Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Abstract

Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the “modern hospital” era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.

Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis

“…The occurrence of ARGs could be due to exposure to health care systems and antibiotics and/or the selection of these genes as a means to enhance trans-kingdom and quorum-sensing communications. 16 These are supported by studies in antibiotic-unexposed and natural systems and in organisms exposed to sub-MIC antibiotic concentrations of antibiotics show ARG expressions that are distinct from the effect seen after exposure to adequate antibiotic concentrations. 40,[44][45][46] Therefore, despite controlling for prior antibiotic exposure and hospitalizations, ARG patterns were associated with poor outcomes in cirrhosis but most of these outcomes were not antibiotic-resistant infections.…”

“…These could be due to exposure to the health care environment, because over the past 6 months they had been hospitalized and/or exposed to antibiotics or because of the greater abundance of organisms with these genes that may be used as a survival mechanism independent of antibiotics. 16 In addition, most of the decompensated patients were on rifaximin and some on SBP prophylaxis. This is important because unlike a prior study in which ciprofloxacin, amoxicillin, and metronidazole exposure over 5 days significantly increased the ARG burden, 21 the use of rifaximin per se was not associated with this.…”

“…[9][10][11] With advancing cirrhosis, there is a higher relative abundance of pathobionts 12 that could express ARGs. [13][14][15] In addition, these ARGs can represent survival and quorum-sensing strategies that can predate antibiotic exposure, 16 regulate the microbial ecological dynamics in the gut, and determine survival in complex multiorganismal mucosal surfaces 17 ; however, whether these are unique to cirrhosis or are a sequelae of chronic diseases per se is unknown. The knowledge of species with ARGs that are associated with poor outcomes could be used as prognosticators and facilitate development of novel or targeted therapeutic strategies directed toward them rather than the broad-spectrum antimicrobial treatments that dominate clinical practice today.…”

Functional characterization of a gene cluster responsible for inositol catabolism associated with hospital-adapted isolates of Enterococcus faecium

“…In addition, in E. faecalis a similar lacI gene encoded upstream the iol gene cluster was considered as putative regulator [35]. In contrast to E. faecium, the E. faecalis iol gene cluster is not encoded on a large mobile genetic element like ICEEfm1 but instead is located on a hot spot for integration, as other types of insertion elements were identified at the same position in other E. faecalis isolates [35,39].…”

A high-throughput multiplexing and selection strategy to complete bacterial genomes

“…In addition, we provide a step-by-step computational workflow to perform an unbiased selection of isolates for long-read sequencing based on the presence/absence of genes. as previously applied in two large bacterial collections of isolates [16,17].…”