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1
Zubair, Mohammad, and Ibrahim Mohammad. "Interrelationship of Extended Spectrum Beta-Lactamase Producers and Biofilm Formation among the Gram-Negative Bacteria from Tabuk, KSA." Open Access Macedonian Journal of Medical Sciences 11, A (2023): 15–22. http://dx.doi.org/10.3889/oamjms.2023.11101.
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AIM: The present study investigates the production of extended-spectrum beta-lactamases (ESBL) and the formation of biofilm among different bacterial pathogens. METHODS: The study conducted prospective analysis on bacteria isolates (Gram-negative) from patients who have diagnosed with infections with bacteria between October 2020 and January 2022. RESULTS: The results showed that there were 53 biofilm producers in Escherichia coli. In contrast, Pseudomonas aeruginosa was observed to have the highest percentage, with 32/40 (80%) isolates being biofilm producers. The least number of isolates were Morganella morganii (n = 2) with two (100%) biofilm producers. The resistance in the biofilm positive isolates was high compared with biofilm negative. About 88% of phenotypic ESBL-positive isolates were biofilm producers, and 97% of cefotaxime-resistant biofilm-positive isolates were genotypic positive for CTX-M, TEM, and SHV genes. CONCLUSION: The present study has shown that protection against antibiotics through mucus production is possible due to bacteria’s reduced metabolic activity and diffusion of antibiotics across the biofilm matrix. In this study, all the bacterial strains of E. coli and Klebsiella pneumoniae were reported to be MDR and competent for establishing biofilm.
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Dropa, Milena, Livia C. Balsalobre, Nilton Lincopan, et al. "Extended-spectrum beta-lactamases among Enterobacteriaceae isolated in a public hospital in Brazil." Revista do Instituto de Medicina Tropical de São Paulo 51, no. 4 (2009): 203–9. http://dx.doi.org/10.1590/s0036-46652009000400005.
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Extended-spectrum β-lactamases (ESBL) in enterobacteria are recognized worldwide as a great hospital problem. In this study, 127 ESBL-producing Enterobacteriaceae isolated in one year from inpatients and outpatients at a public teaching hospital at São Paulo, Brazil, were submitted to analysis by PCR with specific primers for blaSHV, blaTEM and blaCTX-M genes. From the 127 isolates, 96 (75.6%) Klebsiella pneumoniae, 12 (9.3%) Escherichia coli, 8 (6.2%) Morganella morganii, 3 (2.3%) Proteus mirabilis, 2 (1.6%) Klebsiella oxytoca, 2 (1.6%) Providencia rettgeri, 2 (1.6%) Providencia stuartti, 1 (0.8%) Enterobacter aerogenes and 1 (0.8%) Enterobacter cloacae were identified as ESBL producers. BlaSHV, blaTEM and blaCTX-M were detected in 63%, 17.3% and 33.9% strains, respectively. Pulsed field gel eletrophoresis genotyping of K. pneumoniae revealed four main molecular patterns and 29 unrelated profiles. PCR results showed a high variety of ESBL groups among strains, in nine different species. The results suggest the spread of resistance genes among genetically different strains of ESBL-producing K. pneumoniae in some hospital wards, and also that some strongly related strains were identified in different hospital wards, suggesting clonal spread in the institutional environment.
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Emborg, Jette, Paw Dalgaard, and Peter Ahrens. "Morganella psychrotolerans sp. nov., a histamine-producing bacterium isolated from various seafoods." International Journal of Systematic and Evolutionary Microbiology 56, no. 10 (2006): 2473–79. http://dx.doi.org/10.1099/ijs.0.64357-0.
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Mesophilic Morganella morganii (n=6) and psychrotolerant M. morganii-like isolates from various seafoods (n=13), as well as clinical M. morganii isolates (n=3), were characterized by using a polyphasic approach including multi-locus sequencing. Based on the phylogenetic analysis, the 22 strains were divided into two distinct groups comprising mesophilic and psychrotolerant isolates, respectively. This classification was supported by DNA–DNA hybridization studies, whereby a psychrotolerant isolate (strain U2/3T) showed 41.0 and 17.8 % relatedness to the type strains of the mesophilic species Morganella morganii subsp. morganii (strain LMG 7874T) and Morganella morganii subsp. sibonii (strain DSM 14850T), respectively. Analysis of the 16S rRNA gene sequences showed a similarity of 98.6 % between mesophilic and psychrotolerant isolates. However, fragments of seven protein-encoding housekeeping genes (atpD, dnaN, gyrB, hdc, infB, rpoB and tuf) all showed less than 90.9 % sequence similarity between the two groups. The psychrotolerant isolates grew at 0–2 °C and also differed from the mesophilic M. morganii isolates with respect to growth at 37 °C and in 8.5 % (w/v) NaCl and fermentation of d-galactose. The psychrotolerant strains appear to represent a novel species, for which the name Morganella psychrotolerans sp. nov. is proposed. The type strain is U2/3T (=LMG 23374T=DSM 17886T).
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Luo, Xingwei, Yajun Zhai, Dandan He, et al. "Molecular characterization of a novel bla CTX-M-3-carrying Tn6741 transposon in Morganella morganii isolated from swine." Journal of Medical Microbiology 69, no. 8 (2020): 1089–94. http://dx.doi.org/10.1099/jmm.0.001235.
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Introduction. The bla CTX-M-3 gene has rarely been reported in Morganella morganii strains and its genetic environment has not yet been investigated. Aim. To identify the bla CTX-M-3 gene in M. morganii isolated from swine and characterize its genetic environment. Methodology. A M. morganii isolate (named MM1L5) from a deceased swine was identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and subjected to antimicrobial susceptibility testing. The bla genes were detected and then the genetic location and environment of bla CTX-M-3 were investigated by Southern blot and PCR mapping, respectively. The M. morganii bla CTX-M-3 gene was cloned and expressed in Escherichia coli . Results. Isolate MM1L5 harboured the bla CTX-M-3 and bla TEM-1 genes. The bla CTX-M-3 gene, located on the chromosome, was co-carried with an IS26 and bla TEM-1 gene by a novel 6361 bp IS26-flanked composite transposon, designated Tn6741. This transposon consisted of a novel bla CTX-M-3-containing module, IS26-ΔISEcp1-bla CTX-M-3-Δorf477-IS26 (named Tn6710), and a bla TEM-1-containing module, IS26-Δorf477-bla TEM-1-tnpR-IS26, differing from previous reports. Phylogenetic analysis showed a significant variation based on the sequence of Tn6741, as compared to those of other related transposons. Interestingly, although the cloned bla CTX-M-3 gene could confer resistance to ceftiofur, cefquinome, ceftriaxone and cefotaxime, one amino acid substitution (Ile-142-Thr) resulted in a significant reduction of resistance to these antimicrobials. Conclusion. This is the first time that bla CTX-M-3 has been identified on a chromosome from a M. morganii isolate. Furthermore, the bla CTX-M-3 gene was located with an IS26 element and bla TEM-1 gene on a novel IS26-flanked composite transposon, Tn6741, suggesting that Tn6741 might act as a reservoir for the bla CTX-M-3 and bla TEM-1 genes and may become an important vehicle for their dissemination among M. morganii .
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Sun, Zhenxiao, Yi Zhang, Xinping Lin, Sufang Zhang, Yingxi Chen, and Chaofan Ji. "Inhibition Mechanism of Lactiplantibacillus plantarum on the Growth and Biogenic Amine Production in Morganella morganii." Foods 12, no. 19 (2023): 3625. http://dx.doi.org/10.3390/foods12193625.
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Morganella morganii, a spoilage bacterium in fermented foods, produces harmful biogenic amines (BAs). Although Lactiplantibacillus plantarum is widely used to inhibit spoilage bacteria, the inhibition pattern and inhibition mechanism of M. morganii by Lpb. plantarum are not well studied. In this study, we analysed the effects of the addition of Lpb. plantarum cell-free supernatant (CFS) on the growth and BA accumulation of M. morganii and revealed the mechanisms of changes in different BAs by using RNA sequencing transcriptome analysis. The results showed that Lpb. plantarum CFS could significantly inhibit M. morganii BAs in a weak acid environment (pH 6), and the main changes were related to metabolism. Carbohydrate and energy metabolism were significantly down-regulated, indicating that Lpb. plantarum CFS inhibited the growth activity and decreased the BA content of M. morganii. In addition, the change in histamine content is also related to the metabolism of its precursor amino acids, the change in putrescine content may also be related to the decrease in precursor amino acid synthesis and amino acid transporter, and the decrease in cadaverine content may also be related to the decrease in the cadaverine transporter. The results of this study help to inhibit the accumulation of harmful metabolites in fermented foods.
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Taher, Eman M., Basima A. Abdullah, and Anmar A. AL Taie. "Phenotypic and genotypic detection of biofilm genes for<i> </i><i>Proteus, Morganella, Providencia</i> (PMP) bacterial group isolated from clinical samples of some hospitals in Mosul/Iraq." Journal of Applied and Natural Science 16, no. 4 (2024): 1719–30. https://doi.org/10.31018/jans.v16i4.5935.
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The three genera Proteus spp., Morganella spp., Providencia spp. (PMP) is a group of bacteria belonging to the Enterobacteriaceae family that is predominantly implicated in nosocomial infections within hospital environments. The research aimed to ascertain the frequency of PMP in various clinical samples from some hospitals by isolation and confirming the identification of bacteria from biofilms using Viteck-2 and phenotypic and genotypic determinants of biofilm genes. Out of 380 isolates from different clinical sources that were identified phenotypically (microscopic examination, culture, and biochemical tests) confirmed identification of bacteria from biofilms using Viteck-2 and genotypic determinants of biofilm genes DNA were extracted from twenty identified strains, the PCR products derived were utilized for sequencing. The Congo Red Agar and Microplate methods employed encompassed qualitative and quantitative approaches to analyze the formation of biofilms. In this approach, bacteria that develop black colonies were assessed as positive for biofilm formation.Proteus mirabilis showed strong producers (19.8%), Providencia stuartii (100%), and Morganella morganii produced pink colonies. The strains were assessed as non-producers and analyzed quantitatively using the microplate technique. which shows strong biofilm production in most PMP groups. Genetic detection of biofilm genes showed that the mrpA gene was identified in P. mirabilis strains utilizing the PCR technique as positive for all strains at (100%) but M. morganii at (25%), positive amplification for all strains (100%) for the rsm gene in P. mirabilis strains. P. stuartii gave positive detection for the fim A gene by utilizing the PCR technique as (100%). All genes were involved in biofilm formation.
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Barnaud, Guilene, Guillaume Arlet, Charlotte Verdet, Olivier Gaillot, Philippe H. Lagrange та Alain Philippon. "Salmonella enteritidis: AmpC Plasmid-Mediated Inducible β-Lactamase (DHA-1) with anampR Gene from Morganella morganii". Antimicrobial Agents and Chemotherapy 42, № 9 (1998): 2352–58. http://dx.doi.org/10.1128/aac.42.9.2352.
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ABSTRACT DHA-1, a plasmid-mediated cephalosporinase from a single clinicalSalmonella enteritidis isolate, conferred resistance to oxyimino-cephalosporins (cefotaxime and ceftazidime) and cephamycins (cefoxitin and moxalactam), and this resistance was transferable toEscherichia coli HB101. An antagonism was observed between cefoxitin and aztreonam by the diffusion method. Transformation of the transconjugant E. coli strain with plasmid pNH5 carrying the ampD gene (whose product decreases the level of expression of ampC) resulted in an eightfold decrease in the MIC of cefoxitin. A clone with the same AmpC susceptibility pattern with antagonism was obtained, clone E. coliJM101(pSAL2-ind), and its nucleotide sequence was determined. It contained an open reading frame with 98.7% DNA sequence identity with the ampC gene of Morganella morganii. DNA sequence analysis also identified a gene upstream of ampCwhose sequence was 97% identical to the partial sequence of the ampR gene (435 bp) from M. morganii. The gene encoded a protein with an amino-terminal DNA-binding domain typical of transcriptional activators of the LysR family. Moreover, the intercistronic region between the ampC andampR genes was 98% identical to the corresponding region from M. morganii DNA. AmpR was shown to be functional by enzyme induction and a gel mobility-shift assay. An ampGgene was also detected in a Southern blot of DNA from the S. enteritidis isolate. These findings suggest that this inducible plasmid-mediated AmpC type β-lactamase, DHA-1, probably originated from M. morganii.
