Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics.

After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries.

Bartonella infections diagnosed in the French reference center, 2014-2019, and focus on infections in the immunocompromised.

We studied retrospectively 651 PCR-confirmed Bartonella infections diagnosed at the French reference center for bartonellosis from 2014 to 2019. The most common form was cat-scratch disease (89%) followed by endocarditis (9%). Disseminated forms (2%) mainly presented as bacillary angiomatosis or peliosis hepatis in solid organ transplant recipients.

Evaluation of 11 DNA Automated Extraction Protocols for the Detection of the 5 Mains Candida Species from Artificially Spiked Blood.

The molecular detection of plays an important role in the diagnosis of candidaemia, a major cause of morbidity and mortality. The sensitivity of this diagnosis is partly related to the efficiency of yeast DNA extraction. In this monocentric study, we investigated the suitability of 11 recent automated procedures for the extraction of low and high amounts of DNA from spiked blood.

Contribution of VitaPCR SARS-CoV-2 to the emergency diagnosis of COVID-19.

Background: With the persistent COVID-19 pandemic, there is an urgent need to use rapid and reliable diagnostic tools for highly urgent cases. Antigen tests are disappointing with their lack of sensitivity. Among molecular tools allowing a diagnosis in less than an hour, only one, the Cepheid Xpert Xpress SARS-CoV-2 assay, has exhibited a good sensitivity.

Original sequence divergence among Pseudomonas putida CadRs drive specificity.

Bacteria, especially those living in soils, are in constant contact with metals. Transition metals like Fe or Zn, are required for proper growth. Some other metals like Cd or Hg are only toxic.

Metagenomic Analysis of Microdissected Valvular Tissue for Etiological Diagnosis of Blood Culture-Negative Endocarditis.

Background: Etiological diagnosis is a key to therapeutic adaptation and improved prognosis, particularly for infections such as endocarditis. In blood culture-negative endocarditis (BCNE), 22% of cases remain undiagnosed despite an updated comprehensive syndromic approach. This prompted us to develop a new diagnostic approach.

Fluorescence in situ hybridization, a complementary molecular tool for the clinical diagnosis of infectious diseases by intracellular and fastidious bacteria.

Many obligate or facultative intracellular bacteria pose a critical problem in clinical microbiology diagnosis as a result of their fastidious growth or lack of growth in conventional culture media. Molecular diagnosis is based on the analysis and demonstration of nucleic acids (DNA and RNA). In the field of infectiology, it combines laboratory medicine with the technology of molecular genetics to identify infectious pathogens.

Fluorescent in situ hybridization can be used as a complementary assay for the diagnosis of Tropheryma whipplei infection.

Background: Immunohistochemistry and Periodic acid-Schiff (PAS) staining have been routinely used for the diagnosis of Whipple's disease (WD). However, these methods present limitations. As a result, the last years, Fluorescence in situ hybridization (FISH) has been increasingly used as a complementary tool for the diagnosis of WD from various tissue samples.

Fluorescence Hybridization (FISH) and Peptide Nucleic Acid Probe-Based FISH for Diagnosis of Q Fever Endocarditis and Vascular Infections.

Endocarditis and vascular infections are common manifestations of persistent localized infection due to , and recently, fluorescence hybridization (FISH) was proposed as an alternative tool for their diagnosis. In this study, we evaluated the efficiency of FISH in a series of valve and vascular samples infected by We tested 23 -positive valves and thrombus samples obtained from patients with Q fever endocarditis. Seven aneurysms and thrombus specimens were retrieved from patients with Q fever vascular infections.

Coxiella burnetii: A Hidden Pathogen in Interstitial Lung Disease?

We report 7 patients with interstitial lung disease seen at computed tomographic scan review. Coxiella burnetii infection was diagnosed in situ in 1 lung biopsy specimen. Q fever may be a cofactor of interstitial lung disease, especially in endemic areas.

Molecular strategy for the diagnosis of infectious lymphadenitis.

Molecular methods have been considered to be the gold standard for the diagnosis of infectious lymphadenitis. However, culture remains critical in the case of low bacterial concentrations. We used molecular assays and culture to examine fresh lymph node biopsies from patients with suspected infectious lymphadenopathy.

