Iranian Journal of Microbiology
Volume:15 Issue: 3, Jun 2023

Antibacterial resistance (AMR) is a serious threat and major concern, especially in developing countries. Therefore, we aimed to determine phenotypical patterns of resistance to antibiotics in COVID-19 patients with associated bacterial infection in intensive care units.

In this cross-sectional study, 6524 COVID-19 patients admitted for more than 48 h in the ICUs of Imam Khomeini Complex Hospital (IKCH) in Tehran from March 2020 to January 2022 were included in the study with initial diagnosis of COVID-19 (PCR test and chest imaging). Data were collected regarding severity of the illness, primary reason for ICU admission, presence of risk factors, presence of infection, length of ICU and hospital stay, microbial type, and antibiotic resistance. In this study, the pattern of antibiotic resistance was determined using the Kirby–Bauer disk diffusion method.

In this study, 439 (37.5%) were ventilator-related events (VAEs), and 46% of all hospitalized patients had an under- lying disease. The most common microorganisms in COVID-19 patients were carbapenem resistant Klebsiella pneumoniae (KPCs) (31.6%), Escherichia coli (E. coli) (15.8%), and Acinetobacter baumannii (A. baumannii) (15.7%), respectively. Prevalence of vancomycin-resistant enterococci (VRE) and KPCs were 88% and 82%, respectively.

A study on AMR surveillance is the need of the hour as it will help centers to generate local antibiograms that will further help formulate national data. It will guide doctors to choose the appropriate empiric treatment, and these studies will be the basis for establishing antimicrobial surveillance and monitoring and regulating of the use of antimicrobials.

Community-acquired pneumonia (CAP) is one of the most common life-threatening infec- tions, occurring in the community or within the first 48 hours of a patient's hospitalization. The present study aimed to investigate the frequency of pathogenic bacteria and their antibiotic resistance pattern in the sputum of patients with commu- nity-acquired pneumonia in Yasuj from 2018 to 2019.

In the present study, 128 patients with CAP were included. Under aseptic conditions clinical samples including sputum collected from each patient were sent to the Microbiology Laboratory. Specific culture media and biochemical tests were used to identify the bacteria. Antimicrobial resistance patterns of the isolates were examined by disc diffusion. DNA was extracted from sputum using the phenol-chloroform method. The PCR method was used for the molec- ular detection of bacteria. Data were analyzed using SPSS software version 22 and the chi-square test.

The most common clinical symptoms in patients were sputum (68.8%), fever (64.1%), shortness of breath (60.2%), cough (50.8%), and chest pain (24.2%). A total of 133 bacteria were identified by culture and 117 bacteria by PCR. In the current study, the most prevalent organisms were Streptococcus pneumoniae (24.1%), Hemophilus influenzae (18%), Staph- ylococcus aureus (13.5%), and Moraxella catarrhalis (11.4%). Antibiogram test showed that most of the Gram-negative bacteria were resistant to levofloxacin (22.6%), rifampin (20.8%) and ceftriaxone (17%), and the highest resistance rate to clindamycin (43.1%), ciprofloxacin (43.1%) and amoxicillin (41.4%) were detected in the Gram-positive bacteria. Cefepime was the most effective antibiotic against Gram negative bacteria.

S. pneumoniae was the most prevalent bacteria identified by culture and PCR methods in patients with CAP, indicating an important role of this bacterium in the pathogenesis of CAP. According to the results, cefepime can be used to treat patients with CAP with Gram-negative bacteria. In the present study, S. pneumoniae, S. aureus, P. aeruginosa, H. influenzae, M. catarrhalis, and K. pneumoniae have been isolated from the CAP patient population with varying frequencies. This is consistent with various studies in different parts of the world.

This study aimed to investigate epidemiology of Staphylococcus epidermidis (S. epidermidis) and Acinetobacter baumannii (A. baumannii) infections in neonatal intensive care unit (NICU) in a period of 8 years.

This retrospective cohort study was conducted on 46 cases of nosocomial infection by S. epider- midis, and 44 neonates with A. baumannii in NICU of Valiasr hospital, Iran.

