Fecal Test Research Articles

Nutritional status in advanced pancreatic cancer

Background. Exocrine pancreatic insufficiency (EPI) occurs in most patients with advanced pancreatic cancer (PC) and even more often when a tumor is localized in the head of the pancreas. However, insufficient attention is paid to the diagnosis of EPI and assessment of nutritional status, which negatively affects the results of treatment.
 Materials and methods. One hundred fifty eight patients with primary diagnosed locally advanced and metastatic PC were included in the retrospective study. We used the calculation of the odds ratio with 95% CI with an assessment of the p value using the Pearson ÷2 test to compare the incidence of clinical and laboratory parameters of nutritional status with values below the lower limit of normal (LLN) depending on the location of the tumor in the pancreas.
 Results. Fecal elastase test was performed in only 19 (12%) patients. In this group, the incidence of EPI was 73.6%. Pancreatic enzyme replacement therapy in the minimal sufficient dose was prescribed in 17.1% of the general cohort. The level of hemoglobin, erythrocytes and albumin below the LLN was found in patients with the tumor in the pancreatic head, respectively, 2.742 (95% CI 1.27–5.92), 3.788 (95% CI 1.554–9.232) and 9.767 (95% CI 1.255–76.027) times more often than in patients with cancer in the body-tail of the pancreas. In patients with the tumor in the pancreatic head, the lower levels of hemoglobin (median 125 g/l vs 132 g/l, respectively), erythrocytes (4.19 mil/μl vs 4.51 mil/μl), total protein (69.6 g/l vs 71.5 g/l), and albumin (40.1 g/l vs 42 g/l), as well as the values of nutritional indices: prognostic nutritional index, nutritional risk index, hemoglobin, albumin, lymphocyte and platelet ratio index, and prognostic immune nutritional index were observed.
 Conclusion. Diagnosis and treatment of EPI remains inadequately attended. The values of nutritional status parameters in patients with PC in the head are lower than in patients with a tumor in the body-tail of the pancreas, which reflects the contribution of EPI.

Chemoprophylaxis of precancerous lesions in patients who are at a high risk of developing colorectal cancer (Review).

The diagnostics of colorectal cancer (CRC) and precancerous lesions in the colon is one of the most urgent matters to be considered for the modern protocols of complex examination, recommended for use from the age of 45 years, and including both instrumental and laboratory methods of research: Colonoscopy, CT colonography, flexible sigmoidoscopy, fecal occult blood test, fecal immunohistochemistry test and stool DNA test Nevertheless, the removal of those precancerous lesions does not solve the issue, and, apart from the regular endoscopic monitoring of patients who are at a high risk of developing CRC, the pharmacological treatment of certain key pathogenic mechanisms leading to the development of CRC is required. The present review to discusses the function of β-catenin in the transformation of precancerous colorectal lesions into CRC, when collaborating with PI3K/AKT/mTOR signaling pathway and other mechanisms. The existing methods for the early diagnostics and prevention of discovered anomalies are described and categorized. The analysis of the approaches to chemoprophylaxis of CRC, depending on the results of endoscopic, morphological and molecular-genetic tests, is presented.

Comparative Effectiveness and Cost-Effectiveness of Colorectal Cancer Screening With Blood-Based Biomarkers (Liquid Biopsy) vs Fecal Tests or Colonoscopy

Colorectal cancer (CRC) screening is highly effective but underused. Blood-based biomarkers (liquid biopsy) could improve screening participation. Using our established Markov model, screening every 3 years with a blood-based test that meets minimum Centers for Medicare & Medicaid Services' thresholds (CMSmin) (CRC sensitivity 74%, specificity 90%) was compared with established alternatives. Test attributes were varied in sensitivity analyses. CMSmin reduced CRC incidence by 40% and CRC mortality by 52% vs no screening. These reductions were less profound than the 68%-79% and 73%-81%, respectively, achieved with multi-target stool DNA (Cologuard; Exact Sciences) every 3 years, annual fecal immunochemical testing (FIT), or colonoscopy every 10 years. Assuming the same cost as multi-target stool DNA, CMSmin cost $28,500/quality-adjusted life-year gained vs no screening, but FIT, colonoscopy, and multi-target stool DNA were less costly and more effective. CMSmin would match FIT's clinical outcomes if it achieved 1.4- to 1.8-fold FIT's participation rate. Advanced precancerous lesion (APL) sensitivity was a key determinant of a test's effectiveness. A paradigm-changing blood-based test (sensitivity >90% for CRC and 80% for APL; 90% specificity; cost ≤$120-$140) would be cost-effective vs FIT at comparable participation. CMSmin could contribute to CRC control by achieving screening in those who will not use established methods. Substituting blood-based testing for established effective CRC screening methods will require higher CRC and APL sensitivities that deliver programmatic benefits matching those of FIT. High APL sensitivity, which can result in CRC prevention, should be a top priority for screening test developers. APL detection should not be penalized by a definition of test specificity that focuses on CRC only.

