Abstract
Enterococci are ubiquitous microorganisms having diverse ecological niches but most prominently in gastrointestinal tract of humans and animals. Production of enterocins makes them a good probiotic candidate. However, their role as probiotics has become ambiguous in the last few years because of the presence of virulence factors and antibiotic resistance genes. These virulence traits are known to be transferred genetically, which makes them opportunistic pathogens in the gastrointestinal tract leading to serious concerns about their being used as probiotics. In the present study, Enterococcusspp. isolated from the human gut were subjected to Whole-Genome Sequencing (WGS) to determine the presence of resistance and virulence genes. Four human origins Enterococcus spp. including Enterococcus faecalis, Enterococcus casseliflavus, and two Enterococcus gallinarum were isolated from human fecal samples and further cultured on blood agar. Sanger sequencing was done using Applied Biosystems 3730xl DNA Analyzer. These strains were further subjected to WGS using oxford nanopore technology MinION. Raw data were analyzed using the free online tool epi2me. The Comprehensive Antibiotic Resistance Database (CARD) and RAST (Rapid Annotation using Subsystem Technology) software were used to look for the presence of antibiotic resistance genes in these strains. Resistance determinants for clinically important antibiotics (vancomycin) and functional virulence factor genes were detected. G-view server was used for comparative genomics of all strains. The genomic sequencing of Enterococcus suggested that E. faecalis, E. casseliflavus, and E. gallinarum strains are opportunistic pathogens, having antibiotic resistance genes. All isolates had vancomycin resistance genes, which were expressed phenotypically. Genes related to bacteriocin resistance were also present in E. casseliflavus and E. gallinarum.
Highlights
Enterococcus genus is important class of lactic acid bacteria (LAB) of the phylum Firmicutes that can survive in diverse ecological niches [1] including intestine of humans, animals and food products
There is an alarming increase of multidrug resistance among enterococci, mainly vancomycin resistance, more over they have ability to transfer antibiotic and virulence genes [6].Whole genome sequencing is becoming routine practice in many laboratories to characterize various genes related to antimicrobial resistance mainly in gram negative bacteria, very less data is available related to study of genome for antimicrobial resistance among gram positive bacteria[7]
E.gallinarium have AAC (6) li protein homology model belonging to aminoglycoside antibiotics class that work by antibiotics inactivation which is somehow expressed phenotypically that is its resistance towards vancomycin and linezolid
Summary
Enterococcus genus is important class of lactic acid bacteria (LAB) of the phylum Firmicutes that can survive in diverse ecological niches [1] including intestine of humans, animals and food products. There is an alarming increase of multidrug resistance among enterococci, mainly vancomycin resistance, more over they have ability to transfer antibiotic and virulence genes [6].Whole genome sequencing is becoming routine practice in many laboratories to characterize various genes related to antimicrobial resistance mainly in gram negative bacteria, very less data is available related to study of genome for antimicrobial resistance among gram positive bacteria[7] Based upon this background its time of hour to do deep research on enterococcus virulence properties before using them as probiotic strains[8]. This ambiguity in their probiotic role is related to presence of virulence factors and antibiotic resistance genes These virulence traits are known to be transfer genetically which make them opportunistic pathogens in gastrointestinal track. In present study Whole-genome sequencing (WGS) of Enterococcus spp was done for checking presence of resistance and virulence genes, isolated from human gut
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