Iranian Journal of Microbiology最新文献

Background and objectives: Ventilator-associated pneumonia (VAP) caused by carbapenem-resistant Gram-negative bacteria is a serious ICU challenge. This study determined the prevalence, antimicrobial susceptibility profiles, and phenotypic carbapenemase resistance mechanisms of Gram-negative isolates from VAP patients in two tertiary hospitals in Karachi, Pakistan.

Materials and methods: We included 104 consecutive cases of VAP (July 2021-January 2023). A total of 67 carbapenem-resistant Gram-negative isolates were identified and tested. Antibiotic susceptibility was assessed by disk diffusion and broth micro dilution, according to CLSI and EUCAST guidelines. Modified and enhanced carbapenem inactivation methods (mCIM/eCIM) were used to distinguish metallo-β-lactamase (MBL) and serine carbapenemase production.

Results: The mean age was 44.6 ± 18.3 years; 52.2% were male. Early-onset VAP accounted for 37.3% and late-onset for 62.7%. The most frequent pathogens were Acinetobacter baumannii (49.3%, 33/67) and Klebsiella pneumoniae (20.9%, 14/67). Notably, 67% of isolates produced MBLs, and 33% produced serine carbapenemases (phenotypically). The prevalence of multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan drug-resistant (PDR) phenotypes was 42.6%, 31.3%, and 19.4%, respectively.

Conclusion: VAP in our ICUs was dominated by A. baumannii and K. pneumoniae with high levels of MBL-mediated resistance. These findings highlight the urgent need for surveillance, stewardship, and new therapeutic options.

Background and objectives: Probiotics are effective in improving inflammatory bowel disease (IBD). This study assessed the effect of mesalazine and two candidate probiotics on the improvement of acetic acid (AA)-induced colitis model.

Materials and methods: Lactobacillus plantarum MS1and Lactobacillus delbrueckii YN1 were used for IBD model in rat. Twenty-five male Wistar rats weighing 250 ± 50 grams were used in 5 classified groups: Control (CO); Colitis (CL); Colitis, Probiotic (CLP); Colitis, Mesalazine (CLM); Colitis, Probiotic, Mesalazine (CLPM) and the treatment period was 3 weeks. The rats were treated with mesalazine 30 mg/kg and probiotic 10⁹ CFU/ml after induction of colitis. Histopathological and immunological analyses were performed to evaluate the effects of probiotic bacteria on IBD.

Results: The results showed that the probiotic bacteria reduced inflammation (P<0.05), extent (P<0.01), crypt abscesses (P<0.01), edema (P<0.05), inflammatory cell infiltration (P<0.5), and increased mucosa (P<0.001) in rats. Mesalazine administration in animals with colitis did not have a significant effect. Administration of probiotics in both CLP and CLPM groups reduced extent, crypt abscesses, edema, and inflammatory cell infiltration and showed an important role in the down-regulation of consolidation of pro-inflammatory factors (TNFα, IL-6, and IL-17), as well as up-regulation of anti-inflammatory factors such as IL-10.

Conclusion: Lactobacillus plantarum MS1 and Lactobacillus delbrueckii YN1 have shown significant potential in alleviating AA-induced colitis symptoms. Their administration leads to a marked reduction in pro-inflammatory cytokines such as TNF-α, IL-17, and IL-6, while enhancing IL-10 levels, indicating their promise as therapeutic candidates for inflammatory bowel disease (IBD).

Background and objectives: Global health is seriously threatened by the rise of carbapenem-resistant Enterobacterales (CRE). The bla _NDM gene, a key carbapenemase coding gene, causes global health concern due to its multidrug resistance and easy spread through mobile genetic elements. This study aimed to identify and genetically characterize the bla _NDM genes from uropathogens, its antibiotic susceptibility, and its correlation with global sequences.

Materials and methods: Urine samples were processed following microbiological guidelines. Isolates were identified using API-20E. Antibiotic susceptibility was tested using disc diffusion method, and bacterial DNAs were extracted for bla _NDM gene sequencing for phylogenetic analysis.

Results: CREs were detected in 11.92% (n=51) of the 428 Enterobacterales. Among CRE isolates, 45% (n=23) were positive for bla _NDM gene harbored by Klebsiella pneumoniae (57%), followed by Escherichia coli (26%). Uropathogenic CRE, harboring bla _NDM, revealed susceptibility of 34.78%, 60.87%, and 65.22% to amikacin, nitrofurantoin, and fosfomycin respectively. The bla _NDM-5 variant was most common (69.57%), followed by bla _NDM-1 (26.09%) and bla _NDM-7 (4.35%). Phylogenetic analysis revealed that bla _NDM variants exhibit diverse relationships with Pakistani and worldwide sequences.

Conclusion: The significant presence of bla _NDM in uropathogens, along with extensive antibiotic resistance, underscores the urgent need for continuous monitoring and antibiotic stewardship programs to manage the growing threat of CRE infections.

