Multiple-locus variable number of tandem repeats analysis of Salmonella enterica serotype paratyphi A from Yuxi and comparison with isolates from the Chinese Medical Culture Collection Center

YingBo, Yao; Cui, Xiaoyan; Chen, Qingshan; Huang, Xinrong; Elmore, Bradley O.; Pan, Qing; Wang, Shukun; Liu, Jie

doi:10.3892/mmr.2014.2187

Cited by 4 publications

(2 citation statements)

References 30 publications

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“…Just like Nocardiopsis dassonvillei , as we have mentioned above, Salmonella enterica has been recognized as a crucial microbe and pathogen distributed all over the world. However, the specific subtype of such microbe, AKU_1260 has mainly been identified in Yuxi, China and Cambridge, UK, implying that such subtype of Salmonella enterica may specifically distribute in Asian and Europe, validating the accuracy of our prediction algorithm 52 53 .…”

Section: Discussionmentioning

confidence: 52%

Gene expression profiling gut microbiota in different races of humans

Lei

Zhang

Huang

et al. 2016

Sci Rep

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The gut microbiome is shaped and modified by the polymorphisms of microorganisms in the intestinal tract. Its composition shows strong individual specificity and may play a crucial role in the human digestive system and metabolism. Several factors can affect the composition of the gut microbiome, such as eating habits, living environment, and antibiotic usage. Thus, various races are characterized by different gut microbiome characteristics. In this present study, we studied the gut microbiomes of three different races, including individuals of Asian, European and American races. The gut microbiome and the expression levels of gut microbiome genes were analyzed in these individuals. Advanced feature selection methods (minimum redundancy maximum relevance and incremental feature selection) and four machine-learning algorithms (random forest, nearest neighbor algorithm, sequential minimal optimization, Dagging) were employed to capture key differentially expressed genes. As a result, sequential minimal optimization was found to yield the best performance using the 454 genes, which could effectively distinguish the gut microbiomes of different races. Our analyses of extracted genes support the widely accepted hypotheses that eating habits, living environments and metabolic levels in different races can influence the characteristics of the gut microbiome.

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Section: Discussionmentioning

confidence: 52%

Gene expression profiling gut microbiota in different races of humans

Lei

Zhang

Huang

et al. 2016

Sci Rep

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“…Typhimurium (Hiley et al, 2014) and four VNTR loci from S . Paratyphi A (Yao et al, 2014), as well as three VNTR loci from a Mycobacterium avium dataset (Ahlstrom et al, 2015) to determine whether directional mutability applies to VNTRs in other Salmonella serovars or other bacterial species. These datasets are relatively small and consist of a few hundred isolates.…”

Section: Discussionmentioning

confidence: 99%

Evolution of Variable Number Tandem Repeats and Its Relationship with Genomic Diversity in Salmonella Typhimurium

Octavia

Wang

et al. 2016

Front. Microbiol.

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Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing human infections in Australia and many other countries. A total of 12,112 S. Typhimurium isolates from New South Wales were analyzed by multi-locus variable number of tandem repeat (VNTR) analysis (MLVA) using five VNTRs from 2007 to 2014. We found that mid ranges of repeat units of 8–14 in VNTR locus STTR5, 6–13 in STTR6, and 9–12 in STTR10 were always predominant in the population (>50%). In vitro passaging experiments using MLVA type carrying extreme length alleles found that the majority of long length alleles mutated to short ones and short length alleles mutated to longer ones. Both data suggest directional mutability of VNTRs toward mid-range repeats. Sequencing of 28 isolates from a newly emerged MLVA type and its five single locus variants revealed that single nucleotide variation between isolates with up to two MLVA differences ranged from 0 to 12 single nucleotide polymorphisms (SNPs). However, there was no relationship between SNP and VNTR differences. A population genetic model of the joint distribution of VNTRs and SNPs variations was used to estimate the mutation rates of the two markers, yielding a ratio of 1 VNTR change to 6.9 SNP changes. When only one VNTR repeat difference was considered, the majority of pairwise SNP difference between isolates were 4 SNPs or fewer. Based on this observation and our previous findings of SNP differences of outbreak isolates, we suggest that investigation of S. Typhimurium community outbreaks should include cases of 1 repeat difference to increase sensitivity. This study offers new insights into the short-term VNTR evolution of S. Typhimurium and its application for epidemiological typing.

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