A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type

ABSTRACTIn this study, we report a whole-genome single nucleotide polymorphism (SNP)-based evolutionary approach to study the epidemiology of a multistate outbreak ofSalmonella entericasubsp.entericaserovar Montevideo. This outbreak included 272 cases that occurred in 44 states between July 2009 and April 2010. A case-control study linked the consumption of salami made with contaminated black and red pepper to the outbreak. We sequenced, on the SOLiD System, 47 isolates with XbaI PFGE pattern JIXX01.0011, a common pulsed-field gel electrophoresis (PFGE) pattern associated with isolates from the outbreak. These isolates represented 20 isolates collected from human sources during the period of the outbreak and 27 control isolates collected from human, food, animal, and environmental sources before the outbreak. Based on 253 high-confidence SNPs, we were able to reconstruct a tip-dated molecular clock phylogeny of the isolates and to assign four human isolates to the actual outbreak. We developed an SNP typing assay to rapidly discriminate between outbreak-related cases and non-outbreak-related cases and tested this assay on an extended panel of 112 isolates. These results suggest that only a very small percentage of the human isolates with the outbreak PFGE pattern and obtained during the outbreak period could be attributed to the actual pepper-related outbreak (20%), while the majority (80%) of the putative cases represented background cases. This study demonstrates that next-generation-based SNP typing provides the resolution and accuracy needed for outbreak investigations of food-borne pathogens that cannot be distinguished by currently used subtyping methods.

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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

Journal of Clinical Microbiology ◽

10.1128/jcm.02930-14 ◽

2015 ◽

Vol 53 (4) ◽

pp. 1227-1238 ◽

Cited By ~ 11

Author(s):

Erika Scaltriti ◽

Davide Sassera ◽

Francesco Comandatore ◽

Marina Morganti ◽

Carmen Mandalari ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Gel Electrophoresis ◽

Salmonella Enterica ◽

Pulsed Field Gel Electrophoresis ◽

Snp Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Content Type ◽

Pulsed Field ◽

Codon Positions

We retrospectively analyzed a rareSalmonella entericaserovar 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.

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Produce Isolates of the Escherichia coli Ont:H52 Serotype That Carry both Shiga Toxin 1 and Stable Toxin Genes

Applied and Environmental Microbiology ◽

10.1128/aem.72.4.3062-3065.2006 ◽

2006 ◽

Vol 72 (4) ◽

pp. 3062-3065 ◽

Cited By ~ 16

Author(s):

Steven R. Monday ◽

Christina Keys ◽

Patricia Hanson ◽

Yuelian Shen ◽

Thomas S. Whittam ◽

...

Keyword(s):

Escherichia Coli ◽

Single Nucleotide Polymorphism ◽

Shiga Toxin ◽

Gel Electrophoresis ◽

Pulsed Field Gel Electrophoresis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Pulsed Field ◽

Clonal Group ◽

Toxin Genes

ABSTRACT Produce isolates of the Escherichia coli Ont:H52 serotype carried Shiga toxin 1 and stable toxin genes but only expressed Stx1. These strains had pulsed-field gel electrophoresis profiles that were 90% homologous to clinical Ont:H52 strains that had identical phenotypes and genotypes. All Ont:H52 strains had identical single nucleotide polymorphism profiles that are suggestive of a unique clonal group.

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Whole-Genome Single-Nucleotide-Polymorphism Analysis for Discrimination of Clostridium botulinum Group I Strains

Applied and Environmental Microbiology ◽

10.1128/aem.03934-13 ◽

2014 ◽

Vol 80 (7) ◽

pp. 2125-2132 ◽

Cited By ~ 23

Author(s):

Narjol Gonzalez-Escalona ◽

Ruth Timme ◽

Brian H. Raphael ◽

Donald Zink ◽

Shashi K. Sharma

Keyword(s):

