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.

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.

Shiga Toxin-Producing Escherichia coli Outbreaks in the United States, 2010-2017.

Shiga toxin-producing Escherichia coli (STEC) cause illnesses ranging from mild diarrhea to ischemic colitis and hemolytic uremic syndrome (HUS); serogroup O157 is the most common cause. We describe the epidemiology and transmission routes for U.S. STEC outbreaks during 2010-2017. Health departments reported 466 STEC outbreaks affecting 4769 persons; 459 outbreaks had a serogroup identified (330 O157, 124 non-O157, 5 both). Among these, 361 (77%) had a known transmission route: 200 foodborne (44% of O157 outbreaks, 41% of non-O157 outbreaks), 87 person-to-person (16%, 24%), 49 animal contact (11%, 9%), 20 water (4%, 5%), and 5 environmental contamination (2%, 0%). The most common food category implicated was vegetable row crops. The distribution of O157 and non-O157 outbreaks varied by age, sex, and severity. A significantly higher percentage of STEC O157 than non-O157 outbreaks were transmitted by beef (p = 0.02). STEC O157 outbreaks also had significantly higher rates of hospitalization and HUS (p < 0.001).

Disparities in Incidence and Severity of Shigella Infections Among Children-Foodborne Diseases Active Surveillance Network (FoodNet), 2009-2018.

BACKGROUND: Shigella infections are an important cause of diarrhea in young children and can result in severe complications. Disparities in Shigella infections are well documented among US adults. Our objective was to characterize disparities in incidence and severity of Shigella infections among US children. METHODS: We analyzed laboratory-diagnosed Shigella infections reported to FoodNet, an active, population-based surveillance system in 10 US sites, among children during 2009-2018. We calculated the incidence rate stratified by sex, age, race/ethnicity, Shigella species, and disease severity. Criteria for severe classification were hospitalization, bacteremia, or death. The odds of severe infection were calculated using logistic regression. RESULTS: During 2009-2018, 10 537 Shigella infections were reported in children and 1472 (14.0%) were severe. The incidence rate was 9.5 infections per 100 000 child-years and the incidence rate of severe infections was 1.3 per 100 000 child-years. Incidence was highest among children aged 1-4 years (19.5) and lowest among children aged 13-17 years (2.3); however, children aged 13-17 years had the greatest proportion of severe infections (21.2%). Incidence was highest among Black (16.2 total; 2.3 severe), Hispanic (13.1 total; 2.3 severe), and American Indian/Alaska Native (15.2 total; 2.5 severe) children. Infections caused by non-sonnei species had higher odds of severity than infections caused by Shigella sonnei (adjusted odds ratio 2.58; 95% confidence interval 2.12-3.14). CONCLUSIONS: The incidence and severity of Shigella infections among US children vary by age, race/ethnicity, and Shigella species, warranting investigation of unique risk factors among pediatric subpopulations.

Outbreaks Associated with Untreated Recreational Water - California, Maine, and Minnesota, 2018-2019.

Outbreaks associated with fresh or marine (i.e., untreated) recreational water can be caused by pathogens or chemicals, including toxins. Voluntary reporting of these outbreaks to CDC's National Outbreak Reporting System (NORS) began in 2009. NORS data for 2009-2017 are finalized, and data for 2018-2019 are provisional. During 2009-2019 (as of May 13, 2020), public health officials from 31 states voluntarily reported 119 untreated recreational water-associated outbreaks, resulting at least 5,240 cases; 103 of the outbreaks (87%) started during June-August. Among the 119 outbreaks, 88 (74%) had confirmed etiologies. The leading etiologies were enteric pathogens: norovirus (19 [22%] outbreaks; 1,858 cases); Shiga toxin-producing Escherichia coli (STEC) (19 [22%]; 240), Cryptosporidium (17 [19%]; 237), and Shigella (14 [16%]; 713). This report highlights three examples of outbreaks that occurred during 2018-2019, were caused by leading etiologies (Shigella, norovirus, or STEC), and demonstrate the wide geographic distribution of such outbreaks across the United States. Detection and investigation of untreated recreational water-associated outbreaks are challenging, and the sources of these outbreaks often are not identified. Tools for controlling and preventing transmission of enteric pathogens through untreated recreational water include epidemiologic investigations, regular monitoring of water quality (i.e., testing for fecal indicator bacteria), microbial source tracking, and health policy and communications (e.g., observing beach closure signs and not swimming while ill with diarrhea).

