دو ماهنامه میکروب شناسی پزشکی ایران
سال شانزدهم شماره 2 (فروردین و اردیبهشت 1400)

Presently, viral diseases are incrementing all over the world, for which the definitive solutions are difficult since there are no effective drugs. In the 1990s, antiviral probiotics first appeared when they acted as drugs for protecting the intestinal epithelium against viral infection and reducing diarrhea. Thus, further studies have been performed to define the mechanisms behind this antiviral impact. Over 100 years ago, lactic acid bacteria (LAB) were accidentally utilized naturally exist in fermented products, against viral infections. Producing several active ingredients like active ribosomal proteins, acids, hydrogen peroxide, non-ribosomal synthetase peptides (NRPS), and other metabolites is an important feature of lactic acid bacteria. Numerous studies have recently assessed the significance of these active ingredients in both nutrition and medicine. LAB was utilized in food fermentation to present a good taste for food while protecting it from pathogenic microorganisms and spoilage. In this article, the LAB metabolites’ antiviral activity was assessed.

The pervasiveness of urinary tract infections (UTIs) with their clinical manifestations in patients with diabetes mellitus has escalated amidst the past decade or so, as myriad predisposing factors contribute to its occurrence. Although the causative agent of UTI is Escherichia coli, the etiopathogenesis can be traced back to glycosuria in the renal parenchymal region. This has precipitated pyelonephritis and renal complications, including cytopathic and altered metabolism. Furthermore, impaired immunity with scarce IL-6, 8 in urine, urinary retention, and dysfunctional voiding raise susceptibility towards uropathogens, mainly E. coli. Treatment for UTI with diabetes is based on symptoms and severity, urologic abnormalities, renal function, bladder infections, and metabolic alteration. The treatment process or regimens for patients with type 2 diabetes with asymptomatic bacteriuria are very low or negligible. Adequate management with antibiotic regimens in symptomatic patients after critical diagnosis is crucial for prophylaxis and effective treatment.

 A large group of genes associated with extended-spectrum beta-lactamases (ESBL) and AmpC expression is involved in inducing antibiotic resistance in various bacteria. Identifying these genes and assessing their harboring will be crucial in determining the pattern of antibiotic resistance. This study aimed to characterize genetic variants in extended-spectrum beta-lactamases, AmpC-producing gram-negative bacilli, and associated antibiotic resistance.

 This cross-sectional research was conducted on clinical samples of patients admitted to Rasool-e-Akram Hospital, Tehran, Iran (2019 and 2020). The genetic variants were assessed by the Polymerase chain reaction method. The pattern of durability to antibiotics was determined by the disk diffusion system.

Of the 80 isolates that produced ESBL and AmpC beta-lactamase, 75 cases were ESBL producers and 5 cases co-producers of ESBL and AmpC. The most common cultivated strains included Escherichia coli (61.2%) and Klebsiella pneumoniae (31.3%). The highest antibiotic resistance in ESBL producers was related to cefotaxime, trimethoprim-sulfamethoxazole, and cefazolin, and the lowest resistance level was related to colistin, cefoxitin, and ceftriaxone. The total frequencies of common genes of ESBL-producing gram-negative bacilli were blaCTX-M (76.0%), blaTEM (46.7%), and blaSHV (26.7%), while multigenic harboring was also observed in 49.3%. The level of drug resistance to Imipenem, Amikacin, and Ceftazidime in people who harbored the blaSHV gene was significantly higher than in other cases.

The most common cultivated strains included E. coli and K. pneumoniae. blaCTX-M, blaTEM, blaSHV, and multigenic expression were observed. The detection of the blaSHV gene is associated with increased antibiotic resistance to Imipenem, Amikacin, and Ceftazidime.

 Dermatophytosis is a superficial fungal disease. Prosopis farcta has attracted attention for ethnobotany and medical purposes. The present study aimed to investigate the antifungal properties of Prosopis farcta extracts against Trichophyton mentagrophytes (PTCC 5054) and five archived terbinafine resistant clinical isolates of T. mentagrophyte, based on an ethnobotanical report in Yazd province (Iran).

 In vitro drug susceptibility for methanol extract and amphotericin B was carried out according to the CLSI-M38-A2. A topical solution (1%) was formulated by root extract of P. farcta. The nine male Sprague rats were infected by T. mentagrophytes and assessed for in vivo anti-dermatophytic activity.

