Disruption of Mycobacterium avium subsp. paratuberculosis-specific genes impairs in vivo fitness

Background: Mycobacterium avium subsp. paratuberculosis (MAP) is an obligate intracellular pathogen that infects many ruminant species. The acquisition of foreign genes via horizontal gene transfer has been postulated to contribute to its pathogenesis, as these genetic elements are absent from its putative ancestor, M. avium subsp. hominissuis (MAH), an environmental organism with lesser pathogenicity. In this study, high-throughput sequencing of MAP transposon libraries were analyzed to qualitatively and quantitatively determine the contribution of individual genes to bacterial survival during infection. Results: Out of 52384 TA dinucleotides present in the MAP K-10 genome, 12607 had a MycoMarT7 transposon in the input pool, interrupting 2443 of the 4350 genes in the MAP genome (56%). Of 96 genes situated in MAP-specific genomic islands, 82 were disrupted in the input pool, indicating that MAP-specific genomic regions are dispensable for in vitro growth (odds ratio = 0.21). Following 5 independent in vivo infections with this pool of mutants, the correlation between output pools was high for 4 of 5 (R = 0.49 to 0.61) enabling us to define genes whose disruption reproducibly reduced bacterial fitness in vivo. At three different thresholds for reduced fitness in vivo, MAP-specific genes were over-represented in the list of predicted essential genes. We also identified additional genes that were severely depleted after infection, and several of them have orthologues that are essential genes in M. tuberculosis. Conclusions: This work indicates that the genetic elements required for the in vivo survival of MAP represent a combination of conserved mycobacterial virulence genes and MAP-specific genes acquired via horizontal gene transfer. In addition, the in vitro and in vivo essential genes identified in this study may be further characterized to offer a better understanding of MAP pathogenesis, and potentially contribute to the discovery of novel therapeutic and vaccine targets. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-415) contains supplementary material, which is available to authorized users

Deep domain adaptation enhances Amplification Curve Analysis for single-channel multiplexing in real-time PCR

Data-driven approaches for molecular diagnostics are emerging as an alternative to perform an accurate and inexpensive multi-pathogen detection. A novel technique called Amplification Curve Analysis (ACA) has been recently developed by coupling machine learning and real-time Polymerase Chain Reaction (qPCR) to enable the simultaneous detection of multiple targets in a single reaction well. However, target classification purely relying on the amplification curve shapes currently faces several challenges, such as distribution discrepancies between different data sources of synthetic DNA and clinical samples (i.e., training vs testing). Optimisation of computational models is required to achieve higher performance of ACA classification in multiplex qPCR through the reduction of those discrepancies. Here, we proposed a novel transformer-based conditional domain adversarial network (T-CDAN) to eliminate data distribution differences between the source domain (synthetic DNA data) and the target domain (clinical isolate data). The labelled training data from the source domain and unlabelled testing data from the target domain are fed into the T-CDAN, which learns both domains' information simultaneously. After mapping the inputs into a domain-irrelevant space, T-CDAN removes the feature distribution differences and provides a clearer decision boundary for the classifier, resulting in a more accurate pathogen identification. Evaluation of 198 clinical isolates containing three types of carbapenem-resistant genes ( bla NDM , bla IMP and bla OXA-48 ) illustrates a curve-level accuracy of 93.1% and a sample-level accuracy of 97.0% using T-CDAN, showing an accuracy improvement of 20.9% and 4.9% respectively, compared with previous methods. This research emphasises the importance of deep domain adaptation to enable high-level multiplexing in a single qPCR reaction, providing a solid approach to extend qPCR instruments' capabilities without hardware modification in real-world clinical applications

Relationship between ventilator-associated pneumonia and mortality in COVID-19 patients: a planned ancillary analysis of the coVAPid cohort

Background Patients with SARS-CoV-2 infection are at higher risk for ventilator-associated pneumonia (VAP). No study has evaluated the relationship between VAP and mortality in this population, or compared this relationship between SARS-CoV-2 patients and other populations. The main objective of our study was to determine the relationship between VAP and mortality in SARS-CoV-2 patients. Methods Planned ancillary analysis of a multicenter retrospective European cohort. VAP was diagnosed using clinical, radiological and quantitative microbiological criteria. Univariable and multivariable marginal Cox's regression models, with cause-specific hazard for duration of mechanical ventilation and ICU stay, were used to compare outcomes between study groups. Extubation, and ICU discharge alive were considered as events of interest, and mortality as competing event. Findings Of 1576 included patients, 568 were SARS-CoV-2 pneumonia, 482 influenza pneumonia, and 526 no evidence of viral infection at ICU admission. VAP was associated with significantly higher risk for 28-day mortality in SARS-CoV-2 group (adjusted HR 1.65 (95% CI 1.11-2.46), p = 0.013), but not in influenza (1.74 (0.99-3.06), p = 0.052), or no viral infection groups (1.13 (0.68-1.86), p = 0.63). VAP was associated with significantly longer duration of mechanical ventilation in the SARS-CoV-2 group, but not in the influenza or no viral infection groups. VAP was associated with significantly longer duration of ICU stay in the 3 study groups. No significant difference was found in heterogeneity of outcomes related to VAP between the 3 groups, suggesting that the impact of VAP on mortality was not different between study groups. Interpretation VAP was associated with significantly increased 28-day mortality rate in SARS-CoV-2 patients. However, SARS-CoV-2 pneumonia, as compared to influenza pneumonia or no viral infection, did not significantly modify the relationship between VAP and 28-day mortality

