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Ethnic and religious minorities have been disproportionately affected by the SARSCoV-2 pandemic and are less likely to accept coronavirus vaccinations. Orthodox (Haredi) Jewish neighbourhoods in England experienced high incidences of SARSCoV-2 in 2020-21 and measles outbreaks (2018-19) due to suboptimal childhood vaccination coverage. The objective of our study was to explore how the COVID-19 vaccination programme (CVP) was co-delivered between public health services and an Orthodox Jewish health organisation. Methods included 28 semi-structured interviews conducted virtually with public health professionals, community welfare and religious representatives, and household members. We examined CVP delivery from the perspectives of those involved in organising services and vaccine beneficiaries. Interview data was contextualised within debates of the CVP in Orthodox (Haredi) Jewish print and social media. Thematic analysis generated five considerations: i) Prior immunisation-related collaboration with public health services carved a role for Jewish health organisations to host and promote coronavirus vaccination sessions, distribute appointments, and administer vaccines ii) Public health services maintained responsibility for training, logistics, and maintaining vaccination records; iii) The localised approach to service delivery promoted vaccination in a minority with historically suboptimal levels of coverage; iv) Co-delivery promoted trust in the CVP, though a minority of participants maintained concerns around safety; v) Provision of CVP information and stakeholders' response to situated (context-specific) challenges and concerns. Drawing on this example of CVP co-delivery, we propose that a localised approach to delivering immunisation programmes could address service provision gaps in ways that involve trusted community organisations. Localisation of vaccination services can include communication or implementation strategies, but both approaches involve consideration of investment, engagement and coordination, which are not cost-neutral. Localising vaccination services in collaboration with welfare groups raises opportunities for the on-going CVP and other immunisation programmes, and constitutes an opportunity for ethnic and religious minorities to collaborate in safeguarding community health.

IntroductionEbola virus disease (EVD) continues to be a significant public health problem in sub-Saharan Africa, especially in the Democratic Republic of the Congo (DRC). Large-scale vaccination during outbreaks may reduce virus transmission. We established a large population-based clinical trial of a heterologous, two-dose prophylactic vaccine during an outbreak in eastern DRC to determine vaccine effectiveness.Methods and analysisThis open-label, non-randomised, population-based trial enrolled eligible adults and children aged 1 year and above. Participants were offered the two-dose candidate EVD vaccine regimen VAC52150 (Ad26.ZEBOV, Modified Vaccinia Ankara (MVA)-BN-Filo), with the doses being given 56 days apart. After vaccination, serious adverse events (SAEs) were passively recorded until 1 month post dose 2. 1000 safety subset participants were telephoned at 1 month post dose 2 to collect SAEs. 500 pregnancy subset participants were contacted to collect SAEs at D7 and D21 post dose 1 and at D7, 1 month, 3 months and 6 months post dose 2, unless delivery was before these time points. The first 100 infants born to these women were given a clinical examination 3 months post delivery. Due to COVID-19 and temporary suspension of dose 2 vaccinations, at least 50 paediatric and 50 adult participants were enrolled into an immunogenicity subset to examine immune responses following a delayed second dose. Samples collected predose 2 and at 21 days post dose 2 will be tested using the Ebola viruses glycoprotein Filovirus Animal Non-Clinical Group ELISA. For qualitative research, in-depth interviews and focus group discussions were being conducted with participants or parents/care providers of paediatric participants.Ethics and disseminationApproved by Comité National d’Ethique et de la Santé du Ministère de la santé de RDC, Comité d'Ethique de l'Ecole de Santé Publique de l’Université de Kinshasa, the LSHTM Ethics Committee and the MSF Ethics Review Board. Findings will be presented to stakeholders and conferences. Study data will be made available for open access.Trial registration numberNCT04152486.

Funder: World Health Organization, Background: Approval for the use of COVID-19 vaccines has been granted in a number of countries but there are concerns that vaccine uptake may be low amongst certain groups. Methods: This study used a mixed methods approach based on online survey and an embedded quantitative/qualitative design to explore perceptions and attitudes that were associated with intention to either accept or refuse offers of vaccination in different demographic groups during the early stages of the UK's mass COVID-19 vaccination programme (December 2020). Analysis used multivariate logistic regression, structural text modeling and anthropological assessments. Results: Of 4,535 respondents, 85% (n = 3,859) were willing to have a COVID-19 vaccine. The rapidity of vaccine development and uncertainties about safety were common reasons for COVID-19 vaccine hesitancy. There was no evidence for the widespread influence of mis-information, although broader vaccine hesitancy was associated with intentions to refuse COVID-19 vaccines (OR 20.60, 95% CI 14.20-30.30, p < 0.001). Low levels of trust in the decision-making (OR 1.63, 95% CI 1.08, 2.48, p = 0.021) and truthfulness (OR 8.76, 95% CI 4.15-19.90, p < 0.001) of the UK government were independently associated with higher odds of refusing COVID-19 vaccines. Compared to political centrists, conservatives and liberals were, respectively, more (OR 2.05, 95%CI 1.51-2.80, p < 0.001) and less (OR 0.30, 95% CI 0.22-0.41, p < 0.001) likely to refuse offered vaccines. Those who were willing to be vaccinated cited both personal and public protection as reasons, with some alluding to having a sense of collective responsibility. Conclusion: Dominant narratives of COVID-19 vaccine hesitancy are misconceived as primarily being driven by misinformation. Key indicators of UK vaccine acceptance include prior behaviors, transparency of the scientific process of vaccine development, mistrust in science and leadership and individual political views. Vaccine programmes should leverage the sense of altruism, citizenship and collective responsibility that motivated many participants to get vaccinated.

Background In Melanesia, the prevalence of trachomatous inflammation–follicular (TF) suggests that public health–level interventions against active trachoma are needed. However, the prevalence of trachomatous trichiasis is below the threshold for elimination as a public health problem and evidence of conjunctival infection with trachoma’s causative organism (Chlamydia trachomatis [CT]) is rare. Here, we examine the prevalence of ocular infection with CT and previous exposure to CT in three evaluation units (EUs) of Papua New Guinea. Methods All individuals aged 1–9 years who were examined for clinical signs of trachoma in 3 Global Trachoma Mapping Project EUs were eligible to take part in this study (N = 3181). Conjunctival swabs were collected from 349 children with TF and tested by polymerase chain reaction to assess for ocular CT infection. Dried blood spots were collected from 2572 children and tested for anti-Pgp3 antibodies using a multiplex assay. Results The proportion of children with TF who had CT infection was low across all 3 EUs (overall 2%). Anti-Pgp3 seroprevalence was 5.2% overall and there was no association between anti-Pgp3 antibody level and presence of TF. In 2 EUs, age-specific seroprevalence did not increase significantly with increasing age in the 1- to 9-year-old population. In the third EU, there was a statistically significant change with age but the overall seroprevalence and peak age-specific seroprevalence was very low. Conclusions Based on these results, together with similar findings from the Solomon Islands and Vanuatu, the use of TF to guide antibiotic mass drug administration decisions in Melanesia should be reviewed., In Papua New Guinea (PNG), prevalence of trachomatous trichiasis is very low. This study demonstrates that prevalence and transmission of ocular Chlamydia trachomatis, a driver of progressive trachomatous disease, is much lower in PNG than in other settings with similar active trachoma prevalence.

Highlights • In Vanuatu, ocular Chlamydia infection prevalence is low; in Kiribati it is high. • In Vanuatu, Pgp3 seroprevalence does not increase in childhood; in Kiribati it does. • Conjunctival scarring is more common in adults in Kiribati than in Vanuatu. • Trachomatous inflammation—follicular lacks specificity for ocular Chlamydia infection. • Non-TF markers may help to determine need for interventions against active trachoma., Introduction In the peri-elimination setting, the positive predictive value of trachomatous inflammation–follicular (TF), the primary marker used to determine need for antibiotics for trachoma, is suboptimal. Here, three non-TF measures are used to compare two regions where TF prevalence exceeds the threshold for intervention, but where the Chlamydia trachomatis (Ct) prevalence is different. Methods Population prevalence of trachoma was measured in Vanuatu (n = 3470) and Kiribati (n = 2922). Dried blood spots (DBS) and conjunctival photographs were collected from every survey participant, and conjunctival swabs were collected from those aged 1–9 years. Individuals were tested for blood anti-Pgp3 antibodies, Ct DNA at the conjunctiva and severity of conjunctival scarring. Results The prevalence of TF in 1–9-year-olds was 16.5% in Vanuatu and 38.2% in Tarawa. 7% of people aged ≥1 year in Vanuatu had conjunctival scarring compared to 27% in Tarawa. The prevalence of ocular Ct infection in 1–9-year-olds was 1.5% in Vanuatu and 27.4% in Tarawa. The seroconversion rate amongst 1–9-year-old children in Vanuatu and Tarawa was 0.018 and 0.197 events per child per year, respectively. Conclusions Comparing Vanuatu to Tarawa demonstrates several markers that could be used to differentiate the trachoma status of populations in these (and other) locations.

