Analysis of Salmonella enterica Serovar Typhimurium Variable-Number Tandem-Repeat Data for Public Health Investigation Based on Measured Mutation Rates and Whole-Genome Sequence Comparisons

Dimovski, Karolina; Cao, Hanwei; Wijburg, Odilia L. C.; Strugnell, Richard A.; Mantena, Radha Kr; Whipp, Margaret; Hogg, Geoff; Holt, Kathryn E.

doi:10.1128/jb.01820-14

Cited by 31 publications

(47 citation statements)

References 32 publications

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“…This equates to a VNTR mutation rate of 1.49 per year (95% CI, 0.48 to 3.47 per year). This estimate is higher than that reported in a previous study using a mouse model in which S. Typhimurium was passaged in vivo (29), with an estimated VNTR mutation rate of 0.84 per year. The VNTR mutation rate difference could be due to the different hosts or to the mode of infection, as the mouse model used was a systemic infection through intravenous inoculation (29).…”

Section: Resultscontrasting

confidence: 54%

Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage

et al. 2015

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c Salmonella enterica serovar Typhimurium is an important foodborne human pathogen that often causes self-limiting but severe gastroenteritis. Prolonged excretion of S. Typhimurium after the infection can lead to secondary transmissions. However, little is known about within-host genomic variation in bacteria associated with asymptomatic shedding. Genomes of 35 longitudinal isolates of S. Typhimurium recovered from 11 patients (children and adults) with culture-confirmed gastroenteritis were sequenced. There were three or four isolates obtained from each patient. Single nucleotide polymorphisms (SNPs) were analyzed in these isolates, which were recovered between 1 and 279 days after the initial diagnosis. Limited genomic variation (5 SNPs or fewer) was associated with short-and long-term carriage of S. Typhimurium. None of the isolates was shown to be due to reinfection. SNPs occurred randomly, and the majority of the SNPs were nonsynonymous. Two nonsense mutations were observed. A nonsense mutation in flhC rendered the isolate nonmotile, whereas the significance of a nonsense mutation in yihV is unknown. The estimated mutation rate is 1.49 ؋ 10 ؊6 substitution per site per year. S. Typhimurium isolates excreted in stools following acute gastroenteritis in children and adults demonstrated limited genomic variability over time, regardless of the duration of carriage. These findings have important implications for the detection of possible transmission events suspected by public health genomic surveillance of S. Typhimurium infections. Nontyphoid Salmonella (NTS) infections generally result in a short-term, self-limiting gastroenteritis. However, NTS can be excreted continually and asymptomatically in stools for many weeks, even after the initial diarrheal episode has been resolved. Children are the more common carriers, especially children under the age of 3 years (1, 2). Fecal shedding of NTS after an intestinal infection can last for up to 4 weeks in adults and 7 weeks in children (3). In a very small proportion of cases, carriage can last for a year after the initial onset of the disease (3). Carriers excrete large numbers of bacteria in their feces and can facilitate the transmission of Salmonella to other hosts by contaminating water and food sources. The persistence of fecal shedding in asymptomatic patients can have a duration similar to that for patients with clinical disease (4). Antibiotic treatment of NTS disease is rarely indicated, as it does not assist in clearance of infection but may increase the duration of asymptomatic shedding (4).Salmonella enterica serovar Typhimurium is one of the leading causes of NTS gastroenteritis in humans in Australia and other countries. Salmonellosis is a notifiable disease in all Australian states and territories. In the state of New South Wales (NSW), the notification rate has been around 50 cases per 100,000 population (5). Sequencing of S. Typhimurium genomes or analyses of tandem repeats within the genome have increasingly been employed for tracking community ou...

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Section: Resultscontrasting

confidence: 54%

Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage

et al. 2015

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“…The study of the most frequent alleles obtained from the isolates of the different origins and the higher discriminatory index (DI), showed that ST6 was the loci with highest discriminatory index, and it may be of potential use for source attribution. Previous studies supported our results [9,36]. On the other hand, STTR10 and ST8 locus were absent in many strains (46.6% and 48.8%, respectively).…”

Section: Discussionsupporting

confidence: 81%

“…Salmonella serovar Typhimurium (S. Typhimurium) is one of the most important and frequent foodborne pathogens, being responsible of a high number of foodborne outbreaks [9]. In this sense, there is a need for highly discriminatory typing of isolates in order to be able to study the relatedness among strains, which can then aid in the contamination sources tracking [10,11].…”

Section: Introductionmentioning

confidence: 99%

Antimicrobial susceptibility and MLVA analysis of S. Typhimurium strains isolated from human and poultry samples in Tunisia

