Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana

Mills, R. O.; Dadzie, I.; Le-Viet, T.; Baker, D. J.; Addy, H. P. K.; Akwetey, S. A.; Donkoh, I. E.; Quansah, E.; Semanshia, P. S.; Morgan, J.; Mensah, A.; Adade, N. E.; Ampah, E. O.; Owusu, E.; Mwintige, P.; Amoako, E. O.; Spadar, A.; Holt, K. E.; Foster-Nyarko, E.

doi:10.1101/2024.01.20.576413

bioRxiv · 10.1101/2024.01.20.576413

Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana

Mills, R. O.·Dadzie, I.·Le-Viet, T.·Baker, D. J.·Addy, H. P. K.·Akwetey, S. A.·Donkoh, I. E.·Quansah, E.·Semanshia, P. S.·Morgan, J.·Mensah, A.·Adade, N. E.·Ampah, E. O.·Owusu, E.·Mwintige, P.·Amoako, E. O.·Spadar, A.·Holt, K. E.·Foster-Nyarko, E.

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Abstract

Comprehensive data on the genomic epidemiology of hospital-associated Klebsiella pneumoniae in Ghana is scarce. This study sequenced 103 clinical K. pneumoniae isolates from five tertiary hospitals in Southern Ghana, predominantly from paediatric patients under five years (67/103, 65%), with the majority collected from urine (32/103, 31%) and blood (25/103, 24%) cultures. We employed Pathogenwatch for genotyping via Kaptive (K/O antigens) and Kleborate (antimicrobial resistance and hypervirulence) and determined clonal relationships using core-genome multilocus sequence typing (cgMLST). Among the 44 distinct sequence types (STs) detected, ST133 was the most common, comprising 23% of isolates (n=23/103). We discovered 27 different capsular (K) locus antigens and seven lipopolysaccharide (O) types; KL116 (28/103, 27%) and O1 (66/103, 64%) were the most prevalent. Single-linkage clustering highlighted the global spread of multidrug-resistant clones such as ST15, ST307, ST17, ST11, ST101, and ST48, with minimal allele differences (1-5) from publicly available genomes worldwide. Conversely, several isolates (n=17) constituted novel clonal groups and lacked close relatives among publicly available genomes, displaying unique genetic diversity within our study population. A significant proportion of isolates (88/103, 85%) carried resistance genes for three or more antibiotic classes, with the blaCTXM-15 gene present in 78% (n=80/103). Carbapenem resistance, predominantly due to blaOXA-181 and blaNDM-1 genes, was found in 10% (n=10/103) of the isolates. Yersiniabactin was the predominant acquired virulence trait, identified in 70% (n=72/103) of the isolates. Our findings reveal a complex genomic landscape of K. pneumoniae in Southern Ghana, underscoring the critical need for ongoing genomic surveillance to manage the substantial burden of antimicrobial resistance.

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Mills, R. O., Dadzie, I., Le-Viet, T., Baker, D. J., Addy, H. P. K., Akwetey, S. A., Donkoh, I. E., Quansah, E., Semanshia, P. S., Morgan, J., Mensah, A., Adade, N. E., Ampah, E. O., Owusu, E., Mwintige, P., Amoako, E. O., Spadar, A., Holt, K. E., Foster-Nyarko, E.. 2024-01-22. Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana. https://doi.org/10.1101/2024.01.20.576413

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