PCR-positive Cases Research Articles

Severe Acute Respiratory Syndrome Coronavirus 2 Household Transmission During the Omicron Era in Massachusetts: A Prospective, Case-Ascertained Study Using Genomic Epidemiology

Abstract Background Households are a major setting for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, but there remains a lack of knowledge regarding the dynamics of viral transmission, particularly in the setting of preexisting SARS-CoV-2 immunity and evolving variants. Methods We conducted a prospective, case-ascertained household transmission study in the greater Boston area in March–July 2022. Anterior nasal swabs, along with clinical and demographic data, were collected for 14 days. Nasal swabs were tested for SARS-CoV-2 by polymerase chain reaction (PCR). Whole genome sequencing was performed on high-titer samples. Results We enrolled 33 households in a primary analysis set, with a median participant age of 25 years (range, 2–66 years), 98% of whom had received at least 2 doses of a coronavirus disease 2019 (COVID-19) vaccine. Fifty-eight percent of households had a secondary case during follow-up and the secondary attack rate (SAR) for contacts was 39%. We further examined a strict analysis set of 21 households that had only 1 PCR-positive case at baseline, finding an SAR of 22.5%. Genomic epidemiology further determined that there were multiple sources of infection for household contacts, including the index case and outside introductions. When limiting estimates to only highly probable transmissions given epidemiologic and genomic data, the SAR was 18.4%. Conclusions Household contacts of a person newly diagnosed with COVID-19 are at high risk for SARS-CoV-2 infection in the following 2 weeks. This is, however, not only due to infection from the household index case, but also because the presence of an infected household member implies increased SARS-CoV-2 community transmission.

Antibiogram and Salmonella typhi detection in suspected patients using advanced PCR technique, serology, and conventional blood culture

Background & Objectives: Salmonella enterica serovar Typhi is a diverse gram-negative bacillus that causes life-threatening invasive bloodstream infection and remains a public health burden in developing countries. The antimicrobial resistance in Salmonella typhi has led to widespread multidrug resistance strains making complication in the treatment and demanding alternative therapies. Various diagnostics test such as blood culture, serological assay, and molecular assay are available. PCR is a newer gold standard method, but blood culture is still considered a definitive diagnosis of typhoid fever. Materials and Methods: A cross-sectional study was conducted. Venous blood was collected, and a widal test was performed to detect antibodies against O and H antigens in serum. Blood culture, isolation, and identification were performed using the standard techniques. The antibiogram of isolates was performed by the Kirby Bauer method. Amplification of the hilA gene through PCR was used for the molecular diagnosis. Results: Out of 141 suspected typhoid patients, 78 were males, and 63 were females. PCR detected maximum positivity rate (70%) followed by Widal test (43.26%) and blood culture (16.25%). PCR positive cases were highly prevalent in the male in less than 15 years of age group (14.8%), followed by 15-30 (12.7%) and 30-45 (9.1%). The isolated organism was found to be 100% sensitive to most antibiotics studied, except ofloxacin, which showed 71.4% sensitivity. In contrast, all the isolates were 100% resistant to nalidixic acid. None of the isolates showed multi-drug resistance. Conclusion: PCR is a sensitive, rapid, and better alternative than conventional methods that can be used in clinical diagnosis for early detection of the Salmonella typhi.

Impact of the 2022 African Cup of Nations mass-gathering event on the COVID-19 epidemic in Garoua, Cameroon.

The 2022 African Cup of Nations (AFCON) took place in Cameroon from January 9th to February 5th, 2022, including Garoua in the north. We aimed to measure the impact of this event on the local COVID-19 epidemic given the implementation of a preventive strategy based on a health pass. All players, staff and fans involved in the AFCON event were screened with PCR tests. Symptomatic cases were also continuously monitored in the general population and screened for variants of concern. Daily numbers of confirmed cases were compared to neighboring countries numbers retrieved from a public domain source. In total, 1479 and 2481 tests were performed in the general population and on asymptomatic AFCON attendees, respectively. From the latter, 12.5% were PCR-positive; 97% were infected with Omicron, with no significant difference compared to the passive program (G-test, P value=0.162). Surveillance indicated the AFCON did not increase the number of symptomatic PCR-positive cases in the general population compared to neighboring countries. Though the COVID-19 epidemic was fueled by asymptomatic cases infected with the Omicron variant at the time, the non-therapeutic preventive measures implemented for AFCON mitigated an increase in the epidemic in the local population.