Background WHO endorsed the use of epilation as an alternative treatment to surgery for the management of both minor unoperated TT (UTT) and postoperative TT (PTT). However, some trachoma control programmes hesitated to implement epilation citing concerns that it would hamper TT surgical acceptance and result in larger numbers of and stiffer trichiatic eyelashes than the original TT lashes. We investigated the burden and phenotypes of post-epilation trichiatic eyelashes, and willingness to accept surgical management separately in unoperated and postoperative TT cases. Methodology/Principal findings We recruited cases with minor (≤5 eyelashes from the upper eyelid touching the eye or evidence of epilation in, Author summary Trachomatous Trichiasis (TT), the blinding stage of trachoma, ranges from few peripheral eyelashes touching the eye to all eyelashes scratching the cornea. TT is mainly treated with corrective eyelid surgery. However, not all TT cases require surgical correction, and some, particularly, those with few eyelashes decline surgery. Epilation, the repeated removal of eyelashes, is a very common clinical and traditional practice in many trachoma endemic settings. The World Health Organisation recommends that epilation can be offered as an alternative management strategy to surgery for patients with few eyelashes touching the eye or refusing surgery. However, some trachoma control programmes hesitated to implement epilation with the concern that it would hamper surgical acceptance and results in larger numbers of and stiffer eyelashes touching the eye than the original TT eyelashes. In this study, we explored if these concerns are true in epilating minor (≤5 eyelashes from the upper eyelid touching the eye or evidence of epilation in

IntroductionOur project follows community requests for health service incorporation into conservation collaborations in the rainforests of Papua New Guinea (PNG). This protocol is for health needs assessments, our first step in coplanning medical provision in communities with no existing health data.Methods and analysisThe study includes clinical assessments and rapid anthropological assessment procedures (RAP) exploring the health needs and perspectives of partner communities in two areas, conducted over 6 weeks fieldwork. First, in Wanang village (population c.200), which is set in lowland rainforest. Second, in six communities (population c.3000) along an altitudinal transect up the highest mountain in PNG, Mount Wilhelm. Individual primary care assessments incorporate physical examinations and questioning (providing qualitative and quantitative data) while RAP includes focus groups, interviews and field observations (providing qualitative data). Given absence of in-community primary care, treatments are offered alongside research activity but will not form part of the study. Data are collected by a research fellow, primary care clinician and two PNG research technicians. After quantitative and qualitative analyses, we will report: ethnoclassifications of disease, causes, symptoms and perceived appropriate treatment; community rankings of disease importance and service needs; attitudes regarding health service provision; disease burdens and associations with altitudinal-related variables and cultural practices. To aid wider use study tools are in online supplemental file, and paper and ODK versions are available free from the corresponding author.Ethics and disseminationChallenges include supporting informed consent in communities with low literacy and diverse cultures, moral duties to provide treatment alongside research in medically underserved areas while minimising risks of therapeutic misconception and inappropriate inducement, and PNG research capacity building. Brighton and Sussex Medical School (UK), PNG Institute of Medical Research and PNG Medical Research Advisory Committee have approved the study. Dissemination will be via journals, village meetings and plain language summaries.

Background The success of a government’s COVID-19 control strategy relies on public trust and broad acceptance of response measures. We investigated public perceptions of the UK government’s COVID-19 response, focusing on the relationship between trust and perceived transparency, during the first wave (April 2020) of the COVID-19 pandemic in the United Kingdom. Methods Anonymous survey data were collected (2020-04-06 to 2020-04-22) from 9,322 respondents, aged 20+ using an online questionnaire shared primarily through Facebook. We took an embedded-mixed-methods approach to data analysis. Missing data were imputed via multiple imputation. Binomial & multinomial logistic regression were used to detect associations between demographic characteristics and perceptions or opinions of the UK government’s response to COVID-19. Structural topic modelling (STM), qualitative thematic coding of sub-sets of responses were then used to perform a thematic analysis of topics that were of interest to key demographic groups. Results Most respondents (95.1%) supported government enforcement of behaviour change. While 52.1% of respondents thought the government was making good decisions, differences were apparent across demographic groups, for example respondents from Scotland had lower odds of responding positively than respondents in London. Higher educational levels saw decreasing odds of having a positive opinion of the government response and decreasing household income associated with decreasing positive opinion. Of respondents who thought the government was not making good decisions 60% believed the economy was being prioritised over people and their health. Positive views on government decision-making were associated with positive views on government transparency about the COVID-19 response. Qualitative analysis about perceptions of government transparency highlighted five key themes: (1) the justification of opacity due to the condition of crisis, (2) generalised mistrust of politics, (3) concerns about the role of scientific evidence, (4) quality of government communication and (5) questions about political decision-making processes. Conclusion Our study suggests that trust is not homogenous across communities, and that generalised mistrust, concerns about the transparent use and communication of evidence and insights into decision-making processes can affect perceptions of the government’s pandemic response. We recommend targeted community engagement, tailored to the experiences of different groups and a new focus on accountability and openness around how decisions are made in the response to the UK COVID-19 pandemic.

The reported influence of donor Killer-cell Immunoglobulin-like Receptor (KIR) genes on the outcomes of haematopoietic cell transplantation (HCT) are contradictory, in part due to diversity of disease, donor sources, era and conditioning regimens within and between different studies. Here, we describe the results of a retrospective clinical analysis establishing the effect of donor KIR motifs on the outcomes of 119 HLA-matched, unrelated donor HCT for adult acute myeloid leukaemia (AML) using myeloablative conditioning (MAC) in a predominantly T-cell deplete (TCD) cohort. We observed that HCT involving donors with at least one KIR B haplotype were more likely to result in non-relapse mortality (NRM) than HCT involving donors with two KIR A haplotypes (p = 0.019). Upon separation of KIR haplotypes into their centromeric (Cen) and telomeric (Tel) motif structures, we demonstrated that the Cen-B motif was largely responsible for this effect (p = 0.001). When the cause of NRM was investigated further, infection was the dominant cause of death (p = 0.006). No evidence correlating donor KIR B haplotype with relapse risk was observed. The results from this analysis confirm previous findings in the unrelated, TCD, MAC transplant setting and imply a protective role for donor-encoded Cen-A motifs against infection in allogeneic HCT recipients.

Background In the Solomon Islands and Vanuatu, the sign trachomatous inflammation—follicular (TF) is common, but ocular infection with Chlamydia trachomatis is not. It is therefore debatable whether azithromycin mass drug administration (MDA), the recommended antibiotic treatment strategy for trachoma’s elimination as a public health problem, is necessary in this setting. We set out to estimate what proportion of adolescents were at risk of progression of trachomatous scarring. Methods A cross-sectional survey was undertaken of all children aged 10–14 years resident in communities identified as high-TF clusters during previous population-based mapping. Graders examined children for clinical evidence of trachomatous scarring, pannus, and Herbert’s pits (HPs) or limbal follicles in both eyes. A dried blood spot was collected from each child and tested for antibodies to C. trachomatis. Results A total of 492 children in 24 villages of the Solomon Islands and Vanuatu were examined. In total, 35/492 (7%) of children had limbal signs (pannus and/or HPs) plus any conjunctival scarring. And 9/492 (2%) had limbal signs and moderate or severe conjunctival scarring; 22% of children were anti-Pgp3 seropositive. Conclusions Few adolescents here are at risk of future complications from trachoma, supporting the conclusion that further antibiotic MDA is not currently required for trachoma elimination purposes in these settings., In Solomon Islands and Vanuatu communities in which active trachoma prevalence in children was previously high, prevalence of Herbert’s pits or pannus plus conjunctival scarring in 10–14-year-olds is low, suggesting risk of future trachomatous blindness here is also low.

Summary Background Trachomatous trichiasis is treated surgically to prevent sight loss. Unfavourable surgical outcomes remain a major challenge. We investigated the hypothesis that doxycycline might reduce the risk of postoperative trichiasis following surgery in patients with trachomatous trichiasis through anti-matrix metalloproteinase and anti-inflammatory activity. Methods In this randomised, double-blind, placebo-controlled trial, adults (aged >18 years) with upper lid trachomatous trichiasis in association with tarsal conjunctive scarring were recruited through community-based screening and surgical outreach campaigns in Ethiopia. Individuals who had previously had eyelid surgery were excluded. Participants were randomly assigned (1:1), with random block sizes of four or six, to receive oral doxycycline (100 mg once a day) or placebo for 28 days immediately after trichiasis surgery. Randomisation was stratified by surgeon. Patients, investigators, surgeons, and all other study team members were masked to study group allocation and treatment. Participants were examined at 10 days, and 1, 6, and 12 months after surgery. The primary outcome was the cumulative proportion of individuals who developed postoperative trichiasis by 12 months. Primary analyses were done in all participants who attended at least one of the four follow-up assessments. Safety analyses were done in all participants who attended either the 10 day or 1 month follow-up assessments. This trial is registered with the Pan African Clinical Trials Registry, number PACTR201512001370307. Findings Between Dec 21, 2015, and April 6, 2016, 1000 patients with trichiasis were enrolled and randomly assigned to treatment (499 patients to doxycycline, 501 patients to placebo). All but one participant attended at least one follow-up assessment. Thus, 999 participants were assessed for the primary outcome: 498 in the doxycycline group and 501 in the placebo group. By month 12, 58 (12%) of 498 patients in the doxycycline group and 62 (12%) of 501 patients in the placebo group had developed postoperative trichiasis (adjusted odds ratio 0·91, 95% CI 0·61 to 1·34, p=0·63), with a risk difference of −0·5% (–4·5% to 3·5%). Significantly more patients in the doxycycline group had an adverse event than in the placebo group (18 [4%] of 498 vs six [1%] of 501; odds ratio 3·09, 95% CI 1·21–7·84; p=0·02). The most frequent adverse events in the doxycycline group were gastritis symptoms (n=9), constipation (n=4), and diarrhoea (n=4). Interpretation Doxycycline did not reduce the risk of postoperative trichiasis and is therefore not indicated for the improvement of outcomes following trachomatous trichiasis surgery. Surgical programmes should continue to make efforts to strengthen surgical training and supervision to improve outcomes. Funding The Wellcome Trust.

