Shiga Toxin-Producing Escherichia coli O157:H7 Illness Outbreak Associated with Untreated, Pressurized, Municipal Irrigation Water - Utah, 2023.

During July-September 2023, an outbreak of Shiga toxin-producing Escherichia coli O157:H7 illness among children in city A, Utah, caused 13 confirmed illnesses; seven patients were hospitalized, including two with hemolytic uremic syndrome. Local, state, and federal public health partners investigating the outbreak linked the illnesses to untreated, pressurized, municipal irrigation water (UPMIW) exposure in city A; 12 of 13 ill children reported playing in or drinking UPMIW. Clinical isolates were genetically highly related to one another and to environmental isolates from multiple locations within city A's UPMIW system. Microbial source tracking, a method to indicate possible contamination sources, identified birds and ruminants as potential sources of fecal contamination of UPMIW. Public health and city A officials issued multiple press releases regarding the outbreak reminding residents that UPMIW is not intended for drinking or recreation. Public education and UPMIW management and operations interventions, including assessing and mitigating potential contamination sources, covering UPMIW sources and reservoirs, indicating UPMIW lines and spigots with a designated color, and providing conspicuous signage to communicate risk and intended use might help prevent future UPMIW-associated illnesses.

An investigation of an outbreak of Salmonella Newport infections linked to melons - United States, 2020.

The United States are one of the world's leading consumers of melons. In 2020, the Food and Drug Administration (FDA), the Centers for Disease Control and Prevention (CDC), and state health and regulatory partners investigated an outbreak of Salmonella Newport infections linked to melons from southwest Indiana, resulting in 80 ill persons and 18 hospitalizations reported across 15 states. Epidemiologic and traceback data indicated melons as the vehicle for these infections, but the collinearity of melon varieties purchased and consumed together in combination with the traceback investigation that could not rule out either melon type, did not allow investigators to delineate whether the vehicle was cantaloupe alone or, both cantaloupe and watermelons. Analysis of traceback records for cantaloupe and/or watermelon exposures for 12 ill people indicated convergence on a grower in southwest Indiana which supplied cantaloupe to the nine of eleven points of service where ill people purchased cantaloupe; similar convergence was not observed for watermelon. While Salmonella isolates were recovered from environmental samples collected by FDA throughout the growing operation, they were not highly genetically related to the outbreak strain by whole genome sequencing analyses, i.e. greater than a 20 high quality single nucleotide polymorphisms difference. This outbreak illustrates the need for additional efforts to determine the source and extent of environmental contamination in the melon growing region of southwest Indiana and emphasizes the need for outreach and education efforts to help promote farm practices to reduce pathogen contamination of melons.

Salmonella illness outbreaks linked to backyard poultry purchasing during the COVID-19 pandemic: United States, 2020.

Poultry contact is a risk factor for zoonotic transmission of non-typhoidal Salmonella spp. Salmonella illness outbreaks in the United States are identified by PulseNet, the national laboratory network for enteric disease surveillance. During 2020, PulseNet observed a 25% decline in the number of Salmonella clinical isolates uploaded by state and local health departments. However, 1722 outbreak-associated Salmonella illnesses resulting from 12 Salmonella serotypes were linked to contact with privately owned poultry, an increase from all previous years. This report highlights the need for continued efforts to prevent backyard poultry-associated outbreaks of Salmonella as ownership increases in the United States.

Multidrug-Resistant Salmonella Serotype Anatum in Travelers and Seafood from Asia, United States.

A multidrug-resistant Salmonella enterica serotype Anatum strain reported in Taiwan was isolated in the United States from patients and from seafood imported from Asia. Isolates harbored 11 resistance determinants, including quinolone and inducible cephalosporin resistance genes. Most patients had traveled to Asia. These findings underscore the need for global One Health resistance surveillance.

Update on Extensively Drug-Resistant Salmonella Serotype Typhi Infections Among Travelers to or from Pakistan and Report of Ceftriaxone-Resistant Salmonella Serotype Typhi Infections Among Travelers to Iraq - United States, 2018-2019.

