دو ماهنامه میکروب شناسی پزشکی ایران
سال شانزدهم شماره 3 (خرداد و تیر 1401)

The coronavirus disease 2019 (COVID-19) is a deadly viral infection causing death due to impaired immunity. Therefore, an investigation of factors affecting the immune system should be considered. It is well documented that regular sessions of moderate-intensity exercise training with up to 1-hour duration boost the immune functions through anti-inflammatory and antioxidant effects. Besides, a diet containing functional and nutritious foods is also needed to aid the immune system. Herein, we have summarized available data on how exercise and nutritional factors help promote immunity against various infections. More importantly, this review provides practical and valuable guidance for sedentary adult people and non-professional athletes on how to do aerobic and resistance training and stretching exercises at home with no special types of equipment required during the outbreaks of delta variant-COVID-19. Some significant exercise-related nutritional considerations regarding carbohydrates, fibers, vitamins, zinc, and omega-3 fatty acids were also supplied that help to create better adaptations and improve immune responses.

Wound infections are the primary cause of sepsis in burn wound patients and increase burn-related morbidity and mortality. Gram-negative and Gram-positive bacteria induce infections in burn wounds. Conventional antimicrobial therapy is recognized as the most successful therapeutic intervention to combat infections of burn wounds. Unfortunately, antimicrobial resistance could be catastrophic and lead to treatment failure. Burn wound infections need topical treatment. Phages as an alternative for antibiotics can be used as a monotherapy for infections with antibiotic-resistant pathogens or can be applied in combination with antibiotic therapy. Phages are species-specific bacterial natural viruses. Worldwide, many phage-producing companies are emerging. However, not many countries implement phage therapy in their patient management. Clinical trials are needed to convince the health care system in those countries that do not have confidence in phage therapy in infectious diseases. This study reviewed several aspects of phage therapy in burn wound patients.

 Acinetobacter baumannii is a major cause of nosocomial infections and is considered one of the most serious health threats worldwide. Several researchers have attempted to study and report this issue to find a solution. In this regard, the observation and monitoring of topic and conceptual priorities are thus crucial. This study aimed to identify and formulate the relationship among topic research priorities of A. baumannii to accurately understand the intellectual structure concerning A. baumannii.

 This scientometric study is quantitative and applied, conducted by using the co-word analysis technique. A total of 10,898 records indexed at the WOSCC were retrieved and analyzed during 2002-2021, and 102 keywords out of 12,060 keywords were selected for analysis. Following the vocabulary homogenization process, the threshold was determined, and UCINET 6.528.0.0 2017, NetDraw (2017), VOSviewer 1.6.14, and SPSS-16 software were used to analyze and preprocess the data and visualize the maps.

The keyword 'Multidrug Resistance (MDR)' was in first place among the most frequent keywords of A. baumannii articles. The main concepts of the documents published regarding A. baumannii were obtained using the hierarchical clustering with the Ward method (6 topic clusters). The largest cluster had 27 keywords and 680 links with a centrality of 25,185 and a density of 0.969. The distribution of clusters in the strategic diagram indicated that topic clusters were located in quadrants 1 and 3, including mature and central topics and emerging or marginal topics, respectively.

Identifying and monitoring significant topics and conceptual priorities of the A. baumannii area with scientometric techniques is an appropriate tool for determining the intellectual structure of the A. baumannii area, leading optimal and efficient decisions in officials' research financial policy.

 AmpC-producing bacteria are a severe threat to treating infectious diseases caused by gram-negative bacteria. The actual prevalence of these bacteria is not clearly determined as there is no reliable diagnostic method available to detect them. Therefore, this study was performed to determine the frequency of Escherichia coli, Klebsiella, and Enterobacter species producing AmpC among clinical samples by phenotypic and molecular methods.

 In this study, 163 bacteria of Enterobacteriaceae species isolated from different clinical samples in 2018 were examined. Suspected isolates of producing pAmpC were identified using cefoxitin disk (FOX) and disk diffusion method. Three confirmatory phenotypic methods were performed to identify pAmpC production, and blaDHA, blaFOX, blaMOX genes were searched using a molecular method for all bacteria. Specificity and sensitivity of phenotypic tests were obtained compared to the presence of blaDHAgene.

