Mastaneh Alinezhadi, N. Neisi, M. Rasti, M. Arshadi, M. Parsanahad, B. Cheraghian
Background: Fast and precise detection of SARS-CoV-2 RNA in clinical samples and subsequent quarantine are two critical factors in preventing virus transmission and distribution through the community. The false-negative result is a major problem in the SARS-CoV-2 detection because of the kind of sample (swab sample), sampling error, and sensitivity of PCR test, which can be reduced by a much more sensitive test such as nested PCR. Objectives: This study aimed to evaluate the false-negative rate among samples that were negative by a real-time PCR test using RT-nested PCR. Methods: One hundred eighty-four negative samples were included in the study, and nucleic acid was extracted using a commercial kit based on a silica filter column and then subjected to RT-nested PCR using three sets of primers targeting Orf1ab, N, and RdRp regions. Results: Among 184 negative swab samples for SARS-CoV-2, 27 (14.6%) cases were positive for the Orf1ab gene using RT-nested PCR. The samples were tested using N and RdRp primer sets. Also, seven (3.8%) cases were positive for the N gene, and four (2.1%) cases were positive for the RdRp gene. Conclusions: The results indicated that RT-nested PCR could be more sensitive than real-time PCR and reduce the false-negative rate.
{"title":"Evaluation of False Negative Among SARS-COV-2 Patients with Negative Real-time PCR Result Using Nested-RT PCR","authors":"Mastaneh Alinezhadi, N. Neisi, M. Rasti, M. Arshadi, M. Parsanahad, B. Cheraghian","doi":"10.5812/jjm-122889","DOIUrl":"https://doi.org/10.5812/jjm-122889","url":null,"abstract":"Background: Fast and precise detection of SARS-CoV-2 RNA in clinical samples and subsequent quarantine are two critical factors in preventing virus transmission and distribution through the community. The false-negative result is a major problem in the SARS-CoV-2 detection because of the kind of sample (swab sample), sampling error, and sensitivity of PCR test, which can be reduced by a much more sensitive test such as nested PCR. Objectives: This study aimed to evaluate the false-negative rate among samples that were negative by a real-time PCR test using RT-nested PCR. Methods: One hundred eighty-four negative samples were included in the study, and nucleic acid was extracted using a commercial kit based on a silica filter column and then subjected to RT-nested PCR using three sets of primers targeting Orf1ab, N, and RdRp regions. Results: Among 184 negative swab samples for SARS-CoV-2, 27 (14.6%) cases were positive for the Orf1ab gene using RT-nested PCR. The samples were tested using N and RdRp primer sets. Also, seven (3.8%) cases were positive for the N gene, and four (2.1%) cases were positive for the RdRp gene. Conclusions: The results indicated that RT-nested PCR could be more sensitive than real-time PCR and reduce the false-negative rate.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2022-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42437148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Azadeh abedzadeh hajar, M. Dakhili, M. Saghazadeh, S. Aghaei, R. Nazari
Background: There are serious challenges of drug resistance in Candida albicans infection. Therefore, it is essential to identify new antifungal agents against resistant species to effectively treat patients affected by these species. Objectives: The present study aimed to study how zinc oxide nanoparticles (ZnO-NPs) and fluconazole affected the genes encoding resistance to fluconazole (i.e., CDR2 and ERG11) and those encoding adhesins (i.e., ALS1 and HWP1) in C. albicans isolates. Methods: In this descriptive-analytic study, samples of 120 patients with vaginitis were obtained using sterile swabs. After the identification of C. albicans strains, the fluconazole-resistant candida isolates were treated with various sub-minimum inhibitory concentrations of ZnO-NPs, fluconazole, and a combination of ZnO-NPs and fluconazole. Then, the effects of ZnO-NPs and fluconazole on the expression levels of ALS1, HWP1, CDR2, and ERG11 genes were evaluated by real-time polymerase chain reaction. Results: In this study, 50 out (41.6%) of 120 species with C. albicans were isolated, and 13 (26%) of 50 species were resistant to fluconazole. The expression analysis of fluconazole-resistant C. albicans strains showed that the expression of HWP1 and ALS1 genes was decreased by 2.84 and 1.62 times (P < 0.05), respectively. Nevertheless, the expression of CDR2 increased 1.42 - fold after the treatment with fluconazole. The expression of ERG11, CDR2, HWP1, and ALS1 in isolates treated with the combination of ZnO-NPs and fluconazole was downregulated by 2.1, 5.9, 3, and 5.5 times, respectively, compared to that of the control group. Conclusions: Based on the results, ZnO-NPs are helpful for the treatment of vaginitis-related C. albicans isolates in combination with fluconazole.