The trend of A. baumannii and S. epidermidis infection were as follows: 1 and 7 in 2014, 11 and 7 in 2015, 20 and 11 in 2016, 1 and 4 in 2017, 4 and 6 in 2018, 4 and 4 in 2019, 0 and 1 in 2020, and 3 and 6 in 2021-March 2022 respectively. Mortality proportion (%) in neonates with S. epidermidis and A. baumannii infection was at 8.3 and 32.1, respectively. There was a strong positive correlation between number of infected neonates in month and average of prescribed antibiotics before incidence of infection in every baby in that month. Fluconazole prescription before incidence of infection were associated with the A. baumannii infection in month too. Amikacin prescription had adjusted correlation on increasing of A. baumannii and S. epidermidis infection in month.

It seems reducing of hospitalization duration and medication prescriptions management plays an important role in reducing of nosocomial infections

Microorganisms producing Metallo-Beta-Lactamase (MBL) are a threat and cause of concern as they have become one of the most feared resistance mechanisms. This study was designed to explore the prevalence of MBL production in clinical isolates of Gram negative bacteria using phenotypic MBL detection.

A total of 248 isolates were collected from various clinical samples and were evaluated for car- bapenem resistance and MBL production. All strains were screened for MBL production using Double Disk Confirmatory Test (DDCT).

The results of screening for MBL production using phenotypic disk diffusion method showed that in the 85 isolates were carbapenemase positive; including, 10 (16.1%) Klebsiella pneumoniae, 9 (14.5%) Escherichia coli, 58 (93.6%) Acine- tobacter baumannii, and 8 (12.9%) Pseudomonas aeruginosa isolates. Also, 83 (97.6) Carbapenemase-producing isolates were resistant to at least four classes of antimicrobials (MDR).

A. baumannii was the most common carbapenem resistant bacterium in medical centers in Kermanshah. Signif- icant multiple drug resistance (MDR) incidence was observed compared to different classes of antibiotics.

Plasmid-mediated AmpC producers are considered an increasing concern. The aim of this study was to investigate the prevalence of plasmid-mediated AmpC β-lactamases (pAmpCs) in Klebsiella pneumoniae iso- lates.

A total of 228 clinical isolates of K. pneumoniae were collected in Bushehr province, Iran, from December 2017 to February 2019. Cefoxitin disks were applied for screening AmpC-producing isolates. Furthermore, 3 phe- notypic confirmatory tests including combine disk test (CDT), double disk synergy test (DDST) and modified three dimen- sional test (M3DT) were used. Finally, the presence of pAmpC genes was tested by multiplex PCR.

We identified 18 pAmpC-KP isolates among the 228 isolates (7.9%): 12 DHA (66.6%) and 6 CMY (33.3%). In the present study only 47% of cefoxitin-resistant isolates were pAmpC producers. The sensitivity of CDT, DDST, and M3DT was 89%, 67% and 100% and the specificity was 90%, 90% and 85%, respectively. In addition, M3DT displayed a higher rate of efficiency (92%) than CDT (89%) and DDST (79%) in detecting plasmid-meditated AmpC producers.

DHA was the most prevalent pAmpC beta-lactamase in this study. DDST and CDT tests proved inefficient to detect two and six pAmpC producers, respectively, while M3DT represented the best overall performance.

The immediate emergence of resistant bacteria poses an increasingly growing problem to human society and the increasing prevalence of antibiotic resistance in Escherichia coli strains is one of the most important health problems. This study aimed to review the molecular epidemiology of drug resistance among clinical isolates of E. coli in north-west portion of Iran Azerbaijan.

A complete of 219 clinical isolates of E. coli had been collected from the various clinical samples. The disk diffusion and agar dilution assays were used to determine antimicrobial susceptibility. The presence of antibiotics resistance genes was carried out by the PCR method.