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Al Sium, Syed Muktadir, Barna Goswami, Sanjana Fatema Chowdhury, et al. "An insight into the genome-wide analysis of bacterial defense mechanisms in a uropathogenic Morganella morganii isolate from Bangladesh." PLOS ONE 20, no. 1 (2025): e0313141. https://doi.org/10.1371/journal.pone.0313141.
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The gram-negative, facultative anaerobic bacterium Morganella morganii is linked to a number of illnesses, including nosocomial infections and urinary tract infections (UTIs). A clinical isolate from a UTI patient in Bangladesh was subjected to high-throughput whole genome sequencing and extensive bioinformatics analysis in order to gather knowledge about the genomic basis of bacterial defenses and pathogenicity in M. morganii. With an average nucleotide identity (ANI) of more than 97% similarity to a reference genome and phylogenetic analysis verified the isolate as M. morganii. Genome annotation identified 3,718 protein-coding sequences, including genes for metabolism, protein processing, stress response, energy, and membrane transport. The presence of biosynthetic gene clusters points to the isolate’s ability to create bioactive compounds, including antibiotics. Genomic islands contained genes for metal transporters, stress proteins, toxin proteins, and genes related to horizontal gene transfer. The beta-lactam resistance gene blaDHA was found using antimicrobial resistance (AMR) gene analysis across three databases. The virulence genes kdsA and cheY, which may be involved in chemotaxis and lipopolysaccharide production, were also available in the isolate, suggesting its high pathogenicity. The genome contained mobile genetic components and defense mechanisms, such as restriction modification and CRISPR-Cas systems, indicating the bacterium’s ability to defend itself against viral attacks. This thorough investigation sheds important light on M. morganii’s pathogenicity and adaptive tactics by revealing its genetic characteristics, AMR, virulence components, and defense mechanisms. For the development of targeted treatments and preventing the onset of resistance in clinical care, it is essential to comprehend these genetic fingerprints.
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Behera, Dibyajyoti Uttameswar, Sangita Dixit, Mahendra Gaur, et al. "Sequencing and Characterization of M. morganii Strain UM869: A Comprehensive Comparative Genomic Analysis of Virulence, Antibiotic Resistance, and Functional Pathways." Genes 14, no. 6 (2023): 1279. http://dx.doi.org/10.3390/genes14061279.
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Morganella morganii is a Gram-negative opportunistic Enterobacteriaceae pathogen inherently resistant to colistin. This species causes various clinical and community-acquired infections. This study investigated the virulence factors, resistance mechanisms, functional pathways, and comparative genomic analysis of M. morganii strain UM869 with 79 publicly available genomes. The multidrug resistance strain UM869 harbored 65 genes associated with 30 virulence factors, including efflux pump, hemolysin, urease, adherence, toxin, and endotoxin. Additionally, this strain contained 11 genes related to target alteration, antibiotic inactivation, and efflux resistance mechanisms. Further, the comparative genomic study revealed a high genetic relatedness (98.37%) among the genomes, possibly due to the dissemination of genes between adjoining countries. The core proteome of 79 genomes contains the 2692 core, including 2447 single-copy orthologues. Among them, six were associated with resistance to major antibiotic classes manifested through antibiotic target alteration (PBP3, gyrB) and antibiotic efflux (kpnH, rsmA, qacG; rsmA; CRP). Similarly, 47 core orthologues were annotated to 27 virulence factors. Moreover, mostly core orthologues were mapped to transporters (n = 576), two-component systems (n = 148), transcription factors (n = 117), ribosomes (n = 114), and quorum sensing (n = 77). The presence of diversity in serotypes (type 2, 3, 6, 8, and 11) and variation in gene content adds to the pathogenicity, making them more difficult to treat. This study highlights the genetic similarity among the genomes of M. morganii and their restricted emergence, mostly in Asian countries, in addition to their growing pathogenicity and resistance. However, steps must be taken to undertake large-scale molecular surveillance and to direct suitable therapeutic interventions.
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Ramya, D., A. Joseph Thatheyus, S. Jemima Balaselvi Juliana, N. Jennifer Michellin Kiruba, and Deborah Gnana Selvam A. "Physical characterization and kinetic studies of Zn (II) biosorption by Morganella morganii ACZ05." Water Science and Technology 85, no. 4 (2022): 970–86. http://dx.doi.org/10.2166/wst.2022.031.
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Abstract Through this investigation, we establish the mechanism and physical characterization of zinc (II) sequestration by Morganella morganii ACZ05 strain, which was isolated and characterized from soil polluted by effluents from electroplating industries. As far as we know, there is very little literature concerning zinc biosorption using an environmental strain of M. morganii. The SEM analysis shows the dark porous gaps in the aggregated cell-matrix of test bacterial biomass which is inferred as water channels usually seen in biofilms, as compared to metal-unexposed control. M. morganii is not known to produce biofilms unless in the rare nosocomial conditions. Here, SEM analysis shows the production of biofilms after exposure to zinc (II) at 500 ppm, which has not been previously reported. EDX analysis of bacterial biomass also specified the sorption of zinc (II) by the bacterial cells and the presence of new peaks for zinc in contrast to control. Both XRD and FTIR analysis observations strongly implicate the potential of physical adsorption as a mechanism for heavy metal resistance. Analysis of the cell surface by Atomic force microscopy and examination of the topography revealed cell aggregation occurs during biofilm production after zinc biosorption. Unlike other reports, regular models such as Langmuir isotherm and Freundlich isotherm were found insufficient to explain the physisorption of zinc (II) metal ions on complex multicomponent adsorbents such as the exopolymeric surface of the bacterial cells. However, adsorption kinetics of zinc (II) to the bacterial biomass was most effectively elucidated by a pseudo-second-order kinetic model, suggesting a certain kind of chemisorption that requires further study.
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Ullah, Asad, Sajjad Ahmad, Saba Ismail, et al. "Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii." International Journal of Environmental Research and Public Health 18, no. 20 (2021): 10961. http://dx.doi.org/10.3390/ijerph182010961.
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Morganella morganii is one of the main etiological agents of hospital-acquired infections and no licensed vaccine is available against the pathogen. Herein, we designed a multi-epitope-based vaccine against M. morganii. Predicted proteins from fully sequenced genomes of the pathogen were subjected to a core sequences analysis, followed by the prioritization of non-redundant, host non-homologous and extracellular, outer membrane and periplasmic membrane virulent proteins as vaccine targets. Five proteins (TonB-dependent siderophore receptor, serralysin family metalloprotease, type 1 fimbrial protein, flagellar hook protein (FlgE), and pilus periplasmic chaperone) were shortlisted for the epitope prediction. The predicted epitopes were checked for antigenicity, toxicity, solubility, and binding affinity with the DRB*0101 allele. The selected epitopes were linked with each other through GPGPG linkers and were joined with the cholera toxin B subunit (CTBS) to boost immune responses. The tertiary structure of the vaccine was modeled and blindly docked with MHC-I, MHC-II, and Toll-like receptors 4 (TLR4). Molecular dynamic simulations of 250 nanoseconds affirmed that the designed vaccine showed stable conformation with the receptors. Further, intermolecular binding free energies demonstrated the domination of both the van der Waals and electrostatic energies. Overall, the results of the current study might help experimentalists to develop a novel vaccine against M. morganii.
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Naqqash, Tahir, Aeman Aziz, Muhammad Babar, et al. "Lead-Resistant Morganella morganii Rhizobacteria Reduced Lead Toxicity in Arabidopsis thaliana by Improving Growth, Physiology, and Antioxidant Activities." Agriculture 12, no. 8 (2022): 1155. http://dx.doi.org/10.3390/agriculture12081155.
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Biological remediation serves as a powerful technique for addressing heavy metals toxicity in metals-contaminated soils. The present study aimed to evaluate the efficacy of lead (Pb)-resistant rhizobacterial strains on growth, photosynthetic traits, and antioxidant activities of the Arabidopsis plant under lead toxicity in pot conditions. Two pre-isolated and pre-characterized Pb-resistant Morganella morganii (ABT3) and Morganella morganii (ABT9) strains were used for inoculating Arabidopsis plants grown under varying Pb concentrations (1.5 mM and 2.5 mM) using PbNO3 as the lead source. The treatments were set up in a completely randomized design with four replications. Data on growth parameters, physiological characteristics, lipid peroxidation, and antioxidant activities were recorded at harvesting. It was observed that Pb contamination caused a significant reduction in Arabidopsis growth, chlorophyll content and quantum yield at both lead concentrations. The Pb concentration of 2.5 mM, showed a substantial decrease in all parameters, including shoot fresh weight (58.72%), shoot dry weight (59.31%), root fresh weight (67.31%), root dry weight (67.28%), chlorophyll content (48.69%), quantum yield (62.36%), catalase activity (65.30%), superoxide dismutase (60.88%), and peroxidase activity (60.54%) while increasing lipid peroxidation (113.8%). However, the inoculation with Pb-resistant M. morganii strains (ABT3 and ABT9) improved plant growth, photosynthesis and antioxidant activities, while reduced the malondialdehyde content of Arabidopsis compared to control plants without inoculation. The M. morganii strain ABT9 showed a maximum increase in the shoot fresh weight (67.18%), shoot dry weight (67.96%), root fresh weight (94.04%), root dry weight (93.92%), shoot length (148.88%), root length (123.33%), chlorophyll content (52.53%), quantum yield (58.57%), catalase activity (39.46%), superoxide dismutase (21.84%), and peroxidase activity (22.34%) while decreasing lipid peroxidation (35.28%). PCA analysis further showed that all nine treatments scattered differently across the PC1 and PC2, having 81.4% and 17.0% data variance, respectively, indicating the efficiency of Pb-resistant strains. The heatmap further validated that the introduction of Pb-resistant strains positively correlated with the growth parameters, quantum yield, chlorophyll content and antioxidant activities of Arabidopsis seedlings. Both Pb-resistant strains improved Arabidopsis plant growth and photosynthetic efficiency under lead stress conditions. Thus, both Morganella morganii ABT3 and Morganella morganii ABT9 strains can be considered as bio-fertilizer for reducing lead toxicity thereby improving plant growth and physiology in metal-contaminated agricultural soils.
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Wang, Yazhe, Di Wang, Shengjun Chen, et al. "Genomic Analysis of Two Histamine-Producing Strains Isolated from Yellowfin Tuna." Foods 14, no. 9 (2025): 1532. https://doi.org/10.3390/foods14091532.
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Psychrotrophic Morganella spp. is a typical histamine producer commonly found in seafood, exhibiting a high histamine-producing capacity. In this study, two strains of Morganella (GWT 902 and GWT 904) isolated from yellowfin tuna were subjected to phenotypic and genotypic characterization. Phenotypic analysis reveals differences in growth temperature, NaCl tolerance, and D-galactose fermentation capacity between the two strains. Notably, the histamine production capacity of GWT 902 is significantly higher than that of GWT 904 at 4 °C. The complete genome sequences of strains GWT 902 and GWT 904 were sequenced, identifying GWT 902 as Morganella psychrotolerans and GWT 904 as Morganella morganii subsp. sibonii. Genomic analysis confirms the presence of histidine decarboxylase gene clusters (hdcT1, hdc, hdcT2, hisRS) in both strains, and sequence alignment shows that the amino acid sequence similarity of histidine decarboxylase encoded by the hdc gene was 95.24%. Gene function analysis further identified genes associated with putrescine biosynthesis, sulfur metabolism, lipase and protease secretion, and detected key genes in quorum sensing (QS), stress adaptation, and antibiotic resistance. This study provides valuable insights into the taxonomic analysis of psychrotrophic Morganella spp. and contributes to the development of efficient strategies for preventing histamine formation in seafood.
