학술논문
Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria.
Document Type
Article
Author
Afolayan, Ayorinde O; Oaikhena, Anderson O; Aboderin, Aaron O; Olabisi, Olatunde F; Amupitan, Adewale A; Abiri, Oyekola V; Ogunleye, Veronica O; Odih, Erkison Ewomazino; Adeyemo, Abolaji T; Adeyemo, Adeyemi T; Obadare, Temitope O; Abrudan, Monica; Argimón, Silvia; David, Sophia; Kekre, Mihir; Underwood, Anthony; Egwuenu, Abiodun; Ihekweazu, Chikwe; Aanensen, David M; Okeke, Iruka N
Source
Subject
*DNA analysis
*KLEBSIELLA
*HOSPITALS
*SEQUENCE analysis
*PHYLOGENY
*PLASMIDS
*GENOMES
*BACTERIOPHAGE typing
*MULTIDRUG resistance
*BETA lactamases
*DESCRIPTIVE statistics
*DRUG resistance in microorganisms
*MICROBIAL virulence
*MICROBIAL sensitivity tests
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Language
ISSN
1058-4838
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 bla CTX_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. [ABSTRACT FROM AUTHOR]