Rapid identification of oral anaerobic bacteria cultivated from subgingival biofilm by MALDI-TOF-MS

Rapid determination of colistin resistance in Klebsiella pneumoniae by MALDI-TOF peak based machine learning algorithm with MATLAB

INTRODUCTION

To date, limited data exist on demonstrating the usefulness of machine learning (ML) algorithms applied to MALDI-TOF in determining colistin resistance among Klebsiella pneumoniae. We aimed to detect colistin resistance in K. pneumoniae using MATLAB on MALDI-TOF database.

MATERIALS AND METHODS

A total of 260 K. pneumoniae isolates were collected. Three ML models, namely, linear discriminant analysis (LDA), support vector machine, and Ensemble were used as ML algorithms and applied to training data set.

RESULTS

The accuracies for the training phase with 200 isolates were found to be 99.3%, 93.1%, and 88.3% for LDA, support vector machine, and Ensemble models, respectively. Accuracy, sensitivity, specificity, and precision values for LDA in the application test set with 60 K. pneumoniae isolates were 81.6%, 66.7%, 91.7%, and 84.2%, respectively.

CONCLUSION

This study provides a rapid and accurate MALDI-TOF MS screening assay for clinical practice in identifying colistin resistance in K. pneumoniae.

Identification of root canal microbiota profiles of periapical tissue diseases using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

OBJECTIVES

The purpose of this study was to identify microorganisms isolated from various periapical tissue diseases using Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) and classify them via an unsupervised machine learning approach.

METHODS

A total of 150 patients with various apical conditions and teeth in need of endodontic retreatment were divided into five groups, including Retreatment, Acute Apical Abscess, Chronic Apical Abscess, Acute Apical Periodontitis, and Chronic Apical Periodontitis. Samples were collected from root canals using paper points after agitating with a #10 K file then microorganisms were identified using MALDI-TOF-MS. Data were analyzed using a hierarchical clustering method. Quadruple clusters and dendrograms were formed according to similarities and dissimilarities.

RESULTS

A total of 80 species were identified representative of six different phyla. The most similar microorganism species identified were: ''Enterococcus faecalis'' between 21 and 23-year-old female cases in Retreatment group; ''Lactobacillus rhamnosus'' between 20 and 18-year-old male cases in Symptomatic Apical Abscess cases; ''Lactobacillus paracasei'' between 26 and 40-year-old male cases in Asymptomatic Apical Abscess cases; ''Enterococcus faecalis'' between 48 and 50-year-old female cases in Symptomatic Apical Periodontitis cases; ''Lactobacillus rhamnosus'' between 48 and 60-year-old male cases in Asymptomatic Apical Periodontitis cases.

CONCLUSIONS

MALDI-TOF MS can be considered a fast and high-throughput screening technique for microbial species identification in endodontics. Thus, it will provide valuable data for future research designs regarding periapical tissue diseases. As the MALDI-TOF MS database expands and comprehensive data becomes available, the relationship between microbial profiles and disease progression will become increasingly apparent.

Characterization of the salivary microbiome before and after antibiotic therapy via separation technique

In the present research, the MALDI-TOF MS technique was applied as a tool to rapidly identify the salivary microbiome. In this fact, it has been monitored the changes occurred in molecular profiles under different antibiotic therapy. Significant changes in the composition of the salivary microbiota were noticed not only in relation to the non antibiotic (non-AT) and antibiotic treatment (AT) groups, but also to the used media, the antibiotic therapy and co-existed microbiota. Each antibiotic generates specific changes in molecular profiles. The highest number of bacterial species was isolated in the universal culture medium (72%) followed by the selective medium (48% and 38%). In the case of non-AT patients, the prevalence of Streptococcus salivarius (25%), Streptococcus vestibularis (19%), Streptococcus oralis (13%), and Staphylococcus aureus (6%) was identified while in the case of AT, Streptococcus salivarius (11%), Streptococcus parasanguinis (11%), Staphylococcus epidermidis (12%), Enterococcus faecalis (9%), Staphylococcus hominis (8%), and Candida albicans (6%) were identified. Notable to specified that the Candida albicans was noticed only in AT samples, indicating a negative impact on the antibiotic therapy. The accuracy of the MALDI-TOF MS technique was performed by the 16S rRNA gene sequencing analysis-as a reference method. Conclusively, such an approach highlighted in the present study can help in developing the methods enabling a faster diagnosis of disease changes at the cellular level before clinical changes occur. Once the MALDI tool allows for the distinguishing of the microbiota of non-AT and AT, it may enable to monitor the diseases treatment and develop a treatment regimen for individual patients in relation to each antibiotic. KEY POINTS: The salivary microbiota of antibiotic-treated patients was more bacteria variety MALDI-TOF MS is a promising tool for recording of reproducible molecular profiles Our data can allow to monitor the treatment of bacterial diseases for patients.

Chemical and Biological Characterization of Melaleuca alternifolia Essential Oil

The essential oil of Melaleuca alternifolia, commonly known as tea tree oil, has many beneficial properties due to its bioactive compounds. The aim of this research was to characterize the tea tree essential oil (TTEO) from Slovakia and its biological properties, which are specific to the chemical composition of essential oil. Gas chromatography/mass spectroscopy revealed that terpinen-4-ol was dominant with a content of 40.3%. γ-Terpinene, 1,8-cineole, and p-cymene were identified in contents of 11.7%, 7.0%, and 6.2%, respectively. Antioxidant activity was determined at 41.6% radical inhibition, which was equivalent to 447 μg Trolox to 1 mL sample. Antimicrobial activity was observed by the disk diffusion method against Gram-positive (G⁺), Gram-negative (G^-) bacteria and against yeasts, where the best antimicrobial activity was against Enterococcus faecalis and Candida albicans with an inhibition zone of 10.67 mm. The minimum inhibitory concentration showed better susceptibility by G⁺ and G^- planktonic cells, while yeast species and biofilm-forming bacteria strains were more resistant. Antibiofilm activity was observed against Pseudomonas fluorescens and Salmonella enterica by MALDI-TOF, where degradation of the protein spectra after the addition of essential oil was obtained. Good biological properties of tea tree essential oil allow its use in the food industry or in medicine as an antioxidant and antimicrobial agent.

