Iranian Journal of Microbiology最新文献

Background and objectives: Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality in both ICU and non-ICU patients. Timely identification of causative pathogens and antimicrobial resistance (AMR) genes is critical for optimizing therapy. This study evaluated the diagnostic performance of the BioFire FilmArray Pneumonia Panel (BFPP), a multiplex PCR assay, for pathogen and AMR detection in LRTI cases at a tertiary care hospital in India.

Materials and methods: A retrospective study was conducted over 29 months (October 2022-February 2025) on 251 respiratory specimens from clinically suspected LRTIs. BFPP was performed for bacterial, viral, and AMR gene detection, with results compared to conventional aerobic bacterial culture. Diagnostic yield, co-infection rates, and concordance were assessed using kappa statistics.

Results: BFPP detected at least one pathogen in 81.7% of samples versus 44.2% by culture, with 55.8% showing polymicrobial infections. Sensitivity was 94.6%, with moderate agreement with culture (κ = 0.428). Among 251 cases, predominant bacteria included Acinetobacter baumannii (29.5%), Klebsiella pneumoniae (24.7%), and Pseudomonas aeruginosa (19.9%).Major viral agents were human rhinovirus/enterovirus (15.1%) and influenza A virus (13.1%). Among 174 AMR-positive cases, bla _CTX-M (59.2%), bla- _NDM (56.9%), and bla _OXA-48 (46.6%) were the most frequently detected resistance genes.

Conclusion: The BioFire FilmArray Pneumonia Panel (BFPP) demonstrated high diagnostic sensitivity of 94.6% and detected pathogens in 81.7% of suspected LRTI cases, compared to 44.2% positivity by conventional culture. BFPP identified 69 additional pathogens missed by culture, enabling earlier targeted therapy and improved diagnostic stewardship in ICU and non-ICU settings.

Background and objectives: Helicobacter pylori infection has been increasingly linked to extra-gastric diseases. Outer membrane vesicles are a key virulence factor of H. pylori. This study investigates the influence of H. pylori-derived outer membrane vesicles on inflammatory marker expression in human hepatoma cells (HepG2).

Materials and methods: Outer membrane vesicles were isolated through ultracentrifugation and characterized using dynamic light scattering technique (DLS) and a Field Emission Scanning Electron Microscope (FE-SEM). Protein concentrations were measured via the Bradford assay. HepG2 cells treated with outer membrane vesicles were analyzed for IL-6, TNF-α, TLR-4, TGF-β, and PPAR-γ mRNA expression by RT-qPCR. Cell viability was assessed through an MTT assay. The prevalence of H. pylori virulence-associated genes (babA2, sabA, and oipA) was determined by PCR.

Results: The results showed a high prevalence of sabA (91.7%), babA2 (75%), and oipA (66.7%). FE-SEM and DLS analyses confirmed the presence of bleb-shaped nanovesicles ranging in size from 50 to 450 nm. H. pylori-derived outer membrane vesicles significantly upregulated the expression of pro-inflammatory markers (TLR-4, PPAR-γ, TNF-α, and IL-6), while downregulating TGF-β expression.

Conclusion: These findings underscore the potential role of nanoparticles in driving inflammatory responses and influencing host cell signaling, which may play a key role in liver-related pathologies.

Background and objectives: The antimicrobial resistance of Pseudomonas aeruginosa bacteria limits the spectrum of effective antibiotics. Considerable focus has been placed on the identification of more contemporary and cost-effective antimicrobial drugs. In this study, the antibacterial properties of a commonly used solvent, dimethyl sulfoxide (DMSO), against P. aeruginosa were investigated.

Materials and methods: The microtiter broth dilution technique was employed to establish the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of DMSO. The solvent's impact on bacterial growth, biofilm formation and eradication was assessed. A quantitative polymerase chain reaction (qPCR) was carried out to assess the effect of varying DMSO concentrations ranging from 1% to 8% (v/v) on quorum sensing gene expression.

Results: All P. aeruginosa strains exhibited a DMSO MIC of 25% v/v and MBC of 50% v/v. DMSO caused significant growth inhibition and suppression of biofilm formation in all P. aeruginosa strains at sub-inhibitory concentrations, i.e. 1%-8% v/v. At these concentrations, the samples showed a reduction in biomass and reduced metabolic activity. These effects were concentration-dependent. A DMSO strength of 8% v/v was associated with a statistically significant downregulation of most of the quorum sensing genes; at a DMSO titer of 1% v/v, this effect was modest with only a few genes being significantly affected.

