نشریه میکروب شناسی پزشکی ایران
سال هفدهم شماره 3 (خرداد و تیر 1402)

A growing body of research suggests that rising average global temperatures may be one of several causes of disease emergence and reemergence among human and animal populations. Climate change most significantly affects diseases caused by pathogens that spend part of their lifecycle outside the host and are exposed to the environment, such as waterborne diseases, foodborne pathogens, and vector-borne zoonoses. Additionally, the displacement of people and damage to health infrastructures from the projected increase in climate variability could indirectly contribute to transmitting infectious diseases. However, while the globe is significantly warmer than a century ago, not all studies have found a clear link between climate change and disease outbreaks. Analyzing the role of climate in the emergence of infectious diseases will require interdisciplinary collaboration among climatologists, physicians, social researchers, and biologists. Understanding the relationship between climatological and ecological change as disease emergence and redistribution determinants will ultimately help optimize preventive measures. Here, we review the scientific evidence of how global warming and patterns affect different human bacterial infectious diseases.

 Pseudomonas aeruginosa is an important ubiquitous and especially common pathogen in the hospital. Exotoxin A that encoded by exoA gene has a role in pathogenesis of this bacterium. Today, probiotics are widely used in the treatment and prevention of diseases. The present study aimed to study the Saccharomyces cerevisiae S3 effect on the expression of exoA gene.

 S. cerevisiae S3 supernatant and lysate were prepared. Subminimum inhibitory concentrations (sub-MIC) of extracts were used to P. aeruginosa PAO1. The level of exoA expression was measured with real-time PCR method.

Lysate extract had a reducing effect on toxin gene expression, but unlike lysate, supernatant had an increasing effect on gene expression.

 We demonstrated that S. cerevisiae S3 had an inhibitory effect on Exotoxin A virulence factor of P. aeruginosa. We suggest doing more experiments on the effect of S. cerevisiae on other virulence factors of P. aeruginosa and pathogens.

 Rapid antigen and antibody, serological tests, and RT ‑ PCR-based molecular methods are widely used to detect microorganisms worldwide. This study aimed to detect the covid-19 using Isothermal nucleic acid amplification techniques.

 In this study, we collected 200 samples of nasopharynx and oropharynx from Jamaran Heart Hospital in Tehran. Covid -19 was examined by LAMP-RT PCR and Real-Time RT- PCR techniques. The nasopharynx and oropharynx nucleic acids were extracted both by pishtaz RNA extraction kit. LAMP-RT-PCR was performed on direct samples, while Real-Time RT-PCR samples were tested only using RNA extraction samples. The probe-primer mixture of this kit was designed using a dual-target gene method that simultaneously targets the genomic sequences of the spike region and N nucleocapsid. Fluorescence was measured using Real-Time RT-PCR and LAMP-RT PCR.

Clinical specimens (56%) were positive using Real-Time RT-PCR technique, with mean Ct values less than 30. Clinical samples (52%) were positive for Covid-19 in the RT-LAMP technique of RNA extraction samples. RT-LAMP technique indicated a sensitivity of 92.8%. Also in the RT-LAMP method without RNA extraction, the sensitivity of the technique was 85.7%.

 The LAMP-RT PCR technique is emerging as an appropriate alternative to the Real-Time RT-PCR method. This technique has basic advantages, such as constant temperature amplification, thermal cycle elimination, faster results, and potentially greater detection capacity. Therefore, the RT-LAMP-PCR can be used as a quick and cost-effective technique that can be employed in all areas.

 Oral infections are common among people of any age and can trigger systemic inflammation. The microbiota is a diverse group of microorganisms that play important roles in metabolism, immune function, and homeostasis. Oral microbiota in human atherosclerotic plaques has been identified using various techniques. Therefore, the focus of this study was to determine the correlation between metabolic parameters and oral microbiota composition in patients with atherosclerosis using Denaturing Gradient Gel Electrophoresis (DGGE) assays.

 In this case-control study, saliva samples were collected from 139 patients with atherosclerosis and healthy individuals from Imam Ali Cardiovascular Hospital, Kermanshah, Iran.  After DNA extraction, PCR products were examined and evaluated using DGGE assays.

 The study included 89 (36%) patients with a history of atherosclerosis and 50 (36%) healthy individuals. There was a significant relationship between the mean total cholesterol, Low-Density Lipoprotein (LDL), Fasting Blood Sugar (FBS), and Blood Urea Nitrogen (BUN) in the two groups. However, there was no significant difference in the mean high-density lipoprotein (HDL) and Triglyceride levels between the study groups.

