Detection of multiple extensively-drug resistant hypervirulent Klebsiella pneumoniae clones from patients with ventilator-associated pneumonia in Egypt.

Introduction. Hypervirulent-K. pneumoniae (hvKP) is an evolving pathotype that is more virulent than the classical-K. pneumoniae (cKP) and causes serious fatal illnesses.Hypothesis/Gap Statement. Although there are few reports on hvKP isolated from Egyptian patients, the molecular characteristics and clonal relatedness of MDR-hvKP have not been adequately investigated.Aim. To investigate the microbiological and genetic characteristics as well as the epidemiology of hvKP induced ventilator-associated pneumonia (VAP).Methodology. A retrospective study of 59 K. pneumoniae inducing VAP was conducted at Assiut University Hospitals from November 2017 to January 2019. All K. pneumoniae were tested for resistance phenotype, capsular genotype (K1 and K2), virulence gene profile (c-rmpA, p-rmpA, iucA, kfu, iroB, iroN), and the presence of resistance genes (blaNDM-1, blaCTX-M-3-like, blaCTX-M-14-like). Clonal relatedness was assessed by Pulsed field gel electrophoresis (PFGE).Result. HvKP accounted for 89.8 % (53/59) of K. pneumoniae isolates with ~95 % exhibiting extensively-drug resistant (XDR) phenotype. Hypermucoviscous phenotype was detected in 19 (35.8 %) hvKP and K2 capsular gene was identified in 18 (33.9 %) of hvKP. Regarding the virulence genotype of hvKP strains, iucA was the most prevalent virulence gene (98.1%), while p-rmpA and kfu were detected in 75.4 and 52.8 % of hvKP strains, respectively. Resistance genes were highly prevalent in both cKP and hvKP with blaCTX-M-3-like being more prevalent in hvKP (100 % vs 94.3 % for blaNDM-1, 50 % vs 62.2 % for blaCTX-M-3-like and 83.3 % vs 69.8 % for blaCTX-M-14 -like, respectively). PFGE typing of 29 representative K. pneumoniae revealed 15 pulsotypes, with identical hvKP pulsotypes isolated from different ICUs at different times and several hvKP and cKP isolates belonged to the same pulsotype.Conclusion. This study highlights the dominance and clonal spread of XDR-hvKP strains at Assiut University Hospital in Egypt. Physicians should be aware of the increased risk of hvKP induced-VAP and support further epidemiologic studies.

Comorbidities and outcomes among patients hospitalized with COVID-19 in Upper Egypt.

Background: The coronavirus disease 19 (COVID-19) pandemic has spread rapidly around the globe with considerable morbidity and mortality. Coexistence of comorbidities with COVID-19 had consistently been reported as risk factors for unfavorable outcome. We aimed to evaluate the impact of comorbidities in COVID-19 patients on the outcome and determine predictors of prolonged hospital stay, requisite for intensive care unit (ICU) admission. Four hundred and thirty-nine adult patients who are admitted through (June and July 2020) in our University Hospitals were included in the study. All participants were diagnosed with COVID-19 according to Egyptian Ministry of Health guidance as definite case or probable case. Results: Patients with comorbidities represented 61.7% of all cases. Constitutional symptoms especially myalgia and lower respiratory tract (LRT) symptoms such as dyspnea were significantly higher in patients with comorbidities (P < 0.05). Patients with comorbidities had significantly worse laboratory parameters. ICU admission was higher in patients with comorbidities (35.8%). Among different comorbidities 45.4% of cardiovascular diseases (CVD) cases were admitted in ICU followed by diabetes mellitus (DM) cases (40.8%). Also, patients with comorbidities needed invasive mechanical ventilation more than those without comorbidity (31 versus 10.7%, P < 0.001). Significant lower frequency of recovery was found in COVID-19 patients with comorbidities (59% versus 81%, P < 0.001) and death rate was significantly higher in cases with comorbidities (P < 0.001) . The survival rates in cases with pre-existing CVD and neurological diseases were lower than those without disease (P < 0.002 and 0.001, respectively). Conclusions: Association of cardiovascular comorbid conditions including hypertension or neurological diseases including old cerebrovascular strokes together with COVID-19 infections carries higher risks of mortality. However, other comorbidities such as diabetes mellitus, chronic pulmonary or kidney diseases may also contribute to increased COVID-19 severity.