Ceftriaxone-resistant Salmonella enterica serotype Typhi (Typhi), the bacterium that causes typhoid fever, is a growing public health threat. Extensively drug-resistant (XDR) Typhi is resistant to ceftriaxone and other antibiotics used for treatment, including ampicillin, chloramphenicol, ciprofloxacin, and trimethoprim-sulfamethoxazole (1). In March 2018, CDC began enhanced surveillance for ceftriaxone-resistant Typhi in response to an ongoing outbreak of XDR typhoid fever in Pakistan. CDC had previously reported the first five cases of XDR Typhi in the United States among patients who had spent time in Pakistan (2). These illnesses represented the first cases of ceftriaxone-resistant Typhi documented in the United States (3). This report provides an update on U.S. cases of XDR typhoid fever linked to Pakistan and describes a new, unrelated cluster of ceftriaxone-resistant Typhi infections linked to Iraq. Travelers to areas with endemic Typhi should receive typhoid vaccination before traveling and adhere to safe food and water precautions (4). Treatment of patients with typhoid fever should be guided by antimicrobial susceptibility testing whenever possible (5), and clinicians should consider travel history when selecting empiric therapy.

Protracted Outbreak of Salmonella Newport Infections Linked to Ground Beef: Possible Role of Dairy Cows - 21 States, 2016-2017.

In January 2017, CDC identified a cluster of Salmonella enterica serotype Newport infections with isolates sharing an indistinguishable pulsed-field gel electrophoresis (PFGE) pattern, JJPX01.0010 (pattern 10), through PulseNet, the national molecular subtyping network for foodborne disease surveillance. This report summarizes the investigation by CDC, state and local health and agriculture departments, and the U.S. Department of Agriculture's Food Safety and Inspection Service (USDA-FSIS) and discusses the possible role of dairy cows as a reservoir for strains of Salmonella that persistently cause human illness. This investigation combined epidemiologic and whole genome sequencing (WGS) data to link the outbreak to contaminated ground beef; dairy cows were hypothesized to be the ultimate source of Salmonella contamination.

Genetic Diversity in Salmonella enterica in Outbreaks of Foodborne and Zoonotic Origin in the USA in 2006-2017.

Whole genome sequencing is replacing traditional laboratory surveillance methods as the primary tool to track and characterize clusters and outbreaks of the foodborne and zoonotic pathogen Salmonella enterica (S. enterica). In this study, 438 S. enterica isolates representing 35 serovars and 13 broad vehicle categories from one hundred epidemiologically confirmed outbreaks were evaluated for genetic variation to develop epidemiologically relevant interpretation guidelines for Salmonella disease cluster detection. The Illumina sequences were analyzed by core genome multi-locus sequence typing (cgMLST) and screened for antimicrobial resistance (AR) determinants and plasmids. Ninety-three of the one hundred outbreaks exhibited a close allele range (less than 10 allele differences with a subset closer than 5). The remaining seven outbreaks showed increased variation, of which three were considered polyclonal. A total of 16 and 28 outbreaks, respectively, showed variations in the AR and plasmid profiles. The serovars Newport and I 4,[5],12:i:-, as well as the zoonotic and poultry product vehicles, were overrepresented among the outbreaks, showing increased variation. A close allele range in cgMLST profiles can be considered a reliable proxy for epidemiological relatedness for the vast majority of S. enterica outbreak investigations. Variations associated with mobile elements happen relatively frequently during outbreaks and could be reflective of changing selective pressures.

Evaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA.

