Risk Factors Associated with Severity and Death from COVID-19 in Iran: A Systematic Review and Meta-Analysis Study.

Objectives: This study aims to investigate the risk factors associated with severity and death from COVID-19 through a systematic review and meta-analysis of the published documents in Iran. Methods: A systematic search was performed based on all articles indexed in Scopus, Embase, Web of Science (WOS), PubMed, and Google Scholar in English and Scientific Information Database (SID) and Iranian Research Institute for Information Science and Technology (IRA)NDOC indexes in Persian. To assess quality, we used the Newcastle Ottawa Scale. Publication bias was assessed using Egger's tests. Forest plots were used for a graphical description of the results. We used HRs, and ORs reported for the association between risk factors and COVID-19 severity and death. Results: Sixty-nine studies were included in the meta-analysis, of which 62 and 13 had assessed risk factors for death and severity, respectively. The results showed a significant association between death from COVID-19 and age, male gender, diabetes, hypertension, cardiovascular disease (CVD), cerebrovascular disease, chronic kidney disease (CKD), Headache, and Dyspnea. We observed a significant association between increased white blood cell (WBC), decreased Lymphocyte, increased blood urea nitrogen (BUN), increased creatinine, vitamin D deficiency, and death from COVID-19. There was only a significant relationship between CVD and disease severity. Conclusion: It is recommended that the predictive risk factors of COVID-19 severity and death mentioned in this study to be used for therapeutic and health interventions, to update clinical guidelines and determine patients' prognoses.

Antibiotic use during the first 6 months of COVID-19 pandemic in Iran: A large-scale multi-centre study.

WHAT IS KNOWN AND OBJECTIVE: Although antibiotics are ineffective against viral infections, epidemiological studies have revealed that the COVID-19 pandemic resulted in the overuse of antibiotics and disruption of antimicrobial stewardship programmes. We investigated the pattern of antibiotic use during the first 6 months of the COVID-19 pandemic in Iran. METHODS: A multi-centre retrospective study was designed to investigate the use of 16 broad-spectrum antibiotics in 12 medical centres. The rate of antibiotic use was calculated and reported based on the Defined Daily Dose (DDD) per 100 hospital bed-days. The bacterial co-infection rate was also reported. RESULTS AND DISCUSSION: Totally, 43,791 hospitalized COVID-19 patients were recruited in this study. It was found that 121.6 DDD of antibiotics were used per 100 hospital bed-days, which estimated that each patient received approximately 1.21 DDDs of antibiotics every day. However, the bacterial co-infections were detected only in 14.4% of the cases. A direct correlation was observed between the rate of antibiotic use and mortality (r[142] = 0.237, p = 0.004). The rate of antibiotic consumption was not significantly different between the ICU and non-ICU settings (p = 0.15). WHAT IS NEW AND CONCLUSION: In this study, widespread antibiotic use was detected in the absence of the confirmed bacterial coinfection in COVID-19 patients. This over-consumption of broad-spectrum antibiotics may be associated with increased mortality in hospitalized COVID-19 patients, which can be an alarming finding.

Challenges of and corrective recommendations for healthcare-associated infection's case findings and reporting from local to national level in Iran: a qualitative study.

BACKGROUND: The accuracy of health care-associated infections (HAIs) statistics in many countries is questionable and the main reasons of this inaccuracy are not well-known. The study aim was to explore inhibitors of and corrective recommendations for HAIs case findings and reporting in some of Iran hospitals. METHODS: Sixteen face-to-face interviews and an expert panel were performed with expertise of infection prevention and control (IPC) programs in hospitals, and Deputies of Health and Treatment in medical university and Ministry of Health from Feb 2018 to May 2019. Using conventional content analysis, code, subcategories and categories were developed. RESULT: Three categories emerged including improper structure preparation, conflict of interest, and inadequate motivation. Allocating distinct budget and adequate staff to IPC programs, developing a user-friendly surveillance system and engaging physicians and nurses for HAIs reporting are the main corrective recommendations accepted by the expert panel. CONCLUSION: Despite the improvement in growing case-findings and reporting of HAIs in Iran, there are many challenges which inhibit accurate case finding and reporting of HAIs. So it is necessary to update the structure, system and rules to reach accurate HAIs data in Iran.

