Clinical and immunological comparison of COVID-19 disease between critical and non-critical courses: a systematic review and meta-analysis.

Introduction: Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which appeared in 2019, has been classified as critical and non-critical according to clinical signs and symptoms. Critical patients require mechanical ventilation and intensive care unit (ICU) admission, whereas non-critical patients require neither mechanical ventilation nor ICU admission. Several factors have been recently identified as effective factors, including blood cell count, enzymes, blood markers, and underlying diseases. By comparing blood markers, comorbidities, co-infections, and their relationship with mortality, we sought to determine differences between critical and non-critical groups. Method: We used Scopus, PubMed, and Web of Science databases for our systematic search. Inclusion criteria include any report describing the clinical course of COVID-19 patients and showing the association of the COVID-19 clinical courses with blood cells, blood markers, and bacterial co-infection changes. Twenty-one publications were eligible for full-text examination between 2019 to 2021. Result: The standard difference in WBC, lymphocyte, and platelet between the two clinical groups was 0.538, -0.670, and -0.421, respectively. Also, the standard difference between the two clinical groups of CRP, ALT, and AST was 0.482, 0.402, and 0.463, respectively. The odds ratios for hypertension and diabetes were significantly different between the two groups. The prevalence of co-infection also in the critical group is higher. Conclusion: In conclusion, our data suggest that critical patients suffer from a suppressed immune system, and the inflammation level, the risk of organ damage, and co-infections are significantly high in the critical group and suggests the use of bacteriostatic instead of bactericides to treat co-infections.

Aluminum Phosphide Poisoning in the North of Iran: A Register-based Research.

BACKGROUND: Aluminum phosphide (ALP) poisoning is considered one of the health care issues in Iran, which is associated with the mortality outcome of patients. INTRODUCTION: According to the ALP poisoning that commonly results in death, we aimed to evaluate the prevalence of ALP pill poisoning by employing register-based research. METHODS: In this descriptive cross-sectional study, all selected patients diagnosed and confirmed with ALP poisoning by a specialist and referred to the poisoning ward from the beginning of April 2016 to the end of October 2017 were enrolled, and data were registered in the Disease Registration System by a technical expert for daily follow-up during hospitalization. RESULTS: Approximately 12.4% of patients had neurological problems, with the majority having paresis (68.3%). Self-poisoning with the purpose of suicide was documented for 96.2% of cases, with the most common cause being family problems (54.1%). In 97.3% of cases, the method of contact with the toxic substance was oral. Hypotension, cardiac, and respiratory complications were observed in 25.2%, 30.8%, and 25% of the patients, respectively. The most gastrointestinal symptoms were nausea and vomiting (86.7%). CONCLUSION: The results indicate that the rate of ALP pill poisoning is relatively high. Suicide is the most important cause of ALP poisoning, which is more common in men under 40 years of age.

Prevalence of Invasive Streptococcus pneumoniae Infections among Iranian Children: A Systematic Review and Meta-Analysis.

BACKGROUND: Streptococcus pneumoniae is an important pathogen of children, mostly in developing countries. We aimed to investigate the prevalence of invasive S. pneumoniae among Iranian children using a systematic review and meta-analysis. METHODS: A systematic search was carried out to identify papers published by Iranian authors in the Web of Science, PubMed, Scopus, and Google Scholar electronic databases from January of 2010 to December of 2017. Then, seven publications that met our inclusion criteria were selected for data extraction and analysis. RESULTS: Totally, one study was multicenter, and six were single-center based studies. Meanwhile, all of the included studied performed among hospitalized patients. Seven studies reported the prevalence of invasive S. pneumoniae isolated from children, of these the pooled prevalence of S. pneumoniae was 2.5% (95% CI: 0.7%-9.1%). CONCLUSION: The overall prevalence of invasive S. pneumoniae infections among Iranian children is low (2.5%). However, further clinical studies are required to elucidate the burden of infections among Iranian children, especially in eastern regions.

Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the global outbreak of coronavirus disease 2019 (Covid-19), which has been considered as a pandemic by WHO. SARS-CoV-2 encodes four major structural proteins, among which spike protein has always been a main target for new vaccine studies. This in silico study aimed to investigate some physicochemical, functional, immunological, and structural features of spike protein using several bioinformatics tools. METHOD: We retrieved all SARS-CoV-2 spike protein sequences from different countries registered in NCBI GenBank. CLC Sequence Viewer was employed to translate and align the sequences, and several programs were utilized to predict B-cell epitopes. Modification sites such as phosphorylation, glycosylation, and disulfide bonds were defined. Secondary and tertiary structures of all sequences were further computed. RESULTS: Some mutations were determined, where only one (D614G) had a high prevalence. The mutations did not impact the B-cell and physicochemical properties of the spike protein. Seven disulfide bonds were specified and also predicted in several N-link glycosylation and phosphorylation sites. The results also indicated that spike protein is a non-allergen. CONCLUSION: In summary, our findings provided a deep understanding of spike protein, which can be valuable for future studies on SARS-CoV-2 infections and design of new vaccines.

Burden of Clostridium (Clostridioides) difficile Infection among Patients in Western Asia: A Systematic Review and Meta-Analysis.

BACKGROUND: Clostridium difficile is the most common causes of hospital-acquired diarrhea affecting particularly hospitalized patients globally. This organism has re-emerged in recent years with significant morbidity and mortality. The present study aimed to estimate the burden of C. difficile infection (CDI) and to acquire information on the overall rates of community- and hospital-acquired CDI in western Asia. METHODS: A systematic literature search was performed to identify articles published from the eight Persian Gulf countries in western Asia including Iran, Iraq, Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, and the United Arab Emirates in the electronic databases within Jan of 2000 to Dec of 2017. Then, 20 publications which met our inclusion criteria were selected for data extraction and analysis by Comprehensive Meta-Analysis Software. RESULTS: Twenty studies reported the prevalence of toxigenic strains of C. difficile among patients from Persian Gulf countries, of these the pooled prevalence of CDI was 9% (95% CI: 6.5%-12.5%). Totally, 8 studies showed the prevalence of hospital-acquired CDI, from those studies the prevalence of CDI was estimated 8.4% (95% CI: 4.9%-14.1%). Moreover, 7 studies reported the prevalence of community-acquired CDI, from those studies the prevalence of CDI was estimated 1.8% (95% CI: 1.2%-2.9%). CONCLUSION: The prevalence of CDI in western Asia is lower than southern and eastern region. Moreover, the lower prevalence of community-acquired CDI compared to hospital-acquired CDI, indicate that the source of infection in western Asia is more likely in the hospitals.

Prevalence of antibiotic resistance and integrons, sul and Smqnr genes in clinical isolates of Stenotrophomonas maltophilia from a tertiary care hospital in Southwest Iran.

OBJECTIVES: Stenotrophomonas maltophilia has emerged as an important opportunistic nosocomial pathogen due to its intrinsic and acquired resistance to a wide range of antimicrobial agents. The present study aimed to investigate the occurrence of antibiotic resistance and resistance mechanisms among clinical isolates of S. maltophilia from Iranian patients. MATERIALS AND METHODS: This cross-sectional study was performed on 44 S. maltophilia isolates that were recovered from different clinical specimens in 2015 and 2016. Conventional microbiologic methods were used for primary identification of isolates and confirmed by specific polymerase chain reaction (PCR) primers. Minimum inhibitory concentrations (MICs) were determined by the E-test. PCR was applied to determine antibiotic resistance genes. RESULTS: All of S. maltophilia isolates were susceptible to trimethoprim/sulfamethoxazole (TMP/SMX) and colistin. Moreover, the susceptibility rates of isolates toward ceftazidime and ciprofloxacin were 93.2%, and 84.1%, respectively. Class 1 integrons was detected in 24 (54.5%) isolates by the presence of int1 gene. Moreover, the prevalence of antibiotic resistance genes sul1, sul2, and Smqnr were found in 16 (36.4%), 15 (34.1%), and 29 (65.9%) isolates, respectively. CONCLUSION: In summary, the prevalence of sul and Smqnr genes in integrons-contained isolates point out the significant risk of sulfonamides and fluoroquinolones resistance among clinical isolates of S. maltophilia in our region.