Do patients infected with human coronavirus before the COVID-19 pandemic have less risk of being infected with COVID-19?

Although seasonal human coronaviruses (HCoVs) have long been recognized as respiratory tract viruses, the newly identified SARS-CoV-2 caused a pandemic associated with severe respiratory failure. We aimed to evaluate the incidence of COVID-19 infection in patients diagnosed in three tertiary teaching hospitals, both with and without prior confirmed HCoV infection, and to compare these cohorts in terms of COVID-19 contraction. In our study, we examined HCoV PCR-positive cases obtained retrospectively between January 2014 and March 2020 from three University Hospital Microbiology Laboratories (Cohort 1), as well as PCR-negative patients detected in the same PCR cycle as the positive cases (Cohort 2). We also evaluated subgroups of HCoV-positive cases. There was no difference in COVID-19 contraction rates between Cohort 1 and Cohort 2 (p = 0.724). When previous HCoV subgroups of COVID-19-positive patients were examined, no significant difference was found between the betacoronavirus and alphacoronavirus subgroups (p = 0.822), among the four groups (NL63, 229E, OC43, HKU-1) (p = 0.207), or between the OC43 subgroup and the other groups (p = 0.295). Being previously infected with HCoV did not provide protection against COVID-19 in our study group. We suggest evaluating the possible effect of previous OC43 infection on COVID-19 contraction in larger cohorts.

Evidence of Orientia spp. Endemicity among Severe Infectious Disease Cohorts, Uganda.

At 3 severe infection cohort sites in Uganda, Orientia seropositivity was common. We identified 4 seroconversion cases and 1 PCR-positive case. These results provide serologic and molecular support for Orientia spp. circulating in sub-Saharan Africa, possibly expanding its endemic range. Orientia infections could cause severe illness and hospitalizations in this region.

Efficacy and safety of Chinese herbal medicine to prevent and treat COVID-19 household close contacts in Hong Kong: an open-label, randomized controlled trial.

To evaluate the efficacy and safety of CHM in the prevention of COVID-19 infection and treatment for COVID-19 related symptoms. Prospective open-label randomized controlled trial. Participants' home in Hong Kong. Participants who had household close contact with COVID-19-infected family members. Close contacts were stratified into 4 groups (cohort A, B, C, D) based on symptoms and infection status and were randomized in 4:1 ratio to receive CHM granules (9g/sachet, two times daily) or blank control for 7 days with 2 weeks of follow-up. The primary outcome measure was the rate of positive nucleic acid tests. Secondary outcomes were the proportion of developed COVID-19 related symptoms and adverse events during the whole 3-week study period. Subgroup analysis was used to evaluate demographic factors associated with positive infection rates. A total of 2163 contacts were enrolled and randomly assigned to the CHM group (1720 contacts) and blank control (443 contacts) group. During the 21 days, the rate of PCR-positive cases in cohort A was markedly lower in the CHM group (3.6%) compared to the control group (7.0%) (P=0.036). Overall, the rate of infection in the CHM group was significantly lower than that in the control group (10.69% vs. 6.03%; RR 0.56, 95% CI 0.39-0.82) after 7-day treatment. No serious adverse events were reported during the medication period. The preliminary findings indicate that CHM may be effective and safe in preventing COVID-19. Future double-blind, randomized controlled trials and long-term follow-up are needed to fully evaluate the efficacy of CHM in a larger contact population. ClinicalTrials.gov, identifier NCT05269511.

Assessing the Impact of the 2020 Council of State and Territorial Epidemiologists Case Definition for Pertussis on Reported Pertussis Cases.

