نشریه میکروب شناسی پزشکی ایران
سال هفدهم شماره 2 (فروردین و اردیبهشت 1402)

 In December 2019, human-to-human transmission of respiratory illness (pneumonia) with fever and sputum was discovered in the respiratory tract, called COVID-19. Serum amyloid A (SAA) is an acute-phase plasma protein that is considered to be diagnostically superior to CRP in pathological conditions such as viral diseases. Therefore, the study question in this review is whether SAA as an indicator is involved in the early diagnosis of COVID disease.

 To identify related studies, we systematically searched international databases, including PubMed, Scopus, Science Direct, Cochrane, Embase, Web of Science, and Google Scholar search engine, without restriction on time until June 2021. Also, the Reference list of relevant studies was reviewed separately to find all existing articles in this field. Summary standardized mean difference (SMD) was estimated using random effects meta-analysis.

A total of 394 potentially relevant articles were identified from the initial search. After removing the duplicates and reading the title, abstract and full-text review, six studies were entered into the meta-analysis. There was a significant difference between the means of SSA among patients with a severe form of the disease compared to non-sever groups (SMD=-0.91, 95% CI: 1.18-1.59, -0.23) and with the control group (SMD=4.68, 95% CI: 1.18, 8.18). The Beggs and egger test results indicated no evidence of publication bias in the reported SMD.

 The result of our work indicates that SAA might potentially be used for the early diagnosis of COVID disease, but more studies are needed.

During the last years, antimicrobial resistance has become one of the greatest challenges in clinical settings. Staphylococcus aureus and Enterococcus are important nosocomial pathogens worldwide. In different corners of the world, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) have been isolated from various sources including different foods of animal and plant origin; however, information about food-related vancomycin-resistant Staphylococcus aureus (VRSA) is limited. The current review describes the presence of MRSA, VRSA and VRE in different food samples of animal and plant origin in Iran. Databases including PubMed, ScienceDirect, Scopus, SID, and Google Scholar were searched and a total of 65 articles were retrieved (published between 2006 and September 2020) reporting antibiotic-resistant S. aureus and Enterococcus in food in Iran. The overall prevalence meta-analysis was calculated by using “meta prop program” in STATA statistical software. Finally, 42 studies were included in the present review. These reports indicated high rates of MRSA, VRSA and VRE strains in different types of raw and processed meat, raw milk, traditional cheese, restaurant, and hospital foods. The meta-analysis showed that the highest pooled ES of MRSA was for pastry products and the lowest pooled ES of MRSA was for miscellaneous foods. Thus, higher priority should be given to the development of effective surveillance systems which can track the appropriate use of wide-spectrum antibiotics and spread of antimicrobial-resistant organisms throughout food supply chains. Future research should assess the risk of antimicrobial resistance transmission to consumers following intake of MRSA, VRSA, and VRE-contaminated foodstuffs.

 The results from the analysis of COVID-19 literature by employing text-mining techniques are of particular importance for researchers, policymakers, and planners of medical sciences at the national and international levels, avoiding parallel research and waste of time and budget. The paper explore emerging topics and the trend of scientific words at the national and international levels in the subject area of COVID-19.

 This applied research was conducted by employing the text-mining and its related algorithms and classifying texts. The population consists of all COVID-19 articles indexed in PubMed Central® (PMC). The number of records retrieved was 160,862 items until June 10, 2021. Among these, 3143 national and 157,719 international COVID-19 articles. Python and its related libraries were applied. The most significant words were also identified and reported based on TF-IDF weighting. Emerging topics were identified according to the weighted average growth.

"COVID", "infect", and "cell" were among the most important words used in international COVID-19 articles. In addition, the most important words in the national COVID-19 articles were "patient", "SARS-Cov", and "COVID".