Subgingival Microbiota Profile in Association with Cigarette Smoking in Young Adults: A Cross-Sectional Study

While smoking is recognized as one of the factors for the development and progression of periodontal diseases, a relation between the composition of the subgingival microbiota and smoking is yet to be elucidated. The aim of this study was to investigate the prevalence of subgingival bacteria in young smokers and non-smokers without clinical signs of periodontal disease. In this cross-sectional study, performed at the Department of Pharmacology, School of Dental Medicine, University of Zagreb, we enrolled 32 periodontally healthy smokers and 32 non-smokers, aged 25–35 years old. The number of oral bacteria and the prevalence of particular bacteria were assessed for each subject. Subgingival plaque samples were collected with sterile paper points from two first molars for microbiological analyses with MALDI-TOF mass spectrometry. In smokers, a significantly higher prevalence of Actinomyces odontolyticus was observed compared to non-smokers, and a significantly lower prevalence of Streptococcus sanguinis was observed compared to non-smokers. Smoking affects the composition of subgingival microbiota, either via depletion of beneficial bacteria or the increase in pathogenic bacteria.

Thymus serpyllum Essential Oil and Its Biological Activity as a Modern Food Preserver

The aim of this study was to analyze the chemical composition and biological and antibiofilm activity of the essential oil (EO) of Thymus serpyllum with the use of a MALDI-TOF MS Biotyper. The main compounds of the EO were thymol, 18.8%; carvacrol, 17.4%; o-cymene, 15.4%; and geraniol, 10.7%. It was found that free-radical scavenging activity was high. The highest antimicrobial activity was observed against Pseudomonas aeruginosa, Salmonella enteritidis, and biofilm-forming bacteria. The changes in the biofilm structure after T. serpyllum EO application confirmed the inhibitory action and the most pronounced effect was observed on Bacillus subtilis biofilm. The antifungal activity of the vapor phase was the most effective against Penicillium crustosum. T. serpyllum should be a suitable alternative to synthetic antioxidants as well as antimicrobials. The EO of T. serpyllum can be used in the vapor phase in the storage of root vegetables as well as a growth inhibitor of Penicillium on bread.

Markers to Rapidly Distinguish Bacillus paralicheniformis From the Very Close Relative, Bacillus licheniformis

As close relatives, Bacillus paralicheniformis is often wrongly identified as Bacillus licheniformis. In this study, two genetic markers are presented based on fenC and fenD from the fengycin operon of B. paralicheniformis to rapidly distinguish it from B. licheniformis. The fengycin operon is one of the few present in B. paralicheniformis but absent in B. lichenformis up to date. Using these markers, two presumptive B. paralicheniformis isolates each were recovered from a set of isolates previously identified as B. licheniformis by Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) or identified only to genus level as Bacillus by 16S ribosomal RNA (rRNA) gene sequencing, respectively. Whole genome sequencing of the four isolates confirmed their identity as B. paralicheniformis having the closest similarity with B. paralicheniformis ATCC 9945a (GenBank: CP005965.1) with a 7,682 k-mer score and 97.22% Average Nucleotide Identity (ANI). ANI of 100% suggests that the four isolates are highly similar. Further analysis will be necessary to determine if finer differences exist among these isolates at the level of single nucleotide polymorphisms.

Bacterial Identification and Monitoring Around Two-Piece Dental Implants by Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS)

Context  Early microbiological diagnosis and treatment of periodontal pathogens is important for successful retention of dental implants. Aims  This study aimed to identify and monitor oral bacterial colonization after successful two-piece dental implants. Settings and Design  In this study, 50 two-piece dental implant subjects were included and assessed clinically, radiographically, and microbiologically. Methods and Material  All the parameters were recorded at various stages after prosthesis placement. In each stage, nonadherent (peri-implant sulcular fluid) and adherent (curetted inner threads) samples were collected. Semiquantitative anaerobic culture of the samples were done in Anoxomat system. Bacterial colonies were first identified by routine microbiological methods and then by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) method. Statistical Analysis  All the results were analyzed by appropriate statistical methods (Chi-square, one factor analysis of variance, etc.). Results  All the bacterial isolates were identified in the MALDI-TOF MS system with no failure. After implant placement for the nonadherent samples, the frequency (%) of Fusobacterium nucleatum, Prevotella melaninogenica, and Propionibacterium acnes decreased whereas frequency (%) of Escherichia coli, Staphylococcus epidermidis, and Streptococcus mitis increased. For adherent samples, the frequency (%) of E. coli, Enterococcus faecalis, Porphyromonas gingivalis, P. melaninogenica , and Veillonella parvula decreased, whereas frequency (%) of S. mitis and Streptococcus mutans increased. The postimplant mean nonadherent and adherent bacterial load increased with time but not significantly over the periods ( p = 0.302 and 0.123, respectively). Conclusion  Combination of basic (semiquantitative culture method) and advanced microbiological method (MALDI-TOF MS) can be useful for accurate detection and monitoring of potential pathogens around two-piece dental implants.

