bioRxiv - Microbiology最新文献

{"title":"In silico analysis reveals differential targeting of enterovirus species by commonly used PCR assays","authors":"Van N Trinh, Nisha J Mulakken, Kara L Nelson, Nicholas A Be, Rose S Kantor","doi":"10.1101/2024.09.13.612945","DOIUrl":"https://doi.org/10.1101/2024.09.13.612945","url":null,"abstract":"Quantitative polymerase chain reaction (qPCR) assays are sensitive molecular tools commonly used to quantify pathogens in environmental samples. These assays have become a staple of wastewater-based surveillance and often form the basis of quantitative microbial risk assessments. However, PCR assays may fail to capture all of their intended targets due to signature erosion over time. Here, we performed an in silico analysis of four human enterovirus PCR assays to assess signature erosion against the NCBI virus database. The predicted number of genomes hit by each assay rose alongside total genomes in the database through 2010 but the proportion of predicted hits began to level off with the emergence of the clinically important enterovirus D-68. We found that although all assays captured a majority of enterovirus species, only one recently developed assay adequately captured enterovirus D species. Some assays also appeared more likely to capture non-human enteroviruses than others, an important consideration for data interpretation. We conclude that broad-spectrum virus assays applied to environmental samples should be regularly checked against expanding sequence databases and provide methods to do so.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259894","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":"Surface-mediated Bacteriophage Defense Incurs Fitness Tradeoffs for Interbacterial Antagonism","authors":"Chia-En Tsai, Feng-Qi Wang, Chih-Wen Yang, Ling-Li Yang, Yung-Chih Chen, Po-Yin Chen, Ing-Shouh Hwang, See-Yeun Ting","doi":"10.1101/2024.09.13.612980","DOIUrl":"https://doi.org/10.1101/2024.09.13.612980","url":null,"abstract":"Bacteria in polymicrobial habitats are constantly exposed to biotic threats from bacteriophages, antagonistic bacteria, and predatory eukaryotes. These antagonistic interactions play crucial roles in shaping the evolution and physiology of bacteria. To survive, bacteria have evolved mechanisms to protect themselves from such attacks, but the fitness costs of resisting one threat and rendering bacteria susceptible to others remain unappreciated. Here, we examined the fitness consequences of bacteriophage resistance in Salmonella enterica, revealing that phage-resistant variants exhibited significant fitness loss upon co-culture with competitor bacteria. These phage-resistant strains display varying degrees of lipopolysaccharide (LPS) deficiency and increased susceptibility to contact-dependent interbacterial antagonism, such as the type VI secretion system (T6SS). Utilizing mutational analyses and atomic force microscopy, we show that the long-modal length O-antigen of LPS serves as a protective barrier against T6SS-mediated intoxication. Notably, this competitive disadvantage can also be triggered independently by phages possessing LPS-targeting endoglycosidase in their tail spike proteins, which actively cleave the O-antigen upon infection. Our findings reveal two distinct mechanisms of phage-mediated LPS modifications that modulate interbacterial competition, shedding light on the dynamic microbial interplay within mixed populations.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259895","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":"Genomic Reconstruction and Dietary Response Assessment of Three Acutalibacteraceae Bacteria Isolated from Fecal Samples of Singapore Subjects.","authors":"Mi Ae Park, Sharifah Nora Ahmad Almunawar, Rachel Rui Xia Lim, Sumanto Haldar, Christiani Jeyakumar Henry, Oleg V Moskvin","doi":"10.1101/2024.09.13.612987","DOIUrl":"https://doi.org/10.1101/2024.09.13.612987","url":null,"abstract":"Clostridium leptum, a key player in gut butyrate production, has a profound impact on various facets of intestinal health. A recent clinical trial highlighted a significant increase in the relative abundance of this species in response to dietary interventions using beneficial oils. We isolated microbial strains corresponding to 'Clostridium leptum' (at the 16S rRNA gene similarity level) and sequenced their genomes. All three genomes were successfully reconstructed, maintaining the chromosome as a single contig. Subsequent genome-wide analysis unveiled the phylogenetic diversity of the isolates, including the discovery of a new species - Gallacutalibacter singaporense. Based on the reconstructed metabolic model, we predicted growth condition patterns of this new species and confirmed the predictions in vitro. Leveraging the assembled genomes, we dissected the components of the strong dietary intervention response signal previously ascribed to 'C.leptum' and revealed distinct individual dynamics of all three bacteria in the clinical trial context. The transitional behavior of the novel species, in particular, revealed intriguing patterns, blazing the path to uncovering previously unrecognized interactions along the diet - gut microbiome - human health axis.