Evaluation of a novel multiplex qPCR method for rapid detection and quantification of pathogens associated with calf diarrhoea.

AIMS: Diarrhoea is a common health problem in calves and a main reason for use of antimicrobials. It is associated with several bacterial, viral and parasitic pathogens, most of which are commonly present in healthy animals. Methods, which quantify the causative agents, may therefore improve confidence in associating a pathogen to the disease. This study evaluated a novel commercially available, multiplex quantitative polymerase chain reaction (qPCR) assay (Enterit4Calves) for detection and quantification of pathogens associated with calf-diarrhoea. METHODS AND RESULTS: Performance of the method was first evaluated under laboratory conditions. Then it was compared with current routine methods for detection of pathogens in faecal samples from 65 calves with diarrhoea and in 30 spiked faecal samples. The qPCR efficiencies were between 84%-103% and detection limits of 100-1000 copies of nucleic acids per sample were observed. Correct identification was obtained on 42 strains of cultured target bacteria, with only one false positive reaction from 135 nontarget bacteria. Kappa values for agreement between the novel assay and current routine methods varied between 0.38 and 0.83. CONCLUSION: The novel qPCR method showed good performance under laboratory conditions and a fair to good agreement with current routine methods when used for testing of field samples. SIGNIFICANCE AND IMPACT OF STUDY: In addition to having fair to good detection abilities, the novel qPCR method allowed quantification of pathogens. In the future, use of quantification may improve diagnosis and hence treatment of calf diarrhoea.

Investigation of hemogram, oxidative stress, and some inflammatory marker levels in neonatal calves with escherichia coli and coronavirus diarrhea.

Calf diarrhea is the most common disease affecting calves in the neonatal period resulting in economic losses. Although predisposing factors play a role in the etiology of the disease, in most cases, different pathogens are involved in the development of the infection. In this study, hemogram data, glutathione and malondialdehyde levels were examined to determine lipid peroxidation and glutathione levels in E. coli- and coronavirus-infected calves. Serum amyloid A and calprotectin levels were also analyzed to determine inflammatory status. The study included a total of 45 female Montofon calves aged 0-1 week, including the E. coli group (15 calves), the coronavirus group (15 calves), and the control group (15 calves). Analysis revealed that total leukocyte, neutrophil, lymphocyte, malondialdehyde, serum amyloid A, and calprotectin levels increased in the coronavirus-infected calves compared with the E. coli group and the control group. In contrast, the levels of glutathione, one of the antioxidant markers, decreased. In conclusion, the main findings related to the determination of inflammation and oxidative status were characterized by the presence of E. coli and coronavirus diarrhea, and it is suggested that future studies may be guided by the fact that inflammatory conditions are higher in viral disease than in bacterial infection.

The Effect of Helicobacter pylori on the Presentation and Clinical Course of Coronavirus Disease 2019 Infection.

OBJECTIVES: Novel coronavirus 2019 (corona virus disease 2019 [COVID-19]) binds angiotensin-converting enzyme-2 (ACE-2) receptors to enter the cell. These receptors are widely expressed in the intestine, and COVID-19 may cause gastrointestinal symptoms via these receptors during the course of the disease. Helicobacter pylori is known to increase the expression of ACE-2 receptors in the gastrointestinal tract. The aim of this study was to investigate the effects of H pylori on the presentation and clinical course of COVID-19 infections. METHODS: This study was carried out from June 1 to July 20, 2020. Patients diagnosed with COVID-19 infections by PCR tests were included in the study. Antigen screening tests were performed on stool samples to determine the presence of H pylori. All patients were evaluated for manifestations of COVID-19 infection, severity of the course, hospitalized days because of the virus and outcome of the disease process. RESULTS: Of 108 COVID-19 positive patients evaluated, 31 with a mean age of 49.54 ±â€Š17.94 years were H pylori-positive (8 girls [25.8%]) and 77 with a mean age of 47.85 ±â€Š20.51 years; (31 girls [40.3%]) were H pylori-negative. Abdominal pain (19.4% vs 2.6%) and diarrhea (32.3% vs 9.1%) were significantly higher in patients with H pylori than those without (P = 0.007 and P = 0.006, respectively). There was no statistically significant difference between H pylori positivity and the number of hospitalized days, the severity of the course of COVID-19 infection, or the outcome of the disease (P > 0.05). CONCLUSION: Our results revealed that the findings of abdominal pain and diarrhea strongly correlated with the presence of H pylori in COVID-19 patients.

The gut microbiome: a missing link in understanding the gastrointestinal manifestations of COVID-19?

Coronavirus disease 2019 (COVID-19), which is caused by infection with SARS-CoV-2, presents with a broad constellation of both respiratory and nonrespiratory symptoms, although it is primarily considered a respiratory disease. Gastrointestinal symptoms-including nausea, abdominal pain, vomiting, and diarrhea-rank chief among these. When coupled with the presence of viral RNA in fecal samples, the presence of gastrointestinal symptoms raises relevant questions regarding whether SARS-CoV-2 can productively infect the upper or lower gastrointestinal tract. Despite the well-documented prevalence of gastrointestinal symptoms and the high rate of SARS-CoV-2 fecal RNA shedding, the biological, clinical, and epidemiological relevance of these findings is unclear. Furthermore, the isolation of replication-competent virus from fecal samples has not been reproducibly and rigorously demonstrated. Although SARS-CoV-2 shedding likely occurs in a high proportion of patients, gastrointestinal symptoms affect only a subset of individuals. Herein, we summarize what is known about gastrointestinal symptoms and fecal viral shedding in COVID-19, explore the role of the gut microbiome in other respiratory diseases, speculate on the role of the gut microbiota in COVID-19, and discuss potential future directions. Taking these concepts together, we propose that studying gut microbiota perturbations in COVID-19 will enhance our understanding of the symptomology and pathophysiology of this novel devastating disease.

