Escherichia coli population structure and antibiotic resistance at a buffalo/cattle interface in Southern Africa

At a human/livestock/wildlife interface, Escherichia coli populations were used to assess the risk of bacterial and antibiotic resistance dissemination between hosts. We used phenotypic and genotypic characterization techniques to describe the structure and the level of antibiotic resistance of E. coli commensal populations and the resistant Enterobacteriaceae carriage of sympatric African buffalo (Syncerus caffer caffer) and cattle populations characterized by their contact patterns in the southern part of Hwange ecosystem in Zimbabwe. Our results (i) confirmed our assumption that buffalo and cattle share similar phylogroup profiles, dominated by B1 (44.5%) and E (29.0%) phylogroups, with some variability in A phylogroup presence (from 1.9 to 12%); (ii) identified a significant gradient of antibiotic resistance from isolated buffalo to buffalo in contact with cattle and cattle populations expressed as the Murray score among Enterobacteriaceae (0.146, 0.258, and 0.340, respectively) and as the presence of tetracycline-, trimethoprim-, and amoxicillin-resistant subdominant E. coli strains (0, 5.7, and 38%, respectively); (iii) evidenced the dissemination of tetracycline, trimethoprim, and amoxicillin resistance genes (tet, dfrA, and blaTEM-1) in 26 isolated subdominant E. coli strains between nearby buffalo and cattle populations, that led us (iv) to hypothesize the role of the human/animal interface in the dissemination of genetic material from human to cattle and toward wildlife. The study of antibiotic resistance dissemination in multihost systems and at anthropized/natural interface is necessary to better understand and mitigate its multiple threats. These results also contribute to attempts aiming at using E. coli as a tool for the identification of pathogen transmission pathway in multihost systems. (Résumé d'auteur

Escherichia coli population structure and antibiotic resistance at a buffalo/cattle interface in southern Africa

At a human/livestock/wildlife interface, Escherichia coli populations were used to assess the risk of bacterial and antibiotic resistance dissemination between hosts. We used phenotypic and genotypic characterization techniques to describe the structure and the level of antibiotic resistance of E. coli commensal populations and the resistant Enterobacteriaceae carriage of sympatric African buffalo (Syncerus caffer caffer) and cattle populations characterized by their contact patterns in the southern part of Hwange ecosystem in Zimbabwe. Our results (i) confirmed our assumption that buffalo and cattle share similar phylogroup profiles, dominated by B1 (44.5%) and E (29.0%) phylogroups, with some variability in A phylogroup presence (from 1.9 to 12%); (ii) identified a significant gradient of antibiotic resistance from isolated buffalo to buffalo in contact with cattle and cattle populations expressed as the Murray score among Enterobacteriaceae (0.146, 0.258, and 0.340, respectively) and as the presence of tetracycline-, trimethoprim-, and amoxicillin-resistant subdominant E. coli strains (0, 5.7, and 38%, respectively); (iii) evidenced the dissemination of tetracycline, trimethoprim, and amoxicillin resistance genes (tet, dfrA, and blaTEM-1) in 26 isolated subdominant E. coli strains between nearby buffalo and cattle populations, that led us (iv) to hypothesize the role of the human/animal interface in the dissemination of genetic material from human to cattle and toward wildlife. The study of antibiotic resistance dissemination in multihost systems and at anthropized/natural interface is necessary to better understand and mitigate its multiple threats. These results also contribute to attempts aiming at using E. coli as a tool for the identification of pathogen transmission pathway in multihost systems.This study was implemented within the framework of the research Platform Conservation and Production in Partnership (www.rp-pcp.org) and in collaboration with CNRS within the framework of the Zone Atelier in the Hwange area.Agence Nationale de la Recherche (ANR) http://dx.doi.org/10.13039/501100001665ANR-11-CEPL-003.http://aem.asm.org2017-06-30Mammal Research Institut

Escherichia coli population structure and antibioresistance at a buffalo/cattle interface in Southern Africa

At a human/livestock/wildlife interface, Escherichia coli populations were used to assess the risk of bacteria and antibioresistance dissemination between hosts. We used phenotypic and genotypic characterization techniques to describe the structure and the level of antibioresistance of E. coli commensal populations and the resistant Enterobacteriaceae carriage of sympatric African buffalo (Syncerus caffer) and cattle populations characterized by their contact patterns in the southern part of Hwange ecosystem in Zimbabwe. Our results 1) confirmed our assumption that buffalo and cattle share similar phylogroup profiles, 2) identified a significant gradient of antibioresistance from isolated buffalo to buffalo in contact with cattle and cattle populations; 3) evidenced the dissemination of tetracycline, trimethoprim and amoxicillin resistance genes (tet, dfrA, blaTEM-1in 26 isolated sub-dominant E. coli strains between nearby buffalo and cattle populations that led us 4) to hypothesize the role of the human/animal interface in the dissemination of genetic material from human to cattle and towards wildlife. The study of antibiotic resistance dissemination in multi-host systems and at anthropised/natural interface is necessary to better understand and mitigate its multiple threats. These results also contribute to attempts aiming at using E. coli as a tool for the identification of pathogen transmission pathway in multi-host systems. (Texte intégral

