Polish Journal of Microbiology最新文献_第2页

Molecular Epidemiology of Bulgarian Clinically Significant Staphylococcus aureus Isolates. 保加利亚临床意义金黄色葡萄球菌分离株的分子流行病学。

IF 2.1 4区生物学

Polish Journal of Microbiology Pub Date : 2023-06-01 DOI: 10.33073/pjm-2023-018

Raina Gergova, Virna-Maria Tsitou, Svetoslav G Dimov, Ivanka Gergova, Alexandra Alexandrova, Tanya Strateva

{"title":"Molecular Epidemiology of Bulgarian Clinically Significant Staphylococcus aureus Isolates.","authors":"Raina Gergova, Virna-Maria Tsitou, Svetoslav G Dimov, Ivanka Gergova, Alexandra Alexandrova, Tanya Strateva","doi":"10.33073/pjm-2023-018","DOIUrl":"https://doi.org/10.33073/pjm-2023-018","url":null,"abstract":"Severe infections due to highly virulent and resistant Staphylococcus aureus pose a serious health threat in Bulgaria and worldwide. The purpose of this study was to explore the clonal spread of recent clinically significant methicillin-susceptible S. aureus (MSSA) isolates from inpatients and outpatients treated in three university hospitals in Sofia, Bulgaria, during the period 2016-2020 and evaluate the relationship between their molecular epidemiology, virulence profiling, and antimicrobial resistance. A total of 85 isolates (invasive and noninvasive) were studied using RAPD analysis. Ten major clusters (A-K) were identified. The first major cluster A (31.8%) was found to be predominant during 2016 and 2017 and was widespread in two hospitals, unlike its case in the following years, when it was found to be replaced by newer cluster groups. All MSSA members of the second most common cluster F (11.8%) were recovered from the Military Medical Academy, mainly during 2018-2020, and were determined to be susceptible to all other groups of antimicrobials, except for penicillins without inhibitors because they harboured the blaZ gene. The newer cluster I, with 9.4% of the isolates absent in 2016-2017, showed significantly higher virulence and macrolide resistance (42.9%) due to ermB and ermC. All the isolated MSSA in groups F and I were nosocomial and mostly invasive. In conclusion, this 5-year study demonstrates the molecular epidemiology of MSSA infections in three Bulgarian hospitals. Findings can be helpful for the understanding of staphylococcal infection distribution in hospital settings and their prevention.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":"72 2","pages":"169-176"},"PeriodicalIF":2.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/57/4f/pjm-72-2-pjm-2023-018.PMC10266289.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9637002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Molecular Approaches and Challenges of Streptococcus pneumoniae Serotyping for Epidemiological Surveillance in the Vaccine Era. 疫苗时代肺炎链球菌血清分型在流行病学监测中的分子途径和挑战。

IF 2.1 4区生物学

Polish Journal of Microbiology Pub Date : 2023-06-01 DOI: 10.33073/pjm-2023-023

Nurul Asyikin Abdul Rahman, Mohd Nasir Mohd Desa, Siti Norbaya Masri, Niazlin Mohd Taib, Nurshahira Sulaiman, Hazmin Hazman, James John

{"title":"The Molecular Approaches and Challenges of Streptococcus pneumoniae Serotyping for Epidemiological Surveillance in the Vaccine Era.","authors":"Nurul Asyikin Abdul Rahman, Mohd Nasir Mohd Desa, Siti Norbaya Masri, Niazlin Mohd Taib, Nurshahira Sulaiman, Hazmin Hazman, James John","doi":"10.33073/pjm-2023-023","DOIUrl":"https://doi.org/10.33073/pjm-2023-023","url":null,"abstract":"Streptococcus pneumoniae (pneumococcus) belongs to the Gram-positive cocci. This bacterium typically colonizes the nasopharyngeal region of healthy individuals. It has a distinct polysaccharide capsule - a virulence factor allowing the bacteria to elude the immune defense mechanisms. Consequently, it might trigger aggressive conditions like septicemia and meningitis in immunocompromised or older individuals. Moreover, children below five years of age are at risk of morbidity and mortality. Studies have found 101 S. pneumoniae capsular serotypes, of which several correlate with clinical and carriage isolates with distinct disease aggressiveness. Introducing pneumococcal conjugate vaccines (PCV) targets the most common disease-associated serotypes. Nevertheless, vaccine selection pressure leads to replacing the formerly dominant vaccine serotypes (VTs) by non-vaccine types (NVTs). Therefore, serotyping must be conducted for epidemiological surveillance and vaccine assessment. Serotyping can be performed using numerous techniques, either by the conventional antisera-based (Quellung and latex agglutination) or molecular-based approaches (sequetyping, multiplex PCR, real-time PCR, and PCR-RFLP). A cost-effective and practical approach must be used to enhance serotyping accuracy to monitor the prevalence of VTs and NVTs. Therefore, dependable pneumococcal serotyping techniques are essential to precisely monitor virulent lineages, NVT emergence, and genetic associations of isolates. This review discusses the principles, associated benefits, and drawbacks of the respective available conventional and molecular approaches, and potentially the whole genome sequencing (WGS) to be directed for future exploration.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":"72 2","pages":"103-115"},"PeriodicalIF":2.1,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/fa/c1/pjm-72-2-pjm-2023-023.PMC10266295.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10011545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Stethoscopes or Maybe "Bacterioscopes" - Is hand Hygiene Solely Capable of Preventing Hospital-Associated Infections? 听诊器或 "细菌镜"--手部卫生是预防医院相关感染的唯一方法吗？

