CRISPR-based diagnostics.

The accurate and timely diagnosis of disease is a prerequisite for efficient therapeutic intervention and epidemiological surveillance. Diagnostics based on the detection of nucleic acids are among the most sensitive and specific, yet most such assays require costly equipment and trained personnel. Recent developments in diagnostic technologies, in particular those leveraging clustered regularly interspaced short palindromic repeats (CRISPR), aim to enable accurate testing at home, at the point of care and in the field. In this Review, we provide a rundown of the rapidly expanding toolbox for CRISPR-based diagnostics, in particular the various assays, preamplification strategies and readouts, and highlight their main applications in the sensing of a wide range of molecular targets relevant to human health.

Estimating the health impact of vaccination against ten pathogens in 98 low-income and middle-income countries from 2000 to 2030: a modelling study.

BACKGROUND: The past two decades have seen expansion of childhood vaccination programmes in low-income and middle-income countries (LMICs). We quantify the health impact of these programmes by estimating the deaths and disability-adjusted life-years (DALYs) averted by vaccination against ten pathogens in 98 LMICs between 2000 and 2030. METHODS: 16 independent research groups provided model-based disease burden estimates under a range of vaccination coverage scenarios for ten pathogens: hepatitis B virus, Haemophilus influenzae type B, human papillomavirus, Japanese encephalitis, measles, Neisseria meningitidis serogroup A, Streptococcus pneumoniae, rotavirus, rubella, and yellow fever. Using standardised demographic data and vaccine coverage, the impact of vaccination programmes was determined by comparing model estimates from a no-vaccination counterfactual scenario with those from a reported and projected vaccination scenario. We present deaths and DALYs averted between 2000 and 2030 by calendar year and by annual birth cohort. FINDINGS: We estimate that vaccination of the ten selected pathogens will have averted 69 million (95% credible interval 52-88) deaths between 2000 and 2030, of which 37 million (30-48) were averted between 2000 and 2019. From 2000 to 2019, this represents a 45% (36-58) reduction in deaths compared with the counterfactual scenario of no vaccination. Most of this impact is concentrated in a reduction in mortality among children younger than 5 years (57% reduction [52-66]), most notably from measles. Over the lifetime of birth cohorts born between 2000 and 2030, we predict that 120 million (93-150) deaths will be averted by vaccination, of which 58 million (39-76) are due to measles vaccination and 38 million (25-52) are due to hepatitis B vaccination. We estimate that increases in vaccine coverage and introductions of additional vaccines will result in a 72% (59-81) reduction in lifetime mortality in the 2019 birth cohort. INTERPRETATION: Increases in vaccine coverage and the introduction of new vaccines into LMICs have had a major impact in reducing mortality. These public health gains are predicted to increase in coming decades if progress in increasing coverage is sustained. FUNDING: Gavi, the Vaccine Alliance and the Bill & Melinda Gates Foundation.

Assessment of infectious complications in elderly kidney transplant recipients receiving induction with anti-thymocyte globulin vs basiliximab.

BACKGROUND: Elderly transplant recipients experience lower rates of acute rejection with higher rates of infectious complications compared to their younger counterparts. While less intensive immunosuppression may be preferable, there are no recommendations for depleting versus non-depleting induction strategies. We sought to compare infectious complications between anti-thymocyte globulin (ATG) and basiliximab (IL2RA) induction in elderly kidney transplant recipients (KTRs). METHODS: We reviewed 146 KTRs ≥65 years receiving ATG or IL2RA induction. Per institution protocol, ATG was administered to patients with the following characteristics, irrespective of age: African American (AA), PRA ≥20%, and/or re-transplantation. Infectious complications (bacterial, viral, and invasive fungal) at 1 year were compared. RESULTS: There were significantly more AA, deceased donors, and sensitized KTRs in the ATG group, reflecting criteria for induction agent. ATG KTRs experienced higher rates of overall infectious complications (77% vs 56%, P = .01), driven by increased bacterial (54% vs 39%, P = .08) and viral infections (51% vs 35%, P = .05). Urinary tract infections (UTIs) and CMV in particular occurred at high rates among ATG patients (46% and 32%, respectively). In multivariate analysis, the only independent risk factor associated with increased risk for infection was induction with ATG (adjusted HR 1.71 [95% CI 1.04-2.83], P = .04). Overall rates of immunologic outcomes were low. CONCLUSION: Elderly KTRs receiving ATG are at an increased risk for infectious complications, largely attributed to high rates of UTIs and CMV. Additional strategies aimed at mitigating these complications in elderly patients requiring ATG may be beneficial.