a retrospective multicenter study

Funding This study was supported in part by a grant from the French government through the « Programme Investissement d’Avenir» (I-SITE ULNE) managed by the Agence Nationale de la Recherche (coVAPid project). Prof. Ignacio Martin-Loeches has been supported by SFI (Science Foundation Ireland), Grant number 20/COV/0038. The funders of the study had no role in the study design, data collection, analysis or interpretation, writing of the report or deci sion to submit for publication.BACKGROUND: Ventilator-associated pneumonia (VAP) is common in patients with severe SARS-CoV-2 pneumonia. The aim of this ancillary analysis of the coVAPid multicenter observational retrospective study is to assess the relationship between adjuvant corticosteroid use and the incidence of VAP. METHODS: Planned ancillary analysis of a multicenter retrospective European cohort in 36 ICUs. Adult patients receiving invasive mechanical ventilation for more than 48 h for SARS-CoV-2 pneumonia were consecutively included between February and May 2020. VAP diagnosis required strict definition with clinical, radiological and quantitative microbiological confirmation. We assessed the association of VAP with corticosteroid treatment using univariate and multivariate cause-specific Cox's proportional hazard models with adjustment on pre-specified confounders. RESULTS: Among the 545 included patients, 191 (35%) received corticosteroids. The proportional hazard assumption for the effect of corticosteroids on the incidence of VAP could not be accepted, indicating that this effect varied during ICU stay. We found a non-significant lower risk of VAP for corticosteroid-treated patients during the first days in the ICU and an increased risk for longer ICU stay. By modeling the effect of corticosteroids with time-dependent coefficients, the association between corticosteroids and the incidence of VAP was not significant (overall effect p = 0.082), with time-dependent hazard ratios (95% confidence interval) of 0.47 (0.17-1.31) at day 2, 0.95 (0.63-1.42) at day 7, 1.48 (1.01-2.16) at day 14 and 1.94 (1.09-3.46) at day 21. CONCLUSIONS: No significant association was found between adjuvant corticosteroid treatment and the incidence of VAP, although a time-varying effect of corticosteroids was identified along the 28-day follow-up.publishersversionpublishe

a planned ancillary analysis of the coVAPid cohort

Funding: This study was supported in part by a grant from the French government through the «Programme Investissement d’Avenir» (I-SITE ULNE) managed by the Agence Nationale de la Recherche (coVAPid project). The funders of the study had no role in the study design, data collection, analysis, or interpreta tion, writing of the report, or decision to submit for publication.BACKGROUND: Patients with SARS-CoV-2 infection are at higher risk for ventilator-associated pneumonia (VAP). No study has evaluated the relationship between VAP and mortality in this population, or compared this relationship between SARS-CoV-2 patients and other populations. The main objective of our study was to determine the relationship between VAP and mortality in SARS-CoV-2 patients. METHODS: Planned ancillary analysis of a multicenter retrospective European cohort. VAP was diagnosed using clinical, radiological and quantitative microbiological criteria. Univariable and multivariable marginal Cox's regression models, with cause-specific hazard for duration of mechanical ventilation and ICU stay, were used to compare outcomes between study groups. Extubation, and ICU discharge alive were considered as events of interest, and mortality as competing event. FINDINGS: Of 1576 included patients, 568 were SARS-CoV-2 pneumonia, 482 influenza pneumonia, and 526 no evidence of viral infection at ICU admission. VAP was associated with significantly higher risk for 28-day mortality in SARS-CoV-2 (adjusted HR 1.70 (95% CI 1.16-2.47), p = 0.006), and influenza groups (1.75 (1.03-3.02), p = 0.045), but not in the no viral infection group (1.07 (0.64-1.78), p = 0.79). VAP was associated with significantly longer duration of mechanical ventilation in the SARS-CoV-2 group, but not in the influenza or no viral infection groups. VAP was associated with significantly longer duration of ICU stay in the 3 study groups. No significant difference was found in heterogeneity of outcomes related to VAP between the 3 groups, suggesting that the impact of VAP on mortality was not different between study groups. INTERPRETATION: VAP was associated with significantly increased 28-day mortality rate in SARS-CoV-2 patients. However, SARS-CoV-2 pneumonia, as compared to influenza pneumonia or no viral infection, did not significantly modify the relationship between VAP and 28-day mortality. CLINICAL TRIAL REGISTRATION: The study was registered at ClinicalTrials.gov, number NCT04359693.publishersversionpublishe

