Meropenem/colistin synergy testing for multidrug-resistant Acinetobacter baumannii strains by a two-dimensional gradient technique applicable in routine microbiology

Objectives Precise assessment of potential therapeutic synergy, antagonism or indifference between antimicrobial agents currently depends on time-consuming and hard-to-standardize in vitro chequerboard titration methods. We here present a method based on a novel two-dimensional antibiotic gradient technique named Xact™. Methods We used a test comprising a combination of perpendicular gradients of meropenem and colistin in a single quadrant. We compared test outcomes with those obtained with classical chequerboard microbroth dilution testing in a study involving 27 unique strains of multidrug-resistant Acinetobacter baumannii from diverse origins. Results We were able to demonstrate 92% concordance between the new technology and classical chequerboard titration using the A. baumannii collection. Two strains could not be analysed by Xact™ due to their out-of-range MIC of meropenem (>128 mg/L). Conclusions The new test was shown to be diagnostically useful, easy to implement and less labour intensive than the classical metho

Effect of the COVID-19 pandemic on colorectal cancer care in France

International audienc

Relatedness of streptococcus suisSerotype 2 isolates from different geographic origins as evaluated by molecular fingerprinting and phenotyping

NRC publication: Ye

Genome Sequence of a Clinical Staphylococcus aureus Strain from a Prosthetic Joint Infection

International audienceHere, we report the genome sequence of Staphylococcus aureus LYO-S2, an isolate with sequence type (ST) 45 that was isolated in 2001 from a patient suffering from a prosthetic joint infection after total knee arthroplasty in the public hospital of Lyon, Franc

Biomedical mass spectrometry in today's and tomorrow's clinical microbiology laboratories

Clinical microbiology is a conservative laboratory exercise where base technologies introduced in the 19th century remained essentially unaltered. High-tech mass spectrometry (MS) has changed that. Within a few years following its adaptation to microbiological diagnostics, MS has been introduced, embraced, and broadly accepted by clinical microbiology laboratories throughout the world as an innovative tool for definitive bacterial species identification. Herein, we review the current state of the art with respect to this exciting new technology and discuss potential future applications. Copyrigh

1690O Impact of the SARS-CoV-2 outbreak on the initial clinical presentation of new solid cancer diagnoses: A systematic review and meta-analysis

International audienceBackgroundSars Cov-2-related disruptions to health services might have impaired the initial clinical presentation of new solid tumor patients. The aim of this systematic review was to compare the initial tumor stage of solid cancer diagnoses before and after the Sars Cov-2 outbreak.MethodsFollowing PRISMA and MOOSE guidelines, we systematically reviewed articles in MEDLINE and EMBASE on the tumor stage of new solid cancer diagnoses before and after the initial Sars Cov-2 pandemic waves. A random-effects meta-analysis was conducted to compare the rate of metastatic tumors at initial presentation. Subgroup analyses were performed per primary tumor site, and per study country. Interstudy heterogeneity and subgroup differences were assessed with I2 and X2 tests, respectively.ResultsFrom 2,013 studies published between January 2020 and April 2022, we included 58 studies including 109,996 patients. The rate of metastatic tumors was higher after than before the pandemic (OR: 1.29 (95% confidence interval (95%CI), 1.06-1.57) with a I2 of 89% (95%CI, 86%-91%). OR (95%CI) were 1,51 (1.07-2,12) for breast cancers, 1.51 (1.04-2.18) for gynecologic cancers, 0.79 (0.18-3.52) for lung cancers, 1.15 (0.89-1.49) for colorectal cancers, 1.45 (0.62-3.42) for other digestive cancer, 2.26 (0.51-10,05) for prostate cancer, 12.07 (0.57-253,68) for genitourinary cancers and 1.01 (0.59-1.75) for other types of cancer (X2 = 24,60, p<0.01). Only 2 countries out of 17 studied showed a significantly higher rate of metastasis after the pandemic: Italy (OR (95%CI) = 1.55 (1.01-2.39)) and Spain (1.14 (1.02-1.29)) Conversely, Taiwan and Canada showed a significantly lower rate of metastasis after the pandemic: OR (95%CI): 0,51 (0,28-0,93) and 0,14 (0,07-0,29).ConclusionsDespite inter-study heterogeneity, our meta-analysis showed a higher rate of metastatic tumors at initial presentation after the Sars Cov2 outbreak. The burden of social distancing policies might explain those results, as patients may have delayed seeking care