IF 2 4区生物学

Polish Journal of Microbiology Pub Date : 2023-03-24 Print Date: 2023-03-01 DOI: 10.33073/pjm-2023-012

Katarzyna Talaga-Ćwiertnia, Dorota Ochońska, Mateusz Gajda, Monika Kowalczyk, Magdalena Palczewska, Monika Brzychczy-Włoch

{"title":"Stethoscopes or Maybe \"Bacterioscopes\" - Is hand Hygiene Solely Capable of Preventing Hospital-Associated Infections?","authors":"Katarzyna Talaga-Ćwiertnia, Dorota Ochońska, Mateusz Gajda, Monika Kowalczyk, Magdalena Palczewska, Monika Brzychczy-Włoch","doi":"10.33073/pjm-2023-012","DOIUrl":"10.33073/pjm-2023-012","url":null,"abstract":"The stethoscope remains an indispensable diagnostic tool for medical students. Improper stethoscope hygiene may cause bacterial infections, including hospital-associated infections (HAIs), which challenge the Polish medical system. The study's main objective was to evaluate the hygiene habits declared by medical students. Moreover, microbiological control with the characteristics of potentially pathogenic microorganisms was performed. The study included 66 medical students from the Faculty of Medicine at the Jagiellonian University Medical College in Cracow, Poland. The participants filled in an anonymous questionnaire. Stethoscope contamination was assessed through isolation, identification, testing of antibiotic resistance, and clonality of the isolates bacterial pathogens. The survey showed that only 30.3% of students cleaned their stethoscopes after each patient, and 1.5% never did this. Of the 66 stethoscopes tested, 100% were positive for bacterial growth. Staphylococcus spp. was the most frequently isolated contaminant (50.5%). The questionnaire results demonstrated the necessity of the validated procedures for cleaning the stethoscopes. Stethoscopes used by medical students are contaminated with numerous bacterial species, including multidrug-resistant organisms. The clonal structure of the MRSA and MRSE populations acquired from stethoscopes has been demonstrated. Our results confirm the possibility that these medical devices mediate the spread of hazardous pathogens in the hospital environment. Practical exercises are essential to forming the correct hygiene habits involving stethoscopes, which enable practicing and checking the correctness of the established skills.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":"72 1","pages":"79-91"},"PeriodicalIF":2.0,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8f/b5/pjm-72-1-pjm-2023-012.PMC10280307.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10081655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chlorine Dioxide Reprograms Rhizosphere Microbial Communities to Enrich Interactions with Tobacco (Nicotiana tabacum). 二氧化氯重编程根瘤微生物群落，丰富与烟草（Nicotiana tabacum）的相互作用。

IF 2.1 4区生物学

Polish Journal of Microbiology Pub Date : 2023-03-24 Print Date: 2023-03-01 DOI: 10.33073/pjm-2023-009

Shi Qi, Jili Zhang, Xinbo Luan, Junlin Li, Zikang He, Junru Long, Mengyun Xu, Ping Li, Zepeng Chen, Jianyu Wei, Jian Yan