Investigations of Irgm1 during experimental infections with «Mycobacterium avium paratuberculosis»

Introduction: Mycobacterium avium paratuberculosis (MAP) is the causative agent of a chronic granulomatous enteritis of ruminants called Johne's disease (JD). Crohn's disease (CD) is an inflammatory bowel disease of unknown etiology affecting humans. Due to histological similarities between the two conditions, it has been suggested that MAP could be responsible for a subset of cases of CD. Irgm1 (murine ortholog of IRGM, a CD susceptibility gene) has been linked to host defence against mycobacteria. Methods: In the first part of this work, we have attempted to study the immune response of the Irgm1-/- mouse to systemic infection with MAP. In the second part, we have attempted to use the Irgm1-/- mouse as a host susceptible to lead to significant pathology after intra-intestinal infection with MAP (a murine model of JD) and documented its response to therapeutics used in the care of patients with CD. Results: First, we have shown that mice deleted for Irgm1 have a major susceptibility to systemic MAP infection, with accelerated rate of death and uncontrolled bacterial replication. To explain this, we have identified a defect of Irgm1-/- macrophages in controlling the intracellular growth of MAP. We have also identified severe haematological abnormalities leading to their death. Second, we have devised a protocol for the surgical inoculation of ~ 109 MAP colony forming units (CFUs) in the jejunum of Irgm1-/- mice. After 1 and 2 months of infection, we have observed significant intestinal histopathological lesions resembling those seen in Johne's disease, including focal and transmural lympho-histiocytic infiltrates and mesenteric lymphadenopathy. Mice infected according to this protocol were submitted to: 1) a systemic treatment with methylprednisolone, which did not lead to increased mortality; and 2) a treatment with an anti-tumor necrosis factor-alpha (TNF-α) antibody, which did not lead to uncontrolled MAP replication in the host.Conclusion: Irgm1-/- mice are markedly susceptible to systemic MAP infection. When inoculated with ~ 109 MAP CFUs in the lumen of the jejunum, they develop stable histological lesions resembling those of JD. Interestingly, treatments used in the cure of patients with CD did not have a deleterious effect.Titre du mémoire : Etude du rôle d'Irgm1 au cours d'infections expérimentales par Mycobacterium avium paratuberculosis Introduction : Mycobacterium avium paratuberculosis (MAP) est responsable d'une entérite chronique granulomateuse chez les ruminants, la maladie de Johne (ou paratuberculose). La maladie de Crohn est une maladie inflammatoire chronique du tube digestif d'étiologie indéterminée qui affecte les humains. Du fait de similarités histologiques entre les deux conditions, il a été suggéré que MAP pouvait être responsable de certains cas de maladie de Crohn. Irgm1 (orthologue murin de IRGM, un gène de susceptibilité à la maladie de Crohn), a été impliqué dans la réponse immunitaire contre les mycobactéries. Méthodes : Dans la première partie de ce travail, nous avons étudié la réponse immunitaire de la souris Irgm1-/- au cours d'une infection systémique par MAP. Dans la second partie, nous avons cherché à utiliser la souris Irgm1-/- pour induire des lésions histologiques après infection intra-intestinale par MAP (réalisant un modèle murin de maladie de Johne), et avons documenté la réponse de ce modèle à des traitements utilisés chez les patients atteints de maladie de Crohn. Résultats : Nous avons montré que la souris Irgm1-/- présente une susceptibilité majeure à une infection systémique par MAP, avec mortalité accélérée et réplication bactérienne incontrôlée. Nous avons identifié un défaut des macrophages Irgm1-/- à contrôler la croissance intra-cellulaire de MAP. Nous avons aussi identifié des anomalies hématologiques expliquant leur mortalité accélérée. Dans un second temps, nous avons conçu un protocole consistant en l'injection par voie chirurgicale de ~ 109 unités formant colonies (UFC) de MAP au sein de la lumière du jéjunum de souris Irgm1-/-. Nous avons observé qu'à 1 et 2 mois post-infection, nous avions induit des lésions histologiques ressemblant à celles rencontrées dans la maladie de Johne, notamment des infiltrats lympho-histiocytiques focaux et transmuraux et une lymphadénopathie mésenterique. Des souries infectées selon ce protocole ont été soumises à: 1) un traitement systémique par methylprednilosone, qui n'a pas entrainé une augmentation de la mortalité; et 2) un traitement par anticorps anti-tumor necrosis factor-alpha (TNF-α), qui n'a pas provoqué une réplication bactérienne incontrôlée. Conclusion : Les souris Irgm1-/- sont susceptibles à une infection systémique par MAP. Après inoculation par voie chirurgicale de ~ 109 UFC de MAP, elles développent des lésions histologiques stables analogues à celles de la maladie de Johne. Des traitements utilisés pour traiter la maladie de Crohn n'ont pas entrainé d'effet délétère. Des travaux supplémentaires sont nécessaires pour évaluer l'utilité de ce modèle dans les recherches sur la maladie de Johne et sur la maladie de Crohn

