Use of MALDI-TOF mass spectrometry fingerprinting to characterize Enterococcus spp. and Escherichia coli isolates

Rapid and accurate identification of yeast subspecies by MALDI-MS combined with a cell membrane disruption reagent

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been widely used for microbial analysis. However, due to the impenetrable shell of fungi the direct identification of fungi remains challenges. Targeting on this problem, the yeast Saccharomyces cerevisiae (S. cerevisiae) was selected as a model fungus, and a new fungal cell membrane disruption reagent C18-G1 was used before MALDI-MS detection. As a result, much more intensive peaks which distributed in wider m/z range of S. cerevisiae have been identified in comparison with the use of traditional fungal pretreatment methods. Furthermore, a differential peak at m/z 4993 between two subspecies of S. cerevisiae has been identified. The corresponding protein with exclusive sequence of the specific peak was obtained based on MS/MS fragments and database searching. In addition, the method was successfully applied for the discrimination of four commercial yeasts.

Effect of Tryptic Digestion on Sensitivity and Specificity in MALDI-TOF-Based Molecular Diagnostics through Machine Learning

The digestion of protein into peptide fragments reduces the size and complexity of protein molecules. Peptide fragments can be analyzed with higher sensitivity (often > 102 fold) and resolution using MALDI-TOF mass spectrometers, leading to improved pattern recognition by common machine learning algorithms. In turn, enhanced sensitivity and specificity for bacterial sorting and/or disease diagnosis may be obtained. To test this hypothesis, four exemplar case studies have been pursued in which samples are sorted into dichotomous groups by machine learning (ML) software based on MALDI-TOF spectra. Samples were analyzed in 'intact' mode in which the proteins present in the sample were not digested with protease prior to MALDI-TOF analysis and separately after the standard overnight tryptic digestion of the same samples. For each case, sensitivity (sens), specificity (spc), and the Youdin index (J) were used to assess the ML model performance. The proteolytic digestion of samples prior to MALDI-TOF analysis substantially enhanced the sensitivity and specificity of dichotomous sorting. Two exceptions were when substantial differences in chemical composition between the samples were present and, in such cases, both 'intact' and 'digested' protocols performed similarly. The results suggest proteolytic digestion prior to analysis can improve sorting in MALDI/ML-based workflows and may enable improved biomarker discovery. However, when samples are easily distinguishable protein digestion is not necessary to obtain useful diagnostic results.

Discrimination and Characterization of Escherichia coli Originating from Clinical Cases of Femoral Head Necrosis in Broilers by MALDI-TOF Mass Spectrometry Confirms Great Heterogeneity of Isolates

Escherichia coli, a major pathogen in poultry production, is involved in femoral head necrosis (FHN) in broiler birds. So far, the characterization and relationship of isolates in context with this disease are mainly based on phenotypic and genotypic characteristics. Previously, an involvement of diverse E. coli isolates was reported. MALDI-TOF MS has been successfully applied investigating the clonality of different bacteria. Therefore, its application to characterize a well-defined selection of E. coli isolates beyond the species level was tested. The isolates were derived from clinical cases of FHN as well as from healthy birds. Reproducibility studies to perform a standardized protocol were done, and LB agar as well as the usage of fresh bacterial cultures proved most appropriate. No distinct clustering in context with the origin of isolates, association with lesions, serotype, or PFGE profile was found. Most of the isolates belonging to phylogroup B2 revealed a characteristic peak shift at 9716 m/z and could be attributed to the same MALDI-TOF MS cluster. The present study confirmed the previously found pheno- and genotypic heterogeneity of E. coli involved in FHN on the proteomic level. The study also highlights the need for standardized protocols when using MALDI-TOF MS for bacterial typing, especially beyond species level.

