Academic literature on the topic 'Microbiological techniques – Periodicals'

Disposal of untreated olive-mill wastewater (OMW) is a major environmental problem in many Mediterranean countries. This study assessed the impact of OMW application on soil microbiological properties and explored the relationship to soil chemical properties during a 9-month, periodical soil-sampling campaign in a pilot study area in Crete, South Greece. Cases studied involved: direct application of OMW on soil; OMW disposal in active evaporation ponds; sites hosting evaporation ponds that have been inactive for the past 9 years; sites downstream of active evaporation ponds; and control soils, upstream of the waste-disposal ponds. Long-term OMW disposal on land affected the main soil chemical properties. Applicability of the results from the systematic monitoring was confirmed by results obtained in other OMW disposal sites around the pilot area. Soil microbial properties (microbial activity, microbial biomass carbon, and metabolic quotient) were considerably affected by OMW disposal. Moreover, seasonal changes of soil properties revealed short- and long-term residual effects due to OMW disposal. Significant correlations were observed among soil microbial characteristics and soil chemical properties, clearly indicating a close relationship between chemical properties and the transformation of microbial communities in soil after OMW land spreading. The determination of a key set of chemical and microbiological parameters that can be used as indicators for monitoring soil quality at olive-mill waste-disposal areas will verify the efficiency of the techniques used for the land disposal of OMW and will consequently promote their sustainable management.

Organophosphorus compounds (OP) are chemicals widely used as pesticides in different applications such as agriculture and public health (vector control), and some of the highly toxic forms have been used as chemical weapons. After application of OPs in an environment, they persist for a period, suffering a degradation process where the biotic factors are considered the most relevant forms. However, to date, the biodegradation of OP compounds is not well understood. There are a plenty of structure-based biodegradation estimation methods, but none of them consider enzymatic interaction in predicting and better comprehending the differences in the fate of OPs in the environment. It is well known that enzymatic processes are the most relevant processes in biodegradation, and that hydrolysis is the main pathway in the natural elimination of OPs in soil samples. Due to this, we carried out theoretical studies in order to investigate the interactions of these OPs with a chosen enzyme—the phosphotriesterase. This one is characteristic of some soils’ microorganisms, and has been identified as a key player in many biodegradation processes, thanks to its capability for fast hydrolyzing of different OPs. In parallel, we conducted an experiment using native soil in two conditions, sterilized and not sterilized, spiked with specific amounts of two OPs with similar structure—paraoxon-ethyl (PXN) and O-(4-nitrophenyl) O-ethyl methylphosphonate (NEMP). The amount of OP present in the samples and the appearance of characteristic hydrolysis products were periodically monitored for 40 days using analytical techniques. Moreover, the number of microorganisms present was obtained with plate cell count. Our theoretical results were similar to what was achieved in experimental analysis. Parameters calculated by enzymatic hydrolysis were better for PXN than for NEMP. In soil, PXN suffered a faster hydrolysis than NEMP, and the cell count for PXN was higher than for NEMP, highlighting the higher microbiological toxicity of the latter. All these results pointed out that theoretical study can offer a better comprehension of the possible mechanisms involved in real biodegradation processes, showing potential in exploring how biodegradation of OPs relates with enzymatic interactions.

Objectives: The aim of this study was to assess quality status of ground water in Kathmandu valley and describe the antibiotic susceptibility of the isolated Klebsiella pneumoniae. 
 Methods: A total of 100 samples were collected from different places of Kathmandu valley with 50 each from two different groundwater sources namely boring and well. This study was conducted from June to September, 2019 at Environment and Climate Study Laboratory, Nepal Academy of Science and Technology (NAST). The physicochemical analysis of the samples was done according to standard methodology. Membrane filtration technique was performed for the enumeration of total coliform and different biochemical tests were performed for isolation and identification of Klebsiella pneumoniae followed by Kirby-Bauer disc diffusion method for antibiotic susceptibility test.
 Results: This study reveals the poor microbiological aspects of ground water sources as 98% of total water samples crossed the standard value for total coliform count. The pH, turbidity, ammonia, nitrate and iron content were found to be higher than Nepal Drinking Water Quality Standard (NDWQS 2005) in 15%, 26%, 34%, 7% and 26% of total water samples respectively. The chloride and arsenic content in all the water samples were within the NDWQS, 2005. The 12 out of 18 isolates of Klebsiella pneumoniae from ground water source were highly resistant against first generation Cefazolin however, 15 out of 18 isolates were sensitive to Chloramphenicol. Additionally, four isolates showed zone of inhibition in intermediate range provided by Clinical and Laboratory Standard Institute (CLSI) guideline towards Imipenem and Meropenem.
 Conclusion: This study concludes that ground water sources were heavily contaminated by coliform bacteria and most of the physicochemical aspects were under standard limit. Although Klebsiella pneumoniae isolated from ground water were not multidrug resistant, one isolate was recorded to be resistant to Meropenem. These results alarm for circulation of antibiotic resistance in environmental bacterial isolates. Therefore, the appropriate water purification methods should be applied before consumption and should be examined periodically.