Digestive tract methanodrome: Physiological roles of human microbiota-associated methanogens

Methanogens are the archaea most commonly found in humans, in particular in the digestive tract and are an integral part of the digestive microbiota. They are present in humans from the earliest moments of life and represent the only known source of methane production to date. They are notably detected in humans by microscopy, fluorescent in situ hybridization, molecular biology including PCR-sequencing, metagenomics, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and culture. Methanogens present in the human digestive tract play major roles, in particular the use of hydrogen from the fermentation products of bacteria, thus promoting digestion. They are also involved in the transformation of heavy metals and in the use of trimethylamine produced by intestinal bacteria, thus preventing major health problems, in particular cardiovascular diseases. Several pieces of evidence suggest their close physical contacts with bacteria support symbiotic metabolism. Their imbalance during dysbiosis is associated with many pathologies in humans, particularly digestive tract diseases such as Crohn's disease, ulcerative colitis, diverticulosis, inflammatory bowel disease, irritable bowel syndrome, colonic polyposis, and colorectal cancer. There is a huge deficit of knowledge and partially contradictory information concerning human methanogens, so much remains to be done to fully understand their physiological role in humans. It is necessary to develop new methods for the identification and culture of methanogens from clinical samples. This will permit to isolate new methanogens species as well as their phenotypic characterization, to explore their genome by sequencing and to study the population dynamics of methanogens by specifying in particular their exact role within the complex flora associated with the mucous microbiota of human.

Proteome Analysis of Molecular Events in Oral Pathogenesis and Virus: A Review with a Particular Focus on Periodontitis

Some systemic diseases are unquestionably related to periodontal health, as periodontal disease can be an extension or manifestation of the primary disease process. One example is spontaneous gingival bleeding, resulting from anticoagulant treatment for cardiac diseases. One important aspect of periodontal therapy is the care of patients with poorly controlled disease who require surgery, such as patients with uncontrolled diabetes. We reviewed research on biomarkers and molecular events for various diseases, as well as candidate markers of periodontal disease. Content of this review: (1) Introduction, (2) Periodontal disease, (3) Bacterial and viral pathogens associated with periodontal disease, (4) Stem cells in periodontal tissue, (5) Clinical applications of mass spectrometry using MALDI-TOF-MS and LC-MS/MS-based proteomic analyses, (6) Proteome analysis of molecular events in oral pathogenesis of virus in GCF, saliva, and other oral Components in periodontal disease, (7) Outlook for the future and (8) Conclusions. This review discusses proteome analysis of molecular events in the pathogenesis of oral diseases and viruses, and has a particular focus on periodontitis.

Early and accurate detection of bacterial isolates from dental plaque in subjects with primary, mixed, and permanent dentition by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technique

Background:

Bacterial colonization of dentition in different age groups can impact prognosis in different dental diseases. Latest diagnostic technique such as matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF) is increasingly being used for accurate identification of bacteria. This study was undertaken to evaluate the MALDI-TOF MS technique to identify bacterial pathogens from dental plaques in subjects with primary, mixed, and permanent dentition.

Materials and Methods:

The study included 150 subjects of different age groups and were divided into three groups - Group A: Subjects with primary dentition (n = 50), Group B: Subjects with mixed dentition (n = 50), and Group C: Subjects with permanent dentition (n = 50). Subgingival dental plaque samples were collected from buccal and lingual surfaces of premolar and molar teeth. Clinical parameters such as gingival index were recorded. Samples were cultured in routine aerobic and anaerobic medium. Bacterial growths were assessed by semiquantitative methods. Bacterial isolates were confirmed by MALDI-TOF MS technique.

Results:

MALDI-TOF MS detected all the culture-grown bacteria. In primary dentition group, purple and yellow complex bacteria predominated. Streptococcus spp. was the predominant bacteria (51%) followed by Escherichia coli (19%) and Veillonella spp. (19%). In mixed dentition and permanent group also, Streptococcus spp. was predominant (46%) followed by Veillonella spp. (24%) and E. coli(19%). However, in both groups, orange complex bacteria (bridge complex) such as Prevotella nigrescens and red complex bacteria (Porphyromonas gingivalis, 3%) were seen. For majority of bacteria, the load increased with age.

Conclusions:

The bacterial isolates showed a distinct age-specific colonization. The use of advanced technique such as MALDI-TOF MS is helpful in the detection of periodontal pathogens, and the effective oral health programs can be implemented to minimize the risk of periodontal diseases.

Microbiological Aspects of Naturally Occurring Primary Endodontic Infections in Dogs

Dental fractures are common in dogs, but data on microbiology of naturally occurring primary endodontic infections, and their relation to clinical and radiographic signs, are lacking. Samples were obtained from root canals of 32 periodontally healthy fractured teeth under aseptic conditions and immediately cultured for aerobic and anaerobic bacteria. Cultures were further identified by matrix-assisted laser desorption/ionization, time of flight technology. Sixty-one bacteria (30 bacterial species) were isolated from root canals; 54% were Gram-negative bacteria, 53% were facultative anaerobic, and 42% were anaerobic bacteria. Number of bacterial species in the root canals declined with the duration of fractures over 12 months. No statistically significant association was found between the number of bacterial species involved in the root canal infection and any of the clinical or radiographic signs of endodontic disease. Naturally occurring primary endodontic infections in dogs appear to be polymicrobial and involve only a selected number of opportunistic pathogen species.

How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown

Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.

