Jundishapur Journal of Microbiology

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ISSN / EISSN : 2008-3645 / 2008-4161
Published by: Kowsar Medical Institute (10.5812)
Total articles ≅ 1,280
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Seyed Ali Bazghandi, , Hadi Peeridogaheh, , ,
Jundishapur Journal of Microbiology, Volume 14; https://doi.org/10.5812/jjm.118452

Abstract:
Background: Drug resistance and virulence genes are two key factors for the colonization of Pseudomonas aeruginosa in settings with high antibiotic pressure, such as hospitals, and the development of hospital-acquired infections. Objectives: The objective of this study was to investigate the prevalence of drug resistance and virulence gene profiles in clinical isolates of P. aeruginosa in Ardabil, Iran. Methods: A total of 84 P. aeruginosa isolates were collected from clinical specimens of Ardabil hospitals and confirmed using laboratory standard tests. The disk diffusion method was used for antibiotic susceptibility testing and polymerase chain reaction (PCR) for the identification of P. aeruginosa virulence genes. Results: The highest and the lowest antibiotic resistance rates of P. aeruginosa strains were against ticarcillin-clavulanate (94%) and doripenem (33.3%), respectively. In addition, the frequency of multidrug-resistant (MDR) P. aeruginosa was 55.9%. The prevalence of virulence factor genes was as follows: algD 84.5%, lasB 86.9%, plcH 86.9%, plcN 86.9%, exoU 56%, exoS 51.2%, toxA 81%, nan1 13.1%, and pilB 33.3%. A significant association was observed between resistance to some antibiotics and the prevalence of virulence genes in P. aeruginosa. Conclusions: Our results revealed a high prevalence of antibiotic resistance, especially MDR, and virulence-associated genes in clinical isolates of P. aeruginosa in Ardabil hospitals. Owing to the low resistance rates against doripenem, gentamicin, and tobramycin, these antibiotics are recommended for the treatment of infections caused by highly resistant and virulent P. aeruginosa strains.
Zahra Taghinejad, , Vahid Asgharzadeh,
Jundishapur Journal of Microbiology, Volume 14; https://doi.org/10.5812/jjm.117435

Abstract:
: Opportunistic infections, such as mucormycosis, in coronavirus disease 2019 (COVID-19) patients has become a new health challenge. Since opportunistic infections can exacerbate COVID-19 patients' status, it is vital to identify the risk factors to prevent, diagnose, and treat them as soon as possible. Viral, fungal, environmental, and host factors may be responsible for this situation. Long hospital stays, impaired host immune system function due to viral infection, and excessive consumption of glucocorticoids in managing COVID-19 patients are the main risk factors for the increased risk of mucormycosis in COVID-19 patients. Educating health care workers and considering the association between mucormycosis of the paranasal sinuses and different strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the cause of COVID-19 can help prevent invasive fungal sinusitis in COVID-19 patients.
Ali Akbar Heydari, Abas Eslami,
Jundishapur Journal of Microbiology, Volume 14; https://doi.org/10.5812/jjm.116313

Abstract:
Background: Staphylococcus aureus is an important cause of resistant infection with high mortality and morbidity. Objectives: We aimed to evaluate the clinical characteristics and comorbidities of patients with S. aureus infection to define the predictors of adverse outcomes. Methods: In this cross-sectional study, patients (aged ≥ 15 years) with positive S. aureus blood cultures were included. Their demographic and clinical characteristics were recorded, and their association with the main adverse outcomes (methicillin-resistant S. aureus [MRSA], infective endocarditis, source of infection, and the final outcome were analyzed using SPSS software version 16. Results: The male-to-female ratio was 54/51. The mean age was 55.13 years (women: 58.45 ± 20.4 and men: 53.6 ± 17.6). Of 105 cases analyzed, 40% had hospital-, 25.7% community-, and 34.3% healthcare-associated bacteremia. The median duration of hospital admission was 13 days. Thirty-two percent had MRSA, differently based on the source of infection (P = 0.029). Twenty-eight patients had infective endocarditis, differently based on the source of infection, prosthetics, considerable foci of infection, and receipt of blood and its derivatives (P < 0.05). Most patients with neurological and end-stage renal disease (both P = 0.001) did not have infective endocarditis. Finally, 61.9% of the patients were discharged with good condition, 38.1% died, and 9% left the hospital before diagnosis of the foci. Conclusions: Vascular catheters and cardiovascular diseases, including hypertension, are among the most common factors associated with S. aureus bacteremia, and it is necessary to carefully examine the presence of these factors, as well as infective endocarditis in these patients.
Qian Lei, Hao Wang, Xiaohui Lv, Liyun Dang
Jundishapur Journal of Microbiology, Volume 14; https://doi.org/10.5812/jjm.116750

