Incidence of COVID-19 mRNA vaccine symptomatic breakthrough infections during Omicron circulation in adults with or without infection prior to vaccination.

OBJECTIVES: COVID-19 vaccine breakthrough infections were frequently reported during circulation of the Omicron variant. The ANRS|MIE CoviCompareP study investigated these infections in adults vaccinated and boosted with BNT162b2 [Pfizer-BioNTech] and with/without SARS-CoV-2 infection before vaccination. METHODS: In the first half of 2021, healthy adults (aged 18-45, 65-74 and 75 or older) received either one dose of BNT162b2 (n = 120) if they had a documented history of SARS-CoV-2 infection at least five months previously, or two doses (n = 147) if they had no history confirmed by negative serological tests. A first booster dose was administered at least 6 months after the primary vaccination, and a second booster dose, if any, was reported in the database. Neutralizing antibodies (NAbs) against the European (D614G) strain and the Omicron BA.1 variant were assessed up to 28 days after the first booster dose. A case-control analysis was performed for the 252 participants who were followed up in 2022, during the Omicron waves. RESULTS: From January to October 2022, 78/252 (31%) had a documented symptomatic breakthrough infection after full vaccination: 21/117 (18%) in those who had been infected before vaccination vs. 57/135 (42%) in those who had not. In a multivariate logistic regression model, factors associated with a lower risk of breakthrough infection were older age, a higher number of booster doses, and higher levels of Omicron BA.1 NAb titers in adults with infection before vaccination, but not in those without prior infection. CONCLUSION: Our results highlight the need to consider immune markers of protection in association with infection and vaccination history.

Availability of drugs and resistance testing for BPaLM regimen for rifampicin-resistant tuberculosis in Europe.

OBJECTIVES: Multidrug-resistant/Rifampicin-resistant tuberculosis (TB) is a major obstacle to successful TB control. The recommendation by the World Health Organization to use bedaquiline, pretomanid, linezolid and moxifloxacin (BPaL(M)) for 6 months, based on results of three trials with high efficacy and low toxicity, has revolutionized treatment options. METHODS: In this study, representatives of the Tuberculosis Network European Trialsgroup (TBnet) in 44/54 countries of the WHO Europe region document the availability of the medicines and drug susceptibility testing (DST) of the BPaL(M) regimen through a structured questionnaire between September to November 2023. RESULTS: 24/44 (54.5%), 42/44 (95.5%), 43/44 (97.7%), and 43/44 (97.7%) had access to pretomanid, bedaquiline, linezolid, and moxifloxacin, respectively. Overall, 23/44 (52.3%) had access to all the drugs composing the BPaL(M) regimen. 7/44 (15.9%), 28/44 (63.6%), 34/44 (77.3%) and 36/44 (81.8%) had access to DST for pretomanid, bedaquiline, linezolid and moxifloxacin, respectively. DST was available for all medicines composing the BPaL(M) regimen in 6/44 (13.6%) countries. CONCLUSION: Only in about half of the countries participating in the survey clinicians have access to all the BPaL(M) regimen drugs. In less than a fifth of countries, a complete DST is possible. Rapid scale up of DST capacity to prevent unnoticed spread of drug resistance and equal access to new regimens are urgently needed in Europe.

Machine learning to predict antimicrobial resistance: future applications in clinical practice?

