15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils.

Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3--N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different.

Formation of a conceptual framework during the development of a patient-reported outcome measure for early gastrointestinal recovery: phase I of the PRO-diGi study.

AIM: Patients admitted to hospital for abdominal surgery often experience gastrointestinal dysfunction. Many studies have reported outcomes following gastrointestinal dysfunction, yet there is no unified definition of recovery or a validated patient-reported outcome measure (PROM). The first stage of PROM development requires formation of a conceptual framework to identify key themes to patients. The aim of this study was to utilize semistructured interviews to identify core themes and concepts relevant to patients to facilitate development of a conceptual framework. METHOD: Adult patients admitted to hospital for major gastrointestinal, urological or gynaecological surgery, in an emergency or elective setting, were eligible to participate. Patients treated nonoperatively for small bowel obstruction were also eligible. Interviews were conducted by telephone, audio-recorded, transcribed, coded and analysed using NVivo software by two researchers and reviewed by lay members of the steering group. Interviews continued until data saturation was reached. Ethical approval was gained prior to interviews (21/WA/0231). RESULTS: Twenty nine interviews were completed (17 men, median age 64 years) across three specialties (20 gastrointestinal, six gynaecological, three urological). Two overarching themes of 'general recovery' and 'gastrointestinal symptoms' were identified. General recovery included three themes: 'life impact', 'mental impact', including anxiety, and 'physical impact', including fatigue. Gastrointestinal symptoms included three themes: 'abdominal symptoms' such as pain, 'diet and appetite' and 'expulsory function', such as stool frequency. A total of 18 gastrointestinal symptoms were identified during patient recovery-many of which lasted several weeks following discharge. CONCLUSION: This study reports a range of gastrointestinal and nongastrointestinal symptoms experienced by patients during early gastrointestinal recovery. Identified symptoms have been synthesized into a conceptual framework to enable development of a definitive PROM for early gastrointestinal recovery.

Postoperative nonsteroidal anti-inflammatory drugs in relation to recurrence, survival and anastomotic leakage after surgery for colorectal cancer.

AIM: The aim of this work was to investigate whether nonsteroidal anti-inflammatory drugs (NSAIDs) could be beneficial or harmful when used perioperatively for colorectal cancer patients, as inflammation may affect occult disease and anastomotic healing. METHOD: This is a protocol-based retrospective cohort study on colorectal cancer patients operated on between 2007 and 2012 at 21 hospitals in Sweden. NSAID exposure was retrieved from postoperative analgesia protocols, while outcomes and patient data were retrieved from the Swedish Colorectal Cancer Registry. Older or severely comorbid patients, as well as those with disseminated or nonradically operated tumours were excluded. Multivariable regression with adjustment for confounders was performed, estimating hazard ratios (HRs) for long-term outcomes and odds ratios (ORs) for short-term outcomes, including 95% confidence intervals (CIs). RESULTS: Some 6945 patients remained after exclusion, of whom 3996 were treated at hospitals where a NSAID protocol was in place. No association was seen between NSAIDs and recurrence-free survival (HR 0.97, 95% CI 0.87-1.09). However, a reduction in cancer recurrence was detected (HR 0.83, 95% CI 0.72-0.95), which remained significant when stratifying into locoregional (HR 0.68, 95% CI 0.48-0.97) and distant recurrences (HR 0.85, 95% CI 0.74-0.98). Anastomotic leakage was less frequent (HR 0.69%, 95% CI 0.51-0.94) in the NSAID-exposed, mainly due to a risk reduction in colo-rectal and ileo-rectal anastomoses (HR 0.47, 95% CI 0.33-0.68). CONCLUSION: There was no association between NSAID exposure and recurrence-free survival, but an association with reduced cancer recurrence and the rate of anastomotic leakage was detected, which may depend on tumour site and anastomotic location.

The Incidence of Low Anterior Resection Syndrome as Assessed in an International Randomized Controlled Trial (MRC/NIHR ROLARR).

