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

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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.

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Fig. 1

Data availability

Sequences data was submitted to NCBI with Bio project number PRJNA682015.

Code availability

Not applicable.

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Funding

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

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Authors and Affiliations

  1. Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan

    Zumara Younus & Muhammad Imran

  2. Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, MN, 55108, USA

    Zumara Younus, Sagar M. Goyal & Vikash Singh

  3. National Institute of Health (NIH), Park Road, Islamabad, 45550, Pakistan

    Aamer Ikram

Authors
  1. Zumara Younus
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  2. Sagar M. Goyal
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  3. Vikash Singh
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  4. Aamer Ikram
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  5. Muhammad Imran
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Contributions

All authors contributed significantly in this study. Ms. Zumara: did all laboratory work and drafted the manuscript. Prof. Goyal: Supervised the WGS. Dr. Vikash: worked on WGS data analysis. Prof. Aamer: supervised the clinical aspects especially sampling. Dr. Imran: supervised the experiment design and did data analysis.

Corresponding author

Correspondence to Muhammad Imran.

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Authors have no conflict of interest or competing interest in this study.

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The work was approved by the Biological Ethical Committee of Quaid-i-Azam University, Islamabad, Pakistan.

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Written informed consent was obtained from all participants of this study.

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Younus, Z., Goyal, S.M., Singh, V. et al. Genomic-based characterization of Enterococcus spp.: an emerging pathogen isolated from human gut. Mol Biol Rep 48, 5371–5376 (2021). https://doi.org/10.1007/s11033-021-06540-5

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  • DOI: https://doi.org/10.1007/s11033-021-06540-5

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