INTRODUCTION: Machine learning (ML) is increasingly being used to predict antimicrobial resistance (AMR). This review aims to provide physicians with an overview of the literature on ML as a means of AMR prediction. METHODS: References for this review were identified through searches of MEDLINE/PubMed, EMBASE, Google Scholar, ACM Digital Library, and IEEE Xplore Digital Library up to December 2023. RESULTS: Thirty-six studies were included in this review. Thirty-two studies (32/36, 89 %) were based on hospital data and four (4/36, 11 %) on outpatient data. The vast majority of them were conducted in high-resource settings (33/36, 92 %). Twenty-four (24/36, 67 %) studies developed systems to predict drug resistance in infected patients, eight (8/36, 22 %) tested the performances of ML-assisted antibiotic prescription, two (2/36, 6 %) assessed ML performances in predicting colonization with carbapenem-resistant bacteria and, finally, two assessed national and international AMR trends. The most common inputs were demographic characteristics (25/36, 70 %), previous antibiotic susceptibility testing (19/36, 53 %) and prior antibiotic exposure (15/36, 42 %). Thirty-three (92 %) studies targeted prediction of Gram-negative bacteria (GNB) resistance as an output (92 %). The studies included showed moderate to high performances, with AUROC ranging from 0.56 to 0.93. CONCLUSION: ML can potentially provide valuable assistance in AMR prediction. Although the literature on this topic is growing, future studies are needed to design, implement, and evaluate the use and impact of ML decision support systems.

Epidemiology, treatment and outcomes of infected pancreatic necrosis in France: a bicenter study.

INTRODUCTION: Acute necrotizing pancreatitis (ANP) mortality increases when pancreatic necrosis is infected (IPN). Current treatment of IPN relies on prolonged antibiotic therapies associated with a step-up strategy of drainage. The objective of this study was to analyze IPN treatment outcomes in two referral centers in France. METHODS: Data of consecutive patients with documented IPN hospitalized in two expert centers in France between 2014 and 2019 were retrospectively reviewed. The composite primary outcome was the proportion of unsuccessful management outcome, defined as new emergency drainage to treat sepsis with organ failure, an unplanned new antibiotic course, an unplanned prolongation of antibiotic course and/or death by septic shock, within three months following the diagnosis of ANP. RESULTS: All in all, 187 patients (138 males; 74.0%), with documented IPN were included. The most frequently identified microorganism was Escherichia coli (26.2%). Ninety-eight patients (52.4%) were admitted to an intensive care unit or resuscitation ward within the first two days of ANP care. Overall, 126 patients (67.4%) endured an unsuccessful outcome: new emergency drainage to treat acute sepsis (62.0%), unplanned new antibiotic course (47.1%), unplanned prolongation of antibiotic course (44.9%) and/or death by septic shock complicating IPN (8.0%). CONCLUSION: The unfavorable evolution in two thirds of patients shows that determination of optimal drainage timing and choice of antibiotic therapy remain major challenges in 2024.

Statistics of Rare Events.

Rare events can sometime arise in clinical development of treatments. For example, CYPIDES was a single-arm study of the CYP11A1 inhibitor ODM-208 to treat metastatic prostate cancer.1 Preclinical testing of the compound identified elevated thyroid-stimulating hormone (TSH) and bilirubin in rats and dogs. Unusual findings in preclinical testing focus attention and magnify evidence if similar results occur in humans. By analogy, imagine a murder trial in which the only evidence against the defendant arose from a database search of DNA matching the partial profile found at the crime scene. Multiple people could match, so without other evidence, the perpetrator could be any of them.

Epidemiology of Mycobacterium abscessus.