In 2020, the Council of State and Territorial Epidemiologists (CSTE) pertussis case definition was modified; the main change was classifying polymerase chain reaction (PCR)-positive cases as confirmed, regardless of cough duration. Pertussis data reported through Enhanced Pertussis Surveillance (EPS) in 7 sites and the National Notifiable Diseases Surveillance System (NNDSS) were used to evaluate the impact of the new case definition. We compared the number of EPS cases with cough onset in 2020 to the number that would have been reported based on the prior (2014) CSTE case definition. To assess the impact of the change nationally, the proportion of EPS cases newly reportable under the 2020 CSTE case definition was applied to 2020 NNDSS data to estimate how many additional cases were captured nationally. Among 442 confirmed and probable cases reported to EPS states in 2020, 42 (9.5%) were newly reportable according to the 2020 case definition. Applying this proportion to the 6124 confirmed and probable cases reported nationally in 2020, we estimated that the new definition added 582 cases. Had the case definition not changed, reported cases in 2020 would have decreased by 70% from 2019; the observed decrease was 67%. Despite a substantial decrease in reported pertussis cases in the setting of coronavirus disease 2019 (COVID-19), our data show that the 2020 pertussis case definition change resulted in additional case reporting compared with the previous case definition, providing greater opportunities for public health interventions such as prophylaxis of close contacts.

Cytopathological study of pleural effusion in SARS-CoV2 RTPCR positive subjects during pandemic at tertiary care hospital

Introduction and Aim: Respiratory system is the most common system affected by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).Review of literature reveals that pleural effusion were seen in one third of cases with Middle East Respiratory Syndrome(MERS) but were rarely reported in SARS –CoV2.This study aims to study the cytomorphological changes in Pleural effusion seen in SARS CoV-2 positive cases, to correlate the cytological findings with radiological CT COVID-19 Reporting and Data System(CORADS)scorings and to categorize pleural effusion as isolated cause of SARS CoV-2 or aggravation of underlying other etiologies. Materials and Methods: Pleural fluid samples of SARS CoV-2 RT PCR positive cases, obtained from patients of all age groups were included in the study. The samples were predominantly from Covid19 wave 1 (March 2020- February 2021) and few from Covid wave 2(March 2021-April 2021). Biochemical analysis, hematological parameters, cytomorphology and associated comorbidity was recorded, and analysis done. Results: Male predominance was observed. Most common cytological and biochemical finding in pleural fluid analysis was Exudative pleural effusion. Predominant cytological features showed lymphocytic effusion. Radiology showed maximum left sided pleural effusion (42%). CORADS score was 6 in majority of cases and effusion as an isolated cause was seen in few cases. Conclusion: Pleural effusion is a rare finding in SARS COV-2 induced bronchopneumonia. Effusion is seen with a high CORADS score, and they carry a high risk of mortality. This study suggests having SARS CoV-2 infection as a differential diagnostic entity when we find the mentioned morphological and biochemical findings as discussed in the present study.

The Prognosis of Crimean-congo Hemorrhagic Fever in Thiqar City, South of Iraq, in 100 Cases over 2022

Background:: The study of Crimean-Congo hemorrhagic fever (CCHF) worldwide is of low rate as it is an uncommon disease. The outbreak in Iraq in 2022 is high. Aim:: To study the prognosis of hemorrhagic fever patients in Thi-Qar governorate, where the highest rate of the disease is, so that we might expect the fat of the disease. : Patients and Methods: A descriptive cases series of cross-section studies that included all patients with severe or life-threatening Crimean-Congo hemorrhagic fever(CCHF) PCR-positive cases (out of the total 100) admitted and followed up in AL-Hussain Teaching Hospital in 2022. To study patients' features that indicate the prognostic factors of the disease. Results:: All cases proved to be CCHF by PCR were 100 patients of variable severity, 14 cases were admitted to intensive care units (ICU), 13 patients died, 2 pregnant ladies were infected with CCHF unfortunately died, 16 children admitted to hospital 2 of them died and 14 cases completely cured. The most serious cases are intrapulmonary hemorrhage and neuropsychiatric presentation. Conclusion:: There are many clinical and laboratory prognostic markers. The riskiest clinical bad prognostic factor is the neuropsychiatric and pulmonary hemorrhage and CCHF in pregnant ladies.

Risk factors for SARS-CoV-2 infection: a test-negative case–control study with additional population controls in Norway

ObjectivesThis study aims to assess risk factors for SARS-CoV-2 infection by combined design; first comparing positive cases to negative controls as determined by PCR testing and then comparing these two...

Shigella as a Cause of Diarrhea Hospitalization in Children Under Five: Evaluation by Conventional and Molecular Methods.

