Identification of a Salmonellosis Outbreak by Means of Molecular Sequencing

Lienau, E. Kurt; Strain, Errol; Wang, Charles; Zheng, Jie; Ottesen, Andrea; Keys, Christine E.; Hammack, Thomas S.; Musser, Steven M.; Brown, Eric W.; Allard, Marc W.; Cao, Guojie; Meng, Jianghong; Stones, Robert

doi:10.1056/nejmc1100443

Cited by 155 publications

(123 citation statements)

References 5 publications

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“…Moreover, serovar-specific studies on S. enterica subsp. enterica have highlighted microevolutionary differences among clinical, environmental, and food isolates in S. enterica serovars Montevideo (13,14), Enteritidis (4), Newport (15), Typhimurium (16)(17)(18), and Heidelberg (12), which would have been missed by more traditional approaches.…”

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confidence: 99%

Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis

et al. 2015

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We retrospectively analyzed a rare Salmonella enterica serovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients (n ‫؍‬ 15) and food, feed, animal, and environmental sources (n ‫؍‬ 24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB_BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system. Salmonellosis is a major food-borne disease worldwide, with an estimated 93.8 million cases occurring each year, resulting in 155,000 deaths (1). The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks (2) indicated that nontyphoid salmonellosis was the second most reported food-borne zoonosis in Europe in 2012, trailing only behind Campylobacter jejuni infection. The 2012 overall notification rate for human salmonellosis in the European Union (EU) was 22.2 episodes per 100,000 population, for a total of 91,034 confirmed cases, with hospitalization and mortality rates of 45.1% and 0.14%, respectively. The highest proportions of Salmonella-positive foodstuff samples were reported for fresh turkey, poultry, and pork at 4.4%, 4.1%, and 0.7%, respectively (2). In order to manage this food-borne infection and to limit its health and economic burdens, surveillance programs have developed and implemented DNA-based subtyping methods to identify outbreaks in a timely manner and to trace infections back to their food sources. Over the past decades, the two most intensively used protocols for Salmonella subtyping have been pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandemrepeat analysis (MLVA) (3). Unfortunately, these methods rely on just few features of the entire bacterial genome (rare restriction sites for PFGE or few polymorphic loci for MLVA) to assess the relatedness of different isolates. During epidemiological investigations of food-borne outbreaks, this limitation mi...

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confidence: 99%

Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis

et al. 2015

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“…Highresolution WGS is promising to be the most informative typing method (6) and is likely to be more sensitive than the traditional culture-based diagnostic procedures in clinical microbiology (1,2,4,7). As the technology is moving from bench to bedside (8)(9)(10), sample quality and quantity have become a major technical bottleneck in clinical sequencing.…”

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confidence: 99%

“…hole-genome sequencing (WGS) is beginning to provide new and efficient opportunities for the diagnosis and control of many clinically relevant pathogenic infections (1)(2)(3)(4)(5). Highresolution WGS is promising to be the most informative typing method (6) and is likely to be more sensitive than the traditional culture-based diagnostic procedures in clinical microbiology (1,2,4,7).…”

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confidence: 99%

Efficient Depletion of Host DNA Contamination in Malaria Clinical Sequencing

Oyola

Manske

et al. 2013

J Clin Microbiol

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dThe cost of whole-genome sequencing (WGS) is decreasing rapidly as next-generation sequencing technology continues to advance, and the prospect of making WGS available for public health applications is becoming a reality. So far, a number of studies have demonstrated the use of WGS as an epidemiological tool for typing and controlling outbreaks of microbial pathogens. Success of these applications is hugely dependent on efficient generation of clean genetic material that is free from host DNA contamination for rapid preparation of sequencing libraries. The presence of large amounts of host DNA severely affects the efficiency of characterizing pathogens using WGS and is therefore a serious impediment to clinical and epidemiological sequencing for health care and public health applications. We have developed a simple enzymatic treatment method that takes advantage of the methylation of human DNA to selectively deplete host contamination from clinical samples prior to sequencing. Using malaria clinical samples with over 80% human host DNA contamination, we show that the enzymatic treatment enriches Plasmodium falciparum DNA up to ϳ9-fold and generates high-quality, nonbiased sequence reads covering >98% of 86,158 catalogued typeable single-nucleotide polymorphism loci.

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“…Sequence-based analysis of Salmonella organisms from nextgeneration sequencing data has been used to examine outbreak clusters of Salmonella enterica serovar Montevideo (30)(31)(32) and S. Enteritidis (7,11,29). Outbreak-related organisms in these two highly homologous serovars are distinguished by fewer than 20 pairwise single nucleotide polymorphisms (SNPs) compared to the sequence of a reference strain.…”

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confidence: 99%

Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

et al. 2015

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b Salmonella enterica serovar Enteritidis is a significant cause of gastrointestinal illness in the United States; however, current molecular subtyping methods lack resolution for this highly clonal serovar. Advances in next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subtyping tool for outbreak detection and source trace back. Here, we conducted a retrospective analysis of S. Enteritidis isolates from seven epidemiologically confirmed foodborne outbreaks and sporadic isolates (not epidemiologically linked) to determine the utility of WGS to identify outbreaks. A collection of 55 epidemiologically characterized clinical and environmental S. Enteritidis isolates were sequenced. Single nucleotide polymorphism (SNP)-based cluster analysis of the S. Enteritidis genomes revealed well supported clades, with less than four-SNP pairwise diversity, that were concordant with epidemiologically defined outbreaks. Sporadic isolates were an average of 42.5 SNPs distant from the outbreak clusters. Isolates collected from the same patient over several weeks differed by only two SNPs. Our findings show that WGS provided greater resolution between outbreak, sporadic, and suspect isolates than the current gold standard subtyping method, pulsed-field gel electrophoresis (PFGE). Furthermore, results could be obtained in a time frame suitable for surveillance activities, supporting the use of WGS as an outbreak detection and characterization method for S. Enteritidis. Foodborne bacterial pathogen characterization, surveillance, and outbreak detection is an important function of the public health laboratory (1). Current practices involve time-and laborintensive phenotypic typing, including biochemical profiling, phage typing, serotyping, and antimicrobial susceptibility testing. In addition, a variety of species-specific molecular methods for advanced characterization are utilized, including pulsed-field gel electrophoresis (PFGE), multiple-locus variable number tandem repeat analysis (MLVA), and virulence gene typing (2). Often, it is necessary to combine results from multiple techniques to provide an adequate level of discrimination in order to identify outbreak clusters within routine clinical surveillance isolates.Salmonella is an important foodborne pathogen that is estimated to be responsible for approximately 1 million cases of illness and more than 450 deaths annually in the United States (3). Salmonella enterica serovar Enteritidis is responsible for 36% of Salmonella outbreaks in the United States, and in 1990, it replaced Salmonella enterica serovar Typhimurium as the most frequently reported serotype of Salmonella worldwide (4, 5). It is estimated that approximately 64% of S. Enteritidis clinical cases are attributable to contaminated eggs and 18% to poultry products (5, 6).There is limited genetic variation between the strains of S. Enteritidis, which reduces the utility of current subtyping methods (7-9). For example, PFGE, the gold standard s...

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Identification of a Salmonellosis Outbreak by Means of Molecular Sequencing

Cited by 155 publications

References 5 publications

Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis

Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis

Efficient Depletion of Host DNA Contamination in Malaria Clinical Sequencing

Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

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