BACKGROUND: Nontuberculous mycobacteria (NTM) are highly abundant in soil, dust, and water sources, making human-pathogen contact frequent and recurrent. NTM represents over 200 species/subspecies; some are considered strict or opportunistic pathogens. Mycobacterium abscessus, often regarded as one of the most antibiotic-resistant mycobacteria, is the second most frequent NTM pulmonary disease pathogen. OBJECTIVES: To describe the epidemiology of M. abscessus through a literature review focusing on clinical aspects. SOURCES: We conducted searches on PubMed and Web of Knowledge for articles published from 2010 to the present using the keywords 'Mycobacterium abscessus', 'Nontuberculous mycobacteria', and 'epidemiology'. Our search prioritized original reports on the occurrence of NTM and M. abscessus infection/disease. CONTENT: Advanced molecular and genetic diagnostic techniques have refined the M. abscessus complex (MABC) microbiological classification over the last few decades. MABC can adhere to surfaces and form a biofilm. This characteristic and its resistance to common disinfectants allow these microorganisms to persist in the water distribution systems, becoming a constant reservoir. The frequency and manifestation of NTM species vary geographically because of environmental conditions and population susceptibility differences. MABC lung disease, the most frequent site of NTM infection in humans, is often seen in patients with underlying lung diseases such as bronchiectasis, whereas MABC disseminated disease is related to immunosuppression. Skin and soft tissue infections are associated with surgical or injection procedures. Epidemiological evidence suggests an overall increase in MABC infection and disease in the last decade. IMPLICATIONS: Establishing the burden of this disease is challenging because of varying measures of incidence and prevalence, referral bias, and differences in medical practices and reporting. Furthermore, environmental and structural determinants, infection routes, and MABC pulmonary disease mechanisms require additional investigation. This review contributes to a better understanding of the epidemiology of MABC, which could inform clinical practice and future research.

What do medical students and graduated physicians think about infectious disease specialists?

OBJECTIVES: This study evaluated the social representation and stereotypes on infectious disease (ID) specialists among medical students and physicians in France after the COVID-19 pandemic. METHODS: A survey applying the hierarchical evocation model assessed the social representations (SRs) of ID specialists. RESULTS: All in all, 372 answers were analyzed. The positive elements related to the personal and professional qualities of ID specialists ('intellectual prestige", "open-mindedness"), in contrast with negative stereotypes related to their perceived daily life and practice characteristics ("hospital-based", "intense", "overspecialized"). Variables such as "I would not have chosen (or I won't choose) ID after the national ranking exam" and "I know someone who is an ID specialist" were associated with worse SR scores (p < 0.001 and p = 0.022 respectively). CONCLUSIONS: These findings provide insights into the attractiveness of ID as a specialty. Rounds in ID departments may enhance the interest of the specialty as a possible residency choice.

Recent advances in the treatment of tuberculosis.

BACKGROUND: Tuberculosis (TB) is a global health challenge and one of the leading causes of death worldwide. In the last decade, the TB treatment landscape has dramatically changed. After long years of stagnation, new compounds entered the market (bedaquiline, delamanid, and pretomanid) and phase III clinical trials have shown promising results towards shortening duration of treatment for both drug-susceptible (Study 31/A5349, TRUNCATE-TB, and SHINE) and drug-resistant TB (STREAM, NiX-TB, ZeNix, and TB-PRACTECAL). Dose optimization of rifamycins and repurposed drugs has also brought hopes of further development of safe and effective regimens. Consequently, international and WHO clinical guidelines have been updated multiple times in the last years to keep pace with these advances. OBJECTIVES: This narrative review aims to summarize the state-of-the-art on treatment of drug-susceptible and drug-resistant TB, as well as recent trial results and an overview of ongoing clinical trials. SOURCES: A non-systematic literature review was conducted in PubMed and MEDLINE, focusing on the treatment of TB. Ongoing clinical trials were listed according to the authors' knowledge and completed consulting clinicaltrials.gov and other publicly available websites (www.resisttb.org/clinical-trials-progress-report, www.newtbdrugs.org/pipeline/trials). CONTENT: This review summarizes the recent, major changes in the landscape for drug-susceptible and drug-resistant treatment, with a specific focus on their potential impact on patient outcomes and programmatic TB management. Moreover, insights in host-directed therapies, and advances in pharmacokinetics and pharmacogenomics are discussed. A thorough outline of ongoing therapeutic clinical trials is presented, highlighting different approaches and goals in current TB clinical research. IMPLICATIONS: Future research should be directed to individualize regimens and protect these recent breakthroughs by preventing and identifying the selection of drug resistance and providing widespread, affordable, patient-centred access to new treatment options for all people affected by TB.

Infectious Complications of Targeted Therapies for Solid Cancers or Leukemias/Lymphomas.

