Skip to main content
NCBI home page
Scientific Reports logoLink to Scientific Reports
. 2024 Nov 9;14:27337. doi: 10.1038/s41598-024-70910-9

Molecular epidemiology of carbapenemase-producing Klebsiella pneumoniae in Gauteng South Africa

Kafilat T Salvador-Oke 1, Johann D D Pitout 2,3,4, Gisele Peirano 2,3, Kathy-Anne Strydom 4,5, Chanel Kingsburgh 4,5, Marthie M Ehlers 1,4, Arshad Ismail 6,9,10, Faustinos T Takawira 7,8, Marleen M Kock 1,4,✉
PMCID: PMC11550437  PMID: 39521758

Abstract

Klebsiella pneumoniae multidrug-resistant (MDR) high-risk clones drive the spread of antimicrobial resistance (AMR) associated infections, resulting in limited therapeutic options. This study described the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa. Representative carbapenem-resistant [K. pneumoniae carbapenemase (KPC)-2, New-Delhi metallo-beta (β)-lactamase (NDM)-1, oxacillinase (OXA)-181, OXA-232, OXA-48, Verona integron-encoded metallo-β-lactamase (VIM)-1] K. pneumoniae isolates (n = 22) obtained from inpatient and outpatient’s urine (n = 9) and inpatients rectal carriage (n = 13) were selected for short-read whole genome sequencing. Klebsiella pneumoniae population include sequence type (ST)-307 (n = 3), ST2497 (n = 5) and ST17 (n = 4). The ST17 strains were exclusively obtained from rectal screening. Ten isolates co-harboured carbapenemase genes including β-lactamase gene encoding KPC-2 + OXA-181, NDM-1 + OXA-48 and NDM-1 + OXA-181. One ST307 isolate (UP-KT-73CKP) co-harboured three carbapenemase genes (blaNDM-1 + blaOXA-48 + blaOXA-181), while all the ST2497 strains co-harboured (blaNDM-1 + blaOXA-232). Phenotypically, hypermucoviscosity was observed in a single ST307 isolate. The ST307 isolate UP-KT-151UKP harboured colibactin genotoxins. The following mobile genetic elements were detected: plasmids [incompatibility group (Inc)-FIB(K), IncX3], and bacteriophages [e.g. Klebsi_ST16_OXA48phi5.4_NC_049450, Klebsi_3LV2017_NC_047817(36)]. The study highlights the importance of local genomic surveillance systems to characterise K. pneumoniae MDR high-risk clones. This data will aid in designing infection and prevention measures for limiting the spread of carbapenemase-producing K. pneumoniae in Gauteng, South Africa.

Keywords: Carbapenemase-producing Klebsiella pneumoniae, High-risk clones, ST307, IncX3, blaOXA-181, Virulence determinants

Subject terms: Computational biology and bioinformatics, Evolution, Microbiology, Molecular biology, Diseases, Health care, Medical research, Pathogenesis

Introduction

Klebsiella pneumoniae is one of the clinically relevant priority pathogens responsible for hospital- and community-acquired infections such as liver abscesses, and urinary tract infections (UTIs)1,2. Multidrug resistant (MDR) K. pneumoniae high-risk clones are important in the spread of carbapenemases locally and globally, revealing a significant public health threat3–6. The major well-studied K. pneumoniae high-risk clones include those from the multi-locus sequence typing (MLST) clonal group 258 especially, sequence type (ST)-11, ST258, and ST5127.

Klebsiella pneumoniae normally colonises mucosal surfaces such as the gastrointestinal tract, which can harbour numerous K. pneumoniae clones with antimicrobial resistance (AMR), virulence determinants, and diverse plasmids8,9. Classical K. pneumoniae (cKp) mostly include MDR high-risk clones, some of which have been reported to co-harbour carbapenemase genes, which limit therapeutic options for K. pneumoniae infections10–12. Hypervirulent K. pneumoniae (hvKp) are known to be susceptible to most antimicrobials however, it is more virulent compared to the cKp13. Though the MDR-cKp and hvKp populations remain non-overlapping, traits associated with both pathotypes have been described in K. pneumoniae high risk clones (ST101, ST147)14,15. The ongoing global convergence of AMR, especially carbapenemase genes and virulence determinants in K. pneumoniae epidemic clones indicates an alarming evolution, which deserves continuous monitoring to control and prevent further spread16. Whole genome sequencing (WGS) is able to provide a more accurate understanding of the evolution of these epidemic clones17.

Klebsiella pneumoniae high-risk clones have been linked to several outbreaks in South African hospitals, particularly ST307 associated with incompatibility group (Inc)-X3 plasmids carrying beta (β)-lactamase gene encoding oxacillinase (blaOXA)-1814,5,15. Studies investigating K. pneumoniae high-risk clones in South Africa focused on a single clone, and associated AMR genes4–6. There is paucity of information on the distribution of K. pneumoniae high-risk clones linked to AMR, and virulence determinants. This study aimed to describe the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa using WGS.

Methods

Bacterial isolates, identification, susceptibility and genotyping

This descriptive study analysed clinical isolates of carbapenemase-producing K. pneumoniae collected between February 2021 and May 2022. Each isolate was resistant to at least one carbapenem (ertapenem, imipenem and meropenem). Isolates were selected from a total sample of 446 obtained from inpatient and outpatient’s urine (n = 194) as well as rectal screening (n = 252) at hospital admission. The susceptibility profiles of all 446 isolates were obtained. Urine isolates were identified using matrix assisted laser desorption ionization-time of flight mass spectrometry [MALDI-TOF MS, Bruker Daltonics, United States (US)]. Antimicrobial susceptibility testing (AST) was performed by disk diffusion method using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints18. The rectal carriage isolates were cultured on Chrom-ID CARBA SMART (bioMérieux, Marcy l’Étoile, France) according to manufacturer’s instructions. Microbial identification of cultured isolates was confirmed using MALDI-TOF MS (Bruker Daltonics, US) at the Ampath National Reference Laboratory (Ampath-MDRC), Pretoria. Further analysis was performed at the Department of Medical Microbiology, University of Pretoria. The AST of rectal carriage isolates was performed using the VITEK® 2 system (bioMérieux-Vitek, Marcy-l’Étoile, France). String test was performed to determine mucoid phenotype19. Isolates were subjected to rapid polymyxin Nordmann/Poirel (NP) test, microbroth dilution testing, and PCR assays for phenotypic and genotypic detection of colistin resistance respectively. Carbapenemase genes [beta (β)-lactamase gene encoding New Delhi metallo-β-lactamase (blaNDM), K. pneumoniae carbapenemase (blaKPC), Verona integron-encoded metallo-β-lactamase (blaVIM) and blaOXA-48-like] were detected using PCR assays with published primers20,21. Selection criteria are described in Fig. 1. Since ST307 K. pneumoniae high-risk clone is a well-studied AMR clone, endemic to South African hospitals, representative ST307 (n = 36) and all non-ST307 (n = 287) isolates were typed using repetitive extragenic palindromic PCR (REP-PCR) to determine genetic relatedness among isolates. Patients’ demographic data were collected. Twenty-two carbapenem-resistant K. pneumoniae (CRKp) isolated from urine (n = 9) and rectal carriage (n = 13) were selected based on the presence of the PCR detected carbapenemase genes for short-read WGS to explore the genomic context of carbapenemase-producing K. pneumoniae isolates representing different K. pneumoniae lineages circulating in Gauteng, South Africa.

