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

Clostridium paraputrificum Bacteremia and Ectopic Ileal Varices in Underlying Chronic Portal and Superior Mesenteric Vein Thrombosis: Report of a Rare Case

Ischemic bowel disease is considered a high-risk factor for infection from anaerobic bacteria, as the ischemic bowel is the perfect ground for their development. Herein, we present the case of an advance stage colon cancer patient with a rare cause of gastrointestinal bleeding and bacteremia due to Clostridium paraputrificum, a rare anaerobic Gram-positive bacterium. The patient had presented with several episodes of hematochezia in the context of chronic superior mesenteric-portal vein tumor thrombosis and rupture of ectopic varices, and the bacteremia was an unexpected complication of the bowel ischemia due to a combination of arterial ischemia and venous congestion.

Lipidomic approach to identify Escherichia coli and Shigella spp. by matrix-assisted laser desorption/ionization mass spectrometry

PURPOSE

Escherichia coli (E. coli) and Shigella species, being highly similar, present a challenge for differentiation using classical methods such as phenotyping, 16S rRNA sequencing, or protein profiling using matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The paper proposes a method for identifying E. coli, S. flexneri, S. sonnei, and S. boydii by augmenting the Bruker Biotyper database with reference spectra of lipid profiles obtained using MALDI MS in the positive mode.

MATERIALS/METHODS

Lipid extracts were made from cultured E. coli, S. flexneri, S. sonnei and S. boydii using the Bligh & Dyer protocol. MALDI MS spectra in positive ion mode were performed for the extracts. Reference spectra were created from 30 spectra for each bacterium and added to the Bruker Biotyper database.

RESULTS

Identification of bacteria based on lipid profiles in the Biotyper database gave correct results with scores above 2.49. Statistical analysis of the results by Partial Least Squares-Discriminant Analysis (PLS-DA) showed that it is possible to correctly differentiate the microorganisms studied using the lipidomic approach. A panel of six m/z values was proposed for which the value of the area under the ROC curve is 1, thus enabling the identification of E. coli and S. flexneri with 100 ​% accuracy.

CONCLUSIONS

Identification of bacteria from lipid fingerprints obtained by the MALDI MS technique is possible and may become a useful tool in the future, especially for microorganisms that are difficult to distinguish by other methods.

Comparison of the Bruker Microflex LT and Zybio EXS2600 MALDI TOF MS systems for the identification of clinical microorganisms

The emergence of Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI TOF MS) technology has expanded the capabilities for identifying microorganisms in clinical labs, replacing traditional biochemical testing with a proteomic approach. In the present study, we compared results between the two commercial MALDI TOF MS systems, Bruker Microflex LT Biotyper and Zybio EXS2600 Ex-Accuspec, for the identification of 1979 urinary isolates by direct extraction method. Current study found that both systems identified a high percentage of isolates to at least the genus level - Bruker 95.6 % of isolates, Zybio 92.4 %. In the case of 89.5 % of all analyzed spectra, the identification results were consistent between the used devices. The highest score values and the highest percentage of spectra identified to species were obtained for gram-negative bacteria. The results show that both systems are equally good choices in terms of analytical performance for routine microbiological diagnostic procedures.

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.

Development and validation of main spectral profile for rapid identification of Yersinia ruckeri isolated from Atlantic salmon using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows rapid and reliable identification of microorganisms. The accuracy of bacterial identification using MALDI-TOF MS depends on main spectral profiles (MSPs) provided in a quality-assured commercial reference library, which requires ongoing improvement. This study aimed to develop and validate an in-house MALDI-TOF MS MSP to rapidly identify Yersinia ruckeri isolated from Atlantic salmon (Salmo salar). The novel MSP was prepared using an isolate of Y. ruckeri recovered from Atlantic salmon and confirmed by 16S rRNA gene sequencing. Subsequently, a validation set which comprises 29 isolates of Y. ruckeri were examined from three fishes: Atlantic salmon (Salmo salar) (n = 26), American eel (Anguilla rostrata) (n = 1), and Atlantic cod (Gadus morhua) (n = 2). These isolates were randomly selected from the Atlantic Veterinary College, Aquatic Diagnostic Services Bacteriology Laboratory's culture collection to validate the novel MSP. Analytical sensitivity of MALDI-TOF MS using the novel MSP to identify the validation set was 86.2%. Repeatability was assessed by acquiring spectra from 30 different spots of a randomly-selected isolate of Y. ruckeri, and analyzed spectra from each spot were compared against the novel MSP. The coefficient of variation was 3.3%. The novel MSP clustered with Bruker MSPs (n = 3) of Y. ruckeri in the reference library and did not falsely identify any closely related bacteria to Y. ruckeri. This study reports the development of a novel MSP of high analytical sensitivity and specificity for rapid identification of Y. ruckeri using MALDI-TOF MS.