BackgroundAs concerns about the prevalence of infections that are resistant to available antibiotics increase, attention has turned toward the use of these medicines both within and outside of formal healthcare settings. Much of what is known about use beyond formal settings is informed by survey-based research. Few studies to date have used comparative, mixed-methods approaches to render visible patterns of use within and between settings as well as wider points of context shaping these patterns.DesignThis article analyses findings from mixed-methods anthropological studies of antibiotic use in a range of rural and urban settings in Zimbabwe, Malawi and Uganda between 2018 and 2020. All used a ‘drug bag’ survey tool to capture the frequency and types of antibiotics used among 1811 households. We then undertook observations and interviews in residential settings, with health providers and key stakeholders to better understand the stories behind the most-used antibiotics.ResultsThe most self-reported ‘frequently used’ antibiotics across settings were amoxicillin, cotrimoxazole and metronidazole. The stories behind their use varied between settings, reflecting differences in the configuration of health systems and antibiotic supplies. At the same time, these stories reveal cross-cutting features and omissions of contemporary global health programming that shape the contours of antibiotic (over)use at national and local levels.ConclusionsOur findings challenge the predominant focus of stewardship frameworks on the practices of antibiotic end users. We suggest future interventions could consider systems—rather than individuals—as stewards of antibiotics, reducing the need to rely on these medicines to fix other issues of inequity, productivity and security.

© 2017 The Author(s). The frequency and duration of Chlamydia trachomatis (Ct) ocular infections decrease with age, suggesting development of partial immunity. However, there is a lack of clear correlates of immunity to Ct infection in humans. We screened sera from a cohort of Gambian children followed for six-months against a Ct-proteome microarray. At genome sequence level, we detected signatures of selection from a population of ocular Ct isolates from Guinea-Bissau. Together these approaches allowed us to highlight the focus of humoral responses and hypothesise new modes of pathogen immune evasion. Children who were susceptible to frequent and/or prolonged Ct infection had a less focussed antibody response, including preferential recognition of forty-two antigens. There was evidence of positive and purifying selection across the genome, but little balancing selection. In contrast, most antigens that were associated with susceptibility were under neutral selection. These data suggest an evasion strategy in which Ct presents a large panel of irrelevant antigens to the immune system to block or misdirect protective responses. Development of a focused immune response, possibly induced through vaccination, may be an effective strategy to promote protection to Ct infection.

BackgroundTrachoma, a neglected tropical disease, is the leading infectious cause of blindness and visual impairment worldwide. Host responses to ocular chlamydial infection resulting in chronic inflammation and expansion of non-chlamydial bacteria are hypothesised risk factors for development of active trachoma and conjunctival scarringMethodsOcular swabs from trachoma endemic populations in The Gambia were selected from archived samples for 16S sequencing and host conjunctival gene expression. We recruited children with active trachoma and adults with conjunctival scarring, alongside corresponding matched controls.FindingsIn children, active trachoma was not associated with significant changes in the ocular microbiome.Haemophilusenrichment was associated with antimicrobial responses but not linked to active trachoma. Adults with scarring trachoma had a reduced ocular bacterial diversity compared to controls, with increased relative abundance ofCorynebacterium. Increased abundance ofCorynebacteriumin scarring disease was associated with innate immune responses to the microbiota, dominated by altered mucin expression and increased matrix adhesion.InterpretationIn the absence of currentC. trachomatisinfection, changes in the ocular microbiome associate with antimicrobial and inflammatory responses that impair epithelial cell health. In scarring trachoma, expansion of ‘non-pathogenic’ bacteria such asCorynebacteriumand innate responses are coincident, warranting further investigation of this relationship. Comparisons between active and scarring trachoma supported the relative absence of type-1 interferon responses in scarring, whilst highlighting a common suppression of re-epithelialisation with altered epithelial and bacterial adhesion, likely contributing to development of scarring pathology.

Yaws is a neglected tropical disease targeted for eradication by 2020. Kiribati, a Pacific Island nation, was previously endemic for yaws but lacks recent data from which its current endemicity status could be determined. This study tested antibody responses to Treponema pallidum to determine if transmission of yaws is taking place among children in Kiribati. Using a commercially available T. pallidum particle agglutination kit (Serodia®, Fujirebio Inc., Tokyo, Japan), we tested dried blood spots, collected during population-based trachoma prevalence surveys on Tarawa Atoll and Kiritimati Island, for long-lived treponemal antibodies. Dried blood spots from 1,420 children aged 1–9 years were tested. Only two were positive, suggesting T. pallidum is not being widely transmitted among children in the settings sampled. These data require support from additional surveys to demonstrate the absence of clinical signs of disease and molecular evidence of infection, to confirm that yaws is no longer endemic in Kiribati.

Made available in DSpace on 2019-10-06T16:55:02Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 Wisconsin Turfgrass Association National Institutes of Health Wellcome Trust Institute for National Strategic Studies Leukemia and Lymphoma Research Seventh Framework Programme Horizon 2020 Medical Research Council Canada National Institute on Drug Abuse National Institute of Child Health and Human Development Killer cell immunoglobulin-like receptors (KIRs) are expressed predominantly on natural killer cells, where they play a key role in the regulation of innate immune responses. Recent studies show that inhibitory KIRs can also affect adaptive T cell–mediated immunity. In mice and in human T cells in vitro, inhibitory KIR ligation enhanced CD8+ T cell survival. To investigate the clinical relevance of these observations, we conducted an extensive immunogenetic analysis of multiple independent cohorts of HIV-1–, hepatitis C virus (HCV)–, and human T cell leukemia virus type 1 (HTLV-1)–infected individuals in conjunction with in vitro assays of T cell survival, analysis of ex vivo KIR expression, and mathematical modeling of host-virus dynamics. Our data suggest that functional engagement of inhibitory KIRs enhances the CD8+ T cell response against HIV-1, HCV, and HTLV-1 and is a significant determinant of clinical outcome in all three viral infections. Department of Medicine Imperial College London Faculty of Engineering São Paulo State University—UNESP Institute for Infection and Immunity St. George’s University of London International AIDS Vaccine Initiative Human Immunology Laboratory Clinical Research Department London School of Hygiene and Tropical Medicine Divi-sion of Infection and Immunity Cardiff University School of Medicine Nuffield Department of Medicine University of Oxford Oxford NIHR Biomedical Research Centre Immunology Division Department of Pathology University of Cambridge Cancer and Inflammation Program Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research Johns Hopkins University Rho San Francisco Department of Public Health Faculty of Medicine University of Southampton Division of Cancer Epidemiology and Genetics National Cancer Institute Ragon Institute of MGH, MIT and Harvard Faculty of Engineering São Paulo State University—UNESP Wisconsin Turfgrass Association: 090323/Z/09/Z National Institutes of Health: 100326Z/12/Z Wellcome Trust: 103865Z/14/Z Institute for National Strategic Studies: 105609/Z/14/Z Leukemia and Lymphoma Research: 15012 Seventh Framework Programme: 317040 Horizon 2020: 695551 Medical Research Council Canada: G1001052 Medical Research Council Canada: J007439 National Institute on Drug Abuse: K24-AI118591 Medical Research Council Canada: MR/L018373/L Medical Research Council Canada: MR/M019829/1 Medical Research Council Canada: MR/P001602/1 National Institutes of Health: R01 DA13324 National Institute on Drug Abuse: R01-DA-12568 National Institute of Child Health and Human Development: R01-HD-41224 National Institute on Drug Abuse: U01-DA-036297

Introduction Trachoma is endemic in several Pacific Island countries. The aims of this study were to (a) identify future trachoma mapping needs in the Pacific and (b) to examine whether any temporal trends in trachoma prevalence could be ascertained from the historical literature on trachoma in the Pacific Islands. Methods Human studies of trachoma and eye care in the Pacific Islands were identified from a systematic search of PubMed, EMbase, Scopus and Web of Science databases. A published quality assessment system for disease prevalence studies was modified to assess studies for quality and transparency. Results Few general ophthalmic studies in the Pacific mention trachoma. In targeted studies of trachoma, cases have consistently been identified throughout the Pacific since the early twentieth century. The largest number of studies come from Papua New Guinea and Fiji, whereas some countries have no published data on trachoma. The majority of studies identified were published before the Alliance for the Global Elimination of Trachoma 2020 was convened, so lack the standardisation of population-based mapping which has been implemented in the past decade. Conclusions Population-based trachoma prevalence estimates have been recently generated in Papua New Guinea, Solomon Islands, Vanuatu, Kiribati and Fiji. There is insufficient evidence to assess whether there has been temporal change in trachoma prevalence in these countries over the past century. Cases of trachoma have been identified in some countries (for example, Nauru and Samoa) which have no recent population-based mapping data, but may be at risk of trachoma endemcitiy. Deployment of appropriate mapping strategies is warranted to identify whether interventions are required.

