Public Health Investigation Research Articles

Improved genome assembly of Candida auris strain B8441 and annotation of B11205.

Candida auris is a fungal pathogen of significant worldwide concern, typically resistant to one or more antifungal drugs. We report a completed genome for clade Ia isolate B8441 and gene annotations of clade Ic isolate B11205. These resources will support public health investigations and population genomic studies of this pathogen.

Molecular Detection and Characterisation of Coxiella burnetii in Koala (Phascolarctos cinereus) Urogenital Tract Swabs.

Q fever is a zoonosis caused by Coxiella burnetii, primarily affecting those in close contact with domestic ruminants, the main source of human infection. Coxiella burnetii has also been detected in various wildlife species globally. In Australia, serological and molecular studies have shown exposure to and infection by C. burnetii in macropods, bandicoots, and koalas. However, the extent to which these species contribute to human infection remains unclear. An unpublished public health investigation into a Q fever case in a person involved in koala care could not conclusively link the infection to koalas due to the patient's broad animal exposure. This study aimed to explore the potential role of koalas in transmitting C. burnetii to humans by investigating the presence of C. burnetii DNA in urogenital tract (UGT) swabs from koalas. DNA was extracted from UGT swabs from koalas in three regions in New South Wales, Australia. An optimised multiplex qPCR assay detected C. burnetii DNA in 2 out of 225 samples (0.89%) at approximately 10 genome equivalents per reaction. Both positive samples amplified all three gene targets. MLVA genotyping identified two distinct C. burnetii genotypes previously isolated from Australian Q fever cases. These findings highlight the need for vaccination against Q fever for those in close contact with koalas.

A Scoping Review and Assessment of the Area-Level Composite Measures That Estimate Social Determinants of Health Across the United States

Objectives: Evidence-informed population health initiatives often leverage data from various sources, such as epidemiologic surveillance data and administrative datasets. Recent interest has arisen in using area-level composite measures describing a community’s social risks to inform the development and implementation of health policies, including payment reform initiatives. Our objective was to capture the breadth of available area-level composite measures that describe social determinants of health (SDH) and have potential for application in population health and policy work. Methods: We conducted a scoping review of the scientific literature from 2010 to 2022 to identify multifactorial indices and rankings reflected in peer-reviewed literature that estimate SDH and that have publicly accessible data sources. We discovered several additional composite measures incidental to the scoping review process. Literature searches for each composite measure aimed to contextualize common applications in public health investigations. Results: From 491 studies, we identified 31 composite measures and categorized them into 8 domains: environmental conditions and pollution, opportunity and infrastructure, deprivation and well-being, COVID-19, rurality, food insecurity, emergency response and community resilience, and health. Composite measures are applied most often as an independent variable associated with disparities, risk factors, and/or outcomes affecting individuals, populations, communities, and health systems. Conclusions: Area-level composite measures describing SDH have been applied to wide-ranging population health work. Social risk indicators may enable policy makers, evaluators, and researchers to better assess community risks and needs, thereby facilitating the evidence-informed development, implementation, and study of initiatives that aim to improve population health.

Impact of the COVID-19 pandemic on infectious diseases reporting.

COVID-19 pandemic had impacted the reporting of notifiable communicable diseases. Since the beginning of the pandemic and the introduction of relate public health measures, notifications for most notifiable diseases have declined compared to previous years. In this study, we aim to quantify the changes in the incidences of notifiable infectious diseases during and after the pandemic in Siracusa Local Health Authority, Italy. We collected and analysed the infectious disease notifications made in two different three-years periods, 2017-2019 and 2020-2022 in Siracusa Local Health Authority, Italy. Descriptive statistics were used to find the percentages and the 95% confidence interval (CI). Exact "F-tests" was performed to compare the mean values between the studied periods to evaluate the hypothesis that the number of reported cases would not differ significantly between the two periods. Significance was assessed at the p < 0.05 level. The total number of notifications significantly decreased by 69.3% in the pandemic period compared to the pre-pandemic one, with the highest reduction of air-borne transmission diseases (-86.5%), followed by food-borne diseases (-68.2%) and sexually transmitted diseases (-39.3%). Conversely, an increase in number of notifications was found only for legionellosis. The COVID-19 pandemic had the potential to influence communicable disease reporting at multiple points. While the effects could vary considerably, the results would be expected to reduce the number and the detection of notifiable cases. Included would be changes in exposures, diagnostic testing, reporting to public health agencies, and public health investigations.