{"title":"Changes of Gene Expression in Candida albicans Isolates from Vaginal Infections by Effects of Zinc Oxide Nanoparticles and Fluconazole","authors":"Azadeh abedzadeh hajar, M. Dakhili, M. Saghazadeh, S. Aghaei, R. Nazari","doi":"10.5812/jjm-124602","DOIUrl":"https://doi.org/10.5812/jjm-124602","url":null,"abstract":"Background: There are serious challenges of drug resistance in Candida albicans infection. Therefore, it is essential to identify new antifungal agents against resistant species to effectively treat patients affected by these species. Objectives: The present study aimed to study how zinc oxide nanoparticles (ZnO-NPs) and fluconazole affected the genes encoding resistance to fluconazole (i.e., CDR2 and ERG11) and those encoding adhesins (i.e., ALS1 and HWP1) in C. albicans isolates. Methods: In this descriptive-analytic study, samples of 120 patients with vaginitis were obtained using sterile swabs. After the identification of C. albicans strains, the fluconazole-resistant candida isolates were treated with various sub-minimum inhibitory concentrations of ZnO-NPs, fluconazole, and a combination of ZnO-NPs and fluconazole. Then, the effects of ZnO-NPs and fluconazole on the expression levels of ALS1, HWP1, CDR2, and ERG11 genes were evaluated by real-time polymerase chain reaction. Results: In this study, 50 out (41.6%) of 120 species with C. albicans were isolated, and 13 (26%) of 50 species were resistant to fluconazole. The expression analysis of fluconazole-resistant C. albicans strains showed that the expression of HWP1 and ALS1 genes was decreased by 2.84 and 1.62 times (P < 0.05), respectively. Nevertheless, the expression of CDR2 increased 1.42 - fold after the treatment with fluconazole. The expression of ERG11, CDR2, HWP1, and ALS1 in isolates treated with the combination of ZnO-NPs and fluconazole was downregulated by 2.1, 5.9, 3, and 5.5 times, respectively, compared to that of the control group. Conclusions: Based on the results, ZnO-NPs are helpful for the treatment of vaginitis-related C. albicans isolates in combination with fluconazole.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":"1 1","pages":""},"PeriodicalIF":0.6,"publicationDate":"2022-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71285479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Pseudomonas aeruginosa nosocomial infections are among major problems associated with increased mortality and mobility among patients. Objectives: The aim of this research was to determine the molecular epidemiology of extended spectrum beta-lactamase (ESBL)-producing P. aeruginosa genotypes isolated from patients with nosocomial infections. Methods: One hundred forty-six clinical isolates of Pseudomonas spp. were obtained from a tertiary referral hospital. Phenotypic identification and PCR detection of gyrB were used to characterize P. aeruginosa. Extended spectrum beta-lactamases in samples were identified using the disk approximation test and the combination disk test (CDT). The blaSHV and blaTEM genes were detected by PCR. The strains were typed by the pulse field gel electrophoresis (PFGE), repetitive element sequence (Rep)-PCR, and enterobacterial repetitive intergenic consensus (ERIC)–PCR methods. Results: A total of 134 (91.78%) P. aeruginosa isolates were separated, 41.79% of whom were related to nosocomial infections. The extended spectrum beta-lactamase analysis test revealed that 5.97% and 66.41% of the isolates harbored the blaSHV and blaTEM genes, respectively. Enterobacterial repetitive intergenic consensus PCR, Rep-PCR, and PFGE each showed 56, 55, and 55 different patterns, respectively. Pulse-field gel electrophoresis indicated that pulso types C3 were dominant. Conclusions: The associations between ESBL production, blaSHV and blaTEM positivity, and ERIC, Rep-PCR, and PFGE patterns were not significant (P ≥ 0.05). Among nosocomial infections, a relatively high prevalence of ESBL-producing P. aeruginosa isolates was observed in the Kurdistan province of Iran. Periodic review of antibiotic resistance and molecular characterization of P. aeruginosa isolates is recommended to prevent the spread of nosocomial infections in hospitals.