Different epidemiology of bloodstream infections in COVID-19 compared to non-COVID-19 critically ill patients: A descriptive analysis of the Eurobact II study

Background: The study aimed to describe the epidemiology and outcomes of hospital-acquired bloodstream infections (HABSIs) between COVID-19 and non-COVID-19 critically ill patients. Methods: We used data from the Eurobact II study, a prospective observational multicontinental cohort study on HABSI treated in ICU. For the current analysis, we selected centers that included both COVID-19 and non-COVID-19 critically ill patients. We performed descriptive statistics between COVID-19 and non-COVID-19 in terms of patients’ characteristics, source of infection and microorganism distribution. We studied the association between COVID-19 status and mortality using multivariable fragility Cox models. Results: A total of 53 centers from 19 countries over the 5 continents were eligible. Overall, 829 patients (median age 65 years [IQR 55; 74]; male, n = 538 [64.9%]) were treated for a HABSI. Included patients comprised 252 (30.4%) COVID-19 and 577 (69.6%) non-COVID-19 patients. The time interval between hospital admission and HABSI was similar between both groups. Respiratory sources (40.1 vs. 26.0%, p < 0.0001) and primary HABSI (25.4% vs. 17.2%, p = 0.006) were more frequent in COVID-19 patients. COVID-19 patients had more often enterococcal (20.5% vs. 9%) and Acinetobacter spp. (18.8% vs. 13.6%) HABSIs. Bacteremic COVID-19 patients had an increased mortality hazard ratio (HR) versus non-COVID-19 patients (HR 1.91, 95% CI 1.49–2.45). Conclusions: We showed that the epidemiology of HABSI differed between COVID-19 and non-COVID-19 patients. Enterococcal HABSI predominated in COVID-19 patients. COVID-19 patients with HABSI had elevated risk of mortality. Trial registration ClinicalTrials.org number NCT03937245. Registered 3 May 2019

Messages from the second International Conference on Clinical Metagenomics (ICCMg2)

Clinical metagenomics (CMg) refers to as the application of metagenomic sequencing of clinical samples in order to recover clinically-relevant information. Due to the increasing access to next-generation sequencing (NGS) facilities, CMg is a gast-growing field. In this context, we held the second International Conference on Clinical Metagenomics (ICCMg2) in Geneva in October 2017. During the two days of the conference, several aspects of CMg were addressed, which we propose to summarize in the present manuscript. Besides, we also discuss the evolution of CMg from the last conference held in 2016. In brief, many technical issues related to CMg are expected to be successfully addressed in the coming years. Conversely, assessing the clinical value of CMg, implementing a quality process, storage of data and the ethics of CMg are emerging challenges

Résistance aux b-lactamines des Escherichia coli responsables d'infections urinaires communautaires au Cambodge

PARIS-BIUP (751062107) / SudocSudocFranceF

Messages from the third international conference on clinical metagenomics (ICCMg3)

Clinical metagenomics (CMg), referring to as the application of metagenomic sequencing of clinical samples in order to recover clinically-relevant information, has been rapidly evolving these last years. Following this trend, we held the third International Conference on Clinical Metagenomics (ICCMg3) in Geneva in October 2018. During the two days of the conference, several aspects of CMg were addressed, which we propose to summarize in the present manuscript. During this ICCMg3, we kept on following the progresses achieved worldwide on clinical metagenomics, but also this year in clinical genomics. Besides, the use of metagenomics in cancer diagnostic and management was addressed. Some new challenges have also been raised such as the way to report clinical (meta)genomics output to clinicians and the pivotal place of ethics in this expanding field

In 2035, will all bacteria be multidrug resistant? We are not sure

The development of antibiotics revolutionized the management of patients with infectious diseases and may be considered as a defining moment of modern medicine [1]. However, emergence of resistance to antimicrobials is challenging our practice by threatening to reverse decades of progress [2]. Patients with few or no effective antibiotic therapy options due to resistance are increasingly observed and the possibility exists that this will worsen to the point where in some countries or patient populations the antibiotic therapy era will become only of historical relevance over the next two decades [3]. Given the current situation, antibiotic resistance, especially among Gram-negative pathogens, will most likely continue to evolve with low-income countries at greatest risk [4]. We propose that following a continuous rise, resistance will reach an ultimate point where the economic, medical, and social environment will change such that we will have the ability to continue to manage these important infections