Biology subjects

Kigozi, E.

Publications and source records attributed to Kigozi, E..

5 recordsLinked to original sources

bioRxiv2026

Pulmonary Tuberculosis Is Associated with Body Site-Specific Alterations in the Respiratory and Gut Microbiome in Uganda

Abstract Background: Tuberculosis is a major infectious disease whose effects may extend beyond the lungs to influence microbial communities at other body sites. Although studies have reported alterations in the respiratory and gut microbiomes of people with TB, evidence from sub-Saharan Africa remains limited, and the extent to which these alterations differ between body sites is not fully understood. This study characterized sputum and stool microbiomes among Ugandan adults with pulmonary TB and those without TB. Methods: We conducted a cross-sectional study involving 200 participants, comprising 150 adults with pulmonary TB and 50 contacts, at Mulago National Referral Hospital in Kampala, Uganda. Sputum and stool samples were profiled using 16S rRNA gene sequencing. Following quality control and contaminant removal, within-sample diversity was assessed using multiple alpha diversity indices. Beta diversity was evaluated using distance-based methods, with group differences assessed by permutational multivariate analysis of variance (PERMANOVA) and homogeneity of dispersion tests. Differentially abundant taxa were identified using ANCOM-BC2. Results: After quality control, 135 sputum and 151 stool samples were retained for downstream analysis. In sputum, microbial richness estimators Chao1 and ACE were lower among TB cases than controls, whereas differences in overall community composition were not statistically significant after correction for multiple testing. In stool, several richness and diversity measures differed between groups, and beta-diversity analyses detected differences in community composition. However, TB cases exhibited greater within-group dispersion, and the sequencing platform contributed substantially to variation in stool microbial profiles. In multivariable analyses, the sequencing platform was the only factor independently associated with stool community composition after correction for multiple testing. Differential-abundance analyses identified body site-specific taxonomic associations with TB, including differences involving Streptococcus, Parvimonas, and Actinobacillus in sputum, and Dorea, Lachnoclostridium, and Turicibacter in stool. Conclusion: Pulmonary TB was associated with differences in microbial richness and the abundance of specific taxa in both sputum and stool, but evidence for overall community composition differences varied by body site and was influenced by dispersion and sequencing platform. These findings highlight the importance of examining both respiratory and gut microbial communities in TB research. Longitudinal studies using standardized sequencing methods are needed to clarify how these patterns change during treatment and whether they have diagnostic or clinical relevance.

genomics↗

bioRxiv2026

Comparative analyses of Gram-negative bacteria isolated from cancer patients with bacteraemia at the Uganda Cancer Institute

Antimicrobial resistance (AMR) exacerbates bacteraemia in cancer patients, particularly in low-resource settings. At the Uganda Cancer Institute, high rates of Enterobacterales producing extended-spectrum {beta}-lactamases (ESBLs) have been reported, with DNA-based detection of bla genes limited to PCR. This study aimed to determine whether bacterial genomic DNA shipped at ambient temperature from Uganda to the UK retained sufficient quality for whole-genome sequencing (WGS), to allow in-depth genomic analyses of isolates. Genomic DNA was extracted from Gram-negative bloodstream isolates (n=77) in Uganda and shipped to the UK at ambient temperature. rpoB gene (77/77, 100%) and WGS data (72/77, 93.5%) were generated for isolates, with 66/72 (91.7%) genomes of high-quality (Escherichia coli n=34; Klebsiella spp. n=32). Bioinformatic analyses included species identification, sequence typing, SNP analysis, AMR and virulence gene profiling, and comparison with publicly available genomes of Ugandan isolates. Phenotypic-genotypic concordance was generally high: 7/77 (9.1%) isolates were misidentified by phenotypic testing, and two showed unexplained carbapenem resistance. E. coli isolates showed diverse sequence types, with high prevalence of blaCTX-M (91.2%) and blaOXA-1 (47.1%); carbapenemase genes were rare. Klebsiella isolates lacked hypermucoidy loci and displayed diverse capsule types, with a high prevalence of ESBLs. Genomic clustering suggested limited within-hospital transmission of strains. Genomic data can provide important insights into the dissemination of bacterial subclades of global concern. The widespread AMR genotypes reported here highlight the need for improved diagnostics and updated treatment guidelines for bacteraemia in Ugandan cancer patients. IMPACT STATEMENTBloodstream infections are a major threat to cancer patients, particularly in low-resource settings where access to advanced diagnostics is limited and infection prevention may be challenging. This study shows that it is feasible to transport bacterial DNA at room temperature from Uganda to the UK for high-quality whole-genome sequencing, helping to overcome a logistical barrier to genomic surveillance. By applying genomic analysis to bacteria that had caused bloodstream infections at the Uganda Cancer Institute, we found that traditional laboratory methods can misidentify some bacteria, and that genomic analyses can provide more accurate and detailed insights into the bacteria causing these serious infections. Our work also highlights gaps in current treatment guidelines and demonstrates how genomic data could help inform updates to these, facilitating more effective antibiotic use in situations where urgent treatment is needed and there is no time to wait for laboratory test results. While there was limited evidence of direct transmission of bacteria between patients in our dataset, the genetic diversity and resistance patterns we observed are concerning and emphasise the need for ongoing monitoring and more extensive future studies.

