International Journal of Microbiology最新文献

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Full-Length Genome Sequencing and Analysis of Hepatitis B Viruses Isolated from Iraqi Patients. 对从伊拉克患者身上分离出的乙型肝炎病毒进行全长基因组测序和分析。
IF 3.4
International Journal of Microbiology Pub Date : 2024-04-29 eCollection Date: 2024-01-01 DOI: 10.1155/2024/6826495
Yaseen I Mamoori, Ibrahim A Ahmed, Ayhan R Mahmood, Safaa A Al-Waysi
{"title":"Full-Length Genome Sequencing and Analysis of Hepatitis B Viruses Isolated from Iraqi Patients.","authors":"Yaseen I Mamoori, Ibrahim A Ahmed, Ayhan R Mahmood, Safaa A Al-Waysi","doi":"10.1155/2024/6826495","DOIUrl":"10.1155/2024/6826495","url":null,"abstract":"<p><p>Hepatitis B virus (HBV) causes liver diseases (chronic hepatitis, cirrhosis, and hepatocellular carcinoma) and is a leading health problem worldwide. Sequencing of the whole HBV genome provides insight into the virus genotype, subgenotype, serotype, genetic variation, and viral drug resistance. To date, no study has been conducted on the whole genome sequence of HBV obtained from Iraqi patients. Therefore, this is the first study to sequence clinical samples from these patients. Viral genomic DNA was isolated and amplified using five primer sets to amplify five overlapping regions covering the entire HBV genome. The amplicons were sequenced, aligned to a reference sequence, annotated, and submitted to the National Center for Biotechnology Information GenBank database. Sequence analysis showed that the genome size of the tested viral samples was 3,182 bp and belonged to genotype D, subgenotype D1, and serotype ayw2. Missense mutations were found in the four regions (X, PreS1-S, PreC-C, and P) of the tested samples, leading to amino acid substitutions, which were 8.4%, 5.1%, 4.7%, and 4.6%, respectively. These mutations may cause severe liver diseases.</p>","PeriodicalId":14098,"journal":{"name":"International Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11074772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prevalence and Antimicrobial Susceptibility Profile of Salmonella from Poultry Farms and In-Contact Humans and Associated Risk Factors in Addis Ababa, Ethiopia. 埃塞俄比亚亚的斯亚贝巴家禽养殖场和接触人群中沙门氏菌的流行率和抗菌药敏感性概况及相关风险因素。
IF 3.4
International Journal of Microbiology Pub Date : 2024-04-26 eCollection Date: 2024-01-01 DOI: 10.1155/2024/4227460
Aberaw Akalu, Tekalign Tadesse, Haile Alemayehu, Girmay Medhin, Desalegn Woldeyohannes, Tadesse Eguale
{"title":"Prevalence and Antimicrobial Susceptibility Profile of <i>Salmonella</i> from Poultry Farms and In-Contact Humans and Associated Risk Factors in Addis Ababa, Ethiopia.","authors":"Aberaw Akalu, Tekalign Tadesse, Haile Alemayehu, Girmay Medhin, Desalegn Woldeyohannes, Tadesse Eguale","doi":"10.1155/2024/4227460","DOIUrl":"10.1155/2024/4227460","url":null,"abstract":"<p><p>Poultry and poultry products are the common sources of <i>Salmonella,</i>which is one of the serious food-borne bacterial diseases in humans. Little is known about the status of <i>Salmonella</i> and their antimicrobial susceptibility in poultry farms in Addis Ababa. This study was conducted to estimate the prevalence and antimicrobial susceptibility of <i>Salmonella</i> isolates and to investigate possible risk factors for the occurrence of <i>Salmonella</i> in poultry farms in Addis Ababa. We recruited 58 poultry farms, from which 471 poultry-related samples and 44 stool samples from in-contact humans were collected. The isolates were tested for their susceptibility to 11 antimicrobials using the Kirby-Bauer disk diffusion assay. The farm-level prevalence of <i>Salmonella</i> was 36.2% and the sample-level prevalence was 6.4% for samples taken from poultry farms and 4.5% in human stool samples who have contact with poultry. On-farm waste disposal practices and chicken being purchased from different multiplication farms were significantly