Search

Background Produce-associated outbreaks of Shiga toxin–producing Escherichia coli (STEC) were first identified in 1991. In April 2018, New Jersey and Pennsylvania officials reported a cluster of STEC O157 infections associated with multiple locations of a restaurant chain. The Centers for Disease Control and Prevention (CDC) queried PulseNet, the national laboratory network for foodborne disease surveillance, for additional cases and began a national investigation. Methods A case was defined as an infection between 13 March and 22 August 2018 with 1 of the 22 identified outbreak-associated E. coli O157:H7 or E. coli O61 pulsed-field gel electrophoresis pattern combinations, or with a strain STEC O157 that was closely related to the main outbreak strain by whole-genome sequencing. We conducted epidemiologic and traceback investigations to identify illness subclusters and common sources. A US Food and Drug Administration–led environmental assessment, which tested water, soil, manure, compost, and scat samples, was conducted to evaluate potential sources of STEC contamination. Results We identified 240 case-patients from 37 states; 104 were hospitalized, 28 developed hemolytic uremic syndrome, and 5 died. Of 179 people who were interviewed, 152 (85%) reported consuming romaine lettuce in the week before illness onset. Twenty subclusters were identified. Product traceback from subcluster restaurants identified numerous romaine lettuce distributors and growers; all lettuce originated from the Yuma growing region. Water samples collected from an irrigation canal in the region yielded the outbreak strain of STEC O157. Conclusions We report on the largest multistate leafy greens–linked STEC O157 outbreak in several decades. The investigation highlights the complexities associated with investigating outbreaks involving widespread environmental contamination.

Three cases of infant botulism were reported in a small Colorado town between 1981 and 1984. The first two cases occurred in 1981, 6 months apart, and the third case occurred in 1984. Clostridium botulinum type A was isolated from stool of all three case patients and from environmental samples of the patient’s homes. An epidemiological investigation and follow-up study were conducted from 1981 to 1986 and concluded the cases were likely related. In this study, we sought to determine whether the C. botulinum type A clinical isolates were related to each other and to isolates obtained from environmental samples. We performed whole genome sequencing (WGS) for 17 isolates associated with this potential cluster of infant botulism. Fifteen isolates were confirmed to be C. botulinum type A(B) and contained botulinum toxin gene subtypes A1 and B5 by WGS; these strains formed a monophyletic cluster in a phylogeny and were considered closely related to each other (0–18 high-quality single-nucleotide polymorphisms), but distinct from other C. botulinum type A(B) in Colorado and elsewhere in the United States. Results of our study suggest that the three infant botulism cases could have represented a cluster due to a C. botulinum type A(B) strain present in the environment.

Yersinia enterocolitica (YE) bioserotype 1B/O:8 (YE 1B/O:8) was identified in routine culture of a variety of zoo species housed at Omaha's Henry Doorly Zoo and Aquarium (OHDZA) from April to July 2011. Animal cases representing 12 species had YE detected from 34 cases during routine fecal monitoring and/or during postmortem examination: Coquerel's sifakas (Propithecus coquereli, two cases), black & white (BW) ruffed lemurs (Varecia variegata variegata, six cases), red ruffed lemurs (Varecia rubra, seven cases), white handed gibbon (Hylobates lar albimana, one case), black lemurs (Eulemur macaco, three cases), mongoose lemurs (Eulemur mongoz, two cases), African hunting dogs (Lycaon pictus, five cases), agile gibbons (Hylobates agilis, three cases), siamangs (Hylobates syndactylus, two cases), colobus monkey (Colobus angolensis palliates, one case), argus pheasant (Argusianus argus, one case), and orangutan (Pongo pygmaeus, one case). Most species were not symptomatic; however, three symptomatic cases in Coquerel's sifakas (two) and a white handed gibbon (one) showed clinical signs of diarrhea and lethargy that resulted in death for the Coquerel's sifakas. One unexpected death also occurred in a BW ruffed lemur. To the authors' knowledge, this is the first report of YE 1B/O:8 in such a large variety of zoo species. The source of the YE could not be identified, prompting the initiation of a diseases surveillance program to prevent further cases for the species that are sensitive to YE. To date, no additional cases have been identified, thus suggesting a single introduction of the YE 1B/O:8 strain into the zoo environment.

