The MexTAg collaborative cross: host genetics affects asbestos related disease latency, but has little influence once tumours develop.

Objectives: This study combines two innovative mouse models in a major gene discovery project to assess the influence of host genetics on asbestos related disease (ARD). Conventional genetics studies provided evidence that some susceptibility to mesothelioma is genetic. However, the identification of host modifier genes, the roles they may play, and whether they contribute to disease susceptibility remain unknown. Here we report a study designed to rapidly identify genes associated with mesothelioma susceptibility by combining the Collaborative Cross (CC) resource with the well-characterised MexTAg mesothelioma mouse model. Methods: The CC is a powerful mouse resource that harnesses over 90% of common genetic variation in the mouse species, allowing rapid identification of genes mediating complex traits. MexTAg mice rapidly, uniformly, and predictably develop mesothelioma, but only after asbestos exposure. To assess the influence of host genetics on ARD, we crossed 72 genetically distinct CC mouse strains with MexTAg mice and exposed the resulting CC-MexTAg (CCMT) progeny to asbestos and monitored them for traits including overall survival, the time to ARD onset (latency), the time between ARD onset and euthanasia (disease progression) and ascites volume. We identified phenotype-specific modifier genes associated with these traits and we validated the role of human orthologues in asbestos-induced carcinogenesis using human mesothelioma datasets. Results: We generated 72 genetically distinct CCMT strains and exposed their progeny (2,562 in total) to asbestos. Reflecting the genetic diversity of the CC, there was considerable variation in overall survival and disease latency. Surprisingly, however, there was no variation in disease progression, demonstrating that host genetic factors do have a significant influence during disease latency but have a limited role once disease is established. Quantitative trait loci (QTL) affecting ARD survival/latency were identified on chromosomes 6, 12 and X. Of the 97-protein coding candidate modifier genes that spanned these QTL, eight genes (CPED1, ORS1, NDUFA1, HS1BP3, IL13RA1, LSM8, TES and TSPAN12) were found to significantly affect outcome in both CCMT and human mesothelioma datasets. Conclusion: Host genetic factors affect susceptibility to development of asbestos associated disease. However, following mesothelioma establishment, genetic variation in molecular or immunological mechanisms did not affect disease progression. Identification of multiple candidate modifier genes and their human homologues with known associations in other advanced stage or metastatic cancers highlights the complexity of ARD and may provide a pathway to identify novel therapeutic targets.

Uncovering myocardial infarction genetic signatures using GWAS exploration in Saudi and European cohorts.

Genome-wide association studies (GWAS) have yielded significant insights into the genetic architecture of myocardial infarction (MI), although studies in non-European populations are still lacking. Saudi Arabian cohorts offer an opportunity to discover novel genetic variants impacting disease risk due to a high rate of consanguinity. Genome-wide genotyping (GWG), imputation and GWAS followed by meta-analysis were performed based on two independent Saudi Arabian studies comprising 3950 MI patients and 2324 non-MI controls. Meta-analyses were then performed with these two Saudi MI studies and the CardioGRAMplusC4D and UK BioBank GWAS as controls. Meta-analyses of the two Saudi MI studies resulted in 17 SNPs with genome-wide significance. Meta-analyses of all 4 studies revealed 66 loci with genome-wide significance levels of p < 5 × 10-8. All of these variants, except rs2764203, have previously been reported as MI-associated loci or to have high linkage disequilibrium with known loci. One SNP association in Shisa family member 5 (SHISA5) (rs11707229) was evident at a much higher frequency in the Saudi MI populations (> 12% MAF). In conclusion, our results replicated many MI associations, whereas in Saudi-only GWAS (meta-analyses), several new loci were implicated that require future validation and functional analyses.

Identification of Genetic Variants Associated with Sex-Specific Lung-Cancer Risk.

