A novel hybridization capture method for direct whole genome sequencing of clinical specimens to inform Legionnaires' disease investigations

The unprecedented precision and resolution of whole genome sequencing (WGS) can provide definitive identification of infectious agents for epidemiological outbreak tracking. WGS approaches, however, are frequently impeded by low pathogen DNA recovery from available primary specimens or unculturable samples. A cost-effective hybrid capture assay for Legionella pneumophila WGS analysis directly on primary specimens was developed. DNA from a diverse range of sputum and autopsy specimens PCR-positive for L. pneumophila serogroup 1 (LPSG1) was enriched with this method, and WGS was performed. All tested specimens were determined to be enriched for Legionella reads (up to 209,000-fold), significantly improving the discriminatory power to compare relatedness when no clinical isolate was available. We found the WGS data from some enriched specimens to differ by less than five single-nucleotide polymorphisms (SNPs) when compared to the WGS data of a matched culture isolate. This testing and analysis retrospectively provided previously unconfirmed links to environmental sources for clinical specimens of sputum and autopsy lung tissue. The latter provided the additional information needed to identify the source of these culture-negative cases associated with the South Bronx 2015 Legionnaires' disease (LD) investigation in New York City. This new method provides a proof of concept for future direct clinical specimen hybrid capture enrichment combined with WGS and bioinformatic analysis during outbreak investigations.IMPORTANCELegionnaires' disease (LD) is a severe and potentially fatal type of pneumonia primarily caused by inhalation of Legionella-contaminated aerosols from man-made water or cooling systems. LD remains extremely underdiagnosed as it is an uncommon form of pneumonia and relies on clinicians including it in the differential and requesting specialized testing. Additionally, it is challenging to obtain clinical lower respiratory specimens from cases with LD, and when available, culture requires specialized media and growth conditions, which are not available in all microbiology laboratories. In the current study, a method for Legionella pneumophila using hybrid capture by RNA baiting was developed, which allowed us to generate sufficient genome resolution from L. pneumophila serogroup 1 PCR-positive clinical specimens. This new approach offers an additional tool for surveillance of future LD outbreaks where isolation of Legionella is not possible and may help solve previously unanswered questions from past LD investigations.

Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis. However, molecular diagnostics to date have focused largely on first-line drugs and predicting susceptibilities in a binary manner (classifying strains as either susceptible or resistant). Here, we used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration (MIC) in 15,211 Mycobacterium tuberculosis clinical isolates from 23 countries across five continents. We identified 492 unique MIC-elevating variants across 13 drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.

Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis; however, molecular diagnostics to date have focused largely on first-line drugs and predicting binary susceptibilities. We used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration in 15,211 Mycobacterium tuberculosis patient isolates from 23 countries across five continents. This identified 492 unique MIC-elevating variants across thirteen drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.

Mycobacterium tuberculosis complex whole-genome sequencing in New York State: Implementation of a reduced phenotypic drug susceptibility testing algorithm

Whole-genome sequencing (WGS) can predict drug resistance and antimicrobial susceptibility in Mycobacterium tuberculosis complex (MTBC) and has shown promise in partially replacing culture-based phenotypic drug susceptibility testing (pDST). We performed a two-year side by side study comparing the prediction of drug resistance and antimicrobial susceptibility by WGS molecular DST (mDST) to pDST to determine resistance at the critical concentration by Mycobacterial Growth Indicator Tube (MGIT) and agar proportion testing. Negative predictive values of WGS results were consistently high for the first-line drugs: rifampin (99.9%), isoniazid (99.0%), pyrazinamide (98.5%), and ethambutol (99.8%); the rates of resistance to these drugs, among strains in our population, are 2.9%, 10.4%, 46.3%, and 2.3%, respectively. WGS results were available an average 8 days earlier than first-line MGIT pDST. Based on these findings, we implemented a new testing algorithm with an updated WGS workflow in which strains predicted pan-susceptible were no longer tested by pDST. This algorithm was applied to 1177 isolates between October 2018 and September 2020, eliminating pDST for 66.6% of samples and reducing pDST for an additional 22.0%. This algorithm change resulted in faster turnaround times and decreased cost while maintaining comprehensive antimicrobial susceptibility profiles of all culture-positive MTBC cases in New York.

Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis

Drug susceptibility testing of M. tuberculosis is rooted in a binary susceptible/resistant paradigm. While there are considerable advantages in measuring the minimum inhibitory concentrations (MICs) of a panel of drugs for an isolate, it is necessary to measure the epidemiological cut-off values (ECOFF/ECVs) to permit comparison with qualitative data. Here we present ECOFF/ECVs for 13 anti-tuberculosis compounds, including bedaquiline and delamanid, derived from 20 637 clinical isolates collected by 14 laboratories based in 11 countries on five continents. Each isolate was incubated for 14 days on a dry 96-well broth microdilution plate and then read. Resistance to most of the drugs due to prior exposure is expected and the MIC distributions for many of the compounds are complex, and therefore a phenotypically wild-type population could not be defined. Since a majority of samples also underwent genetic sequencing, we defined a genotypically wild-type population and measured the MIC of the 99th percentile by direct measurement and via fitting a Gaussian using interval regression. The proposed ECOFF/ECVs were then validated by comparing with the MIC distributions of high-confidence genetic variants that confer resistance and with qualitative drug susceptibility tests obtained via the Mycobacterial Growth Indicator Tube (MGIT) system or Microscopic-Observation Drug Susceptibility (MODS) assay. These ECOFF/ECVs will inform and encourage the more widespread adoption of broth microdilution: this is a cheap culture-based method that tests the susceptibility of 12-14 antibiotics on a single 96-well plate and so could help personalise the treatment of tuberculosis.

A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics

The Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) presents here a data compendium of 12,289 Mycobacterium tuberculosis global clinical isolates, all of which have undergone whole-genome sequencing and have had their minimum inhibitory concentrations to 13 antitubercular drugs measured in a single assay. It is the largest matched phenotypic and genotypic dataset for M. tuberculosis to date. Here, we provide a summary detailing the breadth of data collected, along with a description of how the isolates were selected, collected, and uniformly processed in CRyPTIC partner laboratories across 23 countries. The compendium contains 6,814 isolates resistant to at least 1 drug, including 2,129 samples that fully satisfy the clinical definitions of rifampicin resistant (RR), multidrug resistant (MDR), pre-extensively drug resistant (pre-XDR), or extensively drug resistant (XDR). The data are enriched for rare resistance-associated variants, and the current limits of genotypic prediction of resistance status (sensitive/resistant) are presented by using a genetic mutation catalogue, along with the presence of suspected resistance-conferring mutations for isolates resistant to the newly introduced drugs bedaquiline, clofazimine, delamanid, and linezolid. Finally, a case study of rifampicin monoresistance demonstrates how this compendium could be used to advance our genetic understanding of rare resistance phenotypes. The data compendium is fully open source and it is hoped that it will facilitate and inspire future research for years to come.

Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms

The emergence of drug-resistant tuberculosis is a major global public health concern that threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly diagnose resistant infections can transform patient treatment and clinical practice. While resistance mechanisms are well understood for some drugs, there are likely many mechanisms yet to be uncovered, particularly for new and repurposed drugs. We sequenced 10,228 Mycobacterium tuberculosis (MTB) isolates worldwide and determined the minimum inhibitory concentration (MIC) on a grid of 2-fold concentration dilutions for 13 antimicrobials using quantitative microtiter plate assays. We performed oligopeptide- and oligonucleotide-based genome-wide association studies using linear mixed models to discover resistance-conferring mechanisms not currently catalogued. Use of MIC over binary resistance phenotypes increased sample heritability for the new and repurposed drugs by 26% to 37%, increasing our ability to detect novel associations. For all drugs, we discovered uncatalogued variants associated with MIC, including in the Rv1218c promoter binding site of the transcriptional repressor Rv1219c (isoniazid), upstream of the vapBC20 operon that cleaves 23S rRNA (linezolid) and in the region encoding an α-helix lining the active site of Cyp142 (clofazimine, all p < 10-7.7). We observed that artefactual signals of cross-resistance could be unravelled based on the relative effect size on MIC. Our study demonstrates the ability of very large-scale studies to substantially improve our knowledge of genetic variants associated with antimicrobial resistance in M. tuberculosis.

