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.

Neurologic Outcomes and Quality of Life in Children After Extracorporeal Membrane Oxygenation

RATIONALE

Use of life support with extracorporeal membrane oxygenation (ECMO) is associated with brain injury. However, the consequences of these injuries on subsequent neurologic development and health-related quality of life (HRQoL) are poorly described in children.

OBJECTIVES

The aim of this preliminary study was to describe short- and long-term neurologic outcomes in survivors of ECMO, as well as their HRQoL.

DESIGN

Retrospective identified cohort with contemporary evaluations.

SETTING

Necker Children's Hospital academic PICU.

PATIENTS

Forty survivors who underwent ECMO (October 2014 to January 2020) were included in follow-up assessments in May 2021.

INTERVENTIONS

None.

MEASUREMENT AND MAIN RESULTS

We first reviewed the outcomes of ECMO at the time of PICU discharge, which included a summary of neurology, radiology, and Pediatric Overall/Cerebral Performance Category (POPC/PCPC) scores. Then, in May 2021, we interviewed parents and patients to assess HRQoL (Pediatric Quality of Life Inventory [PedsQL]) and POPC/PCPC for children 3 years old or older, and Denver II test (DTII) for younger children. An evaluation of DTII in the youngest patients 1 year after ECMO decannulation was also added. Median age at ECMO was 1.4 years (interquartile range [IQR], 0.4-6 yr). Thirty-five children (88%) underwent a venoarterial ECMO. At PICU discharge, 15 of 40 patients (38%) had neurologic impairment. Assessment of HRQoL was carried out at median of 1.6 years (IQR, 0.7-3.3 yr) after PICU discharge. PedsQL scores were over 70 of 100 for all patients (healthy peers mean results: 80/100), and scores were like those published in patients suffering with chronic diseases. In May 2021, seven of 15 patients had a normal DTII, and 36 of 40 patients had a POPC/PCPC score less than or equal to 3.

CONCLUSIONS

None of our patients presented severe disability at long term, and HRQoL evaluation was reassuring. Considering the risk of neurologic impairment after ECMO support, a systematic follow-up of these high-risk survivor patients would be advisable.

Anti-infective prescribing practices in critically ill children on continuous renal replacement therapy: a multicenter survey of French-speaking countries

BACKGROUND

Use of continuous renal replacement therapy in children receiving anti-infective drugs may lead to inappropriate concentrations with risks related to treatment failure, toxicity and emergence of multidrug-resistant bacteria. We aimed to describe anti-infective prescribing practices in critically ill children undergoing continuous renal replacement therapy.

METHODS

An online survey to assess continuous renal replacement therapy, anti-infective prescribing and therapeutic drug monitoring practices was sent by e-mail to physicians working in pediatric intensive care units through the French-speaking Group of Pediatric Intensive Care and Emergency medicine (GFRUP).

RESULTS

From April 1st, 2021 to May 1st, 2021, 26/40 pediatric intensive care units participated in the survey, corresponding to a response rate of 65%. Twenty-one were located in France and five abroad. All pediatric intensive care units administered continuous renal replacement therapy, primarily with Prismaflex™ System. Anti-infective prescriptions were adjusted to the presence of continuous renal replacement therapy in 23 (88%) pediatric intensive care units mainly according to molecular weight in 6 (23%), molecule protein binding in 6 (23%) and elimination routes in 15 (58%) including residual diuresis in 9 (35%), to the continuous renal replacement therapy flow in 6 (23%) and to the modality of continuous renal replacement therapy used in 15 (58%), pediatric intensive care units. There was broad variability among pediatric intensive care units and among physicians within the same unit. Barriers to therapeutic drug monitoring were mainly an excessive delay in obtaining results in 11 (42%) and the lack of an on-site laboratory in 8 (31%) pediatric intensive care units.

CONCLUSIONS

Our survey reported wide variability in anti-infective prescribing practices in children undergoing continuous renal replacement therapy, thus highlighting a gap in knowledge and the need for education and recommendations.

Aminoglycosides for the Treatment of Severe Infection Due to Resistant Gram-Negative Pathogens

Aminoglycosides are a family of rapidly bactericidal antibiotics that often remain active against resistant Gram-negative bacterial infections. Over the past decade, their use in critically ill patients has been refined; however, due to their renal and cochleovestibular toxicity, their indications in the treatment of sepsis and septic shock have been gradually reduced. This article reviews the spectrum of activity, mode of action, and methods for optimizing the efficacy of aminoglycosides. We discuss the current indications for aminoglycosides, with an emphasis on multidrug-resistant Gram-negative bacteria, such as extended-spectrum β-lactamase-producing Enterobacterales, carbapenemase-producing Enterobacterales, multidrug-resistant Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii. Additionally, we review the evidence for the use of nebulized aminoglycosides.

