Editorial Note

Mohammad Medhdi Feizabadi

Editor

Iranian Journal of Microbiology

On the occasion of World Antimicrobial Resistance (AMR) Awareness Week, November 2024, we witnessed a lot of events throughout our country, Iran. Many different specialists throughout the country debated on the current situation, however, no one can predict the future outlook of this ongoing issue. The health policy makers try to find the right solutions for combating the drug-resistant superbugs but they should not ignore Microbiology principles. Carbapenem-resistant Klbesiella pneumoniae infections are definitely the main causes of morbidity and mortality in the Iranian Hospitals. In the current issue of this Journal, Dr. Solgi and his colleagues have raised an important and critical point: New Delhi metallo-beta-lactamase (NDM-MBL). Unfortunately, the number of cases infected with ceftazidime/avibactam-resistant Gram-negative bacteria has increased due to NDM-MBL production (Nearly 87% of K. pneumoniae clinical isolates in Isfahan). Therefore, our country resources are wasted with the current official protocol for administration of ceftazidime/avibactam, despite knowing that NDM-MBL producers are dominant. Physicians should be aware of the current situation of MBL strains in Iran, which is attainable through reviewing works published by Microbiologists in different provinces of Iran.

No abstract

Background and Objectives: Nosocomial pneumonia caused by multidrug-resistant gram-negative bacteria presents a significant challenge for healthcare systems, as there are limited effective treatments available. This systematic review and meta-analysis aim to investigate the outcomes of colistin plus meropenem combination therapy on nosocomial pneumonia.
Materials and Methods: An exhaustive search of PubMed, Scopus, Web of Science (WOS), and Embase databases was conducted, resulting in the extraction of 5 studies for qualitative assessment and meta-analysis. The study sample included 991 patients admitted with nosocomial pneumonia. The outcomes evaluated were clinical improvement, microbiological response, mortality, Sequential Organ Failure Assessment (SOFA) score, Acute Physiology and Chronic Health Evaluation (APACHE II) score, Charlson Comorbidity Index (CCI), Clinical Pulmonary Infection Score (CPIS), C-reactive protein (CRP) levels, procalcitonin (PCT) levels, and intensive care unit (ICU) duration.
Results: The results demonstrated that colistin plus meropenem combination therapy significantly improved clinical outcomes (OR = 1.37, 95% CI = 1.04-1.81, p = 0.027), reduced SOFA scores (OR = -0.28, 95% CI = -0.44 to -0.11, p = 0.001), and increased CCI scores (OR = 0.16, 95% CI = 0.02-0.29, p = 0.021) compared to other medications. However, other evaluated parameters did not show significant differences.
Conclusion: This meta-analysis indicates that colistin-meropenem combination therapy is superior to other colistin-based treatments for nosocomial pneumonia in terms of clinical improvement, SOFA score reduction, and CCI score increase. Nevertheless, other variables assessed did not exhibit remarkable differences between the treatment regimens.

Background and Objectives: The incidence of multidrug-resistant, Gram-negative organisms, isolated as the etiological agents of infections is ascending. The advent of novel antibiotics poses significant challenges, necessitating the optimization and utilization of extant antimicrobial agents. Cefoperazone, a third-generation cephalosporin and β-lactam antimicrobial, when combined with sulbactam, an irreversible β-lactamase inhibitor, mitigates the vulnerability of cefoperazone to β-lactamase-producing organisms. Nonetheless, regional data on the susceptibility patterns for this pharmacological combination remains scarce. The primary objective of this investigation was to assess the efficacy of the cefoperazone-sulbactam combination against prevalent Gram-negative bacteria isolated from blood cultures.
Materials and Methods: A total of 700 Gram-negative isolates, comprising Escherichia coli, Klebsiella pneumoniae, Acinetobacter species, and Pseudomonas aeruginosa, were procured using the BacT/Alert 3D system. The identification and susceptibility testing for cefoperazone-sulbactam were performed using the VITEK Compact ID and AST system. Comparative analysis was conducted against other tested antibiotics.
Results: The study revealed that cefoperazone-sulbactam exhibited commendable in-vitro activity against Gram-negative pathogens isolated from blood, surpassed only by colistin and tigecycline.
Conclusion: Cefoperazone-sulbactam demonstrates robust activity against the most frequently encountered clinical pathogens, suggesting its potential as an efficacious therapeutic agent. The findings underscore the imperative for ongoing surveillance of resistance patterns and trends among commonly used antimicrobials.

