Access Microbiology最新文献

{"title":"Towards a Yersinia pestis lipid A recreated in an Escherichia coli scaffold genome","authors":"N. D. McDonald, Erin E. Antoshak","doi":"10.1099/acmi.0.000723.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000723.v3","url":null,"abstract":"Synthetic biology and genome engineering capabilities have facilitated the utilization of bacteria for a myriad of applications, ranging from medical treatments to biomanufacturing of complex molecules. The bacterial outer membrane, specifically the lipopolysaccharide (LPS), plays an integral role in the physiology, pathogenesis, and serves as a main target of existing detection assays for Gram-negative bacteria. Here we use CRISPR/Cas9 recombineering to insert Yersinia pestis lipid A biosynthesis genes into the genome of an Escherichia coli strain expressing the lipid IVa subunit. We successfully inserted three genes: kdsD, lpxM, and lpxP into the E. coli genome and demonstrated their expression via reverse transcription PCR (RT-PCR). Despite observing expression of these genes, analytical characterization of the engineered strain’s lipid A structure via MALDI-TOF mass spectrometry indicated that the Y. pestis lipid A was not recapitulated in the E. coli background. As synthetic biology and genome engineering technologies advance, novel applications and utilities for the detection and treatments of dangerous pathogens like Yersinia pestis will continue to be developed.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"19 S3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141841035","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}

{"title":"In vitro comparison of viral replication and cytopathology induced by SARS-CoV-2 variants","authors":"Kruttika S. Phadke, Nathaniel B. A. Higdon, B. Bellaire","doi":"10.1099/acmi.0.000716.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000716.v3","url":null,"abstract":"A myriad of coronaviruses cause diseases from a common cold to severe lung infections and pneumonia. SARS-CoV-2 was discovered to be the etiologic agent of the Coronavirus pandemic and many laboratory techniques were examined for virus culture and basic and applied research. Understanding the replication kinetics and characterizing the effect the virus has on different cell lines is crucial for developing in vitro studies. With the emergence of multiple variants of SARS-CoV-2, a comparison between their infectivity and replication in common cell lines will help give us a clear understanding of their characteristic differences in pathogenicity. In this study we compared the cytopathic effect and replication of Wild-Type (USA/WA1), Omicron (B.1.1.529), and Delta (B.1.617.2) variants on five different cell lines; VeroE6, VeroE6 cells expressing high endogenous ACE2, VeroE6 cells expressing human ACE2 and TMPRSS2, Calu3 cells highly expressing human ACE2 and A549 cells. This data will aid researchers with experimental planning and viral pathogenicity analysis and provide a baseline for testing any future variants.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141850221","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}

{"title":"Whole genome sequence of Paracoccus sp. NFXS7, a carotenoid-producing bacterium isolated from a marine saltern","authors":"Constança D F Bertrand, Rodrigo Martins, Francisco Quintas-Nunes, Pedro Reynolds-Brandão, M. B. Barreto Crespo, Francisco X. Nascimento","doi":"10.1099/acmi.0.000862.v2","DOIUrl":"https://doi.org/10.1099/acmi.0.000862.v2","url":null,"abstract":"The study presents the whole genome sequence of the carotenoid-producing Paracoccus sp. NFXS7, isolated from a marine saltern in Setúbal, Portugal. The carotenoid-producing strain NFXS7 contains homologs of the crt genes involved in astaxanthin biosynthesis, making it a promising candidate for biotechnological applications.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"45 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141850292","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}

{"title":"HIV-DRIVES: HIV drug resistance identification, variant evaluation, and surveillance pipeline","authors":"Stephen Kanyerezi, Ivan Sserwadda, A. Ssemaganda, Julius Seruyange, Alisen Ayitewala, Hellen Rosette Oundo, Wilson Tenywa, Brian A. Kagurusi, Godwin Tusabe, Stacy Were, Isaac Ssewanyana, Susan Nabadda, Maria Magdalene Namaganda, Gerald Mboowa","doi":"10.1099/acmi.0.000815.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000815.v3","url":null,"abstract":"The global prevalence of resistance to antiviral drugs combined with antiretroviral therapy (cART) emphasizes the need for continuous monitoring to better understand the dynamics of drug-resistant mutations to guide treatment optimization and patient management as well as check the spread of resistant viral strains. We have recently integrated next-generation sequencing (NGS) into routine HIV drug resistance (HIVDR) monitoring, with key challenges in the bioinformatic analysis and interpretation of the complex data generated, while ensuring data security and privacy for patient information. To address these challenges, here we present HIV-DRIVES (HIV Drug Resistance Identification, Variant Evaluation, and Surveillance), an NGS-HIVDR bioinformatics pipeline that has been developed and validated using Illumina short reads, FASTA, and Sanger ab1.seq files.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"180 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141841922","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}