OBJECTIVE: To investigate the incidence of LARS in patients undergoing elective anterior resection within the MRC/NIHR ROLARR trial and to explore perioperative variables that might be associated with major LARS. SUMMARY BACKGROUND DATA: Sphincter-preserving rectal cancer surgery is frequently accompanied by defaecatory dysfunction known as Low anterior resection syndrome (LARS). This is distressing for patients and is an unmet clinical challenge. METHODS: An international, retrospective cohort study of patients undergoing anterior resection within the ROLARR trial was undertaken. Trial participants with restoration of gastrointestinal continuity and free from disease recurrence completed the validated LARS questionnaire between August 2015 and April 2017. The primary outcome was the incidence of LARS and secondary outcome was severity (minor versus major). RESULTS: LARS questionnaires were received from 132/155 (85%) eligible patients. The median time from surgery to LARS assessment was 1065 days (range 174-1655 d). The incidence of LARS was 82.6% (n = 109/132), which was minor in 26/132 (19.7%) and major in 83/132 (62.9%). The most common symptoms were incontinence to flatus (n = 86/132; 65.2%) and defaecatory clustering (88/132; 66.7%). In a multivariate model, predictors of major LARS were: 1 cm decrease in tumor height above the anal verge (OR = 1.290, 95% CI: 1.101,1.511); and an ASA grade greater than 1 (OR = 2.920, 95% CI: 1.239, 6.883). Treatment allocation (laparoscopic vs robotic) did not predict major LARS. CONCLUSIONS: LARS is a common after rectal cancer surgery and patients should be appropriately counselled preoperatively, particularly before surgery for low tumors or in comorbid populations.

Noninvasive vagus nerve stimulation to reduce ileus after major colorectal surgery: early development study.

AIM: Vagus nerve stimulation has emerged as a plausible intervention to reduce ileus after surgery. An early development study was undertaken with the aim of exploring the feasibility of self-administered, noninvasive vagus nerve stimulation (nVNS) after major colorectal surgery. METHOD: A parallel-group, randomized controlled trial was undertaken between 1 January 2018 and 31 August 2019. Forty patients undergoing colorectal surgery for malignancy were allocated equally to Sham and Active stimulation groups. Electrical vagus nerve stimulation was self-administered bilaterally over the cervical surface landmarks for 5 days before and after surgery. Outcomes of interest were postoperative complications and adverse events measured using the Clavien-Dindo scale, treatment compliance, device usability according to the Systems Usability Scale (SUS) and clinical measures of bowel recovery. RESULTS: Forty patients were randomized and one withdrew, leaving 39 for analysis. Postoperative complications occurred in 9/19 (47.4%) participants receiving Sham and 11/20 (55.0%) receiving Active stimulation and were mostly minor. Compliance with treatment before surgery was 4.7 ± 0.9 days out of 5 days in the Sham group and 4.7 ± 1.1 in the Active group. Compliance with treatment after surgery was 4.1 ± 1.1 and 4.4 ± 1.5, respectively. Participants considered the intervention to be 'acceptable' according to the SUS. The most prominent differences in bowel recovery were days to first flatus (2.35 ± 1.32 vs 1.65 ± 0.88) and tolerance of solid diet (2.18 ± 2.21 vs 1.75 ± 0.91) for Sham and Active groups, respectively. CONCLUSION: This study supports the safety, treatment compliance and usability of self-administered nVNS in patients undergoing major colorectal surgery.

Information needs for recovery after colorectal surgery: a patient focus group study.

AIM: The provision of information to patients is an important part of recovery after colorectal surgery. This study aimed to define patient information needs, barriers to effective understanding and insights into how information provision may be improved. METHOD: A patient focus group was convened. This comprised a broad, convenience sample of 11 participants from across the United Kingdom with experience of major colorectal surgery. A semistructured topic guide was used to facilitate discussion about previous experiences of information provision and how this may be improved. Data were analysed thematically and are presented as major themes. RESULTS: Overall, participants felt that their information needs are poorly prioritized by healthcare professionals. Barriers to understanding and retaining information include highly emotional situations (such as receiving bad news) and inappropriate information design (such as the use of inaccessible language). Participants expressed how information resources should: (a) address patients' individual information needs; (b) empower patients to take an active role in their recovery; (c) support patients with meaningful education and sign-posted resources; and (d) recognize patients' heightened need for information during recovery at home. CONCLUSION: This study provides key insights into the information needs of patients undergoing colorectal surgery. These should inform the development of future information resources, whose format, timing and design are currently supported by low-quality evidence.