Background and Objectives: The global problem of urinary tract infections (UTIs) caused by antibiotic-resistant bacteria is due to limited treatment options. This study aimed to examine the prevalence, etiology, and management implications of Escherichi coli causing UTI at Imam Hospital Ardabil, Iran.
Materials and Methods: 2340 samples of retrospective data on E. coli causing UTIs were collected at Imam Hospital in Ardabil, Iran, spanning from 2012 to 2022. The samples were cultured and isolated, and their antibiotic susceptibility was determined using standard laboratory methods and data were then organized and systematically categorized using Python.
Results: It was found that the lowest level of resistance was related to nitrofurantoin, followed by imipenem. In 2018, the number of E. coli patients resistant to trimethoprim was the highest. Cephalexin and ciprofloxacin trends indicate the reduction of the line during this retrospective period. There was a significant correlation between wards and some antibiotics like Cefepime, Cefotaxime, Ceftazidime, and Trimethoprim (P-Value <0.05).
Conclusion: Significant correlations were identified between specific hospital wards and resistance to antibiotics. These findings underscore the need for continuous surveillance and tailored antibiotic stewardship programs to combat the rising trend of antibiotic resistance.

Background and Objectives: Klebsiella pneumoniae is a common pathogen associated with healthcare-related infections. It is particularly notable for its ability to develop resistance to multiple antibiotics, making treatment challenging. During the COVID-19 pandemic, increased antibiotic use to manage critically ill patients was contributed to the rise of multidrug-resistant Klebsiella pneumoniae. This study evaluated the antibiotic resistance patterns of multidrug-resistant, ESBL-producing Klebsiella pneumoniae in northern Iran after the COVID-19 pandemic.
Materials and Methods: This cross-sectional study was conducted between September 2022 and October 2023. Clinical samples were collected from patients with nosocomial infections at hospitals in Sari. This study included 114 multidrug-resistant ESBLs-producing Klebsiella pneumoniae isolates. Antimicrobial susceptibility was assessed using broth macro-dilution, and resistance genes were detected by multiplex PCR.
Results: Gentamicin, ampicillin-sulbactam, co-amoxiclav, and ceftazidime displayed the lowest activity against multidrug-resistant Klebsiella pneumoniae. In contrast, piperacillin-tazobactam showed the highest activity. The prevalence of resistance genes was as follows: bla_TEM (99.12%), bla_SHV (74.56%), bla_CTX (88.60%), bla_IMP (64.04%), acrA -B (92.98%), and OqXA -B (67.54%).
Conclusion: This study identified over 50% of antibiotic-resistance genes. Over half of multidrug-resistant Klebsiella pneumoniae isolates showed resistance to antibiotics except piperacillin-tazobactam, which is recommended for treating multidrug-resistant Klebsiella pneumoniae infections.

Background and Objectives: Salmonellosis is among the most common food-born infections, caused by Salmonella spp. bacteria. Present study has investigated the frequency and antibiotic resistance pattern of Salmonella spp. isolated from traditional dairy products and raw milk supplied in Yazd, Iran.
Materials and Methods: In a cross-sectional study, 350 samples of raw milk and traditional dairy products were randomly collected from July to September 2018. Following culturing the samples, isolates went through biochemical tests for phenotypic identification. Results were confirmed through PCR technique by targeting invA gene. Antimicrobial susceptibility test was conducted by means of disk diffusion method.
Results: The rate of contamination with Salmonella bacteria was 6.57% in all samples. The PCR assay of all isolates showed that 23 isolates (100%) carried the invA gene. No significant association between the frequency of salmonella spp. and types of dairy and their origin was reported (P>0.05). The highest antibiotic resistance rate among the isolates belonged to tetracycline (34.8%) and the highest sensitivity was seen to imipenem, cefepime, and cefotaxime (each 91.3%).
Conclusion: According to our results there has been a rise in multiple drug resistance and contamination rate in traditional dairy products in Yazd province.