Preliminary Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food - Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2016-2019.

To evaluate progress toward prevention of enteric illnesses, the Foodborne Diseases Active Surveillance Network (FoodNet) of CDC's Emerging Infections Program monitors the incidence of laboratory-diagnosed infections caused by eight pathogens transmitted commonly through food at 10 U.S. sites.* This report summarizes preliminary 2019 data and describes changes in incidence compared with that during 2016-2018. The incidence of enteric infections caused by these eight pathogens reported by FoodNet sites in 2019 continued to increase or remained unchanged, indicating progress in controlling major foodborne pathogens in the United States has stalled. Campylobacter and Salmonella caused the largest proportion of illnesses; trends in incidence varied by Salmonella serotype. Widespread adoption of whole genome sequencing (WGS) of bacteria has improved the ability to identify outbreaks, emerging strains, and sources of pathogens. To maximize the potential of WGS to link illnesses to particular sources, testing of isolates by clinical and public health laboratories is needed. Reductions in Salmonella serotype Typhimurium suggest that targeted interventions (e.g., vaccinating chickens and other food animals) might decrease human infections. Reducing contamination during food production, processing, and preparation will require more widespread implementation of known prevention measures and of new strategies that target particular pathogens and serotypes.

Preliminary Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food - Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2015-2018.

Foodborne diseases represent a major health problem in the United States. The Foodborne Diseases Active Surveillance Network (FoodNet) of CDC's Emerging Infections Program monitors cases of laboratory-diagnosed infection caused by eight pathogens transmitted commonly through food in 10 U.S. sites.* This report summarizes preliminary 2018 data and changes since 2015. During 2018, FoodNet identified 25,606 infections, 5,893 hospitalizations, and 120 deaths. The incidence of most infections is increasing, including those caused by Campylobacter and Salmonella, which might be partially attributable to the increased use of culture-independent diagnostic tests (CIDTs). The incidence of Cyclospora infections increased markedly compared with 2015-2017, in part related to large outbreaks associated with produce (1). More targeted prevention measures are needed on produce farms, food animal farms, and in meat and poultry processing establishments to make food safer and decrease human illness.

Exploration of veterinary shortages in the wake of the Veterinary Feed Directive.

OBJECTIVE To identify geographic areas in the United States where food animal veterinary services may be insufficient to meet increased needs associated with the US FDA's Veterinary Feed Directive. DESIGN Cross-sectional study. SAMPLE Data collected between 2010 and 2016 from the US Veterinary Medicine Loan Repayment Program, the National Animal Health Monitoring System Small-Scale US Livestock Operations Study, and the USDA's National Veterinary Accreditation Program. PROCEDURES Each dataset was analyzed separately to identify geographic areas with greatest potential for veterinary shortages. Geographic information systems methods were used to identify co-occurrence among the datasets of counties with veterinary shortages. RESULTS Analysis of the loan repayment program, Small-Scale Livestock Operations Study, and veterinary accreditation datasets revealed veterinary shortages in 314, 346, and 117 counties, respectively. Of the 3,140 counties in the United States during the study period, 728 (23.2%) counties were identified as veterinary shortage areas in at least 1 dataset. Specifically, 680 counties were identified as shortage areas in 1 dataset, 47 as shortage areas in 2 datasets, and 1 Arizona county as a shortage area in all 3 datasets. Arizona, Kentucky, Missouri, South Dakota, and Virginia had ≥ 3 counties identified as shortage areas in ≥ 2 datasets. CONCLUSIONS AND CLINICAL RELEVANCE Many geographic areas were identified across the United States where food animal veterinary services may be inadequate to implement the Veterinary Feed Directive and meet other producer needs. This information can be used to assess the impact of federal regulations and programs and help understand the factors that influence access to food animal veterinary services in specific geographic areas.

