نشریه میکروب شناسی پزشکی ایران
سال هفدهم شماره 1 (بهمن و اسفند 1401)

The emergence of drug resistance in Mycobacterium tuberculosis is a major challenge in tuberculosis treatment and control. In addition, multidrug resistance (MDR) and, more broadly, extensive drug resistance (XDR) have hampered treatment with common antibiotics. Thus, an herbal medicine containing antimicrobial capability can be a good alternative to antituberculosis drugs. In this study, we reviewed the effect of folk herbs in Iran as anti-Mycobacterium tuberculosis drugs. In this systematic analysis, keywords including medicinal plants, M. Tuberculosis infection, Tuberculosis disease, MTB, essential oils, and extracts were searched in Science Direct, Scopus, PubMed, Ovid, Cochrane, Scientific Information Database (SID), Iran Medex, Iran Doc, Magiran, and Google scholar where articles published from 2000 to 2020 were considered. The results indicated that Iranian native herbs such as Peganum harmala, Humulus lupulus, Capparis spinosa, Thymus vulgaris, Pulicaria gnaphalodes, Perovskia abrotanoides, Peganum harmala, Punica granatum, Digitalis sp., Citrus lemon, Rosa canina, Berberis vulgaris, Aloe vera, Mentha spp., Hypericum perforatum, Humulus lupulus, Trachyspermum copticum, Pelargonium graveolens, Levisticum officinale, and Dracocephalum kotschyi were all effective antibacterial against mycobacterial infection within 0.5 ug to 200 mg. Thymus vulgaris was shown to be the most effective than other antibacterial agents such as Streptomycin, Cycloserin Isoniazid, and Ethambutol (0.5-40 μg/mL). Herbal remedies may be an effective therapeutic option for antibiotic-resistant tuberculosis. Potential adverse effects and antibacterial properties, along with possible synergistic interactions with other plants and drugs, require further studies to clarify.

 This umbrella review presents comprehensive data on the evidence of the association between cerebral venous thrombosis (CVT) and COVID-19 vaccinations.

 We searched related databases to access issue-related systematic reviews both with meta‐analyses and without it that studied the connotation between COVID 19 vaccination and CVT in any languages on March 1, 2022. Two reviewers independently extracted the data using the JBI Form for Data Extraction in Systematic Reviews and Research Syntheses.

The primary search resulted in 886 titles, and finally, 48 full texts were selected, and of these, 12 qualitative systematic reviews or quantitative meta-analyses were eligible for the umbrella review. No study was excluded based on using the JBI checklist for critical appraisal. The results revealed that cerebral venous sinus thrombosis (CVST) from the COVID-19 vaccine could occur in any age group, in both sexes, and with all types of vaccine. However, young females were the predominantly affected cases. Although more common in adenovirus vaccine types, vaccines consisting of mRNA are not free from side effects. Headache was the most typical clinical symptom. Thrombocytopenia, PF4 IgG Assay, and d-Dimer evaluation were positive in many reported studies.

 The results showed that CVST from the COVID-19 vaccine can happen without age limitation for both sexes and all vaccine types. Although CVST is a life-threatening condition, early diagnosis and, most importantly, its management can be life-saving for patients. The overall balance of risk and benefit in favor of vaccination is positive in all of the included studies in the current umbrella review.

 Enteric fever causes serious health problem and brings about significant death and ill health globally because of the absence of decisive diagnostic techniques. The ability of frequently used assay to authenticate the absence of enteric fever is debatable. This research study aimed to appraise the specificity and sensitivity of typhoid diagnosis for establishing highly accurate diagnostic techniques and to recommend appropriate standardized composite reference.

 Published articles indexed in Google scholar, MEDLINE and PubMed were reviewed for hospital-based findings. Independent sample t-test was utilized to ascertain differences in mean percentage specificity and sensitivity.

From the 432 articles identified in this study, 53 were used in the analysis. The result outcome reveals that, Widal techniques show moderate accuracy with percentage average specificity (55%), sensitivity (53.8%), positive predictive value of 57.8% and negative predictive value of 55.6% in comparison to 28%, 29.4%,  29.5%, and 27.8% of Typhidot  respectively. 34.4% of the studies used prospective study design. The results revealed a statistically significant association in the sensitivity between Typhidot and Widal at p<0.05. The finding also presented emerging enteric fever diagnostic tests such as protein biomarkers, metabolite biomarkers, nucleic acid biomarkers and genomics. Antigens that were regularly assayed are lipopolysaccharides (LPS) and hemolysin E (HlyE).  Highest specificity of 96% and sensitivity of 96% was obtained in anti-LPS IgA.