A case of giant cell arteritis associated with culture-proven Coxiella burnetii aortitis.

A case of proven Coxiella burnetii aortitis, possibly associated with giant cell arteritis (GCA), is reported. A 72-year-old man, who is a hunter, presented with weight loss, fever, jaw claudication, and hardened temporal arteries associated with a persistent inflammatory syndrome and arteritis of the whole aorta, including the brachiocephalic arteries, as seen on F-fluorodeoxyglucose positron emission tomography/computed tomography. The diagnosis of GCA was retained, and treatment with prednisolone was started.

Molecular Tests That Target the RTX Locus Do Not Distinguish between Kingella kingae and the Recently Described Kingella negevensis Species.

is an important invasive pathogen in early childhood. The organism elaborates an RTX toxin presumably restricted to this species. Consequently, real-time quantitative PCR (qPCR) assays targeting the RTX locus have been developed in recent years and are gaining increasing use for the molecular diagnosis of infections.

Bartonella henselae is usually not viable in lymph nodes of patients with cat scratch disease.

Bartonella henselae, the agent of cat scratch disease (CSD), appears to be a common organism responsible for lymphadenitis in both adults and children. There is a very low isolation rate for B. henselae from lymph nodes of patients with CSD.

Bacterial host and reporter gene optimization for genetically encoded whole cell biosensors.

Whole-cell biosensors based on reporter genes allow detection of toxic metals in water with high selectivity and sensitivity under laboratory conditions; nevertheless, their transfer to a commercial inline water analyzer requires specific adaptation and optimization to field conditions as well as economical considerations. We focused here on both the influence of the bacterial host and the choice of the reporter gene by following the responses of global toxicity biosensors based on constitutive bacterial promoters as well as arsenite biosensors based on the arsenite-inducible P promoter. We observed important variations of the bioluminescence emission levels in five different Escherichia coli strains harboring two different lux-based biosensors, suggesting that the best host strain has to be empirically selected for each new biosensor under construction.

Noncontiguous finished genome sequence and description of Necropsobacter massiliensis sp. nov.

Strain FF6(T) was isolated from the cervical abscess of a 4-year-old Senegalese boy, in Dakar, Senegal. MALDI-TOF MS did not provide any identification. This strain exhibited a 95.

Prevalence of Mycobacterium lentiflavum in cystic fibrosis patients, France.

Background: Mycobacterium lentiflavum is rarely isolated in respiratory tract samples from cystic fibrosis patients. We herein describe an unusually high prevalence of M. lentiflavum in such patients.

Pushing the limits of nickel detection to nanomolar range using a set of engineered bioluminescent Escherichia coli.

The detection of nickel in water is of great importance due to its harmfulness for living organism. A way to detect Ni is the use of whole-cell biosensors. The aim of the present work was to build a light-emitting bacterial biosensor for the detection of Ni with high specificity and low detection limit properties.

Cost-effective pooling of DNA from nasopharyngeal swab samples for large-scale detection of bacteria by real-time PCR.

We investigated the potential of pooling DNA from nasopharyngeal specimens to reduce the cost of real-time PCR (RT-PCR) for bacterial detection. Lyophilization is required to reconcentrate DNA. This strategy yields a high specificity (86%) and a high sensitivity (96%).

PCR primers to study the diversity of expressed fungal genes encoding lignocellulolytic enzymes in soils using high-throughput sequencing.

Plant biomass degradation in soil is one of the key steps of carbon cycling in terrestrial ecosystems. Fungal saprotrophic communities play an essential role in this process by producing hydrolytic enzymes active on the main components of plant organic matter. Open questions in this field regard the diversity of the species involved, the major biochemical pathways implicated and how these are affected by external factors such as litter quality or climate changes.

Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases.

Molecular tools have shown an added value in the diagnosis of infectious diseases, in particular for those caused by fastidious intracellular microorganisms, or in patients receiving antibiotics before sampling. If 16S rDNA amplification had been gradually implemented in microbiology laboratories, specific real-time polymerase chain reaction (PCR) would have permitted an increase in the sensitivity of molecular methods and a reduction of contamination. Herein, we report our experience in the diagnosis of infectious diseases over two years, during which 32,948 clinical samples from 18,056 patients were received from France and abroad.