Background and objectives: Studies have indicated that Helicobacter pylori (H. pylori) infection could correlate with autophagy dysregulation. This research was undertaken to investigate whether H. pylori can dysregulate the expression of genes related to autophagy in human gastric adenocarcinoma (AGS) cells.

Materials and methods: Ten H. pylori clinical isolates recovered from peptic ulcer disease (PUD) and chronic gastritis (CG) patients were used for cell infection assays. AGS cells infected with H. pylori strains at a multiplicity of infection (MOI) of 100 were incubated at 37°C for 12 h. The expression of autophagy-related genes (atg5, atg12, atg16L1, LC3B, and beclin-1) was determined in AGS cells by RT-qPCR. ELISA was applied to measure IL-8 production.

Results: The gene expression of atg5, atg12, atg16L1, LC3B was upregulated by both CG and PUD strains. The overexpression was more pronounced in PUD than CG strains. On the contrary, beclin-1 gene was downregulated in all H. pylori-infected AGS cells. In addition, H. pylori strains could significantly produce IL-8 in AGS cells.

Conclusion: Our in vitro study demonstrates that H. pylori could alter the expression of autophagy-related genes. Further investigation could precisely uncover the mechanism whereby H. pylori dysregulates host autophagy.

Background and objectives: This study investigated the correlation between high-risk (HR) human papillomavirus (HPV), sexually transmitted disease (STD), and vaginal microbiota in patients with a normal Pap smear.

Materials and methods: For women who were referred for their routine cervical cancer screening, in addition to co-testing, some samples were taken from the vaginal and cervical environment to check the presence of the most common STD pathogens. The diagnosis of the organisms was done by means of PCR and microbial cultures.

Results: HR HPV was detected in 67 women, and STD was positive in 80% of them, while in HR HPV negative women, this was 67%. The HPV positive group reported a significantly higher rate of STD history (92% vs. 82%) and frequency of intercourse weekly (86% vs. 3.96%) (p<0.05). Lactobacilli, streptococcus, and staphylococcus concentrations were significantly lower in the HPV positive group compared to the HPV negative group (p<0.007; OR = 4.17). Ureaplasma urealyticum and Ureaplasma parvum were significantly (p<0.001) more prevalent in the HPV positive group compared to the HPV negative group.

Conclusion: This study showed that the existence of other STDs and the composition of the vaginal and cervical microbiome play an important role in either the clearance or the progression of high-risk HPV.

Background and objectives: Breast tissue microbiota differs between healthy and cancerous tissues, with some bacteria influencing tumor progression. Staphylococcus epidermidis, a common skin commensal found in breast tumors, may play a role in epithelial-mesenchymal transition (EMT), a key step in metastasis. This study evaluated the effects of S. epidermidis culture and cell-free supernatant (CFS) on MDA-MB-231 breast cancer cell survival and expression of EMT-related genes Snail1, fibronectin 1 (FN1), and N-cadherin (CDH2).

Materials and methods: Different concentrations of S. epidermidis cultures and their CFS were applied to MDA-MB-231 cells. Cytotoxic effects were assessed by MTT assay at 2, 4, and 24 hours post-treatment. Real-time PCR analyzed gene expression after 24 hours of exposure to non-toxic concentrations (MOI 50 and 100 for cultures; 14% for CFS).

Results: Low concentrations did not affect viability, while higher doses (MOI 100 and 14% CFS) reduced viability by up to 60% and 90%, respectively, at 24 hours. MOI 50 did not significantly alter gene expression. At MOI 100, Snail1 and FN1 were significantly upregulated, but CDH2 was unchanged. Treatment with 5% and 7% CFS significantly increased all three EMT gene expressions, indicating EMT induction.

Conclusion: S. epidermidis affects EMT gene expression and cell viability, indicating potential involvement in breast cancer progression.

Background and objectives: Rapid and accurate identification of suspicious SARS-CoV-2 patients is essential in controlling the infection. Numerous commercial kits are developed which target diverse regions of the SARS-CoV-2 virus genome. This systematic review addresses the lack of comprehensive analyses comparing the diagnostic value of commercial kits for SARS-CoV-2 detection. We aimed to compare diagnostic value of commercial SARS-CoV-2 kits in clinical samples using a systematic review and meta-analysis method.

Materials and methods: A comprehensive search was conducted on main databases of Medline (PubMed), Embase, Web of Science and Scopus from 2019 to October 2021 using the appropriate keywords. Systematic Reviews and Meta-Analysis guideline PRISMA checklist was used to select eligible studies.

Results: The most frequent introduced kits were from USA (33 cases) and China (27). Among all studies, 11, 9 and 7 papers had assessed FDA -CDC, Sansure and Allplex kits, respectively. The majority of the kits were based on RT-PCR (52 cases) and the most frequent genes target was N protein (63 cases). The overall sensitivity of the kits was 80.5%. The lowest sensitivity was reported for Daan Kit, while the highest sensitivity was seen for many kits. The specificity of the kits ranged from 87.9% to 99.8% and the overall specificity was 97.9%. Both PPV and NPV of the kits ranged from 87.9% to 99.8% for PPV and 82.9% to 99.8% for NPV.

