HaeNa Waechter

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

ABSTRACT In this study, we report a whole-genome single nucleotide polymorphism (SNP)-based evolutionary approach to study the epidemiology of a multistate outbreak of Salmonella enterica subsp. enterica serovar 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.

Increasing Antibiotic Resistance in Shigella spp. from Infected New York City Residents, New York, USA

Approximately 20% of Shigella isolates tested in New York City, New York, USA, during 2013–2015 displayed decreased azithromycin susceptibility. Case-patients were older and more frequently male and HIV infected than those with azithromycin-susceptible Shigella infection; 90% identified as men who have sex with men. Clinical interpretation guidelines for azithromycin resistance and outcome studies are needed.

Reassessing provider reporting in the age of electronic surveillance.

CONTEXT In 2000, the Centers for Disease Control and Prevention began funding health departments to implement integrated electronic systems for disease surveillance. OBJECTIVE Determine the impact of discontinuing provider reporting for chronic hepatitis B and C, hepatitis A, and select enteric diseases. DESIGN Laboratory and provider surveillance reports of chronic hepatitis B and C and enteric infections (Shiga toxin-producing Escherichia coli, Campylobacter, Listeria, noncholera Vibrio [eg, Vibrio parahaemolyticus], Salmonella, Shigella, and hepatitis A) diagnosed on January 1, 2007 to December 31, 2010 were compared for completeness and timeliness. Number of cases submitted by laboratories, providers, or both were assessed. RESULTS From 2007 to 2010, the proportion of cases reported only by providers for enteric disease infections differed by disease, ranging from 4% (Shiga toxin-producing E coli) to 20% (noncholera Vibrio). For chronic hepatitis C, less than 1% of cases were reported by providers only. The number of complete laboratory reports increased over the time period from 80% to 95% for chronic hepatitis and 92% to 94% for enteric infections. Laboratory reports had higher completion for date of birth, sex, and zip codes. Provider reports had less than 60% completion for race/ethnicity versus 20% for laboratories. Laboratories were faster than providers at reporting chronic hepatitis B (median 4 vs 21 days), chronic hepatitis C (4 vs 18 days), Campylobacter (6 vs 10 days), noncholera Vibrio (11 vs 12 days), Salmonella (6 vs 7 days), Shigella (6 vs 13 days), and hepatitis A (3 vs 8 days); providers were faster than laboratories at reporting Shiga toxin-producing E coli (4 vs 7 days) and Listeria (5 vs 6 days). CONCLUSIONS Laboratories reported more cases and their reports were timelier and more complete for all categories except race/ethnicity for chronic hepatitis, Campylobacter, noncholera Vibrio, Salmonella, Shigella, and hepatitis A. For chronic hepatitis, provider reporting could be eliminated in New York City with no adverse effects on disease surveillance. For enteric infections, more work is needed before discontinuing provider reporting.

Salmonellosis and Meat Purchased at Live-Bird and Animal-Slaughter Markets, United States, 2007–2012

