TY - JOUR
T1 - Genomic insights into the expansion of carbapenem-resistant Klebsiella pneumoniae within Portuguese hospitals
AU - Faria, N. A.
AU - Touret, T.
AU - Simões, A. S.
AU - Palos, C.
AU - Bispo, S.
AU - Cristino, J. M.
AU - Ramirez, M.
AU - Carriço, J.
AU - Pinto, M.
AU - Toscano, C.
AU - Gonçalves, E.
AU - Gonçalves, M. L.
AU - Costa, A.
AU - Araújo, M.
AU - Duarte, A.
AU - de Lencastre, H.
AU - Serrano, M.
AU - Sá-Leão, R.
AU - Miragaia, M.
N1 - Funding Information:
This work was partially supported by Projects LISBOA-01-0145-FEDER-007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020 - Programa Operacional Competitividade e Internacionaliza\u00E7\u00E3o (POCI); by ONEIDA project (LISBOA-01-0145-FEDER- 016417) co-funded by FEEI - \"Fundos Europeus Estruturais e de Investimento\" from \"Programa Operacional Regional Lisboa2020\" and by national funds through FCT; N. A. F. was supported by grant SFRH/BPD/111922/2015, from FCT, and DL 57-012/DL/2018. We thank Ana Bela Correia (SAMS Hospital, Lisboa Portugal) and Filomena Martins (Centro hospitalar Lisboa Ocidental, Lisboa, Portugal) for their participation in this study and for providing K. pneumoniae strains.
Funding Information:
This work was partially supported by Projects LISBOA-01-0145-FEDER-007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020 - Programa Operacional Competitividade e Internacionaliza\u00E7\u00E3o (POCI); by ONEIDA project (LISBOA-01-0145-FEDER- 016417) co-funded by FEEI - \"Fundos Europeus Estruturais e de Investimento\" from \"Programa Operacional Regional Lisboa2020\" and by national funds through FCT; N. A. F. was supported by grant SFRH/BPD/111922/2015, from FCT, and DL 57-012/DL/2018.
Publisher Copyright:
© 2024 The Healthcare Infection Society
PY - 2024/6
Y1 - 2024/6
N2 - Carbapenem-resistant Klebsiella pneumoniae (CR-KP) are a public health concern, causing infections with a high mortality rate, limited therapeutic options and challenging infection control strategies. In Portugal, the CR-KP rate has increased sharply, but the factors associated with this increase are poorly explored. In order to address this question, phylogenetic and resistome analysis were used to compare the draft genomes of 200 CR-KP isolates collected in 2017–2019 from five hospitals in the Lisbon region, Portugal. Most CR-KP belonged to sequence type (ST) 13 (29%), ST17 (15%), ST348 (13%), ST231 (12%) and ST147 (7%). Carbapenem resistance was conferred mostly by the presence of KPC-3 (74%) or OXA-181 (18%), which were associated with IncF/IncN and IncX plasmids, respectively. Almost all isolates were multi-drug resistant, harbouring resistance determinants to aminoglycosides, beta-lactams, trimethoprim, fosfomycin, quinolones and sulphonamides. In addition, 11% of isolates were resistant to colistin. Colonizing and infecting isolates were highly related, and most colonized patients (89%) reported a previous hospitalization. Moreover, among the 171 events of cross-dissemination identified by core genome multi-locus sequence typing data analysis (fewer than five allelic differences), 41 occurred between different hospitals and 130 occurred within the same hospital. The results suggest that CR-KP dissemination in the Lisbon region results from acquisition of carbapenemases in mobile genetic elements, influx of CR-KP into the hospitals by colonized ambulatory patients, and transmission of CR-KP within and between hospitals. Prudent use of carbapenems, patient screening at hospital entry, and improvement of infection control are needed to decrease the burden of CR-KP infection in Portugal.
AB - Carbapenem-resistant Klebsiella pneumoniae (CR-KP) are a public health concern, causing infections with a high mortality rate, limited therapeutic options and challenging infection control strategies. In Portugal, the CR-KP rate has increased sharply, but the factors associated with this increase are poorly explored. In order to address this question, phylogenetic and resistome analysis were used to compare the draft genomes of 200 CR-KP isolates collected in 2017–2019 from five hospitals in the Lisbon region, Portugal. Most CR-KP belonged to sequence type (ST) 13 (29%), ST17 (15%), ST348 (13%), ST231 (12%) and ST147 (7%). Carbapenem resistance was conferred mostly by the presence of KPC-3 (74%) or OXA-181 (18%), which were associated with IncF/IncN and IncX plasmids, respectively. Almost all isolates were multi-drug resistant, harbouring resistance determinants to aminoglycosides, beta-lactams, trimethoprim, fosfomycin, quinolones and sulphonamides. In addition, 11% of isolates were resistant to colistin. Colonizing and infecting isolates were highly related, and most colonized patients (89%) reported a previous hospitalization. Moreover, among the 171 events of cross-dissemination identified by core genome multi-locus sequence typing data analysis (fewer than five allelic differences), 41 occurred between different hospitals and 130 occurred within the same hospital. The results suggest that CR-KP dissemination in the Lisbon region results from acquisition of carbapenemases in mobile genetic elements, influx of CR-KP into the hospitals by colonized ambulatory patients, and transmission of CR-KP within and between hospitals. Prudent use of carbapenems, patient screening at hospital entry, and improvement of infection control are needed to decrease the burden of CR-KP infection in Portugal.
KW - Carbapenem resistance
KW - Dissemination
KW - Enterobacterales
KW - Molecular epidemiology
KW - Nosocomial infections
UR - http://www.scopus.com/inward/record.url?scp=85192250663&partnerID=8YFLogxK
U2 - 10.1016/j.jhin.2024.02.028
DO - 10.1016/j.jhin.2024.02.028
M3 - Article
C2 - 38554808
AN - SCOPUS:85192250663
SN - 0195-6701
VL - 148
SP - 62
EP - 76
JO - Journal of Hospital Infection
JF - Journal of Hospital Infection
ER -