Gut microbiota in forty cases of egyptian relapsing remitting multiple sclerosis.

BACKGROUND AND OBJECTIVES: Gut microbiota is assumed to play an essential role in the pathogenesis of multiple sclerosis (MS). This study aimed to investigate the abundance of some gut microbiota among Egyptian patients with relapsing remitting multiple sclerosis (RR-MS). MATERIALS AND METHODS: Forty cases of RR-MS diagnosed according to McDonald diagnostic criteria (2017) were recruited consecutively from the Department of Neurology, Assiut University Hospitals. The results were compared with 22 healthy age and sex matched control subjects. DNA was extracted from stool and measures made of concentration and copy number of bacterial organisms by real-time PCR using group specific primers for 16S rRNA targeting predominant genera of gut microbiota previously hypothesized to participate in MS pathogenesis. RESULTS: The mean age was 31.4 ± 8.8 yrs; 75% of the patients were women. The mean and SD of EDSS score was 3.43 ± 1.35. Seven cases had cervical cord plaques (17%). There were significantly increased copy numbers of Desulfovibrio, Actinobacteria, Firmcutes, and Lactic acid bacteria in patients compared with the control group. In contrast there was a significantly lower level of Clostridium cluster IV in the patients. Patients who had EDSS < 3.5 had a significantly higher copy number of Actinobacteria, Bacteroidetes, and Bifidobacterium, compared with patients who had EDSS > 3.5. There was a significant negative correlation between duration of illness and copy number of Firmcutes, Akkermansia, and Lactic acid bacteria (P = 0.01, 0.04, and 0.004 respectively). CONCLUSION: The changes in gut microbiota are associated with exacerbation of MS disease. Disruption of the intestinal microbiota results in the depletion or enrichment of certain bacteria that may affect the immune balance leading to predisposition to MS.

Characteristics of Carbapenem-Resistant Gram-Negative Bacilli in Patients with Ventilator-Associated Pneumonia.

Carbapenem-resistant Gram-negative bacilli (CR-GNB) has become a global threat. In hospital settings, the association of CR-GNB with ventilator-associated pneumonia (VAP) is a critical public health concern owing to their high resistance rate to most antibiotics. The present study aims to identify the frequency of carbapenem-resistance and to determine the rate of multidrug resistance (MDR), extensive drug resistance (XDR) and pan-drug resistance (PDR) among CR-GNB infections in VAP. Antimicrobial susceptibility testing was carried out using the disk diffusion method and the detection of carbapenemases was screened using the imipenem-E test and the modified carbapenem-inactivation method (mCIM). The isolates were verified by polymerase chain reaction (PCR) for the presence of blaNDM, blaSPM, blaVIM, blaIMP and blaGIM genes. 89.5%, 14%, 17.5%, 10.5%, 3.5% of isolates exhibited the presence of blaNDM, blaVIM, blaSPM, blaIMP and blaGIM, respectively. 76%, 17% and 7% of isolates were PDR, XDR, and MDR, respectively. Carbapenem-resistance genes were identified in a significant percentage and blaNDM was the most predominant gene. All isolates were highly resistant to most antibiotics. This health concern has proven to be a big challenge in developing countries such as Egypt, as it is associated with high morbidity, high mortality, and raised healthcare costs.

Antimicrobial Resistance and Comparative Genome Analysis of Klebsiella pneumoniae Strains Isolated in Egypt.

