دو ماهنامه میکروب شناسی پزشکی ایران
سال شانزدهم شماره 6 (آذر و دی 1401)

 Nosocomial infections caused by gram-negative bacteria are among the most important health-threatening challenges of the current century, particularly following the emergence and spreading of antibiotic-resistance strains. Extended-spectrum beta-lactamase (ESBL), one of the most important antibiotic resistance mechanisms, is spreading worldwide. Surveillance and gathering data on the prevalence of antibiotic resistance and their associated encoding genes could assist in selecting treatment strategies and policies. This systematic review and meta-analysis was designed to assess the prevalence of ESBL-positive bacteria and their resistance genes in medical centers of Kermanshah city, west of Iran.

 All studies published as original articles were retrieved by searching in EMBASE, Scopus, PubMed/Medline, Google Scholar, and Persian databases of SID and Magiran, using appropriate keywords All published studies in the field were included without time restriction until 30-Mar-2022. Comprehensive Meta-Analysis software was used to analyze the data.

The prevalence of ESBL-positive and multidrug resistance (MDR) bacteria in Kermanshah medical centers were 34.8% and 56.1%, respectively. The highest and lowest prevalence of ESBL-positive bacteria was observed for Enterobacter cloacae (59.14%) and Pseudomonas aeruginosa (4.55%), respectively. The highest and lowest prevalence of the resistance genes were observed for blaOXA-51 (99.3%) and blaKPC (0.6%), respectively. The highest resistance was estimated to mezlocillin antibiotic (92.2%).

 This study showed that the prevalence of ESBL-positive and MDR bacteria is high in Kermanshah medical centers, and it provides significant information to health policymakers to implement appropriate strategies to reduce the prevalence of resistant bacteria.

 Mycobacterium tuberculosis is a health problem in countries. Despite the global prevalence of tuberculosis and the lack of appropriate drugs, further progress is still needed with the help of modern methods of preparing epitope-based vaccines for tuberculosis.

 In this study, specific T and B cell epitopes required for producing chimeric vaccines with the help of servers such as IEDB were determined. The antigenicity, allergenicity, and toxicity of the selected epitopes by various other servers such as VaxiJenv2.0, AllerTOP, and Toxinpred were determined, and the vaccine of the epitope was then configured with the help of special linkers. Then, analyze the structure vaccine by some other bioinformatics servers such as PRABI, SWISS-MODEL, PROCHECK, and PEPCALC, was investigated and finally detected using docking techniques to evaluate the interaction with the epitope through MVD software.

The results showed that the vaccine, in terms of in silico evaluations of two-dimensional and three-dimensional structures, has a good condition. Also, the percentage of optimal placement of amino acids and bonds by PROCHECK server, % 99 percent of optimal placement of amino acids in the chimer structure was established. Also, it was non-toxic and nonallergenic and had the desired antigenicity.

 In general, the vaccine that was able to have a favorable interaction with some components of the immune system (HLA) in the docking process, which indicates the optimal identification of this structure by the humoral and cellular immune system, of course, more reliable proof of it requires clinical phase processes.

 Pseudomonas aeruginosa (P. aeruginosa) is an important causative organism of burn infection. Several virulence factors are implicated in P. aeruginosa colonization and invasion, making P. aeruginosa infection's outcome worse. Type III secretion system (T3SS) effector proteins are among these virulence factors. The present study evaluated the frequency of genes encoding T3SS effectors as a virulence determinant in P. aeruginosa isolates from burn patients.

 Wound swabs were collected from burn patients admitted to the Plastic and Reconstructive Surgery Center, Mansoura University, Egypt, and identified by different microbiological testing methods. The modified Kirby Bauer's disc diffusion method was used to test the antibiotic susceptibility of P. aeruginosa isolates against different antibiotics. Prevalence and the presence of exo genes that encode type T3SS proteins (exoS, exoT, exoU, and exoY) in P. aeruginosa isolates were evaluated by the multiplex PCR. Chi-square and Fisher's test were used for statistical analysis.

