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.

Antimicrobial-Resistant Nontyphoidal Salmonella Infection Following International Travel-United States, 2018-2019.

BACKGROUND: Antimicrobial resistance in nontyphoidal Salmonella (NTS) can limit treatment options. We assessed the contribution of international travel to antimicrobial-resistant NTS infections. METHODS: We describe NTS infections that were reported to the Foodborne Diseases Active Surveillance Network during 2018-2019 and screened for genetic resistance determinants, including those conferring decreased susceptibility to first-line agents (ciprofloxacin, ceftriaxone, or azithromycin). We used multivariable logistic regression to assess the association between resistance and international travel during the 7 days before illness began. We estimated the contribution of international travel to resistance using population-attributable fractions, and we examined reported antimicrobial use. RESULTS: Among 9301 NTS infections, 1159 (12%) occurred after recent international travel. Predicted resistance to first-line antimicrobials was more likely following travel; the adjusted odds ratio varied by travel region and was highest after travel to Asia (adjusted odds ratio, 7.2 [95% confidence interval, 5.5-9.5]). Overall, 19% (95% confidence interval, 17%-22%) of predicted resistance to first-line antimicrobials was attributable to international travel. More travelers than nontravelers receiving ciprofloxacin or other fluoroquinolones had isolates with predicted resistance to fluoroquinolones (29% vs 9%, respectively; P < .01). CONCLUSIONS: International travel is a substantial risk factor for antimicrobial-resistant NTS infections. Understanding risks of resistant infection could help target prevention efforts.

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.

Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 in High-Density Settings, Minnesota, USA, March-June 2020.

Coronavirus disease has disproportionately affected persons in congregate settings and high-density workplaces. To determine more about the transmission patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in these settings, we performed whole-genome sequencing and phylogenetic analysis on 319 (14.4%) samples from 2,222 SARS-CoV-2-positive persons associated with 8 outbreaks in Minnesota, USA, during March-June 2020. Sequencing indicated that virus spread in 3 long-term care facilities and 2 correctional facilities was associated with a single genetic sequence and that in a fourth long-term care facility, outbreak cases were associated with 2 distinct sequences. In contrast, cases associated with outbreaks in 2 meat-processing plants were associated with multiple SARS-CoV-2 sequences. These results suggest that a single introduction of SARS-CoV-2 into a facility can result in a widespread outbreak. Early identification and cohorting (segregating) of virus-positive persons in these settings, along with continued vigilance with infection prevention and control measures, is imperative.

Decreased Susceptibility to Azithromycin in Clinical Shigella Isolates Associated with HIV and Sexually Transmitted Bacterial Diseases, Minnesota, USA, 2012-2015.

Shigellosis outbreaks caused by Shigella with decreased susceptibility to azithromycin (DSA-Shigella) among men who have sex with men (MSM) have been reported worldwide. We describe sexual health indicators and antimicrobial drug resistance for shigellosis cases in Minnesota, USA. We analyzed a sample of isolates received during 2012-2015 and cross-referenced cases with the Minnesota Department of Health Sexually Transmitted Disease Database to ascertain patients' HIV status and recent chlamydia, gonorrhea, and syphilis infections. Of 691 Shigella isolates, 46 (7%) were DSA-Shigella; 91% of DSA-Shigella patients were men, of whom 60% were living with HIV. Among men, those with DSA-Shigella infection had greater odds of living with HIV, identifying as MSM, or having a recent diagnosis of a sexually transmitted disease. DSA-Shigella was associated with MSM, HIV infection, and recent sexually transmitted disease. To decrease spread of DSA-Shigella, interventions targeted at communities at high risk are needed.

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.

Can Aggregated Restaurant Inspection Data Help Us Understand Why Individual Foodborne Illness Outbreaks Occur?

