The use of high-throughput sequencing to investigate an outbreak of glycopeptide-resistant Enterococcus faecium with a novel quinupristin-dalfopristin resistance mechanism

Shaw, Timothy D; Fairley, Derek; Schneiders, Thamarai; Pathiraja, Melanie; Hill, Robert L.; Werner, Guido; Elborn, J.S.; McMullan, Ronan

doi:10.1007/s10096-018-3214-x

Cited by 5 publications

(2 citation statements)

References 22 publications

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“…Enterococcal blooms were seen in 11 patients. In six cases, the dominant strain belonged not just to the same species , E. faecium , but also to the same sequence type, ST80, which is a well-documented cause of nosocomial outbreaks across the globe [59–61]. Core phylogenetic analyses with the MAGs identified in this study and complete public E.…”

Section: Resultsmentioning

confidence: 98%

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

et al. 2019

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Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson’s index of <4) at some stage during their stay in the ICU, often accompanied by the absence or loss of potentially beneficial bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but the administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three-quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium . In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species Methanobrevibacter smithii . In conclusion, we have documented a dramatic absence of microbial diversity and pathogen domination of the gut microbiota in a high proportion of critically ill patients using shotgun metagenomics.

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Section: Resultsmentioning

confidence: 98%

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

et al. 2019

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“…faecium DO was specified as a representative genome for this analysis. The DO strain was selected for this analysis because it has a complete genome sequence and has been used in multiple pathogenesis studies [21, 22]. The statistics (as of 4th August 2021) of the genus Enterococcus in the VFDB are the following: number of species and strains is 2 and 13, respectively.…”

Section: Methodsmentioning

confidence: 99%

Genomic insights into antibiotic-resistance and virulence genes of Enterococcus faecium strains from the gut of Apis mellifera

Zaghloul

Halfawy

2022

Microbial Genomics

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Enterococcus faecium is a lactic acid bacterium that confers beneficial health effects in humans. However, lately, a number of E. faecium strains have been linked to the spread of nosocomial infections in the hospital environment. Therefore, any potential commercial usage of E. faecium isolates should be preceded by an assessment of infection risk. In the current study, the genomes of two novel E. faecium strains Am1 (larval isolate) and Bee9 (adult bee isolate) isolated from the gut of Apis mellifera L. (honeybee) were sequenced to allow evaluation of their safety. In particular, their genomes were screened for antibiotic-resistance and virulence genes. In addition, their potential to spread resistance in the environment was evaluated. The analysis revealed that Am1 and Bee9 possess 2832 and 2844 protein-encoding genes, respectively. In each case, the genome size was 2.7 Mb with a G+C content of 37.9 mol%. Comparative analysis with probiotic, non-pathogenic and pathogenic enterococci revealed that there are variations between the two bee E. faecium isolates and pathogenic genomes. They were, however, closely linked to the probiotic comparison strains. Phenotypically, the Am1 and Bee9 strains were susceptible to most antibiotics tested, but showed intermediate sensitivity towards erythromycin, linezolid and trimethoprim/sulfamethoxazole. Notably, no genes associated with antibiotic resistance in clinical isolates (e.g. vancomycin resistance: vanA, vanB, vanS, vanX and vanY) were present. In addition, the insertion sequences (IS16, ISEfa11 and ISEfa5), acting as molecular pathogenicity markers in clinically relevant E. faecium strains, were also absent. Moreover, the analysis revealed the absence of three key pathogenicity-associated genes (acm, sgrA, ecbA) in the Am1 and Bee9 strains that are found in the prominent clinical isolates DO, V1836, Aus0004 and Aus0085. Overall, the findings of this investigation suggest that the E. faecium isolates from the bee gut have not suffered any recent clinically relevant antibiotic exposure. It also suggests that E. faecium Am1 and Bee9 are safe potential probiotic strains, because they lack the phenotypic and genetic features associated with strains eliciting nosocomial infections.

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Dissemination of Quinupristin-Dalfopristin and Linezolid resistance genes among hospital environmental and healthy volunteer fecal isolates of Enterococcus faecalis and Enterococcus faecium

et al. 2022

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The use of high-throughput sequencing to investigate an outbreak of glycopeptide-resistant Enterococcus faecium with a novel quinupristin-dalfopristin resistance mechanism

Cited by 5 publications

References 22 publications

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

Genomic insights into antibiotic-resistance and virulence genes of Enterococcus faecium strains from the gut of Apis mellifera

Dissemination of Quinupristin-Dalfopristin and Linezolid resistance genes among hospital environmental and healthy volunteer fecal isolates of Enterococcus faecalis and Enterococcus faecium

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