 Based on the result outcome, it is recommended that, blood culture and Widal techniques having sensitivity of 60% and 53.8% respectively be used as a harmonized composite reference standard for enteric fever diagnosis to improve prevalence appraisals.

 Nosocomial infections caused by antibiotic-resistant bacteria and their rapid spread threaten public health. This study aimed to determine the frequency of genes encoding Extended-Spectrum Beta-Lactamase (ESBL) in gram-negative bacteria in Kermanshah city, west of Iran.

 Identification and antibiotic susceptibility pattern of 165 isolates were performed by biochemical and disk diffusion methods, respectively. Screening and confirming the presence of ESBL genes were performed according to the double disk combination test (DDCT) method. The presence of genes encoding ESBL in each isolate was identified by Polymerase Chain Reaction (PCR) method.

Out of 165 isolates, 83 strains were resistant to all antibiotics. The lowest frequency of resistance was observed for Gentamicin, while the highest frequency was observed for Cefotaxime and Cefazolin. Among all strains, 50 (30.30 %) and 80 (48.48%) isolates were phenotypically and genotypically ESBL-positive, respectively. The most prevalent genes encoding ESBL were SHVOS and SHV-1, with a frequency of 20.61 % and 21.82 %, respectively.

 The frequency of producing ESBL bacteria and the prevalence of blaSHV and blaCTX-M genes in our studied Klebsiella pneumoniae and Escherichia coli isolates were high. However, unlike some previous reports from Kermanshah, the prevalence of ESBL-encoding genes in Pseudomonas aeruginosa was low, and the blaVEB gene was not found.

 Shigella is the causative agent of shigellosis in the world. Antibiotic treatment is important in this bacterium, but recently Shigella species containing the aph, aadE, aacA-aphD genes have shown resistance to aminoglycosides and have hampered the treatment process. Therefore, the aim of this study is a molecular investigation of Shigella dysenteriae aminoglycoside resistance genes isolated from children and its expression under the influence of curcumin nanoparticles.

 In this study, 60 diarrhea samples collected from Tehran hospitals in 2022 were used. Shigella dysenteriae isolates were identified by biochemical and microbial tests. The presence of aadE, aacA-aphD, and aph genes was confirmed by the Multiplex-PCR method. Then, real-time PCR was used to investigate the expression of aadE gene in the presence of curcumin nanoparticles.

From the 60 diarrhea samples examined, 12 strains (40%) of Shigella dysentery were identified by biochemical tests. Ten isolates (83.3%) carried the aadE gene, six isolates carried the aacA_aphD gene, and one isolate carried the aph gene. The Sub MIC value of curcumin nanoparticles on aadE gene expression is 128 µg/mL, and the Fold Change for this gene is -1.03.

 Considering the presence of aadE gene in 83.3% of Shigella dysenteriae isolates, it is important to investigate the presence of this gene in providing a suitable treatment model for patients infected with this bacterium, as well as the expression of aadE gene as the most common one. The expression of the aminoglycoside resistance gene was reduced to a relative amount in the presence of curcumin nanoparticles. Therefore, curcumin nanoparticles can be a suitable alternative for the treatment of strains carrying aminoglycoside resistance genes.

 Gastric cancer (GC) is a major health problem worldwide. Several studies have shown the virus's role in cancer pathogenesis. Therefore, the aim of this study was to evaluate the presence of human papillomavirus (HPV) in GC by immunohistochemistry (IHC) and polymerase chain reaction (PCR) in hospitals in the East Azerbaijan province, Iran.

 In this descriptive cross-sectional study, 100 tissue samples of paraffin-embedded, including GC (50 samples), benign gastric hyperplasia (25 samples), and a control group (25 samples) were collected from the archives of laboratories in East Azerbaijan province from April to October 2021. The IHC and PCR were used to detect the HPV virus. SPSS software version 22 and t-test and Chi-Square statistical tests were used for data analysis.

8 out of 50 cancer samples were HPV positive by IHC and PCR. HPV-positive samples had a mean age of 62.87 ± 9.67 and a higher Gleason score. Men had the highest number of HPV-positive samples compared to women (5 samples vs. 3 samples). However, no viral genomes were observed in non-malignant and control samples. There was a significant relationship between HPV infection and GC (P=0.03).