The highest susceptibility was shown to imipenem (3%) and fosfomycin (3%), and the most antibiotic resis- tance was presented to ampicillin (99%). The highest frequent ESBL gene among isolates was bla CTXM-15 in 70% followed by bla CMY-2 in 67%, and bla TEM-1 in 46%. The most common fluoroquinolone (FQ) resistance genes were oqxB (34%), fol- lowed by oqxA (25%), and qnrB (18%). The frequency of tetracycline resistance genes (tetA, tetB, tetC, and tetD) were de- tected in 24.8%, 31.6%, 1.8%, and 4.2%, respectively. The highest frequent genes to fosfomycin were fosA 10%, fosA3 30%, fosC 40%, and fosX 20%. The dominant founded aminoglycosides resistant genes were armA (12.96%) and npmA (4.93%).

The prevalence of antibiotics resistance in the tested E. coli isolates was high in Azerbaijan, Iran and these findings showed that E. coli is one of the major drug-resistant pathogens.

Sternum infection increases the time of the patients stay in the hospital and, as a result, increases the treatment costs. This study aimed to evaluate the fungal and bacterial co-infection in the superficial and deep sternal wounds after open cardiac surgery and its relationship with risk factors, as sternal infection increases the time of the patient's stay in the hospital and, as a result, increases the treatment costs.

Data were collected using a questionnaire and sampling with two swabs after open heart surgery and hospitalization from 21 March 2018 to 20 March 2019 and sent to the laboratory for diagnosis of microorganisms effective in wound infection. Susceptibility testing for fluconazole and specific antibiotics was performed by the disk diffusion method.

Out of 210 patients studied, 2% of patients had deep sternal wound infections. The most common coinfection fungal and bacterial agents in sternal wounds were caused by Staphylococcus aureus with Candida glabrata 4% and Escherichia coli with Candida albicans 2%. S. aureus and E. coli showed the highest antibiotic susceptibility to the antibiotics ciproflox- acin, norfloxacin, meropenem, and imipenem. Candida glabrata and Candida albicans had the highest rate of resistance to fluconazole.

According to the results of this study, patients on the 7th day in the cardiac care unit (CCU) and the 28th day are at higher risk of getting confection of fungi with bacteria in the sternal wound. Therefore, timely and appropriate antibiotic therapy, including the use of appropriate antibiotics, can be an important step in the patient's recovery.

In clinical diagnostics, molecular methods are used to detect Mycobacterium tuberculosis bacilli (MTB) and to distinguish them from non-tuberculous mycobacteria (NTM). They are also used to make the right treatment decision for the patient as soon as possible. The aim of this study was to establish a rapid and novel multiplex PCR (mPCR) assay for the detection and differentiation of MTB and NTM in a single tube.

100 sputum samples positive for acid-fast bacilli (AFB) were included in this study. Mycobacterial culture, biochemical tests, and antibiotic susceptibility testing were performed on samples. After alkaline decontamination, total DNA was extracted from the samples. A primer pair targeting the rpoB gene, encoding the beta-subunit of RNA poly- merase, was used to detect MTB and NTM, amplifying a 235-bp fragment of MTB and a 136-bp sequence of NTM. A pair of primers targeting a 190-bp fragment of the IS6110 region of MTB was also used to confirm the results. The sensitivity and specificity of the mPCR assay were evaluated using DNA extracted from standard strains. The amplified products were then analyzed by conventional agarose gel electrophoresis.

Of 100 AFB smear-positive sputum samples, 92 MTB DNA, 7 NTM DNA, and one mixed-infection sample were identified in a single tube using mPCR assay. There was no correlation between the AFB degree of smear positivity and PCR results. Of seven NTM isolates, 6 (86%) were resistant to rifampin, isoniazid, and ethambutol, the three first-line anti-tuber- culosis drugs.

A single-tube mPCR assay based on the rpoB gene provides a rapid and reliable means of detecting and differ- entiating MTB and NTM in sputum specimens.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the main causes of high mor- tality and morbidity in hospitals. This study was aimed to examine virulence factors, molecular typing, and the antibiotic resistance pattern of MRSA isolates in hemodialysis patients and healthy communities.