 The MIC value of amphotericin B was ≤ 0.5 μg/mL against all strains. The methanol extract showed the lowest MIC and MFC values on fungal activity (both with 0.00625 mg/mL). The complete cure of 21-day period with terbinafine is reduced to 10 days with methanol 80% root extract of P. farcta solution.

 Compared with amphotericin B, P. farcta could be considered a potential antifungal agent in terbinafine-resistant clinical isolates of dermatophytes.

 Increasing of resistant bacteria is a major concern globally. The emergence of XDR gram-negative bacteria is a more serious problem due to treatment limitations. This study aimed to evaluate the frequency of extensively drug-resistant (XDR) gram-negative bacterial isolates in different clinical samples from Payvand Clinical and Specialty Laboratory, Tehran, Iran, for 6 months by VITEK 2 system.

 During March 2020-September 2020, different clinical samples were collected from patients referred to Payvand Clinical and Specialty Laboratory. Bacterial identification and antimicrobial susceptibility test (AST) were performed applying an automated VITEK 2 system. The frequency of identified bacteria, their resistance to common antibiotics and also XDR bacteria were calculated and reported, respectively.

 Overall, 4125 urine specimens, 34 sputum samples, and 1 tracheal aspirate tube were submitted to Payvand Laboratory during 6 months. Of them, 486 urine, 32 sputum, and a tracheal aspirate tube samples were culture positive. Gram-negative isolated bacteria were included in this study. Based on AST, 63.3% of the isolated Klebsiella pneumoniae, 100% of Pseudomonas aeruginosa, and all Acinetobacter baumannii isolates were susceptible to amikacin and colistin. Totally, 31 XDR gram-negative bacteria, including: K. pneumonia (ssp. pneumonia (n=20), and ozaenae (n=2), Escherichia coli (n=3), P. aeruginosa (n=5), and A. baumannii (n=1) were identified from 18 urine samples, 12 sputum specimens, and a tracheal aspirate tube. 

 The rate of XDR bacteria was high in the investigated laboratory in this study. Therefore, accurate screening and antimicrobial stewardship is recommended in different medical centers of Iran.

 Klebsiella pneumoniae is one of the three pathogens that has become a global disease control and treatment problem due to its resistance to common antibiotics. For this reason, it is crucial to study the genes that cause antibiotic resistance in it. Therefore, the aim of this study was to investigate the phenotypic and genotypic frequency of tetracycline resistance in clinical isolates of K. pneumoniae in Tehran, Iran.

 In this study, 100 isolates of K. pneumoniae isolated from clinical samples (urine) during 2018-2019 were studied. In addition to microbial and biochemical phenotypic tests, genotypic tests were conducted to determine the frequency of antibiotic resistance genes tet (A, B, C, 39).

 Out of 100 isolates of K. pneumoniae, 49 isolates were resistant to tetracyclines. The results of multiplex PCR showed that 31 samples were positive for tetA gene, 8 isolates for tetB gene, 21 samples for tetC and, and 8 isolates for tet39. None of the isolates were positive for all four tetracycline genes.

 The results of this study showed that the isolates were positive for at least one gene and at most 2 tetracycline resistance genes. The tetA gene showed the highest frequency and the lowest frequency was demonstrated by tetB. The highest binary combination of genes was tetA-tetC, and the lowest was tetA-tet39.

 Alcaligenes sp. is a non-fermentative Gram-negative bacillus, which causes nosocomial infections, including urinary tract infections, pneumonia, sepsis, and may be confused with Pseudomonas aeruginosa. Alcaligenes infections usually are not well identified and due to possible errors and similarities with Pseudomonas, their diagnosis with phenotypic tests is not sufficient. In this case, molecular methods seem to be more effective. We aimed to investigate the real presence of clinical isolates of  Alcaligenes xylosoxidans and  Alcaligenes faecalis by phenotypical, and genetic methods and their antibiotic susceptibility.

 From September 2019 to March 2020, we analyzed 36 clinical isolates from a Sina hospital in Hamadan, Iran, which have been identified as Alcaligenes in the hospital's microbiology lab, by routine phenotypicall methods. Using the PCR method and tracking AX and 77F-r genes, we identified A. xylosoxidans and A. faecalis respectively; the antibiotic resistance of each isolate was determined by the disc diffusion method.