Conclusion: Based on DOR obtained from three different formulas, GeneFinder, InBios, NxTAG, Simplexa and FDA-CDC kit have better detection performance. The GeneFinder Kit appears to be among the more suitable options regarding cost-effectiveness for each reaction.

Background and objectives: Hepatitis B virus (HBV) remains a major public health challenge, particularly in hyperendemic regions. This study assessed the effectiveness of Iran's national HBV vaccination program in Esfandiar village, South Khorasan Province, where HBV prevalence substantially exceeds the national average. We compared hepatitis B surface antigen (HBsAg) prevalence between cohorts born before and after implementation of the universal vaccination program in 1993.

Materials and methods: We conducted a cross-sectional seroprevalence study encompassing both unvaccinated individuals (born before 1993) and vaccinated individuals (born 1993 onwards) in Esfandiar village. Serum samples were analyzed for HBsAg, hepatitis B e antigen (HBeAg), and hepatitis B core antibody (HBcAb) using enzyme-linked immunosorbent assay (ELISA).

Results: HBsAg prevalence was markedly higher among unvaccinated individuals (22.56%, 132/585) compared to vaccinated individuals (1.19%, 3/252), yielding a vaccine effectiveness of 94.74%. Among vaccinated children, 54% maintained protective antibody titers (>10 mIU/mL), with highest levels observed in children born to HBsAg-positive mothers. Conversely, 46% of vaccinated children demonstrated suboptimal antibody titers (<10 mIU/mL), predominantly among those born to HBsAg-negative mothers. Notably, all three HBsAg-positive vaccinated children were born to mothers with concurrent HBsAg and HBeAg positivity.

Conclusion: The national HBV vaccination program demonstrates remarkable effectiveness in reducing HBsAg prevalence, underscoring the critical importance of universal neonatal immunization in endemic settings. Enhanced preventive strategies, including hepatitis B immunoglobulin (HBIG) administration to infants of HBeAg-positive mothers, could further optimize protection. Sustained surveillance and rigorous adherence to vaccination protocols remain essential for achieving comprehensive HBV control.

Background and objectives: Pseudomonas aeruginosa is a Gram-negative bacterium that causes respiratory infections in individuals with cystic fibrosis. Its level of virulence is primarily controlled through Quorum Sensing (QS), a communication mechanism that utilizes small signaling molecules. This study investigates P. aeruginosa antibiotic resistance in CF patients in Imam Khomeini Hospital and examines the presence of QS genes in resistant strains.

Materials and methods: Sixty-five P. aeruginosa samples were identified in CF patients in Imam Khomeini Hospital in Tehran. Antibiotic resistance was assessed using the disk diffusion method, and QS genes (rhlI, rhlR, lasI, lasR) were evaluated by applying PCR.

Results: Approximately 61.5 % of P. aeruginosa strains were multiple-drug-resistant (MDR), with 30.7% classified as extensively drug-resistant (XDR). The highest resistance was observed against amoxicillin, amikacin, and cefepime. The most common QS gene in MDR and XDR strains was rhlR. Additionally, 78.9% of XDR isolates carried rhlI, rhlR, lasI, and lasR genes.

Conclusion: The study specified that more than half of the P. aeruginosa strains exhibited resistance to five antibiotic classes, and effective antibiotics against P. aeruginosa were colistin, meropenem, ciprofloxacin, piperacillin/tazobactam, and cefotaxime. A noteworthy correlation was identified between MDR and XDR strains and the existence of QS genes in the strains.

Background and objectives: Helicobacter and Wolinella are gram-negative bacteria belonging to the Helicobacteraceae family. While Helicobacter species are well-known for their role in gastric disorders, emerging evidence suggests their presence in the oral cavity and potential involvement in periodontal diseases.

Materials and methods: Helicobacter and Wolinella species were investigated in 122 saliva and periodontal plaque samples from dogs and cats by DNA extraction, PCR amplification, and 16S rDNA gene identification.

Results: Comparing the periodontitis group and the healthy group, a higher incidence of positive Wolinella and Helicobacter species was shown in both dog and cat groups. 16S rDNA genes of Helicobacter were detected in 60% of the cats and 67.7% of the dogs. Detection of 16S rDNA genes of the Wolinella group in felines was 78.3% which was higher than in canines (67.7%). Helicobacter felis (35%) was the most common species detected in cats, contrary to dogs, in which Helicobacter heilmannii (30%) detection was higher (in both groups). Helicobacter pylori was not detected in either group.

Conclusion: Comparing the occurrence of Helicobacter and Wolinella in the mouths of dogs and cats, their association with periodontal disease, and the possibility of a common source of infections between humans and companion animals is of great importance for the management of oral health in animals and humans.