Clinical Outcomes of Patients With Nontyphoidal Salmonella Infections by Isolate Resistance-Foodborne Diseases Active Surveillance Network, 10 US Sites, 2004-2018.

BACKGROUND: Nontyphoidal Salmonella causes an estimated 1.35 million US infections annually. Antimicrobial-resistant strains are a serious public health threat. We examined the association between resistance and the clinical outcomes of hospitalization, length-of-stay ≥3 days, and death. METHODS: We linked epidemiologic data from the Foodborne Diseases Active Surveillance Network with antimicrobial resistance data from the National Antimicrobial Resistance Monitoring System (NARMS) for nontyphoidal Salmonella infections from 2004 to 2018. We defined any resistance as resistance to ≥1 antimicrobial and clinical resistance as resistance to ampicillin, azithromycin, ceftriaxone, ciprofloxacin, or trimethoprim-sulfamethoxazole (for the subset of isolates tested for all 5 agents). We compared outcomes before and after adjusting for age, state, race/ethnicity, international travel, outbreak association, and isolate serotype and source. RESULTS: Twenty percent of isolates (1105/5549) had any resistance, and 16% (469/2969) had clinical resistance. Persons whose isolates had any resistance were more likely to be hospitalized (31% vs 28%, P = .01) or have length-of-stay ≥3 days (20% vs 16%, P = .01). Deaths were rare but more common among those with any than no resistance (1.0% vs 0.4%, P = .01). Outcomes for patients whose isolates had clinical resistance did not differ significantly from those with no resistance. After adjustment, any resistance (adjusted odds ratio 1.23, 95% confidence interval 1.04-1.46) remained significantly associated with hospitalization. CONCLUSIONS: We observed a significant association between nontyphoidal Salmonella infections caused by resistant pathogens and likelihood of hospitalization. Clinical resistance was not associated with poorer outcomes, suggesting that factors other than treatment failure (eg, strain virulence, strain source, host factors) may be important.

Trends in Outpatient Medical-Care Seeking for Acute Gastroenteritis During the COVID-19 Pandemic, 2020.

The rate of enteric infections reported to public health surveillance decreased during 2020 amid the coronavirus disease 2019 (COVID-19) pandemic. Changes in medical care-seeking behaviors may have impacted the diagnosis of enteric infections contributing to these declines. We examined trends in outpatient medical care-seeking behavior for acute gastroenteritis (AGE) in Colorado during 2020 compared with the that of previous 3 years using electronic health record data from the Colorado Health Observation Regional Data Service (CHORDS). Outpatient medical encounters for AGE were identified using diagnoses codes from the International Classification of Diseases 10th Revision and aggregated by year, quarter, age group, and encounter type. The rate of encounters was calculated by dividing the number of AGE encounters by the corresponding total number of encounters. There were 9064 AGE encounters in 2020 compared with an annual average of 18,784 from 2017 to 2019 (p < 0.01), representing a 52% decrease. The rate of AGE encounters declined after the first quarter of 2020 and remained significantly lower for the rest of the year. Moreover, previously observed trends, including seasonal patterns and the preponderance of pediatric encounters, were no longer evident. Telemedicine modalities accounted for 23% of all AGE encounters in 2020. AGE outpatient encounters in Colorado in 2020 were substantially lower than during the previous 3 years. Decreases remained stable over the second, third, and fourth quarters of 2020 (April-December) and were especially pronounced for children <18 years of age. Changes in medical care-seeking behavior likely contributed to declines in the number of enteric disease cases and outbreaks reported to public health. It is unclear to what extent people were ill with AGE and did not seek medical care because of concerns about the infection risk during a health care visit or to what extent there were reductions in certain exposures and opportunities for disease transmission resulting in less illness.

Relationship Between Census Tract-Level Poverty and Domestically Acquired Salmonella Incidence: Analysis of Foodborne Diseases Active Surveillance Network Data, 2010-2016.