Respiratory health of American Indian and Alaska Native coal miners participating in the Coal Workers' Health Surveillance Program, 2014-2019

BACKGROUND

In 2014, a federal rule reduced occupational exposure limits to coal mine dust and expanded medical surveillance eligibility beyond underground miners to surface and contract coal miners. This expansion may have provided an opportunity for more American Indian and Alaska Native (AI/AN) coal miners to participate in screening, since many surface coal mines are located near AI/AN communities and may employ AI/AN miners. Therefore we sought to better understand the respiratory health of AI/AN coal miners by characterizing prevalence of coal workers' pneumoconiosis (CWP), progressive massive fibrosis (PMF), and abnormal lung function in this population.

METHODS

Descriptive analysis of 1405 chest radiographs and 627 spirometry test results for AI/AN miners who participated in the Coal Workers' Health Surveillance Program (CWHSP) during 2014-2019 was conducted.

RESULTS

Most AI/AN miners (0-25+ years of tenure) were western United States residents (82.3%) and active surface miners (76.9%) with no underground tenure. Among miners with at least 10 years of tenure, prevalence of CWP was 3.0%, and of PMF was 0.3%. Lung function abnormalities were seen in 9.0% with primarily restrictive patterns.

CONCLUSIONS

The prevalence of CWP, PMF, and lung function abnormality among active and former AI/AN coal miners was higher than seen in a larger CWHSP study of active western miners working primarily underground with 10+ years of tenure. Interventions that eliminate or control coal mine dust exposure, identify miners with CWP early, and limit respiratory disease progression and complications remain vital for eliminating the preventable adverse health effects of coal mining. Comprehensive demographic data on the coal mining workforce are needed to improve CWHSP participation assessment.

Detection of Lymphogranuloma Venereum-Associated Chlamydia trachomatis L2 Serovars in Remnant Rectal Specimens Collected from 7 US Public Health Laboratories

ABSTRACT

The frequency of lymphogranuloma venereum or invasive Chlamydia trachomatis infection with serovar L1, L2, or L3 is unknown in the United States. While no diagnostic test is commercially available, we used a laboratory-developed test and detected lymphogranuloma venereum-associated serovar L2 in 14% of 132 remnant C. trachomatis-positive rectal swabs.

A Comparison of US Clinical Laboratory Chlamydia and Gonorrhea Testing Practices Before and After the 2014 Centers for Disease Control and Prevention Testing Recommendations

BACKGROUND

Adherence to recommended laboratory testing practices is crucial for sexually transmitted infection prevention and control. The objective of this article is to compare Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) testing practices of US clinical laboratories in 2013 before the updated 2014 Centers for Disease Control and Prevention recommendations and in 2015 after the updated recommendations.

METHODS

A total of 236 clinical laboratories participated in surveys about their 2013 and 2015 CT and NG testing practices, including questions on specimen types collected and assays used.

RESULTS

There was an increase of 5 laboratories offering CT nucleic acid amplification testing (NAAT) from 2013 to 2015 and an increase of 5 laboratories offering NG NAAT. There was a net increase of 3 laboratories accepting urine for CT and NG NAAT, the preferred specimen type for male individuals. There was not a net increase in the total number of laboratories accepting vaginal swabs for CT NAAT (n = 89 in 2013 and 2015), the preferred specimen type for female individuals, but there was an increase of 3 laboratories accepting vaginal swabs for NG NAAT. The number of laboratories performing NG susceptibility testing decreased from 100 in 2013 to 89 in 2015 (χ2 = 1.07, P > 0.10).

CONCLUSIONS

There were no major changes in testing practices in the 2-year period from 2013 to 2015. However, there were some small shifts, including increases in the use of NAATs, acceptance of Centers for Disease Control and Prevention-preferred specimen types for CT/NG, and changes in usage of assays by manufacturer.

Inconsistencies in Overdose Suicide Death Investigation Practice and Potential Remedies Using Technology: A Centers for Disease Control and Prevention Consultation Meeting Summary

INTRODUCTION

It is widely accepted that suicides-which account for more than 47 500 deaths per year in the United States-are undercounted by 10% to 30%, partially due to incomplete death scene investigations (DSI) and varying burden-of-proof standards across jurisdictions. This may result in the misclassification of overdose-related suicides as accidents or undetermined intent.

METHODS

Virtual and in-person meetings were held with suicidologists and DSI experts from five states (Spring-Summer 2017) to explore how features of a hypothetical electronic DSI tool may help address these challenges.

RESULTS

Participants envisioned a mobile DSI application for cell phones, tablets, or laptop computers. Features for systematic information collection, scene description, and guiding key informant interviews were perceived as useful for less-experienced investigators.

DISCUSSION

Wide adoption may be challenging due to differences in DSI standards, practices, costs, data privacy and security, and system integration needs. However, technological tools that support consistent and complete DSIs could strengthen the information needed to accurately identify overdose suicides.

Performance and Implementation Evaluation of the Abbott BinaxNOW Rapid Antigen Test in a High-Throughput Drive-Through Community Testing Site in Massachusetts

Rapid diagnostic tests (RDTs) for SARS-CoV-2 antigens (Ag) that can be performed at point of care (POC) can supplement molecular testing and help mitigate the COVID-19 pandemic. Deployment of an Ag RDT requires an understanding of its operational and performance characteristics under real-world conditions and in relevant subpopulations. We evaluated the Abbott BinaxNOW COVID-19 Ag card in a high-throughput, drive-through, free community testing site in Massachusetts using anterior nasal (AN) swab reverse transcriptase PCR (RT-PCR) for clinical testing. Individuals presenting for molecular testing in two of seven lanes were offered the opportunity to also receive BinaxNOW testing. Dual AN swabs were collected from symptomatic and asymptomatic children (≤18 years of age) and adults. BinaxNOW testing was performed in a testing pod with temperature/humidity monitoring. One individual performed testing and official result reporting for each test, but most tests had a second independent reading to assess interoperator agreement. Positive BinaxNOW results were scored as faint, medium, or strong. Positive BinaxNOW results were reported to patients by phone, and they were instructed to isolate pending RT-PCR results. The paired RT-PCR result was the reference for sensitivity and specificity calculations. Of 2,482 participants, 1,380 adults and 928 children had paired RT-PCR/BinaxNOW results and complete symptom data. In this study, 974/1,380 (71%) adults and 829/928 (89%) children were asymptomatic. BinaxNOW had 96.5% (95% confidence interval [CI], 90.0 to 99.3) sensitivity and 100% (95% CI, 98.6 to 100.0) specificity in adults within 7 days of symptoms and 84.6% (95% CI, 65.1 to 95.6) sensitivity and 100% (95% CI, 94.5 to 100.0) specificity in children within 7 days of symptoms. Sensitivity and specificity in asymptomatic adults were 70.2% (95% CI, 56.6 to 81.6) and 99.6% (95% CI, 98.9 to 99.9), respectively, and in asymptomatic children, they were 65.4% (95% CI, 55.6 to 74.4) and 99.0% (95% CI, 98.0 to 99.6), respectively. By cycle threshold (CT ) value cutoff, sensitivity in all subgroups combined (n = 292 RT-PCR-positive individuals) was 99.3% with CT values of ≤25, 95.8% with CT values of ≤30, and 81.2% with CT values of ≤35. Twelve false-positive BinaxNOW results (out of 2,308 tests) were observed; in all 12, the test bands were faint but otherwise normal and were noted by both readers. One invalid BinaxNOW result was identified. Interoperator agreement (positive versus negative BinaxNOW result) was 100% (n = 2,230/2,230 double reads). Each operator was able to process 20 RDTs per hour. In a separate set of 30 specimens (from individuals with symptoms ≤7 days) run at temperatures below the manufacturer's recommended range (46 to 58.5°F), sensitivity was 66.7% and specificity 95.2%. BinaxNOW had very high specificity in both adults and children and very high sensitivity in newly symptomatic adults. Overall, 95.8% sensitivity was observed with CT values of ≤30. These data support public health recommendations for use of the BinaxNOW test in adults with symptoms for ≤7 days without RT-PCR confirmation. Excellent interoperator agreement indicates that an individual can perform and read the BinaxNOW test alone. A skilled laboratorian can perform and read 20 tests per hour. Careful attention to temperature is critical.

Assessment of missed opportunities for vaccination in Kenyan health facilities, 2016

Background

In November 2016, the Kenya National Vaccines and Immunization Programme conducted an assessment of missed opportunities for vaccination (MOV) using the World Health Organization (WHO) MOV methodology. A MOV includes any contact with health services during which an eligible individual does not receive all the vaccine doses for which he or she is eligible.