Plasma and serum exosome markers analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry coupled with electron multiplier

Although matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a simple, rapid, and high-throughput assay, its microchannel plate (MCP) detector is limited by the low sensitivity and ion saturation effect when analyzing macromolecules. Herein, we introduced a strategy that combined MALDI-TOF MS with electron multiplier (EM) for the direct analysis of exosomal proteins isolated from human plasma and serum. The results demonstrated that EM yielded a higher sensitivity than MCP detector in high-mass range (m/z 5000-100000). Through the analysis of MALDI-TOF MS coupled with EM, chemokine (C-X-C motif) ligand 12 (CXCL12) ion at m/z 7960 and its degradation products at m/z 7927, 7587, and 7553 were identified as characteristic exosomal proteins in plasma. CXCL4 ion at m/z 7765 was identified as a characteristic protein in serum exosomes. Additionally, the peak intensity of CXCL12 and CXCL4 standards exhibited great linear relationship (CXCL12, R² = 0.989; CXCL4, R² = 0.986) with the concentrations (ranging from 0.1 to 20 μg/mL) when using EM as detector. In conjunction with ultrasonic assisted matrix coating technology (UAMCT), this assay repeatability in our lab has been excellent with coefficient of variation (CV%) of 4.6% for CXCL12 and 9.3% for CXCL4. Finally, the spectra demonstrated that the intensity of exosome related peaks was significantly enhanced in plasma and serum of patients with Parkinson's disease (PD) (m/z 7553, P < 0.01; m/z 7587, P < 0.01; m/z 7927, P < 0.001; m/z 7980, P < 0.001; m/z 7765, P < 0.01), Alzheimer's disease (AD) (m/z 7553, P < 0.001; m/z 7587, P < 0.001; m/z 7927, P < 0.001; m/z 7980, P < 0.001), and ischemic cerebrovascular disease (ICD) (m/z 7553, P < 0.05; m/z 7587, P < 0.05; m/z 7927, P < 0.01; m/z 7980, P < 0.05; m/z 7765, P < 0.05) compared to that in healthy persons. The fingerprint information of CXCL12 in plasma exosomes has better clinical relevance than serum exosome CXCL4 in MALDI-TOF MS analysis.

Application and Perspectives of MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories

Early diagnosis of severe infections requires of a rapid and reliable diagnosis to initiate appropriate treatment, while avoiding unnecessary antimicrobial use and reducing associated morbidities and healthcare costs. It is a fact that conventional methods usually require more than 24–48 h to culture and profile bacterial species. Mass spectrometry (MS) is an analytical technique that has emerged as a powerful tool in clinical microbiology for identifying peptides and proteins, which makes it a promising tool for microbial identification. Matrix assisted laser desorption ionization–time of flight MS (MALDI–TOF MS) offers a cost- and time-effective alternative to conventional methods, such as bacterial culture and even 16S rRNA gene sequencing, for identifying viruses, bacteria and fungi and detecting virulence factors and mechanisms of resistance. This review provides an overview of the potential applications and perspectives of MS in clinical microbiology laboratories and proposes its use as a first-line method for microbial identification and diagnosis.

Use of MALDI-TOF for identification and surveillance of gram-negative bacteria in captive wild psittacines

Microbiological studies of the sanitary and health status of psittacine birds that will be reintroduced is important in evaluating whether these animals act as carriers of pathogenic agents to other animals and humans. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a faster and more accurate method to identify bacteria than conventional microbiology methods. The aim of this study was to evaluate the health status of psittacines housed in captivity, by assessment of Gram-negative bacteria from fecal microbiota through MALDI- TOF MS identification. The results indicate high frequency of Gram-negative bacteria in feces (96.5%), especially from the Enterobacteriaceae family (88.7%). The most prevalent bacteria were Escherichia coli (39.0%), Proteus vulgaris (12.2%), Klebsiella spp. (12.1%) and Raoultella ornithinolytica (8.7%). Proteus hauseri, Citrobacter spp., Morganella morgannii, Providencia rettgeri, Enterobacter spp. and Escherichia hermannii were isolated with lower frequency. . All these agents are potentially pathogenic for parrots and can cause systemic infections in other animals and humans. These findings reinforce that MALDI- TOF MS proved to be a rapid and accurate method of identification of the microorganism and evaluation of the health status of psittacines, providing relevant data to assist decision-making regarding the sanitary protocols in wildlife centers, and possible future reintroduction of wild birds.