 Among the most important conclusions that can be inferred from the trend of word change used in the COVID-19 literature is that the most significant words in international literature differ significantly from those in national literature, as international research focuses on COVID-19 and the infections caused by it. In contrast, national research focuses on COVID-19 and patients. Another significant result is the annual word-changing national and international literature.

 Determination of HPV genotypes in cervical lesions is essential in screening programs and the impact of current HPV vaccines. Therefore, we investigated the frequency of various HPV genotypes among different grades of cervical lesions.

 In total, 101 biopsy samples of different grades of cervical lesions were collected. Extracted DNA was subjected to PCR amplification of beta-globin to assess sample integrity. Duplex Taq-Man Real-Time PCR was performed to identify HPV types 16 and 18. Nested PCR following sequencing was done on those samples with HPV16/18 negative results.

The mean age of participants was 43±1. Of 101 samples, 91 (90%) were infected with HPVs. In the LSIL group, HPV genotypes 16, 18, and 51; in the HSIL group, genotypes 6, 16, 18, 31, and 53; in the SCC group, genotypes 6, 16, 18, and 3; and in the AD group, HPV genotypes 16 and 18 were detected. Also, 49 (61%) samples had co-infection with HPV16 and HPV18.

 Our results showed that HPV 16 and 18 were the most prevalent genotypes among different grades of lesions. The presence of low-risk HPV types, including genotypes 6 and 53, might need more attention in HPV screening and prevention programs.

 Escherichia coli is the normal flora of the human and animal intestine that sometimes causes pathogenesis within the intestine and urinary tract. The current study investigates resistance genes in Escherichia coli isolated from the toilets at the Islamic Azad University of Mashhad, Iran, and to perform genome sequencing in tetracycline-resistant strains.

 This cross-sectional evaluation was carried out on 200 samples collected over three months. Samples were cultured and isolated using eosin methylene blue agar medium (EMB). E. coli Samples were identified and used to evaluate the resistance genes by polymerase chain reaction (PCR). The E. coli isolates were used for an Antibiogram test to identify resistant strains. For the statistical analysis of antibiotics pattern, SPSS-22 and the Kolmogorov-Smirnov test were used.

Out of 200 samples, 41 isolates were identified as E. coli with the highest resistance rate to cefotaxime (74.60%) and the highest sensitivity rate to gentamicin (58.74%). Among the 20 isolates, 30%, 20%, 25% carried blaTEM-1, blaOXA-10 and blaOXA-48 genes, respectively. Among 38 tetracycline-resistant isolates, three isolates (7.89%) had tetA gene, and two (5.26%) had the tetR gene.

 In this experiment, most of the isolates were identified as E. coli and were resistant to antibiotics. To control the spread of E. coli infectious disease and arbitrary use of antibiotics, it is recommended to conduct some educational programs and social activities with the aim of increasing health awareness.

 Conventional anti-cancer treatments, such as surgery, chemotherapy, radiation therapy, etc., are linked to antimicrobial resistance (AMR) and have negative effects on healthy tissues. The flow cytometry technique was used in this study to evaluate the effectiveness of a modified anti-cancer peptide in treating the AGS gastric cancer cell line.

 This study used bioinformatics software to determine the EntA-PynR-Lac gene sequence. The engineered E. coli BL21 bacterium was used to express recombinant proteins derived from the synthesized fusion gene cloned into the pET22b expression vector. A recombinant protein was designed, and its three-dimensional structure and stability were evaluated. Using Western blotting and nickel column chromatography, the recombinant protein was confirmed and purified. In addition, the MTT technique was used to determine the cell lethality of various concentrations of the recombinant protein in AGS cells. Flow cytometry was used to determine the level of apoptosis in AGS cells treated with the desired protein concentrations.

According to the results of the MTT test, the 80µg/mL concentration of recombinant protein showed significant cytotoxic effects on the AGS cell line. Furthermore, using flow cytometry, it was found that cancer cells treated with this concentration of recombinant protein exhibited higher rates of total apoptosis than untreated cancer cells.

