A study published in Molecular Biology Reports details the molecular epidemiology of carbapenem- and colistin-resistant Escherichia coli sequence types across human, poultry, and environmental reservoirs in Pakistan. The research, led by Muhammad Usman Qamar and colleagues, investigates the prevalence of antimicrobial resistance within a One Health framework, highlighting the interconnected nature of these pathogens.
The investigation involved the aseptical collection of a total of 300 samples, divided equally into 100 each from human clinical, poultry, and environmental sources. Isolates were cultured using standard microbiological methods and identified with the VITEK® 2 Compact system. Antimicrobial susceptibility testing was performed according to Clinical and Laboratory Standards Institute guidelines to determine the resistance profiles of the collected bacteria.
To assign sequence types, the researchers utilized two-locus CH typing. Polymerase chain reaction was then employed to detect specific resistance genes, including blaNDM, blaVIM, blaIMP, blaOXA, and mcr-1.
The results revealed a significant presence of resistant isolates across all three reservoirs. From human samples, the team recovered 27 carbapenem-resistant E. coli and 3 colistin-resistant E. coli isolates. Environmental samples yielded a higher number of resistant strains, with 38 carbapenem-resistant and 5 colistin-resistant isolates. Poultry samples contributed 25 colistin-resistant E. coli isolates.
Among all isolates, sequence type 101 was the most predominant, accounting for 21 out of 90 isolates, or 23.3 percent. Sequence types 131 and 405 were also common, each representing 15 out of 90 isolates, or 16.7 percent. The study found that all three reservoirs harbored ST101, ST131, and ST405, suggesting a widespread circulation of these lineages. Furthermore, ST648 was shared between human and environmental isolates, while ST10 was shared between poultry and environmental isolates.
Analysis of the resistance genes in environmental carbapenem-resistant isolates showed that blaNDM was detected in 20 out of 38 isolates, or 52.6 percent. blaVIM was present in 18 out of 38 isolates, or 47.4 percent, while blaIMP was found in 11 out of 38 isolates, or 28.9 percent. blaOXA was detected in 6 out of 38 isolates, or 15.8 percent, and mcr-1 was present in 5 out of 38 isolates, or 13.2 percent. In contrast, all human carbapenem-resistant isolates carried the blaNDM gene, with 27 out of 27 isolates testing positive.
The study also highlighted the prevalence of colistin resistance in poultry. All 25 colistin-resistant E. coli isolates from poultry samples harbored the mcr-1 gene, with a detection rate of 100 percent.
The conclusion of the study emphasizes that high-risk multidrug-resistant E. coli lineages carrying carbapenemase and colistin resistance genes are widely distributed across human, poultry, and environmental reservoirs. The study provides valuable insights into the molecular epidemiology of resistant E. coli in Pakistan, identifying specific sequence types and resistance genes that are prevalent across different sources.
Subject of Research: Molecular epidemiology of carbapenem- and colistin-resistant Escherichia coli in Pakistan
Article Title: One health molecular epidemiology of carbapenem- and colistin-resistant Escherichia coli sequence types in humans, poultry, and the environment in Pakistan
Article References: Qamar, M. U., Kariuki, S., Zahra, F. T., Beg, S. S., Batool, A., Mahmood, S., Rizwan, M., Rasool, M. H., Aatika, & Palmer, G. H. (2026). One health molecular epidemiology of carbapenem- and colistin-resistant Escherichia coli sequence types in humans, poultry, and the environment in Pakistan. Molecular Biology Reports, 53(1), Article 1953. https://doi.org/10.1007/s11033-026-13132-8
Image Credits: AI Generated
DOI: 10.1007/s11033-026-13132-8
Keywords: Escherichia coli, antimicrobial resistance, carbapenem resistance, colistin resistance, One Health, molecular epidemiology, Pakistan, sequence types, blaNDM, mcr-1, poultry, environmental samples, human clinical samples, resistance genes, Molecular Biology Reports, multidrug-resistant bacteria, CH typing, PCR detection, public health, cross-transmission
News Source: William Thompson. (November 13, 2026). Shared E. coli Lineages Link Human, Poultry, and Environmental Resistance. Scienmag.
