JYNNEOS™ effectiveness as post-exposure prophylaxis against mpox: Challenges using real-world outbreak data.

BACKGROUND: JYNNEOSTM vaccine has been used as post-exposure prophylaxis (PEP) during a mpox outbreak in New York City (NYC). Data on effectiveness are limited. METHODS: Effectiveness of a single dose of JYNNEOSTM vaccine administered subcutaneously ≤ 14 days as PEP for preventing mpox disease was assessed among individuals exposed to case-patients from May 22, 2022-August 24, 2022. Individuals were evaluated for mpox through 21 days post-exposure. An observational study was conducted emulating a sequence of nested "target" randomized trials starting each day after exposure. Results were adjusted for exposure risk and race/ethnicity. Analyses were conducted separately based on last (PEPL) and first (PEPF) exposure date. We evaluated the potential to overestimate PEP effectiveness when using conventional analytic methods due to exposed individuals developing illness before they can obtain PEP (immortal time bias) compared to the target trial. RESULTS: Median time from last exposure to symptom onset (incubation period) among cases that did not receive PEPL was 7 days (range 1-16). Time to PEPL receipt was 7 days (range 0-14). Among 549 individuals, adjusted PEPL and PEPF effectiveness was 19 % (95 % Confidence Interval [CI], -54 % to 57 %) and -7% (95 % CI, -144 % to 53 %) using the target trial emulation, respectively, and 78 % (95 % CI, 50 % to 91 %) and 73 % (95 % CI, 31 % to 91 %) using conventional analysis. CONCLUSIONS: Determining PEP effectiveness using real-world data during an outbreak is challenging. Time to PEP in NYC coupled with the observed incubation period resulted in overestimated PEP effectiveness using a conventional method. The target trial emulation, while yielding wide confidence intervals due to small sample size, avoided immortal time bias. While results from these evaluations cannot be used as reliable estimates of PEP effectiveness, we present important methodologic considerations for future evaluations.

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.

Risk Factors for Death Among Hospitalized Patients Aged 21-64 Years Diagnosed with COVID-19-New York City, March 13-April 9, 2020.

BACKGROUND: COVID-19 mortality studies have primarily focused on persons aged ≥ 65 years; less is known about decedents aged <65 years. METHODS: We conducted a case-control study among NYC residents aged 21-64 years hospitalized with COVID-19 diagnosed March 13-April 9, 2020, to determine risk factors for death. Case-patients (n=343) were hospitalized decedents with COVID-19 and control-patients (n=686) were discharged from hospitalization with COVID-19 and matched 2:1 to case-patients on age and residential neighborhood. Conditional logistic regression models were adjusted for patient sex, insurance status, and marital status. Matched adjusted odds ratios (aORs) were calculated for selected underlying conditions, combinations of conditions, and race/ethnic group. RESULTS: Median age of both case-patients and control-patients was 56 years (range: 23-64 years). Having ≥ 1 selected underlying condition increased odds of death 4.45-fold (95% CI: 2.33-8.49). Patients with diabetes; morbid obesity; heart, kidney, or lung disease; cancer; neurologic/neurodevelopmental conditions; mental health conditions; or HIV had significantly increased odds of death. Compared with having neither condition, having both diabetes and obesity or diabetes and heart disease was associated with approximately threefold odds of death. Five select underlying conditions were more prevalent among non-Hispanic Black control-patients than among control-patients of other races/ethnicities. CONCLUSIONS AND RELEVANCE: Selected underlying conditions were risk factors for death, and most prevalent among racial/ethnic minorities. Social services; health care resources, including vaccination; and tailored public health messaging are important for COVID-19 prevention. Strengthening these strategies for racial/ethnic minority groups could minimize COVID-19 racial/ethnic disparities.

Hepatitis A Virus Infections Among Men Who Have Sex with Men - Eight U.S. States, 2017-2018.

During 1995-2011, the overall incidence of hepatitis A decreased by 95% in the United States from 12 cases per 100,000 population during 1995 to 0.4 cases per 100,000 population during 2011, and then plateaued during 2012─2015. The incidence increased by 294% during 2016-2018 compared with the incidence during 2013-2015, with most cases occurring among populations at high risk for hepatitis A infection, including persons who use illicit drugs (injection and noninjection), persons who experience homelessness, and men who have sex with men (MSM) (1-3). Previous outbreaks among persons who use illicit drugs and MSM led to recommendations issued in 1996 by the Advisory Committee on Immunization Practices (ACIP) for routine hepatitis A vaccination of persons in these populations (4). Despite these long-standing recommendations, vaccination coverage rates among MSM remain low (5). In 2017, the New York City Department of Health and Mental Hygiene contacted CDC after public health officials noted an increase in hepatitis A infections among MSM. Laboratory testing* of clinical specimens identified strains of the hepatitis A virus (HAV) that subsequently matched strains recovered from MSM in other states. During January 1, 2017-October 31, 2018, CDC received reports of 260 cases of hepatitis A among MSM from health departments in eight states, a substantial increase from the 16 cases reported from all 50 states during 2013-2015. Forty-eight percent (124 of 258) of MSM patients were hospitalized for a median of 3 days. No deaths were reported. In response to these cases, CDC supported state and local health departments with public health intervention efforts to decrease HAV transmission among MSM populations. These efforts included organizing multistate calls among health departments to share information, providing guidance on developing targeted outreach and managing supplies for vaccine campaigns, and conducting laboratory testing of clinical specimens. Targeted outreach for MSM to increase awareness about hepatitis A infection and improve access to vaccination services, such as providing convenient locations for vaccination, are needed to prevent outbreaks among MSM.