Klebsiella pneumoniae is an important human pathogen in both developing and industrialised countries that can causes a variety of human infections, such as pneumonia, urinary tract infections and bacteremia. Like many Gram-negative bacteria, it is becoming resistant to many frontline antibiotics, such as carbapenem and cephalosporin antibiotics. In Egypt, K. pneumoniae is increasingly recognised as an emerging pathogen, with high levels of antibiotic resistance. However, few Egyptian K. pneumoniae strains have been sequenced and characterised. Hence, here, we present the genome sequence of a multidrug resistant K. pneumoniae strain, KPE16, which was isolated from a child in Assiut, Egypt. We report that it carries multiple antimicrobial resistance genes, including a blaNDM-1 carbapenemase and extended spectrum ß-lactamase genes (i.e., blaSHV-40, blaTEM-1B, blaOXA-9 and blaCTX-M-15). By comparing this strain with other Egyptian isolates, we identified common plasmids, resistance genes and virulence determinants. Our analysis suggests that some of the resistance plasmids that we have identified are circulating in K. pneumoniae strains in Egypt, and are likely a source of antibiotic resistance throughout the world.

Sero-prevalence of anti-SARS-CoV-2 antibodies among healthcare workers: A multicenter study from Egypt.

BACKGROUND: Healthcare workers (HCWs) are at a high risk for disease exposure. Given the limited availability of nucleic acid testing by PCR in low resource settings, serological assays can provide useful data on the proportion of HCWs who have recently or previously been infected. Therefore, in this study, we conducted an immunologic study to determine the seroprevalence of anti-SARS-CoV-2 antibodies in two university hospitals in Egypt. METHODS: in this cross sectional study, HCWs who were working in SARS-CoV-2 Isolation Hospitals were interviewed. Estimating specific antibodies (IgM and IgG) against SARS-CoV-2 was carried out using an enzyme-linked immunosorbent assay targeting the Spike antigen of SARS-CoV-2 virus. RESULTS: Out of 111, 82 (74%) HCWs accepted to participate with a mean age of 31.5 ± 8.5 years. Anti-SARS-COV2 antibodies were detected in 38/82 (46.3%) of cases with a mean age of 31 years and female HCWs constituted 57.6% of cases. The highest rate of seropositivity was from the nurses (60.5%), and physicians (31.6%) with only (7.9%) technicians. Only 28/82 (34.1%) HCWs reported previous history of COVID19. We reported a statistically significant difference in the timing of exposure (p = 0.010) and the frequency of contact with COVID-19 cases (p = 0.040) between previously infected and on-infected HCWs. Longer time of recovery was reported from IgG positive HCWs (p = 0.036). CONCLUSION: The high frequency of seropositive HCWs in investigated hospitals is alarming, especially among asymptomatic personnel. Confirmation of diseased HCWs (among seropositive ones) are warranted.

Knowledge, perception, and confidence of healthcare workers about COVID-19 preventive measures during the first wave of the pandemic: a cross-sectional study from Egypt.

INTRODUCTION: The ongoing coronavirus-disease-19 (COVID-19) pandemic had a variable history with differences in its various stages. This study evaluates the status of knowledge, perception, and confidence about COVID-19 preventive measures during the first wave of the COVID-19 pandemic among healthcare workers (HCWs) in Egypt. METHODS: A cross-sectional study was conducted during the first wave of the COVID-19 pandemic, in July 2020, in Egypt. An-online-based questionnaire was used to collect data. It included items to record demographic data, and an assessment of knowledge, the perception of healthcare facilities preparedness, and HCW confidence about applying infection prevention measures. RESULTS: A total of 465 responses were analyzed. HCWs' mean age was 36.76 ± 9.57 years, 94.2% (n=438) had an adequate level of knowledge, 31% (n=144) had an adequate perception level, and 39.4% (n=183) had an adequate confidence level. The main source of information was international organizations' websites 46.5% (n=216). The main barriers to applying preventive measures were the overcrowding of patient care areas 73.1% (n=339), and limited infection control supplies 68% (n=316). Factors associated with COVID-19 among HCWs were COVID-19 infected family members (OR: 5.86), inability to protect themselves and their families (OR: 5.73), uncertainty about the available hand hygiene supplies (OR: 3.76), male gender (OR: 3.07), and single HCWs (OR: 2.88). CONCLUSIONS: Although the majority reported an adequate knowledge level, lower rates of adequate perception and confidence were observed. Revision of preparedness plans in different facilities should be further studied. Psychological support and gender differences should be considered in response programs.

