Iranian Journal of Microbiology
Volume:14 Issue: 2, Apr 2022

Health care workers (HCWs) are a high-risk group for acquiring and transmitting severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Aim of the study was the evaluation of sero-prevalence of SARS-CoV-2 in a random sample of HCWs at a large acute care hospital in Iran.

We collected blood samples of 180 medical staffs from September 22, 2020 to January 26, 2021. The enzyme linked immunosorbent assays (ELISA) tests were used for evaluation of the presence of IgG antibodies. Participants completed a self-report questionnaire, comprising demographics, occupational, the work area, and personal protection data.

Of the 180 HCWs who participated in this study, 44 (24.4%) were seropositive for anti-SARS-CoV-2 IgG. The percentage of IgG positivity was higher in males than females (P<0.05). Also, there was statistically significant difference between presence of the antibodies and the occupation, location, and infecting family members with Covid -1 (P<0.05). Other factors did not associate significantly to antibody presence against SARS-CoV-2 (P>0.05).

According to this point that the number of COVID-19 cases is still growing rapidly among HCWs. So, the epidemiological estimate of SARS-CoV-2 infection remains a major challenge that is needed to prevent the spread of infection in the hospitals.

Obligate anaerobic bacteria are known to cause various infections in human beings. We aimed to determine the prevalence and spectrum of obligate anaerobes encountered in pus aspirate, sterile fluids and tissue samples received for routine bacterial culture and sensitivity.

A total of 160 samples including tissue, sterile body fluids and pus aspirate were collected , analysed for prevalence and spectrum of obligate anaerobes. Identification of obligate and facultative anaerobes was done by automated MALDI-TOF and Vitek 2 method.

Among 160 samples, 75 samples (46.8%) yielded obligate anaerobes out of which 41 samples (26%) yielded obligate anaerobes along with facultative anaerobes which was significant (p value=0.031) and 34 samples (21%) yielded only obligate anaerobes. 90 obligate anaerobes were isolated from 75 samples among which only 34 (37.7%) samples yielded only obligate anaerobes and 56 (62.2%) yielded both obligate and facultative anaerobes. Gram stain with polymicrobial appearance (p value 0.02) was found to be significantly associated with growth of obligate anaerobes. Clinical conditions where obligate anaerobes were commonly associated were appendicular abscess, empyema, fournier’s gangrene, diabetic foot, ludwigs angina and deep abscess. Out of 75 positive samples 30 (40%) patients had predisposing conditions like diabetes mellitus, hypertension etc. Total of 90 obligate anaerobes and 49 facultative anaerobes were isolated. The common obligate anaerobes were Bacteroides fragilis 18 (20%), Prevotella spp. 20 (22.2%), and Clostridium spp. 8 (8.88%). Facultative anaerobes like Escherichia coli 25 (34.7%), Klebsiella species 15 (20.8%), Enterococcus faecalis 19 (26.3%) were isolated. Antibiotic sensitivity was performed for facultative anaerobes by Kirby bauer disc diffusion method. Out of 15 Escherichia coli isolates resistance was commonly seen for ampicillin 13 (86.6%), cephalosporins 11 (73.3%), ciprofloxacin 10 (66.6%) and Piperacillin tazobactum 8 (53.3%). In Klebsiella species resistance were commonly seen to Ampicillin 6 (100%), cephalosporins 2 (33.3%) and ciprofloxacin 2 (33.3%).

There was significant isolation of obligate anaerobes along with facultative anaerobes in clinical samples received for aerobic culture and sensitivity. There is a need for isolation of these bacteria routinely and a scope for doing antibiotic susceptibility testing, which will help in evidence-based medicine and a better clinical outcome by giving appropriate therapy.

Urinary tract infections are one of the most common bacterial infections worldwide. The emergence of antibiotic-resistant bacterial strains is a serious problem and greatest challenge in public health care. The purpose of this study was to determine the prevalence of uropathogenic microorganisms and the antibiotic resistance pattern of Escherichia coli in Algeria.

Urine samples were collected from 760 outpatients in the hospital of Tizi-Ouzou (Algeria). From the positive cultures, 120 strains of E. coli were isolated and tested for their susceptibility to antibiotics by disk diffusion method on Mueller Hinton agar medium.