Phenotypic and genotypic characterization of Enterococcus spp. from yolk sac infections in broiler chicks with a focus on virulence factors

Bacterial infections of yolk sacs contribute to increased mortality of chicks, chronic infections during their rearing, or increased selection in the flock, which in turn leads to high economic losses in poultry production worldwide. The aim of this study was a phenotypic and genotypic characterization of enterococci isolated from yolk sac infections (YSI) of broiler chickens from Poland and the Netherlands. Biochemical, matrix-assisted laser desorption/ionization (MALDI)–time-of-flight (TOF) MS, and rpoA gene sequencing identification was performed. Moreover, phenotypic and genotypic characterization of virulence factors and analysis of the clonal relationship of isolates by MALDI-TOF MS and enterobacterial repetitive intergenic consensus—polymerase chain reaction (ERIC-PCR) were performed. The biochemical test identified 70 isolates as Enterococcus faecalis and 6 as Enterococcus mundtii. The results of MALDI-TOF MS were 100% concordant with those obtained by rpoA gene sequencing, and all 76 isolates were identified as E. faecalis. Differences were noted in the β-glucuronidase, β-glucosidase, α-galactosidase, phosphatase, melibiose, lactose, and raffinose tests that is going about the results of biochemical identification. None of the isolates were beta-hemolytic on blood agar in aerobic conditions, but all but one were gelatinase positive. Among biofilm-forming isolates (30/76; 39.5%), as many as 66.7% (20/30) were Polish E. faecalis strains. Most of the isolates carried virulence genes, that is gelE, ace, asa1, efaAfs, fsrA, fsrB, fsrC, cob, cpd, and ccf, but none had the hyl gene. Some isolates harbored cyl operon genes. One Polish strain (ST16) had all of the tested cyl genes and the esp gene, considered clinically important, and showed the highest biofilm-forming ability. Nearly 50% of the isolates showed close genetic relatedness in ERIC typing. In contrast with MALDI-TOF MS cluster analysis, ERIC-PCR results did not show a relationship with the origin of the strains. Using MALDI-TOF MS, 7 peaks were found in Polish and Dutch isolates, which may type them as species-specific biomarkers in E. faecalis from YSI.

Discrimination of major and minor streptococci incriminated in bovine mastitis by MALDI-TOF MS fingerprinting and 16S rRNA gene sequencing

The current work investigated the discriminatory potential of MALDI-TOF MS fingerprinting towards most-relevant major (Streptococcus agalactiae, S. dysgalactiae, S. uberis) and minor (S. canis, S. parauberis, S. salivarius, S. equinus and S. gallolyticus) streptococci involved in bovine mastitis (BM), in comparison to 16S rRNA gene sequencing (GS)-based identification. The MALDI-TOF MS-generated spectral fingerprints were recruited for eliciting a detailed proteomic map that demonstrated clear variability for inter- and intra-species-specific biomarkers. Besides, a phyloproteomic dendrogram was evolved and comparatively analyzed against the phylogenetic one obtained from 16S rRNA GS in order to assess the differentiation of streptococci of bovine origin based on variability of protein fingerprints versus the variation of 16S rRNA gene homology. Results showed that the discrimination of BM-implicated streptococci can be obtained by both approaches; however MALDI-TOF MS was superior, achieving more variability at both intra- and sub-species levels. MALDI-TOF MS spectral analytics revealed that Streptococcus spp. exhibited three genus-specific biomarkers (peaks with m/z values at 2112, 4452 and 5955) and all streptococci exhibited spectral variability at both species and subspecies levels. Remarkably, MALDI-TOF MS fingerprinting was found to be at least as robust as 16S rRNA GS-based identification, allowing much cheaper and faster analysis, and additionally exhibiting high reliability for characterization of BM-implicated streptococci, thus proving to be a powerful tool that can be used independently within dairy diagnostics.

Putative Protein Biomarkers of Escherichia coli Antibiotic Multiresistance Identified by MALDI Mass Spectrometry

The commensal bacteria Escherichia coli causes several intestinal and extra-intestinal diseases, since it has virulence factors that interfere in important cellular processes. These bacteria also have a great capacity to spread the resistance genes, sometimes to phylogenetically distant bacteria, which poses an additional threat to public health worldwide. Here, we aimed to use the analytical potential of MALDI-TOF mass spectrometry (MS) to characterize E. coli isolates and identify proteins associated closely with antibiotic resistance. Thirty strains of extended-spectrum beta-lactamase producing E. coli were sampled from various animals. The phenotypes of antibiotic resistance were determined according to Clinical and Laboratory Standards Institute (CLSI) methods, and they showed that all bacterial isolates were multi-resistant to trimethoprim-sulfamethoxazole, tetracycline, and ampicillin. To identify peptides characteristic of resistance to particular antibiotics, each strain was grown in the presence or absence of the different antibiotics, and then proteins were extracted from the cells. The protein fingerprints of the samples were determined by MALDI-TOF MS in linear mode over a mass range of 2 to 20 kDa. The spectra obtained were compared by using the ClinProTools bioinformatics software, using three machine learning classification algorithms. A putative species biomarker was also detected at a peak m/z of 4528.00.