Identification of microbiota in peri-implantitis pockets by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The purpose of this study was to identify the microbial communities that colonize peri-implantitis pockets using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Subjects having at least one implant with peri-implantitis, no diabetes, and not taking antibiotics in the previous 3 months were selected. Peri-implantitis was defined when surrounding bone loss ≥0.5 mm and bleeding on probing was found. Microbial samples were collected from peri-implantitis pockets using paper points. After incubation and isolation, the colonies were analyzed by MALDI-TOF MS. A total of 126 isolates were cultivated and identified from 12 samples, in identification rates of 82.5% at the species level and 12.72% at the genus level. Although the compositions were highly variable, major habitants in different peri-implant pockets could be identified. Among them the most distinguished were Neisseria flavescens (87%), Streptococcus constellatus (56%), Slackia exigua (46%), Streptococcus intermedius (45%), Fusobacterium nucleatum (45%) and Gemella morbillorum (43%). This preliminary study provides comprehensive and reliable data for future study designs involving MALDI-TOF MS and peri-implantitis in a more specific, easy, rapid and economical way. MALDI-TOF MS could be a new clinical method to evaluate and monitor oral microbiota associated with the disease.

Identification of Porphyromonas isolates from clinical origin using MALDI-TOF Mass Spectrometry

Despite the wide implementation of MALDI-TOF MS for the rapid and reliable identification of most microorganisms, some taxonomic groups such as the Porphyromonas genus remain largely untested. In this study we evaluated the performance of MALDI-TOF MS on this genus using a collection of 39 isolates sent for routine identification to our institution over a 16-year period. All of them were identified by DNA-sequencing analysis of the 16S rRNA gene plus the hsp60 gene when the previous one did not yield species-level assignment. MALDI-TOF MS provided correct identification at least at the genus level of 21/39 isolates (53.9%). Twelve isolates were correctly identified at the species level with a score value ≥ 2.0 and 9 more with score values < 2.0 and ≥ 1.7. The species most represented in the database (P. gingivalis and P. somerae) lay within this category. However, the species poorly represented in this database (P. asaccharolytica and P. uenonis) were mostly identified with lower scores (1.35-1.67) or remained unidentified by MALDI-TOF MS. The addition of two P. asaccharolytica reference spectra to our in-house library allowed 72.9% of genus-level identifications with 17/37 isolates (45.9%) identified with score values ≥ 2.0. Our results showed a high level of correlation between MALDI-TOF MS and DNA-based identification for Porphyromonas spp. strains at the species level, even with score values < 2.0. The reliability provided by MALDI-TOF MS increased when the database was fed with spectra from the species poorly represented in the commercial database.

Critical review on biofilm methods

Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.

Selected Topics in Anaerobic Bacteriology

Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.

Association of clinical parameters with periodontal bacterial haemolytic activity

AIMS

To determine whether haemolytic activity of subgingival bacteria is associated with periodontitis clinical parameters and to identify which bacteria produce the haemolysins.

MATERIALS AND METHODS

Subgingival plaque samples from 22 untreated chronic periodontitis patients were investigated by culture and identified with matrix assisted laser desorption/ionisation time-of-flight mass spectrometry.

RESULTS

Total aerobic and anaerobic bacterial viable counts, percentage distribution of α- and β-haemolytic bacteria were significantly elevated in diseased sites in relation to healthy sites (p < 0.001). Periodontal pathogens were more frequently detected at diseased sites: Porphyromonas gingivalis, Tannerella forsythia, Treponema sp., Prevotella sp., Parvimonas micra, Fusobacterium sp., Campylobacter sp., Capnocytophaga sp., and Selenomonas sp. Haemolytic unidentifiable species and Gram-positive anaerobes such as Slackia exigua, Solobacterium moorei, and Bulledia extructa were also more frequently detected at diseased sites. In diseased sites, the presence of different haemolytic characteristics was more strongly correlated with clinical measures of disease than the mere absence or presence of specific species. The strongest correlation with probing pocket depth was observed for overall β-haemolytic toxicity (r = 0.73, p < 0.001).

CONCLUSION

A strong association was observed between subgingival bacterial haemolytic activity and clinical parameters in patients with chronic periodontitis. Further investigations are warranted to delineate the role of haemolysins in the pathogenesis of periodontitis.

Prevalence of Actinomyces spp. in patients with chronic periodontitis

This study investigated the prevalence of Actinomyces spp. in shallow, deep and very deep pockets of patients with chronic periodontitis compared to healthy controls and correlated the results with clinical status. Twenty patients with chronic periodontitis and 15 healthy subjects were enrolled in this study. Clinical indices were recorded in a six-point measurement per tooth. From each patient samples of supra and subgingival plaque were taken separately from teeth with shallow, deep and very deep pockets. Samples of supragingival plaque and sulcular microflora were collected from the healthy subjects. All the samples were cultivated on different media at 37̊C in an anaerobic atmosphere for 7 days. All the suspect colonies were identified using a rapid ID 32 A system (bioMèrieux) and MALDI-TOF-MS analysis using an Autoflex II Instrument (Bruker Daltonics) together with in house developed identification software and a reference spectra database. A total of 977 strains were identified as Actinomyces. Actinomyces naeslundii/oris/johnsonii (430 isolates) was the most prevalent species and was found in all patients and in almost all of the healthy subjects. Significant differences (p=0.003) between the groups were found for Actinomyces odontolyticus/meyeri and Actinomyces israelii which were associated with periodontitis patients. Actinomyces dentalis was found in higher percentage (p=0.015) in the periodontitis group. Actinomyces gerencseriae and Actinomyces massiliensis were significantly more often found supragingivally than subgingivally (p=0.004, p=0.022, respectively) in the periodontitis group. Whether some Actinomyces species, definitely important plaque formers, are actively involved in the pathogenicity of chronic periodontitis needs further investigation.