Shigella is an important cause of diarrhea in children under five, often missed by conventional laboratory methods. Blood in stools has always been a syndromic indicator for Shigella diarrhea, but most cases present with watery diarrhea without blood. This study aimed to determine the frequency of Shigella detected by molecular and conventional methods in children under five. Additionally, we aimed to study the clinical profile and outcome of children with Shigella diarrhea managed as per current diarrhea treatment guidelines. In this hospital-based prospective observational study, stool samples from 150 children (age range: one month to five years) with acute diarrhea (duration < seven days) were subjected to routine microscopic examination, stool culture, and DNA extraction. The extracted DNA from stored stool samples was subjected to polymerase chain reaction (PCR) amplification using a specific primer for the invasion plasmid antigen Hgenesequence (ipaH) gene at 424 bp. Results were interpreted in the context of the percentage of isolation of Shigella by molecular (PCR) and conventional methods (stool microscopy and culture) and the follow-up outcome in terms of recurrence of diarrhea or dysentery and growth faltering over three months after discharge. Shigella infection was diagnosed in stool samples by PCR from 13 (8.7%) children, whereas it was isolated by conventional stool culture in only one (0.7%) child. The sensitivity of culture was only 7.7% against PCR for the diagnosis of Shigella infection, whereas blood in stools had a sensitivity of 15.4%. The majority of Shigella PCR-positive cases (11 out of 13) presented with non-bloody diarrhea. None of the evaluated clinical predictors had a significant association with the Shigella infection. No statistically significant difference was found between PCR-positive and PCR-negative children at the end of follow-up (P>0.05). The majority of children with Shigella infection present with watery diarrhea rather than bloody diarrhea, and a history of blood in stools is a poor marker for the diagnosis of shigellosis. The diagnostic performance of stool culture is also very low compared to stool PCR for the diagnosis of Shigella diarrhea.

Demographic and Clinical Profiles of PCR Positive Rickettsia felis Infected Patients at A Tertiary Care Hospital in Bangladesh

Background: Rickettsial infections remain relatively unexplored, under recognized and under reported due to a lack of awareness and limited access to diagnosis. Objective: The purpose of the present study was to evaluate the demographic and clinical profile of PCR positive Rickettsia felis infected patients attended at a tertiary care hospital. Methodology: This cross-sectional study was conducted in the Department of Microbiology at Mymensingh Medical College, Mymensingh, Bangladesh from July 2013 to June 2014 for duration of one year. Patients with fever (102° to 104°F) more than 15 days of any age and gender, not responding to commonly used antibiotics and any other additional complaints and clinical features including headache, rash, lymphadenopathy or myalgia and eschars on the skin were included in this study. Patients with evident cause of fever like malaria diagnosed by blood smear or immunochromatography were excluded from the study. Blood was collected according to blood collection guidelines. PCR from blood was performed using standard protocol with specific primers to detect Rickettsia up to species level. Results: A total number of 50 respondents were recruited after fulfilling the inclusion and exclusion criteria. Among them 21(42%) cases were PCR positive. Among 21 PCR positive cases, the predominant age group was more than 15 to 30 years which was 11(52.4%), female patients were predominant than male patients which was 11(52.0%). All the cases with Rickettsial infection had fever 21(100.0%). Other associated features like headache was most commonly noticed in 10(47.6%) cases followed by body-ache, Cough and rash which was 7(33.3%) cases, 5(23.8%) cases and 1/21 (4.7%) cases respectively. Conclusion: This study demonstrated high prevalence of Rickettsia felis infection in patients in Bangladesh with unidentified febrile illness and suggests that this infection is endemic to the north-central area of this country. Females are more prone to get infected and most commonly noticed associated features was headache. Bangladesh Journal of Medical Microbiology, July 2023;17 (2):71-76

Diversity of symptom phenotypes in SARS-CoV-2 community infections observed in multiple large datasets

