Multi-centre evaluation of mass spectrometric identification of anaerobic bacteria using the VITEK® MS system

Lemierre syndrome with pulmonary empyema caused by Prevotella intermedia

Lemierre syndrome is a rare disease that is most often caused by Fusobacterium necrophorum We present a case caused by Prevotella intermedia in a young, healthy man, complicated by multiple cavitary lung lesions, loculated pleural effusions requiring chest tube placement and trapezius abscess. Our case highlights (a) P. intermedia as a rare cause of Lemierre syndrome and (b) clinical response to appropriate antimicrobial therapy may be protracted.

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, screening, and identification of chitinase-producing bacterial strains from riverbank soils at Ambo, Western Ethiopia

Chitinases are hydrolytic enzymes that dissolve the glycosidic linkages in chitin. Chitin is a cell wall component of fungi and fund in exoskeleten of worms and arthropods. Chitinase has been applied in agriculture, as a biopesticide for the control of plant fungal infections, in medicine, and in waste management. This research aimed to isolate, screen, and identification of chitinase-producing bacteria from riverbank soils. Twenty nine chitinolytic bacteria were isolated from the river bank soil samples, from which 9 of them had strong chitinolytic properties. Chitinase production was determined by zones of hydrolysis produced after 96 h of incubation at 37 °C. The different bacterial isolates were characterized morphologically, microscopically, and biochemically and finally eight strain were identified at species level by Matrix Assisted Laser Desorption Ionization - Time of Flight Mass Spectrometry (MALDI-TOF MS). From the eight, bacterial isolates investigated in this study Stenotrophomonas maltophilia showed the highest chitinase enzyme activity (625 μg/mL) followed by Pseudomonas putida with the enzyme activity of (553 μg/mL) and the least enzyme activity was recorded for Lilliottia amnigena (80 μg/mL). An incubation temperature of 45 °C, neutral pH and an incubation period of 96 h are found to be the optimum condition for the chitinase enzyme production from Stenotrophomonas maltophilia. The results of this study indicated the possibility of the production of chitinase from the chitinolytic bacterial isolates, which was highly useful for a variety of applications, including biocontrol of harmful insects and pathogenic fungi as well as in the biochemical, pharmaceutical, and medical sectors.

Analysis of Neutrophil and Monocyte Inflammation Markers in Response to Gram-Positive Anaerobic Cocci

The impact of anaerobic bacteria on the human host is sparsely investigated due to cultivation challenges. Nonetheless, in the last decade increasing research demonstrated the importance of paying attention to these overlooked pathogens. In this chapter, we provide an overview of analyzing surface and intracellular inflammation markers of neutrophils and monocytes in response to Gram-positive anaerobic cocci (GPAC) species Peptoniphilus (P.) harei.

Paediatric pulmonary actinomycosis: A forgotten disease

Actinomycosis is a rare, indolent and invasive infection caused by Actinomyces species. Actinomycosis develops when there is disruption of the mucosal barrier, and invasion and systemic spread of the organism, which can lead to endogenous infection affecting numerous organs. It is known to spread in tissue through fascial planes and most often involves the cervicofacial (55%), abdominopelvic (20%) and thoracic (15%) soft tissue. Pulmonary actinomycosis is rare in patients under the age of five years, with the median reported age in the fifth decade. Clinical findings include chest wall mass (49%), cough (40%), pain (back, chest, shoulders) (36%), weight loss (19%), fever (19%), Draining sinuses (15%) and hemoptysis (9%). Chest x-ray findings in pulmonary actinomycosis are mostly nonspecific and can overlap with pulmonary tuberculosis, foreign body aspiration and malignancy. Endobronchial tissue aggregates may show sulphur granules, with yellow to white conglomerate areas of gram positive Actinomyces. Removal or biopsy of these large endobronchial masses must be done with care, because of the risk of bleeding and large airway obstruction. The cytology on bronchoalveolar lavage fluid may show Periodic acid-Schiff (PAS) positive stain, ZN negative and Gram-positive filamentous bacilli which is morphologically suggestive of Actinomycosis. Actinomyces spp is highly susceptible to beta lactam antibiotics, penicillin G, and amoxicillin. A minimum of 3-6 months is needed but up to 20 months of treatment may be needed. Early diagnosis and correct treatment can lead to a good prognosis with a low mortality.

A side-by-side comparison of the performance and time-and-motion data of VITEK MS

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry systems are designed for rapid and reliable microbial identification. VITEK MS PRIME is the bioMérieux's new generation instrument equipped with a continuous load-and-go sample loading system, urgent slide prioritization for critical patient samples and new internal components for faster identification. The aim of this study was to assess the performance of VITEK MS PRIME and to compare it to that of the VITEK MS system. In addition, at two sites, we performed a time-and-motion study to evaluate the efficiency of sample analysis from colony picking to slide removal from the instrument. We analyzed by VITEK MS and VITEK MS PRIME a total of 1413 isolates (1320 bacterial and 76 yeast) deriving from routine diagnostic samples that came into four laboratories in Canada, France, Italy, and Spain. VITEK MS PRIME and VITEK MS were concordant to the species and genus level for 1354/1413 (95.8%) and to the species level for 1341/1413 (94.9%). The identification and concordance rates in individual centers were largely homogenous. Overall, VITEK MS PRIME identified 1370/1413 (97.0%) of isolates compared to 1367/1413 (96.7%) identified by VITEK MS. Identification rates were consistently high for all microorganism categories. A time-and-motion study showed that the use of VITEK MS PRIME was associated with significant time saving. VITEK MS PRIME performs as well as VITEK MS and reduces the time necessary for pathogen identification. To fully optimize the laboratory process and obtain maximum efficiency, VITEK MS PRIME must be integrated into the laboratory workflow.

