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

Cultivable Microbiome Approach Applied to Cervical Cancer Exploration

Traditional microbiological methodology is valuable and essential for microbiota composition description and microbe role assignations at different anatomical sites, including cervical and vaginal tissues; that, combined with molecular biology strategies and modern identification approaches, could give a better perspective of the microbiome under different circumstances. This pilot work aimed to describe the differences in microbiota composition in non-cancer women and women with cervical cancer through a culturomics approach combining culture techniques with Vitek mass spectrometry and 16S rDNA sequencing. To determine the possible differences, diverse statistical, diversity, and multivariate analyses were applied; the results indicated a different microbiota composition between non-cancer women and cervical cancer patients. The Firmicutes phylum dominated the non-cancer (NC) group, whereas the cervical cancer (CC) group was characterized by the predominance of Firmicutes and Proteobacteria phyla; there was a depletion of lactic acid bacteria, an increase in the diversity of anaerobes, and opportunistic and non-typical human microbiota isolates were present. In this context, we hypothesize and propose a model in which microbial composition and dynamics may be essential for maintaining the balance in the cervical microenvironment or can be pro-oncogenesis microenvironmental mediators in a process called Ying-Yang or have a protagonist/antagonist microbiota role.

Comparison of two MALDI-TOF MS systems for the identification of clinically relevant anaerobic bacteria in Argentina

The aim of this study was to compare the performance of two MALDI-TOF MS systems in the identification of clinically relevant strict anaerobic bacteria. The 16S rRNA gene sequencing was the gold standard method when discrepancies or inconsistencies were observed between platforms. A total of 333 isolates were recovered from clinical samples of different centers in Buenos Aires City between 2016 and 2021. The isolates were identified in duplicate using two MALDI-TOF MS systems, BD Bruker Biotyper (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMèrieux, Marcy-l'Etoile, France). Using the Vitek MS system, the identification of anaerobic isolates yielded the following percentages: 65.5% (n: 218) at the species or species-complex level, 71.2% (n: 237) at the genus level, 29.4% (n: 98) with no identification and 5.1% (n: 17) with misidentification. Using the Bruker Biotyper system, the identification rates were as follows: 85.3% (n: 284) at the species or species-complex level, 89.7% (n: 299) at the genus level, 14.1% (n: 47) with no identification and 0.6% (n: 2) with misidentification. Differences in the performance of both methods were statistically significant (p-values <0.0001). In conclusion, MALDI-TOF MS systems speed up microbial identification and are particularly effective for slow-growing microorganisms, such as anaerobic bacteria, which are difficult to identify by traditional methods. In this study, the Bruker system showed greater accuracy than the Vitek system. In order to be truly effective, it is essential to update the databases of both systems by increasing the number of each main spectrum profile within the platforms.

Isolation, molecular typing and antimicrobial resistance of Clostridium difficile in dogs and cats in Lanzhou city of Northwest China

Clostridium difficile infection (CDI) in human and animals belonged usually to antibiotic-associated diarrhea, ranging in severity from mild to life-threatening intestinal tract illnesses. This study aimed to isolation and characterization, toxin genes test, molecular typing, and drug sensitivity of Clostridium difficile (C. difficile) which were isolated from clinical diseased dogs and cats. A total of 247 clinical samples were collected from five animal hospitals in Lanzhou City of Northwest China, of which dogs and cats accounted for 74.9% (185/247) and 25.1% (62/247), respectively. We successfully identified 24 C. difficile strains by 16S rRNA and Matrix-Assisted Laser Desorption/Ionization Time of Fight Mass Spectroscopy (MALDI-TOF-MS). 10.3% (19/185) of dogs and 8.1% (5/62) of cats were positive for C. difficile. Among them, 16 strains were toxic and 8 were non-toxic, with a toxic rate of 57.9% (11/19) in dogs and 100% (5/5) in cats. A total of 10 STs and 10 RTs were identified in this study. The percentages of ST42 (RT106) and ST2 (RT014/LW01) among 16 toxic strains were 41.7 and 12.5%, respectively. However, ST3 (RT001), ST1 (RT027), ST133 (LW04), and ST-UN (LW04) had only one strain. ST42 (RT106) was the most common genotype and RT027 strain was first isolated in China from pets. Antimicrobial susceptibility test showed that isolates were extremely sensitive to vancomycin and metronidazole but were resistant to erythromycin and ciprofloxacin. The drug resistant rates to clindamycin, levofloxacin, moxifloxacin and meropenem were 62.5, 20.8, 16.7, and 8.3%, respectively. In conclusion, C. difficile was quietly prevalent in dogs and cats in Lanzhou city with RT106 and RT014 as the main ribotypes. The CDI in pets should be paying more attention and further studies are needed.