{"title":"Genotyping of Extended Spectrum Beta-Lactamase-Producing Pseudomonas aeruginosa Isolated from People with Nosocomial Infections","authors":"R. Ramazanzadeh","doi":"10.5812/jjm-119802","DOIUrl":"https://doi.org/10.5812/jjm-119802","url":null,"abstract":"Background: Pseudomonas aeruginosa nosocomial infections are among major problems associated with increased mortality and mobility among patients. Objectives: The aim of this research was to determine the molecular epidemiology of extended spectrum beta-lactamase (ESBL)-producing P. aeruginosa genotypes isolated from patients with nosocomial infections. Methods: One hundred forty-six clinical isolates of Pseudomonas spp. were obtained from a tertiary referral hospital. Phenotypic identification and PCR detection of gyrB were used to characterize P. aeruginosa. Extended spectrum beta-lactamases in samples were identified using the disk approximation test and the combination disk test (CDT). The blaSHV and blaTEM genes were detected by PCR. The strains were typed by the pulse field gel electrophoresis (PFGE), repetitive element sequence (Rep)-PCR, and enterobacterial repetitive intergenic consensus (ERIC)–PCR methods. Results: A total of 134 (91.78%) P. aeruginosa isolates were separated, 41.79% of whom were related to nosocomial infections. The extended spectrum beta-lactamase analysis test revealed that 5.97% and 66.41% of the isolates harbored the blaSHV and blaTEM genes, respectively. Enterobacterial repetitive intergenic consensus PCR, Rep-PCR, and PFGE each showed 56, 55, and 55 different patterns, respectively. Pulse-field gel electrophoresis indicated that pulso types C3 were dominant. Conclusions: The associations between ESBL production, blaSHV and blaTEM positivity, and ERIC, Rep-PCR, and PFGE patterns were not significant (P ≥ 0.05). Among nosocomial infections, a relatively high prevalence of ESBL-producing P. aeruginosa isolates was observed in the Kurdistan province of Iran. Periodic review of antibiotic resistance and molecular characterization of P. aeruginosa isolates is recommended to prevent the spread of nosocomial infections in hospitals.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2022-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47704904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zygmunt Gofron, Klaudia Szarek, M. Aptekorz, Monika Kabała, G. Martirosian
Background: Clostridium spp. spores are resistant to many factors, including alcohol-based disinfectants. The presence of clostridial spores in a hospital environment may lead to infection outbreaks among patients and health care workers. Objective: This study aimed to detect clostridial spores in aurology hospital using C diff Banana Broth™ and assess the antibiotic sensitivity and toxinotypes of isolates. Methods: After diagnosing COVID-19 in medical staff and closing an 86-bed urology hospital in 2020 for H2O2 fogging, 58 swabs from the hospital environment were inoculated to C diff Banana Broth™, incubated at 37°C for 14 days, checked daily, and positive broths were sub-cultured anaerobically for 48 h at 37°C. After identification, multiplex PCR (mPCR) was performed for Clostridium perfringens, C. difficile toxin genes, and MIC determination. Results: In this study, 16.58 (~ 28%) strains of Clostridium spp. were cultured: 11 - C. perfringens, 2 - C. baratii, and 1 each of C. paraputrificum, C. difficile, and C. clostridioforme. Moreover, C. difficile produced all toxins, and 11 C. perfringens consisted of 1 cpa, 7 cpb2, 2 cpiA, and 1 cpb gene-positive. All isolates were sensitive to metronidazole, vancomycin, moxifloxacin, penicillin/tazobactam, and rifampicin. Two out of the 11 C. perfringens strains were resistant to erythromycin and clindamycin. Conclusions: Regardless of the performed H2O2 fogging, antibiotic-resistant, toxigenic strains of C. perfringens (69%) obtained from the urology hospital environment were cultured using C diff Banana Broth™, indicating the need to develop the necessary sanitary and epidemiological procedures in this hospital.