Identification of Peptoniphilus vaginalis-Like Bacteria, Peptoniphilus septimus sp. nov., From Blood Cultures in a Cervical Cancer Patient Receiving Chemotherapy: Case and Implications

A 39-year-old woman with a 3-year human papillomavirus (HPV) 18 infection history was admitted to the hospital for a 16-day history of vaginal bleeding after sex. She was diagnosed with cervical cancer based on the results of the electronic colposcopy, cervical cytology, microscopy, and magnetic resonance imaging (MRI). Then, she received chemotherapy, with paclitaxel 200 mg (day 1), cisplatin 75 mg (day 2), and bevacizumab 700 mg (day 3) twice with an interval of 27 days. During the examination for the diagnosis and treatment, many invasive operations, including removal of intrauterine device, colposcopy, and ureteral dilatation, were done. After that, the patient was discharged and entered the emergency department about 2.5 months later with a loss of consciousness probably caused by septic shock. The patient finally died of multiple organ failure and bacterial infection, although she has received antimicrobial therapy. The blood cultures showed a monobacterial infection with an anaerobic Gram-positive bacterial strain, designated as SAHP1. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI–TOF MS) indicated that the patient was infected with Peptoniphilus asaccharolyticus, while molecular analysis and genome-based taxonomy confirmed the infection with a novel Peptoniphilus species that has a close genetic relationship with Peptoniphilus vaginalis and proposed provisionally as Peptoniphilus septimus sp. nov., which may also act as a commensal of the human vagina. Genomic features of SAHP1 have been fully described, and comparative genomic analysis reveals the known prokaryote relative of Peptoniphilus septimus sp. nov. in the genus Peptoniphilus. The invasive operations on the genital tract during the diagnosis and treatment of the patient and the tumor tissue damage and bleeding may have a certain role in the bloodstream infection. This study casts a new light on the Peptoniphilus bacteria and prompts clinicians to include anaerobic blood cultures as part of their blood culture procedures, especially on patients with genital tract tumors. Furthermore, due to the incomplete database and unsatisfying resolution of the MALDI–TOF MS for Peptoniphilus species identification, molecular identification, especially whole-genome sequencing, is required for those initially identified as bacteria belonging to Peptoniphilus in the clinical laboratory.

Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group

Bacteroides fragilis group (BFG) species are common members of the human microbiota that provide several benefits to healthy hosts, yet BFG are also the most common anaerobes isolated from human infections, including intra-abdominal infections, abscesses, and bloodstream infection. Compared to many other anaerobes associated with disease, members of the BFG are more likely to be resistant to commonly used antimicrobials, including penicillin (>90% resistant), carbapenems (2 to 20% resistant), and metronidazole (0.2 to 4% resistant). As a result, infection with BFG bacteria can be associated with poor clinical outcomes. Here, we discuss the role of BFG in human health and disease, proposed taxonomic reclassifications within the BFG, and updates in methods for species-level identification. The increasing availability of whole-genome sequencing (WGS) supports recent proposals that the BFG now span two families (Bacteroidaceae and "Tannerellaceae") and multiple genera (Bacteroides, Parabacteroides, and Phocaeicola) within the phylum Bacteroidota. While members of the BFG are often reported to "group" rather than "species" level in many clinical settings, new reports of species-specific trends in antimicrobial resistance profiles and improved resolution of identification tools support routine species-level reporting in clinical practice. Empirical therapy may not be adequate for treatment of serious infections with BFG, warranting susceptibility testing for serious infections. We summarize methods for antimicrobial susceptibility testing and resistance prediction for BFG, including broth microdilution, agar dilution, WGS, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). We examine global trends in BFG antimicrobial resistance and review genomics of BFG, revealing insights into rapid activation and dissemination of numerous antimicrobial resistance mechanisms.

Identification of Peptoniphilus harei From Blood Cultures in an Infected Aortic Aneurysm Patient: Case Report and Review Published Literature

Gram-positive anaerobic cocci (GPAC) are a commensal part of human flora but are also opportunistic pathogens. This is possibly the first study to report a case of Peptoniphilus harei bacteremia in an abdominal aortic aneurysm (AAA) patient. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) failed to identify the isolate and molecular analysis confirmed it as P. harei. A comprehensive literature review revealed that P. harei is an emergent pathogen. This study serves as a reminder for practicing clinicians to include anaerobic blood cultures as part of their blood culture procedures; this is particularly important situations with a high level of suspicion of infection factors in some noninfectious diseases, as mentioned in this publication. Clinical microbiologists should be aware that the pathogenic potential of GPAC can be greatly underestimated leading to incorrect diagnosis on using only one method for pathogen identification. Upgradation and correction of the MALDI-TOF MS databases is recommended to provide reliable and rapid identification of GPAC at species level in medical diagnostic microbiology laboratories.

The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS

Bacterial pathogens that cannot be identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) are occasionally encountered in clinical laboratories. The 16S rRNA gene is often used for sequence-based analysis to identify these bacterial species. Nevertheless, traditional Sanger sequencing is laborious, time-consuming and low-throughput. Here, we compared two commercially available 16S rRNA gene sequencing tests, which are based on Illumina and Nanopore sequencing technologies, respectively, in their ability to identify the species of 172 clinical isolates that failed to be identified by MALDI-TOF MS. Sequencing data were analyzed by respective built-in programs (MiSeq Reporter Software of Illumina and Epi2me of Nanopore) and BLAST+ (v2.11.0). Their agreement with Sanger sequencing on species-level identification was determined. Discrepancies were resolved by whole-genome sequencing. The diagnostic accuracy of each workflow was determined using the composite sequencing result as the reference standard. Despite the high base-calling accuracy of Illumina sequencing, we demonstrated that the Nanopore workflow had a higher taxonomic resolution at the species level. Using built-in analysis algorithms, the concordance of Sanger 16S with the Illumina and Nanopore workflows was 33.14% and 87.79%, respectively. The agreement was 65.70% and 83.14%, respectively, when BLAST+ was used for analysis. Compared with the reference standard, the diagnostic accuracy of Nanopore 16S was 96.36%, which was identical to Sanger 16S and was better than Illumina 16S (69.07%). The turnaround time of the Illumina workflow and the Nanopore workflow was 78h and 8.25h respectively. The per-sample cost of the Illumina and Nanopore workflows was US$28.5 and US$17.7, respectively.

