Journal of microbiological methods最新文献

{"title":"Concordance in molecular methods for detection of antimicrobial resistance: A cross sectional study of the influent to a wastewater plant","authors":"Kezia Drane ,&nbsp;Roger Huerlimann ,&nbsp;Rhondda Jones ,&nbsp;Anna Whelan ,&nbsp;Madoc Sheehan ,&nbsp;Ellen Ariel ,&nbsp;Robert Kinobe","doi":"10.1016/j.mimet.2024.107069","DOIUrl":"10.1016/j.mimet.2024.107069","url":null,"abstract":"<div><div>Methods that are used to characterise microbiomes and antimicrobial resistance genes (ARGs) in wastewater are not standardised. We used shotgun metagenomic sequencing (SM-Seq), RNA sequencing (RNA-seq) and targeted qPCR to compare microbial and ARG diversity in the influent to a municipal wastewater treatment plant in Australia. ARGs were annotated with CARD-RGI and MEGARes databases, and bacterial diversity was characterised by 16S rRNA gene sequencing and SM-Seq, with species annotation in SILVA/GreenGenes databases or Kraken2 and the NCBI nucleotide database respectively. CARD and MEGARes identified evenly distributed ARG profiles but MEGARes detected a richer array of ARGs (richness = 475 vs 320). Qualitatively, ARGs encoding for aminoglycoside, macrolide-lincosamide-streptogramin and multidrug resistance were the most abundant in all examined databases. RNA-seq detected only 32 % of ARGs identified by SM-Seq, but there was concordance in the qualitative identification of aminoglycoside, macrolide-lincosamide, phenicol, sulfonamide and multidrug resistance by SM-Seq and RNA-seq. qPCR confirmed the detection of some ARGs, including <em>OXA</em>, <em>VEB</em> and <em>EREB</em>, that were identified by SM-Seq and RNA-seq in the influent. For bacteria, SM-Seq or 16S rRNA gene sequencing were equally effective in population profiling at phyla or class level. However, SM-Seq identified a significantly higher species richness (richness = 15,000 vs 3750). These results demonstrate that SM-Seq with gene annotation in CARD and MEGARes are equally sufficient for surveillance of antimicrobial resistance in wastewater. For more precise ARG identification and quantification however, MEGARes presented a better resolution. The functionality of detected ARGs was not confirmed, but general agreement on the putative phenotypic resistance profile by antimicrobial class was observed between RNA-Seq and SM-Seq.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"228 ","pages":"Article 107069"},"PeriodicalIF":1.7,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Laser Speckle Image analysis for identifying the minimum lethal concentration of ampicillin in Escherichia coli liquid cultures","authors":"Kiran Philip Isaac ,&nbsp;Priya Krishnamurthy ,&nbsp;Sujatha Narayanan Unni ,&nbsp;Sudha Narayani Rao ,&nbsp;Krupakar Parthasarathy","doi":"10.1016/j.mimet.2024.107068","DOIUrl":"10.1016/j.mimet.2024.107068","url":null,"abstract":"<div><div>Understanding a pathogen's sensitivity to antimicrobial drugs through Minimum Lethal Concentration (MLC) is crucial for effective treatment planning for bactericidal drugs. In this paper, we propose a novel approach using Laser Speckle Imaging (LSI) to determine the MLC of <em>Escherichia coli</em> (<em>E. coli</em>), a common pathogenic bacterial species. LSI enables the capture and analysis of the dynamic changes in speckle patterns caused by alterations in optical scattering and shape alterations of bacterial cells as a response to antibiotic treatments through a label-free approach. The observed speckle pattern changes are correlated with the gold standard method to determine the MLC, representing the lowest concentration at which <em>E. coli</em> is lethally affected. The results demonstrate the potential of LSI as a reliable and rapid method for determining the MLC of <em>E. coli</em>. This method has much potential for antimicrobial research since it provides a quick, non-destructive evaluation of bacterial responses to various bactericidal antibiotic doses without requiring labor-intensive processes like pour plate tests to calculate the MLC.