International Journal of Microbiology
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Published By Hindawi Limited

1687-9198, 1687-918x
Updated Friday, 14 January 2022

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Asmae Lamrani Hanchi ◽  
Morad Guennouni ◽  
Meriem Rachidi ◽  
Toufik Benhoumich ◽  
Hind Bennani ◽  
...  

Sever acute respiratory infections (SARIs) are a public health issue that are common in children and are associated with an important morbidity and mortality rate worldwide. Although SARI are mainly caused by viruses, they are still a cause of antibiotic overuse. The use of molecular methods especially real-time multiplex PCR allowed to detect a wide range of respiratory viruses and their subtype as well as some atypical bacteria. The aim of this study was to investigate the epidemiology of respiratory pathogens detected in children admitted with SARI and to highlight the role of real-time multiplex PCR in the rapid diagnosis of viral and bacterial SARI. This work is a descriptive observational study from January 2018 to December 2019 including nasopharyngeal secretions collected from 534 children hospitalised in paediatric department. The detection of respiratory viruses and bacteria was performed by the FilmArray® Respiratory Panel. A total of 387 (72.5%) children were tested positive for at least one respiratory pathogen, and 23.3% of them were coinfected with more than one pathogen. Viral aetiology was found in 91.2% (n = 340). The most common viruses detected were HRV (n = 201) and RSV (n = 124), followed by PIV (n = 35) influenza A (n = 29) and human metapneumovirus (n = 27). Bacteria was found in 8.8% (n = 47), and Bordetella pertussis was the most detected. Respiratory syncytial virus and Bordetella pertussis were significantly higher in infants less than 6 months old. The detection of RSV and influenza A presented a pic in winter, and HMPV was statistically significant in spring ( p < 0.01 ). This study described the epidemiology of respiratory pathogens involved in severe respiratory infections in children that were affected by several factors such as season and age group. It also highlighted the importance of multiplex PCR in confirming viral origin, thus avoiding irrational prescription of antibiotics in paediatric settings.


2021 ◽  
Vol 2021 ◽  
pp. 1-5
Author(s):  
Omid Zarei ◽  
Leili Shokoohizadeh ◽  
Hadi Hossainpour ◽  
Mohammad Yousef Alikhani

Background. Shiga toxin-producing Escherichia coli (STEC) is known as a crucial zoonotic food-borne pathogen. A total of 257 raw chicken meat samples were collected from different markets in Hamadan, west of Iran, from January 2016 to May 2017. Materials and Methods. The samples were cultured in selective and differential culture media, and the virulence genes of E. coli isolates were analyzed by PCR assay. The antibiotic resistance patterns of E. coli isolates were determined by the disk diffusion method. The genetic relatedness of the E. coli O157 isolates was analyzed by ERIC-PCR. Results. In total, 93 (36% ± 3.12) of the isolates were identified as E. coli in this study. Based on serological and microbiological tests, 36 (38.7% ± 9.9), 7 (7.5% ± 5.35), and 12 (12.9% ± 6.81) of the E. coli isolates were characterized as STEC, enteropathogenic E. coli (EPEC), and attaching and effacing E. coli (AEEC) strains, respectively. A high level of resistance to nalidixic acid (91.4% ± 5.7), tetracycline (89.2% ± 6.31), ampicillin (82.8% ± 7.67), and trimotoprime-sulfametoxazole (71% ± 9.22) was detected among the E. coli isolates. The analysis of the ERIC-PCR results showed five different ERIC types among the E. coli O157 isolates. Conclusions. Based on our findings, control and check-up of poultry meats should be considered as a crucial issue for public health.


2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Agustin Krisna Wardani ◽  
Aji Sutrisno ◽  
Titik Nur Faida ◽  
Retno Dwi Yustina ◽  
Untung Murdiyatmo

Background. Oil palm trunk (OPT) with highly cellulose content is a valuable bioresource for bioethanol production. To produce ethanol from biomass, pretreatment is an essential step in the conversion of lignocellulosic biomass to fermentable sugars such as glucose and xylose. Several pretreatment methods have been developed to overcome biomass recalcitrance. In this study, the effects of different pretreatment methods such as alkali pretreatment, microwave-alkali, and alkaline peroxide combined with autoclave on the lignocellulosic biomass structure were investigated. Moreover, ethanol production from the treated biomass was performed by simultaneous saccharification and cofermentation (SSCF) under different temperatures, fermentation times, and cell ratios of Saccharomyces cerevisiae NCYC 479 and pentose-utilizing yeast, Pichia stipitis NCYC 1541. Results. Pretreatment resulted in a significant lignin removal up to 83.26% and cellulose released up to 80.74% in treated OPT by alkaline peroxide combined with autoclave method. Enzymatic hydrolysis of treated OPT resulted in an increase in fermentable sugar up to 93.22%. Optimization of SSCF by response surface method showed that the coculture could work together to produce maximum ethanol (1.89%) and fermentation efficiency (66.14%) under the optimized condition. Conclusion. Pretreatment by alkaline peroxide combined with autoclave method and SSCF process could be expected as a promising system for ethanol production from oil palm trunk and various lignocellulosic biomass.