BACKGROUND: Infections are well known complications of some targeted drugs used to treat solid organ cancer and hematological malignancies. Furthermore, Individual patient risk factors are associated with underlying pathologies, concomitant immunosuppressive treatment, prior treatment and use of anti-infective prophylaxis. Immune-related adverse events (irAEs) are frequent among patients treated with new targeted drugs. OBJECTIVES: In this narrative review, we present the current state of knowledge concerning the infectious complications occurring in patients treated with immune checkpoint inhibitors (ICIs), Bruton's tyrosine kinase (BTK) inhibitors, phosphatidylinositol 3-kinase (PI3K) inhibitors, antiapoptotic protein BCL-2 inhibitors, Janus kinase inhibitors or CAR-T cell infusion. SOURCES: We searched for studies treating infectious complications of ICIs, BTK inhibitors, PI3K inhibitors, antiapoptotic protein BCL-2 inhibitors and CAR-T cell therapy. We included randomized, observational studies and case reports. CONTENT: Immune-related adverse events (irAEs) are frequent among patients treated with new targeted drugs. Treatment of irAEs with corticosteroids and other immunosuppressive agents can lead to opportunistic infections. Bruton's tyrosine kinase (BTK) inhibitors are associated with higher rate of infections, including invasive fungal infections. IMPLICATIONS: Infections, particularly fungal ones, are common in patients treated with BTK inhibitors even though most of the complications occurring among patients treated by ICIs or CART-cells infusion are associated with the treatment of side effects related to the use of these new treatments. The diagnosis of these infectious complications can be difficult and may require extensive investigations.

A recurrent pleuropneumonia revealing Erdheim-Chester Disease.

Erdheim-Chester disease (ECD) is a rare form of L group histiocytosis, accounting for up to 1500 cases to date worldwide, which mainly affects men between their 5th and 7th decade of life. The most frequent manifestations are bone involvement, perirenal infiltration with an evocating appearance of "hairy kidneys", and a "coated aorta" aspect. Lung involvement in ECD is less common and includes pleural infiltration and interstitial lung disease. Herein, we report the case of a 76-year-old woman with recurrent pleuropneumonia revealing ECD.

Machine learning approaches in diagnosing tuberculosis through biomarkers - A systematic review.

Biomarker-based tests may facilitate Tuberculosis (TB) diagnosis, accelerate treatment initiation, and thus improve outcomes. This review synthesizes the literature on biomarker-based detection for TB diagnosis using machine learning. The systematic review approach follows the PRISMA guideline. Articles were sought using relevant keywords from Web of Science, PubMed, and Scopus, resulting in 19 eligible studies after a meticulous screening. All the studies were found to have focused on the supervised learning approach, with Support Vector Machine (SVM) and Random Forest emerging as the top two algorithms, with the highest accuracy, sensitivity and specificity reported to be 97.0%, 99.2%, and 98.0%, respectively. Further, protein-based biomarkers were widely explored, followed by gene-based such as RNA sequence and, Spoligotypes. Publicly available datasets were observed to be popularly used by the studies reviewed whilst studies targeting specific cohorts such as HIV patients or children gathering their own data from healthcare facilities, leading to smaller datasets. Of these, most studies used the leave one out cross validation technique to mitigate overfitting. The review shows that machine learning is increasingly assessed in research to improve TB diagnosis through biomarkers, as promising results were shown in terms of model's detection performance. This provides insights on the possible application of machine learning approaches to diagnose TB using biomarkers as opposed to the traditional methods that can be time consuming. Low-middle income settings, where access to basic biomarkers could be provided as compared to sputum-based tests that are not always available, could be a major application of such models.

Performance of Radiomics in Microvascular Invasion Risk Stratification and Prognostic Assessment in Hepatocellular Carcinoma: A Meta-Analysis.