BACKGROUND: The incidence of lung cancer differs between men and women, suggesting the potential role of sex-specific influences in susceptibility to this cancer. While behavioural differences may account for some of the risk, another possibility is that X chromosome susceptibility genes may have an effect. Little is known about genetic variants on the X chromosome that contribute to sex-specific lung-cancer risk, so we investigated this in a previously characterized cohort. METHODS: We conducted a genetic association reanalysis of 518 lung cancer patients and 844 controls to test for lung cancer susceptibility variants on the X chromosome. Annotated gene expression, co-expression analysis, pathway, and immune infiltration analyses were also performed. RESULTS: 24 SNPs were identified as significantly associated with male, but not female, lung cancer cases. These resided in blocks near the annotated genes DMD, PTCHD1-AS, and AL008633.1. Of these, DMD was differentially expressed in lung cancer cases curated in The Cancer Genome Atlas. A functional enrichment and a KEGG pathway analysis of co-expressed genes revealed that differences in immune function could play a role in sex-specific susceptibility. CONCLUSIONS: Our analyses identified potential genetic variants associated with sex-specific lung cancer risk. Integrating GWAS and RNA-sequencing data revealed potential targets for lung cancer prevention.

Mutations of Helicobacter pylori RdxA are mainly related to the phylogenetic origin of the strain and not to metronidazole resistance.

OBJECTIVES: Drug resistance of Helicobacter pylori is a major clinical problem worldwide. The objective of the present study was to investigate the prevalence of antibiotic-resistant H. pylori in the city of Shenzhen in China, as well as to identify the genetic mutations specifically associated with drug resistance rather than unrelated phylogenetic signals. METHODS: Antibiotic susceptibility testing was performed on 238 clinical strains successfully isolated from H. pylori-positive dyspeptic patients who underwent gastroscopy at the Department of Gastroenterology in Shenzhen People's Second Hospital. Following WGS of all strains using Illumina technology, mutation and phylogenetic analyses were performed. RESULTS: The resistance rates were 84.9%, 35.3%, 25.2% and 2.1% for metronidazole, clarithromycin, ciprofloxacin and rifampicin, respectively. An A2143G conversion in the 23S rRNA gene was the primary mutation observed in clarithromycin-resistant strains, whilst N87K/I and D91G/N/Y in GyrA were detected in ciprofloxacin-resistant strains. In RdxA, our results demonstrated that only R16H/C and M21A are significant contributors to metronidazole resistance; there were 15 other sites, but these are phylogenetically related and thus unrelated to metronidazole resistance. CONCLUSIONS: There is a high prevalence of metronidazole, clarithromycin and ciprofloxacin resistance and a low prevalence of rifampicin resistance in H. pylori from Shenzhen, China. Omission of phylogenetically related sites will help to improve identification of sites genuinely related to antibiotic resistance in H. pylori and, we believe, other species.

Revised Common Rule Changes to the Consent Process and Consent Form.

Background: The Federal Policy for the Protection of Human Subjects-the Common Rule-was revised in 2017 to reduce administrative burdens for low-risk research while enhancing protections for human subjects enrolled in greater-than-minimal-risk trials. These enhanced protections involve changes to the consent process. Methods: We review the general requirements applicable to the consent process, as well as the additional elements of consent mandated by the revisions to the Common Rule. The regulations apply to federally funded studies and are optional for non-federally funded studies. Results: Two new general requirements for the consent process, one basic required element for the consent form, and three optional additional elements for the consent form were added in an effort to improve potential subjects' understanding of research studies and to facilitate the exchange of information between the research staff and potential subjects. Important information about the study should be extracted into a concise key information section to help potential subjects make informed decisions regarding participation. Conclusion: The revisions to the Common Rule are intended to enhance human subject protection by providing more information in an understandable form during the consent process. The new consent elements aim to increase transparency and help improve clarity.

The impact of angiogenesis inhibitors on survival of patients with small cell lung cancer.