Emergence of Nosocomial Pneumonia Caused by Colistin-Resistant Escherichia coli in Patients Admitted to Chest Intensive Care Unit.

(1) Background: Colistin is a last-resort antibiotic used in treating multidrug-resistant Gram-negative infections. The growing emergence of colistin resistance in Escherichia coli (E. coli) represents a serious health threat, particularly to intensive care unit (ICU) patients. (2) Methods: In this work, we investigated the emergence of colistin resistance in 140 nosocomial E. coli isolated from patients with pneumonia and admitted to the chest ICU over 36 months. Virulence and resistance-related genes and E. coli pathotypes in colistin-resistant and colistin-sensitive isolates were determined. (3) Results: Colistin resistance was observed in 21/140 (15%) of the nosocomial E. coli isolates. The MIC50 of the resistant strains was 4 mg/L, while MIC90 was 16 mg/L. Colistin-resistant isolates were also co-resistant to amoxicillin, amoxicillin/clavulanic, aztreonam, ciprofloxacin, and chloramphenicol. The mechanism of colistin resistance was represented by the presence of mcr-1 in all resistant strains. Respectively, 42.9% and 36.1% of colistin-resistant and colistin-sensitive groups were extended-spectrum ß-lactamase (ESBL) producers, while 23.8% and 21% were metallo ß-lactamase (MBL) producers. blaTEM-type was the most frequently detected ESBL gene, while blaIMP-type was the most common MBL in both groups. Importantly, most resistant strains showed a significantly high prevalence of astA (76.2%), aggR (76.2%), and pic (52.4%) virulence-related genes. Enteroaggregative E. coli (76%) was the most frequently detected genotype among the colistin-resistant strains. (4) Conclusion: The high colistin resistance rate observed in E. coli strains isolated from patients with nosocomial pneumonia in our university hospital is worrisome. These isolates carry different drug resistance and virulence-related genes. Our results indicate the need for careful monitoring of colistin resistance in our university hospital. Furthermore, infection control policies restricting the unnecessary use of extended-spectrum cephalosporins and carbapenems are necessary.

Antimicrobial resistance and gene regulation in Enteroaggregative Escherichia coli from Egyptian children with diarrhoea: Similarities and differences.

Enteroaggregative Escherichia coli (EAEC) is a common diarrhoeagenic human pathogen, isolated from patients in both developing and industrialized countries, that is becoming increasingly resistant to many frontline antibiotics. In this study, we screened 50 E. coli strains from children presenting with diarrhea at the outpatients clinic of Assiut University Children's Hospital, Egypt. We show that all of these isolates were resistant to multiple classes of antibiotics and identified two as being typical EAEC strains. Using whole genome sequencing, we determined that both isolates carried, amongst others, blaCTX-M and blaTEM antibiotic resistance genes, as well as many classical EAEC virulence determinants, including the transcriptional regulator, AggR. We demonstrate that the expression of these virulence determinants is dependent on AggR, including aar, which encodes for a repressor of AggR, Aar. Since biofilm formation is the hallmark of EAEC infection, we examined the effect of Aar overexpression on both biofilm formation and AggR-dependent gene expression. We show that whilst Aar has a minimal effect on AggR-dependent transcription it is able to completely disrupt biofilm formation, suggesting that Aar affects these two processes differently. Taken together, our results suggest a model for the induction of virulence gene expression in EAEC that may explain the ubiquity of EAEC in both sick and healthy individuals.

Impact of comorbidities on COVID-19 outcome.