Conclusion: DMSO is a potential therapeutic agent against P. aeruginosa as it has been demonstrated that it exhibits antimicrobial characteristics. Moreover, the impact of DMSO on bacterial growth and biofilm formation complicates its use as a solvent in biologic and clinical research.

Background and objectives: Tuberculosis (TB) is an infectious disease that is among the most common in the world and is a leading cause of high mortality and morbidity. In India, there is very limited data on second line drug susceptibility testing. The aim of the study was to find out the prevalence of Multi Drug Resistant (MDR) isolates among Mycobacterium tuberculosis (MTB) complex strains and to assess the sensitivity pattern to four commonly used 2^nd line anti-tubercular drugs irrespective of their MDR status.

Materials and methods: A 61 culture-positive strains of the tuberculosis complex (smear positive or negative) in Mycobacterium Growth Indicator Tube (MGIT) and Lowenstein Jensen (LJ) from various clinical samples were included. We performed MGIT 1^st and 2^nd line susceptibility testing for tuberculosis.

Results: Among the 61 isolates, 12 (19.6%) were multi drug resistant. Capreomycin resistance was observed in 17 (27.8%) isolates, kanamycin resistance in 30 (49.1%), ofloxacin resistance in 5 (8.1%), and ethionamide resistance in 6 (9.8%) isolates. Resistance to kanamycin and ethionamide was more common among patients with multi drug resistant tuberculosis (MDR-TB) than among those with non-MDR-TB.

Conclusion: The MGIT system has surpassed solid culture and is an excellent method for performing culture and drug sensitivity testing for tuberculosis. However, its use remains limited by economic and logistical challenges. The high prevalence of aminoglycoside resistance suggests the need to preserve these drugs for treating patients with MDR-TB.

Background and objectives: Poultry production generates huge quantities of waste, mainly from slaughterhouses, which can be major reservoirs of pathogenic microorganisms. Escherichia coli is of particular concern due to its ability to acquire antibiotic resistance and virulence factors. This study aimed to characterise E. coli contamination in poultry slaughterhouse waste from ten municipalities in the district of Abidjan (Côte d'Ivoire).

Materials and methods: E. coli strains were isolated from poultry slaughterhouse waste and identified using morphological and biochemical methods. Antibiotic susceptibility was assessed by the disk diffusion method, and virulence genes, including eae and stx1, were detected using a duplex PCR assay.

Results: Between January and April 2023, waste samples were collected, and E. coli strains were isolated and identified. Of 90 isolates, high resistance rates were observed against β-lactams (88.88%), aminoglycosides (77%), and fluoroquinolones (88.87%). MDR was detected in 11.11% of isolates, while 20% produced ESBL. The eae and stx1 genes were detected in 14.47 and 6.57% of isolates, respectively.

Conclusion: These results highlight significant antimicrobial resistance and virulence potential in E. coli from poultry slaughterhouse waste, underscoring the need to improve management strategies.

Background and objectives: Tight junctions (TJs) in the gastrointestinal tract are comprised of various junctional proteins including Occludin and Zonula Occludens (ZO-1) that have a critical role in epithelial barrier function. Gut microbiota and their derived metabolites can maintain and regulate gut epithelial barrier integrity.

Materials and methods: In the present study, the effects of active, heat-inactivated, cell-free supernatant, and outer membrane vesicles (OMVs) of Akkermansia muciniphila were evaluated on the expression of occludin and ZO-1 genes in Caco-2 cell line by quantitative real-time PCR.

Results: Data have shown that both forms of the active (metabolically active, growing, and dividing state), and heat inactivated (by exposure to 56°C for 20 minutes) forms of the bacteria and the cell-free supernatant could affect the expression of occludin and ZO-1 genes (P < 0.05). OMVs significantly increased the expression of the occludin gene but had no effects on the expression of ZO-1.

Conclusion: Akkermansia muciniphila and its derived metabolites might have the potential to be used in the pharmaceutical and medicinal fields as probiotic, paraprobiotic and postbiotic agents to prevent metabolic and inflammatory diseases; Although, further research is needed to understand their interactions within the complex gut microbiome and to evaluate potential side effects or risks associated with their use.

Background and objectives: Insulin resistance and elevated blood glucose levels are the hallmarks of Type 2 Diabetes Mellitus (T2DM), a chronic metabolic condition. Emerging research suggests that gut microbiota may play a causal role in T2DM. This study compares T2DM patients' gut microbiota to healthy controls, focusing on Lactobacillus, Bifidobacterium, Akkermansia muciniphila, Prevotella, Bacteroidetes, and Firmicutes.