Background: Diarrhoea is a major cause of morbidity in Cape Town, South Africa, and mortality is attributed to a failure to recognize the severity of the condition. Cryptosporidium and Giardia are increasingly recognized as important causes of diarrhoea in Africa however, suboptimal diagnostic techniques may lead to underappreciation of their significance. Our objectives are to compare the diagnostic yield of direct immunofluorescent antigen (DFA) microscopy on concentrated stool samples for Cryptosporidium and Giardia, with the current approach of wet mount microscopy for Giardia and auramine fluorescent stain for Cryptosporidium on unconcentrated stool.Methodology: Stool specimens (n=104) received at our hospital laboratory for routine microbiological investigations were used for the study. Direct wet-mount auramine-phenol fluorescent microscopy (auramine) detection of Cryptosporidium oocysts and wet mount iodine microscopy for Giardia detection, were performed on unconcentrated stool samples, while DFA stain for simultaneous detection of Cryptosporidium and Giardia was performed on sodium-acetate formalin concentrated stool samples. The diagnostic yields of the tests were compared using the MEDCALC® version 18.0Results: Of the 104 stool specimens received for microbiological analysis, only 66 (63.5%) had specific Cryptosporidium requests while 38 (36.5%) had no Cryptosporidium specific requests. Of the 66 specimens, 9 (13.6%) were positive for Cryptosporidium oocysts with DFA while only 1 (1.5%) was positive with auramine staining (p=0.013). The one auramine-positive specimen was also positive by DFA. Auramine stain microscopy gave a sensitivity of 11.1% (95%CI: 0.28-48.25%) and specificity of 100% (95%CI: 93.7%-100%) when compared to DFA. Of the 38 stool specimens without specific Cryptosporidium request, DFA yielded 5 (13.2%) additional positive results. Taken together, Cryptosporidium was detected in 14/104 (13.5%; 95%CI: 8.36–21.7%) specimens and only 1 of 14 (7.1%) specimens with the current routine laboratory testing approach. Giardia was detected by DFA in 3/104 (0.9%) specimens, while direct iodine wet mount microscopy did not yield any positive results (0%). All 3 Giardia-positive specimens had Cryptosporidium oocysts detected by DFA.Conclusion: These data suggest that a large proportion of Cryptosporidium cases remain undetected by the laboratory due to suboptimal testing methods, and failure by clinicians to specifically request for Cryptosporidium detection. There is need to periodically assess the effectiveness of diagnostic microbiology laboratory approaches to diarrhoea, and access to improved diagnostic laboratory techniques will contribute to more accurate differential diagnosis and a broadened understanding of local aetiology of diarrhoea diseases in Africa.
 Keywords: Cryptosporidium, Giardia, diarrhoea, stool concentration, DFA, microscopy 
 French Title: Amélioration des découvertes de cas de Cryptosporidium à l'aide de la microscopie immunofluorescente sur des selles concentrées
 Contexte: La diarrhée est une cause majeure de morbidité au Cap, en Afrique du Sud, et la mortalité est attribuée à l'incapacité de reconnaître la gravité de la maladie. Cryptosporidium et Giardia sont de plus en plus reconnus comme des causes importantes de diarrhée en Afrique, cependant, des techniques de diagnostic sous-optimales peuvent conduire à une sous-estimation de leur importance. Nos objectifs sont de comparer le rendement diagnostique de la microscopie à antigène immunofluorescent direct (DFA) sur des échantillons de selles concentrées pour Cryptosporidium et Giardia, avec l'approche actuelle de la microscopie à montage humide pour Giardia et la coloration fluorescente auramine pour Cryptosporidium sur des selles non concentrées.Méthodologie: Des échantillons de selles (n=104) reçus au laboratoire de notre hôpital pour des examens microbiologiques de routine ont été utilisés pour l'étude. La détection directe par microscopie fluorescente auramine-phénol à montage humide (auramine) des oocystes de Cryptosporidium et la microscopie à l'iode à montage humide pour la détection de Giardia, ont été effectuées sur des échantillons de selles non concentrées, tandis que la coloration DFA pour la détection simultanée de Cryptosporidium et de Giardia a été réalisée sur de l'acétate de sodium formaline concentré échantillons de selles. Les rendements diagnostiques des tests ont étécomparés à l'aide de MEDCALC® version 18.0Résultats: Sur les 104 échantillons de selles reçus pour l'analyse microbiologique, seuls 66 (63,5%) avaient des demandes spécifiques de Cryptosporidium tandis que 38 (36,5%) n'avaient pas de demandes spécifiques de Cryptosporidium. Sur les 66 échantillons, 9 (13,6%) étaient positifs pour les oocystes de Cryptosporidium avec DFA tandis que seulement 1 (1,5%) était positif avec coloration à l'auramine (p=0,013). Le seul échantillon positif à l'auramine était également positif au DFA. La microscopie à l'auramine a donné une sensibilité de 11,1% (IC 95%: 0,28-48,25%) et une spécificité de 100% (IC 95%: 93,7% -100%) par rapport au DFA. Sur les 38 échantillons de selles sans demande spécifique de Cryptosporidium, le DFA a donné 5 (13,2%) résultats positifs supplémentaires. Pris ensemble, Cryptosporidium a été détecté dans 14/104 (13,5%; IC à 95%: 8,36–21,7%) et seulement 1 des 14 échantillons (7,1%) avec l'approche actuelle des tests de routine en laboratoire. Giardia a été détecté par DFA dans 3/104 (0,9%) échantillons, tandis que la microscopie directe à l'iode sur monture humide n'a donné aucun résultat positif (0%). Les 3 échantillons positifs à Giardia avaient des oocystes deCryptosporidium détectés par DFA.Conclusion: Ces données suggèrent qu'une grande proportion des cas de Cryptosporidium ne sont pas détectés par le laboratoire en raison de méthodes de test sous-optimales et de l'échec des cliniciens à demander spécifiquement la détection de Cryptosporidium. Il est nécessaire d'évaluer périodiquement l'efficacité des approches de laboratoire de microbiologie diagnostique pour la diarrhée, et l'accès à des techniques de laboratoire de diagnostic améliorées contribuera à un diagnostic différentiel plus précis et à une compréhension élargie de l'étiologie locale des maladies diarrhéiques en Afrique.
 Mots clés: Cryptosporidium, Giardia, diarrhée, concentration des selles, DFA, microscopie