Multi-year comparison of VITEK® MS and 16S rRNA gene sequencing performance for the identification of rarely encountered anaerobes causing invasive human infections in a large Canadian region: can our laboratory abandon 16S rRNA gene sequencing?

BACKGROUND

Our large regional laboratory routinely provides a definitive identification (ID) for 800-1,200 anaerobic bacteria per annum that cause invasive human infections. An increasing number of isolates (i.e., 10-13%) recovered from clinical specimens from these cases were more unusual or rarely isolated genera and/or species (i.e., ≤5 individual cases/annum).

METHODS

VITEK® MS (MALDI-TOF MS)is done initially on all anaerobic bacteria, but rare isolates undergo in-house PCR/sequencing when proteomics provides a wrong ID or no results despite repeat testing. A clinical microbiologist in consultation with the Infectious Diseases service approves molecular analyses. This multi-year comparison (2014-19) of the performance of MALDI-TOF MS and 16S rRNA gene sequencing using the IDNS Smart Gene bacterial dataset shows both method's abilities to provide a genus-level and/or species-level ID for rare isolates.

RESULTS

489 rare anaerobes were recovered from a variety of clinical specimens: 57% blood cultures, 19% other sterile fluids, 14% sterile tissues, 8% deep wounds/abscesses, and 2% prosthetic implants. 16S rRNA gene sequencing gave an accurate genus-vs. species level ID for 487/489 (99.6%) and 401/489 (82.0%) of isolates respectively. Accurate genus-vs species-level ID were obtained by MALDI-TOF MS for 269/489 (53.4%) and 187/489 (37.3%) of isolates respectively. MALDI-TOF MS gave wrong or no results for 35.1% of Gram-negative anaerobic cocci (GNAC), 62% of Gram-negative anaerobic bacilli (GNAB), 30.8% of Gram-positive anaerobic cocci (GPAC) and 46.3% of Gram-positive anaerobic bacilli (GPAB). Neither method gave an ID for one GNAB and one GPAC isolate. MALDI-TOF MS genus-level ID of GNAC and genus/species-level ID of GPAB improved during the study but its performance remained stable for genus- or species-level ID of other organism groups.

CONCLUSIONS

MALDI-TOF MS provides accurate ID for most common anaerobes, but molecular analyses need to be available for rare isolates. Large complex laboratories should have a workflow for sending rare isolates for 16S rRNA gene sequencing in invasive cases where a definitive ID is clinically required.

Does Anti-TNF-α Therapy Affect the Bacteriological Profile of Specimens Collected from Perianal Lesions? A Retrospective Analysis in Patients with Crohn's Disease

Anal abscesses and fistulas are potential complications of Crohn’s disease (CD). Chronic immunosuppression, loose stools, and poor wound healing in this population present challenges to the management of perianal diseases. The purpose of the study was to determine the predominant bacterial species found in specimens from perianal lesions causing anal abscess and/or fistula drainage in hospitalized patients, and to compare the number and type of microorganisms isolated from samples taken from patients undergoing biological therapy or traditionally treated. The outcomes of studies of patients treated for anal abscesses or fistulas from 2017 to 2019 were evaluated. Data obtained from medical records included culture and antibiotic sensitivity results of swabs from perianal lesions of isolated microorganisms. A total of 373 swabs were collected from perianal lesions during the analysis period, including 51 (49 positive samples) from patients with CD. The predominant pathogen was Escherichia coli (55%, p < 0.001), the second most common microorganism was Staphylococcus aureus (14.3%, p < 0.001). In vitro susceptibility testing showed E. coli, ESBL (strain with Extended Spectrum Beta-Lactamase) in five cases, S. aureus, MRSA (methicillin-resistant S. aureus -resistant to all beta-lactam antibiotics: penicillins with inhibitors, cephalosporins, monobactams, carbapenems, except for ceftaroline) in one sample. Biologic therapy does not affect the type of microorganisms isolated from perianal abscesses in patients with CD.