Elevated risk of invasive group A streptococcal disease and host genetic variation in the human leucocyte antigen locus.

Invasive group A streptococcal (GAS) disease is uncommon but carries a high case-fatality rate relative to other infectious diseases. Given the ubiquity of mild GAS infections, it remains unclear why healthy individuals will occasionally develop life-threatening infections, raising the possibility of host genetic predisposition. Here, we present the results of a case-control study including 43 invasive GAS cases and 1540 controls. Using HLA imputation and linear mixed models, we find each copy of the HLA-DQA1*01:03 allele associates with a twofold increased risk of disease (odds ratio 2.3, 95% confidence interval 1.3-4.4, P = 0.009), an association which persists with classical HLA typing of a subset of cases and analysis with an alternative large control dataset with validated HLA data. Moreover, we propose the association is driven by the allele itself rather than the background haplotype. Overall this finding provides impetus for further investigation of the immunogenetic basis of this devastating bacterial disease.

Global academic response to COVID-19: Cross-sectional study.

This study explores the response to COVID-19 from investigators, editors, and publishers and seeks to define challenges during the early stages of the pandemic. A cross-sectional bibliometric review of COVID-19 literature was undertaken between 1 November 2019 and 24 March 2020, along with a comparative review of Middle East respiratory syndrome (MERS) literature. Investigator responsiveness was assessed by measuring the volume and type of research published. Editorial responsiveness was assessed by measuring the submission-to-acceptance time and availability of original data. Publisher-responsiveness was assessed by measuring the acceptance-to-publication time and the provision of open access. Three hundred and ninety-eight of 2,835 COVID-19 and 55 of 1,513 MERS search results were eligible. Most COVID-19 studies were clinical reports (n = 242; 60.8%). The submission-to-acceptance [median: 5 days (IQR: 3-11) versus 71.5 days (38-106); P < .001] and acceptance-to-publication [median: 5 days (IQR: 2-8) versus 22.5 days (4-48·5-; P < .001] times were strikingly shorter for COVID-19. Almost all COVID-19 (n = 396; 99.5%) and MERS (n = 55; 100%) studies were open-access. Data sharing was infrequent, with original data available for 104 (26.1%) COVID-19 and 10 (18.2%) MERS studies (P = .203). The early academic response was characterized by investigators aiming to define the disease. Studies were made rapidly and openly available. Only one-in-four were published alongside original data, which is a key target for improvement. Key points: COVID-19 publications show rapid response from investigators, specifically aiming to define the disease.Median time between submission and acceptance of COVID-19 articles is 5 days demonstrating rapid decision-making compared with the median of 71.5 days for MERS articles.Median time from acceptance to publication of COVID-19 articles is 5 days, confirming the ability to introduce rapid increases at times of crisis, such as during the SARS outbreak.The majority of both COVID-19 and MERS articles are available open-access.

Systematic Review and Meta-analysis of Nonsteroidal Anti-inflammatory Drugs to Improve GI Recovery After Colorectal Surgery.

BACKGROUND: The management of delayed GI recovery after surgery is an unmet challenge. Uncertainty over its pathophysiology has limited previous research, but recent evidence identifies intestinal inflammation and activation of µ-opioid receptors as key mechanisms. Nonsteroidal anti-inflammatory drugs are recommended by enhanced recovery protocols for their opioid-sparing and anti-inflammatory properties. OBJECTIVES: The purpose of this study was to explore the safety and efficacy of nonsteroidal anti-inflammatory drugs to improve GI recovery and to identify opportunities for future research. DATA SOURCES: MEDLINE, Embase, and the Cochrane Library were systematically searched from inception up to January 2018. STUDY SELECTION: Randomized controlled trials assessing the effect of nonsteroidal anti-inflammatory drugs on GI recovery after elective colorectal surgery were eligible. MAIN OUTCOME MEASURES: Postoperative GI recovery, including first passage of flatus, stool, and oral tolerance, were measured. RESULTS: Six randomized controlled trials involving 563 participants were identified. All of the participants received patient-controlled morphine and either nonsteroidal anti-inflammatory drug (nonselective: n = 4; cyclooxygenase-2 selective: n = 1; either: n = 1) or placebo. Patients receiving the active drug had faster return of flatus (mean difference: -17.73 h (95% CI, -21.26 to -14.19 h); p < 0.001), stool (-9.52 h (95% CI, -14.74 to -4.79 h); p < 0.001), and oral tolerance (-12.00 h (95% CI, -18.01 to -5.99 h); p < 0.001). Morphine consumption was reduced in the active groups of 4 studies (average reduction, 12.9-30.0 mg), and 1 study demonstrated significantly reduced measures of systemic inflammation. Nonsteroidal anti-inflammatory drugs were not associated with adverse events, but 1 study was temporarily suspended for safety. LIMITATIONS: The data presented are relatively outdated but represent the best available evidence. CONCLUSIONS: Nonsteroidal anti-inflammatory drugs may represent an effective and accessible intervention to improve GI recovery, but hesitancy over their use after colorectal surgery persists. Additional preclinical research to characterize their mechanisms of action, followed by well-designed clinical studies to test safety and patient-reported efficacy, should be considered.