A total of 45 P. aeruginosa isolates were identified from 101 burn patients, including 27 males and 18 females, with a mean age of 15.78±2.65 years old. P. aeruginosa isolates were mostly susceptible to piperacillin/tazobactam and imipenem (73.33 and 62.22%), respectively; while the lowest susceptibility rates were in ceftazidime (4.44%), Tobramycin (4.44%), and ceftriaxone (6.67%). The exoY and exoT genes were detected in 100% of the P. aeruginosa isolates, while 62.22% and 42.22% of cli nical isolates harbored exoS and exoU genes, respectively.

 This study established a correlation between T3SS proteins, particularly exoS and exoU genes and antimicrobial resistance in P. aeruginosa isolates from burn infection.

 Infectious Bursal Disease is characterized by destroying the Bursa of Fabricius (Primary lymphoid organ), where B cells mature and differentiate. The virus is very stable and resistant to physical and chemical agents, heat, and ultraviolet radiation. Thus, it persists in poultry houses for several weeks after cleaning and disinfection. The present study was designed to develop the IBD immune complex to evaluate immunoprophylactic potential.

 The infectious bursal disease virus (IBDV) was procured from the infected Bursae collected from the disease outbreak areas of the Faisalabad District, and molecular detection was done through RT-PCR. The inactivated IBD virus was injected into the layer birds to raise egg yolk antibodies (IgY). The eggs were collected, and the yolk containing antibodies were processed to separate IgY through the ammonium sulfate precipitation method. The known quantity of antigen and antibodies were mixed to develop the immune complex (Icx) antigen. The immune response of immune complex IBD antigen was determined in rabbits. The comparative immune response of immune complex IBD antigen and IBD commercial vaccine was made in poultry birds, and the comparative mean antibody titers were determined through factorial analysis. Eighty, one day old, semi-specific pathogen-free (SPF) chickens were kept in four groups. Chickens were bled weekly to evaluate infectious bursal virus antibody titers by I-ELISA. All the groups were challenged with local IBD virus strain on day 28, and the Bursa to bodyweight ratios was compared after being challenged on day 35.

The study revealed that the antibody titers of G-III were significantly higher (P ≤ 0.05) than those of other groups on days 28, 35, and 42. On day 35, the Bursa to the bodyweight of group-III was significantly lower (P ≤ 0.05) than the challenged control group.

 The findings showed that the immune complex (Icx) antigen induced a strong and persistent immunogenic response in terms of antibody titer compared to a conventional live vaccine. Icx provoked better protective immunity and protected chickens against the IBD virus challenge and may be considered a substitute for the IBDV vaccine.

 The study was conducted to assess the role of Nitric Oxide (NO) in the pathogenesis of Dengue fever (DF).

 A total of 150 patients with positive Dengue serology and 50 candidates as controls in the age group of 15-65 years were included in the study. NO levels were measured by Griess Nitrate Method (Cadmium granules modified).

The rise in NO was observed in 24 (20.86%) patients out of 115 DF patients, while it was raised in only 01 (2.8%) case out of 35 patients of DHF and the difference was observed to be statistically significant. NO level was within normal limits (Normal Range- 24.8-77.6µmol/L) in 92% (n=50) healthy controls and was raised in (NO value>77.66µmol/L) 4% healthy controls. A positive correlation was observed in the serum NO levels with platelet count. The majority of the patients in the study (41.33%) were in the age group of 21-30 years of age, followed by were < 20 yrs (30%) and 31-40 yrs (12.67%). Male:female ratio observed was 1.78:1. DF was diagnosed in 115 (76.67%) patients, while DHF was diagnosed in 35 (23.33%) patients, while no case of DSS was diagnosed.

 NO plays a protective role in DF, while in DHF patients, the absence of rising NO levels may be one of the contributory factors leading to the progression of the disease and increased morbidity. NO levels can guide the physician about the evolution of a case of Dengue.

