High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates : A Multicentric Retrospective Indian Study. / Nagaraj, G.; Shamanna, V.; Govindan, V.; Sravani, D.; Akshata, K.P.; Shincy, M.R.; Venkatesha, V.T.; Abrudan, M.; Argimón, S.; Kekre, M.; Aanensen, D.M.; Ravikumar, K.L.; Abudahab, K.; Harste, H.; Muddyman, D.; Taylor, B.; Wheeler, N.; Donado-Godoy, P.; Bernal, J.F.; Arevalo, A.; Valencia, M.F.; Osma Castro, E.C.D.; Ravishankar, K.N.; Okeke, I.N.; Oaikhena, A.O.; Afolayan, A.O.; Ajiboye, J.J.; Odih, E.E.; Carlos, C.; Lagrada, M.L.; Macaranas, P.K.V.; Olorosa, A.M.; Gayeta, J.M.; Herrera, E.M.
In: Clinical Infectious Diseases, Vol. 73, No. Suppl. 4, 2021, p. S300–S307.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates
T2 - A Multicentric Retrospective Indian Study
AU - Nagaraj, G.
AU - Shamanna, V.
AU - Govindan, V.
AU - Sravani, D.
AU - Akshata, K.P.
AU - Shincy, M.R.
AU - Venkatesha, V.T.
AU - Abrudan, M.
AU - Argimón, S.
AU - Kekre, M.
AU - Aanensen, D.M.
AU - Ravikumar, K.L.
AU - Abudahab, K.
AU - Harste, H.
AU - Muddyman, D.
AU - Taylor, B.
AU - Wheeler, N.
AU - Donado-Godoy, P.
AU - Bernal, J.F.
AU - Arevalo, A.
AU - Valencia, M.F.
AU - Osma Castro, E.C.D.
AU - Ravishankar, K.N.
AU - Okeke, I.N.
AU - Oaikhena, A.O.
AU - Afolayan, A.O.
AU - Ajiboye, J.J.
AU - Odih, E.E.
AU - Carlos, C.
AU - Lagrada, M.L.
AU - Macaranas, P.K.V.
AU - Olorosa, A.M.
AU - Gayeta, J.M.
AU - Herrera, E.M.
PY - 2021
Y1 - 2021
N2 - BackgroundCarbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India because of its high dissemination, mortality, and limited treatment options. Its genomic variability is reflected in the diversity of sequence types, virulence factors, and antimicrobial resistance (AMR) mechanisms. This study aims to characterize the clonal relationships and genetic mechanisms of resistance and virulence in CRKP isolates in India.Materials and MethodsWe characterized 344 retrospective K. pneumoniae clinical isolates collected from 8 centers across India collected in 2013–2019. Susceptibility to antibiotics was tested with VITEK 2. Capsular types, multilocus sequence type, virulence genes, AMR determinants, plasmid replicon types, and a single-nucleotide polymorphism phylogeny were inferred from their whole genome sequences.ResultsPhylogenetic analysis of the 325 Klebsiella isolates that passed quality control revealed 3 groups: K. pneumoniae sensu stricto (n = 307), K. quasipneumoniae (n = 17), and K. variicola (n = 1). Sequencing and capsular diversity analysis of the 307 K. pneumoniae sensu stricto isolates revealed 28 sequence types, 26 K-locus types, and 11 O-locus types, with ST231, KL51, and O1V2 being predominant. blaOXA-48-like and blaNDM-1/5 were present in 73.2% and 24.4% of isolates, respectively. The major plasmid replicon types associated with carbapenase genes were IncF (51.0%) and Col group (35.0%).ConclusionOur study documents for the first time the genetic diversity of K and O antigens circulating in India. The results demonstrate the practical applicability of genomic surveillance and its utility in tracking the population dynamics of CRKP. It alerts us to the urgency for longitudinal surveillance of these transmissible lineage
AB - BackgroundCarbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India because of its high dissemination, mortality, and limited treatment options. Its genomic variability is reflected in the diversity of sequence types, virulence factors, and antimicrobial resistance (AMR) mechanisms. This study aims to characterize the clonal relationships and genetic mechanisms of resistance and virulence in CRKP isolates in India.Materials and MethodsWe characterized 344 retrospective K. pneumoniae clinical isolates collected from 8 centers across India collected in 2013–2019. Susceptibility to antibiotics was tested with VITEK 2. Capsular types, multilocus sequence type, virulence genes, AMR determinants, plasmid replicon types, and a single-nucleotide polymorphism phylogeny were inferred from their whole genome sequences.ResultsPhylogenetic analysis of the 325 Klebsiella isolates that passed quality control revealed 3 groups: K. pneumoniae sensu stricto (n = 307), K. quasipneumoniae (n = 17), and K. variicola (n = 1). Sequencing and capsular diversity analysis of the 307 K. pneumoniae sensu stricto isolates revealed 28 sequence types, 26 K-locus types, and 11 O-locus types, with ST231, KL51, and O1V2 being predominant. blaOXA-48-like and blaNDM-1/5 were present in 73.2% and 24.4% of isolates, respectively. The major plasmid replicon types associated with carbapenase genes were IncF (51.0%) and Col group (35.0%).ConclusionOur study documents for the first time the genetic diversity of K and O antigens circulating in India. The results demonstrate the practical applicability of genomic surveillance and its utility in tracking the population dynamics of CRKP. It alerts us to the urgency for longitudinal surveillance of these transmissible lineage
U2 - 10.1093/cid/ciab767
DO - 10.1093/cid/ciab767
M3 - Journal article
C2 - 34850832
VL - 73
SP - S300–S307
JO - Clinical Infectious Diseases
JF - Clinical Infectious Diseases
SN - 1058-4838
IS - Suppl. 4
ER -
ID: 323555484