High prevalence of vancomycin and high-level gentamicin resistance in Enterococcus faecalis isolates.

Multiple drug-resistant enterococci are major cause of healthcare-associated infections due to their antibiotic resistance traits. Among them, Enterococcus faecalis is an important opportunistic pathogen causing various hospital-acquired infections. A total of 53 E. faecalis isolates were obtained from various infections. They were identified by phenotypic and genotypic methods. Determination of antimicrobial resistance patterns was done according to CLSI guidelines. The isolates that were non-susceptible to at least one agent in ≥3 antimicrobial categories were defined as multidrug-resistant (MDR). Detection of antimicrobial resistance genes was performed using standard procedures. According to MDR definition, all of the isolates were MDR (100%). High-level gentamicin resistance was observed among 50.9% of them (MIC ≥ 500 µg/ml). The distributions of aac(6')-Ie-aph(2'')-Ia and aph(3')-IIIa genes were 47.2% and 69.8%, respectively. The aph(2'')-Ib, aph(2'')-Ic, aph(2'')-Id, and ant(4')-Ia genes were not detected. Vancomycin resistance was found in 45.3% of strains. The vanA gene was detected in 37.7% of isolates, whereas vanB and vanC1 genes were not observed in any strain. Erythromycin resistance rate was 79.2% and the frequencies of ermB and ermC genes were 88.6% and 69.8%, respectively. The ermA and msrA genes were not present in any of the isolates. Our data indicate a high rate of MDR E. faecalis strains. All of high-level gentamicin-resistant isolates carried at least one of aac(6')-Ie-aph(2'')-Ia or aph(3')-IIIa genes. Distribution of vanA was notable among the isolates. In addition, ermB and ermC were accountable for resistance to erythromycin.

The Occurrence of Nosocomial Pathogens on Cell Phones of Healthcare Workers in an Iranian Tertiary Care Hospital.

BACKGROUND: Cell phones have become one of the necessary means of life and they are commonly used almost everywhere by every population. Colonized microorganisms on cell phones can be easily cross-transmitted. Given the widespread prevalence of nosocomial infections, this study aimed to determine the frequency of bacterial contamination and antibiotic resistance in cell phones of healthcare workers (HCWs) in a tertiary care hospital, from southwest of Iran. In this cross-sectional study conducted between April and June 2016, sampling were performed from cell phones of 25 nurses and 75 medical students. METHODS: Samples were collected from each cell phone by a moistened cotton swap dipped in normal saline prior and after decontamination with available alcohol-based handrubs. Identification of bacterial isolates was performed by conventional microbiologic methods. Antibiotic susceptibility pattern of the isolates was determined using the disk diffusion method. The contamination rates of cell phones prior and after disinfection were 88% and 52%, respectively. Ninety-nine (71.2%) out of 139 isolated distinct bacterial colonies prior to cleaning were potentially nosocomial pathogens. Of them, staphylococci (88.9%) were the most prevalent bacteria, in which 40.9% were methicillin-resistant isolates. The majority of Gram-positive and - negative isolates were susceptible to the tested antimicrobials. Totally, contamination rate of cell phones was significantly reduced after decontamination. Regular disinfection of the hands and cell phones was significantly associated with reduction of colonization of the methicillin-resistant isolates. RESULT & CONCLUSION: These findings emphasize the restricted use of cell phones and encourage the higher compliance with hygienic practices in hospitals to reduce the risk of nosocomial infections.

Molecular Characterization of Vancomycin, Mupirocin and Antiseptic Resistant Staphylococcus aureus Strains.