Soluble ACE2 as a Risk or Prognostic Factor in COVID-19 Patients: A Cross-sectional Study.

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel severe acute respiratory syndrome coronavirus. The first known receptor for this virus in the human body is angiotensin-converting enzyme 2 (ACE2), the same receptor for the SARS virus. Methods: A total of 38 hospitalized adult (18 years) patients with laboratory or clinically confirmed coronavirus disease 2019 (COVID-19) were identified in the infectious disease ward of Tehran Imam Khomeini hospital complex in this single-center cross-sectional study. A blood sample was taken at the time of hospitalization and a second one was taken 48 hours later. Blood samples are kept frozen at -80 degrees Celsius. After the complete collection of samples, the ACE2 level of the samples was measured using a serum sACE2 detection ELISA kit. The data were analyzed using SPSS v26. P value of 0.05 was considered statistically significant. An analysis of covariance was performed to examine the mean differences in day 7 serum ACE2 concentration among the 2 groups after adjusting for the baseline serum ACE2 concentration. The 1-way multivariate analysis of variance was used to determine whether there were any differences between independent groups (mechanical ventilation yes/no) on serum ACE2 levels at 3 different times. Results: The mean age of patients was 64.13 ± 16.49 years, 21 patients (55.3%) were men, 16 patients (42%) were polymerase chain reaction test positive, and 15 patients (39.5%) died. A total of 35 individuals (92.1%) had chest computed tomography images that indicated lung involvement. A comparison of the 2 groups of patients who died and were discharged revealed that serum ACE2 at the first (p=0.033) and third (7th day) measurements were statistically different (p=0.026). Patients had a mean of serum ACE2. The results indicated that the day 7 serum ACE2 concentration did significantly differ between the 2 groups after controlling for the baseline serum ACE2 concentration (p=0.023). The model explained about 73.61% of the variance in the 7-day serum ACE2 concentration. Specifically, after adjusting for the baseline concentration, survived patients had the lowest level of serum ACE2 concentration (1 ± 0.65) on the 7th day compared with the deceased patient group (2.83 ± 1.12). Conclusion: Soluble ACE2 in the serum of COVID-19 patients who died, later on, was significantly higher than the discharged patients when the samples were taken seven days after admission. It is suggested that serum soluble ACE2 level could be used as a prognostic factor for COVID-19 patients' outcomes and also their need for mechanical ventilation.

Epidemiologic characteristics of orthopedic surgical site infections and under-reporting estimation of registries using capture-recapture analysis.

BACKGROUND: Surgical Site Infections (SSIs) are among the leading causes of the postoperative complications. This study aimed at investigating the epidemiologic characteristics of orthopedic SSIs and estimating the under-reporting of registries using the capture-recapture method. METHODS: This study, which was a registry-based, cross-sectional one, was conducted in six educational hospitals in Tehran during a one-year period, from March, 2017 to March, 2018. The data were collected from two hospital registries (National Nosocomial Infection Surveillance System (NNIS) and Health Information Management database (HIM)). First, all orthopedic SSIs registered in these sources were used to perform capture-recapture (N = 503). Second, 202 samples were randomly selected to assess patients` characteristics. RESULTS: Totally, 76.24% of SSIs were detected post-discharge. Staphylococcus aureus (11.38%) was the most frequently detected bacterium in orthopedic SSIs. The median time between the detection of a SSI and the discharge was 17 days. The results of a study done on 503 SSIs showed that the coverage of NNIS and HIM was 59.95 and 65.17%, respectively. After capture-recapture estimation, it was found that about 221 of orthopedic SSIs were not detected by two sources among six hospitals and the real number of SSIs were estimated to be 623 ± 36.58 (95% CI, 552-695) and under-reporting percentage was 63.32%. CONCLUSION: To recognize the trends of SSIs mortality and morbidity in national level, it is significant to have access to a registry with minimum underestimated data. Therefore, according to the weak coverage of NNIS and HIM among Iranian hospitals, a plan for promoting the national Infection Prevention and Control (IPC) programs and providing updated protocols is recommended.