 According to the present study's findings, the presence of HPV infection in GC plays an important role in the development of GC in the hospitals of East Azerbaijan province. Also, the results showed that PCR and IHC are both more sensitive and reliable in detecting HPV because the results of both IHC and PCR were the same. Hence IHC method can be used as an alternative to the PCR method to detect HPV oncoproteins.

 Several methods have been employed to identify Coxiella burnetii isolates based on the specific Coxiella burnetii QpH1 plasmid to distinguish the acute form from the chronic form of Q fever disease in humans and animals owing to the presence of unique gene sequences in this plasmid. Therefore, the present study aimed to investigate the panel of nucleic acid fragments resulting from the enzymatic cleavage in the QpH1 plasmid isolated from cow and buffalo milk by nested polymerase chain reaction (Nested-PCR).

 A total of 86 isolates of Coxiella burnetii QpH1 plasmid, which were confirmed by the Nested-PCR method in 2018, were used to determine the RFLP panel of the QpH1 plasmid. Plasmids were first extracted with the kit and were then affected by the Hph1 restriction enzyme. Additionally, 4 nucleic acid samples were sent to Pishgam Company for sequencing with the IS1111 gene primer.

Based on the results of the PCR-RFLP test, all plasmid samples showed a similar two-fragment pattern under the influence of Hph1. The results of the nucleic acid sequencing of all 4 samples indicated that they had a Coxiella burnetii type (Nine Mile RSA493 strain).

 RFLP patterns exhibited no difference on the Coxiella burnetii QpH1 plasmid isolated from cow and buffalo milk. Hence, all isolates were genetically identical, and the infection in animals could originate from one Coxiella burnetii strain (Nine Mile RSA493 strain).

 The ability to form biofilms is an effective way for Acinetobacter baumannii to survive in stressful conditions. The aim of this study was to investigate the prevalence, antimicrobial susceptibility, and distribution of virulence genes involved in biofilm formation in multidrug-resistant Acinetobacter baumannii isolated from Shahrekord medical centers in Chaharmahal and Bakhtiari Province, Iran.

 In this study, 150 samples from Shahrekord medical centers in Chaharmahal and Bakhtiari Province were isolated and identified using biochemical tests. Then, the antimicrobial susceptibility of A. baumannii isolates was determined using these antibiotics, Ampicillin/Sulbactam, Doxycycline, Ceftazidime, Ciprofloxacin, Erythromycin, Trimethoprim/ Sulfamethoxazole, Gentamicin, Colistin, Imipenem, and Amikacin. Finally, the rate of biofilm formation and the frequency of virulence genes associated with biofilm formation (bap, ompA, csuA, csuE, epsA, bfmS, bfmR, pgaA, pgaD, and surA) were evaluated.

Out of 150 samples, 90 were identified as A. baumannii. The results of antimicrobial susceptibility testing showed that there was the highest resistance rate to Ciprofloxacin and Imipenem (100%), followed by Ceftazidime (90%) and Ampicillin/ Sulbactam (77.77%). The highest frequency of virulence genes associated with biofilm formation was related to bap (100%), ompA (100%), and pgaA/ pgaD (98%).

 Biofilm formation significantly reduces susceptibility to antibiotic agents. Evaluation of biofilm formation showed that all isolates could produce biofilm; hence, they are very important for public health. Therefore, it is necessary to determine antibiotic susceptibility, biofilm formation capacity and the frequency of biofilm-related virulence genes in the clinical setting.

 Otitis media (OM) or middle ear inflammation is an inflammatory disease caused by a bacterial infection such as Pseudomonas aeruginosa (P. aeruginosa), provided with genetic virulence factors. This study aims to detect nan1 and tox A genes of P. aeruginosa isolated from chronic OM patients.

 One hundred thirty OM patients were recruited from Al-Sader medical city and Al-Hakim general hospital in Najaf province from September to January 2021 to collect ear swaps. The Primary identification depends on Gram stain and biochemical tests. We also used Vitek 2 system to make another identification and examine resistance to antibiotics. A polymerase chain reaction (PCR) was used to amplify the required genes. Furthermore, gel electrophoresis was performed to show the amplified genes.