BACKGROUND: The relationships between socioeconomic status and domestically acquired salmonellosis and leading Salmonella serotypes are poorly understood. METHODS: We analyzed surveillance data from laboratory-confirmed cases of salmonellosis from 2010-2016 for all 10 Foodborne Disease Active Surveillance Network (FoodNet) sites, having a catchment population of 47.9 million. Case residential data were geocoded, linked to census tract poverty level, and then categorized into 4 groups according to census tract poverty level. After excluding those reporting international travel before illness onset, age-specific and age-adjusted salmonellosis incidence rates were calculated for each census tract poverty level, overall and for each of the 10 leading serotypes. RESULTS: Of 52 821geocodable Salmonella infections (>96%), 48 111 (91.1%) were domestically acquired. Higher age-adjusted incidence occurred with higher census tract poverty level (P < .001; relative risk for highest [≥20%] vs lowest [<5%] census tract poverty level, 1.37). Children <5 years old had the highest relative risk (2.07). Although this relationship was consistent by race/ethnicity and by serotype, it was not present in 5 FoodNet sites or among those aged 18-49 years. CONCLUSION: Children and older adults living in higher-poverty census tracts have had a higher incidence of domestically acquired salmonellosis. There is a need to understand socioeconomic status differences for risk factors for domestically acquired salmonellosis by age group and FoodNet site to help focus prevention efforts.

Refining historical limits method to improve disease cluster detection, New York City, New York, USA.

Since the early 2000s, the Bureau of Communicable Disease of the New York City Department of Health and Mental Hygiene has analyzed reportable infectious disease data weekly by using the historical limits method to detect unusual clusters that could represent outbreaks. This method typically produced too many signals for each to be investigated with available resources while possibly failing to signal during true disease outbreaks. We made method refinements that improved the consistency of case inclusion criteria and accounted for data lags and trends and aberrations in historical data. During a 12-week period in 2013, we prospectively assessed these refinements using actual surveillance data. The refined method yielded 74 signals, a 45% decrease from what the original method would have produced. Fewer and less biased signals included a true citywide increase in legionellosis and a localized campylobacteriosis cluster subsequently linked to live-poultry markets. Future evaluations using simulated data could complement this descriptive assessment.

Description of a school nurse visit syndromic surveillance system and comparison to emergency department visits, New York City.

OBJECTIVES: We compared school nurse visit syndromic surveillance system data to emergency department (ED) visit data for monitoring illness in New York City schoolchildren. METHODS: School nurse visit data recorded in an electronic health record system are used to conduct daily surveillance of influenza-like illness, fever-flu, allergy, asthma, diarrhea, and vomiting syndromes. We calculated correlation coefficients to compare the percentage of syndrome visits to the school nurse and ED for children aged 5 to 14 years, from September 2006 to June 2011. RESULTS: Trends in influenza-like illness correlated significantly (correlation coefficient = 0.89; P < .001) and 72% of school signals occurred on days that ED signaled. Trends in allergy (correlation coefficient = 0.73; P < .001) and asthma (correlation coefficient = 0.56; P < .001) also correlated and school signals overlapped with ED signals on 95% and 51% of days, respectively. Substantial daily variation in diarrhea and vomiting visits limited our ability to make comparisons. CONCLUSIONS: Compared with ED syndromic surveillance, the school nurse system identified similar trends in influenza-like illness, allergy, and asthma syndromes. Public health practitioners without school-based surveillance may be able to use age-specific analyses of ED syndromic surveillance data to monitor illness in schoolchildren.

Improving occupational health surveillance for enteric infections.

