Evaluation of a multiplex polymerase chain reaction for the diagnosis of infectious diarrhea in intensive care unit patients in Upper Egypt.

The rapid diagnosis of infectious diarrhea is lifesaving for intensive care unit (ICU) patients. This study evaluated a commercially available multiplex polymerase chain reaction (PCR) (BioFire FilmArray) for the diagnosis of parasitic and bacterial infections in ICU patients with secretory diarrhea in comparison to other traditional methods. This cross-sectional study included 50 subjects with infectious diarrhea. Their stool samples were subjected to macroscopic and microscopic examinations, concentration techniques, permanent staining techniques, stool culture, identification of bacterial infection by the Vitek 2 Compact 15 System, and molecular diagnosis of bacterial or parasitic infections by BioFire FilmArray multiplex PCR. Parasitological examination showed that the sensitivity and specificity of BioFire FilmArray multiplex PCR in the diagnosis of Cryptosporidium oocysts were 83.33% and 100.0%, respectively compared with 100% and 92.5% in diagnosis of G. lamblia cysts. Bacteriological examination showed that the sensitivity and specificity of BioFire FilmArray multiplex PCR in the diagnosis of E. coli and salmonella were 100% and 100.0%, respectively. The BioFire FilmArray multiplex PCR gastrointestinal (GI) panel assay was more sensitive and specific in the diagnosis of bacterial infections than parasitic infections. The BioFire FilmArray multiplex PCR GI panel assay was less sensitive in the detection of Cryptosporidium oocysts than traditional methods. In conclusion, the BioFire FilmArray multiplex PCR may be useful for rapid diagnosis of ICU patients with infectious diarrhea.

Assessment of long noncoding RNA CCAT1 using real time-polymerase chain reaction in colorectal cancer patients.

Colorectal cancer (CRC) is linked to high mortality, mainly when discovered in its advanced stages. Several studies have pointed to the role of epigenetic factors in CRC and other cancers. Long non-coding RNAs (lncRNAs) are involved in the initiation, progression, metastasis, and modulation of the response to chemotherapeutic modalities of CRC as vital contributors to epigenetic mechanisms. Colon cancer-associated transcript-1 (CCAT1) is one of the lncRNAs that have been dysregulated in serum samples, providing a non-invasive route for diagnosing CRC patients. This study aimed to determine the role of CCAT1 expression as diagnostic and prognostic markers. We tested the associations of CCAT1 expression with serum carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA 19-9). The study included three groups: 41 patients with colorectal cancer, 39 patients with precancerous benign colorectal diseases, and 20 normal control individuals. CEA and CA 19-9 were measured by an immunoassay automated system. The expression level of CCAT1 was assessed by a real-time polymerase chain reaction. There was a statistically significant elevation of serum CEA levels in patients with CRC compared to patients with precancerous benign colorectal diseases. Furthermore, there was no statistically significant difference in serum CA 19-9 levels between all groups (p = 0.102). Interestingly, CCAT1 expression was significantly upregulated in the blood of CRC patients compared to the precancerous benign colorectal diseases group (p = 0.009) and the control group (p <0.001). Also, expression of CCAT1 was significantly elevated in patients with precancerous benign colorectal diseases compared to the control group (p=0.004). In conclusion, measuring the expression level of CCAT1 is more advised than assessment of CEA and CA 19-9 for the early diagnosis and prognosis of colorectal cancer.

Plasma brain natriuretic peptide, D-Dimer, and serum troponin-I as predictors for in-hospital death in patients with COVID-19.