In memory of Professor Henry Wilde, MD, FACP: infectious disease physician, clinical and public health investigator, and educator.

In memory of Professor Henry Wilde, MD, FACP: infectious disease physician, clinical and public health investigator, and educator.

Investigation of SARS-CoV-2 Infection among Companion Animals in Households with Confirmed Human COVID-19 Cases.

We aimed to characterize SARS-CoV-2 infection in companion animals living in households with COVID-19-positive people and understand the dynamics surrounding how these animals become infected. Public health investigators contacted households with at least one confirmed, symptomatic person with COVID-19 for study recruitment. Blood, nasal, and rectal swab specimens were collected from pet dogs and cats and a questionnaire was completed. Specimens were tested for SARS-CoV-2 by RT-PCR, and for neutralizing antibodies; genomic sequencing was performed on viral-positive samples. A total of 36.4% of 110 pets enrolled had evidence of infection with SARS-CoV-2. Pets were more likely to test positive if the pet was immunocompromised, and if more than one person in the home was positive for COVID-19. Among 12 multi-pet households where at least one pet was positive, 10 had at least one other pet test positive. Whole-genome sequencing revealed the genomes of viral lineages circulating in the community during the time of sample collection. Our findings suggest a high likelihood of viral transmission in households with multiple pets and when pets had very close interactions with symptomatic humans. Further surveillance studies are needed to characterize how new variants impact animals and to understand opportunities for infection and spillover in susceptible species.

Case series of vaping-associated lung illness related to use of nicotine-containing liquids

RATIONALE There is a limited description of cases of vaping-associated lung illness (VALI) associated with users that vape nicotine-based products. OBJECTIVES The objectives of this study were to describe a series of patients that had VALI related to use of nicotine products. METHODS Investigation of reported cases of VALI in the province of Québec, using chart review, public health investigation and analysis of vaping products when available. RESULTS Six VALI cases were reported and investigated in late Summer and Fall 2019. None of the cases used tetrahydrocannabinol (THC)-based vaping products. Three were former tobacco smokers while the rest were still actively smoking. Age ranged from 34 to 82 years old. Vaping products were analyzed for 2 patients, which did not reveal any vitamin E acetate. All cases had respiratory symptoms at presentation, 2 had gastro-intestinal symptoms and 3 had constitutional symptoms. Chest computed tomography (CT)-Scan showed ground glass opacities (GGO) for all 6 cases. Five patients were hospitalized and 2 patients were admitted to the intensive care unit. No patient died. One patient had repeated bouts of hospitalizations without much improvement until VALI was diagnosed. CONCLUSIONS In Quebec, in the second half of 2019, 6 confirmed or probable VALI cases were reported and associated with the use of e-cigarettes with nicotine and flavors only (without THC), suggesting that chemicals present in the vaping liquid and/or the device itself can cause the illness. Former smokers or active smokers may also be at increased risk of developing VALI.

Serogroup B Invasive Meningococcal Disease in Older Adults Identified by Genomic Surveillance, England, 2022-2023.

We report a cluster of serogroup B invasive meningococcal disease identified via genomic surveillance in older adults in England and describe the public health responses. Genomic surveillance is critical for supporting public health investigations and detecting the growing threat of serogroup B Neisseria meningitidis infections in older adults.