Limited effect of planting transgenic rice on the soil microbiome studied by continuous 13CO2 labeling combined with high-throughput sequencing.

The planting of transgenic rice has aroused ongoing controversy, due to the public anxiety surrounding the potential risk of transgenic rice to health and the environment. The soil microbial community plays an important environmental role in the plant-soil-microbe system; however, few studies have focused on the effect of transgenic rice on the soil rhizospheric microbiome. We labeled transgenic gene rice (TT51, transformed with Cry1Ab/1Ac gene), able to produce the Bt (Bacillus thuringiensis) toxin, its parental variety (Minghui 63), and a non-parental variety (9931) with 13CO2. The DNA of the associated soil rhizospheric microbes was extracted, subjected to density gradient centrifugation, followed by high-throughput sequencing of bacterial 16S rRNA gene. Unweighted unifrac analysis of the sequencing showed that transgenic rice did not significantly change the soil bacterial community structure compared with its parental variety. The order Opitutales, affiliated to phylum Verrucomicrobia and order Sphingobacteriales, was the main group of labeled bacteria in soil planted with the transgenic and parental varieties, while the orders Pedosphaerales, Chthoniobacteraceae, also affiliated to Verrucomicrobia, and the genus Geobacter, affiliated to class Deltaproteobacteria, dominated in the soil of the non-parental rice variety. The non-significant difference in soil bacterial community structure of labeled microbes between the transgenic and parental varieties, but the comparatively large difference with the non-parental variety, suggests a limited effect of planting transgenic Bt rice on the soil microbiome.

Fate of tetracycline and sulfonamide resistance genes in a grassland soil amended with different organic fertilizers.

This study provided an assessment of the environmental fate of antibiotic resistance genes (ARGs) in a Scottish grassland field repeatedly treated with different organic fertilizers. The impacts of manure, biosolids and municipal food-derived compost on the relative abundances of tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), sulfonamide ARGs (sul1 and sul2) and class 1 integron-integrase gene (IntI1) in soils were investigated, with inorganic fertilizer (NPK) as a comparison. The background soil with a history of low intensity farming showed a higher total relative abundance of tet ARGs over sul ARGs, with tetracycline efflux genes occurring in a higher frequency. In all treatments, the relative abundances of most ARGs detected in soils decreased over time, especially IntI1 and tet ARGs. This general attenuation of soil ARGs is a reflection of changes in the soil microbial community, which is supported by the result that almost all the soils at the end of the experiment had different bacterial communities from the untreated soil at the beginning of the experiment. Multiple applications of organic fertilizers to some extent counteracted the decreasing trend of soil ARGs relative abundances, which resulted in higher ARGs relative abundances in comparison to NPK, either by a lesser decrease of IntI1 and tet ARGs or an increase of sul ARGs. The enhancement of existing soil ARG prevalence by organic fertilizers was strongly dependent on the organic fertilizer type and the particular ARG. Compost contained the lowest relative abundance of inherent ARGs and had the least effect on the soil ARG decrease after application. The relative increase of tet ARGs caused by biosolids was larger than that of sul ARGs, while manure caused the opposite effect. Fertilization practices did not exert effective impacts on the soil bacterial community, although it caused significant changes in the profile of the ARG pool. Organic fertilization may thus accelerate the dissemination of ARGs in soil mainly through horizontal gene transfer (HGT), consistent with the enrichment of IntI1 in organic fertilized soils.