BACKGROUND: Staphylococcus aureus is a common cause of nosocomial infections leading to a broad spectrum of diseases. Increasing antibiotic resistance among S. aureus strains, particularly methicillin-resistant S. aureus (MRSA), is a serious concern. In addition, the emergence of antiseptics resistance in MRSA helps the organism to persist and spread in healthcare environments easily. The aim of this study was to determine the molecular characteristics of vancomycin, mupirocin, and antiseptic resistant S. aureus strains. MATERIALS AND METHODS: This cross-sectional study was performed on a total of 120 MRSA isolates collected from two major hospitals in Shiraz, Iran. Minimum inhibitory concentrations (MICs) of vancomycin and mupirocin were determined by E-test method according to CLSI and Eucast guidelines. Presence of resistance genes was investigated by PCR method. RESULTS: Antibacterial susceptibility tests for MRSA isolates showed that three isolates (2.5%) were vancomycin-intermediate S. aureus (VISA), seven isolates (5.8%) were vancomycin-resistant S. aureus (VRSA), and 15 isolates (12.5%) were high-level mupirocin-resistant (MuH). None of the isolates had vancomycin resistance gene (vanA), but the frequency of mupirocin resistance gene was significant, and 55 (45.8%) isolates carried the mupA gene. Moreover, norA, smr and qacA/B genes were detected in 110 (91.7%), 55 (45.8%) and 36 (30%) strains, respectively. CONCLUSION: This study showed the existence of VISA and VRSA strains in our region, and we also found a high frequency of mupirocin and biocide resistance genes among them.

Detection of Antimicrobial Susceptibility and Integrons Among Extended-spectrum ß-lactamase Producing Uropathogenic Escherichia coli Isolates in Southwestern Iran.

OBJECTIVES: Urinary tract infections (UTIs) are one of the most prevalent infectious diseases and can lead to a high rate of morbidity and mortality. The emergence of multiple-drug resistant strains, particularly extended-spectrum beta-lactamases (ESBLs) producing strains, has become a global healthcare concern. Our study sought to investigate the antimicrobial resistance pattern and presence of integrons and fimH determinants among uropathogenic Escherichia coli (UPEC) isolates obtained from hospitalized Iranian patients. METHODS: This cross-sectional study was performed on 121 E. coli isolates recovered from patients with clinical symptoms of UTIs, referred to Shiraz Nemazee Hospital, in 2016-17. The isolates were identified by standard microbiologic tests and confirmed by API 20E strip. Antimicrobial susceptibility testing was determined using the disk diffusion method. The presence of fimH and classes 1-3 integron encoding genes was determined using the polymerase chain reaction. RESULTS: Ampicillin (9.1%) and nalidixic acid (19.0%) showed the lowest level of antibiotic susceptibility. The highest level of susceptibility was toward imipenem (77.7%). The rate of ESBL-producing isolates was 42.1%. There was a significant association between production of ESBLs and higher antibiotic resistance in the tested isolates. Of the investigated virulence and resistance genes, fimH, intI1, and intI2 were positive in 98.3%, 59.5%, and 7.4% of isolates, respectively. CONCLUSIONS: The remarkable rate of ESBL-producing UPEC isolates accompanied with the presence of integrons suggest the necessity of restricted infection control policies to prevent further dissemination of resistant strains.

Molecular characteristics of multiple and extensive drug-resistant Acinetobacter baumannii isolates obtained from hospitalized patients in Southwestern Iran.

The emergence of multiple drug-resistant (MDR) Acinetobacter baumannii strains has become a global problem. This study aimed to evaluate the occurrence of antibiotic resistance and to investigate the presence of antibiotic resistance determinants among A. baumannii isolates obtained from hospitalized patients in Iran. This cross-sectional study was performed on 92 A. baumannii isolates in the years 2015-2016. Antimicrobial susceptibility testing was carried out by the disk diffusion method. The presence of antibiotic resistance determinants was detected by the PCR method. All the A. baumannii isolates were resistant to tested carbapenems, fluoroquinolones and sulfonamide agents, and susceptible to polymixins. Of the isolates 92.4% were extensive drug-resistant (XDR) and 7.6% were MDR. PCR screening for the presence of integron genes revealed that class 1 integron presented in 46.7% of isolates and class 2 in 18.5% isolates. Of the investigated antibiotic resistance genes, bla vim, bla imp, bla spm, sul1 and sul2 were positive in 75%, 12%, 12%, 47.8%, and 67.4% of isolates, respectively. The high prevalence of metallo-beta-lactamase (MBL) and sul genes in our results may indicate the importance of these genes in the dissemination of carbapenem- and sulfonamide-resistant A. baumannii isolates. Rational and restricted prescription of carbapenems may be an effective way to minimize the emergence and spread of MBL-harboring strains.

