BMC Microbiology最新文献

{"title":"Enable, empower, succeed: a bioinformatics workshop Harnessing open web-based tools for surveillance of bacterial antimicrobial resistance.","authors":"Luria Leslie Founou, Opeyemi U Lawal, Armando Djiyou, Erkison Ewomazino Odih, Daniel Gyamfi Amoako, Stephane Fadanka, Mabel Kamweli Aworh, Sindiswa Lukhele, Dusanka Nikolic, Alice Matimba, Raspail Carrel Founou","doi":"10.1186/s12866-025-03865-0","DOIUrl":"10.1186/s12866-025-03865-0","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial resistance (AMR) poses a significant threat to global health, particularly in Western sub-Saharan Africa where 27.3 deaths per 100,000 lives are affected, and surveillance and control measures are often limited. Genomics research plays a crucial role in understanding the emergence, spread and containment measures of AMR. However, its implementation in such settings is particularly challenging due to limited human capacity. This manuscript outlines a three-day bioinformatics workshop in Cameroon, highlighting efforts to build human capacity for genomics research to support AMR surveillance using readily accessible and user-friendly web-based tools. The workshop introduced participants to basic next-generation sequencing concepts, data file formats used in bacterial genomics, data sharing procedures and considerations, as well as the use of web-based bioinformatics software to analyse genomic data, including in silico prediction of AMR, phylogenetics analyses, and a quick introduction to Linux© command line.</p><p><strong>Results: </strong>Briefly, a substantial increase in participants' confidence in bioinformatics knowledge and skills was observed before and after the workshop. Notably, before the workshop most participants lacked confidence in their ability to identify next-generation sequencing technologies or workflows (64%) and analyse genetic data using web-based bioinformatics tools (81%). After the workshop, majority of participants were extremely confident using NCBI BLAST and other web-based bioinformatics tools for data analysis with a score ≥ 5 among which 45%, 9% and 18% had a score of 8, 9, and 10, respectively.</p><p><strong>Conclusion: </strong>Our findings highlight the effectiveness of this training approach in empowering local researchers and bridging the bioinformatics gap in genomics surveillance of AMR in resource-constrained settings. We provide a detailed description of the relevant training approaches used, including workshop structure, the selection and planning, and utilization of freely available web-based tools, and the evaluation methods employed. Our approach aimed to overcome limitations such as inadequate infrastructure, limited access to computational resources, and scarcity of expertise. By leveraging the power of freely available web-based tools, we demonstrated how participants can acquire fundamental bioinformatics skills, enhance their understanding of biological data analysis, and contribute to the field, even in an underprivileged environment. Building human capacity for genomics research globally, and especially in resource-constrained settings, is imperative for ensuring global health and sustainable containment of AMR.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"156"},"PeriodicalIF":4.0,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Virulence traits, agr typing, multidrug resistance patterns, and biofilm ability of MDR Staphylococcus aureus recovered from clinical and subclinical mastitis in dairy cows.","authors":"Nada H Eidaroos, Abdelazeem M Algammal, Walaa Ismail Mohamaden, Asma Massad Alenzi, Saad Alghamdi, Ahmed Kabrah, Heba Sayed El-Mahallawy, Hamza M Eid, Alaa Abd Algwad, Samar Ali Asfor, Heinrich Neubauer, Amira A Moawad, Reham M El-Tarabili","doi":"10.1186/s12866-025-03870-3","DOIUrl":"10.1186/s12866-025-03870-3","url":null,"abstract":"<p><strong>Background: </strong>Bovine mastitis caused by Staphylococcus aureus is considered a public health threat globally. Herein, we aimed to investigate the occurrence, agr typing, antimicrobial resistance patterns, biofilm production, and PCR-based detection of the virulence, biofilm, adhesion, and enterotoxins genes of S. aureus strains recovered from clinical and subclinical bovine mastitis.</p><p><strong>Results: </strong>The prevalence of S. aureus in the examined milk samples was 44.4%. Besides, 95% of the retrieved S. aureus strains were identified as MRSA. Herein, all the tested isolates were biofilm producers. PCR revealed that 85% of the retrieved S. aureus strains were positive for the agr I gene. Furthermore, the clfB, clfA, fnbB, fnbA, and cna genes were detected with a prevalence of 100%, 80%, 60%, 55%, and 30%, respectively. Also, all the tested S. aureus strains were positive for the coa gene (100%). Besides, 92.5% and 85% of the recovered strains harbored the lukF and spa genes, respectively. In addition, the prevalence of the hla, hlb, and hlg hemolysin genes was 70%, 50%, and 35%, respectively. Among the enterotoxin genes, the seb gene was detected in 30% of the tested strains. The prevalence of eno and icaA biofilm genes was 95% in the tested strains. Moreover, 15% of S. aureus strains were MDR to 8 antimicrobial agents and harbored the mecA, ermC, and ermB genes. As well, 12.5% of S. aureus strains were MDR to 8 antimicrobial agents and carried the mecA, ermC, ermB, tetK, and tetM genes. Also, 5% of S. aureus strains were XDR to 11 antimicrobial agents and carried the mecA, ermC, and ermB genes.