AbstractSurgical site infections (SSI) remain a common postoperative complication despite use of prophylactic antibiotics and other preventive measures, mainly due to increasing antimicrobial resistance. Here, we present antimicrobial resistance rate of bacteria isolated in clinical cases of SSI. A hospital based descriptive cross sectional study was conducted on 83 consented postoperative patients with clinical SSI. Data on patients was obtained using structured data collection form. Two swabs were collected aseptically from each patient. Bacteriological culture examination and identification was done following standard microbiological techniques. Antibiotic susceptibility test was done by Kirby-Bauer disc diffusion method. Gram negative bacteria (GNB) were predominant (65.59%) with the dominant being Klebsiella species (29.03%). Overall 86% of aerobic bacteria isolated were multidrug resistant (MDR) where 65.63% and 96.72% of Gram positive and Gram negative isolates were MDR respectively. All the isolates with exception of Enterococci species were resistant to ampicillin. GNB showed high resistance to ceftriaxone, sulfamethoxazole/trimethoprim and gentamicin. All the isolated Klebsiella spp were MDR. S. aureus were all resistant to oxacillin. The isolation rate was higher in emergency, males and dirty wounds in relation to nature of surgery, gender and class of surgical wound respectively. These findings necessitate judicious antibiotic use and calls for surveillance of SSIs periodically as well as strict adherence to good sanitation practice to reduce spread of drug-resistant pathogens.