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Prevalence and Study of the Clonality of Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Strains in Neonatology at the University Hospitals of Abidjan by the Pulsed Field Gel Electrophoresis and the Quantitative Antibiogram

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Advances in microbiology 2024年第9期14卷 416-429页

作者： valérie m’bengue gbonon Sidjè Arlette Afran Stanislas Assohoun Egomli Djeda Franck Arnaud Gnahoré Aboubakar Sylla N’Golo David Coulibaly Nathalie Guessennd Assanvo Simon-Pierre N’Guetta mireille Dosso Antibiotics Natural Substances and Anti-Infectious Resistance Surveillance Unit Pasteur Institute of Cte dIvoire Abidjan Cte dIvoire molecular Genetics Platform Pasteur Institute of Cte dIvoire Abidjan Cte dIvoire Genetics and Species Improvement Laboratory Flix Houphout Boigny University Abidjan Cte dIvoire mechanics and Computer Sciences Laboratory Flix Houphout Boigny University Abidjan Cte dIvoire Biology and Health Laboratory Flix Houphout Boigny University Abidjan Cte dIvoire molecular Biology Platform Pasteur Institute of Cte dIvoire Abidjan Cte dIvoire

Background: ESBL-producing strains of Klebsiella pneumoniae, one of the main causes of nosocomial and hospital-acquired infections, are commonly associated with therapeutic impasses. Surveillance of these multidrug-resistant pathogens is a crucial tool for controlling and preventing infections. This surveillance involves the use of appropriate molecular and phenotypic typing techniques. The choice of techniques is based on criteria such as discriminatory power, intra- and inter-laboratory reproducibility, epidemiological concordance, ease of use and cost. The aim of our study was to identify clusters of Extended-Spectrum Beta-Lactamase-producing Klebsiella pneumoniae (ESBL-K. pneumoniae) strains circulating in neonatology using quantitative antibiogram (QA) and Pulsed Field Gel Electrophoresis (PFGE). materials and methods: This cross-sectional study included 55 K. pneumoniae strains isolated from a total of 513 samples. These various samples are taken from newborns, healthcare personnel, and the environment. K. pneumoniae identification followed standard bacteriological procedures and was confirmed using the Vitek® 2 (biomérieux). The detection of the ESBL phenotype was performed using the synergy test. QA and PFGE were used to identify clonal relationships between the various strains isolated. Concordance between these two methods was assessed by calculating Cohen’s KAPPA coefficient and Simpson’s diversity index. Results: Among the 55 K. pneumoniae strains included in this study, 58.2% (32/55) were found to be Extended-Spectrum Beta-Lactamase (ESBL) producers. most of these strains were isolated from neonatal samples (blood samples and rectal swabs). The quantitative antibiogram method applied to 28 out of the 32 ESBL-producing strains revealed that the isolates were grouped into 5 clusters. Pulsed Field Gel Electrophoresis performed on a total of 16 ESBL-producing strains showed the existence of four profiles. A perfect concordance was observed between the two m

关键词： Resistance-Clone-Klebsiella pneumoniae-Pulsed Field Gel Electrophoresis-Quantitative Antibiogram

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Comparative Study of Gut microbiota in Breast Cancer Patients versus Controls in Abidjan, Côte d’Ivoire

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Advances in microbiology 2024年第9期14卷 405-415页

作者： m’bengue gbonon valérie Gnahore Djeda Franck Kouadio Kouamé Assohoun Stanislas Coulibaly Safiatou Diplo Flore Bernadette Sekongo mamadou Osseni Akandji Afran Sidje Arlette N’Guessan Jean-David Dosso mireille molecular Genetics Platform Institut Pasteur de Cte dIvoire Abidjan Cte dIvoire Laboratory of Biology and Health UFR Biosciences Flix Houphout Boigny University Abidjan Cte dIvoire Department of Environment and Health Institut Pasteur de Cte dIvoire Abidjan Cte dIvoire Bioinformatics & Computational Biology Group National Computing Center of Cte dIvoire Flix Houphout Boigny University Bingerville Cte dIvoire National Blood Transfusion Center Abidjan Cte dIvoire Oncology Department Treichville University Hospital Abidjan Cte dIvoire