Diagnostic strategy of irritable bowel syndrome: a low- and middle-income country perspective.

Irritable bowel syndrome (IBS) is a highly prevalent gastrointestinal disorder associated with substantial impairment which considerably burdens healthcare systems worldwide. Research on IBS has largely been conducted in high-income countries posing barriers to the application of diagnostic strategies in low- and middle-income countries (LMICs) due to differences in disease characteristics, healthcare resources, and socioeconomic factors. This review discusses the diagnostic issues associated with LMICs. We present a concise overview of the relevant approaches and propose a diagnostic strategy based on the latest evidence. A positive diagnostic strategy that relies on appropriate symptom-based criteria is crucial within the diagnostic framework. A combination of complete blood count, fecal occult blood test, and complete stool test may reliably identify individuals with suspected IBS who are more likely to have organic diseases, thus justifying the necessity for a colonoscopy. Eventually, we developed a diagnostic algorithm based on a limited setting perspective that summarizes the available evidence and may be applied in LMICs.

Abstract 2160: Utilizing geospatial analytics to identify neighborhood cancer hot spots for recruitment of underserved populations in clinical prevention research

Abstract Background: The term “precision public health” has increasingly been used in literature to describe public health practices that utilize new technologies and big data to precisely target the most vulnerable populations for disease control. Following the principles of precision public health, we used geospatial technologies and population-based health data to identify the locations and socioeconomic status of neighborhoods with high cancer incidences for recruitment of participants in prevention research. Methods: Using Florida cancer registry data, geospatial hot spot analyses were carried out to identify statistically significant clusters of census tracts with high incidences of prostate, gastric, and oral cancers within the catchment area of the Sylvester Comprehensive Cancer Center in South Florida. The locations, social determinants of health (US Census’ American Community Survey), and behavioral risk factor data (CDC’s Behavioral Risk Factor Surveillance System) of these hot spots were analyzed to identify the locations of underserved communities facing high risk for these three cancers. Results: Hot spots with high incidences for each of these three cancers overlap in many neighborhoods with high proportions of Hispanic and Non-Hispanic Black populations and high levels of socioeconomic disparities, such as low income, low education level, rental housing, no vehicles, and no access to health insurance. These neighborhoods also have high rates for behavioral risk factors in smoking, lack of physical activity, obesity, and high incidence of cervical cancer (high risk areas for HPV-associated oral cancers). Mobile screening units called the Game Changer Vehicles have been deployed to the locations to recruit participants who were tested on-site for prostate specific antigen (prostate cancer), H. pylori (gastric cancer), or solCD44 (a soluble tumor marker for squamous cell carcinoma) and total protein levels in oral rinse specimens, which can distinguish individuals with molecular features at risk for oral cancers due to tobacco, alcohol use, and human HPV infection. Conclusions: Geospatial analyses of population health data can be used to produce metrics that precisely target neighborhoods with high cancer risk and health disparities to recruit research participants. The same precision approach can also be applied for cancer screening purposes, such as offering cervical self-sample and fecal blood test kits in disadvantaged communities facing heightened risk for cervical and colorectal cancers. Citation Format: Ming S. Lee, Rebecca Kaiser, Ridhi Vyas, Amando Vera, Daniela Flores Quetant, Nancy Elliott, Valerie Bethel, Amanda Rivera, Shria Kumar, Brandon Mahal, Elizabeth Franzmann, Erin Kobetz. Utilizing geospatial analytics to identify neighborhood cancer hot spots for recruitment of underserved populations in clinical prevention research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2160.