Among the collected urine specimens, 270 (35.5%) yielded positive cultures for urinary tract infection. Females were more affected with a sex ratio F/M of 1.14. E. coli was the most prevalent isolated bacteria with a rate of 44.44%, followed by Klebsiella pneumoniae (12.21%), Pseudomonas aeruginosa (11.1%) and Proteus mirabilis (5.55%). Isolates of E. coli showed high level of resistance to cephalothin (85.83%), ticarcillin (82.5%), ampicillin (73.3%) and amoxicillin-clavulanic acid (58.33%). Imipenem was the most effective antimicrobial agent.

These results highlight the inappropriate utilization of antibiotics and suggest the need to improve prescription practices in our country.

Prostatitis affects about 16% of men in their lifetime and sometimes leading to prostate cancer. Bacterial infections are the most common causes of prostatitis. Diagnosis of the causative agents of bacterial prostate infections plays an essential role in timely treating and preventing secondary complications. This study isolated bacterial infectious agents in patients’ surgical prostate and evaluated them by routine and molecular microbiological methods.

In this cross-sectional study, 72 prostate biopsy specimens were collected from the Orology Departmen of hospitals of Qazvin University of Medical Sciences. All samples were cultured in aerobic and anaerobic conditions. Antibiotic susceptibility test by Kirby-Bauer standard method was performed for all isolated bacteria. In addition, all isolated bacteria were identified using 16S rDNA PCR and sanger sequencing methods. Also, TaqMan real-time PCR was applied to detect Ureaplasm aurealyticum, Mycoplasma hominins, and Mycoplasma genitalium.

In conventional culture method, out of 18 positive samples, 15 samples (83.3%) were Gram-negative bacteria and 3 samples (16.6%) were Gram-positive bacteria, containing Escherichia coli (55.5%), Klebsiella pneumoniae (11.1%), Enterobacter cloacae (5.5%), Pseudomonas aeruginosa (11.1%), Staphylococcus aureus (11.1%), and Enterococcus faecalis (5.5%). The results of molecular identification methods were the same as conventional culture results. Also, four patients were Ureaplasm aurealyticum, and three patients were positive for Mycoplasma hominis.

Most bacteria isolated from prostate specimens belonged to the Enterobacteriaceae family, especially Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae. Staphylococcus aureus and Enterococcus faecalis were cocci isolated in the specimens too. Also, Ureaplasma urealyticum, and Mycoplasma hominis were identified in prostatitis.

Insertion of an External Ventricular Drain (EVD) is a common and important lifesaving procedure that can lead to morbidity and mortality. This study was conducted to assess the infection rate, risk factors, causative organisms, and outcome of EVDs.

A prospective study was undertaken in a tertiary care centre from August 1st to October 30th, 2020. Over 192 patients had undergone insertion of EVDs in the neurosurgical intensive care unit. CSF samples were collected in sterile containers and transported to the laboratory.

A total of 214 EVDs were inserted in 192 patients for 691 days. The median duration for EVD in situ and the mean time between catheter insertion and onset of infection were 14.5 days and 8 days. EVD related infection rate was 19.4 for 1000 EVD days. The most common risk factor for EVD insertion were tumors (55%) followed by hydrocephalus (40%).We identified 25 patients out of 192 (12%) who had clinical signs and symptoms with deranged CSF counts. A total of 13/25 (52%) specimens were culture positives out of which 10 (76.9%) were Gram negative pathogens and 3 (23%) were Gram positive pathogens and 3/10 (30%) Gram negative pathogens were Multidrug resistant organisms (MDROs).

It was observed that longer duration of catheter in situ was an important risk factor for EVD-related infections (ERIs) and also higher frequency of CSF sampling. A proper EVD infection prevention and control protocol must be followed in the form of a checklist at the time of EVD insertion.

Acinetobacter baumannii has emerged as a major organism accounting for hospital acquired infections particularly in intensive care units. Due to production of different kinds of beta lactamases these bacteria have developed drug resistance rendering the treatment of such infections very difficult and expensive. Rapid identification of A. baumannii producing such beta-lactamases is the need of the hour in reducing morbidity and mortality associated with A. baumannii infections.