Peptostreptococcus anaerobius: Pathogenicity, identification, and antimicrobial susceptibility. Review of monobacterial infections and addition of a case of urinary tract infection directly identified from a urine sample by MALDI-TOF MS

Peptostreptococcus anaerobius is a gram-positive anaerobic coccus (GPAC) found in the gastrointestinal and vaginal microbiota. The organism is mainly found in polymicrobial and scarcely in monobacterial infections such as prosthetic and native endocarditis. Anaerobic bacteria have rarely been reported as the cause of urinary tract infection (UTI). Although GPAC are susceptible to most antimicrobials used against anaerobic infections, P. anaerobius has shown to be more resistant. Herein, we report a case of UTI caused by P. anaerobius from a 62-year-old man with a history of urological disease. Surprisingly, the microorganism was directly identified by Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) from the urine sample. The isolate was successfully identified by phenotypic methods, MALDI-TOF MS, and 16S rRNA gene sequencing. P. anaerobius showed no β-lactamase-producing activity, was resistant to penicillin, ampicillin, ciprofloxacin and levofloxacin, and displayed intermediate susceptibility to ampicillin-sulbactam and amoxicillin-clavulanic acid. Successful treatment was achieved with oral amoxicillin-clavulanic acid. Antimicrobial susceptibility testing (AST) should be performed on P. anaerobius isolates due to their unpredictable AST patterns and because empirically administered antimicrobial agents may not be active. This report shows that MALDI-TOF MS, directly used in urine specimens, may be a quick option to diagnose UTI caused by P. anaerobius or other anaerobic bacteria. This review is a compilation of monobacterial infections caused by P. anaerobius published in the literature, their pathogenicity, identification, and data about the antimicrobial susceptibility of P. anaerobius.

Identification of Bacteria Associated with Post-Operative Wounds of Patients with the Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Approach

The bacterial infection of post-operative wounds is a common health problem. Therefore, it is important to investigate fast and accurate methods of identifying bacteria in clinical samples. The aim of the study was to analyse the use of the MALDI-TOF MS technique to identify microorganism wounds that are difficult to heal. The most common bacteria are Escherichia coli, Staphylococcus spp., and Enterococcus spp. We also demonstrate the effect of culture conditions, such as the used growth medium (solid: Brain Heart Infusion Agar, Mueller Hilton Agar, Glucose Bromocresol Purple Agar, and Vancomycin Resistance Enterococci Agar Base and liquid: Tryptic Soy Broth and BACTEC Lytic/10 Anaerobic/F), the incubation time (4, 6, and 24h), and the method of the preparation of bacterial protein extracts (the standard method based on the Bruker guideline, the Sepsityper method) to identify factors and the quality of the obtained mass spectra. By comparing the protein profiles of bacteria from patients not treated with antibiotics to those treated with antibiotics based on the presence/absence of specific signals and using the UniProt platform, it was possible to predict the probable mechanism of the action of the antibiotic used and the mechanism of drug resistance.

Septic hip abscess due to Fusobacterium nucleatum and Actinomyces turicensis in an immunocompetent SARS-CoV-2 positive patient

A 42-year-old man was referred to the Department of Orthopedic Surgery with pain over his right greater trochanter and signs of systemic infection. CT showed an enhanced mass in his gluteus maximus as well as gas in the biceps femoris over the underlying hip joint. Tissue biopsy yielded Fusobacterium nucleatum and Actinomyces turicensis. The patient was successfully treated for 6 weeks with amoxicillin/clavulanic acid 875mg/125mg and metronidazole 500mg.

A tale of two unusual anaerobic bacterial infections in an immunocompetent man: A case report and literature review

We report a case of an immunocompetent man who presented with Desulfovibrio fairfieldensis bacteremia, followed by an epidural abscess due to Parvimonas micra. Only few cases have described unique clinical features related to both organisms, and this report illustrates two distinct sequential, if not concurrent, syndromes due to these anaerobes.

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.

Identifying Anaerobic Bacteria Using MALDI-TOF Mass Spectrometry: A Four-Year Experience

Because of the special culture requirements of anaerobic bacteria, their low growth-rate and the difficulties to isolate them, MALDI-TOF MS has become a reliable identification tool for these microorganisms due to the little amount of bacteria required and the accuracy of MALDI-TOF MS identifications. In this study, the performance of MALDI-TOF MS for the identification of anaerobic isolates during a 4-year period is described. Biomass from colonies grown on Brucella agar was directly smeared onto the MALDI-TOF target plate and submitted to on-plate protein extraction with 1μl of 100% formic acid. Sequencing analysis of the 16S rRNA gene was used as a reference method for the identification of isolates unreliably or not identified by MALDI-TOF MS. Overall, 95.7% of the isolates were identified to the species level using the updated V6 database vs 93.8% with previous databases lacking some anaerobic species; 68.5% of the total were reliably identified with high-confidence score values (≥2.0) and 95.0% with low-confidence values (score value ≥1.7). Besides, no differences between Gram-positive and Gram-negative isolates were detected beyond a slight decrease of correct species assignment for gram positive cocci (94.1% vs 95.7% globally). MALDI-TOF MS has demonstrated its usefulness for the identification of anaerobes, with high correlation with phenotypic and conventional methods. Over the study period, only 2.1% of the isolates could not be reliably identified and required molecular methods for a final identification. Therefore, MALDI-TOF MS provided reliable identification of anaerobic isolates, allowing clinicians to streamline the most appropriate antibiotic therapy and manage patients accordingly.

