Journal of medical microbiology最新文献

{"title":"Towards an update on the antimicrobial use in Adult Care Units in Brazil: insights from multi-hospital prevalence study.","authors":"Luiz Gustavo Machado, Daiane Silva Resende, Paola Amaral de Campos, Melina Lorraine Ferreira, Iara Rossi, Iolanda Alves Braga, Caio Augusto Martins Aires, Maria Tereza Freitas Tenório, Lícia Ludendorff Queiroz, Vitelhe Ferreira de Almeida, Paulo Pinto Gontijo-Filho, Rosineide Marques Ribas","doi":"10.1099/jmm.0.001908","DOIUrl":"10.1099/jmm.0.001908","url":null,"abstract":"<p><p><b>Introduction.</b> Efforts to understand the burden of antibiotic use in low- and middle-income countries such as Brazil are essential for developing strategies that are effective and appropriate in the context of endemic multidrug-resistant organisms.<b>Aim.</b> This study aims to determine antimicrobial-prescribing practices among patients hospitalized in intensive care units (ICUs) for adults in Brazil.<b>Methodology.</b> A 1-day point prevalence multicentre survey was conducted in 58 adult ICUs across the five regions of Brazil. The institutions were categorized according to their type and size. Detailed antimicrobial prescription data were prospectively provided to all patients hospitalized on the day of data collection.<b>Results.</b> A total of 620 patients were included in the study, of whom 63.9% were receiving at least one antimicrobial. Of these, 34.6% were treated for an infection, but only 39.9% of the cases were based on microbiological criteria. Empirical treatment was applied to 72.3% of the patients. Significant differences in antibiotic usage were observed across the different hospitals included in the study. Overall, treatment was most commonly directed towards pneumonia (51.8%) and bloodstream infections (29.6%). Glycopeptides (19.4%) and carbapenems (18.5%) were the most prescribed in teaching hospitals, while in non-teaching hospitals, carbapenems (17.8%) and broad-spectrum cephalosporins (16.8%) were most frequently used.<b>Conclusion.</b> Our study reveals alarming data on antibiotic use in adult ICUs in Brazil, with high frequencies of severe healthcare-associated infections acquired in these units, where patients are frequently subjected to empirical treatment.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396390","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":"Nicotine promotes pathogenic bacterial growth and biofilm formation in peri-implant.","authors":"Rong Hu, Huifen Qian, Xiangyun Wang, Bei Peng, Dahai Huang","doi":"10.1099/jmm.0.001897","DOIUrl":"10.1099/jmm.0.001897","url":null,"abstract":"<p><p><b>Introduction.</b> Peri-implantitis is a plaque-associated disease that leads to implant loss and arises from bacterial biofilms on the surface of the implant. Smoking is a risk factor for peri-implantitis and impedes treatment effectiveness. Additionally, aryl hydrocarbon receptor (AHR), IL-6, and IL-22 levels are related to peri-implantitis.<b>Aim.</b> We aimed to investigate the effects of nicotine on inflammatory response, bacterial growth and biofilm formation.<b>Hypothesis/Gap Statement.</b> We hypothesized that nicotine promoted pathogenic bacterial growth and biofilm formation, thereby aggravating inflammation.<b>Methodology.</b> The expression of AHR, IL-6 and IL-22 was measured in peri-implant sulci fluid using quantitative PCR and Western blot analyses. The cementum was incubated with bacterial suspension including <i>Porphyromonas gingivalis</i>, <i>Streptococcus sanguinis</i> and <i>Fusobacterium nucleatum</i> and treated with 100, 200, 250 and 300 µg ml^-1 nicotine, and then, the absorbance and number of colony-forming units were detected. Biofilm formation was evaluated using the tissue culture plate method and safranin O staining. Carbohydrates and proteins were measured by the phenol-sulfuric acid method and the bicinchoninic acid method, respectively.<b>Results.</b> The results indicated that smoking increased the levels of AHR, IL-6 and IL-22. Functionally, nicotine promoted the growth of <i>P. gingivalis</i>, <i>S. sanguinis</i> and <i>F. nucleatum</i>. Additionally, it promoted the biofilm formation of these bacteria and increased the contents of carbohydrates and proteins.<b>Conclusion.</b> Nicotine promoted bacterial growth and biofilm build-up, suggesting that smoking may aggravate the progression of peri-implantitis.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142368060","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 epidemiology and resistant genes of <i>Acinetobacter baumannii</i> clinical strains in Vietnamese hospitals.","authors":"Vu Nhi Ha, Hoang Tran Huy, Trung Nguyen Đac, Phuong Anh Nguyen, Le Duy Cuong","doi":"10.1099/jmm.0.001922","DOIUrl":"10.1099/jmm.0.001922","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Acinetobacter baumannii</i> is a common cause of multidrug-resistant (MDR) nosocomial infections worldwide, including Vietnam.