Fig. 1.

Fig. 1

Open in a new tab

Description of selection criteria for the representative isolates for whole genome sequencing from the primary data.

Genomic DNA extraction

Genomic DNA (gDNA) was extracted from K. pneumoniae cultures using the Zymo Quick-DNA™ Fungal/Bacteria Mini prep Kit [ZYMO Research, US] according to the manufacturer’s instructions. To ensure adequate quantity and quality of extracted gDNA, the yield, concentration, and purity were evaluated using the Nanodrop spectrophotometer (ND-1000). The gDNA was stored at − 20 °C.

Whole genome sequencing

The Qubit® 3.0 fluorometer (Invitrogen, Oregon, US) was used for quantification of the extracted gDNA to a concentration of > 10 nanogram/microlitre (ng/µL). Multiplexed, paired-end libraries (2 × 150 bp) were prepared using the Illumina DNA Prep kit (Illumina, San Diego, US), followed by sequencing on the Illumina NextSeq 550 platform (Illumina, San Diego, US) with 100 × coverage.

Bioinformatics analysis

Raw sequencing reads were analysed using the Jekesa pipeline v1.0 (https://github.com/stanikae/jekesa), which included the filtering of reads (Q, ≥ 20; length, ≥ 50) with Trim Galore v0.6.10 (https://github.com/FelixKrueger/TrimGalore), and de novo assembly with SPAdes v3.13.2 (https://github.com/ablab/spades)22–24. Sequence types were assigned using the BIGSdb platform curated by the Institute Pasteur (https://bigsdb.pasteur.fr/klebsiella)25. Raw reads were deposited in the National Center for Biotechnology Information (NCBI) under the Bio-Project number: PRJNA922902.

Pathogenwatch was used to infer isolates core genome (cg) MLST classification, capsular serotypes, and plasmid replicons26–32. The AMR and virulence determinants of the genomes were determined using Kleborate30,31.

Phage prediction was performed with the PHAge Search Tool (PHASTER) for the identification, annotation, and visualisation of prophage sequences33. The 22 genomes were run as a query on the Centre for Genomic Epidemiology MobileElementFinder v.1.0.2 to determine the mobile genetic elements (MGEs) associated with AMR and virulence determinants34. ResFinder database was used to determine the molecular basis of chromosomal mutations causing resistance on genomes35.

Phylogenetic analysis of the Klebsiella pneumoniae high-risk clones

Klebsiella pneumoniae publicly available reference genomes corresponding to the STs in this study from Australia, India, South Africa, United Kingdom, and the US, retrieved from Pathogenwatch were used to construct a phylogenetic tree27. The 22 genomes, reconstructed with ROARY, and aligned with MAFFET, were compared against K. pneumoniae reference genomes within the Pathogenwatch27. This was performed via BLASTn with species-specific parameter by default based on core gene pairwise SNP distances between genomes27. This was used to construct the neighbour joining trees to demonstrate the phylogenetic relatedness of the isolates27. The phylogenetic tree was visualised in FigTree v1.4.4, and annotated using the interactive tree of life (iTol) (https://itol.embl.de)36,37. The cgMLST and cg life identification number (cgLN) code information of the genomes were used to confirm the clonality of each ST26.

Ethics

Ethical approval was obtained from the Research Ethics Committee, Faculty of Health Sciences, University of Pretoria, South Africa (Ethics Reference No: 819/2020). Since clinical bacterial isolates were used for this study, the need for informed consent to participates was waived by the Research Ethics Committee, Faculty of Health Sciences, University of Pretoria, South Africa (Ethics Reference No: 819/2020). The study was performed according to the Declaration of Helsinki. The study methods adhered to the relevant guidelines and regulations.

Results

Baseline characteristics of sequenced isolates

A total of 22 CRKp isolates were analysed. Antibiograms of isolates are shown in Table 1. Among the CRKp isolates, 13 (59%) were obtained from rectal carriage and 9 (41%) from urine (Table 2). Urine isolates were collected from one (11%) outpatient and eight (89%) inpatients, of which five (63%) were admitted to the intensive care unit (ICU). Four of the CRKp isolates were resistant to colistin: minimum inhibitory concentrations (MICs) ≥ 64 µg per millilitre (µg/mL).

Table 1.

Antimicrobial susceptibility profile and carbapenemase genes associated with the sequenced isolates.

Isolate Sequence types Patients Antimicrobial resistance Carbapenemase genes
Isolate ID Population AMP AMC TZP CXM CAZ FEP ETP IPMa MEMb AMK GEN CIP CSTc SXT
UP-KT-9CKP ST17 Inpatient/RS* R R R R R R R R R S S R R S blaOXA-181
UP-KT-18CKP ST530 Inpatient/ RS* R R R R R R R R R S S R S R blaKPC-2; blaOXA-181
UP-KT-64CKP ST34 Inpatient/ RS* R R R R R R I R R S S R S S blaVIM-1
UP-KT-73CKP ST307 Inpatient/ RS* R R R R R R R R R R R R S R blaNDM-1; blaOXA-181; blaOXA-48
UP-KT-105CKP ST147 Inpatient/ RS* R R R R R R R R R R R R R R blaOXA-181
UP-KT-118CKP ST2497 Inpatient/ RS* R R R R R R R R R R I R S R blaNDM-1; blaOXA-232
UP-KT-120CKP ST147 Inpatient/ RS* R R R R R R R R R I S R S R blaNDM-1
UP-KT-132CKP ST17 Inpatient/ RS* R R R R R R R R R I R R S R blaOXA-181
UP-KT-162CKP ST152 Inpatient/ RS* R R R R R R R R R R S R S R blaNDM-1; blaOXA-48
UP-KT-190CKP ST2497 Inpatient/ RS* R R R R R R R R R R I R S R blaNDM-1; blaOXA-232
UP-KT-202CKP ST17 Inpatient/ RS* R R R R R R R R R S R R S S blaOXA-181
UP-KT-221CKP ST17 Inpatient/ RS* R R R R R R R S R S R R S R blaOXA-181
UP-KT-228CKP ST2497 Inpatient/ RS* R R R R R R R R R R I R S R blaNDM-1; blaOXA-232
UP-KT-23UKP ST152 Inpatient/urine R R R R R R R I R R R R S R blaNDM-1; blaOXA-181
UP-KT-25UKP ST2497 Inpatient/urine R R R R R R R R R R R R S R blaNDM-1; blaOXA-232
UP-KT-70UKP ST147 Inpatient/urine R R R R R R R R R R R R S R blaNDM-1
UP-KT-74UKP ST353 Inpatient/urine R R R R R R R S S S S S S R blaKPC-2
UP-KT-118UKP ST2795 Inpatient/urine R R R R R R R R R R R R R R blaOXA-181
UP-KT-128UKP ST152 Outpatient/urine R R R R R R R I I R R R S R blaNDM-1; blaOXA-48
UP-KT-139UKP ST307 Inpatient/urine R R R R R R R R R S S R S R blaOXA-181
UP-KT-151UKP ST307 Inpatient/urine R R R R R R R S R S S R S R blaOXA-181
UP-KT-195UKP ST2497 Inpatient/urine R R R R R R R R R R R R R R blaNDM-1; blaOXA-232
Open in a new tab