The severe acute respiratory syndrome coronavirus 2, first appeared in Wuhan, China, in December 2019. Since then, a variety of strains of the virus were spread throughout the world, prompting the World Health Organization to declare a pandemic in March 2020. Additionally, Coronavirus disease 2019 (COVID-19) can cause a variety of symptoms, ranging from fatigue and fever to severe respiratory and cardiovascular complications. This study evaluated the role of brain natriuretic peptide (BNP), troponin-I and D-dimer as biomarkers for death prediction in hospitalized patients with COVID-19. The study included 90 patients with COVID -19 diagnosed with PCR-RNA testing. They were divided into survivors and non-survivors. Also, 20 apparently healthy individuals age and sex matched were included as a control group. Plasma BNP and serum troponin-I were measured by enzyme linked immune-sorbent assay (ELISA) technique. D-dimer was measured by a turbidimetric technique. Patients with COVID-19 had significantly elevated levels of serum Troponin-I and plasma BNP in comparison to controls (p < 0.0001, for both). D-dimer, troponin-I and BNP levels were significantly higher in the non-survivors group when compared to the survivors group. Troponin-1 can predict COVID-19 severity with sensitivity, specificity, and accuracy of 55.1%, 66.7%, and 57.8%, respectively at a cutoff value of 0.075 (ng /ml); and area under the receiver operating characteristic (AUC) curve of 0.670 (95% CI: 0.551 - 0.790, p=0.018). BNP can predict COVID-19 severity with sensitivity, specificity, and accuracy of 98.6%, 71.4%, 92.2%, respectively at a cutoff value of 16.02 (Pg /ml) and AUC of 0.872 (95% CI: 0.778 - 0.965, p < 0.001). Univariate and multivariate logistic regression analysis showed that only BNP level can significantly predict death among COVID-19 infected patients. In conclusion, plasma BNP and serum troponin-I could be used as prognostic biomarkers for determination of the severity of COVID-19 and BNP could predict mortality.

First Report on Abnormal Renal Function in Acute Hepatitis E Genotype 1 Infection.

Impaired renal functions have been reported with Hepatitis E virus (HEV) infections, especially with genotypes 3 and 4. These complications were reported during the acute and chronic phases of infection. HEV genotype 1 causes acute infection, and the effect of HEV-1 infections on renal functions is not known. We examined the kidney function parameters in the serum of HEV-1 patients (AHE, n = 31) during the acute phase of infection. All of the included patients developed an acute self-limiting course of infection, without progression to fulminant hepatic failure. We compared the demographic, laboratory, and clinical data between AHE patients with normal kidney function parameters and those with abnormal renal parameters. Out of 31 AHE patients, 5 (16%) had abnormal kidney function tests (KFTs) during the acute phase of infection. Three patients had abnormal serum urea and creatinine, and two patients had either abnormal urea or creatinine. Four out of five patients had an estimated glomerular filtration rate (eGFR) below 60 mL/min/1.73 m2. AHE patients with abnormal KFTs were older and had a lower level of albumin, but a slightly elevated alanine transaminase (ALT) compared to AHE patients with normal KFTs. There were no significant differences between the two groups in terms of age, sex, liver transaminase levels, and the viral load. Similarly, the clinical presentations were comparable in both groups. Interestingly, these KFTs in patients with abnormal renal parameters returned to normal levels at the recovery. The serum creatinine level was not correlated with patients' age or liver transaminase levels, but it was significantly negatively correlated with albumin level. In conclusion, this study is the first report that evaluated KFTs in patients during the acute phase of HEV-1 infections. Impaired KFTs in some AHE patients resolved at convalescence. KFTs and renal complications should be monitored during HEV-1 infections.

Long noncoding RNA HOTAIR and Midkine as biomarkers in thyroid cancer.

Thyroid cancer is the most common endocrine malignancy, and its incidence is increasing. Differentiated thyroid cancer is the most common type and papillary thyroid carcinoma is the most common type of differentiated thyroid cancer. This work aimed to study long noncoding (Lnc) RNA homeobox transcript antisense RNA (HOTAIR) expression in plasma and serum midkine, a heparin binding growth factor, as biomarkers of thyroid cancer. This study included 27 thyroid cancer patients, 29 patients with benign thyroid disease and 26 individuals as normal controls. HOTAIR expression was assessed by real time polymerase chain reaction and midkine by ELISA. These biomarkers were elevated in thyroid cancer patients than patients with benign thyroid diseases and controls. Patients with thyroid cancer stage III had higher midkine levels in comparison to those with stage-I and stage-II (p < 0.001). Patients with grade II had higher midkine in comparison to those with grade I (p < 0.001). Statistically significant elevation of HOTAIR expression was found in stage III and stage II (p=0.001), compared to stage I. However, no difference was observed between stage II and stage III (p=0.533). There was no difference in both biomarkers in different histopathological types of thyroid cancer. ROC analysis was used for detection of thyroid cancer, midkine had AUC of 0.95 at a cutoff 897.5 pg/ml with a sensitivity of 98.0%, and specificity of 81.5% (p < 0.001). HOTAIR had AUC of 1 at a cutoff 11.8-fold change with a sensitivity and specificity of 100 %, (p < 0.001). We concluded that HOTAIR has high sensitivity and specificity in detection of thyroid cancer. It was correlated with tumor stage but not with histopathological types.