Single Nucleotide Polymorphism ◽

Clostridium Botulinum ◽

Toxin Gene ◽

Polymorphism Analysis ◽

Snp Analysis ◽

Whole Genome ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Content Type ◽

Group I

ABSTRACTClostridium botulinumis a genetically diverse Gram-positive bacterium producing extremely potent neurotoxins (botulinum neurotoxins A through G [BoNT/A-G]). The complete genome sequences of three strains harboring only the BoNT/A1 nucleotide sequence are publicly available. Although these strains contain a toxin cluster (HA+OrfX−) associated with hemagglutinin genes, little is known about the genomes of subtype A1 strains (termed HA−OrfX+) that lack hemagglutinin genes in the toxin gene cluster. We sequenced the genomes of three BoNT/A1-producingC. botulinumstrains: two strains with the HA+OrfX−cluster (69A and 32A) and one strain with the HA−OrfX+cluster (CDC297). Whole-genome phylogenic single-nucleotide-polymorphism (SNP) analysis of these strains along with other publicly availableC. botulinumgroup I strains revealed five distinct lineages. Strains 69A and 32A clustered with theC. botulinumtype A1 Hall group, and strain CDC297 clustered with theC. botulinumtype Ba4 strain 657. This study reports the use of whole-genome SNP sequence analysis for discrimination ofC. botulinumgroup I strains and demonstrates the utility of this analysis in quickly differentiatingC. botulinumstrains harboring identical toxin gene subtypes. This analysis further supports previous work showing that strains CDC297 and 657 likely evolved from a common ancestor and independently acquired separate BoNT/A1 toxin gene clusters at distinct genomic locations.

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Monitoring of Chicken Houses and an Attached Egg-Processing Facility in a Laying Farm for Salmonella Contamination between 1994 and 1998

Journal of Food Protection ◽

10.4315/0362-028x-64.12.1912 ◽

2001 ◽

Vol 64 (12) ◽

pp. 1912-1916 ◽

Cited By ~ 35

Author(s):

TOSHIYUKI MURASE ◽

KAZUKO SENJYU ◽

TAKESHI MAEDA ◽

MASAYUKI TANAKA ◽

HIROSHI SAKAE ◽

...

Keyword(s):

Gel Electrophoresis ◽

Salmonella Enterica ◽

Environmental Samples ◽

Pfge Pattern ◽

Pulsed Field Gel Electrophoresis ◽

Drain Water ◽

Pulsed Field ◽

Processing Facility ◽

Single Clone

Two chicken houses and an attached egg-processing facility in a laying farm were sampled between 1994 and 1998 to investigate Salmonella contamination. Each of the houses was environmentally controlled and fitted with egg belts that transported eggs from the houses to the egg-processing facility. Four hundred twenty-eight Salmonella isolates were obtained from 904 environmental samples collected from the houses. Two hundred fifty-two of the 428 (58.9%) isolates yielded five serotypes as follows: Salmonella enterica subsp. enterica serovar Livingstone, Salmonella serovar Cerro, Salmonella serovar Montevideo, Salmonella serovar Mbandaka, and Salmonella serovar Corvallis. The remaining (41.1%, 176 of 428) isolates included four other serotypes and isolates that were untypeable. Salmonella isolates obtained from the drain water collected after the washing of the eggs in the egg-processing facility yielded the same serotypes as those found in the chicken houses. Strains having an identical pulsed-field gel electrophoresis (PFGE) pattern were continually recovered from a house for more than 1 year. Several strains of Salmonella Cerro, Salmonella Mbandaka, and Salmonella Montevideo obtained from both the houses and from the egg-processing facility were indistinguishable by PFGE, respectively. These results suggest that Salmonella organisms originating from a single clone colonized the chicken houses and that the egg belts are likely to be one of the means by which Salmonella organisms are spread from one house to the others.

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Whole-Genome Sequences of Two Listeria monocytogenes Serovar 1/2a Strains Responsible for a Severe Listeriosis Outbreak in Central Italy

Genome Announcements ◽

10.1128/genomea.00236-18 ◽

2018 ◽

Vol 6 (24) ◽

Cited By ~ 2

Author(s):

Massimiliano Orsini ◽

Alessandra Cornacchia ◽

Claudio Patavino ◽

Marina Torresi ◽

Patrizia Centorame ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Gel Electrophoresis ◽

Central Italy ◽

Pulsed Field Gel Electrophoresis ◽

Single Band ◽

Whole Genome ◽

Genome Sequences ◽

Content Type ◽

Pulsed Field ◽

Pfge Profiles

ABSTRACT We report the whole-genome sequences of two Listeria monocytogenes strains responsible for a severe invasive listeriosis outbreak in central Italy that occurred in 2015 and 2016. These two strains differ by a single band in their pulsed-field gel electrophoresis (PFGE) profiles.

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Pulsed-Field Gel Electrophoresis Supports the Presence of Host-Adapted Salmonella enterica subsp. enterica Serovar Typhimurium Strains in the British Garden Bird Population

Applied and Environmental Microbiology ◽

10.1128/aem.00131-11 ◽

2011 ◽

Vol 77 (22) ◽

pp. 8139-8144 ◽

Cited By ~ 25

Author(s):

Becki Lawson ◽

Laura A. Hughes ◽

Tansy Peters ◽

Elizabeth de Pinna ◽

Shinto K. John ◽

...