Methods

The MOV assessment in Kenya was conducted in 10 geographically diverse counties, comprising exit interviews with caregivers and knowledge, attitudes, and practices (KAP) surveys with health workers. On the survey dates, which covered a 4-day period in November 2016, all health workers and caregivers visiting the selected health facilities with children <24 months of age were eligible to participate. Health facilities (n = 4 per county) were purposively selected by size, location, ownership, and performance. We calculated the proportion of MOV among children eligible for vaccination and with documented vaccination histories (i.e., from a home-based record or health facility register), and stratified MOV by age and reason for visit. Timeliness of vaccine doses was also calculated.

Results

We conducted 677 age-eligible children exit interviews and 376 health worker KAP surveys. Of the 558 children with documented vaccination histories, 33% were visiting the health facility for a vaccination visit and 67% were for other reasons. A MOV was seen in 75% (244/324) of children eligible for vaccination with documented vaccination histories, with 57% (186/324) receiving no vaccinations. This included 55% of children visiting for a vaccination visit and 93% visiting for non-vaccination visits. Timeliness for multi-dose vaccine series doses decreased with subsequent doses. Among health workers, 25% (74/291) were unable to correctly identify the national vaccination schedule for vaccines administered during the first year of life. Among health workers who reported administering vaccines as part of their daily work, 39% (55/142) reported that they did not always have the materials they needed for patients seeking immunization services, such as vaccines, syringes, and vaccination recording documents.

Conclusions

The MOV assessment in Kenya highlighted areas of improvement that could reduce MOV. The results suggest several interventions including standardizing health worker practices, implementing an orientation package for all health workers, and developing a stock management module to reduce stock-outs of vaccines and vaccination-related supplies. To improve vaccination coverage and equity in all counties in Kenya, interventions to reduce MOV should be considered as part of an overall immunization service improvement plan.

Nanopore MinION Sequencing Reveals Possible Transfer of bla KPC-2 Plasmid Across Bacterial Species in Two Healthcare Facilities

Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the United States and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the bla KPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.

Nurse- and Midwife-Led HIV Services in Eastern and Southern Africa: Challenges and Opportunities for Health Facilities

In eastern and southern Africa, much is unknown about implementation of nurse-initiated and managed antiretroviral therapy (NIMART). The purpose of this study was to identify perceived barriers and facilitators of NIMART for the prevention of mother-to-child transmission and pediatric HIV services in high-volume, high HIV-burden health facilities across this region. A total of 211 nurses, midwives, and nurse midwives and 62 supervisors from 30 health facilities in 11 countries participated in this mixed-methods evaluation. The findings show that although nurses, midwives, and nurse midwives clearly had the authority to provide NIMART services, they did not necessarily feel that they were well prepared and supported to do so. Deficits in supportive supervision and clinical mentorship were viewed as substantial challenges to effective provision of NIMART for the prevention of mother-to-child transmission and pediatric HIV services-particularly with respect to pediatric HIV services. Health facilities have important opportunities to advance NIMART practice through strengthening these aspects of in-service support.

Qualitative insights into reasons for missed opportunities for vaccination in Kenyan health facilities

Background

In 2016, Kenya conducted a study of missed opportunities for vaccination (MOV)—when eligible children have contact with the health system but are not fully vaccinated—to explore some of the reasons for persistent low vaccination coverage. This paper details the qualitative findings from that assessment.

Methods

Using the World Health Organization MOV methodology, teams conducted focus group discussions among caregivers and health workers and in-depth interviews of key informants in 10 counties in Kenya. Caregivers of children <24 months of age visiting the selected health facilities on the day of the assessment were requested to participate in focus group discussions. Health workers were purposively sampled to capture a broad range of perspectives. Key informants were selected based on their perceived insight on immunization services at the county, sub-county, or health facility level.

Results

Six focus group discussions with caregivers, eight focus group discussions with health workers, and 35 in-depth interviews with key informants were completed. In general, caregivers had positive attitudes toward healthcare and vaccination services, but expressed a desire for increased education surrounding vaccination. In order to standardize vaccination checks at all health facility visits, health workers and key informants emphasized the need for additional trainings for all staff members on immunization. Health workers and key informants also highlighted the negative impact of significant understaffing in health facilities, and the persistent challenge of stock-outs of vaccines and vaccination-related supplies.

Conclusions

Identified factors that could contribute to MOV include a lack of knowledge surrounding vaccination among caregivers and health workers, inadequate number of health workers, and stock-outs of vaccines or vaccination-related materials. In addition, vaccination checks outside of vaccination visits lacked consistency, leading to MOV in non-vaccinating departments. Qualitative assessments could provide a starting point for understanding and developing interventions to address MOV in other countries.

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.

International Public Health Laboratory Twinning: An Innovative Approach to Strengthen the National Health Laboratory System in Uganda, 2014-2017

International initiatives to strengthen national health laboratory systems in resource-poor countries are often hampered by unfamiliarity with the country's health laboratory environment and turnover of international partners during the initiative. This study provides an overview of, and lessons learned from, the use of a laboratory long-term partnership approach (ie, "twinning") to strengthen the national public health laboratory system in an international setting. We focused on the partnering of the Uganda Ministry of Health Central Public Health Laboratory (CPHL) with the New Mexico State Public Health Laboratory to help the CPHL become Uganda's national public health reference laboratory (Uganda National Health Laboratory Services [UNHLS] Institute) and leader of its nascent Uganda National Health Laboratory Network (UNHLN). Via twinning, CPHL leadership received training on laboratory leadership and management, quality systems, facility management, and the One Health environmental strategy (ie, that the health of persons is connected to the health of animals and the environment), and drafted a National Health Laboratory Policy, UNHLS Institute business plan, and strategic and operating plans for the UNHLS Institute and UNHLN. The CPHL is now responsible for the UNHLS Institute and coordinates the UNHLN. Lessons learned include (1) twinning establishes stable long-term collaborations and (2) success requires commitment to a formal statement of activities and objectives, as well as clear and regular communication among partners.

Characteristics of Campylobacter and Salmonella Infections and Acute Gastroenteritis in Older Adults in Australia, Canada, and the United States

BACKGROUND

The early detection of enteric infections in older adults is challenging because typical signs and symptoms of disease may be less common, absent, or overlooked. Understanding illness characteristics of enteric infections among older adults could improve the timeliness and accuracy of clinical diagnoses, thereby improving patient outcomes and increasing cases reported to surveillance.

METHODS

Here, we describe illness characteristics (percentage reporting bloody diarrhea, fever, vomiting, abdominal pain; percentage hospitalized; duration of hospitalization; and duration of illness) among older adults (≥65 years) with acute gastroenteritis and culture-confirmed Campylobacter and nontyphoidal Salmonella infections in Australia, Canada, and the United States and compare these characteristics with those among younger people (<5 years, 5-24 years, and 25-64 years).

RESULTS

A significant negative correlation was found between all symptoms and increasing age group, except for bloody diarrhea in cases of acute gastroenteritis. Adults aged ≥85 years reported bloody diarrhea in only 9% of nontyphoidal Salmonella and 4% of Campylobacter infections compared with 59% and 55% among children aged <5 years. Conversely, a greater percentage of older adults (≥65) than younger persons (<5, 5-24, 25-64) reported being hospitalized, with an increasing linear relationship in age groups 65 years and older.

CONCLUSIONS

Although older adults are more likely to have severe illness and be hospitalized, we found that the proportion of persons reporting symptoms typically associated with enteric infections decreases with age. These findings have implications for clinical recognition and treatment of gastrointestinal illness, as well as for public health research.

Overview of rabies post-exposure prophylaxis access, procurement and distribution in selected countries in Asia and Africa, 2017-2018

BACKGROUND

Rabies is a neglected zoonotic disease with a global burden of approximately 59,000 human deaths a year. Once clinical symptoms appear, rabies is almost invariably fatal; however, with timely and appropriate post-exposure prophylaxis (PEP) consisting of wound washing, vaccine, and in some cases rabies immunoglobulin (RIG), the disease is almost entirely preventable. Access to PEP is limited in many countries, and when available, is often very expensive.