Culturomics Approaches Expand the Diagnostic Accuracy for Sexually Transmitted Infections

Sexually transmitted infections (STIs) are a major health concern with clinical manifestations being acknowledged to cause severe reproductive impairment. Research in infectious diseases has been centered around the known major pathogens for decades. However, we have just begun to understand that the microbiota of the female genital tract is of particular importance for disease initiation, infection progression, and pathological outcome. Thus, we are now aware that many poorly described, partially not yet known, or cultured bacteria may pave the way for an infection and/or contribute to disease severity. While sequencing-based methods are an important step in diagnosing STIs, culture-based methods are still the gold-standard method in diagnostic routine, providing the opportunity to distinguish phenotypic traits of bacteria. However, current diagnostic culture routines suffer from several limitations reducing the content of information about vaginal microbiota. A detailed characterization of microbiota-associated factors is needed to assess the impact of single-bacterial isolates from the vaginal community on vaginal health and the containment of STIs. Here we provide current concepts to enable modern culture routines and create new ideas to improve diagnostic approaches with a conjunct usage of bioinformatics. We aim to enable scientists and physicians alike to overcome long-accepted limitations in culturing bacteria of interest to the human health. Eventually, this may improve the quality of culture-based diagnostics, facilitate a research interface, and lead to a broader understanding of the role of vaginal microbiota in reproductive health and STIs.

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.

The State of Microbiological Cleanliness of Surfaces and Equipment of an Endoscopic Examination Laboratory-Data from a Reference Tertiary Clinical Endoscopy Center in Southern Poland

The increasing number of endoscopic procedures performed and their increasing invasiveness mean that endoscopy of the gastrointestinal tract is associated with the risk of transmitting pathogenic microorganisms through infected equipment or contact with other patients and medical staff. In order to ensure protection of the health of both patients and medical staff, endoscopy laboratories should meet high hygiene standards. The results of tests of the microbiological cleanliness of surfaces and equipment of an endoscopic examination laboratory performed in the period from January to December 2019 at the Provincial Clinical Hospital No. 2 in Rzeszow were assessed retrospectively. Samples for testing were collected by swabbing from places where microbiological contamination was the most likely and cleaning was the most difficult. In the analyzed period, a total of 86 samples were collected for microbiological tests, of which positive results accounted for 6.9%. Positive results were obtained mainly from swabs collected from wet surfaces (66.7%). Most of the isolated microorganisms were Gram-negative bacteria (66.7% of all positive tests) and they were: Acinetobacter junii, Ralstonia pickettii, and Achromobacter denitrificans. The condition of the microbiological cleanliness of the surfaces and equipment of the endoscopic examination laboratory was satisfactory. A very low level of microbiological contamination of the tested items indicates occasional shortcomings in the decontamination processes. Since microorganisms isolated from the collected samples may be the cause of infection in patients and medical personnel, it is necessary to verify the decontamination procedures applied and to continue periodic microbiological monitoring of their effectiveness.

Application of MALDI-TOF MS to assess clinical characteristics, risk factors, and outcomes associated with anaerobic bloodstream infection: a retrospective observational study

Background

Correctly identifying anaerobic bloodstream infections (BSIs) is difficult. However, a new technique, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), enables more accurate identification and appropriate treatment. Anaerobic BSIs identified by MALDI-TOF MS were retrospectively analyzed to determine the clinical and microbiological features and patient outcomes based on the anaerobic genera or group.

Methods

Medical records of patients with anaerobic BSIs were used to conduct a single-center retrospective cohort study from January 2016 to December 2020 in Nagoya, Japan. Multivariate logistic regression analysis was performed to determine the independent risk factors for in-hospital mortality.

Results

Of the 215 patients with anaerobic BSIs, 31 had multiple anaerobic organisms in the blood culture, including 264 total episodes of anaerobic BSIs. Bacteroides spp. were isolated the most (n = 74), followed by gram-positive non-spore-forming bacilli (n = 57), Clostridium spp. (n = 52), gram-positive anaerobic cocci (GPAC) (n = 27), and gram-negative cocci (n = 7). The median patient age was 76 years; 56.7% were male. The most common focal infection site was intra-abdominal (36.7%). The in-hospital mortality caused by anaerobic BSIs was 21.3%, and was highest with Clostridium spp. (36.5%) and lowest with GPAC (3.7%). Age, solid tumors, and Clostridium spp. were independent risk factors for in-hospital mortality.