A. baumannii was isolated from clinical samples like endotracheal aspirates, sputum, urine, exudates using standard culture techniques. Identification and drug sensitivity was done using Vitek 2 system. All the isolates were subjected to detection of ESBLs using phenotypic confirmatory test, plasmid mediated AmpC beta- lactamase by AmpC disc test, Carbapenemase production by CarbAcineto NP Test and Modified hodge method.

149 A. baumannii isolates were analysed for antimicrobial susceptibility and various beta-lactamase production. Results were evaluated for statistical significance using Chi-Square and P value. 81.8% of isolates were from male patients with majority of them above 50 years of age. 88.5% of samples were from ventilator associated pneumonia patients. 83.8% of isolates were sensitive to tigecycline. Only 10% to 12% of isolates were sensitive to carbapenems. 23.4% of isolates were ESBL producers and 46.9% of them were AmpC producers. Modified Hodge test method identified 63.7% of A. baumannii as carbapenemase producers where as CarbAcineto NP test identified 63% and exibiting 94.74% sensitivity, 93.22% specificity when compared to Modified Hodge test.

Multidrug resistant Acinetobacter spp. is on the rise. Present study showed that high percentage of drug resistance in A. baumannii could be due to production of ESBLs, AmpC and carbapenemases. Among all beta lactamases carbapenemase producers are more and quickly raising in A. baumannii. Rapid, cost effective assay which can be adopted in all clinical laboratories is critical to prevent their further transmission particularly in hospital environment.

Torque Teno virus or transfusion-transmitted virus (TTV) is a non-enveloped virus with a single strand circular DNA genome that currently is classified in the Alphatorquevirus genus and the family of Anelloviridae. Unlike other DNA viruses, TTV has an extremely wide genomic diversity. This virus, based on previous studies, infects both healthy people, as well as those who have HCV and human papillomavirus (HPV). This study aimed to evaluate the coinfection of torque teno virus (TTV) and HPV in cervical samples from Iranian women.

In this case-control study, the fresh cervical cytobrush specimens were collected from 150 women referred to Dena laboratory in Tehran. Viral DNA was extracted from samples. The HPV-DNA was detected and genotyped. Then, nested polymerase chain reaction (Nested PCR) was performed for TTV using specific primers.

Among 50 cervical specimens without HPV, 14 were TTV positive (28%); among 50 low-risk HPV cervical specimen, 23 were TTV positive (46%), and from 50 high-risk HPV cervical specimen, 48 were TTV positive (96%). There is a significantly higher prevalence of TTV virus in low-risk and high-risk papillomavirus-infected specimens than in healthy specimens (p 0.0001). Additionally, TTV is more prevalent in samples containing high-risk papillomaviruses than in samples with low-risk papillomaviruses (P = 0.048).

The higher prevalence of TTV among people infected with papillomavirus than in non-infected people indicates that both viruses are transmitted by the same mechanism (sexual route). In addition, the prevalence of TTV in samples containing high-risk papillomavirus is significantly higher than that in samples containing low-risk papillomavirus. The presence of papillomaviruses, particularly high-risk types, may be associated with TTV proliferation, which requires further research in the future.

DNA extraction is an important step of any molecular experiment. DNA could not be easily extracted from members of actinomycetes by the usual methods of lysis. Due to the low efficiency of the conventional DNA extraction methods, development of an effective technique for DNA extraction of actinobacteria in emergency cases seems to be necessary. Since most of the DNA extraction techniques and commercial kits are not efficient enough to extract DNA from actinobacteria, this study was conducted to improve an efficient method obtained from conventional one to extract DNA from this group of bacteria.

DNA extraction was performed using five methods (an improved method, Invisorb Spin Plant Mini Kit, EZ-10 Spin Column, Sarrbrucken method (HZI, Germany) and Kirby Bauer's method). To evaluate the quantity and quality of extracted genomic DNA, UV absorbance of all samples and efficiency of polymerase chain reaction (PCR) were evaluated.

Overall, the results revealed that the highest quantity (up to 4000 ng/µl) and good quality of DNA was obtained using introduced DNA extraction method.

Results indicated that recently introduced improved method was more efficient for extraction of DNA from actinobacteria for DDH (DNA–DNA hybridization) test and for those require the high concentration of DNA.