METHODS

We distributed a standardized assessment tool electronically to a convenience sample of 25 low- and middle-income countries in Asia and Africa to collect information on rabies PEP procurement, forecasting, distribution, monitoring and reporting. Information was collected from national rabies focal points, focal points at the World Health Organization (WHO) country offices, and others involved in procurement, logistics and distribution of PEP. Because RIG was limited in availability or unavailable in many countries, the assessment focused on vaccine. Data were collected between January 2017 and May 2018.

RESULTS

We received responses from key informants in 23 countries: 11 countries in Asia and 12 countries in Africa. In 9 of 23 (39%) countries, rabies vaccine was provided for free in the public sector and was consistently available. In 10 (43%) countries, all or some patients were required to pay for the vaccine in the public sector, with the cost of a single dose ranging from US$ 6.60 to US$ 20/dose. The primary reason for the high cost of the vaccine for patients was a lack of funding at the central level to subsidize vaccine costs. In the remaining 4 (17%) countries, vaccine was provided for free but was often unavailable so patients were required to purchase it instead. The majority of countries used the intramuscular route for vaccine administration and only 5 countries exclusively used the dose-sparing intradermal (ID) route. Half (11/22; 50%) of all countries assessed had a standardized distribution system for PEP, separate from the systems used for routine childhood vaccines, and almost half used separate storage facilities at both central and health facility levels. Approximately half (9/22; 41%) of all countries assessed reported having regular weekly, monthly or quarterly reporting on rabies vaccination.

CONCLUSIONS

While all countries in our assessment had rabies vaccines available in the public sector to some extent, barriers to access include the high cost of the vaccine to the government as well as to patients. Countries should be encouraged to use ID administration as this would provide access to rabies vaccine for many more people with the same number of vaccine vials. In addition, standardized monitoring and reporting of vaccine utilization should be encouraged, in order to improve data on PEP needs.

Opportunities to improve vaccination coverage in a country with a fledgling health system: Findings from an assessment of missed opportunities for vaccination among health center attendees-Timor Leste, 2016

INTRODUCTION

Since its independence in 2002, Timor Leste has made significant strides in improving childhood vaccination coverage. However, coverage is still below national targets, and children continue to have missed opportunities for vaccination (MOV), when eligible children have contact with the health system but are not vaccinated. Timor Leste implemented the updated World Health Organization methodology for assessing MOV in 2016.

METHODS

The MOV data collection included quantitative (caregiver exit interviews and health worker knowledge, attitudes, practices surveys (KAP)) and qualitative arms (focus group discussions (FGDs) with caregivers and health workers and in-depth interviews (IDIs) with health administrators). During a four-day period, health workers and caregivers with children <24 months of age attending the selected eight facilities in Dili Municipality were invited to participate. The researchers calculated the proportion of MOV and timeliness of vaccine doses among children with documented vaccination histories (i.e., from a home-based record or facility register) and thematically analyzed the qualitative data.

RESULTS

Researchers conducted 365 caregiver exit interviews, 169 health worker KAP surveys, 4 FGDs with caregivers, 2 FGDs with health workers, and 2 IDIs with health administrators. Among eligible children with documented vaccination histories (n = 199), 41% missed an opportunity for vaccination. One-third of health workers (33%) believed their knowledge of immunization practices to be insufficient. Qualitative results showed vaccines were not available at all selected health facilities, and some facilities reported problems with their cold chain equipment.

CONCLUSION

This study demonstrates that many children in Timor Leste miss opportunities for vaccination during health service encounters. Potential interventions to reduce MOV include training of health workers, improving availability of vaccines at more health facilities, and replacing unusable cold chain equipment. Timor Leste should continue to scale up successful MOV interventions beyond Dili Municipality to improve vaccination coverage nationally and strengthen the health system overall.

A Laboratory Medicine Best Practices Systematic Review and Meta-analysis of Nucleic Acid Amplification Tests (NAATs) and Algorithms Including NAATs for the Diagnosis of Clostridioides (Clostridium) difficile in Adults

The evidence base for the optimal laboratory diagnosis of Clostridioides (Clostridium) difficile in adults is currently unresolved due to the uncertain performance characteristics and various combinations of tests. This systematic review evaluates the diagnostic accuracy of laboratory testing algorithms that include nucleic acid amplification tests (NAATs) to detect the presence of C. difficile The systematic review and meta-analysis included eligible studies (those that had PICO [population, intervention, comparison, outcome] elements) that assessed the diagnostic accuracy of NAAT alone or following glutamate dehydrogenase (GDH) enzyme immunoassays (EIAs) or GDH EIAs plus C. difficile toxin EIAs (toxin). The diagnostic yield of NAAT for repeat testing after an initial negative result was also assessed. Two hundred thirty-eight studies met inclusion criteria. Seventy-two of these studies had sufficient data for meta-analysis. The strength of evidence ranged from high to insufficient. The uses of NAAT only, GDH-positive EIA followed by NAAT, and GDH-positive/toxin-negative EIA followed by NAAT are all recommended as American Society for Microbiology (ASM) best practices for the detection of the C. difficile toxin gene or organism. Meta-analysis of published evidence supports the use of testing algorithms that use NAAT alone or in combination with GDH or GDH plus toxin EIA to detect the presence of C. difficile in adults. There is insufficient evidence to recommend against repeat testing of the sample using NAAT after an initial negative result due to a lack of evidence of harm (i.e., financial, length of stay, or delay of treatment) as specified by the Laboratory Medicine Best Practices (LMBP) systematic review method in making such an assessment. Findings from this systematic review provide clarity to diagnostic testing strategies and highlight gaps, such as low numbers of GDH/toxin/PCR studies, in existing evidence on diagnostic performance, which can be used to guide future clinical research studies.

Factors associated with provision of depot medroxyprogesterone acetate to adolescents by US health care providers

OBJECTIVE

Identify factors associated with healthcare providers' frequency of depot medroxyprogesterone acetate (DMPA) provision to adolescents.

STUDY DESIGN

We analyzed data from surveys mailed to a nationally representative sample of public-sector providers and office-based physicians (n=1984). We estimated adjusted odds ratios (aORs) and 95% confidence intervals (CIs) of factors associated with frequent DMPA provision to adolescents in the past year.

RESULTS

Although most providers (>95%) considered DMPA safe for adolescents, fewer reported frequent provision (89% of public-sector providers; 64% of office-based physicians). Among public-sector providers, factors associated with lower odds of frequent provision included working in settings without Title X funding (aOR 0.44, 95% CI 0.30-0.64), reporting primary care as their primary clinical focus versus reproductive or adolescent health (aOR 0.42, 95% CI 0.28-0.61), and providing fewer patients with family planning services. Among office-based physicians, factors associated with lower odds of frequent provision included specializing in obstetrics/gynecology (aOR 0.50, 95% CI 0.27-0.91) and family medicine (aOR 0.21, 95% CI 0.09-0.47) versus adolescent medicine, completing training ≥15 versus <5 years ago (aOR 0.27, 95% CI 0.09-0.83), and reporting that 0-24% of patients pay with Medicaid or other government healthcare assistance versus ≥50% (aOR 0.23, 95% CI 0.09-0.61). The reason most commonly reported by providers for infrequent DMPA provision was patient preference for another method.

CONCLUSIONS

While most providers reported frequently providing DMPA to adolescents, training on evidence-based recommendations for contraception, focused on subgroups of providers with lower odds of frequent DMPA provision, may increase adolescents' access to contraception.

IMPLICATIONS

Although >95% of providers considered depot medroxyprogesterone (DMPA) a safe contraceptive for adolescents, only 89% of public-sector providers and 64% of office-based physicians reported frequently providing DMPA to adolescents. Provider training on evidence-based recommendations for contraception counseling and provision may increase adolescents' access to DMPA and all methods of contraception.

Health Care Provider Attitudes and Practices Related to 'Quick Start' Provision of Combined Hormonal Contraception and Depot Medroxyprogesterone Acetate to Adolescents

PURPOSE

Adolescents may encounter many barriers to initiating contraception. 'Quick Start' is a recommended approach for initiating contraception on the same day as a provider visit. We examined factors associated with health care provider attitudes and practices related to 'Quick Start' provision of combined hormonal contraception (CHC) and depot medroxyprogesterone acetate (DMPA) to adolescents.

METHODS

We analyzed weighted survey data from providers in publicly funded health centers and from office-based physicians (n = 2,056). Using multivariable logistic regression, we estimated adjusted odds ratios (aORs) and 95% confidence intervals (CIs) of the associations between provider characteristics and frequent (very often or often vs. not often or never) 'Quick Start' provision of CHC and DMPA to adolescents in the past year.