Multicenter evaluation of the VITEK MS matrix-assisted laser desorption/ionization-time of flight mass spectrometry system for identification of bacteria, including Brucella, and yeasts

The use of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has proven to be rapid and accurate for the majority of clinical isolates. Some gaps remain concerning rare, emerging, or highly pathogenic species, showing the need to continuously expand the databases. In this multicenter study, we evaluated the accuracy of the VITEK MS v3.2 database in identifying 1172 unique isolates compared to identification by DNA sequence analysis. A total of 93.6% of the isolates were identified to species or group/complex level. A remaining 5.2% of the isolates were identified to the genus level. Forty tests gave a result of no identification (0.9%) and 12 tests (0.3%) gave a discordant identification compared to the reference identification. VITEK MS is also the first MALDI-TOF MS system that is able to delineate the four members of the Acinetobacter baumannii complex at species level without any specific protocol or special analysis method. These findings demonstrate that the VITEK MS v3.2 database is highly accurate for the identification of bacteria and fungi encountered in the clinical laboratory as well as emerging species like Candida auris and the highly pathogenic Brucella species.

Evolution of the liver biopsy and its future

Liver biopsies are commonly used to evaluate a wide variety of medical disorders, including neoplasms and post-transplant complications. However, its use is being impacted by improved clinical diagnosis of disorders, and non-invasive methods for evaluating liver tissue and as a result the indications of a liver biopsy have undergone major changes in the last decade. The evolution of highly effective treatments for some of the common indications for liver biopsy in the last decade (e.g., viral hepatitis B and C) has led to a decline in the number of liver biopsies in recent years. At the same time, the emergence of better technologies for histologic evaluation, tissue content analysis and genomics are among the many new and exciting developments in the field that hold great promise for the future and are going to shape the indications for a liver biopsy in the future. Recent advances in slide scanners now allow creation of "digital/virtual" slides that have image of the entire tissue section present in a slide [whole slide imaging (WSI)]. WSI can now be done very rapidly and at very high resolution, allowing its use in routine clinical practice. In addition, a variety of technologies have been developed in recent years that use different light sources and/or microscopes allowing visualization of tissues in a completely different way. One such technique that is applicable to liver specimens combines multiphoton microscopy (MPM) with advanced clearing and fluorescent stains known as Clearing Histology with MultiPhoton Microscopy (CHiMP). Although it has not yet been extensively validated, the technique has the potential to decrease inefficiency, reduce artifacts, and increase data while being readily integrable into clinical workflows. Another technology that can provide rapid and in-depth characterization of thousands of molecules in a tissue sample, including liver tissues, is matrix assisted laser desorption/ionization (MALDI) mass spectrometry. MALDI has already been applied in a clinical research setting with promising diagnostic and prognostic capabilities, as well as being able to elucidate mechanisms of liver diseases that may be targeted for the development of new therapies. The logical next step in huge data sets obtained from such advanced analysis of liver tissues is the application of machine learning (ML) algorithms and application of artificial intelligence (AI), for automated generation of diagnoses and prognoses. This review discusses the evolving role of liver biopsies in clinical practice over the decades, and describes newer technologies that are likely to have a significant impact on how they will be used in the future.

Clinical characteristics of bloodstream infection by Parvimonas micra: retrospective case series and literature review

Background

Gram-positive anaerobic (GPA) bacteria inhabit different parts of the human body as commensals but can also cause bacteremia. In this retrospective observational study, we analyzed GPA bacteremia pathogens before (2013–2015) and after (2016–2018) the introduction of the matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS).

Method

We conducted a retrospective observational study by searching the microbiology database to identify all positive GPA blood cultures of patients with GPA bacteremia diagnosed using the new technique, MALDI-TOF MS, between January 1, 2016 and December 31, 2018; and using a conventional phenotypic method between January 1, 2013 and December 31, 2015 at a single tertiary center in Japan. Parvimonas micra (P. micra) (17.5%) was the second most frequently identified GPA (MALDI-TOF MS); we then retrospectively reviewed electronic medical records for 25 P. micra bacteremia cases at our hospital. We also conducted a literature review of published cases in PubMed from January 1, 1980, until December 31, 2019; 27 cases were retrieved.

Results

Most cases of P. micra bacteremia were identified after 2015, both, at our institute and from the literature review. They were of mostly elderly patients and had comorbid conditions (malignancies and diabetes). In our cases, laryngeal pharynx (7/25, 28%) and gastrointestinal tract (GIT; 6/25, 24%) were identified as the most likely sources of bacteremia; however, the infection source was not identified in 9 cases (36%). P. micra bacteremia were frequently associated with spondylodiscitis (29.6%), oropharyngeal infection (25.9%), intra-abdominal abscess (14.8%), infective endocarditis (11.1%), septic pulmonary emboli (11.1%), and GIT infection (11.1%) in the literature review. Almost all cases were treated successfully with antibiotics and by abscess drainage. The 30-day mortalities were 4 and 3.7% for our cases and the literature cases, respectively.

Conclusions

Infection sites of P. micra are predominantly associated with GIT, oropharyngeal, vertebral spine, intra-abdominal region, pulmonary, and heart valves. Patients with P. micra bacteremia could have good prognosis following appropriate treatment.

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.