House-keeping genes are generally selected as reference genes in gene expression analysis. However, some genes may not be stably expressed across all experimental conditions. Thus, this study aimed to validate seven house-keeping genes for gene expression analysis in Bacillus siamensis 1021.

Strain 1021 was grown in potato dextrose broth, nutrient broth and mineral salt medium. Reverse-transcription quantitative PCR was used to determine Cq values of seven reference genes including gyrA, gyrB, ssb and dnaB, rpsU, gat_Yqey and udp in these media. Expression stability of these genes was analyzed, using geNorm and Normfinder applications. The target gene ftsZ was used for assessment of the best candidate genes.

Based on geNorm and Normfinder, ssb was the most-stably expressed gene, while udp was the least-stably expressed gene. Pairwise variation indicated the combination of ssb, gyrA, gyrB and gatB_Yqey was suitable for the normalization of ftsZ expression. ftsZ expression in potato dextrose broth and mineral salt medium was higher than that in nutrient broth. In contrast, the normalization against udp resulted in an under- and overestimation of ftsZ expression in potato dextrose broth and mineral salt medium, respectively.

The combination of ssb, gyrA, gyrB and gatB_Yqey was the best candidate for normalization of target gene expression in B. siamensis 1021 in these media. This study emphasized the significance of reference gene validation for gene expression analysis and provided a guideline for future gene expression studies in B. siamensis.

With the emergence of Pseudomonas aeruginosa antibiotic-resistant strains, using the antibacterial potential of bacteriophages could be an effective approach to combat bacterial infections.

In this study, after evaluation of antibiotic sensitivity of 20 clinical bacterial isolates of Pseudomonas aeruginosa, isolation of lytic phages was performed against 15 isolates using double-layer agar overlay technique. Molecular analysis of isolated phages was carried out using EcoRV and HindIII endonucleases. Then, the host range of the phages was evaluated and the phage with the broadest host range (PPaMa1/18) was selected to morphological characteristics by TEM. Also, its one-step growth curve was determined and the stability of the phage to environmental parameters (temperature and pH) was evaluated.

All isolates of Pseudomonas aeruginosa were resistant to five antibiotics. In total, 15 phages were successfully isolated from the sewage sources against each of 15 used bacterial isolates. Molecular analysis of the phages showed a high rate of genomic variation. In the morphological analysis of the selected phage (PPaMa1/18) using TEM, an icosahedral head with a size of 90 nm × 75 nm and a long contractile tail (215 nm) were observed which indicated its similarity to the Myoviridae family. The latent period of the PPaMa1/18 was about 20 minutes and its burst size was estimated to be 58 PFU/cell. Also, the PPaMa1/18 phage antibacterial activity was not significantly affected at pH 4-10 and temperature 4-40C°.

Findings demonstrated that isolated bacteriophage (PPaMa1/18) with wide host range, strong lytic effect and high stability can be used as a promising candidate for the treatment of antibiotic-resistant infections caused by Pseudomonas aeruginosa.

Human health and development have been related to dietary intake of essential fatty acids (omega 3, 6 and 9) and important for brain development, immune system function, and blood pressure regulation. Microbial essential oils are more natural and safer alternatives to synthetic preservatives. These oils have been demonstrated to have antibacterial activity within food systems and may be ideal additives to food formulations. Zygomycete fungi are well-known as good candidate for production of essential oils.

Essential oils of fungi Mucor rouxii, Mucor circinelloides and Cuninghamella echinulata were extracted and fatty acids were analyzed by GC, for the first, antimicrobial activity of the fungi essential oils against foodborne pathogenic bacteria E. coli, S. aureus, B. cereus, B. subtilis, and S. enterica was examined by disc diffusion and well diffusion methods and the minimal inhibitory concentrations (MIC) of oils were determined by microtiter plate.

The fungi oils were exhibited the stron g antibacterial effect against Gram-positive bacteria, B. cereus, S. aureus and B. subtilis higher than Gram-negative and commercial oleic acid and linoleic acid. The MIC of the fungi oil extracts was 0.25 mg/ml for B. cereus and B. subtilis and 0.5 mg/ml about S. aureus. This research demonstrated microbial essential oils may be suitable for their antimicrobial properties in food.

