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

Harvard

Afolayan, AO, Oaikhena, AO, Aboderin, AO, Olabisi, OF, Amupitan, AA, Abiri, OV, Ogunleye, VO, Odih, EE, Adeyemo, AT, Adeyemo, AT, Obadare, TO, Abrudan, M, Argimón, S, Kekre, M, Egwuenu, A, Ihekweazu, C, Aanensen, DM, Okeke, IN, Abudahab, K, Harste, H, Muddyman, D, Taylor, B, Wheeler, N, Donado-Godoy, P, Fabian Bernal, J, Arevalo, A, Fernanda Valencia, M, Osma Castro, ECD, Ravikumar, KL, Nagaraj, G, Shamanna, V, Govindan, V, Prabhu, A, Sravani, D, Shincy, MR, Ravishankar, KN, Ajiboye, JJ, Carlos, C, Lagrada, ML, Macaranas, PKV, Olorosa, AM, Gayeta, JM, Herrera, EM, Molloy, A, Stelling, J & Vegvari, C 2021, 'Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria', Clinical Infectious Diseases, vol. 73, no. Suppl. 4, pp. S308–S315. https://doi.org/10.1093/cid/ciab769

APA

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., ... Vegvari, C. (2021). Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria. Clinical Infectious Diseases, 73(Suppl. 4), S308–S315. https://doi.org/10.1093/cid/ciab769

Vancouver

Afolayan AO, Oaikhena AO, Aboderin AO, Olabisi OF, Amupitan AA, Abiri OV et al. Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria. Clinical Infectious Diseases. 2021;73(Suppl. 4):S308–S315. https://doi.org/10.1093/cid/ciab769

Author

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. / Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria. In: Clinical Infectious Diseases. 2021 ; Vol. 73, No. Suppl. 4. pp. S308–S315.

Bibtex

@article{cee70bc2b2184b8abfa946a30dc2a121,
title = "Clones and Clusters of Antimicrobial-Resistant Klebsiella from Southwestern Nigeria",
abstract = "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.",
author = "A.O. Afolayan and A.O. Oaikhena and A.O. Aboderin and O.F. Olabisi and A.A. Amupitan and O.V. Abiri and V.O. Ogunleye and E.E. Odih and A.T. Adeyemo and A.T. Adeyemo and T.O. Obadare and M. Abrudan and S. Argim{\'o}n and M. Kekre and A. Egwuenu and C. Ihekweazu and D.M. Aanensen and I.N. Okeke and K. Abudahab and H. Harste and D. Muddyman and B. Taylor and N. Wheeler and P. Donado-Godoy and {Fabian Bernal}, J. and A. Arevalo and {Fernanda Valencia}, M. and {Osma Castro}, E.C.D. and K.L. Ravikumar and G. Nagaraj and V. Shamanna and V. Govindan and A. Prabhu and D. Sravani and M.R. Shincy and K.N. Ravishankar and J.J. Ajiboye and C. Carlos and M.L. Lagrada and P.K.V. Macaranas and A.M. Olorosa and J.M. Gayeta and E.M. Herrera and A. Molloy and J. Stelling and C. Vegvari",
year = "2021",
doi = "10.1093/cid/ciab769",
language = "English",
volume = "73",
pages = "S308–S315",
journal = "Clinical Infectious Diseases",
issn = "1058-4838",
publisher = "Oxford University Press",
number = "Suppl. 4",

}

RIS

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