Abstract:
Background: The prevalence of nontuberculous mycobacteria (NTM) infection has been increasing globally. Many cases of NTM infection are misdiagnosed as Mycobacterium tuberculous (MTB) because of similar clinicoradiological features. Objectives: To determine the burden and characteristics of NTM infection, this study was done to evaluate clinical isolates collected from tuberculous (TB) suspects in a population from Northwest China. Methods: From January to December 2020, the clinical samples of 9,142 TB suspects were collected for the PCR-fluorescent probe and mycobacterial culture. The PCR-fluorescent probe-positive nucleic acid samples were further subjected to a DNA microarray for confirmation and species identification. Drug susceptibility testing (DST) was also carried out using the micropore plate method (MicroDSTTM) on isolates from NTM patients. Results: Of 9,412 TB suspects, 85 cases (0.9%) were clinically diagnosed with NTM infection according to the American Thoracic Society (ATS) guidelines. For the laboratory samples, a total of 169 NTM strains, identified by molecular biology methods, were classified into 10 species. The most common species were Mycobacterium chelonae/ Mycobacterium abscessus (64/169, 37.7%) and M. intracellulare (40/169, 23.7%). All strains showed the highest resistance to imipenem/cilastatin (85/85, 100%) and the highest susceptibility to linezolid (4/85, 4.7%). In comparison with the rapidly growing mycobacteria (RGM) group, the slowly growing mycobacteria (SGM) group showed a lower resistance and a shorter hospital inpatient stay (t = 6.66, P < 0.001 and t = 2.40, P = 0.020, respectively). Conclusions: Mycobacterium chelonae/M. abscessus and M. intracellulare were the most frequently detected NTM pathogens in Northwest China. The differences in drug sensitivity and clinical characteristics were giant for different strains. Timely identification and accurate DST play important roles in NTM management.
Sunarno Sunarno, Nelly Puspandari, Dwi Febriyana, Tati Febrianti, Ratih Dian Saraswati, Novi Sulistyaningrum, Noer Endah Pracoyo
Jundishapur Journal of Microbiology, Volume 14; https://doi.org/10.5812/jjm.117884

Abstract:
Background: Indonesia is one of the five countries with the highest number of diphtheria cases worldwide. Diphtheria is caused by the toxigenic strains Corynebacterium diphtheriae, C. ulcerans, and C. pseudotuberculosis. The diphtheria-causing bacteria can be identified using conventional and molecular methods, including polymerase chain reaction (PCR) assay. We used the PCR assay as additional testing, because in island countries like Indonesia, specimen transport is a serious challenge to maintaining bacterial survival. Objectives: This study aimed to evaluate the PCR assay as additional testing to identify diphtheria-causing bacteria in the diphtheria laboratory. Methods: In this cross-sectional study, a total of 178 pairs of the throat and nasal swabs from diphtheria suspected cases and close contacts were collected from seven provinces in Indonesia in 2016. All samples were directly identified by the conventional method and multiplex PCR assay. Statistical analysis was conducted using the 2 × 2 tables to determine the sensitivity and specificity of both methods, while the χ2 test was used to examine the correlation between specimen examination delay and the differentiation of results. A P-value < 0.05 was considered as statistically significant. Results: Out of 178 examined samples, eight samples were identified as diphtheria-positive by both the conventional method and PCR assay, while nine samples were only detected by the PCR assay. All diphtheria-causing bacteria found in the positive samples were toxigenic C. diphtheriae. The diphtheria-causing bacteria were found in 27.6% of cases and 6.0% of close contacts using the PCR assay versus 13.8% of cases and 2.7% of close contacts using the conventional method. Statistical analysis showed that the PCR assay is about twice more sensitive than the conventional method. There was a significant correlation between the differentiation of results and > 72 hours’ specimen examination delay with a P-value of 0.04 (< 0.05). Conclusions: The PCR assay is more sensitive than the conventional method to identify diphtheria-causing bacteria and may be applied as additional testing to increase the positivity rate of diphtheria-confirmed cases in Indonesia as an archipelago country where geographical factors and specimen transport are real obstacles.
Sulaiman A Al Yousef, Khalid AbdelRahim, Ahmed Mohamed Ali
Jundishapur Journal of Microbiology, Volume 14; https://doi.org/10.5812/jjm.116162