</p><p><strong>Conclusions: </strong>The existence of MDR and XDR MRSA strains in bovine milk is a public health hazard. The mecA, ermC, ermB, tetK, and tetM resistance genes and the coa, clfB, eno, icaA, lukF, spa, clfA, and hla virulence genes are commonly associated with the MDR and XDR MRSA strains. Moreover, the seb gene was the predominant enterotoxin gene in the MRSA strains recovered from milk.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"155"},"PeriodicalIF":4.0,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adoption of an in-silico analysis approach to assess the functional and structural impacts of rpoB-encoded protein mutations on Chlamydia pneumoniae sensitivity to antibiotics.","authors":"Sanae Esskhayry, Ichrak Benamri, Afaf Lamzouri, Ouafae Kaissi, Rachida Fissoune, Ahmed Moussa, Fouzia Radouani","doi":"10.1186/s12866-025-03860-5","DOIUrl":"10.1186/s12866-025-03860-5","url":null,"abstract":"<p><strong>Background: </strong>Antibiotics are frequently used to treat infections caused by Chlamydia pneumoniae; an obligate intracellular gram-negative bacterium commonly associated with respiratory diseases. However, improper or overuse of these drugs has raised concerns about the development of antibiotic resistance, which poses a significant global health challenge. Previous studies have revealed a link between mutations in the rpoB-encoded protein of C. pneumoniae and antibiotic resistance. This study assessed these mutations via various bioinformatics tools to predict their impact on function, structural stability, antibiotic binding, and, ultimately, their effect on bacterial sensitivity to antibiotics.</p><p><strong>Results: </strong>Eight mutations in the rpoB-encoded protein (R421S, F450S, L456I, S454F, D461E, S476F, L478S, and S519Y) are associated with resistance to rifampin and rifalazil. These mutations occur in conserved regions of the protein, leading to decreased stability and affecting essential functional sites of RNA polymerase, the target of these antibiotics. Although the structural differences between the native and mutant proteins are minimal, notable changes in local hydrogen bonding have been observed. Despite similar binding energies, variations in hydrogen bonds and hydrophobic interactions in certain mutants (for instance, D461E for rifalazil and S476F for rifampin) indicate that these changes may diminish ligand affinity and specificity. Furthermore, protein-protein network analysis demonstrated a strong correlation between wild-type rpoB and ten C. pneumoniae proteins, each fulfilling specific functional roles. Consequently, some of these mutations can reduce the bacterium's sensitivity to rifampin and rifalazil, thereby contributing to antibiotic resistance.</p><p><strong>Conclusion: </strong>The findings of this study indicate that mutations in the rpoB gene, which encodes the beta subunit of RNA polymerase, are pivotal in the resistance of C. pneumoniae to rifampin and rifalazil. Some of these mutations may result in reduced protein stability and changes in the structure, function, and antibiotic binding. As a consequence, the efficacy of these drugs in inhibiting RNA polymerase is compromised, allowing the bacteria to persist in transcription and replication even in the presence of antibiotics. Overall, these insights enhance our understanding of the resistance mechanisms in C. pneumoniae and could guide the development of strategies to address this challenge.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"157"},"PeriodicalIF":4.0,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921668/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cellulase enhancing rumen microbiome of Tan sheep indicates plastic responses to seasonal variations of diet in the typical steppe.","authors":"Hairen Shi, Pei Guo, Zhen Wang, Jieyan Zhou, Meiyue He, Liyuan Shi, Xiaojuan Huang, Penghui Guo, Zhaoxia Guo, Yuwen Zhang, Fujiang Hou","doi":"10.1186/s12866-025-03799-7","DOIUrl":"10.1186/s12866-025-03799-7","url":null,"abstract":"<p><strong>Background: </strong>Climate and geographical changes significantly influence food availability and nutrient composition over time and space, Which in turn affects the selection of microbial communities essential for maintaining gastrointestinal homeostasis and facilitating dietary adaptation. Therefore, it is essential to understand the specific responses of the gut microbiota to dietary and seasonal variations in order to improve animal conservation strategies based on solid scientific knowledge.