BACKGROUND AND AIMS: The coronavirus disease 19 (COVID-19) pandemic has spread rapidly around the globe with considerable morbidity and mortality. Coexistence of comorbidities with COVID-19 have consistently been reported as risk factors for unfavorable prognosis. We aim at this study to evaluate the impact of comorbidities in COVID-19 patients on the outcome and determine predictors of prolonged hospital stay, requisite for ICU admission or decease. METHODS: Four hundreds and thirty nine adult patients who are admitted through (June and July 2020) in Assiut and Aswan University Hospitals were included in the study. All participants were diagnosed with COVID-19 according to Egyptian Ministry of Health guidance as definite case or Probable case. Detection of SARS-CoV-2 RNA was done by (TaqManâ"¢ 2019-nCoV Control Kit v1 (Cat. No. A47532) supplied by QIAGEN, Germany on the Applied Biosystem 7500 Fast RT PCR System, USA. RESULTS: Patients with comorbidities represented 61.7% of all cases. Constitutional symptoms especially myalgia and LRT symptoms such as dyspnea were significantly higher in patients with comorbidities (P < 0.05). Patients with comorbidities had significantly worse laboratory parameters. ICU admission was higher in patients with comorbidities (35.8%). Among different comorbidities 45.4% of CVD cases were admitted in ICU followed by DM cases (40.8%). Also, patients with comorbidities needed invasive mechanical ventilation more than those without comorbidity (31 vs. 10.7%, P<0.001). Significant lower frequency of recovery was found in COVID-19 patients with comorbidities (59% vs. 81%, P<0.001) and death rate was significantly higher in cases with comorbidities (P< 0.001). The survival rates in cases with pre-existing CVD and neurological diseases were lower than those without disease (P<0.002 and 0.001 respectively). CONCLUSION: Association of cardiovascular comorbid conditions including hypertension or neurological diseases together with COVID-19 infections carries higher risks of mortality. However, other comorbidities such as diabetes mellitus, chronic pulmonary or kidney diseases may also contribute to increased COVID-19 severity.

Patterns of Fluoroquinolone Resistance in Enterobacteriaceae Isolated from the Assiut University Hospitals, Egypt: A Comparative Study.

Background: An increasing pattern of fluoroquinolone resistance (FQR) among bacterial pathogens has been described worldwide. In this study, we compared the patterns of genetic mechanisms that confer FQR for Escherichia coli and Klebsiella pneumoniae isolated from the Assiut University Hospitals in Egypt. Methods: Eighty-seven clinical E. coli and K. pneumoniae isolates were tested for mutations in gyrA, gyrB, parC, and parE genes by polymerase chain reaction (PCR) amplification and DNA sequencing. The presence of plasmid-mediated quinolone resistance (PMQR) genes qnrA, qnrB, qnrS, aac(6')-Ib, qepA was screened by PCR and characterized by conjugation. Correlations between different FQR mechanisms and ciprofloxacin minimal inhibitory concentration (MIC) levels were determined. Results: A higher number of quinolone resistance-determining region (QRDR) mutations was detected in E. coli, while the number of PMQR determinants was significantly higher in K. pneumoniae. However, K. pneumoniae showed stronger correlations than E. coli between MIC levels and number of mutations in the QRDR per isolate (rs = 0.8, p < 0.0001 and rs = 0.7, p < 0.0001, respectively) as well as between MIC levels and number of plasmids (rs = 0.4, p = 0.005 and rs = 0.3, p = 0.02, respectively). Conclusions: Although we observed a prevalence of chromosomal mutations for E. coli and the presence of plasmid-encoded genes for K. pneumoniae that resulted in FQR phenotype, high levels of FQR appeared to occur as a result of gradual accumulation of mutations in QRDR for both bacteria. To our best of knowledge, this is the first study to report and compare the correlation between FQ MIC levels and different genetic mechanisms for FQR in Enterobacteriaceae.

Bloodstream Infections in Febrile Neutropenic Pediatric Cancer Patients: Microbiological and Sepsis Biomarkers Insight.