AMP Ampicillin, AMC Amoxicillin/Clavulanate, TZP Piperacillin/tazobactam, CXM Cefuroxime, CAZ Ceftazidime, FEP Cefepime, ETP Ertapenem, IPM Imipenem, MEM Meropenem, AMK Amikacin, GEN Gentamicin, CIP Ciprofloxacin, CST Colistin, SXT Trimethoprim/Sulfamethoxazole.

*Rectal screening (RS).

aIPM MIC range of isolates: susceptible (S) (0.5 to 2 µg/mL); intermediate (I) (4 to 8 µg/mL); resistant (R) (16 to > 32 µg/mL).

bMEM MIC range of isolates: susceptible (S) (0.5 µg/mL); intermediate (I) (8 µg/mL); resistant (R) (16 to > 32 µg/mL).

cCST MIC range of isolates: susceptible (S) (≤ 0.5 to 2 µg/mL); resistant (R) (64 to > 64 µg/mL).

Table 2.

Characteristics of the ST307 and non-ST307 Klebsiella pneumoniae clones in this study.

Profile Sequence types detected
ST307 ST2497 ST17 ST147 ST152 ST2975 ST530 ST34 ST353
No of isolates (n = 22) 3 5 4 3 3 1 1 1 1
Isolates type
Urine 2 2 0 1 2 1 0 0 1
Rectal carriage 1 3 4 2 1 0 1 1 0
Patient population
Inpatients/urine 2 2 0 1 1 1 0 0 1
Outpatient 0 0 0 0 1 0 0 0 0
Inpatients/rectal screening 1 3 4 2 1 0 1 1 0
Ward type
ICU 1 1 0 1 0 1 0 0 1
General 1 1 0 0 0 0 0 0 0
Rehabilitation 0 0 0 0 1 0 0 0 0
Outpatient 0 0 0 0 1 0 0 0 0
Unknown 1 3 4 2 1 0 1 1 0
Capsule (K) serotype
KL25 (wzi141) 0 0 4 0 0 0 0 0 0
KL102 (wzi173) 3 0 0 1 0 1 0 0 0
KL64 (wzi64) 0 4 0 3 0 0 0 0 0
KL149 (wzi110) 0 0 0 0 3 0 0 0 0
KL54 (wzi115) 0 0 0 0 0 0 1 0 0
KL14 (wzi-unknown) 0 0 0 0 0 0 0 1 0
KL110 (wzi346) 0 0 0 0 0 0 0 0 1
KL111 (wzi113) 0 0 0 0 0 0 0 0 0
O serotype
O1 0 5 0 0 0 0 1 0 0
O2a 0 0 0 2 0 0 0 0 0
o2afg 3 0 0 1 0 1 0 0 0
O3b 0 0 0 0 0 0 0 0 1
O4 0 0 0 0 3 0 0 0 0
O5 0 0 4 0 0 0 0 0 0
OL104 0 0 0 0 0 0 0 1 0
Antimicrobial resistance genes
ESBLs
CTX-M-15 2 5 4 3 3 1 1 0 1
TEM- 1 5 4 3 3 0 1 0 1
SHV- 3 5 4 3 3 1 1 1 1
Aminoglycosides
aac(6’)Ib-cr 1 4 3 2 3 1 1 1 1
aac-IIa 1 1 4 2 2 0 0 1 0
aadA 1 4 3 2 3 1 1 1 1
Fluoroquinolones
qnrS1 2 1 4 3 1 1 1 0 0
qnrB- 1 5 0 2 3 1 0 0 0
Trimethoprim/Sulfamethoxazole
dfrA- 3 5 3 3 3 1 1 0 1
sul1-2 3 5 3 3 3 1 1 1 1
Clonal group 307 10190 17 147 152 307 530 13050* 353
Sublineage 307 395 17 147 152 307 530 34 353
Open in a new tab

*New clonal group.

Genomic assembly, quality control and phylogenetic tree of the Klebsiella pneumoniae high-risk clones

Genome sequencing of isolates generated a collective length of contigs from assembled genomes within a length range of 5.5 mega bp (Mbp) to 6.0 Mbp, with the total assembly genome length (N50) ranging from 34 kilo bp (Kbp) to 215 Kbp. Neighbour-joining phylogenetic trees are shown in Figs. 2 and 3. Core genome SNPs grouped the genomes into eight clonal groups and eight sublineages. The phylogenetic tree (Fig. 2) showed that the CRKp isolates clustered into nine distinct STs, five of which represented ≥ 3 isolates: ST2497 (n = 5), ST17 (n = 4) and ST307 (n = 3). Comparison of the virulence determinants, plasmids, and bacteriophage diversity of the isolates is shown in Fig. 3.

Fig. 2.

Fig. 2

Open in a new tab

Phylogenetic tree of the Klebsiella pneumoniae high-risk clones showing accessory genome. The 22 study isolates reconstructed with ROARY and aligned with MAFFET compared against reference genomes within Pathogenwatch via BLASTn. The tree branches (n = 35) indicate isolate names with respective STs (colours) and 13 K. pneumoniae reference genomes from Pathogenwatch database. The outgroup was not shown. Isolate branches tips are coloured by the metadata columns showing accessory genome (showing the presence of carbapenemase genes in filled squares), heatmap of ESBL and other acquire AMR genes in purple and red, chromosomal mutation and efflux pump genes in filled circles.

Fig. 3.