Rocky mountain spotted fever characterization and comparison to similar illnesses in a highly endemic area-Arizona, 2002-2011.

BACKGROUND: Rocky Mountain spotted fever (RMSF) has emerged as a significant cause of morbidity and mortality since 2002 on tribal lands in Arizona. The explosive nature of this outbreak and the recognition of an unexpected tick vector, Rhipicephalus sanguineus, prompted an investigation to characterize RMSF in this unique setting and compare RMSF cases to similar illnesses. METHODS: We compared medical records of 205 patients with RMSF and 175 with non-RMSF illnesses that prompted RMSF testing during 2002-2011 from 2 Indian reservations in Arizona. RESULTS: RMSF cases in Arizona occurred year-round and peaked later (July-September) than RMSF cases reported from other US regions. Cases were younger (median age, 11 years) and reported fever and rash less frequently, compared to cases from other US regions. Fever was present in 81% of cases but not significantly different from that in patients with non-RMSF illnesses. Classic laboratory abnormalities such as low sodium and platelet counts had small and subtle differences between cases and patients with non-RMSF illnesses. Imaging studies reflected the variability and complexity of the illness but proved unhelpful in clarifying the early diagnosis. CONCLUSIONS: RMSF epidemiology in this region appears different than RMSF elsewhere in the United States. No specific pattern of signs, symptoms, or laboratory findings occurred with enough frequency to consistently differentiate RMSF from other illnesses. Due to the nonspecific and variable nature of RMSF presentations, clinicians in this region should aggressively treat febrile illnesses and sepsis with doxycycline for suspected RMSF.

Risk factors for fatal outcome from rocky mountain spotted Fever in a highly endemic area-Arizona, 2002-2011.

BACKGROUND: Rocky Mountain spotted fever (RMSF) is a disease that now causes significant morbidity and mortality on several American Indian reservations in Arizona. Although the disease is treatable, reported RMSF case fatality rates from this region are high (7%) compared to the rest of the nation (<1%), suggesting a need to identify clinical points for intervention. METHODS: The first 205 cases from this region were reviewed and fatal RMSF cases were compared to nonfatal cases to determine clinical risk factors for fatal outcome. RESULTS: Doxycycline was initiated significantly later in fatal cases (median, day 7) than nonfatal cases (median, day 3), although both groups of case patients presented for care early (median, day 2). Multiple factors increased the risk of doxycycline delay and fatal outcome, such as early symptoms of nausea and diarrhea, history of alcoholism or chronic lung disease, and abnormal laboratory results such as elevated liver aminotransferases. Rash, history of tick bite, thrombocytopenia, and hyponatremia were often absent at initial presentation. CONCLUSIONS: Earlier treatment with doxycycline can decrease morbidity and mortality from RMSF in this region. Recognition of risk factors associated with doxycycline delay and fatal outcome, such as early gastrointestinal symptoms and a history of alcoholism or chronic lung disease, may be useful in guiding early treatment decisions. Healthcare providers should have a low threshold for initiating doxycycline whenever treating febrile or potentially septic patients from tribal lands in Arizona, even if an alternative diagnosis seems more likely and classic findings of RMSF are absent.

Forewarning of poliovirus outbreaks in the Horn of Africa: an assessment of acute flaccid paralysis surveillance and routine immunization systems in Kenya.

