Whole-genome sequencing in hierarchy with pulsed-field gel electrophoresis: the utility of this approach to establish possible sources of MRSA cross-transmission

SUMMARYSalmonella enterica subsp. enterica serovar Dublin is an uncommon cause of human salmonellosis; however, a relatively high proportion of cases are associated with invasive disease. The serotype is associated with cattle. A geographically diffuse outbreak of S. Dublin involving nine patients occurred in Ireland in 2013. The source of infection was not identified. Typing of outbreak associated isolates by pulsed-field gel electrophoresis (PFGE) was of limited value because PFGE has limited discriminatory power for S. Dublin. Whole genome sequencing (WGS) showed conclusively that the isolates were closely related to each other, to an apparently unrelated isolate from 2011 and distinct from other isolates that were not readily distinguishable by PFGE.

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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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Carriage of a Single Strain of NontoxigenicCorynebacterium diphtheriaebv. Belfanti (Corynebacterium belfantii) in Four Patients with Cystic Fibrosis

Journal of Clinical Microbiology ◽

10.1128/jcm.00042-19 ◽

2019 ◽

Vol 57 (5) ◽

Cited By ~ 3

Author(s):

Diane Pivot ◽

Annlyse Fanton ◽

Edgar Badell-Ocando ◽

Marion Benouachkou ◽

Karine Astruc ◽

...

Keyword(s):

Cystic Fibrosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Antimicrobial Agents ◽

Care Center ◽

Whole Genome ◽

Single Strain ◽

Content Type ◽

Microbiological Methods ◽

Cross Transmission

ABSTRACTCystic fibrosis (CF) patients are commonly colonized by bacterial pathogens, which can induce persistent lung inflammation and may contribute to clinical deterioration. Colonization of CF patients and cross-transmission byCorynebacterium diphtheriaehave not been reported so far. The aim of this article was to investigate the possibility of a cross-transmission ofC. diphtheriaebiovar Belfanti between four patients of a CF center.C. diphtheriaebiovar Belfanti (now formally calledC. belfantii) isolates were collected from four patients in a single CF care center over a period of 6 years and analyzed by microbiological methods and whole-genome sequencing. Epidemiological links among patients were investigated. Ten isolates were collected from 4 patients. Whole-genome sequencing of one isolate from each patient showed that a single strain was shared among them. In addition, one patient was found to have the same strain in two consecutive samplings performed 9 months apart. The strain was nontoxigenic and was susceptible to most antimicrobial agents. Ciprofloxacin resistance was observed in one patient. The idea of transmission of the strain among patients was supported by the occurrence of same-day visits to the CF center. This study demonstrated colonization of CF patients byC. diphtheriaebiovar Belfanti (C. belfantii), and the data suggest persistence and transmission of a unique strain during at least 6 years in a single CF patient care center.

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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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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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