 Circulating microRNAs have the potential to serve as biomarkers in diagnostics and monitoring of disease progression, including liver diseases. Therefore, this study investigated the alteration in the expression levels of microRNA-222 (miR-222) in patients with chronic hepatitis B (CHB) as a potential diagnostic biomarker.

 MiR-222 expression was analyzed in the 86 plasma samples, including 43 patients with CHB and 43 healthy individuals as a control group. RNA extraction and cDNA synthesis processes were done, and then the expression of the miR-222 was measured by qRT-PCR. The Mann-Whitney U-test Spearman analyzed the results to show the correlation between miR-222 and clinical parameters.

MiR-222 had a difference in expression levels between the patient and control groups (miRNA-222 Fold change= 1.384). Nevertheless, a statically significant difference was not observed (p value=0.269).

 Our study showed that even though changes in miR-222 expression levels in the group of patients with chronic hepatitis B compared to the healthy group, it could not be utilized as a precise diagnostic biomarker, and more studies, on a broader scale, are needed to determine the role of this microRNA in patients with CHB.

 Evidence linking the BK virus (BKV), John Cunningham virus (JCV), and Cytomegalovirus (CMV) to ovarian cancer is inconclusive. Therefore, this study aimed to evaluate the association of BKV, JCV, and CMV in malignant, borderline, benign, and normal ovarian tissues to shed light on the potential role of viral infections in the process of ovarian carcinogenesis.

 Paraffin-embedded ovarian tissues of 205 patients and 45 normal controls were included in this case-control study conducted from January 2015 to January 2020. The patient group was divided into three subgroups: malignant, borderline, and benign. Amplifying the β-globin gene was conducted to confirm the quality of the DNA extracted. Real-time PCR was used to identify BKV, JCV, and CMV genomes in all specimens.

The mean age of the patients and the control group was 44.0 ± 11.4 and 34.2 ± 12.1 years old, respectively. One, two, and three malignant lesions were positive for the presence of BKV, JCV, and CMV, respectively. These viruses were not detected in any borderline, benign, or control lesions.

 The results of this study indicated no association between CMV, BKV, and JCV with ovarian cancer. Therefore, major studies are recommended to confirm these findings.

 Carbapenem resistant- Pseudomonas aeruginosa (CRPA) is one of the most important causes of severe and persistent infections. The contributions of different resistance mechanisms to Carbapenems and biofilm formation among a collection of imipenem susceptible and non-susceptible P. aeruginosa isolates were investigated.

 In this cross-sectional study, a total of 117 P. aeruginosa isolates were collected. The disc diffusion method assessed the susceptibility of isolates to various antimicrobials. The Carbazole method was used for the detection of alginate producers. Multiplex-PCRs were performed for the detection of biofilm and resistance genes. The expression mRNA levels of efflux pumps were assessed by phenotypic and genotypic (Quantitative Real-time PCR) approaches.

The highest resistance rate was related to ceftazidime, chloramphenicol, ceftriaxone, tetracycline, and levofloxacin. MDR phenotype was observed in 8.4% of strains. The frequency of carbapenem resistance was also 24.7%. The Carbazole test was positive at 53.8%. In general, 62.4% of isolates were able to form a biofilm, 28.8% of which were resistant to carbapenem. The distribution of algD and algU genes were 41.8% and 26.5%, respectively. The frequency of MBL-encoded genes was as follows; blaIMP (62.1%), blaVIM (31.0%), and blaNDM (6.8%). The relative levels of MexX, MexC, MexB and MexA mRNA in CRPA strains with active efflux pump were 81.8%, 63.6%, 54.5%, and 36.4%, respectively.

 The existence of different resistant mechanisms in P. aeruginosa can cause cross antibiotic resistance, lead to the appearance of resistant strains, and make the treatment difficult. Biofilm production is directly related to antibiotic resistance. Efflux pumps are actively expressed in carbapenem-resistant strains.