</p><p><strong>Results: </strong>In summer, due to the higher nutritional quality of forage, Tan sheep exhibited enhanced forage degradation and fermentation. This was reflected by increased populations of key rumen bacteria, including Bacteroidetes, Prevotella_1, Prevotellaceae_UCG-003, Ruminococcus_1, Saccharofermentans, and Ruminococcaceae_UCG-014. Supplementation with cellulase further facilitated these processes, optimizing the utilization of available nutrients. In contrast, during winter, when the nutritional quality of forage decline, we observed lower indicators of forage degradation and fermentation in Tan sheep. Additionally, there was a significant increase in the Firmicutes/Bacteroidetes ratio, microbial diversity, microbial interactions, and metabolic activity.</p><p><strong>Conclusions: </strong>The rumen microbiota adapts to enhance the breakdown of forage biomass and maintain energy balance during periods of inadequate nutritional value. Supplementing the diet with cellulase during these times can help mitigate the reduced digestibility associated with low-quality forage. This study highlights the dynamic adaptation of the rumen microbiota to seasonal variations in forage quality and emphasizes the potential benefits of cellulase supplementation in supporting rumen function and improving animal performance under varying environmental conditions.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"154"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11917088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential of a phage cocktail in the treatment of multidrug-resistant Klebsiella pneumoniae pulmonary infection in mice.","authors":"Zong Gou, Pu Yao, Lirong Xiong, Xiaowen Wang, Qian Yuan, Fengjun Sun, Yimei Cheng, Peiyuan Xia","doi":"10.1186/s12866-025-03851-6","DOIUrl":"10.1186/s12866-025-03851-6","url":null,"abstract":"<p><p>The emergence of multidrug-resistant Klebsiella pneumoniae, including carbapenem-resistant K. pneumoniae (CRKP), as one of the most common and notable superbugs, has long been a major threat to public health. As natural predators of bacteria, bacteriophages (or phages) can induce the lysis of bacterial cells. Herein, we report the isolation and characterization of two phages and their efficacy in the control of CRKP. Using the sequence type 11 (ST11) CRKP strain THR60 and its related strain THR60r as the host bacteria, phages GZ7 and GZ9 were isolated from hospital sewage, respectively. GZ7 is a myovirus with a head of 64 nm in diameter and a tail of 97 nm in length, and GZ9 is a siphovirus with a head of 67 nm in diameter and a tail of 175 nm in length. The host spectrum of a phage cocktail consisting of phages GZ7 and GZ9 was 82.4% (42/51 strains). An in vitro antibacterial activity assay demonstrated that the phage cocktail consisting of GZ7 and GZ9 effectively inhibited bacterial growth and suppressed the production of phage-resistant bacteria. In vivo experiment revealed that phage-treated mice exhibited lower K. pneumoniae burdens in the lungs compared to untreated control mice. Additionally, phage-treated mice experienced less body weight loss and had reduced levels of inflammatory cytokines in their lungs. Lung lesion conditions were significantly improved by phage therapy. Notably, the therapeutic effects of the GZ7 + GZ9 cocktail and GZ7 alone on mouse pulmonary infections were nearly equivalent. Therefore, phages GZ7 and GZ9 showed potential as alternatives to antibiotics for treating pneumonia caused by multidrug-resistant K. pneumoniae.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"151"},"PeriodicalIF":4.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of relative genes expression and mutation of pstB and efpA efflux pumps in Mycobacterium simiae isolates from suspected tuberculosis patients by using quantitative Real-time PCR.","authors":"Mohammad Hashemzadeh, Maryam Hasanvand, Effat Abbasi Montazeri","doi":"10.1186/s12866-025-03843-6","DOIUrl":"10.1186/s12866-025-03843-6","url":null,"abstract":"<p><strong>Background: </strong>Mycobacterium simiae is commonly found in people with weak immune systems such as the elderly and people with tuberculosis and other lung diseases. The aim of this study is the epidemiology of M. simiae infections in Iran and the world, therefore, in this study, analysis of relative gene expression and mutation of pstB and efpA efflux pumps in Mycobacterium simiae isolates from suspected tuberculosis patients by using Real-time quantitative PCR. Sixty-five sputa samples of suspected tuberculosis specimens were collected. The identification of NTM Species by PCR sequencing and determining drug sensitivity by micro broth dilution method. The investigate mutations in pstB and efpA efflux pump genes using the PCR-sequencing method. Comparative evaluation of the replication efficiency of internal control gene 16SrDNA and target genes pstB and efpA.