An AcciMap approach to analyse the Chinese melamine milk scandal

PurposeThe 2008 Chinese melamine milk scandal resulted in six reported fatalities and affected around 300,000 children, of whom 54,000 were hospitalised. Previous studies have used linear approaches to examine the root causes of the melamine milk scandal.Design/methodology/approachIn the present study, we applied a systems approach to the melamine milk scandal to identify the complex systems-level failures across the supply chain leading to the incident and why food fraud incidents such as this occurred in the dairy sector. Additionally, systemic failures associated with food fraud vulnerability factors were considered (i.e. opportunities, motivation and control measures).Findings48 contributory factors of influence were identified and grouped across six sociotechnical levels across the Chinese dairy system, from government to equipment and surroundings. Lack of vertical integration (processes and communication) contributed to the failure. When viewed from a broader perspective, the melamine milk scandal can be linked to a series of human errors and organisational issues associated with government bodies, the dairy supply chain, individual organisations and management decisions and individual actions of staff or processes.Practical implicationsThis approach is of value to policymakers and the industry as it supports public health investigations of food fraud incidents and proactive food safety management.Originality/valueTo the best of our knowledge, this is the first study to analyse a food safety or fraud incident using the AcciMap approach and the food fraud vulnerability assessment (FFVA) technique. AcciMap analysis is applied to both unintentional and intentional aspects of the incident.

Persistence of A-234 nerve agent on indoor surfaces

Understanding the fundamental physical characteristics of extremely toxic compounds and their behavior across different environments plays a crucial role in assessing their danger. Additionally, this knowledge informs the development of protocols for gathering forensic evidence related to harmful chemicals misuse. In 2018, former Russian spy Sergei Skripal and his daughter were poisoned in Salisbury, England, with a substance later identified as the unconventional nerve agent A-234. Contamination with the compound was found on items inside Skripal's home. The aim of this paper was to determine the persistence of A-234 on selected indoor surfaces. Ceramics, aluminum can, laminated chipboard, polyvinyl chloride (PVC) floor tile, polyethylene terephthalate (PET) bottle, acrylic paint and computer keyboard were used as matrices. The decrease in surface contamination and further fate of the compound was monitored for 12 weeks. Persistence determination involved optimizing the wipe sampling method. Simultaneously, evaporation from the surface and permeation of the contaminant into the matrix were closely monitored. The experimental findings indicate that the nerve agent exhibits remarkable persistence, particularly on impermeable surfaces. Notably, the process of A-234 evaporation plays a minor role in determining its fate, with detectable concentrations observed solely above solid, non-porous surfaces such as ceramics and aluminum can. The surface persistence half-life varied significantly, ranging from 12 min to 478 days, depending on the material. The article has implications for emergency response protocols, decontamination strategies, public health and crime scene investigations.

Human exposures to Brucella canis from a pregnant dog during an international flight: Public health risks, diagnostic challenges and future considerations.

This report documents the exposure of passengers and crew of a commercial international flight to the zoonotic pathogen Brucella canis after an infected dog aborted in the passenger cabin of the aircraft. This case demonstrates the challenges associated with brucellosis screening and the risks that airline personnel, airport employees and travellers face when animals with unrecognized zoonotic infections are transported. The public health investigation of this case was conducted by the Centers for Disease Control, the Illinois Department of Health and the Illinois Department of Agriculture, in collaboration with a local veterinary clinic and several academic and federal diagnostic laboratories. It included an extensive diagnostic evaluation of the dam and aborted foetuses to confirm a diagnosis of canine brucellosis. Passengers, airline personnel and staff from the veterinary clinic where the dogs were treated underwent risk assessments, and clinic staff also received detailed guidance regarding infection prevention practices. Animal shelters and breeding programs are recommended to screen dogs routinely for brucellosis, but it is not unusual for domestic or imported animals to have unknown health histories, including the dog's brucellosis status, at the time of purchase, adoption, or re-homing. Testing recommendations and requirements vary by state, making it challenging for state public health and animal health agencies to monitor and respond appropriately. This case highlights the importance of Brucella spp. screening in sexually intact dogs prior to breeding, purchase, or domestic or international transportation of the dogs. The transportation of pregnant dogs may present a previously unrecognized public health threat in addition to contributing to unnecessary stress and health risks for pregnant animals.