Background and Objectives: The most common cause of severe foodborne salmonellosis is S. Typhimurium. Its interaction with intestinal epithelial cells is little known. Lactic acid bacteria (LAB) were recognized as a prominent probiotic gastrointestinal microbiota of humans and animals that confer health-promoting and protective effects. This study aims to determine the anti-invasion and antibacterial effects of heat-killed LAB (HK-LAB) isolates against S. Typhimurium towards human intestinal cells.
Materials and Methods: 12 HK-LAB isolates from 3 sources of origin (stingless bee, plant, and food) were tested to determine the adhesion of HK-LAB to Caco-2 cells, anti-invasion and antibacterial activities against S. Typhimurium, the adhesion and invasion pattern of S. Typhimurium on intestinal epithelial cells (Caco-2) and assessing the effect of LAB on the S. Typhimurium-host cell interaction.
Results: Tairu isolates from food have the highest adhesion rate with 19 ± 1.32/10 Caco-2 cells followed by HK-LAB R-isolate from plant 17 ± 0.70/10 Caco-2 cells, which is similar to the control (Lactobacillus casei). In the anti-invasion assay, the two HK-LAB isolates that had the strongest adherence to Caco-2 cells, Tairu-isolate inhibited at 78.1 ± 3.06% and R-isolate inhibited at 64.76 ± 9.02% compared to the positive control (63.81 ± 1.15%), which led to increased suppression of S. Typhimurium accordingly. Tairu and R isolates were tested for their antibacterial ability against S. Typhimurium. Both R and Tairu isolates displayed strong inhibition zones (27 ± 0.06 mm, 23 ± 0.06 mm) respectively.
Conclusion: These findings suggest that the anti-invasion activities of HK-LAB R and Tairu may correlate to their bactericidal effects that serve to protect the host from infection.

Background and Objectives: Helicobacter pylori (H. pylori) is a bacterium involved in gastrointestinal disorders with a high prevalence in Iran. We have determined the seroprevalence of H. pylori in the young adult population of Mashhad city for the first time.
Materials and Methods: We carried out a cross-sectional study on 933 individuals between the ages of 15 and 35 in Mashhad. The serum level of IgG, IgM, and IgA H. pylori antibodies was determined using enzyme linked immunosorbent assay (ELISA) method.
Results: The average age of the participants including 290 (31.0%) male and 643 (68.9%) female cases was 25.47 ± 5.76. H. pylori IgG was seropositive in 365 (39.1%) of subjects. Occupation (p=0.002), body mass index (p=0.002), marital status (p<0.0001), and age (p<0.007) were meaningfully related to H. pylori IgG seropositivity. Other factors such as sex, educational attainment, history of chronic diseases, and smoking cigarette had no significant relationship with the presence of H. pylori antibodies.
Conclusion: The seroprevalence of H. pylori IgG antibodies in Mashhad's 15 to 35 years old citizens was determined 39.1%. We suggest further studies with larger sample sizes and different age groups as the target population.

Background and Objectives: Recently, the anti-herpetic activities of different plant species have been investigated. This study evaluated the effects of Teucrium stocksianum aqueous extract on the HSV-1 virus-infected Vero cell.
Materials and Methods: The IC₅₀ of the aqueous extract was obtained by the maceration of the plant in boiling water and has been measured with the MTT method, also the q-PCR was used to study viral gene expression reduction.
Results: Results of the MTT test indicated that the highest percentage of metabolic activity was observed in the 75 μg/ml concentration of Teucrium stocksianum’s aqueous extracts (IC₅₀=45.5μg/ml). Time intervals of 24 and 48 hours after viral infection revealed that the cell viability is reduced by the viral infection time (MOI=0.1), log 10^-3, p <0.001). Furthermore, the plant’s aqueous extract concentration almost avoids cell viability reduction. Through Q-PCR results; the reduction of viral proliferation revealed that the low expression of genes UL46 and US6 were significant in the presence of different treatments utilized in the experiment.
Conclusion: T. stocksianum, has an anti-viral property and may be considered as a remedy for anti-HSV-1 agents.

