Suchergebnisse

Enterococci are Gram-positive bacteria that are found in plants, soil and as commensals of the gastrointestinal tract of humans, mammals, and insects. Despite their commensal nature, they have also become globally important nosocomial pathogens. Within the genus Enterococcus, Enterococcus faecium, and Enterococcus faecalis are clinically most relevant. In this review, we will discuss how E. faecium and E. faecalis have evolved to become a globally disseminated nosocomial pathogen. E. faecium has a defined sub-population that is associated with hospitalized patients and is rarely encountered in community settings. These hospital-associated clones are characterized by the acquisition of adaptive genetic elements, including genes involved in metabolism, biofilm formation, and antibiotic resistance. In contrast to E. faecium, clones of E. faecalis isolated from hospitalized patients, including strains causing clinical infections, are not exclusively found in hospitals but are also present in healthy individuals and animals. This observation suggests that the division between commensals and hospital-adapted lineages is less clear for E. faecalis than for E. faecium. In addition, genes that are reported to be associated with virulence of E. faecalis are often not unique to clinical isolates, but are also found in strains that originate from commensal niches. As a reflection of more ancient association of E. faecalis with different hosts, these determinants Thus, they may not represent genuine virulence genes but may act as host-adaptive functions that are useful in a variety of intestinal environments. The scope of the review is to summarize recent trends in the emergence of antibiotic resistance and explore recent developments in the molecular epidemiology, population structure and mechanisms of adaptation of E. faecium and E. faecalis. ; WS is funded through a NWO-Vidi grant (917.13.357). TC and FB are supported by grants PI12-01581 and PI15-01307 from the ISCIII-Ministry of Economy and Competitiveness of Spain (to TC), S2010/BMD2414 from the Regional Government of Madrid (to FB) and the CIBERESP Network for Biomedical Research in Epidemiology and Public Health (Instituto Carlos III, Spanish Ministry of Science and Innovation, reference number CB06/02/0053). ; Peer reviewed ; Peer Reviewed

[Background]: Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype. Here, we describe a novel strategy that combines targeted metagenomics using last generation in-solution capture platforms, with novel bioinformatics tools to establish a standardized framework that allows both quantitative and qualitative analyses of resistomes. [Methods]: We developed ResCap, a targeted sequence capture platform based on SeqCapEZ (NimbleGene) technology, which includes probes for 8667 canonical resistance genes (7963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), and 2517 relaxase genes (plasmid markers) and 78,600 genes homologous to the previous identified targets (47,806 for antibiotics and 30,794 for biocides or metals). Its performance was compared with metagenomic shotgun sequencing (MSS) for 17 fecal samples (9 humans, 8 swine). ResCap significantly improves MSS to detect "gene abundance" (from 2.0 to 83.2%) and "gene diversity" (26 versus 14.9 genes unequivocally detected per sample per million of reads; the number of reads unequivocally mapped increasing up to 300-fold by using ResCap), which were calculated using novel bioinformatic tools. ResCap also facilitated the analysis of novel genes potentially involved in the resistance to antibiotics, metals, biocides, or any combination thereof. [Conclusions]: ResCap, the first targeted sequence capture, specifically developed to analyze resistomes, greatly enhances the sensitivity and specificity of available metagenomic methods and offers the possibility to analyze genes related to the selection and transfer of antimicrobial resistance (biocides, heavy metals, plasmids). The model opens the possibility to study other complex microbial systems in which minority populations play a relevant role. ; This study was supported by the European Commission, Seven Framework Program (EVOTARFP7-HEALTH-282004 for VFL, FB, JLM, AA, DE, ER, RJLW, WvS, FdlC, and TMC), the Joint Programming Initiative in Antimicrobial Resistance (JPIAMR Third call, STARCS, JPIAMR2016-AC16/00039 to TMC, RJLW, WvS), the Joint Programming Initiative in Water (JPI Water StARE JPIW2013-089-C02-01 to JLM) and the Ministry of Economy and Competitiveness of Spain (BIO2014-54507-R to JLM, and PLASWIRES-612146/FP7-ICT-2013-10 and BFU2014-55534-C2-1-P for FdlC). The authors also acknowledge the European Development Regional Fund "A way to achieve Europe" (ERDF) for co-founding the Spanish R&D National Plan 2012-2019 (BIO2014-54507-R to JLM, PI15-0512 to TMC, PI15-00818 to FB, and BFU2014-55534-C2-1-P to FdlC), CIBER (CIBER in Epidemiology and Public Health, CIBERESP; CB06/02/0053 to FB), the Spanish Network for Research on Infectious Diseases (REIPI RD12/0015 to JLM) and the Regional Government of Madrid (InGeMICS- B2017/BMD-3691). Val F. Lanza was further funded by a Research Award Grant 2016 of the European Society for Clinical Microbiology and Infectious Diseases (ESCMID). Additional funding was from the Metagenopolis grant ANR-11-DPBS-0001 to DE. ; Peer reviewed

