Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria
Author:
Afolayan Ayorinde O1, Oaikhena Anderson O1, Aboderin Aaron O2, Olabisi Olatunde F2, Amupitan Adewale A2, Abiri Oyekola V2, Ogunleye Veronica O3, Odih Erkison Ewomazino1, Adeyemo Abolaji T4, Adeyemo Adeyemi T2, Obadare Temitope O2, Abrudan Monica56, Argimón Silvia56, David Sophia56, Kekre Mihir56, Underwood Anthony56, Egwuenu Abiodun7, Ihekweazu Chikwe7, Aanensen David M5, Okeke Iruka N1, Abudahab Khalil, Harste Harry, Muddyman Dawn, Taylor Ben, Wheeler Nicole, Donado-Godoy Pilar, Fabian Bernal Johan, Arevalo Alejandra, Fernanda Valencia Maria, Osma Castro Erik C D, Ravikumar K L, Nagaraj Geetha, Shamanna Varun, Govindan Vandana, Prabhu Akshata, Sravani D, Shincy M R, Rose Steffimole, Ravishankar K N, Ajiboye Jolaade J, Carlos Celia, Lagrada Marietta L, Macaranas Polle Krystle V, Olorosa Agnettah M, Gayeta June M, Herrera Elmer M, Molloy Ali, Stelling John, Vegvari Carolin,
Affiliation:
1. Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria 2. Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria 3. Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Nigeria 4. Department of Medical Microbiology and Parasitology, Osun State University Teaching Hospital, Teaching Hospital, Osogbo, Nigeria 5. Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom 6. Wellcome Genome Campus, Hinxton, United Kingdom 7. Nigeria Centre for Disease Control, Jabi, Abuja, Nigeria
Abstract
Abstract
Background
Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria.
Methods
We 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.
Results
Phylogenetic 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.
Conclusions
This 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.
Funder
National Institute for Health Research Department for International Development, UK Government
Publisher
Oxford University Press (OUP)
Subject
Infectious Diseases,Microbiology (medical)
Cited by
29 articles.
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