Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis

Abstract

The enterococci, which are among the leading causes of multidrug-resistant (MDR) hospital infection, are notable for their environmental ruggedness, which extends to intrinsic antibiotic resistance. To identify genes that confer this unique property, we used Tn-seq to comprehensively explore the genome of MDR Enterococcus faecalis strain MMH594 for genes important for growth in nutrient-containing medium and with low-level antibiotic challenge. As expected, a large core of genes for DNA replication, expression, and central metabolism, shared with other bacteria, are intolerant to transposon disruption. However, genes were identified that are important to E. faecalis that are either absent from or unimportant for Staphylococcus aureus and Streptococcus pneumoniae fitness when similarly tested. Further, 217 genes were identified that when challenged by sub-MIC antibiotic levels exhibited reduced tolerance to transposon disruption, including those previously shown to contribute to intrinsic resistance, and others not previously ascribed this role. E. faecalis is one of the few Gram-positive bacteria experimentally shown to possess a functional Entner-Doudoroff pathway for carbon metabolism, a pathway that contributes to stress tolerance in other microbes. Through functional genomics and network analysis we defined the unusual structure of this pathway in E. faecalis and assessed its importance. These approaches also identified toxin-antitoxin and related systems that are unique and active in E. faecalis. Finally, we identified genes that are absent in the closest nonenterococcal relatives, the vagococci, and that contribute importantly to fitness with and without antibiotic selection, advancing an understanding of the unique biology of enterococci. IMPORTANCE Enterococci are leading causes of antibiotic-resistant infection transmitted in hospitals. The intrinsic hardiness of these organisms allows them to survive disinfection practices and then proliferate in the gastrointestinal tracts of antibiotic-treated patients. The objective of this study was to identify the underlying genetic basis for its unusual hardiness. Using a functional genomic approach, we identified traits and pathways of general importance for enterococcal survival and growth that distinguish them from closely related pathogens as well as ancestrally related species. We further identified unique traits that enable them to survive antibiotic challenge, revealing a large set of genes that contribute to intrinsic antibiotic resistance and a smaller set of uniquely important genes that are rare outside enterococci.

Heme cross-feeding can augment Staphylococcus aureus and Enterococcus faecalis dual species biofilms

“…Aerobic respiration in E. faecalis requires exogenous heme as a cofactor for cytochrome bd [ 58 , 59 ]. Enterococci are unable to synthesize heme due to an absent TCA cycle that prevents the formation of porphyrin precursors.…”

Listeria monocytogenes gene essentiality under laboratory conditions and during macrophage infection

“…With 394 genes, almost 14% of all genes are indispensable for growth in rich medium. Similar numbers of essential genes were discovered by Tn-Seq in other bacteria, such as Staphylococcus aureus (420), Streptococcus pyogenes (298), Enterococcus faecalis (349), Escherichia coli (358) or Pseudomonas aeruginosa (352 essential genes) (94)(95)(96)(97)(98). In Mycoplasma genitalium, which contains one of the smallest genomes of self-replicating organisms, 382 out of 482 protein encoding genes are essential (99).…”

Antistaphylococcal Activities and ADME-Related Properties of Chlorinated Arylcarbamoylnaphthalenylcarbamates

“…An explanation for the observed differences in the susceptibility of staphylococci and enterococci to the tested carbamates can be found in the naturally much greater resistance of enterococci to disinfection procedures [47,48]. Recent functional genomic stud-ies [49,50] identified unique properties of enterococci that allow them to survive exposure to antibiotics.…”