Sewage sludge as a source of triclosan-resistant bacteria

Subinhibitory concentrations of antibiotics and biocides in wastewaters and sewage sludge have a great impact on the development of antibiotic resistance and its spread among bacteria. The aim of this work was to determine the occurrence of coliform bacteria and enterococci resistant to biocide triclosan in samples of sewage sludge. Subsequently, isolated strains of coliform bacteria were identified and characterized in terms of their antibiotic susceptibility and ability to form a biofilm. Occurrence of the studied bacteria was monitored in three samples of stabilized sludge from three different wastewater treatment plants (Vrakuňa, Petržalka, and Senec). The number of triclosan-resistant coliforms was the highest in the sludge sample from the wastewater treatment plant in Senec and the lowest in the sludge sample from the wastewater treatment plant in Petržalka. Triclosan-resistant Enterococcus spp. were not found in any sample of stabilized sludge. Most isolates were identified as Citrobacter freundii and Serratia spp. Triclosan-resistant isolates showed also resistance to antibiotics and the majority of them were strong biofilm producers.

Annual changes in the occurrence of antibiotic-resistant coliform bacteria and enterococci in municipal wastewater

Wastewater contains subinhibitory concentrations of different micropollutants such as antibiotics that create selective pressure on bacteria. This phenomenon is also caused by insufficient wastewater treatment technology leading to the development and spread of antibiotic-resistant bacteria and resistance genes into the environment. Therefore, this work focused on monitoring of antibiotic-resistant coliform bacteria and enterococci in influent and effluent wastewaters taken from the second biggest wastewater treatment plant (Petržalka) in the capital of Slovakia during 1 year. Antibiotic-resistant strains were isolated, identified, and characterized in terms of susceptibility and biofilm production. All of 27 antibiotic-resistant isolates were identified mainly as Morganella morganii, Citrobacter spp., and E. coli. Multidrug-resistance was detected in 58% of isolated strains. All tested isolates could form biofilm; two strains were very strong producers, and 74% formed biofilm by strong intensity. The flow rate of the influent wastewater had a more significant impact on the number of studied bacteria than the temperature. Graphical abstract.

Tuberculosis in the 21th century: Current status of diagnostic methods

Tuberculosis is an infectious bacterial disease with a high mortality rate worldwide constituting a serious public health problem. The diagnostic methods commonly used by health professionals are slow and expensive and the results may take about sixty days which will cause a delay in administrating the most proper treatment to the patient, as well as increase health care costs and infection transmission possibility. Patients infected simultaneously with human immunodeficiency virus and Mycobacterium tuberculosis are a constant and worrying challenge for the scientific community which will research and develop new methods of diagnosis, new drugs and new therapies. Nowadays there are new tuberculosis diagnosis methods and some of which are already in clinical trial phases. These methods have high sensitivity, but do not replace the microbiological examination for isolation and culture of Mycobacterium spp. However, in clinical practice, microbiological, imaging, clinical and epidemiological data integration provide the best diagnosis and treatment possible. Consequently, throughout this paper, the different methods of diagnosis of human tuberculosis with its advantages and disadvantages will be covered, describing new omics and ultra-fast methods to increase knowledge and obtain a rapid diagnosis of tuberculosis.

Analysis of copper response inAcinetobactersp. by comparative proteomics

Metal contamination exerts environmental pressure on several lifeforms.