Abstract:
Background: Fast, reliable, and cost-effective tests are recommended for tuberculosis diagnosis and drug susceptibility testing, especially in resource-limited settings. Objectives: This study aimed to evaluate the performance of thin-layer agar for tuberculosis diagnosis and drug susceptibility testing. Methods: Samples were collected from patients with presumptive tuberculosis and tested using thin-layer agar for tuberculosis and drug susceptibility testing in parallel with Lowenstein Jensen culture method for tuberculosis diagnosis and proportion method for drug susceptibility testing as the gold standard. Receiver operating characteristic curve analysis was performed to calculate the performance parameters. Results: Thin-layer agar method showed sensitivity and specificity values of 96.63% and 62.50%, respectively, for the isolation of Mycobacterium tuberculosis directly from specimens. Drug susceptibility results using thin-layer agar showed sensitivity values for isoniazid, rifampicin), ethambutol and streptomycin were 94.74%, 86.84%, 94.74% and 81.58%, respectively, while the specificity values were 100%, 100%, 86.27% and 100% for isoniazid, rifampicin, ethambutol and streptomycin, respectively. Results were available in a median time of 16 days for thin-layer agar and 25 days for the conventional method. Conclusions: The thin-layer agar method is a relatively rapid, simple, and cost-effective method for the diagnosis and drug susceptibility testing of M. tuberculosis. It may be a useful tool for establishing tuberculosis laboratories in resource-limited settings because it does not require expensive equipment and a high level of training. Our study may help in choosing the appropriate treatment and control of tuberculosis.
Umar Saeed, Zahra Zahid Piracha, Sara Rizwan Uppal, Rizwan Uppal
Jundishapur Journal of Microbiology, Volume 14; https://doi.org/10.5812/jjm.114374

Abstract:
: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) preferentially infects respiratory tract cells, but it has organotropism. Middle East respiratory syndrome coronavirus (MERS-CoV) is significantly distinct from common cold and SARS coronavirus. In past few years, the SARS-CoV-2 and MERS-CoV caused several deaths in South Korea. The aim of current study was to assess SARS-CoV-2 and MERS-CoV awareness and epidemic prevention ability in South Koreans.According to our results, out of 1500 participants, 98.8% and 64.3% were aware of SARS-CoV-2 and MERS-CoV, respectively. Moreover, 97% of the participants used masks for prevention of airborne diseases, while 65.3% of the participants reused the same mask for several days. In addition, 50% of the participants were not satisfied with the government support. Future viral epidemics can be prevented by disseminating advanced knowledge and awareness among general public.
Nasrin Aliabadi, , , Nahid Heydari Marandi, Atoosa Ziyaeyan, Ali Amanati, Mazyar Ziyaeyan
Jundishapur Journal of Microbiology, Volume 14; https://doi.org/10.5812/jjm.117928

Abstract:
Background: Mutations in herpes simplex virus Thymidine kinase (TK, UL23) and DNA polymerase (pol, UL30) genes may confer resistance to acyclovir (ACV). Phenotypic resistance must be determined along with genotypic resistance to achieve complete acyclovir susceptibility. Objectives: The present study aimed to characterize HSV-1 clinical isolates from outpatients and organ transplant recipients in terms of phenotypic ACV resistance. Moreover, genotypic resistance to ACV was assessed through sequencing the viral TK and pol genes amplified from virus-infected cell DNA. Methods: Twenty-six HSV-1 clinical isolates collected between 2016 and 2019 were examined for drug susceptibility. The samples were collected from eyes, oropharyngeal, facial, and other skin parts of immunocompetent and immunocompromised individuals. Phenotypic susceptibility was determined by using three different concentrations of ACV. The results were expressed based on the ability of ACV in reducing viral plaques by 50%. Genotyping was carried out by polymerase chain reaction and sequencing of TK and pol genes. Results: All the strains were characterized as sensitive at 0.01 and 0.05 µg.ml-1 concentrations to ACV. Seventy percent inhibition was observed at 0.1 mg/mL of ACV for three isolates (two from patients who received transplants and one from an outpatient). Nine natural polymorphisms were detected in the TK gene and 31 in the Pol gene. Furthermore, four susceptible-associated mutations in the DNA pol gene were analyzed. A substitution was encoded in the conserved region of the pol Exo III motif (M553L), and nine amino acid substitutions in TK were detected. The phylogenetic analysis of partial genome sequences revealed high diversity in the TK and pol genes of HSV-1. Conclusions: A higher number of mutations were observed in patients who received transplants and underwent long-term treatment compared with outpatients. The high genetic variability of HSV-1 TK and DNA pol was not associated with phenotypic resistance.
, Maryam Zadsar, Shahram Samiei
Jundishapur Journal of Microbiology, Volume 14; https://doi.org/10.5812/jjm.117424