Fig. 3

Open in a new tab

Neighbour-joining phylogenetic tree displaying the relationship of the Klebsiella pneumoniae high-risk clones based on virulence, bacteriophages and plasmids. Relationship among isolates sequenced in this study and similar strains obtained from the Pathogenwatch database (details in Fig. 1). Public K. pneumoniae genomes were obtained from Australia, India, South Africa, United Kingdom and the US. Clonality of the isolates were confirmed using cgMLST and cgLIN code information from Pathogenwatch. Isolate branch tips are coloured by metadata columns showing the presence of virulence determinants in filled star, the commonly detected bacteriophages in filled triangle and heatmap of plasmids in green and red filled squares.

Among the 22 sequenced isolates, three (14%) were ST307 (Table 2). Commonly detected non-ST307 K. pneumoniae clones were ST2497 (5/22; 23%), followed by ST17 (4/22; 18%). The ST17 clones were only identified from rectal carriage isolates. Most of the isolates were assigned to capsular serotype KL64 (wzi64) (ST147, ST2497), and six O1 (ST2497, ST530) antigen types were identified (Table 2). Isolates belonging to ST307 clustered with ST2975 [ST307 single-locus variant (SLV)].

Klebsiella pneumoniae high-risk clones harbouring multiple carbapenemases and other antimicrobial resistance determinants

Among the 22 sequenced isolates, 10 isolates carried two or more carbapenemase genes (Fig. 2). The ST307 UP-KT-73CKP isolate harboured blaNDM-1, blaOXA-48 and blaOXA-181. All the ST2497 strains carried blaNDM-1 and blaOXA-232. The most prevalent carbapenemase genes were blaNDM-1 (n = 11) and blaOXA-181 (n = 11). Eight out of the 10 isolates co-harbouring carbapenemases have carbapenem MICs of 16 to > 32 µg/mL (Table 1).

All isolates also harboured extended-spectrum β-lactamase (ESBL) genes (e.g., blaCTX-M-15) with high prevalence as shown in Fig. 2. Two of the four colistin-resistant CRKp isolates carried mutations in the mgrB gene, while the other isolates possess an unknown colistin resistance mechanism. Plasmid-mediated colistin resistant genes mcr-1 to mcr-9 were not detected. Chromosomal mutations were observed for parC encoding topoisomerase IV, and gyrA (n = 21) encoding DNA gyrase. Defects in the outer membrane proteins [e.g., ompK37(n = 22)] were identified.

Klebsiella pneumoniae high-risk clones ST307 harbouring unusual virulence traits

Isolate ST307 UP-KT-139UKP K. pneumoniae strain exhibited a hypermucoviscosity phenotype. The ST307 UP-KT-151UKP harboured siderophore genes encoding yersiniabactin [ybt17 on integrative and conjugate element (ICEKp1)], and colibactin genotoxin (clb3) associated with hvKp (Fig. 3).

Plasmid replicons and bacteriophages associated with Klebsiella pneumoniae high-risk clones

Several plasmid replicons (Fig. 2), most commonly IncFIB(K) (n = 14), IncX3 (n = 13), and ColKP3 (n = 13) were identified. Each isolate harboured at least two intact bacteriophages, most commonly Klebsi_ST16_OXA48phi5.4_NC_049450 (n = 8) and Klebsi_3LV2017_NC_047817(36) (n = 8).

Genetic environment of the antimicrobial resistance and virulence genes

Antimicrobial resistance gene clusters, conferring resistance to multiple antimicrobial classes, flanked by MGEs were identified in 12 isolates (Table 3). In ST147 UP-KT-105CKP isolate, blaOXA-181 and qnrS1 encoding quinolone resistance on ColKP3 plasmid was coupled with virulence gene cluster irp2; fyuA on ICEKp1in the same contig. Further details regarding the genomic characteristics of the study isolates can be found in the supplementary file 1-Table S1.

Table 3.

Mobile genetic elements associated with antimicrobial resistance and virulence genes among the Klebsiella pneumoniae high-risk clones.

Isolates Sequence types Plasmids Transposon Insertion sequences ICE AMR determinants Virulence genes
UP-KT-9CKP ST17 ColKP3; IncFIB(K) – ISKra4; IS1; IS5; IS66 – OXA-181; CTX-M-15; TEM1B; aac-Iia; qnrS1 –
UP-KT-18CKP ST530 IncHI1B; IncX3; IncFII Tn6196 IS481; ISL3; IS3 – KPC2; TEM-40; TEM-150; TEM-171; TEM-1A; TEM-1C –
UP-KT-73CKP ST307 ColKP3; IncFIB(K); IncX3 Tn5403 IS110; IS5; ISKra4; IS5; ISL3; IS630; IS5 – OXA-181; qnrS1; TEM-1B; sul2 –
*UP-KT-105CKP ST147 ColKP3 – ISKra4 ICEKp1 OXA181; qnrS1 irp2; fyuA
UP-KT-118CKP ST2497 IncFIB(pQil) Tn6196 IS5; IS6; ISL3 – sul1; dfrA14 –
UP-KT-120CKP ST147 – – ISL3 – OXA-1; sul1; dfrA12 –
UP-KT-132CKP ST17 ColKP3; IncFIB(K) – ISKra4; IS1380; IS6; IS3; IS5 – OXA181; qnrS1; TEM-1C; CTX-M; SHV-172; SHV-94; SHV-96 –
UP-KT-162CKP ST152 IncFIB(K); IncFIB(pB171) – IS1380; IS48; IS3 – TEM-1B; CTX-M-15 –
UP-KT-190CKP ST2497 IncHI1B; IncFIB(pQil) Tn6196 IS5; IS110; ISL3 – aadA(homolog); sul1; cmlA1 –
UP-KT-202CKP ST17 ColKP3; IncX3 – ISKra4; IS1380 (truncated); ISL3 – qnrS1; OXA-181; CTX-M-15 –
UP-KT-221CKP ST17 ColKP3 – IS3; ISKra4; IS1380 – OXA-181; qnrS1; CTX-M-15 fimH; mrkA: ABW83989
UP-KT-228CKP ST2497 IncFIB(pQil) Tn6196 IS630; IS5; IS6; ISL3 – NDM-1; sul1; dfrA14 –
UP-KT-25UKP ST2497 – Tn6196 IS4 – aadA1; cmlA1; sul1 –
UP-KT-70UKP ST147 IncFIB(K) – ISKra4; IS91; IS1380; IS66; IS110 – CTX-M-15; NDM-1; qnrS1; sul2 –
UP-KT-74UKP ST353 – Tn6196 IS6; IS3 ICEKp1 OXA-10; aadA1; cmlA1; sul1; dfrA23; dfrA14 irp2; fyuA
UP-KT-118UKP ST2795 ColKP3; IncFIB(pNDM-Mar); IncFIB(K) – ISKra4; IS1380; IS630; IS481; IS5; IS110 – CTX-M-15, OXA-181; qnrS1; sul1; aadA2; dfrA12, –
UP-KT-128UKP ST152 IncFII – IS1380; ISL3 – TEM-1B; CTX-M-15; sul2 –
UP-KT-139UKP ST307 ColKP3; IncHI1B Tn5403 ISKra4; IS110 – OXA-181; qnrS1 –
UP-KT-151UKP ST307 ColKP3 Tn5403; Tn6196 ISKra4 – OXA-181; qnrS1; aadA1; cmlA1; sul1; dfrA15 –
UP-KT-195UKP ST2497 IncFIB(pQil) Tn6196 IS5; IS6; ISL3 – aadA1; cmlA1; sul1; dfrA14 –
Open in a new tab

*Bold indicate the isolate harbouring both AMR genes on plasmid, and virulent determinants on ICE.