Ruminococcus gnavus bacteremia, an uncommon presentation of a common member of the human gut microbiota: case report and literature review

Case report: We present a case of a 66-year-old female diagnosed with R. gnavus bacteremia associated with fecal peritonits secondary to small-bowel herniation and perforation. Identification  as R. gnavus was delayed because of absence of this species in the MALDI-TOF MS database (Vitek MS, bioMérieux). Identification was provided by 16S rRNA gene sequencing. Review: R. gnavus, a Gram-positive, strictly anaerobic bacterium, is a member of the human gut microbiota. Dysbiosis in the gut microbiota, with increased amounts of R. gnavus, has been described in inflammatory bowel disease. R. gnavus has only been reported occasionally as the cause of infections. Hence the potential pathogenicity is not yet fully recognized, and data regarding the antimicrobial susceptibility profile are rare. Identification of anaerobic bacteria such as R. gnavus is greatly accelerated  as a result of the introduction of MALDI-TOF MS. However, as illustrated in this case report, an extensive and up-to-date MALDI-TOF MS database is necessary for providing an accurate identification.

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.

Current status of MALDI-TOF mass spectrometry in clinical microbiology

Mass spectrometry (MS) is a type of analysis used to determine what molecules make up a sample, based on the mass spectrum that are created by the ions. Mass spectrometers are able to perform traditional target analyte identification and quantitation; however, they may also be used within a clinical setting for the rapid identification of bacteria. The causative agent in sepsis is changed over time, and clinical decisions affecting the management of infections are often based on the outcomes of bacterial identification. Therefore, it is essential that such identifications are performed quickly and interpreted correctly. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometer is one of the most popular MS instruments used in biology, due to its rapid and precise identification of genus and species of an extensive range of Gram-negative and-positive bacteria. Microorganism identification by Mass spectrometry is based on identifying a characteristic spectrum of each species and then matched with a large database within the instrument. The present review gives a contemporary perspective on the challenges and opportunities for bacterial identification as well as a written report of how technological innovation has advanced MS. Future clinical applications will also be addressed, particularly the use of MALDI-TOF MS in the field of microbiology for the identification and the analysis of antibiotic resistance.

Actinomyces turicensis Necrotizing Soft-Tissue Infection of the Thigh in a Diabetic Male

Background: Necrotizing soft-tissue infections are a devastating infection that is rarely caused by Actinomyces spp. Case Report: A 45-year-old obese previously healthy male presented to the emergency department with diabetic ketoacidosis. The patient developed systemic signs of infections and right medial thigh pain subsequently diagnosed as a necrotizing soft-tissue infection. Successful treatment included prompt surgical intervention and initiation of broad-spectrum antimicrobial drugs. Conclusion: Actinomyces turicensis may be the pathogen causing certain necrotizing soft-tissue infections. Clinicians should consider the possibility that this organism represents a true pathogen and not colonization/contamination.

Evaluation of VITEK MS, Clin-ToF-II MS, Autof MS 1000 and VITEK 2 ANC card for identification of Bacteroides fragilis group isolates and antimicrobial susceptibilities of these isolates in a Chinese university hospital

BACKGROUND AND PURPOSE

Bacteroides fragilis group isolates are most frequently isolated anaerobic pathogens. This study aimed to evaluate the accuracy of VITEK MS, Clin-ToF-II MS, Autof MS 1000 and VITEK 2 ANC card on the identification of clinical B. fragilis group isolates, as well as to determine their antimicrobial susceptibilities.

METHODS

A total of 138 isolates of B. fragilis group isolates were identified with the three MALDI-TOF MS systems and VITEK 2 ANC cards. 16S rRNA gene sequencing was used as the reference identification method for comparison. Antimicrobial susceptibilities were determined by agar dilution method to 19 antimicrobial agents recommended by Clinical and Laboratory Standards Institute (CLSI).

RESULTS

Hundred thirty three isolates of Bacteroides spp. and 5 isolates of Parabacteroides spp. were identified by 16S rRNA sequencing. The rates of accurate identification at species level of VITEK MS, Clin-ToF-II MS, Autof MS 1000 and VITEK 2 ANC card were 94.2%, 94.2%, 98.6% and 94.9%, respectively, while that at genus level were 99.3%, 100%, 100% and 97.8%, respectively. Metronidazole and chloramphenicol were the most susceptible agents (99.3% and 92.8%, respectively), followed by meropenem, ertapenem, imipenem and piperacillin/tazobactam to which the susceptible rates ranged from 76.8% to 79.0%. The susceptible rates to carbapenems decreased 12.4-15.3% from 2010-2013 to 2014-2017.

CONCLUSION

All the four systems provided high accurate rate on the identification of B. fragilis group isolates. Metronidazole showed highest activity against these isolates. Attention should be paid to the higher resistant rates to carbapenems, clindamycin, moxifloxacin and tigecycline than the other countries.

A comparison of Sensititre™ Anaerobe MIC plate with ATB ANA® test for the routine susceptibility testing of common anaerobe pathogens

The accuracy of the Thermo Scientific™ Sensititre™ Anaerobe MIC plate was assessed against the ATB ANA® test (bioMérieux) on 56 clinically relevant anaerobic strains collected at Geneva University Hospitals. The overall categorical agreement between both methods reached 95%. The Sensititre™ Anaerobe MIC plate had excellent accuracy for most antibiotics tested. When the Sensititre™ Anaerobe MIC plate disagreed with ATB ANA® test, the gradient strip method resolved the antimicrobial susceptibility categories of all the antibiotics tested, except for piperacillin, piperacillin-tazobactam, and penicillin, in favor of the Sensititre™ Anaerobe MIC plate (58% [21 out of 36]). Several very major errors were observed for piperacillin (12.5% [7 out of 56]), piperacillin-tazobactam (12.5% [7 out of 56]), and penicillin (2% [1 out of 56]). The gradient strip method revealed that the categorical differences for piperacillin, piperacillin-tazobactam, and penicillin were at least partly explained by heterogeneity in resistance expression. The Sensititre™ Anaerobe MIC plate offers therefore a useful alternative to the ATB ANA® test for the routine antimicrobial susceptibility testing of anaerobes in clinical microbiology 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.