Kalai

Martinez

Bikandi

et al. 2018

J Infect Dev Ctries

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Introduction: Salmonella enterica infections are a significant public health concern worldwide, being Salmonella Typhimurium one of the most prevalent serovars. Human salmonellosis is typically associated with the consumption of contaminated foods, such as poultry, eggs and processed meat. The extensive use of antimicrobials in humans and animals has led to an increase in multidrug resistance among Salmonella strains, becoming multidrug-resistant (MDR) strains a major public health concern. Methodology: This study was designed to investigate the antimicrobial susceptibility and the genotypic diversity of Salmonella Typhimurium strains isolated in Tunisia from human and poultry sources from 2009 to 2015. Fortyfive strains were analyzed by disk-diffusion test to determine the antimicrobial susceptibility. The presence of antimicrobial resistance genes was tested by PCR, and genotyping was performed using multiple-locus variable-number tandem repeats analysis (MLVA). Results: About 50% of the strains were resistant to at least 3 antibiotics (multidrug-resistant strains, MDR). The most frequent resistance profile in clinical strains was AMP-TIC-TET-MIN-SXT (n = 7) and TET-MIN in poultry origin strains (n = 7). The MLVA typing grouped the strains in 2 main clusters. Cluster I was mostly formed by human isolates, whereas in cluster II both human and poultry isolates were grouped. Simpson's diversity index was 0.870 and 0.989 for antimicrobial resistance profiles and MLVA, respectively. Conclusions: Multiresistance is common in Salmonella Typhimurium isolated from human and poultry sources in Tunisia. The genotyping results suggest that some strains isolated from both sources may descend from a common subtype.

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“…Previous investigations using MLVA revealed a high diversity in isolates from Danish broiler breeding flocks and it was concluded that no persisting clones of DT41 was present in Danish poultry production, but that the reoccurring infections was due to an outside source (Litrup et al, 2010). However, the instability of the MLVA loci could make it hard to draw correct conclusions from MLVA data (Litrup et al, 2010;Barua et al, 2013;Wuyts et al, 2013;Dimovski et al, 2014). Highest variation has previously been noted for the STTR6 and STTR5 loci, which is consistent with the data generated in the present study where STTR6 was found to be the most variable, followed by STTR10 and STTR5.…”

Section: Discussionmentioning

confidence: 95%

Outbreak of Salmonella enterica serovar Typhimurium phage type DT41 in Danish poultry production

Löfström

Hintzmann

Sørensen

et al. 2015

Veterinary Microbiology

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Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium) is one of the most prevalent serovars in Europe - where both poultry and poultry related products are common sources of human salmonellosis. Due to efficient control programs, the prevalence of S. Typhimurium in Danish poultry production is very low. Despite this, during the past decades there has been a reoccurring problem with infections with S. Typhimurium phage type DT41 in the Danish poultry production without identifying a clear source. In the end of 2013 and beginning of 2014 an increased isolation of S. Typhimurium DT41 was noted mainly in this production, but also in other samples. To investigate this is in more detail, 47 isolates from egg layers (n=5, 1 flock), broilers (n=33, 13 flocks), broiler breeding flocks and hatches (n=5; 2 flocks and 1 environmental hatchery sample), feed (n=1), poultry slaughter house (n=3, environmental sample and meat) were typed with multi locus variable number of tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE) to investigate the epidemiology of the outbreak. Based on PFGE results isolates were divided into four groups (Simpson's index of diversity (DI)=0.24±0.15). Due to the low DI, PFGE was not sufficient to provide information to unravel the outbreak. Based on MLVA typing the DT41 (42/47 isolates) and the RDNC isolates (5/47) were split into nine groups (DI=0.65±0.14). When a maximum divergence at one locus was permitted these could be gathered into four groups. Using this criterion, combined with epidemiological information, a spread of one type from broiler breeders to broilers and further to the poultry slaughter house was plausible. In conclusion, although it could be concluded that a spread within the broiler production pyramid had taken place the source of the sudden increase of S. Typhimurium DT41 remains unclear. To investigate this in more detail, further studies using whole genome sequencing to obtain a higher discriminatory strength and including isolates from a longer period of time and from various sources are in progress.

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Analysis of Salmonella enterica Serovar Typhimurium Variable-Number Tandem-Repeat Data for Public Health Investigation Based on Measured Mutation Rates and Whole-Genome Sequence Comparisons

Cited by 31 publications

References 32 publications

Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage

Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage

Antimicrobial susceptibility and MLVA analysis of S. Typhimurium strains isolated from human and poultry samples in Tunisia

Outbreak of Salmonella enterica serovar Typhimurium phage type DT41 in Danish poultry production

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