To the Editor: Salmonella spp. cause ≈1.2 million human illnesses annually in the United States (1). Infections are primarily acquired through exposure to contaminated food or infected animals (1,2). Since 2007, state and local health departments and the Centers for Disease Control and Prevention have investigated multiple salmonellosis outbreaks linked to meat purchased at live-bird markets (LBMs) and live-animal markets (LAMs), where poultry and livestock are sold for onsite slaughter. These markets typically operate in large cities and serve populations of diverse ethnic backgrounds (3). In 2007, an outbreak involving 62 case-patients infected with 1 of 3 S. enterica serotype Schwarzengrund strains was investigated in Massachusetts; 61% were children <5 years of age, including 14 (23%) infants <1 year of age, and 96% were Asian (Table). A case-patient was defined as a person infected with S. enterica who had a pulsed-field gel electrophoresis XbaI restriction enzyme pattern indistinguishable from the outbreak strain. Exposure to poultry purchased at LBMs was reported, and environmental sampling at an implicated LBM identified 6 S. enterica serotypes, including 1 outbreak strain. Table Characteristics of outbreaks of human Salmonella enterica serotype Schwarzengrund infections linked to meat purchased at live-bird markets, United States, 2007–2012* Three subsequent investigations of S. enterica serotype Schwarzengrund infections were conducted: a 2009 outbreak of 50 cases in New York, New York; a 2010–2011 multistate outbreak of cases predominantly in New York, New Jersey, and Massachusetts; and a 2012 multistate outbreak of cases mostly in Illinois and Michigan. Most case-patients in these outbreaks were of Asian race or Hispanic ethnicity, but 3/5 case-patients in Michigan reported Arab ethnicity; >50% were infants or children <5 years of age. Among case-patients with available information, exposure to poultry from LBMs was reported by 88% of case-patients in the 2009 New York investigation, 35% in the 2010–2011 multistate investigation, and 50% in the 2012 multistate investigation. In Michigan, the outbreak strain was isolated from chicken purchased at an LBM and collected from households of 2 case-patients. During 2011–2012, the Centers for Disease Control and Prevention investigated a nationwide increase in S. enterica serotype I,4,[5],12:i- infections (pulsed-field gel electrophoresis XbaI restriction enzyme pattern JPXX01.1314). Although no single vehicle was implicated, clusters linked to LAMs were identified. In Minnesota, 14 illnesses were linked to meat from 3 neighboring LAMs. Environmental sampling identified the outbreak strain from an animal-holding pen at 1 of the markets. Seven case-patients were infants <1 year of age, and 10 reported Hmong ethnicity. In California, 10 illnesses likely associated with pork, lamb, and beef purchased at 3 LAMs were identified; case-patients reported Ethiopian and Hmong ethnicity. The outbreak strain was isolated from a pork leg collected from the freezer of a case-patient. LBMs and LAMs appear to be preferred by certain populations for cultural, culinary, or religious reasons. Exposure to meat from these markets is being increasingly recognized as a potential source of salmonellosis. The cause is uncertain, but one factor may be an increased number of markets: in New York, New York, the number of LBMs nearly doubled from 44 to >80 during 1994–2002 (4). Most case-patients in these outbreaks had minimal direct contact with poultry or livestock at these markets; many case-patients were infants or young children who had not visited the markets or consumed meat. Therefore, one risk factor appears to be living in a household where the meat purchased from these markets is handled or consumed. Several factors could make meats from these markets more risky for acquiring salmonellosis. Although LBMs and LAMs must meet sanitation requirements and prevent product adulteration (5–7), most are exempt from Food Safety and Inspection Service pathogen reduction performance standards (8,9) and probably do not require suppliers to use pathogen control measures on the farm or employ them during slaughter. Regulatory oversight by state agencies varies. Investigation findings, including environmental sampling, indicate that these markets could be heavily contaminated with S. enterica. Preliminary results of a Massachusetts study found that fresh-killed chickens from LBMs had higher Salmonella and Campylobacter spp. contamination rates than those for chickens purchased at grocery stores (10; T. Stiles, unpub. data). High-risk cultural preferences identified in these outbreaks included consuming raw or undercooked meat and cooking parts (e.g., feet, intestines) that are more likely to harbor Salmonella spp. Further processing (e.g., de-feathering, butchering) conducted inside homes could lead to cross-contamination in the household environment. Because of language and cultural barriers, existing food safety messages may not have been effective. The number and type of LBMs and LAMs, the populations these markets serve, and regulatory authority vary considerably by state, and many case-patients and market owners have been reluctant to speak with public health authorities. Therefore, illness prevention requires a local, targeted approach. To strengthen regulations, some states have created guidelines and begun regular inspection of these markets. Educational outreach has included distribution of posters, flyers, and magnets with safe food handling messages in multiple languages; collaboration with community groups; and education of market owners and workers. Given the various communities who use LBMs and LAMs, multifaceted interventions, including collaboration between human and animal health agencies, are needed to reduce disease risk among market patrons and their families.

Two Listeria monocytogenes Pseudo-outbreaks Caused by Contaminated Laboratory Culture Media

ABSTRACT Listeriosis is a serious foodborne infection that disproportionately affects elderly adults, pregnant women, newborns, and immunocompromised individuals. Diagnosis is made by culturing Listeria monocytogenes from sterile body fluids or from products of conception. This report describes the investigations of two listeriosis pseudo-outbreaks caused by contaminated laboratory media made from sheep blood.

Discovering foodborne illness in online restaurant reviews

Objective We developed a system for the discovery of foodborne illness mentioned in online Yelp restaurant reviews using text classification. The system is used by the New York City Department of Health and Mental Hygiene (DOHMH) to monitor Yelp for foodborne illness complaints. Materials and Methods We built classifiers for 2 tasks: (1) determining if a review indicated a person experiencing foodborne illness and (2) determining if a review indicated multiple people experiencing foodborne illness. We first developed a prototype classifier in 2012 for both tasks using a small labeled dataset. Over years of system deployment, DOHMH epidemiologists labeled 13 526 reviews selected by this classifier. We used these biased data and a sample of complementary reviews in a principled bias-adjusted training scheme to develop significantly improved classifiers. Finally, we performed an error analysis of the best resulting classifiers. Results We found that logistic regression trained with bias-adjusted augmented data performed best for both classification tasks, with F1-scores of 87% and 66% for tasks 1 and 2, respectively. Discussion Our error analysis revealed that the inability of our models to account for long phrases caused the most errors. Our bias-adjusted training scheme illustrates how to improve a classification system iteratively by exploiting available biased labeled data. Conclusions Our system has been instrumental in the identification of 10 outbreaks and 8523 complaints of foodborne illness associated with New York City restaurants since July 2012. Our evaluation has identified strong classifiers for both tasks, whose deployment will allow DOHMH epidemiologists to more effectively monitor Yelp for foodborne illness investigations.

Hepatitis A Cases Among Food Handlers: A Local Health Department Response-New York City, 2013.

During 2013, the New York City Department of Health and Mental Hygiene (DOHMH) received reports of 6 hepatitis A cases among food handlers. We describe our decision-making process for public notification, type of postexposure prophylaxis (PEP) offered, and lessons learned. For 3 cases, public notification was issued and DOHMH offered only hepatitis A vaccine as PEP. Subsequent outbreaks resulted from 1 case for which no public notification was issued or PEP offered, and 1 for which public notification was issued and PEP was offered too late. DOHMH continues to use environmental assessments to guide public notification decisions and offer only hepatitis A vaccine as PEP after public notification but recognizes the need to evaluate each situation individually. The PEP strategy employed by DOHMH should be considered because hepatitis A vaccine is immunogenic in all age groups, can be obtained by local jurisdictions more quickly, and is logistically easier to administer in mass clinics than immunoglobulin.