A Chlorhexidine- Agar Plate Culture Medium Protocol to Complement Standard Broth Culture of Mycobacterium tuberculosis

International audienceThe culture of Mycobacterium tuberculosis using parallel inoculation of a solid culture medium and a liquid broth provides the gold standard for the diagnosis of tuberculosis. Here, we evaluated a chlorhexidine decontamination-MOD9 solid medium protocol versus the standard NALC-NaOH-Bactec 960 MGIT protocol for the diagnosis of pulmonary tuberculosis by culture. Three-hundred clinical specimens comprising 193 sputa, 30 bronchial aspirates, 10 broncho-alveolar lavages, 47 stools, and 20 urines were prospectively submitted for the routine diagnosis of tuberculosis. The contamination rates were 5/300 (1.7%) using the MOD9 protocol and 17/300 (5.7%) with the Bactec protocol, respectively (P < 0.05, Fisher exact test). Of a total of 50 Mycobacterium isolates (48 M. tuberculosis and two Mycobacterium abscessus) were cultured. Out of these 50, 48 (96%) isolates were found using the MOD9 protocol versus 35 (70%) when using the Bactec protocol (P < 05, Fisher exact test). The time to positivity was 10.1 +/- 3.9 days versus 14.7 +/- 7.3 days, respectively, (P < 0.05, Student's t-test). These data confirmed the usefulness of parallel inoculation of a solid culture medium with broth for the recovery of M. tuberculosis in agreement with current recommendations. More specifically, chlorhexidine decontamination and inoculation of the MOD9 solid medium could be proposed to complement the standard Bactec 960 MGIT broth protocol

Why Are Data Missing in Clinical Data Warehouses? A Simulation Study of How Data Are Processed (and Can Be Lost)

International audienceIn recent years, the development of clinical data warehouses (CDW) has put Electronic Health Records (EHR) data in the spotlight. More and more innovative technologies for healthcare are based on these EHR data. However, quality assessments on EHR data are fundamental to gain confidence in the performances of new technologies. The infrastructure developed to access EHR data – CDW – can affect EHR data quality but its impact is difficult to measure. We conducted a simulation on the Assistance Publique – Hôpitaux de Paris (AP-HP) infrastructure to assess how a study on breast cancer care pathways could be affected by the complexity of the data flows between the AP-HP Hospital Information System, the CDW, and the analysis platform. A model of the data flows was developed. We retraced the flows of specific data elements for a simulated cohort of 1,000 patients. We estimated that 756 [743;770] and 423 [367;483] patients had all the data elements necessary to reconstruct the care pathway in the analysis platform in the “best case” scenarios (losses affect the same patients) and in a random distribution scenario (losses affect patients at random), respectively

Conséquences de la crise Covid-19 en oncologie médicale : promesses, réalisations et défis d'un entrepôt de données de santé

International audience(EDS) regroupent de nombreuses informations disponibles sur les patients traités au sein d'un établissement hospitalier. Ces données ont été largement utilisées pendant la pandémie de Covid-19 pour informer rapidement des conséquences de la crise Covid-19 sur l'état de santé des patients, notamment en cancérologie. Néanmoins, ces analyses nécessitent une grande prudence car différents types de biais peuvent survenir lors de l'exploitation de ces données. Nous présentons un bilan réflexif du travail réalisé sur l'EDS de l'Assistance Publique-Hôpitaux de Paris (AP-HP) pour analyser l'impact de la Covid19 sur la prise en charge des patients atteints de cancer. Nous analysons différents biais constatés sur les données structurées et non-structurées, et leur impact sur l'étude. Une fois ces points pris en compte, les EDS présentent un potentiel indéniable. Pour l'illustrer, nous présentons brièvement les résultats obtenus sur l'impact du Covid19 sur la prise en charge en cancérologie à l'AP-HP