Neutralizing antibody responses in asymptomatic close contacts of COVID-19 patients and in asymptomatic healthcare workers.

The identification of novel antibodies that could neutralize SARS-CoV-2 is one of the novel approaches to use in combating COVID-19. This study aimed to explore the level of neutralizing antibodies (NAbs) in asymptomatic close contacts of COVID-19 patients and asymptomatic healthcare workers. In vitro qualitative detection of serum antibodies of participants from both populations was done using an anti-SARS-CoV-2 immunoassay. The study included 107 participants, of which 59.8% were healthcare workers and 40.2% were family contacts of confirmed COVID-19 cases. Their median age was 22 years. The percentage of positivity and median titer for NAbs were significantly higher among family contacts than mong healthcare workers (P = 0.013 and < 0.001, respectively). We also measured C-reactive protein (CRP) levels and the median value of CRP was significantly higher in the family members who had been in contact with COVID-19 patients than in healthcare workers (P < 0.001). In the family contact group, there was a significant negative correlation between the absolute lymphocyte count and CRP (r = -0.409, P = 0.034). There was no significant correlation between neutralizing antibody titers and either CRP or absolute lymphocyte count (P > 0.05 for both). In conclusion, the indication of elevated NAb titers in asymptomatic family contacts could help lay the groundwork for further studies to explore the potential utility of these antibodies to provide future immunity from infection within a family as well as for potential use in general during passive antibody therapies for COVID-19 patients.

Correlation Between Vascular Endothelial Growth Factor and Long-Term Occurrence of HCV-Related Hepatocellular Carcinoma After Treatment with Direct-Acting Antivirals.

We aimed to evaluate the correlation between vascular endothelial growth factor (VEGF) and long-term occurrence of hepatocellular carcinoma after HCV treatment with direct-acting antivirals (DAAs) and the HCC stage. Two groups with HCV-related liver cirrhosis and HCC were included: group 1, HCC following DAAs; group 2, HCC did not receive DAAs. The serum level of VEGF and HCC staging was evaluated. The duration between DAAs and HCC was 21.81 ± 11.66 months. Portal vein thrombosis (PVT) was observed more in group 1 (31%). VEGF was relatively elevated in group 1 compared to group 2. HCC patients after DAAs, showed elevated VEGF with frequent PVT.

No evidence of HEV genotype 1 infections harming the male reproductive system.

Extrahepatic disorders are recorded with hepatitis E virus (HEV) infection. The impact of HEV infection on the male reproductive system is a query. In this study, we retrospectively analyzed semen from infertile men and prospectively examined the semen from acute hepatitis E patients (AHE) for HEV markers. HEV RNA and HEV Ag were not detectable in the semen of infertile men nor the semen of AHE patients. Although HEV markers were detectable in the urine of patients infected with HEV-1, these markers were absent in their semen. There is no significant difference in the level of reproductive hormones between AHE patients and healthy controls. Semen analysis of AHE patients did not show a notable abnormality and there was no significant difference in the semen quality and sperm characteristics between AHE and healthy controls.

Predictors of Cardiovascular Affection in Patients with Active Rheumatoid Arthritis: Secondary Analysis of a Randomized Controlled Trial.