<b>Hypothesis.</b> Analysis of crucial genetic factors may link to epidemiological characteristics and antibiotic resistance of <i>A. baumannii</i> clinical strains in Vietnamese hospitals.<b>Methodology.</b> Fifty-one <i>A</i>. <i>baumannii</i> clinical strains from six different tertiary hospitals in Vietnam were analysed using whole genome sequencing (WGS), between 2017 and 2019.<b>Results.</b> Eleven sequence types (STs) were identified, including four STs reported for the first time in Vietnam based on the PubMLST database and three new STs not previously documented. ST1336, ST1260 and ST575 were found exclusively in Vietnam. These STs were widely distributed in all hospitals in Vietnam, with ST2 and ST571 being the most dominant. Resistant rates to eight antibiotics, belonging to four antibiotic groups, were very high (72.5-94.1 %) with high MIC values, while resistance to colistin was 29.4%. Fifty-one isolates were identified as MDR, with 100% (51/51) isolates carrying antimicrobial-resistant (AMR) genes, and 52 antibiotic-resistant genes were detected among these strains, including β-lactam (22 genes), chloramphenicol (5 genes), lincosamide (2 genes), aminoglycoside (11 genes), rifampicin (1 gene), quinolone (2 genes), sulfonamide and trimethoprim (4 genes) and tetracycline (5 genes) resistance. The most commonly found mobile structures carried partial or complete transposons: ISaba24/ISEc29/ISEc35 contains a series of antibiotic-resistant genes.<b>Conclusion.</b> The WGS results of the 51 strains of <i>A. baumannii</i> provided important information regarding the distribution of STs and associated antibiotic-resistant genes among <i>A. baumannii</i> strains.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142549785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of GeneXpert MTB/Rif Ultra assay performance on formalin-fixed paraffin-embedded tissues for <i>Mycobacterium tuberculosis</i> detection.","authors":"Calvin Ka-Fung Lo, Dale Purych, Inna Sekirov, Jaswinder Khattra, Trevor J Hird, Shazia Masud","doi":"10.1099/jmm.0.001918","DOIUrl":"10.1099/jmm.0.001918","url":null,"abstract":"<p><p>We evaluated the Xpert MTB/Rif Ultra assay performance for <i>Mycobacterium tuberculosis</i> (MTB) detection in formalin-fixed paraffin-embedded tissue (FFPET) compared to mycobacterial culture or laboratory-developed MTB PCR test (LDT). FFPET samples with histological features suggestive of tuberculosis from 2018 to 2023 were selected. Five hundred microlitres of tissue lysis buffer was added to FFPET scrolls and incubated at 75 °C for 5 min. After adding 50 µl of proteinase K and overnight incubation at 56 °C, sample aliquots were processed as per the manufacturer's instructions. MTB culture or LDT assay results were used as a reference for sensitivity and specificity calculations. Of 51 eligible FFPET, 32 were positive for MTB either by culture or LDT PCR on FFPET. Xpert MTB/Rif Ultra detected MTB in 23/32 positive specimens [71.9%, 95% confidence interval (CI) 54.6-84.4%]. Of nine discordant specimens, seven were MTB positive by culture and two were identified by LDT MTB PCR only, as no specimen was submitted for MTB culture. Of 19 negative samples, 100% specificity (95% CI 83.2-100.0%) was attained via Xpert MTB/Rif Ultra. Implementation of Xpert MTB/Rif Ultra on FFPET within clinical laboratories is promising, given its improved turnaround time compared to MTB culture and ability to detect MTB in cases where no tissue is available for culture.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11495408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic characterization of <i>Haemophilus influenzae</i> harbouring an exogenous resistance gene.","authors":"Emi Tanaka, Takeaki Wajima, Sonoe Hirano, Shoji Seyama, Hidemasa Nakaminami, Kei-Ichi Uchiya","doi":"10.1099/jmm.0.001904","DOIUrl":"10.1099/jmm.0.001904","url":null,"abstract":"<p><p><b>Introduction.</b> Reports of β-lactamase-producing <i>Haemophilus influenzae</i> are increasing worldwide.<b>Aim</b>. This study aimed to elucidate the molecular characteristics and evolution of β-lactamase-producing <i>H. influenzae</i>.<b>Methodology.</b> A total of 159 clinical isolates were characterized using multi-locus sequence typing. Antimicrobial resistance genes and integrative and conjugative element (ICE) types were identified through PCR and DNA sequencing. The genetic structure of ICE was further investigated using whole-genome sequencing.<b>Results.