Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia

Souradeep Das; Anish K. Pandey; Denise E Morris; Rebecca Anderson; Victor Lim; Chong Chun Wie; Ivan Kok Seng Yap; Ahmed Ghazi Alattraqchi; Hafis Simin; Ramle Abdullah; Chew Chieng Yeo; Stuart C. Clarke; David W. Cleary

doi:10.1186/s12864-024-10276-4

Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia

Souradeep Das, Anish K. Pandey, Denise E Morris, Rebecca Anderson, Victor Lim, Chong Chun Wie, Ivan Kok Seng Yap, Ahmed Ghazi Alattraqchi, Hafis Simin, Ramle Abdullah, Chew Chieng Yeo, Stuart C. Clarke, David W. Cleary^*

^*Corresponding author for this work

Microbiology and Infection

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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.

Original language	English
Article number	381
Number of pages	9
Journal	BMC Genomics
Volume	25
Issue number	1
Early online date	17 Apr 2024
DOIs	https://doi.org/10.1186/s12864-024-10276-4
Publication status	E-pub ahead of print - 17 Apr 2024

Bibliographical note

Funding
This work was funded by a Newton Fund Institutional Links award to Prof Stuart C. Clarke and Prof Mohd Nor Norazmi [grant number 172686537], an International Medical University grant awarded to Dr Chong Chun Wie and Dr Ivan Kok Seng Yap (BP I-01/12 (09) 2015), and two University of Southampton HEFCE Newton Fund Official Development Assistance (ODA) awards, one each to Prof Stuart C. Clarke and Dr David W. Cleary. Dr Cleary was supported by the National Institute for Health Research through the NIHR Southampton Biomedical Research Centre.

Keywords

Klebsiella pneumoniae
ESBL
Malaysia
Antimicrobial resistance
Hypervirulent

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Das, S., Pandey, A. K., Morris, D. E., Anderson, R., Lim, V., Wie, C. C., Yap, I. K. S., Alattraqchi, A. G., Simin, H., Abdullah, R., Yeo, C. C., Clarke, S. C., & Cleary, D. W. (2024). Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia. BMC Genomics, 25(1), Article 381. Advance online publication. https://doi.org/10.1186/s12864-024-10276-4

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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.",

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author = "Souradeep Das and Pandey, {Anish K.} and Morris, {Denise E} and Rebecca Anderson and Victor Lim and Wie, {Chong Chun} and Yap, {Ivan Kok Seng} and Alattraqchi, {Ahmed Ghazi} and Hafis Simin and Ramle Abdullah and Yeo, {Chew Chieng} and Clarke, {Stuart C.} and Cleary, {David W.}",

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AU - Das, Souradeep

AU - Pandey, Anish K.

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AU - Lim, Victor

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AU - Yap, Ivan Kok Seng

AU - Alattraqchi, Ahmed Ghazi

AU - Simin, Hafis

AU - Abdullah, Ramle

AU - Yeo, Chew Chieng

AU - Clarke, Stuart C.

AU - Cleary, David W.

N1 - Funding This work was funded by a Newton Fund Institutional Links award to Prof Stuart C. Clarke and Prof Mohd Nor Norazmi [grant number 172686537], an International Medical University grant awarded to Dr Chong Chun Wie and Dr Ivan Kok Seng Yap (BP I-01/12 (09) 2015), and two University of Southampton HEFCE Newton Fund Official Development Assistance (ODA) awards, one each to Prof Stuart C. Clarke and Dr David W. Cleary. Dr Cleary was supported by the National Institute for Health Research through the NIHR Southampton Biomedical Research Centre.

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N2 - 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.

AB - 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.

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KW - ESBL

KW - Malaysia

KW - Antimicrobial resistance

KW - Hypervirulent

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DO - 10.1186/s12864-024-10276-4

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SN - 1471-2164

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JO - BMC Genomics

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IS - 1

M1 - 381

ER -

Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia

Abstract

Bibliographical note

Keywords

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