Proven Aspergillus flavus pulmonary aspergillosis in a COVID-19 patient: A case report and review of the literature.

Severe COVID-19 patients complicated with aspergillosis are increasingly reported. We present a histopathological proven case of fatal COVID-19-associated pulmonary aspergillosis (CAPA), due to Aspergillus flavus. This report and existing published literature indicate diagnostic challenges and poor outcomes of CAPA in ICU patients.

Oropharyngeal candidiasis in hospitalised COVID-19 patients from Iran: Species identification and antifungal susceptibility pattern.

BACKGROUND: Emergence of coronavirus disease 2019 (COVID-19) is a major healthcare threat. Apparently, the novel coronavirus (SARS-CoV-2) is armed by special abilities to spread and dysregulate the immune mechanisms. The likelihood of oropharyngeal candidiasis (OPC) development in COVID-19 patients with a list of attributable risk factors for oral infections has not yet been investigated. OBJECTIVES: We here aim to investigate the prevalence, causative agents and antifungal susceptibility pattern of OPC in Iranian COVID-19 patients. PATIENTS AND METHODS: A total of 53 hospitalised COVID-19 patients with OPC were studied. Relevant clinical data were mined. Strain identification was performed by 21-plex PCR and sequencing of the internal transcribed spacer region (ITS1-5.8S-ITS2). Antifungal susceptibility testing to fluconazole, itraconazole, voriconazole, amphotericin B, caspofungin, micafungin and anidulafungin was performed according to the CLSI broth dilution method. RESULTS: In 53 COVID-19 patients with OPC, cardiovascular diseases (52.83%) and diabetes (37.7%) were the principal underlying conditions. The most common risk factor was lymphopaenia (71%). In total, 65 Candida isolates causing OPC were recovered. C albicans (70.7%) was the most common, followed by C glabrata (10.7%), C dubliniensis (9.2%), C parapsilosis sensu stricto (4.6%), C tropicalis (3%) and Pichia kudriavzevii (=C krusei, 1.5%). Majority of the Candida isolates were susceptible to all three classes of antifungal drugs. CONCLUSION: Our data clarified some concerns regarding the occurrence of OPC in Iranian COVID-19 patients. Further studies should be conducted to design an appropriate prophylaxis programme and improve management of OPC in critically ill COVID-19 patients.

Pulmonary adenocarcinoma mimicking miliary tuberculosis in a 20-year-old man: A clinical case report.

Lung adenocarcinoma (LA) is the most common subtype of lung cancer with nonsignificant manifestations. Some benign conditions can mimic LA in symptoms and even chest imaging. In this case report, we are discussing a young man without any significant medical history with metastatic LA, initially presumed military TB.

A clinical prediction model for predicting the surgical site infection after an open reduction and internal fixation procedure considering the NHSN/SIR risk model: a multicenter case-control study.

