Frontiers in Bacteriology最新文献

{"title":"Genomic characterisation of generic Escherichia coli from food-producing animals and products of animal origin in South Africa","authors":"Refiloe Malesa, R. Pierneef, Kudakwashe Magwedere, T. Mafuna, I. Matle","doi":"10.3389/fbrio.2024.1432292","DOIUrl":"https://doi.org/10.3389/fbrio.2024.1432292","url":null,"abstract":"Escherichia coli is found in diverse environmental niches, including meat and meat products, and is known for its significance in both food safety and public health. In South Africa, whole genomic sequencing (WGS) efforts for E. coli are overwhelmingly skewed toward human isolates with limited studies conducted on non-human isolates. Therefore, the aim of this study was to use WGS to characterise generic strains of E. coli isolated from animal specimens, meat, and meat-based products in South Africa. Based on WGS analysis, a total of 35 E. coli strains were grouped into five phylogroups (A, B1, B2, C, and E), with A (46%) being the most predominant. Virulence-associated genes identified the isolates as either extra-intestinal pathogenic E. coli (69%) or intestinal pathogenic E. coli (31%) pathotypes. Twenty-three different serotypes were identified, with O101:H37 (17%), O2:H4 (17%), O6:H5 (13%), and O64:H19 (9%) being the predominant ones. Among the 19 different sequence types (STs), ST1858, ST975, and ST10 were the most prevalent (11% each). Various virulence genes, antimicrobial resistance genes, and genetic mobile elements carrying Tn2, IS26, and Tn6196 elements were detected, with the disinfectant resistance sitABCD being the most predominant. The type 1 CRISPR system which functions by storing records of previous invasions to provide immunological memory for a rapid and robust response upon subsequent viral infections was detected in all isolates, consisting of subtypes I-E (86%), I-A (57%), and I-F (11%). The findings of this study provide an insight into the genetic diversity of generic E. coli isolates from animal species, meat, and meat-based products in South Africa.","PeriodicalId":510337,"journal":{"name":"Frontiers in Bacteriology","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141641734","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":"Oral origin of the placenta microbiome in pregnant women with preeclampsia","authors":"Shontreal M. Cooper, Adam Borgida, Sejal Thacker, Erica Hammer, Amirtha Hariharan, C. Kuo, Nyle Blanck, Hanshu Yuan, Hunter Panier, Qingqi Lin, Kendra Maas, Winston Campbell, Yanjiao Zhou","doi":"10.3389/fbrio.2023.1322165","DOIUrl":"https://doi.org/10.3389/fbrio.2023.1322165","url":null,"abstract":"Preeclampsia (PE) is a leading cause of morbidity and mortality in pregnancy with elusive etiology. Patients with PE are thought to be associated with a higher rate of periodontal diseases (PDs) and changes of oral bacteria with targeted PCR techniques. However, few studies have investigated the associations between oral microbiome dysbiosis and secondarily disseminated microbes in the placenta simultaneously in patients with PE. The association between detected microbiome in placenta and systemic inflammation in PE is also unclear. We enrolled 54 pregnant patients with and without PE and PD, and profiled the subgingival and placenta microbiome by the V4 region of 16S rRNA gene sequencing. Systemic inflammatory markers tumor necrosis factor-alpha (TNF-α), C-reactive protein (CRP), lipopolysaccharide binding protein (LBP), and interleukins 6 and 8 (IL-6 and IL-8) in blood were measured by ELISA. We found that PD significantly increased the risk of PE after adjusting for age and smoking status (OR = 2.26, 95% CI = 1.14–4.48, p = 0.024). A combined group of oral-associated bacteria Veillonella, Fusobacterium, Haemophilus, Granulicatella, Streptococcus, Gemella, and Neisseria in placenta had a significantly higher prevalence in women with PE compared to women without PE (53.8% vs. 19.0%, p = 0.018), with the highest prevalence in patients with both PE and PD (58.8%). The relative abundance of Haemophilus, Veillonella, and Fusobacterium in subgingival samples was significantly higher in patients with PE than those without PE. The relative abundance of Haemophilus in subgingival samples was associated with increased risk of PE (OR = 2.11, 95% CI = 1.11–4.52, p = 0.032). Proinflammatory cytokine analysis showed that PE patients with PD had higher blood IL-8 levels than PE patients without PD (p = 0.026). CRP, LBP, and TNF-α showed no statistical difference in patients with and without PE or PD. Blood IL-6 levels were significantly higher in patients with detectable placenta microbiome compared to those without placenta microbiome (p = 0.028). Together, our data suggest a potential oral origin of the placental microbiota present in patients with PE, and the microbiota detected in placenta is associated with increased IL-6 level in the blood.","PeriodicalId":510337,"journal":{"name":"Frontiers in Bacteriology","volume":"10 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140244642","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":"Emerging applications of artificial intelligence in pathogen genomics","authors":"Carl J. E. Suster, David Pham, Jen Kok, V. Sintchenko","doi":"10.3389/fbrio.2024.1326958","DOIUrl":"https://doi.org/10.3389/fbrio.2024.1326958","url":null,"abstract":"The analysis of microbial genomes has long been recognised as a complex and data-rich domain where artificial intelligence (AI) can assist. As AI technologies have matured and expanded, pathogen genomics has also contended with exponentially larger datasets and an expanding role in clinical and public health practice. In this mini-review, we discuss examples of emerging applications of AI to address challenges in pathogen genomics for precision medicine and public health. These include models for genotyping whole genome sequences, identifying novel pathogens in metagenomic next generation sequencing, modelling genomic information using approaches from computational linguistics, phylodynamic estimation, and using large language models to make bioinformatics more accessible to non-experts. We also examine factors affecting the adoption of AI into routine laboratory and public health practice and the need for a renewed vision for the potential of AI to assist pathogen genomics practice.","PeriodicalId":510337,"journal":{"name":"Frontiers in Bacteriology","volume":"27 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140262555","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":"Bacterial hypothetical proteins may be of functional interest","authors":"Antony T. Vincent","doi":"10.3389/fbrio.2024.1334712","DOIUrl":"https://doi.org/10.3389/fbrio.2024.1334712","url":null,"abstract":"Genomic analysis is part of the daily routine for many microbiology researchers. These analyses frequently unveil genes that encode proteins with uncertain functions, and for many bacterial species, these unknown genes constitute a significant proportion of their genomic coding sequences. Because these genes do not have defined functions, they are often overlooked in analyses. Experimentally determining the function of a gene can be challenging; however, ongoing advancements in bioinformatics tools, especially in protein structural analysis, are making it progressively easier to assign functions to hypothetical sequences. Leveraging various complementary tools and automated pipelines for annotating hypothetical sequences could ultimately enhance our comprehension of microbial functions and provide direction for new laboratory experiments.","PeriodicalId":510337,"journal":{"name":"Frontiers in Bacteriology","volume":"17 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140263398","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}