</b> Out of 159 clinical isolates, 20.8% (<i>n</i>=33) were β-lactamase producers. Thirteen sequence types (STs) were identified. ST 103, 155, 165 and 388 have been identified in previous studies, suggesting that strains with these STs tend to acquire the β-lactamase gene <i>bla</i> _TEM-1. Among β-lactamase producers, 66.7% (<i>n</i>=22) of <i>bla</i> _TEM-1 were located on ICE. The ICEs could be classified into two groups based on their sequence (types I and II). Among these strains, 2017-Y3 harboured a macrolide resistance gene, <i>mef (A/E)</i>, in ICE. A comparative analysis of the ICE region of this strain and those from other countries suggested that each isolate was derived from ICE type I or II. These regions, including <i>mef (A/E</i>), were similar to those of Tn<i>6822</i>, which is commonly found in <i>Streptococcus</i>.<b>Conclusions.</b> This study revealed several STs associated with the acquisition of β-lactamase genes on ICEs. Additionally, ICE evolution involved the acquisition of exogenous genes. The accumulation of resistance genes in ICE raises concerns regarding the emergence of multidrug-resistant <i>H. influenzae</i>.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142368059","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":"Effect of simethicone on the bactericidal efficacy of a high-level disinfectant.","authors":"Gregory G Anderson, Katharine Segars, Anastacia M Sanchez, Jon W Weeks, Shanil P Haugen, Ruchi Pandey","doi":"10.1099/jmm.0.001902","DOIUrl":"https://doi.org/10.1099/jmm.0.001902","url":null,"abstract":"<p><p><b>Introduction.</b> Simethicone is an over-the-counter product that is frequently used by clinicians during endoscopic procedures to reduce foaming and improve visualization. Published studies have found simethicone residue on endoscopes after cleaning and disinfecting the devices as per the manufacturer's instructions. Some literature suggests that simethicone residue may reduce disinfection efficacy and increase the risk of patient infections.<b>Gap Statement.</b> However, there appears to be a lack of direct evidence in the literature to either disprove this or correlate simethicone presence with an increased microbial risk.<b>Aim</b>: Research was conducted to evaluate the <i>in vitro</i> impact of simethicone on disinfection efficacy.<b>Methodology.</b> Bacteria were grown in a microtitre plate assay in the presence of a range of simethicone concentrations and then treated with a disinfectant. Bacterial growth was assessed by spotting each microtitre well onto an agar plate.<b>Results.</b> The results demonstrated that, under the conditions tested, simethicone did not reduce the efficacy of Cidex ortho-phthalaldehyde disinfectant, which demonstrated at least a 6-log unit reduction in bacterial viability. Additional experiments showed that direct exposure to 66 mg ml^-1 of simethicone reduced bacterial viability.<b>Conclusion.</b> These results indicate that simethicone may not reduce the bactericidal efficacy of disinfectant during reprocessing, under certain conditions.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373942","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":"Impact of periodontal therapy on oral bacterial composition in individuals diagnosed with advanced periodontal disease.","authors":"Huixia Chen, Liqin Zhao, Yan Liang, Hui Xie, Siyu Chen, Lin Wang, Xiao Han","doi":"10.1099/jmm.0.001913","DOIUrl":"https://doi.org/10.1099/jmm.0.001913","url":null,"abstract":"<p><p><b>Introduction.</b> Negative changes in the microbial composition have been extensively studied in individuals with periodontal disease.<b>Gap Statement.</b> The changes in the oral microbiota after treating this disease are still unknown.<b>Aim.</b> We sought to elucidate the distinctive traits of salivary microbiota in individuals displaying healthy gums and those with severe periodontitis (SP) and examine the influence of periodontal therapy.<b>Methodology.</b> Periodontal pocket depths were examined to determine disease severity. The presence and quantity of oral <i>Helicobacter pylori</i> (associated with periodontal disease) were determined. Sequencing of 16S ribosomal DNA and bioinformatic analyses were performed to assess oral bacterial compositions in patients.<b>Results.