OBJECTIVE: This is a secondary analysis of a randomized controlled trial that aimed to assess subclinical atherosclerosis in patients with rheumatoid arthritis (RA) by measuring carotid artery intima-media thickness (CIMT) and correlating it with disease activity and inflammatory markers (including levels of matrix metalloproteinase-3(MMP-3) and matrix metalloproteinase-9 (MMP-9)) and to detect the effectiveness of agents that inhibit matrix metalloproteinases (MMPs) as doxycycline in RA therapy. METHODS: One hundred and sixty RA patients were assigned in a randomized clinical trial (clinicaltrial. gov NCT03194204). Disease activity score 28(DAS28), laboratory markers, including erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), MMP-3, and MMP-9 were evaluated and mean CIMT was measured. Subjects were allocated randomly into one of two treatment arms, either methotrexate (MTX) alone or MTX with doxycycline 200mg per day orally. Follow up ESR, CRP, DAS28, MMP-3, and MMP-9 levels were re-evaluated after 3 months. RESULTS: There were positive significant correlations between CIMT and disease duration (r = 0.461, p = 0.001), age (r=0.459, p= 0.001), DAS28 score (r= 0.547, p = 0.001), ESR (r =0.413, p = 0.001), CRP (r = 0.281, p = 0.001), MMP-3 (r = 0.476, p = 0.001), and MMP-9 (r = 0.593, p =0.001). Patients treated with MTX and doxycycline showed lower levels of DAS28, ESR, CRP, MMP-3, and MMP-9 and this was statistically significant. CONCLUSION: CIMT seems to be the ultimate method to screen for subclinical atherosclerosis in RA patients. MMP-3 and 9 play a key role in both RA synovitis and cardiovascular changes, making them important therapeutic targets, especially with safe and cost-effective agents like doxycycline. This clinical trial was carried out in Assiut University Hospital (AUH), Assiut, Egypt (Clinical Trial Registration No. clinicaltrial.gov NCT03194204).

Ledipasvir/Sofosbuvir in Adolescents With Chronic Hepatitis C Genotype 4 With and Without Hematological Disorders: Virological Efficacy and Impact on Liver Stiffness.

BACKGROUND: Egypt has the highest prevalence of hepatitis C virus (HCV) infection. Anti-HCV antibodies were detectable in 3% of children in Upper Egypt. Our aim was to evaluate the efficacy of ledipasvir/sofosbuvir for chronic HCV genotype 4 in adolescents with/without hematological disorders and to determine the effect of sustained virological response (SVR) on liver stiffness. METHODS: Sixty-five adolescents were recruited. There were 3 patient groups: group 1, 44 treatment-naive without hematological disorders; group 2, 6 previously treated; and group 3, 15 treatment-naive with hematological disorders. All patients received sofosbuvir 400 mg/ledipasvir 90 mg per day for 12 weeks. Serum HCV RNA levels were measured before treatment, at week 12, and at 12 weeks after the end of treatment (SVR12). Liver stiffness and the aspartate aminotransferase-platelet ratio index (APRI) score were estimated at baseline and at SVR12. RESULTS: SVR12 was 100%. At SVR12, there was a significant improvement in liver stiffness in all groups. The APRI score showed significant improvements in groups 1 and 3 (P < .001 and P = .004, respectively). The treatment was well tolerated, with minimal and self-limited side effects. CONCLUSIONS: Treatment of chronic HCV in adolescents using ledipasvir/sofosbuvir was effective, with a cure rate (at SVR12) of 100%. Significant improvement in liver stiffness was found in all groups.

COVID-19-associated sleep disorders: A case report.

PURPOSE: We reported one patient infected with acute respiratory syndrome coronavirus-2 (SARS-CoV-2) presented with sleep disorders; insomnia and restless leg syndrome. METHODS: Patient data were obtained from medical records from Al-Raghy Isolation Hospital in Assuit University. RESULTS: A 49-year-old female patient presented with insomnia and restless leg syndrome associated with anosmia, ageusia. Three days before, she had developed a cough, malaise and athenia, headache, arthralgia, myalgia affecting mainly upper limbs, diarrhea and a fever followed by tachypnea. The naso-oropharyngeal swab test for coronavirus disease 2019 (COVID-19) by qualitative real-time reverse-transcriptase-polymerase-chain-reaction assay was positive. The patient was treated with Oseltamivir 75mg and clarithromycin 500 mg (12 hourly for each respectively) for 10 days with paracetamol. Two weeks later, the patient made a complete neurological and respiratory recovery. CONCLUSION: Our case highlighted the rare occurrence of restless leg syndrome and insomnia during the COVID-19 pandemic. The era of sleep disorders spectrum in patients with COVID-19 remains to be characterized suggesting a frightening scientific association between COVID-19 and neuropsychiatric illness.