First case of an invasive Bacteroides dorei infection detected in a patient with a mycotic aortic aneurysm-raising a rebellion of major indigenous bacteria in humans: a case report and review

Background

Bacteroides dorei is an anaerobic gram-negative bacterium first described in 2006. Because of the high similarity in mass spectra between B. dorei and Bacteroides vulgatus, discriminating between these species is arduous in clinical practice. In recent decades, 16S rRNA gene sequencing has been a complementary method for distinguishing taxonomically close bacteria, including B. dorei and B. vulgatus, at the genus and species levels. Consequently, B. dorei has been shown to contribute to some diseases, including type 1 autoimmune diabetes mellitus and atherosclerotic diseases. However, there are no reports on invasive infectious diseases caused by B. dorei. This report describes the first case of direct invasion and colonisation of human tissue by B. dorei, thus providing a warning regarding the previously proposed application of B. dorei as a live biotherapeutic for atherosclerotic diseases.

Case presentation

A 78-year-old Japanese man complained of intermittent chest/back pain and was diagnosed with a mycotic thoracic aortic aneurysm by enhanced computed tomography on admission. Despite strict blood pressure control and empirical antibiotic therapy, the patient’s condition worsened. To prevent aneurysmal rupture and eliminate infectious foci, the patient underwent surgical treatment. The resected specimen was subjected to tissue culture and 16S rRNA gene sequencing analysis to identify pathogenic bacteria. A few days after the surgery, culture and sequencing results revealed that the pathogen was B. dorei/B. vulgatus and B. dorei, respectively. The patient was successfully treated with appropriate antibacterial therapy and after improvement, was transferred to another hospital for rehabilitation on postoperative day 34. There was no recurrence of infection or aneurysm after the patient transfer.

Conclusions

This report describes the first case of invasive infectious disease caused by B. dorei, casting a shadow over its utilisation as a probiotic for atherosclerotic diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06345-8.

Innovative and Highly Sensitive Detection of Clostridium perfringens Enterotoxin Based on Receptor Interaction and Monoclonal Antibodies

Clostridium perfringens enterotoxin (CPE) regularly causes food poisoning and antibiotic-associated diarrhea; therefore, reliable toxin detection is crucial. To this aim, we explored stationary and mobile strategies to detect CPE either exclusively by monoclonal antibodies (mAbs) or, alternatively, by toxin-enrichment via the cellular receptor of CPE, claudin-4, and mAb detection. Among the newly generated mAbs, we identified nine CPE-specific mAbs targeting five distinct epitopes, among them mAbs recognizing CPE bound to claudin-4 or neutralizing CPE activity in vitro. In surface plasmon resonance experiments, all mAbs and claudin-4 revealed excellent affinities towards CPE, ranging from 0.05 to 2.3 nM. Integrated into sandwich enzyme-linked immunosorbent assays (ELISAs), the most sensitive mAb/mAb and claudin-4/mAb combinations achieved similar detection limits of 0.3 pg/mL and 1.0 pg/mL, respectively, specifically detecting recombinant CPE from spiked feces and native CPE from 30 different C. perfringens culture supernatants. The implementation of mAb- and receptor-based ELISAs into a mobile detection platform enabled the fast detection of CPE, which will be helpful in clinical laboratories to diagnose diarrhea of assumed bacterial origin. In conclusion, we successfully employed an endogenous receptor and novel high affinity mAbs for highly sensitive and specific CPE-detection. These tools will be useful for both basic and applied research.

Prevalence and Characteristics of Bacillus cereus Group Isolated from Raw and Pasteurised Milk

The elimination of spore-forming bacteria is not guaranteed by current pasteurisation processes and is a challenging problem for the dairy industry. Given that Bacillus cereus sensu lato (B. cereus group) is an important foodborne pathogen and spoiler in the dairy industry, this study aimed at evaluating the prevalence and characteristics of B. cereus group in raw and pasteurised milk samples collected in Victoria, Australia. Isolated B. cereus group were tested for antimicrobial susceptibility, biofilm formation and virulence properties. Genetic diversity was assessed using ERIC-PCR. Proteomic profiling using MALDI-TOF MS and chemical profiling using Fourier-transform infrared (FTIR) spectroscopy were also applied for clustering of the isolates. Results showed 42.3% of milk samples contained B. cereus group, with a higher contamination level for pasteurised milk. Virulence studies identified genes nheA, nheB, hblA and nheC in most isolates and cyk gene in 46% of all isolates. Antimicrobial susceptibility testing showed a high prevalence of resistance towards ampicillin, ceftriaxone and penicillin. The biofilm-forming capacity of our isolates showed that most (53.7%) had the ability to form a biofilm. Genetic profiling using ERIC-PCR placed most B. cereus group isolates from pasteurised milk in the same cluster, indicating that they probably originated from a similar source. Raw milk isolates showed greater diversity indicating various sources. FTIR spectroscopy showed high agreement with genetic profiling. In contrast, low agreement between proteomic (MALDI-TOF MS) and genetic typing was observed. The present study showed that the FTIR spectroscopy could be adopted as a rapid tool for the typing of B. cereus group. Overall, the virulence and antimicrobial resistance characteristics, together with the ability of isolates to produce biofilm, indicate the importance of B. cereus group in the Australian dairy industry.