Escherichia coli, Escherichia albertii, and Escherichia fergusonii are closely related bacteria that can cause illness in humans, such as bacteremia, urinary tract infections and diarrhea. Current identification strategies for these three species vary in complexity and typically rely on the use of multiple phenotypic and genetic tests. To facilitate their rapid identification, we developed a multiplex PCR assay targeting conserved, species-specific genes. We used the Daydreamer™ (Pattern Genomics, USA) software platform to concurrently analyze whole genome sequence assemblies (WGS) from 150 Enterobacteriaceae genomes (107 E. coli, 5 Shigella spp., 21 E. albertii, 12 E. fergusonii and 5 other species) and design primers for the following species-specific regions: a 212 bp region of the cyclic di-GMP regulator gene (cdgR, AW869_22935 from genome K-12 MG1655, CP014225) for E. coli/Shigella; a 393 bp region of the DNA-binding transcriptional activator of cysteine biosynthesis gene (EAKF1_ch4033 from genome KF1, CP007025) for E. albertii; and a 575 bp region of the palmitoleoyl-acyl carrier protein (ACP)-dependent acyltransferase (EFER_0790 from genome ATCC 35469, CU928158) for E. fergusonii. We incorporated the species-specific primers into a conventional multiplex PCR assay and assessed its performance with a collection of 97 Enterobacteriaceae strains. The assay was 100% sensitive and specific for detecting the expected species and offers a quick and accurate strategy for identifying E. coli, E. albertii, and E. fergusonii in either a single reaction or by in silico PCR with sequence assemblies.

BACKGROUND: In 2017, we conducted a multistate investigation to determine the source of an outbreak of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infections, which occurred primarily in children. METHODS: We defined a case as infection with an outbreak strain of STEC O157:H7 with illness onset between January 1 and April 30, 2017. Case-patients were interviewed to identify common exposures. Traceback and facility investigations were conducted; food samples were tested for STEC. RESULTS: We identified 32 cases from 12 states. Twenty-six (81%) cases occurred in children

SUMMARYIn July 2011, a cluster ofYersinia enterocoliticainfections was detected in southwestern Pennsylvania, USA. We investigated the outbreak's source and scope in order to prevent further transmission. Twenty-two persons were diagnosed with yersiniosis; 16 of whom reported consuming pasteurized dairy products from dairy A. Pasteurized milk and food samples were collected from this dairy.Y. enterocoliticawas isolated from two products. Isolates from both food samples and available clinical isolates from nine dairy A consumers were indistinguishable by pulsed-field gel electrophoresis. Environmental and microbiological investigations were performed at dairy A and pasteurization deficiencies were noted. Because consumption of pasteurized milk is common and outbreaks have the potential to become large, public health interventions such as consumer advisories or closure of the dairy must be implemented quickly to prevent additional cases if epidemiological or laboratory evidence implicates pasteurized milk as the outbreak source.

We identified a novel serotype 1/2a outbreak strain and 2 novel epidemic clones of Listeria monocytogenes while investigating a foodborne outbreak of listeriosis associated with consumption of cantaloupe during 2011 in the United States. Comparative analyses of strains worldwide are essential to identification of novel outbreak strains and epidemic clones.

Four Vibrio spp. isolates from the historical culture collection at the Centers for Disease Control and Prevention, obtained from human blood specimens (n=3) and river water (n=1), show characteristics distinct from those of isolates of the most closely related species, Vibrio navarrensis and Vibrio vulnificus , based on phenotypic and genotypic tests. They are specifically adapted to survival in both freshwater and seawater, being able to grow in rich media without added salts as well as salinities above that of seawater. Phenotypically, these isolates resemble V. navarrensis , their closest known relative with a validly published name, but the group of isolates is distinguished from V. navarrensis by the ability to utilize l-rhamnose. Average nucleotide identity and percent DNA–DNA hybridization values obtained from the pairwise comparisons of whole-genome sequences of these isolates to V. navarrensis range from 95.4–95.8 % and 61.9–64.3 %, respectively, suggesting that the group represents a different species. Phylogenetic analysis of the core genome, including four protein-coding housekeeping genes (pyrH, recA, rpoA and rpoB), places these four isolates into their own monophyletic clade, distinct from V. navarrensis and V. vulnificus . Based on these differences, we propose these isolates represent a novel species of the genus Vibrio , for which the name Vibrio cidicii sp. nov. is proposed; strain LMG 29267T (=CIP 111013T=2756-81T), isolated from river water, is the type strain.