Discussion

The spread of carbapenemases causing outbreaks in South African hospitals has been linked to horizontal gene transfer (HGT), and clonal expansion via diverse K. pneumoniae clonal lineages, of which few have been investigated individually4–6. This study described the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa.

In this study, ST307 isolates were clonally related, and possessed similar traits as the South African ST307 from clade VI [e.g. blaOXA-181, IncX3, KL102 (wzi173), parC and gyrA]4,5. This is evidence that similar ST307 strains are circulating in South Africa. The majority (80%) of isolates co-harbouring carbapenemases showed high carbapenem MICs (16 to > 32 µg/mL). Additionally, evolutionary development was observed among ST307 isolates: ST307 UP-KT-73CKP isolate co-harboured multiple carbapenemase genes (blaNDM-1, blaOXA-48 and blaOXA-181), similarly to a recent Chinese study, where a ST307 isolate co-harboured blaKPC-2, blaNDM-1 and blaIMI-312. The ST307 UP-KT-73CKP also harboured plasmids such as IncX3 with the highest number of bacteriophages, which might aid in its acquisition of new AMR traits, and increased virulence via HGT38–40. The ST307 UP-KT-139UKP isolate lacked virulence determinants, but possess iutA, which is usually associated with hvKp. Similarly, a case study in India reported a clinical isolate exhibiting hypermucoviscosity phenotype, but lacked hypervirulence determinants [e.g. regulator of mucoid phenotype (rmp)-A]41. A ST307 UP-KT-151UKP isolate acquired ybt17 on ICEKp1 and colibactin genotoxin. These virulence traits have been associated with hvKp causing invasive and life-threatening infections such as sepsis42,43. Studies have shown the presence of colibactin among ST11 K. pneumoniae clone, but it has not been linked to ST307 until now44,45. Acquisition of virulence determinants can further enhance K. pneumoniae pathogenicity45. However, increased virulence of colibactin-carrying strains in the absence of a virulence plasmid has not been well established31.

The non-ST307 K. pneumoniae high-risk clone ST2497 (n = 5) exhibited a high level of AMR harbouring double carbapenemase genes (blaNDM-1 and blaOXA-232). The ST2497 strains were linked to other AMR mechanisms, and several MGEs, consistent with a case report in the US, in which the strain was resistant to numerous antimicrobials, except tigecycline and colistin46. The ST2497 in this study exhibited pandrug resistant (PDR) and extensively drug resistant (XDR) phenotypes. This is worrisome because three of these ST2497 strains were obtained from rectal carriage of patients, who might be colonised by CRKp. This may cause person-to-person transmission within the hospital and community settings or possible development of subsequent ST2497 infection47.

Klebsiella pneumoniae co-harbouring blaNDM-1 and blaOXA-232 was first reported in the US in 2014 in ST1448. It was later reported in other STs in Italy, Malaysia, South Korea and recently in France in ST249749–52. Resistance of K. pneumoniae strains harbouring blaNDM-1 and blaOXA-232 to the last-resort antimicrobials including the combination therapy like ceftazidime/avibactam have been reported46,52. The reported resistance might be because ceftazidime/avibactam is highly active against OXA-48-like carbapenemases but lacks activity against strains producing NDM and other metallo-β-lactamases53,54. There is a need for antimicrobials active against metallo-β-lactamases-producing strains such as cefiderocol or aztreonam with ceftazidime/avibactam combinations53,54.

The ST2497 associated plasmids IncHI1B(pNDM-MAR) and Col(pHAD28) have been linked to strains co-harbouring blaNDM-1 and blaOXA-23255. The ColE-type plasmid carrying blaOXA-232 was isolated from patients returning from India, indicating travel-related transmission56. The blaOXA-232 differs from blaOXA-181 by one amino acid substitution, but both share similar genetic environments57. The presence of OXA-232 with NDM in a region like South Africa, where OXA-181 is highly prevalent might lead to a significant treatment challenge. The combination therapy available presently in South Africa are partly effective against this mechanism of resistance58. The IncHI1B-like plasmid carrying blaNDM-1 was suggested to have been transferred from Acinetobacter spp. to K. pneumoniae via transpositional events47,59. The possible transfer of AMR genes by plasmids between diverse strains and species of bacteria are a threat to human health. This present study reported the occurrence of ST2497 co-harbouring blaNDM-1 and blaOXA-232 in South Africa. Limited therapeutic options available against this clone might result in poor patient outcomes and high mortality rates. As evidenced in a recent outbreak of NDM-1 and OXA-181 CRKp among neonates resulting in a 64% (9/14) mortality rate in South Africa60. Continuous genomic surveillance of carbapenem-resistant Enterobacterales (CRE) is needed to monitor and control the spread into the community.

The ST2975 clone isolated from an inpatient in the ICU originated from ST307 via a SLV (mutation in rpoB allele). This fact highlights the potential expansion of ST307 as a persistent nosocomial pathogen61. This ST2975 may pose a risk of acquiring additional AMR traits, which might result in effective transmission of extensive AMR in hospitals, and thus community spread61. The ST2975 and a PDR ST147 UP-KT-105CKP K. pneumoniae high-risk clone were phenotypically resistant to colistin (MIC = 64 µg/mL) however, colistin resistance mechanisms were unknown. This is worrisome because colistin in combination with other antimicrobials is currently used as a last-resort treatment for severe CRE infections in South Africa. The available β-lactam/β-lactamase inhibitor combinations (e.g. ceftazidime/avibactam) in South African hospitals are expensive, and not easily accessible62. There is a need for further investigation into the colistin resistance mechanisms. It is concerning that within the same contig of the PDR ST147, AMR genes and virulence determinants were found on a ColKP3 plasmid associated with other MGEs. Similar to an outbreak in Italy linked to NDM-1-producing ST147, which harboured numerous virulence determinants14. This might be an indication of evolutionary development through mutation, which might result in the emergence of a convergence clone (MDR-hvKp)13,63.