Abstract:
Background: With the rapidly increasing incidence of the novel coronavirus disease 2019 (COVID-19) and the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in plasma, blood supply safety has become a main concern. Objectives: Due to some reports on the detection of RNAemia in SARS-CoV-2-infected blood donors, this study examined the presence of SARS-CoV-2 RNA in asymptomatic blood donors. Methods: In this cross-sectional study, about 400 blood donors from the Tehran Blood Transfusion Center with negative results for viral serological markers of hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) were included in the study. Moreover, all samples were tested for anti-SARS-CoV-2 ELISA (IgG) to detect antibodies against SARS-CoV-2. The Presence of SARS-CoV-2 RNA in blood donors was identified by targeting RNA-dependent, RNA polymerase (RdRp), and N (nucleocapsid protein) genes using Real-Time PCR. Furthermore, the RNase P gene was used as an internal control. Results: The SARS-CoV-2 ELISA test showed that 60 (15%) of blood donors had antibodies against SARS-CoV-2 nucleocapsid protein, and 340 (85%) of the participants have not been exposed to the virus. The cycle threshold (Ct) for positive control in the RT-PCR test for nucleocapsid (N) and RdRP SARS-CoV-2 genes was < 40 (CT = 20.37). Moreover, internal control (RNase P gene) in all samples had Ct < 40. The presence of SARS-CoV-2 RNA was detected in the blood sample of none of the blood donors. In this regard, there has been no report of SARS-CoV-2 transmission to blood recipients yet. Conclusions: The blood-borne transmission of SARS-CoV-2 seems to be highly unlikely, and coronavirus RNA screening is unnecessary among blood donors. Preventive measures should be adopted to reduce the theoretical risk of transmitting SARS-CoV-2 by the blood from asymptomatic COVID-19 cases.
Shaghayegh Rostami Yasuj, Maral Gharaghani, , Marjan Salahi, Ali Keshtkari, Jabar Taghavi, Khadigeh Nazari, Saham Ansari, , Sadegh Nouripour-Sisakht
Jundishapur Journal of Microbiology, Volume 14; https://doi.org/10.5812/jjm.117643

Abstract:
Background: Candidemia is the most common systemic infection in hospitalized patients causing high mortality. Hence, the diagnosis of this infection in the early stage with appropriate antifungal therapy is paramount. Objectives: The study aimed at molecular identification of Candida species isolated from candidemia patients and evaluation of the in vitro antifungal susceptibility patterns of these strains to fluconazole, amphotericin B, and caspofungin. Methods: In the present study, 800 hospitalized patients who were suspected to have candidemia were sampled. Candida species were isolated and identified based on morphological characteristics and PCR-sequencing of the ITS1-5.8S-ITS2 region. Antifungal susceptibility tests for fluconazole, amphotericin B, and caspofungin were performed according to the Clinical and Laboratory Standards Institute protocol M27-A3. Also, clinical data were recorded from the patients' records. Results: Twenty-seven patients among the sample of hospitalized patients were found to have candidemia. A total of 33.3% of candidemia patients were treated with amphotericin B, in which case the mortality rate was 14.8%. The majority of patients (59%) were from the neonatal intensive care unit, and premature birth was the most common underlying condition. Candida albicans (n = 18; 66.6%) was the most common species isolated from blood cultures, followed by C. parapsilosis (n = 7; 25.9%), C. pelliculosa (n = 1; 3.7%), and C. tropicalis (n = 1; 3.7%). Only one C. albicans isolate resistant to fluconazole (minimum inhibitory concentration = 32 µg/mL). Conclusions: Generally, C. albicans has been the most frequent causative agent of candidemia. Resistance to antifungal drugs among candidemia agents was rare. Also, the identification of Candida isolates at the species level with in vitro antifungal susceptibility tests helps manage candidemia patients better and decrease the mortality rate among them.
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