Total of 231 and 400 nasal samples were obtained from hemodialysis patients and healthy com- munities, respectively. Virulence factors profile was examined in two groups by PCR reaction. Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR) was used as a molecular typing approach.

Overall, 35.49% (82/231) of hemodialysis patients were positive for S. aureus, and 47.56% (39/82) of isolates were positive for mecA. In a healthy community, 15% (60/400) of samples were positive for S. aureus, and 36.66% (22/60) were positive for mecA. The frequency of MDR was significantly higher in patients group (p-value < 0.00001). The frequency of pvl (p.value = 0.003932, P<0.05) and tsst-1 (p.value = 0.003173, p < .05) were significantly higher in patients group. The highest frequency virulence factors in healthy individuals were related to hla (68.33%, 41/60), hlb (53.33%, 32/60), and Acme/arcA (46.66%) genes. Two groups were clustered by the ERIC-PCR method into 7 clusters and 2 single isolate with a 0.74 similarity index. Based on the results, each cluster was combination with healthy and patient isolates.

Our findings indicate a notable variation in the frequency of virulence factors between S. aureus isolates ob- tained from dialysis patients and the healthy community.

The study aimed to investigate whether Achromobacter mucicolens IA strain biofilm forma- tion, which contributes to antibiotic resistance, could be enhanced by readily available nutrient sources like carbohydrates and environmental factors such as pH and NaCl. Additionally, the study aimed to identify any inherent genes that support biofilm formation in this strain, which is an opportunistic pathogen that affects immunocompromised patients and is resistant to many antibiotics.

Biofilm growth in different carbohydrate, pH, and NaCl concentrated media was measured using crystal violet microtiter assay. All the treatments were subjected to biostatistics analysis for normality, Test of Homogeneity, one way ANOVA analysis. Whole-genome sequencing of our IA strain was conducted to identify various gene sequences.

Biofilm formation was measured at different carbohydrate concentrations, and the optimum biofilm formation was observed at 3M glucose and 0.5M NaCl, while the lowest results were seen at 2M maltose concentration. Whole-genome sequencing identified potential genes involved in biofilm formation, pathogenicity, protein metabolism, flagellar motility, cell wall component synthesis, and a multidrug efflux pump.

These findings suggest that biofilm formation is influenced by extrinsic and intrinsic factors, which could aid in the development of effective treatments for resistant infections.

Biosurfactants are amphiphilic surface-active agents that mainly produced by various micro- organisms. In this study, the anti-biofilm and inhibition of bacterial adhesion activities of two bacterial biosurfactants were investigated.

After extraction and evaluation of Bacillus cereus and Serratia nematodiphila biosurfctants, inhi- bition of bacterial adhesion and anti-biofilm effects of them on Staphylococcus aureus and Pseudomonas aeruginosa were determined.

On average, the synergistic effect of two bacterial biosurfactants, caused about 60% decrease in adhesion and about 80% decrease in biofilm formation of S. aureus and P. aeruginosa.

The results of this study showed that combination of B. cereus and S. nematodiphila biosurfactants would in- crease the potential of attachment inhibition and biofilm eradication with very low toxicity.

Anaplasmosis is a zoonotic disease caused by Gram- negative bacterium from Anaplasmata- ceae family. Anaplasma causes high economic losses worldwide. 16S rRNA analysis was used to diagnose Anaplasma platys in Cattle. Phylogenetic tree and estimation of evolutionary divergence between A. platys isolates were performed.

A total of 60 blood samples were collected from a cattle farm in AL- Diwaniyah province. 16S rRNA gene was identified using nested PCR. Overall, 40% of cattle that were chosen to collect the blood were identified to be infected with A. platys.

The results have shown presence of targeting partial region of 16S rRNA gene in 24 samples out of 60. Sequenc- ing results of 10 samples have revealed that the phylogenetic tree was divided in to two separate clades. Five isolates of A. platys- Iraq (accession no. OP646782, OP646783, OP646784, OP646790, and OP646791) were located in one clade with the A. platys- China (accession no. MN193068.1). While, five isolates (accession no. OP646785, OP646786, OP646787, OP646788, OP646789) were in different clade with two isolates of A. platys- Africa and A. platys- Zambia in distinct branch- es, close to the Rickettsiales.