2021 ◽  
Vol 2021 ◽  
pp. 1-6
Author(s):  
Kiandokht Babolhavaeji ◽  
Leili Shokoohizadeh ◽  
Morteza Yavari ◽  
Abbas Moradi ◽  
Mohammad Yousef Alikhani

Background. The aims of the current study are the identification of O157 and non-O157 Shiga Toxin-Producing Escherichia coli (STEC) serogroups isolated from fresh raw beef meat samples in an industrial slaughterhouse, determination of antimicrobial resistance patterns, and genetic linkage of STEC isolates. Materials and Methods. A total of 110 beef samples were collected from the depth of the rump of cattle slaughtered at Hamadan industrial slaughterhouse. After detection of E. coli isolates, STEC strains were identified according to PCR for stx1, stx2, eaeA, and hlyA virulence genes, and STEC serogroups (O157 and non-O157) were identified by PCR. The genetic linkage of STEC isolates was analyzed by the ERIC- (Enterobacterial Repetitive Intergenic Consensus-) PCR method. The antimicrobial susceptibility of STEC isolates was detected by the disk diffusion method according to CLSI guidelines. Results. Among 110 collected beef samples, 77 (70%) were positive for E. coli. The prevalence of STEC in E. coli isolates was 8 (10.4%). The overall prevalence of O157 and non-O157 STEC isolates was 12.5% (one isolate) and 87.5% (7 isolates), respectively. The hemolysin gene was detected in 25% (2 isolates) of STEC strains. Evaluation of antibiotic resistance indicated that 100% of STEC isolates were resistant to ampicillin, ampicillin-sulbactam, amoxicillin-clavulanic acid, and cefazolin. Resistance to tetracycline and ciprofloxacin was detected in 62.5% and 12.5% of isolates, respectively. The analysis of the ERIC-PCR results showed five different ERIC types among the STEC isolates. Conclusion. The isolation of different clones STECs from beef and the presence of antibiotic-resistant isolates indicate that more attention should be paid to the hygiene of slaughterhouses.


2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Meera Maharjan ◽  
Anil Kumar Sah ◽  
Susil Pyakurel ◽  
Sabita Thapa ◽  
Susan Maharjan ◽  
...  

Staphylococcus aureus, a commensal on the skin and in the nasal cavity of humans, is one of the most serious cases of nosocomial infections. Moreover, methicillin-resistant S. aureus (MRSA) is a leading cause of morbidity and mortality worldwide. For the treatment of MRSA infections, vancomycin is considered as a drug of choice. However, the emergence of vancomycin resistance among MRSA isolates has been perceived as a formidable threat in therapeutic management. To estimate the rate of vancomycin-resistant S. aureus (VRSA) and to detect the vancomycin-resistant genes, namely, vanA and vanB, among the isolates, a hospital-based cross-sectional study was conducted from July to December 2018 in Annapurna Neurological Institute and Allied Science, Kathmandu, Nepal. S. aureus was isolated and identified from different clinical samples and processed for antibiotic susceptibility testing by the modified Kirby–Bauer disc diffusion method. The screening of MRSA was performed as per Clinical and Laboratory Standard Institute (CLSI) guidelines. VRSA was confirmed by the minimum inhibitory concentration (MIC) method by employing E-test strips. All the phenotypically confirmed VRSA were further processed to detect the vanA and vanB gene by using the conventional polymerase chain reaction (PCR) method. A total of 74 (20.3%) S. aureus were isolated, and the highest percentage of S. aureus was from the wound samples (36.5%). Of 74 S. aureus isolates, the highest number (89.2%) was resistant to penicillin, and on the other hand, linezolid was found to be an effective drug. Likewise, 45 (60.81%) were found to be MRSA, five (11.11%) were VRSA, and 93.2% of S. aureus isolates showed an MAR index greater than 0.2. Two VRSA isolates (40%) were positive for the vanA gene. The higher prevalence of MRSA and significant rate of VRSA in this study recommend routine surveillance for the MRSA and VRSA in hospital settings before empirical therapy.