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Li, Heling, Zhigang Chen, Qing Ning, Faliang Zong, and Hong Wang. "Isolation and Identification of Morganella morganii from Rhesus Monkey (Macaca mulatta) in China." Veterinary Sciences 11, no. 5 (2024): 223. http://dx.doi.org/10.3390/vetsci11050223.
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A bacterium was isolated and identified from the secretion of a rhesus monkey with endometritis. The morphological results showed that the strain exhibited round, convex, gray-white colonies with smooth surfaces and diameters ranging from 1 to 2 mm when cultured on Columbia blood agar at 37 °C for 24 h; on salmonella–shigella agar (S.S.) at 37 °C for 24 h, the colonies appeared round, flat, and translucent. Gram staining showed negative results with blunt ends and non-spore-forming characteristics. Molecular biology results showed that the 16S rRNA sequence of the strain revealed over 96.9% similarity with published sequences of M. morganii from different sources in the NCBI GenBank database. Morphological and molecular biology analysis confirmed that the strain (RM2023) isolated from cervical secretions of rhesus monkey was M. morganii. Drug sensitivity testing demonstrated that the isolated strain (RM2023) was sensitive to ceftriaxone, amikacin, gentamicin, cefazolin, cefuroxime, ceftazidime, levofloxacin, cotrimoxazole, norfloxacin, and tetracycline; moderately sensitive to ampicillin; and resistant to penicillin, vancomycin, ciprofloxacin, and clindamycin. The research findings provide valuable insights for disease prevention in rhesus monkeys and contribute to molecular epidemiological studies.
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Sheng, Wang-Huei, Robert E. Badal та Po-Ren Hsueh. "Distribution of Extended-Spectrum β-Lactamases, AmpC β-Lactamases, and Carbapenemases among Enterobacteriaceae Isolates Causing Intra-Abdominal Infections in the Asia-Pacific Region: Results of the Study for Monitoring Antimicrobial Resistance Trends (SMART)". Antimicrobial Agents and Chemotherapy 57, № 7 (2013): 2981–88. http://dx.doi.org/10.1128/aac.00971-12.
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ABSTRACTThe increasing trend of β-lactam resistance amongEnterobacteriaceaeis a worldwide threat.Enterobacteriaceaeisolates causing intra-abdominal infections (IAI) from the Study for Monitoring Antimicrobial Resistance Trends (SMART) collected in 2008 and 2009 from the Asia-Pacific region were investigated. Detection of extended-spectrum β-lactamases (ESBLs), AmpC β-lactamases, and carbapenemases was performed by multiplex PCR. A total of 699Enterobacteriaceaeisolates with positive genotypic results, includedEscherichia coli(n= 443),Klebsiella pneumoniae(n= 187),Enterobacter cloacae(n= 45),Klebsiella oxytoca(n= 9),Citrobacter freundii(n= 5),Proteus mirabilis(n= 3),Enterobacter aerogenes(n= 2),Morganella morganii(n= 2), and one each ofEnterobacter asburiae,Proteus vulgaris, andProvidencia rettgeriwere analyzed. Nearly 20% of these β-lactamase-producingEnterobacteriaceaeisolates were from community-associated IAI. CTX-M (588 isolates, including 428 [72.8%] with CTX-M-15) was the most common ESBL, followed by SHV (n= 59) and TEM (n= 4). CMY (n= 110, including 102 [92.7%] with CMY-2) was the most common AmpC β-lactamase, followed by DHA (n= 46) and ACT/MIR (n= 40). NDM (n= 65, including 62 [95.4%] with NDM-1) was the most common carbapenemase, followed by IMP (n= 7) and OXA (n= 7). Isolates from hospital-associated IAI had more complicated β-lactamase combinations than isolates from the community. Carbapenemases were all exclusively detected inEnterobacteriaceaeisolates from India, except that IMP β-lactamases were also detected in Philippines and Australia. CTX-M β-lactamases were the predominant ESBLs produced byEnterobacteriaceaecausing IAI in the Asia-Pacific region. Emergence of CTX-M-15-, CMY-2-, and NDM-1-producingEnterobacteriaceaeisolates is of major concern and highlights the need for further surveillance in this area.
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Krutko, V. S., L. H. Nikolaieva, T. V. Maistat, O. A. Oparin, and Anton Viktorovych Rohozhyn. "INFLUENCE OF GENOTYPIC VARIABILITY OF M. TUBERCULOSIS ON THE COURSE OF TUBERCULOSIS WITH MULTIPLE DRUG RESISTANCE." International Medical Journal, no. 1 (March 5, 2020): 68–71. http://dx.doi.org/10.37436/2308-5274-2020-1-15.
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Tuberculosis is infectious and socially dependent disease, being now one of the most pressing issues in practical health care. As well the usual types of tuberculosis infection, chemoresistant tuberculosis is spreading rapidly in the world. The WHO estimates that about 500,000 people on the planet are infected with M. tuberculosis, which is resistant to standard anti−tuberculosis drugs. The probability of successful treatment decreases with emergence of new genotypes of M. tuberculosis with total resistance. In the modern epidemiology of tuberculosis, it is important to identify genotypes on certain signs, allowing to address issues such as their origin, identification of the infection source, possible routes and factors of transmission, as well as to reveal cases and spread of resistance to anti−tuberculosis drugs. To evaluate the therapy efficiency of multidrug−resistant tuberculosis patients with revealed genotypic variability during treatment, 10 patients with chemoresistant pulmonary tuberculosis having M. tuberculosis genotypic variability were treated. In these patients, the clinical, laboratory and radiological dynamics of disease in intensive phase of treatment were studied. Analysis of treatment results for patients with chemoresistant tuberculosis with genotypic variability of M. tuberculosis was evaluated by the intoxication syndrome dynamics of, the timing of closure of the decay cavities and cessation of bacterial excretion. The study found that the genotypic variability of M. tuberculosis is characterized by the change of less virulent genotypes of M. tuberculosis to more virulent. Signs of intoxication have been shown to change from less virulent M. tuberculosis genotypes to M. tuberculosis Beijing genotypes. Genotypic variability of mycobacteria in hospital suggests that hospitalization in tuberculosis facilities is a risk of exogenous tuberculosis superinfection. Studying the influence of genotypic variability of M. tuberculosis on the course of multidrug−resistant tuberculosis requires more extensive research, being a very relevant and promising area in phthisiology. Key words: Mycobacterium tuberculosis, genotypic variability, VNTR−genotyping, treatment.
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Choi, Sang-Ho, Jung Eun Lee, Su Jin Park та ін. "Emergence of Antibiotic Resistance during Therapy for Infections Caused by Enterobacteriaceae Producing AmpC β-Lactamase: Implications for Antibiotic Use". Antimicrobial Agents and Chemotherapy 52, № 3 (2007): 995–1000. http://dx.doi.org/10.1128/aac.01083-07.
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ABSTRACT Enterobacter spp., Serratia marcescens, Citrobacter freundii, and Morganella morganii are characterized by chromosomally encoded AmpC β-lactamases and possess the ability to develop resistance upon exposure to broad-spectrum cephalosporins. To determine the incidences of the emergence of resistance during antimicrobial therapy for infections caused by these organisms and the effect of the emergence of resistance on patient outcomes, all patients who were admitted to the Asan Medical Center (Seoul, Republic of Korea) from January 2005 to June 2006 and whose clinical specimens yielded Enterobacter spp., S. marcescens, C. freundii, or M. morganii were monitored prospectively. The main end point was the emergence of resistance during antimicrobial therapy. A total of 732 patients with infections were included for analysis. The overall incidence of the emergence of antimicrobial resistance during antimicrobial therapy was 1.9% (14/732). Resistance to broad-spectrum cephalosporins, cefepime, extended-spectrum penicillin, carbapenem, fluoroquinolones, and aminoglycosides emerged during treatment in 5.0% (11/218), 0% (0/20), 2.0% (2/100), 0% (0/226), 0% (0/153), and 1.1% (1/89) of patients, respectively. The emergence of resistance to broad-spectrum cephalosporins occurred more often in Enterobacter spp. (8.3%, 10/121) than in C. freundii (2.6%, 1/39), S. marcescens (0%, 0/37), or M. morganii (0%, 0/21). Biliary tract infection associated with malignant bile duct invasion was significantly associated with the emergence of resistance to broad-spectrum cephalosporins (P = 0.024 at a significance level of 0.042, by use of the Bonferroni correction). Only 1 of the 14 patients whose isolates developed resistance during antimicrobial therapy died. The emergence of resistance was more frequently associated with broad-spectrum cephalosporins than with the other antimicrobial agents tested, especially in Enterobacter spp. However, the emergence of resistance was associated with a low risk of mortality.
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Bonilla-Aldana, D. Katterine, Jorge Luis Bonilla-Aldana, Juan R. Ulloque-Badaracco, et al. "Snakebite-Associated Infections: A Systematic Review and Meta-Analysis." American Journal of Tropical Medicine and Hygiene 110, no. 5 (2024): 874–86. http://dx.doi.org/10.4269/ajtmh.23-0278.
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ABSTRACT. Snakebites still constitute a significant public health problem in developing countries and are considered a neglected tropical condition by the WHO. Snake accidents are associated with substantial morbidity and mortality and may produce secondary complications, such as severe infections. The objective of this systematic review was to determine the prevalence of snakebite infections and characterize the bacteria isolated from these infections. A systematic literature review in five databases was carried out to assess the prevalence of snakebite infection. A meta-analysis was performed using a random-effects model to calculate the pooled prevalence and 95% CIs. Cochran’s Q test and the I2 statistic were used to assess between-study heterogeneity. The pooled prevalence of infection due to snakebite was 27.0% (95% CI: 22.0–32.0%), with high heterogeneity among studies (I2 = 99.7%). The prevalence was higher in Asia (32%) than in the Americas (21%). Snakebite infections required surgical interventions in 68% (95% CI: 37.0–98.0%). The leading group of pathogens identified corresponded to Gram-negative bacteria (63%), particularly Morganella morganii (32%), but also, Gram-positive cocci (40%), especially Enterococcus spp. (23%) and Staphylococcus aureus (15%). However, multiple other pathogens, including anaerobes, were found. A high prevalence of snakebite-associated infection has been described, primarily due to M. morganii, with the corresponding implications for empirical therapy. Rational use of antimicrobials is recommended, and this should guide initial empirical treatment. Moreover, isolation and identification of the possible bacteria present in snakebite wounds is recommended in all cases to confirm or rule out associated infection.
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Akter, A., MJ Hasan, MA Latif, et al. "Genetic Variability, Heritability, Correlation and Path Coefficient Studies for Yield and Yield Components of Some Promising Rice Hybrids." Bangladesh Rice Journal 23, no. 2 (2020): 27–34. http://dx.doi.org/10.3329/brj.v23i2.48245.