Efficacy and safety of baricitinib in hospitalized adults with severe or critical COVID-19 (Bari-SolidAct): a randomised, double-blind, placebo-controlled phase 3 trial

BACKGROUND

Baricitinib has shown efficacy in hospitalized patients with COVID-19, but no placebo-controlled trials have focused specifically on severe/critical COVID, including vaccinated participants.

METHODS

Bari-SolidAct is a phase-3, multicentre, randomised, double-blind, placebo-controlled trial, enrolling participants from June 3, 2021 to March 7, 2022, stopped prematurely for external evidence. Patients with severe/critical COVID-19 were randomised to Baricitinib 4 mg once daily or placebo, added to standard of care. The primary endpoint was all-cause mortality within 60 days. Participants were remotely followed to day 90 for safety and patient related outcome measures.

RESULTS

Two hundred ninety-nine patients were screened, 284 randomised, and 275 received study drug or placebo and were included in the modified intent-to-treat analyses (139 receiving baricitinib and 136 placebo). Median age was 60 (IQR 49-69) years, 77% were male and 35% had received at least one dose of SARS-CoV2 vaccine. There were 21 deaths at day 60 in each group, 15.1% in the baricitinib group and 15.4% in the placebo group (adjusted absolute difference and 95% CI - 0.1% [- 8·3 to 8·0]). In sensitivity analysis censoring observations after drug discontinuation or rescue therapy (tocilizumab/increased steroid dose), proportions of death were 5.8% versus 8.8% (- 3.2% [- 9.0 to 2.7]), respectively. There were 148 serious adverse events in 46 participants (33.1%) receiving baricitinib and 155 in 51 participants (37.5%) receiving placebo. In subgroup analyses, there was a potential interaction between vaccination status and treatment allocation on 60-day mortality. In a subsequent post hoc analysis there was a significant interaction between vaccination status and treatment allocation on the occurrence of serious adverse events, with more respiratory complications and severe infections in vaccinated participants treated with baricitinib. Vaccinated participants were on average 11 years older, with more comorbidities.

CONCLUSION

This clinical trial was prematurely stopped for external evidence and therefore underpowered to conclude on a potential survival benefit of baricitinib in severe/critical COVID-19. We observed a possible safety signal in vaccinated participants, who were older with more comorbidities. Although based on a post-hoc analysis, these findings warrant further investigation in other trials and real-world studies. Trial registration Bari-SolidAct is registered at NCT04891133 (registered May 18, 2021) and EUClinicalTrials.eu ( 2022-500385-99-00 ).

Novel mutations in antiviral multiresistant HSV-2 genital lesion: A case report

HSV-2 antiviral resistance mainly occurs in immunocompromised patients and especially in HIV-positive individuals receiving long-term antiviral treatment. Those situations can be challenging as few alternatives are available for HSV infection management. To describe clinical and virological significance of two novel potential HSV-2 resistance mutations after treating an obese patient with a pseudotumoral genital HSV-related lesion. Consecutive different antiviral treatments were used: valacyclovir (VACV) then foscarnet (FOS) then topical cidofovir (CDV) and finally imiquimod. Under VACV, genotypic resistance testing revealed a novel mutation within viral thymidine kinase (TK, gene UL23) not previously reported but probably accounting for antiviral resistance: W89G, similar to W88R mutation reported in HSV-1 TK, known to be associated with ACV resistance for HSV-1. Under FOS, while initial mutations were still present, a second genotypic resistance testing performed on persisting lesions showed a novel mutation within viral DNA polymerase (DNA pol, gene UL30): C625R. All three antivirals used in this case are small molecules and pharmacokinetics of VACV, FOS, and CDV have not been evaluated in animals and there are very few studies in human. As small molecules are poorly bound to proteins and distribution volume is increased in obese patients, there is risk of underdosage. This mechanism is suspected to be involved in emergence of resistance mutation and further data is needed to adapt, closely to patient profile, antiviral dosage. This report describes a chronic HSV-2 genital lesion, with resistance to current antivirals and novel mutations within viral TK and DNA pol which may confer antiviral resistance.