Human genetic susceptibility to infectious disease.

Recent genome-wide studies have reported novel associations between common polymorphisms and susceptibility to many major infectious diseases in humans. In parallel, an increasing number of rare mutations underlying susceptibility to specific phenotypes of infectious disease have been described. Together, these developments have highlighted a key role for host genetic variation in determining the susceptibility to infectious disease. They have also provided insights into the genetic architecture of infectious disease susceptibility and identified immune molecules and pathways that are directly relevant to the human host defence.

A Cross-Sectional Review of Reporting Variation in Postoperative Bowel Dysfunction After Rectal Cancer Surgery.

BACKGROUND: Postoperative bowel dysfunction affects quality of life after sphincter-preserving rectal cancer surgery, but the extent of the problem is not clearly defined because of inconsistent outcome measures used to characterize the condition. OBJECTIVE: The purpose of this study was to assess variation in the reporting of postoperative bowel dysfunction and to make recommendations for standardization in future studies. If possible, a quantitative synthesis of bowel dysfunction symptoms was planned. DATA SOURCES: MEDLINE and EMBASE databases, as well as the Cochrane Library, were queried systematically between 2004 and 2015. STUDY SELECTION: The studies selected reported at least 1 component of bowel dysfunction after resection of rectal cancer. MAIN OUTCOME MEASURES: The main outcome measures were reporting, measurement, and definition of postoperative bowel dysfunction. RESULTS: Of 5428 studies identified, 234 met inclusion criteria. Widely reported components of bowel dysfunction were incontinence to stool (227/234 (97.0%)), frequency (168/234 (71.8%)), and incontinence to flatus (158/234 (67.5%)). Urgency and stool clustering were reported less commonly, with rates of 106 (45.3%) of 234 and 61 (26.1%) of 234. Bowel dysfunction measured as a primary outcome was associated with better reporting (OR = 3.49 (95% CI, 1.99-6.23); p < 0.001). Less than half of the outcomes were assessed using a dedicated research tool (337/720 (46.8%)), and the remaining descriptive measures were infrequently defined (56/383 (14.6%)). LIMITATIONS: Heterogeneity in the reporting, measurement, and definition of postoperative bowel dysfunction precluded pooling of results and limited interpretation. CONCLUSIONS: Considerable variation exists in the reporting, measurement, and definition of postoperative bowel dysfunction. These inconsistencies preclude reliable estimates of incidence and meta-analysis. A broadly accepted outcome measure may address this deficit in future studies.

Systematic Review and Meta-analysis of Prophylactic Mesh During Primary Stoma Formation to Prevent Parastomal Hernia.

BACKGROUND: Implantation of mesh at the time of stoma formation may reduce the rate of parastomal hernia. Until recently, the evidence has been limited to only a few small randomized controlled trials. OBJECTIVE: We present an updated systematic review and meta-analysis to assess the effect of mesh prophylaxis on rates of parastomal hernia. We examine ongoing and unpublished trials via online registries and propose recommendations for future research. DATA SOURCES: MEDLINE, EMBASE, and the Cochrane Library were searched up to March 2016 for published randomized controlled trials. Sixteen international trial registries were inspected for ongoing and unpublished trials. STUDY SELECTION: Randomized controlled trials comparing mesh versus no mesh on the incidence of parastomal hernia after colostomy or ileostomy formation were selected. MAIN OUTCOME MEASURES: The primary outcome measure was rate of parastomal hernia at least 12 months after stoma formation. Secondary outcomes included rates of stoma-related complications. RESULTS: Of 3005 studies identified, 7 randomized controlled trials (432 patients) were eligible for inclusion in the final analysis. All were at high risk of bias. Mesh reduced the incidence of clinically detected parastomal hernia (10.8% vs 32.4%; p = 0.001) (risk ratio, 0.34; 95% CI, 0.18-0.65; I = 39%) and the rate of radiologically detected parastomal hernia (34.6% vs 55.3%; p = 0.01) (risk ratio, 0.61; 95% CI, 0.42-0.89; I = 44%). No increase in the incidence of stoma-related complications was observed with the use of prophylactic mesh. Results from ongoing and unpublished randomized controlled trials are expected, but few will report on alternative mesh types or surgical techniques. LIMITATIONS: Heterogeneity of interventions, small patient populations, and a high risk of bias seen in all studies implicate cautious interpretation of the results. CONCLUSION: Mesh prophylaxis at the time of stoma formation appears safe and effective in preventing parastomal hernia; however, limitations of the primary evidence justify larger, more rigorous randomized controlled trials.

