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. 2024 Apr 17;25(1):381.
doi: 10.1186/s12864-024-10276-4.

Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia

Souradeep Das  1 , Anish K Pandey  1   2 , Denise E Morris  1 , Rebecca Anderson  1 , Victor Lim  3 , Chong Chun Wie  4   5 , Ivan Kok Seng Yap  5 , Ahmed Ghazi Alattraqchi  6 , Hafis Simin  7 , Ramle Abdullah  8 , Chew Chieng Yeo  6 , Stuart C Clarke  1   2   4   9 , David W Cleary  10
Affiliations

Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia

Souradeep Das et al. BMC Genomics. .

Abstract

Klebsiella pneumoniae is a Gram-negative Enterobacteriaceae that is classified by the World Health Organisation (WHO) as a Priority One ESKAPE pathogen. South and Southeast Asian countries are regions where both healthcare associated infections (HAI) and community acquired infections (CAI) due to extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant K. pneumoniae (CRKp) are of concern. As K. pneumoniae can also exist as a harmless commensal, the spread of resistance genotypes requires epidemiological vigilance. However there has been no significant study of carriage isolates from healthy individuals, particularly in Southeast Asia, and specially Malaysia. Here we describe the genomic analysis of respiratory isolates of K. pneumoniae obtained from Orang Ulu and Orang Asli communities in Malaysian Borneo and Peninsular Malaysia respectively. The majority of isolates were K. pneumoniae species complex (KpSC) 1 K. pneumoniae (n = 53, 89.8%). Four Klebsiella variicola subsp. variicola (KpSC3) and two Klebsiella quasipneumoniae subsp. similipneumoniae (KpSC4) were also found. It was discovered that 30.2% (n = 16) of the KpSC1 isolates were ST23, 11.3% (n = 6) were of ST65, 7.5% (n = 4) were ST13, and 13.2% (n = 7) were ST86. Only eight of the KpSC1 isolates encoded ESBL, but importantly not carbapenemase. Thirteen of the KpSC1 isolates carried yersiniabactin, colibactin and aerobactin, all of which harboured the rmpADC locus and are therefore characterised as hypervirulent. Co-carriage of multiple strains was minimal. In conclusion, most isolates were KpSC1, ST23, one of the most common sequence types and previously found in cases of K. pneumoniae infection. A proportion were hypervirulent (hvKp) however antibiotic resistance was low.

Keywords: Klebsiella pneumoniae; Antimicrobial resistance; ESBL; Hypervirulent; Malaysia.

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Conflict of interest statement

DWC was a post-doctoral researcher on projects funded by Pfizer and GSK between April 2014 and October 2017. SCC acts as principal investigator on studies conducted on behalf of University Hospital Southampton NHS Foundation Trust/University of Southampton that are sponsored by vaccine manufacturers but receives no personal payments from them. SCC has participated in advisory boards for vaccine manufacturers but receives no personal payments for this work. SCC has received financial assistance from vaccine manufacturers to attend conferences. All grants and honoraria are paid into accounts within the respective NHS Trusts or Universities, or to independent charities. All other authors have no conflicts of interest.

Figures

Fig. 1
Fig. 1
Minimum-spanning tree generated using goeBurst and MLST. Node numbers are STs and edge numbers represent allelic differences. Node size is proportional to number of isolates belonging to that ST and are coloured by location of isolation
Fig. 2
Fig. 2
Antibiotic resistance (A) and acquired virulence (B) scores for isolates with known capsular types. Resistance scores are on a scale of 0 (low) to 3 (high), and virulence 0 (low) to 5 (high). Resistance scores of 0 indicates no ESBL and no carbapenemase, 1 indicates the presence of an ESBL but still without carbapenemase, 2 indicates the presence of a carbapenemase without colistin resistance and 3 a carbapenemase with colistin resistance. Scores of 0/1 are irrespective of colistin resistance with scores of 2/3 irrespective of the presence of an ESBL. Virulence scores are based on the presence of yersinibactin (ybt), colibactin (clb) and/or aerobactin (iuc). A score of 0 indicates none of these genes were found with a score of 5 showing all three were present. Scores of 1–4 indicate the following: 1 - yersiniabactin only, 2 - yersiniabactin and colibactin (or colibactin only), 3 aerobactin only, 4– aerobactin and yersiniabactin. Bars are ordered by frequency of capsule type
Fig. 3
Fig. 3
Correlation between capsule (K) and serotype (O) loci. Each point displays the number of isolates within each K/O group. Most isolates were characterized by O1 or O2 polysaccharide which were found in KL1, KL2, KL3, KL109 and KL124 (bottom left quadrant)
Fig. 4
Fig. 4
Phylogeny of K. pneumoniae. Phylogenetic tree based on core-genome SNPs and constructed using FastTree (GTR + GAMMA). Leaves are colored by ST. The presence of virulence genes are shown in black, with antibiotic resistance markers in blue (white indicates absence). Virulence: Ybt yersiniabactin, Clb colibactin, Iuc aerobactin, Iro salmochelin, Rmp and RmpA2 hypermucoidy. Antibiotics: Agly aminoglycosides, Col colistin, Fcyn Fosfomycin, Flq fluoroquinolones, Gly glycopeptides, MLS macrolides, Ntmdz nitroimidazoles, Phe phenicols, Rif rifampin, Sul sulfonamides, Tet tetracyclines, Tgc tigecycline, Tmt trimethoprim, Omp osmoporin mutations, Bla beta-lactamases, Carb carbapenemase, ESBL extended spectrum beta-lactamases, ESBL(inhR) extended spectrum beta-lactamases with resistance to beta-lactamase inhibitors, B.broad beta-lactamases, B.broad.inhR beta-lactamases with resistance to beta-lactamase inhibitors
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