Variability in case severity and in the range of symptoms experienced has been apparent from the earliest months of the COVID-19 pandemic. From a clinical perspective, symptom variability might indicate various routes/mechanisms by which infection leads to disease, with different routes requiring potentially different treatment approaches. For public health and control of transmission, symptoms in community cases were the prompt upon which action such as PCR testing and isolation was taken. However, interpreting symptoms presents challenges, for instance, in balancing the sensitivity and specificity of individual symptoms with the need to maximise case finding, whilst managing demand for limited resources such as testing. For both clinical and transmission control reasons, we require an approach that allows for the possibility of distinct symptom phenotypes, rather than assuming variability along a single dimension. Here we address this problem by bringing together four large and diverse datasets deriving from routine testing, a population-representative household survey and participatory smartphone surveillance in the United Kingdom. Through the use of cutting-edge unsupervised classification techniques from statistics and machine learning, we characterise symptom phenotypes among symptomatic SARS-CoV-2 PCR-positive community cases. We first analyse each dataset in isolation and across age bands, before using methods that allow us to compare multiple datasets. While we observe separation due to the total number of symptoms experienced by cases, we also see a separation of symptoms into gastrointestinal, respiratory and other types, and different symptom co-occurrence patterns at the extremes of age. In this way, we are able to demonstrate the deep structure of symptoms of COVID-19 without usual biases due to study design. This is expected to have implications for the identification and management of community SARS-CoV-2 cases and could be further applied to symptom-based management of other diseases and syndromes.

Value of pneumococcal PCR in respiratory samples for exclusion of pneumococcal pneumonia.

Streptococcus pneumoniae is the main aetiological agent in bacterial pneumonia. Therefore pneumococcal PCR is often included in respiratory multiplex PCR panels, both commercial and in-house. But respiratory PCR results for S. pneumoniae are difficult to interpret due to frequent non-pathogenic colonization on the mucosal surface of the upper airways with pneumococci or to cross-reaction of the PCR target in non-pneumococcal streptococci. In this study we investigated the value of lytA gene pneumococcal PCR in patients presenting with pneumonia. To assess the utility of lytA gene detection for S. pneumoniae in a respiratory multiplex quantitative PCR (qPCR) panel for patients presenting with pneumonia. A retrospective study was conducted for lytA gene results as target for S. pneumoniae in hospitalized patients who were diagnosed with pneumonia and for which a respiratory multiplex PCR panel was performed. Patients were classified as 'probable', 'possible' or 'unlikely' of having a pneumococcal pneumonia. A sensitivity of 71.4% and specificity of 89.6% were found, corresponding to a negative predictive value and positive predictive value of 97.6% and 34.2%, respectively, when considering 'probable' versus 'possible/unlikely'. In the PCR-positive cases we found a statistically significant difference in semi-quantitative Ct values between the 'probable' and the 'possible/unlikely' groups. We conclude that a negative qPCR for the lytA gene in a respiratory sample is highly predictive of a negative S. pneumoniae culture and is possibly sufficient to exclude S. pneumoniae as a causative agent. Respiratory pneumococcal PCR has a high negative predictive value for pneumococcal disease but the positive predictive value is low.

Evidence of autoinflammation as a principal mechanism of myocardial injury in SARS-CoV-2 PCR-positive medical examiner cases

BackgroundDisease from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) remains the seventh leading cause of death in the United States. Many patients infected with this virus develop later cardiovascular complications including myocardial infarctions, stroke, arrhythmia, heart failure, and sudden cardiac death (20–28%). The purpose of this study is to understand the primary mechanism of myocardial injury in patients infected with SARS-CoV-2.MethodsWe investigated a consecutive cohort of 48 medical examiner cases who died with PCR-positive SARS-CoV-2 (COVpos) infection in 2020. We compared them to a consecutive cohort of 46 age- and sex-matched controls who were PCR-negative for SARS-CoV-2 (COVneg). Clinical information available at postmortem examination was reviewed on each patient. Formalin-fixed sections were examined using antibodies directed against CD42 (platelets), CD15 (myeloid cells), CD68 (monocytes), C4d, fibrin, CD34 (stem cell antigen), CD56 (natural killer cells), and myeloperoxidase (MPO) (neutrophils and neutrophil extracellular traps(NETs)). We used a Welch 2-sample T-test to determine significance. A cluster analysis of marker distribution was also done.ResultsWe found a significant difference between COVpos and COVneg samples for CD42, CD15, CD68, C4d, fibrin, and MPO, all of which were significant at p < 0.001. The most prominent features were neutrophils (CD15, MPO) and MPO-positive debris suggestive of NETs. A similar distribution of platelets, monocytes, fibrin and C4d was seen in COVpos cases. Clinical features were similar in COVpos and COVneg cases for age, sex, and body mass index (BMI).ConclusionThese findings suggest an autoinflammatory process is likely involved in cardiac damage during SARS-CoV-2 infection. No information about clinical cardiac disease was available.