Underreporting of Secondary Endpoints in Randomized Trials: Cross-sectional, Observational Study.

OBJECTIVE: To determine if underreporting of secondary endpoints in randomized controlled trials occurs, using surgical site infection (SSI) as an example. BACKGROUND: SSI is a commonly measured endpoint in surgical trials and can act as a proxy marker for primary and secondary endpoint assessments across trials in a range of medical specialties. METHODS: Cross-sectional observational study of randomized trials including patients undergoing gastrointestinal surgery published in a representative selection of general medical and general surgical journals. Studies were included if SSI assessment was a prespecified endpoint. Adjusted binary logistic regression was used to identify factors associated with a high rate of SSI detection (≥10%). RESULTS: From 216 trials including 45,633 patients, the pooled SSI rate was 7.7% (3519/45,633), which was significantly higher when assessed as a primary endpoint (12.6%, 1993/15,861, 49 studies) vs as a secondary endpoint (5.1%, 1526/29,772, 167 studies, P < 0.001). When assessed as a secondary outcome, standardized definitions and formal clinical reviews were used significantly less often. When adjusted for surgical contamination and methodological confounders, secondary assessment was associated with reduced SSI detection compared with primary assessment (adjusted odds ratio 0.24, 95% confidence interval 0.08-0.69, P = 0.008). CONCLUSIONS: Secondary endpoint assessment of SSI in randomized trials was associated with significantly reduced rigor and subsequent detection rates compared with assessment as a primary endpoint. Trial investigators should ensure that primary and secondary endpoint assessments are equally robust. PRISMA guidelines should be updated to promote the conduct of meta-analysis based only on primary outcomes from randomized controlled trials.

Genetic variants associated with non-typhoidal Salmonella bacteraemia in African children.

BACKGROUND: Non-typhoidal Salmonella (NTS) causes invasive and frequently fatal disease in African children. Existing strategies to prevent, diagnose, and treat NTS disease are inadequate. An improved understanding of the biology of invasive Salmonella infection will facilitate the development of novel NTS control measures. Despite evidence in mice and man showing a clear role for host genetics in NTS susceptibility, there are no published studies investigating host genetic susceptibility to NTS in African populations. METHODS: We conducted a genome-wide association study (SNP Array 6.0, Affymetrix, CA, USA) of NTS bacteraemia in Kenyan children, with replication in Malawian children. We assessed the function of NTS-associated variants in an expression quantitative trait locus (eQTL) dataset of interferon γ (IFNγ) and lipopolysaccharide-stimulated monocytes from 432 healthy European adults. Serum IFNγ (Bio-Plex immunoassay, Bio-Rad Laboratories, CA, USA) in Malawian NTS cases (n=106) during acute disease was correlated with genotype by linear regression. FINDINGS: After whole-genome imputation and quality control, 180 Kenyan cases and 2677 controls were included in an association analysis at 7 951 614 (additive model) and 4 669 537 (genotypic model) loci. After quality control, 143 Malawian cases and 336 controls were included in the replication analysis. An intronic variant in STAT4 was associated (recessive model) with NTS in both Kenyan and Malawian children (Kenya p=5·6 × 10(-9), Malawi p=0·02, combined p=1·4 × 10(-9); odds ratio 7·2, 95% CI 3·8-13·5). The NTS-associated variant was an eQTL for STAT4 expression in IFNγ-stimulated monocytes (p=9·59 × 10(-6)), the NTS risk allele being associated with lower STAT4 expression. In Malawian children with NTS bacteraemia, the same NTS risk allele was associated with lower serum concentrations of IFNγ (p=0·02) at presentation. INTERPRETATION: STAT4 is highly plausible as a susceptibility locus for invasive NTS disease. STAT4 mediates IFNγ release in T cells and natural killer cells in response to interleukin 12 (IL12). Individuals with rare mutations elsewhere in the IL12-IFNγ axis are at risk of disseminated NTS infection. We provide the first evidence, to our knowledge, of a host genetic determinant of NTS disease in African children, and of a STAT4 variant conferring susceptibility to an infectious disease in man. FUNDING: Wellcome Trust.

