scholarly journals Evaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis.

2020 ◽  
Author(s):  
Manal Mohammed ◽  
Salina Thapa
Keyword(s):  
Salmonella Typhimurium ◽  
Multilocus Sequence Typing ◽  
Bacterial Infections ◽  
Outbreak Investigation ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Whole Genome ◽  
Salmonella Dublin ◽  
Source Of Infection ◽  
Investigation Methods

Abstract Background: Salmonellosis is one of the most common foodborne diseases worldwide. Although human infection by non-typhoidal Salmonella (NTS) enterica subspecies enterica is associated primarily with a self-limiting diarrhoeal illness, invasive bacterial infections (such as septicaemia, bacteraemia and meningitis) were also reported. Human outbreaks of NTS were reported in several countries all over the world including developing as well as high-income countries. Conventional laboratory methods such as pulsed field gel electrophoresis (PFGE) do not display adequate discrimination and have their limitations in epidemiological surveillance. It is therefore very crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation. Methods: Here, we used different whole genome sequence (WGS)-based subtyping methods for retrospective investigation of two different outbreaks of Salmonella Typhimurium and Salmonella Dublin that occurred in 2013 in UK and Ireland respectively. Results: Single nucleotide polymorphism (SNP)-based cluster analysis of Salmonella Typhimurium genomes revealed well supported clades, that were concordant with epidemiologically defined outbreak and confirmed the source of outbreak is due to consumption of contaminated mayonnaise. SNP-analyses of Salmonella Dublin genomes confirmed the outbreak however the source of infection could not be determined. The core genome multilocus sequence typing (cgMLST) was discriminatory and separated the outbreak strains of Salmonella Dublin from the non-outbreak strains that were concordant with the epidemiological data however cgMLST could neither discriminate between the outbreak and non-outbreak strains of Salmonella Typhimurium nor confirm that contaminated mayonnaise is the source of infection, On the other hand, other WGS-based subtyping methods including multilocus sequence typing (MLST), ribosomal MLST (rMLST), whole genome MLST (wgMLST), clustered regularly interspaced short palindromic repeats (CRISPRs), prophage sequence profiling, antibiotic resistance profile and plasmid typing methods were less discriminatory and could not confirm the source of the outbreak. Conclusions: Foodborne salmonellosis is an important concern for public health therefore, it is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological surveillance and outbreak investigation. In this study, we showed that SNP-based analyses do not only have the ability to confirm the occurrence of the outbreak but also to provide definitive evidence of the source of the outbreak in real-time.

scholarly journals Evaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis.

2020 ◽  
Author(s):  
Manal Mohammed ◽  
Salina Thapa
Keyword(s):  
Salmonella Typhimurium ◽  
Multilocus Sequence Typing ◽  
Bacterial Infections ◽  
Rapid Development ◽  
Outbreak Investigation ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Whole Genome ◽  
Salmonella Dublin ◽  
Investigation Methods

Abstract Background: Salmonellosis is one of the most common foodborne diseases worldwide. Although human infection by non-typhoidal Salmonella (NTS) enterica subspecies enterica is associated primarily with a self-limiting diarrhoeal illness, invasive bacterial infections (such as septicaemia, bacteraemia and meningitis) were also reported. Human outbreaks of NTS were reported in several countries all over the world including developing as well as high-income countries. Conventional laboratory methods such as pulsed field gel electrophoresis (PFGE) do not display adequate discrimination and have their limitations in epidemiological surveillance. It is therefore very crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation. Methods: Here, we used different whole genome sequence (WGS)-based subtyping methods for retrospective investigation of two different outbreaks of Salmonella Typhimurium and Salmonella Dublin that occurred in 2013 in UK and Ireland respectively. Results: The core genome multilocus sequence typing (cgMLST) was discriminatory and separated the outbreak strains of Salmonella Dublin from the non-outbreak strains that were concordant with the epidemiological data however cgMLST could not discriminate between outbreak and non-outbreak strains of Salmonella Typhimurium, On the other hand, other WGS-based subtyping methods including multilocus sequence typing (MLST), ribosomal MLST (rMLST), whole genome MLST (wgMLST), clustered regularly interspaced short palindromic repeats (CRISPRs), prophage sequence profiling, antibiotic resistance profile and plasmid typing methods were less discriminatory. Conclusions: Foodborne salmonellosis is an important concern for public health therefore, it is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological surveillance and outbreak investigation. The rapid development of next-generation sequencing (NGS) technology and bioinformatics tools have enabled WGS of any bacterial strain feasible. Various typing tools have been proposed by using WGS data but currently, the adoption of WGS-based methods have proved to be difficult due to lack of standardization. There are many layers on obtaining WGS data and there is need of standardization from the type of sequencers used to the bioinformatics analysis. Therefore, the emerging genetic analysis techniques should be combined with conventional phenotypic and molecular methods for routine surveillance and outbreak investigation until the WGS-based methods can be fully exploited, improved and standardized.