The diagnosis of blood steam infections (BSIs) in febrile neutropenic pediatric cancer patients (FNPCP) remains a challenge. Although blood culture is the most accurate method; yet the delay in results has urged the need for reliable biomarkers for early diagnosis. The objectives of this study were to identify the bacterial causes of BSIs in FNPCP at SECI and their antimicrobial susceptibility patterns. Also, to assess the value of procalcitonin (PCT), interleukin 6 (IL6), and interleukin 10 (IL 10) for early diagnosis of BSIs. This study included 68 FNPCP with a total of 85 fever episodes. Blood cultures were done at the onset of fever. Identification of the organisms was carried by Vitek 2 system and the antimicrobial susceptibility testing by disc diffusion. The levels of PCT, IL-6 and IL-10 serum levels were measured by ELISA. Blood stream bacterial infection was detected in 29.4% (25/85). Most were Gram positive cocci in 53.6 % (15/28). There were high percentages of multidrug resistant organism (MDRO) (73.3% and 92.3% among Gram positive and negative bacteria, respectively). The least percentage of resistance was to linezolid (0%) and amikacin (15.4%). The levels of the biomarkers were significantly higher in patients with positive bacterial cultures compared to those with negative cultures (P < 0.001). IL -6 had the best sensitivity (96%) (AUC 0.975, cut off 0.925ng/L) with considerable specificity (88.3%). Combined PCT & IL-6 had the highest sensitivity (96%) and specificity (98.3%). We conclude that the percentage of BSIs among FNPCP was considerable. Gram positive bacteria were the commonest causes. High percentages of MDRO were reported. The most efficient antimicrobials were linezolid and amikacin. IL-6 alone had the best sensitivity for early diagnosis of BSIs. The combination of PCT and IL 6 showed the best performance.

Serological and Molecular Diagnosis of Occult Hepatitis B Virus Infection in Hepatitis C Chronic Liver Diseases.

Occult Hepatitis B infection (OBI), defined as the presence of serum HBV DNA without detectable HBsAg, can be classified into seropositive OBI [anti-HBc and/or anti-hepatitis B surface (anti- HBs) positive] and seronegative OBI (anti-HBc and anti- HBs negative). We examined the role of anti-HBc as a screening test for OBI in HCV patients with chronic liver diseases and evaluated the possible impact of OBI on liver disease progression. 90 patients with hepatitis C related chronic liver diseases (CLD) and negative for HBsAg were divided into three equal groups; chronic hepatitis, liver cirrhosis and hepatocellular carcinoma (HCC). Patients were tested for anti-HBc by ELISA and by PCR for S-gene. Total anti-HBc was found in 26 patients (28.9%). 8 patients (8.9%) had positive serum HBV DNA. Of these, 2 were positive for anti-HBc and 6 negative for anti-HBc. No correlation between OBI and severity of HCV related CLD was observed. In conclusion, as OBI was not associated with total anti-HBc, it is invaluable surrogate marker for OBI detection.

Incidence and characteristics of hepatitis E virus infection in children in Assiut, Upper Egypt.

Objective To describe the characteristics of hepatitis E virus (HEV) infection in a cohort of children from Upper Egypt using data from a large multicentre prospective study of acute viral hepatitis (AVH). Methods Data from subjects aged 2-18 years with AVH or close contacts of those with AVH found to have asymptomatic AVH were included in the analysis. Information concerning medical history, clinical examination, liver function tests and screening for hepatotropic viruses was recorded and analysed. Results A total of 123 patients (73 boys, 50 girls) were included in the analysis. Of these, 33 (26.8%) had HEV infection, 17 (13.8%) had hepatitis A virus infection, 10 (8.1%) had hepatitis B virus infection, 14 (11.4%) had cytomegalovirus hepatitis, five (4.1%) had autoimmune hepatitis, 11 (8.9%) had hepatitis due to mixed viral infections and 33 (26.8%) had non A-E hepatitis. Overall, 38 (30.9%) had infection with HEV. HEV infection was significantly higher among those using underground wells as a water source compared with tap water. Liver enzymes were significantly raised in patients with non-HEV infection compared with those with HEV infection. Conclusions HEV is a significant cause of AVH among children in Upper Egypt. Contamination of drinking water appears to be a major source of infection. Screening for HEV should be considered in all Egyptian children with AVH.

Association between IL28B rs12979860 single nucleotide polymorphism and the frequency of colonic Treg in chronically HCV-infected patients.

