Molecular Detection of Carbapenemase and mcr-1 Resistance Genes in Enterobacterales at the Animal–Human Interface in Pakistan: A One Health Perspective

Abstract

Carbapenem-and colistin-resistant Enterobacterales (CRE and Col-R) are critical-priority pathogens within the One Health framework and pose a significant public health threat. This study investigated the prevalence and molecular characteristics of resistance across clinical, veterinary, and environmental sources. A total of 600 samples were collected, including clinical (urine and blood), veterinary (poultry cloacal swabs), and environmental (hospital and surface wastewater) specimens. Enterobacterales were identified using culture, biochemical tests and VITEK® 2. Antimicrobial susceptibility testing, MIC determination, Modified Hodge ’s Test, and PCR-based detection of carbapenemase genes and mcr-1 were performed. Enterobacterales were detected in 41% of clinical, 100% of veterinary and 98 – 100% of environmental samples. Carbapenem resistance in clinical isolates was 32.4% in E. coli and 33.3% in K. pneumoniae , while colistin resistance was 10.8 and 5.6%, respectively. Veterinary E. coli showed 12.5% carbapenem resistance and 28% colistin resistance. Environmental isolates exhibited carbapenem resistance in 29.8% of K. pneumoniae and 11.1% of E. coli , with colistin resistance of 22.2 and 6%, respectively. Co-resistance to carbapenems and colistin was observed in environmental (11.1%), veterinary (4%) and clinical (2.7%) E. coli . High meropenem MICs reached 1024µg/mL and colistin MICs 32µg/mL. Genotypically, bla NDM (66.7%) predominated, followed by bla VIM (58.3%), bla IMP (37.5%) and bla OXA (33.3%). The mcr-1 was detected in all phenotypically colistin-resistant isolates. High MAR indices (>0.5) were most frequent in environmental (68%) and veterinary (39%) isolates. These findings highlight widespread cross-sector transmission and emphasize the urgent need for integrated One Health surveillance and antimicrobial stewardship in Pakistan.