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"227 ","pages":"Article 107068"},"PeriodicalIF":1.7,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142622188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a MALDI-TOF MS model for differentiating haemorrhagic septicaemia-causing strains of Pasteurella multocida from other capsular groups","authors":"Kelli Maddock ,&nbsp;Brianna L.S. Stenger ,&nbsp;Jill C. Roberts ,&nbsp;Emily L. Wynn ,&nbsp;Michael L. Clawson ,&nbsp;John Dustin Loy","doi":"10.1016/j.mimet.2024.107067","DOIUrl":"10.1016/j.mimet.2024.107067","url":null,"abstract":"<div><div><em>Pasteurella multocida</em> capsular types A, D, and F cause disease in many animal hosts, including bovine respiratory disease in cattle, which is one of the most globally significant animal diseases. Additionally, <em>P. multocida</em> capsular types B and E cause haemorrhagic septicaemia, a devastating disease primarily of cattle, water buffalo, and bison that develops rapidly with high mortality. Haemorrhagic septicaemia mostly occurs in developing countries and has potential to emerge elsewhere in the world. The diagnosis of haemorrhagic septicaemia currently requires recognition of compatible gross or histologic lesions and serotyping or molecular characterization of strains. In this study, we performed genomic characterization of 84 <em>P. multocida</em> strains, which were then used to develop and validate a matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) biomarker-based method for differentiating non-haemorrhagic septicaemia strains of <em>P. multocida</em> from haemorrhagic septicaemia-causing strains. Haemorrhagic septicaemia strain types B:2,5, E:2,5, and B:3,4 were used to maximize diversity. Three automated classification models were generated and then used to develop an assisted model, which utilized two peaks (6419 and 7729 <em>m/z</em>) to accurately differentiate non-haemorrhagic septicaemia-causing strains from haemorrhagic septicaemia-causing strains of <em>P. multocida.</em> The assisted model performed with 98.2 % accuracy for non-haemorrhagic septicaemia strains, 100 % accuracy for classic B:2,5 and E:2,5 strains, and 84.4 % accuracy for combined haemorrhagic septicaemia-causing strains (B:2,5, E:2,5, and B:3,4) with an overall accuracy of 96.9 %. Our results suggest that MALDI-TOF MS may be used to routinely screen <em>P. multocida</em> isolated from diagnostic cases for initial identification of haemorrhagic septicaemia-causing strains, and to determine whether additional characterizations are warranted.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"227 ","pages":"Article 107067"},"PeriodicalIF":1.7,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR: New promising biotechnological tool in wastewater treatment","authors":"L.S. Mamatha Bhanu ,&nbsp;Sampriti Kataki ,&nbsp;Soumya Chatterjee","doi":"10.1016/j.mimet.2024.107066","DOIUrl":"10.1016/j.mimet.2024.107066","url":null,"abstract":"<div><div>The increasing demand for water resources with increase in population has sparked interest in reusing produced water, especially in water-scarce regions. The clustered regularly interspaced short palindromic repeats (CRISPR) technology is an emerging genome editing tool that has the potential to trigger significant impact with broad application scope in wastewater treatment. We provide a comprehensive overview of the scope of CRISPR-Cas based tool for treating wastewater that may bring new scope in wastewater management in future in controlling harmful contaminants and pathogens. As an advanced versatile genome engineering tool, focusing on particular genes and enzymes that are accountable for pathogen identification, regulation of antibiotic/antimicrobial resistance, and enhancing processes for wastewater bioremediation constitute the primary focal points of research associated with this technology. The technology is highly recommended for targeted mutations to incorporate desirable microalgal characteristics and the development of strains capable of withstanding various wastewater stresses. However, concerns about gene leakage from strains with modified genome and off target mutations should be considered during field application. A comprehensive interdisciplinary approach involving various fields and an intense research focus concerning delivery systems, target genes, detection, environmental conditions, and monitoring at both lab and ground level should be considered to ensure its successful application in sustainable and safe wastewater treatment.