Chlamydia trachomatis is the most commonly diagnosed bacterial sexually transmitted infection and can lead to tubal factor infertility, a disease characterised by fibrosis of the fallopian tubes. Genetic polymorphisms in molecular pathways involving G protein-coupled receptor signalling, the Akt/PI3K cascade, the mitotic cell cycle, and immune response have been identified in association with the development of trachomatous scarring, an ocular form of chlamydia-related fibrotic pathology. In this case-control study, we performed genome-wide association and pathways-based analysis in a sample of 71 Dutch women who attended an STI clinic who were seropositive for Chlamydia trachomatis antibodies and 169 high-risk Dutch women who sought similar health services but who were seronegative. We identified two regions of within-gene SNP association with Chlamydia trachomatis serological response and found that GPCR signalling and cell cycle pathways were also associated with the trait. These pathway-level associations appear to be common to immunological sequelae of chlamydial infections in both ocular and urogenital tropisms. These pathways may be central mediators of human refractoriness to chlamydial diseases.

Trachoma is a blinding disease usually caused by infection withChlamydia trachomatis (Ct)serovars A, B, and C in the upper tarsal conjunctiva. Individuals in endemic regions are repeatedly infected withCtthroughout childhood. A proportion of individuals experience prolonged or severe inflammatory episodes that are known to be significant risk factors for ocular scarring in later life. Continued scarring often leads to trichiasis and in-turning of the eyelashes, which causes pain and can eventually cause blindness. The mechanisms driving the chronic immunopathology in the conjunctiva, which largely progresses in the absence of detectableCtinfection in adults, are likely to be multifactorial. Socioeconomic status, education, and behavior have been identified as contributing to the risk of scarring and inflammation. We focus on the contribution of host and pathogen genetic variation, bacterial ecology of the conjunctiva, and host epigenetic imprinting including small RNA regulation by both host and pathogen in the development of ocular pathology. Each of these factors or processes contributes to pathogenic outcomes in other inflammatory diseases and we outline their potential role in trachoma.

The health impact of many copy number variants in our genome remains still largely to be discovered. Detecting and genotyping this often complex variation presents a technical challenge. Here we describe a 96-well format droplet digital PCR (ddPCR) protocol for genotyping a common copy variant in the human haptoglobin gene. ddPCR allows for high-throughput and accurate quantitation of gene copy numbers.

Objective In some Pacific Island countries, such as Solomon Islands and Fiji, active trachoma is common, but ocular Chlamydia trachomatis (Ct) infection and trachomatous trichiasis (TT) are rare. On Tarawa, the most populous Kiribati island, both the active trachoma sign “trachomatous inflammation—follicular” (TF) and TT are present at prevalences warranting intervention. We sought to estimate prevalences of TF, TT, ocular Ct infection, and anti-Ct antibodies on Kiritimati Island, Kiribati, to assess local relationships between these parameters, and to help determine the need for interventions against trachoma on Kiribati islands other than Tarawa. Methods As part of the Global Trachoma Mapping Project (GTMP), on Kiritimati, we examined 406 children aged 1–9 years for active trachoma. We collected conjunctival swabs (for droplet digital PCR against Ct plasmid targets) from 1–9-year-olds with active trachoma, and a systematic selection of 1–9-year-olds without active trachoma. We collected dried blood spots (for anti-Pgp3 ELISA) from all 1–9-year-old children. We also examined 416 adults aged ≥15 years for TT. Prevalence of TF and TT was adjusted for age (TF) or age and gender (TT) in five-year age bands. Results The age-adjusted prevalence of TF in 1–9-year-olds was 28% (95% confidence interval [CI]: 24–35). The age- and gender-adjusted prevalence of TT in those aged ≥15 years was 0.2% (95% CI: 0.1–0.3%). Twenty-six (13.5%) of 193 swabs from children without active trachoma, and 58 (49.2%) of 118 swabs from children with active trachoma were positive for Ct DNA. Two hundred and ten (53%) of 397 children had anti-Pgp3 antibodies. Both infection (p, Author summary Ocular infection with Chlamydia trachomatis causes trachoma. It is the leading infectious cause of blindness, and the target of an international campaign for elimination as a public health problem. Trachoma is endemic to Tarawa, the most populated island of Kiribati, housing approximately half the national population. However, the country has 20 inhabited islands and there were no previous trachoma prevalence data from Kiribati outside Tarawa. We set out to determine the prevalence of trachoma in the second most populated island, Kiritimati, located over 3000 km from Tarawa. In some other Pacific Island countries, ocular C. trachomatis infection is much less prevalent than the clinical signs that are used to guide interventions; we therefore looked for PCR-based evidence of current infection and antibodies to chlamydial proteins, in addition to recording clinical signs of trachoma. Our results indicate that trachoma and ocular C. trachomatis infection are prevalent on Kiritimati, and suggest that interventions are required here. The combined application of antibody, nucleic acid and clinical tools in an intervention-naïve population provides insight into their inter-relationships and the data are, therefore, of considerable interest to elimination programmes within and beyond the Pacific.

Killer-cell immunoglobulin-like receptors (KIRs) are expressed predominantly on natural killer cells, where they play a key role in the regulation of innate immune responses. Recent studies show that inhibitory KIRs can also impact adaptive T cell-mediated immunity. In mice and in human T cells in vitro, inhibitory KIR ligation enhanced CD8(+) T cell survival. To investigate the clinical relevance of these observations, we conducted an extensive immunogenetic analysis of multiple, independent cohorts of HIV-1, hepatitis C virus (HCV) and human T cell leukemia virus (HTLV-1)-infected individuals in conjunction with in vitro assays of T cell survival, analysis of ex vivo KIR expression and mathematical modeling of host-virus dynamics. Our data suggest that functional engagement of inhibitory KIRs enhances the CD8(+) T cell response against HIV-1, HCV and HTLV-1 and is a significant determinant of clinical outcome in all three viral infections.

Trachoma is caused byChlamydia trachomatis(Ct). It is targeted for global elimination as a public health problem. In 2014, a population-based cross-sectional study was performed in two previously trachoma-endemic areas of The Gambia. Participants of all ages from Lower River Region (LRR) (N = 1028) and Upper River Region (URR) (N = 840) underwent examination for trachoma and had blood collected for detection of antibodies against the Ct antigen Pgp3, by ELISA. Overall, 30 (1.6%) individuals had active trachoma; the prevalence in children aged 1–9 years was 3.4% (25/742) with no statistically significant difference in prevalence between the regions. There was a significant difference in overall seroprevalence by region: 26.2% in LRR and 17.1% in URR (p

The work was supported by the National Institute on Aging in the United States (grants 2RO1AG7644-01A1 and 2RO1AG017644) and a consortium of UK government departments coordinated by the Office for National Statistics. Background: Frail older adults are heavy users of health and social care. In order to reduce the costs associated with frailty in older age groups, safe and cost-effective strategies are required that will reduce the incidence and severity of frailty. Objective: We investigated whether self-reported intensity of physical activity (sedentary, mild, moderate or vigorous) performed at least once a week can significantly reduce trajectories of frailty in older adults who are classified as non-frail at baseline (Rockwood’s Frailty Index [FI] ≤ 0.25). Methods: Multi-level growth curve modelling was used to assess trajectories of frailty in 8649 non-frail adults aged 50 and over and according to baseline self-reported intensity of physical activity. Frailty was measured in five-year age cohorts based on age at baseline (50–54; 55–59; 60–64; 65–69; 70–74; 75–79; 80+) on up to 6 occasions, providing an average of 10 years of follow-up. All models were adjusted for baseline sex, education, wealth, cohabitation, smoking, and alcohol consumption. Results: Compared with the sedentary reference group, mild physical activity was insufficient to significantly slow the progression of frailty, moderate physical activity reduced the progression of frailty in some age groups (particularly ages 65 and above) and vigorous activity significantly reduced the trajectory of frailty progression in all older adults. Conclusion: Healthy non-frail older adults require higher intensities of physical activity for continued improvement in frailty trajectories. Publisher PDF