AIMS: Enteric pathogens with a livestock reservoir pose a unique risk to people in occupations with regular contact with animals. However, public health surveillance of occupational exposures is inadequate, with surveillance for occupation typically focusing on the risk of transmission and the need for worker exclusion, rather than workplace exposures. To improve surveillance for occupational zoonoses, the Colorado Integrated Food Safety Center of Excellence convened a group of subject matter experts who developed a set of variables on occupation, industry, and exposures, which were integrated into Colorado's surveillance system in 2017. We evaluated the quality and completeness of these new occupational fields for interviewed cases with laboratory-confirmed zoonotic infections and compared occupations to cases with a non-zoonotic infection (Shigella) and to employment data from the Bureau of Labor Statistics. METHODS AND RESULTS: From March 2017 through December 2019, 3668 domestically acquired, laboratory-confirmed sporadic infections of Campylobacter, Cryptosporidium, Shiga toxin-producing Escherichia coli, and non-typhoidal Salmonella among individuals ≥14 years of age were interviewed by public health. We found asking explicitly about occupational exposure risks and focusing on animal exposures, improved data quality and accuracy. Of the cases who stated that they were employed, 262 (13%) reported working in an occupation with regular animal exposure, and 254 (14%) reported an industry with regular animal exposure. Cases with an animal exposure occupation were more likely to be male and live in a rural or frontier county compared to other occupations. All occupations with regular animal contact were reported at a higher frequency than among Shigella cases or the general population. CONCLUSIONS: Public health efforts, both in occupational health and communicable disease sectors, should be made to improve surveillance for enteric zoonoses and identify opportunities for prevention strategies.

Modelling counterfactual incidence during the transition towards culture-independent diagnostic testing.

BACKGROUND: Culture-independent diagnostic testing (CIDT) provides rapid results to clinicians and is quickly displacing traditional detection methods. Increased CIDT use and sensitivity likely result in higher case detection but might also obscure infection trends. Severe illness outcomes, such as hospitalization and death, are likely less affected by changes in testing practices and can be used as indicators of the expected case incidence trend had testing methods not changed. METHODS: Using US Foodborne Diseases Active Surveillance Network data during 1996-2019 and mixed effects quasi-Poisson regression, we estimated the expected yearly incidence for nine enteric pathogens. RESULTS: Removing the effect of CIDT use, CIDT panel testing and culture-confirmation of CIDT testing, the modelled incidence in all but three pathogens (Salmonella, Shigella, STEC O157) was significantly lower than the observed and the upward trend in Campylobacter was reversed from an observed 2.8% yearly increase to a modelled -2.8% yearly decrease (95% credible interval: -4.0, -1.4). CONCLUSIONS: Severe outcomes may be useful indicators in evaluating trends in surveillance systems that have undergone a marked change.

Syndromic Gastrointestinal Panel Diagnostic Tests Have Changed our Understanding of the Epidemiology of Yersiniosis-Foodborne Diseases Active Surveillance Network, 2010-2021.

Background: In the US, yersinosis was understood to predominantly occur in winter and among Black or African American infants and Asian children. Increased use of culture-independent diagnostic tests (CIDTs) has led to marked increases in yersinosis diagnoses. Methods: We describe differences in the epidemiology of yersiniosis diagnosed by CIDT versus culture in 10 US sites, and identify determinants of health associated with diagnostic method. Results: Annual reported incidence increased from 0.3/100 000 in 2010 to 1.3/100 000 in 2021, particularly among adults ≥18 years, regardless of race and ethnicity, and during summer months. The proportion of CIDT-diagnosed infections increased from 3% in 2012 to 89% in 2021. An ill person's demographic characteristics and location of residence had a significant impact on their odds of being diagnosed by CIDT. Conclusions: Improved detection due to increased CIDT use has altered our understanding of yersinosis epidemiology, however differential access to CIDTs may still affect our understanding of yersinosis.

Changing Diagnostic Testing Practices for Foodborne Pathogens, Foodborne Diseases Active Surveillance Network, 2012-2019.

