Genomic analysis of Fosfomycin resistance in multi-drug resistant uropathogens and comparison of in-vitro susceptibility methods uropathogens

Raunak  Bir; Sarita Mohapatra; Arvind Kumar; Nazneen Arif; Sonu Tyagi; Aswin Pius AK; Hitender Gautam; Seema Sood; Bimal Kumar Das; Arti Kapil

doi:10.18502/ijm.v14i5.10956

Raunak Bir Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
Sarita Mohapatra Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
Arvind Kumar Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
Nazneen Arif Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
Sonu Tyagi Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
Aswin Pius AK Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
Hitender Gautam Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
Seema Sood Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
Bimal Kumar Das Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
Arti Kapil Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India

DOI: https://doi.org/10.18502/ijm.v14i5.10956

Keywords: Fosfomycin; Agar dilution; Disc diffusion; E-test; Enterobacterales

Abstract

Background and Objectives: Urinary tract infection is one of the most common bacterial infections causing high morbidity and mortality. Thealarming rise of multidrug-resistant uropathogens worldwide forced the clinician to re- think the old drugs like Fosfomycin for its therapeutic management. Our objective was to compare agar dilution, disc diffusion and E-test method for antimicrobial susceptibility testing of Fosfomycin againstdifferent drug-resistant uropathogens.

Materials and Methods: Consecutive 181 uropathogens were tested for Fosfomycin susceptibility using agar dilution, disc diffusion and E-test. Resultswere interpreted using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST)breakpoints. Whole genome sequencing analysis was done on the 4 XDR/PDR Fosfomycin resistant Klebsiella pneumoniae isolates.

Results: Escherichia coli was found as the most common (62.4%) uropathogen followed by Klebsiella pneumoniae (21%). Considering agar dilution as thegold standard, 6.1% of isolates were resistant to Fosfomycin. Following CLSI breakpoints, the susceptibility of Escherichia coli, Klebsiella pneumoniae,other Enterobacterales and Pseudomonas aeruginosa were 92.9%, 92.1%, 100%, 100%; whereas using EUCAST breakpoints the susceptibility rates were 85.7%, 86.9%, 92.9%, and 100%, respectively. The essential agreement, categorical agreement, major error, and very major error for E-test/ disc diffu- sion for all the organisms were91.2%/Not Applicable, 95%/93.9%, 1.8%/4.7%, 9.1%/9.1%, respectively. Whole-genome sequencing showed mutation UhpT gene as well as the presence of plasmid-mediated fosA5 or fosA6 genes conferring Fos- fomycin resistance.

Conclusion: This result supports very low resistance of Enterobacterales against Fosfomycin; hence should be considered a valuable option to treat multidrug-resistant uropathogens. Disc diffusion was observed to be a convenient method for Fosfo- mycin susceptibility testing compared to agar dilution.