Genomics Analysis of Clinical Bacterial Isolates from Surgical Site and Urinary Tract Infections in Kilombero, Tanzania
Abstract
Background
Hospital-acquired infections (HAIs) remain a global public-health concern, particularly in low- and middle-income countries where infection-prevention resources are limited. Surgical-site infections (SSIs) and urinary-tract infections (UTIs) are among the most frequent HAIs and contribute to increased morbidity and healthcare costs. Genomic surveillance provides insights into the diversity, antimicrobial resistance (AMR), and virulence potential of causative bacteria.
Methods
Four bacterial isolates collected from Tanzanian healthcare facilities were analysed: Pseudomonas aeruginosa SS01 and SS89 (from SSIs), Alcaligenes faecalis UP17 (from a UTI), and Lysinibacillus sphaericus SS48 (from an SSI). Genomic DNA was extracted and sequenced on the Illumina platform. Reads were quality-filtered and assembled de novo using SPAdes. Genomes were annotated with Prokka. AMR genes were identified using AMRFinderPlus, CARD-RGI, and ResFinder. Virulence determinants were detected using VFDB. P. aeruginosa isolates were typed by multilocus sequence typing (MLST). Phylogenetic analysis based on single-nucleotide polymorphisms (SNPs) was performed using Snippy and IQ-TREE, and trees were visualised with iTOL.
Results
Genome sizes ranged between approximately 6.0 and 6.7 Mb with GC contents consistent with species references. MLST revealed two distinct P. aeruginosa sequence types: SS01 was closest to ST2317 (incomplete ppsA locus) and SS89 matched ST4714, indicating non-clonal origins. AMR screening detected β-lactamase, aminoglycoside-modifying enzyme, and efflux-pump genes in P. aeruginosa , multidrug-efflux genes in A. faecalis , and intrinsic resistance determinants in L. sphaericus . Virulence-factor profiling identified type III-secretion, quorum-sensing, and biofilm-formation genes in P. aeruginosa ; adhesion and stress-tolerance genes in A. faecalis ; and sporulation and surface-adhesion genes in L. sphaericus . Phylogenetic analysis positioned the Tanzanian isolates as unique local lineages distinct from global references.
Conclusions
This study demonstrates the genomic diversity and complex AMR mechanisms of clinically important bacteria in Tanzania. The coexistence of resistance and virulence determinants underscores the need for routine genomic surveillance and strengthened antimicrobial-stewardship programs.
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