microbiology↗

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↗

bioRxiv2025

Patterns of compensatory mutations in rpoA/B/C genes of multidrug resistant M. tuberculosis in Uganda

Mutations in rpoB, a gene that encodes the bacterial RNA polymerase (RNAP) beta-subunit, can cause high-level resistance to rifampicin. Approximately 95% of rifampicin-resistant Mycobacterium tuberculosis clinical isolates possess mutations in an 81-base pair rpoB region referred to as the rifampicin-resistance determining region (rpoB/RRDR). Also, rifampicin-resistant M. tuberculosis clinical isolates carry multiple mutations in RNAP genes (i.e., rpoA, rpoB, rpoC, rpoD), particularly rpoA and rpoC, which encode the alpha-(2) and beta'-({beta}') subunits, respectively. Such secondary mutations offset the fitness cost associated with rifampicin-resistance mutations in M. tuberculosis, resulting in resistant strains that are as fit as the wildtype drug-susceptible strains. To analyse the patterns of compensatory mutations in RNAP encoding genes of rifampicin-resistant M. tuberculosis clinical isolates in Uganda, whole genome sequencing and Sanger DNA sequencing were performed on 52 M. tuberculosis clinical isolates - 20 drug-susceptible and 32 multidrug resistant (MDR). A total of 24 (75%) MDR-TB isolates had high-level rifampicin-resistance conferring mutations in rpoB/RRDR i.e., Ser531Leu (31%); His526Asp (6%); His526Leu (3%); His526Tyr (3%); His526Arg (3%); His526Gly (3%); Asp516Tyr (13%); Asp516Val (6%); Glu513Lys (3%); Leu511Pro (3%); Leu492Leu (3%); Gln490Arg (3%). Further, two putative compensatory mutations (Gln490Arg & Lys1025Glu) outside the RRDR and not resistance conferring were found in rpoB. Altogether, 16 (50%) MDR-TB isolates with rpoB/RRDR resistance conferring mutations had non-synonymous mutations in rpoC of the following patterns Leu39Phe (3%); Tyr61His (3%); Asp271Gly (3%); Ser377Ala (3%); Pro481Thr (3%); Val483Ala (6%); Leu516Pro (3%); Ala521Asp (3%); Gly594Glu (13%); Asn698Ser (3%); Leu823Pro (3%). In conclusion, putative compensatory mutations are prevalent in rifampicin-resistant M. tuberculosis clinical isolates in Uganda, with rpoC/Gly594Glu and rpoC/Val483Ala as the most frequent. Further studies will determine their association with strain genetic background, fitness and transmission in an endemic setting with a high burden of HIV-TB coinfection.

microbiology↗

bioRxiv2020

Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda

Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based improvement of antibiotic stewardship measures in the hospital. To address this, we combined existing antimicrobial susceptibility testing (AST) from FPRRH, with whole genome sequencing (WGS) of 41 Staphylococcus aureus isolates (2017-2019). AST revealed 73% (30/41) of isolates were resistant to one or more antibiotics and 29% (12/41) were multi-drug resistant (MDR). Resistance phenotypes were largely explained by the presence of antibiotic resistance genes in WGS data. Five isolates were methicillin-resistant S. aureus (MRSA) and MDR. Although all isolates were susceptible to clindamycin, a 24% carriage of erm genes suggests potential for rapid development of resistance. We inferred a population structure for the S. aureus isolates by comparing their core genomes. Twenty isolates formed a tight cluster corresponding to multilocus sequence typing clonal complex (CC) 152, a CC found to be particularly prevalent in northern Africa. The frequency of genes associated with methicillin, chloramphenicol and ciprofloxacin resistance were significantly lower among CC152 strains than non-CC152 strains; thus, in keeping with previous work, we find that CC152 is almost exclusively methicillin-sensitive S. aureus (MSSA). Also, in agreement with other studies, we observed that the occurrence of Panton-Valentine leukocidin toxin-encoding genes was significantly higher among CC152 strains than non-CC152 strains. However, we also observed that the coagulase gene was over-represented in this CC, further defining the virulence strategy of this important pathogen. By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, our study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.

microbiology↗