Introduction Trachoma, caused by the intracellular bacterium Chlamydia trachomatis (Ct), is the leading infectious cause of preventable blindness. Many commercial platforms are available that provide highly sensitive and specific detection of Ct DNA. However, the majority of these commercial platforms are inaccessible for population-level surveys in resource-limited settings typical to trachoma control programmes. We developed two low-cost quantitative PCR (qPCR) tests for Ct using readily available reagents on standard real-time thermocyclers. Methods Each multiplex qPCR test targets one genomic and one plasmid Ct target in addition to an endogenous positive control for Homo sapiens DNA. The quantitative performance of the qPCR assays in clinical samples was determined by comparison to a previously evaluated droplet digital PCR (ddPCR) test. The diagnostic performance of the qPCR assays were evaluated against a commercial assay (artus C. trachomatis Plus RG PCR, Qiagen) using molecular diagnostics quality control standards and clinical samples. We examined the yield of Ct DNA prepared from five different DNA extraction kits and a cold chain-free dry-sample preservation method using swabs spiked with fixed concentrations of human and Ct DNA. Results The qPCR assay was highly reproducible (Ct plasmid and genomic targets mean total coefficients of variance 41.5% and 48.3%, respectively). The assay detected 8/8 core specimens upon testing of a quality control panel and performed well in comparison to commercially marketed comparator test (sensitivity and specificity > 90%). Optimal extraction and sample preservation methods for research applications were identified. Conclusion We describe a pipeline from collection to diagnosis providing the most efficient sample preservation and extraction with significant per test cost savings over a commercial qPCR diagnostic assay. The assay and its evaluation should allow control programs wishing to conduct independent research within the context of trachoma control, access to an affordable test with defined performance characteristics., Graphical abstract Image 1, Highlights • Current WHO guidelines for trachoma control do not recommend tests for infection. • A Chlamydia trachomatis diagnostic more suited to low-income economies was developed. • A complete sample-to-result pipeline is evaluated. • The assay offers high throughput and comparable performance to commercial diagnostics. • The assay was significantly cheaper than commercial alternatives.

Background Healthcare and other front-line workers are at particular risk of infection with Ebola virus (EBOV). Despite the large-scale deployment of international responders, few cases of Ebola virus disease have been diagnosed in this group. Since asymptomatic or pauci-symptomatic infection has been described, it is plausible that infections have occurred in healthcare workers but have escaped being diagnosed. We aimed to assess the prevalence of asymptomatic or pauci-symptomatic infection, and of exposure events, among returned responders to the West African Ebola epidemic 2014–2016. Methods and findings We used snowball sampling to identify responders who had returned to the UK or Ireland, and used an online consent and questionnaire to determine their exposure to EBOV and their experience of illness. Oral fluid collection devices were sent and returned by post, and samples were tested using an EBOV IgG capture assay that detects IgG to Ebola glycoprotein. Blood was collected from returnees with reactive samples for further testing. Unexposed UK controls were also recruited. In all, 300 individuals consented, of whom 268 (89.3%) returned an oral fluid sample (OFS). The majority had worked in Sierra Leone in clinical, laboratory, research, and other roles. Fifty-three UK controls consented and provided samples using the same method. Of the returnees, 47 (17.5%) reported that they had had a possible EBOV exposure. Based on their free-text descriptions, using a published risk assessment method, we classified 43 (16%) as having had incidents with risk of Ebola transmission, including five intermediate-risk and one high-risk exposure. Of the returnees, 57 (21%) reported a febrile or diarrhoeal illness in West Africa or within 1 mo of return, of whom 40 (70%) were not tested at the time for EBOV infection. Of the 268 OFSs, 266 were unreactive. Two returnees, who did not experience an illness in West Africa or on return, had OFSs that were reactive on the EBOV IgG capture assay, with similar results on plasma. One individual had no further positive test results; the other had a positive result on a double-antigen bridging assay but not on a competitive assay or on an indirect EBOV IgG ELISA. All 53 controls had non-reactive OFSs. While the participants were not a random sample of returnees, the number participating was high. Conclusions This is the first study, to our knowledge, of the prevalence of EBOV infection in international responders. More than 99% had clear negative results. Sera from two individuals had discordant results on the different assays; both were negative on the competitive assay, suggesting that prior infection was unlikely. The finding that a significant proportion experienced “near miss” exposure events, and that most of those who experienced symptoms did not get tested for EBOV at the time, suggests a need to review and standardise protocols for the management of possible exposure to EBOV, and for the management of illness, across organisations that deploy staff to outbreaks., In a cross-sectional study, Catherine Frances Houlihan and colleagues surveyed international responders to the West African Ebola crisis, after they returned to the UK or Ireland, to analyze their experience of risk., Author summary Why was this study done? A large number of international volunteers worked in West Africa during the largest Ebola outbreak ever seen, but only a small number of international staff were diagnosed with Ebola virus disease. Since asymptomatic or unrecognised infections can occur, it is possible that some infections in international responders to the epidemic were missed. What did the researchers do and find? We carried out an online survey and antibody testing of oral fluid samples from 268 individuals who returned to the UK and Ireland after working in West Africa during the Ebola outbreak. A high number of near miss events were reported, and less than a third of individuals who experienced illness whilst in West Africa or soon after return were tested for Ebola virus while they were unwell. Of the 268 who were tested for antibodies, two had reactive test results, but these were not reactive on further testing. What do these findings mean? Although our study could not reach every individual who returned to the UK after working in West Africa during the Ebola outbreak, we demonstrated that asymptomatic or pauci-symptomatic Ebola virus infection was rare in international healthcare and other workers in our study who responded to the epidemic in West Africa. The descriptions of near miss events and the finding that many of those who experienced illness were not tested at the time suggest that protocols for the management of possible exposure to Ebola virus and for the management of illness should be reviewed and standardised across organisations that deploy staff to outbreaks.

Trachoma is endemic in several Pacific Island states. Recent surveys across the Solomon Islands indicated that whilst trachomatous inflammation-follicular (TF) was present at levels warranting intervention, the prevalence of trachomatous trichiasis (TT) was low. We set out to determine the relationship between chlamydial infection and trachoma in this population.We conducted a population-based trachoma prevalence survey of 3674 individuals from two Solomon Islands provinces. Participants were examined for clinical signs of trachoma. Conjunctival swabs were collected from all children aged 1-9 years. We tested swabs for Chlamydia trachomatis (Ct) DNA using droplet digital PCR. Chlamydial DNA from positive swabs was enriched and sequenced for use in phylogenetic analysis.We observed a moderate prevalence of TF in children aged 1-9 years (n = 296/1135, 26.1%) but low prevalence of trachomatous inflammation-intense (TI) (n = 2/1135, 0.2%) and current Ct infection (n = 13/1002, 1.3%) in children aged 1-9 years, and TT in those aged 15+ years (n = 2/2061, 0.1%). Ten of 13 (76.9%) cases of infection were in persons with TF or TI (p = 0.0005). Sequence analysis of the Ct-positive samples yielded 5/13 (38%) complete (95% coverage of reference) genome sequences, and 8/13 complete plasmid sequences. Complete sequences all aligned most closely to ocular serovar reference strains.The low prevalence of TT, TI and Ct infection that we observed are incongruent with the high proportion of children exhibiting signs of TF. TF is present at levels that apparently warrant intervention, but the scarcity of other signs of trachoma indicates the phenotype is mild and may not pose a significant public health threat. Our data suggest that, whilst conjunctival Ct infection appears to be present in the region, it is present at levels that are unlikely to be the dominant driving force for TF in the population. This could be one reason for the low prevalence of TT observed during the study.

Background Efforts are underway to eliminate trachoma as a public health problem by 2020. Programmatic guidelines are based on clinical signs that correlate poorly with Chlamydia trachomatis (Ct) infection in post-treatment and low-endemicity settings. Age-specific seroprevalence of anti Ct Pgp3 antibodies has been proposed as an alternative indicator of the need for intervention. To standardise the use of these tools, it is necessary to develop an analytical approach that performs reproducibly both within and between studies. Methodology Dried blood spots were collected in 2014 from children aged 1–9 years in Laos (n = 952) and Uganda (n = 2700) and from people aged 1–90 years in The Gambia (n = 1868). Anti-Pgp3 antibodies were detected by ELISA. A number of visual and statistical analytical approaches for defining serological status were compared. Principal Findings Seroprevalence was estimated at 11.3% (Laos), 13.4% (Uganda) and 29.3% (The Gambia) by visual inspection of the inflection point. The expectation-maximisation algorithm estimated seroprevalence at 10.4% (Laos), 24.3% (Uganda) and 29.3% (The Gambia). Finite mixture model estimates were 15.6% (Laos), 17.1% (Uganda) and 26.2% (The Gambia). Receiver operating characteristic (ROC) curve analysis using a threshold calibrated against external reference specimens estimated the seroprevalence at 6.7% (Laos), 6.8% (Uganda) and 20.9% (The Gambia) when the threshold was set to optimise Youden’s J index. The ROC curve analysis was found to estimate seroprevalence at lower levels than estimates based on thresholds established using internal reference data. Thresholds defined using internal reference threshold methods did not vary substantially between population samples. Conclusions Internally calibrated approaches to threshold specification are reproducible and consistent and thus have advantages over methods that require external calibrators. We propose that future serological analyses in trachoma use a finite mixture model or expectation-maximisation algorithm as a means of setting the threshold for ELISA data. This will facilitate standardisation and harmonisation between studies and eliminate the need to establish and maintain a global calibration standard., Author Summary Trachoma is caused by the bacterium Chlamydia trachomatis (Ct). Individuals who have previously been infected with Ct carry specific antibodies in their blood. Recent studies have suggested that these antibodies may be a good way to estimate the intensity of transmission of this bacterium in a population. Among people who do have antibodies (seropositives) there is variation in the amount that is detectable in their blood. Some people have such low levels that differentiating them from those who don’t have antibodies (seronegatives) is challenging. We used a new test for Ct antibodies on blood specimens from three countries. Our test worked extremely well, giving reproducible results when we tested the same samples multiple times. We compared four different methods for setting the position of the threshold line between seronegatives and seropositives. The estimated transmission intensity in each country varied depending on the threshold method used, but two methods that used statistical modelling algorithms to define the two groups performed consistently across all three countries’ samples. We recommend that future studies should consider adopting the statistical modelling approaches, as they are objective tests that require no reference material and allow for standardisation between studies.

