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Category Archives: PFGE
Research – Whole-Genome Sequencing of Shiga Toxin-Producing Escherichia coli for Characterization and Outbreak Investigation
Shiga toxin-producing Escherichia coli (STEC) causes high frequencies of foodborne infections worldwide and has been linked to numerous outbreaks each year. Pulsed-field gel electrophoresis (PFGE) has been the gold standard for surveillance until the recent transition to whole-genome sequencing (WGS). To further understand the genetic diversity and relatedness of outbreak isolates, a retrospective analysis of 510 clinical STEC isolates was conducted. Among the 34 STEC serogroups represented, most (59.6%) belonged to the predominant six non-O157 serogroups. Core genome single nucleotide polymorphism (SNP) analysis differentiated clusters of isolates with similar PFGE patterns and multilocus sequence types (STs). One serogroup O26 outbreak strain and another non-typeable (NT) strain, for instance, were identical by PFGE and clustered together by MLST; however, both were distantly related in the SNP analysis. In contrast, six outbreak-associated serogroup O5 strains clustered with five ST-175 serogroup O5 isolates, which were not part of the same outbreak as determined by PFGE. The use of high-quality SNP analyses enhanced the discrimination of these O5 outbreak strains into a single cluster. In all, this study demonstrates how public health laboratories can more rapidly use WGS and phylogenetics to identify related strains during outbreak investigations while simultaneously uncovering important genetic attributes that can inform treatment practices.
Posted in Decontamination Microbial, Food Micro Blog, Food Microbiology, Food Microbiology Blog, Food Microbiology Research, Food Microbiology Testing, microbial contamination, Microbial growth, Microbiological Risk Assessment, Microbiology, Microbiology Investigations, Microbiology Risk, MLST, PFGE, Shigatoxin, STEC, STEC E.coli, WGS
Research – Phenotypic and genotypic characterization of salmonella Enteritidis isolated from two consecutive Food-Poisoning outbreaks in Sichuan, China
Abstract
Salmonella enterica serotype Enteritidis (SE) is a primary pathogen that causes foodborne diseases in humans. Although whole-genome sequencing (WGS) -based typing analyses have been increasingly used to investigate food-poisoning outbreaks, they are rarely applied to the epidemiology of multiple Salmonella outbreaks in Sichuan, China. This study therefore isolated SE from patients and food of two consecutive food-poisoning outbreaks during 2020 in Sichuan, China. We tracked outbreak origin using epidemiological investigation, serotyping, antimicrobial susceptibility testing (AST), pulsed-field gel electrophoresis (PFGE), and WGS. We also determined phylogenetic relationships using PFGE, whole and core genome multilocus sequence typing (wg/cgMLST), and whole-genome single nucleotide polymorphism (wgSNP) analyses. Epidemiological investigations identified a correlation between cake consumption and food poisoning. Thirteen strains isolated from patients and one strain isolated from the cake were confirmed as SE. Among the 14 strains, only six shared the same AST pattern (AMP-AMS-Sul-STR). Isolates from patients and cakes were indistinguishable in PFGE results. All four methods, namely PFGE, wgMLST, cgMLST, and wgSNP were appropriate for bacterial typing in SE-related outbreak investigation. However, wgSNP can assign 12 SE strains from the first outbreak to one cluster and assign two SE strains from the second outbreak to another cluster, while PFGE, wgMLST, cgMLST did not successfully distinguish the SE strains from different outbreaks. Thus, we conclude that SNP-based phylogenetic analysis might be a viable method for differentiating SE strains at the outbreak level.
Posted in food bourne outbreak, Food Micro Blog, Food Microbiology, Food Microbiology Blog, Food Microbiology Research, Food Microbiology Testing, foodborne outbreak, foodbourne outbreak, microbial contamination, Microbiological Risk Assessment, Microbiology, Microbiology Investigations, Microbiology Risk, MLST, outbreak, PFGE, Research, WGS
Research – Multistate Outbreak Investigation of Salmonella Infections Linked to Kratom: A Focus on Traceback, Laboratory, and Regulatory Activities

During the spring of 2018, the U.S. Food and Drug Administration (FDA), U.S. Centers for Disease Control and Prevention (CDC), states and local public health agencies responded to a multistate outbreak of gastrointestinal illnesses caused by multiple Salmonella serovars and associated with consumption of kratom, a product harvested from a tropical tree native to Southeast Asia. The outbreak included 199 case-patients reported by 41 U.S. states, with illness onset dates ranging from January 11, 2017 to May 8, 2018, leading to 54 hospitalizations, and no deaths. Case-patients reported purchasing kratom products from physical and online retail points of service (POS). Products distributed to 16 POS where 24 case-patients from 17 states purchased kratom were selected for traceback investigation. Traceback revealed that the kratom was imported from several countries, the most common being Indonesia. Local and state officials collected product samples from case-patients and retail POS. The FDA collected 76 product samples from POS and distributors, of which 42 (55%) tested positive for Salmonella . The positive samples exhibited a wide range of pulsed field gel electrophoresis (PFGE) patterns and whole genome sequence (WGS) genetic heterogeneity, and a total 25 of 42 (60%) yielded at least one isolate indistinguishable from one or more outbreak-related clinical isolates. While it does not exclude a possibility of a single contamination source, the extent of genetic diversity exhibited by the Salmonella isolates recovered from product samples and a lack of traceback convergence, suggested that kratom was widely contaminated across multiple sites from which it was grown, harvested, and packaged. As a result of the contamination, kratom products were recalled by numerous firms (both voluntarily and mandatory). Epidemiologic, traceback, and laboratory evidence supported the conclusion that kratom products were associated with illnesses.
Posted in Decontamination Microbial, food bourne outbreak, Food Illness, Food Micro Blog, Food Microbiology, Food Microbiology Blog, Food Microbiology Research, Food Microbiology Testing, Foodborne Illness, foodborne outbreak, foodbourne outbreak, Illness, microbial contamination, Microbiological Risk Assessment, Microbiology, Microbiology Investigations, outbreak, PFGE, Research, Salmonella, WGS