Viral Forecasting, Pathogen Cataloging, and Disease Ecosystem Mapping: Measuring Returns on Investments.

Infectious disease emergence into humans from animals or the environment occurs primarily due to genetic changes in the microbe through mutation or re-assortment making it either more transmissible or virulent or through a change in the disease "ecosystem". Research into infectious disease emergence can be grouped into different strategic approaches. One strategic approach is to study a specific or model disease system to understand the ecology of an infectious disease and how is transmitted and propagated through the environment and different hosts and then extrapolate that disease system knowledge to related pathogens. The other strategic approach follows the genomics and phylogenetics-tracking how pathogens are evolving and changing at the amino acid level. Here we argue that for understanding complex zoonotic diseases and for the purposes of preventing emergence and re-emergence into humans, that the Return on Investment be considered for the best research strategy.

Assessment of eight nucleic acid amplification technologies for potential use to detect infectious agents in low-resource settings.

Nucleic acid amplification technologies (NAATs) are high-performance tools for rapidly and accurately detecting infectious agents. They are widely used in high-income countries to diagnose disease and improve patient care. The complexities associated with test methods, reagents, equipment, quality control and assurance require dedicated laboratories with trained staff, which can exclude their use in low-resource and decentralized healthcare settings. For certain diseases, fully integrated NAAT devices and assays are available for use in environmentally-controlled clinics or emergency rooms where relatively untrained staff can perform testing. However, decentralized settings in many low- and middle-income countries with large burdens of infectious disease are challenged by extreme environments, poor infrastructure, few trained staff and limited financial resources. Therefore, there is an urgent need for low-cost, integrated NAAT tools specifically designed for use in low-resource settings (LRS). Two essential components of integrated NAAT tools are: 1) efficient nucleic acid extraction technologies for diverse and complex sample types; and 2) robust and sensitive nucleic acid amplification and detection technologies. In prior work we reported the performance and workflow capacity for the nucleic acid extraction component. In the current study we evaluated performance of eight novel nucleic acid amplification and detection technologies from seven developers using blinded panels of RNA and/or DNA from three pathogens to assess both diagnostic accuracy and suitability as an essential component for low-cost NAAT in LRS. In this exercise, we noted significant differences in performance among these technologies and identified those most promising for potential further development.

Infections and associated behaviors among deceased organ donors: Informing the assessment of risk.

BACKGROUND: For infectious disease risk assessment among deceased organ donors, pre-donation clinical, microbiological, and behavioral information are reviewed; however, uncertainty may arise due to false negative screening results of recently acquired infections. METHOD: The burden of hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV), and residual risks (RR) of undetected virus was estimated, with the impact of more sensitive screening. RESULTS: For United Kingdom potential deceased organ donors between 2010 and 2014, prevalence of HBsAg was 0.1%, HIV 0.06% and HCV 0.9%, increasing to 25.7% in people who injected drugs (PWID). Incidence, derived from new blood donors, was multiplied by duration of screening assay window periods to give RR per 100 000 donors as 0.43 (95% confidence interval [CI] 0.03-3.99) for HBV, 0.08 (95% CI 0.02-0.21) for HIV, and 5.96 (95% CI 0.82-37.89) for HCV. For PWID, HCV RR was 163.3 (95% CI 22.8-1107.8) compared to 2.76 (95% CI 0.35-17.36) for non-PWID. RR decreased significantly with nucleic acid testing (NAT), and, for HCV, antigen testing had a similar impact. CONCLUSION: While the burden of HCV risk lies within PWID, these are in small numbers therefore few HCV antigen or NAT tests would be needed to more accurately assess risk.