associated with <i>Salmonella</i> positivity of the farms (<i>p</i> < 0.05). Eleven (34.4%) <i>Salmonella</i> isolates were resistant to streptomycin, and nine (28.1%) were resistant to tetracycline. Thirteen (40.6%) <i>Salmonella</i> isolates were resistant to two or more antimicrobials tested in this study, whereas resistance to 3 or more antimicrobials was detected in seven (21.9%) isolates. In conclusion, a high prevalence of <i>Salmonella</i> and a high rate of resistance to multiple antimicrobials were detected in poultry farms in Addis Ababa. Hence, implementation of strong biosecurity measures and rational use of antimicrobials are recommended.</p>","PeriodicalId":14098,"journal":{"name":"International Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11102108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Spiritual Holy Water Sites in Ethiopia: Unrecognized High-Risk Settings for Transmission of Pulmonary Tuberculosis 埃塞俄比亚的圣水圣地:未被发现的肺结核传播高风险场所
IF 3.4
International Journal of Microbiology Pub Date : 2024-04-08 DOI: 10.1155/2024/3132498
M. Reta, N. Maningi, G. Wubetu, Steve A. S. Olorunju, P. B. Fourie
{"title":"Spiritual Holy Water Sites in Ethiopia: Unrecognized High-Risk Settings for Transmission of Pulmonary Tuberculosis","authors":"M. Reta, N. Maningi, G. Wubetu, Steve A. S. Olorunju, P. B. Fourie","doi":"10.1155/2024/3132498","DOIUrl":"https://doi.org/10.1155/2024/3132498","url":null,"abstract":"Ethiopia is a high-tuberculosis (TB) burden country with 157 new cases per 100,000 people, with 23,800 TB-related deaths in 2020. In Ethiopia, TB patients have different healthcare-seeking behaviors. They frequently visit spiritual places, such as holy water sites (HWSs), to seek treatment for their illness spiritually. This study examined the prevalence of pulmonary TB (PTB) and drug susceptibility profiles of Mycobacterium tuberculosis (MTB) isolates among spiritual HWS attendees in Northwest Ethiopia. A cross-sectional study was conducted from June 2019 to March 2020. Sputum samples were collected, processed, and cultured using Löwenstein–Jensen (LJ) culture medium. Second-generation line probe assays (LPAs), GenoType®MTBDRplus VER2.0 and GenoType®MTBDRsl VER2.0, were used to detect anti-TB drug-resistant isolates. STATA 17 was utilized to perform descriptive statistics, bivariate, and multivariate regression analyses. Of 560 PTB-symptomatic participants, 21.8% ((95% confidence interval (95 CI): 18.4–25.2%)) were culture-positive, resulting in a point prevalence of 1,183/100,000 attendees. Amongst HWS attendees, culture-positive TB occurred most commonly in persons 18–33 years of age (28.5% (95 CI 23.4–34.3%)). Other participant characteristics significantly associated with culture-positive PTB were as follows: rural residents (adjusted odds ratio (aOR) 2.65; 95 CI 1.38–5.10), married participants (aOR 2.43; 95 CI 1.28–4.63), family members >5 per household (aOR 1.84; 95 CI 1.04–3.24), and sharing living space (aOR 10.57; 95 CI 3.60–31.13). Also, among 438 participants followed for 12 months after showing negative TB culture results while at the HWS, 6.8% (95 CI 4.4–9.4%) developed or contracted culture-positive TB post-residency at the HWSs. Of the 122 tested isolates, 20 (16.4%) were isoniazid (INH) and/or rifampicin (RIF) resistant. Multidrug-resistant (MDR) TB was detected in 15 cases (12.3%), five of which were fluoroquinolones (FLQs) resistant. The findings from this study should raise a concern about HWSs as potential high-risk settings for TB transmission. It is recommended that appropriate control measures be instituted that include compulsory TB testing and tightened infection control at HWSs, where an increased risk exists for transmission of TB.","PeriodicalId":14098,"journal":{"name":"International Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140730202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effect of Mixed Probiotics on Ovalbumin-Induced Atopic Dermatitis in Juvenile Mice 混合益生菌对卵清蛋白诱导的幼年小鼠特应性皮炎的影响
