Iranian Journal of Microbiology最新文献

Background and objectives: Viral infections of the respiratory system are a major public problem due to their ease of spread, pandemic potential, and significant rate of death. Diagnosing these infections requires laboratory testing, as clinical symptoms alone are often insufficient. Influenza A, Influenza B, and COVID-19 are common infections that burden the population, especially during winter. We developed a multiplex real-time PCR method to simultaneously detect Influenza A and B, as well as COVID-19. Compared to existing detection kits, it offers higher accuracy, lower costs, and faster results, making it an efficient diagnostic tool.

Materials and methods: We designed primer/TaqMan probes for the M2 gene of Influenza A, N gene of SARS-CoV-2, and NS1 gene of Influenza B. Reaction components were optimized and functional parameters were tested using standard samples with known viral copy numbers.

Results: The method's detection limit is 10 copies for Influenza A and B, and 60 for SARS-CoV-2. Sensitivity and specificity for Influenza A are 88% and 100%, for Influenza B, 95.6% and 100%, and for SARS-CoV-2, 90.4% and 100%.

Conclusion: This multiplex real-time PCR method can accurately detect and distinguish SARS-CoV-2, Influenza B, and Influenza A infections.

Background and objectives: We assessed the susceptibility of ceftazidime+avibactam (CZA/AVI) in Klebsiella pneumoniae and Pseudomonas aeruginosa isolated from intensive care units of our hospital.

Materials and methods: Clinical samples from Jan 2022 to Dec 2023 at SKIMS Soura, were processed for the recovery of K. pneumoniae and P. aeruginosa. Susceptibility testing was done by disc diffusion (DD) method and minimum inhibitory concentration (MIC) for CZA/AVI and meropenem was assessed using E-test strips. Categorical agreement (CA), very major errors (VME), major errors (ME) and minor errors (mE) between DD and MIC were measured. Statistical analyses were performed using SPSS version 22.0.

Results: A total of 111 K. pneumoniae and 81 P. aeruginosa were part of the study. Of these, 56.8% K. pneumoniae and 45.7% P. aeruginosa isolates were susceptible to CZA/AVI. MIC of CZA/AVI for K. pneumoniae ranged from 0.125 to ≥ 256 μg/ml and for P. aeruginosa it ranged from 0.032 to 128 μg/ml. CA was 97.29% between DD and E-Test for CZA/AVI in K. pneumoniae isolates, with a ME of 2.70%. For P. aeruginosa CA between DD and E-Test for CZA/AVI was 98.76% with a VME of 1.23%. MIC values of meropenem were higher than CZA/AVI even in sensitive isolates.

Conclusion: CZA/AVI shows good in-vitro activity against clinical isolates of K. pneumoniae and P. aeruginosa and can be part of empirical therapy for treating infections caused by these bacteria.

Background and objectives: The emergence of carbapenem resistance in Escherichia coli (E. coli) poses an urgent threat. The study aims to assess carbapenem resistance and the presence of carbapenemase genes in E. coli clinical isolates from Thi-Qar Hospital, Iraq.

Materials and methods: A total of 2203 specimens were collected from patients at two hospitals between January and October 2024. E. coli was identified via biochemical tests and confirmed with the Vitek2® system. Antibiotic sensitivity was evaluated using disc diffusion, and carbapenemase production was investigated through combined disc tests (CDT) and modified Hodge tests (MHT). PCR was used to detect carbapenemase genes.

Results: Out of 2203 specimens, 1212 (55.02%) exhibited bacterial growth, with E. coli accounting for 15.35% (186/1212) of isolates. Among these, 40 (21.51%) were resistant to at least one carbapenem. CDT identified 10, and MHT identified 1 as a carbapenemase producer. The most detected gene was bla _NDM (60.00%), followed by bla _OXA (40.00%) and bla _OXA-48 (15.00%). bla _OXA-51 and bla _VIM were found in 5.00% of isolates each. No bla _KPC, bla _NMC, bla _IMI, bla _GES, bla _SPM, bla _GIM, or bla _SIM was detected.

Conclusion: The high prevalence of carbapenem resistance and the corresponding encoding genes in E. coli in Thi-Qar province pose a concerning challenge for managing serious infections caused by this pathogen.

Background and objectives: We assessed the susceptibility of ceftazidime+avibactam (CZA/AVI) in Klebsiella pneumoniae and Pseudomonas aeruginosa isolated from intensive care units of our hospital.

