Anaerobic blood culture isolates in a Norwegian university hospital: identification by MALDI-TOF MS vs 16S rRNA sequencing and antimicrobial susceptibility profiles

Contamination rate of rare bacterial species detected by MALDI-TOFMS: a retrospective cohort study

When rare bacterial species are identified in blood cultures, determining the clinical significance is sometimes difficult. This study aimed to analyze the clinical significance of rare bacterial species detected in blood cultures using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOFMS) by comparing their contamination rates with those of common species. We retrospectively analyzed medical records of adult patients with positive blood cultures at Kyoto City Hospital from 2014 to 2022. Rare species were defined by low detection rates and few PubMed reports. Of 4880 microorganisms identified from 3441 individuals, 1150 (23.6%) were classified as contamination. Meanwhile, 24 rare microorganisms were identified, of which 14 (58.3%) were classified as contamination, which was significantly higher than common species (odds ratio 4.56, 95% confidence Interval 1.88-11.50, P < 0.001). These findings may help in determining the clinical significance of rare bacterial species in blood cultures with few reported cases.

Tannerella forsythia, Fusobacterium nucleatum, and Suspected Actinomyces Causing Massive Empyema: A Case Report

This report presents the case of a polymicrobial empyema due to Fusobacterium nucleatum, Tannerella forsythia, and suspected Actinomyces spp., presenting as several weeks of progressive shortness of breath and malaise. The patient had many risk factors for a lower respiratory tract infection, including chronic alcohol abuse, a flu-like illness months prior, and a recent invasive dental procedure. An admission CT scan showed a large right pleural effusion. Blood cultures were negative, but an aspirate from the pleural effusion showed abundant gram-positive rods that did not grow aerobically. Subsequent anaerobic cultures at a reference laboratory grew Tannerella forsythia and Fusobacterium nucleatum. This report will review the diagnostic difficulties associated with anaerobic causes of empyema in general and the specific organisms implicated in this case.

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.

Metronidazole: an update on metabolism, structure-cytotoxicity and resistance mechanisms

Metronidazole, a nitroimidazole, remains a front-line choice for treatment of infections related to inflammatory disorders of the gastrointestinal tract including colitis linked to Clostridium difficile. Despite >60 years of research, the metabolism of metronidazole and associated cytotoxicity is not definitively characterized. Nitroimidazoles are prodrugs that are reductively activated (the nitro group is reduced) under low oxygen tension, leading to imidazole fragmentation and cytotoxicity. It remains unclear if nitroimidazole reduction (activation) contributes to the cytotoxicity profile, or whether subsequent fragmentation of the imidazole ring and formed metabolites alone mediate cytotoxicity. A molecular mechanism underpinning high level (>256 mg/L) bacterial resistance to metronidazole also remains elusive. Considering the widespread use of metronidazole and other nitroimidazoles, this review was undertaken to emphasize the structure-cytotoxicity profile of the numerous metabolites of metronidazole in human and murine models and to examine conflicting reports regarding metabolite-DNA interactions. An alternative hypothesis, that DNA synthesis and repair of existing DNA is indirectly inhibited by metronidazole is proposed. Prokaryotic metabolism of metronidazole is detailed to discuss new resistance mechanisms. Additionally, the review contextualizes the history and current use of metronidazole, rates of metronidazole resistance including metronidazole MDR as well as the biosynthesis of azomycin, the natural precursor of metronidazole. Changes in the gastrointestinal microbiome and the host after metronidazole administration are also reviewed. Finally, novel nitroimidazoles and new antibiotic strategies are discussed.

MALDI-TOF MS versus 16S rRNA sequencing: Minor discrepancy between tools in identification of Bacteroides isolates

Members of the genus Bacteroides are important components of the normal microbiota of gastrointestinal tract; however, as opportunistic pathogens are also associated with severe or even life-threatening infections with significant mortality. Various species within Bacteroides fragilis group are phenotypically very similar; thus, their identifications with traditional-automated biochemical methods are frequently inaccurate. The identification of the newly discovered or reclassified bacteria can be doubtful because of the lack of biochemical profile in the database of these tests. The aim of this study was to determine the accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method by testing of 400 Hungarian Bacteroides clinical isolates. Inaccurate identification results with MALDI-TOF MS were confirmed by 16S rRNA gene sequencing and findings were compared with traditional-automated biochemical test rapid ID 32A method as well.

First report of metronidazole resistant, nimD-positive, Bacteroides stercoris isolated from an abdominal abscess in a 70-year-old woman

We here present the first case of a metronidazole resistant nimD positive Bacteroides stercoris. The isolate originated from a polymicrobial intra-abdominal abscess in a 70-year-old woman. The nimD gene was detected by use of whole-genome shotgun sequencing and the subsequent use of the ResFinder 2.1 web service.

High-Throughput Sequencing of Viable Microbial Communities in Raw Pork Subjected to a Fast Cooling Process

This study aimed to investigate the effect of the fast cooling process on the microbiological community in chilled fresh pork during storage. We established a culture-independent method to study viable microbes in raw pork. Tray-packaged fresh pork and chilled fresh pork were completely spoiled after 18 and 49 d in aseptic bags at 4 °C, respectively. 16S/18S ribosomal RNAs were reverse transcribed to cDNA to characterize the activity of viable bacteria/fungi in the 2 types of pork. Both cDNA and total DNA were analyzed by high-throughput sequencing, which revealed that viable Bacteroides sp. were the most active genus in rotten pork, although viable Myroides sp. and Pseudomonas sp. were also active. Moreover, viable fungi were only detected in chilled fresh pork. The sequencing results revealed that the fast cooling process could suppress the growth of microbes present initially in the raw meat to extend its shelf life. Our results also suggested that fungi associated with pork spoilage could not grow well in aseptic tray-packaged conditions.

Matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology

The microbiological management of patients with suspected bacterial infection includes the identification of the pathogen and the determination of the antibiotic susceptibility. These traditional approaches, based on the pure culture of the microorganism, require at least 36-48h. A new method, Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS), has been recently developed to profile bacterial proteins from whole cell extracts and obtain a bacterial fingerprint able to discriminate microorganisms from different genera and species. By whole cell-mass spectrometry, microbial identification can be achieved within minutes from cultured isolate, rather than traditional phenotypic or genotypic characterizations. From the year 2009 an explosion of applications of this technology has been observed with promising results. Several studies have been performed and showed that MALDI-TOF represents a reliable alternative method for rapid bacteria and fungi identification in clinical setting. A future area of expansion is represented by the application of MALDI-TOF technology to the antibiotic susceptibility test. In conclusion, the revision of the literature available up to date demonstrated that MALDI-TOF MS represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates in clinical settings. By an earlier microbiological diagnosis, MALDI-TOF MS contributes to a reduced mortality and hospitalization time of the patients and consequently has a significant impact on cost savings and public health.