Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Dec 1;73(Suppl_4):S308-S315.
doi: 10.1093/cid/ciab769.

Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria

Ayorinde O Afolayan  1 , Anderson O Oaikhena  1 , Aaron O Aboderin  2 , Olatunde F Olabisi  2 , Adewale A Amupitan  2 , Oyekola V Abiri  2 , Veronica O Ogunleye  3 , Erkison Ewomazino Odih  1 , Abolaji T Adeyemo  4 , Adeyemi T Adeyemo  2 , Temitope O Obadare  2 , Monica Abrudan  5   6 , Silvia Argimón  5   6 , Sophia David  5   6 , Mihir Kekre  5   6 , Anthony Underwood  5   6 , Abiodun Egwuenu  7 , Chikwe Ihekweazu  7 , David M Aanensen  5 , Iruka N Okeke  1 ; NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance
Collaborators, Affiliations

Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria

Ayorinde O Afolayan et al. Clin Infect Dis. .

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.

Keywords: Klebsiella; Nigeria; antimicrobial resistance; genomic surveillance.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Epidemiological data, virulence determinants, antibiotic profile (phenotypic resistance), and AMR determinants in Klebsiella pneumoniae genomes ordered by phylogeny. The heat map shows the presence (red) or absence (blank) of virulence determinants, phenotypic resistance, AMR genes, and plasmid replicon genes. Tree nodes represent the origin of isolate collection. The shape of the tree nodes depicts the outbreak (star) and non-outbreak (circle) isolates. The data are available at https://microreact.org/project/GHRUNigeriaKpneumoniae/2a856694. Abbreviation: AMR, antimicrobial resistance.
Figure 2.
Figure 2.
The timeline of likely outbreak of Klebsiella pneumoniae clones belonging to STs 17 (a), 25 (b), 307(c), and 5241(d) from the OAU sentinel site. The shape of the tree nodes depicts the outbreak (star) and non-outbreak (circle) isolate, while the color of the tree nodes depicts the sentinel site. The data are available at https://microreact.org/project/brfq17BXzwmqptfcrNRfZR/71b2f0f1 (ST17), https://microreact.org/project/8FP4F1D5fSQMv6FDxbR39b/bd381f0b (ST25), https://microreact.org/project/sV5NsJ8szcorvFAeFQgV4E/6498edf1 (ST307), and https://microreact.org/project/u5RPX7CjyitjRYMQ9ByW4W/1a3570e2 (ST5241). Abbreviations: OAU, Obafemi Awolowo University; ST, sequence type.
See this image and copyright information in PMC

References

    1. Podschun R, Ullmann U. Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev 1998; 11:589-603. - PMC - PubMed
    1. Wyres KL, Holt KE. Klebsiella pneumoniae population genomics and antimicrobial-resistant clones. Trends Microbiol 2016; 24:944-56. - PubMed
    1. Wyres KL, Nguyen TNT, Lam MMC, et al. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. Genome Med 2020; 12:11. - PMC - PubMed
    1. Olalekan A, Onwugamba F, Iwalokun B, Mellmann A, Becker K, Schaumburg F. High proportion of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae among extended-spectrum β-lactamase-producers in Nigerian hospitals. J Glob Antimicrob Resist 2020; 21:8-12. - PubMed
    1. Müller-Schulte E, Tuo MN, Akoua-Koffi C, Schaumburg F, Becker SL. High prevalence of ESBL-producing Klebsiella pneumoniae in clinical samples from central Côte d’Ivoire. Int J Infect Dis 2020; 91:207-9. - PubMed

Publication types