{"title":"Comparative analysis of virulence gene profiles of Escherichia coli from human and non-human sources in Rivers State, Nigeria","authors":"B. A. Abeni, N. Frank-Peterside, K. Otokunefor","doi":"10.1099/acmi.0.000776.v6","DOIUrl":"https://doi.org/10.1099/acmi.0.000776.v6","url":null,"abstract":"Traditionally, the presence of virulence features has been thought to be a key factor in differentiating pathogenic from commensal strains. An understanding of the virulence potential of Escherichia coli isolates from various sources is essential to shed light on potential contamination/transmission rates between the various sources. This study was therefore aimed at exploring the occurrence of specific virulence genes and gene profiles associated with E. coli from human and non-human sources in Rivers State, Nigeria. Two hundred samples from human (urine and faeces) and non-human (soil and poultry droppings) sources (50 each) were analysed using standard microbiological procedures. DNA was extracted from isolates presumptively identified as E. coli using the Presto Mini gDNA Bacteria-Kit Quick protocol following the manufacturer’s instructions. Isolate identities were confirmed using E. coli-specific 16S rRNA primers, and confirmed isolates were screened for the presence of six virulence genes [afimbriae binding adhesin (afa), type 1 fimbriae (fimH) and P-fimbrial usher protein (papC)], iron acquisition systems: aerobactin (aer), cytotoxic necrotizing factor I (cnf1) and alpha-hemolysin (hly). Results showed that all isolates harboured at least one of the tested virulence genes, with fimH (97%) as the most prevalent virulence gene and papC the least commonly occurring (35%). A higher occurrence of virulence genes was noted in non-human isolates, though hly and cnf were not detected at all in any of the isolates studied (0%). Ten different profiles were observed with the afaCc-aer-fimH profile the most commonly occurring virulence gene profile being in general (33.3%). For non-human isolates, however, aer-afaCc-fimH-papC was the most commonly occurring profile (42.9%). This study shows that the test E. coli from human and non-human sources do not carry distinct virulence gene profiles. Studies on a larger subset of isolates would however be necessary to determine if the virulence genes tested in this study really cannot be used to tell whether an isolate is from a human source or not in the South–South of Nigeria.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"47 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854040","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}

{"title":"An evaluation of ChatGPT and Bard (Gemini) in the context of biological knowledge retrieval","authors":"R. Caspi, Peter D. Karp","doi":"10.1099/acmi.0.000790.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000790.v3","url":null,"abstract":"ChatGPT and Bard (now called Gemini), two conversational AI models developed by OpenAI and Google AI, respectively, have garnered considerable attention for their ability to engage in natural language conversations and perform various language-related tasks. While the versatility of these chatbots in generating text and simulating human-like conversations is undeniable, we wanted to evaluate their effectiveness in retrieving biological knowledge for curation and research purposes. To do so we asked each chatbot a series of questions and scored their answers based on their quality. Out of a maximal score of 24, ChatGPT scored 5 and Bard scored 13. The encountered issues included missing information, incorrect answers, and instances where responses combine accurate and inaccurate details. Notably, both tools tend to fabricate references to scientific papers, undermining their usability. In light of these findings, we recommend that biologists continue to rely on traditional sources while periodically assessing the reliability of ChatGPT and Bard. As ChatGPT aptly suggested, for specific and up-to-date scientific information, established scientific journals, databases, and subject-matter experts remain the preferred avenues for trustworthy data.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"18 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141396905","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}