{"title":"Chlorine Dioxide Reprograms Rhizosphere Microbial Communities to Enrich Interactions with Tobacco (Nicotiana tabacum).","authors":"Shi Qi, Jili Zhang, Xinbo Luan, Junlin Li, Zikang He, Junru Long, Mengyun Xu, Ping Li, Zepeng Chen, Jianyu Wei, Jian Yan","doi":"10.33073/pjm-2023-009","DOIUrl":"10.33073/pjm-2023-009","url":null,"abstract":"For decades chlorine dioxide has been used in water disinfection with excellent results. As the scope of application expands, chlorine dioxide has the potential for soil disinfection. We used amplicon sequencing and gas chromatography-mass spectrometry to compare the changes of four mixed rhizosphere microbial community samples and 12 tobacco leaf volatile samples four months after the flood irrigation with chlorine dioxide in different concentrations (0, 2, 4, 8 mg/l). Phenotypic data of 60 tobacco plants were also collected. The effects of chlorine dioxide on rhizosphere microorganisms were positively correlated with dose gradients. Bacteria responded more strongly in both community structure and metabolic pathways than fungi. Five new bacterial phyla (Firmicutes, Bacteroidota, Myxococcota, Patescibacteria, Verrucomicroboata) appeared in chlorine dioxide treatment groups, while the fungal community only appeared as one new fungal phylum (Basidomycota). Alterations in 271 predicted metabolic bacterial pathways were found. However, in the fungal community were only 10 alternations. The correlations between leaf volatile compounds and rhizosphere microorganisms under the influence of chlorine dioxide treatment could be observed based on network results. However, natural connectivity had already been declining rapidly when less than 20% of the network's nodes were removed. Therefore, the microbe-metabolite network is not stable. It might be why chlorine dioxide treatments did not significantly affect tobacco quality (p = 0.754) and phenotype (p = 0.867). As a comprehensive investigation of chlorine dioxide in agriculture, this study proves the effectiveness and safety of chlorine dioxide soil disinfection and widens the application range of chlorine dioxide.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":"72 1","pages":"47-60"},"PeriodicalIF":2.1,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2d/ce/pjm-72-1-pjm-2023-009.PMC10280303.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9705078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Changes in the Protein Profile in Staphylococcal Strains from Patients Infected with the SARS-CoV-2 Virus. SARS-CoV-2病毒感染患者葡萄球菌菌株蛋白谱的变化

IF 2.1 4区生物学

Polish Journal of Microbiology Pub Date : 2023-03-01 DOI: 10.33073/pjm-2023-001

Tomasz Jarzembowski, Lidia Piechowicz, Marek Bronk, Anna Pałubicka, Łukasz Naumiuk

引用次数: 0

A Molecular and Epidemiological Study of Cholera Outbreak in Sulaymaniyah Province, Iraq, in 2022. 2022年伊拉克苏莱曼尼亚省霍乱暴发的分子和流行病学研究

IF 2.1 4区生物学

Polish Journal of Microbiology Pub Date : 2023-03-01 DOI: 10.33073/pjm-2023-008

Dana Khdr Sabir, Zhwan Talib Hama, Karzan Jalal Salih, Karzan Ghafur Khidhir

{"title":"A Molecular and Epidemiological Study of Cholera Outbreak in Sulaymaniyah Province, Iraq, in 2022.","authors":"Dana Khdr Sabir, Zhwan Talib Hama, Karzan Jalal Salih, Karzan Ghafur Khidhir","doi":"10.33073/pjm-2023-008","DOIUrl":"https://doi.org/10.33073/pjm-2023-008","url":null,"abstract":"Cholera is a disease caused by a Gram-negative bacterium Vibrio cholerae and is among the significant threats to global public health. The disease is mainly spread in the hot months of the year; low sanitation and lack of clean water are the major causes of the disease. In this study, we conducted a molecular and epidemiological study of the recent outbreak in the city of Sulaymaniyah in Iraq. Based on the bacteriological, serological, and molecular identification of the bacterium, it was shown that V. cholerae O1 serotype Ogawa caused the disease. Additionally, the number of positive cholera cases were higher in June compared to July (391 positive cases in June and 23 in July). Moreover, the majority (> 60%) of the cholera cases were recorded among 20-44-year-old people in both months; however, there was no significant difference in the patient genders diagnosed every month. Overall, this is the first report on the recent cholera outbreak in the city of Sulaimaniyah in Iraq.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":"72 1","pages":"39-46"},"PeriodicalIF":2.1,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/71/c6/pjm-72-1-pjm-2023-008.PMC10280330.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9705076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","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 of Closely Related Candida albicans Species among Patients with Vulvovaginal Candidiasis in Southern Poland Based on the hwp1 Gene Amplification. 基于hwp1基因扩增的波兰南部外阴阴道念珠菌病患者中密切相关白色念珠菌的流行

IF 2.1 4区生物学

Polish Journal of Microbiology Pub Date : 2023-03-01 DOI: 10.33073/pjm-2023-011

Karolina Klesiewicz, Paulina Mrowiec, Katarzyna Kania, Iwona Skiba-Kurek, Joanna Białecka, Magdalena Namysł, Marianna Małek