IF 3.4
International Journal of Microbiology Pub Date : 2024-03-31 DOI: 10.1155/2024/7172386
Jinli Huang, Xingzhi Wang, Qiuhong Li, Panpan Zhang, Z. Jing, Juan Zhang, Hui Su, Xin Sun
{"title":"Effect of Mixed Probiotics on Ovalbumin-Induced Atopic Dermatitis in Juvenile Mice","authors":"Jinli Huang, Xingzhi Wang, Qiuhong Li, Panpan Zhang, Z. Jing, Juan Zhang, Hui Su, Xin Sun","doi":"10.1155/2024/7172386","DOIUrl":"https://doi.org/10.1155/2024/7172386","url":null,"abstract":"Atopic dermatitis is one of the most common dermatologic problems, especially in children. Given the ability of symbiotic microorganisms in modulating the immune system, probiotics administration has been studied in previous research in the management of atopic dermatitis. However, there are conflicting results between studies. In this study, we aimed to assess the effectiveness of mixed probiotics as a treatment option for atopic dermatitis induced by ovalbumin. BALB/c juvenile mice were classified and divided into the ovalbumin group, mixed probiotic group (ovalbumin + LK), and control group. Except for the control group, all mice were sensitized with ovalbumin to establish a model of atopic dermatitis. The mixed probiotics were given by gavage for 14 days. Mice body weight, skin lesions, skin inflammation, ovalbumin-specific Ig, the number of Treg and CD103+DC, and the expression level of PD-1/PD-L1 were examined. The results showed that mixed probiotics can improve body weight and alleviate skin symptoms. Mixed probiotics reduced serum Th2 inflammatory factors, eosinophils, mast cell degranulation, mast cell count, and the expression of ovalbumin-specific immunoglobulin E/G1 and increased the anti-inflammatory cytokine interleukin-10, Treg cells, CD103+DC cells, and the expression level of PD-1/PD-L1. These findings suggest that mixed probiotics could be a viable treatment option for atopic dermatitis and provide insight into the underlying mechanisms involved.","PeriodicalId":14098,"journal":{"name":"International Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140359429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Management of Inoculation with Bradyrhizobium japonicum and Application of Vitamins for Hydroponic Soybean Cultivation 水培大豆接种日本农杆菌的管理和维生素的应用
IF 3.4
International Journal of Microbiology Pub Date : 2024-03-31 DOI: 10.1155/2024/4463693
A. H. F. D. Lima, J. S. Salles, E. P. Vendruscolo, C. D. C. Seron, R. S. de Freitas, S. F. de Lima, Gabriela R. Sant’Ana, E. Costa
{"title":"Management of Inoculation with Bradyrhizobium japonicum and Application of Vitamins for Hydroponic Soybean Cultivation","authors":"A. H. F. D. Lima, J. S. Salles, E. P. Vendruscolo, C. D. C. Seron, R. S. de Freitas, S. F. de Lima, Gabriela R. Sant’Ana, E. Costa","doi":"10.1155/2024/4463693","DOIUrl":"https://doi.org/10.1155/2024/4463693","url":null,"abstract":"The exchange of technologies used in field cultivation for hydroponic systems can potentially increase plant development and grain production, requiring studies to verify the best management forms, such as growth-promoting bacteria and biostimulant compounds. With this in mind, the study aimed to evaluate the effect of the application of thiamine and niacin, alone and combined, to soybean plants in the absence and presence of inoculation with B. japonicum on the agronomic and physiological characteristics of the crop grown in an ebb and flow hydroponic system. Eight treatments were evaluated using t-test (LSD) and Tukey’s test, both at 5% probability (P<0.05), in addition to Pearson correlation and canonical variables. The treatments consist of inoculation with B. japonicum at 1 mL 500 g−1 seeds (with and without) and foliar application of four solutions (water, niacin (0.1 g·L−1), thiamine (0.1 g·L−1), and niacin + thiamine (0.05 g·L−1 + 0.05 g·L−1)). We found that inoculation significantly improved the parameters evaluated and resulted in a gain of approximately 84.8% in yield when compared by t-test (P<0.05). In addition, the action of the vitamins was more significant when they were applied without the presence of B. japonicum, especially niacin, either alone or combined with thiamine, which increased yield parameters in this condition, identified when the Tukey’s test (P<0.05) was applied. We conclude that inoculation with Bradyrhizobium japonicum in soybean seeds grown in a hydroponic system significantly benefits the development and grain yield, mainly when combined with vitamin solutions. Niacin also has the potential to be used alone or combined with thiamine in noninoculated or inoculated hydroponic soybean crops, respectively.","PeriodicalId":14098,"journal":{"name":"International Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140358122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Absence of Tuberculosis-Causing Mycobacteria from Slaughtered Livestock Tissues and Environmental Samples, Gauteng Province, South Africa. 南非豪登省屠宰牲畜组织和环境样本中未发现结核病致病分枝杆菌。
IF 3.4
International Journal of Microbiology Pub Date : 2024-03-15 eCollection Date: 2024-01-01 DOI: 10.1155/2024/4636652
Vuyokazi Mareledwane, Abiodun A Adesiyun, Tiny M Hlokwe
{"title":"Absence of Tuberculosis-Causing <i>Mycobacteria</i> from Slaughtered Livestock Tissues and Environmental Samples, Gauteng Province, South Africa.","authors":"Vuyokazi Mareledwane, Abiodun A Adesiyun, Tiny M Hlokwe","doi":"10.1155/2024/4636652","DOIUrl":"10.1155/2024/4636652","url":null,"abstract":"<p><p><i>Mycobacterium tuberculosis</i> complex (MTBC) is a group of bacteria responsible for causing tuberculosis in animals and humans. In South Africa (S.A), slaughterhouses are registered by the government and closely inspected and audited for hygienic slaughter practices. Meat inspection to detect lesions has been used for passive surveillance, monitoring, and diagnosis of the disease status. Information on the current status of bovine tuberculosis (bTB) in livestock in the country is limited. Hence, we investigated the occurrence of <i>Mycobacterium</i> spp. in the tissues of slaughtered livestock and environmental samples in abattoirs in Gauteng province of South Africa (S.A). The cross-sectional study employing random sampling from cattle, pigs, and sheep (with the collection of liver, lung, spleen, and different lymph nodes) irrespective of lesions was carried out in 19 red meat abattoirs. Five hundred animals were sampled, comprising cattle (<i>n</i> = 369), pigs (<i>n</i> = 90), and sheep (<i>n</i> = 41). Additionally, 19 environmental samples were collected from feedlots, or where animals drink water while awaiting slaughter, to identify mycobacterial species using culture, acid-fast bacteria staining, and polymerase chain reaction (PCR). The Chi-square and Fisher's Exact tests were used to detect statistically significant differences in the frequency of detection of <i>Mycobacterium</i> spp. according to the variables investigated (types of tissues, livestock, abattoirs, etc.). The PCR assays detected no MTBC complex species DNA in the bacterial isolates from cattle (<i>n</i> = 32). Sequence analysis (16S rDNA) of the isolates from eight cattle confirmed only two species, namely <i>Mycobacterium colombiense</i> (99.81% identity) and <i>Mycobacterium simiae</i> (99.42% identity). The remaining isolates were identified as members of the <i>Actinomadura</i> species. From the environmental samples, bacterial isolation was made from three samples, and two could only be identified up to the genus level (<i>Mycobacterium</i> species) while the remaining isolate was identified as <i>Mycobacterium senuense</i> (99.22% identity). The study revealed the absence of bovine tuberculosis-causing pathogens in red meat abattoirs of the Gauteng province. Although non-tuberculous <i>Mycobacteria</i> have been implicated as potentially causing tuberculosis-like diseases in livestock, their occurrence in the current study was found to be low, but the potential to cause disease cannot be ignored.