Conclusions

We identified current anaerobic BSI trends using MALDI-TOF MS and reported that mortality in patients with anaerobic BSIs patients was highest with Clostridium spp. infections.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

The Pathogenic Role of Actinomyces spp. and Related Organisms in Genitourinary Infections: Discoveries in the New, Modern Diagnostic Era

Actinomycosis is a chronic, suppurative, granulomatous infectious disease, caused by different species of Actinomyces bacteria. To date, 26 validly published Actinomyces species have been described as part of a normal human microbiota or from human clinical specimens. Due to the rapid spread of new, modern diagnostic procedures, 13 of 26 of these species have been described in this century and the Actinomycetaceae family has undergone several taxonomic revisions, including the introduction of many novel species termed Actinomyces-like organisms (ALOs). There is scarce data available on the role of these novel bacterial species in various infectious processes in human medicine. The aim of this review is to provide a comprehensive overview of Actinomyces and closely related organisms involved in human diseases-with a special focus on newly described species-in particular their role in genitourinary tract infections in females and males.

Relevance of anaerobic bacteremia in adult patients: A never-ending story?

Obligate anaerobic bacteria are considered important constituents of the microbiota of humans; in addition, they are also important etiological agents in some focal or invasive infections and bacteremia with a high level of mortality. Conflicting data have accumulated over the last decades regarding the extent in which these pathogens play an intrinsic role in bloodstream infections. Clinical characteristics of anaerobic bloodstream infections do not differ from bacteremia caused by other pathogens, but due to their longer generation time and rigorous growth requirements, it usually takes longer to establish the etiological diagnosis. The introduction of matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) has represented a technological revolution in microbiological diagnostics, which has allowed for the fast, accurate and reliable identification of anaerobic bacteria at a low sample cost. The purpose of this review article is to summarize the currently available literature data on the prevalence of anaerobic bacteremia in adults for physicians and clinical microbiologists and to shed some light on the complexity of this topic nowadays.

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.

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.

Isolation, identification and biodiversity of antiscalant degrading seawater bacteria using MALDI-TOF-MS and multivariate analysis

Seawater reverse osmosis (SWRO) is a commonly used desalination technique owing to its lesser environmental and economic impacts as compared to thermal desalination techniques. Antiscalants are used in SWRO to reduce membrane scaling caused by the supersaturation of salts present in feed water. However, to remain effective in reducing membrane scaling, antiscalants should be highly stable and resistant to biological degradation by seawater microorganisms. In this research, several bacteria from Qatar's seawater were isolated and screened for their ability to use antiscalants as a carbon and energy source. The biodiversity of antiscalant degrading seawater bacteria was demonstrated through combining the techniques of MALDI-TOF MS and principle component analysis. It was found that the bacteria isolated from Qatar's seawater such as H. aquamarina, H. elongata, P. fragi, P. stutzeri and others can degrade antiscalants and use them as a carbon and energy source. It was observed that the growth rates varied based on the type of antiscalant and the bacteria used. Among the tested strains, H. aquamarina, which is also known for its potential to cause biofouling, demonstrated the highest growth rates in antiscalants media. Thus, it was concluded that there is wide variety of bacteria in Qatar's seawater that can biodegrade the antiscalants; reducing their efficiency to combat membrane scaling. Since, these antiscalants will be used as a source of carbon and energy, microbial growth will increase resulting in enhanced membrane biofouling in SWRO.

Routine use of MALDI-TOF MS for anaerobic bacterial identification in clinical microbiology

In 2013, we adopted MALDI-TOF MS using the Bruker Biotyper system for identification of anaerobic bacteria into our routine clinical practice. Here, we describe our experience with the use of MALDI-TOF MS for anaerobic bacterial identification, highlighting its value in replacing the more costly and time-consuming 16S ribosomal RNA gene PCR plus sequencing-based approach as the primary method of anaerobic bacterial identification. We also describe our more recent experience with the use of early/rapid MALDI-TOF MS for identification of anaerobic bacteria performed on short incubation (4-6 h) plated aerobic media from anaerobic blood culture bottles positive for Gram-negative bacilli.

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.

