Fernando Cobo, Virginia Pérez-Carrasco, Lina Martín-Hita, José Antonio García-Salcedo, José María Navarro-Marí
{"title":"MALDI-TOF MS和16S rRNA基因测序用于鉴定临床相关厌氧菌的比较评估:差异结果的关键评估。","authors":"Fernando Cobo, Virginia Pérez-Carrasco, Lina Martín-Hita, José Antonio García-Salcedo, José María Navarro-Marí","doi":"10.1016/j.anaerobe.2023.102754","DOIUrl":null,"url":null,"abstract":"<div><h3>Objectives</h3><p>The main study objective was to evaluate the correlation between matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing results for the identification of anaerobes.</p></div><div><h3>Methods</h3><p>A retrospective study was conducted of all anaerobic bacteria isolated from clinically significant specimens. MALDI-TOF (Bruker Byotyper) and 16S rRNA gene sequencing were performed in all strains. Identifications were considered correct when the concordance with gene sequencing was ≥99%.</p></div><div><h3>Results</h3><p>The study included 364 isolates of anaerobic bacteria: 201 (55.2%) Gram-negative and 163 (44.8%) Gram-positive, mostly belonging to the genus <em>Bacteroides</em>. Isolates were largely obtained from blood cultures (128/35.4%) and intra-abdominal samples (116/32.1%). Overall, 87.3% of isolates were identified at species level using the version 9 database (89.5% of Gram-negative and 84.6% of Gram-positive anaerobic bacteria). All isolates belonging to the species <em>B. fragilis sensu stricto</em> were correctly identified by MALDI-TOF MS, but five cases of <em>Phocaeicola (Bacteroides) dorei</em> were misidentified as <em>Phocaeicola</em> (<em>Bacteroides) vulgatus;</em> all <em>Prevotella</em> isolates were correctly identified at the genus level, and most were correctly identified at the species level. Among Gram-positive anaerobes, 12 <em>Anaerococcus</em> species were not identified by MALDI-TOF MS, while six cases identified as <em>Peptoniphilus indolicus</em> were found to belong to other genera/species.</p></div><div><h3>Conclusions</h3><p>MALDI-TOF is a reliable technique for identifying most anaerobic bacteria, although the database needs frequent updating to identify rare, infrequent, and newly discovered species.</p></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"82 ","pages":"Article 102754"},"PeriodicalIF":2.5000,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"2","resultStr":"{\"title\":\"Comparative evaluation of MALDI-TOF MS and 16S rRNA gene sequencing for the identification of clinically relevant anaerobic bacteria: critical evaluation of discrepant results\",\"authors\":\"Fernando Cobo, Virginia Pérez-Carrasco, Lina Martín-Hita, José Antonio García-Salcedo, José María Navarro-Marí\",\"doi\":\"10.1016/j.anaerobe.2023.102754\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Objectives</h3><p>The main study objective was to evaluate the correlation between matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing results for the identification of anaerobes.</p></div><div><h3>Methods</h3><p>A retrospective study was conducted of all anaerobic bacteria isolated from clinically significant specimens. MALDI-TOF (Bruker Byotyper) and 16S rRNA gene sequencing were performed in all strains. Identifications were considered correct when the concordance with gene sequencing was ≥99%.</p></div><div><h3>Results</h3><p>The study included 364 isolates of anaerobic bacteria: 201 (55.2%) Gram-negative and 163 (44.8%) Gram-positive, mostly belonging to the genus <em>Bacteroides</em>. Isolates were largely obtained from blood cultures (128/35.4%) and intra-abdominal samples (116/32.1%). Overall, 87.3% of isolates were identified at species level using the version 9 database (89.5% of Gram-negative and 84.6% of Gram-positive anaerobic bacteria). All isolates belonging to the species <em>B. fragilis sensu stricto</em> were correctly identified by MALDI-TOF MS, but five cases of <em>Phocaeicola (Bacteroides) dorei</em> were misidentified as <em>Phocaeicola</em> (<em>Bacteroides) vulgatus;</em> all <em>Prevotella</em> isolates were correctly identified at the genus level, and most were correctly identified at the species level. Among Gram-positive anaerobes, 12 <em>Anaerococcus</em> species were not identified by MALDI-TOF MS, while six cases identified as <em>Peptoniphilus indolicus</em> were found to belong to other genera/species.</p></div><div><h3>Conclusions</h3><p>MALDI-TOF is a reliable technique for identifying most anaerobic bacteria, although the database needs frequent updating to identify rare, infrequent, and newly discovered species.</p></div>\",\"PeriodicalId\":8050,\"journal\":{\"name\":\"Anaerobe\",\"volume\":\"82 \",\"pages\":\"Article 102754\"},\"PeriodicalIF\":2.5000,\"publicationDate\":\"2023-08-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"2\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Anaerobe\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S107599642300063X\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Anaerobe","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S107599642300063X","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
Comparative evaluation of MALDI-TOF MS and 16S rRNA gene sequencing for the identification of clinically relevant anaerobic bacteria: critical evaluation of discrepant results
Objectives
The main study objective was to evaluate the correlation between matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing results for the identification of anaerobes.
Methods
A retrospective study was conducted of all anaerobic bacteria isolated from clinically significant specimens. MALDI-TOF (Bruker Byotyper) and 16S rRNA gene sequencing were performed in all strains. Identifications were considered correct when the concordance with gene sequencing was ≥99%.
Results
The study included 364 isolates of anaerobic bacteria: 201 (55.2%) Gram-negative and 163 (44.8%) Gram-positive, mostly belonging to the genus Bacteroides. Isolates were largely obtained from blood cultures (128/35.4%) and intra-abdominal samples (116/32.1%). Overall, 87.3% of isolates were identified at species level using the version 9 database (89.5% of Gram-negative and 84.6% of Gram-positive anaerobic bacteria). All isolates belonging to the species B. fragilis sensu stricto were correctly identified by MALDI-TOF MS, but five cases of Phocaeicola (Bacteroides) dorei were misidentified as Phocaeicola (Bacteroides) vulgatus; all Prevotella isolates were correctly identified at the genus level, and most were correctly identified at the species level. Among Gram-positive anaerobes, 12 Anaerococcus species were not identified by MALDI-TOF MS, while six cases identified as Peptoniphilus indolicus were found to belong to other genera/species.
Conclusions
MALDI-TOF is a reliable technique for identifying most anaerobic bacteria, although the database needs frequent updating to identify rare, infrequent, and newly discovered species.
期刊介绍:
Anaerobe is essential reading for those who wish to remain at the forefront of discoveries relating to life processes of strictly anaerobes. The journal is multi-disciplinary, and provides a unique forum for those investigating anaerobic organisms that cause infections in humans and animals, as well as anaerobes that play roles in microbiomes or environmental processes.
Anaerobe publishes reviews, mini reviews, original research articles, notes and case reports. Relevant topics fall into the broad categories of anaerobes in human and animal diseases, anaerobes in the microbiome, anaerobes in the environment, diagnosis of anaerobes in clinical microbiology laboratories, molecular biology, genetics, pathogenesis, toxins and antibiotic susceptibility of anaerobic bacteria.