Salmonella enterica is a leading cause of bacterial foodborne and zoonotic illnesses in the United States. For this study, we applied four different whole genome sequencing (WGS)-based subtyping methods: high quality single-nucleotide polymorphism (hqSNP) analysis, whole genome multilocus sequence typing using either all loci [wgMLST (all loci)] and only chromosome-associated loci [wgMLST (chrom)], and core genome multilocus sequence typing (cgMLST) to a dataset of isolate sequences from 9 well-characterized Salmonella outbreaks. For each outbreak, we evaluated the genomic and epidemiologic concordance between hqSNP and allele-based methods. We first compared pairwise genomic differences using all four methods. We observed discrepancies in allele difference ranges when using wgMLST (all loci), likely caused by inflated genetic variation due to loci found on plasmids and/or other mobile genetic elements in the accessory genome. Therefore, we excluded wgMLST (all loci) results from any further comparisons in the study. Then, we created linear regression models and phylogenetic tanglegrams using the remaining three methods. K-means analysis using the silhouette method was applied to compare the ability of the three methods to partition outbreak and sporadic isolate sequences. Our results showed that pairwise hqSNP differences had high concordance with cgMLST and wgMLST (chrom) allele differences. The slopes of the regressions for hqSNP vs. allele pairwise differences were 0.58 (cgMLST) and 0.74 [wgMLST (chrom)], and the slope of the regression was 0.77 for cgMLST vs. wgMLST (chrom) pairwise differences. Tanglegrams showed high clustering concordance between methods using two statistical measures, the Baker's gamma index (BGI) and cophenetic correlation coefficient (CCC), where 9/9 (100%) of outbreaks yielded BGI values ≥ 0.60 and CCCs were ≥ 0.97 across all nine outbreaks and all three methods. K-means analysis showed separation of outbreak and sporadic isolate groups with average silhouette widths ≥ 0.87 for outbreak groups and ≥ 0.16 for sporadic groups. This study demonstrates that Salmonella isolates clustered in concordance with epidemiologic data using three WGS-based subtyping methods and supports using cgMLST as the primary method for national surveillance of Salmonella outbreak clusters.

Sequencing and Characterization of Five Extensively Drug-Resistant Salmonella enterica Serotype Typhi Isolates Implicated in Human Infections from Punjab, Pakistan.

A large outbreak of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi infections is ongoing in Pakistan, predominantly in Sindh Province. Here, we report the sequencing and characterization of five XDR Salmonella Typhi isolates from the Punjab province of Pakistan that are closely related to the outbreak strain and carry the same IncY plasmid.

Pulsed-field gel electrophoresis subtypes of shiga toxin-producing Escherichia coli O157 isolated from ground beef and humans, United States, 2001-2006.

Pulsed-field gel electrophoresis XbaI patterns of Shiga toxin-producing Escherichia coli O157 (STEC O157) isolates (n = 156) found in ground beef sampled from U.S. processing plants and retail stores during 2001 to 2006 were summarized and compared with XbaI patterns from human STEC O157 isolates (n = 14,591) in the national PulseNet E. coli database. Four ground beef samples contained more than one pulsed-field gel electrophoresis subtype of STEC O157. Of the 117 unique patterns found in ground beef, 100 (85%) appeared only once, and 17 (15%) were found in more than one isolate. The six patterns that appeared most frequently in human isolates were also found among the eight most common ground beef patterns. The yearly proportion of human isolates with the two most common patterns changed inversely, such that these patterns traded dominance over the study period. Human isolates with patterns that were first detected in both ground beef and humans contemporaneously were clustered in a 6-month window around the time of the respective ground beef sample. Of the 156 ground beef isolates, 82 (53%) were indistinguishable from at least one human isolate in this 6-month window. The yearly proportions of human STEC O157 isolates that were indistinguishable from ground beef isolates decreased significantly from 2002 to 2003 (12.3-0.8%), and then increased significantly from 2003 to 2006 (overall 0.8-12.6%). This increase in the numbers of human isolates that matched a ground beef isolate occurred during a period of relatively consistent rates of ground beef contamination with STEC O157. Pattern similarity of STEC O157 isolates derived from ground beef and clinical cases may serve as a good predictor of human incidence trends.

An investigation of Salmonella Fluntern illnesses linked to leopard geckos-United States, 2018.

