TY - JOUR
T1 - Whole‐Genome Sequencing Enables Molecular Characterization of Non‐Clonal Group 258 High‐Risk Clones (ST13, ST17, ST147 and ST307) Among Carbapenem‐Resistant Klebsiella pneumoniae From a Tertiary University Hospital Centre in Portugal
AU - Mendes, Gabriel
AU - Ramalho, João F.
AU - Bruschy‐fonseca, Ana
AU - Lito, Luís
AU - Duarte, Aida
AU - Melo‐cristino, José
AU - Caneiras, Cátia
N1 - Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2022/2
Y1 - 2022/2
N2 - The carbapenem‐resistant Enterobacterales (CRE) strains have been identified by the World Health Organization as critical priority pathogens in research and development of diagnostics, treatments, and vaccines. However, recent molecular information about carbapenem-resistant K. pneumoniae (CRK) epidemiology in Portugal is still scarce. Thus, this study aimed to provide the molecular epidemiology, resistome, and virulome of CRK clinical strains recovered from a tertiary care hospital centre (2019–2021) using polymerase chain reaction (PCR) and the advanced molecular technique whole‐genome sequencing (WGS). PCR amplification of carbapenemase genes was performed in 437 carbapenem‐resistant K. pneumoniae strains. The most frequent carbapenemases were: KPC‐3 (42%), followed by OXA‐181 (20%), GES‐5 (0.2%), and NDM‐ 1 (0.2%). Additionally, 10 strains (2%) coproduced KPC‐3 and OXA‐181, and 1 strain coproduced KPC‐3 and OXA‐48 (0.2%). The genomic population structure of 68 strains characterized by WGS demonstrated the ongoing dissemination of four main high‐risk clones: ST13, ST17, ST147, and ST307, while no clones belonging to the European predominant clonal groups (CG15 and CG258) were found. Moreover, we describe one K. pneumoniae ST39‐KL62 that coproduced the NDM‐1 carbapenemase and the extended‐spectrum beta‐lactamase CTX‐M‐15, and one K. pneumoniae ST29‐ KL54 GES‐5 and BEL‐1 coproducer. Furthermore, a high prevalence of iron siderophores were present in all CRK strains, with several strains presenting both colibactin and the hypermucoviscosity phenotype. Thus, the data presented here highlight an uncommon molecular epidemiology pattern in Portugal when compared with most European countries, further supporting the emergence and dissemination of nonclonal group 258 hypervirulent multidrug high-risk clones and the need to promote in‐depth hospital molecular surveillance studies.
AB - The carbapenem‐resistant Enterobacterales (CRE) strains have been identified by the World Health Organization as critical priority pathogens in research and development of diagnostics, treatments, and vaccines. However, recent molecular information about carbapenem-resistant K. pneumoniae (CRK) epidemiology in Portugal is still scarce. Thus, this study aimed to provide the molecular epidemiology, resistome, and virulome of CRK clinical strains recovered from a tertiary care hospital centre (2019–2021) using polymerase chain reaction (PCR) and the advanced molecular technique whole‐genome sequencing (WGS). PCR amplification of carbapenemase genes was performed in 437 carbapenem‐resistant K. pneumoniae strains. The most frequent carbapenemases were: KPC‐3 (42%), followed by OXA‐181 (20%), GES‐5 (0.2%), and NDM‐ 1 (0.2%). Additionally, 10 strains (2%) coproduced KPC‐3 and OXA‐181, and 1 strain coproduced KPC‐3 and OXA‐48 (0.2%). The genomic population structure of 68 strains characterized by WGS demonstrated the ongoing dissemination of four main high‐risk clones: ST13, ST17, ST147, and ST307, while no clones belonging to the European predominant clonal groups (CG15 and CG258) were found. Moreover, we describe one K. pneumoniae ST39‐KL62 that coproduced the NDM‐1 carbapenemase and the extended‐spectrum beta‐lactamase CTX‐M‐15, and one K. pneumoniae ST29‐ KL54 GES‐5 and BEL‐1 coproducer. Furthermore, a high prevalence of iron siderophores were present in all CRK strains, with several strains presenting both colibactin and the hypermucoviscosity phenotype. Thus, the data presented here highlight an uncommon molecular epidemiology pattern in Portugal when compared with most European countries, further supporting the emergence and dissemination of nonclonal group 258 hypervirulent multidrug high-risk clones and the need to promote in‐depth hospital molecular surveillance studies.
KW - Carbapenem‐resistance
KW - Hypermucoviscosity (HMV)
KW - Hypervirulent
KW - KPC‐3
KW - Klebsiella pneumoniae
KW - Molecular epidemiology
KW - NDM‐1
KW - OXA‐181
KW - Portugal
KW - ST13
KW - ST147
KW - ST17
KW - ST307
KW - ST39‐KL62
KW - Whole‐genome sequencing (WGS)
UR - http://www.scopus.com/inward/record.url?scp=85124290772&partnerID=8YFLogxK
U2 - 10.3390/microorganisms10020416
DO - 10.3390/microorganisms10020416
M3 - Article
AN - SCOPUS:85124290772
SN - 2076-2607
VL - 10
JO - Microorganisms
JF - Microorganisms
IS - 2
M1 - 416
ER -