Prevalence of Clostridioides difficile and Other Gastrointestinal Pathogens in Patients with COVID-19.

BACKGROUND: Gastrointestinal symptoms are common in patients with COVID-19, but prevalence of co-infection with enteric pathogens is unknown. AIMS: This study assessed the prevalence of enteric infections among hospitalized patients with COVID-19. METHODS: We evaluated 4973 hospitalized patients ≥ 18 years of age tested for COVID-19 from March 11 through April 28, 2020, at two academic hospitals. The primary exposure was a positive COVID-19 test. The primary outcome was detection of a gastrointestinal pathogen by PCR stool testing. RESULTS: Among 4973 hospitalized individuals, 311 were tested for gastrointestinal infections (204 COVID-19 positive, 107 COVID-19 negative). Patients with COVID-19 were less likely to test positive compared to patients without COVID-19 (10% vs 22%, p < 0.01). This trend was driven by lower rates of non-C.difficile infections (11% vs 22% in COVID-19 positive vs. negative, respectively, p = 0.04), but not C. difficile infection (5.1% vs. 8.2%, p = 0.33). On multivariable analysis, infection with COVID-19 remained significantly associated with lower odds of concurrent GI infection (aOR 0.49, 95% CI 0.24-0.97), again driven by reduced non-C.difficile infection. Testing for both C.difficile and non-C.difficile enteric infection decreased dramatically during the pandemic. CONCLUSIONS: Pathogens aside from C.difficile do not appear to be a significant contributor to diarrhea in COVID-19 positive patients.

Probiotics for treating novel coronavirus with diarrhea: A protocol for systematic review and meta analysis.

BACKGROUND: The study aims to evaluate the efficacy and safety of probiotic therapy for coronavirus disease 2019 with diarrhea. METHODS: The following electronic bibliographic databases will be searched to identify relevant studies from December 2019 to December 2020: MEDLINE, PubMed, Embase, the Cochrane Central Register of Controlled Trials, China National Knowledge Infrastructure, Chinese Technical Periodicals, Wan-fang data, Chinese Biological Medicine Database, and other databases. The search results will not be restricted by language, all included articles were randomized controlled trial. Two independent researchers will conduct article retrieval, de-duplication, filtering, quality assessment, and data analysis through the Review Manager (V.5.3). Meta-analysis, subgroup analysis and/or descriptive analysis were performed on the included data. RESULTS: High-quality synthesis and/or descriptive analysis of current evidence will be provided from outcomes. CONCLUSION: This study will provide the evidence of whether probiotics is an effective and safe intervention for coronavirus disease 2019 with diarrhea.PROSPERO registration number: CRD42020192657.

Risk factors for symptoms of infection and microbial carriage among French medical students abroad.

OBJECTIVES: To investigate symptoms of infections and their risk factors among French medical students undertaking an internship abroad. METHODS: Clinical follow up, and qPCR-based respiratory, gastrointestinal, and vaginal pathogen carriages were prospectively assessed pre-travel and post-travel, in a cohort of medical students departing from Marseille, France. RESULTS: 293 students were included. 63.5%, 35.8%, and 3.6% of students reported gastrointestinal, respiratory, and vaginal symptoms, respectively. The acquisition rate of Enteroaggregative Escherichia coli and Enteropathogenic E. coli was 40.9% and 18.6%, respectively. A significant increase was observed for rhinovirus and Streptococcus pneumoniae by comparing the prevalence of pathogens in pre-travel and post-travel samples. Gardnerella vaginalis and Atopobium vaginae acquisition rates were 12.9% and 13.9%, respectively. Being female, primarily traveling to Vietnam, and living in basic accommodation conditions were independent risk factors for reporting respiratory symptoms. Students reporting respiratory symptoms were three times more likely to acquire S. pneumoniae. Traveling primarily to north India and Senegal were independent risk factors for diarrhea. CONCLUSION: This study makes it possible to identify the leading infectious diseases linked to travel in a group of French medical students undertaking an internship abroad and the risk factors on which to base targeting students for reinforced pre-travel advice.

Prior infection with intestinal coronaviruses moderates symptom severity and mortality in patients with COVID-19: A hypothesis and preliminary evidence.

The pandemic of acute respiratory illness caused by the novel betacoronavirus SARS-CoV-2, officially designated COVID-19, has attained the proportions of a global health crisis. Though all nations of the world have been affected by this disease, there have been marked cross-national variations in prevalence, severity and mortality rates. Various explanations, based on demographic, social and climatic factors, have been suggested to account for this variability, but these remain unverified to date. Based on recent research findings suggesting that human enterocytes may serve as a point of entry for SARS-CoV-2, leading to intestinal viral replication, this paper puts forward the hypothesis that prior intestinal infection with coronaviruses, either symptomatic or asymptomatic, may moderate this process and minimize the severity of SARS-CoV-2 infection. This hypothesis is supported by evidence on the gastrointestinal manifestations of SARS-CoV-2 and related infections, on the geographical patterns observed in the variability of COVID-19 mortality, and on the occurrence and geographical distribution of outbreaks of diarrheal disease, as well as asymptomatic infection, with human coronaviruses as verified by direct or serological testing. Preliminary supporting evidence based on national and international health statistics is presented, along with suggestions on more robust methods by which this hypothesis may be tested. If the proposal put forth in this paper can be confirmed either wholly or in part, it would have significant implications in terms of strategies aimed at minimizing the severity of COVID-19 in a clinical setting.