scholarly journals Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shingo Nishiki ◽  
Kenichi Lee ◽  
Mizue Kanai ◽  
Shu-ichi Nakayama ◽  
Makoto Ohnishi
Keyword(s):  
Genetic Difference ◽  
Phylogenetic Analyses ◽  
Treponema Pallidum ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Global Perspectives ◽  
Most Recent Common Ancestor ◽  
Sex With Men

AbstractJapan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.

scholarly journals Whole genome sequencing provides an unambiguous link between Salmonella Dublin outbreak strain and a historical isolate

2015 ◽  
Vol 144 (3) ◽  
pp. 576-581 ◽  
Author(s):  
M. MOHAMMED ◽  
N. DELAPPE ◽  
J. O'CONNOR ◽  
P. McKEOWN ◽  
P. GARVEY ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Gel Electrophoresis ◽  
Invasive Disease ◽  
Pulsed Field Gel Electrophoresis ◽  
Whole Genome ◽  
Outbreak Strain ◽  
Salmonella Dublin ◽  
Source Of Infection ◽  
Human Salmonellosis

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.

scholarly journals Genomic Epidemiology of the Haitian Cholera Outbreak: a Single Introduction Followed by Rapid, Extensive, and Continued Spread Characterized the Onset of the Epidemic

mBio ◽  
2014 ◽  
Vol 5 (6) ◽  
Author(s):  
Mark Eppinger ◽  
Talima Pearson ◽  
Sara S. K. Koenig ◽  
Ofori Pearson ◽  
Nathan Hicks ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Molecular Evidence ◽  
Whole Genome ◽  
Cholera Outbreak ◽  
Content Type ◽  
Genomic Epidemiology ◽  
Southern Asia ◽  
Strain Collection

ABSTRACT For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons. Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade. IMPORTANCE In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and evolutionary relationships. The established phylogenomic framework showed how outbreak isolates fit into the global phylogeographic patterns compared to a comprehensive globally and temporally diverse strain collection and provides strong molecular evidence that points to a nonindigenous source of the 2010 Haitian cholera outbreak and refines epidemiological standards used in outbreak investigations for outbreak inclusion/exclusion following the concept of genomic epidemiology. The generated phylogenomic data have major public health relevance in translating sequence-based information to assist in future diagnostic, epidemiological, surveillance, and forensic studies of cholera.

Outbreak of Burkholderia contaminans endophthalmitis traced to a clinic ventilation system

2021 ◽  
pp. 1-3
Author(s):  
Theodore Spilker ◽  
Jens Kratholm ◽  
Eliza Depoorter ◽  
Peter Vandamme ◽  
John J. LiPuma
Keyword(s):  
Sequence Analysis ◽  
Cataract Surgery ◽  
Genome Sequence ◽  
Ventilation System ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis ◽  
Source Of Infection ◽  
Burkholderia Contaminans

Abstract We describe the follow-up investigation of an outbreak of endophthalmitis due to Burkholderia contaminans following cataract surgery in a single clinic. Whole-genome sequence analysis of bacteria recovered from affected patients and the clinic identified the clinic’s ventilation system as the source of infection.

scholarly journals Salmonella Typhimurium: experiences from recent European outbreaks

2008 ◽  
Vol 13 (44) ◽  
Author(s):  
T Westrell
Keyword(s):  
Salmonella Typhimurium ◽  
European Countries ◽  
Outbreak Investigation ◽  
Molecular Subtyping ◽  
Investigation Methods

In this week’s issue of Eurosurveillance, four European countries present recent outbreaks of Salmonella Typhimurium. The articles present a variety of innovative outbreak investigation methods, in particular molecular subtyping which permits to compare strains within and between countries.

scholarly journals Characteristics of Salmonella recovered from stools of children enrolled in the Global Enteric Multicenter Study