 Our results showed a relationship between metabolic parameters and oral microbiota composition in patients with atherosclerosis. Additionally, our results indicated that the DGGE assay is a useful method for diagnosing and comparing the oral microbiota of people with atherosclerosis and healthy individuals. Therefore, further examination of the oral microbiota is necessary to determine its potential as a biomarker for atherosclerosis.

 There is little in vitro evidence of potential hepatotoxicity of Remdesivir (RDV). Regarding the effective results of RDV in patients with COVID-19 and the impact of COVID-19 on liver function, we investigated the effects of RDV on the expression and activity of liver enzymes in chicken embryo-derived hepatocytes.

 In this in vitro study, 20 embryonated chicken eggs (stage X) were incubated (37.5 °C, 60-65% humidity) for 10 days (stage HH35). The hepatocytes were cultured in DMEM/F12+10% FBS medium and treated with four concentrations of RDV (2.00, 3.00, 4.00, and 5.00 µM). Serum levels of alanine (ALT) and aspartate (AST) aminotransferases were measured by enzyme-linked immunosorbent assay (ELISA), and gene expression was measured by quantitative real-time PCR (qPCR).

Each hepatocyte had a hexagonal structure with a large nucleus and nucleolus. In the PAS-positive cells with a pink color confirmed the glycogen content of hepatocytes. In the presence of 4 and 5 μM RDV resulted in a significant decrease in hepatocyte viability, up to 50% increase in the proportion of non-viable hepatocytes after 48 hr (P<0.001). Besides, the expression of both ALT and AST significantly increased after treatment with RDV (P<0.001). Our data demonstrated a significant increase in the function of both ALT and AST in the RDV+ group.

 We concluded that treatment with RDV led to increased expression and function of hepatocyte enzymes in vitro.

 The aim of this study was to evaluate the relationship between salivary cortisol levels and the viable count of mutans streptococci in drug abusers.

 The study was conducted from March 2022 to May 2022 and included 86 participants aged between 17 to 30 years, who were equally divided into two groups:  cases (n= 43) and controls (n= 43). All participants underwent a urine drug line test to confirm their drug use status. Saliva was collected, and centrifuged at 3000 for 10 min, and the supernatant was stored at -20°C for later estimation of salivary cortisol levels using a Cobas device. The viable count of Mutans streptococci was determined using an identification and culturing method to calculate the colony-forming units per milliliter (CFU/ml).

The drug abusers exhibited a significantly higher concentration of salivary cortisol as compared to the control group. In addition, the cases showed a positive correlation between salivary cortisol levels and the count of Mutans Streptococci. In contrast, the control group demonstrated a negative and non-significant relationship.

 The data from the current study indicated a higher concentration of salivary cortisol associated with an increasing count of Mutans streptococci compared to the control group.

 Adalimumab is a highly human monoclonal antibody that binds to tumor necrosis factor, a key proinflammatory cytokine pathogenic in psoriasis. It is considered as an influential factor in controlling moderate to severe psoriasis. This study aimed to evaluate the impact of Adalimumab on COVID-19 incidence in patients with psoriasis.

 This cross-sectional study was performed at Baqiyatallah Hospital in 2021. Eighty patients with psoriasis who referred to Baqiyatallah Hospital were included in the study. Patients were divided into two groups, one group was treated with Adalimumab, and the other group received the control treatment. The incidence of the disease was assessed by the history of COVID-19 signs and symptoms, positive RT‐ PCR testing and graphing, and physician diagnosis.

The mean age of patients was 39.5 (±7.9 S.D.). 36(45%) patients were infected with COVID-19, and 44 (55%) patients were not infected, and there was no significant difference between the two groups in the infection with COVID-19 (P value = 0.36). There was a significant relationship between infection with COVID-19 and the severity of psoriasis (P value=0.01).  Although, in the severe psoriasis group, which was significantly more affected by COVID-19, there was no statistically significant relationship between Adalimumab consumption and COVID-19 affection (P value = 0.19).

 PPsoriasis patients treated with Adalimumab are not more prone to COVID-19 infection. However, patients with severe psoriasis are more likely to develop COVID-19; this matter is not related to the use of Adalimumab, and it is not necessary to discontinue or change Adalimumab.

 The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still an ongoing challenge in health system worldwide. Molecular detection methods including reverse transcription loop-mediated isothermal amplification (RT-LAMP) can help cutting off the transmission chain of the virus. In this study, prompt setting up of the RT-LAMP assays were investigated using gene construct design approach.

 RT-LAMP assays were initially setup and optimized using gene constructs as positive controls which worked simultaneously for RT-LAMP and RT-PCR assays. Constructed genes included T7 promoter sequence and partial sequences of SARS-CoV-2 RdRp, N and E genes cloned into pUC57 multiple cloning site (MCS) via synthetic and subcloning procedures. These templates were then used for artificial RNA synthesis. Finally, the RT-LAMP assay parameters were optimized and applied to clinical RNA specimens.