 Of 36 samples of phenotypically identified Alcaligenes, only 13 (36.11%) were confirmed as A. xylosoxidans and 3 (8.33%)  as A. faecalis by PCR test. Among A. xylosoxidans isolates, the highest susceptibility(92.3%) was against cephalosporin and the highest resistance (76.92%) was against ciprofloxacin. Among A. faecalis isolates, the most susceptibility (100%) was against ceftazidime, piperacillin/tazobactam, imipenem, meropenem, and cefepime, and the most resistance (66.66%) was against gentamicin and ceftriaxone.

 Regarding the importance of accurate diagnosis of Alcaligenes in combating nosocomial infections, it seems with phenotypic and biochemical tests, there is a possibility of error in their diagnosis; so using the PCR method, each species can be determined more accurately.

Acinetobacter baumannii is one of the most nosocomial pathogens as it can form biofilm on hospital surfaces. The objective of this work was to analyze the production of exopolysaccharides, extracellular proteins, and biofilm formation of carbapenem-resistant A. baumannii on silicone and ceramic surfaces.

Qualitative and quantitative tests were conducted to evaluate the production of exopolysaccharides in different culture conditions. The Biuret method was applied for protein determination. Furthermore, the count of viable cultivable cells was used to study biofilm formation. For physicochemical characterization, the surfaces were subjected to contact angle measurements.

Incubation at 37°C with glucose (1.5%) was the optimal condition for producing exopolysaccharides. Glucose supplementation has also impacted the protein production by A. baumannii. Moreover, proteins were abundant in the extracellular matrix compared to exopolysaccharides (0.46 mg/mL for exopolysaccharides and 2.48 mg/mL for proteins). The strains formed biofilms on both surfaces but with different capacities, possibly due to the hydrophilic nature of ceramic and the hydrophobic nature of silicone. The addition of 1.5% glucose enhanced biofilm formation on ceramic for all strains. A positive correlation was established between the EPS concentration and the number of cells forming biofilm on silicone with 0.2% of glucose and between protein production and biofilm formed on ceramic with 0.2% and 1.5% of glucose. On the contrary, a negative correlation was detected between protein production and biofilm formation on the silicone surface with 0.2% glucose concentration.

  The environmental conditions significantly affect A. baumannii biofilm and its extracellular matrix compounds.

 Antibiotic resistance is the ability of microbes to survive antibiotic exposure with standard doses. Regular updating of antibiotics is one solution to overcome antibiotic resistance. One source with potential new antibiotics is moonmilk from caves because it contains various bacteria proven to have antibacterial activity. The objective of the present study is to explore the potential of moonmilk microbes from Pindul cave, Indonesia, as a source of new antibiotic compounds.

 The antibiotic potency test was divided into six groups with various concentrations of isolated moonmilk bacteria (IMM) supernatant 25%, 50%, 75%, 100%, negative control (-), and positive control (+). All groups were further tested for antibiotic susceptibility using the disk diffusion (Kirby and Bauer) method to pathogenic resistant bacteria Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 25923 on Mueller Hinton agar medium. PCR and Sanger sequencing method using 16S rRNA primers was performed to identify species of isolated moonmilk bacteria.

 The 16S rRNA sequence analysis showed that the IMM shared a 99,64% (1399 nucleotide match) similarity with Bacillus licheniformis strain IND706. The results showed that moonmilk bacteria had antibacterial activity against E. coli ATCC 25922 and S. aureus ATCC 25923. The highest inhibition zone was observed for the bacterial extract concentration of 75% (42 mm) in E. coli ATCC 25922 and 100% (23 mm) in S. aureus ATCC 25923 medium.

 IMM supernatant extract from Pindul cave, Indonesia, has the potential to control antibiotic-resistant bacterial pathogens.

Before interventional clinical studies in humans, researchers usually perform preclinical studies in vitro or in vivo to evaluate the initial efficacy, toxicity, and pharmacokinetics of interventions. Sample size determination in animal studies is necessary both in terms of correct and scientific inference and in terms of ethics. Therefore, the purpose of this paper is a brief description of how to determine the sample size in a study on laboratory animals.