All the ST17 strains harboured blaOXA-181, blaCTX-M-15, several plasmids and capsular serotypes. The ST17 strains were exclusively obtained from rectal carriage, which might be related to colonisation. There has been an indication that ST17 infections occurs mostly by colonising strains, rather than causing outbreaks due to clonal expansion64. The divergence of ST17 to many sublineages with several AMR genes, virulence determinants, and plasmids has been attributed to the recombination of the K and O loci64.

This current descriptive study was limited by a small sample size, so it cannot be concluded that the K. pneumoniae clones were dominant or emerging. It was inconclusive that the urine isolates were solely from patients who had UTIs due to lack of access to the clinical information. The patients screened for CRKp colonisation had no documented history of exposure to the healthcare facilities, so it cannot be concluded that the colonisation was exclusively from the community settings. Short-read sequencing did not provide full description of the plasmids as compared to long-read sequencing. However, this study provided a detailed view of the genomic and evolutionary relationship of the circulating K. pneumoniae high-risk clones in Gauteng, South Africa using short-read WGS.

Conclusion

This study revealed the importance of diverse multiple clonal lineages, and HGT through MGEs especially plasmids in the spread of carbapenemases and virulence determinants in South Africa. This study highlights the importance of local genomic surveillance systems to characterise K. pneumoniae MDR high-risk clones. The generated data will aid in designing infection and prevention measures for limiting the spread of K. pneumoniae with carbapenemases in Gauteng, South Africa.

Supplementary Information

Supplementary Information. (20.8KB, docx)

Acknowledgements

The authors would like to thank the Ampath laboratory representatives for providing isolates for this project. The authors would like to express their gratitude to Dr Samuel Ogundare for data analysis support. The authors would like to thank the University of Pretoria for the 2022 PhD student (K.T.S) bursary. This work is based on the research supported wholly by the National Research Foundation (NRF) of South Africa; Competitive Support for Unrated Researchers (Grant Number: 129376). The authors acknowledge the Institut Pasteur team for the curation and maintenance of BIGSdb-Pasteur databases at http://bigsdb.pasteur.fr/.

Disclaimer

The opinions, findings and conclusions expressed in this publication generated by the NRF supported research are from the authors. Study funders had no role in the study design, data collection, data analysis, interpretation or writing of the publication.

Author contributions

Conceptualization: K.T.S.-O., J.D.D.P., M.M.K.; Methodology: K.T.S.-O., J.D.D.P., M.M.K.; Formal analysis and investigation: K.T.S.-O., J.D.D.P., G.P., K.-A.S., C.K., A.I., F.T.T., M.M.K.; Writing—original draft preparation: K.T.S.-O., J.D.D.P., M.M.K.; Writing—review and editing: K.T.S.-O., J.D.D.P., G.P., K.-A.S., C.K., M.M.E., A.I., F.T.T., M.M.K.; Funding acquisition: M.M.K..; Resources: K.-A.S., C.K., M.K.; Supervision: J.D.D.P., M.M.K.; Data curation: K.T.S.-O., J.D.D.P, M.M.K. All authors have read the manuscript and approved submission.

Funding

This work is based on the research supported wholly by the NATIONAL RESEARCH FOUNDATION (NRF) of South Africa; Competitive Support for Unrated Researchers (Grant Number: 129376) (M.M.K). The PhD student (K.T.S) received support through the University of Pretoria, PhD student bursary (2022).

Data availability

All short-reads and assemblies associated with this study are available at NCBI under Bio-Project number: PRJNA922902; with individual BioSamples details. The raw data supporting the conclusions of this manuscript will be made available by the authors, without undue reservation, to any qualified researcher. Anyone interested in using the data for scientific purposes is free to request permission from the corresponding author.

Competing interests

The authors declare no competing interests.

Footnotes

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

The online version contains supplementary material available at 10.1038/s41598-024-70910-9.