BACKGROUND: Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype. Here, we describe a novel strategy that combines targeted metagenomics using last generation in-solution capture platforms, with novel bioinformatics tools to establish a standardized framework that allows both quantitative and qualitative analyses of resistomes. METHODS: We developed ResCap, a targeted sequence capture platform based on SeqCapEZ (NimbleGene) technology, which includes probes for 8667 canonical resistance genes (7963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), and 2517 relaxase genes (plasmid markers) and 78,600 genes homologous to the previous identified targets (47,806 for antibiotics and 30,794 for biocides or metals). Its performance was compared with metagenomic shotgun sequencing (MSS) for 17 fecal samples (9 humans, 8 swine). ResCap significantly improves MSS to detect "gene abundance" (from 2.0 to 83.2%) and "gene diversity" (26 versus 14.9 genes unequivocally detected per sample per million of reads; the number of reads unequivocally mapped increasing up to 300-fold by using ResCap), which were calculated using novel bioinformatic tools. ResCap also facilitated the analysis of novel genes potentially involved in the resistance to antibiotics, metals, biocides, or any combination thereof. CONCLUSIONS: ResCap, the first targeted sequence capture, specifically developed to analyze resistomes, greatly enhances the sensitivity and specificity of available metagenomic methods and offers the possibility to analyze genes related to the selection and transfer of antimicrobial resistance (biocides, heavy metals, plasmids). The model opens the possibility to study other complex microbial systems in which minority populations play a relevant role. ; This study was supported by the European Commission, Seven Framework Program (EVOTARFP7-HEALTH-282004 for VFL, FB, JLM, AA, DE, ER, RJLW, WvS, FdlC, and TMC), the Joint Programming Initiative in Antimicrobial Resistance (JPIAMR Third call, STARCS, JPIAMR2016-AC16/00039 to TMC, RJLW, WvS), the Joint Programming Initiative in Water (JPI Water StARE JPIW2013-089-C02-01 to JLM) and the Ministry of Economy and Competitiveness of Spain (BIO2014-54507-R to JLM, and PLASWIRES-612146/FP7-ICT-2013-10 and BFU2014-55534-C2-1-P for FdlC). The authors also acknowledge the European Development Regional Fund "A way to achieve Europe" (ERDF) for co-founding the Spanish R&D National Plan 2012-2019 (BIO2014-54507-R to JLM, PI15-0512 to TMC, PI15-00818 to FB, and BFU2014-55534-C2-1-P to FdlC), CIBER (CIBER in Epidemiology and Public Health, CIBERESP; CB06/02/0053 to FB), the Spanish Network for Research on Infectious Diseases (REIPI RD12/0015 to JLM) and the Regional Government of Madrid (InGeMICSB2017/BMD-3691). Val F. Lanza was further funded by a Research Award Grant 2016 of the European Society for Clinical Microbiology and Infectious Diseases (ESCMID). Additional funding was from the Metagenopolis grant ANR-11-DPBS-0001 to DE.