We used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates of Listeria monocytogenes serotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or “epidemic clones” that have been previously associated with outbreaks, suggesting that epidemic potential may be widespread in L. monocytogenes and is not limited to the recognized epidemic clones. Pairwise comparisons between epidemiologically related isolates within clonal complexes showed that genome-level variation differed by 2 orders of magnitude between different comparisons, and the distribution of point mutations (core versus accessory genome) also varied. In addition, genetic divergence between one closely related pair of isolates from a single outbreak was driven primarily by changes in phage regions. The evolutionary analysis showed that the changes could be attributed to horizontal gene transfer; members of the diverse bacterial community found in the production facility could have served as the source of novel genetic material at some point in the production chain. The results raise the question of how to best utilize information contained within the accessory genome in outbreak investigations. The full magnitude and complexity of genetic changes revealed by genome sequencing could not be discerned from traditional subtyping methods, and the results demonstrate the challenges of interpreting genetic variation among isolates recovered from a single outbreak. Epidemiological information remains critical for proper interpretation of nucleotide and structural diversity among isolates recovered during outbreaks and will remain so until we understand more about how various population histories influence genetic variation.

Vibrio navarrensis is an aquatic bacterium recently shown to be associated with human illness. We report the first genome sequences of three V. navarrensis strains obtained from clinical and environmental sources. Preliminary analyses of the sequences reveal that V. navarrensis contains genes commonly associated with virulence in other human pathogens.

We characterized 18 Vibrio isolates, including 15 recovered from human clinical specimens, and found that they clustered with two previously characterized Vibrio navarrensis isolates in a phylogenetic analysis. Four of the 18 strains may represent a new Vibrio species, distinct from V. navarrensis . The potential role of V. navarrensis in human disease needs further investigation.

MI agar is routinely used for quantifying Escherichia coli in drinking water. A suspect E. coli colony isolated from a water sample was identified as Buttiauxella agrestis . The whole genome sequence of B. agrestis was determined to understand the genetic basis for its phenotypic resemblance to E. coli on MI agar.

We isolated Raoultella planticola from a river water sample, which was phenotypically indistinguishable from Escherichia coli on MI agar. The genome sequence of R. planticola was determined to gain information about its metabolic functions contributing to its false positive appearance of E. coli on MI agar. We report the first whole genome sequence of Raoultella planticola .

Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of Vibrio cholerae O1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and >7,500 deaths in the first two years of the epidemic. We applied whole-genome sequencing to a temporal series of V. cholerae isolates from Haiti to gain insight into the mode and tempo of evolution in this isolated population of V. cholerae O1. Phylogenetic and Bayesian analyses supported the hypothesis that all isolates in the sample set diverged from a common ancestor within a time frame that is consistent with epidemiological observations. A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates. Nine nearly closed genomes assembled from continuous-long-read data showed evidence of genome rearrangements and supported the observation of no gene acquisition among isolates. Thus, intrinsic mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT). Consistent with this, the 12 Haiti isolates tested by laboratory HGT assays were severely impaired for transformation, although unlike previously characterized noncompetent V. cholerae isolates, each expressed hapR and possessed a functional quorum-sensing system. Continued monitoring of V. cholerae in Haiti will illuminate the processes influencing the origin and fate of genome variants, which will facilitate interpretation of genetic variation in future epidemics., IMPORTANCE Vibrio cholerae is the cause of substantial morbidity and mortality worldwide, with over three million cases of disease each year. An understanding of the mode and rate of evolutionary change is critical for proper interpretation of genome sequence data and attribution of outbreak sources. The Haiti epidemic provides an unprecedented opportunity to study an isolated, single-source outbreak of Vibrio cholerae O1 over an established time frame. By using multiple approaches to assay genetic variation, we found no evidence that the Haiti strain has acquired any genes by horizontal gene transfer, an observation that led us to discover that it is also poorly transformable. We have found no evidence that environmental strains have played a role in the evolution of the outbreak strain.

Vibrio furnissii in the blood is rarely reported, which may explain why clinical features of bloodstream infections with this organism have not been described. We describe a patient who developed skin lesions and V. furnissii bacteremia and was successfully treated with fluoroquinolones. V. furnissii may be a serious pathogen in patients with underlying comorbidities who are exposed to seafood.