Phenotypic and genotypic characterization of salmonella isolates from chickens and humans in South Sudan.
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Date
2022
Authors
Saad, Shereen Ahmed Mohamed
Journal Title
Journal ISSN
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Publisher
The University of Zambia
Abstract
Salmonellae are known to be among the most important food-borne pathogens of public health significance. A Cross sectional study was conducted in Wau, Municipality Western Bahr El- Ghazal State, South Sudan, to assess the phenotypic and genotypic characteristic of Salmonella isolates from chickens and humans. The fecal samples were randomly collected from 147 chicken keepers and 270 chicken’s cloacal swabs from selected household levels. The samples were cultured on Xylose Lysine Deoxycholate Agar for the isolation of Salmonella and further confirmed using a series of biochemical tests and PCR.
Following confirmation of Salmonella, the phenotypic and genotypic characterization was done. Phenotypic characterization was done through serology, biotyping and antimicrobial susceptibility profiles while the genetic diversity was determined through molecular typing methods that included the detection of virulence genes by PCR and whole genome sequencing of targeted genes. The data was analyzed using SPSS-23 software, for descriptive statistics to obtain frequencies of Salmonella occurrence while the Bioinformatics specialist software was used for determining antimicrobial resistance gene (ARG) and virulence gene distribution.
The phenotypic results revealed that, 9 (3.3%) out of the 270 chicken faecal samples were found to be positive for Salmonella, while 11 isolates (7.5%) out of 147 human samples were obtained. The identified species for both, humans and chicken included Salmonella aberdeen (4), Salmonella enteritidis (3), Salmonella uganda (1), Salmonella typhimurium (6), Salmonella serovar montevideo (1) and non-typhi (5). On antibiotic susceptibility, seven isolates from humans showed 100% sensitivity to co-trimoxazole, chloramphenicol, streptomycin, nalidixic acid, cefotaxime and gentamicin. However, some isolates showed resistance to ciprofloxacin 1 (9.1%), tetracycline 1 (9.1%), and ampicillin 2 (18.2%). All the chicken isolates were susceptible to chloramphenicol, cefotaxime, streptomycin, sulfamethoxazole/trimethoprim, nalidixic acid and gentamicin.
Eight isolates (Salmonella sentfenberg (1), Salmonella enteritidis (1), Salmonella typhimurium (1) and Salmonella typhi (5)) were chosen for further characterization using whole genome sequencing. Following WGS analysis, ARG were found for sulfonamides 8 (100%), tetracycline 7 (87%), erythromycin 4 (50%), β-lactamases 6 (75%), erythromycin 4 (50%), streptomycin 4 (50%) and chloramphenicol 2 (25%). The gene sul1 and sul2 (8 isolates) was the most frequently detected followed by the gene tet(D) and tet(A) (7 isolates), and blaCTX-M-15 (6 isolates). The ARG against streptomycin were very diverse and included genes aac(3), aph(3) and aph(6). The ARG against β-lactamases included blaCTX-M-15, blaTEM-1, blaOXA-10, blaOXA-1, and blaTEM-1. The dfrA19 was the only resistance gene found for trimethoprim. All the chosen eight Salmonella serotypes were negative for the presence of spiA, pagC, msgA, sipB, ivpan, and spvB virulence genes while they were positive for iroB, sinH, iroC and cdtB virulence genes.
Thirty mobile genetic elements were identified of which the majority belonged to the insertion sequence, miniature inverted repeat, unit transposon and integrative conjugative element. Human isolates showed twenty-four (80%) mobile genetic elements compared to chicken which had only six (20%) mobile genetic elements only. The identified mobile genetic elements were found to be associated with antibiotic resistance of aac(6)-Iaa and blaCTX-M-15 Beta-lactamases genes. This study has demonstrated the diversity of Salmonella isolated from humans and animals in South Sudan requiring efforts for a conclusive one health intervention.
Description
Thesis of Doctor of Philosophy in Microbiology.