Background Trachoma is the leading infectious cause of blindness and is caused by ocular infection with the bacterium Chlamydia trachomatis (Ct). While the majority of the global disease burden is found in sub-Saharan Africa, the Western Pacific Region has been identified as trachoma endemic. Population surveys carried out throughout Fiji have shown an abundance of both clinically active trachoma and trachomatous trichiasis in all divisions. This finding is at odds with the clinical experience of local healthcare workers who do not consider trachoma to be highly prevalent. We aimed to determine whether conjunctival infection with Ct could be detected in one administrative division of Fiji. Methods A population-based survey of 2306 individuals was conducted using the Global Trachoma Mapping Project methodology. Population prevalence of active trachoma in children and trichiasis in adults was estimated using the World Health Organization simplified grading system. Conjunctival swabs were collected from 1009 children aged 1–9 years. DNA from swabs was tested for the presence of the Ct plasmid and human endogenous control. Results The prevalence of active trachoma in 1–9 year olds was 3.4%. The age-adjusted prevalence was 2.8% (95% CI: 1.4–4.3%). The unadjusted prevalence of ocular Ct infection in 1–9 year-olds was 1.9% (19/1009), and the age-adjusted infection prevalence was 2.3% (95% CI: 0.4–2.5%). The median DNA load was 41 Ct plasmid copies per swab (min 20, first quartile 32, mean 6665, third quartile 161, max 86354). There was no association between current infection and follicular trachoma. No cases of trachomatous trichiasis were identified. Discussion The Western Division of Fiji has a low prevalence of clinical trachoma. Ocular Ct infections were observed, but they were predominantly low load infections and were not correlated with clinical signs. Our study data suggest that trachoma does not meet the WHO definition of a public health problem in this Division of Fiji, but the inconsistency with previous studies warrants further investigation., Author Summary Trachoma, caused by ocular strains of Chlamydia trachomatis, represents a major global public health issue, and is the subject of an international elimination campaign. Until recently, data on trachoma in the Pacific Island states have been sparse. The most recent studies have conflicted in their estimates of trachomatous disease burden in Fiji, therefore, surveys using alternative markers (infection testing plus grading) to those already used (grading alone) are warranted to try to shed further light on trachoma epidemiology in this setting. We used an externally validated clinical assessment protocol to show that evidence of active trachoma is present at a low prevalence, and we did not find any cases of trichiasis, the sight-threatening stage of trachoma. From testing of conjunctival swabs with a validated, next-generation PCR, we also found that C. trachomatis was present at a low prevalence. Our clinical data suggest that trachoma does not meet the WHO definition of a public health problem in this Division of Fiji, but the inconsistency with previous studies warrants further investigation.

Sequence-based typing (SBT) is a powerful method of genotyping in highly polymorphic gene systems. In standard SBT methods, both strands of a double-stranded template amplicon are sequenced in separate reactions in order to achieve high quality data across the region of interest. The amount of informative data that is obtained from the second strand sequence is often low, whilst the impact of performing second strand sequencing on costs and throughput are significant. Here we present short template amplicon and multiplex megaprimer-enabled relay (STAMMER) sequencing, a novel simultaneous sequence-based typing methodology that allows the detection of any practical amount of useful sequence from a plurality of distinct polymerase chain reaction products in a single sequencing reaction. In addition to simultaneous bidirectional sequencing, we show how the STAMMER approach can be used to simultaneously sequence a number of regions of interest that are not physically linked within the range of a single sequencing reaction. The efficiencies of this method could impact significantly on the output of SBT laboratories.

The European Searchable Tumour line Database (ESTDAB) ( http://www.ebi.ac.uk/ipd/estdab ) is a freely available and fully searchable database of melanoma-derived cell lines, which have been characterised for over 250 immunologically relevant markers by a consortium of European scientists. The database is linked to a cell bank, which can provide melanoma cell lines to non-profit investigators for a nominal handling charge. All cells are fully HLA typed at the genomic and surface expression levels. The expression of a number of surface antigens, apoptotic markers, tumour-associated antigens and extracellular matrix proteins has also been determined. Cytokine secretion has been tested and polymorphisms in cytokine genes have been identified. Glycans at the cell surface were identified and glycosyltransferase activity quantified. Cell lines with a particular constellation of these parameters can be sought online via the ESTDAB interface, which is included as part of the Immuno-Polymorphism Database (IPD) section of the European Bioinformatics Institute's (EBI) website.

Killer-cell immunoglobulin-like receptor (KIR) genes are highly polymorphic and polymorphisms have been found in all KIR exons. Although less is known of the introns, these also appear to be polymorphic. To generate a comprehensive database of KIR genomic sequences, which will aid in the design of KIR typing reagents, we have established a method for cloning and sequencing of KIR genes from genomic DNA. We cloned and sequenced the entire KIR2DL4 gene from genomic DNA using long template touchdown PCR and high capacity cloning vectors. Overlapping secondary amplicons were modified to include a nucleotide analogue that reduced sequencing problems associated with secondary structure formation in the KIR sequence. Using a modified sequencing chemistry we were able to sequence approximately 11,000 bases confirming the previously published KIR2DL4*005 allele sequence.

Chlamydia trachomatis causes both trachoma and sexually transmitted infections. These diseases have similar pathology and potentially similar genetic predisposing factors. We aimed to identify polymorphisms and pathways associated with pathological sequelae of ocular Chlamydia trachomatis infections in The Gambia. We report a discovery phase genome-wide association study (GWAS) of scarring trachoma (1090 cases, 1531 controls) that identified 27 SNPs with strong, but not genome-wide significant, association with disease (5 × 10−6 > P > 5 × 10−8). The most strongly associated SNP (rs111513399, P = 5.38 × 10−7) fell within a gene (PREX2) with homology to factors known to facilitate chlamydial entry to the host cell. Pathway analysis of GWAS data was significantly enriched for mitotic cell cycle processes (P = 0.001), the immune response (P = 0.00001) and for multiple cell surface receptor signalling pathways. New analyses of published transcriptome data sets from Gambia, Tanzania and Ethiopia also revealed that the same cell cycle and immune response pathways were enriched at the transcriptional level in various disease states. Although unconfirmed, the data suggest that genetic associations with chlamydial scarring disease may be focussed on processes relating to the immune response, the host cell cycle and cell surface receptor signalling.

Background Trachoma, a preventable blinding eye disease, is initiated by ocular infection with Chlamydia trachomatis (Ct). We previously showed that microRNAs (miR) -147b and miR-1285 were up-regulated in inflammatory trachomatous scarring. During the initial stage of disease, follicular trachoma with current Ct infection, the differential expression of miR has not yet been investigated. Methods Conjunctival samples were collected from 163 children aged 1–9 years old living in a trachoma-endemic region of Guinea Bissau, West Africa. Small RNA sequencing (RNAseq) was carried out on samples from five children with follicular trachoma and current Ct infection and five children with healthy conjunctivae and no Ct infection. Small RNAseq was also carried out on human epithelial cell lines infected with ocular Ct strains A2497 and isogenic plasmid-free A2497 in vitro. Results were validated by quantitative PCR (qPCR) in 163 clinical samples. Results Differential expression of RNAseq data identified 12 miR with changes in relative expression during follicular trachoma, of which 9 were confirmed as differentially expressed by qPCR (miR-155, miR-150, miR-142, miR-181b, miR-181a, miR-342, miR-132, miR-4728 and miR-184). MiR-155 and miR-184 expression had a direct relationship with the degree of clinical inflammation. MiR-155 was up-regulated (OR = 2.533 ((95 % CI = 1.291–4.971); P = 0.0069) and miR-184 was down-regulated (OR = 0.416 ((95 % CI = 0.300–0.578); P = 1.61*10−7) as the severity of clinical inflammation increased. Differential miR expression was not detected in HEp-2 or HCjE epithelial cells 48 h post infection with Ct in vitro. HCjE cells, a conjunctival epithelial cell line, had a markedly different miR background expression compared to HEp-2 cells. Conclusions In follicular trachoma, expression of miR-155 and miR-184 is correlated with the severity of inflammation. This likely reflects host regulation of the immune response and a prolonged period of wound healing following the clearance of Ct. Prolonged healing may be associated with subsequent development of scarring trachoma. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1367-8) contains supplementary material, which is available to authorized users.

