Iranian Journal of Microbiology最新文献

Background and objectives: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51'51″N 75°32'07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics.

Materials and methods: In the present study, physiochemical parameters including temperature (65-75°C), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis.

Results: Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs).

Conclusion: The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries.

Background and objectives: Bisphenol A (BPA) is a toxic compound with broad applications in the plastics industry. BPA has harmful effects on various organisms and its efficient removal is necessary. The microbial degradation of BPA is a safe and economical approach. In this research, soil samples containing decaying plants were screened to isolate a BPA-degradable bacterial strain.

Materials and methods: Soil samples were collected from different locations in Damghan, Semnan province, Iran. To enrich BPA-degrading bacteria, the samples were cultured in a stepwise manner in a mineral medium containing increasing BPA concentrations (5 to 40 mg/L). The ability of isolated bacteria in degrading BPA was assayed by Folin-Ciocalteu and high-performance liquid chromatography methods. The biodegradation efficiency of the most efficient isolate was assayed under distinct conditions and it was identified through the sequencing of the 16S rRNA gene.

Results: Among the isolated bacteria, Pseudomonas aeruginosa DU2 (GenBank accession number: OP919484) showed the most BPA biodegradation ability. The highest BPA degradation (52.98%) was observed in the mineral medium containing 5 mg/L BPA and the inoculum size of 6 × 10⁷ CFU/mL at pH 9 and in the presence of 0.05% (w/v) NaCl during 10 days.

Conclusion: These results offer soil containing decaying plants as a promising source for finding BPA-degrading bacteria. P. aeruginosa DU2 has basal BPA removal ability, which could be improved by optimization of medium components and growth conditions.

Background and objectives: Group A Rotavirus (RVA) is the most important causative agent of acute diarrheal disease in pediatrics 5 years and below. This study aimed to determine the distribution of circulating RVA in Mashhad, Iran to develop health improvement strategies and vaccine decision making.

Materials and methods: A total of 106 fecal specimens were collected from children admitted to Akbar and Dr. Sheikh referral pediatric hospitals of Mashhad City during the December 2020 to March 2021 and December 2021 to March 2022. All specimens were tested for specific bacterial, parasitic, and amoebic infections. Negative samples were analyzed for RVA infections using the RT-PCR method.

Results: RVA was detected in 31.3% of the specimens, indicating no statistical significance in gender distribution or between fall and winter positivity rates. The number of RVA-positive specimens increased following age increasing in the range of 1 to 60 months.

Conclusion: Today, acute diarrheal disease (ADD) is still caused mostly by Rotavirus infections in pediatrics in Mashhad. Comprehensive studies are needed to determine the genetic diversity of circulating Rotavirus strains in this era.

Background and objectives: Coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Monitoring the humoral immune responses during the natural course of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection and the duration of them provide useful information for the development of vaccination strategies against this virus and its emerging variants. The importance of the antibody response especially neutralizing antibodies in long-term immunity to SARS-CoV-2 is significant.

Materials and methods: The present study is a cross-sectional study of sero-epidemiological type that has been proposed to compare the persistence of Immunoglobulin G (IgG) against N (nucleocapsid), S (spike) and RBD (receptor-binding domain) proteins in the community after the time of primary disease. A total of 652 serum samples were collected from hospital staff working in COVID wards, as well as a number of community members with different occupations, among those with positive antibody titers, 86 participated in the resampling test before vaccination.

Results: There was no association between antibody titer and disease severity (p>0.05). A significant decrease in Ab levels was observed in the paired second samples. The highest rate of decrease was related to anti-N, then anti-RBD and anti-S IgG levels, respectively. There is a significant relationship between the initial antibody titer and its reduction over time (p-value <0.05).

Conclusion: Our data revealed that humoral immunity following natural infection of SARS-CoV-2 is detectable for at least 4 months, regardless of disease severity. The most decrease in antibody titer over time was related to anti-N IgG levels.

Background and objectives: A new type of corona virus has caused Corona virus disease-19 and, subsequently, a global pandemic. All individuals are prone to the disease, so drastic measures were taken to prevent its spread. This study aimed to evaluate the impact of COVID-19 on the progression of the antimicrobial resistance rate by comparing two periods: before and during COVID-19.

Materials and methods: We used a cross-sectional design to investigate the Antimicrobial Resistance (AMR) rate before (03/2019 to 03/2020) and during COVID-19 (03/2020 to 03/2021) in a University Hospital in Marrakech. The data were analyzed using SPSS Version 25.0.

Results: Among the 7106 specimens, there was a significant increase in the multidrug-resistant bacterial from 27.38% to 35.87% during COVID-19 (p<0.001), particularly in blood culture, cerebrospinal fluid, catheter, and pus. However, there was a non-significant change in puncture fluid, expectoration, protected distal sampling, joint fluid, stool culture, and genital sampling. A decrease in Multidrug-resistant bacteria (MDRB) was observed only in cytobacteriological urine tests (p<0.05). According to species, there was an increase in extended-spectrum beta-lactamase-producing Enterobacteriaceae, carbapenem-resistant Enterobacteriaceae, and methicillin-resistant Staphylococcus aureus.

Conclusion: In our study, it is particularly noticeable that the MDRB has increased. These results highlight the importance that the pandemic has not been able to slow the progression.