The association between organised colorectal cancer screening strategies and reduction of its related mortality: a systematic review and meta-analysis

BackgroundTo assess the long-term association between organised colorectal cancer (CRC) screening strategies and CRC-relate mortality.MethodsWe systematically reviewed studies on organised CRC screening through PubMed, Ovid Medline, Embase and Cochrane from the inception. We retrieved characteristics of organised CRC screening from included literature and matched mortality (over 50 years) of those areas from the International Agency for Research on Cancer in May 2023. The variations of mortality were reported via the age-standardised mortality ratio. A random-effects model was used to synthesis results.ResultsWe summarised 58 organised CRC screening programmes and recorded > 2.7 million CRC-related deaths from 22 countries where rollout screening programmes were performed. The CRC screening strategy with faecal tests (guaiac faecal occult blood test (gFOBT) or faecal immunochemical tests (FIT)) or colonoscopy as the primary screening offer was associated with a 41.8% reduction in mortality, which was higher than those offered gFOBT (4.4%), FIT (16.7%), gFOBT or FIT (16.2%), and faecal tests (gFOBT or FIT) or flexible sigmoidoscopy (16.7%) as primary screening test. The longer duration of screening was associated with a higher reduction in the pooled age-standardised mortality ratio. In particular, the pooled age-standardised mortality ratio became non-significant when the screening of FIT was implemented for less than 5 years.ConclusionsA CRC screening programme running for > 5 years was associated with a reduction of CRC-related mortality. Countries with a heavy burden of CRC should implement sustainable, organised screening providing a choice between faecal tests and colonoscopy as a preferred primary test.

Screening for potential infections in fecal microbiota transplantation guidelines and an experience of microbiota bank operation in Korea: a narrative review

Fecal microbiota transplantation (FMT) involves the transfer of fecal microbiota from healthy donors to patients to rectify dysbiosis and restore the functionality of the gut microbiota to a healthy state. Donor selection is important to minimize the risk of FMT. Donor selection for FMT is primarily focused on screening for potential infections. A complete consensus on screening tests and checkpoints is lacking and controversial; nevertheless, most guidelines agree to rule out certain infections, such as syphilis; hepatitis A, B, and C; and HIV. In most guidelines, stool testing includes testing for Clostridioides difficile and other enteric pathogens. The Korean FMT guidelines for C. difficile infections were published in 2022. The guidelines recommend serological and stool testing for donor candidates, with recommendations for stool testing providing targets for screening using specific test methods. Donor screening by Microbiotix Inc., a fecal microbiota bank in Korea, between 2017 and 2023 showed that only 5% of potential FMT donors were eligible for repeat donation. The future of FMT remains uncertain, with possibilities ranging from continuation to restrictions, and the development of synthetic microbiota preparations. Legislative support is crucial for advancing this field and providing hope and a potential cure for previously incurable patients.

The projected health and economic impact of increased colorectal cancer screening participation among Canadians by income quintile

ObjectivesDisparities in colorectal cancer (CRC) screening uptake by socioeconomic status have been observed in Canada. We used the OncoSim-Colorectal model to evaluate the health and economic outcomes associated with increasing the participation rates of CRC screening programs to 60% among Canadians in different income quintiles.MethodsBaseline CRC screening participation rates were obtained from the 2017 Canadian Community Health Survey. The survey participants were categorized into income quintiles using their reported household income and 2016 Canadian Census income quintile thresholds. Within each quintile, the participation rate was the proportion of respondents aged 50–74 who reported having had a fecal test in the past two years. Using the OncoSim-Colorectal model, we simulated an increase in CRC screening uptake to 60% across income quintiles to assess the effects on CRC incidence, mortality, and associated economic costs from 2024 to 2073.ResultsIncreasing CRC screening participation rates to 60% across all income quintiles would prevent 69,100 CRC cases and 36,600 CRC deaths over 50 years. The improvement of clinical outcomes would also translate to increased person-years and health-adjusted person-years. The largest impact was observed in the lowest income group, with 22,200 cases and 11,700 deaths prevented over 50 years. Increased participation could lead to higher screening costs ($121 million CAD more per year) and lower treatments costs ($95 million CAD less per year), averaged over the period 2024–2073.ConclusionIncreased screening participation will improve clinical outcomes across all income groups while alleviating associated treatment costs. The benefits of increased participation will be strongest among the lowest income quintile.

Association between time to colonoscopy after positive fecal testing and colorectal cancer outcomes in Alberta, Canada.