As an initial rapid approach, RT-LAMP assays were successfully setup for SARS-CoV-2 diagnostic using in vitro RNA transcripts from gene constructs. The assays were then examined on clinical samples with reaction times of 35 and 40 min required for assay one and two respectively. The detection limit was 100 copies of the target gene per reaction for each assay.

 Here, prompt setting up of RT-LAMP assays was carried out initially on designed gene constructs containing different SARS-CoV-2 target genes and simultaneous validation by RT-PCR. This approach could be used as an efficient solution where the clinical specimens may not initially be available, with the feasibility for new target gene of interest to be inserted into the MCS position.

 Due to the widespread use of antimicrobials in veterinary medicine and the increase in livestock production, it seems that the risk of spreading antibiotic resistance in human societies is more related to animals and the veterinary field. In this study, antibiotic resistance, high-level aminoglycoside resistance and frequency of aminoglycoside resistance associated genes among Enterococcus spp. isolated from Caspian horse feces were studied.

 One year from 2021-2022, Enterococcus spp. were isolated from 140 Caspian horse fecal samples and identified by biochemical tests. The disk diffusion and determination of minimum inhibitory concentration by broth microdilution method were used to examine the antibiotic resistance of isolates and PCR method was used to determine the frequency of four aminoglycoside resistance associated genes. The data were analyzed using SPSS software and the Chi-square test.

A total of 100 Enterococcus spp. was isolated from equine fecal samples. Antibacterial susceptibility testing revealed that 72% of isolates were resistant to at least one tested aminoglycoside and 38% of isolates showed high-level gentamicin and/or streptomycin resistance phenotype. Bifunctional gene aac(6′)-Ie-aph(2″)-Ia was the most common resistance associated gene and was detected in 73.61% (53/72) isolates. The frequency of aph (3´)-IIIa, aph(2'')-Ib and ant(6)Ia was 69.44%, 48.61% and 70.83% respectively, among aminoglycoside resistant isolates. Aminoglycoside resistance genes' frequency was higher in biofilm-positive isolates (P<0.05).

 Our findings demonstrate the presence of multi aminoglycoside resistance encoding genes in Enterococcus spp., isolated from equine normal microflora in northern Iran, and support the ongoing concern about proper monitoring of antimicrobial use in veterinary.

 Bacillus cereus is accountable for several outbreaks of diseases spread by food. Therefore, the study aimed to use routine culture methods and direct PCR to detect the foodborne bacterial pathogen and its enterotoxins.

 In the present study, a total of 75 Kibda sandwiches, Sausage sandwiches, Chicken Luncheons, Beef Meat luncheons, and Chicken shawarma (Fifteen samples of each) were collected from different places in Kafr El-Sheikh governorate, Egypt, from July to September 2022. isolation, identification, and rapid analysis by PCR were done to find Foodborne bacterial pathogens in samples.

Bacterial isolation revealed 17 positive samples from different food types. From 17 infected samples, 40% were Kibda, 26.6% were Sausage, 20% were Chicken luncheon, and 13.3% were positive for Meat luncheon and Chicken shawarma sandwiches. Using PCR to identify B. cereus from positive isolates (group A), 8 isolates were detected having groEL, nhe & cytK genes amplified at 533, 766, and 421 bp respectively. Also, the PCR, which was used to detection of Bacillus cereus directly in positive samples (group B) and revealed that 8 B. cereus in samples with its enterotoxins genes nhe & cytK, while group C which represents some random food samples of negative isolation results revealed that 3 samples were infected by Bacillus cereus.

 PCR assay was a sensitive & specific diagnostic tool in detecting Bacillus cereus with its enterotoxins genes directly from food samples, even in the presence of low numbers of B. cereus bacteria that traditional isolation and identification methods cannot detect.

 Staphylococcus haemolyticus is a prominent pathogen in hospital-related infections, exhibiting high antibiotic resistance. This study aimed to investigate antibiotic sensitivity, biofilm formation, and the presence of virulence-associated genes in S. haemolyticus isolated from pregnant women with urinary tract infections.

 Clinical samples were collected from pregnant women with urinary tract infections between October 2021 and December 2022. S. haemolyticus isolates were identified using cultural, biochemical, and molecular methods. Antibiotic susceptibility was determined using the VITEK-2 system. Biofilm formation was assessed, and virulence-associated genes (hla, hlb, fnbA, and fnbB) were detected using PCR.