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"227 ","pages":"Article 107066"},"PeriodicalIF":1.7,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extraction of high-quality metagenomic DNA from the lichens Flavoparmelia caperata and Peltigera membranacea","authors":"Kalea Gregoris,&nbsp;Welkin H. Pope","doi":"10.1016/j.mimet.2024.107065","DOIUrl":"10.1016/j.mimet.2024.107065","url":null,"abstract":"<div><div>Lichens are composite organisms found throughout temperate terrestrial forests, with species-specific associations with industrial air pollution. Metagenomic analysis of lichen samples requires robust nucleic acid extraction methodology, a process that is challenging due to the protective cortex layers, high polysaccharide content, and the vast diversity of the internal microbiome. Our method includes physical lysis through garnet bead beating, chemical lysis using a sodium dodecyl sulfate buffer, phenol:chloroform:isoamyl alcohol extraction, and ethanol precipitation. The method was tested on three different lichen samples from two distinct species and yielded metagenomic DNA suitable for sequencing and PCR amplification. This procedure addresses the issues associated with DNA extraction from lichen using common laboratory equipment and reagents without the utilization of liquid nitrogen. This paper presents a cost-effective and accessible DNA extraction method for obtaining high-quality genetic material from dried and preserved lichen specimens.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"227 ","pages":"Article 107065"},"PeriodicalIF":1.7,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142554584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of a nucleic acid amplification system, GENECUBE, for rapid detection of staphylococcal nuc and mecA in blood culture samples","authors":"Yasuka Hara ,&nbsp;Daiki Tanno ,&nbsp;Masahiro Toyokawa ,&nbsp;Yukiko Takano ,&nbsp;Kazutaka Ohashi ,&nbsp;Rie Harada ,&nbsp;Hiroko Suzuki ,&nbsp;Mariko Usui ,&nbsp;Suguru Yui ,&nbsp;Shuko Kobari ,&nbsp;Mitsuki Kitabatake ,&nbsp;Tomoo Hidaka ,&nbsp;Yoshihiro Soya ,&nbsp;Kiwamu Nakamura ,&nbsp;Keiji Kanemitsu","doi":"10.1016/j.mimet.2024.107063","DOIUrl":"10.1016/j.mimet.2024.107063","url":null,"abstract":"<div><h3>Objective</h3><div>This study determined whether the GENECUBE rapid nucleic acid amplification test could directly detect <em>nuc</em> and <em>mecA</em> genes in clinical blood culture samples of <em>Staphylococcus</em> and various other pathogens.</div></div><div><h3>Methods</h3><div>Between September 2020 and December 2021, 537 blood culture samples from 192 patients with suspected bacteremia were tested using conventional assays (MicroScan WalkAway96 or VITEK 2 systems) and GENECUBE <em>nuc</em> and <em>mecA</em> assays. Isolates from samples with discrepant results between the conventional and GENECUBE assays were further evaluated using MALDI-TOF mass spectrometry, disk diffusion testing using cefoxitin, broth microdilution testing using oxacillin, and sequencing for <em>mecA</em>. Bacterial solutions containing a mixture of methicillin-susceptible <em>Staphylococcus aureus</em> (MSSA) and methicillin-resistant <em>Staphylococcus epidermidis</em> (MRSE) were prepared to evaluate the limit of detection (LOD) of <em>mecA</em>.</div></div><div><h3>Results</h3><div>Using conventional assays as the reference, the sensitivity, specificity, and positive and negative predictive values (95 % confidence interval) of GENECUBE were 100 % (96.8–100 %), 100 % (99.1–100 %), 100 % (96.8–100 %), and 100 % (99.1–100 %), respectively, for <em>nuc</em> detection and 100 % (96.1–100 %), 98.9 % (97.4–99.6 %), 94.9 % (88.5–98.3 %), and 100 % (99.2–100 %), respectively, for <em>mecA</em> detection. Sequencing analysis of five samples identified as methicillin-sensitive staphylococci using conventional assays and methicillin-resistant staphylococci using GENECUBE revealed the presence of methicillin-resistant isolates in all samples. The estimated LOD of <em>mecA</em> was 10⁴ colony-forming units (CFU)/mL of MRSE with GENECUBE, compared with 10⁵ CFU/mL with conventional assays.