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142259896","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":"Discovery of novel quinoline papain-like protease inhibitors for COVID-19 through topology constrained molecular generative model","authors":"Jinsai Shang, Ting Ran, Yongzhi Lu, Qi Yang, Guihua Zhang, Peiqi Zhou, Wenqi Li, Minyuan Xu, Jielin Tang, Minxian Dai, Jinpeng Zhong, Hua Chen, Pan He, Anqi Zhou, Bao Xue, Jiayi Chen, Jiyun Zhang, Kunzhong Wu, Xinyu Wu, Miru Tang, Xinwen Chen, Hongming Chen","doi":"10.1101/2024.09.07.611841","DOIUrl":"https://doi.org/10.1101/2024.09.07.611841","url":null,"abstract":"Papain-like protease (PL^pro) plays a critical role in both viral polyprotein processing and host antiviral immune suppression in SARS-CoV-2 infection, which causes COVID-19. Although several drugs have been approved for COVID-19, such as Remdesivir, Nirmatrelvir, etc., none of the PL^pro inhibitors have been approved for the treatment of COVID-19. The advent of artificial intelligence-based drug design methods has significantly accelerated the process of drug discovery. In current study, by harnessing the power of a topology constrained molecular generative model, we discovered a novel series of PL^pro inhibitors with strong potency against prevalent SARS-CoV-2 variants. Following a structure based computational approach for optimization, our lead compound, GZNL-2002, achieved decent PL^pro inhibitory potency and favorable pharmacokinetic properties, which warrants further development as a potential candidate compound for COVID-19 disease.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213987","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":"Vaginal microbiota as a predictor of preterm birth: an observational cohort study","authors":"Laura Lesimple, Jessica Rousseau, Celine Plainvert, Luce Landraud, Nathalie Grall, Francois Goffinet, Pierre-Yves Ancel, Christophe Pannetier, Claire Poyart, Laurent Mandelbrot, Asmaa Tazi","doi":"10.1101/2024.09.11.612423","DOIUrl":"https://doi.org/10.1101/2024.09.11.612423","url":null,"abstract":"Background: Preterm birth (birth before 37 weeks of gestational age) is a frequent and severe adverse pregnancy outcome. Despite the growing number of scientific studies highlighting the link between vaginal microbiota composition and adverse pregnancy outcomes, data remain controversial.\u0000Objectives: To identify microbiota signatures of preterm labor and premature rupture of outer membranes; to determine microbiological risk factors for preterm birth. Study Design: We conducted an observational, prospective, longitudinal cohort study from August 2018 until June 2023 in 3 maternity wards from university hospitals in the Paris, France, area. Women were categorized in 4 groups including a control group, and 3 groups of increasing risk of intrauterine infection and preterm birth: prelabor rupture of membranes at term, preterm labor, and preterm premature rupture of membranes. Demographic, clinical data, past medical and obstetrical history and pregnancy outcome were collected. Vaginal swabs were collected at admission and were analyzed using culturomics. The association between bacterial species and the cohort groups and eventually preterm birth was studied in univariate analyses. Adjusted odds ratio (aOR) and 95% confidence intervals (95% CI) were calculated in multivariable analyses. Results: A total of 2,476 women were included, of whom 1,068 (43.1%) in the control group, 477 (19.3%) with term premature rupture of outer membranes, 495 (20.0%) with preterm labor, and 436 (17.6%) with preterm premature rupture of outer membranes. Together with demographic features such as ethnicity and obstetrical history, several vaginal microbiota signatures were identified as correlated with pregnancy outcome. In multivariable analysis, prelabor rupture of membranes at term was associated with enterobacteria (aOR 1.97, 95% CI 1.46-2.65) and Gardnerella vaginalis (aOR 5.19, 95% CI 2.22-13.78); preterm labor with lactobacilli depletion (aOR 1.49, 95% CI 1.08-2.06), enterobacteria (aOR 1.86, 95% CI 1.36-2.53) and G. vaginalis (aOR 4.62, 95% CI 1.86-13.34); preterm premature rupture of membranes with lactobacilli depletion (aOR 2.04, 95% CI 1.49-2.80) and enterobacteria (aOR 2.38, 95% CI 1.74-3.24). Finally, together with gestational diabetes, lactobacilli depletion and enterobacteria both represented risk factors for preterm birth, especially in singleton pregnancies (aOR 1.54, 95% CI 1.05-2.28 and aOR 1.62, 95% CI 1.11-2.36, respectively).