Genomic-based characterization of Enterococcus spp.: an emerging pathogen isolated from human gut

Zumara Younus; Sagar M. Goyal; Vikash Singh; Aamer Ikram; Muhammad Imran

doi:10.1007/s11033-021-06540-5

Genomic-based characterization of Enterococcus spp. an emerging pathogen isolated from human gut

Zumara Younus, Sagar M. Goyal, Vikash Singh, Aamer Ikram, Muhammad Imran

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

Background: 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. Methods and results: 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. Conclusion: 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.

Original language	English (US)
Pages (from-to)	5371-5376
Number of pages	6
Journal	Molecular Biology Reports
Volume	48
Issue number	6
DOIs	https://doi.org/10.1007/s11033-021-06540-5
State	Published - Jun 2021

Bibliographical note

Funding Information:
This research was funded by Higher Education Commission (HEC) of Pakistan (IRSIP: 43 BMS 79).

Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature B.V.

Keywords

Antimicrobial resistance
Enterococcus spp
MinION
Probiotics
Sanger sequencing
Vancomycin
Whole genome sequencing

PubMed: MeSH publication types

Journal Article

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10.1007/s11033-021-06540-5

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@article{aa3bd9fe31c741949a1cdf165ba364f0,

title = "Genomic-based characterization of Enterococcus spp.: an emerging pathogen isolated from human gut",

abstract = "Background: 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. Methods and results: 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. Conclusion: 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.",

keywords = "Antimicrobial resistance, Enterococcus spp, MinION, Probiotics, Sanger sequencing, Vancomycin, Whole genome sequencing",

author = "Zumara Younus and Goyal, {Sagar M.} and Vikash Singh and Aamer Ikram and Muhammad Imran",

note = "Funding Information: This research was funded by Higher Education Commission (HEC) of Pakistan (IRSIP: 43 BMS 79). Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature B.V.",

year = "2021",

month = jun,

doi = "10.1007/s11033-021-06540-5",

language = "English (US)",

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journal = "Molecular Biology Reports",

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T1 - Genomic-based characterization of Enterococcus spp.

T2 - an emerging pathogen isolated from human gut

AU - Younus, Zumara

AU - Goyal, Sagar M.

AU - Singh, Vikash

AU - Ikram, Aamer

AU - Imran, Muhammad

N1 - Funding Information: This research was funded by Higher Education Commission (HEC) of Pakistan (IRSIP: 43 BMS 79). Publisher Copyright: © 2021, The Author(s), under exclusive licence to Springer Nature B.V.

PY - 2021/6

Y1 - 2021/6

N2 - Background: 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. Methods and results: 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. Conclusion: 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.

AB - Background: 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. Methods and results: 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. Conclusion: 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.

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KW - Vancomycin

KW - Whole genome sequencing

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