Background and Objectives: Medicinal plants are the primary treatment for many infectious and non-infectious diseases. In this study, we evaluated the antiviral activity of Ferula assa-feotida against herpes simplex viruses 1 and 2, and compared it with the antiviral drug acyclovir.
Materials and Methods: In our experimental study, Ferula assa-feotida was dissolved in DMSO, then diluted in DMEM medium. Acyclovir was used at a concentration of 100 μM in all procedures. The antiherpetic activity and Antiviral activity of Ferula were evaluated in Vero cells (African green monkey kidney cells) by using the plaque reduction assay.
Results: Inhibitory concentrations of 50% (IC₅₀) of Ferula assa-feotida for HSV-1 and HSV-2 were determined at 0.00025% and 0.00015%, respectively. Ferula was introduced at various stages of viral infection and significantly inhibited HSV-1 and HSV-2 infectivity by > 95.5% and 89%, respectively, when virus was pre-treated before addition to the cells. No HSV-1 or HSV-2 activity was detected in cells treated prior to and following viral infection.
Conclusion: These results indicate that Ferula assa-feotida demonstrates antiherpetic activity in the early phase of viral infection and could be used as potential antiviral agent.

Background and Objectives: Airway fungal infection is a severe clinical problem, especially in patients with compromised immune functions. Here, we examined the distribution and antifungal susceptibility profiles of fungal agents isolated from respiratory tract of symptomatic patients hospitalized in pulmonary units.
Materials and Methods: This descriptive cross-sectional study took place from 2023 to 2024, involving 360 patients. Bronchoalveolar lavage (BAL) or sputum specimens were collected and analyzed using mycological and molecular methods for this study. Antifungal susceptibility testing (AFST) was carried out using the broth micro dilution method.
Results: Of a total of 360 respiratory specimens, 114 (31.6%) were positive. The male-to-female ratio was 63:51 (1.3%). Candida albicans and Aspergillus flavus were the most common yeast and mold species. Chronic obstructive pulmonary disease (COPD) had the highest rate of colonization with fungal agents (47/114, 41%). The isolates associated with COPD in this study included Aspergillus species (4/12, 3.5%), Candida species (41/96, 36%), and other fungal species (2/6, 1.5%). Coughing (87%) was the predominant symptom, and malignancy (52%) was the predominant comorbidity factor. The result of AFST for antifungal agents showed that 9 (22.5%) Candida isolates were resistant, and the highest rate of resistance was related to voriconazole agent (5/9, 55.5%). Resistance to antifungal agents was not observed among Aspergillus isolates.
Conclusion: This study showed a significant relationship between the frequency of Aspergillus and Candida species in patients with underlying lung diseases. In addition, voriconazole was more effective than itraconazole, especially against Aspergillus flavus.

Background and Objectives: Understanding the epidemiology of Candida species among cancer patients is crucial for preventing invasive infections. This study aimed to identify Candida species and assess risk factors among cancer patients receiving chemotherapy in Birjand, eastern Iran.
Materials and Methods: The samples were obtained from the oral cavity of 140 patients and the initial identification of Candida species was carried out through fungal cultures. Subsequently, Candida isolates were molecularly identified using the PCR-RFLP method with the restriction enzyme Msp1. Furthermore, the demographic characteristics, risk factors, and clinical history of the patients were extracted and scrutinized using a multiple logistic regression model.
Results: Among the 140 patients examined, 55 individuals (39.3%) tested positive for oral candidiasis (OC). Notably, Hemorrhagic cancer emerged as the most common type of cancer associated with OC (46.7%). The predominant species isolated was the Candida albicans complex (64.8%), followed by the Candida glabrata complex (26.8%). A noteworthy finding was the significant association between the occurrence of OC and the number of chemotherapy sessions (P<0.05). Conversely, no significant correlations were detected between OC and variables such as sex, age, type of cancer, occupation, residence, underlying disease, and drug use (P>0.05).
Conclusion: The prevalence of Candida spp. and its correlation with the number of chemotherapy sessions underscored the importance of preventive measures. These findings provided valuable insights for designing targeted interventions to mitigate the burden of oral candidiasis in this vulnerable population.