Large Clusters of Invasive emm49 Group A Streptococcus Identified Within Arizona Health Care Facilities Through Statewide Genomic Surveillance System, 2019-2021.

A statewide genomic surveillance system for invasive Group A Streptococcus was implemented in Arizona in June 2019, resulting in 1046 isolates being submitted for genomic analysis to characterize emm types and identify transmission clusters. Eleven of the 32 identified distinct emm types comprised >80% of samples, with 29.7% of all isolates being typed as emm49 (and its genetic derivative emm151). Phylogenetic analysis initially identified an emm49 genomic cluster of 4 isolates that rapidly expanded over subsequent months (June 2019 to February 2020). Public health investigations identified epidemiologic links with 3 different long-term care facilities, resulting in specific interventions. Unbiased genomic surveillance allowed for identification and response to clusters that would have otherwise remained undetected.

Lead exposure sources and public health investigations for children with elevated blood lead in England, 2014 to 2022.

Lead exposure at any concentration can adversely impact health, with children being more vulnerable to its effects. In England, children with an elevated blood lead concentration (BLC) are reported to Health Protection Teams (HPTs) for public health investigation. A detailed review of these cases has not yet been conducted. The objectives of this study were to describe the demographics, likely setting and sources of lead exposure, risk behaviours, public health investigations and outcomes for children aged <16 years with a BLC requiring public health action reported to HPTs between 2014-2022 in England. Data were collected via a lookback questionnaire and a live enhanced surveillance questionnaire. Data were deduplicated, cleaned and results summarised as numbers and percentages using R studio. A thematic analysis was conducted on qualitative responses to a question relating to problems experienced during case investigation. There were 340 cases in our study: the majority were aged 1-4 years old (53%) and male (69%). Ethnicity data was poorly recorded. A higher than expected proportion (31%) lived in the most deprived areas. Pica (76%) and learning difficulties (60%) were often present. Cases were primarily exposed to lead in the domestic setting (92%) with paint (43%) and soil (29%) the most common exposures. Most cases lived in rented accommodation (63%), with a higher proportion in social rentals (48%) than privately rented (37%). Case investigations were resource intensive and poor stakeholder engagement/response was most frequently identified as challenging by HPTs. Lead exposure is harmful to children and requires public health and clinical management, which can be complex and challenging. Prevention of lead exposure in children should be the focus of intervention efforts. Outreach, engagement and preventative work should focus on both renters and homeowners. Collecting ethnicity data consistently may enable identification of more specific groups at increased risk of lead exposure in England.

Racial, socioeconomic, and neighborhood characteristics in relation to COVID-19 severity of illness for adolescents and young adults.

This study tests the hypotheses that insurance status, race and ethnicity, and neighborhood characteristics are associated with hospital admission and severe health outcomes (Intensive Care Unit [ICU] admission and oxygen assistance) for youth and young adults who present to the emergency department (ED) with COVID-19 in a single, academic health system in Illinois, Rush University System for Health (RUSH). Demographic and clinical data from the electronic health record were collected for all 13- to 24-y-old patients seen at RUSH who tested positive for COVID-19 between March 2020 and 2021. Individual-level and neighborhood characteristics were analyzed to determine their association with hospital admission and severe health outcomes through generalized estimating equations. As of March 2021, 1,057 patients were seen in the ED within RUSH in which non-Hispanic White (odds ratio [OR], 2.96; 95% CI, 1.61-5.46; P = 0.001) and Hispanic (OR, 3.34; 95% CI, 1.84-6.10; P < 0.001) adolescents and youth were more likely to be admitted to the hospital compared with non-Hispanic Black/other adolescents and youth. Patients with public insurance or who were uninsured were less likely to be admitted to the ICU compared with those with private insurance (OR, 0.24; 95% CI, 0.09-0.64; P = 0.004). None of the neighborhood characteristics were significantly associated with hospital admission or severe health outcomes after adjusting for covariates. Our findings demonstrated that race and ethnicity were related to hospitalization, while insurance was associated with presentation severity due to COVID-19 for adolescents and young adults. These findings can aid public health investigators in understanding COVID-19 disparities among adolescents and young adults.