Parasitemia and antibody response to benznidazole treatment in a cohort of patients with chronic Chagas disease

BackgroundEvaluating the effectiveness of Chagas disease treatment poses challenges due to the lack of biomarkers for disease progression and therapeutic response. In this study, we aimed to assess the clearance of Trypanosoma cruzi (T. cruzi) parasites in a group of benznidazole (BNZ)-treated chronic Chagas disease patients using high-sensitivity quantitative PCR (qPCR) and track T. cruzi antibody levels through a semiquantitative chemiluminescent assay.MethodsA total of 102 T. cruzi seropositive patients with previous PCR-positive results were enrolled in the study. We collected samples 30 days before treatment (T-30d), on the day before initiating BNZ treatment (T0d), and at follow-up visits 60 days (T60d), 6 months (T6M), 12 months (T12M), and 36 months (T36M) after treatment initiation. Treatment efficacy was assessed by testing of serial samples using a target-capture qPCR assay specific to satellite T. cruzi DNA and the ORTHO T. cruzi ELISA Test System for antibody quantitation.ResultsOf the enrolled individuals, 87 completed at least 50% of the treatment course, and 86 had PCR results at follow-up visits T6M, T12M, and T36M. PCR results exhibited fluctuations before and after treatment, but levels were significantly lower post-treatment. Only 15 cases consistently tested PCR-negative across all post-treatment visits. Notably, nearly all participants demonstrated a declining antibody trajectory, with patients who tested PCR-negative at T36M exhibiting an earlier and more pronounced decline compared to PCR-positive cases at the same visit.ConclusionOur study suggests that serial PCR results pose challenges in interpretation. In contrast, serial antibody levels may serve as an ancillary, or even a more reliable indicator of parasite decline following BNZ treatment. Monitoring antibody levels can provide valuable insights into the efficacy of treatment and the persistence of parasites in Chagas disease patients.

A seromolecular study to determine the prevalence of cytomegalovirus in pregnant women referred to health centers in the north of Iran.

Because of the controversial aspects of the CMV virus during pregnancy, it should be considered a serious health threat, especially in developing countries. The present seromolecular study aimed to determine cytomegalovirus prevalence in pregnant women referred to health centers in the north of Iran. One hundred and twenty-five pregnant women who were referred to health centers in Mazandaran province for regular health checks were randomly selected from Jan 2022 to Oct 2022. To detect the presence of the CMV genome and specific IgM and IgG antibodies against cytomegalovirus, the conventional PCR and ELISA tests were applied respectively. All 125 pregnant women that attended the study were from Mazandaran province with a mean age of 30 years ranging from 20 to 42 years. The result showed that 2 (1.6%), 92 (73.6%), and 2 (1.6%) of the cases were positive for IgM, IgG, and IgM/IgG, respectively. The PCR test results indicated that the CMV DNA was present in 10 (8%) pregnant women. Our study shows that all PCR-positive cases were negative for the IgM test. Of the 10 PCR-positive samples 3 were positive and 1 was suspicious for the IgG test. Our study revealed that there is an urgent need for vaccination or other strategies to prevent and treat congenital CMV infection. Reducing the burden of congenital CMV infection requires global awareness. Further studies are recommended to obtain accurate estimates of the risk of congenital CMV infection.

Effect of COVID-19 infection on the gastrointestinal tract considering preventive methods during endoscopic procedures.

This study aimed to prevent the infection risk of environmental contamination by feces during endoscopic procedures. We evaluated the effect of coronavirus disease 2019 (COVID-19) on the gastrointestinal tract using fecal polymerase chain reaction (PCR) and examined risk factors affecting endoscopic procedures, to develop infection prevention strategies. This single-center prospective observational study enrolled 32 patients diagnosed with COVID-19 at Tokyo Medical University Hospital between January and December 2022. We performed reverse transcriptase-PCR to detect severe acute respiratory syndrome coronavirus 2 in human stool specimens and evaluated the COVID-19 positivity rate in stool, the effect of vaccination on infection detection, and differences in positivity rates considering different patient backgrounds. Among the 32 nasal PCR-positive patients who underwent fecal PCR testing, the fecal PCR positivity rate was 21.8%. Compared to the negative cases, 71.4% vs. 32% were older than 65 years (p < 0.016), 71.4% vs. 0.8% (p < 0.001) had malignant tumors, the rate during BA.5 variant outbreaks was significantly higher (100% vs. 60% [p = 0.044]), and the rate of diarrheal symptoms was also higher (42.9% vs. 24%). The median collection period for fecal PCR-positive cases was 2 days after sampling. The severe acute respiratory syndrome coronavirus 2 affects not only the upper respiratory tract but also the gastrointestinal tract. These findings may indicate the risk of digestive fluid infection in older patients with gastrointestinal symptoms and immunocompromised patients with malignant tumor comorbidities, especially during the early stages of viral infection. Therefore, it is advisable to establish a system to prevent infection by using personal protective equipment, including eye guards, in future endoscopic procedures.