RESULTS

The prevalence of considering 'Quick Start' as safe was high for CHC (public-sector providers [87.5%]; office-based physicians [80.2%]) and DMPA (public-sector providers [80.9%]; office-based physicians [78.8%]). However, the prevalence of frequent 'Quick Start' provision was lower, particularly among office-based physicians (CHC: public-sector providers [74.2%]; office-based physicians [45.2%]; DMPA: public-sector providers [71.4%]; office-based physicians [46.9%]). Providers who considered 'Quick Start' unsafe or were uncertain about its safety had lower odds of frequent 'Quick Start' provision compared with those who considered it safe (public-sector providers: CHC aOR = 0.09 95% CI 0.06-0.13, DMPA aOR = 0.07 95% CI 0.05-0.10; office-based physicians: CHC aOR = 0.06 95% CI 0.02-0.22, DMPA aOR = 0.07 95% CI 0.02-0.20).

CONCLUSIONS

While most providers reported that 'Quick Start' initiation of CHC and DMPA among adolescents is safe, fewer providers reported frequent 'Quick Start' provision in this population, particularly among office-based physicians.

Can vaccination coverage be improved by reducing missed opportunities for vaccination? Findings from assessments in Chad and Malawi using the new WHO methodology

Background

In 2015, the World Health Organization (WHO) updated the global methodology for assessing and reducing missed opportunities for vaccination (MOV), when eligible children have contact with the health system but are not vaccinated. This paper presents the results of two pilot assessments conducted in Chad and Malawi.

Methods

Using the ten-step global WHO MOV strategy, we purposively selected districts and health facilities, with non-probabilistic sampling of <24 month old children for exit interviews of caregivers and self-administered knowledge, attitudes, and practices (KAP) surveys of health workers. MOV were calculated based on a child’s documented vaccination history (i.e., from a home-based record (HBR) or a health facility vaccination register), including selected vaccines in the national schedule.

Results

Respondents included caregivers of 353 children in Chad and of 580 children in Malawi. Among those with documented vaccination history, 82% (195/238) were eligible for vaccination in Chad and 47% (225/483) in Malawi. Among eligible children, 51% (99/195) in Chad, and 66% (149/225) in Malawi had one or more MOV on the survey date. During non-vaccination visits, 77% (24/31) of children eligible for vaccination in Chad and 92% (119/129) in Malawi had a MOV compared to 46% (75/164) and 31% (30/96) during vaccination visits, respectively. Among health workers, 92% in Chad and 88% in Malawi were unable to correctly identify valid contraindications for vaccination.

Conclusion

The new MOV tool was able to characterize the type and potential causes of MOV. In both countries, the findings of the assessments point to two major barriers to full vaccination of eligible children—a lack of coordination between vaccination and curative health services and incomplete vaccination during vaccination visits. National immunization programs should explore tailored efforts to improve health worker practices and to increase vaccine delivery by making better use of existing health service contacts.

Performance of the Alere Determine™ HIV-1/2 Ag/Ab Combo Rapid Test with algorithm-defined acute HIV-1 infection specimens

BACKGROUND

The capacity of HIV Antigen/Antibody (Ag/Ab) immunoassays (IA) to detect HIV-1 p24 antigen has resulted in improved detection of HIV-1 infections in comparison to Ab-only screening assays. Since its introduction in the US, studies have shown that the Determine HIV-1/2 Ag/Ab Combo assay (Determine Ag/Ab) detects HIV infection earlier than laboratory-based IgM/IgG-sensitive IAs, but its sensitivity for HIV-1 p24 Ag detection is reduced compared to laboratory-based Ag/Ab assays. However, further evaluation is needed to assess its capacity to detect acute HIV-1 infection.

OBJECTIVE

To assess the performance of Determine Ag/Ab in serum from acute HIV-1 infections.

STUDY DESIGN

Select serum specimens that screened reactive on a laboratory-based Ag/Ab IA or IgM/IgG Ab-only IA, with a negative or indeterminate supplemental antibody test and detectable HIV-1 RNA were retrospectively tested with Determine Ag/Ab. Results were compared with those of the primary screening immunoassay to evaluate concordance within this set of algorithm-defined acute infections.

RESULTS

Of 159 algorithm-defined acute HIV-1 specimens, Determine Ag/Ab was reactive for 105 resulting in 66.0% concordance. Of 125 that were initially detected by a laboratory-based Ag/Ab IA, 81 (64.8%) were reactive by Determine Ag/Ab. A total of 34 acute specimens were initially detected by a laboratory-based IgM/IgG Ab-only IA and 24 (70.6%) of those were reactive by Determine Ag/Ab.

CONCLUSIONS

Due to their enhanced sensitivity, laboratory-based Ag/Ab IAs continue to be preferred over the Determine Ag/Ab as the screening method used by laboratories conducting HIV diagnostic testing on serum and plasma specimens.

Evaluation of the impact of the ARC program on national nursing and midwifery regulations, leadership, and organizational capacity in East, Central, and Southern Africa

BACKGROUND

The African Health Professions Regulatory Collaborative (ARC) was launched in 2011 to support countries in East, Central, and Southern Africa to safely and sustainably expand HIV service delivery by nurses and midwives. While the World Health Organization recommended nurse initiated and managed antiretroviral therapy, many countries in this region had not updated their national regulations to ensure nurses and midwives were authorized and trained to provide essential HIV services. For four years, ARC awarded annual grants, convened regional meetings, and provided technical assistance to country teams of nursing and midwifery leaders to improve national regulations related to safe HIV service delivery. We examined the impact of the program on national regulations and the leadership and organizational capacity of country teams.

METHODS

Data was collected to quantify the level of participation in ARC by each country (number of grants received, number of regional meetings attended, and amount of technical assistance received). The level of participation was analyzed according to two primary outcome measures: 1) changes in national regulations and 2) improvements in leadership and organizational capacity of country teams. Changes in national regulations were defined as advancement of one "stage" on a capability maturity model; nursing and midwifery leadership and organizational capacity was measured by a group survey at the end of the program.

RESULTS

Seventeen countries participated in ARC between 2012 and 2016. Thirty-three grants were awarded; the majority addressed continuing professional development (20; 61%) and scopes of practice (6; 18%). Fourteen countries (representing approximately two-thirds of grants) progressed at least one stage on the capability maturity model. There were significant increases in all five domains of leadership and organizational capacity (p < 0.01). The number of grants (Kendall's tau = 0.56, p = 0.02), duration of technical assistance (Kendall's tau = 0.50, p = 0.03), and number of learning sessions attended (Kendall's tau = 0.46, p = 0.04) were significantly associated with improvements in in-country collaboration between nursing and midwifery organizations.

CONCLUSIONS

The ARC program improved national nursing regulations in participating countries and increased reported leadership, organizational capacity, and collaboration among national nursing and midwifery organizations. These changes help ensure national policies and professional regulations underpin nurse initiated and managed treatment for people living with HIV.

Assessing prevalence of missed laboratory-confirmed sexually transmitted infections among women in Kingston, Jamaica: results from a secondary analysis of the Sino-Implant clinical trial

OBJECTIVES

To assess potentially missed sexually transmitted infections (STIs), we compared clinically diagnosed STIs to laboratory-confirmed diagnoses of gonorrhoea (GC), chlamydia (CT) and trichomonas (Tvag).

DESIGN

Secondary analysis of a randomised controlled trial.

SETTING

We used data and specimens previously collected for the Sino-Implant Study in Kingston, Jamaica.

PARTICIPANTS

The Sino-Implant Study randomised 414 women to receive a levonorgestrel implant at either baseline or 3 months post-enrolment to evaluate unprotected sex after implant initiation. This analysis used 254 available vaginal swab samples.

OUTCOME MEASURES

Clinically diagnosed STIs were determined from medical records by assessing clinical impressions and prescriptions. Laboratory-confirmed STIs included GC, CT and Tvag tested by Aptima Combo 2 for CT/GC and Aptima Tvag assays (Hologic, San Diego, California, USA). Log-binomial regression models fit with generalised estimating equations were used to estimate associations of clinically diagnosed STIs with laboratory-confirmed diagnoses and demographic and behavioural characteristics.