</p>","PeriodicalId":14098,"journal":{"name":"International Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10959579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140206837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Detection of Pathogenic Serogroups and Virulence Genes in Listeria monocytogenes Strains Isolated from Beef and Beef Products Retailed in Gauteng Province, South Africa, Using Phenotypic and Polymerase Chain Reaction (PCR)-Based Methods. 利用表型和聚合酶链式反应 (PCR) 方法检测从南非豪登省零售的牛肉和牛肉制品中分离出的单核细胞增生李斯特菌株的致病性血清群和毒性基因。
IF 3.4
International Journal of Microbiology Pub Date : 2024-03-13 eCollection Date: 2024-01-01 DOI: 10.1155/2024/8891963
James Gana, Nomakorinte Gcebe, Rebone Moerane, Yusuf B Ngoshe, Khomotso Moabelo, Abiodun A Adesiyun
{"title":"Detection of Pathogenic Serogroups and Virulence Genes in <i>Listeria monocytogenes</i> Strains Isolated from Beef and Beef Products Retailed in Gauteng Province, South Africa, Using Phenotypic and Polymerase Chain Reaction (PCR)-Based Methods.","authors":"James Gana, Nomakorinte Gcebe, Rebone Moerane, Yusuf B Ngoshe, Khomotso Moabelo, Abiodun A Adesiyun","doi":"10.1155/2024/8891963","DOIUrl":"10.1155/2024/8891963","url":null,"abstract":"<p><p>South Africa recently (2017-18) experienced the largest outbreak of human listeriosis in the world caused by <i>L. monocytogenes</i> following the consumption of \"polony,\" a ready-to-eat meat product. Most (59%) cases originated from Gauteng province, South Africa. As a follow-up study to the outbreak, we used standard bacteriological and molecular methods to determine the prevalence of pathogenic and virulent serogroups of <i>L. monocytogenes</i> in various beef and beef products retailed in Gauteng province, South Africa. The overall prevalence of <i>Listeria</i> spp. was 28% (112/400), comprising <i>Listeria monocytogenes</i> (9.3%), <i>Listeria innocua</i> (16.3%), and <i>Listeria welshimeri</i> (2.5%) (<i>p</i> < 0.001). It is crucial to have detected that the region (<i>p</i>=0.036), type of product (<i>p</i>=0.032), and temperature at storage (<i>p</i>=0.011) significantly affected the occurrence of <i>L. monocytogenes</i> in beef products. It is alarming that pathogenic serogroups 4b-4d-4e (51.4%) and 1/2a-3a (43.2%) were detected among the isolates of <i>L. monocytogenes</i>. Importantly, they were all carriers of seven virulence-associated genes (<i>hlyA, inlB, plcA, iap, inlA, inlC, and inlJ</i>). Our study also demonstrated that 16.7% of \"polony\" samples investigated were contaminated with <i>L. monocytogenes.</i> Considering that pathogenic and virulent <i>L. monocytogenes</i> contaminated beef and beef products retailed in South Africa, the food safety risk posed to consumers remains and cannot be ignored. Therefore, it is imperative to reduce the contamination of these products with <i>L. monocytogenes</i> during beef production, processing, and retailing to avoid future outbreaks of human listeriosis in the country.</p>","PeriodicalId":14098,"journal":{"name":"International Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10954364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140174606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Development and Optimization of a Multiplex Real-Time RT-PCR to Detect SARS-CoV-2 in Human Samples. 开发和优化用于检测人体样本中 SARS-CoV-2 的多重实时 RT-PCR 技术
IF 3.4
International Journal of Microbiology Pub Date : 2024-03-11 eCollection Date: 2024-01-01 DOI: 10.1155/2024/4894004