Challenges in the identification of Chryseobacterium indologenes and Elizabethkingia meningoseptica in cases of nosocomial infections and patients with cystic fibrosis

Rare nonfermenting Gram-negative bacilli, such as Chryseobacterium indologenes and Elizabethkingia meningoseptica, have clinical importance in nosocomial infections and cystic fibrosis (CF), and their identification is a challenge to microbiology laboratories. Thus, the objective of this study was to verify the performance of phenotypic and mass spectrometry (matrix-assisted desorption ionization–time of flight mass spectrometry, MALDI-TOF MS) methods to identify C. indologenes and E. meningoseptica. In this context, the results obtained with phenotypic methods—namely manual biochemical and automated VITEK 2 (bioMérieux, Marcy l’Etoile, France) and Phoenix tests (Becton Dickinson (BD), San Diego, CA, USA)—and by MALDI-TOF MS—namely MALDI-TOF VITEK MS (MALDI-MS; bioMérieux) and MALDI-TOF BioTyper (MALDI-BD; BD)—of 22 isolates (blood cultures of patients with nosocomial infection (n = 15) and from patients with CF (n = 7)), initially identified as C. indologenes and E. meningoseptica, were compared. As result, using the manual phenotypic method, it was possible to identify the species level in 18/22; no identification was found in 4/22. There was a low agreement level between manual and VITEK 2 automated phenotypic methods when considering the genus level. The greatest agreement for genus-level identification occurred in MALDI-TOF MS equipment (15/22). When comparing all methods to identify the 22 isolates, there was agreement of 4/22 at the genus level and of 4/22 at the species level. In conclusion, there is low agreement level among identification methods of C. indologenes and E. meningoseptica. Although MALDI-TOF MS equipment shows a higher agreement level among them, results present low levels of confidence.

Evaluation of VITEK matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of anaerobes

Rapid and adequate identification of anaerobic bacterial species still presents a challenge for most diagnostic laboratories, hindering the selection of appropriate therapy. In this study, the identification capacity of 16S rRNA sequence analysis, VITEK 2 (BioMérieux, Lyon, France) compact analysis and VITEK MS-mediated identification for anaerobic bacterial species was compared. Eighty-five anaerobic bacterial isolates from 11 provinces in China belonging to 14 genera were identified by these three methods. Differences in identification between these three methods were compared. Consistent identification results were obtained for 54 (54/85, 63.5%) isolates by all three methods, the most discordant results being concentrated in Clostridium XI (n = 8) and Bacteroides fragilis (n = 9) clusters. Using the VITEK MS system, 74 (74/90, 82.2%) isolates were identified as single species consistent with 16S rRNA sequence analysis, which was significantly better than the results obtained with VITEK 2 Compact (P < 0.01). Misidentifications by the Vitek 2 Compact and Vitek MS systems were mainly observed in the Clostridium XI (n = 8)and B. fragilis clusters (n = 9). VITEK MS identified anaerobic bacteria even after they had been exposed to oxygen for a week. Identification by the Vitek MS system was more consistent with 16S rRNA sequence analysis than identification by Vitek 2 Compact. Continuous expansion of the VITEK MS database with rare described anaerobic species is warranted to improve both the efficiency and accuracy of VITEK MS identification in routine diagnostic microbiology.

Differences in sheep and goats milk microbiological profile between conventional and organic farming systems in Greece

The aim of this study was to examine differences in the microbiological profile and antimicrobial resistance of bacteria isolated from milk from organic and conventional sheep and goat farms. Twenty-five organic and 25 conventional sheep and goat farms in the region of Thessaly, Greece participated in this study. A standardised detailed questionnaire was used to describe farming practices. A total of 50 samples were collected and analysed for total viable count (TVC), total coliform count (TCC) and somatic cell count (SCC), while Staphylococcus aureus and Escherichia coli were isolated using standard methods. Isolates were identified at species level by Api-test and Matrix-Assisted Laser Desorption/Ionisation-Time of Flight Mass Spectrometry (MALDI-TOF MS). Susceptibility to a panel of 20 for E. coli and 16 for S. aureus antimicrobials was determined by the agar dilution method. Pulsed Field Gel Electrophoresis (PFGE) was performed for S. aureus and E. coli isolates to determine predominant clones. Lower counts of TVC, TCC and SCC were identified in milk from the organic farms, possibly due to differences in the hygienic farming practices found on those farms. API-tests and MALDI-TOF MS showed no significant differences in the S. aureus and E. coli isolates. Overall, antimicrobial resistance rates were low, while a statistically higher percentage was estimated among strains originating from conventional farms in comparison with organic farms, possibly due to the restriction of antibiotic use in organic farming. PFGE revealed diversity among S. aureus and E. coli populations in both organic and conventional farms indicating circulation of 2-3 main clones changing slightly during their evolution. Consequently, there is evidence that milk from the organic farms presents a better microbiological profile when compared with milk from conventional farms.

Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS

Identification of bacteria in aquatic and environmental applications, for monitoring purposes and research, for health assessments and therapy considerations of farmed and free-living aquatic organisms, still relies on conventional phenotypic and biochemical protocols. Although molecular techniques based on DNA amplification and sequencing are finding ways into diagnostic laboratories, they are time-consuming, costly and difficult in the case of multiplex assays. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate proteomic method reliable for identification of unknown bacteria to the genus and species level. Upon extension of databases, it will certainly find its position in environmental sciences. The paper presents an overview of the principle of the method, its effectiveness in comparison with conventional and molecular identification procedures, and applicability on environmental and aquatic isolates, discussing its advantages and shortcomings, as well as possible future implementations.

Advances in Clinical Mass Spectrometry

Although mass spectrometry has been used clinically for decades, the advent of immunoassay technology moved the clinical laboratory to more labor saving automated platforms requiring little if any sample preparation. It became clear, however, that immunoassays lacked sufficient sensitivity and specificity necessary for measurement of certain analytes or for measurement of analytes in specific patient populations. This limitation prompted clinical laboratories to revisit mass spectrometry which could additionally be used to develop assays for which there was no commercial source. In this chapter, the clinical applications of mass spectrometry in therapeutic drug monitoring, toxicology, and steroid hormone analysis will be reviewed. Technologic advances and new clinical applications will also be discussed.

Evaluation of MALDI-TOF MS (Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry) for routine identification of anaerobic bacteria

Information regarding the use of MALDI-TOF MS as an alternative to conventional laboratory methods for the rapid and reliable identification of bacterial isolates is still limited. In this study, MALDI-TOF MS was evaluated on 295 anaerobic isolates previously identified by 16S rRNA gene sequencing and with biochemical tests (Rapid ID 32A system, BioMérieux). In total, 85.8% of the isolates were identified by MALDI-TOF MS at the species level vs 49.8% using the Rapid ID 32A system (p < 0.0001). None of the isolates was discordantly identified at the genus level using MALDI-TOF MS and only 9 of them could not be identified using the method. Thus, our results show that MALDI-TOF MS is a robust and reliable tool for the identification of anaerobic isolates in the microbiology laboratory. Its implementation will reduce the turnaround time for a final identification and the number of isolates that require 16S rRNA sequencing.

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.

Routine identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: Success rate, economic analysis, and clinical outcome

BACKGROUND

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used in microbial identification. This study evaluated the performance of MALDI-TOF MS and investigated the economic and medical impact of MALDI-TOF MS implementation.

METHODS

A total of 12,202 clinical isolates collected from April to September 2013 were identified using MALDI-TOF MS, and the success rates in identifying isolates were analyzed. The differences in the processing time, cost of consumables, weight of waste, and clinical impact between MALDI-TOF MS and biochemical reaction were compared.

RESULTS

MALDI-TOF MS successfully identified 96% of 12,202 isolates, including 96.8% of 10,502 aerobes, 90.5% of 1481 anaerobes, 93.8% of 81 yeasts, and 90.6% of 138 nontuberculous mycobacteria at the genus level. By using MALDI-TOF MS, the processing time for aerobes decreased from 32.5 hours to 4.1 hours, and that for anaerobes decreased from 71.5 hours to 46 hours. For detection of aerobes and anaerobes, the cost of consumables was estimated to decrease by US$0.9 per isolate, thus saving US$94,500 in total annual isolation. Furthermore, the weight of waste decreased six-fold, resulting in a reduction of 350 kg/month or 4.2 tons/year. MALDI-TOF MS also increased the percentage of correct antibiotics treatment for Escherichia coli and Klebsiella pneumonia from 56.1% to 75% and shortened the initiation time of the correct antibiotic action from 3.3 hours to 2.5 hours.