2021 ◽  
Author(s):  
Irene N Kasumba ◽  
Caisey V Pulford ◽  
Blanca M Perez-Sepulveda ◽  
Sunil Sen ◽  
Nurulla Sayed ◽  
...  
Keyword(s):  
Salmonella Typhimurium ◽  
Multicenter Study ◽  
Antimicrobial Susceptibility ◽  
Sequence Data ◽  
Sub Saharan Africa ◽  
Whole Genome Sequence ◽  
Diffusion Method ◽  
Whole Genome ◽  
Disk Diffusion Method ◽  
Severe Diarrhea

Abstract Background The Global Enteric Multicenter Study (GEMS) determined the etiologic agents of moderate-to-severe diarrhea (MSD) in children under 5 years old in Africa and Asia. Here, we describe the prevalence and antimicrobial susceptibility of non-typhoidal Salmonella (NTS) serovars in GEMS and examine the phylogenetics of Salmonella Typhimurium ST313 isolates. Methods Salmonella isolated from children with MSD or diarrhea-free controls were identified by classical clinical microbiology and serotyped using antisera and/or whole genome sequence data. We evaluated antimicrobial susceptibility using the Kirby-Bauer disk diffusion method. Salmonella Typhimurium sequence types were determined using multi-locus sequence typing and whole genome sequencing was performed to assess the phylogeny of ST313. Results Out of 370 Salmonella-positive individuals, 190 (51.4%) were MSD cases and 180 (48.6%) were diarrhea-free controls. The most frequent Salmonella serovars identified were Salmonella Typhimurium, serogroup O:8 (C2-C3), serogroup O:6,7 (C1), Salmonella Paratyphi B Java and serogroup O:4 (B). The prevalence of NTS was low but similar across sites, regardless of age, and was similar amongst both cases and controls except in Kenya, where Salmonella Typhimurium was more commonly associated with cases than controls. Phylogenetic analysis showed that these Salmonella Typhimurium isolates, all ST313, were highly genetically related to isolates from controls. Generally, Salmonella isolates from Asia were resistant to ciprofloxacin and ceftriaxone but African isolates were susceptible to these antibiotics. Conclusion Our data confirms that NTS is prevalent, albeit at low levels, in Africa and South Asia. Our findings provide further evidence that multi-drug resistant Salmonella Typhimurium ST313 can be carried asymptomatically by humans in sub-Saharan Africa.

scholarly journals Whole-genome sequence-based comparison and profiling of virulence-associated genes of Bacillus cereus group isolates from diverse sources in Japan

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Akiko Okutani ◽  
Satoshi Inoue ◽  
Akira Noguchi ◽  
Yoshihiro Kaku ◽  
Shigeru Morikawa
Keyword(s):  
Bacillus Cereus ◽  
Core Genome ◽  
Genetic Relationships ◽  
Significant Risk ◽  
Clinical Isolates ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Whole Genome ◽  
Genome Sequences ◽  
Snp Typing

Abstract Background The complete genome sequences of 44 Bacillus cereus group isolates collected from diverse sources in Japan were analyzed to determine their genetic backgrounds and diversity levels in Japan. Multilocus sequence typing (MLST) and core-genome single-nucleotide polymorphism (SNP) typing data from whole-genome sequences were analyzed to determine genetic diversity levels. Virulence-associated gene profiles were also used to evaluate the genetic backgrounds and relationships among the isolates. Results The 44 B. cereus group isolates, including soil- and animal-derived isolates and isolates recovered from hospitalized patients and food poisoning cases, were genotyped by MLST and core-genome SNP typing. Genetic variation among the isolates was identified by the MLST and core-genome SNP phylogeny comparison against reference strains from countries outside of Japan. Exploratory principal component analysis and nonmetric multidimensional scaling (NMDS) analyses were used to assess the genetic similarities among the isolates using gene presence and absence information and isolate origins as the metadata. A significant correlation was seen between the principal components and the presence of genes encoding hemolysin BL and emetic genetic determinants in B. cereus, and the capsule proteins in B. anthracis. NMDS showed that the cluster of soil isolates overlapped with the cluster comprising animal-derived and clinical isolates. Conclusions Molecular and epidemiological analyses of B. cereus group isolates in Japan suggest that the soil- and animal-derived bacteria from our study are not a significant risk to human health. However, because several of the clinical isolates share close genetic relationships with the environmental isolates, both molecular and epidemiological surveillance studies could be used effectively to estimate virulence in these important pathogens.

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