RESULTS

Overall, 195 (76.8%) women had laboratory-confirmed STI (CT, GC or Tvag) while only 65 (25.6%) women had clinically diagnosed cervicitis and/or vaginitis during the study period. Clinical diagnosis missed 79.7% of laboratory-confirmed STIs: 85% of GC (n=17/20), 78.8% of CT (n=141/179) and 80.0% of Tvag (n=180/225). Hormonal contraceptive use in the month prior to the study visit was significantly associated with clinical diagnosis at any time point (prevalence ratio (PR): 1.65, 95% CI 1.07 to 2.54). As age increased, clinically missed infections significantly decreased (PR: 0.98 per year increase, 95% CI 0.97 to 1.00).

CONCLUSIONS

The prevalence of laboratory-confirmed STIs was much higher than what was captured by clinical diagnosis. GC, CT and Tvag were not accurately detected without lab confirmation. Missed diagnoses decreased with older age. Increased laboratory capacity and refinement of the syndromic approach are needed to protect the health of sexually active Jamaican women.

TRIAL REGISTRATION NUMBER

NCT01684358.

Prevalence and Medical Costs of Chronic Diseases Among Adult Medicaid Beneficiaries

INTRODUCTION

This review summarizes the current literature for the prevalence and medical costs of noncommunicable chronic diseases among adult Medicaid beneficiaries to inform future program design.

METHODS

The databases MEDLINE and CINAHL were searched in August 2016 using keywords, including Medicaid, health status, and healthcare cost, to identify original studies that were published during 2000-2016, examined Medicaid as an independent population group, examined prevalence or medical costs of chronic conditions, and included adults within the age group 18-64 years. The review and data extraction was conducted in Fall 2016-Spring 2017. Disease-related costs (costs specifically to treat the disease) and total costs (all-cause medical costs for a patient with the disease) are presented separately.

RESULTS

Among the 29 studies selected, prevalence estimates for enrollees aged 18-64 years were 8.8%-11.8% for heart disease, 17.2%-27.4% for hypertension, 16.8%-23.2% for hyperlipidemia, 7.5%-12.7% for diabetes, 9.5% for cancer, 7.8%-19.3% for asthma, 5.0%-22.3% for depression, and 55.7%-62.1% for one or more chronic conditions. Estimated annual per patient disease-related costs (2015 U.S. dollars) were $3,219-$4,674 for diabetes, $3,968-$6,491 for chronic obstructive pulmonary disease, and $989-$3,069 for asthma. Estimated hypertension-related costs were $687, but total costs per hypertensive beneficiary ranged much higher. Estimated total annual healthcare costs were $29,271-$51,937 per beneficiary with heart failure and $11,446-$20,585 per beneficiary with schizophrenia. Costs among beneficiaries with cancer were $29,384-$46,194 for the 6 months following diagnosis.

CONCLUSIONS

These findings could help inform the evaluation of interventions to prevent and manage noncommunicable chronic diseases and their potential to control costs among the vulnerable Medicaid population.

Safety and Accuracy of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Highly Pathogenic Organisms

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) sample preparation methods, including the direct, on-plate formic acid, and ethanol/formic acid tube extraction methods, were evaluated for their ability to render highly pathogenic organisms nonviable and safe for handling in a biosafety level 2 laboratory. Of these, the tube extraction procedure was the most successful, with none of the tested strains surviving this sample preparation method. Tube extracts from several agents of bioterrorism and their near neighbors were analyzed in an eight-laboratory study to examine the utility of the Bruker Biotyper and Vitek MS MALDI-TOF MS systems and their in vitro diagnostic (IVD), research-use-only, and Security-Relevant databases, as applicable, to accurately identify these agents. Forty-six distinct strains of Bacillus anthracis, Yersinia pestis, Francisella tularensis, Burkholderia mallei, Burkholderia pseudomallei, Clostridium botulinum, Brucella melitensis, Brucella abortus, Brucella suis, and Brucella canis were extracted and distributed to participating laboratories for analysis. A total of 35 near-neighbor isolates were also analyzed.

A Systematic Review of Economic Evidence on Community Hypertension Interventions

CONTEXT

Effective community-based interventions are available to control hypertension. It is important to determine the economics of these interventions.

EVIDENCE ACQUISITION

Peer-reviewed studies from January 1995 through December 2015 were screened. Interventions were categorized into educational interventions, self-monitoring interventions, and screening interventions. Incremental cost-effectiveness ratios were summarized by types of interventions. The review was conducted in 2016.

EVIDENCE SYNTHESIS

Thirty-four articles were included in the review (16 from the U.S., 18 from other countries), including 25 on educational interventions, three on self-monitoring interventions, and six on screening interventions. In the U.S., five (31.3%) studies on educational interventions were cost saving. Among the studies that found the interventions cost effective, the median incremental costs were $62 (range, $40-$114) for 1-mmHg reduction in systolic blood pressure (SBP) and $13,986 (range, $6,683-$58,610) for 1 life-year gained. Outside the U.S., educational interventions cost from $0.62 (China) to $29 (Pakistan) for 1-mmHg reduction in SBP. Self-monitoring interventions, evaluated in the U.S. only, cost $727 for 1-mmHg reduction in SBP and $41,927 for 1 life-year gained. For 1 quality-adjusted life-year, screening interventions cost from $21,734 to $56,750 in the U.S., $613 to $5,637 in Australia, and $7,000 to $18,000 in China. Intervention costs to reduce 1 mmHg blood pressure or 1 quality-adjusted life-year were higher in the U.S. than in other countries.

CONCLUSIONS

Most studies found that the three types of interventions were either cost effective or cost saving. Quality of economic studies should be improved to confirm the findings.

Medical Expenditures Associated With Diabetes in Myocardial Infarction and Ischemic Stroke Patients

INTRODUCTION

The coexistence of diabetes among people with acute myocardial infarction (AMI) or acute ischemic stroke (AIS) is common. However, little is known about the extent of excess medical expenditures associated with having diabetes among AMI and AIS patients.

METHODS

Data on 3,307 AMI patients and 2,460 AIS patients aged ≥18 years from the 2008 to 2014 Medical Expenditure Panel Survey were analyzed. Per capita annual medical expenditures associated with diabetes were separately estimated by healthcare components with generalized linear models and two-part models. Excess expenditure associated with diabetes is the difference between estimated expenditure conditional on having both diabetes and AMI (or AIS) and the estimated expenditure conditional on having AMI (or AIS) but not diabetes. All expenditures were adjusted to 2014 U.S. dollars. The analysis was conducted in 2017.

RESULTS

Per capita annual total excess expenditures associated with diabetes were $5,117 (95% CI=$4,989, $5,243) for AMI patients and $5,734 (95% CI=$5,579, $5,887) for AIS patients. Of the total excess expenditures, prescription drugs accounted for 40% among AMI patients and 42% among AIS patients. Higher expenditures associated with diabetes were explained more by higher volume of utilization than higher per unit expenditures.

CONCLUSIONS

Excess expenditures associated with diabetes were substantial among both AMI and AIS patients. These results highlight the needs for both prevention and better management of diabetes among AMI and AIS patients, which in turn may lower the financial burden of treating these conditions.

Annual Total Medical Expenditures Associated with Hypertension by Diabetes Status in U.S. Adults

INTRODUCTION

Hypertension and diabetes, both independent risk factors for cardiovascular disease, often coexist. The hypertension-increased medical expenditures by diabetes status is unclear, however. This study estimated annual total medical expenditures in U.S. adults by hypertension and diabetes status.

METHODS

The study population consisted of 40,746 civilian, non-institutionalized adults aged ≥18 years who participated in the 2013 or 2014 Medical Expenditure Panel Survey. The authors separately estimated hypertension-increased medical expenditures using two-part econometric and generalized linear models for the total; diabetes (n=4,396); and non-diabetes (n=36,250) populations and adjusted the results into 2014 U.S. dollars. Data were analyzed in 2017 and estimated the hypertension-increased medical expenditures by type of medical service and payment source.

RESULTS

The prevalence of hypertension was 34.9%, 78.3%, and 30.1% for the total, diabetes, and non-diabetes populations, respectively. The respective mean unadjusted annual per capita medical expenditures were $5,225, $12,715, and $4,390. After controlling for potential confounders, hypertension-increased expenditures were $2,565, $4,434, and $2,276 for total, diabetes, and non-diabetes populations, respectively (all p<0.001). The hypertension-increased expenditure was highest for inpatient stays among the diabetes population ($1,730, p<0.001), and highest for medication among the non-diabetes population ($687, p<0.001). By payment source, Medicare ranked first in hypertension-increased expenditures for the diabetes ($2,753) and second for the non-diabetes ($669) populations (both p<0.001).

