Genomic characterization of high-risk Escherichia coli and Enterobacter hormaechei clones recovered from a single tertiary-care hospital in Pakistan

J Appl Microbiol. 2022 May;132(5):3907-3914. doi: 10.1111/jam.15482. Epub 2022 Feb 21.

Abstract

Aims: Spread of carbapenem-resistant Enterobacterales have become a global problem. We characterized extended-spectrum β-lactamase (ESBL)-producing Enterobacterales from urinary tract infections cases from Allied Hospital Faisalabad, Pakistan.

Methods and results: Eleven (22%, 11/50) ESBL-producing Enterobacterales (Escherichia coli; n = 10 and Enterobacter hormaechei; n = 1) were recovered and processed through VITEK-2, PCR, rep-PCR followed by whole-genome sequencing (WGS) of ESBL-producing Ent. hormaechei and carbapenem-resistant E. coli isolates. Plasmid transferability of blaNDM-1 -producers was assayed by conjugation experiments. All ESBL strains carried the blaCTX-M-15 gene. Of these blaCTX-M-15 producing E. coli, four also carried blaNDM-1 located on transferable plasmids. All E. coli strains belonged to ST448 and displayed similar genetic features including genes for antimicrobial resistance, heavy metal, biocides and virulence. Genomic features of a multidrug-resistant (MDR) Ent. hormaechei were also reported for the first time in Pakistan.

Conclusion: Our findings indicate that blaNDM-1 producing E. coli ST448 is a multidrug, heavy metals and biocides-resistant strain. Therefore, the screening of these isolates may be effective in limiting the MDR bacteria spread in hospitalized patients and within the community.

Significance and impact of this study: Spread of multi-drug-resistant ESBL-producing bacteria in the clinical settings of Pakistan is a serious challenge and further limiting treatment options in the country. WGS could be used as a tool in the nationwide antibiotic surveillance programme to explore insights of spread and outbreak.

Keywords: bla NDM-1; ESBL; Enterobacterales; Pakistan; antimicrobial resistance; genomics.

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Carbapenems / pharmacology
  • Clone Cells
  • Disinfectants* / pharmacology
  • Enterobacter
  • Escherichia coli
  • Escherichia coli Infections* / microbiology
  • Humans
  • Male
  • Microbial Sensitivity Tests
  • Pakistan
  • Plasmids / genetics
  • Tertiary Care Centers
  • beta-Lactamases / genetics

Substances

  • Anti-Bacterial Agents
  • Carbapenems
  • Disinfectants
  • beta-Lactamases

Supplementary concepts

  • Enterobacter hormaechei