To quantify the associations between time to colonoscopy after a positive fecal immunochemical test (FIT+) and colorectal cancer (CRC)-related outcomes in the context of a provincial, population-based CRC screening program. Population-based, retrospective cohort study in Alberta, Canada, including Albertans aged 50-74 with at least one FIT+ in 2014-2017. Study outcomes were CRC diagnosis after a FIT+ and a diagnostic follow-up colonoscopy in 2014-2019 and CRC stage at diagnosis. Multivariable logistic regression models were used to evaluate the relative risk of any CRC or advanced-stage CRC. Results were presented as crude odds ratio (OR) and adjusted OR (aOR) with 95% confidence intervals (CIs). Of the 787,967 participants who had a FIT, 63,232 (8%) had a FIT+ and met the study's eligibility criteria. The risk of any CRC or advanced-stage CRC stayed high and was relatively consistent for follow-up colonoscopies performed within 1-12 months of the FIT+. After 12 months, the risk of CRC was considerably higher, particularly for advanced-stage CRC. The OR and aOR for any CRC were 1.40 (95% CI: 1.13-1.73; p < 0.05) and 1.20 (95% CI: 0.96-1.49), respectively, and the OR and aOR for advanced-stage CRC were 1.42 (95% CI: 0.98-2.08) and 0.88 (95% CI: 0.59-1.32), respectively, for colonoscopy follow-up within 12-18 months versus 1-2 months. For Albertans who used FIT for CRC screening, a longer time interval between a FIT+ and follow-up colonoscopy, particularly over 12 months, increases the risk of having CRC and decreases the effectiveness of CRC screening programs.

Medical Home Implementation and Follow-Up of Cancer-Related Abnormal Test Results in the Veterans Health Administration

Lack of timely follow-up of cancer-related abnormal test results can lead to delayed or missed diagnoses, adverse cancer outcomes, and substantial cost burden for patients. Care delivery models, such as the Veterans Affairs' (VA) Patient-Aligned Care Team (PACT), which aim to improve patient-centered care coordination, could potentially also improve timely follow-up of abnormal test results. PACT was implemented nationally in the VA between 2010 and 2012. To evaluate the long-term association between PACT implementation and timely follow-up of abnormal test results related to the diagnosis of 5 different cancers. This multiyear retrospective cohort study used 14 years of VA data (2006-2019), which were analyzed using panel data-based random-effects linear regressions. The setting included all VA clinics and facilities. The participants were adult patients who underwent diagnostic testing related to 5 different cancers and had abnormal test results. Data extraction and statistical analyses were performed from September 2021 to December 2023. Calendar years denoting preperiods and postperiods of PACT implementation, and the PACT Implementation Progress Index Score denoting the extent of implementation in each VA clinic and facility. Percentage of potentially missed timely follow-ups of abnormal test results. This study analyzed 6 data sets representing 5 different types of cancers. During the initial years of PACT implementation (2010 to 2013), percentage of potentially missed timely follow-ups decreased between 3 to 7 percentage points for urinalysis suggestive of bladder cancer, 12 to 14 percentage points for mammograms suggestive of breast cancer, 19 to 22 percentage points for fecal tests suggestive of colorectal cancer, and 6 to 13 percentage points for iron deficiency anemia laboratory tests suggestive of colorectal cancer, with no statistically significant changes for α-fetoprotien tests and lung cancer imaging. However, these beneficial reductions were not sustained over time. Better PACT implementation scores were associated with a decrease in potentially missed timely follow-up percentages for urinalysis (0.3-percentage point reduction [95% CI, -0.6 to -0.1] with 1-point increase in the score), and laboratory tests suggestive of iron deficiency anemia (0.5-percentage point reduction [95% CI,-0.8 to -0.2] with 1-point increase in the score). This cohort study found that implementation of PACT in the VA was associated with a potential short-term improvement in the quality of follow-up for certain test results. Additional multifaceted sustained interventions to reduce missed test results are required to prevent care delays.