Introduction: Surgical site infection (SSI) is one of the most common surgical-related complications worldwide, particularly in developing countries. SSI is responsible for mortality, long hospitalization period, and a high economic burden. Method: This hospital-based case-control study was conducted in six educational hospitals in Tehran, Iran. A total of 244 patients at the age of 18-85 years who had undergone open reduction and internal fixation (ORIF) surgery were included in this study. Among the 244 patients, 122 patients who developed SSIs were selected to be compared with 122 non-infected patients used as controls. At the second stage, all patients (n = 350) who underwent ORIF surgery in a hospital were selected for an estimation of the standardized infection ratio (SIR). A logistic regression model was used for predicting the most important factors associated with the occurrence of SSIs. Finally, the performance of the ORIF prediction model was evaluated using discrimination and calibration indices. Data were analyzed using R.3.6.2 and STATA.14 software. Results: Klebsiella (14.75%) was the most frequently detected bacterium in SSIs following ORIF surgery. The results revealed that the most important factors associated with SSI following an ORIF procedure were found to be elder age, elective surgery, prolonged operation time, American Society of Anesthesiologists score of ≥2, class 3 and 4 wound, and preoperative blood glucose levels of >200 mg/dl; while preoperative higher hemoglobin level (g/dl) was found to be a protective factor. The evidence for the interaction effect between age and gender, body mass index and gender, and age and elective surgery were also observed. After assessing the internal validity of the model, the overall performance of the models was found to be good with an area under the curve of 95%. The SIR of SSI for ORIF surgery in the selected hospital was 0.66 among the patients aged 18-85 years old. Conclusion: New risk prediction models can help in detecting high-risk patients and monitoring the infection rate in hospitals based on their infection prevention and control programs. Physicians using prediction models can identify high-risk patients with these factors prior to ORIF procedure.

Dissemination of the Acinetobacter baumannii isolates belonging to global clone 2 containing AbGRI resistance islands in a referral hospital.

Acinetobacter baumannii strains belonging to global clone 2 (GC2) contain resistance islands (AbGRIs), which are composed of genes conferring resistance to older and newer antibiotics. Here, to locate these genes in AbGRIs, the GC2 strains from Tehran, Iran were examined. Among the 170 A. baumannii, 90 isolates were identified as GC2. Of the genes that confer resistance to older antibiotics, tetA(B), tetR(B) (tetracyclines), strA, and strB (aminoglycosides) were located in AbGRI1 of 65 GC2 isolates (72.2%). Of the other aminoglycosides, the aphA1b was located in AbGRI2-12b (63.6%), AbGRI2-12a (21.2%), or AbGRI2-1 (15.1%). The aacC1 and aadA1 genes were co-located within AbGRI2-1 (5.5%). The armA was located in AbGRI3-4 (77.7%) and AbGRI3ABI221 (22.2%). Of sulfonamides, the sul1 was located within AbGRI2-1 (5.5%). Of beta-lactams, the blaTEM was located in AbGRI2-12b (42%), AbGRI2-12a (14%), AbGRI2-1 (10%), or AbGRI2ABI257 (34%). The oxa23 gene conferring resistance to newer antibiotics (carbapenems) was located in AbaR4 (81.1%); of them, the AbaR4 was located within AbGRI1 in 45.2% of the isolates. This study showed that the GC2 isolates, which contained at least one AbGRI, disseminate in the hospital. Hence, it is likely that the AbGRIs play a significant role in conferring resistance to older and newer antibiotics in GC2 isolates from Iran. IMPORTANCE The majority of Acinetobacter baumannii isolates that are resistant to multiple antibiotics belong to one of the two major global clones, namely global clone 1 (GC1) and global clone 2 (GC2). The resistance islands, which contain variable assortments of transposons, integrons, and specific resistance genes, have been characterized in the genome of these GCs. In GC2 A. baumannii, the chromosomally located A. baumannii genomic resistance islands (AbGRIs) carry the genes conferring resistance to older and newer antibiotics. In this context, we tested whether GC2 isolates collected from a referral hospital carry the AbGRIs containing these genes. This study provided evidence for the circulation of the GC2 A. baumannii strains harboring AbGRI resistance islands between different wards of a referral hospital.

Clinical and microbiological patterns in critically ill patients with catheter-associated UTI: A report from Iran.