{"title":"Clostridium perfringens Spores in Urology Hospitals","authors":"Zygmunt Gofron, Klaudia Szarek, M. Aptekorz, Monika Kabała, G. Martirosian","doi":"10.5812/jjm-124129","DOIUrl":"https://doi.org/10.5812/jjm-124129","url":null,"abstract":"Background: Clostridium spp. spores are resistant to many factors, including alcohol-based disinfectants. The presence of clostridial spores in a hospital environment may lead to infection outbreaks among patients and health care workers. Objective: This study aimed to detect clostridial spores in aurology hospital using C diff Banana Broth™ and assess the antibiotic sensitivity and toxinotypes of isolates. Methods: After diagnosing COVID-19 in medical staff and closing an 86-bed urology hospital in 2020 for H2O2 fogging, 58 swabs from the hospital environment were inoculated to C diff Banana Broth™, incubated at 37°C for 14 days, checked daily, and positive broths were sub-cultured anaerobically for 48 h at 37°C. After identification, multiplex PCR (mPCR) was performed for Clostridium perfringens, C. difficile toxin genes, and MIC determination. Results: In this study, 16.58 (~ 28%) strains of Clostridium spp. were cultured: 11 - C. perfringens, 2 - C. baratii, and 1 each of C. paraputrificum, C. difficile, and C. clostridioforme. Moreover, C. difficile produced all toxins, and 11 C. perfringens consisted of 1 cpa, 7 cpb2, 2 cpiA, and 1 cpb gene-positive. All isolates were sensitive to metronidazole, vancomycin, moxifloxacin, penicillin/tazobactam, and rifampicin. Two out of the 11 C. perfringens strains were resistant to erythromycin and clindamycin. Conclusions: Regardless of the performed H2O2 fogging, antibiotic-resistant, toxigenic strains of C. perfringens (69%) obtained from the urology hospital environment were cultured using C diff Banana Broth™, indicating the need to develop the necessary sanitary and epidemiological procedures in this hospital.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2022-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47551067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Enterococcus faecalis rapidly develops resistance to different antibiotics, thereby resulting in serious nosocomial infections associated with high mortality rates and different problems in the healthcare systems. Objectives: This study aimed to analyze the genetic diversity, antimicrobial resistance, and virulence factors of E. faecalis isolates obtained from the stool samples of patients in a hospital in the center of Iran. Methods: In this cross-sectional descriptive-analytical study, 108 stool samples were collected from September 2019 to February 2020 from 108 patients hospitalized in a hospital in the center of Iran. Enterococcus faecalis isolates were detected using the ddlE gene detection technique, and antimicrobial resistance testing was performed using the disc agar diffusion method. Moreover, polymerase chain reaction (PCR) was used to detect antimicrobial resistance genes and virulence factors. Genetic diversity was also analyzed by enterobacterial repetitive intergenic consensus using PCR (ERIC-PCR). The BioNumerics software was used to construct a dendrogram. Results: Of 108 isolates, 50 samples were E. faecalis (46.2%). The prevalence of multidrug resistance among E. faecalis isolates was 62%, and most isolates were resistant to antibiotics tetracycline (70%), erythromycin (68%), and rifampin (60%). Among the E. faecalis isolates, the most prevalent antimicrobial resistance genes were ermB (96%), aph (2′′) Ia (66%), aac(6′)-Ie (40%), and ermC (30%), and the most prevalent virulence genes were gelE (78%), asa1 (74%), and esp (74%). The genetic diversity analysis showed 25 ERIC types in two major clusters (ie, clusters H and J) and eight minor clusters (ie, clusters A-G and I). There was no significant difference between clusters H and J in terms of antimicrobial resistance and resistance genes (P > 0.05). In contrast, the prevalence of the asa1 gene was significantly higher in cluster J than in cluster H (P < 0.05). Conclusions: This study showed the high prevalence of multidrug resistance, and high heterogeneity among the E. faecalis isolates obtained from the stool samples of hospitalized patients.
{"title":"Genetic Diversity, Antimicrobial Resistance, and Virulence Factors of Enterococcus Faecalis Isolates Obtained from Stool Samples of Hospitalized Patients","authors":"Mitra Motallebi, Z. Seyyedi, M. Azadchehr","doi":"10.5812/jjm-121379","DOIUrl":"https://doi.org/10.5812/jjm-121379","url":null,"abstract":"Background: Enterococcus faecalis rapidly develops resistance to different antibiotics, thereby resulting in serious nosocomial infections associated with high mortality rates and different problems in the healthcare systems. Objectives: This study aimed to analyze the genetic diversity, antimicrobial resistance, and virulence factors of E. faecalis isolates obtained from the stool samples of patients in a hospital in the center of Iran. Methods: In this cross-sectional descriptive-analytical study, 108 stool samples were collected from September 2019 to February 2020 from 108 patients hospitalized in a hospital in the center of Iran. Enterococcus faecalis isolates were detected using the ddlE gene detection technique, and antimicrobial resistance testing was performed using the disc agar diffusion method. Moreover, polymerase chain reaction (PCR) was used to detect antimicrobial resistance genes and virulence factors. Genetic diversity was also analyzed by enterobacterial repetitive intergenic consensus using PCR (ERIC-PCR). The BioNumerics software was used to construct a dendrogram. Results: Of 108 isolates, 50 samples were E. faecalis (46.2%). The prevalence of multidrug resistance among E. faecalis isolates was 62%, and most isolates were resistant to antibiotics tetracycline (70%), erythromycin (68%), and rifampin (60%). Among the E. faecalis isolates, the most prevalent antimicrobial resistance genes were ermB (96%), aph (2′′) Ia (66%), aac(6′)-Ie (40%), and ermC (30%), and the most prevalent virulence genes were gelE (78%), asa1 (74%), and esp (74%). The genetic diversity analysis showed 25 ERIC types in two major clusters (ie, clusters H and J) and eight minor clusters (ie, clusters A-G and I). There was no significant difference between clusters H and J in terms of antimicrobial resistance and resistance genes (P > 0.05). In contrast, the prevalence of the asa1 gene was significantly higher in cluster J than in cluster H (P < 0.05). Conclusions: This study showed the high prevalence of multidrug resistance, and high heterogeneity among the E. faecalis isolates obtained from the stool samples of hospitalized patients.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2022-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42590185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G. Rasool, M. Shams, M. Siraj, W. Latif, Robina Sheikh, S. Jahan, N. Naseem, A. Nagi