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Eight promising hybrids along with three checks were evaluated for yield and yield contributing traits to observe their genetic variability, heritability, correlation and path coefficient analysis during T. Aman season 2014. The results indicated that the highest genotypic variance was recorded in spikelet panicle-1 followed by effective tiller m-2. Similarly, the highest phenotypic variances were also found with these two characters. Phenotypic coefficient of variation (PCV) was slightly higher than genotypic coefficient of variation (GCV) for all the traits under this study. Hence, slight differences indicate less or minor environmental influence and greater role of genetic factors on the expression of the traits. High heritability was observed in all the characters studied except effective tiller m-2. Highly significant and positive correlations of grain yield with effective tiller m-2, spikelet panicle-1 at genotypic level were observed. Spikelet fertility was found significant at both genotypic and phenotypic level. Path analysis revealed that spikelet fertility had highly positive direct effect on grain yield followed by effective tiller m-2. On the other hand, spikelet panicle-1 showed positive indirect effect on grain yield. Thus, the results suggested that effective tiller m-2; number of spikelet panicle-1 and spikelet fertility (%) could be considered as effective selection criteria for the development of heterotic rice hybrids.
 Bangladesh Rice j. 2019, 23(2): 27-34
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Hadrich, Ines, Nahed Khemakhem, Amin Ilahi, et al. "Genotypic Analysis of the Population Structure in Malassezia globosa and Malassezia restricta." Journal of Fungi 9, no. 2 (2023): 263. http://dx.doi.org/10.3390/jof9020263.
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The molecular characterization of Malassezia spp. isolates from animals and humans has not been thoroughly studied. Although a range of molecular methods has been developed for diagnosing Malassezia species, they have several drawbacks, such as inefficiency in differentiating all the species, high cost and questionable reproducibility. The present study aimed to develop VNTR markers for genotyping Malassezia isolated from clinical and animal samples. A total of 44 M. globosa and 24 M. restricta isolates were analyzed. Twelve VNTR markers were selected on seven different chromosomes (I, II, III, IV, V, VII and IX), six for each Malassezia species. The highest discriminatory power for a single locus was obtained with the STR-MG1 marker (0.829) and STR-MR2 marker (0.818) for M. globosa and M. restricta, respectively. After the analysis of multiple loci, 24 genotypes were noted among 44 isolates in M. globosa, with a discrimination index D of 0.943 and 15 genotypes were noted among 24 isolates in M. restricta, with a discrimination index D of 0.967. An endogenous infection was detected in two patients. Different genotypes of M. globosa strains colonized one patient. Interestingly, VNTR markers analysis revealed a carriage between a breeder and his dog in three cases for M. globosa and two for M. restricta. The FST (0.018 to 0.057) values indicate a low differentiation between the three populations of M. globosa. These results suggest a dominant clonal mode of reproduction in M. globosa. The typing of M. restricta showed a genotypic diversity of the strains, which can cause various skin pathologies. However, patient five was colonized with strains having the same genotype collected from different body parts (back, shoulder). VNTR analysis was capable of identifying species with high accuracy and reliability. More importantly, the method would facilitate monitoring Malassezia colonization in domestic animals and humans. It was shown that the patterns are stable and the method is discriminant, making it a powerful tool for epidemiological purposes.
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Angadi, Airadevi P., B. S. Reddy, R. C. Jagadeesha, Balaji S. Kulkarni, and S. Nishani. "Effect of summer season on correlation coefficient in bird of paradise (Strelitzia reginae) progenies." Journal of Applied and Natural Science 9, no. 1 (2017): 364–69. http://dx.doi.org/10.31018/jans.v9i1.1197.
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The study pertaining to the effect of summer season on correlation analysis in bird of paradise (Strelitzia reginae) was carried out among forty progenies. The results of correlation analysis for twelve parameters (plant height, stem girth, leaf length, leaf width, number of leaves per plant, number of suckers/m 2 , flower stalk length, flower stalk girth, spath length, no. of bracts, vase life and no. of flowers/ m 2 ) at genotypic and phenotypic levels revealed that number of flowers per m 2 of progenies during summer, 2011 showed positive and significant correlations with plant height (0.357 and 0.237) and number of suckers/ m2 (0.880 and 0.899). Whereas, it showed positive and significant correlation with stem girth (0.203), leaf width (0.202) and flower stalk girth (0.265) at genotypic level only. While during summer 2012, number of flowers per m 2 showed positive correlations with plant height (0.265 and 0.242), stem girth (0.232 and 0.215), number of suckers/ m 2 (0.913 and 0.900) and flower stalk length (0.268 and 0.249) at genotypic and phenotypic levels. Hence, the selection of these characters would be effective in improving yield in bird of paradise crop.
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Petrova, L. V., E. V. Sevastyanova, E. E. Larionova, and T. G. Smirnova. "GENOTYPIC AND PHENOTYPIC COMPARISON OF DRUG RESISTANCE PROFILES OF M. tuberculosis ISOLATES." Вестник ЦНИИТ 7, no. 4 (2023): 23–28. http://dx.doi.org/10.57014/2587-6678-2023-7-4-23-28.
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We conducted a comparative analysis of drug resistance of M. tuberculosis isolates to first-line TB drugs. The diagnostic samples and cultures of M. tuberculosis from TB patients were tested in the Mari El Republic. It was established that the divergence between genotypic and phenotypic isoniazid resistance did not exceed 4%, and rifampicin resistance – 3.9%. In most cases there was lack of mutations associated with resistance to isoniazid or rifampicin in the presence of phenotypic resistance. However, the divergence between results obtained by genotypic and different phenotypic methods was not only seen for M. tuberculosis isolates genotypically referred to sensitive, but also for M. tuberculosis isolates genotypically referred to resistant.
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Frothingham, Richard, Percy L. Strickland, Gisela Bretzel, Srinivas Ramaswamy, James M. Musser, and Diana L. Williams. "Phenotypic and Genotypic Characterization ofMycobacterium africanum Isolates from West Africa." Journal of Clinical Microbiology 37, no. 6 (1999): 1921–26. http://dx.doi.org/10.1128/jcm.37.6.1921-1926.1999.
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The Mycobacterium tuberculosis complex includesM. tuberculosis, M. bovis, M. africanum, and M. microti. Most clinical isolates areM. tuberculosis or M. bovis. These species can be distinguished by phenotypes and genotypes. However, there is no simple definition of M. africanum, and some authors question the validity of this species. We analyzed 17 human isolates from Sierra Leone, identified as M. africanum by biochemical and growth characteristics. We sequenced polymorphic genes and intergenic regions. We amplified DNA from six loci with variable numbers of tandem repeats (VNTRs) and determined the exact number of repeats at each locus in each strain. All M. africanumisolates had the ancestral CTG Leu at katG codon 463. Drug-resistant M. africanum isolates had katGand rpoB mutations similar to those found in drug-resistantM. bovis and M. tuberculosis. Fourteen Sierra Leone M. africanum isolates (designated group A) hadkatG codon 203 ACC Thr, also found in M. africanum T (the T indicates type strain) from Senegal. Group A isolates clustered with M. africanum T by VNTR analysis. Three M. africanum isolates (group B) had katG codon 203 ACT Thr, found in M. tuberculosis T, and clustered with M. tuberculosis T by VNTR analysis. Phenotypic identification of M. africanumyielded a heterogeneous collection of strains. Genotypic analyses identified a cluster (M. africanum group A) which includedM. africanum T and was distinct from the rest of the M. tuberculosis complex. Future studies ofM. africanum should include both phenotypic and genotypic analyses.
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Borelli, Tiago Cabral, Gabriel Lencioni Lovate, Ana Flavia Tonelli Scaranello, et al. "Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital." Antibiotics 10, no. 4 (2021): 419. http://dx.doi.org/10.3390/antibiotics10040419.
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(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. (2) Methods: We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 34 strains of Gram-negative and Gram-positive bacteria, providing the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. (3) Results: We identified a high abundance of beta-lactamase genes in resistant organisms, including seven extended-spectrum beta-lactamases (OXA-1, OXA-10, CTX-M-1, KPC, TEM, HYDRO, BLP) shared between organisms from different species. Additionally, we identified several ARG-carrying plasmids indicating the potential for a fast transmission of resistance mechanism between bacterial strains. Furthermore, we uncovered two pairs of (near) identical plasmids exhibiting multi-drug resistance. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identified six beta-lactamase genes out of 15 predicted in silico as those mainly responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms. (4) Conclusions: Systematic studies similar to the one presented here should help to prevent outbreaks of novel multidrug-resistant bacteria in healthcare facilities.
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Hayat, Fawad, Sumera Afzal Khan, Muddasir Khan, et al. "Biological activity of silver nanoparticles synthesized from untapped secondary metabolites of Olea europea endophytic Bacillus amyloliquefaciens." PLOS One 20, no. 5 (2025): e0321134. https://doi.org/10.1371/journal.pone.0321134.
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Endophytic microbes offer frequent contributions to the identification of novel biologically active compounds. The current study aimed to isolate untapped Olea europaea-associated Bacillus amyloliquefaciens and to explore their bioactive secondary metabolites as well as its mediated silver nanoparticles (AgNPs). B. amyloliquefaciens analysis revealed the existence of 23 compounds in metabolite extract by using Gas chromatography-mass spectrometry (GC-MS) analysis. AgNPs were synthesized by using metabolite extract and confirmed by using UV-Vis spectrophotometry, Energy Dispersive Spectroscopy (EDS), and Fourier Transform Infrared Spectroscopy (FTIR). B. amyloliquefaciens metabolite extract displays a high inhibition zone (19 mm) against Morganella morganii and Escherichia coli, while AgNPs exhibit high inhibition zone (22 mm) against M. morganii. The extract shows 64.8% and AgNPs display 99.8% antioxidant activity in 5mg/mL concentration. In analgesic effect, after 90 minutes at 100 mg/mL concentration, the extract shows a mean latency time of 17 seconds while AgNPs show 19 seconds, respectively. In conclusion, B. amyloliquefaciens metabolite extract and AgNPs exhibited significant antibacterial, antioxidant, and analgesic activities in various concentrations while comparatively AgNPs displayed higher bioactive potential. Endophytic bacteria associated with O. europaea have diverse bioactive metabolites with promising pharmaceutical activities, as well as their mediated AgNPs increase these activities. Further research on the exploration of endophytic bacterial metabolites and its mediated nanoparticles will prompt the discovery of novel bioactive compounds.
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Hirabayashi, Aki, Koji Yahara, Satomi Mitsuhashi та ін. "Plasmid analysis of NDM metallo-β-lactamase-producing Enterobacterales isolated in Vietnam". PLOS ONE 16, № 7 (2021): e0231119. http://dx.doi.org/10.1371/journal.pone.0231119.
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Carbapenem-resistant Enterobacterales (CRE) represent a serious threat to public health due to the lack of treatment and high mortality. The rate of antimicrobial resistance of Enterobacterales isolates to major antimicrobials, including carbapenems, is much higher in Vietnam than in Western countries, but the reasons remain unknown due to the lack of genomic epidemiology research. A previous study suggested that carbapenem resistance genes, such as the carbapenemase gene blaNDM, spread via plasmids among Enterobacterales in Vietnam. In this study, we characterized blaNDM-carrying plasmids in Enterobacterales isolated in Vietnam, and identified several possible cases of horizontal transfer of plasmids both within and among species of bacteria. Twenty-five carbapenem-nonsusceptible isolates from a medical institution in Hanoi were sequenced on Illumina short-read sequencers, and 13 blaNDM-positive isolates, including isolates of Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii, Morganella morganii, and Proteus mirabilis, were further sequenced on an Oxford Nanopore Technologies long-read sequencer to obtain complete plasmid sequences. Almost identical 73 kb IncFII(pSE11)::IncN hybrid plasmids carrying blaNDM-1 were found in a P. mirabilis isolate and an M. morganii isolate. A 112 kb IncFII(pRSB107)::IncN hybrid plasmid carrying blaNDM-1 in an E. coli isolate had partially identical sequences with a 39 kb IncR plasmid carrying blaNDM-1 and an 88 kb IncFII(pHN7A8)::IncN hybrid plasmid in a C. freundii isolate. 148–149 kb IncFIA(Hl1)::IncA/C2 plasmids and 75–76 kb IncFII(Yp) plasmids, both carrying blaNDM-1 were shared among three sequence type 11 (ST11) isolates and three ST395 isolates of K. pneumoniae, respectively. Most of the plasmids co-carried genes conferring resistance to clinically relevant antimicrobials, including third-generation cephalosporins, aminoglycosides, and fluoroquinolones, in addition to blaNDM-1. These results provide insight into the genetic basis of CRE in Vietnam, and could help control nosocomial infections.