MALDI mass spectrometry imaging and in situ microproteomics of Listeria monocytogenes biofilms

MALDI-TOF Mass spectrometry Imaging (MSI) is a surface-sampling technology that can determine spatial information and relative abundance of analytes directly from biological samples. Human listeriosis cases are due to the ingestion of contaminated foods with the pathogenic bacteria Listeria monocytogenes. The reduction of water availability in food workshops by decreasing the air relative humidity (RH) is one strategy to improve the control of bacterial contamination. This study aims to develop and implement an MSI approach on L. monocytogenes biofilms and proof of concept using a dehumidified stress condition. MSI allowed examining the distribution of low molecular weight proteins within the biofilms subjected to a dehumidification environment, mimicking the one present in a food workshop (10 °C, 75% RH). Furthermore, a LC-MS/MS approach was made to link the dots between MSI and protein identification. Five identified proteins were assigned to registered MSI m/z, including two cold-shock proteins and a ligase involved in cell wall biogenesis. These data demonstrate how imaging can be used to dissect the proteome of an intact bacterial biofilm giving new insights into protein expression relating to a dehumidification stress adaptation. Data are available via ProteomeXchange with identifier PXD010444.

BIOLOGICAL SIGNIFICANCE

The ready-to-eat food processing industry has the daily challenge of controlling the contamination of surfaces and machines with spoilage and pathogenic microorganisms. In some cases, it is a lost cause due to these microorganisms' capacity to withstand the cleaning treatments, like desiccation procedures. Such a case is the ubiquitous Gram-positive Bacterium Listeria monocytogenes. Its surface proteins have particular importance for the interaction with its environment, being important factors contributing to adaptation to stress conditions. There are few reproducibly techniques to obtain the surface proteins of Gram-positive cells. Here, we developed a workflow that enables the use of MALDI imaging on Gram-positive bacterium biofilms to study the impact of dehumidification on sessile cells. It will be of the most interest to test this workflow with different environmental conditions and potentially apply it to other biofilm-forming bacteria.

A novel method to rapidly distinguish the geographical origin of traditional fermented-salted vegetables by mass fingerprinting

The geographical origin of kimchi is of interest to consumers and producers because the prices of commercial kimchi products can vary significantly according to the geographical origin. Hence, social issues related to the geographical origin of kimchi in Korea have emerged as a major problem. In this study, the geographical origin of kimchi was determined by comparing the mass fingerprints obtained for Korean and Chinese kimchi samples by MALDI-TOF MS with multivariate analysis. The results obtained herein provide an accurate, powerful tool to clearly discriminate kimchi samples based on their geographical origin within a short time and to ensure food authenticity, which is of significance in the kimchi industry. Furthermore, our MALDI-TOF MS method could be applied to determining the geographical origin of other fermented-salted vegetables at a reduced cost in shorter times.

Themis: Batch Preprocessing for Ultrahigh-Resolution Mass Spectra of Complex Mixtures

Fourier transform ion cyclotron resonance mass spectrometry affords the resolving power to determine an unprecedented number of components in complex mixtures, such as petroleum. The software tools required to also analyze these data struggle to keep pace with advancing instrument capabilities and increasing quantities of data, particularly in terms of combining information efficiently across multiple replicates. Improved confidence in data and the use of replicates is particularly important where strategic decisions will be based upon the analysis. We present a new algorithm named Themis, developed using R, to jointly preprocess replicate measurements of a sample with the aim of improving consistency as a preliminary step to assigning peaks to chemical compositions. The main features of the algorithm are quality control criteria to detect failed runs, ensuring comparable magnitudes across replicates, peak alignment, and the use of an adaptive mixture model-based strategy to help distinguish true peaks from noise. The algorithm outputs a list of peaks reliably observed across replicates and facilitates data handling by preprocessing all replicates in a single step. The processed data produced by our algorithm can subsequently be analyzed by use of relevant specialized software. While Themis has been demonstrated with petroleum as an example of a complex mixture, its basic framework will be useful for complex samples arising from a variety of other applications.