Reptile contact can result in zoonotic non-typhoidal salmonellosis. In April 2018, Oregon Public Health Division contacted CDC about a cluster of four Salmonella serovar Fluntern (SF) illnesses in four states (OR, CA, IA, NY); patients reported contact with geckos, a popular reptile pet. PulseNet, the national molecular subtyping network of food-borne disease surveillance, subsequently identified additional SF clinical isolates. Twelve cases in 11 states were identified; median age was 5 years (range: <1-58 years). Three patients were hospitalized; no deaths were reported. Of those with exposure information (n = 10), all reported reptile exposure; 9 (90%) specified contact with leopard geckos. No common source of geckos was identified from reported purchase locations. Los Angeles County (LAC) health officials isolated SF from one patient's leopard gecko. Five reptile/gecko isolates were identified from the USDA National Veterinary Services Laboratories (NVSL) from 2015 to 2018. Five countries responded to an Epidemic Intelligence Information System post by PulseNet; reptile isolate sequence data were received from Czech Republic. A clinical case from England was identified through the National Center for Biotechnology Information pathogen detection pipeline; the patient did not report contact with leopard geckos. Whole genome sequencing analysis revealed substantial genetic diversity between clinical and animal isolates; however, gecko and clinical isolates from LAC were highly related (1 allele difference). This investigation linking SF illnesses to leopard geckos highlights an important public health risk from pets. A better understanding of how geckos are distributed by the pet industry in the United States could improve traceability to points of origin and mitigate Salmonella transmission at gecko breeders. Earlier NVSL reports of SF isolates from geckos suggest the risk of human SF infection from geckos is not new. This investigation demonstrates a need to educate gecko breeders, retailers and gecko owners about the continued Salmonella infection risk from pet geckos.

Multidrug-Resistant Salmonella I 4,[5],12:i:- and Salmonella Infantis Infections Linked to Whole Roasted Pigs from a Single Slaughter and Processing Facility.

We describe two outbreaks of multidrug-resistant (MDR) Salmonella I 4,[5],12:i:- infection, occurring in 2015 to 2016, linked to pork products, including whole roaster pigs sold raw from a single Washington slaughter and processing facility (establishment A). Food histories from 80 ill persons were compared with food histories reported in the FoodNet 2006 to 2007 survey of healthy persons from all 10 U.S. FoodNet sites who reported these exposures in the week before interview. Antimicrobial susceptibility testing and whole genome sequencing were conducted on selected clinical, food, and environmental isolates. During 2015, a total of 192 ill persons were identified from five states; among ill persons with available information, 30 (17%) of 180 were hospitalized, and none died. More ill persons than healthy survey respondents consumed pork (74 versus 43%, P < 0.001). Seventeen (23%) of 73 ill persons for which a response was available reported attending an event where whole roaster pig was served in the 7 days before illness onset. All 25 clinical isolates tested from the 2015 outbreak and a subsequent 2016 smaller outbreak (n = 15) linked to establishment A demonstrated MDR. Whole genome sequencing of clinical, environmental, and food isolates (n = 69) collected in both investigations revealed one clade of highly related isolates, supporting epidemiologic and traceback data that establishment A as the source of both outbreaks. These investigations highlight that whole roaster pigs, an uncommon food vehicle for MDR Salmonella I 4,[5],12:i:- outbreaks, will need further attention from food safety researchers and educators for developing science-based consumer guidelines, specifically with a focus on the preparation process.

Multistate Outbreak of Escherichia coli O157:H7 Infections Associated with Consumption of Fresh Spinach: United States, 2006.

During September to October, 2006, state and local health departments and the Centers for Disease Control and Prevention investigated a large, multistate outbreak of Escherichia coli O157:H7 infections. Case patients were interviewed regarding specific foods consumed and other possible exposures. E. coli O157:H7 strains isolated from human and food specimens were subtyped using pulsed-field gel electrophoresis and multiple-locus variable-number tandem repeat analyses (MLVA). Two hundred twenty-five cases (191 confirmed and 34 probable) were identified in 27 states; 116 (56%) case patients were hospitalized, 39 (19%) developed hemolytic uremic syndrome, and 5 (2%) died. Among 176 case patients from whom E. coli O157:H7 with the outbreak genotype (MLVA outbreak strain) was isolated and who provided details regarding spinach exposure, 161 (91%) reported fresh spinach consumption during the 10 days before illness began. Among 116 patients who provided spinach brand information, 106 (91%) consumed bagged brand A. E. coli O157:H7 strains were isolated from 13 bags of brand A spinach collected from patients' homes; isolates from 12 bags had the same MLVA pattern. Comprehensive epidemiologic and laboratory investigations associated this large multistate outbreak of E. coli O157:H7 infections with consumption of fresh bagged spinach. MLVA, as a supplement to pulsed-field gel electrophoresis genotyping of case patient isolates, was important to discern outbreak-related cases. This outbreak resulted in enhanced federal and industry guidance to improve the safety of leafy green vegetables and launched an independent collaborative approach to produce safety research in 2007.