Evaluation of the Vitek MS v3.0 Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Identification of Mycobacterium and Nocardia Species

This multicenter study was designed to assess the accuracy and reproducibility of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system for identification of Mycobacterium and Nocardia species compared to DNA sequencing. A total of 963 clinical isolates representing 51 taxa were evaluated. In all, 663 isolates were correctly identified to the species level (69%), with another 231 (24%) correctly identified to the complex or group level. Fifty-five isolates (6%) could not be identified despite repeat testing. All of the tuberculous mycobacteria (45/45; 100%) and most of the nontuberculous mycobacteria (569/606; 94%) were correctly identified at least to the group or complex level. However, not all species or subspecies within the M. tuberculosis, M. abscessus, and M. avium complexes and within the M. fortuitum and M. mucogenicum groups could be differentiated. Among the 312 Nocardia isolates tested, 236 (76%) were correctly identified to the species level, with an additional 44 (14%) correctly identified to the complex level. Species within the N. nova and N. transvalensis complexes could not always be differentiated. Eleven percent of the isolates (103/963) underwent repeat testing in order to get a final result. Identification of a representative set of Mycobacterium and Nocardia species was highly reproducible, with 297 of 300 (99%) replicates correctly identified using multiple kit lots, instruments, analysts, and sites. These findings demonstrate that the system is robust and has utility for the routine identification of mycobacteria and Nocardia in clinical practice.

Accuracy of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacteria: a systematic review and meta-analysis

Mycobacterium species are a significant cause of morbidity and mortality worldwide. The present study was carried out to systematically evaluate the accuracy of Matrix-assisted laser desorption ionization-time of flight mass spectroscopy (MALDI-TOF MS) for the identification of clinical pathogenic mycobacteria. After a rigid selection process, 19 articles involving 2,593 mycobacteria isolates were included. The pooled result agreed with the reference method identification for 85% of the isolates to genus level, with 71% (95% CI of 69% to 72%) correct to the species level. The MALDI-TOF MS correctly identified 92% of the M.tuberculosis isolates (95% CI of 0.87 to 0.96), and 68% of M. bovisisolates (95% CI of 27% to 100%) to the species level. Mycobacterium tuberculosis complex in solid media with reference strains using augmented database showing more accurate identification. The identifying accuracy rate of bioMérieuxVitek MS was slight higher than Bruker MALDI Biotyper (75% vs 72%). However, opposite results were obtained in identifications of M. fortuitum, M. kansasii, M. marinum, and M. terrae with these two systems. In summary, our results demonstrate that application of MALDI-TOF MS in clinical pathogenic mycobacteria identification is less satisfactory to date. Increasing need for improvement is important especially at species level.

How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories

BACKGROUND

There has been increased interest in the study of anaerobic bacteria that cause human infection during the past decade. Many new genera and species have been described using 16S rRNA gene sequencing of clinical isolates obtained from different infection sites with commercially available special culture media to support the growth of anaerobes. Several systems, such as anaerobic pouches, boxes, jars and chambers provide suitable anaerobic culture conditions to isolate even strict anaerobic bacteria successfully from clinical specimens. Beside the classical, time-consuming identification methods and automated biochemical tests, the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has revolutionized identification of even unusual and slow-growing anaerobes directly from culture plates, providing the possibility of providing timely information about anaerobic infections.

AIMS

The aim of this review article is to present methods for routine laboratories, which carry out anaerobic diagnostics on different levels.

SOURCES

Relevant data from the literature mostly published during the last 7 years are encompassed and discussed.

CONTENT

The review involves topics on the anaerobes that are members of the commensal microbiota and their role causing infection, the key requirements for collection and transport of specimens, processing of specimens in the laboratory, incubation techniques, identification and antimicrobial susceptibility testing of anaerobic bacteria. Advantages, drawbacks and specific benefits of the methods are highlighted.

IMPLICATIONS

The present review aims to update and improve anaerobic microbiology in laboratories with optimal conditions as well as encourage its routine implementation in laboratories with restricted resources.

Multicenter Evaluation of the Vitek MS v3.0 System for the Identification of Filamentous Fungi

Invasive fungal infections are an important cause of morbidity and mortality affecting primarily immunocompromised patients. While fungal identification to the species level is critical to providing appropriate therapy, it can be slow and laborious and often relies on subjective morphological criteria. The use of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has the potential to speed up and improve the accuracy of identification. In this multicenter study, we evaluated the accuracy of the Vitek MS v3.0 system in identifying 1,601 clinical mold isolates compared to identification by DNA sequence analysis and supported by morphological and phenotypic testing. Among the 1,519 isolates representing organisms in the v3.0 database, 91% (n = 1,387) were correctly identified to the species level. An additional 27 isolates (2%) were correctly identified to the genus level. Fifteen isolates were incorrectly identified, due to either a single incorrect identification (n = 13) or multiple identifications from different genera (n = 2). In those cases, when a single identification was provided that was not correct, the misidentification was within the same genus. The Vitek MS v3.0 was unable to identify 91 (6%) isolates, despite repeat testing. These isolates were distributed among all the genera. When considering all isolates tested, even those that were not represented in the database, the Vitek MS v3.0 provided a single correct identification 98% of the time. These findings demonstrate that the Vitek MS v3.0 system is highly accurate for the identification of common molds encountered in the clinical mycology laboratory.