BACKGROUND: Small cell lung cancer (SCLC) is a highly invasive and lethal neuroendocrine tumor. Antiangiogenic drugs have been reported in the treatment of SCLC. We aimed to provide a comprehensive evaluation of the impact of angiogenic inhibitors on SCLC survival using network meta-analysis. METHODS: The impact of five angiogenesis inhibitors, that is, vandetanib (Van), bevacizumab (Bev), Rh-endostatin (End), sunitinib (Sun), and thalidomide (Tha), on progression-free survival (PFS) and overall survival (OS) was evaluated by conducting a network meta-analysis. RNA sequencing data were downloaded from publicly available databases. RESULTS: Nine phase II and III randomized controlled trials (RCTs), that involved 1599 participants, that investigated angiogenesis inhibitors in the treatment of SCLC were included in this meta-analysis. Sun and Bev achieved better PFS than Tha (Bev VS. Tha, HR = 0.88, 95% CI: 0.79-0.98, Sun VS. Tha, HR = 0.80, 95% CI: 0.65-1.00). Moreover, Sun and Bev were superior to placebo in terms of PFS (Bev VS. Placebo, HR = 0.89, 95%CI: 0.81-0.97, Sun VS. Placebo, HR = 0.81, 95% CI: 0.66-1.00). Based on this study, we found no significant difference of OS of SCLC. The angiogenesis pathway and expression of target genes were globally deactivated in SCLC tissue. CONCLUSION: Results of this network meta-analysis indicate that the PFS outcome of SCLC with Sun or Bev drugs is superior to that of Tha. The improved therapeutic impact of angiogenesis inhibitors on SCLC needs more evidence, such as long-term observation in clinical trials, to be validated.

The Influence of Modernization and Disease on the Gastric Microbiome of Orang Asli, Myanmars and Modern Malaysians.

The present study explored the differences in gastric microbiome between three distinct populations of Southeast Asia. These include the isolated Orang Asli population and modern Malaysians, as well as patients from Myanmar, the least developed country in the region. All 79 subjects recruited in this study had Helicobacter pylori infection. Based on alpha diversity analysis, Orang Asli had the richest and most diverse gastric microbiome, followed by Myanmar and modern Malaysian groups. Beta diversity analysis revealed significant separation of samples between different populations. These observations are likely to be associated with the level of modernization of each population. Our data further suggested increased bacterial species richness and diversity of the gastric microbiome in individuals who were less modernized, particularly in the Orang Asli group, could suppress the growth of H. pylori. In addition, there were significant variations in the gastric microbiome between modern Malaysians with different types of gastric diseases. Notably, Cutibacterium acnes was present at significantly greater abundance level in patients with non-ulcerative dyspepsia than those with peptic-ulcer diagnosis. This suggests that C. acnes may also play a role in gastritis besides H. pylori, which merits further investigation.

The impact of household hygiene on the risk of bacterial diarrhea among Egyptian children in rural areas, 2004-2007.

INTRODUCTION: The present study, conducted between January 2004 and April 2007, explored the impact of household hygiene on the risk of bacterial diarrhea, using data from a prospective birth cohort of 348 infants in five villages in the Nile Delta in Egypt. METHODOLOGY: Neonates were enrolled at birth and followed up until 24 months of age. Children were visited twice a week to survey them for acute diarrhea. A detailed observational household hygiene survey was completed in-house every six months. Adjusted relative risk (aRR) of developing bacterial diarrhea was calculated for exposure to different hygiene variables and examined for specific bacterial pathogens. RESULTS: Exclusive breastfeeding reduced the risk of bacterial diarrhea by 70%, while bacterial diarrhea cases were 2.6 times higher in the warm season. Risk of Campylobacter diarrhea increased with the absence of barriers to keep birds and animals out of the eating area, the presence of garbage containers and a bathing facility within the compound, and the presence of feces on the floor of the bathing facility. Use of municipal water for drinking and cooking was associated with a lower risk of Campylobacter diarrhea. Risk of enterotoxigenic Escherichia coli diarrhea increased with uncovered garbage containers and the presence of liquid materials in the garbage containers, but decreased with the use of tap water in the washing facility. CONCLUSION: The results highlight some potential targets for interventions, such as expanding municipal water supply to all houses and comprehensive mass-media awareness programs to change hygiene-promoting behaviors and practices.

Pathogenicity and phenotypic characterization of enterotoxigenic Escherichia coli isolates from a birth cohort of children in rural Egypt.