</div></div><div><h3>Conclusion</h3><div>The GENECUBE assay accurately detected <em>mecA</em> in positive blood culture samples and had higher sensitivity than conventional assays.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"227 ","pages":"Article 107063"},"PeriodicalIF":1.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The future in diagnostic tools for TB outbreaks: A review of the approaches with focus on LAMP and RPA diagnostics tests","authors":"Richa Prasad Mahato ,&nbsp;Saurabh Kumar","doi":"10.1016/j.mimet.2024.107064","DOIUrl":"10.1016/j.mimet.2024.107064","url":null,"abstract":"<div><div>Tuberculosis (TB) is still the most frequent cause of morbidity and mortality in the world caused by <em>Mycobacterium tuberculosis</em> (MTB). Due to slow diagnostic and treatment options, the disease is a major concern for public health and also increases the burden on the global economy. Rapid, sensitive, and cheaper TB diagnosis test is urgent to lower their rates by point of care testing (POCT). Therefore, molecular detection techniques <em>like</em> recombinase polymerase assay (RPA) and Loop-mediated isothermal amplification (LAMP) play a significant role in this regard as they work on the principle of isothermal nucleic acid amplification. RPA and LAMP bridge the research gap between the previous PCR-based detection tool and other reported isothermal tools for MTB. In this review, we endeavor to provide an overview of the assay that will be a novel approach toward a rapid amplification and visualization of DNA by the naked eye in natural light. RPA and LAMP can prove to be a highly specific pathogen detection technique in combination with lateral flow (LF) strips and SYBR Green I. Optimization of amplification conditions also made the assay ideally suited to the resource-limited field application at POCT. Additionally, RPA and LAMP have paved the way for meeting a key component of the POC diagnosis of TB <em>like</em> universal drug susceptibility testing. However, RPA is more suitable at the POC level than LPA as it requires a lower amplification temperature of around 37–42 °C and a simpler primer design.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"227 ","pages":"Article 107064"},"PeriodicalIF":1.7,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A TaqMan real-time PCR assay for detection of qacEΔ1 gene in Gram-negative bacteria","authors":"Svetlana N. Kovalchuk ,&nbsp;Anna L. Arkhipova ,&nbsp;Svetlana V. Bondar ,&nbsp;Dmitry N. Konanov ,&nbsp;Danil V. Krivonos ,&nbsp;Polina S. Chulkova ,&nbsp;Vladimir A. Ageevets ,&nbsp;Lyudmila S. Fedorova ,&nbsp;Elena N. Ilina","doi":"10.1016/j.mimet.2024.107054","DOIUrl":"10.1016/j.mimet.2024.107054","url":null,"abstract":"<div><div>The transfer of biocide and antibiotic resistance genes by mobile genetic elements is the most common mechanism for rapidly acquiring and spreading resistance among bacteria. The <em>qacEΔ1</em> gene confers the resistance to quaternary ammonium compounds (QACs). It has also been considered a genetic marker for the presence of class 1 integrons associated with multidrug-resistant (MDR) phenotypes in Gram-negative bacteria. In this study, a TaqMan real-time PCR assay was developed to detect the <em>qacEΔ1</em> gene in Gram-negative bacteria. The assay has a detection limit of 80 copies of the <em>qacEΔ1</em> gene per reaction. No false-positive or false-negative results have been observed. Simultaneous amplification and detection of the 16S rRNA gene is performed as an endogenous internal amplification control (IAC). The TaqMan real-time PCR assay developed is a rapid, sensitive, and specific method that could be used to monitor resistance to QACs, the spread of class 1 integrons, and the prediction of associated MDR phenotypes in Gram-negative bacteria.