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

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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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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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

Applied and Environmental Microbiology ◽

10.1128/aem.06538-11 ◽

2011 ◽

Vol 77 (24) ◽

pp. 8648-8655 ◽

Cited By ~ 72

Author(s):

Henk C. den Bakker ◽

Andrea I. Moreno Switt ◽

Craig A. Cummings ◽

Karin Hoelzer ◽

Lovorka Degoricija ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Gel Electrophoresis ◽

Salmonella Enterica ◽

Pfge Pattern ◽

Pulsed Field Gel Electrophoresis ◽

Whole Genome ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Content Type ◽

Pulsed Field

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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Plasmid-Borne Type E Neurotoxin Gene Clusters in Clostridium botulinum Strains

Applied and Environmental Microbiology ◽

10.1128/aem.00080-13 ◽

2013 ◽

Vol 79 (12) ◽

pp. 3856-3859 ◽

Cited By ~ 17

Author(s):

Zhen Zhang ◽

Hannamari Hintsa ◽

Ying Chen ◽

Hannu Korkeala ◽

Miia Lindström

Keyword(s):

Gene Cluster ◽

Gel Electrophoresis ◽

Clostridium Botulinum ◽

Southern Hybridization ◽

Gene Clusters ◽

Pulsed Field Gel Electrophoresis ◽

Content Type ◽

Pulsed Field ◽

Large Plasmids

ABSTRACTA collection of 36Clostridium botulinumtype E strains was examined by pulsed-field gel electrophoresis (PFGE) and Southern hybridization with probes targeted tobotEandorfX1in the neurotoxin gene cluster. Three strains were found to contain neurotoxin subtype E1 gene clusters in large plasmids of about 146 kb in size.

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Differentiation of Bacillus anthracis, B. cereus, and B. thuringiensis by Using Pulsed-Field Gel Electrophoresis

Applied and Environmental Microbiology ◽

10.1128/aem.02478-06 ◽

2007 ◽

Vol 73 (10) ◽

pp. 3446-3449 ◽

Cited By ~ 19

Author(s):

Wenwan Zhong ◽

Yulin Shou ◽

Thomas M. Yoshida ◽

Babetta L. Marrone

Keyword(s):

Cluster Analysis ◽

Bacillus Anthracis ◽

Gel Electrophoresis ◽

Pulsed Field Gel Electrophoresis ◽

Enzyme Digestion ◽

Whole Genome ◽

Pulsed Field ◽

High Profile

ABSTRACT A pulsed-field gel electrophoresis (PFGE) method was developed for discriminating Bacillus anthracis from B. cereus and B. thuringiensis. A worldwide collection of 25 B. anthracis isolates showed high-profile homology, and these isolates were unambiguously distinguished from B. cereus and B. thuringiensis isolates by cluster analysis of the whole-genome macrorestriction enzyme digestion patterns generated by NotI.

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Study of genetic diversity of Salmonella typhi using pulsed-field gel electrophoresis

Medical Journal of Indonesia ◽

10.13181/mji.v10i3.25 ◽

2001 ◽

pp. 158 ◽

Cited By ~ 1

Author(s):

Lucky H. Moehario ◽

Retno K. Soemanto

Keyword(s):

Genetic Diversity ◽

Gel Electrophoresis ◽

Salmonella Typhi ◽

Pulsed Field Gel Electrophoresis ◽

Pulsed Field

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Genetic diversity of canine gastric helicobacters, Helicobacter bizzozeronii and H. salomonis studied by pulsed-field gel electrophoresis

Journal of Medical Microbiology ◽

10.1099/00222615-48-4-341 ◽

1999 ◽

Vol 48 (4) ◽

pp. 341-347 ◽

Cited By ~ 7

Author(s):

M-L. HäUNNINEN ◽

U. HIRVI

Keyword(s):

Genetic Diversity ◽

Gel Electrophoresis ◽

Pulsed Field Gel Electrophoresis ◽

Pulsed Field

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Comparison of Virulence Gene Identification, Ribosomal Spacer PCR, and Pulsed-Field Gel Electrophoresis for Typing of Staphylococcus aureus Strains Isolated from Cases of Subclinical Bovine Mastitis in the United States

Journal of Clinical Microbiology ◽

10.1128/jcm.03282-15 ◽

2016 ◽

Vol 54 (7) ◽

pp. 1871-1876 ◽

Cited By ~ 5

Author(s):

Pamela R. F. Adkins ◽

John R. Middleton ◽

Lawrence K. Fox

Keyword(s):

United States ◽

Staphylococcus Aureus ◽

Gel Electrophoresis ◽

Virulence Gene ◽

The United States ◽

Pulsed Field Gel Electrophoresis ◽

Gene Identification ◽

Content Type ◽

Pulsed Field

Staphylococcus aureusis one of the most important pathogens causing contagious mastitis in dairy cattle worldwide. The objectives of this study were to determine if recently describedS. aureusgenotype B was present among previously characterized isolates from cases of bovine intramammary infection in the United States and to compare pulsed-field gel electrophoresis (PFGE) to the combination of ribosomal spacer PCR (RS-PCR) and virulence gene identification for typing ofS. aureusstrains. The hypothesis was that isolates that were previously characterized as contagious would be identified as genotype B and that the results of the two strain-typing methods would be comparable. Isolates were selected from a collection ofS. aureusisolates from eight dairy farms. Mammary quarter milk somatic cell count (SCC) andN-acetyl-β-d-gluconaminidase (NAGase) activity data were known and used to evaluate strain pathogenicity. RS-PCR was performed with conventional gel electrophoresis, and PCR was used for toxin gene identification. RS-PCR patterns were associated with a specific virulence gene pattern, as previously reported. Five RS-PCR banding patterns were identified. None of the isolates were characterized as genotype B. No association between RS-PCR types and milk SCC was found; however, NAGase activity was significantly higher in milk from mammary glands infected with RS-PCR banding type 1 (RSP type 1) than in milk from those infected with RSP type 2. The discriminatory power values were 1.0 and 0.46 for PFGE and RS-PCR, respectively. These data suggest that genotype B may have a limited geographic distribution and that PFGE is more discriminatory than RS-PCR performed with conventional gel electrophoresis for typing ofS. aureusisolates of bovine origin.

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