BACKGROUND: Primary liver cancer is the sixth most commonly diagnosed cancer and the third leading cause of cancer death. Advances in phenomenal imaging are paving the way for application in diagnosis and research. The poor prognosis of advanced HCC warrants a personalized approach. The objective was to assess the value of imaging phenomics for risk stratification and prognostication of HCC. METHODS: We performed a meta-analysis of manuscripts published to January 2023 on MEDLINE addressing the value of imaging phenomics for HCC risk stratification and prognostication. Publication information for each were collected using a standardized data extraction form. RESULTS: Twenty-seven articles were analyzed. Our study shows the importance of imaging phenomics in HCC MVI prediction. When the training and validation datasets were analyzed separately by the random-effects model, in the training datasets, radiomics had good MVI prediction (AUC of 0.81 (95% CI 0.76-0.86)). Similar results were found in the validation datasets (AUC of 0.79 (95% CI 0.72-0.85)). Using the fixed effects model, the mean AUC of all datasets was 0.80 (95% CI 0.76-0.84). CONCLUSIONS: Imaging phenomics is an effective solution to predict microvascular invasion risk, prognosis, and treatment response in patients with HCC.

Landscape of TB Infection and Prevention among People Living with HIV.

Tuberculosis (TB) is one of the leading causes of mortality in people living with HIV (PLHIV) and contributes to up to a third of deaths in this population. The World Health Organization guidelines aim to target early detection and treatment of TB among PLHIV, particularly in high-prevalence and low-resource settings. Prevention plays a key role in the fight against TB among PLHIV. This review explores TB screening tools available for PLHIV, including symptom-based screening, chest radiography, tuberculin skin tests, interferon gamma release assays, and serum biomarkers. We then review TB Preventive Treatment (TPT), shown to reduce the progression to active TB and mortality among PLHIV, and available TPT regimens. Last, we highlight policy-practice gaps and barriers to implementation as well as ongoing research needs to lower the burden of TB and HIV coinfection through preventive activities, innovative diagnostic tests, and cost-effectiveness studies.

Preventive Therapy for Contacts of Drug-Resistant Tuberculosis.

Preventing the progression of a drug-resistant tuberculosis (DR-TB) infection to disease is an important pillar of the DR-TB elimination strategy. International guidelines have recently proposed fluoroquinolones for tuberculosis preventive therapy (TPT) in DR-TB contacts, although the available evidence is low quality. The pooled data from small observational studies suggest that a fluoroquinolone-based TPT is safe, effective and cost-effective as a preventive treatment in DR-TB contacts. Three clinical trials are currently ongoing to generate higher quality evidence on the efficacy of levofloxacin and delamanid as a DR-TB preventive therapy. Additional evidence is also needed, regarding TPT treatment in fluoroquinolone-resistant-TB contacts, patient and health care worker perceptions on DR-TB preventive therapy for contacts, and the service delivery models to increase DR-TPT access. This state-of-the-art review presents the current literature on TPT for contacts of DR-TB cases, focusing on the available evidence and international guidelines.

COVID-19 Vaccines against Omicron Variant: Real-World Data on Effectiveness.

The efficacy of vaccines against coronavirus disease 2019 (COVID-19) has now been well established in phase III clinical trials. However, clinical studies based on real-world data remain critical to assess vaccines effectiveness (VE), especially in specific populations and against variants of concern (VOC). This review presents the principles and methods of VE studies and the main available results on VE of COVID-19 vaccines at the time of Omicron circulation. References for this narrative review were identified through searches of PubMed database up to 13 September 2022. The results of phase III clinical trials have been globally confirmed by VE in real-life studies, including in the elderly. Emergence of VOC Omicron emphasized the importance of booster doses to maintain a high level of protection against severe forms. There are still numerous challenges regarding booster(s) and duration of immunity, particularly in specific subpopulations, and regarding the need for adapted vaccines.

Machine learning, antimicrobial stewardship, and solid organ transplantation: Is this the future?