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"227 ","pages":"Article 107054"},"PeriodicalIF":1.7,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142441261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mycobacterium tuberculosis complex sample processing by mechanical lysis, an essential step for reliable whole genome sequencing","authors":"Noud Hermans ,&nbsp;Rina de Zwaan ,&nbsp;Arnout Mulder ,&nbsp;Joyce van den Dool ,&nbsp;Dick van Soolingen ,&nbsp;Kristin Kremer ,&nbsp;Richard Anthony","doi":"10.1016/j.mimet.2024.107053","DOIUrl":"10.1016/j.mimet.2024.107053","url":null,"abstract":"<div><div><em>Mycobacterium tuberculosis</em> complex (MTBC) whole genome sequencing (WGS) turnaround time and WGS success rates are highly influenced by DNA extraction protocols even from cultures. Efficient mycobacterial lysis is crucial for obtaining sufficient DNA from cultures to facilitate reliable genomic drug susceptibility prediction and accurate genotyping with WGS. We compared four DNA extraction protocols from BD BACTEC™ Mycobacterial Growth Indicator Tubes (MGIT) for WGS with a focus on the lysis step: protocol A) column-based protocol without mechanical lysis; protocol B) an adapted protocol including a bead beating step; protocol C) DNA extraction from primary received cultures using bead beating: and protocol D) DNA extraction from pre MGIT-positive (enriched) cultures. Protocol B increased DNA yield approximately 60-fold, and significantly improved the sequencing success rate. The increased yield also allowed DNA extraction from primary cultures with high success rates (protocol C). Additionally, by using pre-positive enriched MGIT cultures, we demonstrated that bead beating opens the possibility of reliable WGS up to five days before a MGIT tube would be flagged positive (protocol D). The most optimal bead beating-based DNA extraction was also evaluated for Nanopore sequencing. Shortening bead beating duration to 15 s resulted in longer read lengths (N50 from 1.4 kb to 2.6 kb) while still providing efficient lysis. Furthermore, AmpureXP bead beating-based DNA capture / purification proved to be as efficient as Qiagen column-based DNA extraction, further simplifying and shortening the DNA extraction protocol. Adding a mechanical lysis step to our routine MTBC DNA extraction protocol has allowed us to reduce the turnaround time while maintaining DNA quality sequencing success rates.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"227 ","pages":"Article 107053"},"PeriodicalIF":1.7,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142441309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of protein extraction protocols for MALDI-TOF Biotyper analysis of mycobacteria","authors":"Katarzyna Machnik,&nbsp;Jakub Smoliński,&nbsp;Mariola Paściak","doi":"10.1016/j.mimet.2024.107052","DOIUrl":"10.1016/j.mimet.2024.107052","url":null,"abstract":"<div><div>Infections caused by <em>Mycobacterium tuberculosis</em> and nontuberculous mycobacteria represent a significant global threat and medical concern. Therefore, accurate and reliable methods must be employed to identify mycobacteria rapidly. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a technique that compares the cellular protein profiles of unknown isolates with reference mass spectra in a database to identify microorganisms. However, the thick and waxy lipid layer, which is rich in mycolic acids and is present in mycobacterial cells, makes protein extraction challenging. To identify the optimal protocol for correctly identifying bacilli using MALDI-TOF mass spectrometry, this study compared four different cellular protein extraction methods. Four strains of <em>M. bovis</em> BCG were selected as representatives of slow-growing mycobacteria, while three strains of fast-growing mycobacteria were also included: <em>M. peregrinum</em>, <em>M. smegmatis,</em> and <em>M. farcinogenes</em>. The extraction method that proved most effective was the extraction of inactivated cells with chloroform and methanol, which partially delipidates the cells. These cells were then extracted with formic acid, as is standard practice for protein extraction. The advantage of this method is that it allows the parallel analysis of cellular lipids and proteins from a single sample. It is therefore important to optimize mycobacterial protein extraction for MALDI-TOF MS analysis in clinical microbiology laboratories.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"227 ","pages":"Article 107052"},"PeriodicalIF":1.7,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}