Microbial essential oil with good antibacterial activity could also be used in selected cases like foodborne disease.

Bacteriocins are antimicrobial peptides produced by many genera of bacteria especially Lactobacillus spp. against many pathogens, adapt bacterial composition in the gut and inhibit dysbiosis that can lead to inflammation disorders like inflammatory bowel disease (IBD). The aim of this study was to compare the prevalence of bacteriocin genes in health, IBD disease and recovery conditions.

In this survey 115 Lactobacillus spp. from 58 fecal samples of three different groups were evaluated. Comparison of the presence of bacteriocin genes in different groups were assayed by purified samples and PCR method, followed by statistical analysis to identify the effect of inflammation in the proportion of Lactobacillus spp. and presence of their bacteriocin genomes.

Of 115 Lactobacillus spp. 60% of samples had positive bacteriocin-encoding genes which included: gassericin-A 29.56%, acidocin 15.65%, plantaricin-NC8 18.26%, plantaricin-S 13.04%, lactacin-F 9.5%, sakacin-P 6.08% and gassericin-T 6.08%. Results indicated that the percentage of positive bacteriocin genes were much more in healthy volunteer and IBD-recovered in comparison to IBD-patients which showed the effect of inflammation in the presence of bacteriocin genes.

The results obtained in this study demonstrated that the presence of bacteriocin genes can be related to health and disease states and inflammatory disease affected the prevalence of bacteriocin-encoding genes. This approach can help to identify bacterial functions that can be targeted in future concepts of IBD therapy.

Probiotics are added into the food or feed systems and provide beneficial effects to the human or animal health. This study aimed to isolate the gastrointestinal native Lactobacillus strains with high probiotic, cholesterol-assimilation and aflatoxin-degradation capabilities from native chickens.

About 70 Lactobacillus isolates were isolated from ileum of the Fars province native chickens and were investigated for their probiotic properties.

Of 70 Lactobacillus isolates, 10 showed high probiotic capabilities, including survival at acidic conditions (pH up to 2.5), tolerance of 0.5% bile and 6-10% NaCl salts, growth in a wide range of temperature from 15 to 45°C, antagonistic effects against different important bacterial pathogens (Pseudomonas aeruginosa, Escherichia coli, Streptococcus mutans, Clostridium defficile, Enterococcus hirae, Salmonella enterica and Staphylococcus aureus) and sensitivity to some important antibiotics. The selected strains had an aggregation time less than 120 min. The 16S-rDNA sequencing showed that the selected strains were highly related to Lactobacillus reuteri and L. casei. Finally, the selected strains in this study along with 10 other probiotic strains isolated and characterized in our pervious study were used to evaluate their cholesterol assimilation and aflatoxin B1 degradation capabilities. The potentials of cholesterol assimilation of the selected strains were significantly different (P<0.05) and ranged from 2.3% to 99%. The highest content of cholesterol assimilation was obtained in isolates M20 and M4 with more than 98% absorption. Moreover, four strains 43, OR7, M21 and OR9 were able to absorb AFB1 with 58.6%, 52.33%, 47% and 31.6% efficiency respectively.

It could be concluded that the strains 43, M21 and OR7 showed high probiotic potentials for application in the poultry industry.

Honey has excellent antibacterial properties against various microorganisms of several different species. To date, there is no comparative evaluation of the antibacterial activity of Jarrah honey (JH), Kelulut Madu honey (KMH), Gelam honey (GH), and Acacia honey (AH) with that of Manuka honey (MH). The purpose of this study was to conduct such study and to compare the antibacterial activity of JH, KMH, GH, and AH with that of MH against Pseudomonas aeruginosa and Streptococcus pyogenes.

Activity was assessed using broth microdilution, time kill viability, microtiter plate, scanning electron microscope (SEM) and Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR).

The susceptibility tests revealed promising antibacterial activities of all honeys against both bacteria. The MICs of JH, KMH, GH, and AH ranged from 20% to 25% compared to MH (12.5%) against both bacteria. The MBCs of JH, KMH, GH, and AH ranged from 20% to 50% compared to MH (20%) against both bacteria. Treatment of both bacteria with 2× MIC (Minimum inhibitory concentration) of MH, JH, KMH, GH, and AH for 9 hours resulted in reduction in colony-forming unit (CFU/ml). SEM images showed that the morphological changes, cell destruction, cell lysis and biofilm disruption in both bacteria after exposure to all honeys. RT-qPCR analysis revealed that the expression of all genes in both bacteria were downregulated following treatment with all honeys. Among the all-tested honeys, MH showed the highest total antibacterial and antivirulence activities.

