Optimization of Mycobacterium tuberculosis DNA processing prior to whole genome sequencing.

The process of whole genome sequencing of the Mycobacterium tuberculosis complex is dependent on complete the inactivation of the strain and subsequent DNA extraction. The objective of this study was to optimise the two steps. Firstly, the efficacy of Triton X-100 as a solvent for the inactivation step was evaluated.

Extensive buruli ulcer in a patient returning from Mali and Senegal.

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Towards the reconstruction of a global TB history using a new pipeline "TB-Annotator".

Mycobacterium tuberculosis complex (MTBC) has a population structure consisting of 9 human and animal lineages. The genomic diversity within these lineages is a pathogenesis factor that affects virulence, transmissibility, host response, and antibiotic resistance. Hence it is important to develop improved information systems for tracking and understanding the spreading and evolution of genomes.

Performances of bioinformatics tools for the analysis of sequencing data of Mycobacterium tuberculosis complex strains.

Whole-genome sequencing of Mycobacterium tuberculosis complex (MTBC) strains is a rapidly growing tool to obtain results regarding the resistance and phylogeny of the strains. We evaluated the performances of two bioinformatics tools for the analysis of whole-genome sequences of MTBC strains. Two hundred and twenty-seven MTBC strains were isolated and whole-genome sequenced at the laboratory of Avicenne Hospital between 2015 and 2021.

Tuberculosis treatment outcomes among precarious patients in France.

Objectives: Patients lost to follow-up and treatment failure in tuberculosis disease (TB) are major public health issues. In the absence of appropriate treatment, approximately 70 % of smear-positive patients will die within 10 years of disease progression. This study, conducted in the French region with the highest incidence, aimed to assess tuberculosis treatment outcomes and its determinants.

Prevalence and risk factors for carriage of extended-spectrum β-lactamase-producing enterobacteriaceae in rehabilitation wards in France.

Objectives: Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) are a major public health concern worldwide. Little is known about the prevalence of ESBL-PE colonization in rehabilitation wards in France. Our aim was to determine the prevalence of ESBL-PE colonization in rehabilitation wards in the Parisian area and to identify potential risk factors for ESBL-PE carriage.

Molecular detection of isoniazid monoresistance improves tuberculosis treatment: A retrospective cohort in France.

Objectives: Isoniazid-monoresistant tuberculosis (HR-TB) requires early diagnosis and adapted treatment to achieve optimal outcomes. The primary aim of the study was to assess the impact of the implementation of rapid diagnostic tests on HR-TB treatment in France.

Methods: We designed a retrospective multicentre study including consecutive HR-TB patients diagnosed in 2016 and 2017.

Isoniazid-monoresistant tuberculosis in France: Risk factors, treatment outcomes and adverse events.

Objectives: Isoniazid-monoresistant tuberculosis (HR-TB) is the most prevalent form of drug-resistant TB worldwide and in France and is associated with poorer treatment outcomes compared with drug-susceptible TB (DS-TB). The objective of this study was to determine the characteristics of HR-TB patients in France and to compare outcomes and safety of treatment for HR-TB and DS-TB.

Methods: We performed a case-control multicenter study to identify risk factors associated with HR-TB and compare treatment outcomes and safety between HR-TB patients and DS-TB patients.

Molecular identification of Actinomadura madurae isolated from a patient originally from Algeria; observations from a case report.

Background: Mycetoma is a chronic granulomatous subcutaneous infection caused by anaerobic pseudofilamentous bacteria or fungi. It is commonly prevalent in tropical and subtropical countries. Men are more susceptible to the disease due to greater participation in agricultural works.

A recurrent lung abscess caused by delayed diagnosis of unique co-infection with Abiotrophia defectiva.

We report the case of a lung abscess due to Prevotella baroniae with a co-infection by Abiotrophia defective, which is a 'nutritionally variant streptococci' (NVS), in a 48-year-old patient. The delayed diagnosis of this co-infection led to multiple failures of medical treatment and need for surgery. Pathogenicity of these bacteria is well known, particularly in endocarditis, but not in lung infection.

Pulmonary tuberculosis: Evaluation of current diagnostic strategy.

Objective: To identify tools that will result in faster diagnosis, making the current pulmonary tuberculosis strategy more efficient.

Patients And Methods: A 4-year (2015-2018) retrospective study. The gold standard for diagnosis was a positive culture from a respiratory specimen.