Occupation and Industry Data Quality Among Select Notifiable Conditions in Washington State.

Occupation and industry are basic data elements that, when collected during public health investigations, can be key to understanding patterns of disease transmission and developing effective prevention measures. To assess the completeness and quality of occupation and industry data among select notifiable conditions in Washington and discuss potential improvements to current data collection efforts. We evaluated occupation and industry data, collected by local health departments during routine case investigations, for 11 notifiable conditions, selected for inclusion based on an established or plausible link to occupational exposure. Confirmed cases of select notifiable conditions among Washington residents aged 16 to 64 years, for years 2019-2021. We calculated the percentage of cases among working-age adults reported as employed, the percentage with occupation and industry data collected, and the percentage assigned standard occupation and industry codes. We identified the most common responses for occupation and industry and challenges of assigning codes to those responses. Among the 11 conditions evaluated, one-third of cases aged 16 to 64 years were reported as employed. Among the cases reported as employed, 91.5% reported occupation data and 30.5% reported industry data. "Self-employed" was among the top responses for occupation, a response that does not describe a specific job and could not be assigned an occupation code. In the absence of additional information, 4 of the most common responses for industry could not be coded: "health care," "technology," "tech," and "food." Routine collection of informative occupation and industry data among working-age adults is largely absent from case investigations in Washington. Methods of data collection that improve quality while minimizing the burden of collection should be pursued. Suggestions for improving data quality are discussed.

A field‐based evaluation of portable XRF to screen for toxic metals in seafood products

AbstractPortable X‐Ray Fluorescence (XRF) has become increasingly popular where traditional laboratory methods are either impractical, time consuming, and/or too costly. While the Limit of Detection (LOD) is generally poorer for XRF compared to laboratory‐based methods, recent advances have improved XRF LODs and increased its potential for field‐based studies. Portable XRF can be used to screen food products for toxic elements such as lead (Pb), cadmium (Cd), mercury (Hg), arsenic (As), manganese, (Mn), zinc (Zn), and strontium (Sr). In this study, 23 seafood samples were analyzed using portable XRF in a home setting. After XRF measurements were completed in each home, the same samples were transferred to the laboratory for re‐analysis using microwave‐assisted digestion and Inductively Coupled Plasma Tandem Mass Spectrometry (ICP‐MS/MS). Four elements (Mn, Sr, As, and Zn) were quantifiable by XRF in most samples, and those results were compared to those obtained by ICP‐MS/MS. Agreement was judged reasonable for Mn, Sr, and As, but not for Zn. Discrepancies could be due to (1) the limited time available to prepare field samples for XRF, (2) the heterogeneous nature of “real samples” analyzed by XRF, and (3) the small beam spot size (~1 mm) of the XRF analyzer. Portable XRF is a cost‐effective screening tool for public health investigations involving exposure to toxic metals. It is important for practitioners untrained in XRF spectrometry to (1) recognize the limitations of portable instrumentation, (2) include validation data for each specific analyte(s) measured, and (3) ensure personnel have some training in sample preparation techniques for field‐based XRF analyses.

Increased reports of severe myocarditis associated with enterovirus infection in neonates, United Kingdom, 27 June 2022 to 26 April 2023.

Enteroviruses are a common cause of seasonal childhood infections. The vast majority of enterovirus infections are mild and self-limiting, although neonates can sometimes develop severe disease. Myocarditis is a rare complication of enterovirus infection. Between June 2022 and April 2023, twenty cases of severe neonatal enteroviral myocarditis caused by coxsackie B viruses were reported in the United Kingdom. Sixteen required critical care support and two died. Enterovirus PCR on whole blood was the most sensitive diagnostic test. We describe the initial public health investigation into this cluster and aim to raise awareness among paediatricians, laboratories and public health specialists.

The utility of SARS-CoV-2 genomic data for informative clustering under different epidemiological scenarios and sampling.

Clustering pathogen sequence data is a common practice in epidemiology to gain insights into the genetic diversity and evolutionary relationships among pathogens. We can find groups of cases with a shared transmission history and common origin, as well as identifying transmission hotspots. Motivated by the experience of clustering SARS-CoV-2 cases using whole genome sequence data during the COVID-19 pandemic to aid with public health investigation, we investigated how differences in epidemiology and sampling can influence the composition of clusters that are identified. We performed genomic clustering on simulated SARS-CoV-2 outbreaks produced with different transmission rates and levels of genomic diversity, along with varying the proportion of cases sampled. In single outbreaks with a low transmission rate, decreasing the sampling fraction resulted in multiple, separate clusters being identified where intermediate cases in transmission chains are missed. Outbreaks simulated with a high transmission rate were more robust to changes in the sampling fraction and largely resulted in a single cluster that included all sampled outbreak cases. When considering multiple outbreaks in a sampled jurisdiction seeded by different introductions, low genomic diversity between introduced cases caused outbreaks to be merged into large clusters. If the transmission and sampling fraction, and diversity between introductions was low, a combination of the spurious break-up of outbreaks and the linking of closely related cases in different outbreaks resulted in clusters that may appear informative, but these did not reflect the true underlying population structure. Conversely, genomic clusters matched the true population structure when there was relatively high diversity between introductions and a high transmission rate. Differences in epidemiology and sampling can impact our ability to identify genomic clusters that describe the underlying population structure. These findings can help to guide recommendations for the use of pathogen clustering in public health investigations.

Transmission of yellow fever vaccine virus through blood transfusion and organ transplantation in the USA in 2021: report of an investigation

In 2021, four patients who had received solid organ transplants in the USA developed encephalitis beginning 2-6 weeks after transplantation from a common organ donor. We describe an investigation into the cause of encephalitis in these patients. From Nov 7, 2021, to Feb 24, 2022, we conducted a public health investigation involving 15 agencies and medical centres in the USA. We tested various specimens (blood, cerebrospinal fluid, intraocular fluid, serum, and tissues) from the organ donor and recipients by serology, RT-PCR, immunohistochemistry, metagenomic next-generation sequencing, and host gene expression, and conducted a traceback of blood transfusions received by the organ donor. We identified one read from yellow fever virus in cerebrospinal fluid from the recipient of a kidney using metagenomic next-generation sequencing. Recent infection with yellow fever virus was confirmed in all four organ recipients by identification of yellow fever virus RNA consistent with the 17D vaccine strain in brain tissue from one recipient and seroconversion after transplantation in three recipients. Two patients recovered and two patients had no neurological recovery and died. 3 days before organ procurement, the organ donor received a blood transfusion from a donor who had received a yellow fever vaccine 6 days before blood donation. This investigation substantiates the use of metagenomic next-generation sequencing for the broad-based detection of rare or unexpected pathogens. Health-care workers providing vaccinations should inform patients of the need to defer blood donation for at least 2 weeks after receiving a yellow fever vaccine. Despite mitigation strategies and safety interventions, a low risk of transfusion-transmitted infections remains. US Centers for Disease Control and Prevention (CDC), the Biomedical Advanced Research and Development Authority, and the CDC Epidemiology and Laboratory Capacity Cooperative Agreement for Infectious Diseases.

Detection of Hantavirus during the COVID-19 Pandemic, Arizona, USA, 2020.

We identified 2 fatal cases of persons infected with hantavirus in Arizona, USA, 2020; 1 person was co-infected with SARS-CoV-2. Delayed identification of the cause of death led to a public health investigation that lasted ≈9 months after their deaths, which complicated the identification of a vector or exposure.