Genetic identification and antimicrobial susceptibility of clinically isolated anaerobic bacteria: A prospective multicenter surveillance study in Japan

This prospective multicenter surveillance study was designed to provide antimicrobial susceptibility profiles of clinical anaerobic bacteria with genetic species identification in Japan. In 2014, a total of 526 non-duplicate clinical anaerobic isolates were collected from 11 acute-care hospitals in the Kyoto and Shiga regions of Japan. Genetic identification was performed using 16S rRNA sequencing. Minimum inhibitory concentrations were determined in the central laboratory and were interpreted using the CLSI criteria. Genetic analysis provided species-level identification for 496 isolates (83 species in 40 genera) and genus-level identification for 21 isolates (13 genera). Among these 517 isolates, the most frequent anaerobes were Bacteroides spp. (n = 207), Prevotella spp. (n = 43), Clostridium spp. (n = 40), and Peptoniphilus spp. (n = 40). B. fragilis was the most common species (n = 107) and showed 91.6%-97.2% susceptibility to β-lactam/β-lactamase inhibitor combinations (BLBLIs; ampicillin-sulbactam, amoxicillin-clavulanate, and piperacillin-tazobactam) and carbapenems (imipenem and meropenem) as well as 100% susceptibility to metronidazole. Gram-negative anaerobes were highly susceptible to metronidazole (99.0%) followed by BLBLIs and carbapenems (>90% each). BLBLIs or carbapenems also retained activity against Gram-positive anaerobes (99.5%-100%) except Clostridioides difficile. All isolates were susceptible to combinations of metronidazole with BLBLIs or carbapenems. Thus, BLBLIs or carbapenems are first choices for empirical therapy of anaerobic infections in Japan, and these antimicrobials in combination with metronidazole should be reserved for very severe infections and targeted therapy.

Head-to-head comparison of Microflex LT and Vitek MS systems for routine identification of microorganisms by MALDI-TOF mass spectrometry in Chile

Background

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a new and revolutionary identification method for microorganisms and has recently been introduced into clinical microbiology in many industrialized countries in Europe and North America.

Objectives

Our study aimed to compare the performance and practicality of two commercial MALDI-TOF MS platforms in a head-to head manner at a routine laboratory in Chile.

Methods

During a five-month period in 2012–13, the diagnostic efficiency (correct identification rate) and agreement between Microflex LT (Bruker Daltonics) and Vitek MS (bioMérieux) was compared in a parallel manner to conventional identification including genotypic analysis for difficult-to-identify strains. The study included 804 microbial isolates: 252 Enterobacteriaceae, 126 non-fermenters, 36 other gram-negative rods, 279 gram-positive cocci, 32 gram-positive rods, 32 anaerobes, and 47 yeasts. Other relevant factors of the two devices such as user friendliness and connectivity were also evaluated and compared.

Results

Both systems correctly identified the vast majority (98%) of the isolates to the genus level. Vitek MS reached higher rates of identification to species and species complex level than Microflex LT (81% vs. 85% and 87% vs. 93%, respectively), which was mainly based on the higher performance among coagulase negative staphylococci and Candida isolates. The evaluation of user friendliness and other technical aspects showed only marginal differences, which slightly favored Vitek MS, mainly due to its ready-to-use supplies, easier connectivity and workflow integration, and availability of local technical support.

Conclusions

Both MALDI-TOF MS systems permitted fast and accurate identification of most microbial strains and showed a high level of user-friendliness. The observed differences were marginal and slightly favored Vitek MS, mainly due to practicality and connectivity issues within our setting.

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.

Evaluation of Correlation between Pretest Probability for Clostridium difficile Infection and Clostridium difficile Enzyme Immunoassay Results

The objective of this study was to evaluate the clinical characteristics and outcomes of hospitalized patients tested for Clostridium difficile and determine the correlation between pretest probability for C. difficile infection (CDI) and assay results. Patients with testing ordered for C. difficile were enrolled and assigned a high, medium, or low pretest probability of CDI based on clinical evaluation, laboratory, and imaging results. Stool was tested for C. difficile by toxin enzyme immunoassay (EIA) and toxigenic culture (TC). Chi-square analyses and the log rank test were utilized. Among the 111 patients enrolled, stool samples from nine were TC positive and four were EIA positive. Sixty-one (55%) patients had clinically significant diarrhea, 19 (17%) patients did not, and clinically significant diarrhea could not be determined for 31 (28%) patients. Seventy-two (65%) patients were assessed as having a low pretest probability of having CDI, 34 (31%) as having a medium probability, and 5 (5%) as having a high probability. None of the patients with low pretest probabilities had a positive EIA, but four were TC positive. None of the seven patients with a positive TC but a negative index EIA developed CDI within 30 days after the index test or died within 90 days after the index toxin EIA date. Pretest probability for CDI should be considered prior to ordering C. difficile testing and must be taken into account when interpreting test results. CDI is a clinical diagnosis supported by laboratory data, and the detection of toxigenic C. difficile in stool does not necessarily confirm the diagnosis of CDI.

Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults

Topical antimicrobials are often employed for decolonization and infection prevention and may alter the endogenous microbiota of the skin. The objective of this study was to compare the microbial communities and levels of richness and diversity in community-dwelling subjects and intensive care unit (ICU) patients before and after the use of topical decolonization protocols. We enrolled 15 adults at risk for Staphylococcus aureus infection. Community subjects (n = 8) underwent a 5-day decolonization protocol (twice daily intranasal mupirocin and daily dilute bleach-water baths), and ICU patients (n = 7) received daily chlorhexidine baths. Swab samples were collected from 5 anatomic sites immediately before and again after decolonization. A variety of culture media and incubation environments were used to recover bacteria and fungi; isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Overall, 174 unique organisms were recovered. Unique communities of organisms were recovered from the community-dwelling and hospitalized cohorts. In the community-dwelling cohort, microbial richness and diversity did not differ significantly between collections across time points, although the number of body sites colonized with S. aureus decreased significantly over time (P = 0.004). Within the hospitalized cohort, richness and diversity decreased over time compared to those for the enrollment sampling (from enrollment to final sampling, P = 0.01 for both richness and diversity). Topical antimicrobials reduced the burden of S. aureus while preserving other components of the skin and nasal microbiota.

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.