Among 260 clinical samples, 36 S. haemolyticus isolates were identified. The isolates exhibited high resistance to Benzylpencillin, Erythromycin, oxacillin, Trimethoprim/sulfamethoxazole, Levofloxacin, and Gentamicin. Resistance was lower to Tigecycline, linezolid, tobramycin, Rifampin, vancomycin, Moxifloxacin, Tetracycline, and Ticoplanin. Biofilm formation was negative in 69.4% and weak in 30.6% of isolates. The hla gene was present in all isolates, while hlb was detected in 77.7%. Detection rates of fnbA and fnbB were 88.8% and 38.8%, respectively.

 This study highlights the high antibiotic resistance, limited biofilm formation ability, and prevalence of virulence-associated genes in S. haemolyticus isolates from pregnant women with urinary tract infections. These findings underscore the clinical significance of this bacterium and the need for infection control measures.

 Entamoeba histolytica and Giardia intestinalis are two common parasites associated with gastrointestinal infections and diarrheal diseases worldwide. This study investigated the prevalence, molecular characterization, and phylogenetic relationships of E. histolytica and G. intestinalis among patients with diarrhea and intestinal disorders in hospitals across Iraq.

 Stool samples were collected from individuals presenting with gastrointestinal symptoms, and a microscopic examination was performed to screen for the presence of E. histolytica and G. intestinalis. DNA was extracted from positive samples, and PCR amplification targeting the 16S rRNA gene for E. histolytica and the triose phosphate isomerase (TPI) gene for G. intestinalis was carried out. The resulting PCR products were subjected to agarose gel electrophoresis, purified, and sequenced. Phylogenetic trees were constructed using the Maximum Likelihood method based on the Tamura-Nei model, and bootstrap analysis was performed.

Among the studied samples, 27.8% (n=85) were positive for E. histolytica, while 19.6% (n=60) were positive for G. intestinalis. Sequence analysis confirmed the presence of E. histolytica and G. intestinalis by matching the obtained sequences with those available in the NCBI gene bank. The phylogenetic analysis revealed the genetic diversity and relatedness of the E. histolytica and G. intestinalis isolates. Clustering patterns specific to the Iraqi population were observed, suggesting potential regional transmission dynamics.

 This study provides valuable insights into the prevalence, molecular characterization, and phylogenetic relationships of E. histolytica and G. intestinalis in Iraqi patients with diarrhea and intestinal disorders.

 Urinary tract infections (UTIs) caused by urease-producing organisms, including ureaplasmas, may contribute to urolithiasis formation. We aimed to determine the frequency of Ureaplasma parvum and Ureaplasma urealyticum among urology hospital patients with urinary stones.

 The study group included 30 men with urolithiasis from Katowice, Poland. Urine samples were examined routinely for bacteria and by RT-PCR for ureaplasma DNA. Statistical analysis was done by chi-square and Fisher test (p<0.05 was statistically significant).

 In patients with urolithiasis, DNAs of Ureaplasma spp. were detected 2 times more frequently (20%) compared with controls (10%). We suggest including the detection of Ureaplasma spp. in the group of patients with urolithiasis and sterile leukocyturia.

During the Coronavirus disease 2019 (COVID-19) pandemic, children are less affected than adults, and underlying conditions and older age are associated with severe disease. Following the SARS-CoV-2 pandemic, outbreaks of cases with Kawasaki-like disease and a few others with the multisystem inflammatory syndrome in children related to COVID-19 (MIS-C) have been reported. Here, we report a two-year-old girl initially admitted to urgent pediatric care and was diagnosed with Kawasaki disease associated with COVID-19 infection to highlight the clinical features and signs. Physical examination showed a fussy infant with swelling of the hands, feet, and lips, red lips, restlessness, anorexia, and fever. According to the clinical and laboratory findings, Kawasaki disease was diagnosed. Laboratory tests for SARS-CoV-2 were positive. The patient's clinical symptoms improved after receiving medications such as IVIG and ascorbic acetyl acid.

The covid-19 pandemic began in China in November 2019 and spread globally by March 2020. In India Vaccine research, trials, and production were ramped up gradually. The Covishield vaccine trial was completed by December 2020 and the mass vaccination program started in January 2021. The mortality was far more in western and European countries (despite better health infrastructure) than in Asia or Africa. This shows how a virus can behave differently based on race. True reasons for the decline of the epidemic are still to be well established. Is it due to vaccines? Or is it just that the virus lethality has waned naturally so that it is now living in perfect sync with a human? Despite vaccines, many people suffered from breakthrough infections. When the rest of the world was recovering, China was a cause of worry. In spite of good vaccination coverage with an indigenous and efficacious vaccine, it caused havoc in the last 6 months. It may be related to their zero covid policy of theirs. Always remember that the virus will never vanish; it is still active someplace. When they have the opportunity to mutate, they will create new varieties and return.