INTRODUCTION: Catheter-associated urinary tract infections (CAUTIs) are among the most common nosocomial infections with different clinical and microbiological characteristics. We studied these characteristics in critically ill patients. METHODOLOGY: This research was a cross-sectional study conducted on intensive care unit (ICU) patients with CAUTI. Patients' demographic and clinical information and laboratory data, including causative microorganisms and antibiotic susceptibility tests, were recorded and analyzed. Finally, the differences between the patients who survived and died were compared. RESULTS: After reviewing 353 ICU cases, 80 patients with CAUTI were finally included in the study. The mean age was 55.9 ± 19.1 years, 43.7% were male and 56.3% were female. The mean length of infection development since hospitalisation and hospital stay were 14.7 (3-90) and 27.8 (5-98) days, respectively. The most common symptom was fever (80%). The microbiological identification showed that the most isolated microorganisms were Multidrug-resistant (MDR) Enterobacteriaceae (75%), Pseudomonas aeruginosa (8.8%), Gram-positive uropathogens (8.8%) and Acinetobacter baumannii (5%). Fifteen patients (18.8%) died among whom infections with A. baumannii (75%) and P. aeruginosa (57.1%) were associated with more death (p = 0.005). CONCLUSIONS: Although A. baumannii and P. aeruginosa can be the most important pathogens for death, MDR Enterobacteriaceae are still a serious concern as causes of CAUTIs.

Determine phenotypical patterns of resistance to antibiotics in COVID-19 patients with associated bacterial infection: largest medical center in Iran.

Background and Objectives: Antibacterial resistance (AMR) is a serious threat and major concern, especially in developing countries. Therefore, we aimed to determine phenotypical patterns of resistance to antibiotics in COVID-19 patients with associated bacterial infection in intensive care units. Materials and Methods: In this cross-sectional study, 6524 COVID-19 patients admitted for more than 48 h in the ICUs of Imam Khomeini Complex Hospital (IKCH) in Tehran from March 2020 to January 2022 were included in the study with initial diagnosis of COVID-19 (PCR test and chest imaging). Data were collected regarding severity of the illness, primary reason for ICU admission, presence of risk factors, presence of infection, length of ICU and hospital stay, microbial type, and antibiotic resistance. In this study, the pattern of antibiotic resistance was determined using the Kirby-Bauer disk diffusion method. Results: In this study, 439 (37.5%) were ventilator-related events (VAEs), and 46% of all hospitalized patients had an underlying disease. The most common microorganisms in COVID-19 patients were carbapenem resistant Klebsiella pneumoniae (KPCs) (31.6%), Escherichia coli (E. coli) (15.8%), and Acinetobacter baumannii (A. baumannii) (15.7%), respectively. Prevalence of vancomycin-resistant enterococci (VRE) and KPCs were 88% and 82%, respectively. Conclusion: A study on AMR surveillance is the need of the hour as it will help centers to generate local antibiograms that will further help formulate national data. It will guide doctors to choose the appropriate empiric treatment, and these studies will be the basis for establishing antimicrobial surveillance and monitoring and regulating of the use of antimicrobials.

Effect of famotidine on cognitive and behavioral dysfunctions induced in post-COVID-19 infection: A randomized, double-blind, and placebo-controlled study.

OBJECTIVES: This is an investigation of the efficacy and safety of famotidine, a selective histamine H2 receptor antagonist, on improvement of cognitive impairment, depression and anxiety symptoms developing post-COVID-19, in a 12-week, randomized controlled trial. METHODS: A total of 50 patients with a confirmed diagnosis of COVID-19 and a score ≤ 23 on the Mini-Mental State Examination (MMSE) test or a score ≤ 22 on the Montreal Cognitive Assessment (MoCA) were randomly assigned to either the famotidine (40 mg twice daily) or the placebo group. Changes in MMSE scores at weeks 6 and 12 were the primary outcome, while changes in other scales were the secondary outcomes. Participants and evaluators were blinded. RESULTS: At weeks 6 and 12, patients in the famotidine group had significantly higher MMSE scores (p = 0.014, p < 0.001, respectively). Regarding the MoCA scale, the famotidine group had a significantly higher score at weeks 6 and 12 (p = 0.001, p < 0.001, respectively). Considering the HAM-D scale (Hamilton Depression Rating Scale), at weeks 6 and 12, the famotidine group experienced a larger reduction (p = 0.009, p = 0.02, respectively). Additionally, comparison of the HAM-A scale scores (Hamilton Anxiety Rating Scale) at weeks 6 and 12 showed a statistically significant larger reduction in the famotidine group (p = 0.04, p = 0.02, respectively). The two groups did not differ in the frequency of adverse effects. CONCLUSION: Our study supports safety and efficacy of famotidine in treating cognitive impairment, depression and anxiety symptoms induced by COVID-19. TRIAL REGISTRATION: This trial was registered at the Iranian registry of clinical trials (IRCT: www.irct.ir; registration number: IRCT20090117001556N138).