Camilo Castellar-Mendoza, María-Angélica Calderón-Peláez, Jaime E Castellanos, Myriam L Velandia-Romero, Carolina Coronel-Ruiz, Sigrid Camacho-Ortega, Lilia J Bernal-Cepeda, Lady López-Ibarra, Jhann A Arturo, Félix G Delgado, Hernando Gutierrez-Barbosa, Sonia Bohorquez-Avila, Johanna Madroñero, Zayda L Corredor-Rozo, Sandra J Perdomo-Lara, Angela Fonseca-Benitez, Eliana Calvo
{"title":"Development and Optimization of a Multiplex Real-Time RT-PCR to Detect SARS-CoV-2 in Human Samples.","authors":"Camilo Castellar-Mendoza, María-Angélica Calderón-Peláez, Jaime E Castellanos, Myriam L Velandia-Romero, Carolina Coronel-Ruiz, Sigrid Camacho-Ortega, Lilia J Bernal-Cepeda, Lady López-Ibarra, Jhann A Arturo, Félix G Delgado, Hernando Gutierrez-Barbosa, Sonia Bohorquez-Avila, Johanna Madroñero, Zayda L Corredor-Rozo, Sandra J Perdomo-Lara, Angela Fonseca-Benitez, Eliana Calvo","doi":"10.1155/2024/4894004","DOIUrl":"10.1155/2024/4894004","url":null,"abstract":"<p><p>PCR and its variants (RT-PCR and qRT-PCR) are valuable and innovative molecular techniques for studying nucleic acids. qPCR has proven to be highly sensitive, efficient, and reproducible, generating reliable results that are easy to analyze. During the COVID-19 pandemic, qPCR became the gold standard technique for detecting the SARS-CoV-2 virus that allowed to confirm the infection event, and those asymptomatic ones, and thus save millions of lives. In-house multiplex qPCR tests were developed worldwide to detect different viral targets and ensure results, follow the infections, and favor the containment of a pandemic. Here, we present the detailed fundamentals of the qPCR technique based on fluorogenic probes and processes to develop and optimize a successful multiplex RT-qPCR test for detecting SARS-CoV-2 that could be used to diagnose COVID-19 accurately.</p>","PeriodicalId":14098,"journal":{"name":"International Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10948217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140158109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mycobacterium tuberculosis Lineage Distribution Using Whole-Genome Sequencing and Bedaquiline, Clofazimine, and Linezolid Phenotypic Profiles among Rifampicin-Resistant Isolates from West Java, Indonesia 印度尼西亚西爪哇耐利福平分枝杆菌中结核分枝杆菌的全基因组测序谱系分布以及贝达喹啉、氯法齐明和利奈唑胺的表型特征
IF 3.4
International Journal of Microbiology Pub Date : 2024-03-04 DOI: 10.1155/2024/2037961
Andriansjah Rukmana, Cynthia Gozali, Linda Erlina
{"title":"Mycobacterium tuberculosis Lineage Distribution Using Whole-Genome Sequencing and Bedaquiline, Clofazimine, and Linezolid Phenotypic Profiles among Rifampicin-Resistant Isolates from West Java, Indonesia","authors":"Andriansjah Rukmana, Cynthia Gozali, Linda Erlina","doi":"10.1155/2024/2037961","DOIUrl":"https://doi.org/10.1155/2024/2037961","url":null,"abstract":"Tuberculosis (TB) is caused by Mycobacterium tuberculosis infection. Indonesia is ranked second in the world for TB cases. New anti-TB drugs from groups A and B, such as bedaquiline, clofazimine, and linezolid, have been shown to be effective in curing drug resistance in TB patients, and Indonesia is already using these drugs to treat patients. However, studies comparing the TB strain types with anti-TB resistance profiles are still relevant to understanding the prevalent strains in the country and their phenotypic characteristics. This study aimed to determine the association between the TB lineage distribution using whole-genome sequencing and bedaquiline, clofazimine, and linezolid phenotypic profile resistance among M. tuberculosisrifampicin-resistant isolates from West Java. M. tuberculosis isolates stock of the Department of Microbiology, Faculty of Medicine, Universitas Indonesia, was tested against bedaquiline, clofazimine, and linezolid using a mycobacteria growth indicator tube liquid culture. All isolates were tested for M. tuberculosis and rifampicin resistance using Xpert MTB/RIF. The DNA genome of M. tuberculosis was freshly extracted from a Löwenstein–Jensen medium