Background: Pathogen detection has changed with increased use of culture-independent diagnostic tests (CIDTs). CIDTs do not yield isolates, which are necessary to detect outbreaks using whole-genome sequencing. The Foodborne Diseases Active Surveillance Network (FoodNet) monitors clinical laboratory testing practices to improve interpretation of surveillance data and assess availability of isolates. We describe changes in practices over 8 years. Methods: During 2012-2019, 10 FoodNet sites collected standardized data about practices in clinical laboratories (range, 664-723 laboratories) for select enteric pathogens. We assessed changes in practices. Results: During 2012-2019, the percentage of laboratories that used only culture methods decreased, with the largest declines for Vibrio (99%-57%) and Yersinia (99%-60%). During 2019, the percentage of laboratories using only CIDTs was highest for Shiga toxin-producing Escherichia coli (43%), Campylobacter (34%), and Vibrio (34%). From 2015 to 2019, the percentage of laboratories that performed reflex culture after a positive CIDT decreased, with the largest declines for Shigella (75%-42%) and Salmonella (70%-38%). The percentage of laboratories that routinely submitted isolates to a public health laboratory decreased for all bacterial pathogens examined from 2015 to 2019. Conclusions: By increasing use of CIDTs and decreasing reflex culture, clinical laboratories have transferred the burden of isolate recovery to public health laboratories. Until technologies allow for molecular subtyping directly from a patient specimen, state public health laboratories should consider updating enteric disease reporting requirements to include submission of isolates or specimens. Public health laboratories need resources for isolate recovery.

Disparities in Shigellosis Incidence by Census Tract Poverty, Crowding, and Race/Ethnicity in the United States, FoodNet, 2004-2014.

BACKGROUND: Shigella causes an estimated 500 000 enteric illnesses in the United States annually, but the association with socioeconomic factors is unclear. METHODS: We examined possible epidemiologic associations between shigellosis and poverty using 2004-2014 Foodborne Diseases Active Surveillance Network (FoodNet) data. Shigella cases (n = 21 246) were geocoded, linked to Census tract data from the American Community Survey, and categorized into 4 poverty and 4 crowding strata. For each stratum, we calculated incidence by sex, age, race/ethnicity, and FoodNet site. Using negative binomial regression, we estimated incidence rate ratios (IRRs) comparing the highest to lowest stratum. RESULTS: Annual FoodNet Shigella incidence per 100 000 population was higher among children <5 years old (19.0), blacks (7.2), and Hispanics (5.6) and was associated with Census tract poverty (incidence rate ratio [IRR], 3.6; 95% confidence interval [CI], 3.5-3.8) and household crowding (IRR, 1.8; 95% CI, 1.7-1.9). The association with poverty was strongest among children and persisted regardless of sex, race/ethnicity, or geographic location. After controlling for demographic variables, the association between shigellosis and poverty remained significant (IRR, 2.3; 95% CI, 2.0-2.6). CONCLUSIONS: In the United States, Shigella infections are epidemiologically associated with poverty, and increased incidence rates are observed among young children, blacks, and Hispanics.

Assessment of reportable disease incidence after Hurricane Sandy, New York City, 2012.