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Recordon-Pinson, Patricia, Cathia Soulié, Philippe Flandre, et al. "Evaluation of the Genotypic Prediction of HIV-1 Coreceptor Use versus a Phenotypic Assay and Correlation with the Virological Response to Maraviroc: the ANRS GenoTropism Study." Antimicrobial Agents and Chemotherapy 54, no. 8 (2010): 3335–40. http://dx.doi.org/10.1128/aac.00148-10.
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ABSTRACT Genotypic algorithms for prediction of HIV-1 coreceptor usage need to be evaluated in a clinical setting. We aimed at studying (i) the correlation of genotypic prediction of coreceptor use in comparison with a phenotypic assay and (ii) the relationship between genotypic prediction of coreceptor use at baseline and the virological response (VR) to a therapy including maraviroc (MVC). Antiretroviral-experienced patients were included in the MVC Expanded Access Program if they had an R5 screening result with Trofile (Monogram Biosciences). V3 loop sequences were determined at screening, and coreceptor use was predicted using 13 genotypic algorithms or combinations of algorithms. Genotypic predictions were compared to Trofile; dual or mixed (D/M) variants were considered as X4 variants. Both genotypic and phenotypic results were obtained for 189 patients at screening, with 54 isolates scored as X4 or D/M and 135 scored as R5 with Trofile. The highest sensitivity (59.3%) for detection of X4 was obtained with the Geno2pheno algorithm, with a false-positive rate set up at 10% (Geno2pheno10). In the 112 patients receiving MVC, a plasma viral RNA load of <50 copies/ml was obtained in 68% of cases at month 6. In multivariate analysis, the prediction of the X4 genotype at baseline with the Geno2pheno10 algorithm including baseline viral load and CD4 nadir was independently associated with a worse VR at months 1 and 3. The baseline weighted genotypic sensitivity score was associated with VR at month 6. There were strong arguments in favor of using genotypic coreceptor use assays for determining which patients would respond to CCR5 antagonist.
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Cao Yao, Juan Carlos, Jesús Navas Méndez, and María Teresa Tórtola Fernández. "Analysis of Phenotypic and Genotypic Susceptibility to Clarithromycin and Amikacin of Mycobacterium abscessus Complex Strains Isolated from Cystic Fibrosis Patients." Microorganisms 11, no. 12 (2023): 2897. http://dx.doi.org/10.3390/microorganisms11122897.
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Mycobacterium abscessus complex infections are ever on the rise. To curb their increasing evolution, we performed an in-depth study of 43 clinical isolates of cystic fibrosis patients obtained from 2009 to 2020. We identified their subspecies, uncovered their genotypic resistance profiles, characterised their antibiotic-resistant genes, and assessed their phenotypic antibiotic susceptibilities. The phenotypic and genotypic methods showed total agreement in terms of resistance to clarithromycin and amikacin. Of the 43 clinical strains, 28 belonged to M. abscessus subsp. abscessus (65.1%), 13 to M. abscessus subsp. massiliense (30.2%), and 2 to M. abscessus subsp. bolletii (4.6%). The resistant rates for clarithromycin and amikacin, the two main drugs against M. abscessus complex pulmonary infections, were 64.2% and 14.2%, respectively. We found three strains of M. abscessus subsp. abscessus that showed heteroresistance in the rrl and rrs genes, and these strains also presented double-resistance since they were macrolide- and aminoglycoside-resistant. M. abscessus subsp. abscessus showed a high minimum inhibitory concentration (MIC) and a resistant percentage larger than or equal to 88% to cefoxitin, ciprofloxacin, moxifloxacin, doxycycline, imipenem, and trimethoprim-sulfamethoxazole. These results show a panorama of the high resistance of Mycobacterium abscessus complex to current drugs for cystic fibrosis patients. Thus, other treatment methods are urgently needed.
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KIM, SHIN-HEE, BEGOÑA BEN-GIGIREY, JORGE BARROS-VELÁZQUEZ, ROBERT J. PRICE, and HAEJUNG AN. "Histamine and Biogenic Amine Production by Morganella morganii Isolated from Temperature-Abused Albacore." Journal of Food Protection 63, no. 2 (2000): 244–51. http://dx.doi.org/10.4315/0362-028x-63.2.244.
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Histamine-producing bacteria were isolated from albacore stored at 0, 25, 30, and 37°C. They were screened using Niven's differential medium, and their histamine production was confirmed by high-pressure liquid chromatography analysis. The optimum temperature for growth of histamine-producing bacteria was 25°C. The bacterium producing the highest level of histamine was isolated from fish abused at 25°C. It was identified as Morganella morganii by morphological, cultural, biochemical, and antimicrobial characteristics and by the Vitek microbial identification system. The M. morganii isolate was inoculated into tuna fish infusion broth medium, and the effect of temperature was determined for microbial growth and formation of histamine and other biogenic amines. The isolate produced the highest level of histamine, 5,253 ppm, at 25°C in the stationary phase. At 15°C, histamine production was reduced to 2,769 ppm. Neither microbial growth nor histamine formation was detected at 4°C. To determine whether the isolate can also produce other biogenic amines that can potentiate histamine toxicity, production of cadaverine, putrescine, serotonin, tryptamine, tyramine, phenylethylamine, spermidine, and spermine by the isolate was also monitored. Cadaverine, putrescine, and phenylethylamine were detected with microbial growth in the tuna fish infusion broth medium. The optimum temperature for cadaverine, putrescine, and phenylethylamine formation was found to be 25°C, as it was for histamine.
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Lu, Yanzhi, Jinman Li, and Xuewen Qin. "Study on extended-spectrum beta-lactamases genes and drug resistance in patients with urinary tract infection of enterohemorrhagic Escherichia coli after bladder cancer surgery." Medicine 104, no. 17 (2025): e42098. https://doi.org/10.1097/md.0000000000042098.
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To explore of the detection of enterohemorrhagic Escherichia coli with extended-spectrum beta-lactamase (ESBLs) in patients with urinary tract infections (UTIs) after bladder cancer surgery, and analysis of their genotypic distribution and drug resistance. From February 2022 to February 2024, patients who underwent bladder cancer surgery at our hospital were collected. Among them, those who developed UTIs with enterohemorrhagic E coli postoperatively had their urine specimens isolated and cultured, resulting in 87 strains of enterohemorrhagic E coli. Cultures were conducted on the obtained enterohemorrhagic E coli samples, ESBLs production was screened, and drug sensitivity tests were performed to investigate the resistance rate and antibacterial effects. Additionally, genotypic testing was conducted. This study successfully isolated 87 strains of E coli, among which 49 strains (56.32%) were found to produce ESBLs after screening. The resistance rates of these ESBL-producing E coli to cefotaxime and ampicillin were relatively high (93.88% and 97.96%, respectively), while the resistance rate to imipenem was the lowest (2.04%). Genotypic testing revealed that among the 49 strains of ESBL-producing E coli, the detection rate of blaCTX-M-14 was the highest at 53.06%, followed by bla-TEM at 30.61%. The detection rates of bla-SHV (4.08%), bla-OXA (2.04%), blaCTX-M-3 (2.04%), blaCTX-M-15 (2.04%), as well as combinations of several genotypes (blaCTX-M-3 + bla-TEM, blaCTX-M-14 + bla-TEM, blaCTX-M-15 + bla-TEM, all with a detection rate of 2.04%), were relatively low. Strains carrying the bla-TEM genotype exhibited 100% resistance rates to ampicillin and tetracycline. Strains carrying the blaCTX-M-14 genotype showed a 100% resistance rate to ampicillin and a 96.15% resistance rate to cefotaxime. Bladder cancer patients with postoperative complications of E coli urinary tract infection have a detection rate of 56.32% for ESBL-producing E coli. The detected ESBL-producing strains show a high resistance rate to ampicillin and cefotaxime, with the lowest resistance rate observed against imipenem. Genotypic analysis reveals that blaCTX-M-14 and bla-TEM are the main ESBL genes, with blaCTX-M-14 having the highest detection rate.
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KIM, SHIN-HEE, KATHARINE G. FIELD, MICHAEL T. MORRISSEY, ROBERT J. PRICE, CHENG-I. WEI, and HAEJUNG AN. "Source and Identification of Histamine-Producing Bacteria from Fresh and Temperature-Abused Albacore†." Journal of Food Protection 64, no. 7 (2001): 1035–44. http://dx.doi.org/10.4315/0362-028x-64.7.1035.
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Histamine-producing bacteria were isolated from fresh and temperature-abused albacore using two different isolation procedures. Typically, the bacterial isolates on Niven's or modified Niven's medium produced negligible or low levels of histamine (&lt;300 ppm) in histamine enumeration broth. The most frequently found species using this approach was Hafnia alvei. By prescreening on selective media (eosin methylene blue [EMB] agar for enteric bacteria; deMan Rogosa Sharpe agar for lactic acid bacteria; KF streptococcus agar for streptococci; pseudomonas isolation [PI] agar for pseudomonads; and staphylococcus medium 110 agar for staphylococci) prior to plating on histidine decarboxylase differential media, detection rate of true histamine formers increased. Prolific histamine producers capable of forming &gt;1,000 ppm histamine in culture broth were isolated when PI and EMB agars were used for prescreening. Among the selective media tested, EMB agar was most effective in selecting high histamine producers, as demonstrated by the highest rate of true positives based on histamine analysis. Histamine-producing isolates were mostly enteric bacteria, including Morganella morganii, H. alvei, Klebsiella spp., Citrobacter freundii, Enterobacter spp., and Serratia spp. M. morganii isolated on PI agar from temperature-abused albacore muscle was found to be the highest histamine former. This species was not isolated from fresh albacore, while other enteric bacteria were frequently detected on the gills. However, only a few species isolated from both fresh and temperature-abused muscles were identified as high histamine formers.
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Terradot, L., J. C. Simon, N. Leterme, et al. "Molecular characterization of clones of the Myzus persicae complex (Hemiptera: Aphididae) differing in their ability to transmit the potato leafroll luteovirus (PLRV)." Bulletin of Entomological Research 89, no. 4 (1999): 355–63. http://dx.doi.org/10.1017/s0007485399000498.
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AbstractA prerequisite to studying the specific interactions involved in the persistent transmission of luteoviruses such as the potato leafroll virus (PLRV) is the characterization of both the virus and its vectors. A range of techniques was used to assess genetic differentiation among 27 clones belonging to the Myzus persicae complex (M. persicae (Sulzer), M. antirrhinii (Macchiati) and M. nicotianaeBlackman) and showing different efficiencies in transmitting PLRV isolates. All M. persicae/M. nicotianae clones belonged to one of two karyotypes, both 2n = 12, either normal or carrying an autosomal translocation (A1,3), and all M. antirrhinii clones had 13 or 14 chromosomes. Amplified esterase 4 genes were detected by PCR–REN assay in M. persicae/M. nicotianae taxa, with gene expression being modified by methylation. Similarly, amplified E4 genes were revealed in M. antirrhinii but they all showed unmethylated. Two allozyme and 11 microsatellite loci discriminated 10 different genotypic classes among the 27 clones. Analysis of genetic relatedness between these genotypic classes revealed that M. nicotianae clones were very closely related to M. persicaeclones, whereas the genetic differentiation between M. antirrhinii and M. persicae was greater. The implications of these results for the taxonomic status of these genotypes within the complex, and the transmission of PLRV, are discussed.