In vivo Antibacterial and Wound Healing Activities of Roman Chamomile (Chamaemelum nobile).

BACKGROUND: Today considerable number of drugs are produced from plants. Several plants with antibacterial and healing applications are used in medicine such as Roman chamomile (Chamaemelum nobile L.). Wound infection is one of the most prevalent infections among infectious diseases around the world. Due to appearance of drug resistance, researchers are now paying attention to medicinal plants. Therefore, this study was designed to investigate the antimicrobial and wound healing properties of C. nobile against Pseudomonas aeruginosa using in vivo conditions. METHODS: Ethanolic extract of C. nobile was provided using standard method. The 5% C. nobile ointment was prepared by dissolving lyophilized extract in eucerin. Forty five male rats were obtained from Ilam university. After anesthetization and wound creation, wounds were infected by P. aeruginosa. The rats were divided into three groups, group I was treated with C. nobile ointment, group II was treated with tetracycline ointment and the third group was treated with base gel as control group. RESULTS: Antibacterial and wound healing activities of C. nobile ointment were more than tetracycline ointment significantly. Our results indicated that extract of C. nobile had effective antibacterial activity and accelerated the progression of wound healing. CONCLUSION: Our study indicated that antibacterial and wound healing activities of C. nobile ointment were notable. C. nobile therapy in combination with antibiotics can also be useful because medicinal plants contents operate in synergy with antibiotics. These results revealed the value of plant extracts to control antibiotic resistant bacteria in wound infections.

WITHDRAWN: Molecular characterization of glycopeptide and macrolide resistance genes among multidrug-resistant Enterococcus faecalis strains.

This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.

High Incidence of Virulence Factors Among Clinical Enterococcus faecalis Isolates in Southwestern Iran.

BACKGROUND: Over the past two decades, enterococci have emerged as an important agent responsible for hospital acquired infection. Several virulence factors contribute to the adherence, colonization, evasion of the host immune response, and pathogenicity and severity of the infection. Enterococcus faecalis is the most common and virulent species causing infections in hospitalized patients. The aim of the present study was to examine the prevalence of genes encoding virulence factors and antimicrobial resistance patterns of E. faecalis strains isolated from hospitalized patients in Shiraz, south west of Iran. MATERIALS AND METHODS: A total of 51 E. faecalis isolates from the urine, blood, pleural fluid, peritoneal fluid, eye discharge, endotracheal tube (ETT) and transjugular intrahepatic portosystemic shunt (TIPS) specimens of patients were identified by phenotypic and genotypic methods. Antimicrobial sensitivity tests and detection of virulence factors were performed using standard methods. RESULTS: The efa and asa1 were the most frequently detected gene (100%) among the isolates, followed by esp (94.1%), ace (90.2%), gelE (80.4%), cylA (64.7%), and hyl (51%). More than half of the isolates (52.9%) were high level gentamicin resistant (HLGR). Vancomycin resistance was observed among 23 (45.1%) isolates. The lowest antimicrobial activity was related to erythromycin (3.9%), tetracycline (5.9%) and ciprofloxacin (9.8%). No isolate was found resistant to fosfomycin and linezolid. CONCLUSION: Our data indicated a high incidence of virulence factors among E. faecalis strains isolated from clinical samples. Colonization of drug resistant virulent isolates in hospital environment may lead to life threatening infection in hospitalized patients. Therefore, infection control procedures should be performed.