The phylogenetic study of A. platys sequences indicated that the isolates were collected from a cattle farm in Al- Dewaniyah were similar and close related to A. platys- China, A. platys- Zambia and A. platys- Africa). This study suggests that cattle can be considered a reservoir of A. platys.

The lactobacilli are abundant in honey, helping protect against pathogens and providing antimicrobial properties. This study aimed to isolate lactobacillus species from different honey regions and evaluate their potential probiotic properties.

Eighty-eight samples were collected from different regions, including the northern, central, and southern areas, and obtained through retail stores. All samples were independently examined for the presence of Lactoba- cillus using both culture and real-time PCR methods. Probiotic tests were performed on the isolated Lactobacillus strains, including hemolytic activity, bile, acid, and pepsin resistance. Additionally, the antibiotic resistance of the obtained strains was investigated using seven different antibiotics.

Thirteen Lactobacillus isolates were obtained from 7 (8.0%) honey samples. Of these, eight isolates were identified as L. plantarum (61.54%), four isolates as L. rhamnosus (30.77%), and one isolate as L. acidophilus (7.69%). All strains were devoid of hemolytic activity, and three isolates (23.07%) were found to be resistant to acid, while 2 (15.38%) showed resistance to bile and pepsin. All isolates were resistant to vancomycin (100%). Additionally, only one strain exhibited resis- tance to all tested antibiotics. Furthermore, the present study demonstrates a significant association (p-value<0.05) between the presence of Lactobacillus in various regions of Iran.

Various factors, such as climatic conditions and geographical location, can influence honey's composition and microbial diversity. Identifying and isolating potential probiotic species in honey could significantly expand their use in the food and pharmaceutical industries, offering numerous health benefits and potential therapeutic applications.

17 β- estradiol (E2) is an important pollutant of the aquatic system. It is responsible for sexual disruptions in the majority of aquatic organisms. This study aimed to search for bacteria with high potential degradation of E2 as an important method for bioremediation.

Sewage water samples were collected and treated to isolate bacterial strains which were identified by conventional methods and 16S ribosomal RNA gene sequence analysis. The biodegradation of E2 by the isolated strains was evaluated under different environmental conditions.

Two bacterial strains were recovered from sewage water samples and identified as Stenotrophomonas tumulicola and Serratia marcescens, (named ASc2 and ASc5 respectively). Co-culture of the two strains showed biodegradation of approximately 93.6 % of E2 (50 mg. L-1) within 48 hours. However, the biodegradation capacity of the same E2 concentra- tion was 69.4% and 71.2% for ASc2 and ASc5 each alone, respectively. The optimum cultivation conditions for efficient E2 biodegradation by co-culture were 5% (v/v) inoculation volume with 50 mg. L-1 of E2 as the initial concentration at pH 7 and 30°C within 48 hours inoculation period.

This study detected new bacterial strains that are capable of rapid degradation of estrogen as an environmental pollutant.

The aim of this study was to investigate the in vitro antifungal potency of the moronecidin-like peptide against Candida albicans, Candida glabrata, and Candida tropicalis.

To evaluate the antifungal effect of moronecidin-like peptide, the protocol presented in CLSI M27-A3 and CLSI M27-S4 was used and the minimum inhibitory concentration was determined.

The minimum inhibitory effect of moronecidin-like peptide composition was 8 μg/ml for Candida tropicalis and Candida albicans and 32 μg/ml for Candida glabrata. The MIC of nystatin was determined to be 1.25 μg/ml for Candida glabrata and Candida albicans and 0.625 μg/ml for Candida tropicalis strains. The MFC composition of the moroneci- din-like peptide was determined for Candida tropicalis and Candida albicans strains 8 μg/ml and for Candida glabrata strain 64 μg/ml. The results of cytotoxicity and hemolysis of the moronecidin peptide test on macrophage showed that moronecidin peptide has no cytotoxicity and toxicity properties.

