Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia
Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia
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.
Anti-Bacterial Agents, Carbapenems, Humans, Indigenous Peoples, Klebsiella Infections, Klebsiella pneumoniae/genetics, Malaysia, Virulence/genetics, beta-Lactamases/genetics, Hypervirulent, ESBL, Antimicrobial resistance, Klebsiella pneumoniae
Das, Souradeep
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Pandey, Anish K.
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Morris, Denise E.
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Anderson, Rebecca
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Lim, Victor
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Wie, Chong Chun
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Yap, Ivan Kok Seng
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Alattraqchi, Ahmed Ghazi
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Simin, Hafis
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Abdullah, Ramle
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Yeo, Chew Chieng
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Clarke, Stuart C.
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Cleary, David W.
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17 April 2024
Das, Souradeep
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Pandey, Anish K.
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Morris, Denise E.
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Anderson, Rebecca
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Lim, Victor
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Wie, Chong Chun
392fda42-5d71-45ca-85cd-925ea94022ea
Yap, Ivan Kok Seng
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Alattraqchi, Ahmed Ghazi
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Simin, Hafis
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Abdullah, Ramle
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Yeo, Chew Chieng
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Clarke, Stuart C.
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Cleary, David W.
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Das, Souradeep, Pandey, Anish K., Morris, Denise E., Anderson, Rebecca, Lim, Victor, Wie, Chong Chun, Yap, Ivan Kok Seng, Alattraqchi, Ahmed Ghazi, Simin, Hafis, Abdullah, Ramle, Yeo, Chew Chieng, Clarke, Stuart C. and Cleary, David W.
(2024)
Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia.
BMC Genomics, 25 (1), [381].
(doi:10.1186/s12864-024-10276-4).
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.
Text
s12864-024-10276-4
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Accepted/In Press date: 1 April 2024
Published date: 17 April 2024
Keywords:
Anti-Bacterial Agents, Carbapenems, Humans, Indigenous Peoples, Klebsiella Infections, Klebsiella pneumoniae/genetics, Malaysia, Virulence/genetics, beta-Lactamases/genetics, Hypervirulent, ESBL, Antimicrobial resistance, Klebsiella pneumoniae
Identifiers
Local EPrints ID: 489989
URI: http://eprints.soton.ac.uk/id/eprint/489989
ISSN: 1471-2164
PURE UUID: 068fe74e-1c77-4c1d-bd72-ae4d50fed0d1
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Date deposited: 09 May 2024 16:45
Last modified: 10 May 2024 01:45
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Contributors
Author:
Souradeep Das
Author:
Anish K. Pandey
Author:
Denise E. Morris
Author:
Rebecca Anderson
Author:
Victor Lim
Author:
Chong Chun Wie
Author:
Ivan Kok Seng Yap
Author:
Ahmed Ghazi Alattraqchi
Author:
Hafis Simin
Author:
Ramle Abdullah
Author:
Chew Chieng Yeo
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