References

  • 1.Podschun, R. & Ullmann, U. Klebsiella spp. as nosocomial pathogens: Epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin. Microbiol. Rev.11, 589–603 (1998). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Fazili, T. et al.Klebsiella pneumoniae liver abscess: An emerging disease. Am. J. Med. Sci.351, 297–304. 10.1016/j.amjms.2015.12.018 (2016). [DOI] [PubMed] [Google Scholar]
  • 3.Villa, L. et al. Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone. Microb. Genom.3, e000110. 10.1099/mgen.0.000110 (2017). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Lowe, M. et al.Klebsiella pneumoniae ST307 with blaOXA-181, South Africa, 2014–2016. Emerg. Infect. Dis.25, 739–747. 10.3201/eid2504.181482 (2019). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Strydom, K. A. et al.Klebsiella pneumoniae ST307 with OXA-181: Threat of a high-risk clone and promiscuous plasmid in a resource-constrained healthcare setting. J. Antimicrob. Chemother.75, 896–902. 10.1093/jac/dkz550 (2020). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Ramsamy, Y. et al. Genomic analysis of carbapenemase-producing extensively drug-resistant Klebsiella pneumoniae isolates reveals the horizontal spread of p18–43_01 plasmid encoding blaNDM-1 in South Africa. Microorganisms8, 137. 10.3390/microorganisms8010137 (2020). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Wyres, K. L., Lam, M. M. & Holt, K. E. Population genomics of Klebsiella pneumoniae. Nat. Rev. Microbiol.10.1038/s41579-019-0315-1 (2020). [DOI] [PubMed] [Google Scholar]
  • 8.Ashurst, J. V. & Dawson, A. in StatPearls [Internet] (StatPearls Publishing, 2019). https://www.ncbi.nlm.nih.gov/pubmed/30085546.
  • 9.Sun, Q. L. et al. Dynamic colonization of Klebsiella pneumoniae isolates in gastrointestinal tract of intensive care patients. Front. Microbiol.10, 230. 10.3389/fmicb.2019.00230 (2019). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Rojas, L. J. et al. NDM-5 and OXA-181 beta-lactamases, a significant threat continues to spread in the Americas. Antimicrob. Agents Chemother.61, 1–6. 10.1128/AAC.00454-17 (2017). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Balm, M. N. et al. Emergence of Klebsiella pneumoniae co-producing NDM-type and OXA-181 carbapenemases. Clin. Microbiol. Infect.19, E421-423. 10.1111/1469-0691.12247 (2013). [DOI] [PubMed] [Google Scholar]
  • 12.Bai, J. et al. Antibiotic resistance and virulence characteristics of four carbapenem-resistant Klebsiella pneumoniae strains coharbouring bla(KPC) and bla(NDM) based on whole genome sequences from a tertiary general teaching hospital in central China between 2019 and 2021. Microb. Pathog.175, 105969. 10.1016/j.micpath.2023.105969 (2023). [DOI] [PubMed] [Google Scholar]
  • 13.Russo, T. A. & Marr, C. M. Hypervirulent Klebsiella pneumoniae. Clin. Microbiol. Rev.32, e00001–e000019. 10.1128/CMR.00001-19 (2019). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Turton, J. et al. Hybrid resistance and virulence plasmids in “high-risk” clones of Klebsiella pneumoniae, including those carrying blaNDM-5. Microorganisms7, 1–11. 10.3390/microorganisms7090326 (2019). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Peirano, G., Chen, L., Kreiswirth, B. N. & Pitout, J. D. D. Emerging antimicrobial-resistant high-risk Klebsiella pneumoniae clones ST307 and ST147. Antimicrob. Agents Chemother.64, 1–14. 10.1128/AAC.01148-20 (2020). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Di Pilato, V. et al. Resistome and virulome accretion in an NDM-1-producing ST147 sublineage of Klebsiella pneumoniae associated with an outbreak in Tuscany, Italy: a genotypic and phenotypic characterisation. Lancet Microbe3, e224–e234. 10.1016/s2666-5247(21)00268-8 (2022). [DOI] [PubMed] [Google Scholar]
  • 17.Parkhill, J. & Wren, B. W. Bacterial epidemiology and biology–lessons from genome sequencing. Genome Biol.12, 230. 10.1186/gb-2011-12-10-230 (2011). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.EUCAST, ECoAST. Breakpoint tables for interpretation of MICs and zone diameters (2020). https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.pdf.
  • 19.Shon, A. S., Bajwa, R. P. & Russo, T. A. Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: A new and dangerous breed. Virulence4, 107–118. 10.4161/viru.22718 (2013). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Poirel, A., Walsh, T. R., Cuvillier, V. & Nordmann, P. Multiplex PCR for detection of acquired carbapenemase genes. Diagn. Microbiol. Infect. Dis.70, 119–123. 10.1016/j.diagmicrobio.2010.12.002 (2011). [DOI] [PubMed] [Google Scholar]
  • 21.Poirel, L., Heritier, C., Tolun, V. & Nordmann, P. Emergence of oxacillinase-mediated resistance to imipenem in Klebsiella pneumoniae. Antimicrob. Agents Chemother.48, 15–22. 10.1128/aac.48.1.15-22.2004 (2004). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol.19, 455–477. 10.1089/cmb.2012.0021 (2012). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Kwenda S., A. M., Khumalo Z.T.H., Mtshali S., Mnyameni F., Ismail A. Jekesa: An Automated Easy-to-Use Pipeline for Bacterial Whole Genome Typing Github. Github, https://github.com/stanikae/jekesa (2021).
  • 24.Krueger, F. et al. (2023). FelixKrueger/TrimGalore: v0. 6.10-add default decompression path (0.6. 10). Zenodo. https://github.com/FelixKrueger/TrimGalore.
  • 25.Hennart, M. et al. A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains. Mol. Biol. Evol.10.1093/molbev/msac135 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Tian, L., Huang, C., Mazloom, R., Heath, L. S. & Vinatzer, B. A. LINbase: A web server for genome-based identification of prokaryotes as members of crowdsourced taxa. Nucleic Acids Res.48, W529-w537. 10.1093/nar/gkaa190 (2020). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Argimón, S. et al. Rapid genomic characterization and global surveillance of Klebsiella using Pathogenwatch. Clin. Infect. Dis.73, S325-s335. 10.1093/cid/ciab784 (2021). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Wyres, K. L. et al. Identification of Klebsiella capsule synthesis loci from whole genome data. Microb. Genom.2, e000102. 10.1099/mgen.0.000102 (2016). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Lam, M. M. C., Wick, R. R., Judd, L. M., Holt, K. E. & Wyres, K. L. Kaptive 2.0: Updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex. Microb. Genom.10.1099/mgen.0.000800 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Lam, M. M. C. et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat. Commun.12, 4188. 10.1038/s41467-021-24448-3 (2021). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Lam, M. M. C. et al. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. Microb. Genom.10.1099/mgen.0.000196 (2018). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Carattoli, A. et al.In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother.58, 3895–3903. 10.1128/aac.02412-14 (2014). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Arndt, D. et al. PHASTER: A better, faster version of the PHAST phage search tool. Nucleic Acids Res.44, W16-21. 10.1093/nar/gkw387 (2016). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Johansson, M. H. K. et al. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J. Antimicrob. Chemother.76, 101–109. 10.1093/jac/dkaa390 (2021). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Florensa, A. F., Kaas, R. S., Clausen, P., Aytan-Aktug, D. & Aarestrup, F. M. ResFinder—An open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb. Genom.10.1099/mgen.0.000748 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Rambaut, A. FigTree, Version 1.4.4. Institute of Evolutionary Biology (University of Edinburgh, 2018). http://tree.bio.ed.ac.uk/software/figtree/.
