The increasing worldwide incidence of nontuberculous mycobacterial lung disease (NTM-LD) and the similarity of its manifestations to those of tuberculosis (TB) pose huge challenges in the diagnosis and treatment of NTM-LD, which is commonly misdiagnosed and mistreated as TB. Proper diagnosis and treatment at an early stage can greatly improve patient outcomes.
Mycobacterium avium was identified by mNGS in lung tissue of case 1 and bronchioalveolar fluid from case 2 that was not identified using conventional microbiological methods. Multiple NTM species were detected in the blood mNGS samples from case 3 who had disseminated NTM infection. Although NTM was isolated from blood culture, conventional methods failed to identify the organisms to the level of species. All three patients were suffering from and being treated for myelodysplastic syndrome, rheumatoid arthritis, systemic lupus erythematosus, or acute lymphoblastic leukemia, making them immunosuppressed and susceptible to NTM infections. Case 1 and Case 2 significantly improved after anti-NTM treatment, but case 3 succumbed to the infection due to her underlying medical illness despite aggressive treatment.
The cases in this study demonstrate the effectiveness of mNGS in facilitating and improving the clinical diagnosis of NTM infections. We propose combining mNGS with traditional diagnostic methods to identify pathogens at the early stages of the disease so that targeted treatment can be implemented.

The new European In Vitro Diagnostic (IVD) Regulation 2017/746 (IVDR) restricts the use of lab-developed tests (LDT) after 26th May 2022. There are no data on the impact of the IVDR on laboratories in the European Union.
Laboratory tests performed in UZ Leuven were divided in four groups: core laboratory, immunology, special chemistry, and molecular microbiology testing. Each test was classified as Conformité Européenne (CE)-IVD, modified/off-label CE-IVD, commercial Research Use Only (RUO) or LDT. Each matrix was considered a separate test.
We found that 97.6% of the more than 11.5 million results/year were generated with a CE-IVD method. Of the 922 different laboratory tests, however, only 41.8% were CE-IVD, 10.8% modified/off-label CE-IVD, 0.3% RUO, and 47.1% LDT. Off-label CE-IVD was mainly used to test alternative matrices not covered by the claim of the manufacturer (e.g., pleural or peritoneal fluid). LDTs were mainly used for special chemistry, flow cytometry, and molecular testing. Excluding flow cytometry, the main reasons for the use of 377 LDTs were lack of a CE-IVD method (71.9%), analytical requirements (14.3%), and the fact the LDT was in use before CE-IVD available (11.9%).
While the large majority of results (97.6%) were generated with a CE-IVD method, only 41.8% of laboratory tests were CE-IVD. There is currently no alternative on the market for 71.5% of the 537 LDTs performed in our laboratory which do not fall within the scope of the current IVD directive (IVDD). Compliance with the IVDR will require a major investment of time and effort.

BACKGROUND: Pertussis, caused by Bordetella pertussis (B. pertussis), is a highly transmissible, acute respiratory disease that occurs in many countries. Diagnosis of pertussis continues to be a challenge using traditional tests due to their turn-around time and sensitivity. Herein, we rapidly and accurately screened a family cluster of pertussis from a child and her mother.
METHODS: We used an automated nested multiplex PCR system which included B. pertussis, influenza A virus, and 19 other respiratory pathogens.
RESULTS: We detected B. pertussis, influenza A virus H1-2009 (FluA-2009), adenovirus, and respiratory syncytial virus (RSV) in the child, and the mother of the child was positive for B. pertussis and FluA-2009.
CONCLUSIONS: Active and timely screening for pertussis of adult family members should be considered. The detection of multiple respiratory pathogens may guide effective antibiotic therapies. This could be a novel test for the prevention of pertussis.

In the aseptic manufacture of parenteral drug products and low bioburden, cell, and gene therapy products, the control and monitoring of environmental- and personnel-associated microorganisms is an imperative for the confirmation of controlled conditions and the assessment of microbial risks. Environmental and personnel monitoring programs exist to assure product quality and serve as one of the several means of removing the emphasis on finished drug product testing. Therefore, these programs must adequately assess these risks and identify situations in which increased microbial risks occur. The major source of microbial risks in the controlled clean room environments for parenteral drug product manufacture are personnel. Modern microbial analytical methods, including metagenomic analysis, have identified a greater abundance of Cutibacterium acnes; traditional culture-based monitoring fails to consistently recover and assist in the identification of the potential risk that this microorganism represents. This review provides a case-study assessment of this microorganism in the context of parenteral manufacture for the purpose of assisting in the deciding the necessary controls and the potential monitoring addressing this microbial risk.