Of 163 bacteria, 80 (49.1%) isolates were resistant to FOX, and 21 (12.9%) carried the blaDHA gene. Among the bacteria carrying the gene, 5 (6%) isolates were sensitive to FOX. 49 (61.3%) FOX-resistance bacteria were positive in one of the chromosomal and/or plasmid phenotypic tests. The highest specificity and sensitivity were observed in the AmpC disk (90.8%) and CAM (42.7%) methods, respectively.

It seems phenotypic methods are more successful in distinguishing true negatives (higher specificity). Also, sensitivity to cefoxitin is not a criterion for not producing the enzyme AmpC. For this reason, it is recommended that national monitoring be performed to identify the genes of AmpC producing bacteria.

 COVID-19 is a highly contagious infectious disease, and it has affected people's daily life and has raised great concern for governments and public health officials. Forecasting its future behavior may be useful for allocating medical resources and defining effective strategies for disease control, etc.

 The collected data was the cumulative and the absolute number of confirmed, death, and recovered cases of COVID-19 from February 20 to July 03, 2021. We used hierarchical cluster analysis. To forecast the future behavior of COVID-19, the Auto-Regressive Integrated Moving Average (ARIMA), Exponential Smoothing (ETS), Automatic Forecasting Procedure (Prophet), Naive, Seasonal Naive (s-Naive), boosted ARIMA, and boosted Prophet models were used.

The results of clustering showed a similar behavior of coronavirus in Iran and other countries such as France, Russia, Turkey, United Kingdom (UK), Argentina, Colombia, Italy, Spain, Germany, Poland, Mexico, and Indonesia. It also revealed similar patterns of SARS-CoV-2 for the same countries in six groups. Results showed that XGBoost models' family had higher accuracy than other models.

In Iran, COVID-19 showed similar behavior patterns compared to the studied developed countries. The family of XGBoost models showed practical results and high precision in forecasting behavior patterns of the virus. Concerning the rapid spread of the virus worldwide, these models can be used to forecast the behavior patterns of SARS-CoV-2. Preventing the spread of the coronavirus, controlling the disease, and breaking down its chain necessitates community assistance, and in this mission, the role of statisticians cannot be neglected.

 Proteus bacteria, a key contributor to several gastrointestinal diseases, is known to survive in the wide pH range offered by different locations of the GI tract. The bacterial enzyme Choline TMA Lyase found in several opportunistic gut commensals catalyzes choline conversion to trimethylamine, a precursor of the pro-atherosclerotic metabolite trimethylamine N oxide. This study evaluates the pathogenic potential of Proteus gut bacteria in patients with coronary artery disease. We also sought to create a simple predictive model for assessing risk factors of coronary artery disease using a sample of Indian patients.

 The study included 14 patients with coronary artery disease and 6 controls. Optimal conditions were devised, and standardized protocols were followed to culture Proteus bacteria in vitro and isolate the protein of interest, Choline TMA Lyase. FTIR analysis and UV spectrophotometry were employed to quantify choline and trimethylamine N oxide levels, respectively. Finally, receiver operating characteristic analysis and multivariate logistic regression established the predictive power of the entire model and trimethylamine N oxide.

The findings demonstrated an optimum activity of this protein and the bacterial growth in the pH range of 7.4 - 9. Quantitative analysis showed trimethylamine N oxide levels to be significantly higher in coronary artery disease patients (1.81 µM) than in controls (0.86 µM).

Optimum activity in the alkaline condition indicates the strong pathological potential of Proteus bacteria in the progression of coronary artery disease. The prediction model can serve as a helpful tool within the medical community to assess the risk factors for coronary artery disease.

 Anaplasmosis caused by Anaplasma spp. is an important arthropod-borne disease of various vertebrates with health concerns to humans. The present study aimed to investigate the detection and genotype of Anaplasma phagocytophilum using microscopic examination, real-time PCR technique, and phylogenetic analysis in dogs from Mashhad shelters, Khorasan-Razavi province.

 For this purpose, 250 blood specimens were collected during routine health checkups from dogs in different shelters in Mashhad, Iran, in 2020. First, smears were prepared from the blood specimens, stained with Giemsa, and examined under the light microscope for Anaplasma inclusions. Then, the genomic DNAs were extracted from buffy coats of blood specimens and screened by real-time PCR for the presence of Anaplasma infection by amplifying a 1400 bp sequence of 16S rRNA belonging to the Anaplasma genus. Finally, sequencing and BLAST analyses were carried out on the amplified fragments for the phylogenetic assessments in positive specimens.