Comparing identification of clinically relevant Prevotella species by VITEK MS and MALDI biotyper

In this multicenter study, we aimed to evaluate the performance of MALDI Biotyper and VITEK MS, for identification of Prevotella species. Three hundred and fourteen clinical isolates, collected in eight European countries between January 2014 and April 2016, were identified at the collecting sites by MALDI Biotyper (versions 3.0 and 3.1) and then reidentified by VITEK MS (version 3.0) in the central laboratory. 16S rRNA gene sequencing was used as a standard method. According to sequence analysis, the 314 Prevotella strains belonged to 19 species. MALDI Biotyper correctly identified 281 (89.5%) isolates to the species level and 33 (10.5%) only at the genus level. VITEK MS correctly identified 253 (80.6%) isolates at the species level and 276 (87.9%) isolates at the genus level. Thirty-three isolates belonging to P. bergensis, P. conceptionensis, P. corporis, P. histicola, and P. nanciensis, unavailable in the VITEK MS 3.0 database, were resulted in genus level or no identification. Six Prevotella strains, belonged to P. veroralis, P. timonensis, and P. conceptionensis not represented in the MALDI Biotyper system database, were misidentified at the genus level. In conclusion, both VITEK MS and MALDI Biotyper provided reliable and rapid identification. However, the permanent extension of the databases is needed.

Performance evaluation of a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, ASTA MicroIDSys system, in bacterial identification against clinical isolates of anaerobic bacteria

INTRODUCTION

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced for bacterial identification. The ASTA MicroIDSys system (ASTA, Suwon, Korea) is a new MALDI-TOF MS system developed for species identification of microorganisms. We evaluated the performance of MicroIDSys against clinical isolates of anaerobic bacteria.

MATERIAL AND METHODS

A total of 370 non-duplicated clinical isolates of anaerobic bacteria were tested in this study. Bacterial identification with MicroIDSys was performed with a direct smear method, and measured spectra were analyzed using respective software. The results of MicroIDSys were compared with the results of Bruker Biotyper and 16S rRNA sequencing.

RESULTS

The overall agreement rates for the 370 clinical isolates (34 genera and 99 species) were 95.4% (353/370) at the genus level and 91.6% (n = 340) at the species level. Only 17 isolates were incorrectly identified at the genus level: five misidentifications and 12 unidentifications. The MicroIDSys system exhibited excellent performance in the identification of clinically relevant bacterial species. Most of the Bacteroides isolates (98.0%, 99/101) and all of the Clostridium difficile (100%, n = 11), Clostridium perfringens (100%, n = 10), Finegoldia magna (100%, n = 11), and Parvimonas micra (100%, n = 10) isolates were correctly identified at the species level.

CONCLUSION

The MicroIDSys system proved useful in the identification of anaerobic bacteria, especially clinically relevant species. This system could be of use in clinical microbiology laboratories as a primary tool for identifying anaerobic bacteria.

Application of MALDI-TOF MS to rapid identification of anaerobic bacteria

BACKGROUND

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been rapidly developed and widely used as an analytical technique in clinical laboratories with high accuracy in microorganism identification.

OBJECTIVE

To validate the efficacy of MALDI-TOF MS in identification of clinical pathogenic anaerobes.

METHODS

Twenty-eight studies covering 6685 strains of anaerobic bacteria were included in this meta-analysis. Fixed-effects models based on the P-value and the I-squared were used for meta-analysis to consider the possibility of heterogeneity between studies. Statistical analyses were performed by using STATA 12.0.

RESULTS

The identification accuracy of MALDI-TOF MS was 84% for species (I² = 98.0%, P < 0.1), and 92% for genus (I² = 96.6%, P < 0.1). Thereinto, the identification accuracy of Bacteroides was the highest at 96% with a 95% CI of 95-97%, followed by Lactobacillus spp., Parabacteroides spp., Clostridium spp., Propionibacterium spp., Prevotella spp., Veillonella spp. and Peptostreptococcus spp., and their correct identification rates were all above 90%, while the accuracy of rare anaerobic bacteria was relatively low. Meanwhile, the overall capabilities of two MALDI-TOF MS systems were different. The identification accuracy rate was 90% for VITEK MS vs. 86% for MALDI biotyper system.

CONCLUSIONS

Our research showed that MALDI-TOF-MS was satisfactory in genus identification of clinical pathogenic anaerobic bacteria. However, this method still suffers from different drawbacks in precise identification of rare anaerobe and species levels of common anaerobic bacteria.

Microbiological and Clinical Aspects of Cervicofacial Actinomyces Infections: An Overview

Similarly to other non-spore-forming Gram-positive anaerobes, members of the Actinomyces genus are important saprophytic constituents of the normal microbiota of humans. Actinomyces infections are considered to be rare, with cervicofacial infections (also known as ‘lumpy jaw syndrome’) being the most prevalent type in the clinical practice. Actinomycoses are characterized by a slowly progressing (indolent) infection, with non-specific symptoms, and additionally, the clinical presentation of the signs/symptoms can mimic other pathologies, such as solid tumors, active Mycobacterium tuberculosis infections, nocardiosis, fungal infections, infarctions, and so on. The clinical diagnosis of actinomycosis may be difficult due to its non-specific symptoms and the fastidious, slow-growing nature of the pathogens, requiring an anaerobic atmosphere for primary isolation. Based on 111 references, the aim of this review is to summarize current advances regarding the clinical features, diagnostics, and therapy of cervicofacial Actinomyces infections and act as a paper for dentistry specialists, other physicians, and clinical microbiologists.