Materials and methods: Clinical samples from Jan 2022 to Dec 2023 at SKIMS Soura, were processed for the recovery of K. pneumoniae and P. aeruginosa. Susceptibility testing was done by disc diffusion (DD) method and minimum inhibitory concentration (MIC) for CZA/AVI and meropenem was assessed using E-test strips. Categorical agreement (CA), very major errors (VME), major errors (ME) and minor errors (mE) between DD and MIC were measured. Statistical analyses were performed using SPSS version 22.0.

Results: A total of 111 K. pneumoniae and 81 P. aeruginosa were part of the study. Of these, 56.8% K. pneumoniae and 45.7% P. aeruginosa isolates were susceptible to CZA/AVI. MIC of CZA/AVI for K. pneumoniae ranged from 0.125 to ≥ 256 μg/ml and for P. aeruginosa it ranged from 0.032 to 128 μg/ml. CA was 97.29% between DD and E-Test for CZA/AVI in K. pneumoniae isolates, with a ME of 2.70%. For P. aeruginosa CA between DD and E-Test for CZA/AVI was 98.76% with a VME of 1.23%. MIC values of meropenem were higher than CZA/AVI even in sensitive isolates.

Conclusion: CZA/AVI shows good in-vitro activity against clinical isolates of K. pneumoniae and P. aeruginosa and can be part of empirical therapy for treating infections caused by these bacteria.

Background and objectives: Q fever is a frequently occurring illness that is induced by the bacterium Coxiella burnetii (C. burnetii) that can infect humans and various animals. It targets the macrophage cells in the tissues, and circulating monocytes.

Materials and methods: This study was conducted between 2022 and 2023 in the West Azerbaijan and Ardabil provinces of northwestern Iran to examine the presence infection of C. burnetii. Specimens were obtained by swabbing from 140 mares (70 from each province) and 20 stallions (10 from each province) which were apparently healthy, and their DNA was analyzed using quantitative PCR assay detecting the IS1111 element of the bacterium.

Results: The findings indicated that a mere 0.625% of the examined specimens tested positive for C. burnetii. Among the entire set of specimens, a single female horse from the region of Ardabil was found to be the carrier of the bacterium.

Conclusion: This suggested that even though horses may not display any clinical symptoms, they can still harbor C. burnetii and contribute to its transmission. Therefore, the potential contribution of horses to Q fever transmission should be considered.

Background and objectives: The azole antifungals are the most frequent class used to treat Candida infections. It is essential to elucidate the potential of natural compounds as an alternative in eliminating Candida albicans (C. albicans). Therefore, in the present study, the antagonistic effect of Pseudomonas aeruginosa toxins on azole antifungal resistance in C. albicans species was investigated.

Materials and methods: In this study, 28 C. albicans species with azole antifungal resistance were obtained from patients at Shohadaye Tajrish Hospital. The effect of toxins, such as phenazine, pyocyanin, pyoverdine, and fluorescein, was examined on C. albicans species. The antifungal activity of these toxins against C. albicans spp. was determined using methods such as minimal inhibitory concentration (MIC ₉₀), radial diffusion assay (RDA), and detection of reactive oxygen species (ROS).

Results: The prevalence of C. albicans strains in urinary catheters, surgical wounds, respiratory tracts, blood, and standard strains was 46.3%, 21.4%, 25%, 7.14%, and 3.57%, respectively. The MIC values were reported as 32 μg/ml for phenazine, and 128 μg/ml for pyoverdine, pyocyanin, and fluorescein. The results showed that phenazine exhibited higher inhibitory effects against C. albicans isolated from clinical samples compared to the other toxins. After exposure to phenazines (20 μg/ml), 65-70% of yeast cells of C. albicans spp. showed rhodamine 123 fluorescence, indicating high intracellular reactive oxygen species (ROS) production.

Conclusion: The antifungal effect of different toxins in C. albicans spp. may be due to ROS-mediated apoptotic death. The results suggest that phenazine has high potential in controlling C. albicans. This natural compounds are a potential alternative for eliminating this yeast.

Background and objectives: Staphylococcus aureus (S. aureus) is one of the most important pathogens, responsible for a range of infections. This study aimed to assess resistance patterns in S. aureus isolates obtained from certain private-sector laboratories against commonly used antimicrobial agents.

Materials and methods: The process involved collecting various samples from several private laboratories and then identifying S. aureus isolates using biochemical characterization. The antibiotic susceptibility of these isolates was determined by disc diffusion method. Furthermore, Rt-PCR was employed to identify two genes namely the methicillin/oxacillin resistance genes (mecA), and (SCCmec).