BACKGROUND: Although the Horn of Africa region has successfully eliminated endemic poliovirus circulation, it remains at risk for reintroduction. International partners assisted Kenya in identifying gaps in the polio surveillance and routine immunization programs, and provided recommendations for improved surveillance and routine immunization during the health system decentralization process. METHODS: Structured questionnaires collected information about acute flaccid paralysis (AFP) surveillance resources, training, data monitoring, and supervision at provincial, district, and health facility levels. The routine immunization program information collected included questions about vaccine and resource availability, cold chain, logistics, health-care services and access, outreach coverage data, microplanning, and management and monitoring of AFP surveillance. RESULTS: Although AFP surveillance met national performance standards, widespread deficiencies and limited resources were observed and reported at all levels. Deficiencies were related to provider knowledge, funding, training, and supervision, and were particularly evident at the health facility level. CONCLUSIONS: Gap analysis assists in maximizing resources and capacity building in countries where surveillance and routine immunization lag behind other health priorities. Limited resources for surveillance and routine immunization systems in the region indicate a risk for additional outbreaks of wild poliovirus and other vaccine-preventable illnesses. Monitoring and evaluation of program strengthening activities are needed.

Trends in encephalitis-associated deaths in the United States, 1999-2008.

BACKGROUND: While encephalitis may be caused by numerous infectious, immune and toxic processes, the etiology often remains unknown. METHODS: We analyzed multiple cause-of-death mortality data during 1999-2008 for the USA, using the 10th revision of International Classification of Diseases codes for encephalitis, listed anywhere on the death record, including 'specified' and 'unspecified' encephalitis. Annual and average annual age-adjusted and age-specific death rates were calculated. RESULTS: For 1999-2008, 12,526 encephalitis-associated deaths were reported with 68.5% as unspecified encephalitis. The average annual age-adjusted encephalitis-associated death rate was 4.3 per 1 million persons, 1.3 for specified and 2.9 for unspecified encephalitis. Annual encephalitis-associated death rates had a significant downward trend (p < 0.01). The most common specified encephalitis deaths were herpesviral encephalitis (36.7%), Toxoplasma meningoencephalitis (27.8%) and Listeria meningitis/meningoencephaltis (6.8%). HIV was colisted with 15.0% of encephalitis-associated deaths, 58.4% of these with a specified code. CONCLUSION: Encephalitis-associated death rates decreased during 1999-2008, and herpesvirus was the most commonly identified infectious agent associated with encephalitis deaths. The high proportion of unspecified encephalitis deaths highlights the continued challenge of laboratory confirmation for causes of encephalitis and the importance of monitoring trends to assess the impact of new diagnostics and guide potential interventions.

Enhancing health care worker ability to detect and care for patients with monkeypox in the Democratic Republic of the Congo.

BACKGROUND: Monkeypox (MPX) is an endemic disease of public health importance in the Democratic Republic of the Congo (DRC). In 2010, the DRC Ministry of Health joined with external partners to improve MPX surveillance in the Tshuapa Health District of DRC. A pivotal component of the program is training of health zone personnel in surveillance methods and patient care. In this report we evaluate outcomes of the training program. METHODS: Health care worker knowledge of key concepts in the MPX training curriculum was assessed using an anonymous self-administered survey. Additionally, evaluators collected feedback about the capacity of participants to perform the surveillance tasks. Training impacts were determined by assessing various surveillance performance metrics. RESULTS: Correct trainee responses to questions about MPX symptoms and patient care increased significantly upon completion of training events. During the 12 months after the initial training, the proportion of suspected cases investigated increased significantly (from 6.7 to 37.3%), as compared to the 5 months prior. However, the proportion of reported cases that were ultimately confirmed remained unchanged, 20.1% (5/24) vs 23.3% (60/257). CONCLUSIONS: We have demonstrated that the MPX curriculum developed for this initiative was effective in transferring knowledge and was associated with improved detection of human MPX cases.

Evaluation of knowledge, attitudes, and practices of deer owners following identification of a cluster of captive deer with rabies in Pennsylvania in July 2010.