{"title":"Prevalence of Closely Related Candida albicans Species among Patients with Vulvovaginal Candidiasis in Southern Poland Based on the hwp1 Gene Amplification.","authors":"Karolina Klesiewicz, Paulina Mrowiec, Katarzyna Kania, Iwona Skiba-Kurek, Joanna Białecka, Magdalena Namysł, Marianna Małek","doi":"10.33073/pjm-2023-011","DOIUrl":"https://doi.org/10.33073/pjm-2023-011","url":null,"abstract":"Candida albicans remains the most common species isolated from women with vulvovaginal candidiasis. However, closely related species such as Candida africana and Candida dubliniensis may also occur, although they are often misidentified. The aim of the study was to confirm the phenotypic identification of C. albicans and its closely related species isolated from women with genital tract infections by amplification of the hwp1 (hyphal wall protein 1) gene in a PCR assay. We report a detailed molecular identification of C. albicans and its closely related species among 326 patients in the Małopolska region, Poland. Initial phenotypic identifications were confirmed by amplification of the hwp1 gene. Based on molecular analysis, we revealed 307 strains (94.17%) as C. albicans and 17 as C. dubliniensis (5.22%). No strain of C. africana was detected. Two patients h ad co-infection with C. albicans and C. dubliniensis (0.61%). A PCR assay targeting the hwp1 gene was reliable for correctly identifying species among the C. albicans complex.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":"72 1","pages":"69-77"},"PeriodicalIF":2.1,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/92/1e/pjm-72-1-pjm-2023-011.PMC10280305.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10062276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insight into the Antibiotic Resistance of Bacteria Isolated from Popular Aquatic Products Collected in Zhejiang, China. 浙江省常见水产品中细菌耐药性的初步研究

IF 2.1 4区生物学

Polish Journal of Microbiology Pub Date : 2023-03-01 DOI: 10.33073/pjm-2023-010

Jiajia Wu, Fan Ye, Jiong Qu, Zhiyuan Dai

{"title":"Insight into the Antibiotic Resistance of Bacteria Isolated from Popular Aquatic Products Collected in Zhejiang, China.","authors":"Jiajia Wu, Fan Ye, Jiong Qu, Zhiyuan Dai","doi":"10.33073/pjm-2023-010","DOIUrl":"https://doi.org/10.33073/pjm-2023-010","url":null,"abstract":"The present study was aimed to obtain a close insight into the distribution and diversity of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) among the aquatic products collected in Zhejiang, China. A total of 136 presumptive ARB picked up from six aquatic samples were classified into 22 genera and 49 species based on the 16S rDNA sequencing. Aeromonas spp., Shewanella spp., Acinetobacter spp., Myroides spp., Pseudomonas spp., and Citrobacter spp. accounted for 80% of the ARB. Among them, 109 isolates (80.15%) exhibited resistance to at least one antibiotic. Most isolates showed resistance to not only the originally selected drug but also to one to three other tested drugs. The diversity of ARB distributed in different aquatic products was significant. Furthermore, the resistance data obtained from genotypic tests were not entirely consistent with the results of the phenotypic evaluation. The genes qnrS, tetA, floR, and cmlA were frequently detected in their corresponding phenotypic resistant isolates. In contrast, the genes sul2, aac(6')-Ib, and bla PSE were less frequently found in the corresponding phenotypically resistant strains. The high diversity and detection rate of ARB and ARGs in aquaculture might be a significant threat to the food chains closely related to human health.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":"72 1","pages":"61-67"},"PeriodicalIF":2.1,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/df/d4/pjm-72-1-pjm-2023-010.PMC10280302.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9705083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Emergence of Colistin- and Imipenem-Associated Multidrug Resistance in Escherichia coli Isolates from Retail Meat. 从零售肉类中检出的大肠埃希菌出现了与考利司汀和亚胺培南相关的多重耐药性。

IF 2 4区生物学

Polish Journal of Microbiology Pub Date : 2022-12-06 eCollection Date: 2022-12-01 DOI: 10.33073/pjm-2022-046