Assessment of Welfare in Transhumance Yak Hybrids (Chauris) in the Lower Himalayan Region of Nepal

In order to develop a yak/chauri-specific welfare assessment protocol, we sent a set of 31 potential welfare measures to 120 Nepalese experts and asked them to identify the measures that they thought would be useful and propose additional useful measures. Eighty-three experts responded, with 13 measures being identified by &gt;50% of respondents as likely to be useful. These thirteen measures plus one new measure (hematology) were included in an assessment protocol that was tested in the second phase of this study in five chauri herds in two districts in northern Nepal. Animal-based evaluations along with sampling for mastitis, intestinal parasites, and hematology were undertaken during or just after morning milking. Resource- and record-based measures were assessed through structured interviews, with verifications on-site where possible. No chauris exhibited poor body conditions, skin injuries, significant locomotion issues, or significant subclinical mastitis. Fecal testing suggested a high prevalence of intestinal parasites at the herd level, while blood testing suggested no evidence of hematological abnormalities. However, for both results, we need more data to use these effectively as measures of welfare. The resource-based assessment revealed significant challenges across all resources, and veterinary services were reported as being inadequate. A high estimated annual mortality rate (10–21%) needs further investigation. This protocol provided a useful start towards developing a welfare assessment protocol for yak/chauri and identified issues that need addressing to optimize chauri welfare.

Next-Generation Screening for Colorectal Cancer, an Incremental Approach to a Global Disease.

New screening tests for early detection of colorectal cancer and its precursors are rapidly emerging with the focus on noninvasive tests which can be used in both structured opportunistic and population-based organized screening programs. Novel technologies are identifying new combinations of promising markers. Conducting large prospective clinical trials of efficacy requires very large numbers of subjects constituting intended-use populations. These trials are often preceded by studies using smaller numbers of "convenience" samples to derive panels of relevant markers and algorithms to combine them and define what constitutes a positive test. The article by Gagrat and colleagues in this issue reports results from one such study designed to yield a "next-generation" multitargeted (mt-sDNA) stool test. This report exemplifies the advantages and limitations of this approach. See related article by Gagrat et al., p. 119.

Improved DNA Extraction and Amplification Strategy for 16S rRNA Gene Amplicon-Based Microbiome Studies.

Next-generation sequencing technology has driven the rapid advancement of human microbiome studies by enabling community-level sequence profiling of microbiomes. Although all microbiome sequencing methods depend on recovering the DNA from a sample as a first critical step, lysis methods can be a major determinant of microbiome profile bias. Gentle enzyme-based DNA preparation methods preserve DNA quality but can bias the results by failing to open difficult-to-lyse bacteria. Mechanical methods like bead beating can also bias DNA recovery because the mechanical energy required to break tougher cell walls may shear the DNA of the more easily lysed microbes, and shearing can vary depending on the time and intensity of beating, influencing reproducibility. We introduce a non-mechanical, non-enzymatic, novel rapid microbial DNA extraction procedure suitable for 16S rRNA gene-based microbiome profiling applications that eliminates bead beating. The simultaneous application of alkaline, heat, and detergent ('Rapid' protocol) to milligram quantity samples provided consistent representation across the population of difficult and easily lysed bacteria equal to or better than existing protocols, producing sufficient high-quality DNA for full-length 16S rRNA gene PCR. The novel 'Rapid' method was evaluated using mock bacterial communities containing both difficult and easily lysed bacteria. Human fecal sample testing compared the novel Rapid method with a standard Human Microbiome Project (HMP) protocol for samples from lung cancer patients and controls. DNA recovered from both methods was analyzed using 16S rRNA gene sequencing of the V1V3 and V4 regions on the Illumina platform and the V1V9 region on the PacBio platform. Our findings indicate that the 'Rapid' protocol consistently yielded higher levels of Firmicutes species, which reflected the profile of the bacterial community structure more accurately, which was confirmed by mock community evaluation. The novel 'Rapid' DNA lysis protocol reduces population bias common to bead beating and enzymatic lysis methods, presenting opportunities for improved microbial community profiling, combined with the reduction in sample input to 10 milligrams or less, and it enables rapid transfer and simultaneous lysis of 96 samples in a standard plate format. This results in a 20-fold reduction in sample handling time and an overall 2-fold time advantage when compared to widely used commercial methods. We conclude that the novel 'Rapid' DNA extraction protocol offers a reliable alternative for preparing fecal specimens for 16S rRNA gene amplicon sequencing.

