Abstract
Enterobacter cloacae complex (Ecc) species are widely distributed opportunistic pathogens mainly associated with humans and plants. In this study, the genomes of clinical isolates including E. hormaechei, E. kobei, and E. ludwigii and non-clinical isolate including E. nimipressuralis were analysed in combination with the genome of E. asburiae by using the reference strain E. cloacae subsp. cloacae ATCC 13047; the Ecc strains were tested on artificial sputum media (ASM), which mimics the host, to evaluate T6SS genes as a case study. All five Ecc strains were sequenced in our lab. Comparative genome analysis of the Ecc strains revealed that genes associated with the survival of Ecc strains, including genes of metal-requiring proteins, defence-associated genes and genes associated with general physiology, were highly conserved in the genomes. However, the genes involved in virulence and drug resistance, specifically those involved in bacterial secretion, host determination and colonization of different strains, were present in different genomic regions. For example, T6SS accessory and core components, T4SS, and multidrug resistance genes/efflux system genes seemed vital for the survival of Ecc strains in various environmental niches, such as humans and plants. Moreover, the ASM host-mimicking growth medium revealed significantly high expression of T6SS genes, including PrpC, which is a regulatory gene of the T6SS, in all tested Ecc strains compared to the control medium. The variations in T6SS gene expression in ASM vs. control showed that the ASM system represents a simple, reproducible and economical alternative to animal models for studies such as those aimed at understanding the divergence of Ecc populations. In summary, genome sequencing of clinical and environmental Ecc genomes will assist in understanding the epidemiology of Ecc strains, including the isolation, virulence characteristics, prevention and treatment of infectious disease caused by these broad-host-range niche-associated species.
Highlights
The Enterobacter genus was reported in 1960 by Hormaeche and Edwards[1]
In order to look into the genetic makeup of the T6SS in Enterobacter cloacae complex (Ecc), genome-wide prediction of Ecc genomes followed by gene expression profiling could be vital to understand the physiology of these bacteria isolated from plant and clinical niches[7]
The literature shows that these genes might play a significant role in either increasing the general fitness or the competitiveness of Ecc bacterial species, which help them to better survive in diverse environments
Summary
The Enterobacter genus was reported in 1960 by Hormaeche and Edwards[1]. The List of Prokaryotic Names with Standing in Nomenclature (LPSN) reports that 12 species and 2 subspecies are included in this genus. The species of the Enterobacter cloacae complex (Ecc) are opportunistic and can cause lower respiratory tract infections and bacteraemia[2,3]. These bacteria are notorious for causing nosocomial infections in intensive care units. The T6SS is important for bacterial competition as well as virulence in many gram-negative bacteria, and its dynamics and regulation vary significantly between species. In order to look into the genetic makeup of the T6SS in Ecc, genome-wide prediction of Ecc genomes followed by gene expression profiling could be vital to understand the physiology of these bacteria isolated from plant and clinical niches[7]. Genome-wide analysis, including the characterization of specific virulence genes and antimicrobial resistance genes, has only been fully conducted for a few Ecc members
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