Risk assessment of Ebola Reston virus in humans in the Philippines.

OBJECTIVE: There have been five documented outbreaks of Ebola Reston virus (RESTV) in animals epidemiologically linked to the Philippines. This assessment was conducted to determine the risk of RESTV occurring in humans in the Philippines and its potential pathogenicity in humans. METHODS: The World Health Organization Rapid Risk Assessment of Acute Public Health Events Manual was used for the assessment. A literature review was done and a risk assessment matrix was used for the risk characterization of the outbreaks in the Philippines. The risk assessment was conducted by the Philippines Field Epidemiology Training Program. RESULTS: The risk of RESTV occurring in humans in the Philippines and its potential pathogenicity in humans were both assessed as moderate. Animals involved in RESTV outbreaks in the Philippines were non-human primates and domestic pigs. The presence of RESTV in pigs poses a possibility of genetic evolution of the virus. Although RESTV has been identified in humans, there was no death or illness attributed to the infection. The Philippines Inter-agency Committee on Zoonoses oversees collaboration between the animal and human health sectors for the prevention and control of zoonoses. However, there is no surveillance of risk animals or previously affected farms to monitor and facilitate early identification of cases. DISCUSSION: The moderate risk of RESTV recurring among humans in the Philippines and its potential pathogenicity in humans reinforces the need for early detection, surveillance and continued studies of RESTV pathogenesis and its health consequences. The One Health approach, with the involvement and coordination of public health, veterinary services and the community, is essential in the detection, control and management of zoonosis.

Human Resources for Treating HIV/AIDS: Are the Preventive Effects of Antiretroviral Treatment a Game Changer?

Shortages of human resources for treating HIV/AIDS (HRHA) are a fundamental barrier to reaching universal antiretroviral treatment (ART) coverage in developing countries. Previous studies suggest that recruiting HRHA to attain universal ART coverage poses an insurmountable challenge as ART significantly increases survival among HIV-infected individuals. While new evidence about ART's prevention benefits suggests fewer infections may mitigate the challenge, new policies such as treatment-as-prevention (TasP) will exacerbate it. We develop a mathematical model to analytically study the net effects of these countervailing factors. Using South Africa as a case study, we find that contrary to previous results, universal ART coverage is achievable even with current HRHA numbers. However, larger health gains are possible through a surge-capacity policy that aggressively recruits HRHA to reach universal ART coverage quickly. Without such a policy, TasP roll-out can increase health losses by crowding out sicker patients from treatment, unless a surge capacity exclusively for TasP is also created.

Imported infections: What information should be collected by surveillance systems to inform public health policy?

BACKGROUND: International travel carries the risk of imported diseases, which are an increasingly significant public health problem. There is little guidance about which variables should be collected by surveillance systems for strategy-based surveillance. METHODS: Surveillance forms for dengue, malaria, hepatitis A, typhoid and measles were collected from Australia and New Zealand and information on these compared with national surveillance forms from the UK and Canada by travel health experts. Variables were categorised by information relating to recent travel, demographics and disease severity. RESULTS: Travel-related information most commonly requested included country of travel, vaccination status and travel dates. In Australia, ethnicity information requested related to indigenous status, whilst in New Zealand it could be linked to census categories. Severity of disease information most frequently collected were hospitalisation and death. CONCLUSIONS: Reviewing the usefulness of variables collected resulted in the recommendation that those included should be: overseas travel, reason for travel, entry and departure dates during the incubation period, vaccination details, traveller's and/or parents' country of birth, country of usual residence, time resident in current country, postcode, hospitalisation and death details. There was no agreement about whether ethnicity details should be collected. The inclusion of these variables on surveillance forms could enable imported infection-related policy to be formulated nationally and internationally.