\u0000Conclusions: In this large cohort study, we identified on the one hand, G. vaginalis as associated with prelabor rupture of membranes at term and preterm labor, and on the other hand, lactobacilli depletion and enterobacteria as risk factors for preterm labor, preterm premature rupture of outer membranes, and preterm birth, emphasizing the importance of a healthy microbiota in pregnancy outcome. Further studies are needed to address the benefits of adapted antibiotic prophylaxes and probiotics aiming at restoring a healthy microb","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213986","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":"Targeted syndromic next-generation sequencing panel for simultaneous detection of pathogens associated with bovine reproductive failure","authors":"Dhinesh Periyasamy, Yanyun Huang, Janet E Hill","doi":"10.1101/2024.09.10.612295","DOIUrl":"https://doi.org/10.1101/2024.09.10.612295","url":null,"abstract":"Bovine reproductive failure, which includes infertility, abortion, and stillbirth in cattle, leads to significant economic losses for beef and milk producers. Diagnosing the infectious causes of bovine reproductive failure is challenging as there are multiple pathogens associated with it. The traditional stepwise approach to diagnostic testing is time-consuming and can cause significant delays. In this study, we have developed a syndromic next-generation sequencing panel (BovReproSeq), for the simultaneous detection of 17 pathogens associated with bovine reproductive failure. This targeted approach involves amplifying multiple pathogen-specific targets using ultra-multiplex PCR, followed by sequencing with the Oxford Nanopore platform and subsequent analysis of the data using a custom bioinformatic pipeline to determine the presence or absence of pathogens. We tested 116 clinical samples and found that BovReproSeq results matched with current diagnostic methods for 93% of the samples, and most of the disagreements occurring in samples with very low pathogen loads (Ct > 35). At the optimal read-count threshold of 10 reads (minimum number of reads to classify the sample as positive), the sensitivity of the assay was approximately 82%, while specificity was 100%. The overall accuracy of the assay was 98.8%. Matthew's Correlation Coefficient was approximately 0.90 and F1 score (harmonic mean of Precision and Recall) was 0.90, indicating excellent overall performance. Our study presents a significant advancement in detecting the infectious agents associated with bovine reproductive failure and the BovReproSeq panel's ability to detect 17 pathogens makes it a promising tool for veterinary diagnostics.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"95 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213991","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":"Synergistic cross-kingdom host cell damage between Candida albicans and Enterococcus faecalis","authors":"Mario Kapitan, Maria Joanna Niemiec, Nicolas Millet, Philipp Brandt, Md Estiak Khan Chowdhury, Anna Czapka, Ketema Abdissa, Franziska Hoffmann, Anna Lange, Mark Veleba, Sandor Nietzsche, Alexander Sandy Mosig, Bettina Loffler, Mike Marquet, Oliwia Makarewicz, Kimberly A. Kline, Slavena Vylkova, Marc Swidergall, Ilse D. Jacobsen","doi":"10.1101/2024.09.11.612452","DOIUrl":"https://doi.org/10.1101/2024.09.11.612452","url":null,"abstract":"The fungus Candida albicans and the Gram-positive bacterium Enterococcus faecalis share mucosal niches in the human body. As opportunistic pathogens, both are found to expand population size during dysbiosis, and can cause severe systemic infections in susceptible individuals. Here, we show that the presence of C. albicans results in increased host cell damage by E. faecalis. Furthermore, E. faecalis aggravates oropharyngeal candidiasis in mice. Increased damage is mediated by enterococcal cytolysin, and involves both physical interaction and altered glucose availability. Physical interaction promotes accumulation of bacteria on host cells, facilitating contact of cytolysin with host cells. Glucose depletion by the metabolic activity of the fungus sensitized host cells to cytolysin. This work illustrates how a complex interplay between fungi and bacteria can result in detrimental consequences for the host.