Results: The findings of the current study exhibited that females constituted a larger proportion of the participants (59.1%) compared to males (40.9%), with a mean participant age of 40.82 years. Gram-positive bacteria were more prevalent (71.3%) than Gram-negative bacteria (18.3%), with S. aureus being the most frequent isolate (60.9%). Urine samples represented the highest collected sample type (47.8%). Out of the 115 bacterial isolates, 85.2% exhibited multidrug resistance to antibiotics such as cefazolin, gentamicin, vancomycin, and ceftazidime. Clindamycin was the most effective antibiotic, with a sensitivity rate of 62.9%, followed by teicoplanin and meropenem, each with a sensitivity rate of 52.9%. Methicillin-resistant Staphylococcus aureus (MRSA) strains were susceptabile to vancomycin and teicoplanin. The methicillin/oxacillin resistant isolates showed significant association with mecA and SCCA genes.

Conclusion: This study highlighted the multi-drug resistance in S. aureus isolates, stressing the need for stringent antibiotic stewardship, continuous surveillance, and further research into alternative treatments, including novel antibiotics and combination therapy, to combat resistant strains.

Background and objectives: Staphylococcal enterotoxin B (SEB), a potent superantigenic toxin produced by Staphylococcus aureus (S. aureus), plays a crucial role in S. aureus systemic infection. This investigation sought to determine whether immunising animals with SEB toxoid could protect against an experimental acute systemic infection caused by S. aureus.

Materials and methods: This study involved three groups of animals: one group was administered with SEB toxoid, and the second group was administered with intramuscular injections of normal saline, after which both were subjected to systemic S. aureus infection. The third group served as the negative control. After two weeks, the outcomes of the experimental systemic infection demonstrated that SEB immunisation significantly shielded organs (lung and liver) from damage in comparison to the control group.

Results: Regarding the histopathological analysis of liver and lung tissues, the control group showed minimal alterations, indicating a normal tissue state. Infected individuals exhibited severe pathology, including inflammation, necrosis, and fibrosis. The immunised group displayed a mixed profile with elevated inflammation but lower necrosis and fibrosis. Immunisation mitigated pathological changes induced by infection, fostering a more controlled response.

Conclusion: SEB plays an important role in S. aureus pathogenesis and immunisation, and this toxoid might protect against fatal infections of S. aureus.

Background and objectives: The COVID-19 pandemic was mitigated by the rapid development and deployment of vaccines. While vaccines reduce infection severity, breakthrough infections (BTIs) still occur. The CDC defines BTI as a positive SARS-CoV-2 test ≥14 days post-vaccination. This study investigates the occurrence of COVID-19 BTIs at a tertiary care hospital in Puducherry, South India.

Materials and methods: This retrospective study analysed hospital tested qRT-PCR data of individuals from the ICMR portal (March 2021-March 2022). Demographic and vaccination details were extracted.

Results: Among 8001 tested individuals, 1452 were vaccinated. The BTI rate decreased from 16.6% to 1.2% after the first dose and from 58% to 40% after the second one. Odds ratio indicated a 74% reduction in infection risk for vaccinated individuals compared to unvaccinated. Males had higher infection rates than females, regardless of vaccination status.

Conclusion: Our study demonstrates a higher BTI rate after one vaccine dose compared to two doses. The BTI rate also increased four months post-vaccination, even with two doses, potentially due to waning immunity and the emergence of new variants. Therefore, continued adherence to preventive measures in conjunction with vaccination is crucial for minimizing COVID-19 transmission.

Background and objectives: The increasing prevalence of fungal infections due to antifungal resistance underscores the need for novel treatment strategies. The present study aimed to investigate the inhibitory effects of soil-originated antagonistic bacteria against Aspergillus and Trichophyton species.

Materials and methods: Fifty soil samples collected from Isfahan and Khuzestan provinces by using the Zig-Zag method were cultured on glucose-yeast extract (GY) agar around fungal colonies to isolate antagonistic bacteria. Antifungal activity was assessed by measuring clear zones around the colonies of A. niger, A. fumigatus, T. rubrum, and T. mentagrophytes by co-culture linear method. Potent antagonistic bacteria were identified by 16S rRNA sequencing, and evaluated for antifungal activity using disk diffusion assays compared with amphotericin B and ketoconazole.

Results: Among 50 samples, fifteen showed antifungal effects, yielding 55 bacterial strains. Four isolates with strong antifungal activity against all tested fungi were identified as Bacillus subtilis, B. licheniformis, B. axarquiensis, and Bacillus sp. These bacteria were distributed in distinct clusters phylogenitically and showed diverse antifungal activity.

Conclusion: The results suggest the potential of soil-derived Bacillus species as promising antifungal agents. Further studies are recommended to identify their inhibitory metabolites, their ability as biocontrol agents against soil habitated fungi and to explore their mechanism of action and spectrum of activity.