 Acinetobacter baumannii is one of the most important pathogens found in ICUs as it is responsible for nosocomial infection with a high mortality rate and a rising level of resistance to most antibiotics. One of the main mechanisms of resistance is the production of extended-spectrum beta-lactamase (ESBL) genes such as veb, per, tem, and shv. The current study aimed to determine the antibiotic resistance pattern and the frequency of per, tem, veb, and shv genes in A. baumannii strains isolated from Zahedan, Iran.

 The current study was conducted on 150 strains of A. baumannii isolated from different clinical samples from January to September 2018. The antibiotic resistance pattern was determined by the disk diffusion method for 18 antibiotics and the minimum inhibitory concentration for colistin. Later, the bacterial genome was extracted, and PCR detected ESBL genes.

Out of the 150 studied isolates, 141 were A. baumannii and only nine isolates were A. nosocomialis. A. baumannii strains were strongly resistant to many selected antibiotics such as CAZ (99.3%), CTX (97.9), PTZ (97.2%), SXT (97.2%), IMI (97.2%), and LEV (96.5%); while this value was low for a few antibiotics including MN (69.5%), DXT (52.5%), SAM (21.3), and TN (16.7). The eb, per, tem, and shv genes were detected in 20 (13.3%), 15 (10%), 23 (15.4%), and 11 (7.3%) isolates, respectively.

 The isolates were highly resistant to ceftazidime, ceftriaxone, piperacillin-tazobactam, cotrimoxazole, imipenem, and levofloxacin; in addition, the frequency of per, veb, tem, and genes was lower in the current study than those reported in other regions.

 Carbapenem-resistant Enterobacteriaceae (CRE) are rapidly growing, which makes it vital to detect antibacterial activity. However, the carbapenem family does not have an automated antimicrobial susceptibility testing card. So the aim of this study was to identify the prevalence of carbapenemase-producing strains of Gram-negative bacteria and determine their antibiotic susceptibility pattern in Tehran, Iran.

 In this cross-sectional study, between 2019 and 2020, 1600 samples were taken from the Masih Daneshvari hospital's laboratory in Iran. Utilizing standard biochemical methods, all isolated bacteria were identified. The common Kirby-Bauer Disc diffusion method was used for antimicrobial susceptibility testing. A real-time polymerase chain reaction was used to evaluate the molecular detection of genes producing carbapenemase.

Of 1502 (94.7) Gram-negative bacilli, 37.3% isolates were Pseudomonas aeruginosa, 30.6% Acinetobacter baumannii, 16.5% Klebsiella, 9.3% Escherichia coli, 0.6% Pseudomonas multophila, 0.4% Neisseria1105 (73.5%) isolates were carbapenem-sensitive, while the remaining 397 (26.5%) isolates were carbapenem-resistant. Molecular testing of this sample showed that 80% of tested isolates had resistance genes to at least one antibiotic resistance gene. The following carbapenemase genes were most frequently detected among resistant strains: blaimp (35%), blavim (20%), blakpc (15%), blaoxa -48 (10%), blandm (10%), and blages (10%).

 From this study authors can conclude that carbapenemase-producing Enterobacteriaceae is increasing in Iran and the use of phenotypic methods for detection of CPEs showed good sensitivity. Before prescribing antibiotics to patients, this test should be performed.

 Uropathogenic Escherichia coli (UPEC) is the most prevalent causative agent of urinary tract infections (UTIs) in both community and hospital settings. Annually about 150 million people globally develop UTIs, resulting in increased healthcare costs. The current study examined the identification and the frequency distribution of virulence factors among fluoroquinolones-resistant (FQs-R) and fluoroquinolones-susceptible (FQs-S) UPEC strains in Hamadan hospitals, west of Iran.

 One hundred-seventy urine samples were collected consecutively from inpatients at three hospitals in Hamadan from March to September 2018. The UPEC isolates were identified using biochemical tests and polymerase chain reaction (PCR). The disk diffusion and the broth microdilution methods determined the antimicrobial susceptibility and the minimum inhibitory concentration (MIC) of Ciprofloxacin. The multiplex-PCR method investigated the prevalence of pap, aer, and hly genes.