Identification of mycobacterium spp. and nocardia spp. from solid and liquid cultures by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)

Identification of microorganisms by MALDI-TOF MS has been widely accepted in clinical microbiology. However, for Mycobacterium spp. and Nocardia spp. such identification has not yet reached the optimal level of routine testing. Here we describe the development of an identification tool for 49 and 15 species of Mycobacterium spp. and Nocardia spp., respectively. During database construction, a number of ambiguous reference identifications were revealed and corrected via molecular analyses. Eventually, more than 2000 individual mass spectra acquired from 494 strains were included in a reference database and subjected to bio-statistical analyses. This led to correct species identification and correct combination of species into several complexes or groups, such as the Mycobacterium tuberculosis complex. With the Advanced Spectrum Classifier algorithm, class-specific bin weights were determined and tested by cross-validation experiments with good results. When challenged with independent isolates, overall identification performance was 90% for identification of Mycobacterium spp. and 88% for Nocardia spp. However, for a number of Mycobacterium sp. isolates, no identification could be achieved and in most cases, this could be attributed to the production of polymers that masked the species-specific protein peak patterns. For the species where >20 isolates were tested, correct identification reached 95% or higher. With the current spectral database, the identification of Mycobacterium spp. and Nocardia spp. by MALDI-TOF MS can be performed in routine clinical diagnostics although in some complicated cases verification by sequencing remains mandatory.

Acute kidney injury prediction in cardiac surgery patients by a urinary peptide pattern: a case-control validation study

Background

Acute kidney injury (AKI) is a prominent problem in hospitalized patients and associated with increased morbidity and mortality. Clinical medicine is currently hampered by the lack of accurate and early biomarkers for diagnosis of AKI and the evaluation of the severity of the disease.

In 2010, we established a multivariate peptide marker pattern consisting of 20 naturally occurring urinary peptides to screen patients for early signs of renal failure. The current study now aims to evaluate if, in a different study population and potentially various AKI causes, AKI can be detected early and accurately by proteome analysis.

Methods

Urine samples from 60 patients who developed AKI after cardiac surgery were analyzed by capillary electrophoresis-mass spectrometry (CE-MS). The obtained peptide profiles were screened by the AKI peptide marker panel for early signs of AKI. Accuracy of the proteomic model in this patient collective was compared to that based on urinary neutrophil gelatinase-associated lipocalin (NGAL) and kidney injury molecule-1 (KIM-1) ELISA levels. Sixty patients who did not develop AKI served as negative controls.

Results

From the 120 patients, 110 were successfully analyzed by CE-MS (59 with AKI, 51 controls). Application of the AKI panel demonstrated an AUC in receiver operating characteristics (ROC) analysis of 0.81 (95 % confidence interval: 0.72–0.88). Compared to the proteomic model, ROC analysis revealed poorer classification accuracy of NGAL and KIM-1 with the respective AUC values being outside the statistical significant range (0.63 for NGAL and 0.57 for KIM-1).

Conclusions

This study gives further proof for the general applicability of our proteomic multimarker model for early and accurate prediction of AKI irrespective of its underlying disease cause.

Electronic supplementary material

The online version of this article (doi:10.1186/s13054-016-1344-z) contains supplementary material, which is available to authorized users.

Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi

Invasive fungal infections have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. With the increasing incidence of invasive disease attributed to filamentous fungi, rapid and accurate species-level identification of these pathogens is necessary. Traditional methods for identification of filamentous fungi can be slow and may lack resolution. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and accurate method for identification of bacteria and yeasts, but a paucity of data exists on the performance characteristics of this method for identification of filamentous fungi. The objective of our study was to evaluate the accuracy of the Vitek MS for mold identification. A total of 319 mold isolates representing 43 genera recovered from clinical specimens were evaluated. Of these isolates, 213 (66.8%) were correctly identified using the Vitek MS Knowledge Base, version 3.0 database. When a modified SARAMIS (Spectral Archive and Microbial Identification System) database was used to augment the version 3.0 Knowledge Base, 245 (76.8%) isolates were correctly identified. Unidentified isolates were subcultured for repeat testing; 71/319 (22.3%) remained unidentified. Of the unidentified isolates, 69 were not in the database. Only 3 (0.9%) isolates were misidentified by MALDI-TOF MS (including Aspergillus amoenus [n = 2] and Aspergillus calidoustus [n = 1]) although 10 (3.1%) of the original phenotypic identifications were not correct. In addition, this methodology was able to accurately identify 133/144 (93.6%) Aspergillus sp. isolates to the species level. MALDI-TOF MS has the potential to expedite mold identification, and misidentifications are rare.

Development of a MALDI MS-based platform for early detection of acute kidney injury

PURPOSE

Septic acute kidney injury (AKI) is associated with poor outcome. This can partly be attributed to delayed diagnosis and incomplete understanding of the underlying pathophysiology. Our aim was to develop an early predictive test for AKI based on the analysis of urinary peptide biomarkers by MALDI-MS.

EXPERIMENTAL DESIGN

Urine samples from 95 patients with sepsis were analyzed by MALDI-MS. Marker search and multimarker model establishment were performed using the peptide profiles from 17 patients with existing or within the next 5 days developing AKI and 17 with no change in renal function. Replicates of urine sample pools from the AKI and non-AKI patient groups and normal controls were also included to select the analytically most robust AKI markers.

RESULTS

Thirty-nine urinary peptides were selected by cross-validated variable selection to generate a support vector machine multidimensional AKI classifier. Prognostic performance of the AKI classifier on an independent validation set including the remaining 61 patients of the study population (17 controls and 44 cases) was good with an area under the receiver operating characteristics curve of 0.82 and a sensitivity and specificity of 86% and 76%, respectively.

CONCLUSION AND CLINICAL RELEVANCE

A urinary peptide marker model detects onset of AKI with acceptable accuracy in septic patients. Such a platform can eventually be transferred to the clinic as fast MALDI-MS test format.