Infectious disease burden and cognitive function in young to middle-aged adults.

Prior research has suggested an association between exposure to infectious disease and neurocognitive function in humans. While most of these studies have explored individual viral, bacterial, and even parasitic sources of infection, few have considered the potential neurocognitive burden associated with multiple infections. In this study, we utilized publically available data from a large dataset produced by the Centers for Disease Control and Prevention that included measures of neurocognitive function, sociodemographic variables, and serum antibody data for several infectious diseases. Specifically, immunoglobulin G antibodies for toxocariasis, toxoplasmosis, hepatitis A, hepatitis B, and hepatitis C, cytomegalovirus, and herpes 1 and 2 were available in 5662 subjects. We calculated an overall index of infectious-disease burden to determine if an aggregate measure of exposure to infectious disease would be associated with neurocognitive function in adults aged 20-59 years. The index predicted processing speed and learning and memory but not reaction time after controlling for age, sex, race-ethnicity, immigration status, education, and the poverty-to-income ratio. Interactions between the infectious-disease index and some sociodemographic variables were also associated with neurocognitive function. In summary, an index aggregating exposure to several infectious diseases was associated with neurocognitive function in young- to middle-aged adults.

[THE CONDITION AND TENDENCIES OF DEVELOPMENT OF CLINICAL AND SANITARY MICROBIOLOGY IN THE RUSSIAN FEDERATION AND PROBLEM OF IMPORT SUBSTITUTION].

The import substitution becomes one of the strategic tasks of national economy as a result of prolongation of economic sanctions concerning the Russian Federation of part of the USA, EU countries, Japan and number of other countries. It is not proper to be limited in import substitution only by goods because in conditions ofsanctions when access toforeign technologies is complicated Russia is needed to substitute foreign technologies by national designs in faster manner One of directions of effective import substitution is localization of production of laboratory equipment and consumables for clinical and sanitary microbiology on the territory ofthe Russian Federation and countries of Customs union. In Russia, in the field ofdiagnostic of dangerous and socially significant infections, all components for import substitution to implement gene diagnostic, immune diagnostic. bio-sensory and biochip approaches, isolation and storage of live microbial cultures, implementation of high-tech methods of diagnostic are available. At the same time, national diagnostic instrument-making industry for microbiology is factually absent. The few devices of national production more than on 50% consist of import components. The microbiological laboratories are to be equipped only with import devices of open type for applying national components. The most perspective national designs to be implemented are multiplex polimerase chain reaction test-systems and biochips on the basis of national plotters and readers. The modern development of diagnostic equipment and diagnostic instruments requires supplement of national collections of bacterial and viral pathogens and working-through of organizational schemes of supplying collections with strains. The presented data concerning justification of nomenclature of laboratory equipment and consumables permits to satisfy in fill scope the needs of clinical and sanitary microbiology in devices, growth mediums, consumables of national production and to refuse import deliveries without decreasing quality of microbiological analysis. This approach will ensure appropriate response to occurring challenges and new biological dangers and maintenance of biosecurity of the Russian Federation at proper level.

Lifecourse infectious origins of sexual inequalities in central adiposity.