2021 ◽  
Vol 2021 ◽  
pp. 1-5
Author(s):  
Mojtaba Moosavian ◽  
Mahtab Khoshkholgh Sima ◽  
Nazanin Ahmad Khosravi ◽  
Effat Abbasi Montazeri

Antibiotic resistance mechanisms in Enterobacteriaceae are causative agents of global health problems. Bacterial infections due to multidrug resistance (MDR) may be mediated by the overexpression of efflux pumps. In this study, we investigated the prevalence of oqxA and oqxB genes as two encoding agents of efflux pumps and the determination of antibiotic resistance rate in clinical isolates of Enterobacteriaceae. In this study, 100 Enterobacteriaceae isolates collected from different clinical specimens of infectious patients, such as wounds, urine, blood, discharge, and abscesses except stool, were examined. Identification of the isolates was performed using standard biochemical tests such as TSI, citrate, urea, lysine, SIM, MR-VP, and gas production. The antimicrobial susceptibility test was carried out by the Kirby–Bauer disk diffusion method according to CLSI guidelines, and finally, the oqxA and oqxB genes were detected by the PCR method. Among 100 Enterobacteriaceae isolates, Escherichia coli and Enterobacter gergoviae were the most common isolates with 71% and 20%, respectively. Also, the lowest isolates belonged to Enterobacter cloacae (3%) and Klebsiella pneumoniae (1%). Out of 100 Enterobacteriaceae isolates, 37 isolates (37%) were positive for at least one of oqxA or oqxB genes, while both of these genes were detected among 12% of them. oqxAB genes were detected in 8 cases of 20 (40%) Enterobacter gergoviae and 4 cases of 71 (5.7%) E. coli isolates. The antimicrobial susceptibility test showed that all isolates (100%) were susceptible to imipenem, while the maximum resistance to piperacillin, ceftriaxone, and cefotaxime were 69%, 55%, and 55%, respectively. Also, the results of this study showed that antibiotic resistance in Enterobacteriaceae isolates caused by oqxAB genes is increasing among patients in Iran. Therefore, identification of resistant isolates and antibiotic monitoring programs are essential to prevent the spread of MDR isolates.


2021 ◽  
Vol 2021 ◽  
pp. 1-5
Author(s):  
Ândrea Celestino de Souza ◽  
Luciano Z. Goldani ◽  
Eliane Würdig Roesch ◽  
Larissa Lutz ◽  
Patricia Orlandi Barth ◽  
...  

Determination of the susceptibility profile of isolates of Candida from blood culture bottles is extremely important for correctly guiding patient pharmacotherapy. The aim of this study was to compare the results of analysis of Candida isolated directly from blood culture bottles by the VITEK MS MALDI-TOF identification system and the fluconazole disk diffusion assay with those of standard identification methods. Testing directly from the bottle allowed results 24 to 48 hours quicker than the standard method. There was a categorical agreement of 51.64% (47 of 91 samples) between the results of analysis directly from the bottle and analysis by the standard method. Regarding species identification, there was 96.15% agreement for Candida parapsilosis (25 of 26 samples). Categorical agreement between the rapid and standard disk diffusion methods was 95%, and the agreement between the rapid disk diffusion method and the broth microdilution method was 97%. Only minor errors in the rapid method were observed: 3 (5%) in the standard disk diffusion method and 2 (3%) in the broth microdilution method. Our study concluded that the rapid disk diffusion method for fluconazole is a fast, easy, reproducible, and consistent method. Its timely implementation for testing antifungal agents in the clinical microbiology laboratory can help reduce profile release times, thus helping to determine the most appropriate antifungal treatment.


2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Neli Korsun ◽  
Svetla Angelova ◽  
Ivelina Trifonova ◽  
Silvia Voleva ◽  
Iliana Grigorova ◽  
...  

Нuman bocaviruses (hBoVs) are often associated with acute respiratory infections (ARIs). Information on the distribution and molecular epidemiology of hBoVs in Bulgaria is currently limited. The objectives of this study were to investigate the prevalence and genetic characteristics of hBoVs detected in patients with ARIs in Bulgaria. From October 2016 to September 2019, nasopharyngeal/oropharyngeal swabs were prospectively collected from 1842 patients of all ages and tested for 12 common respiratory viruses using a real-time RT-PCR. Phylogenetic and amino acid analyses of the hBoV VP1/VP2 gene/protein were performed. HBoV was identified in 98 (5.3%) patients and was the 6th most prevalent virus after respiratory-syncytial virus (20.4%), influenza A(H1N1)pdm09 (11.1%), A(H3N2) (10.5%), rhinoviruses (9.9%), and adenoviruses (6.8%). Coinfections with other respiratory viruses were detected in 51% of the hBoV-positive patients. Significant differences in the prevalence of hBoVs were found during the different study periods and in patients of different age groups. The detection rate of hBoV was the highest in patients aged 0–4 years (6.9%). In this age group, hBoV was the only identified virus in 9.7%, 5.8%, and 1.1% of the children diagnosed with laryngotracheitis, bronchiolitis, and pneumonia, respectively. Among patients aged ≥5 years, hBoV was detected as a single agent in 2.2% of cases of pneumonia. Phylogenetic analysis showed that all Bulgarian hBoV strains belonged to the hBoV1 genotype. A few amino acid substitutions were identified compared to the St1 prototype strain. This first study amongst an all-age population in Bulgaria showed a significant rate of hBoV detection in some serious respiratory illnesses in early childhood, year-to-year changes in the hBoV prevalence, and low genetic variability in the circulating strains.