Enterotoxigenic Escherichia coli (ETEC) has consistently been the predominant bacterial cause of diarrhea in many birth cohort- and hospital-based studies conducted in Egypt. We evaluated the pathogenicity of ETEC isolates in a birth cohort of children living in a rural community in Egypt. Between 2004 and 2007, we enrolled and followed 348 children starting at birth until their second year of life. A stool sample and two rectal swabs were collected from children during twice-weekly visits when they presented with diarrhea and were collected every 2 weeks if no diarrhea was reported. From routine stool cultures, five E. coli-like colonies were screened for ETEC enterotoxins using a GM1 enzyme-linked immunosorbent assay (ELISA). The isolates were screened against a panel of 12 colonization factor antigens (CFAs) by a dot blot assay. A nested case-control study evaluated the association between initial or repeat excretion of ETEC and the occurrences of diarrhea. The pathogenicity of ETEC was estimated in symptomatic children compared to that in asymptomatic controls. ETEC was significantly associated with diarrhea (crude odds ratio, 1.37; 95% confidence interval [CI], 1.24 to 1.52). The distribution of ETEC enterotoxins varied between the symptomatic children (44.2% heat-labile toxin [LT], 38.5% heat-stable toxin [ST], and 17.3% LT/ST) and asymptomatic children (55.5% LT, 34.6% ST, and 9.9% LT/ST) (P < 0.001). The CFAs CFA/I (n = 61), CS3 (n = 8), CS1 plus CS3 (n = 24), CS2 plus CS3 (n = 18), CS6 (n = 45), CS5 plus CS6 (n = 11), CS7 (n = 25), and CS14 (n = 32) were frequently detected in symptomatic children, while CS6 (n = 66), CS12 (n = 51), CFA/I (n = 43), and CS14 (n = 20) were detected at higher frequencies among asymptomatic children. While all toxin phenotypes were associated with diarrheal disease after the initial exposure, only ST and LT/ST-expressing ETEC isolates (P < 0.0001) were associated with disease in repeat infections. The role of enterotoxins and pathogenicity during repeat ETEC infections appears to be variable and dependent on the coexpression of specific CFAs.

Phenotypic and genotypic characterization of enterotoxigenic Escherichia coli isolated from U.S. military personnel participating in Operation Bright Star, Egypt, from 2005 to 2009.

Enterotoxigenic Escherichia coli (ETEC) is a major health problem for travelers to the Middle East. During the autumn months of 2005, 2007, and 2009, U.S. military personnel participated in Operation Bright Star (OBS) exercises in Egypt. Out of 181 military personnel enrolled in a diarrheal surveillance study, E. coli-like colonies were isolated from 170 patients. Isolates were tested for the detection of ETEC enterotoxins and colonization factors (CFs) using phenotypic and genotypic methods. Additionally, we studied the secular trends of ETEC isolates obtained from OBS studies since 1999. ETEC was isolated from 51.2% and 60.0% of the patients based on enzyme-linked immunosorbent assay and polymerase chain reaction (PCR), respectively. Heat stable (ST) was the dominant enterotoxin detected followed by heat labile (LT) and LTST. Additionally, we detected a CF in 59.7% and 67.6% of the ETEC-positive isolates using dot blot and PCR assays, respectively. The predominant CF isolated was CS6 followed by CS3.

Kernel methods and haplotypes used in selection of sparse DNA markers for protein yield in dairy cattle.

Recently, genome wide DNA markers have been used in breeding value estimation of livestock species. The computational technique is known as genomic selection. Typically, a large number of marker effects are estimated from a small number of animals, which presents an under-determined problem. In this paper, we propose sparse marker selection methods using haplotypes for both breeding value estimation and QTL mapping. By applying a two-stage regression strategy, markers are selected in the first stage, then in the second stage the selected markers are fitted in a range of models including linear, kernel and semi-parametric models. The estimation accuracy of breeding values is measured by the correlation coefficient, as well as the regression coefficient, between the true breeding values and the estimated breeding values by the models. We show that the estimation accuracy by using sparse markers, as low as 5000 or 500 dimensions, is comparable to that obtained from genome wide markers of about 230,000 dimensions of DNA haplotypes. The selected sparse markers can also be used for QTL mapping. In this paper we use protein yield to demonstrate the methods, and show that loci of large effects confirm published QTL.