Traditional approaches versus mass spectrometry in bacterial identification and typing

Biochemical methods such as metabolite testing and serotyping are traditionally used in clinical microbiology laboratories to identify and categorize microorganisms. Due to the large variety of bacteria, identifying representative metabolites is tedious, while raising high-quality antisera or antibodies unique to specific biomarkers used in serotyping is very challenging, sometimes even impossible. Although serotyping is a certified approach for differentiating bacteria such as E. coli and Salmonella at the subspecies level, the method is tedious, laborious, and not practical during an infectious disease outbreak. Mass spectrometry (MS) platforms, especially matrix assisted laser desorption and ionization-time of flight mass spectrometry (MALDI-TOF-MS), have recently become popular in the field of bacterial identification due to their fast speed and low cost. In the past few years, we have used liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based approaches to solve various problems hindering serotyping and have overcome some insufficiencies of the MALDI-TOF-MS platform. The current article aims to review the characteristics, advantages, and disadvantages of MS-based platforms over traditional approaches in bacterial identification and categorization.

Characterization of Enterococcus species isolated from marine recreational waters by MALDI-TOF MS and Rapid ID API® 20 Strep system

MALDI-TOF Mass Spectrometry Biotyping has proven to be a reliable method for identifying bacteria at the species level based on the analysis of the ribosomal proteins mass fingerprint. We evaluate the usefulness of this method to identify Enterococcus species isolated from marine recreational water at Brazilian beaches. A total of 127 Enterococcus spp. isolates were identified to species level by bioMérieux's API® 20 Strep and MALDI-TOF systems. The biochemical test identified 117/127 isolates (92%), whereas MALDI identified 100% of the isolates, with an agreement of 63% between the methods. The 16S rRNA gene sequencing of isolates with discrepant results showed that MALDI-TOF and API® correctly identified 74% and 11% of these isolates, respectively. This discrepancy probably relies on the bias of the API® has to identify clinical isolates. MALDI-TOF proved to be a feasible approach for identifying Enterococcus from environmental matrices increasing the rapidness and accuracy of results.

Characterization of Multidrug Resistant E. faecalis Strains from Pigs of Local Origin by ADSRRS-Fingerprinting and MALDI -TOF MS; Evaluation of the Compatibility of Methods Employed for Multidrug Resistance Analysis

The aim of this study was to characterize multidrug resistant E. faecalis strains from pigs of local origin and to analyse the relationship between resistance and genotypic and proteomic profiles by amplification of DNA fragments surrounding rare restriction sites (ADSRRS-fingerprinting) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI -TOF MS). From the total pool of Enterococcus spp. isolated from 90 pigs, we selected 36 multidrug resistant E. faecalis strains, which represented three different phenotypic resistance profiles. Phenotypic resistance to tetracycline, macrolides, phenicols, and lincomycin and high-level resistance to aminoglycosides were confirmed by the occurrence of at least one corresponding resistance gene in each strain. Based on the analysis of the genotypic and phenotypic resistance of the strains tested, five distinct resistance profiles were generated. As a complement of this analysis, profiles of virulence genes were determined and these profiles corresponded to the phenotypic resistance profiles. The demonstration of resistance to a wide panel of antimicrobials by the strains tested in this study indicates the need of typing to determine the spread of resistance also at the local level. It seems that in the case of E. faecalis, type and scope of resistance strongly determines the genotypic pattern obtained with the ADSRRS-fingerprinting method. The ADSRRS-fingerprinting analysis showed consistency of the genetic profiles with the resistance profiles, while analysis of data with the use of the MALDI- TOF MS method did not demonstrate direct reproduction of the clustering pattern obtained with this method. Our observations were confirmed by statistical analysis (Simpson’s index of diversity, Rand and Wallace coefficients). Even though the MALDI -TOF MS method showed slightly higher discrimination power than ADSRRS-fingerprinting, only the latter method allowed reproduction of the clustering pattern of isolates based on phenotypic resistance and analysis of resistance and virulence genes (Wallace coefficient 1.0). This feature seems to be the most useful for epidemiological purposes and short-term analysis.

Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria

Identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. With the certification of some MS platforms in recent years, more applications and tests of MS‐based diagnosis methods for bacteria identification and typing have been created, not only on well‐accepted MALDI‐TOF‐MS‐based fingerprint matches, but also on solving the insufficiencies of MALDI‐TOF‐MS‐based platforms and advancing the technology to areas such as targeted MS identification and typing of bacteria, bacterial toxin identification, antibiotics susceptibility/resistance tests, and MS‐based diagnostic method development on unique bacteria such as Clostridium and Mycobacteria. This review summarizes the recent development in MS platforms and applications in bacteria identification and typing of common pathogenic bacteria.