 Inhibition of proliferation and growth of gastric cancer cells by this recombinant protein has been shown to be effective. The anti-apoptotic characteristics of the fusion protein make it useful for both therapeutic and preventative purposes when treating cancer cells.

 Pseudomonas aeruginosa exotoxins are responsible for pathogenicity and antibiotic resistant. The aim of this study was to investigate the effects of the Ammi. visnaga (A. visnaga) extract on the P. aeruginosa exotoxin A and S genes expression.

 Antibacterial effects of the A. visnaga ethanolic extract were performed using the micro dilution technique in sequential dilutions. Then, the Real-Time- RT PCR method was used to analyze the level of expression of the exotoxin A and S genes of the bacterium. Real-Time PCR data were analyzed using Graph Pad Software Inc. San Diego (GRAPHPAD PRISM 6CA, USA).

Results showed that, the expression of Exotoxin A and S genes was significantly (P <0.001) reduced in comparing the expression level of the reference gene and control. It had a significant effect on the inhibition of bacterial growth at different concentrations but the lowest inhibitory concentration was observed at 3.125 µg/well.

 Accordingly, the extract of A. visnaga can decrease the expression of the Exotoxin A and S genes of P. aeruginosa and consequently it may decrease the pathogenicity of bacteria. These phenomena (exoA and exoS expression inhibition) may involve reducing the antibiotic resistance of P. aeruginosa.

 One of the main reasons for the ongoing pandemic is the substitutions in the Receptor binding domain (RBD), which is involved in binding to the ACE2 receptor.

 Oro-nasopharyngeal swabs were collected from 41 confirmed patients between September 2020 and May 2021 to analyze the mutations of SARS-CoV-2 RBD in Khuzestan Province. Bi-Directional sequencing was used, and Mutation analysis was performed using multiple Bioinformatics tools.

A total of 35 Single nucleotide polymorphisms (SNPs) were observed in 26 samples. Nonsynonymous substitutions occurred only in the receptor-binding motif (RBM), which accounted for 97% of the detected mutations. 37.14% of observed mutations were N501Y. L452R, T478K, and S477N accounted for 22.86%, 20%, and 11.43% of detected substitutions, respectively. Subsequently, the S477G and Y449N were identified in only one sample. The only synonymous substitution of this study was observed in C432 of one sample. It was found that December 2020 and May 2021 could be the probable prevalence times of the Alpha and Delta variants in Khuzestan, respectively. Also, in a December 2020 sample, a mutation was detected that was only seen in Epsilon among the Variants of interest and Variants of concern.

 Our study showed the existence of some Omicron-related mutations before the emergence of this variant in Khuzestan Province, Iran. In addition, it strengthened the possibility of unconfirmed variants, such as Epsilon entering Iran. It also provided a reference for studies that need to be aware of the circulating variants in Iran.

 The novel coronavirus 2019 can lead to a vast range of respiratory complications, from mild to severe, driving to acute respiratory distress syndrome (ARDS). Common symptoms of COVID-19 include fever, fatigue, and dry cough, which can lead to complications, such as gastrointestinal disorders, and liver, cardiac, and renal dysfunctions. Alteration in the hematological markers is one of the COVID-19 diseases evaluated by our study.

 In this study, hematological markers, including the levels of ESR, BS, Hb, HCT, MCV, MCH, MCHC, platelet, WBC, RBC, neutrophil, and lymphocyte, have been assessed and compared in both case and control groups. Furthermore, we assessed the associations between hematological parameters, clinical manifestations, and underlying medical conditions.

Our data showed that RBC, HCT, and ESR were significantly associated with the novel coronavirus 2019 infection according to the disease progression. ESR (P= 0.022), Hb (P= 0.032), and BS (P= 0.01) levels in male people infected by SARS-CoV-2 proved to have a significant relationship with the control group. Moreover, BS, Hb, HCT, ESR, and neutrophil showed significant variations in diabetic individuals suffering from SARS-CoV-2 infection.