Keyword(s):

Gel Electrophoresis ◽

Salmonella Enterica ◽

Phage Type ◽

Pulsed Field Gel Electrophoresis ◽

Phage Typing ◽

Molecular Technique ◽

Content Type ◽

Pulsed Field ◽

Phage Types ◽

Serovar Typhimurium

ABSTRACTSalmonellosis is a frequently diagnosed infectious disease of passerine birds in garden habitats within Great Britain with potential implications for human and domestic animal health. Postmortem examinations were performed on 1,477 garden bird carcasses of circa 50 species from England and Wales, 1999 to 2007 inclusive. Salmonellosis was confirmed in 263 adult birds of 10 passerine species in this 11-year longitudinal study. A subset of 124 fully biotypedSalmonella entericasubsp.entericaserovar Typhimurium isolates was examined using pulsed-field gel electrophoresis to investigate the hypothesis that these strains are host adapted and to determine whether this molecular technique offers greater resolution in understanding the epidemiology ofSalmonellaTyphimurium infection than phage typing alone. For the two most common phage types, definitive type (DT) 40 and DT56v, which together accounted for 97% (120/124) of isolates, pulsed-field gel electrophoresis groupings closely correlated with phage type with remarkably few exceptions. A high degree of genetic similarity (>90%) was observed within and between the two most common pulsed-field gel electrophoresis groups. No clustering or variation was found in the pulsed-field gel electrophoresis groupings by bird species, year, or geographical region beyond that revealed by phage typing. These findings support the hypothesis that there are currently two host-adaptedSalmonellaphage types,S. Typhimurium DT40 and DT56v, circulating widely in British garden birds and that the reservoir of infection is maintained within wild bird populations. Large-scale multilocus sequence typing studies are required to further investigate the epidemiology of this infection.

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Emergence of Enterohemorrhagic Escherichia coli Serovar O157 Strains in Clade 8 with Highly Similar Pulsed-Field Gel Electrophoresis Patterns

Journal of Food Protection ◽

10.4315/0362-028x.jfp-10-461 ◽

2011 ◽

Vol 74 (8) ◽

pp. 1324-1327 ◽

Cited By ~ 7

Author(s):

EIJI YOKOYAMA ◽

YOSHIKI ETOH ◽

SACHIKO ICHIHARA ◽

KAZUMI HORIKAWA ◽

NORIKO KONISHI ◽

...

Keyword(s):

Escherichia Coli ◽

Gel Electrophoresis ◽

Pulsed Field Gel Electrophoresis ◽

Enterohemorrhagic Escherichia Coli ◽

Common Source ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Pulsed Field ◽

Genetic Features ◽

Insertion Sites

Enterohemorrhagic Escherichia coli serovar O157 (O157) strains with highly similar pulsed-field gel electrophoresis (PFGE) patterns were isolated in Japan during 2007 and 2008. Several genetic features related to O157 evolution were investigated to indicate whether homoplasy might have contributed to the highly similar PFGE patterns in these strains. The O157 strains were classified in lineage I/II, as defined by a lineage-specific polymorphism assay-6 with an atypical allele in Z5935 (code: 231111). Analysis of the insertion sites of stx2 phage in these strains showed that the sites were “occupied” in yehV and “intact” in wrbA, indicating that the strains were derived from “Cluster 1” of “Subgroup C.” When a specific single-nucleotide polymorphism in ECs2357 in clade 8 strains was investigated, all of the strains in the present study were confirmed to be clade 8 strains. These results indicated that the O157 strains in this study had common genetic features, suggesting that the highly similar PFGE patterns of these strains were not due to homoplasy. Because no common source of these strains could be identified in 2007 to 2008 in Japan, these strains may have emerged from a unique O157 clade 8 clone and then spread by dissemination in Japan.

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Efficacy of Pulsed-Field Gel Electrophoresis and Repetitive Element Sequence-Based PCR in Typing ofSalmonellaIsolates from Assam, India

Journal of Clinical Microbiology ◽

10.1128/jcm.02043-17 ◽

2018 ◽

Vol 56 (5) ◽

Author(s):

Purnima Gogoi ◽

Probodh Borah ◽

Iftikar Hussain ◽

Leena Das ◽

Girin Hazarika ◽

...