Our results indicate that all honeys activity included inhibition of both bacteria due to a decrease in expression of essential genes associated with both bacteria, suggesting that all honeys could potentially be used as an alternative therapeutic agent against certain microorganisms particularly against P. aeruginosa and S. pyogenes.

Mahyaveh is a traditional Iranian fish sauce produced by fermentation and hydrolysis. The main production of Mahyaveh has been traditionally and scientific research and industrial measures has not been done on it with the aim to achieve a production with less microbial load. Therefore, the aim of this research was to study the type of fish, salt concentration and fermentation time on the bacterial population of Iranian fish sauce (Mahyaveh).

For this purpose, the effects of fish type (tuna, anchovy and sardine), salt concentration (15%, 25% and 35%) and fermentation time (30, 75 and 120 days) on the total microbial count, Micrococcus, Enterobacteriaceae and Bacillus were investigated. 15 treatments were designed according to the Box-Behnken Response Surface Methodology.

Simultaneous optimization to achieve the minimum total microbial count, Micrococcus, Enterobacteriaceae and Bacillus in the Mahyaveh sauce was obtained with 99.49% desirability at the time of 103.63 days of fermentation with the third type of fish (Sardine) and at a salt concentration of 29.38%.

By optimizing the conditions of producing Mahyaveh sauce, fish sauce can be produced with the least amount of microbial load with more health safety.

Candida species are antifungal-resistant opportunistic infections that spread through contaminated medical staff hands and hospital surfaces creating a nosocomial infection risk. Iodine´s antibacterial properties are well established; however, its antifungal properties remain unknown. The objective of this study was to investigate the antifungal effects of lugol on cell viability and oxidative stress on Candida albicans and Candida glabrata strains.

MTT reduction test and sensitivity growth assay were used to determine viability and minimal inhibitory concentration, colorimetric tests were used to analyzing lipoperoxidation and antioxidant status in C. albicans, parental C. glabrata, C. glabrata lacking catalase gene (cta1) and superoxide dismutase 1 and 2 double mutants (sod1∆ sod2∆) strains exposure to lugol were used.

In both C. albicans and C. glabrata wild types lugol treatment decreased cellular viability in a dose-dependent manner at 30 mm. The cytotoxic lugol effect was characterized by the increase of oxidative stress and the reduction of superoxide dismutase and catalase enzyme activities. C. glabrata strains lacking catalase (cta1) and superoxide dismutase 1 and 2 double mutants (sod1∆ sod2∆) were less resistant to lugol than parental C. glabrata strains.

In Candida strains iodine lugol solution has antifungal properties, producing cytotoxicity and oxidative stress. Superoxide dismutase 1 and 2 activities are involved in resistance of Candida to iodine.

Onychomycosis is caused by dermatophyte species, non- dermatophyte moulds (NDMs), and accounts for roughly 50% of all nail diseases. As the prevalence of onychomycosis is increasing, new epidemiologic documents may help with treatment and prevention. The present investigation aims to determine the epidemiological profile of onychomycosis in 2 mycology laboratories.

A cross-sectional study conducted during eight months (2019-2020) on 169 patients with positive nail mycology tests referred to two mycological laboratory centers affiliated with Tehran University of Medical Science. The nail clippings were examined by direct smear and culture. Also, molecular assays were performed if needed.

10% of nail lesions referred to Razi Hospital (RH), and 30% of nail lesions referred to TUMS mycology laboratory were positive. Middle age (40-60) suffer more from onychomycosis. Aspergillus flavus, Trichophyton mentagrophytes, and Candida albicans were the most common etiologic agents in each of the three main classes of fungi causing onychomycosis. Females were more infected. NDMs were the predominant etiologic agents, and toenails were the most common site of onychomycosis.

The pattern of etiologic agents and clinical signs of onychomycosis differs according to geographical region and age, so repeated epidemiological surveys of onychomycosis seem to be fundamental.