Ahmed Algahawi , Inka Harju , Eija Könönen , Kaisu Rantakokko-Jalava , Mervi Gürsoy
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The identification rate did not show a significant difference (<em>P</em> = 0.05) between the two incubation times, except that <em>C. haemolytica</em> needed a longer incubation time to be recognized at the genus level. The reproducibility of spotting between two examiners was ensured by following the manufacturer's instructions. At the species level, formic acid extraction improved the identification of species with limited representation in the database, such as <em>C. haemolytica</em> and <em>C. granulosa</em>. The storage of plates for one week decreased the identification scores. No significant difference (<em>P</em> = 0.39) was observed between the 60 Hz and 120 Hz laser repetition rates for identifying <em>Capnocytophaga</em> species to the genus or species level. In conclusion, the MALDI TOF MS offers a reliable <em>Capnocytophaga</em> identification after following the universal protocol, while the formic acid extraction is restricted to species with a limited number of strains in the database.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":null,"pages":null},"PeriodicalIF":1.7000,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S016770122400023X/pdfft?md5=d309baea60ab954aed5c2116e2589bc3&pid=1-s2.0-S016770122400023X-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Factors affecting the quality and reproducibility of MALDI-TOF MS identification for human Capnocytophaga species\",\"authors\":\"Ahmed Algahawi , Inka Harju , Eija Könönen , Kaisu Rantakokko-Jalava , Mervi Gürsoy\",\"doi\":\"10.1016/j.mimet.2024.106911\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Reproducibility and quality of MALDI-TOF MS spectra are critical in the identification process, however, information on the factors affecting the identification scores are scarce. Here, we studied the influence of various factors during the identification process of human oral <em>Capnocytophaga</em> species. The influence of two incubation times, plate-spotting reproducibility of two examiners, extraction technique, storage period of plates, and different laser repetition rates on the quality of MALDI-TOF MS identification of 34 human <em>Capnocytophaga</em> strains (including <em>C. gingivalis, C. granulosa, C. haemolytica, C. leadbetteri, C. ochracea, C. sputigena,</em> and <em>Capnocytophaga</em> genospecies AHN8471) was examined. The identification rate did not show a significant difference (<em>P</em> = 0.05) between the two incubation times, except that <em>C. haemolytica</em> needed a longer incubation time to be recognized at the genus level. The reproducibility of spotting between two examiners was ensured by following the manufacturer's instructions. At the species level, formic acid extraction improved the identification of species with limited representation in the database, such as <em>C. haemolytica</em> and <em>C. granulosa</em>. The storage of plates for one week decreased the identification scores. No significant difference (<em>P</em> = 0.39) was observed between the 60 Hz and 120 Hz laser repetition rates for identifying <em>Capnocytophaga</em> species to the genus or species level. 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引用次数: 0
摘要
MALDI-TOF MS 图谱的可重复性和质量在鉴定过程中至关重要,但有关影响鉴定分数的因素的信息却很少。在此,我们研究了人口腔嗜帽毛囊虫鉴定过程中各种因素的影响。我们考察了两种培养时间、两名检验员的平板点样重现性、提取技术、平板的储存期以及不同的激光重复率对 34 个人类 Capnocytophaga 菌株(包括 C. gingivalis、C. granulosa、C. haemolytica、C. leadbetteri、C. ochracea、C. sputigena 和 Capnocytophaga genospecies AHN8471)的 MALDI-TOF MS 鉴定质量的影响。两种培养时间的鉴定率没有明显差异(P = 0.05),只是溶血杆菌需要更长的培养时间才能鉴定出其属。两名检测人员按照制造商的说明进行检测,确保了斑点检测的重现性。在种的水平上,甲酸提取提高了对数据库中代表性有限的物种的鉴定,如溶血杆菌和粒细胞溶血杆菌。将平板存放一周会降低鉴定得分。60 Hz 和 120 Hz 激光重复率对 Capnocytophaga 属或种的鉴定无明显差异(P = 0.39)。总之,在遵循通用方案后,MALDI TOF MS 可提供可靠的 Capnocytophaga 鉴定,而甲酸提取仅限于数据库中菌株数量有限的物种。
Factors affecting the quality and reproducibility of MALDI-TOF MS identification for human Capnocytophaga species
Reproducibility and quality of MALDI-TOF MS spectra are critical in the identification process, however, information on the factors affecting the identification scores are scarce. Here, we studied the influence of various factors during the identification process of human oral Capnocytophaga species. The influence of two incubation times, plate-spotting reproducibility of two examiners, extraction technique, storage period of plates, and different laser repetition rates on the quality of MALDI-TOF MS identification of 34 human Capnocytophaga strains (including C. gingivalis, C. granulosa, C. haemolytica, C. leadbetteri, C. ochracea, C. sputigena, and Capnocytophaga genospecies AHN8471) was examined. The identification rate did not show a significant difference (P = 0.05) between the two incubation times, except that C. haemolytica needed a longer incubation time to be recognized at the genus level. The reproducibility of spotting between two examiners was ensured by following the manufacturer's instructions. At the species level, formic acid extraction improved the identification of species with limited representation in the database, such as C. haemolytica and C. granulosa. The storage of plates for one week decreased the identification scores. No significant difference (P = 0.39) was observed between the 60 Hz and 120 Hz laser repetition rates for identifying Capnocytophaga species to the genus or species level. In conclusion, the MALDI TOF MS offers a reliable Capnocytophaga identification after following the universal protocol, while the formic acid extraction is restricted to species with a limited number of strains in the database.
期刊介绍:
The Journal of Microbiological Methods publishes scholarly and original articles, notes and review articles. These articles must include novel and/or state-of-the-art methods, or significant improvements to existing methods. Novel and innovative applications of current methods that are validated and useful will also be published. JMM strives for scholarship, innovation and excellence. This demands scientific rigour, the best available methods and technologies, correctly replicated experiments/tests, the inclusion of proper controls, calibrations, and the correct statistical analysis. The presentation of the data must support the interpretation of the method/approach.
All aspects of microbiology are covered, except virology. These include agricultural microbiology, applied and environmental microbiology, bioassays, bioinformatics, biotechnology, biochemical microbiology, clinical microbiology, diagnostics, food monitoring and quality control microbiology, microbial genetics and genomics, geomicrobiology, microbiome methods regardless of habitat, high through-put sequencing methods and analysis, microbial pathogenesis and host responses, metabolomics, metagenomics, metaproteomics, microbial ecology and diversity, microbial physiology, microbial ultra-structure, microscopic and imaging methods, molecular microbiology, mycology, novel mathematical microbiology and modelling, parasitology, plant-microbe interactions, protein markers/profiles, proteomics, pyrosequencing, public health microbiology, radioisotopes applied to microbiology, robotics applied to microbiological methods,rumen microbiology, microbiological methods for space missions and extreme environments, sampling methods and samplers, soil and sediment microbiology, transcriptomics, veterinary microbiology, sero-diagnostics and typing/identification.