Clustering of SARS-CoV-2 in Households in New York City: A Building-Level Analysis, March-December 2020.

OBJECTIVES: To identify the proportion of coronavirus disease 2019 (COVID-19) cases that occurred within households or buildings in New York City (NYC) beginning in March 2020 during the first stay-at-home order to determine transmission attributable to these settings and inform targeted prevention strategies. DESIGN: The residential addresses of cases were geocoded (converting descriptive addresses to latitude and longitude coordinates) and used to identify clusters of cases residing in unique buildings based on building identification number (BIN), a unique building identifier. Household clusters were defined as 2 or more cases within 2 weeks of onset or diagnosis date in the same BIN with the same unit number, last name, or in a single-family home. Building clusters were defined as 3 or more cases with onset date or diagnosis date within 2 weeks in the same BIN who do not reside in the same household. SETTING: NYC from March to December 2020. PARTICIPANTS: NYC residents with a positive SARS-CoV-2 nucleic acid amplification or antigen test result with a specimen collected during March 1, 2020, to December 31, 2020. MAIN OUTCOME MEASURE: The proportion of NYC COVID-19 cases in a household or building cluster. RESULTS: The BIN analysis identified 65 343 building and household clusters: 17 139 (26%) building clusters and 48 204 (74%) household clusters. A substantial proportion of NYC COVID-19 cases (43%) were potentially attributable to household transmission in the first 9 months of the pandemic. CONCLUSIONS: Geocoded address matching assisted in identifying COVID-19 household clusters. Close contact transmission within a household or building cluster was found in 43% of noncongregate cases with a valid residential NYC address. The BIN analysis should be utilized to identify disease clustering for improved surveillance.

Extensively Drug-Resistant Typhoid Fever in the United States.

Cases of extensively drug-resistant (XDR) typhoid fever have been reported in the United States among patients who did not travel internationally. Clinicians should consider if and where the patient traveled when selecting empiric treatment for typhoid fever. XDR typhoid fever should be treated with a carbapenem, azithromycin, or both.

Cost Comparison Between 2 Responses to Hepatitis A Virus Incidents in Restaurant Food Handlers-New York City, 2015 and 2017.

CONTEXT: While the New York City Department of Health and Mental Hygiene (DOHMH) can use agency-wide emergency activation to respond to a hepatitis A virus-infected food handler, there is a need to identify alternative responses that conserve scarce resources. OBJECTIVE: To compare the costs incurred by DOHMH of responding to a hepatitis A case in restaurant food handlers using an agency-wide emergency activation (2015) versus the cost of collaborating with a private network of urgent care clinics (2017). DESIGN: We partially evaluate the costs incurred by DOHMH of responding to a hepatitis A case in a restaurant food handler using agency-wide emergency activation (2015) with the cost of collaborating with a private network of urgent care clinics (2017) estimated for a scenario in which DOHMH incurred the retail cost of services rendered. RESULTS: Costs incurred by DOHMH for emergency activation were $65 831 ($238 per restaurant employee evaluated) of which DOHMH personnel services accounted for 85% ($55 854). Costs of collaboration would have totaled $50 914 ($253 per restaurant employee evaluated) of which personnel services accounted for 6% ($3146). CONCLUSIONS: Accounting for incident size, collaborating with the clinic network was more expensive than agency-wide emergency activation, though required fewer DOHMH personnel services.

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.

Notes from the Field: Increase in Reported Hepatitis A Infections Among Men Who Have Sex with Men - New York City, January-August 2017.

Since 2011, the New York City (NYC) Department of Health and Mental Hygiene (DOHMH) has typically been notified of three or fewer cases of hepatitis A virus (HAV) infection each year among men who have sex with men (MSM) who reported no travel to countries where HAV is endemic. This year, DOHMH noted an increase in HAV infections among MSM with onsets in January-March 2017, and notified other public health jurisdictions via Epi-X, CDC's communication exchange network. As a result, 51 patients with HAV infection involving MSM were linked to the increase in NYC.

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.

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.

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

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.

Challenges to implementing communicable disease surveillance in New York City evacuation shelters after Hurricane Sandy, November 2012.

Hurricane Sandy hit New York City (NYC) on October 29, 2012. Before and after the storm, 73 temporary evacuation shelters were established. The total census of these shelters peaked at approximately 6,800 individuals. Concern about the spread of communicable diseases in shelters prompted the NYC Department of Health and Mental Hygiene (DOHMH) to rapidly develop a surveillance system to report communicable diseases and emergency department transports from shelters. We describe the implementation of this system. Establishing effective surveillance in temporary shelters was challenging and required in-person visits by DOHMH staff to ensure reporting. After system establishment, surveillance data were used to identify some potential disease clusters. For the future, we recommend pre-event planning for disease surveillance.