Mobile genetic elements carrying aminoglycoside resistance genes in Acinetobacter baumannii isolates belonging to global clone 2.

Aminoglycosides are used to treat infections caused by carbapenem-resistant Acinetobacter baumannii (CRAB) strains. However, resistance to aminoglycosides has increased remarkably in the last few years. Here, we aimed to determine the mobile genetic elements (MGEs) associated with resistance to aminoglycosides in the global clone 2 (GC2) A. baumannii. Among the 315 A. baumannii isolates, 97 isolates were identified as GC2, and 52 of GC2 isolates (53.6%) were resistant to all the aminoglycosides tested. The AbGRI3s carrying armA were detected in 88 GC2 isolates (90.7%), and of them, 17 isolates (19.3%) carried a new variant of AbGRI3 (AbGRI3ABI221). aphA6 was located in TnaphA6 of 30 isolates out of 55 aphA6-harboring isolates, and 20 isolates were found to harbor TnaphA6 on a RepAci6 plasmid. Tn6020 carrying aphA1b was detected in 51 isolates (52.5%), which was located within AbGRI2 resistance islands. The pRAY* carrying the aadB gene was detected in 43 isolates (44.3%), and no isolate was found to contain a class 1 integron harboring this gene. The GC2 A. baumannii isolates contained at least one MGE carrying the aminoglycoside resistance gene, located mostly either in the chromosome within AbGRIs or on the plasmids. Thus, it is likely that these MGEs play a role in the dissemination of aminoglycoside resistance genes in GC2 isolates from Iran.

The comparison of clinical, laboratory, and radiological findings in immunocompromised and immunocompetent patients with COVID-19: A case-control study.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) with significant morbidity and mortality. We reported and compared the clinical and para-clinical findings of immunocompromised and immunocompetent COVID-19 patients in a case-control study at the Imam Khomeini hospital in Tehran, Iran. METHODS: In this study, 107 immunocompromised COVID-19 patients were recruited as the case group, and 107 immunocompetent COVID-19 patients as the control group. The participants were matched based on age and sex. The patients' information was retrieved from the hospital records in an information sheet. Associations between clinical and para-clinical findings with the immune status were assessed using bivariate and multivariate analyses. RESULTS: The initial pulse rate and recovery time were significantly higher in immunocompromised patients (p < .05). Myalgia, nausea/vomiting, loss of appetite, headache, and dizziness were more frequently reported by the control group (p < .05). Regarding the prescribed medications' duration, Sofosbovir was used longer in the case group, while Ribavirin was used longer in the control groups (p < .05). The most common complication in the case group was acute respiratory distress syndrome, although no major complications were observed in the control group. According to the multivariate analysis, recovery time and Lopinavir/Ritonavir (Kaletra) prescription were significantly higher in the immunocompromised compared to the immunocompetent group. CONCLUSION: Recovery time was significantly longer in the immunocompromised compared to the immunocompetent group, which emphasizes the necessity of prolonged care in these high-risk patients. Also, it is recommended to investigate the effect of novel therapeutic interventions to reduce the recovery time in addition to improving the prognosis of immunodeficient patients with COVID-19.

Intensive care unit admission and associated factors in patients hospitalised for COVID-19: A national retrospective cohort study in Iran.