CONCLUSIONS

MALDI-TOF MS is a rapid, reliable, economical, and environmentally friendly method for routine microbial identification and may contribute to early appropriate antibiotic treatment in clinical settings.

Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry

Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia and Escherichia coli DH5α were employed as reference bacteria to optimize various parameters for identification and classification of species of rhizobia by matrix-assisted laser desorption/ionization time-of-flight MS (MALDI TOF MS). The parameters optimized included culture medium states (liquid or solid), bacterial growth phases, colony storage temperature and duration, and protein data processing to enhance the bacterial identification resolution, accuracy and reliability. The medium state had little effects on the mass spectra of protein profiles. A suitable sampling time was between the exponential phase and the stationary phase. Consistent protein mass spectral profiles were observed for E. coli colonies pre-grown for 14 days and rhizobia for 21 days at 4°C or 21°C. A dendrogram of 75 rhizobial strains of 4 genera was constructed based on MALDI TOF mass spectra and the topological patterns agreed well with those in the 16S rDNA phylogenetic tree. The potential of developing a mass spectral database for all rhizobia species was assessed with blind samples. The entire process from sample preparation to accurate identification and classification of species required approximately one hour.

Emerging technologies for the clinical microbiology laboratory

In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.

MALDI-TOF MS for the Diagnosis of Infectious Diseases

BACKGROUND

First introduced into clinical microbiology laboratories in Europe, MALDI-TOF MS is being rapidly embraced by laboratories around the globe. Although it has multiple applications, its widespread adoption in clinical microbiology relates to its use as an inexpensive, easy, fast, and accurate method for identification of grown bacteria and fungi based on automated analysis of the mass distribution of bacterial proteins.

CONTENT

This review provides a historical perspective on this new technology. Modern applications in the clinical microbiology laboratory are reviewed with a focus on the most recent publications in the field. Identification of aerobic and anaerobic bacteria, mycobacteria, and fungi are discussed, as are applications for testing urine and positive blood culture bottles. The strengths and limitations of MALDI-TOF MS applications in clinical microbiology are also addressed.

SUMMARY

MALDI-TOF MS is a tool for rapid, accurate, and cost-effective identification of cultured bacteria and fungi in clinical microbiology. The technology is automated, high throughput, and applicable to a broad range of common as well as esoteric bacteria and fungi. MALDI-TOF MS is an incontrovertibly beneficial technology for the clinical microbiology laboratory.

Evaluation of VITEK mass spectrometry (MS), a matrix-assisted laser desorption ionization time-of-flight MS system for identification of anaerobic bacteria

Background

By conventional methods, the identification of anaerobic bacteria is more time consuming and requires more expertise than the identification of aerobic bacteria. Although the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems are relatively less studied, they have been reported to be a promising method for the identification of anaerobes. We evaluated the performance of the VITEK MS in vitro diagnostic (IVD; 1.1 database; bioMérieux, France) in the identification of anaerobes.

Methods

We used 274 anaerobic bacteria isolated from various clinical specimens. The results for the identification of the bacteria by VITEK MS were compared to those obtained by phenotypic methods and 16S rRNA gene sequencing.

Results

Among the 249 isolates included in the IVD database, the VITEK MS correctly identified 209 (83.9%) isolates to the species level and an additional 18 (7.2%) at the genus level. In particular, the VITEK MS correctly identified clinically relevant and frequently isolated anaerobic bacteria to the species level. The remaining 22 isolates (8.8%) were either not identified or misidentified. The VITEK MS could not identify the 25 isolates absent from the IVD database to the species level.

Conclusions

The VITEK MS showed reliable identifications for clinically relevant anaerobic bacteria.

Real-time comparative evaluation of bioMerieux VITEK MS versus Bruker Microflex MS, two matrix-assisted laser desorption-ionization time-of-flight mass spectrometry systems, for identification of clinically significant bacteria

Background

Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) recently became available for the identification of bacteria in routine diagnostic laboratories. It is rapid and cost-effective and likely to replace phenotypic identification. This study was undertaken to compare two MALDI-TOF MS-based, Bruker Microflex MS (BMS) and VITEK MS (VMS) systems, for identification (ID) of clinically significant bacterial isolates. Clinically relevant broad diversity of bacterial isolates obtained during a 6-consecutive months of routine laboratory processing of clinical specimens were subjected to ID by the BMS and VMS in parallel with Vitek 2, a conventional phenotypic system (CPS). For the BMS, the isolates were tested in duplicates directly and after pretreatment. Identification was provided with accompanying scores according to manufacturers’ instructions. With VMS, single deposits of the same sets of isolates were tested in duplicates directly on MALDI-plate. Results were interpreted according to the manufacturer’s protocols. Discrepant results were resolved by 16S rRNA gene amplification and sequencing.

