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

Abstract

Background 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.

Keywords: Klebsiella pneumoniae; antibiotic resistance; carriage; community; genomic diversity; low-income countries.

Figure 1.

Rates of Kp carriage and genotype diversity.

Figure 2.

Phylogenetic relationships. The scale bar corresponds to 0.01 substitutions per site. iTOL (https://itol.embl.de/) was used to visualize country of origin (circles at branch tips), phylogroups (background color in first circle comprising the isolates names), the ancestral or acquired character of isolates’ resistome (second circle), ESBL phenotype (third circle), and virulence genes as indicated in front of each external circle.

Figure 3.

Antimicrobial resistance.