Klebsiella pneumoniae carriage in low-income countries: antimicrobial resistance, genomic diversity and risk factors

Bich Tram Huynh, Virginie Passet, Andriniaina Rakotondrasoa, Thierno Diallo, Alexandra Kerleguer, Melanie Hennart, Agathe De Lauzanne, Perlinot Herindrainy, Abdoulaye Seck, Raymond Bercion, Laurence Borand, Maria Pardos de la Gandara, Elisabeth Delarocque-Astagneau, Didier Guillemot, Muriel Vray, Benoit Garin, Jean Marc Collard, Carla Rodrigues, Sylvain Brisse

Research output: Contribution to journalArticlepeer-review


Klebsiella pneumoniae: (hereafter, Kp) is a major public health threat responsible for high levels of multidrug resistant (MDR) human infections. Besides, Kp also causes severe infections in the community, especially in Asia and Africa. Although most Kp infections are caused by endogenous intestinal carriage, little is known about the prevalence and microbiological characteristics of Kp in asymptomatic human carriage, and attached risk factors including environmental sources exposure. Methods: Here, 911 pregnant women from communities in Madagascar, Cambodia, and Senegal were screened for gut colonization by Kp. Characteristics of Kp strains (antimicrobial susceptibility, genomic diversity, virulence, and resistance genes) were defined, and associated risk factors were investigated. Results: Kp carriage rate was 55.9%, and Kp populations were highly heterogeneous (6 phylogroups, 325 sequence types, Simpson index 99.6%). One third of Kp isolates had acquired antimicrobial resistance genes. MDR-Kp (11.7% to 39.7%) and extended spectrum beta-lactamase (ESBL)-producing Kp (0.7% to 14.7%) varied among countries. Isolates with virulence genes were detected (14.5%). Environmental exposure factors including food, animal contacts, or hospitalization of household members were associated with carriage of Kp, antimicrobial resistance and hypervirulence. However, risk factors were country-specific and Kp subpopulation-specific. Conclusion: This large-scale multicenter study uncovers the huge diversity of Kp in human gut carriage, demonstrates that antimicrobial resistance is widespread in communities of three low-income countries, and underlines the challenges posed by Kp colonization to the control of antimicrobial resistance.

Original languageEnglish (US)
Pages (from-to)1287-1299
Number of pages13
JournalGut Microbes
Issue number5
StatePublished - Sep 2 2020
Externally publishedYes


  • Klebsiella pneumoniae
  • antibiotic resistance
  • carriage
  • community
  • genomic diversity
  • low-income countries

ASJC Scopus subject areas

  • Microbiology
  • Gastroenterology
  • Microbiology (medical)
  • Infectious Diseases


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