Malignant transformation of cells is frequently associated with abnormalities in human leukocyte antigen (HLA) expression. MHC class I loss or down-regulation in cancer cells is a major immune escape route used by a large variety of human tumours to evade antitumour immune responses mediated by cytotoxic T lymphocytes. The goal of our study was to explore HLA genotyping and phenotyping in a variety of melanoma tumour cell lines. A total of 91 melanoma cell lines were characterised for HLA class I and II genotype. In addition, 61 out of the 91 cell lines were also analysed for HLA class I and II cell surface molecule expression by flow cytometry. Unexpectedly, we found that 19.7% of the melanoma cell lines were homozygous for HLA class I genotypes, sometimes associated with HLA class II homozygosity (8.79%) and sometimes not (10.98%). The frequency of homozygosity was significantly higher compared with the control groups (1.6%). To identify the reasons underlying the high frequency of HLA homozygosity we searched for genomic deletions using eight pairs of highly polymorphic microsatellite markers covering the entire extended HLA complex on the short arm of chromosome 6. Our results were compatible with hemizygous deletions and suggest that loss of heterozygosity on chromosome arm 6p is a common feature in melanoma cell lines. In fact, although autologous normal DNA from the patients was not available and could not be tested, the retention in some cases of heterozygosity for a number of microsatellite markers would indicate a hemizygous deletion. In the rest of the cases, markers at 6p and 6q showed a single allele pattern indicating the probable loss of part or the whole of chromosome 6. These results led us to conclude that loss of heterozygosity in chromosome 6 is nonrandom and is possibly an immunologically relevant event in human malignant melanoma. Other well-established altered HLA class I phenotypes were also detected by flow cytometry that correspond to HLA class I total loss and HLA-ABC and/or specific HLA-B locus down-regulation.

Vitamin D deficiency may increase susceptibility to opportunistic infections in HIV-infected individuals. We found no evidence that vitamin D deficiency increases risk of cryptococcal meningitis or leads to impaired immune responses or microbiological clearance in HIV-infected patients with cryptococcal meningitis., Background. Vitamin D deficiency is associated with impaired immune responses and increased susceptibility to a number of intracellular pathogens in individuals infected with human immunodeficiency virus (HIV). It is not known whether such an association exists with Cryptococcus neoformans. Methods. Levels of 25-hydroxyvitamin D (25[OH]D) were measured in 150 patients with cryptococcal meningitis (CM) and 150 HIV-infected controls in Cape Town, South Africa, and associations between vitamin D deficiency and CM were examined. The 25-hydroxyvitamin D levels and cryptococcal notifications were analyzed for evidence of reciprocal seasonality. Associations between 25(OH)D levels and disease severity, immune responses, and microbiological clearance were investigated in the patients with CM. Results. Vitamin D deficiency (plasma 25[OH]D ≤50 nmol/L) was present in 74% of patients. Vitamin D deficiency was not associated with CM (adjusted odds ratio, 0.93 [95% confidence interval, .6–1.6]; P = .796). Levels of 25(OH)D showed marked seasonality, but no reciprocal seasonality was seen in CM notifications. No significant associations were found between 25(OH)D levels and fungal burden or levels of tumor necrosis factor α, interferon γ, interleukin 6, soluble CD14, or neopterin in cerebrospinal fluid. Rates of fungal clearance did not vary according to vitamin D status. Conclusions. Vitamin D deficiency does not predispose to the development of CM, or lead to impaired immune responses or microbiological clearance in HIV-infected patients with CM.

Background Chlamydia trachomatis is globally the predominant infectious cause of blindness and one of the most common bacterial causes of sexually transmitted infection. Infections of the conjunctiva cause the blinding disease trachoma, an immuno-pathological disease that is characterised by chronic conjunctival inflammation and fibrosis. The polymorphic Killer-cell Immunoglobulin-like Receptors (KIR) are found on Natural Killer cells and have co-evolved with the Human Leucocyte Antigen (HLA) class I system. Certain genetic constellations of KIR and HLA class I polymorphisms are associated with a number of diseases in which modulation of the innate responses to viral and intracellular bacterial pathogens is central. Methodology A sample of 134 Gambian pedigrees selected to contain at least one individual with conjunctival scarring in the F1 generation was used. Individuals (n = 830) were genotyped for HLA class I and KIR gene families. Family Based Association Tests and Case Pseudo-control tests were used to extend tests for transmission disequilibrium to take full advantage of the family design, genetic model and phenotype. Principle findings We found that the odds of trachomatous scarring increased with the number of genome copies of HLA-C2 (C1/C2 OR = 2.29 BHP-value = 0.006; C2/C2 OR = 3.97 BHP-value = 0.0004) and further increased when both KIR2DL2 and KIR2DL3 (C2/C2 OR = 5.95 BHP-value = 0.006) were present. Conclusions To explain the observations in the context of chlamydial infection and trachoma we propose a two-stage model of response and disease that balances the cytolytic response of KIR expressing NK cells with the ability to secrete interferon gamma, a combination that may cause pathology. The data presented indicate that HLA-C genotypes are important determinants of conjunctival scarring in trachoma and that KIR2DL2/KIR2DL3 heterozygosity further increases risk of conjunctival scarring in individuals carrying HLA-C2., Author Summary Chlamydia trachomatis is a pathogen that causes sexually transmitted infections (STIs) and the blinding disease trachoma. Natural Killer (NK) cells are part of the host immune system's first line of defence against infection. NK cell functions are genetically encoded and differences between individuals mean that some people are better able to respond to infections than others. We found that in certain combinations, specific variants of the gene HLA-C (Human Leucocyte Antigen, C) and of a complex set of genes called the Killer-cell Immunoglobulin-like Receptors (KIR) were associated with a six-fold increase in the relative risk of scarring tissue damage resulting from ocular C. trachomatis infection (trachoma). This combination of genetic variants may reduce the host's ability to effectively resolve infections and result in a harmful immune response that ultimately leads to tissue damage and scarring. KIR+ NK cells are potential cellular mediators of the damaging immune response. Previous studies have identified that the same HLA-KIR genetic constellation that associates with trachoma is actually protective against infectious diseases such as malaria and tuberculosis. The high frequency of the trachoma-associated constellation in African populations may therefore be explained by the evolutionary benefits of protection from the complications of severe disease.

In ophthalmological studies, the need to take photographs as evidence introduces additional complications to fieldwork. A recent report1 highlighted the usefulness of smartphones in the collection and grading of photographic evidence of trachoma. We have recently considered the wider potential of portable computerised equipment to integrate the recording and management of trachoma photographs with field data and biological specimens. While the overall resolution of smartphone cameras increases rapidly, an outstanding issue with smartphone photography is the phenomenon of shutter lag, a significant time interval between actuation and the recording of an image. Shutter lag is associated with image blurring as the subject or camera may have moved out of focus by the time of image recording. Recently released smartphones such as the HTC One X and Samsung Galaxy S3 are robust against shutter lag, but are currently the exceptions in a telephony market that has responded slowly to the problem. Light Field Photography (LFP) technology (http://www.lytro.com) has the potential to eliminate blurring …

In the last fifteen years published reports have described KIR gene-content frequency distributions in more than 120 populations worldwide. However, there have been limited studies examining these data in aggregate in order to detect overall patterns of variation at regional and global levels. Here, we present a summary of the collection of KIR gene-content data for 105 worldwide populations collected as part of the 15th and 16th International Histocompatibility and Immunogenetics Workshops, and preliminary results for data analysis.

Background Leprosy, a chronic granulomatous disease affecting the skin and nerves, is caused by Mycobacterium leprae (M. leprae). The type of leprosy developed depends upon the host immune response. Type 1 reactions (T1Rs), that complicate borderline and lepromatous leprosy, are due to an increase in cell-mediated immunity and manifest as nerve damage and skin inflammation. Owing to the increase in inflammation in the skin of patients with T1Rs, we sought to investigate the activation of the innate immune system during reactionary events. Specifically, we investigated the expression levels of human beta-defensins (hBDs) 2 and 3 in the skin of patients with T1Rs, in keratinocytes, and in macrophages stimulated with M. leprae and corticosteroids. Results Skin biopsies from twenty-three patients with Type 1 reactions were found to have higher transcript levels of hBD3 as compared to fifteen leprosy patients without Type 1 reactions, as measured by qPCR. Moreover, we observed that keratinocytes but not macrophages up-regulated hBD2 and hBD3 in response to M. leprae stimulation in vitro. Corticosteroid treatment of patients with T1Rs caused a suppression of hBD2 and hBD3 in skin biopsies, as measured by qPCR. In vitro, corticosteroids suppressed M. leprae-dependent induction of hBD2 and hBD3 in keratinocytes. Conclusions This study demonstrates that hBD3 is induced in leprosy Type 1 Reactions and suppressed by corticosteroids. Furthermore, our findings demonstrate that keratinocytes are responsive to M. leprae and lend support for additional studies on keratinocyte innate immunity in leprosy and T1Rs. Trial Registration Controlled-Trials.com ISRCTN31894035, Author Summary Leprosy, caused by Mycobacterium leprae (M. leprae), is a chronic infection leading to potentially debilitating nerve damage. Although the infection is curable with multi-drug therapy, many patients continue to suffer from episodes of inflammation, called Type 1 reactions. These reactions may lead to nerve damage and deformation. Patients with Type 1 reactions are treated with corticosteroids to reduce the inflammation. Elucidating the immune factors contributing to leprosy Type 1 reactions will further clarify why many leprosy patients develop nerve and skin inflammation. We conducted a study to understand whether the antimicrobial peptides, human beta-defensins (hBD) 2 and 3, are increased in the skin of leprosy patients with Type 1 reactions. We also investigated keratinocyte expression of hBD2 and hBD3 in response to M. leprae. In this study, we found that hBD3 was significantly increased in the skin of leprosy patients with Type 1 reactions. Moreover, we demonstrated that corticosteroid treatment reduced the expression of hBD3 in patients with Type 1 reactions. We also found that keratinocytes incubated with M. leprae upregulated hBD2 and hBD3 in vitro; corticosteroids were found to suppress this response. These studies suggest a role for the innate immune system in leprosy Type 1 reactions.