Background: Helicobacter pylori colonizes gastric tissue in obese patients and mostly remains undetected clinically, as histological and molecular analysis is seldom ordered in such cases. Objectives: This study aimed to detect the frequency of H. pylori using different techniques in sleeve gastrectomy specimens of obese patients with minimal or no symptoms suggestive of gastritis. Methods: This longitudinal study was carried out at Farooq Hospital Westwood Lahore, Morbid Anatomy and Histopathology Department and Resource Laboratory at the University of Health Sciences, Lahore, Pakistan, from February 2021 to September 2021. This study selected 80 cases who underwent sleeve gastrectomy within six months. Helicobacter pylori was detected by rapid urease test (RUT), modified Giemsa staining, and polymerase chain reaction (PCR) techniques. Results: Most patients (83.7%) were clinically asymptomatic, while 10% had mild and 6.3% had moderate to severe gastritis symptoms. Of the asymptomatic patients, 56.7% of biopsies showed chronic gastritis. Rapid urease test and modified Giemsa staining showed positive evidence for H. pylori in 47.3% of cases, whereas an additional 13.2% of biopsies that were negative on conventional methods showed the amplification of H. pylori DNA by PCR. Patients were discharged with proton-pump inhibitors therapy (40 mg/day) that showed no adverse post-surgical event over a follow-up of six months. Conclusions: Persistent obesity and other socioeconomic factors may lead to colonizing asymptomatic H. pylori infection. More sensitive techniques for detecting H. pylori may be employed in resource-constrained settings for better patient outcomes and to minimize the complications after sleeve gastrectomy.
{"title":"Is Molecular Analysis Mandatory for Better Post-surgical Outcome in Sleeve Gastrectomy Specimens with Asymptomatic Helicobacter pylori Colonization? A Study from Pakistan","authors":"G. Rasool, M. Shams, M. Siraj, W. Latif, Robina Sheikh, S. Jahan, N. Naseem, A. Nagi","doi":"10.5812/jjm-122528","DOIUrl":"https://doi.org/10.5812/jjm-122528","url":null,"abstract":"Background: Helicobacter pylori colonizes gastric tissue in obese patients and mostly remains undetected clinically, as histological and molecular analysis is seldom ordered in such cases. Objectives: This study aimed to detect the frequency of H. pylori using different techniques in sleeve gastrectomy specimens of obese patients with minimal or no symptoms suggestive of gastritis. Methods: This longitudinal study was carried out at Farooq Hospital Westwood Lahore, Morbid Anatomy and Histopathology Department and Resource Laboratory at the University of Health Sciences, Lahore, Pakistan, from February 2021 to September 2021. This study selected 80 cases who underwent sleeve gastrectomy within six months. Helicobacter pylori was detected by rapid urease test (RUT), modified Giemsa staining, and polymerase chain reaction (PCR) techniques. Results: Most patients (83.7%) were clinically asymptomatic, while 10% had mild and 6.3% had moderate to severe gastritis symptoms. Of the asymptomatic patients, 56.7% of biopsies showed chronic gastritis. Rapid urease test and modified Giemsa staining showed positive evidence for H. pylori in 47.3% of cases, whereas an additional 13.2% of biopsies that were negative on conventional methods showed the amplification of H. pylori DNA by PCR. Patients were discharged with proton-pump inhibitors therapy (40 mg/day) that showed no adverse post-surgical event over a follow-up of six months. Conclusions: Persistent obesity and other socioeconomic factors may lead to colonizing asymptomatic H. pylori infection. More sensitive techniques for detecting H. pylori may be employed in resource-constrained settings for better patient outcomes and to minimize the complications after sleeve gastrectomy.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2022-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44557839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Faezeh Ahmadi, R. Daie Ghazvini, S. Hashemi, Zahra Ramezanalipour, J. Chabavizadeh, Z. Rafat, Davoud Roostaei
Background: One of the most prevalent infections in hospitalized patients is candiduria. As the prevalence of this infection is increasing, new epidemiologic and therapeutic data can be used as a guide for the management of patients. Objectives: This research aimed to determine the epidemiological and antifungal susceptibility profile of candiduria. Methods: A total of 104 patients admitted to the nephrology and ICU wards of Bu Ali and Labbafinezhad hospitals in Tehran, Iran, were studied in this cross-sectional investigation. Urine samples were examined using direct smear, culture, and PCR-sequencing techniques. The culture plates were subjected to colony count. The clinical and laboratory standards institute (CLSI) document M27 4th ed was used to assess susceptibility to amphotericin B, itraconazole, caspofungin, and fluconazole. Results: Out of 104 patients, 26 (25%) were diagnosed with candiduria. Most patients were between the ages of 64 - 79 years (n = 9, 34.61%) and female (n = 17, 23.94%). Stroke and urinary catheterization were the most common underlying diseases. Candida glabrata (n = 10, 38.64%) was the most common cause of candiduria. Caspofungin and amphotericin B were the most effective antifungal medicines. Conclusions: Candida glabrata has been identified as the most common cause of candiduria. Due to the increasing antifungal resistance in this species, proper treatment of patients is a crucial concern. Caspofungin exhibited potent antifungal activity against all tested isolates. Still, regardless of its favorable in vitro activity, due to its poor glomerular filtration or tubular secretion in vivo, it has sub-therapeutic antifungal concentrations in the urine.