Keyword(s):

Molecular Typing ◽

Gel Electrophoresis ◽

Salmonella Enterica ◽

Repetitive Element ◽

Pulsed Field Gel Electrophoresis ◽

Fecal Samples ◽

Content Type ◽

Pulsed Field ◽

Typing Methods ◽

Element Sequence

ABSTRACTA total of 12Salmonellaisolates belonging to different serovars,viz.,Salmonella entericaserovar Enteritidis (n= 4),Salmonella entericaserovar Weltevreden (n= 4),Salmonella entericaserovar Newport (n= 1),Salmonella entericaserovar Litchifield (n= 1), and untypeable strains (n= 2) were isolated from 332 diarrheic fecal samples collected from animals, birds, and humans. Of the two molecular typing methods applied,viz., repetitive element sequence-based PCR (REP-PCR) and pulsed-field gel electrophoresis (PFGE), PFGE could clearly differentiate the strains belonging to different serovars as well as differentiate between strains of the same serovar with respect to their source of isolation, whereas REP-PCR could not differentiate between strains of the same serovar. Thus, it can be suggested that PFGE is more useful and appropriate for molecular typing ofSalmonellaisolates during epidemiological investigations than REP-PCR.

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Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing

Applied and Environmental Microbiology ◽

10.1128/aem.02616-15 ◽

2015 ◽

Vol 82 (1) ◽

pp. 384-393 ◽

Cited By ~ 11

Author(s):

Kristin M. Schill ◽

Yun Wang ◽

Robert R. Butler ◽

Jean-François Pombert ◽

N. Rukma Reddy ◽

...

Keyword(s):

Genetic Diversity ◽

Gel Electrophoresis ◽

High Throughput Sequencing ◽

Pulsed Field Gel Electrophoresis ◽

Rrna Gene ◽

Snp Analysis ◽

Whole Genome ◽

Clostridium Sporogenes ◽

Content Type ◽

Pulsed Field

ABSTRACTClostridium sporogenesPA 3679 is a nonpathogenic, nontoxic model organism for proteolyticClostridium botulinumused in the validation of conventional thermal food processes due to its ability to produce highly heat-resistant endospores. Because of its public safety importance, the uncertain taxonomic classification and genetic diversity of PA 3679 are concerns. Therefore, isolates ofC. sporogenesPA 3679 were obtained from various sources and characterized using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. The phylogenetic relatedness and genetic variability were assessed based on 16S rRNA gene sequencing and whole-genome single nucleotide polymorphism (SNP) analysis. AllC. sporogenesPA 3679 isolates were categorized into two clades (clade I containing ATCC 7955 NCA3679 isolates 1961-2, 1990, and 2007 and clade II containing PA 3679 isolates NFL, UW, FDA, and Campbell and ATCC 7955 NCA3679 isolate 1961-4). The 16S maximum likelihood (ML) tree clustered both clades within proteolyticC. botulinumstrains, with clade I forming a distinct cluster with otherC. sporogenesnon-PA 3679 strains. SNP analysis revealed that clade I isolates were more similar to the genomic reference PA 3679 (NCTC8594) genome (GenBank accession numberAGAH00000000.1) than clade II isolates were. The genomic referenceC. sporogenesPA 3679 (NCTC8594) genome and clade IC. sporogenesisolates were genetically distinct from those obtained from other sources (University of Wisconsin, National Food Laboratory, U.S. Food and Drug Administration, and Campbell's Soup Company). Thermal destruction studies revealed that clade I isolates were more sensitive to high temperature than clade II isolates were. Considering the widespread use ofC. sporogenesPA 3679 and its genetic information in numerous studies, the accurate identification and genetic characterization ofC. sporogenesPA 3679 are of critical importance.

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

Journal of Clinical Microbiology ◽

10.1128/jcm.01280-15 ◽

2015 ◽

Vol 53 (10) ◽

pp. 3334-3340 ◽

Cited By ~ 77

Author(s):

Angela J. Taylor ◽

Victoria Lappi ◽

William J. Wolfgang ◽

Pascal Lapierre ◽

Michael J. Palumbo ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Outbreak Detection ◽

Whole Genome ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Molecular Subtyping ◽

Foodborne Outbreaks

Salmonella entericaserovar 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 ofS. 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 environmentalS. Enteritidis isolates were sequenced. Single nucleotide polymorphism (SNP)-based cluster analysis of theS. 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 forS. Enteritidis.

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