Association of virulence factors, phylogenetic groups and antimicrobial resistance markers in Escherichia coli from Badin city, Pakistan

Abstract

Background: Escherichia coli, the most frequent cause of UTIs has extensive genetic substructure and can be assigned to eight phylogroups, A, B1, B2, C, D, E, F and Escherichia cryptic clade I. We investigated the distribution of virulence determinants and antimicrobial resistance genes in relation to phylogenetic groups.

Methods: A total of 77 E. coli isolates were collected from Civil Hospital Badin, Pakistan. Isolates were assigned phylogroups using quadruplex PCR method, while virulence and antibiotic resistance genes, bla_CTX-M and bla_NDM-1 were also detected using PCR.

Results: Thirty-four isolates were assigned to group B2, while 23, 2, 1, 7 and 10 isolates were assigned to F, B1, A/C, clade I/II and negative, respectively. Among virulence genes, prevalence of papC (83%) was highest followed by aer (57%), papGII (16%), papGIII (14%), cnf (9%), hly (5%) and sfa (6%). Of these isolates, 23% and 9% were positive for bla_CTX-M and bla_NDM-1, respectively.

Keywords:

• E. coli
• Phylogroups
• Virulence factors
• UTI
• NDM-1
• CTX-M
• ESBL
• Pakistan