{"title":"Epidemiologic and Antifungal Susceptibility Profile of Candiduria Among Patients Hospitalized in The Nephrology and Intensive Care Unit Wards, Tehran, Iran","authors":"Faezeh Ahmadi, R. Daie Ghazvini, S. Hashemi, Zahra Ramezanalipour, J. Chabavizadeh, Z. Rafat, Davoud Roostaei","doi":"10.5812/jjm-126418","DOIUrl":"https://doi.org/10.5812/jjm-126418","url":null,"abstract":"Background: One of the most prevalent infections in hospitalized patients is candiduria. As the prevalence of this infection is increasing, new epidemiologic and therapeutic data can be used as a guide for the management of patients. Objectives: This research aimed to determine the epidemiological and antifungal susceptibility profile of candiduria. Methods: A total of 104 patients admitted to the nephrology and ICU wards of Bu Ali and Labbafinezhad hospitals in Tehran, Iran, were studied in this cross-sectional investigation. Urine samples were examined using direct smear, culture, and PCR-sequencing techniques. The culture plates were subjected to colony count. The clinical and laboratory standards institute (CLSI) document M27 4th ed was used to assess susceptibility to amphotericin B, itraconazole, caspofungin, and fluconazole. Results: Out of 104 patients, 26 (25%) were diagnosed with candiduria. Most patients were between the ages of 64 - 79 years (n = 9, 34.61%) and female (n = 17, 23.94%). Stroke and urinary catheterization were the most common underlying diseases. Candida glabrata (n = 10, 38.64%) was the most common cause of candiduria. Caspofungin and amphotericin B were the most effective antifungal medicines. Conclusions: Candida glabrata has been identified as the most common cause of candiduria. Due to the increasing antifungal resistance in this species, proper treatment of patients is a crucial concern. Caspofungin exhibited potent antifungal activity against all tested isolates. Still, regardless of its favorable in vitro activity, due to its poor glomerular filtration or tubular secretion in vivo, it has sub-therapeutic antifungal concentrations in the urine.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2022-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47186217","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background: Urinary tract infections represent a major expensive, common public health problem worldwide due to their high prevalence and the difficulties associated with their management. Objectives: This study aimed to characterize the Enterobacter cloacae strains isolated from urinary tract infections in the medical diagnostic laboratories of Shahrekord, Iran. Methods: Urine samples from patients with urinary tract infections from the Shahrekord medical diagnostic laboratories located in Chaharmahal and Bakhtiari Province, Iran, were collected from June 2019 to February 2020. When the samples were cultured, the different isolates of E. cloacae were identified by biochemical tests. Biofilm production capacity was evaluated. Bacterial susceptibility to antibiotics was determined using the Kirby Bauer method, and antibiotic resistance genes were researched by the multiplex PCR technique. Results: In this study, 65 isolates of E. cloacae were obtained. The highest percentage of resistance was observed for co-trimoxazole (84.62%), ampicillin (76.93%), tetracycline (73.85%), and above half of the E. cloacae strain isolates (53,85%) were strongly involved in biofilm production. Some genes, including qnr A, qnr B, qnr S, tetA, tet B, sul1, bla CTXM, bla SHV, and(2)la, ant(3)la, and aac(3)IIa, were detected in the genome of these isolates. Conclusions: The strains are multi-resistant, and their resistance has already reached the carbapenem class. This requires further investigation, and urgent measures must be adopted.