Etude des courants du lac Léman

Kreitmann Louis. Etude des courants du lac Léman. In: Les Études rhodaniennes, vol. 7, n°2, 1931. pp. 109-130

Etude thermique de « La Bataillère » sur le Léman

Gorceix Charles, Kreitmann L. Etude thermique de « La Bataillère » sur le Léman. In: Revue de géographie alpine, tome 18, n°3, 1930. pp. 537-551

ICU-Acquired Colonization and Infection Related to Multidrug-Resistant Bacteria in COVID-19 Patients: A Narrative Review

A large proportion of ICU-acquired infections are related to multidrug-resistant bacteria (MDR). Infections caused by these bacteria are associated with increased mortality, and prolonged duration of mechanical ventilation and ICU stay. The aim of this narrative review is to report on the association between COVID-19 and ICU-acquired colonization or infection related to MDR bacteria. Although a huge amount of literature is available on COVID-19 and MDR bacteria, only a few clinical trials have properly evaluated the association between them using a non-COVID-19 control group and accurate design and statistical methods. The results of these studies suggest that COVID-19 patients are at a similar risk of ICU-acquired MDR colonization compared to non-COVID-19 controls. However, a higher risk of ICU-acquired infection related to MDR bacteria has been reported in several studies, mainly ventilator-associated pneumonia and bloodstream infection. Several potential explanations could be provided for the high incidence of ICU-acquired infections related to MDR. Immunomodulatory treatments, such as corticosteroids, JAK2 inhibitors, and IL-6 receptor antagonist, might play a role in the pathogenesis of these infections. Additionally, a longer stay in the ICU was reported in COVID-19 patients, resulting in higher exposure to well-known risk factors for ICU-acquired MDR infections, such as invasive procedures and antimicrobial treatment. Another possible explanation is the surge during successive COVID-19 waves, with excessive workload and low compliance with preventive measures. Further studies should evaluate the evolution of the incidence of ICU-acquired infections related to MDR bacteria, given the change in COVID-19 patient profiles. A better understanding of the immune status of critically ill COVID-19 patients is required to move to personalized treatment and reduce the risk of ICU-acquired infections. The role of specific preventive measures, such as targeted immunomodulation, should be investigated

Ventilator-Associated Pneumonia in Immunosuppressed Patients

Immunocompromised patients—including patients with cancer, hematological malignancies, solid organ transplants and individuals receiving immunosuppressive therapies for autoimmune diseases—account for an increasing proportion of critically-ill patients. While their prognosis has improved markedly in the last decades, they remain at increased risk of healthcare- and intensive care unit (ICU)-acquired infections. The most frequent of these are ventilator-associated lower respiratory tract infections (VA-LTRI), which include ventilator-associated pneumonia (VAP) and tracheobronchitis (VAT). Recent studies have shed light on some of the specific features of VAP and VAT in immunocompromised patients, which is the subject of this narrative review. Contrary to previous belief, the incidence of VAP and VAT might actually be lower in immunocompromised than non-immunocompromised patients. Further, the relationship between immunosuppression and the incidence of VAP and VAT related to multidrug-resistant (MDR) bacteria has also been challenged recently. Etiological diagnosis is essential to select the most appropriate treatment, and the role of invasive sampling, specifically bronchoscopy with bronchoalveolar lavage, as well as new molecular syndromic diagnostic tools will be discussed. While bacteria—especially gram negative bacteria—are the most commonly isolated pathogens in VAP and VAT, several opportunistic pathogens are a special concern among immunocompromised patients, and must be included in the diagnostic workup. Finally, the impact of immunosuppression on VAP and VAT outcomes will be examined in view of recent papers using improved statistical methodologies and treatment options—more specifically empirical antibiotic regimens—will be discussed in light of recent findings on the epidemiology of MDR bacteria in this population