Surgical site infection after hip replacement due to a novel Peptoniphilus species, provisionally named 'Peptoniphilus nemausus' sp. nov

We report a case of surgical site infection after total hip prosthesis replacement due to an ofloxacin-resistant Peptoniphilus isolate belonging to an unknown species for which the name 'Peptoniphilus nemausus' sp. nov. is proposed. Follow-up was favourable under clindamycin and rifampin for 3 months in this patient whom had a Proteus mirabilis infection treated by fluoroquinolone.

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 Clostridium spp. derived from a sheep and cattle slaughterhouse by matrix-assisted laser desorption and ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing

Clostridia are widespread and some of them are serious human pathogens. Identification of Clostridium spp. is important for managing microbiological risks in the food industry. Samples derived from sheep and cattle carcasses from a slaughterhouse in Iran were analyzed by MALDI-TOF MS using direct transfer and extended direct transfer sample preparation methods and 16S rDNA sequencing. MALDI-TOF MS could identify ten species in 224 out of 240 Clostridium isolates. In comparison to the 16S rDNA sequencing, correct identification rate of the Clostridium spp. at the species level by MALDI-TOF MS technique was 93.3%. 16 isolates were not identified by MALDI-TOF MS but 16s rDNA sequencing identified them as C. estertheticum, C. frigidicarnis, and C. gasigenes species. The most frequently identified Clostridium species were: C. sporogenes (13%), C. cadaveris (12.5%), C. cochlearium (12%) and C. perfringens (10%). Extended direct transfer method [2.26 ± 0.18 log (score)] in comparison to direct transfer method [2.15 ± 0.23 log (score)] improved Clostridium spp.

IDENTIFICATION

Using a cut-off score of 1.7 was sufficient for accurate identification of Clostridium species. MALDI-TOF MS identification scores for Clostridium spp. decreased with longer incubation time. Clostridium species predominantly were isolated from carcasses after skinning and evisceration steps in the slaughterhouse. MALDI-TOF MS could be an accurate way to identify Clostridium species. Moreover, continuous improvement of the database and MALDI-TOF MS instrument enhance its performance in food control laboratories.

Performance of mass spectrometric identification of clinical Prevotella species using the VITEK MS system: A prospective multi-center study

Prevotella species, members of the human microbiota, can cause opportunistic infections. Rapid and accurate identification of Prevotella isolates plays a critical role in successful treatment, especially since the antibiotic susceptibility profile differs between species. Studies, mostly carried out using the Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Biotyper system, showed that MALDI-TOF MS is an accurate, rapid and satisfactory method for the identification of clinically important anaerobes. In this multi-center study, we assessed the performance of the MALDI-TOF MS VITEK MS system for the identification of clinical Prevotella isolates. A total of 508 Prevotella isolates, representing 19 different species, collected from 11 European countries, Kuwait and Turkey between January 2014 and April 2016, were identified using VITEK MS (v3.0). The reliability of the identification was assessed by 16S rRNA gene sequencing. Using VITEK MS, 422 (83.1%) of the 508 isolates were identified on the species level, 459 (90.4%) on the genus level. A total of 49 (9.6%) isolates were not identified correctly. 16S rRNA gene sequencing results showed that this was partly due to the fact that several species were not represented in the database. However, some species that were represented in the database were also not identified. Five Prevotella strains were misidentified at the genus level, 2 of these strains belonged to a species not represented in the database. In general, the VITEK MS offers a reliable and rapid identification of Prevotella species, however the databases needs to be expanded.

Identification of Clostridium species using the VITEK® MS

The genus Clostridium is of high clinical relevance, as some species may cause rapid and even lethal infections. Thus, a timely identification of these anaerobic bacteria is desirable. Conventional identification methods rely on biochemical properties of these organisms, however, establishing these is time-consuming and not always reliable. Alternatively, 16S rRNA gene sequence based diagnostic methods may be used, but they are expensive and not ubiquitously available. This study was designed to assess the possibility to identify Clostridium species employing the matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). For this purpose, 848 Clostridium strains representing 42 species were analyzed with the VITEK^® MS instrument (bioMérieux, Marcy l'Etoile, France), comparing mass spectra derived from these organisms with the spectra provided in the available database. 90.3% of the strains were correctly identified at species level and another 3.6% at genus level. Since the number of Clostridium species included in the database was rather limited (21 altogether), the spectra obtained were also analyzed employing the Shimadzu Pro Series software. Thus, it became possible to create a dendrogram of the species included in this study.

Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik's Cube of Clinical Microbiology?

Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically. In the past, antimicrobial susceptibility of these microorganisms showed predictable patterns and empirical therapy could be safely administered but recently a steady and clear increase in the resistance for several important drugs (β-lactams, clindamycin) has been observed worldwide. For this reason, antimicrobial susceptibility testing of anaerobic isolates for surveillance purposes or otherwise is of paramount importance but the availability of these testing methods is usually limited. In this present review, our aim was to give an overview of the methods currently available for the identification (using phenotypic characteristics, biochemical testing, gas-liquid chromatography, MALDI-TOF MS and WGS) and antimicrobial susceptibility testing (agar dilution, broth microdilution, disk diffusion, gradient tests, automated systems, phenotypic and molecular resistance detection techniques) of anaerobes, when should these methods be used and what are the recent developments in resistance patterns of anaerobic bacteria.

Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems for the identification of clinical filamentous fungi

Infections caused by filamentous fungi have become a health concern, and require rapid and accurate identification in order for effective treatment of the pathogens. To compare the performance of two MALDI-TOF MS systems (Bruker Microflex LT and Xiamen Microtyper) in the identification of filamentous fungal species. A total of 374 clinical filamentous fungal isolates sequentially collected in the Clinical Laboratory at the Beijing Tongren Hospital between January 2014 and December 2015 were identified by traditional phenotypic methods, Bruker Microflex LT and Xiamen Microtyper MALDI-TOF MS, respectively. The discrepancy between these methods was resolved by sequencing for definitive identification. Bruker Microflex LT and Xiamen Microtyper had similar correct species ID (98.9 vs. 99.2%), genus ID (99.7 vs. 100%), mis-ID (0.3 vs. 0%) and no ID (0 vs. 0). The rate of correct species identification by both MALDI-TOF MS (98.9 and 99.2%, respectively) was much higher compared with phenotypic approach (91.9%). Both MALDI-TOF MS systems provide accurate identification of clinical filamentous fungi compared with conventional phenotypic method, and have the potential to replace identification for routine identification of these fungi in clinical mycology laboratories. Both systems have similar performance in the identification of clinical filamentous fungi.

MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species

All 50 Clostridium difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF. For 18 non-difficile Clostridium strains, the identification results were correct in 2, 0, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively [corrected].

Performances and Reliability of Bruker Microflex LT and VITEK MS MALDI-TOF Mass Spectrometry Systems for the Identification of Clinical Microorganisms

In clinical microbiology laboratories, routine microbial identification is mostly performed using culture based methodologies requiring 24 to 72 hours from culturing to identification. Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technology has been established as a cost effective, reliable, and faster alternative identification platform. In this study, we evaluated the reliability of the two available MALDI-TOF MS systems for their routine clinical level identification accuracy and efficiency in a clinical microbiology laboratory setting. A total of 1,341 routine phenotypically identified clinical bacterial and fungal isolates were selected and simultaneously analyzed using VITEK MS (bioMérieux, France) and Microflex LT (Bruker Diagnostics, Germany) MALDI-TOF MS systems. For any isolate that could not be identified with either of the systems and for any discordant result, 16S rDNA gene or ITS1/ITS2 sequencing was used. VITEK MS and Microflex LT correctly identified 1,303 (97.17%) and 1,298 (96.79%) isolates to the species level, respectively. In 114 (8.50%) isolates initial phenotypic identification was inaccurate. Both systems showed a similar identification efficiency and workflow robustness, and they were twice as more accurate compared to routine phenotypic identification in our sample pool. MALDITOF systems with their accuracy and robustness offer a good identification platform for routine clinical microbiology laboratories.

Rapid identification of oral Actinomyces species cultivated from subgingival biofilm by MALDI-TOF-MS

BACKGROUND

Actinomyces are a common part of the residential flora of the human intestinal tract, genitourinary system and skin. Isolation and identification of Actinomyces by conventional methods is often difficult and time consuming. In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has become a rapid and simple method to identify bacteria.

OBJECTIVE

The present study evaluated a new in-house algorithm using MALDI-TOF-MS for rapid identification of different species of oral Actinomyces cultivated from subgingival biofilm.

DESIGN

Eleven reference strains and 674 clinical strains were used in this study. All the strains were preliminarily identified using biochemical methods and then subjected to MALDI-TOF-MS analysis using both similarity-based analysis and classification methods (support vector machine [SVM]). The genotype of the reference strains and of 232 clinical strains was identified by sequence analysis of the 16S ribosomal RNA (rRNA).

RESULTS

The sequence analysis of the 16S rRNA gene of all references strains confirmed their previous identification. The MALDI-TOF-MS spectra obtained from the reference strains and the other clinical strains undoubtedly identified as Actinomyces by 16S rRNA sequencing were used to create the mass spectra reference database. Already a visual inspection of the mass spectra of different species reveals both similarities and differences. However, the differences between them are not large enough to allow a reliable differentiation by similarity analysis. Therefore, classification methods were applied as an alternative approach for differentiation and identification of Actinomyces at the species level. A cross-validation of the reference database representing 14 Actinomyces species yielded correct results for all species which were represented by more than two strains in the database.

CONCLUSIONS

Our results suggest that a combination of MALDI-TOF-MS with powerful classification algorithms, such as SVMs, provide a useful tool for the differentiation and identification of oral Actinomyces.