The results have revealed that 115 samples (88.46%) give a positive result, while 15 samples (11.54%) are negative for culture bacteria. Only 49 (42.76 %) of the 115 clinical specimens showed positive tests for P. aeruginosa. However, the toxA gene is found in 67.3% of P. aeruginosa isolates, while the nan1 gene is found in 38.77 % of the isolates.

 Our findings suggest that P. aeruginosa is one of the most common causes of OM infection in Iraqi patients. Most bacterial isolates show the presence of nan1 and tox A genes, with a high prevalence of tox A than nan1. The presence of these genes is one of the virulence factors and probably partly explains the resistance to antibiotics.

 Carbapenem-resistant Acinetobacter baumannii (CRAb) has ability to develop and acquire resistance makes it one of the most critical nosocomial pathogens globally. Whole genome sequemcing (WGS) technology was employed to map genes associated with antimicrobial resistance (AMR),virulene factors and to identify multilocus sequence types (MLST). In order to understand the resistance mechanism for A. baumannii species, this study set out to establish the genetic makeup of the species.

 Whole-genome sequencing (WGS) of A.b4, A.b49 and A.b75 was performed using Illumina MiSeq and the genomes were assembled with SPAdes. ARG-ANNOT, CARD-RGI, VFDB, PHAST, PlasmidFinder were used to analyse all genomes.

Genome analysis revealed that Ab4 belongs to ST944, represented singletons that could not be attributed to any, A.b49 belongs to ST1104, represented unique ST.While A.b75 belongs to ST195 which represented known international clones of high risk .Molecular characterisation showed the presence 23 antibiotic resistance genes in all straines of A. baumannii. 12 of them are shared by all 3 strains and 11 are common between A. baumannii 4(ST/944), 49 (ST/1104) and 75(ST/195). The common drug-resistance genes shared by all 3 strains include bla OXA-72 (resistance to carbapenems), ade genes, RND (adeFJK, adeLN & adeR), and SMR   (abeS) encoding for efflux pumps.

 We present WGS analysis of three A. baumannii strains belonging to three different STs. The presence of strains harboring acquired AMR genes makes them more dangerous. Acquired resistance genes and chromosomal gene mutation are successful routes for disseminating AMR determinants among A. baumannii. Identification of chromosomal and plasmid-encoded AMR in the genome of A. baumannii may help understand the mechanism behind the genetic mobilization and spread of AMR genes.

 Ventilator associated Tracheobronchitis (VAT) is a common nosocomial respiratory tract infection which develops in intubated critically ill patients. Their etiology changes with time, hospital and ICU setting and duration of hospital stay. This study was aimed at detecting the microbiological etiology of VAT, reporting the antimicrobial susceptibility pattern and impact on outcome.

 This observational study was conducted for 12 months in the Microbiology Department and intensive care unit of a tertiary care center. A total of 39 endotracheal secretions from suspected cases of VAT were subjected to routine bacterial culture and antimicrobial susceptibility testing. The outcome of the patients with VAT was measured in terms of duration of ventilation, hospital stay and mortality.

VAT was found to occur most commonly between 60-69 years of age and among the male population (79%). A total of 47 isolates were recovered from 39 samples. Monomicrobial growth was obtained from 34 (87.18%) of endotracheal samples, while 5 (12.82%) showed polymicrobial growth of at least two pathogens. The predominant organism isolated was Acinetobacter baumannii (27.65%), followed by Klebsiella pneumoniae (23.40%) and Pseudomonas aeruginosa (21.27%) and all were found to be multidrug resistant. The mean duration of ventilation, ICU Stay and hospital stay for VAT was 10.87 days, 12.20 and 16.27 respectively.

 It is imperative to timely diagnose and monitor cases of VAT as this would help in deriving an effective early therapeutic intervention and in implementing timely preventive strategies that could help reduce progression of VAT to Ventilator associated pneumonia (VAP).

 Leptospirosis is a zoonotic bacterial disease caused by the genus Leptospira. This disease is observed in human, domestic and wild mammals. Abortion is known as the most important side effect of Leptospira in infected sheep. Molecular tests such as PCR is considered for the early detection of disease which cannot trigger production of species-specific antibodies. This study was designed to detect Leptospira spp. as a cause of abortion in sheep using PCR in Lorestan province, Iran.

 In the current study a total of 150 samples of vaginal swabs were randomly collected from a sheep that had an abortion in some areas of Lorestan province, Iran. The collected samples were accurately investigated to trace DNA of Leptosoira spp. using specific primers.