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Verhaegh, Suzanne J. C., Martine L. Snippe, Foster Levy, et al. "Colonization of healthy children by Moraxella catarrhalis is characterized by genotype heterogeneity, virulence gene diversity and co-colonization with Haemophilus influenzae." Microbiology 157, no. 1 (2011): 169–78. http://dx.doi.org/10.1099/mic.0.042929-0.
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The colonization dynamics of Moraxella catarrhalis were studied in a population comprising 1079 healthy children living in Rotterdam, The Netherlands (the Generation R Focus cohort). A total of 2751 nasal swabs were obtained during four clinic visits timed to take place at 1.5, 6, 14 and 24 months of age, yielding a total of 709 M. catarrhalis and 621 Haemophilus influenzae isolates. Between January 2004 and December 2006, approximate but regular 6-monthly cycles of colonization were observed, with peak colonization incidences occurring in the autumn/winter for M. catarrhalis, and winter/spring for H. influenzae. Co-colonization was significantly more likely than single-species colonization with either M. catarrhalis or H. influenzae, with genotypic analysis revealing no clonality for co-colonizing or single colonizers of either bacterial species. This finding is especially relevant considering the recent discovery of the importance of H. influenzae–M. catarrhalis quorum sensing in biofilm formation and host clearance. Bacterial genotype heterogeneity was maintained over the 3-year period of the study, even within this relatively localized geographical region, and there was no association of genotypes with either season or year of isolation. Furthermore, chronological and genotypic diversity in three immunologically important M. catarrhalis virulence genes (uspA1, uspA2 and hag/mid) was also observed. This study indicates that genotypic variation is a key factor contributing to the success of M. catarrhalis colonization of healthy children in the first years of life. Furthermore, variation in immunologically relevant virulence genes within colonizing populations, and even within genotypically identical M. catarrhalis isolates, may be a result of immune evasion by this pathogen. Finally, the factors facilitating M. catarrhalis and H. influenzae co-colonization need to be further investigated.
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Zambounis, Antonios, Eleni Stefanidou, Panagiotis Madesis, Jovana Hrustić, Milica Mihajlović, and Brankica Tanović. "Genotypic differentiation of Monilinia spp. populations in Serbia using a high-resolution melting (HRM) analysis." Plant Protection Science 57, No. 1 (2020): 38–46. http://dx.doi.org/10.17221/35/2020-pps.
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Monilinia laxa, Monilinia fructicola and Monilinia fructigena are the three main causal agents of brown rot, which is one of the most important diseases of stone fruits in pre- and postharvest conditions. Nowadays, the need for the precise genotyping of these Monilinia species in terms of the genetic diversity of their populations or differences in their pathogenicity and host range is a prerequisite for any efficient disease management. In our study, the genetic structure of Monilinia populations in Serbia from three geographically distinct regions was investigated employing <br /> a high-resolution melting (HRM) analysis which is a sensitive and rapid molecular approach in fungal genotyping and diagnostics. Using species-specific primer pairs genotype-specific HRM melting curve profiles were generated allowing to efficiently decipher the genetic diversity of the Monilinia populations. The Monilinia genotypes could be easily distinguished according to their melting curves. The isolates from the northern region were assigned to distinct genotypes and grouped rather independently compared to the isolates of the other two regions among all three tested Monilinia spp. M. fructicola and M. fructigena showed a higher genetic diversity among their populations (44%) compared with the genetic diversity among the M. laxa populations (7%). In contrast, the genetic variance within the pathogen populations was higher in the case of M. laxa (93%). Our data revealed an absence of host specificity in the Monilinia spp. populations.
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Peng, Yousheng, Chenchen Li, Xueke Hui, Xiaoning Huo, Nigus Abebe Shumuyed, and Zhong Jia. "Phenotypic and genotypic analysis of drug resistance in M. tuberculosis isolates in Gansu, China." PLOS ONE 19, no. 9 (2024): e0311042. http://dx.doi.org/10.1371/journal.pone.0311042.
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Tuberculosis has posed a serious threat to human health. It is imperative to investigate the geographic prevalence of tuberculosis and medication resistance, as this information is essential for informing strategies for its prevention and treatment. Drug resistance was identified using a proportion method. Drug-resistant genes and pathways were predicted using whole genome sequencing. The drug resistance range of bedaquiline was identified using the microporous plate two-fold dilution method, and drug resistance genes were studied using sequencing. The study revealed that 19.99% of the tuberculosis cases had multidrug resistance. The genes of M. tuberculosis are predominantly involved in the synthesis of ABC transporters, two-component systems, and bacterial secretion systems, as well as in energy production and conversion, and lipid transport and metabolism. The genes encode for 82.45% of carbohydrate-related enzymes such as glycoside hydrolases, glycosyl transferases, and carbohydrate esterases. The minimum inhibitory concentration (MIC) of bedaquiline against clinical strains was approximately 0.06 μg/mL, with identified mutations in drug-resistant genes Rv0678, atpE, and pepQ, specifically V152A, P62A, and T222N, respectively. The multidrug resistance tuberculosis development was attributed to the strong medication resistance exhibited. It was concluded that tuberculosis had presented a high level of drug resistance. Phenotypic resistance was related to genes, existing potential genetic resistance in M. tuberculosis. Bedaquiline was found to possess effective antibacterial properties against M. tuberculosis.
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Maekawa, Masato, Kayoko Sudo, StevenS L. Li, and Takashi Kanno. "Genotypic analysis of families with lactate dehydrogenase A(M) deficiency by selective DNA amplification." Human Genetics 88, no. 1 (1991): 34–38. http://dx.doi.org/10.1007/bf00204925.
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Huys, G., L. Rigouts, K. Chemlal, F. Portaels, and J. Swings. "Evaluation of Amplified Fragment Length Polymorphism Analysis for Inter- and Intraspecific Differentiation ofMycobacterium bovis, M. tuberculosis, andM. ulcerans." Journal of Clinical Microbiology 38, no. 10 (2000): 3675–80. http://dx.doi.org/10.1128/jcm.38.10.3675-3680.2000.
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The usefulness of amplified fragment length polymorphism (AFLP) analysis was evaluated for the discrimination of Mycobacterium bovis (17 strains), M. tuberculosis (15 strains), andM. ulcerans (12 strains) at the inter- and intraspecific level. The AFLP technique is a whole-genome coverage genotypic fingerprinting method based on the selective PCR amplification of modified restriction fragments obtained through a double enzymatic digest and subsequent ligation of double-stranded restriction site-specific adapter oligonucleotides. Selective amplification ofApaI/TaqI templates with primer combination A02-T02 (both having an additional C at their 3′ end) generated autoradiographic AFLP fingerprints that were grouped by numerical analysis in two main AFLP clusters allowing clear separation ofM. ulcerans (cluster I) from the M. tuberculosis complex members M. bovis and M. tuberculosis (cluster II). Calculation of similarities using the band-based Dice correlation coefficient instead of the Pearson product-moment correlation coefficient revealed a further subgrouping in cluster II. The two resulting subclusters corresponded with the phenotypic identity of M. bovis and M. tuberculosis, respectively, and could also be visually identified by two AFLP marker bands. Because of the relatively low degree of genotypic variation among the AFLP band patterns of the latter two taxa, no correlation could be found with previously reported molecular typing data or with geographical origin. The use of primer combination A02-T01 (the latter having an A as selective base) did not increase the resolving power within the M. tuberculosis complex but resulted in a visual subgrouping of the M. ulcerans strains that was not observed with primer combination A02-T02. Based on the presence or absence of a single AFLP marker band, the M. ulcerans isolates could be unambiguously classified in two continental types corresponding with the African and Australian origin of the strains, respectively. In conclusion, the radioactive AFLP method proved to be a reproducible and reliable taxonomic tool for the differentiation of the three mycobacterial species under study and also demonstrated its potential use for typing of M. ulceransstrains when employing multiple primer combinations.
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Liu, Y. P., M. A. Behr, P. M. Small, and N. Kurn. "Genotypic Determination of Mycobacterium tuberculosisAntibiotic Resistance Using a Novel Mutation Detection Method, the Branch Migration Inhibition M. tuberculosis Antibiotic Resistance Test." Journal of Clinical Microbiology 38, no. 10 (2000): 3656–62. http://dx.doi.org/10.1128/jcm.38.10.3656-3662.2000.
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A novel method for the detection of any alteration within a defined sequence has recently been demonstrated (A. Lishanski, N. Kurn, and E. F. Ullman, Nucleic Acids Res. 28:E42, 2000; A. Lishanski, Clin. Chem. 46:9, 2000). Essential to this method are the generation of partial duplexes that are capable of forming four-stranded structures and the ability to detect inhibition of branch migration in these structures (I. G. Panyutin and P. Hsieh, J. Mol. Biol. 230:413–424, 1993). Inhibition of branch migration indicates the presence of sequence alteration. This mutation detection method, termed branch migration inhibition (BMI), is suitable for the detection of drug resistance in M. tuberculosis, which is frequently associated with multiple mutations within known genes. We describe the genotypic determination of the rifampin (RMP) and pyrazinamide (PZA) susceptibilities of M. tuberculosis isolates, using BMI coupled with the luminescence oxygen channeling immunoassay (LOCI) (E. F. Ullman et al., Proc. Natl. Acad. Sci. USA 91:5426–5430, 1994). RMP and PZA resistances are associated with multiple mutations within the rpoB and pncA genes, respectively.M. tuberculosis genomic DNA samples prepared from 46 clinical isolates were used for genotypic determination of RMP resistance in a “blind study.” Similarly, PZA resistance was determined using genomic DNA samples prepared from 37 clinical isolates. Full agreement of the genotypic and phenotypic determinations of drug susceptibility was demonstrated. RMP susceptibility determination directly from cells of 10 clinical isolates grown in culture was also demonstrated. The genotypic result of only 1 out of 10 isolates did not agree with the phenotypic susceptibility testing result. Sequence analysis of the rpoB gene of this clinical isolate revealed a single base substitution, most likely a silent point mutation. The new BMI-LOCI mutation detection method is a rapid and accurate procedure for the genotypic determination of the RMP and PZA susceptibilities of M. tuberculosis clinical isolates. BMI can also be detected by using commercially available automated enzyme-linked immunosorbent assay plate formats (Lishanski et al., Nucleic Acids Res. 28:E42, 2000).
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Khomphet, Thanet, Warin Intana, Athakorn Promwee, and Shams Shaila Islam. "Genetic Variability, Correlation, and Path Analysis of Thai Commercial Melon Varieties." International Journal of Agronomy 2022 (March 10, 2022): 1–6. http://dx.doi.org/10.1155/2022/7877239.
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In the selection phase of melon breeding programs, genetic variability is a critical component for yield improvement. The goals of this study were to discover the variables that affect melon fruit weight and examine genetic variability, correlation, and path analysis of eight melon varieties. The experiment was arranged as a completely randomized block design with 4 blocks. It was conducted between July and September 2021 at the School of Agricultural Technology, Walailak University, Nakhon Si Thammarat, Thailand. The result found that stem diameter and length, leaf length, width, number, and chlorophyll, day to 50% male and female flowering, and fruit perimeter, height, and weight were highly significant across the varieties. The genotypic coefficients of variation (GCV) of observed variables were all lower than phenotypic coefficients of variation (PCV). Fruit weight (15.462 and 19.865%) had the highest GCV and PCV. High broad-sense heritability was linked to high (H) or moderate (M) genetic advance as a percentage of the mean from stem length (67.606%: H and 21.992%: H), fruit weight (60.586%: H and 24.793%: H), fruit perimeter (76.395%: H and 12.258%: M), and fruit height (69.828%: H and 12.122%: M). The maximum and significant genotypic correlation value was obtained between leaf length and leaf width (r = 1.000). Fruit weight is positively correlated with fruit perimeter (r = 0.940) and fruit height (r = 0.831). According to correlation and path analyses, stem diameter and length, leaf chlorophyll, and fruit perimeter and height were considered variables for fruit weight improvement in the breeding programs. It suggests that the increase in traits with a favorable direct influence on fruit weight may directly contribute to fruit weight.
