Search bioRxiv⌕ Search

Biology subjects

Katagirya, E.

Publications and source records attributed to Katagirya, E..

2 recordsLinked to original sources
bioRxiv2026

Whole genome sequencing-based characterization of mobile genetic elements in Staphylococcus aureus isolated from patients in Fort Portal Regional Referral Hospital, Western Uganda

BackgroundThe ability of Staphylococcus aureus to evolve through horizontal gene transfer mechanisms aids its success as a versatile pathogen. Mobile genetic elements (MGEs) are linked to potent virulence factors in S. aureus, e.g., the Panton-Valentine leukocidin and toxic shock syndrome toxins, as well as antibiotic resistance genes, e.g., mecA that encodes methicillin resistance. Despite their clinical relevance, molecular surveillance of MGEs in Africa remains limited. Here, we characterize the MGE repertoire of clinically relevant S. aureus isolates from Fort Portal Regional Referral Hospital (FPRRH), western Uganda. MethodsWe assembled a total of 40 genome sequences from previously sequenced S. aureus isolates cultured from patients (skin wounds, urinary tract, and bloodstream infections) at FPRRH during 2017-2019. spaTyper was used to determine the spa genotypes, while the presence of MGEs was screened and annotated for using PlasmidFinder, PHASTEST, Mobile Element Finder, SCCmecFinder, Bakta, MobileOG-db, and IslandViewer tools. ResultsEleven spa types were identified, with spa type t355 predominating. We detected 74 plasmid-derived sequences and 31 insertion sequences. Two SCCmec types, SCCmec type III and SCCmec type IV, were detected, indicating both hospital-associated MRSA (HA-MRSA) and community-associated MRSA (CA-MRSA). Forty-seven intact prophages (all Siphoviridae) were identified, carrying dfrG, sak, and lukPV genes. A total of 191 genomic islands were detected, and these harbored the virulence, immunoevasion, drug, and heavy metal resistance genes, such as nuc, tuf, tst, pvl, tet, blaZ, and mer genes. ConclusionsS. aureus at FPRRH harbors a diverse and functionally rich MGE repertoire, including genomic islands, prophages, insertion sequences, transposons, and plasmids, that contribute to the dissemination of virulence, AMR, and metal resistance determinants. The coexistence of HA-MRSA and CA-MRSA, as seen in other regions of Uganda, underscores the importance of continued genomic surveillance to inform infection control strategies.

genomics↗
bioRxiv2024

High KIR diversity in Uganda and Botswana children living with HIV

Killer-cell immunoglobulin-like receptors (KIRs) are essential components of the innate immune system found on the surfaces of natural killer (NK) cells. The KIRs encoding genes are located on chromosome 19q13.4 and are genetically diverse across populations. KIRs are associated with various disease states including HIV progression, and are linked to transplantation rejection and reproductive success. However, there is limited knowledge on the diversity of KIRs from Uganda and Botswana HIV-infected paediatric cohorts, with high endemic HIV rates. We used next-generation sequencing technologies on 312 (246 Uganda, 66 Botswana) samples to generate KIR allele data and employed customised bioinformatics techniques for allelic, allotype and disease association analysis. We show that these sample sets from Botswana and Uganda have different KIRs of different diversities. In Uganda, we observed 147 vs 111 alleles in the Botswana cohort, which had a more than 1 % frequency. We also found significant deviation towards homozygosity for the KIR3DL2 gene for both rapid (RPs) and long-term non-progressors (LTNPs)in the Ugandan cohort. The frequency of the bw4-80I ligand was also significantly higher among the LTNPs than RPs (8.9 % Vs 2.0%, P-value: 0.032). In the Ugandan cohort, KIR2DS4*001 (OR: 0.671, 95 % CI: 0.481-0.937, FDR adjusted Pc=0.142) and KIR2DS4*006 (OR: 2.519, 95 % CI: 1.085-5.851, FDR adjusted Pc=0.142) were not associated with HIV disease progression after adjustment for multiple testing. Our study results provide additional knowledge of the genetic diversity of KIRs in African populations and provide evidence that will inform future immunogenetics studies concerning human disease susceptibility, evolution and host immune responses.

genomics↗