Is detection of enteropathogens and human or animal faecal markers in the environment associated with subsequent child enteric infections and growth: an individual participant data meta-analysis

Quantifying contributions of environmental faecal contamination to child diarrhoea and growth faltering can illuminate causal mechanisms behind modest health benefits in recent water, sanitation, and hygiene (WASH) trials. We aimed to assess associations between environmental detection of enteropathogens and human or animal microbial source tracking markers (MSTM) and subsequent child health outcomes. In this individual participant data meta-analysis we searched we searched PubMed, Embase, CAB Direct Global Health, Agricultural and Environmental Science Database, Web of Science, and Scopus for WASH intervention studies with a prospective design and concurrent control that measured enteropathogens or MSTM in environmental samples, or both, and subsequently measured enteric infections, diarrhoea, or height-for-age Z-scores (HAZ) in children younger than 5 years. We excluded studies that only measured faecal indicator bacteria. The initial search was done on Jan 19, 2021, and updated on March 22, 2023. One reviewer (AM) screened abstracts, and two independent reviewers (AM and RT) examined the full texts of short-listed articles. All included studies include at least one author that also contributed as an author to the present Article. Our primary outcomes were the 7-day prevalence of caregiver-reported diarrhoea and HAZ in children. For specific enteropathogens in the environment, primary outcomes also included subsequent child infection with the same pathogen ascertained by stool testing. We estimated associations using covariate-adjusted regressions and pooled estimates across studies. Data from nine published reports from five interventions studies, which included 8603 children (4302 girls and 4301 boys), were included in the meta-analysis. Environmental pathogen detection was associated with increased infection prevalence with the same pathogen and lower HAZ (ΔHAZ -0·09 [95% CI -0·17 to -0·01]) but not diarrhoea (prevalence ratio 1·22 [95% CI 0·95 to 1·58]), except during wet seasons. Detection of MSTM was not associated with diarrhoea (no pooled estimate) or HAZ (ΔHAZ -0·01 [-0·13 to 0·11] for human markers and ΔHAZ -0·02 [-0·24 to 0·21] for animal markers). Soil, children's hands, and stored drinking water were major transmission pathways. Our findings support a causal chain from pathogens in the environment to infection to growth faltering, indicating that the lack of WASH intervention effects on child growth might stem from insufficient reductions in environmental pathogen prevalence. Studies measuring enteropathogens in the environment should subsequently measure the same pathogens in stool to further examine theories of change between WASH, faecal contamination, and health. Given that environmental pathogen detection was predictive of infection, programmes targeting specific pathogens (eg, vaccinations and elimination efforts) can environmentally monitor the pathogens of interest for population-level surveillance instead of collecting individual biospecimens. The Bill & Melinda Gates Foundation and the UK Foreign and Commonwealth Development Office.

Evaluation of infection prevention and control programmes according to the European Centre for Disease Prevention and Control and the World Health Organization in Spain 2012–2022: indicators of core component 1

Key and core components of effective infection prevention and control programmes (IPCPs) issued by the European Centre for Disease Prevention and Control (ECDC) and the World Health Organization (WHO) have been described. WHO core component 1 relates to the structure, organization and management of IPCPs. The objective of this study was to assess the status and the time trends of some indicators of core component 1 of IPCPs in acute hospitals in Spain throughout the period 2012-2022. Hospital-level data from the Spanish point prevalence survey for years 2012-2022 were analysed. Core component 1 indicators were calculated and tested for association to healthcare-associated infections (HAIs). In addition, trends were also examined. Overall, 67.0% and 57.2% of Spanish hospitals reported having an annual infection prevention and control (IPC) plan and an annual IPC report that was approved by the hospital managing director, respectively. The global median number of full-time equivalent (FTE) IPC nurses per 250 beds for the period was 0.87 and the global median number of FTE IPC doctors was 0.70. The rates of blood cultures and stool tests for Clostridioides difficile were 39.9 and 6.1 per 1000 patient-days, respectively. No significant correlation was found between core component 1 indicators and HAI prevalence. Spain is currently at a basic level on the structure, organization and management of IPCPs. Profound differences were found between hospitals depending on size and type.

Population-based screening for colorectal cancer in Wuhan, China.

https://www.chictr.org.cn/showproj.html?proj=192838, identifier ChiCTR2300070520.

Automated detection and classification of polioviruses from nanopore sequencing reads using piranha.