  • 37.Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res.49, W293-w296. 10.1093/nar/gkab301 (2021). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 38.Wagner, P. L. & Waldor, M. K. Bacteriophage control of bacterial virulence. Infect. Immun.70, 3985–3993. 10.1128/iai.70.8.3985-3993.2002 (2002). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Xia, G. & Wolz, C. Phages of Staphylococcus aureus and their impact on host evolution. Infect. Genet. Evol.21, 593–601. 10.1016/j.meegid.2013.04.022 (2014). [DOI] [PubMed] [Google Scholar]
  • 40.Guo, X. et al. Global prevalence, characteristics, and future prospects of IncX3 plasmids: A review. Front. Microbiol.13, 979558. 10.3389/fmicb.2022.979558 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 41.Dey, T. et al. Unusual hypermucoviscous clinical isolate of Klebsiella pneumoniae with no known determinants of hypermucoviscosity. Microbiol. Spectr.10, e0039322. 10.1128/spectrum.00393-22 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 42.Vizcaino, M. I. & Crawford, J. M. The colibactin warhead crosslinks DNA. Nat. Chem.7, 411–417. 10.1038/nchem.2221 (2015). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 43.Marcq, I. et al. The genotoxin colibactin exacerbates lymphopenia and decreases survival rate in mice infected with septicemic Escherichia coli. J. Infect. Dis.210, 285–294. 10.1093/infdis/jiu071 (2014). [DOI] [PubMed] [Google Scholar]
  • 44.Morgado, S., Fonseca, E. & Vicente, A. C. Genomics of Klebsiella pneumoniae species complex reveals the circulation of high-risk multidrug-resistant pandemic clones in human, animal, and environmental sources. Microorganisms10.3390/microorganisms10112281 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 45.Cho, Y. Y. et al. Comparison of virulence between two main clones (ST11 and ST307) of Klebsiella pneumoniae isolates from South Korea. Microorganisms10.3390/microorganisms10091827 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 46.Contreras, D. A. et al. Coinfections of two strains of NDM-1- and OXA-232-coproducing Klebsiella pneumoniae in a kidney transplant patient. Antimicrob. Agents Chemother.10.1128/aac.00948-19 (2020). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 47.Martin, R. M. et al. Molecular epidemiology of colonizing and infecting isolates of Klebsiella pneumoniae. mSphere1, e00261–e00316. 10.1128/mSphere.00261-16 (2016). [DOI] [PMC free article] [PubMed]
  • 48.Doi, Y. et al. Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing. Antimicrob. Agents Chemother.58, 5947–5953. 10.1128/aac.03180-14 (2014). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 49.Avolio, M., Vignaroli, C., Crapis, M. & Camporese, A. Co-production of NDM-1 and OXA-232 by ST16 Klebsiella pneumoniae, Italy, 2016. Future Microbiol.12, 1119–1122. 10.2217/fmb-2017-0041 (2017). [DOI] [PubMed] [Google Scholar]
  • 50.Kwon, T. et al. Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae KP617, Coproducing OXA-232 and NDM-1 Carbapenemases, Isolated in South Korea. Genome Announc.10.1128/genomeA.01550-15 (2016). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 51.Al-Marzooq, F., Ngeow, Y. F. & Tay, S. T. Emergence of Klebsiella pneumoniae producing dual carbapenemases (NDM-1 and OXA-232) and 16S rRNA methylase (armA) isolated from a Malaysian patient returning from India. Int. J. Antimicrob. Agents45, 445–446. 10.1016/j.ijantimicag.2014.12.013 (2015). [DOI] [PubMed] [Google Scholar]
  • 52.Emeraud, C. et al. Polyclonal dissemination of OXA-232 Carbapenemase-producing Klebsiella pneumoniae, France, 2013–2021. Emerg. Infect. Dis.28, 2304–2307. 10.3201/eid2811.221040 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 53.Shaw, E. et al. Clinical outcomes after combination treatment with ceftazidime/avibactam and aztreonam for NDM-1/OXA-48/CTX-M-15-producing Klebsiella pneumoniae infection. J. Antimicrob. Chemother.73, 1104–1106. 10.1093/jac/dkx496 (2018). [DOI] [PubMed] [Google Scholar]
  • 54.Tamma, P. D. et al. Comparing the activity of novel antibiotic agents against carbapenem-resistant Enterobacterales clinical isolates. Infect. Control Hosp. Epidemiol.44, 762–767. 10.1017/ice.2022.161 (2023). [DOI] [PubMed] [Google Scholar]
  • 55.Zhu, C. et al. Longitudinal genomic characterization of carbapenemase-producing Enterobacteriaceae (CPE) reveals changing pattern of CPE isolated in Hong Kong hospitals. Int. J. Antimicrob. Agents58, 106430. 10.1016/j.ijantimicag.2021.106430 (2021). [DOI] [PubMed] [Google Scholar]
  • 56.Potron, A. et al. Genetic and biochemical characterisation of OXA-232, a carbapenem-hydrolysing class D β-lactamase from Enterobacteriaceae. Int. J. Antimicrob. Agents41, 325–329. 10.1016/j.ijantimicag.2012.11.007 (2013). [DOI] [PubMed] [Google Scholar]
  • 57.Pitout, J. D. D., Peirano, G., Kock, M. M., Strydom, K. A. & Matsumura, Y. The global ascendency of OXA-48-type carbapenemases. Clin. Microbiol. Rev.33, e00102–e00119. 10.1128/CMR.00102-19 (2019). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 58.Brink, A. J. et al. Best practices: appropriate use of the new β-lactam/β-lactamase inhibitor combinations, ceftazidime-avibactam and ceftolozane-tazobactam in South Africa. S. Afr. J. Infect. Dis.37, 453. 10.4102/sajid.v37i1.453 (2022). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 59.Dolejska, M., Villa, L., Poirel, L., Nordmann, P. & Carattoli, A. Complete sequencing of an IncHI1 plasmid encoding the carbapenemase NDM-1, the ArmA 16S RNA methylase and a resistance-nodulation-cell division/multidrug efflux pump. J. Antimicrob. Chemother.68, 34–39. 10.1093/jac/dks357 (2013). [DOI] [PubMed] [Google Scholar]
  • 60.Magobo, R. E. et al. Outbreak of NDM-1- and OXA-181-producing Klebsiella pneumoniae bloodstream infections in a neonatal unit, south Africa. Emerg. Infect. Dis.29, 1531–1539. 10.3201/eid2908.230484 (2023). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 61.Roe, C. C., Vazquez, A. J., Esposito, E. P., Zarrilli, R. & Sahl, J. W. Diversity, virulence, and antimicrobial resistance in isolates from the newly emerging Klebsiella pneumoniae ST101 lineage. Front. Microbiol.10, 542. 10.3389/fmicb.2019.00542 (2019). [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 62.Tootla, H. D., Copelyn, J., Botha, A., Brink, A. J. & Eley, B. Using ceftazidime-avibactam for persistent carbapenem-resistant Serratia marcescens infection highlights antimicrobial stewardship challenges with new beta-lactam-inhibitor combination antibiotics. S. Afr. Med. J.111, 729–731. 10.7196/SAMJ.2021.v111i8.15762 (2021). [DOI] [PubMed] [Google Scholar]
  • 63.Gu, D. et al. A fatal outbreak of ST11 carbapenem-resistant hypervirulent Klebsiella pneumoniae in a Chinese hospital: A molecular epidemiological study. Lancet Infect. Dis.18, 37–46. 10.1016/S1473-3099(17)30489-9 (2018). [DOI] [PubMed] [Google Scholar]
  • 64.Hetland, M. A. K. et al. Within-patient and global evolutionary dynamics of Klebsiella pneumoniae ST17. bioRxiv. 10.1101/2022.11.01.514664 (2022). [DOI] [PMC free article] [PubMed]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary Information. (20.8KB, docx)

Data Availability Statement

All short-reads and assemblies associated with this study are available at NCBI under Bio-Project number: PRJNA922902; with individual BioSamples details. The raw data supporting the conclusions of this manuscript will be made available by the authors, without undue reservation, to any qualified researcher. Anyone interested in using the data for scientific purposes is free to request permission from the corresponding author.

Articles from Scientific Reports are provided here courtesy of Nature Publishing Group

RESOURCES