OBJECTIVES: This study aimed to determine factors associated with intensive care unit (ICU) admission in patients hospitalised due to COVID-19. DESIGN: Retrospective cohort. SETTING: Confirmed hospitalised patients from all over Iran were considered for the study. PARTICIPANTS: All patients with COVID-19 admitted to the hospital from March 2020 to May 2021 were included by census. ICU admission was defined by the following criteria: (1) admission to the ICU ward; (2) level of consciousness (loss of consciousness); and (3) use of invasive ventilation. METHODS: This is a secondary data analysis from the Medical Care Monitoring Center. The association between different variables and ICU admission was assessed by forward Logistic regression and restricted cubic spline method. RESULTS: The mean age of the 1 469 620 patients with COVID-19 was 54.49±20.58 years old, and 51.32% of the patients were male. The prevalence of ICU admission was 19.19%. The mean age of patients admitted to the ICU was higher than that of other hospitalised patients (62.49±19.73 vs 52.59±20.31 years). The prevalence of ICU admission was 17.17% in the first, 21.52% in the second, 19.72% in the third, 21.43 in the fourth and 17.4% in the fifth wave. In the multivariable model, age groups, sex, waves of the epidemic, comorbidities and saturation of peripheral oxygen (SpO2) <93% and acute respiratory distress syndrome (ARDS) were associated with an increased odds of ICU admission. The OR for ICU admission indicates a significant protective effect at a young age and then a significant risk factor for admission to the ICU ward at an old age. CONCLUSIONS: Men, older adults, people who suffer from ARDS, patients with SpO2 levels of less than 93% and cases with comorbidities had the highest odds of ICU admission. Therefore, these groups should take all necessary precautions to avoid contracting COVID-19.

Genome Analysis of the Enterococcus faecium Entfac.YE Prophage.

Background: Bacteriophages are viruses that infect bacteria. Bacteriophages are widely distributed in various environments. The prevalence of bacteriophages in water sources, especially wastewaters, is naturally high. These viruses affect evolution of most bacterial species. Bacteriophages are able to integrate their genomes into the chromosomes of their hosts as prophages and hence transfer resistance genes to the bacterial genomes. Enterococci are commensal bacteria that show high resistance to common antibiotics. For example, prevalence of vancomycin-resistant enterococci has increased within the last decades. Methods: Enterococcal isolates were isolated from clinical samples and morphological, phenotypical, biochemical, and molecular methods were used to identify and confirm their identity. Bacteriophages extracted from water sources were then applied to isolated Enterococcus faecium (E. faecium). In the next step, the bacterial genome was completely sequenced and the existing prophage genome in the bacterial genome was analyzed. Results: In this study, E. faecium EntfacYE was isolated from a clinical sample. The EntfacYE genome was analyzed and 88 prophage genes were identified. The prophage content included four housekeeping genes, 29 genes in the group of genes related to replication and regulation, 25 genes in the group of genes related to structure and packaging, and four genes belonging to the group of genes associated with lysis. Moreover, 26 genes were identified with unknown functions. Conclusion: In conclusion, genome analysis of prophages can lead to a better understanding of their roles in the rapid evolution of bacteria.

An Update to Enterococcal Bacteremia: Epidemiology, Resistance, and Outcome.

BACKGROUND: An increase in resistant gram-positive cocci, especially enterococci, requires an epidemiologic re-assay and its results may affect empirical treatments for these infections. OBJECTIVE: In this study, we investigated the microbial epidemiology and resistance pattern of enterococcal bacteremia. METHODS: This study was a cross-sectional study that investigated all cases of positive blood cultures with Enterococcus spp. at a tertiary referral colligates hospital in Tehran in 2018. RESULTS: Enterococcus spp. was isolated from blood cultures of a total of 73 patients. Most of the patients were male i.e: 42 (57.7%). The mean age of the patients was 58.8 (±18.8) years. Hospital- acquired infection was the most prevalent type of infection involving enterococcal bacteremia (80.8%) compared with community-acquired (6.7%) and the health care-associated one (12.3%). Renal failure and cancer were the most underlying disease in E. faecalis and E. faecium, respectively. Mortality for Vancomycin-resistant enterococci (VRE) was approximately two times more than the sensitive ones. Between the dead/alive groups, the following items were significantly different (P.Value<0.05): Vancomycin resistance for enterococcus isolated, immunodeficiency as an underlying disease, Mechanical ventilation, hospitalization period, and the empiric regimen. CONCLUSION: Increased antibiotic-resistant strains, especially Vancomycin-resistant enterococci (VRE), pose a serious threat to the general public, especially hospitalized patients, causing an increase in mortality. Surveillance of microorganisms and antimicrobial resistance is a crucial part of an efficient health care system.