Background and Objectives: Plant growth-promoting rhizobacteria (PGPR) with a diverse set of traits can improve crop yield in agriculture. The current study aimed to evaluate the potential of multi-trait PGPR isolates as inoculants for maize (Zea mays L.) growth.
Materials and Methods: In this study, 23 bacterial isolates were initially screened from maize plant rhizosphere. Ten isolates (A1–A10) were selected based on N fixation, P and K solubilization and their in vitro specific PGPR traits, such as solubilization of Zn, and Mn, the production of IAA, siderophore, ammonia, and HCN were assayed. Finally, the potential of selected isolates in enhancing the germination, height, shoot collar diameter, shoot fresh and dry weight biomass, and root dry weight of maize were evaluated.
Results: Among the positive-PGPR colonies, the selected isolates demonstrated the better performance of PGPR traits such as highest nitrogen fixation, P, K, Mn, and Zn solubilization, and production of siderophore, HCN, NH3, and IAA. In addition, the maize seed germination and improvement of maize yield in a pot experiment were observed after their treatment by bacterial inoculants. Biochemical characteristics, 16S rDNA amplification, and sequencing demonstrated a high similarity of PGPR isolates to the strains of Enterobacter, Pantoea, Kluyvera, Lelliottia, Klebsiella, Pectobacterium, and Stenotrophomonas.
Conclusion: The findings demonstrated that these strains could prove effective PGPR inoculants for the improvement of maize crops as multiple bio-fertilizers.

Background and Objectives: The study focused on the amylase enzyme, widely used in the industrial starch liquefaction process. We looked into the best way to immobilize the native strain Bacillus licheniformis, which is the only alpha-amylase-producing bacterium, by trapping it in calcium alginate gel. This is a promising way to increase enzyme output.
Materials and Methods: We examined the effects of alginate content, biomass age, initial cell loading (ICL), bead size, and solidification duration in calcium chloride solution on enzyme synthesis. We conducted batch fermentations using both immobilized and free cells.
Results: Alpha-amylase production significantly increased with the alginate concentration ratio, achieving a maximum enzyme yield of 23.5 U/mL at a 30 g/l alginate concentration, utilizing an initial cell loading of 1.5 g in 150-200 beads per flask. These involved cells from a 12-hour culture with a bead size of 5.0 mm, were solidified for 24 hours in a 2.5% (w/v) calcium chloride solution. The yield of the immobilized cells was approximately 111.71% higher than that of the free cells, which produced 11.1 U/ml. The immobilized cells consistently generated alpha-amylase over five repeated cycles, attaining a peak value of 23.5 U/ml during the first cycle, which was 2.2-fold more than the control (free cells).
Conclusion: We used a basic mass balance analysis to understand the growth of both fractions and the dynamics of amylase production in free cells and cells immobilized in Ca-alginate beads. The production of alpha-amylase in immobilized cells results in enhanced volumetric activities during fermentation. Notable advantages of this technique encompass prolonged stability, reuse and recycling, and the potential for adaptable regeneration.

Background and Objectives: The study aimed to investigate the epidemiology and clinical therapy of candidemia in burn patients hospitalized in Velayat Hospital, Rasht, Iran.
Materials and Methods: The blood samples of suspected patients were cultured and PCR-sequencing was performed. Antifungal susceptibility testing was done by the CLSI M27-A4 document.
Results: Four blood samples were identified as positive. Candida parapsilosis complex (3 out of 4, 75%) was the predominant leading cause of candidemia. MIC values showed that all isolates were susceptible to itraconazole, amphotericin B, and 5-flucytosine.
Conclusion: It seems necessary to pay attention to Candida non-albicans species in antifungal therapy.