A brief case study demonstrating the applicability of MALDI mass spectrometry for detecting bacteria in dental samples

MALDI-MS detection of bacteria in dental infection.

Special application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiological diagnostics

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry as a new possibility for rapid identification of bacteria and fungi revolutionized the clinical microbiological diagnostics. It has an extreme importance in the routine microbiological laboratories, as identification of the pathogenic species rapidly will influence antibiotic selection before the final determination of antibiotic resistance of the isolate. The classical methods for identification of bacteria or fungi, based on biochemical tests, are influenced by many environmental factors. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a rapid method which is able to identify a great variety of the isolated bacteria and fungi based on the composition of conserved ribosomal proteins. Recently several other applications of the method have also been investigated such as direct identification of pathogens from the positive blood cultures. There are possibilities to identify bacteria from the urine samples in urinary tract infection or from other sterile body fluids. Using selective enrichment broth Salmonella sp from the stool samples can be identified more rapidly, too. The extended spectrum beta-lactamase or carbapenemase production of the isolated bacteria can be also detected by this method helping the antibiotic selection in some cases. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry based methods are suitable to investigate changes in deoxyribonucleic acid or ribonucleic acid, to carry out rapid antibiotic resistance determination or other proteomic analysis. The aim of this paper is to give an overview about present possibilities of using this technique in the clinical microbiological routine procedures. Orv. Hetil., 2014, 155(38), 1495–1503.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a new possibility for the identification and typing of anaerobic bacteria

ABSTRACT: 

Anaerobic bacteria predominate in the normal flora of humans and are important, often life-threatening pathogens in mixed infections originating from the indigenous microbiota. The isolation and identification of anaerobes by phenotypic and DNA-based molecular methods at a species level is time-consuming and laborious. Following the successful adaptation of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the routine laboratory identification of bacteria, the extensive development of a database has been initiated to use this method for the identification of anaerobic bacteria. Not only frequently isolated anaerobic species, but also newly recognized and taxonomically rearranged genera and species can be identified using direct smear samples or whole-cell protein extraction, and even phylogenetically closely related species can be identified correctly by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Typing of anaerobic bacteria on a subspecies level, determination of antibiotic resistance and direct identification of blood culture isolates will revolutionize anaerobe bacteriology in the near future.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology

Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.

Advancement in the routine identification of anaerobic bacteria by MALDI-TOF mass spectrometry

We evaluated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) Biotyper as a tool for the identification of anaerobic bacteria compared with 500 base-pair (bp) 16S ribosomal ribonucleic acid (rRNA) gene sequencing analysis, which is considered to be the "gold standard" method. A total of 484 anaerobic bacteria were retrieved from the clinical specimens of 318 pediatric patients. Molecular identification resulted in 18 genera and 51 species. The most prevalent genus was Clostridium (76.85 %), with 70 % C. difficile isolates. The concordance and sensitivity determined by MALDI-TOF MS for C. difficile, the most prevalent species isolated, was 94.08 %, whereas the specificity was 100 %. For the other anaerobes, the sensitivity and specificity were 94.07 % and 81.82 %, respectively, with a concordance of 93.15 %. Low performance was observed for Propionibacterium acnes and Fusobacterium nucleatum, for which a dedicated pretreatment procedure should likely be set up. MALDI-TOF MS was shown to be a valid alternative for the fast and reliable identification of the most clinically relevant anaerobic bacteria; moreover, it is less time-consuming, the cost for reagents is minimized, and it does not require dedicated personnel.

Association of periodontitis with increased colonization by Prevotella nigrescens

AIM

To estimate differences in the prevalence of Prevotella intermedia and Prevotella nigrescens in the subgingival plaque of patients with periodontitis (including aggressive and advanced chronic periodontitis) compared to healthy controls, and to search for significant associations with clinical status.

METHODS

Sixteen patients and 16 healthy controls were enrolled in this study. Interproximal plaque index, oral hygiene index, gingival index, bleeding on probing, probing depth, and clinical attachment level were recorded. Samples of subgingival plaque were taken with paper points from four teeth of each individual and immediately plated on appropriate supplemented Columbia agar. Black pigmented colonies were identified with the Rapid ID32 A system, and further differentiated using matrix-assisted laser desorption ionization-time of flight mass spectrometry. For the statistical analysis, chi-squared test and the Mann-Whitney U-test were used.

RESULTS

Prevotella nigrescens was isolated from 10 patients and three controls, while P. intermedia was isolated from only two patients. P. nigrescens was found more frequently in the subgingival plaque of patients (P = 0.029), and was significantly associated with high values of clinical indices (P ≤ 0.025). Significant differences for P. intermedia were not found.

CONCLUSIONS

Periodontitis seems to be associated with increased colonization with P. nigrescens. Whether or not it is a major pathogen needs to be determined.

[Reliability of MALDI-TOF mass spectrometry in the identification of anaerobic bacteria]

AIM OF THE STUDY

MALDI-TOF mass spectrometry (MS) is becoming a major resource in the Clinical Microbiology laboratory. Results on some groups of microorganisms are still controversial. We have studied the reliability of MALDI-TOF MS for the identification of anaerobic clinical isolates was studied compared to conventional biochemical methods, with rRNA 16S sequencing being used as a reference when discrepancies arose.

MATERIAL AND METHODS

A total of 126 anaerobic bacteria clinical isolates were studied by using API20A kits (bioMérieux, Marcy l'Étoile, France) and MALDI-TOF MS (Autoflex II, Bruker Daltonics, Germany), and using the data library BioTyper 2.0 (Bruker Daltonics, Germany). When discrepancies arose, or MALDI-TOF MS was not able to identify any microorganism, rRNA 16S sequencing was used as the reference standard.