</p><p><strong>Results: </strong>In total, 15 isolates of M. simiae were evaluated and a drug sensitivity test was performed for them against the antibiotic ethambutol, moxifloxacin, clarithromycin, and linezolid. The highest resistance to moxifloxacin and linezolid antibiotics and the lowest resistance to clarithromycin antibiotics were observed. The results of expression levels of two efflux PstB and efpA showed that there was a significant difference in the expression level of the efpA efflux pump gene in M. simiae three-resistant and double-resistant isolates compared to the sensitive group and the standard.</p><p><strong>Conclusions: </strong>The high level of antibiotic resistance In M. simiae isolates is an alarm and monitoring all factors related to antibiotic resistance, including efflux pumps, is an important research topic.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"144"},"PeriodicalIF":4.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long-term safety of fecal microbiota transplantation in Chinese children from 2013 to 2023: a single-center retrospective study.","authors":"Pei Xiao, Youran Li, Xiaolu Li, Ting Ge, Dan Li, Qiao Xu, Yangming Ruan, Fangfei Xiao, Yongmei Xiao, Ting Zhang","doi":"10.1186/s12866-025-03858-z","DOIUrl":"10.1186/s12866-025-03858-z","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiome plays a vital role in influencing various health conditions. Fecal Microbiota Transplantation (FMT) has emerged as a rapid, safe, and effective method for modifying the microbiome. However, there is a lack of long-term safety data regarding FMT in children. This study presents the largest single-center analysis of the long-term safety outcomes of FMT in pediatric patients in China, featuring a substantial sample size and an extended follow-up period to thoroughly examine its safety in children.</p><p><strong>Methods: </strong>A retrospective study was conducted on 813 patients who underwent FMT treatments at our hospital from December 2013 to December 2023. All FMT procedures adhered to standardized protocols. The safety of these treatments was retrospectively assessed, focusing on adverse events (AEs) and serious adverse events (SAEs). AEs associated with FMT were categorized as short-term (within 48 h post-FMT) and long-term (within 3 months). Various potential influencing factors for AEs, including sex, age, route of administration, disease type, and consanguineous donor, were examined as independent variables. Significant independent factors and their associated risk ratios with 95% confidence intervals (CI) were determined through multivariate logistic regression analysis. A p-value of less than 0.05 was considered statistically significant.</p><p><strong>Results: </strong>A total of 813 patients underwent FMT, with a median age of 93 months (range 4-215) and 68.0% being males. The average follow-up time was 32.3 months (range 1-122). All short-term AEs resolved within 48 h, with an overall occurrence rate of 5.8% (47/813). The most common short-term AEs included vomiting (2.0%), abdominal pain (1.6%), diarrhea (0.9%), fever (0.7%), dysphoria (0.4%), and nausea (0.4%). Multivariable analysis revealed that patients with inflammatory bowel disease (IBD) (OR: 3.98, 95% CI: 1.78-8.92, P = 0.001) and those who received FMT via capsules (OR: 0.09, 95% CI: 0.03-0.27, P = 0.000) were independent risk factors for FMT-related AEs. All 813 patients were followed up for at least 1 month, with 78.8% followed for more than 12 months. No long-term AEs occurred during the longest follow-up period of 122 months.</p><p><strong>Conclusions: </strong>FMT is a promising treatment option that appears to be safe and well tolerated. This study stands out for its substantial sample size, making it's the largest reported series in pediatrics, as well as for having the longest follow-up period for FMT in this population.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"152"},"PeriodicalIF":4.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912669/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study on molecular characteristics of Staphylococcus from yak milk-Xizang.","authors":"Fanxing Meng, Qingxia Wu, Jiangyong Zeng, Hongcai Ma","doi":"10.1186/s12866-025-03868-x","DOIUrl":"10.1186/s12866-025-03868-x","url":null,"abstract":"<p><p>This study investigated the biological characteristics of Staphylococcus strains isolated from Xizangan yak milk by examining the antibiotic resistance phenotypes of 69 isolates against 18 antibiotics, detecting 31 associated resistance genes, identifying 16 virulence genes, and assessing biofilm formation capability. Furthermore, molecular typing techniques including spa typing, multilocus sequence typing (MLST), and Staphylococcus cassette chromosome mec (SCCmec) were used for detailed characterization of the isolates. The findings revealed a high penicillin resistance rate of 72.46%. Resistance genes such as gyrA (100.00%), glrB (92.75%), and gyrB (44.93%) were prevalent. The detection rates were 81.16% and 55.07% for the beta-lactamase gene blaZ and the mecA gene, respectively. Among the tested virulence genes, lukS, lukF, hla, clfA, and icaD were detected in 40.58% of isolates, while sec was detected in 24.64%. MLST typing identified four isolates belonging to the ST62623 type and 24 other isolates representing novel ST types not reported on PubMLST.org. Spa typing revealed spa types t1940 (n = 9), t3022 (n = 8), t4558 (n = 6), t4236 (n = 3), t4445 (n = 1), and one unreported spa type. For SCCmec typing, 11 isolates were typed as SCCmec IVb and 9 as SCCmec V. These findings significantly enhance our understanding of the biological characteristics of Staphylococcus strains derived from Xizangan yak milk.