{"title":"Galleria mellonella as a superficial model for Malassezia globosa and its treatment","authors":"Maritza Torres, Juliana Diaz-Ortiz, Michael G. Davis, Jim Schwartz, Adriana Marcela Celis Ramírez","doi":"10.1099/acmi.0.000745.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000745.v3","url":null,"abstract":"\u0000 Introduction.\u0000 Malassezia globosa is a yeast species that belongs to the mycobiota of humans and animals, associated with dermatological disorders, such as dandruff. This is a chronic scalp skin disorder characterized by flaking and itching. Treatments include commercial shampoo with different formulations that contain antifungal activities like zinc pyrithione (ZPT) or piroctone olamine (PO). The effectiveness of these formulations has been evaluated for decades for dandruff symptom relief of volunteers. To date, non-mammalian, in vivo methods exist to test formulations of these actives.\u0000 \u0000 Aim. To evaluate in vivo in Galleria mellonella larva, two commercial antifungal shampoos (shampoo with 1 % ZPT and 1.6 % zinc Carbonate and shampoo with 0.5 % PO) against this species.\u0000 \u0000 Methodology.\u0000 G. mellonella larvae were inoculated with M. globosa on abraded cuticular surface. Then, integument cell viability, histological changes, and fungal burden were evaluated.\u0000 \u0000 Results. Larvae inoculated with M. globosa showed higher lesion melanization and tissue damage. In addition, M. globosa population showed to increase over time. Concerning the shampoo’s effectiveness, both formulations significantly reduced M. globosa burden and tissue damage.\u0000 \u0000 Conclusion.\u0000 G. mellonella larvae were allowed to evaluate M. globosa superficial infection and antifungal effectiveness. Shampoos with ZPT and PO showed a positive effect on inoculated larvae.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"22 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141396082","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}

{"title":"Sequence and origin of the Streptomyces intergenetic-conjugation helper plasmid pUZ8002","authors":"Daniel E. Larcombe, Robyn E. Braes, James T. Croxford, James W. Wilson, David H. Figurski, P. Hoskisson","doi":"10.1099/acmi.0.000808.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000808.v3","url":null,"abstract":"Conjugation of plasmids from Escherichia coli is essential for the genetic manipulation of Streptomyces spp. To facilitate intergeneric conjugation from E. coli to Streptomyces the conjugative machinery required for genetic transfer is usually provided by the non-transferable helper plasmid, pUZ8002. Here we present the complete nucleotide sequence of pUZ8002, describe the previously undocumented creation process, and provide details of the sequence relative to the parental pUZ8 plasmid and another previously published pUZ8002 sequence.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"2 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141407654","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}

{"title":"Prevalence of SARS-CoV-2 virus in saliva, stool, and urine samples of COVID-19 patients in Bihar, India","authors":"Nupur Meghna, Archana Archana, D. Bhushan, Abhyuday Kumar, A. Sarfraz, B. Naik, B. Pati","doi":"10.1099/acmi.0.000693.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000693.v4","url":null,"abstract":"\u0000 Introduction. The coronavirus illness caused by SARS-CoV-2 can cause multiple organ involvement, with varying degrees of severity. Besides inhalation as a route for transmission, feco-oral has also been proposed. Its transmission to sewage systems is a growing public health issue.\u0000 \u0000 Objective. To detect SARS-CoV-2 RNA in non-respiratory samples (saliva, urine, and stool) collected from COVID-19 cases, in Bihar.\u0000 \u0000 Methods. This cross-sectional observational study was conducted from January 2021 to March 2022 on human non-respiratory samples. A total of 345 samples including saliva (116), stool (97), and urine (132) were collected from 143 COVID-19 cases. Samples were analysed for SARS-CoV-2 by multiplex RT-PCR targeted against E, ORF 1ab, and RdRp genes.\u0000 \u0000 Results. In this study, out of 143 cases, a total of 107 (74.8 %) were positive for SARS-CoV-2 RNA in at least one of the non-respiratory samples.\u0000 \u0000 Conclusion. There is a high prevalence of SARS-CoV-2 virus in non-respiratory samples.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"49 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141411937","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}

{"title":"Sarcina ventriculi in association with gastric ulcer: a case report","authors":"Ankita Simkhada, Pritha Acharya, S. Shrivastav","doi":"10.1099/acmi.0.000550.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000550.v3","url":null,"abstract":"\u0000 Sarcina ventriculi is a species of Gram-positive bacteria which has been reported in patients with delayed gastric emptying as well as in association with cases of gastric ulcer and gastric carcinoma. Although it has been reported frequently in veterinary cases as a cause of fatal diseases, the exact pathogenesis in humans has yet to be identified. We report here a case of an elderly male who presented with haematemesis following which an upper gastrointestinal endoscopy was done and a gastric ulcer was revealed. Histopathological examination revealed S. ventriculi in association with the ulcer.","PeriodicalId":6956,"journal":{"name":"Access Microbiology","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141405979","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}