RESULTS

The biochemical method and MALDI-TOF MS agreed in identifying 60.9% of isolates at species level, and 20.3% of isolates at genus level. Among the 48 discrepancies observed, rRNA 16S sequencing supported MALDI-TOF MS identification, at species level, in 32 isolates (66.7%), and in 8 isolates (16.7%) at genus level. rRNA 16S sequencing supported biochemical identification in only two isolates (4.2%) at species level, and in 26 isolates (54.2%) at genus level. The eight isolates for which MALDI-TOF MS did not manage to identify, or the identification obtained was rejected by sequencing, belonged to species that are still not added to the BioTyper II data library.

CONCLUSIONS

Results obtained in this study show that, overall, MALDI-TOF MS identification of anaerobic bacteria is more reliable than identification obtained by conventional biochemical methods (24% more correct identifications at species level). The number of major errors (incorrect identification at the genus level) is also 2.5-times lower. Moreover, all the major errors obtained by MALDI-TOF MS were due to the absence of some species in the data library. Thus, when data libraries are more complete, reliability differences between both methods will probably be even higher.

Species identification of clinical Prevotella isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry

The performance of matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) for species identification of Prevotella was evaluated and compared with 16S rRNA gene sequencing. Using a Bruker database, 62.7% of the 102 clinical isolates were identified to the species level and 73.5% to the genus level. Extension of the commercial database improved these figures to, respectively, 83.3% and 89.2%. MALDI-TOF MS identification of Prevotella is reliable but needs a more extensive database.

[Proteomic applications in the Clinical Microbiology laboratory]

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is rapidly becoming a new routine resource in Clinical Microbiology laboratories. Its usefulness for bacterial identification is now generally accepted, although there is still some reluctance as regards specific bacterial groups and some other microorganisms, such as moulds. There are other potential applications of this technology in Clinical Microbiology, which are beginning to be developed. A review is presented on the current data on the identification of microorganisms, including the most problematic groups, such as mycobacteria, anaerobic bacteria and moulds. We also analyse its applications for direct sample identification, its impact on pathogenic characteristics of microorganisms, and its potential epidemiological applications. Finally, we review the studies published on its applications for determining antimicrobial susceptibility, and its applications on amplicons, instead of microorganism protein extracts.

Actinobaculum schaalii: review of an emerging uropathogen

Actinobaculum schaalii is a facultative anaerobic, Gram-positive rod-shaped species phylogenetically related to Actinomyces that is likely part of the commensal flora of the human genitourinary tract. Because of its fastidious growth under aerobic conditions and its resemblance to bacteria of the resident flora, A. schaalii is frequently overlooked or considered as a contaminant. It is also difficult to identify phenotypically, still requiring molecular identification. Note that the recent technology of matrix-assisted laser desorption/ionisation time-of-flight-mass spectrometry could be a promising tool for its identification. Recent studies using sensitive PCR assays showed that its clinical significance was largely underestimated. Since its first description in 1997, A. schaalii has been responsible for numerous urinary tract infections (UTIs), mainly in elderly (usually >60 years) and patients with underlying urological conditions. Infected urines usually show many Gram-positive rods with significant leukocyturia and a negative test for nitrites. Numerous cases of severe infections have also been described, such as urosepsis, bacteremia, cellulitis, spondylodiscitis, and endocarditis. In vitro, A. schaalii is highly susceptible to β-lactams but it is resistant to ciprofloxacin and cotrimoxazole, first-choice antimicrobials for the oral treatment of UTIs. A penicillin (e.g. amoxicillin) or a cephalosporin (e.g. cefuroxime, ceftriaxone) should be the preferred treatment.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of Archaea: towards the universal identification of living organisms

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) identification of Archaea has been limited to some environmental extremophiles belonging to distant taxa. We developed a specific protocol for MALDI-TOF-MS identification of Archaea and applied it to seven environmental human-associated Methanobrevibacter smithii, Methanobrevibacter oralis, Methanosphaera stadtmanae, and the recently described Methanomassiliicoccus luminyensi Archaea. After mechanical lyse, we observed a unique protein profile for each organisms comprising 7-24 peaks ranging from 3,015 to 10,632 Da with a high quality score of 7.38 ± 1.26. Profiles were reproducible over successive experiments performed at 1, 2, and 3-week growth durations and unambiguously distinguished the Archaea from all of the 3,995 bacterial spectra in the Brüker database. After the incorporation of the determined profiles into a local database, archaeal isolates were blindly identified within 10 min with an identification score of 1.9-2.3. The MALDI-TOF-MS-based clustering of these archaeal organisms was consistent with their 16S rDNA sequence-based phylogeny. These data prove that MALDI-TOF-MS profiling could be used as a first-line technique for the identification of human Archaea. In complement to previous reports for animal cells, Bacteria and giant viruses, MALDI-TOF-MS therefore appears as a universal method for the identification of living unicellular and multicellular organisms.