CONCLUSIONS

Hypertension-increased medical expenditures were substantial and varied by medical service type and payment sources. These findings may be useful as inputs for cost- effectiveness evaluations of hypertension interventions by diabetes status.

Promoting Regulatory Reform: The African Health Profession Regulatory Collaborative (ARC) for Nursing and Midwifery Year 4 Evaluation

As countries across sub-Saharan Africa work towards universal health coverage and HIV epidemic control, investments seek to bolster the quality and relevance of the health workforce. The African Health Profession Regulatory Collaborative (ARC) partnered with 17 countries across East, Central, and Southern Africa to ensure nurses and midwives were authorized and equipped to provide essential HIV services to pregnant women and children with HIV. Through ARC, nursing leadership teams representing each country identify a priority regulatory function and develop a proposal to strengthen that regulation over a 1-year period. Each year culminates with a summative congress meeting, involving all ARC countries, where teams present their projects and share lessons learned with their colleagues. During a recent ARC Summative Congress, a group survey was administered to 11 country teams that received ARC Year 4 grants to measure advancements in regulatory function using the five-stage Regulatory Function Framework, and a group questionnaire was administered to 16 country teams to measure improvements in national nursing capacity (February 2011-2016). In ARC Year 4, eight countries implemented continuing professional development projects, Botswana revised their scope of practice, Mozambique piloted a licensing examination to assess HIV-related competencies, and South Africa developed accreditation standards for HIV/tuberculosis specialty nurses. Countries reported improvements in national nursing leaders' teamwork, collaborations with national organizations, regional networking with nursing leaders, and the ability to garner additional resources. ARC provides an effective, collaborative model to rapidly strengthen national regulatory frameworks, which other health professional cadres or regions may consider using to ensure a relevant health workforce, authorized and equipped to meet the emerging demand for health services.

A Conceptual Framework for the Evaluation of Emergency Risk Communications

OBJECTIVES

To articulate a conceptual framework in support of evaluation activities in emergency risk communications (ERC).

METHODS

The framework proposed is based on a systematic review of the scientific literature (2001-2016) combined with data derived from a series of semistructured interviews with experts and practitioners in ERC, and it is designed to support local, national, and international public health organizations in implementing evaluation studies in ERC.

RESULTS

We identified a list of ERC outcomes from the full-text review of 152 articles and categorized these into 3 groups, depending upon the level at which the outcome was measured: (1) information environment, (2) population, and (3) public health system. We analyzed interviewees' data from 18 interviews to identify practices and processes related to the effectiveness of ERC and included these as key structural components and processes in the developed evaluation framework.

CONCLUSIONS

Researchers and public health practitioners interested in the evaluation of ERC can use the conceptual framework described in this article to guide the development of evaluation studies and methods for assessing communication outcomes related to public health emergencies.

Use of Emergency Department Data to Monitor and Respond to an Increase in Opioid Overdoses in New Hampshire, 2011-2015

OBJECTIVES

Opioid-related overdoses and deaths in New Hampshire have increased substantially in recent years, similar to increases observed across the United States. We queried emergency department (ED) data in New Hampshire to monitor opioid-related ED encounters as part of the public health response to this health problem.

METHODS

We obtained data on opioid-related ED encounters for the period January 1, 2011, through December 31, 2015, from New Hampshire's syndromic surveillance ED data system by querying for (1) chief complaint text related to the words "fentanyl," "heroin," "opiate," and "opioid" and (2) opioid-related International Classification of Diseases ( ICD) codes. We then analyzed the data to calculate frequencies of opioid-related ED encounters by age, sex, residence, chief complaint text values, and ICD codes.

RESULTS

Opioid-related ED encounters increased by 70% during the study period, from 3300 in 2011 to 5603 in 2015; the largest increases occurred in adults aged 18-29 and in males. Of 20 994 total opioid-related ED visits, we identified 18 554 (88%) using ICD code alone, 690 (3%) using chief complaint text alone, and 1750 (8%) using both chief complaint text and ICD code. For those encounters identified by ICD code only, the corresponding chief complaint text included varied and nonspecific words, with the most common being "pain" (n = 3335, 18%), "overdose" (n = 1555, 8%), "suicidal" (n = 816, 4%), "drug" (n = 803, 4%), and "detox" (n = 750, 4%). Heroin-specific encounters increased by 827%, from 4% of opioid-related encounters in 2011 to 24% of encounters in 2015.

CONCLUSIONS

Opioid-related ED encounters in New Hampshire increased substantially from 2011 to 2015. Data from New Hampshire's ED syndromic surveillance system provided timely situational awareness to public health partners to support the overall response to the opioid epidemic.

Cross-sectional description of nursing and midwifery pre-service education accreditation in east, central, and southern Africa in 2013

BACKGROUND

In 2013, the World Health Organization issued guidelines, Transforming and Scaling Up Health Professional Education and Training, to improve the quality and relevance of health professional pre-service education. Central to these guidelines was establishing and strengthening education accreditation systems. To establish what current accreditation systems were for nursing and midwifery education and highlight areas for strengthening these systems, a study was undertaken to document the pre-service accreditation policies, approaches, and practices in 16 African countries relative to the 2013 WHO guidelines.

METHODS

This study utilized a cross-sectional group survey with a standardized questionnaire administered to a convenience sample of approximately 70 nursing and midwifery leaders from 16 countries in east, central, and southern Africa. Each national delegation completed one survey together, representing the responses for their country.

RESULTS

Almost all countries in this study (15; 94%) mandated pre-service nursing education accreditation However, there was wide variation in who was responsible for accrediting programs. The percent of active programs accredited decreased by program level from 80% for doctorate programs to 62% for masters nursing to 50% for degree nursing to 35% for diploma nursing programs. The majority of countries indicated that accreditation processes were transparent (i.e., included stakeholder engagement (81%), self-assessment (100%), evaluation feedback (94%), and public disclosure (63%)) and that the processes were evaluated on a routine basis (69%). Over half of the countries (nine; 56%) reported limited financial resources as a barrier to increasing accreditation activities, and seven countries (44%) noted limited materials and technical expertise.

CONCLUSION

In line with the 2013 WHO guidelines, there was a strong legal mandate for nursing education accreditation as compared to the global average of 50%. Accreditation levels were low in the programs that produce the majority of the nurses in this region and were higher in public programs than non-public programs. WHO guidelines for transparency and routine review were met more so than standards-based and independent accreditation processes. The new global strategy, Workforce 2030, has renewed the focus on accreditation and provides an opportunity to strengthen pre-service accreditation and ensure the production of a qualified and relevant nursing workforce.

Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State

Whole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics and is capable of providing rapid drug resistance profiles while performing species identification and capturing the data necessary for genotyping. Our laboratory developed and validated a comprehensive and sensitive WGS assay to characterize Mycobacterium tuberculosis and other M. tuberculosis complex (MTBC) strains, composed of a novel DNA extraction, optimized library preparation, paired-end WGS, and an in-house-developed bioinformatics pipeline. This new assay was assessed using 608 MTBC isolates, with 146 isolates during the validation portion of this study and 462 samples received prospectively. In February 2016, this assay was implemented to test all clinical cases of MTBC in New York State, including isolates and early positive Bactec mycobacterial growth indicator tube (MGIT) 960 cultures from primary specimens. Since the inception of the assay, we have assessed the accuracy of identification of MTBC strains to the species level, concordance with culture-based drug susceptibility testing (DST), and turnaround time. Species identification by WGS was determined to be 99% accurate. Concordance between drug resistance profiles generated by WGS and culture-based DST methods was 96% for eight drugs, with an average resistance-predictive value of 93% and susceptible-predictive value of 96%. This single comprehensive WGS assay has replaced seven molecular assays and has resulted in resistance profiles being reported to physicians an average of 9 days sooner than with culture-based DST for first-line drugs and 32 days sooner for second-line drugs.

Analytic Validation of Immunohistochemical Assays: A Comparison of Laboratory Practices Before and After Introduction of an Evidence-Based Guideline

CONTEXT

- Laboratories must demonstrate analytic validity before any test can be used clinically, but studies have shown inconsistent practices in immunohistochemical assay validation.

OBJECTIVE

- To assess changes in immunohistochemistry analytic validation practices after publication of an evidence-based laboratory practice guideline.