A Mal functional variant is associated with protection against invasive pneumococcal disease, bacteremia, malaria and tuberculosis.

Toll-like receptors (TLRs) and members of their signaling pathway are important in the initiation of the innate immune response to a wide variety of pathogens. The adaptor protein Mal (also known as TIRAP), encoded by TIRAP (MIM 606252), mediates downstream signaling of TLR2 and TLR4 (refs. 4-6). We report a case-control study of 6,106 individuals from the UK, Vietnam and several African countries with invasive pneumococcal disease, bacteremia, malaria and tuberculosis. We genotyped 33 SNPs, including rs8177374, which encodes a leucine substitution at Ser180 of Mal. We found that heterozygous carriage of this variant associated independently with all four infectious diseases in the different study populations. Combining the study groups, we found substantial support for a protective effect of S180L heterozygosity against these infectious diseases (N = 6,106; overall P = 9.6 x 10(-8)). We found that the Mal S180L variant attenuated TLR2 signal transduction.

Promoting research and audit at medical school: evaluating the educational impact of participation in a student-led national collaborative study.

BACKGROUND: Medical students often struggle to engage in extra-curricular research and audit. The Student Audit and Research in Surgery (STARSurg) network is a novel student-led, national research collaborative. Student collaborators contribute data to national, clinical studies while gaining an understanding of audit and research methodology and ethical principles. This study aimed to evaluate the educational impact of participation. METHODS: Participation in the national, clinical project was supported with training interventions, including an academic training day, an online e-learning module, weekly discussion forums and YouTube® educational videos. A non-mandatory, online questionnaire assessed collaborators' self-reported confidence in performing key academic skills and their perceptions of audit and research prior to and following participation. RESULTS: The group completed its first national clinical study ("STARSurgUK") with 273 student collaborators across 109 hospital centres. Ninety-seven paired pre- and post-study participation responses (35.5%) were received (male = 51.5%; median age = 23). Participation led to increased confidence in key academic domains including: communication with local research governance bodies (p < 0.001), approaching clinical staff to initiate local collaboration (p < 0.001), data collection in a clinical setting (p < 0.001) and presentation of scientific results (p < 0.013). Collaborators also reported an increased appreciation of research, audit and study design (p < 0.001). CONCLUSIONS: Engagement with the STARSurg network empowered students to participate in a national clinical study, which increased their confidence and appreciation of academic principles and skills. Encouraging active participation in collaborative, student-led, national studies offers a novel approach for delivering essential academic training.

Human genetic susceptibility to intracellular pathogens.

Intracellular pathogens contribute to a significant proportion of infectious disease morbidity and mortality worldwide. Increasing evidence points to a major role for host genetics in explaining inter-individual variation in susceptibility to infectious diseases. A number of monogenic disorders predisposing to infectious disease have been reported, including susceptibility to intracellular pathogens in association with mutations in genes of the interleukin-12/interleukin-23/interferon-γ axis. Common genetic variants have also been demonstrated to regulate susceptibility to intracellular infection, for example the CCR5Δ32 polymorphism that modulates human immunodeficiency virus-1 (HIV-1) disease progression. Genome-wide association study approaches are being increasingly utilized to define genetic variants underlying susceptibility to major infectious diseases. This review focuses on the current state-of-the-art in genetics and genomics as pertains to understanding the genetic contribution to human susceptibility to infectious diseases caused by intracellular pathogens such as tuberculosis, leprosy, HIV-1, hepatitis, and malaria, with a particular emphasis on insights from recent genome-wide approaches. The results from these studies implicate common genetic variants in novel molecular pathways involved in human immunity to specific pathogens.