Matrix-assisted laser-desorption/ionization biotyper: experience in the routine of a University hospital

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) is positioned at the forefront of bacterial identification in the future. Its performance needed to be evaluated in a routine Bacteriology laboratory to determine its true benefits. A prospective study was carried out in the Bacteriology laboratory of the Pellegrin University Hospital in Bordeaux, France, from April to May 2009. Bacterial isolates from clinical samples were identified by conventional phenotypic bacteriological methods [Phoenix (Becton-Dickinson) or API strips (bioMérieux)] and in parallel with a mass spectrometer (Ultraflex III TOF/TOF and the biotyper database from Bruker Daltonics). In case of a discrepancy between these results at the genus level, a 16S rRNA and/or rpoB gene sequencing was performed. Of the 1013 bacteria tested, 837 (82.6%) were correctly identified at the species level by MALDI-TOF mass spectrometry (MS) without extraction and 189 after extraction, i.e. 986 (97.3%) were correctly identified at the species level by MALDI-TOF MS, vs. 945 (93.2%) by phenotypic methods. Indeed, the extraction step was necessary for only 15% of the isolates. These results were even better when considering the genus, reaching almost 99% with MALDI-TOF MS and 98% with phenotypic methods. The performance of MALDI-TOF MS is very attractive considering its efficiency and rapidity, and the technique constitutes a precious tool for bacteriological identification in a routine laboratory.

The identification of anaerobic bacteria using MALDI-TOF MS

Matrix Assisted Laser Desorption and Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has gained more and more popularity for the identification of bacteria. Several studies show that bacterial diagnosticis is being revolutionized by the application of MALDI-TOF MS. For anaerobic bacteria, MALDI-TOF MS has been used for the identification of Prevotella spp., Fusobacterium spp., Clostridium spp., Bacteroides spp. and Gram-positive anaerobic cocci. However, to identify bacteria reliably, an extensive database is essential. For routine identification of anaerobic bacteria available databases need to be optimised.

Application and use of various mass spectrometry methods in clinical microbiology

When confronted with a septic patient or dealing with an emerging epidemic, clinicians, infection control specialists and microbiologists have often felt an immense 'need for speed' while waiting for culture results. Various mass spectrometry (MS) applications are about to answer most of their demands. Matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) MS of whole bacterial cells has already greatly shortened the time needed for identification of a positive culture in major diagnostic laboratories in Europe. MS is described in this article, with a special emphasis on the different systems currently commercially available for routine identification. MALDI-TOF MS remains, however, limited by the previous time-consuming culture steps, and is not suited for strain typing in epidemic contexts. These limitations can be overcome by other applications of MS in microbiology. MALDI-resequencing is a rapid method for genotyping, offering comparable results to multilocus sequence typing. New systems of broad-range PCR, associated with analyses of amplicons by electrospray ionization MS, might allow nearly full automation for the direct identification of pathogens in blood, thus bypassing the culture stage. This article describes various applications of MS methods in clinical microbiology, and provides a comparative table of these technologies.

New insights into Prevotella diversity and medical microbiology

In light of recent studies based on cultivation-independent methods, it appears that the diversity of Prevotella in human microbiota is greater than was previously assumed from cultivation-based studies, and that the implication of these bacteria in several human diseases was unrecognized. While some Prevotella taxa were found during opportunistic infections, changes in Prevotella abundance and diversity were discovered during dysbiosis-associated diseases. As member of the microbiota, Prevotella may also be considered as a reservoir for resistance genes. Greater knowledge on Prevotella diversity, as well as new insights into its pathogenic potential and implication in dysbiosis are expected from the use of human microbe identification microarrays, from whole-genome sequence analyse, and from the NIH Human Microbiome Project data. New approaches, including molecular-based methods, could contribute to improve the diagnosis of Prevotella infections.

Comparison of two matrix-assisted laser desorption ionisation-time of flight mass spectrometry methods for the identification of clinically relevant anaerobic bacteria

Two commercially available MALDI-TOF MS systems, Bruker MS and Shimadzu MS, were compared for the identification of clinically relevant anaerobic bacteria. A selection of 79 clinical isolates, representing 19 different genera, were tested and compared with identification obtained by 16S rRNA gene sequencing. Correct genus identification was achieved for 71% of isolates by Shimadzu MS and for 61% by Bruker MS. Correct identification at the species level occurred in 61% and 51%, respectively. Shimadzu showed markedly better results for identification of Gram-positive anaerobic cocci. In contrast, the Bruker system performed better than Shimadzu for the Bacteroides fragilis group. When strains not present in the database were excluded from the analyses for each database, both systems performed equally well, with 76.7% and 75.0% correct genus identification for Shimadzu and Bruker, respectively. Similarly, when the most recently updated Bruker database was applied, no difference was observed. We conclude that the composition and quality of the database is crucial for a correct identification. The databases currently available for both systems need to be optimized before MS can be implemented for routine identification of anaerobic bacteria.

Identification of HACEK clinical isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry is a rapid and accurate tool for the identification of many microorganisms. We assessed this technology for the identification of 103 Haemophilus parainfluenzae, Aggregatibacter aphrophilus, Aggregatibacter actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, and Kingella kingae (HACEK) clinical isolates and 20 Haemophilus influenzae clinical isolates. Ninety-three percent of HACEK organisms were identified correctly to the genus level using the Bruker database, and 100% were identified to the genus level using a custom database that included clinical isolates.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of environmental organisms: the Planctomycetes paradigm