A total of 9 dogs (3.60%), including 5 females (3.40%) and 4 males (3.88%) were found to be positive for Anaplasma infection in real-time PCR. Moreover, in blood smear observation, A. phagocytophilum morulae were detected in the neutrophils of 3 PCR positive animals.

This study provides important data regarding A. phagocytophilum in dogs and the degree of genetic homology/heterogeneities among these pathogen strains from dogs and humans in Iran and other countries. To our knowledge, this is the first molecular evidence on the infection of A. phagocytophilum in sheltered dogs of the region.

 Enterococcus faecalis (E. faecalis) is a major opportunistic pathogen that causes nosocomial infections in humans, especially in immunocompromised and elderly people. This bacterium can survive and grow in harsh conditions and low-nutrient environments, so it is usually found in water and can easily be transmitted via the fecal-oral route. Due to the high usage of antibiotics, many antibiotic-resistant strains of E. faecalis have been evolved, especially vancomycin-resistant ones (VRE). Water-borne VRE is an environmental and health problem. Since the monitoring of recreational waters is so important in human health, the aim of the present study was to investigate the prevalence of VRE isolates and their antibiotics patterns in the environmental samples from recreational waters in Guilan Province, Iran.

 The environmental samples were obtained from recreational waters in six cities in Guilan Province, North of Iran, 4 stations in Anzali wetland, and 5 main rivers entering Anzali wetland from January to September 2019. E. faecalis samples were identified by microscopic analysis, biochemical tests, and molecular identification. Antibiotic resistance patterns of the isolates were determined by an antibiogram test. The molecular identification of the isolates was performed using polymerase chain reaction (PCR) with specific primers for the ddlE gene.

Overall, in 268 samples, Enterococci were detected in 154 samples (57.46%), of which 35 isolates (29.68%) were VRE. From VRE isolates 32 isolates (91.42%) belonged to E. faecalis, 2 isolates (5.71%) belonged to E. faecium, and one isolate (2.86%) belonged to other Enterococcus species.

This study shows the high prevalence and antibiotic resistance rate of VRE strains of E. faecalis in water resources in Guilan province, which can be alarming and needs to be considered.

 In December 2019, a new type of Coronavirus (SARS-CoV-2) pneumonia (COVID-19) was reported in Wuhan and quickly spread worldwide. This study was designed to investigate the clinical symptoms of the COVID-19 patients.

 In this retrospective study, we collected data of 132 COVID-19 dead patients. Demographic, epidemiological, and clinical data and laboratory test results were analyzed on days 1, 3, and 6 of admission.

Most cases were in the 66-75 age group, 64.39% of which were males. Three days after admission, 55.3% of patients died. The most frequent clinical manifestations were dry cough (70.45%) and fever (54.54%), which increased during hospitalization. Diabetes and blood pressure were reported as the most prevalent underlying diseases. Lymphopenia and an increase in leucocyte number were observed in most patients. ESR (92.5%) and LDH (94.64%) levels were above normal. Furthermore, 42.85% and 44.73% of patients had elevated ALT and AST levels, respectively.

 The results of this study revealed that males are more likely to be infected with SARS-CoV-19. Underlying diseases were common among patients and clinical and laboratory symptoms aggravated with a rise in hospitalization time.

Strongyloides stercoralis (S. stercoralis) is a helminth, which infects humans widely in tropical and subtropical countries. This parasitic infestation usually does not produce symptoms in humans; however, severe and life-threatening forms of this infection can occur in immunocompromised individuals. Patients with Coronavirus disease 2019 (COVID-19) with concurrent immunosuppressive therapy are at risk of developing Strongyloides hyperinfection syndrome (SHS). We present a 70-year-old male with a history of high-dose dexamethasone therapy due to severe COVID-19 who was referred to our hospital with chest discomfort, nausea, and anorexia. Histological assessment of the gastric and duodenal mucosae revealed numerous eggs and filariform larvae of S. stercoralis indicative of SHS. Ivermectin and albendazole were administered to the patient. Following the treatment, the patient's symptoms improved. Clinicians must be aware of the risk of SHS, especially in S. stercoralis endemic countries before and during corticosteroid therapy for COVID-19 because early diagnosis and appropriate treatment can significantly reduce mortality in these patients.