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"153"},"PeriodicalIF":4.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912705/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A rapid detection of Avian Pathogenic Escherichia coli (APEC) strains based on minimal number of virulence markers identified by whole genome sequencing.","authors":"Joanna Kazimierczak, Karolina Pospiech, Patrycja Sowińska, Anna Pękala, Paulina Borówka, Ewelina A Wójcik, Błażej Marciniak, Marcin W Lis, Dominik Strapagiel, Jarosław Dastych","doi":"10.1186/s12866-025-03861-4","DOIUrl":"10.1186/s12866-025-03861-4","url":null,"abstract":"<p><strong>Background: </strong>Colibacillosis is an important epidemiological and economic issue in poultry farming and breeding. A common problem with avian pathogenic Escherichia coli strains (APEC) that cause this disease is a lack of an uniform identification system, resulting from a variety of serotypes, phylogenetic groups, sequence types and combinations of virulence factors. There are no clearly defined features that can be associated with pathogenicity. Therefore, without precise identification of pathogenic strains and differentiation from commensal strains, there is no possibility of appropriate selection of targeted therapy. The widespread use of whole genome sequencing (WGS) in recent years creates new possibilities in diagnostics. Therefore, the purpose of this study was to select features defining the APEC pathotype, based on next generation sequencing (NGS), and design a diagnostic test based on selected factors.</p><p><strong>Results: </strong>A PCR diagnostic test is proposed. Three predictors of virulence were chosen according to in silico analysis: two virulence genes: iroC and hlyF, as well as one molecular marker of O78 serotype (wzx-O-antigen flippase of the O78 serotype). A choice of markers was supported by a chicken embryo model.</p><p><strong>Conclusions: </strong>Whole genome sequencing of E. coli genomes allowed for the development of a rapid diagnostic method identifying pathogenic strains for poultry: APEC. The developed test can support field observations connected with the strain isolation source and clinical symptoms of the disease.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"147"},"PeriodicalIF":4.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Full-length 16S rRNA Sequencing Reveals Gut Microbiome Signatures Predictive of MASLD in children with obesity.","authors":"Yu-Cheng Lin, Chi-Chien Wu, Yun-Er Li, Chun-Liang Chen, Chia-Ray Lin, Yen-Hsuan Ni","doi":"10.1186/s12866-025-03849-0","DOIUrl":"10.1186/s12866-025-03849-0","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota plays a crucial role in metabolic dysfunction-associated steatotic liver disease (MASLD). Next-generation sequencing technologies are essential for exploring the gut microbiome. While recent advancements in full-length 16S (FL16S) rRNA sequencing offer better taxonomic resolution, whether they establish stronger associations with the risk of MASLD remains to be determined.</p><p><strong>Method: </strong>This study utilized long-read FL16S and short-read V3-V4 16S rRNA sequencing to profile gut microbiome compositions in age-, sex-, and BMI-matched case-control pairs of obese children with and without MASLD. A random forest predictive model was employed, using gut-microbiota features selected based on the top 35 most abundant taxa or a linear discriminant analysis score greater than 3. The model's performance was evaluated by comparing the area under the receiver operating characteristic curve (AUC) through a tenfold cross-validation method.</p><p><strong>Results: </strong>Subjects with MASLD exhibited significantly elevated serum alanine aminotransferase, triglycerides, and homeostasis model assessment of insulin resistance levels compared to controls. At the genus level, the gut microbiome compositions detected by both FL16S and V3-V4 sequencing were similar, predominantly comprising Phocaeicola and Bacteroides, followed by Prevotella, Bifidobacterium, Parabacteroides, and Blautia. The AUC for the model based on FL16S sequencing data (86.98%) was significantly higher than that based on V3-V4 sequencing data (70.27%), as determined by DeLong's test (p = 0.008).</p><p><strong>Conclusion: </strong>FL16S rRNA sequencing data demonstrates stronger associations with the risk of MASLD in obese children, highlighting its potential for real-world clinical applications.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"146"},"PeriodicalIF":4.0,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}