Phenomics and genomic features of Enterococcus avium IRMC1622a isolated from a clinical sample of hospitalized patient.

BACKGROUND: Enterococcus avium (E. avium) is a Gram-positive nosocomial pathogen that is commonly isolated from the alimentary tract. The objective of this functional genomics study was to identify the resistant genes by analyzing the genome of E. avium IRMC1622a, a type of bacteria found in feces collected from a patient at a Saudi Arabian tertiary hospital. METHODS: The bacterial strain IRMC1622a was identified by 16 S rRNA sequencing as Enterococcus sp. The resistance phenomics were performed using VITEK® 2, and morphological analysis was achieved using a scanning electron microscope (SEM). Finally, the whole bacterial genome of the bacterial strain IRMC1622a was subjected to sequencing during October 2023 using Oxford Nanopore long-read sequencing technology, and mining for resistant genes. RESULTS: The results of antimicrobial resistant phenomics indicated that the IRMC1622a strain was sensitive to all tested antimicrobial agents except for erythromycin, and the same result was confirmed by genomic analysis in addition to other classes of antibiotics. SEM showed E. avium IRMC1622a is ovoid shape, in single cells (L 1.2797 ± 0.1490 µm), in pairs (L 1.7333 ± 0.1054 µm), and in chains (L 2.44033 ± 0.1978 µm). The E. avium IRMC1622a genome has 14 (in CARD) antimicrobial resistance genes that were identified with several mechanisms of antimicrobial resistance, such as the efflux pump and conferring antibiotic resistance. The present study revealed that the E. avium IRMC1622a genome contains a high number of genes associated with virulence factors, and 14 matched pathogenic protein families and predicted as human pathogen (probability score 0.855). We report two (ISEnfa4 and ISEfa5) mobile genetic elements for the first time in the E. avium genome. CONCLUSIONS: The study concludes that E. avium IRMC1622a is susceptible to all tested antibacterials except erythromycin. The IRMC1622a has 14 genes encoding antimicrobial resistance mechanisms, including the efflux pump and conferring antibiotic resistance. This could indicate a potential rise in E. avium resistance in healthcare facilities. These observations may raise concerns regarding E. avium resistance in healthcare. We need more research to understand the pathophysiology of E. avium, which leads to hospital-acquired infections.

Cytokine expression, protection and shedding reduction induced by the combination of lipopolysaccharide with Montanoid ISA71 in oil-based Newcastle disease vaccine.

Oil-based inactivated ND vaccines are a commonly used control strategy for this endemic disease in Egypt. One of the major limitations of these inactivated vaccines is the time taken to develop a protective response in vaccinated birds. In the present study, we aimed to formulate an inactivated oil-based ND vaccine incorporated with lipopolysaccharide (LPS) that stimulates the early onset innate response to inactivated vaccines via proinflammatory cytokine production. Five groups of 21-day old SPF chicks were reared in isolators and were treated as follows: G1: Montanoid ISA71 adjuvanted NDV vaccinated group, G2: LPS and Montanoid ISA71 adjuvanted NDV vaccinated group, G3: LPS and Montanoid ISA71 with phosphate buffer saline received group and two non-vaccinated control groups. NDV specific antibodies and cell mediated immune responses were evaluated by hemagglutination inhibition and lymphocyte proliferation tests, respectively. Transcriptional responses of the TLR4, IFN-γ and IL-2 genes were analyzed in peripheral blood mononuclear cells (PBMCs) following vaccination by qRT-PCR. Protection % was determined after challenge with a lethal strain of NDV 106 EID50/0.5 ml. Viral shedding was assessed on oropharyngeal swabs by qRT-PCR and infectivity titration on SPF-ECE. The results revealed that the incorporation of LPS with ISA71 in the oil-based ND vaccine induced a synergistic response confirmed by significant humoral and lymphoproliferative responses with a significant increase in Th1 cytokine transcripts. The simultaneous use of both adjuvants in G2 demonstrated complete protection and a significant reduction in viral shedding compared to the ISA71-adjuvated ND vaccine in G1, which conferred 90 % protection.

Genomic Landscape of Multidrug Resistance and Virulence in Enterococcus faecalis IRMC827A from a Long-Term Patient.