Can environmental contamination be explained by particular traits associated with patients?

Background: Little is known about patient risk factors associated with environmental contamination.

Aim: To evaluate the rate of environmental contamination and to investigate individual risk factors.

Methods: A prospective cohort study was conducted.

Fatal serogroup 1 pleural empyema: A case report.

Background: () is a gram-negative intracellular bacillus composed of sixteen different serogroups. It is mostly known to cause pneumonia in individuals with known risk factors as immunocompromised status, tobacco use, chronic organ failure or age older than 50 years. Although parapneumonic pleural effusion is frequent in legionellosis, pleural empyema is very uncommon.

Using SNOMED-CT to Help the Transition from Microbiological Data to ICD-10 Sepsis Codes.

Assigning ICD-10 code of sepsis in regard of a pathogenic bacterium found in an haemoculture requires knowledge of microbiology because of the difference of granularity. The aim of this paper is to automate this coding thanks to the use of SNOMED-CT. A dichotomous classification of bacteria causing sepsis has been generated in respect of ICD-10.

Specialization of small non-conjugative plasmids in according to their family types.

We undertook a comprehensive comparative analysis of a collection of 30 small (<25 kb) non-conjugative plasmids previously classified by the gene sharing approach into 10 families, as well as plasmids found in the National Center for Biotechnology Information (NCBI) nucleotide database sharing similar genomic sequences. In total, 302 mobilizable (belonging to 2 MOB and 5 MOB families) and 106 non-transferable/relaxase-negative (belonging to three ReL families) plasmids were explored. The most striking feature was the specialization of the plasmid family types that was not related to their transmission mode and replication system.

Proposition of a safe Mycobacterium tuberculosis complex denaturation method that does not compromise the integrity of DNA for whole-genome sequencing.

Whole-genome sequencing plays now a leading role in epidemiologic studies of tuberculosis. DNA extraction of Mycobacterium tuberculosis complex (MTBC) requires complete inactivation of the strains, to be handled for further molecular procedures. In this study we compared two chloroform-based denaturation methods (one with a step of heat killing, one without) to a traditional heat inactivation method.

The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-β-Lactamase-Producing Strains of Escherichia coli.

We previously identified an operon involved in an arginine deiminase (ADI) pathway ( operon) on a CTX-M-producing plasmid from an O102-ST405 strain of As the ADI pathway was shown to be involved in the virulence of various Gram-positive bacteria, we tested whether the ADI pathway could be involved in the epidemiological success of extended-spectrum-β-lactamase (ESBL)-producing strains. We studied two collections of human isolated in France ( = 493) and England ( = 1,509) and show that the prevalence of the operon (i) is higher in ESBL-producing strains (12.1%) than in nonproducers (2.

Prediction of methicillin-resistant Staphylococcus aureus bloodstream infection: do we need rapid diagnostic tests?

Staphylococcus aureus (SA) is the leading cause of bloodstream infection (BSI). The incidence of methicillin-resistant SA (MRSA) has decreased in France and Europe since one decade. Early and precise prediction of methicillin susceptibility is needed to improve probabilistic antibiotic therapy of MRSA-BSI.

Pneumonia-Specific Escherichia coli with Distinct Phylogenetic and Virulence Profiles, France, 2012-2014.

In a prospective, nationwide study in France of Escherichia coli responsible for pneumonia in patients receiving mechanical ventilation, we determined E. coli antimicrobial susceptibility, phylotype, O-type, and virulence factor gene content. We compared 260 isolates with those of 2 published collections containing commensal and bacteremia isolates.

Oropharyngeal Bacterial Colonization after Chlorhexidine Mouthwash in Mechanically Ventilated Critically Ill Patients.

What We Already Know About This Topic: WHAT THIS ARTICLE TELLS US THAT IS NEW: BACKGROUND:: Oropharyngeal care with chlorhexidine to prevent ventilator-associated pneumonia is currently questioned, and exhaustive microbiologic data assessing its efficacy are lacking. The authors therefore aimed to study the effect of chlorhexidine mouthwash on oropharyngeal bacterial growth, to determine chlorhexidine susceptibility of these bacteria, and to measure chlorhexidine salivary concentration after an oropharyngeal care.

Methods: This observational, prospective, single-center study enrolled 30 critically ill patients under mechanical ventilation for over 48 h.

Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins.

To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs.