Association Of Public Health Laboratories Research Articles

Strengthening the US Public Health Lab System: Summary of Coronavirus Disease (COVID-19) After Action Review Workshop.

The COVID-19 pandemic highlighted the significance of public health laboratories across the United States, while also revealing weaknesses in the laboratory system. To identify actionable recommendations for building a more resilient public health laboratory system based on previously published lessons learned from COVID-19. In April 2023, the Association of Public Health Laboratories, in cooperation with RAND , convened a 1.5-day after action review workshop of approximately 30 public health laboratory stakeholders to reevaluate priorities, improve processes, and affect policies. Analysis of workshop discussions identified 5 priority areas and 19 recommendations related to clarifying laboratories' unique role and promoting workforce capacity/agility, technology, and collaboration with governmental and nongovernmental partners. Within the identified priority areas, workshop participants described how the recommendations would address challenges encountered during COVID-19 and contribute to strengthening the system. As the risk of novel infectious diseases persists and grows, the importance of maintaining laboratory response capabilities is likely to increase. Addressing the system's weaknesses will require active engagement of laboratories and the many stakeholders who depend on them, along with consistent, adequate funding to strengthen and sustain capabilities.

Investing in health preparedness, response and resilience: a genomics costing tool focused on next generation sequencing.

The world has seen unprecedented gains in the global genomic surveillance capacities for pathogens with pandemic and epidemic potential within the last 4 years. To strengthen and sustain the gains made, WHO is working with countries and partners to implement the Global Genomic Surveillance Strategy for Pathogens with Pandemic and Epidemic Potential 2022-2032. A key technical product developed through these multi-agency collaborative efforts is a genomics costing tool (GCT), as sought by many countries. This tool was developed by five institutions - Association of Public Health Laboratories, FIND, The Global Fund to Fight AIDS, Tuberculosis and Malaria, UK Health Security Agency, and the World Health Organization. These institutions developed the GCT to support financial planning and budgeting for SARS-CoV-2 next-generation sequencing activities, including bioinformatic analysis. The tool costs infrastructure, consumables and reagents, human resources, facility and quality management. It is being used by countries to (1) obtain costs of routine sequencing and bioinformatics activities, (2) optimize available resources, and (3) build an investment case for the scale-up or establishment of sequencing and bioinformatics activities. The tool has been validated and is available in English and Russian at https://www.who.int/publications/i/item/9789240090866. This paper aims to highlight the rationale for developing the tool, describe the process of the collaborative effort in developing the tool, and describe the utility of the tool to countries.

A simple undergraduate laboratory exercise for teaching the role of sentinel-level clinical microbiology testing in biological threat identification.

Undergraduate students in the biomedical sciences are mostly unaware of how clinical microbiology laboratories handle suspected agents of bioterrorism or emerging infectious diseases. The Public Health Security Bioterrorism Preparedness and Response Act of 2002 requires the US Department of Health and Human Services (HHS) to maintain a list of microbes that pose serious biological threats to human health and safety, including Tier 1 agents with the potential for use in bioterrorism. The Laboratory Response Network (LRN), founded by the Centers for Disease Control and Prevention, the Federal Bureau of Investigation, and the Association of Public Health Laboratories, coordinates the response of sentinel, reference, and national laboratories to these biothreats. The sentinel laboratories, which comprise most hospital-based and commercial laboratories, are the first to encounter a suspicious agent. For this reason, the LRN has published a series of testing guidelines to assist the sentinel laboratories in deciding whether a microbial isolate should be considered potentially hazardous and thus sent to a reference or national laboratory for further characterization. Here, we describe a simple laboratory exercise that teaches sentinel-level testing requirements in the context of an applied setting of a potential outbreak of anthrax that would require a sentinel laboratory to recognize a potential threat, attempt to rule it out, and refer to a national laboratory for identification.

Laboratory Criteria for Exclusion and Readmission of Potentially Infectious Persons in Sensitive Settings in the Age of Culture-Independent Diagnostic Tests: Report of a Multidisciplinary Workgroup

Culture-independent diagnostic tests (CIDTs) are increasingly used for clinical diagnosis of gastrointestinal diseases such as salmonellosis, Shiga toxin-producing E. coli disease, and shigellosis because of their speed, convenience, and generally high-performance characteristics. These tests are also used to screen potentially infectious asymptomatic persons during outbreak investigations in sensitive settings such as childcare, food service, and healthcare. However, only limited performance data are available for CIDTs used on specimens from asymptomatic persons. The Association of Public Health Laboratories (APHL) and Council of State and Territorial Epidemiologists (CSTE) convened a workgroup to examine the available scientific data to inform interim decision-making related to exclusion and readmission criteria for potentially infectious persons in sensitive settings, the risks and benefits of different testing strategies, and to identify knowledge gaps for further research. This is the report on the Workgroup findings.

Evaluation of Three Automated Nontreponemal Rapid Plasma Reagin (RPR) Tests for the Laboratory Diagnosis of Syphilis.

Automated nontreponemal rapid plasma reagin (RPR) tests were recently introduced in the United States for syphilis testing and limited performance data are available. In collaboration with the Association of Public Health Laboratories, three public health laboratories (PHL) were chosen through a competitive selection process to evaluate the performance of three FDA-cleared automated RPR test systems: BioPlex 2200 Syphilis Total & RPR assay (Bio-Rad Laboratories), AIX 1000 (Gold Standard Diagnostics), and ASI Evolution (Arlington Scientific). Panels prepared at the CDC included: a qualitative panel comprised of 734 syphilis reactive/nonreactive sera; a quantitative panel of 50 syphilis reactive sera (RPR titer 1:64 to 1:1,024); and a reproducibility panel of 15 nonreactive and reactive sera (RPR titer 1:1 to 1:64). Panels were shipped frozen to the PHL and tested on the automated RPR systems following manufacturers' instructions. Prior test results were blinded to all laboratories. When compared to manual RPR (Arlington Scientific) performed at the CDC as a reference test, the qualitative panel results demonstrated an overall concordance of 95.9% for AIX 1000, 94.6% for ASI Evolution, and 92.6% for Bioplex RPR; quantitative panel showed within range titer of 2-fold for 94% of specimens for AIX 1000, 68% for ASI Evolution, and 64% for BioPlex RPR, and the reproducibility testing panel demonstrated point estimates ranging from 69 to 95%. Automated RPR instruments could reduce turnaround time and minimize interpretation errors. However, additional evaluations with more specimens could assist laboratories with implementing automated RPR tests and understanding their limitations.

Developing an Online Dashboard to Visualize Performance Data-Tennessee Newborn Screening Experience.

Newborn screening (NBS) is a vital public health program and delays in the screening process can lead to catastrophic outcomes for infants and their families. Efforts to improve screening quality in Tennessee are proactive and ongoing. From these efforts, an open-access dashboard has been developed to address a need for methods to better visualize performance data, promote data transparency, and drive quality improvement. Dashboard development was a collaboration between a fellow from the Association of Public Health Laboratories (APHL) and Tennessee NBS staff. Iterative dashboard prototypes were developed using Tableau software and incorporated feedback from Tennessee birthing facility staff and health experts. Infrastructure and procedures were created to reduce the burden of future dashboards. Eight NBS performance indicators are visualized across several views. These views are designed to provide an overview of NBS performance data when first accessed, then allow for a drill-down into specific data. This dashboard drives introspection at the state and facility level, making it possible to identify potential issues and necessary corrective actions earlier, therefore improving the completeness and timeliness of NBS in Tennessee. The experiences from developing this dashboard can be applied to future dashboard development in Tennessee NBS and other public health programs implementing similar measures.

Electronic case reporting (eCR) of COVID-19 to public health: implementation perspectives from the Minnesota Department of Health.

Electronic case reporting (eCR) is the automated generation and transmission of case reports from electronic health records to public health for review and action. These reports (electronic initial case reports: eICRs) adhere to recommended exchange and terminology standards. eCR is a partnership of the Centers for Disease Control and Prevention (CDC), Association of Public Health Laboratories (APHL) and Council of State and Territorial Epidemiologists (CSTE). The Minnesota Department of Health (MDH) received eICRs for COVID-19 from April 2020 (3 sites, manual process), automated eCR implementation in August 2020 (7 sites), and on-boarded ∼1780 clinical units in 460 sites across 6 integrated healthcare systems (through March 2022). Approximately 20 000 eICRs/month were reported to MDH during high-volume timeframes. With increasing provider/health system implementation, the proportion of COVID-19 cases with an eICR increased to 30% (March 2022). Evaluation of data quality for select demographic variables (gender, race, ethnicity, email, phone, language) across the 6 reporting health systems revealed a high proportion of completeness (>80%) for half of variables and less complete data for rest (ethnicity, email, language) along with low ethnicity data (<50%) for one health system. Presently eCR implementation at MDH includes only one EHR vendor. Next steps will focus on onboarding other EHRs, additional eICR data extraction/utilization, detailed analysis, outreach to address data quality issues, and expanding to other reportable conditions.

Newborn Screening Practices for Beta-Thalassemia in the United States.

Beta-thalassemia, a heritable condition of abnormal hemoglobin production, is not a core condition on the United States Recommended Uniform Screening Panel (RUSP) for state and territorial newborn screening (NBS) programs. However, screening for sickle cell disease (which is on the core RUSP) also detects reduced or absent levels of hemoglobin (Hb) A and certain other Hb variants associated with beta-thalassemia and, thus, allows for a timely referral to appropriate healthcare to minimize sequalae of the disease. The Association of Public Health Laboratories’ Hemoglobinopathy Workgroup administered a comprehensive survey of all U.S. NBS programs to assess beta-thalassemia testing methodologies, the cutoffs for defining beta-thalassemia major, and the reporting and follow-up practices. Forty-six (87%) of the programs responded. Thirty-nine of the 46 responding programs (85%) report some form of suspected beta-thalassemia; however, the screening methods, the percentage of Hb A used as a cutoff for an indication of beta-thalassemia major, and the screening follow-up vary widely. The standardization of technical and reporting procedures may improve access to specialty care prior to severe complications, increase genetic counseling, and provide data needed to better understand the public health impact and clinical outcomes of beta-thalassemia in the United States.

Establishing a National Community of Practice for Newborn Screening Follow-Up.

Newborn screening (NBS) follow-up programs in the United States are managed at the state level, leaving limited opportunities for collaboration across programs and coordinated resource sharing. The Newborn Screening Technical assistance and Evaluation Program (NewSTEPs), a program of the Association of Public Health Laboratories (APHL), has established a national community of practice for NBS follow-up by creating a network of follow-up staff and stakeholders through education and engagement opportunities. The activities of NewSTEPs in support of NBS follow-up have strengthened information dissemination, collaboration, data collection and technical assistance-driven mentorship across the national system.

How To Prepare for the Unexpected: a Public Health Laboratory Response.

Public health laboratories (PHLs) continue to face internal and external challenges to their abilities to provide successful, timely responses to public health crises and emerging threats. These laboratories are mandated to maintain the health of their communities by identifying, diagnosing, and warning constituents of potential and real health emergencies. Due to the changing characteristics of public health threats and their cross-jurisdictional nature, laboratories are facing increased pressure to ensure that they respond in a consistent and coordinated manner. Here, the Association of Public Health Laboratories (APHL) Emerging Leader Program Cohort 11 members have compiled stories from subject matter experts (SMEs) at PHLs with direct involvement in crises to determine the characteristics of a successful response. Experts examined a diverse selection of emerging threats from across PHLs, including infectious diseases, opioids, natural disasters, and government shutdowns. While no public health crisis will be identical to another, overarching themes were consistent across subjects. Experiences from SMEs that could improve future responses to emerging threats are highlighted.

Improved detection of microbiological pathogens: role of partner and non-governmental organizations

BackgroundProper detection of disease-causing organisms is very critical in controlling the course of outbreaks and avoiding large-scale epidemics. Nonetheless, availability of resources to address these gaps have been difficult due to limited funding. This report sought to highlight the importance of in-country partners and non-governmental organizations in improving detection of microbiological organisms in Ghanaian Public Health Laboratories (PHLs).Methods/contextThis study was conducted between June, 2018 to August, 2019. U. S CDC engaged the Centre for Health Systems Strengthening (CfHSS) through the Association of Public Health Laboratories to design and implement strategies for strengthening three PHLs in Ghana. An assessment of the three PHLs was done using the WHO/CDS/CSR/ISR/2001.2 assessment tool. Based on findings from the assessments, partner organizations (CfHSS/APHL/CDC) serviced and procured microbiological equipment, laboratory reagents and logistics. CfHSS provided in-house mentoring and consultants to assist with capacity building in detection of epidemic-prone infectious pathogens by performing microbiological cultures and antimicrobial susceptibility tests.ResultsA total of 3902 samples were tested: blood (1107), urine (1742), stool (249) and cerebrospinal fluid (CSF) (804). All-inclusive, 593 pathogenic bacteria were isolated from blood cultures (70; 11.8%); urine cultures (356; 60%); stool cultures (19; 3.2%) and from CSF samples (148; 25%). The most predominant pathogens isolated from blood, urine and stool were Staphylococcus aureus (22/70; 31%), Escherichia coli (153/356; 43%) and Vibrio parahaemolyticus (5/19; 26.3%), respectively. In CSF samples, Streptococcus pneumoniae was the most frequent pathogen detected (80/148; 54.1%). New bacterial species such as Pastuerella pneumotropica, Klebsiella oxytoca, Vibrio parahaemolyticus, and Halfnia alvei were also identified with the aid of Analytical Profile Index (API) kits that were introduced as part of this implementation. Streptococcus pneumoniae and Neisseria meningitidis detections in CSF were highest during the hot dry season. Antimicrobial susceptibility test revealed high rate of S. aureus, K. pneumoniae and E. coli resistance to gentamicin (35–55%). In urine, E. coli was highly resistant to ciprofloxacin (39.2%) and ampicillin (34%).ConclusionDetection of epidemic-prone pathogens can be greatly improved if laboratory capacity is strengthened. In-country partner organizations are encouraged to support this move to ensure accurate diagnosis of diseases and correct antimicrobial testing.

Creating a Blueprint for the Future: Lessons Learned From Public Health Laboratories in the COVID-19 Response.

Public health laboratories have played a central role in the US response to COVID-19. Since the earliest days, myriad issues have impeded the laboratory community's ability to keep pace with the overwhelming demand for effective tests. In this article, the Association of Public Health Laboratories and a subset of its members examine the response to date and evaluate lessons learned from 4 main categories: testing surges, supplies, staffing, and regulations and policy. Within these categories, the authors offer recommendations intended both to improve the ongoing COVID-19 response and to strengthen planning for future outbreaks.

THE STATE OF BROWN CARPATHIAN AND BROWN CAUCASIAN CATTLE BREEDS ON FAO PROJECT TCP/RER/3604 “CONSERVATION AND DEVELOPMENT OF DUAL-PURPOSE CATTLE BREEDS IN EASTERN EUROPE”

During 2018–2019 Ukraine took part in the project of Food and Agriculture Organization (FAO) «Conservation and development of double-purpose cattle breeds in Eastern Europe» (TCP/RER/3604). The project covered Brown Carpathian and Brown Caucasian breeds of Armenia, Georgia and Ukraine. On the results of the project, experts from the FAO Regional Office for Europe and Central Asia, international experts prepared reports on gender, social and economic characteristics of the studied regions, genomic analysis of samples and provided recommendations for breeding in the regions with the breeds. It was considered expedient to present these results to the general scientific community.&#x0D; At each country FAO have chosen service-provider (organization), which should make survey on productive environment of targeted breed (in Ukraine – Brown Carpathian), conclude the general state of the breed, visit at least 100 farms where Caucasian/Carpathian Brown cattle breed was kept, collect information from 300 cows and 20 bulls, and genetic samples from at least 100 cows and 20 bulls kept for breeding. Service-provider in Ukraine was M.V.Zubets Institute of Animal Breeding and Genetics, NAAS.&#x0D; Scientists of M.V.Zubets Institute of Animal Breeding and Genetics and other sub-contracting organizations during February-June, 2019 investigated 265 heads of cattle in 31 villages 5 districts of the Transcarpathian region, phenotypically classified as Brown Carpathian breed, including 6 breeding bulls of mating age (1.5–2 years). Each animal was photographed, linearly descriptive features of the exterior were evaluated, the necessary body measurements were taken with the help of appropriate tools, live weight and constitutional features were determined, and samples were taken for genetic testing.&#x0D; A total of 554 hair samples were taken from the project (123 – from Armenia, 141 – from Georgia and 290 – from Ukraine).&#x0D; The basis for classifying the animals as Brown Carpathian was phenotypic examination and strict compliance with the main characteristics of the breed: uniform grey or brown colour with different shades of it, general conformation typical for the breed, lighter belt along the back, black muzzle with lighter hair around it, black hooves and horn tips, lighter "glasses" around the eyes, thick light hair inside outer ears.&#x0D; To form the genetic passport of the population, hair was selected from the tail switch of selected animals using equipment provided by FAO, sent to the laboratories of the International Atomic Energy Agency, Austria. In the laboratory in the district of Siebersdorf, DNA was isolated from the obtained samples, the genetic diversity of populations, the degree of inbreeding and their effective number, kinship between populations were assessed and the genetic structure and level of influence of other breeds were analysed.&#x0D; DNA was extracted from each hair follicle using a MasterPure kit (Biozym, Illumina, USA) according to the protocol of the Association of Public Health Laboratories (APHL). The isolated DNA was subjected to a two-step quality control procedure before preparation for wide-genome typing. DNA samples were measured using a Nanodrop spectrophotometer to obtain a concentration with a ratio of 260/280 and 260/230. According to the results obtained using a spectrophotometer, DNA samples were diluted to measure high-quality double-stranded DNA (dsDNA) by PicoGreen Assay. The final working DNA was prepared based on PicoGreen measurements and stored at – 20°C for further processing.&#x0D; Sample genotyping was performed using a third-generation 384-cell matrix to assess Bovine individuals on the Affymetrix-Axiom platform (Axiom Bovine Genotyping v3 array). Within the project, 48 individuals of Austrian Simmental and 18 – Ayrshire breeds were also genotyped for comparison. The matrix included 64.000 SNPs, providing a high probability of covering genomic variations of the Bos taurus and Bos indicus breeds.&#x0D; Intra-breed genetic diversity was assessed using PLINK v1.09 to calculate actual heterozygosity (H0) and inbreeding coefficient (FIS).&#x0D; Analysis of genetic parameters of population diversity evidenced a rather low inbreeding rate of Brown Carpathian breed and a fairly high effective population size compared to European breeds, which can indicate a very limited practice of artificial insemination and lack of selection among bulls.&#x0D; Analysis of genetic differentiation and relationship between populations, principal components analysis and determination of admixtures of other breeds proved the uniqueness of the Brown Carpathian breed from a genetic point of view.&#x0D; Based on the conducted genomic analysis of populations, consultations with project participants, reports of service providers of each country, an international consultant on animal genetic resources, chairman of the ICAR working group on functional traits, formed a breeding program for the studied populations. The breeding program included proposals for further selection work, calculation of basic selection-genetic parameters, selection effect, number of bulls and heifers for selection nucleus, number of doses to maintain genetic diversity of the population, cost of population restoration, breeding work of breeding centre and work plan by years to implement a breeding program.&#x0D; Gender analysis of service providers' reports showed some gender differentiation in livestock care, processing and everyday life of owners of Brown Carpathian cattle.

Population Heath Informatics Can Advance Interoperability: National Program of Cancer Registries Electronic Pathology Reporting Project.

Given the reach, breadth, and volume of data collected from multiple clinical settings and systems, US central cancer registries (CCRs) are uniquely positioned to test and advance cancer health information exchange. This article describes a current Centers for Disease Control and Prevention (CDC) National Program of Cancer Registries (NPCR) cancer informatics data exchange initiative. CDC is using an established cloud-based platform developed by the Association of Public Health Laboratories (APHL) for national notifiable disease reporting to enable direct transmission of standardized electronic pathology (ePath) data from laboratories to CCRs in multiple states. The APHL Informatics Messaging Services (AIMS) Platform provides an infrastructure to enable a large national laboratory to submit data to a single platform. State health departments receive data from the AIMS Platform through a secure portal, eliminating separate data exchange routes with each CCR. Key factors enabling ePath data exchange from laboratories to CCRs are having established cancer registry data standards and using a single platform/portal to reduce data streams. NPCR plans to expand this approach in alignment with ongoing cancer informatics efforts in clinical settings. The 50 CCRs supported by NPCR provide a variety of scenarios to develop and disseminate cancer data informatics initiatives and have tremendous potential to increase the implementation of cancer data exchange.

The Landscape of Severe Combined Immunodeficiency Newborn Screening in the United States in 2020: A Review of Screening Methodologies and Targets, Communication Pathways, and Long-Term Follow-Up Practices.

Severe combined immunodeficiency (SCID) is T cell development disorders in the immune system and can be detected at birth. As of December 2018, all 53 newborn screening (NBS) programs within the United States and associated territories offer universal screening for SCID. The Association of Public Health Laboratories (APHL), along with the Immune Deficiency Foundation (IDF), surveyed public health NBS system laboratory and follow-up coordinators regarding their NBS program’s screening methodologies and targets, protocols for stakeholder notifications, and long-term follow-up practices. This report explores the variation that exists across NBS practices, revealing needs for efficiencies and educational resources across the NBS system to ensure the best outcomes for newborns.

Newborn Screening Practices and Alpha-Thalassemia Detection - United States, 2016.

Alpha-thalassemia comprises a group of inherited disorders in which alpha-hemoglobin chain production is reduced. Depending on the genotype, alpha-thalassemia results in moderate to profound anemia, hemolysis, growth delays, splenomegaly, and increased risk for thromboembolic events; certain patients might require chronic transfusions. Although alpha-thalassemia is not a core condition of the United States Recommended Uniform Screening Panel* for state newborn screening programs, methodologies used by some newborn screening programs to detect sickle cell disease, which is a core panel condition, also detect a quantitative marker of alpha-thalassemia, hemoglobin (Hb) Bart's, an abnormal type of hemoglobin. The percentage of Hb Bart's detected correlates with alpha-thalassemia severity. The Association of Public Health Laboratories' Hemoglobinopathy Workgroup conducted a survey of state newborn screening programs' alpha-thalassemia screening methodologies and reporting and follow-up practices. Survey findings indicated that 41 of 44 responding programs (93%) report some form of alpha-thalassemia results and 57% used a two-method screening protocol. However, the percentage of Hb Bart's used for thalassemia classification, the types of alpha-thalassemia reported, and the recipients of this information varied widely. These survey findings highlight the opportunity for newborn screening programs to revisit their policies as they reevaluate their practices in light of the recently released guideline from the Clinical and Laboratory Standards Institute (CLSI) on Newborn Screening for Hemoglobinopathies (1). Although deferring to local programs for policies, the report used a cutoff of 25% Hb Bart's in its decision tree, a value many programs do not use. Standardization of screening and reporting might lead to more timely diagnoses and health care services and improved outcomes for persons with a clinically significant alpha-thalassemia.

Expanding Newborn Screening for Pompe Disease in the United States: The NewSTEPs New Disorders Implementation Project, a Resource for New Disorder Implementation.

Public health programs in the United States screen more than four million babies each year for at least 30 genetic disorders. The Health and Human Services (HHS) Advisory Committee on Heritable Disorders in Newborns and Children (ACHDNC) recommends the disorders for state newborn screening (NBS) programs to screen. ACHDNC updated the Recommended Uniform Screening Panel (RUSP) to include Pompe disease in March 2015. To support the expansion of screening for Pompe disease, the Association of Public Health Laboratories (APHL) proposed the Newborn Screening Technical assistance and Evaluation Program (NewSTEPs) New Disorders Implementation Project, funded by the HHS’ Health Resources and Services Administration (HRSA) Maternal and Child Health Bureau (MCHB). Through this project, APHL provided financial support to 15 state NBS programs to enable full implementation of screening for Pompe disease. As of April 27, 2020, nine of the 15 programs had fully implemented Pompe disease newborn screening and six programs are currently pursuing implementation. This article will discuss how states advanced to statewide implementation of screening for Pompe disease, the challenges associated with implementing screening for this condition, the lessons learned during the project, and recommendations for implementing screening for Pompe disease.

Genetic characterization of mumps viruses associated with the resurgence of mumps in the United States: 2015–2017

Despite high coverage with measles, mumps, and rubella vaccine in the United States, outbreaks of mumps occur in close contact settings such as schools, colleges, and camps. Starting in late 2015, outbreaks were reported from several universities, and by the end of 2017, greater than 13,800 cases had been reported nation-wide. In 2013, the CDC and the Association of Public Health Laboratories contracted four Vaccine Preventable Diseases Reference Centers (VPD-RCs) to perform real-time reverse transcription PCR (RT-qPCR) to detect mumps RNA in clinical samples and to determine the genotype. Twelve genotypes of mumps virus are currently recognized by the World Health Organization, and the standard protocol for genotyping requires sequencing the entire gene coding for the small hydrophobic (SH) protein. Phylogenetic analysis of the 1862 mumps samples genotyped from 2015 through 2017 showed that the overall diversity of genotypes detected was low. Only 0.8 % of the sequences were identified as genotypes C, H, J, or K, and 0.5 % were identified as vaccine strains in genotypes A or N, while most sequences (98.7 %) were genotype G. The majority of the genotype G sequences could be included into one of two large groups with identical SH sequences. Within genotype G, a small number of phylogenetically significant outlier sequences were associated with epidemiologically distinct chains of transmission. These results demonstrate that molecular and epidemiologic data can be used to track transmission pathways of mumps virus; however, the limited diversity of the SH sequences may be insufficient for resolving transmission in all outbreaks.

Testing for Sexually Transmitted Diseases in US Public Health Laboratories, 2016.

Background:Laboratory testing practices are an important part of sexually transmitted disease (STD) diagnosis and control. The goal of this article is to describe the volume and types of STD tests performed in public health laboratories (PHLs) in the United States in 2016.Methods:A total of 105 state and local PHLs who were members of the Association of Public Health Laboratories were invited to participate in a survey between May and August 2017. This web-based survey included questions on types of tests offered for different types of STDs, the number of tests offered in 2016, and number of samples that tested positive for each STD.Results:Eighty-one (77.1%) of 105 member PHLs responded. Overall in 2016, 2,242,728 Chlamydia trachomatis tests, 2,298,596 Neisseria gonorrhoeae (GC) tests, 1,235,037 Treponema pallidum (syphilis) tests, 177,571 Trichomonas vaginalis tests, 37,101 herpes simplex virus tests, and 8707 human papillomavirus tests were performed in 2016 in surveyed laboratories. Sixty-seven (82.7%) of PHLs offered C. trachomatis and GC nucleic acid amplification testing. Ninety percent of laboratories performed syphilis testing, 42% performed T. vaginalis testing, and 28.4% performed herpes simplex virus type–specific nucleic acid amplification testing. Few laboratories tested for human papillomavirus.Conclusions:This survey collected important information on PHL STD laboratory testing practices. Capacity for important reference laboratory testing, such as GC culture and antimicrobial susceptibility, are needed to support STD programs. Public health laboratories play a key role in STD screening, surveillance, and prevention by offering test methods that are not available at commercial laboratories. Funding constraints affect the resources available for STD screening and surveillance, and thus, it is important to continue to monitor testing practices and the capacity of PHLs to test for STDs.

PulseNet and the Changing Paradigm of Laboratory-Based Surveillance for Foodborne Diseases.

PulseNet, the National Molecular Subtyping Network for Foodborne Disease Surveillance, was established in 1996 through a collaboration with the Centers for Disease Control and Prevention; the US Department of Agriculture, Food Safety and Inspection Service; the US Food and Drug Administration; 4 state public health laboratories; and the Association of Public Health Laboratories. The network has since expanded to include 83 state, local, and food regulatory public health laboratories. In 2016, PulseNet was estimated to be helping prevent an estimated 270 000 foodborne illnesses annually. PulseNet is undergoing a transformation toward whole-genome sequencing (WGS), which provides better discriminatory power and precision than pulsed-field gel electrophoresis (PFGE). WGS improves the detection of outbreak clusters and could replace many traditional reference identification and characterization methods. This article highlights the contributions made by public health laboratories in transforming PulseNet's surveillance and describes how the transformation is changing local and national surveillance practices. Our data show that WGS is better at identifying clusters than PFGE, especially for clonal organisms such as Salmonella Enteritidis. The need to develop prioritization schemes for cluster follow-up and additional resources for both public health laboratory and epidemiology departments will be critical as PulseNet implements WGS for foodborne disease surveillance in the United States.