Among 170 urine samples collected from inpatients, E. coli was the most common isolate, with a frequency of 125 (73.5%). Resistance to Nalidixic acid and fluoroquinolones, including Ciprofloxacin, Norfloxacin, and Ofloxacin, was detected in 88.8%, 71.2%, 70.4%, and 68.8% of UPEC isolates, respectively. The prevalence of hly and pap genes in FQs-R strains was significantly lower than in FQs-S strains.

 The high-level antibiotic resistance to quinolones & fluoroquinolones and heterogeneity of virulence genes among clinical UPEC isolates need strong attention.

 Photodynamic inactivation (PDI) is a new strategy for eliminating pathogenic microorganisms, especially in infectious wounds. PDI occurs using light in combination with a photosensitizer. A new approach in PDI applies natural compounds as a photosensitizer. This study aimed to introduce brewed saffron (Crocus sativus) as a new natural photosensitizer in combination with blue light to induce a phototoxic reaction in Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) strains.

 Isolated and standard S. aureus and E. coli strains and a Candida albicans standard strain were used for PDI. Various final concentrations (2.5-10 mg/mL) of brewed saffron as a photosensitizer was employed with 15 minutes of incubation. A blue LED with 5 minutes of illumination was applied as a light source. Control and treatments were compared using the colony count method.

Using the saffron extract in combination with blue LED could induce a phototoxic reaction in Gram-negative bacteria similar to Gram-positive bacteria. After PDI, there was no significant difference between Gram-positive and Gram-negative strains in terms of cellular death. The highest phototoxic reaction in all bacteria was observed at 10 mg/mL of the final saffron concentration combined with blue light by 0.65-0.75log10 (CFU/mL) cellular death. At the concentration of 2.5 mg/mL of the extract (the lowest concentration), the highest phototoxic reaction was found in the S. aureus isolated strain by a 0.65log10 (CFU/mL) reduction.

 The brewed saffron combined with blue light induces a sub-lethal phototoxic reaction in bacteria. Accordingly, it can be suggested as a natural source for new photosensitizers.

 Coxiella burnetii is a mandatory gram-negative and intracellular bacterium. The most common pathogens are Query Fever in humans and Coxiellosis in animals. Due to the variety of ways of infection and the lack of accurate, comprehensive, and reliable research, and the lack of statistics on the percentage of infection with C. burnetiii and the high resistance of this bacterium in the environment, it is important to investigate the presence of nosocomial infections with this bacterium. Therefore, this study aimed to molecularly detect C. burnetiii bacteria that cause infective endocarditis in military hospitals.

 100 negatively cultured endocarditis specimens were collected for this purpose, and DNA was extracted from C. burnetii with an extraction kit. Also, a PCR reaction was performed on the genome of negative control samples to evaluate the specificity of primers and determine the method's specificity. After ligation steps, JM107 E. coli susceptible to calcium chloride was used to accept the plasmid containing the gene.

In quantitative DNA analysis, its amount was calculated between 1.69 and 1.8. The last dilution of the PUC18 plasmid for C. burnetii with an initial concentration of 700 ng / µl, which formed a detectable band on the gel, was calculated to be 7-10, and the minimum number of detectable copies in a 25 μL PCR reaction equal to 22 copies.

 Although C. burnetii was not detected in any of the blood samples in this study. However, C. burnetii has a broad and varied host spectrum in the Epizootic and Enzootic foci.

 Toxoplasmosis is a common parasitic infection that can endanger mother's and neonates' health during pregnancy. The disease is also prevalent in Iran. This study intended to evaluate the seroepidemiology of toxoplasmosis in neonates and postpartum mothers referred to health centers of Yazd in Iran in 2020.

