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

Abstract

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.