According to the results of the present study, the moronecidin-like peptide could be a new strategy in the treat- ment of infections caused by Candida strains. The discovery of the exact mechanism of which requires extensive clinical studies in this field.

Human rhinovirus (HRV), a major cause of common cold, was associated to the hospitaliza- tion of children and adults. This cross-sectional study aimed to determine the prevalence, and genotype distribution of HRV in the patients with mild to severe respiratory infections who were negative for SARS-Cov-2.

Nasopharyngeal swab specimens (n = 356) from the patients aged 29 days to 82 years, received for the respiratory virus detection from January to December 2021, were analyzed for human rhinovirus (HRV) by RT- PCR. As a final step, genotyping was performed on obtained sequences.

A total of 37 HRV infections were identified (37/356, 10%). The highest rates of positive HRV tests were observed in February (21.6%), and January (18.9%), compared with June and August (0%). HRV-positive cases mainly appeared in winter. Among the age groups, those 2-<5 years of age had the highest detection rate (21%), however, those >55 years of age had the lowest detection rate (3%). Among HRV-positive samples, 30 (81%) were identified as type HRV-A, 5 (13.5%) as HRV-B, and 2 (5.5%) as HRV-C.

Our results suggested that HRV frequency gradually decreased with the age of patients which is more active in Iran, especially in the cold months.

HPV infections cause a wide spectrum of pathological changes in lower anogenital epithe- lium. The aim of this study was to investigate the HPV DNA status and histological findings in cervical biopsy specimens diagnosed as flat condyloma.

This study included 20 cervical biopsy specimens diagnosed as flat condyloma. The histopatholog- ical criteria and presence of HPV DNA were evaluated. HPV genotyping was determined in HPV-positive specimens using BioEdit software and the results were analyzed in SPSS software.

HPV DNA was not found in 30% of specimens and relative frequency of HPV genotypes was: 15% HPV6, 15% HPV11, 5% HPV16, 5% HPV18, 5% HPV53, 5% HPV68, 5% HPV84, 10% HPV45. Relative frequency of histopathologi- cal criteria was as below: 100% of specimens had koilocytosis, 100% acanthosis, 15% nuclear immaturity, 100% atypia, 15% mitotic activity, 50% dyskeratosis, 35% parakeratosis and 10% hyperkeratosis.

There were significant differences between HPV positivity and two pathologic criteria; multinucleation and hyperkeratosis (P Value: 0.02). Nuclear immaturity was significantly more prevalent in high risk HPV-positive specimens (P Value: 0.03).

HTLV-1 is responsible for two important diseases, HAM/TSP and ATLL. Approximately 10 to 20 million people are infected with HTLV-1 worldwide. Identifying altered genes in different cancers is crucial for finding potential treatment strategies. One of the proteins of the RAS/MAPK signaling pathway is MEK1, which is made from the MAP2K1 gene. The effects of the MAP2K1 gene on the MAPK signaling pathway are not yet fully elucidated. The current study aims to determine the MAP2K1 gene mutations and the level of MAP2K1 gene expression in ATLL patients compared to healthy individuals.

Ten ATLL and 10 healthy control individuals were investigated in this study. We used ELISA test to screen anti-HTLV-I antibodies and PCR for confirmation of infection. Then, we extracted total RNA from fresh whole blood, and cDNA was synthesized. The expression levels of the MAP2K1 gene were examined by qRT-PCR, and to check possible mutations in the MAP2K1 gene; all samples were sequenced and analyzed by BioEdite Software.

MAP2K1 gene expression in the ATLL group was significantly higher than in the healthy control (P=0.001). The mutational sequencing analysis showed nucleotide 212 (S→R) change and identification mutations at different nucleotides that were entirely different from the nucleotide mutations defined in the UniProt database.

These results could be a perspective in the prevention, prognosis, and targeted treatment of diseases in which the MAP2K1 gene plays a vital role.