ABSTRACT: Restaurant inspections seek to identify and correct risk factors for foodborne illness, but restaurant inspection data are not typically used more broadly as a food safety surveillance tool. In 2015, there was an outbreak of Salmonella serotype Newport infections associated with multiple restaurants in a chain (chain A), primarily in Minnesota. The outbreak was associated with tomatoes that were likely contaminated at the point of production. The objective of this study was to demonstrate the potential usefulness of aggregated restaurant inspection data in aiding individual outbreak investigations. Reports of the last inspection for all chain A restaurants that preceded the first reported case meal date in the outbreak were obtained from local health departments and the Minnesota Department of Health. Ordinal logistic regression was used to assess differences in risk factor and good retail practice violation categories and specific violations in restaurants with zero cases (nonoutbreak restaurants) (n = 25), one to two cases (n = 16), and at least three cases (n = 13). For restaurants with a "protection from contamination" violation in the routine inspection that preceded the outbreak, the proportional odds ratio for outbreak level was 4.92 (95% confidence interval: 1.57, 15.39; P = 0.01). These findings suggest that food handling practices in the outbreak restaurants may have increased contamination of foods through cross-contamination, which in turn increased transmission at outbreak restaurants. These data suggest that aggregated data from routine inspection reports can provide useful information to aid in outbreak investigations and other foodborne illness surveillance and prevention activities.

Multistate Outbreak of Salmonella Virchow Infections Linked to a Powdered Meal Replacement Product-United States, 2015-2016.

Background: Nontyphoidal Salmonella is the leading cause of bacterial gastroenteritis in the United States. Meal replacement products containing raw and "superfood" ingredients have gained increasing popularity among consumers in recent years. In January 2016, we investigated a multistate outbreak of infections with a novel strain of Salmonella Virchow. Methods: Cases were defined using molecular subtyping procedures. Commonly reported exposures were compared with responses from healthy people interviewed in the 2006-2007 FoodNet Population Survey. Firm inspections and product traceback and testing were performed. Results: Thirty-five cases from 24 states were identified; 6 hospitalizations and no deaths were reported. Thirty-one of 33 (94%) ill people interviewed reported consuming a powdered supplement in the week before illness; of these, 30 (97%) reported consuming product A, a raw organic powdered shake product consumed as a meal replacement. Laboratory testing isolated the outbreak strain of Salmonella Virchow from leftover product A collected from ill people's homes, organic moringa leaf powder (an ingredient in product A), and finished product retained by the firm. Firm inspections at 3 facilities linked to product A production did not reveal contamination at the facilities. Traceback investigation identified that the contaminated moringa leaf powder was imported from South Africa. Conclusions: This investigation identified a novel outbreak vehicle and highlighted the potential risk with similar products not intended to be cooked by consumers before consuming. The company issued a voluntary recall of all implicated products. As this product has a long shelf life, the recall likely prevented additional illnesses.

Notes from the Field: Outbreaks of Shigella sonnei Infection with Decreased Susceptibility to Azithromycin Among Men Who Have Sex with Men - Chicago and Metropolitan Minneapolis-St. Paul, 2014.

Increasing rates of shigellosis among adult males, particularly men who have sex with men (MSM), have been documented in the United States, Canada, and Europe, and MSM appear to be at greater risk for infection with shigellae that are not susceptible to ciprofloxacin or azithromycin. Azithromycin is the first-line empiric antimicrobial treatment for shigellosis among children and is a second-line treatment among adults. Isolates collected in 2014 in two U.S. cities from outbreaks of shigellosis displayed highly similar pulsed-field gel electrophoresis (PFGE) patterns and decreased susceptibility to azithromycin (DSA). This report summarizes and compares the findings from investigations of the two outbreaks, which occurred among MSM in metropolitan Minneapolis-St. Paul, Minnesota, and Chicago, Illinois.

Two concurrent enteric disease outbreaks among men who have sex with men, minneapolis-st paul area.

Between 1 November 2013 and 31 March 2014, concurrent shigellosis and cryptosporidiosis outbreaks occurred among men who have sex with men in the Minneapolis-St. Paul area, 75% of whom were HIV-infected. Current HIV/AIDS strategy emphasizing treatment as prevention may effectively decrease HIV transmission, but raises concerns about other diseases if safer sex messages are de-emphasized.