Materials and methods: This case-control research involved 50 T2DM patients and 50 healthy controls, aged 39-75. Quantitative real-time PCR (qPCR) employing 16S rRNA gene primers was used to detect and quantify bacterial diversity in fecal samples. Statistical analyses were performed to compare the microbiota composition between groups.

Results: The gut microbiome of patients with Type 2 Diabetes Mellitus differed significantly from that of healthy controls. In T2DM patients, Lactobacillus spp. and the Firmicutes phylum had higher relative fold differences, while A. muciniphila had lower abundance. No substantial alterations were seen in Bifidobacterium spp., Prevotella, or Bacteroidetes. T2DM patients had more Lactobacillus spp. and Firmicutes and less A. muciniphila in their gut microbiome.

Conclusion: While gut microbiota is linked to T2DM, this study analyzes the bacterial composition to identify taxa that change significantly. Further research is essential to unravel the complex relationships between gut microbiota and T2DM pathogenesis, particularly through species-level analysis and genomic studies to identify the primary associated clades.

Background and objectives: The vaginal microbiome represents a dynamic ecosystem that undergoes significant transformations throughout a woman's lifespan, influenced by hormonal fluctuations and physiological changes. Interpreting pathogen distribution and developing suitable therapeutic care techniques for women's reproductive health depends on an understanding of these age-related patterns. This study aims to thoroughly describe age-related changes in the makeup of the vaginal microbiome and the distribution of pathogenic species.

Materials and methods: Vaginal swab samples were collected from 29 subjects, categorized into different age groups (A: 15-30 years, B: 31-40 years, C: 41-50 years, and D: 51-60 years old females). Microbiome DNA was extracted from the collected vaginal swabs and shotgun next generation sequencing was performed. Post-sequencing, data was analysed using in-house pipeline followed by statistical analysis using R programming.

Results: The results showed that microbial diversity varied significantly with age. Group C displayed the most severe pathogenic burden; Group A had the highest overall species diversity with 350 bacterial species. Group D displayed the greatest overall relative abundance levels of microorganisms, primarily due to Lactobacillus rhamnosus dominance.

Conclusion: This study shows that the composition of the vaginal microbiome changes fundamentally over the course of a woman's life, with each stage bringing with it its own set of microbial signatures, pathogenic risks, and therapeutic prospects.

Background and objectives: Human milk provides nutrients, prebiotics, and probiotics that support infants' physical and mental growth. Human milk microbiota, as a potential source of probiotics and an indicator of the safety of donor milk, is of great importance. Akkermansia muciniphila, a core member of next-generation probiotics (NGPs), with the ability to degrade human milk oligosaccharides (HMOs), may be present in human milk. This study was carried out to assess the total bacterial count and presence of A. muciniphila in raw freshly expressed mothers' milk and pasteurized donor milk from human milk banks (HMBs).

Materials and methods: 15 raw and 20 pasteurized milk samples were collected and analyzed using a real-time PCR technique with specific primers for A. muciniphila and universal 16S rRNA bacterial primers.

Results: Results showed that the average total bacterial count was 4.95 log CFU/ml, which is lower than the normal range reported for human milk. Samples with bacterial count over the standard range were related to the HMBs. Prevalence of A. muciniphila in human milk was 35% and was higher in raw milk samples than in pasteurized samples.

Conclusion: In conclusion, raw human milk can serve as a potential source for A. muciniphila isolation as a candidate for NGPs.

Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is one of the leading causes of nosocomial infections, particularly in vulnerable patients. However, treating these infections is challenging due to its various antibiotic resistance mechanisms and biofilm formation ability. As traditional antibiotic development struggles to keep pace with evolving resistance, this review explores a promising alternative strategy which is enhancing existing antibiotic efficacy by combining them with nutritional supplements that modulate P. aeruginosa physiology. Specifically, it focuses on studies investigating the effects of diverse carbon, nitrogen, and iron sources on bacterial response to antibiotics, and the mechanisms underlying observed synergy. To achieve this, published literature on P. aeruginosa metabolism, antibiotic resistance, and nutritional influences was comprehensively analyzed and summarized. The findings highlight specific carbon, nitrogen, and iron sources that can enhance various antibiotic classes against P. aeruginosa. These include supplements capable of disrupting biofilm formation, reducing efflux pump activity, or interfering with other resistance mechanisms, thereby increasing antibiotic susceptibility. The specific mechanisms by which these supplements interact with bacterial physiology and antibiotic action are thoroughly discussed. Ultimately, modulating P. aeruginosa physiology through strategic supplementation alongside existing antibiotics offers a promising approach to overcome drug resistance in this pathogen.