Background and objectives: Despite progress in diagnosing and managing ventilator-associated pneumonia (VAP), ongoing monitoring of ventilator-associated events (VAE) is crucial due to VAP's persistent prominence as the primary cause of Hospital-Acquired Infection (HAI) among Intensive Care unit patients. This study was done to illuminate the prevalence of VAE and antibiogram of bacterial isolates of VAP in a tertiary care hospital of Uttarakhand.

Materials and methods: This cross-sectional study focused on ICU patients. Adult patients ventilated for > 2 days were monitored daily, with VAE data analyzed using Center of Disease Control & Prevention (CDC) criteria. Specimens were sent to the Microbiology Department and cultured on Blood agar and MacConkey agar. Identification and antimicrobial profiles of isolates were determined using Vitek-2 Compact.

Results: 1220 ventilated individuals were assessed in total. VAE was diagnosed in 6.4% (78/1220) of the patients, the same later developed ventilator associated condition (VAC), 74 developed the infection-related VAC (IVAC), and 60 developed the possible/probable VAP (PVAP) among the 78 VAE cases. Klebsiella pneumoniae (35%), Acinetobacter baumannii (33%), and Pseudomonas aeruginosa (16%) were the most common isolated organisms. Colistin (57%) was the most effective against Klebsiella pneumoniae, followed by amikacin (28.5%) and trimethoprim+sulfamethoxazole (24%). Pseudomonas aeruginosa was most susceptible to imipenem (70%), meropenem, cefoperazone+sulbactam, and colistin (60%). Acinetobacter baumannii was most susceptible to colistin (85%), tigecycline (65%), and trimethoprim+sulfamethoxazole (25%).

Conclusion: The most common cause of HAI is VAP. The purpose of this study is to determine the importance of starting suitable antibiotics early for prognosis and the difficulty of diagnosing VAP.

Background and objectives: Respiratory infections are the most serious condition in cystic fibrosis (CF) patients; therefore, a thorough comprehension of the diversity and dominant microbial species in CF airways has a crucial role in treatment. Our objective was to determine the antibiotic resistance profile of CF airways microbiota and compare culture methods and PCR-DGGE to evaluate bacterial diversity.

Materials and methods: Pharyngeal swabs from 121 CF patients were collected. The samples were then cultured, identified and antibiotic resistance testing was performed. Thirty samples were subjected to further molecular surveys. DNA contents of these samples were extracted and amplified using nested-PCR technique and their bacterial diversity was assessed by DGGE. The DGGE patterns were visualized and certain bands were excised and purified. Next, the DNA was amplified by another round of PCR and sent out for sequencing.

Results: Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae were the most prevalent species isolated using culture methods. S. aureus was the most common bacteria among 6 years and younger patients; while, P. aeruginosa had more prevalence among older ones. The PCR-DGGE results showed more diversity than culture methods, particularly in younger patients who exhibited more bacterial diversity than the older groups. Sequencing results unveiled the presence of certain bacterial species including Haemophilus parainfluenzae and Stenotrophomonas maltophilia which were completely missed in culture.

Conclusion: Even though culture-dependent methods are cost-effective, PCR-DGGE appeared to be more efficient to determine bacterial diversity. PCR-DGGE detects less abundant species, though their viability could not be determined using this method.

Cryptococcosis, a relatively uncommon infection in cancer patients is often associated with delayed diagnosis and high fatality rate due to its highly heterogeneous and protean manifestations. Early recognition and initiation of appropriate antifungal therapy might have a favourable outcome in such cases. Here we report three cases of Cryptococcosis among cancer patients in a tertiary care cancer centre in South India. All three patients were males of different ages at presentation with immunosuppression in the form of solid organ or hematologic malignancy and were using immunosuppressive medications like steroids or chemotherapeutic agents. They presented with cryptococcemia and cryptococcal meningitis. Patients with microbiologically proven cryptococcosis had poor outcome in this subgroup of patients.

Background and objectives: AmpC-producing Gram-negative bacterial (GNB) pathogens are distributed worldwide, especially in clinical settings. This study aimed to determine the antibiogram and the type of AmpC-β-lactamase gene harboured by GNB pathogens implicated in chronic suppurative otitis media (CSOM) cases.

Materials and methods: Ear swab samples (300) collected from patients with active CSOM were analysed using standard microbiological techniques. Phenotypic and molecular detection of AmpC β-lactamase production was done by cefoxitin/cloxacillin double-disk synergy test and PCR respectively. Antibiogram was determined by disk diffusion technique.

Results: Among the GNB pathogens isolated from CSOM patients, P. aeruginosa was the most predominant (36.3%); followed by K. pneumoniae (22.3%), and E. coli (13.7%). Patients with active CSOM showed increased bacteria isolation rate from bilateral ear discharges than unilateral ear discharges. E. coli and P. aeruginosa were more prevalent among patients with duration of discharge >2 weeks; recording 9.0% and 20.3% respectively. AmpC β-lactamase producers accounted for 14.0%; they were highly resistant (60%-100%) to cephalosporins, trimethoprim-sulfamethoxazole, ofloxacin, amoxicillin, and tetracycline, but very susceptible (70.4%-100%) to ciprofloxacin, imipenem, and amikacin. Multiple antibiotic resistance indices of isolates ranged from 0.7-0.8. FOX-AmpC-β-lactamase gene was detected in 3.9% of the isolates.

Conclusion: The detection of AmpC β-lactamase-producing multidrug-resistant GNB pathogens harbouring FOX-AmpC-β-lactamase gene among patients with CSOM infections in our study is a serious public health problem which needs urgent intervention.