Descriptive Epidemiology and Comparative Genomic Analysis of Non-Typhoidal Salmonella Serotypes from Rwanda
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- Nontyphoidal Salmonella enterica subsp. enterica (NTS) serotypes remain a major global public health problem. While foodborne Salmonella infections occur worldwide, the most severe and life-threatening infections most frequently occur in low-income countries, such as Rwanda. Due to the lack of comprehensive epidemiologic investigations in Rwanda, and likewise in many sub-Saharan African countries, little is known about the distribution of Salmonella serotypes and their descriptive and molecular epidemiology. A comprehensive study was conducted to ascertain the descriptive epidemiology and comparative genomic analyses of Salmonella isolated from humans, animals and retail meat in Rwanda. Salmonella was isolated from 4.72%, 3.75% and 22.2% of human participants, animals raised by household, and retail meat, respectively. Five serotypes including, Karamoja (n=3), Mikawasima (n=4), Moero (n=3), Waycross (n=3) and I 43:a:1,7 (Tampa) (n=4) were isolated from human participants with symptoms of gastro-intestinal illness. Isolates from animals belonged to six serotypes including Stanleyville (n=7), Moero (n=2), Bareilly (n=1), Typhimurium (n=1) and serotype II 42:r:- of subspecies salamae (n=1). Isolates from meats belonged to serotypes Stanleyville (n =8), Karamoja (n=1) and II 42:r:- (n=5). The most prevalent serotypes in humans were isolated neither in animals nor from meat. It was also noted that the serotypes isolated from animals were not observed in meat from the same species. Eating out was identified as a risk factor for NTS in human participants, while raising goats by households was found to be the only risk factor associated with Salmonella. None of the other risk factors were associated with NTS. Interestingly, all 43 NTS isolates were susceptible to all 15 antimicrobials examined in this study. The genomes of recently sequenced NTS genomes from Rwanda that are publicly available in the NCBI databases were used for comparative genomic analysis. The comparative genome analysis showed that the isolates of S. Stanleyville belonged to two major clades and four different core genome sequence types (cgST). The genomes of each of the other serotypes belonged to single sequences types except, S. Mikawasima that had two different sequence types. Salmonella Pathogenicity Islands (SPIs) 1-6, SPI-9 and C36PI were identified in all serotypes except 43:a:1,7 (S. Tampa) that lacked SPIs 3 & 6. SPIs 8, 12-14, 19 were differentially distributed in the genomes of different serotypes. Twenty-one prophage elements were identified in the analyzed genomes, but they were dissimilarly distributed among different serotypes. The genes cdtB, pltA and pltB that encode the typhoid toxin were identified in 6 serotypes. They were absent only in serotypes Mikwasima and Karamoja. The only antimicrobial resistance gene identified in most of the genomes of S. Stanleyville was aac(6)-Iaa carried on the chromosomes. Plasmid sequences for S. Stanleyville, S. Karamoja, S. Mikawasima, S. Waycross and S. Typhimurium were also analyzed. Only the S. Typhimurium plasmid carried virulence factor genes.The findings of this study are the first of its kind to be reported on the prevalence of NTS and distribution of serotypes in human participants, food animals raised by rural households, and retail meat in Rwanda. The results of comparative genomic analysis show that the serotypes of NTS from Rulindo district of Rwanda have various degrees virulence potential depending not only on the serotype but also on the intra-serotype phylogenetic clades. Overall the findings of the study provide valuable insight on NTS in Rwanda which can serve as guidelines for conducting large systematic studies to determine the public health significance of NTS in rural populations.
- Dissertation Note:
- Ph.D. Pennsylvania State University 2019.
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- The full text of the dissertation is available as an Adobe Acrobat .pdf file ; Adobe Acrobat Reader required to view the file.
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