</b> Sequencing analysis of 16S ribosomal DNA revealed a significant reduction in the abundance of operational taxonomic units (OTUs) and Chao1 and Abundance coverage-based estimator(ACE) indices in the oral cavities of individuals with SP compared to those of the healthy controls. However, these parameters showed significant recovery after appropriate treatment severe periodontitis after treatment (TSP). Additionally, the levels of harmful Bacillales and Spirochetes significantly increased, whereas the presence of beneficial <i>Euryarchaeota</i> significantly decreased in the SP group. The TSP group exhibited considerably augmented abundances of Burkholderiaceae and Veillonella, while noteworthy reductions in the pathogenic microbiota (Clostridia, Fusobacteria and Spirochaetes) were noticed compared to those of the SP group. Functionally, these modified OTUs were extensively implicated in 41 metabolic pathways.<b>Conclusion.</b> Our study demonstrates that nonsurgical periodontal therapy can effectively reduce the diversity of the oral microbiota, thereby potentially enhancing the treatment efficacy in patients with periodontal disease.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484391","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":"Phenotypic diversity of type III secretion system activity in enteropathogenic <i>Escherichia coli</i> clinical isolates.","authors":"Carmen A Contreras, Tracy H Hazen, Carmen Guadarrama, Ramón Cervantes-Rivera, Theresa J Ochoa, Pablo Vinuesa, David A Rasko, Jose L Puente","doi":"10.1099/jmm.0.001907","DOIUrl":"10.1099/jmm.0.001907","url":null,"abstract":"<p><p><b>Introduction.</b> Enteropathogenic <i>Escherichia coli</i> (EPEC) strains pose a significant threat as a leading cause of severe childhood diarrhoea in developing nations. EPEC pathogenicity relies on the type III secretion system (T3SS) encoded by the locus of enterocyte effacement (LEE), facilitating the secretion and translocation of bacterial effector proteins.<b>Gap Statement.</b> While the regulatory roles of PerC (plasmid-encoded regulator) and GrlA (global regulator of LEE-activator) in <i>ler</i> expression and LEE gene activation are well-documented in the EPEC prototype strain E2348/69, understanding the variability in LEE gene expression control mechanisms among clinical EPEC isolates remains an area requiring further investigation.<b>Aim.</b> This study aims to explore the diversity in LEE gene expression control mechanisms among clinical EPEC isolates through a comparative analysis of secretion profiles under defined growth conditions favouring either PerC- or GrlA-mediated activation of LEE expression.<b>Methodology.</b> We compared T3SS-dependent secretion patterns and promoter expression in both typical EPEC (tEPEC) and atypical EPEC (aEPEC) clinical isolates under growth conditions favouring either PerC- or GrlA-mediated activation of LEE expression. Additionally, we conducted promoter reporter activity assays, quantitative real-time PCR and Western blot experiments to assess gene expression activity.<b>Results.</b> Significant differences in T3SS-dependent secretion were observed among tEPEC and aEPEC strains, independent of LEE sequence variations or T3SS gene functionality. Notably, a clinical tEPEC isolate exhibited increased secretion levels under repressive growth conditions and in the absence of both PerC and GrlA, implicating an alternative mechanism in the activation of Ler (LEE-encoded regulator) expression.<b>Conclusion.</b> Our findings indicate that uncharacterized LEE regulatory mechanisms contribute to phenotypic diversity among clinical EPEC isolates, though their impact on clinical outcomes remains unknown. This challenges the conventional understanding based on reference strains and highlights the need to investigate beyond established models to comprehensively elucidate EPEC pathogenesis.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11493143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predictors of the severity of the course of COVID-19: demographic factors, clinical signs and laboratory markers.","authors":"Klaudia Bartoszewicz, Mateusz Bartoszewicz, Samuel Stróż, Anna Stasiak-Barmuta, Piotr Kosiorek","doi":"10.1099/jmm.0.001911","DOIUrl":"10.1099/jmm.0.001911","url":null,"abstract":"<p><p><b>Introduction.</b> The Coronavirus Disease 2019 (COVID-19) pandemic has had a significant impact on global healthcare, with high mortality and severe complications remaining a major concern. Understanding the predictors of COVID-19 severity may improve patient management and outcomes. While considerable research has focused on the pathogenesis of the virus and vaccine development, the identification of reliable demographic, clinical and laboratory predictors of severe disease remains critical.<b>Hypothesis.</b> Specific demographic factors, clinical signs and laboratory markers can reliably predict the severity of COVID-19. A comprehensive analysis integrating these predictors could provide a more accurate prognosis and guide timely interventions.<b>Aim.