DESIGN

- A survey on current immunohistochemistry assay validation practices and on the awareness and adoption of a recently published guideline was sent to subscribers enrolled in one of 3 relevant College of American Pathologists proficiency testing programs and to additional nonsubscribing laboratories that perform immunohistochemical testing. The results were compared with an earlier survey of validation practices.

RESULTS

- Analysis was based on responses from 1085 laboratories that perform immunohistochemical staining. Of 1057 responses, 65.4% (691) were aware of the guideline recommendations before this survey was sent and 79.9% (550 of 688) of those have already adopted some or all of the recommendations. Compared with the 2010 survey, a significant number of laboratories now have written validation procedures for both predictive and nonpredictive marker assays and specifications for the minimum numbers of cases needed for validation. There was also significant improvement in compliance with validation requirements, with 99% (100 of 102) having validated their most recently introduced predictive marker assay, compared with 74.9% (326 of 435) in 2010. The difficulty in finding validation cases for rare antigens and resource limitations were cited as the biggest challenges in implementing the guideline.

CONCLUSIONS

- Dissemination of the 2014 evidence-based guideline validation practices had a positive impact on laboratory performance; some or all of the recommendations have been adopted by nearly 80% of respondents.

Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens

BACKGROUND

Ocular infections remain a major cause of blindness and morbidity worldwide. While prognosis is dependent on the timing and accuracy of diagnosis, the etiology remains elusive in ~50 % of presumed infectious uveitis cases. The objective of this study is to determine if unbiased metagenomic deep sequencing (MDS) can accurately detect pathogens in intraocular fluid samples of patients with uveitis.

METHODS

This is a proof-of-concept study, in which intraocular fluid samples were obtained from five subjects with known diagnoses, and one subject with bilateral chronic uveitis without a known etiology. Samples were subjected to MDS, and results were compared with those from conventional diagnostic tests. Pathogens were identified using a rapid computational pipeline to analyze the non-host sequences obtained from MDS.

RESULTS

Unbiased MDS of intraocular fluid produced results concordant with known diagnoses in subjects with (n = 4) and without (n = 1) uveitis. Samples positive for Cryptococcus neoformans, Toxoplasma gondii, and herpes simplex virus 1 as tested by a Clinical Laboratory Improvement Amendments-certified laboratory were correctly identified with MDS. Rubella virus was identified in one case of chronic bilateral idiopathic uveitis. The subject's strain was most closely related to a German rubella virus strain isolated in 1992, one year before he developed a fever and rash while living in Germany. The pattern and the number of viral identified mutations present in the patient's strain were consistent with long-term viral replication in the eye.

CONCLUSIONS

MDS can identify fungi, parasites, and DNA and RNA viruses in minute volumes of intraocular fluid samples. The identification of chronic intraocular rubella virus infection highlights the eye's role as a long-term pathogen reservoir, which has implications for virus eradication and emerging global epidemics.

Draft Genome Sequence of Branchiibius sp. NY16-3462-2, Isolated from a Mixed Clinical Sample

Here, we report the release of a draft genome assembly of a Gram-positive cocci Branchiibius sp. NY16-3462-2 with a high-GC content, sequenced from a mixed clinical sample containing Mycobacterium tuberculosis This genome is the first publicly available sequence from a representative of the genus Branchiibius.

Effect of Asthma Call-back Survey methodology changes on work-related asthma estimates, 19 states, 2007-2012

OBJECTIVE

Asthma Call-back Survey methodology has been changed recently, as a new sampling design, weights calculation (2011-2012), and revised work-related asthma (WRA) section (2012) were implemented. To assess the effect of these changes on the WRA and possible WRA estimates among ever-employed adults with current asthma, we analyzed 2007-2012 data for 37 505 ever-employed adults (≥18 years) collected from 19 US states (representing an estimated 10 million adults each year).

METHODS

Using data from landline telephone (LLP) households, we calculated estimates applying poststratification weights (2007-2010) and "raking" weights (2011-2012). Also, using data from LLP/cellular telephone (CP) households combined, we calculated estimates applying "raking" weights (2012).

RESULTS

Based on LLP household data, the WRA estimates ranged from 7.8% to 9.7% during 2007-2010, was 9.1% in 2011 and 15.4% in 2012. Possible WRA estimates ranged from 35.1% to 38.1% during 2007-2010, was 38.1% in 2011 and 39.8% in 2012. Using the 2012 LLP/CP household data, the WRA and possible WRA estimates were 15.4% and 38.9%, respectively.

CONCLUSIONS

Implementation of "raking" weights did not substantially change the WRA or possible WRA estimates among ever-employed adults with current asthma. The WRA and possible WRA estimates based on LLP and LLP/CP samples in 2012 were comparable, as CP users are younger and less likely to have WRA. The substantial upward shift in the 2012 WRA estimates likely was associated with the revision to the WRA section.

Informing the scale-up of Kenya's nursing workforce: a mixed methods study of factors affecting pre-service training capacity and production

BACKGROUND

Given the global nursing shortage and investments to scale-up the workforce, this study evaluated trends in annual student nurse enrolment, pre-service attrition between enrolment and registration, and factors that influence nurse production in Kenya.

METHODS

This study used a mixed methods approach with data from the Regulatory Human Resources Information System (tracks initial student enrolment through registration) and the Kenya Health Workforce Information System (tracks deployment and demographic information on licensed nurses) for the quantitative analyses and qualitative data from key informant interviews with nurse training institution educators and/or administrators. Trends in annual student nurse enrolment from 1999 to 2010 were analyzed using regulatory and demographic data. To assess pre-service attrition between training enrolment and registration with the nursing council, data for a cohort that enrolled in training from 1999 to 2004 and completed training by 2010 was analyzed. Multivariate logistic regression was used to test for factors that significantly affected attrition. To assess the capacity of nurse training institutions for scale-up, qualitative data was obtained through key informant interviews.

RESULTS

From 1999 to 2010, 23,350 students enrolled in nurse training in Kenya. While annual new student enrolment doubled between 1999 (1,493) and 2010 (3,030), training institutions reported challenges in their capacity to accommodate the increased numbers. Key factors identified by the nursing faculty included congestion at clinical placement sites, limited clinical mentorship by qualified nurses, challenges with faculty recruitment and retention, and inadequate student housing, transportation and classroom space. Pre-service attrition among the cohort that enrolled between 1999 and 2004 and completed training by 2010 was found to be low (6%).

CONCLUSION

To scale-up the nursing workforce in Kenya, concurrent investments in expanding the number of student nurse clinical placement sites, utilizing alternate forms of skills training, hiring more faculty and clinical instructors, and expanding the dormitory and classroom space to accommodate new students are needed to ensure that increases in student enrolment are not at the cost of quality nursing education. Student attrition does not appear to be a concern in Kenya compared to other African countries (10 to 40%).

Effects of exposure uncertainties in the TSCE model and application to the Colorado miners data

The simulations in this paper show that exposure measurement error affects the parameter estimates of the biologically motivated two-stage clonal expansion (TSCE) model. For both Berkson and classical error models, we show that likelihood-based techniques of correction work reliably. For classical errors, the distribution of true exposures needs to be known or estimated in addition to the distribution of recorded exposures conditional on true exposures. Usually the exposure uncertainty biases the model parameters toward the null and underestimates the precision. But when several parameters are allowed to be dependent on exposure, e.g. initiation and promotion, then their relative importance is also influenced, and more complicated effects of exposure uncertainty can occur. The application part of this paper shows for two different types of Berkson errors that a recent analysis of the data for the Colorado plateau miners with the TSCE model is not changed substantially when correcting for such errors. Specifically, the conjectured promoting action of radon remains as the dominant radiation effect for explaining these data. The estimated promoting action of radon increases by a factor of up to 1.2 for the largest assumed exposure uncertainties.

Surfactant-induced increases of permeability of rat oral mucosa to non-electrolytes in vivo

The effect of non-ionic, cationic and anionic surfactants on non-electrolyte permeability of rat oral mucosa in vivo was tested. The surfactants caused an increase in mucosal permeability to oil-soluble compounds and small and large water-soluble compounds. The effect was concentration-dependent, and both the cationic and anionic surfactants were more potent than the non-ionic compounds. Surfactant-treated tissue showed widening of the stratum corneum due to separation of layers and loss of surface layers. Measurement of the permeability to sodium lauryl sulphate indicated that this anionic surfactant produced damage to the permeability barrier.