Creating student sleuths: how a team of graduate students helped solve an outbreak of Salmonella Heidelberg infections associated with kosher broiled chicken livers.

Since 2009, the New York City Department of Health and Mental Hygiene (DOHMH) has received FoodCORE funding to hire graduate students to conduct in-depth food exposure interviews of salmonellosis case patients. In 2011, an increase in the number of Salmonella Heidelberg infections with pulsed-field gel electrophoresis Xba I pattern JF6X01.0022 among observant Jewish communities in New York and New Jersey was investigated. As this pattern is common nationwide, some cases identified were not associated with the outbreak. To reduce the number of background cases, DOHMH focused on the community initially identified in the outbreak and defined a case as a person infected with the outbreak strain of Salmonella Heidelberg with illness onset from 1 April to 17 November 2011 and who consumed a kosher diet, spoke Yiddish, or self-identified as Jewish. Nationally, 190 individuals were infected with the outbreak strain of Salmonella Heidelberg; 63 New York City residents met the DOHMH case definition. In October 2011, the graduate students (Team Salmonella) interviewed three case patients who reported eating broiled chicken livers. Laboratory testing of chicken liver samples revealed the outbreak strain of Salmonella Heidelberg. Although they were only partially cooked, the livers appeared fully cooked, and consumers and retail establishment food handlers did not cook them thoroughly before eating or using them in a ready-to-eat spread. This investigation highlighted the need to prevent further illnesses from partially cooked chicken products. Removing background cases helped to focus the investigation. Training graduate students to collect exposure information can be a highly effective model for conducting foodborne disease surveillance and outbreak investigations for local and state departments of public health.

Using online reviews by restaurant patrons to identify unreported cases of foodborne illness - New York City, 2012-2013.

While investigating an outbreak of gastrointestinal disease associated with a restaurant, the New York City Department of Health and Mental Hygiene (DOHMH) noted that patrons had reported illnesses on the business review website Yelp (http://www.yelp.com) that had not been reported to DOHMH. To explore the potential of using Yelp to identify unreported outbreaks, DOHMH worked with Columbia University and Yelp on a pilot project to prospectively identify restaurant reviews on Yelp that referred to foodborne illness. During July 1, 2012-March 31, 2013, approximately 294,000 Yelp restaurant reviews were analyzed by a software program developed for the project. The program identified 893 reviews that required further evaluation by a foodborne disease epidemiologist. Of the 893 reviews, 499 (56%) described an event consistent with foodborne illness (e.g., patrons reported diarrhea or vomiting after their meal), and 468 of those described an illness within 4 weeks of the review or did not provide a period. Only 3% of the illnesses referred to in the 468 reviews had also been reported directly to DOHMH via telephone and online systems during the same period. Closer examination determined that 129 of the 468 reviews required further investigation, resulting in telephone interviews with 27 reviewers. From those 27 interviews, three previously unreported restaurant-related outbreaks linked to 16 illnesses met DOHMH outbreak investigation criteria; environmental investigation of the three restaurants identified multiple food-handling violations. The results suggest that online restaurant reviews might help to identify unreported outbreaks of foodborne illness and restaurants with deficiencies in food handling. However, investigating reports of illness in this manner might require considerable time and resources.

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.

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.

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.

A subset of dendritic cells induces CD4+ T cells to produce IFN-gamma by an IL-12-independent but CD70-dependent mechanism in vivo.

Interferon (IFN)-gamma, a cytokine critical for resistance to infection and tumors, is produced by CD4(+) helper T lymphocytes after stimulation by cultured dendritic cells (DCs) that secrete a cofactor, interleukin (IL)-12. We have identified a major IL-12-independent pathway whereby DCs induce IFN-gamma-secreting T helper (Th)1 CD4(+) T cells in vivo. This pathway requires the membrane-associated tumor necrosis family member CD70 and was identified by targeting the LACK antigen from Leishmania major within an antibody to CD205 (DEC-205), an uptake receptor on a subset of DCs. Another major DC subset, targeted with 33D1 anti-DCIR2 antibody, also induced IFN-gamma in vivo but required IL-12, not CD70. Isolated CD205(+) DCs expressed cell surface CD70 when presenting antigen to T cell receptor transgenic T cells, and this distinction was independent of maturation stimuli. CD70 was also essential for CD205(+) DC function in vivo. Detection of the IL-12-independent IFN-gamma pathway was obscured with nontargeted LACK, which was presented by both DC subsets. This in situ analysis points to CD70 as a decision maker for Th1 differentiation by CD205(+) DCs, even in Th2-prone BALB/c animals and potentially in vaccine design. The results indicate that two DC subsets have innate propensities to differentially affect the Th1/Th2 balance in vivo and by distinct mechanisms.