Phenotypic and genotypic characterization of antimicrobial-resistant uropathogens in community settings of India: A multicentric cross-sectional study.

OBJECTIVE

This study determines the prevalence and genomic characterisation of uropathogens causing community-acquired urinary tract infections.

MATERIALS AND

METHODS

This is a first multicentric cross-sectional community study conducted across different regions of India, in patients aged >1.5 y suspected with urinary tract infection. Uropathogens causing significant bacteriuria were identified, and susceptibility testing was performed. Whole-genome sequencing was done to characterise antimicrobial resistance genes, virulence genes, and sequence types (ST). The effect of age and gender on significant bacteriuria was assessed by Multivariable random-effects logistic regression.

RESULTS

Significant bacteriuria was seen in 11.8% (711/6009) of the specimens, out of which 63% (448/711) were Escherichia coli, and 15.7% (112/711) were Klebsiella pneumoniae. The prevalence of extended-spectrum beta-lactamase positive, multidrug-resistant and carbapenem resistant E. coli was 65.4% (293/448), 64.5% (289/448) and 9.8% (44/448); among K. pneumoniae isolates, similar resistance was seen in 56.2% (63/112), 39.2% (44/112), and 9.8% (11/112), respectively. Genomic analysis showed high-risk clones of E. coli (ST131, ST1193) and K. pneumoniae (ST15, ST16, and ST231) carrying multiple plasmids with blaCTX-M-15, blaOXA-232, blaNDM-5, and blaNDM-7 genes.

CONCLUSIONS

This study revealed a wider presence of drug-resistant high-risk clones of uropathogens in community settings of India. A multifaceted approach through routine antimicrobial resistance surveillance, judicious choice of empiric antibiotics in a community setting, is deemed necessary. Whole-genome sequencing analysis of extended-spectrum beta-lactamase-producing E. coli isolates revealed a predominance of ST131 lineage (25%), while ST1193 strains carried IncFIA and ColKP3 plasmids associated with blaCTX-M-15 and blaTEM-1B. ST231 K. pneumoniae isolates harboured blaOXA-32 gene along with ColKP3 plasmid.