OBJECTIVE: Hurricane Sandy's October 29, 2012 arrival in New York City caused flooding, power disruption, and population displacement. Infectious disease risk may have been affected by floodwater exposure, residence in emergency shelters, overcrowding, and lack of refrigeration or heating. For 42 reportable diseases that could have been affected by hurricane-related exposures, we developed methods to assess whether hurricane-affected areas had higher disease incidence than other areas of NYC. METHODS: We identified post-hurricane cases as confirmed, probable, or suspected cases with onset or diagnosis between October 30 and November 26 that were reported via routine passive surveillance. Pre-hurricane cases for the same 4-week period were identified in 5 prior years, 2007-2011. Cases were geocoded to the census tract of residence. Using data compiled by the NYC Office of Emergency Management, we determined (1) the proportion of the population in each census tract living in a flooded block and (2) the subset of flooded tracts severely "impacted", e.g., by prolonged service outages or physical damage. A separate multivariable regression model was constructed for each disease, modeling the outcome of case counts using a negative binomial distribution. Independent variables were: neighborhood poverty; whether cases were pre- or post-hurricane (time); the proportion of the population flooded in impacted and not impacted tracts; and interaction terms between the flood/impact variables and time. Models used repeated measures to adjust for correlated observations from the same tract and an offset term of the log of the population size. Sensitivity analyses assessed the effects of case count fluctuations and accounted for variations in reporting volume by using an offset term of the log of total cases. RESULTS: Only legionellosis was statistically significantly associated with increased occurrence in flooded/impacted areas post-hurricane, adjusting for baseline differences (P = .04). However, there was only 1 legionellosis case post-hurricane in a flooded/impacted area. CONCLUSIONS: Hurricane Sandy did not appear to elevate reportable disease incidence in NYC. Defining and acquiring reliable data and meta-data regarding hurricane-affected areas was a challenge in the weeks post-storm. Relevant metrics could be developed during disaster preparedness planning. These methods to detect excess disease can be adapted for future emergencies.

Implementation of non-pharmaceutical interventions by New York City public schools to prevent 2009 influenza A.

INTRODUCTION: Children are important transmitters of influenza in the community and a number of non-pharmaceutical interventions (NPIs), including hand washing and use of hand sanitizer, have been recommended to mitigate the transmission of influenza, but limited information is available regarding schools' ability to implement these NPIs during an influenza outbreak. We evaluated implementation of NPIs during fall 2009 in response to H1N1 pandemic influenza (pH1N1) by New York City (NYC) public schools. METHODS: From January 25 through February 9, 2010, an online survey was sent to all the 1,632 NYC public schools and principals were asked to participate in the survey or to designate a school nurse or other school official with knowledge of school policies and characteristics to do so. RESULTS: Of 1,633 schools, 376(23%) accessed and completed the survey. Nearly all respondents (99%) implemented at least two NPIs. Schools that had a Flu Response Team (FRT) as a part of school emergency preparedness plan were more likely to implement the NPI guidelines recommended by NYC public health officials than schools that did not have a FRT. Designation of a room for isolating ill students, for example, was more common in schools with a FRT (72%) than those without (53%) (p<0.001). CONCLUSIONS: Implementing an NPI program in a large school system to mitigate the effects of an influenza outbreak is feasible, but there is potential need for additional resources in some schools to increase capacity and adherence to all recommendations. Public health influenza-preparedness plans should include school preparedness planning and FRTs.

The effect of school dismissal on rates of influenza-like illness in New York City schools during the spring 2009 novel H1N1 outbreak.

BACKGROUND: The effects of individual school dismissal on influenza transmission have not been well studied. During the spring 2009 novel H1N1 outbreak, New York City implemented an individual school dismissal policy intended to limit influenza transmission at schools with high rates of influenza-like illness (ILI). METHODS: Active disease surveillance data collected by the New York City Health Department on rates of ILI in schools were used to evaluate the impact. Sixty-four schools that met the Health Department's criteria for considering dismissal were included in the analysis. Twenty-four schools that met criteria subsequently dismissed all classes for approximately 1 school week. A regression model was fit to these data, estimating the effect of school dismissal on rates of in-school ILI following reconvening, adjusting for potential confounders. RESULTS: The model estimated that, on average, school dismissal reduced the rate of ILI by 7.1% over the entire average outbreak period. However, a large proportion of in-school ILI occurred before dismissal criteria were met. A separate model estimated that school absenteeism rates were not significantly affected by dismissal. CONCLUSION: Results suggest that individual school dismissal could be considered in situations where schools have a disproportionate number of high-risk students or may be unable to implement recommended preventive or infection control measures. Future work should focus on developing more sensitive indicators of early outbreak detection in schools and evaluating the impact of school dismissal on community transmission.