Characterization of the Secreted Acid Phosphatase SapS Reveals a Novel Virulence Factor of Staphylococcus aureus That Contributes to Survival and Virulence in Mice

Staphylococcus aureus possesses a large arsenal of immune-modulating factors, enabling it to bypass the immune system’s response. Here, we demonstrate that the acid phosphatase SapS is secreted during macrophage infection and promotes its intracellular survival in this type of immune cell. In animal models, the SA564 sapS mutant demonstrated a significantly lower bacterial burden in liver and renal tissues of mice at four days post infection in comparison to the wild type, along with lower pathogenicity in a zebrafish infection model. The SA564 sapS mutant elicits a lower inflammatory response in mice than the wild-type strain, while S. aureus cells harbouring a functional sapS induce a chemokine response that favours the recruitment of neutrophils to the infection site. Our in vitro and quantitative transcript analysis show that SapS has an effect on S. aureus capacity to adapt to oxidative stress during growth. SapS is also involved in S. aureus biofilm formation. Thus, this study shows for the first time that SapS plays a significant role during infection, most likely through inhibiting a variety of the host’s defence mechanisms

Molecular diagnosis of community-acquired meningitis : a direct metagenomic-based sequencing approach

Les méningites communautaires sont des urgences vitales, dont le pronostic est partiellement associé au génotype de l'agent pathogène. plus de 100 microbes sont impliqués dans les méningites infectieuses, identifiés dans le liquide céphalorachidien (LCR). La culture de LCR est le gold standard du diagnostic des méningites, mais actuellement ce diagnostic de routine est basé sur la détection par PCR multiplexe en temps réel des pathogènes les plus fréquents. Cependant, le génotypage des microbes responsables tel que les Entérovirus qui couvrent plus de 300 sérotypes différents, ainsi que le génotypage et l’antibiogramme des bactéries pathogènes, nécessitent des investigations in-vitro supplémentaires. Notre étude rétrospective de 20,779 LCR prélevés dans le cadre du diagnostic des méningites communautaires au cours de 61 mois, analysés dans les laboratoires de microbiologie clinique de Nîmes et Marseille a montré l’absence de documentation dans plus de 89% des cas. La métagénomique NGS est un outil potentiel pour le diagnostic direct des méningites infectieuses à partir de LCR en détectant le génome pathogène sans PCR préalable. Dans ce travail de Thèse, nous avons répondu à quatre problématiques : 1) Mise à jour du répertoire des agents pathogènes causatifs de méningites, détectés par métagénomique NGS directe du LCR. 2) Epidémiologie des méningites communautaires à Nîmes et Marseille. 3) Amélioration de diagnostic et génotypage des méningites à Entérovirus. 4) Développement et implantation d’un protocole “one-shot” utilisant la métagénomique en temps réel pour le diagnostic, le génotypage et l’antibiogramme in-silico des méningites au laboratoire point-de-soins (POC).Community-acquired meningitis is a life-threatening condition, whose prognosis is partially dependent on the pathogen genotype. More than 100 different pathogens were involved in central nervous system infections identified in cerebrospinal fluid (CSF), worldwide. CSF culture was for a long time the gold standard for the diagnosis infectieuse meningitis , this routine microbiological diagnosis is based on the detection by multiplexed RT-PCR of the most frequent pathogens. However, the genotyping of causative pathogens such as Enteroviruses which cover more than 300 different serotypes, of which 110 infect humans, as well as the genotyping and antibiogram of pathogenic bacteria, require additional in-vitro investigations. Our retrospective study of 20,779 CSFs collected for the diagnosis of community-acquired meningitis during 61 months, analyzed in the clinical microbiology laboratories of Nîmes and Marseille showed the absence of documentation in more than 89% of cases. Metagenomics NGS is a potential tool for the direct diagnosis of infectious meningitis from CSF samples by detecting the pathogenic genome without prior PCR. In this thesis work, we have addressed four issues: 1) Update of the repertoire of meningitis causative pathogens detected by direct metagenomic NGS of CSF. 2) Epidemiology of community-acquired meningitis in Nîmes and Marseille. 3) Improvement of the diagnostic and genotyping of Enterovirus meningitis. 4) Development and implementation of a "one-shot" protocol using real-time metagenomics for diagnosis, genotyping, and in-silico antibiotic susceptibility testing of community-acquired meningitis in the point-of-care (POC) laborator

Haemophilus influenzae Meningitis Direct Diagnosis by Metagenomic Next-Generation Sequencing: A Case Report

Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influenzae meningitis. Real-time PCR diagnosed H. influenzae meningitis in a 22-year-old male patient, during his hospitalisation following a more than six-metre fall. Using an Oxford Nanopore Technologies real-time sequencing run in parallel to real-time PCR, we detected the H. influenzae genome directly from the cerebrospinal fluid sample in six hours. Furthermore, BLAST analysis of the sequence encoding for a partial DUF417 domain-containing protein diagnosed a non-b serotype, non-typeable H.influenzae belonging to lineage H. influenzae 22.1-21. The Oxford Nanopore metagenomic next-generation sequencing approach could be considered for the point-of-care diagnosis of infectious meningitis, by direct identification of pathogenic genomes and their genotypes/serotypes

Direct Metagenomic Diagnosis of Community-Acquired Meningitis: State of the Art

International audienceCurrent routine diagnosis of community-acquired meningitis (CAM) by multiplex real-time polymerase chain reaction (RT-PCR) is limited in the number of tested pathogens and their full characterisation, requiring additional in vitro investigations to disclose genotype and antimicrobial susceptibility. We reviewed 51 studies published through December 2021 reporting metagenomic next generation sequencing (mNGS) directly applied to the cerebrospinal fluid (CSF). This approach, potentially circumventing the above-mentioned limitations, indicated 1,248 investigated patients, and 617 patients dually investigated by routine diagnosis and mNGS, in whom 116 microbes were detected, including 50 by mNGS only, nine by routine methods only, and 57 by both routine methods and mNGS. Of 217 discordant CSF findings, 103 CSF samples were documented by mNGS only, 87 CSF samples by routine methods only, and 27 CSF samples in which the pathogen identified by mNGS was different than that found using routine methods. Overall, mNGS allowed for diagnosis and genomic surveillance of CAM causative pathogens in real-time, with a cost which is competitive with current routine multiplex RT-PCR. mNGS could be implemented at point-of-care (POC) laboratories as a part of routine investigations to improve the diagnosis and molecular epidemiology of CAM, particularly in the event of failure of routine assays

Direct Diagnosis of Echovirus 12 Meningitis Using Metagenomic Next Generation Sequencing

International audienceThe current point-of-care diagnosis of enterovirus meningitis does not identify the viral genotype, which is prognostic. In this case report, more than 81% of an Echovirus 12 genome were detected and identified by metagenomic next-generation sequencing, directly from the cerebrospinal fluid collected in a 6-month-old child with meningeal syndrome and meningitis: introducing Echovirus 12 as an etiological agent of acute meningitis in the pediatric population

A Tetragenococcus halophilus human gut isolate

International audienc

Emergence of multi-drug-resistant Mycobacterium tuberculosis in Niger: A snapshot based on whole-genome sequencing.

BackgroundAmong other West African countries experiencing the high endemicity of deadly tuberculosis, the situation in Niger is poorly evidenced by microbiological investigations.Methodology/principal findingsThe study of 42 isolates of Mycobacterium tuberculosis from Niger by whole genome sequencing using Illumina iSeq technology yielded four M. tuberculosis lineages: Indo-Oceanic L1 (n = 1) (2.3%), East-Asian (n = 1) (2.3%), East-African Indian L3 (n = 2) (4.7%) and Euro-American L4 (n = 38) (90.4%). The sub-lineage L4.1.3 comprising 18 isolates (47.3%) was predominant, followed by the L4.6.2.2 sub-lineage (Cameroon genotype, n = 13 isolates) (34.2%). Investigating drug resistance profile for 12 antibiotics found 8/42 (19%) pan-susceptible isolates and 34/42 (81%) resistant isolates; with 40/42 (95.2%) isolates being susceptible to clofazimine-bedaquiline.Conclusions/significanceThese unprecedented data from Niger highlight the dynamics of tuberculosis transmission and drug resistance in Niger and may assist tuberculosis control in this country which continues to support a high burden of tuberculosis

Direct next-generation sequencing diagnosis of echovirus 9 meningitis, France

International audienc

Bulevirtide 2mg-based real-life treatment of hepatitis Delta with genotypes 1 and 5 viruses at more than 20 months of follow-up

NoneInternational audienceNot available

Haemophilus influenzae Meningitis Direct Diagnosis by Metagenomic Next-Generation Sequencing: A Case Report

International audienceCurrent routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influenzae meningitis. Real-time PCR diagnosed H. influenzae meningitis in a 22-year-old male patient, during his hospitalisation following a more than six-metre fall. Using an Oxford Nanopore Technologies real-time sequencing run in parallel to real-time PCR, we detected the H. influenzae genome directly from the cerebrospinal fluid sample in six hours. Furthermore, BLAST analysis of the sequence encoding for a partial DUF417 domain-containing protein diagnosed a non-b serotype, non-typeable H.influenzae belonging to lineage H. influenzae 22.1-21. The Oxford Nanopore metagenomic next-generation sequencing approach could be considered for the point-of-care diagnosis of infectious meningitis, by direct identification of pathogenic genomes and their genotypes/serotypes