Hepatitis D virus infection among hepatitis B virus surface antigen positive individuals in Upper Egypt: Prevalence and clinical features.

BACKGROUND/PURPOSE: About 248 million people are chronic HBV surface antigen carriers in the world. Hepatitis D virus (HDV) infection present in more than 15 million people worldwide. HDV needs hepatitis B surface antigen (HBsAg) to help its replication. We aimed to estimate the prevalence of HDV infection among HBsAg positive individuals and to determine the clinical, laboratory and virological characters of HDV infected patients. METHODS: This study was prospective cross-sectional analytic one including 186 HBsAg positive cases. Anti-HBc total, IgM and HBV PCR were done for all of these cases. Anti-HDV ELISA analysis was done for all cases. Positive samples for Anti-HDV by ELISA were then tested by HDV PCR. RESULTS: Of the 186 HBsAg positive cases, 80 were reactive for anti-HDV antibodies, resulting in an overall anti-HDV seropositivity of 43%. Higher prevalence of liver cirrhosis (43.8%), HCC on top of cirrhosis (8.8%) were found in anti-HDV positive compared to anti-HDV negative cases (17.9%) and (3.8%) respectively (p value<0.001). Portal hypertension and Child-Pugh grade B, C were significantly higher in anti-HDV-positive cases as compared to the anti-HDV-negative ones (47.5% versus 18.9%) and (11.3% versus 6.6%); (16.3% versus 3.8%) respectively (p value<0.001 for each). HDV RNA was positive in 25 out of 80 anti-HDV-positive cases (31.3%). CONCLUSION: Anti-HDV was seropositive in 43% among HBsAg positive cases in Upper Egypt. HDV RNA was positive by PCR in 25 out of 80 anti-HDV-positive cases (31.3%). HDV prevalence using PCR was 25/186 (13.4%) in Upper Egypt.

Role of vitamin D deficiency as a risk factor for infections in cirrhotic patients.

BACKGROUND: Vitamin D plays a role in innate and acquired immunity. The risk for bacterial infections is increased in cirrhotic patients due to low levels of vitamin D. This study aimed to determine serum 25-(OH) vitamin D levels among cirrhotic patients in the presence and absence of infections and correlate this level with liver disease severity. METHODS: This cross-sectional analytic study recruited 87 hospitalised cirrhotic patients who were divided into the following groups: group with evidence of infection (45 cases) and group without infection (42 cases). Urine analysis, ascetic fluid study and chest X-rays were performed to find the site of infection. Serum 25-(OH) vitamin D was also measured. RESULTS: Vitamin D levels were lower in the cirrhotic with infection group than in the cirrhotic without infection group (17.3 ± 2.5 vs. 41.1 ± 3.1, respectively) (P-value < 0.001). Approximately 71.4% cirrhotic patients without infection had sufficient vitamin D levels, while 60% of cirrhotic patients with infection had insufficient vitamin D levels, and 28.9% had vitamin D deficiency (P-value < 0.001). Spontaneous bacterial peritonitis was the most common infection (62.2%). The cutoff point of vitamin D levels for cirrhotic patients with infection was 21 ng/mL. CONCLUSION: Vitamin D deficiency was found to be an independent predictor of infection in cirrhotic patients suggesting that vitamin D supplementation may be useful in these patients. No significant correlations were found between the vitamin D level and the Child-Pugh class and MELD score among the infected group and non-infected group.