Background The clinical signs of active trachoma are often present in the absence of ocular Chlamydia trachomatis infection in low prevalence and mass treated settings. Treatment decisions are currently based on the prevalence of clinical signs, and this may result in the unnecessary distribution of mass antibiotic treatment. We aimed to evaluate the diagnostic accuracy of a prototype point-of-care (POC) test, developed for field diagnosis of ocular C. trachomatis, in low prevalence settings of The Gambia and Senegal. Methodology/Principal Findings Three studies were conducted, two in The Gambia and one in Senegal. Children under the age of 10 years were screened for the clinical signs of trachoma. Two ocular swabs were taken from the right eye. The first swab was tested by the POC test in the field and the result independently graded by two readers. The second swab was tested for the presence of C. trachomatis by Amplicor Polymerase Chain Reaction. In Senegal, measurements of humidity and temperature in the field were taken. A total of 3734 children were screened, 950 in the first and 1171 in the second Gambian study, and 1613 in Senegal. The sensitivity of the prototype POC test ranged between 33.3–67.9%, the specificity between 92.4–99.0%, the positive predictive value between 4.3–21.0%, and the negative predictive value between 98.0–99.8%. The rate of false-positives increased markedly at temperatures above 31.4°C and relative humidities below 11.4%. Conclusions/Significance In its present format, this prototype POC test is not suitable for field diagnosis of ocular C. trachomatis as its specificity decreases in hot and dry conditions: the environment in which trachoma is predominantly found. In the absence of a suitable test for infection, trachoma diagnosis remains dependent on clinical signs. Under current WHO recommendations, this is likely resulting in the continued mass treatment of non-infected communities., Author Summary Trachoma, caused by infection of the eye with the bacterium Chlamydia trachomatis, is the leading infectious cause of blindness and is associated with poverty. Antibiotic treatment of all community members is one of the recommended control strategies for trachoma. However, in places where the prevalence of clinical signs is low, C. trachomatis eye infection is often absent. Laboratory testing for C. trachomatis infection by polymerase chain reaction (PCR) is highly sensitive but expensive and requires well-trained staff. A simple point-of-care (POC) test that can be used in trachoma-affected communities could help trachoma control efforts. We evaluated a POC test for C. trachomatis eye infection. Children under 10 years of age were screened for clinical signs of trachoma and C. trachomatis eye infection. The POC test result was compared with laboratory PCR test results. The POC test detected just over half of PCR test positives correctly. However, the POC test tended to give false-positive results in hot and dry conditions, which is the typical environment of trachoma. The POC test requires high specificity since it would be used to make treatment decisions at the community level. Therefore, its present format requires improvement before it can be utilized in trachoma control.

Background Trachoma has been endemic in The Gambia for decades. National trachoma control activities have been in place since the mid-1980's, but with no mass antibiotic treatment campaign. We aimed to assess the prevalence of active trachoma and of actual ocular Chlamydia trachomatis infection as measured by polymerase chain reaction (PCR) in the two Gambian regions that had had the highest prevalence of trachoma in the last national survey in 1996 prior to planned national mass antibiotic treatment distribution in 2006. Methodology/Principal Findings Two stage random sampling survey in 61 randomly selected Enumeration Areas (EAs) in North Bank Region (NBR) and Lower River Region (LRR). Fifty randomly selected children aged under 10 years were examined per EA for clinical signs of trachoma. In LRR, swabs were taken to test for ocular C. trachomatis infection. Unadjusted prevalences of active trachoma were calculated, as would be done in a trachoma control programme. The prevalence of trachomatous inflammation, follicular (TF) in the 2777 children aged 1–9 years was 12.3% (95% CI 8.8%–17.0%) in LRR and 10.0% (95% CI 7.7%–13.0%) in NBR, with significant variation within divisions (p, Author Summary Trachoma is the leading infectious cause of blindness worldwide, and is mainly found in tropical and poor countries. It is caused by infection of the eyes with the bacterium Chlamydia trachomatis. However, sometimes the clinical signs of disease can be present without infection being detected. Control efforts involve surgery, antibiotic treatment, face washing, and environmental improvement for better hygiene. Surveys of trachoma help countries to know whether and where they should implement control interventions. The Gambia is found in West Africa and has suffered from trachoma for decades. We conducted a survey of two Gambian regions to look at how much trachoma disease and C. trachomatis infection there is in the eyes. We found that although there was enough disease (≥10%) to warrant antibiotic treatment for everyone in the regions, there was nearly no infection (0.3%). This means that using clinical signs alone to make treatment decisions in low prevalence settings like The Gambia can lead to the waste of scarce resources. Our results also suggest that since less than 1% of children are infected with C. trachomatis, The Gambia is on course to achieve the World Health Organization's aim of eliminating blinding trachoma by the year 2020.

DNA enrichment by allele-specific hybridization (DEASH) was used as a means to isolate individual alleles of the killer cell immunoglobulin-like receptor (KIR2DL4) gene from heterozygous genomic DNA. Using long-template polymerase chain reaction (LT-PCR), the complete KIR2DL4 gene was amplified from a cell line that had previously been characterized for its KIR gene content by PCR using sequence-specific primers (PCR-SSP). The whole gene amplicons were sequenced and we identified two heterozygous positions in accordance with the predictions of the PCR-SSP. The amplicons were then hybridized to allele-specific, biotinylated oligonucleotide probes and through binding to streptavidin-coated beads, the targeted alleles were enriched. A second PCR amplified only the exonic regions of the enriched allele, and these were then sequenced in full. We show DEASH to be capable of enriching single alleles from a heterozygous PCR product, and through sequencing the enriched DNA, we are able to produce complete coding sequences of the KIR2DL4 alleles in accordance with the typing predicted by PCR-SSP.

Purpose Trachoma is a fibrotic disease of the conjunctiva initiated by Chlamydia trachomatis infection. This blinding disease affects over 40 million people worldwide yet the mechanisms underlying its pathogenesis remain poorly understood. We have investigated host microRNA (miR) expression in health (N) and disease (conjunctival scarring with (TSI) and without (TS) inflammation) to determine if these epigenetic differences are associated with pathology. Methods We collected two independent samples of human conjunctival swab specimens from individuals living in The Gambia (n = 63 & 194). miR was extracted, and we investigated the expression of 754 miR in the first sample of 63 specimens (23 N, 17 TS, 23 TSI) using Taqman qPCR array human miRNA genecards. Network and pathway analysis was performed on this dataset. Seven miR that were significantly differentially expressed between different phenotypic groups were then selected for validation by qPCR in the second sample of 194 specimens (93 N, 74 TS, 22 TSI). Results Array screening revealed differential expression of 82 miR between N, TS and TSI phenotypes (fold change >3, p, Author Summary Trachoma is a debilitating disease that affects 40 million people worldwide. It can cause progressive fibrosis of the upper eyelid and blindness, yet the mechanism is poorly understood. We have investigated the expression of short sequences of genetic material (microRNA) that regulate gene expression. We screened for the expression of 754 microRNA sequences (miR) in genetic material isolated from conjunctival swab samples from individuals in trachoma-endemic communities in The Gambia. This sample included healthy controls, individuals with trachomatous scarring and individuals with trachomatous scarring in the presence of clinically significant inflammation. We found 82 miR that were differentially expressed. Computer simulations predict that these miR regulate genes in epithelial cell differentiation, inflammation and fibrosis pathways, all of which are involved in the scarring process. We then validated the expression of seven of these differentially expressed miR in a second larger biological sample set from The Gambia. We confirmed that miR-147b and miR-1285 have increased expression in individuals with trachomatous scarring in the presence of clinically significant inflammation. Further investigation into the functions of these miR will aid our understanding of this disease and present opportunities to develop treatments for ocular fibrotic diseases.