Genotypic characterization of Egypt enterotoxigenic Escherichia coli isolates expressing coli surface antigen 6.

INTRODUCTION: One approach to control enterotoxigenic Escherichia coli (ETEC) infections has been to develop vaccines focused on inducing protective immunity against surface expressed antigenic factors. One such factor is coli surface antigen 6 (CS6); ETEC isolates expressing CS6 may also simultaneously co-express surface antigens CS4 or CS5. However, there is little information regarding the inter-relationships of isolates expressing the CS6 antigen alone or in combination with CS4 or CS5. METHODOLOGY: A total of 62 CS6-associated ETEC isolates were evaluated for their antimicrobial susceptibility, mechanisms of resistance, toxin genes, colonization factor expression, and XbaI-pulsed-field gel electrophoretic profiles. RESULTS: We observed 46 XbaI profiles; 31 were exclusive to ETEC expressing CS6 alone and 15 among the ETEC co-expressing CS4 or CS5. Nearly half (47%) of these isolates were resistant to ampicillin, a third (37%) of the isolates were resistant to trimethoprim-sulfamethoxazole, and 24% of the isolates were tetracycline-resistant. A blaTEM gene was detected in 24 (83%) ampicillin-resistant isolates. Trimethoprim-sulfamethoxazole-resistant isolates (n = 23) carried either sulI (n = 1, 4%), sulII (n = 8, 35%) or both genes (n = 10, 43%); 4 had no detectable sul gene. CONCLUSIONS: Our results show a lack of clonality among Egypt CS6 E. coli isolates and supports the use and the further research on vaccines targeting this cell surface antigen.

Enteric viral infections as potential risk factors for intussusception.

INTRODUCTION: We aimed to identify potential risk factors for intussusception (ISS) among children presenting to two pediatric hospitals in Egypt. METHODOLOGY: In this case-control study,  enrolled children < 3 years old with ISS (confirmed radiologically and/or surgically) were  matched by age and gender to controls admitted with acute non-abdominal surgical illnesses. Stool samples were collected and tested for various enteric bacteria, rotavirus, enteric adenoviruses (EA, 40 and 41) and astroviruses using commercially available ELISA diagnostic kits. RESULTS: From December 2004 to May 2009, 158 cases and 425 matched controls were enrolled. A history of diarrhoea and cough over the preceding four weeks of interview were more common in cases than controls, respectively. Children with mothers who had secondary education and above were 2.2 times more likely to have ISS than those whose mothers had a lower level of education. In spite of the low detection rate of EA infection (regardless of diarrhoea history) and asymptomatic rotavirus infection, they were detected in higher frequencies in cases than controls; however, infection with astrovirus and bacterial pathogens did not appear to be associated with increased risk of ISS. CONCLUSIONS: History of diarrhoea and cough over the four weeks preceding the study and maternal education above secondary level were potential risk factors for ISS. EA and asymptomatic rotavirus infection were detected in higher frequencies among cases than controls; however, association with ISS cannot be confirmed. Additional research is needed to confirm these findings and evaluate the pathogenesis which may link such infections with ISS.

Hotel clinic-based diarrheal and respiratory disease surveillance in U.S. service members participating in Operation Bright Star in Egypt, 2009.

We conducted clinic-based, influenza-like illness and diarrheal disease surveillance among U.S. service members participating in Operation Bright Star 2009. Epidemiologic data and samples were collected. Nasopharyngeal swab specimens were tested for viruses, and feces was tested for microbiologic, immunologic, and molecular diagnostics. A survey was used to collect self-reported data. From 1,529 surveys, 41% reported diarrheal disease and 25% reported respiratory illness (incidence rate = 62 of 100 versus 37 of 100 person-months; incidence rate ratio = 1.7, 95% confidence interval = 1.5-1.9). Enterotoxigenic Escherichia coli was identified in 74% (69 of 93) of fecal samples. In the influenza-like illness case series, 17% (9 of 52) were positive for influenza A; all were positive for pandemic (pH1N1) 2009 virus. Rates of decreased work performance reported by patients with diarrhea and influenza-like illness were similar (46% versus 48%; P = 0.8). Diarrheal diseases and respiratory illness remain common among deployed military personnel, with important operational impact. Despite an ongoing influenza pandemic, diarrheal disease incidence was higher than that of respiratory illness.