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Khromova, P. A., S. N. Zhdanova, N. S. Solovieva, et al. "Genotypic and phenotypic characteristics of <i>Mycobacterium tuberculosis</i> drug resistance in TB children." Acta Biomedica Scientifica 7, no. 6 (2022): 82–91. http://dx.doi.org/10.29413/abs.2022-7.6.8.
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Background. Russian Federation is included in the list of 30 countries with the highest burden of tuberculosis, including MDR tuberculosis. The most important part of this problem is the primary MDR/XDR TB in children.The aim: a comparative analysis of the phenotypic and genotypic profile of drug resistance to anti-tuberculosis drugs (ATP) according to whole genome sequencing of M. tuberculosis strains from children.Materials and methods. Whole genome sequencing (WGS) results of 61 M. tuberculosis isolates from children with tuberculosis in 2006–2020 in the Russian Federation were analyzed for anti-TB drug resistance mutations, according to the WHO catalog and were compared with the results of phenotypic drug sensitivity.Results. The M. tuberculosis belonged to two genetic groups: Beijing genotype – 82 % (50/61) dominant Central Asian Russian (31/50) and B0/W148 (16/50) subtypes, and non-Beijing (Ural, S, LAM) – 18 % (11/61). Three isolates belonged to Asian Ancestral subtype (3/50). Of the 61 isolates, only 14.7 % (9/61) were sensitive to antiTB drugs, 49.2 % (30/61) were MDR and 14.7 % (9/61) were pre-XDR. Comparison of the resistance profile (MDR/pre-XDR) with genotype revealed an upward shift for Beijing isolates, in particular Beijing B0/W148 (15/16) subline compared to other Beijing (19/34) (Chi-square with Yates correction = 5.535; p < 0.05) and nonBeijing (5/12) (Chi-square with Yates correction = 6.741; p < 0.05) subtypes. Discrepancies between genotypic and phenotypic drug resistance profiles were found in 11.5 % (7/61) of cases.Conclusions. Based on the analysis of WGS data, the genotypic characteristics of M. tuberculosis and the most complete set of drug resistance mutations were obtained, indicating a significant prevalence in MDR and pre-XDR TB of cases caused by epidemic subtypes of Beijing (B0/W148 and Central Asian Russian). The molecular mechanisms of adaptation of M. tuberculosis to the treatment of anti-TB drugs are not unique for the child population but reflect the general processes of the spread of MDR/XDR in Russia.
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Yadav, Chandra Bhan, Prakash I. Gangashetty, Manfred Beckmann, Luis A. J. Mur, and Rattan S. Yadav. "Genotype-by-Environment Interaction Analysis of Metabolites in Pearl Millet Genotypes with High Concentrations of Slowly Digestible and Resistant Starch in Their Grains." Cells 11, no. 19 (2022): 3109. http://dx.doi.org/10.3390/cells11193109.
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Genotype × environment interactions (GEIs) should play an important role in the selection of suitable germplasm in breeding programmes. We here assessed GEI effects on pearl millet (Pennisetum glaucum L.) genotypes, selected to possess a high concentration of slowly digestible starch (SDS) and resistant starch (RS) in their grains. Entries were grown in a randomized complete block design with three replications at locations in Bawku-Ghana, Sadore-Niger, Bamako-Mali, Konni-Nigeria, and Gampella-Burkina Faso across West Africa. Harvested grains from these locations were metabolomically profiled using flow injection ionization-high-resolution mass spectrometry (FIE-HRMS). A total of 3144 mass features (m/z) (1560 negative ion mode and 1584 positive ion mode) were detected, of which, 475 m/z were linked to metabolites be involved in starch, antioxidant and lipid biosynthesis, and vitamin metabolism. Combined ANOVA revealed that the GEI was significantly evident for 54 health-benefiting metabolites, many associated with sugar, especially galactose, metabolism. Additive main effects and multiplicative interaction (AMMI) analysis examined genotype variation and GEI effects, which, when combined with principal component analysis (PCA), found that m/z 171.14864 (positive ionisation, propenyl heptanoate) accounted for 89% of the GEI variation along PC1. The AMMI-based stability parameter (ASTAB), modified AMMI stability value (MASV), and modified AMMI stability index (MASI) were then applied to identify stable and high-performing genotypes for all the health-benefiting metabolites. Similarly, the best-linear-unbiased-prediction (BLUP)-based stability estimation was also performed using the harmonic mean of genotypic values (HMGV), relative performance of genotypic values (RPGV), and harmonic mean of relative performance of genotypic values (HMRPGV), to identify genotype rankings across multiple environments. The multi-trait stability index (MTSI) was calculated and found that the genotypes G1 (ICMH-177111) and G24 (ICMX-207137) were the most stable and were the best mean performers across 52 health-benefiting metabolic traits. These findings demonstrate the potential of G × E assessments on the delivery of health-benefiting metabolite-rich grains in future varieties and hybrids of pearl millet.
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VOUGIDOU (Χ. ΒΟΥΓΙΔΟΥ), C., V. SANDALAKIS (Β. ΣΑΝΤΑΛΑΚΗΣ), A. PSAROULAKI (Α. ΨΑΡΟΥΛΑΚΗ), E. PETRIDOU (Ε.Ι. ΠΕΤΡΙΔΟΥ), W. DONACHIE, and L. EKATERINIADOU (Λ.ΑΙΚΑΤΕΡΙΝΙΑΔΟΥ). "Serotypic diversity and sequence variation of the ompA gene among Mannheimia haemofytica isolates from domestic ruminants." Journal of the Hellenic Veterinary Medical Society 63, no. 1 (2017): 13. http://dx.doi.org/10.12681/jhvms.15389.
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Pneumonia caused by Mannheìmia haemolytica is an important disease of ruminants. Because of its economic significance, several methods have been used to study the pathogenicity and epidemiology of M. haemolytica. The objectives of this study were to provide data about the prevalence of the different serotypes of the bacterium and to investigate the genetic diversity of a significant virulence factor, the ompA gene. Two methods, DNA sequencing analysis and DGGli, were used to study the polymorphisms of the ompA gene. Ninety-four isolates from pneumonic lungs were investigated. Capsular scrotyping showed that serotype Λ2 was the predominant serotype among ovine strains and the only serotype found in caprine strains. This is the first reported analysis of the ompA gene of M haemolytica strains isolated from goats. Analysis of the gene revealed five DGGli patterns and nine genotypic groups. The ovine isolates, which belonged to four DC G li patterns, showed a much greater diversity than the caprine strains, which belonged to just two DGGF patterns, Sequence analysis was used to verify the DGGE results and revealed eight genotypic groups among the ovine isolates and three among the caprine ones. Furthermore, the correlation of these results showed a great diversity of the ompA gene among serotype A2 isolates.
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Voinescu, Adela, Corina Musuroi, Monica Licker, et al. "Comparative Analysis of Bacterial Conjunctivitis in the Adult and Pediatric Inpatient vs. Outpatient Population." Microorganisms 13, no. 3 (2025): 473. https://doi.org/10.3390/microorganisms13030473.
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The etiology and resistance pattern of bacterial conjunctivitis varies depending on the patient’s care setting and age. A retrospective, observational study was conducted in a tertiary care teaching hospital. A total of 126 patients—76 adults and 50 children—diagnosed with conjunctival infection during inpatient or ambulatory care were analyzed. In the samples of adult patients, isolates were represented by Gram-positive cocci (57.7%; Staphylococcus spp., S. pneumoniae) followed by Enterobacterales (17.97%; P. mirabilis, E. coli, Klebsiella spp.), and non-fermenters (7.69%; Pseudomonas spp., A. baumannii). Multidrug-resistant (52.17%) and extensively drug-resistant (21.73%) pathogens (predominantly Gram-negative bacilli) were identified in conjunctival swabs of hospitalized adult patients. The main isolates (55.77%) identified in children’s conjunctival swabs belonged to S. aureus, H. influenzae, and S. pneumoniae, followed by Enterobacterales (19.22%; E. coli, P. mirabilis, M. morganii) and fungi (3.48%). Methicillin-resistant S. aureus (35.71%) and extended-spectrum beta-lactamase-producing K. pneumoniae (8.7%) were identified in the pediatric subgroup of patients. In critically ill adult patients assisted in the intensive care or burn functional units, bacterial conjunctivitis followed the pattern of infections and antimicrobial resistance specific to these categories of patients. In the case of hospitalized children, conjunctivitis was an integral part of the age-related pathology.
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Yousfi, Salima, Maria Dolores Serret та José Luis Araus. "Shoot δ15N gives a better indication than ion concentration or Δ13C of genotypic differences in the response of durum wheat to salinity". Functional Plant Biology 36, № 2 (2009): 144. http://dx.doi.org/10.1071/fp08135.
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We compared the performance of different physiological traits that reveal genotypic variations in tolerance to salinity in durum wheat. A set of 114 genotypes was grown in hydroponics for over 3 months. Three conditions: control, moderate (12 dS m−1) and severe (17 dS m−1) salinity, were maintained for nearly 8 weeks before harvest. The genotype biomass in control conditions correlated with the biomass at the two salinity levels. Subsequently, two subsets of 10 genotypes each were selected on the basis of extreme differences in biomass at the two salinity levels while showing relatively similar biomass in control conditions. Carbon isotope discrimination (Δ13C), nitrogen isotope composition (δ15N), and the concentration of nitrogen, phosphorus and several ions (K+, Na+, Ca2+, Mg2+) were analysed in the two subsets for the three treatments. At 12 dS m−1, K+ concentration, K+/Na+ ratio, Δ13C and δ15N correlated positively and Na+ correlated negatively with shoot biomass. Under control conditions and at 17 dS m−1 no correlation was observed. However, the trait that correlated best with genotypic differences in biomass was δ15N at 12 dS m−1. This trait was the first variable chosen at each of the two salinity levels in a stepwise analysis. We consider the possible mechanisms relating δ15N to biomass and the use of this isotopic signature as a selection trait.
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Sinkov, V. V., and O. V. Ogarkov. "Population structure of the B0/W148 Mycobacterium tuberculosis subtype: Phylogenetic analysis and characteristics of genotypic drug resistance." Acta Biomedica Scientifica 9, no. 4 (2024): 248–59. http://dx.doi.org/10.29413/abs.2024-9.4.27.
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Background. The B0/W148 subtype belongs to the L2phylogenetic lineage of Mycobacterium tuberculosis and is most common in the former Soviet Union. Test systems capable of detecting genetic variants of the pathogen are needed for effective epidemiological surveillance. Studying the genetic diversity of B0/W148 strains and finding molecular markers suitable for their genotyping are key steps in the development of such diagnostic tools.The aim of the work. To study the phylogenetic diversity of the B0/W148 subtype circulating in the territory of the Russian Federation and neighboring countries in order to identify unique clades and search for specific molecular markers suitable for their precise identification.Materials and methods. The study used DNA samples of B0/W148 strains (n = 34) isolated in different regions of the Russian Federation, as well as genomic data obtained from the SRA NCBI (Sequence Read Archive of the National Center for Biotechnology Information) (n = 419). Phylogenetic analysis and principal component analysis (PCA) of whole genome sequencing (WGS) data were used to analyze genetic diversity and to identify molecular markers. An evolutionary reconstruction of the age of the identified clades was carried out.Results. The analysis of the B0/W148 genomes (n = 453) revealed that they are divided into three phylogenetic clades: B – basal, M – minor and P – principal. It was found that specific mutations in the M and P clades allow for their differential diagnosis. The 4137219T>G mutation is unique for the M clade, and the 2241091C>T mutation is unique for the P clade. No characteristic mutations were found among the strains of B clade. In addition, unique mutation profiles in the genes responsible for drug resistance were identified for the clades.Conclusion. The study showed that B0/W148 strains represent a genetically heterogeneous population divided into B, M and P clades. M and P Clades have unique mutations that allow for their identification. It was also found that all clades are characterized by the presence of specific mutation profiles in drug resistance genes.