{"title":"Molecular Characterization of Enterobacter cloacae Isolated from Urinary Tract Infections","authors":"Elahe Barzam Dehkordi, E. Tajbakhsh, H. Momtaz","doi":"10.5812/jjm-122718","DOIUrl":"https://doi.org/10.5812/jjm-122718","url":null,"abstract":"Background: Urinary tract infections represent a major expensive, common public health problem worldwide due to their high prevalence and the difficulties associated with their management. Objectives: This study aimed to characterize the Enterobacter cloacae strains isolated from urinary tract infections in the medical diagnostic laboratories of Shahrekord, Iran. Methods: Urine samples from patients with urinary tract infections from the Shahrekord medical diagnostic laboratories located in Chaharmahal and Bakhtiari Province, Iran, were collected from June 2019 to February 2020. When the samples were cultured, the different isolates of E. cloacae were identified by biochemical tests. Biofilm production capacity was evaluated. Bacterial susceptibility to antibiotics was determined using the Kirby Bauer method, and antibiotic resistance genes were researched by the multiplex PCR technique. Results: In this study, 65 isolates of E. cloacae were obtained. The highest percentage of resistance was observed for co-trimoxazole (84.62%), ampicillin (76.93%), tetracycline (73.85%), and above half of the E. cloacae strain isolates (53,85%) were strongly involved in biofilm production. Some genes, including qnr A, qnr B, qnr S, tetA, tet B, sul1, bla CTXM, bla SHV, and(2)la, ant(3)la, and aac(3)IIa, were detected in the genome of these isolates. Conclusions: The strains are multi-resistant, and their resistance has already reached the carbapenem class. This requires further investigation, and urgent measures must be adopted.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2022-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43343744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. Shokouhi, S. Tehrani, Parviz Saleh, Atousa Yazdanpanah, Amirreza Keyvanfar
Introduction: Brucella prosthetic joint infection is a rare condition. We report a case of bilateral prosthetic knee joint infection caused by Brucella melitensis, which was cured by prolonged antibiotic therapy without implant removal. Case Presentation: A 62-year-old woman was admitted to the Labbafinejad Hospital (Tehran, Iran), complaining of pain and swelling in her knee joints from two months ago. She was also suffering from intermittent fever and night sweats. She underwent bilateral total knee arthroplasty five years ago because of a severe degenerative joint disease. Agglutination tests (wright and 2-mercaptoethanol (2-ME)) were positive. Her knee joint fluid and blood cultures yielded B. melitensis. The polymerase chain reaction result from her knee joint fluid was positive for Brucella spp. The patient was cured after taking a combination of therapies with doxycycline, rifampin, and gentamicin. The prosthesis was retained due to the lack of loosening in radiography. Ten months after the treatment, the patient had no symptoms and could walk with no pain. Conclusions: Clinicians should consider brucellosis in the differential diagnosis of prosthetic joint infection in the endemic regions. They should also be aware that if patients have no sign of implant loosening, they can achieve favorable outcomes only by using antibiotics and with no need for implant removal.
{"title":"Bilateral Prosthetic Knee Joint Infection Caused by Brucella melitensis: A Rare Case Report from Iran","authors":"S. Shokouhi, S. Tehrani, Parviz Saleh, Atousa Yazdanpanah, Amirreza Keyvanfar","doi":"10.5812/jjm-128097","DOIUrl":"https://doi.org/10.5812/jjm-128097","url":null,"abstract":"Introduction: Brucella prosthetic joint infection is a rare condition. We report a case of bilateral prosthetic knee joint infection caused by Brucella melitensis, which was cured by prolonged antibiotic therapy without implant removal. Case Presentation: A 62-year-old woman was admitted to the Labbafinejad Hospital (Tehran, Iran), complaining of pain and swelling in her knee joints from two months ago. She was also suffering from intermittent fever and night sweats. She underwent bilateral total knee arthroplasty five years ago because of a severe degenerative joint disease. Agglutination tests (wright and 2-mercaptoethanol (2-ME)) were positive. Her knee joint fluid and blood cultures yielded B. melitensis. The polymerase chain reaction result from her knee joint fluid was positive for Brucella spp. The patient was cured after taking a combination of therapies with doxycycline, rifampin, and gentamicin. The prosthesis was retained due to the lack of loosening in radiography. Ten months after the treatment, the patient had no symptoms and could walk with no pain. Conclusions: Clinicians should consider brucellosis in the differential diagnosis of prosthetic joint infection in the endemic regions. They should also be aware that if patients have no sign of implant loosening, they can achieve favorable outcomes only by using antibiotics and with no need for implant removal.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2022-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49543393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Hajihasani, M. Ebrahimi-Rad, Masoumeh Rasoulinasab, M. Aslani, F. Shahcheraghi