Results

A total of 806 pathogens comprising 507 Gram-negative bacilli (GNB), 16 Gram-negative cocci (GNC), 267 Gram-positive cocci (GPC), and 16 Gram-positive bacilli (GPB) were tested. BMS and VMS correctly identified isolates to genus and species levels (ID 97.3% and 93.2%, and 99.8% and 99.0%, respectively). Both systems as well as the CPS correctly identified the majority of the species in the family Enterobacteriaceae, Pseudomonas spp., and Acinetobacter baumannii. Turnaround time for identification by BMS and VMS was <20 min compared with 24-48 h by the CPS.

Conclusions

VMS performed slightly better than BMS with GPC ID, especially the Streptococcus spp. Some S. mitis isolates were identified as S. pneumoniae by BMS. BMS and VMS were rapid and proved to be consistently accurate for producing bacterial identification in a fraction of time it takes for identification by CPS.

Evaluation of the Bruker Biotyper and VITEK MS MALDI-TOF MS systems for the identification of unusual and/or difficult-to-identify microorganisms isolated from clinical specimens

The purpose of this investigation was to evaluate the analytical performance characteristics of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of unusual organisms. We evaluated the accuracy of two MALDI-TOF MS systems, bioMérieux VITEK MS (database v2.0) and Bruker Biotyper (software version 3.0), for the identification of the most difficult and/or unusual microorganisms isolated from clinical specimens. Our study included 174 bacterial isolates recovered from clinical cultures at Barnes-Jewish Hospital, St. Louis, MO, from 2009 to 2013, representing 50 genera and 52 species. MS identifications were compared to the identification reported by the reference laboratory. Discrepancies were resolved using molecular methods, including 16S rRNA gene sequencing and additional molecular methods. When performed, molecular methods were considered the gold standard. Of the 168 isolates resolved to the genus level, VITEK MS identified 145 (86.3 %), and of the 114 isolates resolved to the species level, 97 (85.1 %) were correctly identified. Bruker Biotyper identified 155 (92.3 %) of 168 isolates to the genus level and 97 (85.1 %) of 114 isolates to the species level. VITEK MS and Bruker Biotyper provided no identification for 17 (10.1 %) and 12 (7.1 %) organisms, respectively, and misidentified six (3.6 %) and one (0.6 %) isolate, respectively. Six isolates (3.6 %) were not resolvable to the genus level and were excluded from data analysis due to the lack of a gold standard for comparison. There was no significant difference in the number of organisms identified to the genus level, species level, unidentified, or misidentified by the two MALDI-TOF MS systems (p = 0.11, 1.0, 0.44, and 0.12, respectively).

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.

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.

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.

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.

Performance of the Vitek MS v2.0 system in distinguishing Streptococcus pneumoniae from nonpneumococcal species of the Streptococcus mitis group

The Vitek MS v2.0 matrix-assisted laser desorption ionization-time of flight mass spectrometry system accurately distinguished Streptococcus pneumoniae from nonpneumococcal S. mitis group species. Only 1 of 116 nonpneumococcal isolates (<1%) was misidentified as S. pneumoniae. None of 95 pneumococcal isolates was misidentified. This method provides a rapid, simple means of discriminating among these challenging organisms.

Multicenter evaluation of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of Gram-positive aerobic bacteria

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting.

Advances in identification of clinical yeast isolates by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification is being adopted by clinical laboratories for routine identification of microorganisms. To date, the majority of studies have focused on the performance and optimization of MALDI-TOF MS for the identification of bacterial isolates. We review recent literature describing the use of MALDI-TOF MS for the routine identification of a variety of yeasts and yeast-like isolates. Specific topics include the effect of optimized or streamlined extraction methods, modified scoring thresholds, expanded reference libraries, and the possibility of conducting antifungal susceptibility testing using MALDI-TOF MS.