Emergence of SCCmec Type I Obtained From Clinical Samples in Shiraz Teaching Hospitals, South-West of Iran.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) continues to be a major cause of nosocomial infections. Methicillin resistance in S. aureus is caused by the acquisition of the mecA gene, located on a mobile genetic element called the staphylococcal cassette chromosome (SCC). OBJECTIVES: The aim of this study was to evaluate the presence of the predominant SCCmec type present among clinical isolates. MATERIALS AND METHODS: This cross-sectional study was performed on a total of 146 MRSA isolates obtained from clinical specimens between 2012 and 2013 from two major hospitals in Shiraz, Southwest of Iran. Antibiotic susceptibility profiles were determined by the disc diffusion method according to the guidelines of The Clinical and Laboratory Standards Institute. Bacterial DNA was extracted using the small-scale phenol-chloroform extraction method and was employed as polymerase chain reaction (PCR) templates for the assigned current SCCmec types. RESULTS: The assigned SCCmec types by PCR revealed the SCCmec type I as the predominant type with 86 (58.9%) samples, followed by the SCCmec type II with 29 (19.9%), type III with 16 (11.0%), and type IV with 12 (8.2%) samples, respectively. The SCCmec type I MRSA isolates were significantly recovered from blood (80%) and sputum (67.2%). The results of antibacterial susceptibility tests for the MRSA isolates showed that all of those carrying the SCCmec type I and II had significantly greater resistance rates to Gentamicin and Rifampin than the isolates containing the SCCmec type III. Also, a significant difference was detected for susceptibility to Co-trimoxazole between the SCCmec type I and II MRSA isolates and the SCCmec type III, which was more resistant. CONCLUSIONS: The frequency of the isolates containing type I in the current study can indicate an emergence of this SCCmec type in the studied medical centers.

First Outcome of MDR-TB among Co-Infected HIV/TB Patients from South-West Iran.

BACKGROUND: Tuberculosis (TB) is the leading cause of mortality among human immunodeficiency virus (HIV) patients and the majority of them occur in developing countries. The aims of the present study were to determine the frequency of HIV/TB co-infection and other probable associated factors. METHODS: This 10 year retrospective study was conducted on 824 HIV patients in the south-west of Iran. HIV infection was diagnosed by the enzyme linked immunosorbent assay and confirmed by Western blot. TB diagnosis was based on consistency of the clinical manifestations, chest X-ray, and microscopic examination. Drug susceptibility testing was done by the proportional method on Löwenstein-Jensen media. RESULTS: Of 824 HIV patients, 59 (7.2%) were identified as TB co-infected and the majority (86.4%) of them were male. Of the overall TB infected patients, 6 cases (10.2%) showed multidrug-resistant with the mean CD4+ lymphocyte count of 163±166 cells/mm(3). The main clinical forms of TB were pulmonary (73%). There was a significant (p<0.05) correlation between TB infection and CD4+ lymphocyte counts ≤200 cells/mm(3), gender, prison history, addiction history, and highly active anti-retroviral therapy. CONCLUSION: We reported novel information on frequency of HIV/TB co-infection and multidrug resistant-TB outcome among co-infected patients that could facilitate better management of such infections on a global scale.

Frequency of the toxic shock syndrome toxin-1 gene in methicillin-susceptible and -resistant Staphylococcus aureus isolates from teaching hospitals in Shiraz, Iran.

INTRODUCTION: Staphylococcus aureus produces a range of virulence factors such as toxic shock syndrome toxin-1. METHODS: In this cross-sectional study of 345 clinical S. aureus isolates, the presence of the tst gene was assessed by polymerase chain reaction (PCR). RESULTS: The study revealed 53/345 (15.4%) isolates were positive for the tst gene. The tst gene was present in 18.1% of methicillin-susceptible S. aureus (MSSA) isolates and 11.6% of methicillin-resistant S. aureus (MRSA) isolates (p = 0.136). CONCLUSIONS: These results reveal the remarkable risk of S. aureus infections in hospitals, regardless of methicillin-resistance status.