BACKGROUND: Social disparities in obesity are often more marked among women than men, possibly due to social factors. Taking a life-history perspective, we hypothesized that childhood infections could be relevant via sex-specific effects of immune system activation on sexual development and, hence, body shape. METHODS: We used multivariable linear regression to assess the sex-specific, adjusted associations of 'childhood' pathogens [0 (n = 1002), 1 (n = 2199), 2 (n = 3442) or 3 (n = 4833) of HSV1, CMV and hepatitis A antibodies] and 'adult' pathogens [0 (n = 5836), 1 (n = 3018) or ≥ 2 (n = 720) of HSV2, HHV8 and hepatitis B or C) with waist-hip ratio (WHR) and body mass index (BMI) standard deviations (SDs) using NHANES III (1988-94). As validation, we assessed associations with height. RESULTS: 'Childhood' pathogens were positively associated with WHR among women [0.18 SD, 95% confidence interval (95% CI) 0.04-0.32 for 3, compared with 0], but not men (-0.04 SD, 95% CI -0.15 to 0.08), adjusted for age, education, race/ethnicity, smoking and alcohol. Further adjustments for leg length barely changed the estimates. There were no such sex-specific associations for BMI or for adult pathogens. 'Childhood', but not 'adult', pathogens were negatively associated with height, adjusted for age, sex, education and race/ethnicity. CONCLUSIONS: These observations are consistent with the lifecourse hypothesis that early exposure to infections makes women vulnerable to central obesity. This hypothesis potentially sheds new light on the developmental origins of obesity, and is consistent with the generally higher levels of central obesity among women than men in developing populations.

QMRAspot: a tool for Quantitative Microbial Risk Assessment from surface water to potable water.

In the Netherlands, a health based target for microbially safe drinking water is set at less than one infection per 10,000 persons per year. For the assessment of the microbial safety of drinking water, Dutch drinking water suppliers must conduct a Quantitative Microbial Risk Assessment (QMRA) at least every three years for the so-called index pathogens enterovirus, Campylobacter, Cryptosporidium and Giardia. In order to collect raw data in the proper format and to automate the process of QMRA, an interactive user-friendly computational tool, QMRAspot, was developed to analyze and conduct QMRA for drinking water produced from surface water. This paper gives a description of the raw data requirements for QMRA as well as a functional description of the tool. No extensive prior knowledge about QMRA modeling is required by the user, because QMRAspot provides guidance to the user on the quantity, type and format of raw data and performs a complete analysis of the raw data to yield a risk outcome for drinking water consumption that can be compared with other production locations, a legislative standard or an acceptable health based target. The uniform approach promotes proper collection and usage of raw data and, warrants quality of the risk assessment as well as enhances efficiency, i.e., less time is required. QMRAspot may facilitate QMRA for drinking water suppliers worldwide. The tool aids policy makers and other involved parties in formulating mitigation strategies, and prioritization and evaluation of effective preventive measures as integral part of water safety plans.

STOPFLU: is it possible to reduce the number of days off in office work by improved hand-hygiene?

BACKGROUND: Acute infectious diseases are major causes of short periods of days off from work, day care and school. These diseases are mainly caused by viruses and hands have a key role in their transmission. Thus, hypothetically, they can be controlled with means of intensified hand hygiene. In this study we aim to elucidate the effect of acute infectious diseases on the work contribution in common office work and study the influence of improved hand hygiene on possible reduction of infectious disease episodes and days off from work due to acute infectious diseases. DESIGN: The voluntary participants have been recruited from six companies in the Helsinki region. The designated 21 study clusters were identified as operationally distinct working units each containing at least 50 people. The clusters were matched and randomized based on results of a pre-trial contagion risk survey. Improved hand hygiene is being executed with guided hand-washing with soap and water in one intervention arm and with alcohol based hand rubbing disinfectant in the other. Participants in both arms have received guidance on how to avoid infections and how to implement contagion stopping habits. A control arm is acting as before regarding hand hygiene. Data collection for evaluation of the efficacy of the interventions is based on self-reporting through weekly electronic reports. The questionnaire is enquiring about possible respiratory or gastrointestinal symptoms during the preceding week, and requests a daily report of presence of symptoms and working capacity. Etiology of the symptoms is not searched for individually, but contribution of different viruses is evaluated by sentinel surveillance, where occupational health clinics located in the premises of the participating companies collect specimens from employees visiting the clinic. Common causative agents of the diseases are being searched for using real-time PCR techniques. The duration of the intervention will be 16 months. Primary endpoints of the study are the number of reported infection episodes in a cluster within a time frame of 100 reporting weeks and the number of reported sick leave episodes in a cluster within a time frame of 100 reporting weeks. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT00821509.