Salmonella Typhi genotypic diversity, cluster identification and antimicrobial resistance determinants in Mukuru settlement, Nairobi Kenya

BACKGROUND

Understanding the source of typhoid infections and the genetic relatedness of Salmonella Typhi (S. Typhi) by cluster identification in endemic settings is critical for establishing coordinated public health responses for typhoid fever management. This study investigated the genotypic diversity, antibiotic resistance mechanisms, and clustering of 35 S.Typhi strains isolated from cases and carriers in the Mukuru Informal Settlement.

METHODS

We studied 35 S.Typhi isolates, including 32 from cases and 3 from carriers, from study participants in the informal settlement of Mukuru, Nairobi, Kenya. Genomic DNA was extracted, and whole-genome sequencing (WGS) was performed to determine the phylogenetic relatedness of strains and detect antimicrobial resistance determinants (AMR). WGS data were analyzed using bioinformatics tools available at the Center for Genomic Epidemiology and Pathogenwatch platforms.

RESULTS

Genotype 4.3.1.2 EA3 was found to be dominant at 46% (16/35), followed by 4.3.1.2 EA2 at 28% (10/35), and 4.3.1.1 EA1 at 27% (9/35). A comparison of the isolates with global strains from Pathogenwatch identified close clustering with strains from Uganda, Tanzania, Rwanda, and India. Three isolates (9%) distributed in each cluster were isolated from carriers. All genotype 4.3.1.2 EA3 isolates were genotypically multidrug-resistant to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole. Single mutations in the quinolone resistance-determining region were identified in the gyrA (S83Y) and gyrB (S464F) genes. All isolates associated with multidrug resistance showed the presence of the IncQ1 plasmid with the following genes: blaTEM-1B, catA1, sul1, sul2, and dfrA7.

CONCLUSION

The close phylogenetic relatedness between antimicrobial-resistant case isolates and carriage isolates indicates that typhoid carriage is a possible source of infection in the community. Comparative analysis with global isolates revealed that the Kenyan isolates share common lineages with strains from neighboring East African countries and India, suggesting regional dissemination of specific MDR clones. AMR was a major feature of the isolates. Surveillance and testing for antimicrobial susceptibility should inform options for the management of cases.

Quantification of fluoroquinolones in wastewaters by liquid chromatography-tandem mass spectrometry

Antibiotics are the most consumed therapeutic classes worldwide and are released to the environment in their original form as well as potentially active metabolites and/or degradation products. Consequences of the occurrence of these compounds in the environment are primarily related to bacterial resistance development. This work presents a validated analytical method based on solid phase extraction (SPE) using HLB cartridges, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) for quantification of seven different fluoroquinolone antibiotics, namely ciprofloxacin (CPF), enrofloxacin (ENR), lomefloxacin (LOM), norfloxacin (NOR), ofloxacin (OFL), prulifloxacin (PLF) and moxifloxacin (MOX) and its application to detect the target compounds in influents and effluents of wastewater treatment plants (WWTP). Linearity was established through calibration curves in solvent and matrix match using internal calibration method in the range of 50-1300 ng L^-1 and all the fluoroquinolones showed good linear fit (r² ≥ 0.991). Accuracy ranged between 80.3 and 92.9%, precision was comprised between 7.2 and 14.6%, and 10.7 and 18.1% for intra- and inter-batch determinations, respectively. Method detection and quantification limits ranged from 6.7 to 59.0 ng L^-1 and 22.3-196.6 ng L^-1, respectively. Influents and effluents of fifteen WWTPs of North of Portugal were analyzed. OFL was the fluoroquinolone found at the highest concentration, up to 4587.0 ng L^-1 and 987.9 ng L^-1, in influent and effluent, respectively. NOR and PLF were not detected.