 The dropping of the hematological markers in COVID-19 is linked with a noticeably increased mortality rate, while high neutrophil and BS levels are related to aggravation of the disease. Monitoring the hematological markers can contribute significantly to selecting the proper treatment and hamper of disease worsening.

 Infection with the hepatitis C virus (HCV) is an endemic public health problem with long-term consequences, especially in Egypt. Egypt has one of the highest incidence rates of HCV worldwide. The current cross-sectional study aims to determine how prevalent occult HCV infection is and how it affects the individual's immune response.

 The studied adult patients the study had chronic HCV infection and underwent a combination of sofosbuvir 400 mg plus daclatasvir 60 mg once daily ribavirin regimen for 12 weeks from March to September 2019. Quantitative real-time PCR was used to detect HCV-RNA in the plasma. In addition, Cytometric Bead Array (CBA) technique was used to assess cytokines levels.

31 participants from Misr University for Science and Technology University hospitals outpatient clinics were included in the study. The median levels of cytokines of the included patients were as follow: the median IL-6 was 6.56 (5.7- 7.9) pg./mL, and 19% of the patients had higher serum IL-6 levels. None of the patients had abnormal serum levels 28b. in addition, the median serum NF-κB was 232 (18.7- 609.89), and 29% had high serum NF-κB levels. Six (19.4%) patients had positive occult HCV infection. Patients with occult HCV infection exhibited significantly higher values of serum IL-6 (P<0.001), NF-κB (P<0.001), serum AST (P<0.001), ALT (P<0.001), albumin (P<0.001), and total bilirubin (P<0.001).

 We support the evidence about the significant association between occult HCV infection and impaired immunological response in patients who achieved sustained viral response (SVR) following direct-acting antivirals (DAA) regimens.

 Gram-negative pathogens are considered the common cause of wound infections associated with increased mortality and morbidity rates. Antibiotics combination has been used to overcome this problem. In this study, we identify Gram-negative pathogens found in wound infections and assess the in-vitro efficacy of a combination of amikacin and imipenem against the resistant isolated pathogens.

 One hundered fifty gram-negative bacteria were collected from two hundered patients suffering from different wound infections. Patients attended Minia University Hospitals,Egypt at period from January 2019- January 2020 and they were  followed up periodically as a routine work in the hospitals. Swabs streaked on various media as Nutrient agar, MacConkey agar, Eosin methylene blue agar and cetrimide agar. The antimicrobial susceptibility of the identified pathogens was tested using the Kirby-Bauer method. Conventional PCR was used to detect the prevalence of bla-IMP and AAC (6’)-Ib genes. The effect of the tested combination was assessed by checkerboard technique and time-killing assay.

Escherichia coli 38.6% was the most common isolated pathogen, followed by Proteus spp 30%, P. aeruginosa 21.4%, Klebsiella spp. 5.7%, and Acinetobacter baumannii 4.3%. The isolates were completely resistant to Ampicillin/sulbactam, Amoxicillin/clavulanic, Cephalothin, Cefadroxil, Ciprofloxacin, Ceftazidime and Ofloxacin. Bla-IMP was detected in all Klebsiella spp., E. coli (85.2%), A. baumannii (66.7%), Proteus spp. (38.1%) and P. aeruginosa (33.35%). aac(6’)-Ib was detected among E. coli, P. aeruginosa and Proteus spp. The Checkerboard test showed a significant decrease in bacterial count in the presence of combination indicating a synergistic effect with FICIs ≤0.5. Time-kill assay showed a significant decrease in the bacterial count after 12h.

 The studied combinations of antibiotics showed synergistic effects against the tested Gram-negative bacteria which can help in the control and treatment of serious wound infections.

