The Diversity, Resistance Profiles and Plasmid Content of Klebsiella spp. Recovered from Dairy Farms Located around Three Cities in Pakistan

Samia Habib, Marjorie Gibbon, Natacha Monge Gomes Do Couto, Khadija Kakar , Safia Habib, Abdul Samad, Asim Munir, Fariha Fatima, Mashkoor Mohsin, Edward Feil

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The rise of antimicrobial resistance (AMR) in bacterial pathogens such as Klebsiella pneumoniae (Kp) is a pressing public health and economic concern. The ‘One-Health’ framework recognizes that effective management of AMR requires surveillance in agricultural as well as clinical settings, particularly in low-resource regions such as Pakistan. Here, we use whole-genome sequencing to characterise 49 isolates of Klebisella spp. (including 43 Kp) and 2 presumptive Providencia rettgeri isolates recovered from dairy farms located near 3 cities in Pakistan—Quetta (n = 29), Faisalabad (n = 19), and Sargodha (n = 3). The 43 Kp isolates corresponded to 38 sequence types (STs), and 35 of these STs were only observed once. This high diversity indicates frequent admixture and limited clonal spread on local scales. Of the 49 Klebsiella spp. isolates, 41 (84%) did not contain any clinically relevant antimicrobial resistance genes (ARGs), and we did not detect any ARGs predicted to encode resistance to carbapenems or colistin. However, four Kp lineages contained multiple ARGs: ST11 (n = 2), ST1391-1LV (n = 1), ST995 (n = 1) and ST985 (n = 1). STs 11, 1391-1LV and 995 shared a core set of five ARGs, including blaCTX-M-15, harboured on different AMR plasmids. ST985 carried a different set of 16 resistance genes, including blaCTX-M-55. The two presumptive P. rettgeri isolates also contained multiple ARGs. Finally, the four most common plasmids which did not harbour ARGs in our dataset were non-randomly distributed between regions, suggesting that local expansion of the plasmids occurs independently of the host bacterial lineage. Evidence regarding how dairy farms contribute to the emergence and spread of AMR in Pakistan is valuable for public authorities and organizations responsible for health, agriculture and the environment, as well as for industrial development.
Original languageEnglish
Article number539
Number of pages12
Issue number3
Publication statusPublished - 8 Mar 2023

Bibliographical note

Funding: SamH is sponsored by a Schlumberger Foundation Faculty for the Future Fellowship.
Additional funding was provided by grant MR/S004769/1 (OH-DART) from the Antimicrobial Resistance Cross Council Initiative supported by the seven United Kingdom research councils and
the National Institute for Health Research. The APC was funded by the University of Bath

Data Availability Statement: The genome data have been deposited under BioProject ID PRJNA935981.


  • AMR
  • Klebsiella pneumoniae
  • One-Health
  • Pakistan
  • agriculture
  • plasmids

ASJC Scopus subject areas

  • Microbiology
  • Biochemistry
  • Pharmacology, Toxicology and Pharmaceutics(all)
  • Microbiology (medical)
  • Infectious Diseases
  • Pharmacology (medical)


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