Widespread surveillance, rapid detection, and appropriate intervention will be critical for successful eradication of poliovirus. Using deployable next-generation sequencing (NGS) approaches, such as Oxford Nanopore Technologies' MinION, the time from sample to result can be significantly reduced compared to cell culture and Sanger sequencing. We developed piranha (poliovirus investigation resource automating nanopore haplotype analysis), a 'sequencing reads-to-report' solution to aid routine poliovirus testing of both stool and environmental samples and alleviate the bioinformatic bottleneck that often exists for laboratories adopting novel NGS approaches. Piranha can be used for efficient intratypic differentiation of poliovirus serotypes, for classification of Sabin-like polioviruses, and for detection of wild-type and vaccine-derived polioviruses. It produces interactive, distributable reports, as well as summary comma-separated values files and consensus poliovirus FASTA sequences. Piranha optionally provides phylogenetic analysis, with the ability to incorporate a local database, processing from raw sequencing reads to an interactive, annotated phylogeny in a single step. The reports describe each nanopore sequencing run with interpretable plots, enabling researchers to easily detect the presence of poliovirus in samples and quickly disseminate their results. Poliovirus eradication efforts are hindered by the lack of real-time detection and reporting, and piranha can be used to complement direct detection sequencing approaches.

Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study

Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.

Performance of three techniques for diagnosing equine tapeworm infection

Tapeworm infection in horses can cause serious health concerns, and recent data have documented treatment failures in the most common species, Anoplocephala perfoliata. The threat of anthelmintic resistance in A. perfoliata is of particular concern because of poor diagnostic performance of standard egg counting techniques for detecting this parasite. This study compared the performance of three diagnostic techniques 1) Mini-FLOTAC, 2) Cornell-Wisconsin, and 3) Proudman and Edwards used to detect and quantify A. perfoliata eggs in naturally infected horses. Eighteen adult female horses from the University of Kentucky’s historic parasitology herd were included in this study. Fecal samples were collected from all horses at five collection time points two weeks apart and analyzed with the three techniques. A total of 90 samples were collected and 270 counts determined in the study. The proportions of positive samples determined by the three techniques were significantly different from each other (p<0.05): Mini-FLOTAC (16%), Cornell-Wisconsin (47%), and Proudman and Edwards (70%). The Proudman and Edwards technique counted consistently higher numbers of tapeworm eggs compared to the other two techniques throughout the study [p < 0.05]. Total raw counts of tapeworm eggs across the study for each technique were 16, 88, and 410 for the Mini-FLOTAC, Cornell-Wisconsin, and Proudman and Edwards, respectively. This study demonstrated that the Proudman and Edwards technique was superior in diagnosing A. perfoliata infection. Future work needs to assess this technique’s potential for Fecal Egg Count Reduction Testing (FECRT).

The multispecies microbial cluster of Fusobacterium, Parvimonas, Bacteroides and Faecalibacterium as a precision biomarker for colorectal cancer diagnosis.

The incidence of colorectal cancer (CRC) has increased worldwide, and early diagnosis is crucial to reduce mortality rates. Therefore, new noninvasive biomarkers for CRC are required. Recent studies have revealed an imbalance in the oral and gut microbiomes of patients with CRC, as well as impaired gut vascular barrier function. In the present study, the microbiomes of saliva, crevicular fluid, feces, and non-neoplastic and tumor intestinal tissue samples of 93 CRC patients and 30 healthy individuals without digestive disorders (non-CRC) were analyzed by 16S rRNA metabarcoding procedures. The data revealed that Parvimonas, Fusobacterium, and Bacteroides fragilis were significantly over-represented in stool samples of CRC patients, whereas Faecalibacterium and Blautia were significantly over-abundant in the non-CRC group. Moreover, the tumor samples were enriched in well-known periodontal anaerobes, including Fusobacterium, Parvimonas, Peptostreptococcus, Porphyromonas, and Prevotella. Co-occurrence patterns of these oral microorganisms were observed in the subgingival pocket and in the tumor tissues of CRC patients, where they also correlated with other gut microbes, such as Hungatella. This study provides new evidence that oral pathobionts, normally located in subgingival pockets, can migrate to the colon and probably aggregate with aerobic bacteria, forming synergistic consortia. Furthermore, we suggest that the group composed of Fusobacterium, Parvimonas, Bacteroides, and Faecalibacterium could be used to design an excellent noninvasive fecal test for the early diagnosis of CRC. The combination of these four genera would significantly improve the reliability of a discriminatory test with respect to others that use a single species as a unique CRC biomarker.