Genetic landscape of ESBL producing international clone ST410 of Escherichia coli from pediatric infections in Shenzhen, China

Front Cell Infect Microbiol. 2024 Sep 11:14:1403234. doi: 10.3389/fcimb.2024.1403234. eCollection 2024.

Abstract

Background: The emergence of ESBLs producing cephalosporin-resistant Escherichia coli isolates poses a threat to public health. This study aims to decipher the genetic landscape and gain insights into ESBL-producing E. coli strains belonging to the high-risk clone ST410 from pediatric patients.

Methods: 29 E. coli ST410 isolates were collected from young children and subjected to antimicrobial susceptibility testing, Whole-genome sequencing (WGS), serotype analysis, MLST, ESBL genes, virulence genes, and plasmid profiling.

Results: Antimicrobial susceptibility testing demonstrated a high level of resistance to cephalosporins followed by aminoglycoside, sulfonamide, carbapenem and penicillin group of antibiotics. However, n=20/29 shows MDR phenotype. Phylogenetic group B2 (n=15) dominated, followed by group D (n=7), group A (n=4), and group B1 (n=3). Serotyping analysis identified O1:H7 (n=8), O2:H1 (n=6), O8:H4 (n=5), O16:H5 (n=4), and O25:H4 (n=3). Other serotypes identified included O6:H1, O15:H5, and O18:H7 (n=1 each). The most commonly detected ESBL genes were bla CTX-M, (n=26), followed by bla TEM (n=23), and bla SHV (n=18). Additionally, bla OXA-1 (n=10), bla OXA-48 (n=5), bla KPC-2 (n=3), bla KPC-3 (n=2), bla NDM-1 (n=4), bla NDM-5 (n=1), bla GES-1 (n=2), bla GES-5 (n=1), and bla CYM-1 (n=3). Notable virulence genes identified within the ST410 isolates included fimH (n=29), papC (n=24), hlyA (n=22), and cnf1 (n=18), among others. Diverse plasmids were observed including IncFIS, IncX4, IncFIA, IncCol, IncI2 and IncFIC with transmission frequency ranges from 1.3X10-2 to 2.7X10-3.

Conclusion: The ST410 clone exhibited a complex resistance profile, diverse serotypes, the presence of specific resistance genes (ESBL genes), virulence gene repertoire, and diverse plasmids. The bla CTX-M was the most prevalent ESBL gene detected.

Keywords: E. coli; ESBL; WGS; antimicrobial susceptibility; cephalosporin resistance; international high-risk clone ST410; pediatric patients.

MeSH terms

  • Anti-Bacterial Agents* / pharmacology
  • Child
  • Child, Preschool
  • China / epidemiology
  • Drug Resistance, Multiple, Bacterial / genetics
  • Escherichia coli Infections* / epidemiology
  • Escherichia coli Infections* / microbiology
  • Escherichia coli* / drug effects
  • Escherichia coli* / genetics
  • Escherichia coli* / isolation & purification
  • Female
  • Genotype
  • Humans
  • Infant
  • Male
  • Microbial Sensitivity Tests*
  • Multilocus Sequence Typing*
  • Phylogeny*
  • Plasmids* / genetics
  • Serogroup
  • Serotyping
  • Virulence Factors* / genetics
  • Whole Genome Sequencing*
  • beta-Lactamases* / genetics

Substances

  • beta-Lactamases
  • Anti-Bacterial Agents
  • Virulence Factors

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by Shenzhen Fund for Guangdong Provincial High level Clinical Key Specialties (no. SZGSP012), and Shenzhen Key Medical Discipline Construction Fund (no. SZXK034), Upgrading project of Shenzhen Public Service Platform of Molecular Medicine in Pediatric Hematology and Oncology from Development and Reform Commission of Shenzhen Municipality no. XMHT20220104044), Guangdong High-Level hospital Construction Fund.