culture and then sequenced. The isolates showed phenotypically resistance to bedaquiline, clofazimine, and linezolid at 5%, 0%, and 0%, respectively. We identified gene mutations on phenotypically bedaquiline-resistant strains (2/3), and other mutations also found in phenotypically drug-sensitive strains. Mykrobe analysis showed that most (88.33%) of the isolates could be classified as rifampicin-resistant TB. Using Mykrobe and TB-Profiler to determine the lineage distribution, the isolates were found to belong to lineage 4 (Euro-American; 48.33%), lineage 2 (East Asian/Beijing; 46.67%), and lineage 1 (Indo-Oceanic; 5%). This work underlines the requirement to increase the representation of genotype-phenotype TB data while also highlighting the importance and efficacy of WGS in predicting medication resistance and inferring disease transmission.","PeriodicalId":14098,"journal":{"name":"International Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140080536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Biofilm Formation, Pyocyanin Production, and Antibiotic Resistance Profile of Pseudomonas aeruginosa Isolates from Wounds. 伤口铜绿假单胞菌分离物的生物膜形成、焦花青素产生和抗生素耐药性概况
IF 3.4
International Journal of Microbiology Pub Date : 2024-02-20 eCollection Date: 2024-01-01 DOI: 10.1155/2024/1207536
Larissa Yetendje Chimi, Michel Noubom, Borel Ndezo Bisso, Guy Sedar Singor Njateng, Jean Paul Dzoyem
{"title":"Biofilm Formation, Pyocyanin Production, and Antibiotic Resistance Profile of <i>Pseudomonas aeruginosa</i> Isolates from Wounds.","authors":"Larissa Yetendje Chimi, Michel Noubom, Borel Ndezo Bisso, Guy Sedar Singor Njateng, Jean Paul Dzoyem","doi":"10.1155/2024/1207536","DOIUrl":"10.1155/2024/1207536","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> is one of the most frequently resistant and dangerous bacteria isolated from infected wounds of patients. This study aimed to determine the prevalence of <i>P. aeruginosa</i> from infected wounds of patients in the Dschang District Hospital to evaluate their antibiotic susceptibility profiles and their ability to swarm and swim and correlate pyocyanin production with biofilm formation. Wound swab samples were collected and the identification of <i>P. aeruginosa</i> was performed using microbiological and biochemical tests. Their antimicrobial susceptibility was determined by the broth microdilution method. Swarming and swimming were determined by measuring the diameters of motility in semisolid/low-viscosity media. Furthermore, pyocyanin production and biofilm formation were evaluated spectrophotometrically using a microtiter plate. The prevalence of <i>P. aeruginosa</i> from infected wounds in our study population was 26%. All <i>P. aeruginosa</i> isolates were resistant to streptomycin and paromomycin, and the frequency of multidrug resistance (MDR) was 65.8%. All <i>P. aeruginosa</i> isolates showed the ability to produce biofilm and pyocyanin. Out of the 37 isolates screened, 19 including the reference strains (51.4%) were strong biofilm producers. A significant positive correlation was observed among biofilm formation, pyocyanin production, and the antibiotic resistance profile of the isolates. Findings from this study suggest that infected wounds could act as a reservoir for MDR and virulent <i>P. aeruginosa</i>. The presence of strong biofilm producers of <i>P. aeruginosa</i> in infected wounds is a serious public health concern. Therefore, surveillance programs to monitor and control MDR <i>P. aeruginosa</i> in these patients are required to prevent their dissemination in hospital settings.</p>","PeriodicalId":14098,"journal":{"name":"International Journal of Microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10898945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139982842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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