The Role of Genetic Polymorphisms in Nrf2 and P73 in Egyptian Women with Breast Cancer

Background: Breast cancer is the commonest cancer in Egyptian females. Nrf2 is involved in oxidative stress while P73 functions in response to DNA damage. This study aimed to assess the role of Nrf2 promoter and P73 G4C14 to A4T14 SNPs in breast cancer in Egypt. Patients: Eighty-five female patients with breast tumours (41 malignant, 44 benign) were included. Nrf2 (rs6721961) and p73 (G4A) SNPs were determined by PCR- CTPP assay. Results: Genotype frequencies of the Nrf2 promoter SNP were 34.2% and 37.9% for AA in benign and malignant groups respectively, and 43.9% and 40.5% for CC and, 21.9 % and 21.6% for CA. Genotype frequencies for the P73 G4A SNP were 52.9% and 44.7% for GA in benign and malignant groups respectively, and 47.1% and 55.3% for GG. Discussion: Nrf2 genotypes in pre - and post-menopausal patients, showed significantly different distributions in the 2 patient groups, the AA genotype being significantly more common in pre-menopausal patients. The P73 G4A SNP showed no relation to age of disease onset. Conclusion: The Nrf2 (rs6721961) AA genotype might be related to early breast cancer onset. In contrast the P73 G4A polymorphism showed no relation to either disease risk or age at presentation.

Galactin-3 and brain natriuretic peptide versus conventional echocardiography in the early detection of cirrhotic cardiomyopathy.

BACKGROUND/AIMS: Cirrhotic cardiomyopathy (CCM) is defined as an abnormal heart structure and function in cirrhotic patients. CCM includes systolic and diastolic dysfunction, electrophysiological abnormalities, and structural changes, both microscopic and macroscopic. Currently, there is no one diagnostic test that can identify patients with CCM. Evaluation of the validity of galactin-3 and brain natriuretic peptide (BNP) as biomarkers in the early detection of CCM in comparison to conventional echocardiography. MATERIALS AND METHODS: A case control study was carried out in the Departments of internal medicine and tropical Medicine, Assuit University, Egypt. Seventy-one subjects were divided into the following three groups: 26 cirrhotic patients without ascites, 25 cirrhotic patients with ascites, and 20 healthy controls. All groups underwent clinical examination, and laboratory investigation including BNP, galactin-3, and echocardiography. RESULTS: There was a significant difference between the three groups (p < 0.001) with regard to corrected QT (cQT), BNP and galactin-3. Left ventricular diastolic dysfunction with different grades was the most recorded cardiac abnormality in the patient group I and II (88.5% and 96%; respectively) with significantly increased frequency and severity in ascetic patients and with the advancement of liver cirrhosis. BNP and galactin-3 were sensitive and specific biomarkers for the detection of diastolic dysfunction in cirrhotic patients (77.6%, 95.5%, 89.9% and 86.4%; respectively). CONCLUSION: Diastolic dysfunction is a common cardiac abnormality in cirrhotic patients that worsens with the advancement of cirrhosis. BNP and galactin-3 had higher sensitivity and specificity in the early detection of CCM compared with those of conventional echocardiography.

Evaluation of serum PIVKA-II and MIF as diagnostic markers for HCV/HBV induced hepatocellular carcinoma.

Viral hepatitis is the most significant predisposing factor for hepatocellular carcinoma (HCC). Liver cancer grows silently with mild or no symptoms until the disease is advanced and with little hope of cure. Early recognition of the onset of HCC would help to select more effective therapies for patients leading to a better prognosis and life span. The current study aims to evaluate two diagnostic and prognostic markers - Prothrombin induced by vitamin K absence-II (PIVKA-II) and macrophage migration inhibitory factor (MIF) in the serum of patients with HCC and those with a high risk of developing hepatic cancers. Serum samples from hepatocellular carcinoma, hepatitis C and normal subjects were subjected to quantitative determinations of different parameters including alpha-fetoprotein (AFP), PIVKA-II and MIF. Significant differences between the various groups were recorded. PIVKA-II and AFP showed a higher specificity and sensitivity compared to MIF, and there was considerable correlation between AFP and both PIVKA and MIF. It is concluded that analysis of PIVKA-II and AFP can serve as useful non-invasive markers for the early detection of HCC with good sensitivity and specificity.