 Totally, 184 postpartum mothers and 184 neonatal umbilical cords in health centers of Yazd were evaluated for Toxoplasma infection through a specific IgM and IgG antibodies kit. The obtained data were analyzed by SPSS18.

Out of 184 samples of postpartum mothers, 8 cases (4.35%) were seropositive, and 176 (95.65%) were seronegative for IgG antibody; moreover, 7 cases (3.80%) were seropositive, and 177 (96.20%) seronegative for IgM antibody. Also, 184 neonatal umbilical cords were IgM negative, and no toxoplasmosis infection was reported. No significant correlation was found between seroprevalence of Toxoplasma infection and caring for pets, consumption of raw meat, level of education, blood type, job, living area and type of delivery (P>0.05). However, a significant correlation was identified between the number of deliveries and the prevalence of toxoplasmosis (P=0.014). This study also illustrated a low prevalence of Toxoplasma infection in postpartum mothers and no congenital transmission of the disease in diverse health centers of the province. However, there was no statistically significant relationship between risk factors and the prevalence of Toxoplasma.

Monkeypox is a rare zoonotic infectious disease caused by the Monkeypox viruses, a type of Orthopoxvirus of the family Poxviridae, which is endemic to Africa. Monkeypox, which is usually a self-limiting illness, starts with flu-like symptoms (fever, muscle aches, chills, and fatigue). Usually, within 1 to 3 days (sometimes longer) after the onset of fever, the patient develops a rash that often starts on the face and then spreads to other parts of the body. Lesions may appear all over the body. Decreased immunity of populations due to the cessation of smallpox vaccination in the past, has paved the way for Monkeypox. This is shown by the increase in the number of cases as well as the recurrence of the disease in some countries. Due to the importance of the Monkeypox and the limited number of Persian language sources in this regard, the present article aimed to introduce this disease as a zoonotic infectious disease that has recently, been reported in several countries.

 E.coli is a member of Enterobacteriaceae family and gram negative bacilli. Many genus of bacteria can caused urinary tract infection. In fact, uropathogenic E.coli is responsible of 80 - 90% of urinary tract infections in the global. This study was proceeded to determine the prevalence rate of uropathogenic E.coli isolated from Women Patients and study the multi-drug resistance patterns of these isolates, in Kirkuk city, Iraq.

 Collection of 200 Urine samples from women patients with different ages were achieved over a period January to May 2022, from women's and children's Hospital in Kirkuk city, Iraq. Then inoculated on , Nutrient, MacConkey and blood agar and incubated for 24 hours at 37°C. E.coli colonies were identified by culturing and biochemical tests, then antibiotic susceptibility of these isolates were done.

The prevalence of bacterial positive growth was 132(66%), distributed as the following: E.coli 47(35.6%), S.aureus 37(28.03%), Staphylococcus spp. 9(6.81), Proteus mirabilis 9(6.81), Klebsiella sp. 9(6.81), Pseudomonas aeruginosa 7(5.3%), Streptococcus spp. 7(5.3%), Acinetobacter baumannii 4(3%) and shigella spp. 3(2.27%). Most of E.coli isolates were isolated from women patients with age group 18-38 years. Meropenem is showed the highest effect with no resistant E. coli isolates followed by Amikacin, Ciprofloxacin, Azithromycin, Levofloxacin, Trimethoprim and Nitrofurantoin (10.63%,19.14%,19.14%, 31.91%, 38.29% and 38.29)respectively. In contrast to Augmentin, which revealed no effect towards these isolates with 100% resistance followed by Ceftazidime, Rifampicin and Ceftriaxone (78.72%, 72.34%and 59.57%) respectively. The current data revealed that the isolates were multidrug resistance to four, five, six and seven antimicrobial classes : 18(38.29%), 15(31.91%), 9(19.14%), and 5(10.63%) of E. coli  isolates, respectively.

 The sensitivity of all E. coli isolates towards meropenem, calls for attention that the overuse/misuse of this antibiotic will caused the selection pressure and increased the rate of resistance.