Knowledge and perception of hand hygiene: A survey using WHO standardized tools in Tehran, Iran.

BACKGROUND: Proper hand hygiene is the most important action in preventing healthcare-associated infections (HCAIs). In this study, the knowledge and perception of hand hygiene assessed among nurses as the most exposed personnel to patients. METHODS: In this analytical cross-sectional study, the nurses working in different wards of a collegiate tertiary hospital in Tehran were investigated by standardized WHO questionnaires. RESULTS: Of the 101 participating nurses 89 (88.1%) were females. 81 (80.2%) had received formal related training. The 69 respondents estimated the mean prevalence of HCAI to be 38.91% and 98 (97.1%) considered hand hygiene an effective prevention in this regard. 78 (77.3%) perceived hand hygiene as the center priority; 82, 83 and 79 of participants would think that good hand hygiene matters for their superiors, colleagues and patients, respectively. The practice of hand hygiene was stated to be difficult by 48 (47.5%) respondents. There was no significant difference in self-reporting of hand hygiene practice among nurses in age (P=0.68), the degree of education (P=0.574), work experience (P=0.64), nor their wards (P=0.131). There was a significant reverse relationship with the supposed difficulty level of doing hand hygiene (P=0.049). The mean score of the nurses' knowledge was 66.53 (±9.41) based on the answers to the questions of the knowledge questionnaire. CONCLUSION: Knowledge and perception of hand hygiene, as this study showed, might not to be satisfactory; therefore, planning to improve these indicators and regular monitoring using standard tools is necessary for all healthcare centers.

Post-neurosurgical meningitis; gram negative bacilli vs. gram positive cocci.

Background: Post-neurosurgical meningitis is a significant cause of mortality and morbidity. In this study we aimed to compare the differences of clinical, laboratory features and outcomes between the post-neurosurgical meningitis caused by gram-negative bacilli (GNB) and gram-positive cocci (GPC). Methods: Cases of post-neurosurgical meningitis (with positive CSF culture) were included. After classifying patients as GNB and GPC groups, clinical and paraclinical data were compared. Results: Out of 2667 neurosurgical patients, CSF culture was positive in 45 patients. 25 (54.3%) were GNB, 19 (41.3%) GPC. The most common microorganisms were Klebsiella pneumoniae (n=14, 31.1%), Coagulase negative staphylococcus (n=8, 17.8%), Staphylococcus aureus (n=6, 13.3%), Acinetobacter baumannii (n=4, 8.9%), Pseudomonas aeruginosa (n=2, 4.4%), and Escherichia coli (n=2, 4.4%). There were no correlation between CSF Leakage, Surgical site appearance, presence of drain, Age and GCS between two groups (P=0.11, P=0.28, P=0.06, P=0.86, P=0.11 respectively). The only different laboratory indexes were ESR (86.8 mm/h vs. 59.5 mm/h, P=0.01) and PCT (13.1 ng/ml vs. 0.8 ng/ml, P=0.02) which were higher in GNB cases. 20% (n=5) of patients with GNB meningitis received preoperative corticosteroid, while none of GPC cases received (P=0.03). The median length of hospitalization for GNB and GPC cases was 56 and 44.4 days respectively (P=0.3). Conclusion: The GNB antibiotic coverage should be designed more carefully in post-neurosurgical meningitis especially in patients with recent corticosteroid therapy and elevated ESR and procalcitonin.