We report on a highly virulent, multidrug-resistant strain of Enterococcus faecalis IRMC827A that was found colonizing a long-term male patient at a tertiary hospital in Khobar, Saudi Arabia. The E. faecalis IRMC827A strain carries several antimicrobial drug resistance genes and harbours mobile genetic elements such as Tn6009, which is an integrative conjugative element that can transfer resistance genes between bacteria and ISS1N via an insertion sequence. Whole-genome-sequencing-based antimicrobial susceptibility testing on strains from faecal samples revealed that the isolate E. faecalis IRMC827A is highly resistant to a variety of antibiotics, including tetracycline, doxycycline, minocycline, dalfopristin, virginiamycin, pristinamycin, chloramphenicol, streptomycin, clindamycin, lincomycin, trimethoprim, nalidixic acid and ciprofloxacin. The isolate IRMC827A carries several virulence factors that are significantly associated with adherence, biofilm formation, sortase-assembled pili, manganese uptake, antiphagocytosis, and spreading factor of multidrug resistance. The isolate also encompasses two mutations (G2576T and G2505A) in the 23S rRNA gene associated with linezolid resistance and three more mutations (gyrA p.S83Y, gyrA p.D759N and parC p.S80I) of the antimicrobial resistance phenotype. The findings through next-generation sequencing on the resistome, mobilome and virulome of the isolate in the study highlight the significance of monitoring multidrug-resistant E. faecalis colonization and infection in hospitalized patients. As multidrug-resistant E. faecalis is a serious pathogen, it is particularly difficult to treat and can cause fatal infections. It is important to have quick and accurate diagnostic tests for multidrug-resistant E. faecalis, to track the spread of multidrug-resistant E. faecalis in healthcare settings, and to improve targeted interventions to stop its spread. Further research is necessary to develop novel antibiotics and treatment strategies for multidrug-resistant E. faecalis infections.

Selective IgA Deficiency a Probable Risk of Recurrent Chest Infections in Asthmatics.

BACKGROUND: Selective immunoglobulin A (IgA) deficiency is characterized by a high incidence of both recurrent infections and atopic diseases. Asthma is one of the most common lung diseases affecting around 300 million people worldwide and is associated with risk of serious pneumococcal disease and microbial infections. Multiple studies have attributed this to impaired innate and adaptive immunity in asthmatics. An additional probable hypothesis is the existence of an underlying primary immunodeficiency (PID), such as selective IgA deficiency (sIgAD). AIM: To assess the prevalence of selective IgA deficiency and its correlation to recurrent infections in asthmatic patients. METHODS: A case-control study was conducted on 80 subjects who were divided into 3 groups: 20 Asthmatic patients with recurrent chest infections (Group A), 20 asthmatic patients without recurrent chest infections (Group B) and 40 healthy controls (Group C). RESULTS: On comparing the 3 studied groups, there was a statistically significant difference between the three groups (p = ˂0.001) concerning serum IgA. The mean serum IgA was statistically significantly lower in Group A&B than in Group C. Furthermore, it was significantly lower in Group A than in Group B and C (p1,2 <0.002 and <0.001*, respectively). The percentage of selective IgA deficiency or partial IgA deficiency in asthmatic patients was 56% (26 patients). Group A showed a statistically significant higher percentage of selective/partial IgA deficiency.

Cardiovascular system and coronavirus disease-2019 (COVID-19): mutual injuries and unexpected outcomes.

BACKGROUND: Cardiovascular system involvement in coronavirus disease-2019 (COVID-19) has gained great interest in the scientific community. MAIN BODY: Several studies reported increased morbidity and mortality among COVID-19 patients who had comorbidities, especially cardiovascular diseases like hypertension and acute coronary syndrome (ACS). COVID-19 may be associated with cardiovascular complications as arrhythmia, myocarditis, and thromboembolic events. We aimed to illustrate the interactions of COVID-19 disease and the cardiovascular system and the consequences on clinical decision as well as public health. CONCLUSIONS: COVID-19 has negative consequences on the cardiovascular system. A high index of suspicion should be present to avoid poor prognosis of those presenting with unusual presentation.

Diagnostic deficiencies of C. difficile infection among patients in a tertiary hospital in Saudi Arabia: A laboratory-based case series.

Clostridioides difficile infection (CDI) has become a threatening public health problem in the developed world. In the kingdom of Saudi Arabia, prevalence of CDI is still unknown due to limited surveillance protocols and diagnostic resources. We used a two-step procedure to study and confirm C. difficile cases. We also studied toxin profiles of these isolates. Stool samples were collected from symptomatic patients and clinically suspected of CDI for almost 12 months. Isolates were confirmed by culture method followed by 16S rRNA sequencing. Multiplex PCR was performed for the identification of toxin A, toxin B and binary toxin genes and compared to Gene Expert results. Out of the 47 collected samples, 27 were successfully grown on culture media. 18 samples were confirmed as C. difficile by both culture and 16S rRNA sequencing. Interestingly, the rest of the isolates (9 species) belonged to different genera. Our results showed 95% of samples were positive for both toxin A and B (tcdA, tcdB) and all samples exhibited the toxin gene regulator tcdC. All samples were confirmed negative for the binary toxin gene ctdB and 11% of the isolates were positive for ctdA gene. Interestingly, one isolate harbored the binary toxin gene (cdtA +) and tested negative for both toxins A and B. We believe that combining the standard culture method with molecular techniques can make the detection of C. difficile more accurate.