Burden of Aeromonas hydrophila-associated diarrhea among children younger than 2 years in rural Egyptian community.

INTRODUCTION: Between 2004 and 2007, a birth cohort of Egyptian children was analysed to evaluate the epidemiology of enteric diseases. METHODOLOGY: A stool sample was collected from the study children every two weeks as well as whenever they experienced diarrhea. Samples were tested for routine bacterial pathogens as well as enteropathogenic viruses and parasites. A secondary goal of the study was to evaluate the burden of less commonly reported pathogens including Aeromonas hydrophila. RESULTS: Of the 348 study subjects, 79 had A. hydrophila isolated from their stool at some point during the study.  Thirty-six children had exclusively symptomatic (S) infections while 33 had exclusively asymptomatic (AS) infections. However, 10 children had both S and AS infections. Among symptomatic cases, A. hydrophila was the sole pathogen isolated 36% of the time. An important aspect of A. hydrophila associated diarrhea was the high level of resistance to cephalosporins. CONCLUSION: Although relatively uncommon, A. hydrophila was found to be associated with diarrhea among children living in Egypt and was frequently multi-drug resistant.

Increase in the detection rate of viral and parasitic enteric pathogens among Egyptian children with acute diarrhea.

INTRODUCTION: Acute diarrhea continues to be a major cause of morbidity and mortality in children from developing countries. Determination of the frequency of diarrhea in an area, along with the proportion of disease caused by specific enteric agents of different origins, is considered the first step in controlling diarrheal diseases. METHODOLOGY: From 2005 to 2007, a hospital-based surveillance was conducted in two locations in Egypt to determine the causes of acute diarrhea in children younger than 5-years seeking treatment. Five additional enteric viral and parasitic pathogens were tested using commercially-available enzyme immunoassays (EIA) to re-evaluate the prevalence of diarrheal pathogens in undiagnosed cases. RESULTS: Adenovirus, astrovirus, norovirus and G. lamblia were detected as the sole pathogen in 2% (n=34), 3% (n=56), 9% (n=191) and 7% (n=146) of the cases, respectively. E. histolytica was never detected as the sole pathogen. The percentage of diarrheal cases with a known cause increased significantly, from 48% (n=1,006) to 74% (n=1,568) (P < 0.0001). CONCLUSION: In our study, the incorporation of immunoassays yielded useful data in identifying pathogens in previously pathogen-negative diarrhea cases.

Enteric disease surveillance under the AFHSC-GEIS: current efforts, landscape analysis and vision forward.

The mission of the Armed Forces Health Surveillance Center, Division of Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) is to support global public health and to counter infectious disease threats to the United States Armed Forces, including newly identified agents or those increasing in incidence. Enteric diseases are a growing threat to U.S. forces, which must be ready to deploy to austere environments where the risk of exposure to enteropathogens may be significant and where routine prevention efforts may be impractical. In this report, the authors review the recent activities of AFHSC-GEIS partner laboratories in regards to enteric disease surveillance, prevention and response. Each partner identified recent accomplishments, including support for regional networks. AFHSC/GEIS partners also completed a Strengths, Weaknesses, Opportunities and Threats (SWOT) survey as part of a landscape analysis of global enteric surveillance efforts. The current strengths of this network include excellent laboratory infrastructure, equipment and personnel that provide the opportunity for high-quality epidemiological studies and test platforms for point-of-care diagnostics. Weaknesses include inconsistent guidance and a splintered reporting system that hampers the comparison of data across regions or longitudinally. The newly chartered Enterics Surveillance Steering Committee (ESSC) is intended to provide clear mission guidance, a structured project review process, and central data management and analysis in support of rationally directed enteric disease surveillance efforts.