 The increasing demand for the discovery of next-generation antimicrobials necessitates the use of plant extracts as alternatives. This study investigates the antibacterial efficacy of extracted cinnamon essential oil (CEO) and commercial cinnamaldehyde (CN) against foodborne pathogens.

 Kirby-Bauer disc diffusion method was used to screen the antimicrobial potency of CEO and CN. MIC and MBC were determined by the broth microdilution method. Kinetic destruction pattern was studied by time killing assay. CEO and CN mediated inactivation dynamics of S. typhimurium (ALM40) and L. monocytogenes were studied on the ground chicken meat model.

Both CEO and CN showed remarkable antimicrobial efficacy against the test strains, with highest and lowest efficacy against V. metschnikovii and E. coli, respectively. The agents inhibited gram-positive and negative bacteria equally. CN showed higher efficacy than CEO although the results were very close. MIC of CEO and CN ranged from 0.625%-5% (v/v) and 0.078%-0.3125% (v/v), respectively. Heat treatment and pH alteration did not hamper the antibacterial potency of CEO. CEO and CN mediated destruction kinetics were faster in L. monocytogenes than S. typhimurium (ALM 40). Inactivation dynamics study showed CEO and CN to have slightly dose-dependent antimicrobial effects. Besides, storage conditions and time did not reduce the antimicrobial potency. The significant microbial reduction was observed in both CEO and CN treated meat samples than untreated controls. Notably, a complete reduction of viable count in meat model was observed in selective medium just after 24hrs storage.

 Both CEO and CN showed promising antimicrobial effects to be used in combating foodborne pathogens.

 Tocilizumab is a monoclonal antibody against the Interleukin-6 (IL6) receptor, but its effect on improving the clinical condition of coronavirus disease of 2019 (COVID-19) patients is debated. Accordingly, this study investigated the impact of Tocilizumab as an alternative treatment on the outcomes of COVID-19 patients.

 In this retrospective case-control study, 300 COVID-19 patients in Afzalipour Hospital in Kerman, Iran, from November 2021 to January 2022 diagnosed by Real Time-PCR test with severe pneumonia were classified into two groups: 150 patients in the control group, treated with standard treatment, and 150 patients in the case group, that treated with intravenous Tocilizumab in addition to those treatments. Prognostic factors such as the hospitalization period, need for mechanical ventilation, and the patient's discharge condition were investigated.

Effect of Tocilizumab on outcomes of COVID-19 patients, like demanding mechanical ventilation, and length of hospitalization in the case group, despite the presence of poor biological symptoms such as severe lymphopenia in admission, show a significant difference in comparison to the control group. Tocilizumab does not affect the patient's discharge condition and the mortality rate.

 The results of this study showed that Tocilizumab, despite the lack of an apparent effect on the outcome of the COVID-19 disease (recovery or death), reduced length of hospitalization and the necessity for mechanical ventilation and can be used as an alternative therapy with other treatments.

 MRSA, or methicillin-resistant Staphylococcus aureus, has arisen as a nosocomial and community-acquired infection throughout the world. MRSA identification in the laboratory is difficult for a variety of reasons. The aim of this study was to investigate several phenotypic methods for the detection of MRSA compared with the PCR-based method as the gold standard.

 A total of 220 clinical isolates of S. aureus were recovered from diverse clinical specimens between August 1, 2019 and June 30, 2020 at Milad Hospital in Tehran, Iran. Cefoxitin discs, CHROMagar™ MRSA medium, and identification of the mecA gene by Polymerase Chain Reaction (PCR) as the gold standard method were used to assess methicillin resistance.

PCR testing revealed that 105 (47.72%) of 220 S. aureus isolates were positive for the mecA gene. The results of the Cefoxitin disc diffusion method showed that it has similar sensitivity and specificity to PCR method. The sensitivity and specificity of CHROMagar™ MRSA medium were both 100%. The Cefoxitin disc diffusion method had the same sensitivity and specificity as the PCR method for detecting the mecA gene. For MRSA detection, the Cefoxitin disc diffusion method can be employed as an alternative to PCR.