Clinical and microbiological characteristics of Eggerthella lenta bacteremia

Eggerthella lenta is an emerging pathogen that has been underrecognized due to historical difficulties with phenotypic identification. Until now, its pathogenicity, antimicrobial susceptibility profile, and optimal treatment have been poorly characterized. In this article, we report the largest cohort of patients with E. lenta bacteremia to date and describe in detail their clinical features, microbiologic characteristics, treatment, and outcomes. We identified 33 patients; the median age was 68 years, and there was no gender predominance. Twenty-seven patients (82%) had serious intra-abdominal pathology, often requiring a medical procedure. Of those who received antibiotics (28/33, 85%), the median duration of treatment was 21.5 days. Mortality from all causes was 6% at 7 days, 12% at 30 days, and 33% at 1 year. Of 26 isolates available for further testing, all were identified as E. lenta by both commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems, and none were found to harbor a vanA or vanB gene. Of 23 isolates which underwent susceptibility testing, all were susceptible to amoxicillin-clavulanate, cefoxitin, metronidazole, piperacillin-tazobactam, ertapenem, and meropenem, 91% were susceptible to clindamycin, 74% were susceptible to moxifloxacin, and 39% were susceptible to penicillin.

Evaluation of MALDI-TOF mass spectrometry for identification of anaerobic bacteria

In this study MALDI-TOF MS was evaluated in the identification of anaerobic bacteria comparing it with Rapid ID 32A system. Discrepancies were solved by 16S r-RNA gene sequencing. At the species level MALDI-TOF MS identified 94.82% and Rapid ID 32A 86.67%, showing the superiority of MALDI-TOF MS to conventional methods.

Comparison of Biolog GEN III MicroStation semi-automated bacterial identification system with matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S ribosomal RNA gene sequencing for the identification of bacteria of veterinary interest

Recent advances in phenotypic and chemotaxonomic methods have improved the ability of systems to resolve bacterial identities at the species level. Key to the effective use of these systems is the ability to draw upon databases which can be augmented with new data gleaned from atypical or novel isolates. In this study we compared the performance of the Biolog GEN III identification system (hereafter, GEN III) with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing in the identification of isolates of veterinary interest. The use of strains that had proven more difficult to identify by routine methods was designed to test the systems' abilities at the extremes of their performance range. Over an 18month period, 100 strains were analysed by all three methods. To highlight the importance of identification to species level, a weighted scoring system was devised to differentiate the capacity to identify at genus and species levels. The overall relative weighted scores were 0.869:0.781:0.769, achieved by 16S rRNA gene sequencing, GEN III and MALDI-TOF MS respectively, when compared to the 'gold standard'. Performance to the genus level was significantly better using 16S rRNA gene sequencing; however, performance to the species level was similar for all three systems.

Rapid high-throughput characterisation, classification and selection of recombinant mammalian cell line phenotypes using intact cell MALDI-ToF mass spectrometry fingerprinting and PLS-DA modelling

Despite many advances in the generation of high producing recombinant mammalian cell lines over the last few decades, cell line selection and development is often slowed by the inability to predict a cell line's phenotypic characteristics (e.g. growth or recombinant protein productivity) at larger scale (large volume bioreactors) using data from early cell line construction at small culture scale. Here we describe the development of an intact cell MALDI-ToF mass spectrometry fingerprinting method for mammalian cells early in the cell line construction process whereby the resulting mass spectrometry data are used to predict the phenotype of mammalian cell lines at larger culture scale using a Partial Least Squares Discriminant Analysis (PLS-DA) model. Using MALDI-ToF mass spectrometry, a library of mass spectrometry fingerprints was generated for individual cell lines at the 96 deep well plate stage of cell line development. The growth and productivity of these cell lines were evaluated in a 10L bioreactor model of Lonza's large-scale (up to 20,000L) fed-batch cell culture processes. Using the mass spectrometry information at the 96 deep well plate stage and phenotype information at the 10L bioreactor scale a PLS-DA model was developed to predict the productivity of unknown cell lines at the 10L scale based upon their MALDI-ToF fingerprint at the 96 deep well plate scale. This approach provides the basis for the very early prediction of cell lines' performance in cGMP manufacturing-scale bioreactors and the foundation for methods and models for predicting other mammalian cell phenotypes from rapid, intact-cell mass spectrometry based measurements.

MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria

BACKGROUND

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an accurate, rapid and inexpensive technique that has initiated a revolution in the clinical microbiology laboratory for identification of pathogens. The Vitek 2 anaerobe and Corynebacterium (ANC) identification card is a newly developed method for identification of corynebacteria and anaerobic species. The aim of this study was to evaluate the effectiveness of the ANC card and MALDI-TOF MS techniques for identification of clinical anaerobic isolates.

METHODS

Five reference strains and a total of 50 anaerobic bacteria clinical isolates comprising ten different genera and 14 species were identified and analyzed by the ANC card together with Vitek 2 identification system and Vitek MS together with version 2.0 database respectively. 16S rRNA gene sequencing was used as reference method for accuracy in the identification.

RESULTS

Vitek 2 ANC card and Vitek MS provided comparable results at species level for the five reference strains. Of 50 clinical strains, the Vitek MS provided identification for 46 strains (92%) to the species level, 47 (94%) to genus level, one (2%) low discrimination, two (4%) no identification and one (2%) misidentification. The Vitek 2 ANC card provided identification for 43 strains (86%) correct to the species level, 47 (94%) correct to the genus level, three (6%) low discrimination, three (6%) no identification and one (2%) misidentification.