Background: Commensal extended-spectrum β-lactamase (ESBL) producing Escherichia coli isolates in the gut can be the reservoir of virulence factors and resistance genes. Objectives: We investigated the molecular feature, risk factors, and quinolone/fluoroquinolone (Q/FQ) resistance in sequence type 131 (ST131) and non-ST131: ESBL-producing E. coli (EPE) isolates in healthy fecal carriers. Methods: A total of 540 fecal samples and its demographic data were collected from healthy adults in Tehran in 2018. ST131 isolates were identified by MLST analysis, and the characteristics of the virulence factor, phylogenic assay, and Q/FQ resistance genes in ST131 and non-ST131 were determined by polymerase chain reaction (PCR). Results: The EPE isolates mainly belonged to the commensal phylogenetic groups A (54.9%) and D (18.1%). The type 1 fimbriae (fimH; 89.6%) gene was the predominant virulence factor, and there was a significant correlation between ferric yersiniabactin uptake (fyuA; 52.9%), aerobactin receptor (iutA; 17.6%), and group II capsule synthesis (kpsMII; 35.3%) with ST131. In Q/FQ-resistant isolates, qnrS (19%) was the predominant gene, and mutations mostly occurred at codon S83 in GyrA The number of mutations in gyrA and parC genes was significantly higher in ST131 isolates than in non-ST131 isolates. There was a significant positive correlation between diabetes, male gender, and living in the south of the city with EPE carriage (P < 0.05). Conclusions: Accumulation of multiple virulence factors and high- level resistance to Q/FQ in some phylogroups (B2 and D), particularly ST131 isolates, require to be considered in detecting resistant isolates in healthy carriers. According to the risk factor for spreading of EPE isolates (diabetes, living in low-income parts of the city, and male gender), the necessary strategies are required to be developed to control the dissemination of antimicrobial-resistant isolates in the community.
{"title":"The Molecular Characterization and Risk Factors of ST131 and Non-ST131 Escherichia coli in Healthy Fecal Carriers in Tehran, Iran","authors":"A. Hajihasani, M. Ebrahimi-Rad, Masoumeh Rasoulinasab, M. Aslani, F. Shahcheraghi","doi":"10.5812/jjm-122468","DOIUrl":"https://doi.org/10.5812/jjm-122468","url":null,"abstract":"Background: Commensal extended-spectrum β-lactamase (ESBL) producing Escherichia coli isolates in the gut can be the reservoir of virulence factors and resistance genes. Objectives: We investigated the molecular feature, risk factors, and quinolone/fluoroquinolone (Q/FQ) resistance in sequence type 131 (ST131) and non-ST131: ESBL-producing E. coli (EPE) isolates in healthy fecal carriers. Methods: A total of 540 fecal samples and its demographic data were collected from healthy adults in Tehran in 2018. ST131 isolates were identified by MLST analysis, and the characteristics of the virulence factor, phylogenic assay, and Q/FQ resistance genes in ST131 and non-ST131 were determined by polymerase chain reaction (PCR). Results: The EPE isolates mainly belonged to the commensal phylogenetic groups A (54.9%) and D (18.1%). The type 1 fimbriae (fimH; 89.6%) gene was the predominant virulence factor, and there was a significant correlation between ferric yersiniabactin uptake (fyuA; 52.9%), aerobactin receptor (iutA; 17.6%), and group II capsule synthesis (kpsMII; 35.3%) with ST131. In Q/FQ-resistant isolates, qnrS (19%) was the predominant gene, and mutations mostly occurred at codon S83 in GyrA The number of mutations in gyrA and parC genes was significantly higher in ST131 isolates than in non-ST131 isolates. There was a significant positive correlation between diabetes, male gender, and living in the south of the city with EPE carriage (P < 0.05). Conclusions: Accumulation of multiple virulence factors and high- level resistance to Q/FQ in some phylogroups (B2 and D), particularly ST131 isolates, require to be considered in detecting resistant isolates in healthy carriers. According to the risk factor for spreading of EPE isolates (diabetes, living in low-income parts of the city, and male gender), the necessary strategies are required to be developed to control the dissemination of antimicrobial-resistant isolates in the community.","PeriodicalId":17803,"journal":{"name":"Jundishapur Journal of Microbiology","volume":" ","pages":""},"PeriodicalIF":0.6,"publicationDate":"2022-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47431304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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