Benson Chuks Iweriebor, Olivia Sochi Egbule, Larry C Obi

{"title":"The Emergence of Colistin- and Imipenem-Associated Multidrug Resistance in Escherichia coli Isolates from Retail Meat.","authors":"Benson Chuks Iweriebor, Olivia Sochi Egbule, Larry C Obi","doi":"10.33073/pjm-2022-046","DOIUrl":"10.33073/pjm-2022-046","url":null,"abstract":"To determine the prevalence of Escherichia coli and their drug resistance profiles in fresh pork sold at two retail outlets (open-air market and closed retail stores) in Alice, South Africa. Retail meat samples (n = 176) collected from four shops (two from open-air markets and two from closed stores) were analyzed by conventional biochemical and PCR-based molecular confirmatory tests. The confirmed isolates were profiled for antimicrobial susceptibility to a panel of 12 commercial antibiotics: tetracycline, ampicillin, sulphamethoxazole trimethoprim, erythromycin, gentamycin, colistin sulphate, cefotaxime, chloramphenicol, norfloxacin, ciprofloxacin, cefuroxime, and imipenem. Colistin, ampicillin, and erythromycin resistance genes were profiled with the gene-specific primers. Multidrug resistance (MDR) and the association of imipenem and colistin in the MDR profile were determined. A total of 68 (39.08%) E. coli isolates were confirmed by PCR analysis. Resistance was most common to erythromycin (100%), followed by cefotaxime (95.58%), ampicillin (88.23%), cefuroxime (88.23%), trimethoprim-sulphamethoxazole (88.23%), and tetracycline (60.29%). Overall, 27/68 (39.70%) were MDR (≥ 3antibiotics classes). MDR E. coli isolates associated with imipenem resistance (50.00%) and colistin resistance (33.82%) were detected. The resistance genes were detected among the isolates though not in all the phenotypically resistant isolates. The detection of colistin resistance among MDR E. coli isolates from retail meat is troubling as the drug is a last resort antibiotic. Overall, the epidemiological implications of the findings are of public health importance.","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":"71 4","pages":"519-528"},"PeriodicalIF":2.0,"publicationDate":"2022-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/38/7a/pjm-71-519.PMC9944967.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9309829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Omicron SARS-CoV-2 Variants in an In Silico Genomic Comparison Study with the Original Wuhan Strain and WHO-Recognized Variants of Concern. SARS-CoV-2基因组变异与原武汉株和世卫组织认可的关注变异的计算机基因组比较研究

IF 2.1 4区生物学

Polish Journal of Microbiology Pub Date : 2022-12-01 DOI: 10.33073/pjm-2022-053

Elmutuz H Elssaig, Tarig M S Alnour, Mohammad Fahad Ullah, Eltayib H Ahmed-Abakur

{"title":"Omicron SARS-CoV-2 Variants in an In Silico Genomic Comparison Study with the Original Wuhan Strain and WHO-Recognized Variants of Concern.","authors":"Elmutuz H Elssaig, Tarig M S Alnour, Mohammad Fahad Ullah, Eltayib H Ahmed-Abakur","doi":"10.33073/pjm-2022-053","DOIUrl":"https://doi.org/10.33073/pjm-2022-053","url":null,"abstract":"This study aimed to determine the genetic alterations in the Omicron variants compared to other variants of concern (VOCs) to trace the evolutionary genetics of the SARS-CoV-2 variants responsible for the multiple COVID-19 waves globally. The present study is an in silico analysis determining the evolution of selected 11 VOCs compared to the original Wuhan strain. The variants included six Omicrons and one variant of Alpha, Beta, Delta, Gamma, and Mu. The pairwise alignment with the local alignment search tool of NCBI Nucleotide-BLAST and NCBI Protein-BLAST were used to determine the nucleotide base changes and corresponding amino acid changes in proteins, respectively. The genomic analysis revealed 210 nucleotide changes; most of these changes (127/210, 60.5%) were non-synonymous mutations that occurred mainly in the S gene (52/127, 40.1%). The remaining 10.5% (22/210) and 1.9% (4/210) of the mutations were frameshift deletions and frameshift insertions, respectively. The frameshift insertion (Ins22194T T22195G) led to frameshift deletion (Δ211N). Only four mutations (C241T, C3037T, C14408T, and A23403G) were shared among all the VOCs. The nucleotide changes among Omicron variants resulted in 61 amino acid changes, while the nucleotide changes in other VOCs showed 11 amino acid changes. The present study showed that most mutations (38/61, 62.3%) among Omicron variants occurred in the S gene; and 34.2% of them (13/38) occurred in the receptor-binding domain. The present study confirmed that most of mutations developed by Omicron variants occurred in the vaccine target gene (S gene).","PeriodicalId":20272,"journal":{"name":"Polish Journal of Microbiology","volume":"71 4","pages":"577-587"},"PeriodicalIF":2.1,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/6b/28/pjm-71-577.PMC9944972.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9310346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1