CONCLUSIONS

Both Vitek MS and Vitek 2 ANC card can be used for accurate routine clinical anaerobe identification. Comparing to the Vitek 2 ANC card, Vitek MS is easier, faster and more economic for each test. The databases currently available for both systems should be updated and further developed to enhance performance.

Maldi-tof mass spectrometry for microorganism identification

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid, reliable, and high-throughput diagnostic tool for the identification of microorganisms. The technology is unique in clinical microbiology, allowing laboratories to definitively identify bacterial and fungal isolates within minutes. The rapid turnaround time and minimal cost for consumables per specimen compared with conventional identification methods have resulted in MALDI-TOF MS being increasingly used in clinical laboratories worldwide. This article summarizes the current literature on MALDI-TOF MS for microbial identification and provides a preview of the method's potential future applications in clinical microbiology.

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.

Prospective evaluation of the VITEK MS for the routine identification of bacteria and yeast in the clinical microbiology laboratory: assessment of accuracy of identification and turnaround time

This study assessed the accuracy of bacterial and yeast identification using the VITEK MS, and the time to reporting of isolates before and after its implementation in routine clinical practice. Three hundred and sixty-two isolates of bacteria and yeast, consisting of a variety of clinical isolates and American Type Culture Collection strains, were tested. Results were compared with reference identifications from the VITEK 2 system and with 16S rRNA sequence analysis. The VITEK MS provided an acceptable identification to species level for 283 (78 %) isolates. Considering organisms for which genus-level identification is acceptable for routine clinical care, 315 isolates (87 %) had an acceptable identification. Six isolates (2 %) were identified incorrectly, five of which were Shigella species. Finally, the time for reporting the identifications was decreased significantly after implementation of the VITEK MS for a total mean reduction in time of 10.52 h (P<0.0001). Overall, accuracy of the VITEK MS was comparable or superior to that from the VITEK 2. The findings were also comparable to other studies examining the accuracy of the VITEK MS, although differences exist, depending on the diversity of species represented as well as on the versions of the databases used. The VITEK MS can be incorporated effectively into routine use in a clinical microbiology laboratory and future expansion of the database should provide improved accuracy for the identification of micro-organisms.

Proteomics boosts translational and clinical microbiology

The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for identification of clinically significant bacteria that are difficult to identify in clinical laboratories

AIMS

Although the revolutionary matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been evaluated for identification of various groups of bacteria, its application in bacteria that are 'difficult-to-identify' by phenotypic tests has been less well studied. We aim to evaluate the usefulness of MALDI-TOF MS for identification of 'difficult-to-identify' bacterial isolates.

METHODS

We evaluated the performance of the Bruker MALDI-TOF MS system for a collection of 67 diverse clinically important bacterial isolates that were less commonly encountered, possessed ambiguous biochemical profiles or belonged to newly discovered species. The results were compared with 16S rRNA gene sequencing as a reference method for species identification.

RESULTS

Using 16S rRNA gene sequencing as the reference method, 30 (45%) isolates were identified correctly to species level (score ≥2.0), 20 (30%) were only identified to genus level (score ≥1.7), four (6%) were misidentified (incorrect species with score ≥2.0 or incorrect genus with score ≥1.7) and 13 (19%) showed 'no identification' (score <1.7). Aerobic Gram-positive bacteria showed the highest percentage of correct species identification, followed by aerobic Gram-negative, anaerobic Gram-positive and anaerobic Gram-negative bacteria. Sixteen isolates identified to genus level actually showed the correct species but with scores below the threshold for species identification. Most isolates which showed 'no identification' were due to the absence of the corresponding species in the Bruker database.

CONCLUSIONS

Expansion of commercial databases to include reference spectra of less commonly encountered and newly discovered species and to increase available spectra for each species is required to improve the accuracy of MALDI-TOF MS for identifying 'difficult-to-identify' bacteria.

[Anaerobic bacteria 150 years after their discovery by Pasteur]

In 2011 we celebrated the 150th anniversary of the discovery of anaerobic bacteria by Louis Pasteur. The interest of the biomedical community on such bacteria is still maintained, and is particularly focused on Clostridium difficile. In the past few years important advances in taxonomy have been made due to the genetic, technological and computing developments. Thus, a significant number of new species related to human infections have been characterised, and some already known have been reclassified. At pathogenic level some specimens of anaerobic microflora, that had not been isolated from human infections, have been now isolated in some clinical conditions. There was emergence (or re-emergence) of some species and clinical conditions. Certain anaerobic bacteria have been associated with established infectious syndromes. The virulence of certain strains has increased, and some hypotheses on their participation in certain diseases have been given. In terms of diagnosis, the routine use of MALDI-TOF has led to a shortening of time and a cost reduction in the identification, with an improvement directly related to the improvement of data bases. The application of real-time PCR has been another major progress, and the sequencing of 16srRNA gene and others is currently a reality for several laboratories. Anaerobes have increased their resistance to antimicrobial agents, and the emergence of resistance to carbapenems and metronidazole, and multi-resistance is a current reality. In this situation, linezolid could be an effective alternative for Bacteroides. Fidaxomicin is the only anti-anaerobic agent introduced in the recent years, specifically for the diarrhoea caused by C.difficile. Moreover, some mathematical models have also been proposed in relation with this species.

