ArticleNature communications2024
Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producingMicrobial genomics · 2026Article
- Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli.Nature microbiology · 2026Article
- Antibiotic and healthcare exposure impact on dynamics of third-generation cephalosporin-resistant Enterobacterales colonisation in Cambodian children: a six-month cohort study.Antimicrobial resistance and infection control · 2026Article
- Improving antibiotic prescribing in LMICs: Insights from an outpatient clinic in Pakistan.New microbes and new infections · 2026Article
- Insights Into Global Antimicrobial Resistance Dynamics Through the Sequencing of Enteric Bacteria From US International Travelers.The Journal of infectious diseases · 2026Article
- Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.Microbial genomics · 2026Article
- Antibiotic Resistance Patterns of Bacteria Involved in Colonization and/or Infection of Patients in Intensive Care Units in Northeastern Romania.Antibiotics (Basel, Switzerland) · 2025Article
- Quantifying the effects of antibiotic resistance and within-host competition on strain fitness in Streptococcus pneumoniae.PLoS biology · 2025Article
- Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples.Genome medicine · 2025Article
- Insights into global antimicrobial resistance dynamics through the sequencing of enteric bacteria from U.S. international travelers.bioRxiv : the preprint server for biology · 2025Article
- Analyzing Antibiotic Resistance in Bacteria from Wastewater in Pakistan Using Whole-Genome Sequencing.Antibiotics (Basel, Switzerland) · 2024Article
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Authors and funding
13 authors.
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Abstract
Multi-drug resistant (MDR) E. coli constitute a major public health burden globally, reaching the highest prevalence in the global south yet frequently flowing with travellers to other regions. However, our comprehension of the entire genetic diversity of E. coli colonising local populations remains limited. We quantified this diversity, its associated antimicrobial resistance (AMR), and assessed the impact of antibiotic use by recruiting 494 outpatients and 423 community dwellers in the Punjab province, Pakistan. Rectal swab and stool samples were cultured on CLED agar and DNA extracted from plate sweeps was sequenced en masse to capture both the genetic and AMR diversity of E. coli. We assembled 5,247 E. coli genomes from 1,411 samples, displaying marked genetic diversity in gut colonisation. Compared with high income countries, the Punjabi population generally showed a markedly different distribution of genetic lineages and AMR determinants, while use of antibiotics elevated the prevalence of well-known globally circulating MDR clinical strains. These findings implicate that longitudinal multi-regional genomics-based surveillance of both colonisation and infections is a prerequisite for developing mechanistic understanding of the interplay between ecology and evolution in the maintenance and dissemination of (MDR) E. coli.
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