Based on results of Leptosoira spp. lipL32 gene, 2 positive samples (1.3%) were identified. Hence, it was concluded that there is nosignification relation between abortion rate and Leptospirosis in Lorestan province, Iran. It must be mentioned that due to the zoonotic nature of this bacterium, rapid diagnosis of this disease in livestock can extremely decrease outbreak of this disease in humans.

 About one billion people have infected with the influenza A virus each year. The continued spread of SARS-CoV-2 especially in the winter season may increase the co-infection of SARS-CoV-2 with other respiratory viruses, which may worsen the severity of the disease and increase mortality. In respiratory infections, primary identification of the underlying source of infection is necessitated to find appropriate treatment and to improve individual patient management. Therefore, it is essential to accurately and immediately diagnose these two diseases. This study aimed to assess the frequency of influenza A, influenza B, and COVID-19 among individuals suspected of having a respiratory infection.

 In this study, 861 patients presenting from 19 November 2021 to 18 January 2022 in Kavosh medical laboratory (Golestan, Gorgan, Iran) with suspected viral respiratory tract infection who underwent RT-PCR testing for SARS-CoV-2/influenza were included. Data analysis was performed using appropriate descriptive statistics.

A total of 184 patients were confirmed with COVID-19/influenza. 90 patients with COVID-19 (48.9%) and 94 patients (51.1%) with influenza (92 with influenza A and 2 with influenza B) were collected in the present study. The influenza/COVID-19 ratio was 1/0.95. Two cases of co-infection with COVID-19/influenza were observed. During the influenza season, the influenza/COVID-19 ratio in patients with suspected respiratory infection was 1/0.95. Patients with influenza were significantly younger than patients with COVID-19 and the proportion of males and females was not meaningfully different in the COVID-19 and influenza patients.

 Malaria is considered one of the most serious life-threatening diseases in Yazd, a central province of Iran, which hosts both domestic and foreign immigrants. This study aimed to investigate the trend of Malaria in Yazd during 2011-2020.

 In this descriptive retrospective study, all episodes of the disease (imported malaria) recorded at Yazd health center in Iran were carefully evaluated and reported. After preparing the peripheral blood smear and fixation with methanol, it was stained with Giemsa and examined with a light microscope by a skilled technician.

Totally, 95 confirmed malaria patients were investigated from 2011 to 2020. Plasmodium falciparum was the predominant species with 81 cases (85.26%). The highest rate of infection was observed in 49 cases (51.6.3%), in the age group of 50 years with 27 cases (42.86%), and in the working class with 69 cases (72.63%). Despite a decrease in Malaria cases through the implementation of the eradication program compared to the last two decades, its imported type is still showing up in the country, especially in the cosmopolitan city of Yazd, where domestic and foreign workers and tourists usually travel; thus it requires to be further monitored and controlled.

In issue 4 of the Iranian Journal of Medical Microbiology (Volume 12, Issue 4, 2018, pp.230-238), an article entitled “History of Bacterial Infection Diseases in Iran" was published by Akbar Mirsalehian and Mosayeb Dalvand (http://dx.doi.org/10.30699/ijmm.12.4.230). Respected authors of the article with the aim of re-reading the history of common bacterial infectious diseases in Iran in a part of the study examined the history of trachoma infectious disease. Despite some important therapeutic measures in the fight against trachoma, but historical sources and documents show that important aspects of trachoma have not been carefully considered by researchers. Owing to the importance of medical history studies in medical research, please publish the following points in one of the journal's issues as a letter to the editor.

Coronavirus disease 2019 (COVID-19) is the highly viral infectious disease caused by the severe acute respiratory syndrome 2 (SARS-CoV-2) virus (WHO, 2021). As of 5 August 2022, more than 587 million people had already been infected with around 6.4 million deaths (https://ourworldindata.org/covid-vaccinations, 5 August). After the alpha, beta, gamma, and delta variants, the omicron (B.1.1.529) was emerged in Botswana. The original variant of omicron was named as B.1 and following the original BA.1 variant, several subvariants of Omicron have detected: BA.2, BA.3, BA.4, and BA.5 (Yao et al., 2022). Although the data related to the sub-variants before BA.5 show that the percentage of hospitalization due to Omicron has decreased compared to the previous variants (alpha, beta, gamma and delta), but the coronavirus is still considered as a serious threat to humans.