Diversity of human small intestinal Streptococcus and Veillonella populations

Molecular and cultivation approaches were employed to study the phylogenetic richness and temporal dynamics of Streptococcus and Veillonella populations in the small intestine. Microbial profiling of human small intestinal samples collected from four ileostomy subjects at four time points displayed abundant populations of Streptococcus spp. most affiliated with S. salivarius, S. thermophilus, and S. parasanguinis, as well as Veillonella spp. affiliated with V. atypica, V. parvula, V. dispar, and V. rogosae. Relative abundances varied per subject and time of sampling. Streptococcus and Veillonella isolates were cultured using selective media from ileostoma effluent samples collected at two time points from a single subject. The richness of the Streptococcus and Veillonella isolates was assessed at species and strain level by 16S rRNA gene sequencing and genetic fingerprinting, respectively. A total of 160 Streptococcus and 37 Veillonella isolates were obtained. Genetic fingerprinting differentiated seven Streptococcus lineages from ileostoma effluent, illustrating the strain richness within this ecosystem. The Veillonella isolates were represented by a single phylotype. Our study demonstrated that the small intestinal Streptococcus populations displayed considerable changes over time at the genetic lineage level because only representative strains of a single Streptococcus lineage could be cultivated from ileostoma effluent at both time points.

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.

Development of a clinically comprehensive database and a simple procedure for identification of molds from solid media by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a powerful tool for the rapid and highly accurate identification of clinical pathogens but has not been utilized extensively in clinical mycology due to challenges in developing an effective protein extraction method and the limited databases available. Here, we developed an alternate extraction procedure and constructed a highly stringent database comprising 294 individual isolates representing 76 genera and 152 species. To our knowledge, this is the most comprehensive clinically relevant mold database developed to date. When challenged with 421 blinded clinical isolates from our institution, by use of the BioTyper software, accurate species-level (score of ≥ 2.0) and genus-level (score of ≥ 1.7) identifications were obtained for 370 (88.9%) and 18 (4.3%) isolates, respectively. No isolates were misidentified. Of the 33 isolates (7.8%) for which there was no identification (score of <1.7), 25 were basidiomycetes not associated with clinical disease and 8 were Penicillium species that were not represented in the database. Our library clearly outperformed the manufacturer's database that was obtained with the instrument, which identified only 3 (0.7%) and 26 (6.2%) isolates at species and genus levels, respectively. Identification was not affected by different culture conditions. Implementation into our routine workflow has revolutionized our mycology laboratory efficiency, with improved accuracy and decreased time for mold identification, eliminating reliance on traditional phenotypic features.

Identification of anaerobic bacteria by Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry with on-plate formic acid preparation

Identification of anaerobic bacteria using phenotypic methods is often time-consuming; methods such as 16S rRNA gene sequencing are costly and may not be readily available. We evaluated 253 clinical isolates of anaerobic bacteria using the Bruker MALDI Biotyper (Bruker Daltonics, Billerica, MA) matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system with a user-supplemented database and an on-plate formic acid-based preparation method and compared results to those of conventional identification using biochemical testing or 16S rRNA gene sequencing. A total of 179 (70.8%) and 232 (91.7%) isolates were correctly identified to the species and genus levels, respectively, using manufacturer-recommended score cutoffs. MALDI-TOF MS offers a rapid, inexpensive method for identification of anaerobic bacteria.

Comparison of two matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry methods and API 20AN for identification of clinically relevant anaerobic bacteria

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid microbial diagnosis at relatively low cost and can be considered an alternative to conventional biochemical and molecular identification systems in clinical microbiological laboratories, including anaerobe laboratories. Two commercially available MALDI-TOF MS systems, Bruker Microflex MS and bioMérieux VITEK MS, were evaluated for the identification of 274 isolates of clinically significant anaerobic bacteria recovered from routine cultures of clinical specimens in parallel with blinded comparison with conventional biochemical (API 20AN) or molecular methods. All were recovered cultures obtained from patients attending the Mubarak Al Kabir Hospital, Kuwait, during a 6 month period. Discrepant results after two attempts at direct colony testing had failed to provide acceptable MALDI-TOF identification were resolved by gold-standard 16S gene sequencing. The VITEK MS gave high-confidence identification of the 274 isolates, all of which were correctly identified. The Bruker Microflex MS system also gave high-confidence identification for 272 of the 274. After discrepancy testing, the Bruker MS results agreed with biochemical or molecular methods for 89.1 % of the isolates at species level and 10.2 % at genus level (0.72 % were misidentified). The level of agreement with the VITEK MS was 100 % at both species and genus level; no isolates were misidentified. Our data suggest that implementation of MALDI-TOF MS as a first step for identification will shorten the turnaround time and reduce the cost in the anaerobe laboratory.