Mensah, A. | bioRxiv Science

bioRxiv2024

Genomic Analysis of Salmonella enterica from cattle, beef and humans in the Greater Tamale Metropolis of Ghana

Salmonella enterica is a bacterial foodborne pathogen notorious for infecting humans and animals. Proper control of Salmonella requires routine surveillance and interventions across the food-production chain. However, due to limited resources the dynamics and transmission of non-typhoidal Salmonella serotypes remain poorly understood in several African settings, including within Ghana. Here, we employed bacterial culture and whole genome sequencing (WGS) to investigate the prevalence, virulence and antimicrobial resistance determinants of Salmonella enterica isolates from beef, cattle blood and human patient stool in Greater Tamale Metropolis, Ghana. Enrichment and culture of the specimens yielded 62 isolates in total from beef (31), bovine blood (28) and human diarrhoeal specimens (3). We identified at least 15 STs and 18 different Salmonella serovars. The most common serovars detected were Poona (n=13), Montevideo (n=10) and Poano (n=7) with S. Montevideo being the most common from cattle blood. Thirty-two isolates belonged to novel sequence types (STs), with ST2609 (n=9) being most common. Four raw beef isolates harboured at least one gene conferring resistance to beta-lactam (blaTEM-1), chloramphenicol (catA), fosfomycin (fosA7), quinolone (qnrD1) or tetracycline (tet(A)). Eight isolates carried at an IncF, IncI and/orCol3M plasmid replicon. This study recovered Salmonella, often belonging to previously undocumented STs, at high frequencies from cattle and beef and demonstrated that isolates from human diarrhoeal patients are closely related to bovine isolates. The data highlight the need for broader and sustained surveillance and the urgent need for food safety interventions in Ghana.

microbiology↗

bioRxiv2024

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

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.

genomics↗