The IL28B gene is associated with spontaneous or treatment-induced HCV viral clearance. However, the mechanism by which the IL28B single nucleotide polymorphism (SNP) affects the extra-hepatic HCV immune responses and its relationship to HCV pathogenesis have not been thoroughly investigated. To examine the mechanism by which IL28B affects HCV clearance. Forty Egyptian patients with chronic HCV infection receiving an Interferon/ribavirin treatment regimen were enrolled into this study. There were two groups: non-responders (NR; n = 20) and sustained virologic responders (SVR; n = 20). The initial plasma HCV viral loads prior to treatment and IL28B genotypes were determined by quantitative RT-PCR and sequencing, respectively. Liver biopsies were examined to determine the inflammatory score and the stage of fibrosis. Colonic regulatory T cell (Treg) frequency was estimated by immunohistochemistry. No significant association between IL28B genotypes and response to therapy was identified, despite an odds ratio of 3.4 to have the TT genotype in NR compared to SVR (95 % confidence interval 0.3-35.3, p = 0.3). Patients with the TT-IL28Brs12979860 genotype (unfavorable genotype) have significantly higher frequencies of colonic Treg compared to the CT (p = 0.04) and CC (p = 0.03) genotypes. The frequency of colonic Treg cells in HCV-infected patients had a strong association with the IL-28B genotype and may have a significant impact on HCV clearance.

Extra-hepatic infection of hepatitis C virus in the colon tissue and its relationship with hepatitis C virus pathogenesis.

Extra-hepatic compartments might contribute to hepatitis C virus (HCV) persistence and extra-hepatic manifestations. Therefore, we investigated HCV infection in colonic tissue in patients with chronic hepatitis C (CHC) and its relationship with HCV pathogenesis. Colonic biopsies were collected from three groups with CHC infection: treatment naïve (TN; n=12), non-responders (NR; n=10) to anti-HCV therapy (pegylated interferon-α and ribavirin) and sustained virologic response (SVR; n=10) and from a fourth healthy control group (n=10). Liver biopsies were examined to assess inflammation and fibrosis. HCV infection and colonic T regulatory (Treg) frequency were detected by immunohistochemistry. HCV core and NS3 proteins were detected in B cells and macrophage/monocytes of 42 % and 25 % of TN and 50 % and 30 % of NR, respectively, but not in SVR or control group. The numbers of cells expressing HCV proteins were positively correlated with both HCV viral load and colonic Treg frequency. A significant negative correlation between HCV-expressing cells with both liver inflammation and fibrosis was identified. Our study provides evidence that HCV can infect B cells and macrophages of the colon. The correlations between HCV infection in colonic tissue and HCV viral load and liver pathology underline the significance of this extra-hepatic infection in HCV pathogenesis and response to therapy.

Association of colonic regulatory T cells with hepatitis C virus pathogenesis and liver pathology.

BACKGROUND AND AIM: Forkhead box protein P3 (FoxP3)(+) regulatory T (Treg ) cells play a fundamental role in maintaining the balance between the tissue-damaging and protective immune response to chronic hepatitis C (CHC) infection. Herein, we investigated the frequency of Treg cells in the colon and their potential relationship to the various CHC outcomes and hepatic histopathology. METHODS: Colonic biopsies were collected from three groups with CHC: treatment naïve (TN; n = 20), non-responders (NR; n = 20), sustained virologic response (SVR; n = 20), and a fourth healthy control group (n = 10). The plasma viral loads and cytokines levels were determined by quantitative real-time polymerase chain reaction, and ELISA, respectively. Liver biopsies were examined to assess inflammatory score and fibrosis stage. Colonic Treg frequency was estimated by immunohistochemistry using confocal microscopy. RESULTS: A significant increase in the frequency of colonic Treg was found in TN, and NR groups compared with the control and SVR group. The frequency of colonic Treg , plasma interleukin (IL)-10 and IL-4 levels were significantly positively correlated with viral load and negatively correlated with METAVIR inflammatory score, and fibrosis stages. CONCLUSION: Colonic Treg cells are negatively correlated with liver inflammation and hepatitis C virus (HCV) viral load, which suggests a strong linkage between gut-derived Treg cell populations and HCV infection.

Evaluation of chromogenic media and seminested PCR in the identification of Candida species.