Drug Resistance-Associated Mutations in ERG11 of Multidrug-Resistant Candida auris in a Tertiary Care Hospital of Eastern Saudi Arabia.

Candida auris is an emerging multi-drug resistant pathogen with high mortality rate; nosocomial infections have been reported worldwide, causing a major challenge for clinicians and microbiological laboratories. The study aims to describe new cases of C. auris and detect drug resistance-associated mutations of C. auris by the sequencing of ERG11 and FKS1 genes. A total of six specimens were collected from blood, urine, ear swab, and groin screening samples. Isolates were incubated for 48 h on Sabouraud Dextrose agar (SDA) at 42 °C, then confirmed by MALDI-TOF MS. Furthermore, antifungal susceptibility testing was performed using the Vitek 2 system to detect Minimum Inhibitory Concentrations (MICs) of six antifungals. Sequences of 18S rRNA gene and ITS regions from isolates and phylogenetic analysis were performed. Gene sequencing was analysed to detect drug resistance-associated mutations by FKS1 and ERG11 genes sequencing. All C. auris isolates were confirmed by MALDI-TOF MS, and evolutionary analyses using sequences of 18S rRNA gene and ITS region. Antifungal susceptibility testing showed that all isolates were resistant to fluconazole. Sequencing of ERG11 and FKS1 genes from the isolates revealed the presence of two (F132Y and K143R) drug resistance-associated mutations in ERG11, however, FKS1 gene was devoid of mutations. The study sheds light on a public health threat of an emerging pathogen, and the hospital implemented strict contact screening and infection control precautions to prevent C. auris infection. Finally, there is a critical need to monitor the antifungal resistance in different geographical areas and implementation of efficient guidelines for treatment.

Genotypes II and VIId-based inactivated Newcastle disease vaccine reduces virus shedding.

In Egypt, recent outbreaks were reported in NDV-vaccinated flocks. The isolated strain was characterized as class II velogenic genotype VIId of Newcastle disease virus (NDV). In this study, three inactivated NDV vaccine formulations were prepared, the first one is LaSota (genotype II), the second one is genotype VIId and the third one is combined Lasota and genotype VIId at a proportion of 1:1. The challenge trials were conducted in SPF chicks to evaluate the efficacy of the prepared vaccines using 106 EID50/0.5 ml of the Egyptian genotype VIId strain of Newcastle disease virus (NDV-B7-RLQP-CH-EG-12). Our results revealed that all three prepared vaccine formulations conferred 100% protection in the vaccinated chicks. However, the combined vaccine induced the highest haemagglutination inhibition (HI) titers and neutralization indices with significant reduction in virus shedding compared to other vaccine formulations. Histopathology examination of different organs collected from vaccinated chicks post challenge indicated the protective efficacy in vaccinated groups compared to the positive control group where a score of severe lesions was shown. This study reports the efficacy of combined inactivated Lasota and genotype VIId vaccine in reducing virus shedding which is very important in controlling NDV infection in chicken.

Factors associated with irritable bowel syndrome among medical students at Ain Shams University.

BACKGROUND: Irritable bowel syndrome (IBS) is one of the most common and potentially disabling gastrointestinal disorders. The pathogenesis of this disorder remains obscure. However, many etiological explanations point toward bacterial etiology. Also, several studies have documented that psychological and social factors may play a role. Medical education is among the most challenging and stressful education, and this may predispose to high rates of IBS. OBJECTIVES: The aims of this study are to estimate the frequency of IBS in a selected sample of students of Faculty of Medicine in Ain Shams University and to find out the determinants associated with this disorder. STUDY DESIGN: A cross-sectional study was carried out among medical students from October 2017 to February 2018 at Faculty of Medicine-Ain Shams University. All participants were asked to complete a confidential self-administered questionnaire. An interview questionnaire was used for diagnosis of IBS according to Rome III criteria, while morbid anxiety and depression were diagnosed by using the Arabic version of Hospital Anxiety and Depression Scale (HADS). RESULTS: Three hundred eighty-two students completed the questionnaire. The frequency of IBS was 31.7% with higher proportion among females and among students with positive family history of IBS. However, IBS was significantly less prevalent among students practicing regular exercise. Lastly, based on (HADS), there was a statistical significant relationship between IBS and anxiety (p < 0.05), but not depression. CONCLUSION: The study revealed that around 31% of the studied group was suffering from IBS. Female gender, suffering from anxiety, and positive family history of IBS were the main associated factors for IBS. Screening of all medical students in the faculty for IBS is suggested. Providing psychological and emotional support along with stress management is highly recommended.