Deep learning for AI-based diagnosis of skin-related neglected tropical diseases: A pilot study.

Deep learning, which is a part of a broader concept of artificial intelligence (AI) and/or machine learning has achieved remarkable success in vision tasks. While there is growing interest in the use of this technology in diagnostic support for skin-related neglected tropical diseases (skin NTDs), there have been limited studies in this area and fewer focused on dark skin. In this study, we aimed to develop deep learning based AI models with clinical images we collected for five skin NTDs, namely, Buruli ulcer, leprosy, mycetoma, scabies, and yaws, to understand how diagnostic accuracy can or cannot be improved using different models and training patterns. This study used photographs collected prospectively in Côte d'Ivoire and Ghana through our ongoing studies with use of digital health tools for clinical data documentation and for teledermatology. Our dataset included a total of 1,709 images from 506 patients. Two convolutional neural networks, ResNet-50 and VGG-16 models were adopted to examine the performance of different deep learning architectures and validate their feasibility in diagnosis of the targeted skin NTDs. The two models were able to correctly predict over 70% of the diagnoses, and there was a consistent performance improvement with more training samples. The ResNet-50 model performed better than the VGG-16 model. A model trained with PCR confirmed cases of Buruli ulcer yielded 1-3% increase in prediction accuracy across all diseases, except, for mycetoma, over a model which training sets included unconfirmed cases. Our approach was to have the deep learning model distinguish between multiple pathologies simultaneously-which is close to real-world practice. The more images used for training, the more accurate the diagnosis became. The percentages of correct diagnosis increased with PCR-positive cases of Buruli ulcer. This demonstrated that it may be better to input images from the more accurately diagnosed cases in the training models also for achieving better accuracy in the generated AI models. However, the increase was marginal which may be an indication that the accuracy of clinical diagnosis alone is reliable to an extent for Buruli ulcer. Diagnostic tests also have their flaws, and they are not always reliable. One hope for AI is that it will objectively resolve this gap between diagnostic tests and clinical diagnoses with the addition of another tool. While there are still challenges to be overcome, there is a potential for AI to address the unmet needs where access to medical care is limited, like for those affected by skin NTDs.

Tissue quantitative RT-PCR test for diagnostic significance of cytomegalovirus infection in patients with inflammatory bowel disease and treatment response: Cytomegalovirus infection in patients with inflammatory bowel disease.

Cytomegalovirus (CMV) is an opportunistic pathogen that exacerbates inflammatory bowel disease (IBD). There are no clear diagnostic criteria for CMV infection in IBD patients. The aim of this study was to evaluate the importance of the diagnosis of CMV infection with CMV-DNA polymerase chain reaction (PCR) in the colonic mucosa and the response to antiviral treatment. We retrospectively analyzed the clinical data of 30 patients with IBD (24 men, 6 women; median age: 42 years) who were hospitalized because of IBD exacerbation and whose samples were assessed by tissue CMV-DNA PCR positivity. Most of the IBD patients had ulcerative colitis (90%). The CMV-DNA PCR median value was 8848 copies/mL of tissue (range 90-242,936 copies/mL). Blood CMV-DNA PCR was found to be positive in a small group (33.3%, 10/30) of tissue CMV-DNA PCR-positive cases. immunohistochemistry tests were positive in only 5 of the 23 patients positive for CMV-DNA PCR in the colonic mucosa, and high remission (25/30, 83.3%) was detected with antiviral therapy. Recurrence of CMV colitis infection was observed in 9 of 25 patients who had remission with antiviral therapy. The tissue CMV-DNA PCR test was found to be more useful than blood CMV-DNA PCR and immunohistochemistry tests for diagnosing CMV colitis, and the tissue CMV-DNA PCR test enabled rapid and appropriate treatment.