OBJECTIVE: To evaluate knowledge, attitudes, and practices of deer owners following identification of a cluster of captive deer with rabies as an aid for the development of rabies prevention educational materials. DESIGN: Cross-sectional study. POPULATION: Captive-deer owners who were members of the pennsylvania deer farmers association. PROCEDURES: Information was obtained via a mailed, self-administered questionnaire. RESULTS: The questionnaire response rate was 59% (249/425). One hundred three of 206 (50%) respondents had incomplete knowledge of rabies virus vectors, transmission, severity, and prevention measures. Birds or snakes were incorrectly identified as rabies vectors by 96 of 213 (45%) respondents, and most (≥ 94%) respondents identified rabies virus reservoirs as vectors. Ninety of 231 (39%) respondents identified death as an outcome of rabies, and 184 of 235 (78%) respondents would seek emergency treatment if they suspected exposure. Only 62 of 235 (26%) respondents would wash a wound immediately. The majority of respondents (173/239 [72%]) did not know the clinical signs of rabies in deer. Nine respondents indicated that they vaccinated their deer against rabies, and the majority of respondents (158/214 [74%]) would be willing to vaccinate. CONCLUSIONS AND CLINICAL RELEVANCE: Findings suggested that deer owners in Pennsylvania have a basic knowledge of rabies; however, knowledge, attitudes, and practices regarding prevention of rabies transmission could be improved considerably. Rabies educational materials for deer owners should focus on postexposure procedures, disease severity, recognition of rabies in deer, and changes in management practices such as vaccination to prevent rabies.

Unintentional transfer of vaccinia virus associated with smallpox vaccines: ACAM2000(®) compared with Dryvax(®).

BACKGROUND: Routine vaccination against smallpox (variola) ceased in the US in 1976. However, in 2002 limited coverage for military personnel and some healthcare workers was reinstituted. In March 2008, ACAM2000® replaced Dryvax® as the vaccine used in the United States against smallpox. Unintentional transfer of vaccinia virus from a vaccination site by autoinoculation or contact transmission, can have significant public health implications. We summarize unintentional virus transfer AEs associated with ACAM2000® since March 2008 and compare with Dryvax®. RESULTS: We identified 309 reports for ACAM2000® with skin or ocular involvement, of which 93 were autoinoculation cases and 20 were contact transmission cases. The rate for reported cases of autoinoculation was 20.6 per 100,000 vaccinations and for contact transmission was 4.4 per 100,000 vaccinations. Eighteen contact transmission cases could be attributed to contact during a sporting activity (45%) or intimate contact (45%). Of the 113 unintentional transfer cases, 6 met the case definition for ocular vaccinia. The most common locations for all autoinoculation and contact cases were arm/elbow/shoulder (35/113; 31%) and face (24/113; 21%). Methods We reviewed 753 reports associated with smallpox in the Vaccine Adverse Event Reporting System and CDC Poxvirus consultation log, reported from March 2008 to August 2010. Reports were classified into categories based upon standard case definitions. CONCLUSION: Overall, unintentional transfer events for ACAM2000® and Dryvax® are similar. We recommend continued efforts to prevent transfer events and continuing education for healthcare providers focused on recognition of vaccinia lesions, proper sample collection, and laboratory testing to confirm diagnosis.

Rabies in captive deer, Pennsylvania, USA, 2007-2010.

Since January 2007, a total of 11 rabid deer from 4 deer farms have been identified in 2 neighboring Pennsylvania counties. Vaccination of deer against rabies, decreasing wildlife animal contact with deer, and education of deer farmers may prevent further cases of rabies in captive deer and exposures to humans.

Zoonotic Poxviruses Associated with Companion Animals.

Understanding the zoonotic risk posed by poxviruses in companion animals is important for protecting both human and animal health. The outbreak of monkeypox in the United States, as well as current reports of cowpox in Europe, point to the fact that companion animals are increasingly serving as sources of poxvirus transmission to people. In addition, the trend among hobbyists to keep livestock (such as goats) in urban and semi-urban areas has contributed to increased parapoxvirus exposures among people not traditionally considered at high risk. Despite the historic notoriety of poxviruses and the diseases they cause, poxvirus infections are often missed. Delays in diagnosing poxvirus-associated infections in companion animals can lead to inadvertent human exposures. Delays in confirming human infections can result in inappropriate treatment or prolonged recovery. Early recognition of poxvirus-associated infections and application of appropriate preventive measures can reduce the spread of virus between companion animals and their owners. This review will discuss the epidemiology and clinical features associated with the zoonotic poxvirus infections most commonly associated with companion animals.