BACKGROUND: The use of machine learning (ML) in infectious diseases is expanding. OBJECTIVES: This review aims to provide an overview of the literature on ML for clinical decision support in antimicrobial stewardship in the particular context of solid organ transplantation (SOT). METHODS: References for this review were identified through searches of MEDLINE/PubMed and Google Scholar databases up to July 2022. RESULTS: ML may improve the prediction of infectious complications and the diagnosis and treatment of infectious diseases in SOT recipients. One of the most studied applications for antimicrobial stewardship is the individual prediction of antimicrobial resistance that could guide the empiric use of anti-infective treatments. ML may also guide the choice of antimicrobial dose taking into account the interactions with immunosuppressive drugs. The main challenge to the development of ML clinical decision support systems (CDSSs) in SOT is the development of large clinical databases, accessible to all, with good quality, comprehensive, and diversified data. ML-driven CDSSs are still at an experimental stage, and the education of clinicians about the benefits and limits of ML is essential. CONCLUSION: ML could improve antimicrobial stewardship for SOT, but literature on that specific topic is scarce. Future studies are needed to design ML-CDSS in the particular population of solid organ recipients and report clinical outcomes following use in routine practice.

Revised Definitions of Tuberculosis Resistance and Treatment Outcomes, France, 2006-2019.

Definitions of resistance in multidrug-resistant tuberculosis (MDR TB) and extensively drug-resistant tuberculosis (XDR TB) have been updated. Pre-XDR TB, defined as MDR TB with additional resistance to fluoroquinolones, and XDR TB, with additional resistance to bedaquiline or linezolid, are frequently associated with treatment failure and toxicity. We retrospectively determined the effects of pre-XDR/XDR TB resistance on outcomes and safety of MDR TB treatment in France. The study included 298 patients treated for MDR TB at 3 reference centers during 2006-2019. Of those, 205 (68.8%) cases were fluoroquinolone-susceptible MDR TB and 93 (31.2%) were pre-XDR/XDR TB. Compared with fluoroquinolone-susceptible MDR TB, pre-XDR/XDR TB was associated with more cavitary lung lesions and bilateral disease and required longer treatment. Overall, 202 patients (67.8%) had favorable treatment outcomes, with no significant difference between pre-XDR/XDR TB (67.7%) and fluoroquinolone-susceptible MDR TB (67.8%; p = 0.99). Pre-XDR/XDR TB was not associated with higher risk for serious adverse events.

Streptococcal and Staphylococcus aureus prosthetic joint infections: are they really different?

BACKGROUND: Staphylococci and streptococci are the most frequent pathogens isolated from prosthetic joint infections (PJIs). The aim of this study was to analyze the outcome of streptococcal and methicillin-susceptible Staphylococcus aureus (MSSA) PJIs. METHODS: All monomicrobial streptococcal and MSSA PJIs managed in a French Referral Center (2010-2017) were sampled from the prospective PJIs cohort study. The primary outcome of interest was the cumulative reinfection-free survival at a 2-year follow-up. RESULTS: Two hundred and nine patients with 91 streptococcal and 132 staphylococcal infections were analyzed. Patients with streptococcal PJI were older, and infection was more frequently hematogenous. Reinfection-free survival rates at 2-years after all treatment strategies were higher for patients with streptococcal PJI (91% vs 81%; P = .012), but differed according to the strategy. After exchange arthroplasty, no outcome differences were observed (89% vs 93%; P = .878); after debridement, antibiotics and implant retention (DAIR), the reinfection-free survival rate was higher for patients with streptococcal PJI (87% vs 60%; P = .062). For patients managed with prolonged suppressive antibiotic therapy (SAT) alone, those with streptococcal PJIs had a 100% infection-free survival (100% vs 31%; P < .0001). CONCLUSIONS: Reinfection-free survival after DAIR and SAT was better for patients with streptococcal than those with MSSA PJIs. No difference was observed after prosthesis exchange.