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Piatek, Amy S., Amalio Telenti, Megan R. Murray, et al. "Genotypic Analysis of Mycobacterium tuberculosis in Two Distinct Populations Using Molecular Beacons: Implications for Rapid Susceptibility Testing." Antimicrobial Agents and Chemotherapy 44, no. 1 (2000): 103–10. http://dx.doi.org/10.1128/aac.44.1.103-110.2000.
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ABSTRACT Past genotypic studies of Mycobacterium tuberculosismay have incorrectly estimated the importance of specific drug resistance mutations due to a number of sampling biases including an overrepresentation of multidrug-resistant (MDR) isolates. An accurate assessment of resistance mutations is crucial for understanding basic resistance mechanisms and designing genotypic drug resistance assays. We developed a rapid closed-tube PCR assay using fluorogenic reporter molecules called molecular beacons to detect reportedly common M. tuberculosis mutations associated with resistance to isoniazid and rifampin. The assay was used in a comparative genotypic investigation of two different study populations to determine whether these known mutations account for most cases of clinical drug resistance. We analyzed samples from a reference laboratory in Madrid, Spain, which receives an overrepresentation of MDR isolates similar to prior studies and from a community medical center in New York where almost all of the resistant isolates and an equal number of susceptible controls were available. The ability of the molecular beacon assay to predict resistance to isoniazid and rifampin was also assessed. The overall sensitivity and specificity of the assay for isoniazid resistance were 85 and 100%, respectively, and those for rifampin resistance were 98 and 100%, respectively. Rifampin resistance mutations were detected equally well in isolates from both study populations; however, isoniazid resistance mutations were detected in 94% of the isolates from Madrid but in only 76% of the isolates from New York (P = 0.02). In New York, isoniazid resistance mutations were significantly more common in the MDR isolates (94%) than in single-drug-resistant isolates (44%; P < 0.001). No association between previously described mutations in thekasA gene and isoniazid resistance was found. The first mutations that cause isoniazid resistance may often occur in sequences that have not been commonly associated with isoniazid resistance, possibly in other as yet uncharacterized genes. The molecular beacon assay was simple, rapid, and highly sensitive for the detection of rifampin-resistant M. tuberculosis isolates and for the detection of isoniazid resistance in MDR isolates.
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Akhter, S., JM Ferdous, MR Hossain, and G. Rabbani. "Genetic Analysis and Character Association in Jamir (Citrus jambhiri) Accessions of Bangladesh by Using Morphological Traits." Progressive Agriculture 20, no. 1-2 (2013): 17–26. http://dx.doi.org/10.3329/pa.v20i1-2.16843.
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An experiment was carried out to study the morphological variability, characters association, correlation and path coefficient analysis of 14 Jamir accessions during the period from January 2007 to March 2008. Significant variations were observed for all the plant characters studied. The accession CJ09 was characterized with the maximum plant height (6.20m), spreading of branch (north-south 4.90 m and east-west 4.87m), base girth (58cm), plant growth (102.76m3), tree volume (24.64m3) and segment length (9.70). The accession CJ15 showed maximum spine length (25.33mm), CJ05 was characterized with high lamina area (14.94cm3). The accession CJ12 showed the highest % fruit set (36.67%). The highest fruit weight (1753.33g), fruit diameter (46cm), rind thickness (2.73cm) was observed in CJ11. The accession CJ09 was characterized with maximum number of segment (15.33) and pulp weight (746.67). Maximum TSS (12.20%) was found in CJ12. The accession CJ09 was characterized with minimum number of seeds (14). Correlation coefficient study indicated that fruit diameter, rind thickness, length of segment and number of segment had positive and highly significant phenotypic association with fruit weight and also genotypic positive association. Percent Fruit set had negative genotypic and phenotypic association with fruit weight. In respect of path analysis, fruit diameter, rind thickness, number of segment, length of segment contributed to maximum phenotypic and genotypic direct effects on fruit weight indicating their importance as selection parameters.DOI: http://dx.doi.org/10.3329/pa.v20i1-2.16843 Progress. Agric. 20(1 & 2): 17 26, 2009
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Polizzi, G., A. Vitale, I. Castello, J. Z. Groenewald, and P. W. Crous. "Cylindrocladium Leaf Spot, Blight, and Crown Rot, New Diseases of Mastic Tree Seedlings Caused by Cylindrocladium scoparium." Plant Disease 90, no. 8 (2006): 1110. http://dx.doi.org/10.1094/pd-90-1110b.
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The mastic tree (Pistacia lentiscus L., Anacardiaceae) is an important sclerophyllous evergreen shrub in the Mediterranean area where it is the dominant component of maquis and garrigues, which is vegetation composed of shrubs, or scrub, usually not exceeding 3 m high. In October 2005, new widespread diseases were noticed in a nursery in eastern Sicily (Italy) affecting container-grown, 1-year-old mastic tree seedlings. Symptoms were detected on approximately 40% of the 5,000 plants and consisted of minute, brown spots, stem lesions, blight, and defoliation. Occasionally, symptoms of crown and root rot were observed. A Cylindrocladium sp. was consistently isolated from rotted crown and roots, leaf spots, and stem lesions on potato dextrose agar. Morphological features of the fungus including conidiophores, conidia, and terminal vesicles were studied under a light microscope. Five Cylindrocladium isolates were cultured on carnation leaf agar (CLA) and identified as C. scoparium Morgan (teleomorph Calonectria morganii Crous, Alfenas & M.J. Wingf.) on the basis of their pyriform to broadly ellipsoidal terminal vesicles, conidiophore branching pattern, conidium and perithecial morphology, as well as their ability to mate with tester strains of selected C. scoparium isolates (2,3). Sequences of partial β-tubulin (GenBank Accessions Nos. DQ521599 and DQ521600) and histone H3 genes (GenBank Accessions Nos. DQ521601 and DQ521602) were generated as described previously (1) for two of the isolates (CBS 119669 and CBS 119670, respectively). A BLAST analysis of the β-tubulin sequences revealed 100% similarity with C. morganii (GenBank Accessions Nos. AF210872, AF210874, and AF210875). No histone H3 sequences are currently available in the GenBank database for C. morganii, and the two sequences generated in this study, therefore, represent the first publicly available histone H3 sequences for this species. Koch's postulates were fulfilled by inoculating 20 1-year-old mastic tree seedlings with a spore suspension of the fungus (105 conidia per ml) obtained from 14-day-old single-spore colonies grown on CLA at 24°C under fluorescent cool white lights on a 12-h light/dark regimen. Following inoculation, all plants were maintained in plastic bags in a growth chamber in which the temperature was 25 ± 1°C and relative humidity was 90 to 95%. The same number of seedlings was used as a control. After 5 to 7 days, foliar symptoms resembling those seen in the nursery were detected on inoculated plants. Crown and root rot symptoms appeared on two plants after 1 month. C. scoparium was reisolated from the artificially infected tissues. No symptoms were detected on the control plants. To our knowledge, this is the first record of this disease in mastic tree and the first record of C. scoparium in Italy. This report also represents the first definitive confirmation of C. scoparium in Europe. References: (1) P. W. Crous et al. Stud. Mycol. 50:415–430, 2004. (2) P. W. Crous and M. J. Wingfield. Mycotaxon 51:341, 1994. (3) C. L. Schoch et al. Mycologia 91:286, 1999.
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Nonghanphithak, Ditthawat, Orawee Kaewprasert, Pratchakan Chaiyachat, Wipa Reechaipichitkul, Angkana Chaiprasert, and Kiatichai Faksri. "Whole-genome sequence analysis and comparisons between drug-resistance mutations and minimum inhibitory concentrations of Mycobacterium tuberculosis isolates causing M/XDR-TB." PLOS ONE 15, no. 12 (2020): e0244829. http://dx.doi.org/10.1371/journal.pone.0244829.
Full textAbstract:
Drug resistance (DR) remains a major challenge for tuberculosis (TB) control. Whole-genome sequencing (WGS) provides the highest genetic resolution for genotypic drug-susceptibility tests (DST). We compared DST profiles of 60 Mycobacterium tuberculosis isolates which were drug resistant according to agar proportion tests (one poly DR-TB, 34 multidrug-resistant TB and 25 extensively drug-resistant TB). We additionally performed minimum inhibitory concentration (MIC) tests using Sensititre MYCOTBI plates (MYCOTB) and a WGS-based DST. Agreement between WGS-based DST and MYCOTB was high for all drugs except ethambutol (65%) and ethionamide (62%). Isolates harboring the -15 c/t inhA promoter mutation had a significantly lower MIC for isoniazid than did isolates with the katG Ser315Thr mutation (p < 0.001). Similar patterns were seen for ethambutol (embB Gly406Asp vs. embB Met306Ile), streptomycin (gid Gly73Ala vs. rpsL Lys43Arg), moxifloxacin (gyrA Ala90Val vs. gyrA Asp94Gly) and rifabutin (rpoB Asp435Phe/Tyr/Val vs. rpoB Ser450Leu). For genotypic heteroresistance, isolates with lower proportion of mapped read tended to has lower MIC of anti-TB drugs than those with higher proportion. These results emphasize the high applicability of WGS for determination of DR-TB and the association of particular mutations with MIC levels.
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Voltas, J., I. Romagosa, A. Lafarga, A. P. Armesto, A. Sombrero, and J. L. Araus. "Genotype by environment interaction for grain yield and carbon isotope discrimination of barley in Mediterranean Spain." Australian Journal of Agricultural Research 50, no. 7 (1999): 1263. http://dx.doi.org/10.1071/ar98137.
Full textAbstract:
Carbon isotope discrimination (Δ) has been found to be either positively or negatively related to grain yield of small grain cereals when grown in contrasting environments. In order to clarify a possible association between grain yield of barley (Hordeum vulgare L.) and Δ of mature kernels, five 6-rowed and five 2-rowed barley cultivars were evaluated in 22 rainfed environments of northern Mediterranean Spain. Analyses of variance suggested that the genotypic Δ values were more consistent across environments than the genotypic yields. Genotype×environment (G×E) interaction for grain yield was further explored by fitting an AMMI (additive main effects and multiplicative interaction) model. The first 2 multiplicative axes were found significant. The AMMI2 model provided more accurate estimates of genotypic yields within environments than the conventional unadjusted means across replicates. AMMI2 estimates were used for input into cluster analysis, grouping environments that ranked genotypic yields similarly. Three major groups were obtained, with average yields of 2.42 t/ha (cluster I), 3.06 t/ha (cluster II), and 5.16 t/ha (cluster III). The genotypic ranking for Δ did not vary substantially across clusters, but it changed for grain yield. The average genotypic yields in the low-yielding cluster I ranked opposite to those in the high-yielding cluster III, suggesting the existence of a crossover point at an intermediate yield level. The association between grain yield and Δ for genotypic means within clusters was variable. In cluster I, yield and Δ tended to be negatively related, whereas they were positively related in clusters II and III. Genotypes with lower Δ, i.e. with higher transpiration efficiency, performed better in low-yielding environments (mostly those grouped in cluster I). On the contrary, a high genotypic Δ was of advantage in medium (cluster II) and high-yielding environments (cluster III). This observation supports the assumption that drought tolerance and high yield potential under non-limiting growing conditions may be antagonistic concepts in barley. Genotypic means for kernel number per m 2 and Δ were consistently and positively related within clusters, suggesting that a constitutively high Δ may have been driven by a large genotypic reproductive sink. The convenience of using Δ as a selection criterion in areas exhibiting a considerable G×E interaction for grain yield is discussed.