2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Tewodros Tamire ◽  
Temesgen Eticha ◽  
Temesgen Bati Gelgelu

Background. In healthcare facilities, a gradual increase in methicillin-resistant Staphylococcus aureus (MRSA) infections has been seen over the past 2 decades. Similarly, it has been responsible for the most frequent and invasive pathogens associated with admitted patient infection. Currently, it is considered an urgent threat to public health and classified as one of the top-priority antimicrobial-resistant pathogens. This study aimed to determine the magnitude and associated risk factors of MRSA infection among admitted patients. Methods. A facility-based cross-sectional examination was led on 413 patients admitted to Tikur Anbessa Specialized Hospital from January 2018 to January 2019. A convenient sampling technique was used. Clinical specimens of pus and blood were collected from admitted patients who developed the infection after 48 hours of admission. Gram stain, culture media preparations, and biochemical tests were conducted to identify and isolate the causative agent. Staphylococcus aureus (S. aureus) were identified as MRSA strains after having a zone of inhibition less than or equal to 21 mm to the cefoxitin (30 ug) disc. Bivariate and multivariable logistic regression analyses were computed. The odds ratio, along with 95% CI, was estimated to identify associated risk factors for MRSA infection. Results. Out of 413 collected specimens, 38.7% had coagulase-positive S. aureus of which 35.6% (95% CI: 28.2%–43.0%) were MRSA. Being within the age group of 19–29 years and 30–39 years with AOR = 5.02 and 95% CI: 1.24–20.35 and AOR = 6.65 and 95% CI: 1.78–24.78, respectively, admitting in the hematology ward and the pediatric ward with AOR = 7.80 and 95% CI: 1.82–33.49 and AOR = 10.54 and 95% CI: 1.78–62.42, respectively, and experiencing poor prognosis with AOR = 10.97 and 95% CI: 4.57–26.36 were significantly associated with MRSA infection. Conclusion and Recommendation. The significant magnitude of MRSA was found among patients admitted to this hospital. Therefore, identified risk factors should be considered when executing hospital-acquired infection prevention programs. We also suggest that healthcare providers should consider the identified risk factors while prescribing the antibiotic.


2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Aishath Maharath ◽  
Mariyam Shabeena Ahmed

Background. Bloodstream infections pose a significant health problem worldwide and is a major cause of morbidity and mortality in many countries. It is important to have country-specific data for major pathogens causing bloodstream infections, in light of emerging resistance patterns of common bacterial isolates. Due to the scarcity of reports in this area, the aim of this study was to identify bacterial pathogens causing bloodstream infections among the study population. Methods. A retrospective analysis of blood culture samples received at the Department of Laboratory Medicine, Indira Gandhi Memorial Hospital, Malé, Maldives, was performed for reports between January 2016 and December 2017. Results. Out of the 471 culture-positive samples, 278 (59%) were males and 193 (41%) were females. Amongst the culture-positive samples, 338 (71.8%) Gram-positive organisms were isolated and 133 (28.2%) Gram-negative organisms were isolated. Coagulase-negative Staphylococcus (CoNS) was the most frequently isolated blood-borne bacterial pathogen in this study, accounting for 53.6% and 50.9% of the isolates in 2016 and 2017, respectively. Other frequently isolated pathogens included Staphylococcus aureus (15.9% and 10.3%), Klebsiella spp. (10.5% and 16.4%), and Escherichia coli (7.1% and 10.8%). Coagulase-negative Staphylococcus (CoNS) revealed high percentage of resistance among the tested antimicrobials, ampicillin, cephalexin, cefotaxime, and gentamicin. Over the two years, a significant difference between the percentage resistance among paediatric and adult patients was observed for coagulase-negative Staphylococcus (CoNS) isolate resistance to ampicillin p ≤ 0.001 , cephalexin p ≤ 0.001 , cefotaxime p ≤ 0.001 , gentamicin p = 0.008 , and cotrimoxazole (SXT) p ≤ 0.001 . When comparing the significant antimicrobial resistance trends, it can be seen that Enterobacteriaceae isolates also demonstrated high resistance to ampicillin and gentamicin as well as second- and third-generation cephalosporins. Conclusions. This study highlights the major bacterial pathogens involved in bloodstream infections in the healthcare setting of Malé, Maldives, and antibiotic resistance patterns. The results indicate that further characterization of bacteremia and its resistance patterns is needed to combat bloodstream infections.


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