Context: The gut microbiota represents a complex ecosystem encompassing all unicellular microorganisms residing in the digestive tract, primarily bacteria, fungi, archaea, and even viruses. The relationship between the host and the microbiota is symbiotic: bacteria benefit from a stable environment, while the host gains numerous capabilities in terms of digestion, metabolism, nutrition, and immunity. However, numerous studies suggest that the gut microbiota plays a crucial role in various non-communicable diseases, including obesity, chronic inflammatory bowel diseases, allergic and immune disorders, behavioral disorders, and even certain cancers. The objective of our study was to characterize the gut microbiota of a group of breast cancer patients by comparing it to that of control subjects in Côte d’Ivoire, using a metagenomic approach. method: A case-control study was conducted from may 2020 to September 2023. A total of 85 women (39 cases and 46 controls) were recruited, and stool samples were collected from both breast cancer patients and healthy women. Among these, ten (10) samples from patients and ten (10) samples from healthy women were randomly selected for the study of the gut microbiota. The gut microbiota was characterized by sequencing the V4 region of 16S rRNA using metagenomic NGS technology, and bioinformatic analysis was performed using the mothur pipeline. Results: In women with breast cancer, we observed a reduction in the relative abundance of the phyla Firmicutes and Bacteroidetes, as well as an increase in the phyla Actinobacteria and Verrucomicrobia. Additionally, their microbiota exhibited lower Chao1 and Sobs diversities compared to the control women (p molecular variance analysis (AmOVA) revealed a significant difference between the case and control groups (p major phyla within the gut microbiota of cases compared to healthy controls. It wil

关键词： Gut microbiota 16S metagenomic Sequencing Breast Cancer Dysbiosis

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Dissemination of Resistance Integrons and Genes Coding for Blse and Cabapenemases in the Urban Drainage Network in Cote d’Ivoire

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Advances in microbiology 2024年第5期14卷 268-286页

作者： Coulibaly Kalpy Julien Diaby Aboubakar Sidik Vakou N’dri Sabine m’bengue gbonon valérie Carole Claon Jean Stephane Yao Kouamé Eric Gnali Gbohounou Fabrice Yéo Yéfougnini Bagré Issa Djaman Allico Joseph Dosso mireille Pasteur Institute of Ivory Coast Abidjan C&#244te d&#8217Ivoire Fé lix Houphou&#235t-Boigny University Abidjan C&#244te d&#8217Ivoire

Antibiotic resistance has become a major threat to human health worldwide. Environment, particularly the water environment, has long been overlooked as a player in the antibiotic resistance cycle, although its role remains unclear. These can provide an ideal setting for the acquisition and dissemination of antibiotic resistance, as they are frequently affected by anthropogenic activities. The objective of this study was to establish a diffusion map of resistance integrons used as genetic markers of resistance associated with antibiotic resistance conferring genes (ARGs). Total DNA extracts from non-cultivable bacterial communities were used for the analyses. These communities were obtained from wastewater samples from 14 sites upstream and downstream of drainage channels or effluents in the cities of Abidjan, Bouaké, and Yamoussoukro. The results obtained correspond to the number of positives among the treated samples (n = 39). Among the genetic markers of dissemination, class 1 integrons were the most evident in 94.8% of samples in Abidjan (93.3%), Bouaké (100%) and Yamoussoukro (91.6%). Class 2 integrons and class 3 integrons were found respectively in 41% and 51% of all samples. Genes coding for β-lactamases and blaTEm was identified in almost all samples at a rate of 97.4%. A co-presence of the three genes blaTEm, blaSHV and blaCTX-m is also remarkable in the sites of the city of Yamoussoukro. Among the genes coding for carbapenemases, only blaKPC 17.94%, blaNDm 30.76% and blaOXA48 38.46% were detected in the samples.

关键词： Antibiotic Resistance Wastewater Resistance Integrons (RIs) Resistance Genes

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Dissemination of Resistance Integrons and Genes Coding for Blse and Cabapenemases in the Urban Drainage Network in Cote d’Ivoire

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Advances in microbiology（微生物学） 2024年第5期 268页

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