Laboratory models are a cornerstone of modern microbiology, but the accuracy of these models has not been systematically evaluated. As a result, researchers often choose models based on intuition or incomplete data. We propose a general quantitative framework to assess model accuracy from RNA sequencing data and use this framework to evaluate models of Pseudomonas aeruginosa cystic fibrosis (CF) lung infection. We found that an in vitro synthetic CF sputum medium model and a CF airway epithelial cell model had the highest genome-wide accuracy but underperformed on distinct functional categories, including porins and polyamine biosynthesis for the synthetic sputum medium and protein synthesis for the epithelial cell model. We identified 211 \"elusive\" genes that were not mimicked in a reference strain grown in any laboratory model but found that many were captured by using a clinical isolate. These methods provide researchers with an evidence-based foundation to select and improve laboratory models.IMPORTANCE Laboratory models have become a cornerstone of modern microbiology. However, the accuracy of even the most commonly used models has never been evaluated. Here, we propose a quantitative framework based on gene expression data to evaluate model performance and apply it to models of Pseudomonas aeruginosa cystic fibrosis lung infection. We discovered that these models captured different aspects of P. aeruginosa infection physiology, and we identify which functional categories are and are not captured by each model. These methods will provide researchers with a solid basis to choose among laboratory models depending on the scientific question of interest and will help improve existing experimental models.

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.

Cardiobacterium hominis est un bacille à Gram négatif responsable d\'endocardites infectieuses, principalement chez les patients atteints de pathologies cardiaques ou porteurs de valves. L\'identification de cette bactérie est souvent complexe et peut être la cause d\'un diagnostic et d\'une prise en charge tardifs, source de complications cardiaques. Cet article présente la prise en charge d\'une endocardite infectieuse associée à un sepsis à Cardiobacterium hominis, les difficultés d\'identification de cette bactérie, ainsi qu\'une revue de la littérature sur les infections dues à cette bactérie.

The growing commercial interest in multi-strain formulations marketed as probiotics has not been accompanied by an equal increase in the evaluation of quality levels of these biotechnological products. The multi-strain product VSL#3 was used as a model to setup a microbiological characterization that could be extended to other formulations with high complexity. Shotgun metagenomics by deep Illumina sequencing was applied to DNA isolated from the commercial VSL#3 product to confirm strains identity safety and composition. Single-cell analysis was used to evaluate the cell viability, and β-galactosidase and urease activity have been used as marker to monitor the reproducibility of the production process. Similarly, these lots were characterized in detail by a metaproteomics approach for which a robust protein extraction protocol was combined with advanced mass spectrometry. The results identified over 1600 protein groups belonging to all strains present in the VSL#3 formulation. Of interest, only 3.2 % proteins showed significant differences mainly related to small variations in strain abundance. The protocols developed in this study addressed several quality criteria that are relevant for marketed multi-strain products and these represent the first efforts to define the quality of complex probiotic formulations such as VSL#3.

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Histoplasmosis is occasionally encountered in non-endemic countries owing to more frequent international travel and migration, as well as an increase in the number of vulnerable hosts (e.g., patients with cellular immunodeficiencies). However, the diagnosis of endemic mycoses may be challenging because of its rarity and the limited availability of diagnostic tests. We report a case of disseminated histoplasmosis in a human immunodeficiency virus (HIV)-infected Japanese man who had often travelled to histoplasmosis-endemic countries. We also reviewed the reported cases of HIV-associated histoplasmosis in Japan. To the best of our knowledge, this is the ninth case report of co-infection with Histoplasma and HIV in Japan and the second involving a Japanese patient. This case emphasizes the importance of noting the details of not only the present residence of patients, but also their previous residence and travels. If histoplasmosis is suspected, physicians should inform laboratory personnel that fungal cultures should be incubated for 6 weeks, and compliance with biosafety guidelines for handling the specimens should be practiced. Since death occurs in nearly 50% of HIV-associated histoplasmosis cases in Japan, early recognition, timely diagnosis, and appropriate treatment are mandatory.