Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria
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Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria. / Afolayan, A.O.; Oaikhena, A.O.; Aboderin, A.O.; Olabisi, O.F.; Amupitan, A.A.; Abiri, O.V.; Ogunleye, V.O.; Odih, E.E.; Adeyemo, A.T.; Adeyemo, A.T.; Obadare, T.O.; Abrudan, M.; Argimón, S.; Kekre, M.; Egwuenu, A.; Ihekweazu, C.; Aanensen, D.M.; Okeke, I.N.; Abudahab, K.; Harste, H.; Muddyman, D.; Taylor, B.; Wheeler, N.; Donado-Godoy, P.; Fabian Bernal, J.; Arevalo, A.; Fernanda Valencia, M.; Osma Castro, E.C.D.; Ravikumar, K.L.; Nagaraj, G.; Shamanna, V.; Govindan, V.; Prabhu, A.; Sravani, D.; Shincy, M.R.; Ravishankar, K.N.; Ajiboye, J.J.; Carlos, C.; Lagrada, M.L.; Macaranas, P.K.V.; Olorosa, A.M.; Gayeta, J.M.; Herrera, E.M.; Molloy, A.; Stelling, J.; Vegvari, C.
In: Clinical Infectious Diseases, Vol. 73, No. Suppl. 4, 2021, p. S308–S315.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria
AU - Afolayan, A.O.
AU - Oaikhena, A.O.
AU - Aboderin, A.O.
AU - Olabisi, O.F.
AU - Amupitan, A.A.
AU - Abiri, O.V.
AU - Ogunleye, V.O.
AU - Odih, E.E.
AU - Adeyemo, A.T.
AU - Adeyemo, A.T.
AU - Obadare, T.O.
AU - Abrudan, M.
AU - Argimón, S.
AU - Kekre, M.
AU - Egwuenu, A.
AU - Ihekweazu, C.
AU - Aanensen, D.M.
AU - Okeke, I.N.
AU - Abudahab, K.
AU - Harste, H.
AU - Muddyman, D.
AU - Taylor, B.
AU - Wheeler, N.
AU - Donado-Godoy, P.
AU - Fabian Bernal, J.
AU - Arevalo, A.
AU - Fernanda Valencia, M.
AU - Osma Castro, E.C.D.
AU - Ravikumar, K.L.
AU - Nagaraj, G.
AU - Shamanna, V.
AU - Govindan, V.
AU - Prabhu, A.
AU - Sravani, D.
AU - Shincy, M.R.
AU - Ravishankar, K.N.
AU - Ajiboye, J.J.
AU - Carlos, C.
AU - Lagrada, M.L.
AU - Macaranas, P.K.V.
AU - Olorosa, A.M.
AU - Gayeta, J.M.
AU - Herrera, E.M.
AU - Molloy, A.
AU - Stelling, J.
AU - Vegvari, C.
PY - 2021
Y1 - 2021
N2 - BackgroundKlebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria.MethodsWe performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria. We conducted in silico multilocus sequence typing; AMR gene, virulence gene, plasmid, and K and O loci profiling; as well as phylogenetic analyses, using publicly available tools and Nextflow pipelines.ResultsPhylogenetic analysis revealed that the majority of the 134 K. pneumoniae and 5 K. quasipneumoniae isolates from Nigeria characterized are closely related to globally disseminated multidrug-resistant clones. Of the 39 K. pneumoniae sequence types (STs) identified, the most common were ST307 (15%), ST5241 (12%), ST15 (~9%), and ST25 (~6%). ST5241, 1 of 10 novel STs detected, is a single locus variant of ST636 carrying dfrA14, tetD, qnrS, and oqxAB resistance genes. The extended-spectrum β-lactamase (ESBL) gene blaCTX_M-15 was seen in 72% of K. pneumoniae genomes, while 8% encoded a carbapenemase. No isolate carried a combination of carbapenemase-producing genes. Four likely outbreak clusters from 1 facility, within STs 17, 25, 307, and 5241, were ESBL but not carbapenemase-bearing clones.ConclusionsThis study uncovered known and novel K. pneumoniae lineages circulating in 3 hospitals in Southwest Nigeria that include multidrug-resistant ESBL producers. Carbapenemase-producing isolates remain uncommon. WGS retrospectively identified outbreak clusters, pointing to the value of genomic approaches in AMR surveillance for improving infection prevention and control in Nigerian hospitals.
AB - BackgroundKlebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria.MethodsWe performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria. We conducted in silico multilocus sequence typing; AMR gene, virulence gene, plasmid, and K and O loci profiling; as well as phylogenetic analyses, using publicly available tools and Nextflow pipelines.ResultsPhylogenetic analysis revealed that the majority of the 134 K. pneumoniae and 5 K. quasipneumoniae isolates from Nigeria characterized are closely related to globally disseminated multidrug-resistant clones. Of the 39 K. pneumoniae sequence types (STs) identified, the most common were ST307 (15%), ST5241 (12%), ST15 (~9%), and ST25 (~6%). ST5241, 1 of 10 novel STs detected, is a single locus variant of ST636 carrying dfrA14, tetD, qnrS, and oqxAB resistance genes. The extended-spectrum β-lactamase (ESBL) gene blaCTX_M-15 was seen in 72% of K. pneumoniae genomes, while 8% encoded a carbapenemase. No isolate carried a combination of carbapenemase-producing genes. Four likely outbreak clusters from 1 facility, within STs 17, 25, 307, and 5241, were ESBL but not carbapenemase-bearing clones.ConclusionsThis study uncovered known and novel K. pneumoniae lineages circulating in 3 hospitals in Southwest Nigeria that include multidrug-resistant ESBL producers. Carbapenemase-producing isolates remain uncommon. WGS retrospectively identified outbreak clusters, pointing to the value of genomic approaches in AMR surveillance for improving infection prevention and control in Nigerian hospitals.
U2 - 10.1093/cid/ciab769
DO - 10.1093/cid/ciab769
M3 - Journal article
C2 - 34850837
VL - 73
SP - S308–S315
JO - Clinical Infectious Diseases
JF - Clinical Infectious Diseases
SN - 1058-4838
IS - Suppl. 4
ER -
ID: 323554628