We have developed a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based identification technique for Planctomycetes organisms, which are used here as bacteria of suitable diversity at genus and species level for testing resolution of the method. Planctomyces maris ATCC 29201, Planctomyces brasiliensis ATCC 49424(T) , P. brasiliensis ATCC 49425, Planctomyces limnophilus ATCC 43296(T) , Blastopirellula marina ATCC 49069(T) , Rhodopirellula baltica DSM 10527(T) and Gemmata obscuriglobus DSM 5831(T) were cultured on half-strength marine broth and agar, or alternatively on caulobacter broth and agar. The resulting pellets of organisms (liquid) or colonies (solid agar) were directly applied to a MALDI-TOF plate. This yielded a reproducible, unique protein profiles comprising 23-39 peaks ranging in size from 2403 to 12 091 Da. These peaks were unambiguously distinguished from any of the 3038 bacterial spectra in the Brüker database. Matrix-assisted laser desorption/ionization time-of-flight patterns were similar for isolates grown in solid and in liquid medium, albeit the patterns from solid growth were more easily interpretable. After the incorporation of the herein determined profiles into the Brüker database, Planctomycetes isolates were blindly identified within 10 min, with an identification score in the range of 1.8 to 2.3. Matrix-assisted laser desorption/ionization time-of-flight-based clustering of these Planctomycetes organisms was consistent with 16S rDNA-based phylogeny. However, the incorporation of additional non-Planctomycetes MALDI-TOF profiles in the analysis resulted in inconsequential clustering. In conclusion, MALDI-TOF protein profiling is a new approach for the rapid and accurate identification of cultured environmental organisms, as illustrated in this study through the analysis of Planctomycetes.

MALDI-TOF-mass spectrometry applications in clinical microbiology

MALDI-TOF-mass spectrometry (MS) has been successfully adapted for the routine identification of microorganisms in clinical microbiology laboratories in the past 10 years. This revolutionary technique allows for easier and faster diagnosis of human pathogens than conventional phenotypic and molecular identification methods, with unquestionable reliability and cost–effectiveness. This article will review the application of MALDI-TOF-MS tools in routine clinical diagnosis, including the identification of bacteria at the species, subspecies, strain and lineage levels, and the identification of bacterial toxins and antibiotic-resistance type. We will also discuss the application of MALDI-TOF-MS tools in the identification of Archaea, eukaryotes and viruses. Pathogenic identification from colony-cultured, blood-cultured, urine and environmental samples is also reviewed.

Actinomycosis of the temporal bone and brain: case report and review of the literature

OBJECTIVES

Actinomycosis is a rare disease with a typically indolent course in the head and neck. During the modern era, only 12 cases within the ear and temporal bone and 75 intracranial cases have been reported. We present a case of actinomycosis of the petrous apex that led to meningitis and encephalitis.

METHODS

The patient was a 12-year-old girl who presented with mental status changes. After 48 hours of treatment with empiric antibiotics for meningitis without improvement, imaging revealed an enhancing mass in the right petrous apex, destruction of the cochlea, meningeal enhancement, and left temporoparietal encephalitis.

RESULTS

The initial therapy included broad-spectrum antibiotic, antifungal, and antiviral agents, as well as myringotomy and tympanostomy tube placement. When the patient's clinical status worsened, she underwent subtotal petrosectomy with drainage of the petrous apex. The final pathologic findings were consistent with actinomycosis.

CONCLUSIONS

Actinomycosis is a rare infection in the temporal bone and central nervous system that can have a high mortality risk if not treated appropriately. Often, these bacteria do not grow well in culture, and diagnosis must be made on the basis of histopathologic features. Good clinical outcomes can be obtained with surgical debridement followed by long-term antibiotic treatment.

Identification of clinically important anaerobic bacteria by an oligonucleotide array

Anaerobic bacteria can cause a wide variety of infections, and some of these infections can be serious. Conventional identification methods based on biochemical tests are often lengthy and can produce inconclusive results. An oligonucleotide array based on the 16S-23S rRNA intergenic spacer (ITS) sequences was developed to identify 28 species of anaerobic bacteria and Veillonella. The method consisted of PCR amplification of the ITS regions with universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of 35 oligonucleotide probes (17- to 30-mers) immobilized on a nylon membrane. The performance of the array was determined by testing 310 target strains (strains which we aimed to identify), including 122 reference strains and 188 clinical isolates. In addition, 98 nontarget strains were used for specificity testing. The sensitivity and the specificity of the array for the identification of pure cultures were 99.7 and 97.1%, respectively. The array was further assessed for its ability to detect anaerobic bacteria in 49 clinical specimens. Two species (Finegoldia magna and Bacteroides vulgatus) were detected in two specimens by the array, and the results were in accordance with those obtained by culture. The whole procedure of array hybridization took about 8 h, starting with the isolated colonies. The array can be used as an accurate alternative to conventional methods for the identification of clinically important anaerobes.

Rapid identification of Legionella species by mass spectrometry

Legionella species are facultative, intracellular bacteria that infect macrophages and protozoa, with the latter acting as transmission vectors to humans. These fastidious bacteria mostly cause pulmonary tract infections and are routinely identified by various molecular methods, mainly PCR targeting the mip gene and sequencing, which are expensive and time-consuming. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has emerged as a rapid and inexpensive method for identification of bacterial species. This study evaluated the use of MALDI-TOF-MS for rapid species and serogroup identification of 21 Legionella species recognized as human pathogens. To this end, a reference MS database was developed including 59 Legionella type strains, and a blind test was performed using 237 strains from various species. Two hundred and twenty-three of the 237 strains (94.1 %) were correctly identified at the species level, although ten (4.2 %) were identified with a score lower than 2.0. Fourteen strains (5.9 %) from eight species were misidentified at the species level, including seven (3.0 %) with a significant score, suggesting an intraspecific variability of protein profiles within some species. MALDI-TOF-MS was reproducible but could not identify Legionella strains at the serogroup level. When compared with mip gene sequencing, MALDI-TOF-MS exhibited a sensitivity of 99.2 and 89.9 % for the identification of Legionella strains at the genus and species level, respectively. This study demonstrated that MALDI-TOF-MS is a reliable tool for the rapid identification of Legionella strains at the species level.