Identification of Candida cultured from various clinical specimens to the species level is increasingly necessary for clinical laboratories. Although sn PCR identifies the species within hours but its cost-effectiveness is to be considered. So there is always a need for media which help in the isolation and identification at the species level. The study aimed to evaluate the performance of different chromogenic media and to compare the effectiveness of the traditional phenotypic methods vs. seminested polymerase chain reaction (sn PCR) for identification of Candida species. One hundred and twenty seven Candida strains isolated from various clinical specimens were identified by conventional methods, four different chromogenic media and sn PCR. HiCrome Candida Differential and CHROMagar Candida media showed comparably high sensitivities and specificities in the identification of C. albicans, C. tropicalis, C. glabrata and C. krusei. CHROMagar Candida had an extra advantage of identifying all C. parapsilosis isolates. CHROMagar-Pal's medium identified C. albicans, C. tropicalis and C. krusei with high sensitivities and specificities, but couldn't identify C. glabrata or C. parapsilosis. It was the only medium that identified C. dubliniensis with a sensitivity and specificity of 100%. Biggy agar showed the least sensitivities and specificities. The overall concordance of the snPCR compared to the conventional tests including CHROMAgar Candida in the identification of Candida species was 97.5%. The use of CHROMAgar Candida medium is an easy and accurate method for presumptive identification of the most commonly encountered Candida spp.

Evaluation of chromogenic media and seminested PCR in the identification of Candida species

Identification of Candida cultured from various clinical specimens to the species level is increasingly necessary for clinical laboratories. Although sn PCR identifies the species within hours but its cost-effectiveness is to be considered. So there is always a need for media which help in the isolation and identification at the species level. The study aimed to evaluate the performance of different chromogenic media and to compare the effectiveness of the traditional phenotypic methods vs. seminested polymerase chain reaction (sn PCR) for identification of Candida species. One hundred and twenty seven Candida strains isolated from various clinical specimens were identified by conventional methods, four different chromogenic media and sn PCR. HiCrome Candida Differential and CHROMagar Candida media showed comparably high sensitivities and specificities in the identification of C. albicans, C. tropicalis, C. glabrata and C. krusei. CHROMagar Candida had an extra advantage of identifying all C. parapsilosis isolates. CHROMagar-Pal's medium identified C. albicans, C. tropicalis and C. krusei with high sensitivities and specificities, but couldn't identify C. glabrata or C. parapsilosis. It was the only medium that identified C. dubliniensis with a sensitivity and specificity of 100%. Biggy agar showed the least sensitivities and specificities. The overall concordance of the snPCR compared to the conventional tests including CHROMAgar Candida in the identification of Candida species was 97.5%. The use of CHROMAgar Candida medium is an easy and accurate method for presumptive identification of the most commonly encountered Candida spp.

Protective role of humoral immune responses during an outbreak of hepatitis E in Egypt.

Although the seroprevalence of hepatitis E virus (HEV) is approximately 80% in adult Egyptians living in rural areas, symptomatic HEV-caused acute viral hepatitis (AVH) is sporadic and relatively uncommon. To investigate the dichotomy between HEV infection and clinical AVH, HEV-specific immune responses in patients with symptomatic and asymptomatic HEV infection during a waterborne outbreak in Egypt were examined. Of 235 acute hepatitis patients in Assiut hospitals screened for HEV infection, 42 (17.9%) were acute hepatitis patients confirmed as HEV-caused AVH; 37 (88%) of the 42 patients were residents of rural areas, and 14 (33%) were from one village (Kom El-Mansoura). Another 200 contacts of AVH cases in this village were screened for HEV and 14 (7.0%), all of whom were family members of AVH cases, were asymptomatic HEV IgM-positive. HEV infections in this village peaked during the summer. Asymptomatic HEV seroconverters had significantly higher levels of epitope-specific neutralising (p=0.006) and high avidity (p=0.04) anti-HEV antibodies than the corresponding AVH cases. In conclusion, naturally acquired humoral immune responses appear to protect HEV-exposed subjects from AVH during an HEV outbreak in Egypt.