 Since the incidence of various infections caused by Staphylococcus aureus increases, the use of effective antibiotics such as clindamycin has been growing to treat the systemic and local infections caused by such organisms. Antibiotic-resistant species are emerging and spreading in today's communities due to misuse of antibiotics and incomplete treatment, turning into a serious challenge for the health care system of countries, even in the advanced ones. Therefore, this study aims to investigate the prevalence of clindamycin-resistant S. aureus induced by macrolide resistance.

 In this cross-sectional descriptive study, 117 S. aureus isolates were collected from clinical samples of patients referred to Beâsat Hospital, Aja University of Medical Science, in Tehran, in Jan. 2019 to Jan. 2021, Tehran, Iran and were approved after diagnostic, microbiological, biochemical tests. Then, the data of antibiogram test were collected.

 The results showed that 47% and 43% of the isolated samples were resistant to erythromycin and clindamycin, respectively. The prevalence of isolates with erythromycin resistance and induction resistance to clindamycin was approximately 38% and total induction resistance to clindamycin was 12%. The results indicate that antibiogram tests are required to identify induced resistance to clindamycin and to inform physicians about how to prescribe antibiotics in the treatment of infections caused by S. aureus.

 In Indonesia, diphtheria cases caused by Corynebacterium diphtheriae are still occurring. One of the causes is probably the diphtheria toxin repressor (dtxR) gene, which influences toxin expression. In this study, the gene was characterized to determine the mutations that affect the DtxR protein.

 The dtxR genes of 10 C. diphtheria strains isolated in Jakarta were amplified by conventional PCR. The PCR products were directed to DNA sequencing by using overlapping primers.

No mutations showed amino acid changes. We propose that the DtxR protein is conserved among bacterial strains isolated from Jakarta.

For the last few years, antibiotic resistance has become one of the major concerns within medical society. On one hand, pathogens have mostly acquired resistance against the major conventional antibiotics used in the treatment of microbial infections. These included even first-line antibiotics, which are critical in the treatment of severe infections. This catastrophic situation has occurred due to the extensively irresponsible use of antibiotics in humans and veterinary medicines, agriculture, aquaculture and animal breeding. On the other hand, the long absence of novel antibiotic introduction to the market by the pharmaceutical industry has exacerbated the situation. In fact, industrial giants are not interested in, or at least have lost their fascination with, the development of novel formulations. One of the greatest reasons that pharmaceutical industries are not fascinated by antimicrobial development is that the process is a greatly expensive wander since the development of novel antimicrobial drugs costs an estimated $1.5 billion [1] while incomes from the marketing of the antimicrobial agent include nearly $46 million annually. As far as it is known, very few novel antibiotics have been commercialized by the pharmaceutical industries within the last three decades, mostly semi or fully synthetic ones, while the necessity of these biochemicals is urgently felt. As a response to this failure, medical researchers have shifted to other antimicrobial alternatives, including bacteriophages, short peptides, bacteriocins and herbals. However, the potential rapid effectiveness of conventional antibiotics may force researchers to rethink further investigations of microbial antibiotics. But (as always there must be a big “BUT”) why?

Pandemic – this word we learned in our community medicine and public health chapters during medical school. Till 2019 November, many people have even not heard about the pandemic but after the SARS CoV-2 pandemic occurred and the whole world has now faced it. SARS CoV-2 (COVID-19) was first notified in Wuhan city of China and it spread all over the world very rapidly. In India, a lockdown was declared all over the country after a short time when cases started to rise. COVID-19 spreads globally and affects more than 200 countries in the world.  Previously the world faced a lot of pandemics but this was a unique pandemic of all time. It not only affected the health system but also the world economy, education, society, and much more. It reached first place in the cause of human death in this century. It stopped the world for some time and still, the world has not recovered from the loss due to the COVID-19 pandemic.