Whole-genome sequencing analysis of Klebsiella aerogenes among men who have sex with men in Guangzhou, China

Abstract

Klebsiella aerogenes is a common infectious bacterium that poses a threat to human health. Nevertheless, there are limited data on the population structure, genetic diversity, and pathogenicity of K. aerogenes, especially among men who have sex with men (MSM). The present study aimed to clarify the sequence types (STs), clonal complexes (CCs), resistance genes, and virulence factors of popular strains. Multilocus sequence typing was used to describe the population structure of K. aerogenes. The Virulence Factor Database and Comprehensive Antibiotic Resistance Database were used to assess the virulence and resistance profiles. In this study, next-generation sequencing was performed on nasal swabs specimens collected in an HIV Voluntary Counseling Testing outpatient department in Guangzhou, China, from April to August 2019. The identification results showed that a total of 258 K. aerogenes isolates were collected from 911 participants. We found that the isolates were most resistant to furantoin (89.53%, 231/258) and ampicillin (89.15%, 230/258), followed by imipenem (24.81%, 64/258) and cefotaxime (18.22%, 47/258). The most common STs in carbapenem-resistant K. aerogenes were ST4, ST93, and ST14. The population has at least 14 CCs, including several novel ones identified in this study (CC11-CC16). The main mechanism of drug resistance genes was antibiotic efflux. Based on the presence of the iron carrier production genes irp and ybt, we identified two clusters according to virulence profiles. In cluster A, CC3 and CC4 carry the clb operator encoding the toxin. Increased monitoring is needed for the three main ST type strains carried by MSM. The main clone group CC4 has a large number of toxin genes, and it spreads among MSM. Caution is needed to prevent further spread of this clone group in this population. In sum, our results may provide a foundation for the development of new therapeutic and surveillance strategies for treating MSM.

Keywords: Enterobacteriaceae; antimicrobial resistance; multidrug-resistant (MDR); pathogens; whole genome sequencing (WGS).

Figure 1

Population structure of Klebsiella aerogenes based on multilocus sequence typing (MLST). Each circle represents a sequence type, and each color represents a different clonal complex (CC). The size of the circle is proportional to the frequency of the sequence type. A total of 258 K. aerogenes isolates are included.

Figure 2

Detected antibiotic resistance genes. The prediction of antimicrobial resistance genes was performed using a Resistance Gene Identifier (RGI) search of the Comprehensive Antibiotic Resistance Database. Columns and rows represent antibiotic resistance genes and strains, respectively. Blue means that the gene was detected, and tan means that it was not detected. CRKA, carbapenem-resistant K. aerogenes; CSKA, carbapenem-susceptible K. aerogenes.

Figure 3

Relative frequencies of antibiotic genes per clonal complex (CC). Each box shows the percentage of genes associated with resistance to each class of antibiotics. For better visualization, the “multidrug-resistant” category is not shown here.

Figure 4

Prevalence of acquired virulence factors. The prediction of virulence genes was performed using a BLAST search of the Virulence Factor Database. Columns and rows represent virulence factors and strains, respectively. Blue means that the gene was detected, and tan means that it was not detected.

Figure 5

Maximum likelihood phylogenomic analysis of Klebsiella aerogenes in our circulating strains. Discriminatory single-nucleotide polymorphisms (SNPs) based on core-genome comparisons were used to plot the tree. Carbapenem-resistant K. aerogenes (CRKA) strains are shown as solid blue squares; multidrug-resistant (MDR) strains are shown as solid red squares. Different colored squares represent different clonal complexes (CCs). Resistant species are shown in brown, and resistance genes are shown in orange. The scale bar indicates their number.

Figure 6

Maximum likelihood phylogenomic comparison of Klebsiella aerogenes genomes to global K. aerogenes from GenBank. Discriminatory single-nucleotide polymorphisms (SNPs) based on core-genome comparisons were used to plot the tree. Different color squares represent different clonal complexes (CCs) and regions. Carbapenem-resistant K. aerogenes strains are shown as green squares.