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"42 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213985","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":"pr-independent biogenesis of infectious mature Zika virus particles","authors":"Kimberly A Dowd, Michelle Schroeder, Egan Sanchez, Beniah Brumbaugh, Bryant M Foreman, Katherine E Burgomaster, Wei Shi, Lingshu Wang, Natalie Caputo, David Gordon, Cindi L Schwartz, Bryan T Hansen, Maya Aleshnick, Wing-Pui Kong, Kaitlyn M Morabito, Heather D Hickman, Barney S Graham, Elizabeth R Fischer, Theodore C Pierson","doi":"10.1101/2024.09.12.612520","DOIUrl":"https://doi.org/10.1101/2024.09.12.612520","url":null,"abstract":"Flavivirus assembly at the endoplasmic reticulum is driven by the structural proteins envelope (E) and premembrane (prM). Here, contrary to the established paradigm for flavivirus assembly, we demonstrate that the biogenesis of flavivirus particles does not require an intact prM nor proteolytic activation. The expression of E preceded by a truncated version of prM (M-E) was sufficient for the formation of non-infectious Zika virus subviral particles and pseudo-infectious reporter virions. Subviral particles encoded by a ZIKV M-E DNA vaccine elicited a neutralizing antibody response that was insensitive to the virion maturation state, a feature of flavivirus humoral immunity shown to correlate with protection. M-E vaccines that uniformly present structural features shared with mature virions offer a higher quality and broadly applicable approach to flavivirus vaccination.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213988","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":"Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance","authors":"Erica R Fuhrmeister, Sooyeol Kim, Shruteek A Mairal, Caroline McCormack, Benard Chieng, Jenna M Swarthout, Abigail Harvey Paulos, Sammy M Njenga, Amy J Pickering","doi":"10.1101/2024.09.12.612745","DOIUrl":"https://doi.org/10.1101/2024.09.12.612745","url":null,"abstract":"Antimicrobial resistance (AMR) aligns with a One Health framework in that resistant bacteria and antibiotic resistance genes (ARGs) can be transmitted between humans, animals, and the environment. However, there is a critical need to more precisely understand how and to what extent AMR is exchanged between animals and humans. Metagenomic sequencing has low detection for rare targets such as ARGs, while whole genome sequencing of isolates is burdensome and misses exchange between uncultured bacterial species. We developed a novel, targeted sequencing assay using CRISPR-Cas9 to selectively sequence ARGs and their genomic context with long-read sequencing. Using this method, termed Context-Seq, we investigated overlapping AMR elements containing the ARGs blaCTX-M and blaTEM between adults, children, poultry, and dogs in animal-owning households in Nairobi, Kenya. We identified 22 genetically distinct clusters (> 80%ID over ≥ 3000 bp) containing blaTEM and one cluster containing blaCTX-M that were shared within and between households. Half of the clusters were shared between humans and animals, while the other half were shared only between animals (poultry-poultry, dog-dog, and dog-poultry). We identified potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumonia, and Haemophilus influenzae across sample types. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214008","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":"Electromagnetic waves destabilize the SARS-CoV-2 Spike protein and reduce SARS-CoV-2 Virus-Like Particle (SC2-VLP) infectivity","authors":"Skyler Granatir, Francisco M. Acosta, Christina Pantoja, Johann Tailor, Angus Fuori, Bill Dower, Henry Marr, Peter W Ramirez","doi":"10.1101/2024.09.11.612487","DOIUrl":"https://doi.org/10.1101/2024.09.11.612487","url":null,"abstract":"Infection and transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to pose a global public health concern. Using electromagnetic waves represents an alternative strategy to inactivate pathogenic viruses such as SARS-CoV-2 and reduce overall transmission. However, whether electromagnetic waves reduce SARS-CoV-2 infectivity is unclear. Here, we adapted a coplanar waveguide (CPW) to identify electromagnetic waves that could neutralize SARS-CoV-2 virus-like particles (SC2-VLPs). Treatment of SC2-VLPs, particularly at frequencies between 2.5-3.5 GHz at an electric field of 400 V/m for 2 minutes, reduced infectivity. Exposure to a frequency of 3.1 GHz decreased the binding of SC2-VLPs to antibodies directed against the Spike S1 subunit receptor binding domain (RBD). These results suggest that electromagnetic waves alter the conformation of Spike, thereby reducing viral attachment to host cell receptors. Overall, this data provides proof-of-concept in using electromagnetic waves for sanitation and prevention efforts to curb the transmission of SARS-CoV-2 and potentially other pathogenic enveloped viruses.","PeriodicalId":501357,"journal":{"name":"bioRxiv - Microbiology","volume":"95 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142214019","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}