COVID-19 Outbreak - New York City, February 29-June 1, 2020.

New York City (NYC) was an epicenter of the coronavirus disease 2019 (COVID-19) outbreak in the United States during spring 2020 (1). During March-May 2020, approximately 203,000 laboratory-confirmed COVID-19 cases were reported to the NYC Department of Health and Mental Hygiene (DOHMH). To obtain more complete data, DOHMH used supplementary information sources and relied on direct data importation and matching of patient identifiers for data on hospitalization status, the occurrence of death, race/ethnicity, and presence of underlying medical conditions. The highest rates of cases, hospitalizations, and deaths were concentrated in communities of color, high-poverty areas, and among persons aged ≥75 years or with underlying conditions. The crude fatality rate was 9.2% overall and 32.1% among hospitalized patients. Using these data to prevent additional infections among NYC residents during subsequent waves of the pandemic, particularly among those at highest risk for hospitalization and death, is critical. Mitigating COVID-19 transmission among vulnerable groups at high risk for hospitalization and death is an urgent priority. Similar to NYC, other jurisdictions might find the use of supplementary information sources valuable in their efforts to prevent COVID-19 infections.

Salmonellosis Outbreak Detected by Automated Spatiotemporal Analysis - New York City, May-June 2019.

In May 2019, the New York City Department of Health and Mental Hygiene (NYCDOHMH) detected an unusual cluster of five salmonellosis patients via automated spatiotemporal analysis of notifiable diseases using free SaTScan software (1). Within 1 day of cluster detection, graduate student interviewers determined that three of the patients had eaten prepared food from the same grocery store (establishment A) located inside the cluster area. NYCDOHMH initiated an investigation to identify additional cases, establish the cause, and provide control recommendations. Overall, 15 New York City (NYC) residents with laboratory-diagnosed salmonellosis who reported eating food from establishment A were identified. The most commonly consumed food item was chicken, reported by 10 patients. All 11 clinical isolates available were serotyped as Salmonella Blockley, sequenced, and analyzed by core genome multilocus sequence typing; isolates had a median difference of zero alleles. Environmental assessments revealed food not held at the proper temperature, food not cooled properly, and potential cross-contamination during chicken preparation. Elevated fecal coliform counts were found in two of four ready-to-eat food samples collected from establishment A, and Bacillus cereus was detected in three. The outbreak strain of Salmonella was isolated from one patient's leftover chicken. Establishing automated spatiotemporal cluster detection analyses for salmonellosis and other reportable diseases could aid in the detection of geographically focused, community-acquired outbreaks even before laboratory subtyping results become available.

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.

Serving high-risk foods in a high-risk setting: survey of hospital food service practices after an outbreak of listeriosis in a hospital.

BACKGROUND AND OBJECTIVES: Prepared ready-to-eat salads and ready-to-eat delicatessen-style meats present a high risk for Listeria contamination. Because no foodborne illness risk management guidelines exist specifically for US hospitals, a survey of New York City (NYC) hospitals was conducted to characterize policies and practices after a listeriosis outbreak occurred in a NYC hospital. METHODS: From August through October 2008, a listeriosis outbreak in a NYC hospital was investigated. From February through April 2009, NYC's 61 acute-care hospitals were asked to participate in a telephone survey regarding food safety practices and policies, specifically service of high-risk foods to patients at increased risk for listeriosis. RESULTS: Five patients with medical conditions that put them at high risk for listeriosis had laboratory-confirmed Listeria monocytogenes infection. The Listeria outbreak strain was isolated from tuna salad prepared in the hospital. Fifty-four (89%) of 61 hospitals responded to the survey. Overall, 81% of respondents reported serving ready-to-eat deli meats to patients, and 100% reported serving prepared ready-to-eat salads. Pregnant women, patients receiving immunosuppressive drugs, and patients undergoing chemotherapy were served ready-to-eat deli meats at 77%, 59%, and 49% of hospitals, respectively, and were served prepared ready-to-eat salads at 94%, 89%, and 73% of hospitals, respectively. Only 4 (25%) of 16 respondents reported having a policy that ready-to-eat deli meats must be heated until steaming hot before serving. CONCLUSIONS: Despite the potential for severe outcomes of Listeria infection among hospitalized patients, the majority of NYC hospitals had no food preparation policies to minimize risk. Hospitals should implement policies to avoid serving high-risk foods to patients at risk for listeriosis.