</b> The aim of this study is to identify and evaluate the demographic, clinical and laboratory factors that can serve as reliable predictors of severe COVID-19, thereby aiding in the prediction and prevention of adverse outcomes.<b>Methodology.</b> The methods of analysis, synthesis, generalization and descriptive statistics were used to achieve this objective.<b>Results.</b> The analysis showed that demographic factors such as age over 60 and male sex are significant predictors of severe COVID-19. Clinical predictors include respiratory symptoms, especially dyspnoea, and comorbidities such as hypertension, coronary artery disease, chronic obstructive pulmonary disease, respiratory failure, asthma, diabetes mellitus and obesity. Laboratory markers with high prognostic value include elevated levels of C-reactive protein, interleukin-6, ferritin, neutrophil/lymphocyte ratio, d-dimer, aspartate aminotransferase enzyme and decreased lymphocyte count.<b>Conclusion.</b> The study concludes that a holistic approach incorporating demographic, clinical and laboratory data is essential to accurately predict the severity of COVID-19. This integrated model may significantly improve patient prognosis by facilitating early identification of high-risk individuals and allowing timely, targeted interventions. The results highlight the importance of comprehensive patient assessment in managing and mitigating the impact of COVID-19.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396388","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":"Robust prediction of colorectal cancer via gut microbiome 16S rRNA sequencing data.","authors":"Annamaria Porreca, Eliana Ibrahimi, Fabrizio Maturo, Laura Judith Marcos Zambrano, Melisa Meto, Marta B Lopes","doi":"10.1099/jmm.0.001903","DOIUrl":"https://doi.org/10.1099/jmm.0.001903","url":null,"abstract":"<p><p><b>Introduction.</b> The study addresses the challenge of utilizing human gut microbiome data for the early detection of colorectal cancer (CRC). The research emphasizes the potential of using machine learning techniques to analyze complex microbiome datasets, providing a non-invasive approach to identifying CRC-related microbial markers.<b>Hypothesis/Gap Statement.</b> The primary hypothesis is that a robust machine learning-based analysis of 16S rRNA microbiome data can identify specific microbial features that serve as effective biomarkers for CRC detection, overcoming the limitations of classical statistical models in high-dimensional settings.<b>Aim.</b> The primary objective of this study is to explore and validate the potential of the human microbiome, specifically in the colon, as a valuable source of biomarkers for colorectal cancer (CRC) detection and progression. The focus is on developing a classifier that effectively predicts the presence of CRC and normal samples based on the analysis of three previously published faecal 16S rRNA sequencing datasets.<b>Methodology.</b> To achieve the aim, various machine learning techniques are employed, including random forest (RF), recursive feature elimination (RFE) and a robust correlation-based technique known as the fuzzy forest (FF). The study utilizes these methods to analyse the three datasets, comparing their performance in predicting CRC and normal samples. The emphasis is on identifying the most relevant microbial features (taxa) associated with CRC development via partial dependence plots, i.e. a machine learning tool focused on explainability, visualizing how a feature influences the predicted outcome.<b>Results.</b> The analysis of the three faecal 16S rRNA sequencing datasets reveals the consistent and superior predictive performance of the FF compared to the RF and RFE. Notably, FF proves effective in addressing the correlation problem when assessing the importance of microbial taxa in explaining the development of CRC. The results highlight the potential of the human microbiome as a non-invasive means to detect CRC and underscore the significance of employing FF for improved predictive accuracy.<b>Conclusion.</b> In conclusion, this study underscores the limitations of classical statistical techniques in handling high-dimensional information such as human microbiome data. The research demonstrates the potential of the human microbiome, specifically in the colon, as a valuable source of biomarkers for CRC detection. Applying machine learning techniques, particularly the FF, is a promising approach for building a classifier to predict CRC and normal samples. The findings advocate for integrating FF to overcome the challenges associated with correlation when identifying crucial microbial features linked to CRC development.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396389","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}