Diagnostic des pneumonies aiguës communautaires aux urgences et distinction entre étiologie virale ou bactérienne

La pandémie actuelle liée à l’émergence du SARSCoV-2 en 2019 a considérablement modifié la perception des médecins de l’impact des virus respiratoires et de leur rôle dans les pneumonies aiguës communautaires (PAC). Alors que plus de 25 % des tableaux de PAC chez l’adulte étaient d’origine virale, les virus respiratoires étaient souvent perçus comme des agents pathogènes peu graves. Devant le défi que représente encore à nos jours la documentation microbiologique d’une PAC, l’instauration d’un traitement empirique par antibiotiques est souvent réalisée aux urgences. La pandémie de COVID-19 a surtout mis en exergue le rôle déterminant de la biologie moléculaire et du scanner thoracique dans l’algorithme diagnostique de la PAC. En effet, un diagnostic rapide et fiable est la clé pour améliorer les mesures de précaution et réduire la prescription inutile d’antibiotiques. Du fait de prises en charges très différentes, il est nécessaire de distinguer l’étiologie virale de la bactérienne d’une PAC.

Life-threatening hemophagocytic syndrome triggered by disseminated toxoplasmosis in a young patient with previously unknown AIDS

Hemophagocytic syndrome is a rare life-threatening disorder that can be triggered by various conditions such as HIV infection and opportunistic agents. We report a case of disseminated toxoplasmosis complicated with severe hemophagocytic syndrome and revealing an unknown acquired immunodeficiency syndrome. The patient presented with multiple organ failure in intensive care unit. Once diagnosed, he benefitted from etoposide infusion, administration of specific anti-toxoplasmosis treatments and secondary antiretroviral therapy. He was alive at intensive care unit discharge and returned home with little sequalae. This case illustrates both the importance of rapid investigations of hemophagocytic syndrome etiologies in HIV positive patients and the necessity to prompt etoposide and specific treatments in order to improve potentially dramatic outcomes.

Étude pilote sur la corrélation entre le score d'aération pulmonaire par échographie et la performance au test de marche de 6 minutes chez les patients hospitalisés pour COVID-19

Introduction

La kinésithérapie joue un rôle important dans la prise en charge des patients présentant des lésions pulmonaires associées au COVID-19. L'échographie pulmonaire permet une évaluation mais a été peu étudiée avec la récupération fonctionnelle des patients.

L'objectif principal était d'étudier la corrélation entre le score échographique validé d'aération pulmonaire (LUS) et la performance au test de marche de 6 minutes (TM6M) évaluée par les kinésithérapeutes du service.

Matériels et méthodes

L'étude a été proposée à la sortie de tous les patients hospitalisés depuis >48h dans le service de maladies infectieuses pour COVID-19 du 06/06/2021 au 21/07/2021 en recueillant le LUS, le TM6M et autres variables d'intérêt (atteinte scannographique, durée d'hospitalisation, niveau d'oxygénorequérance).

Résultats

Onze patients (5 femmes et 6 hommes) ont été inclus, âgés en moyenne de 53 ±13.5, 27% avec des comorbidités. Vingt-et-un patients ont été exclus (13 pour marche impossible, 4 pour des troubles cognitifs, 3 décès, 1 barrière de la langue). Au total, 82% venaient des Urgences et 18% de réanimation. L'atteinte pulmonaire scannographique initiale était évaluée entre 10 et 50%. La durée moyenne d'hospitalisation était de 15.5 ±19.6jours. Il existait une corrélation linéaire négative (-0.24) entre le score d'aération et la performance au TM6M. Les hommes ont parcouru 403,6 ± 18 m en moyenne tandis que les femmes ont fait 269.5 ±59m avec une diminution de la saturation d'oxygène pendant l'effort et une augmentation de la fréquence cardiaque.

Conclusion

Bien que la taille de notre échantillon soit restreinte, cela montre une étude faisable avec des premiers résultats montrant que les patients qui ont des scores d'aération élevés auraient de moins bonnes performances au TM6M.

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How and why do French medical students choose the specialty of infectious and tropical diseases? A national cross-sectional study

BACKGROUND

Infectious and tropical diseases (ID) physicians are needed now more than ever to tackle existing and emerging global threats. However, in many countries, ID is not recognized as a qualifying specialty. The creation of ID residency in 2017 in France offers the opportunity to know how and why the specialty is chosen by medical students.

METHODS

We first analyzed the choice of specialty of all French medical students in 2017 and 2018 according to their rank at the national exam that ends medical studies. A web questionnaire was then sent in January 2019 to all ID residents in France (n = 100) to assess the factors influencing their choice of specialty and their career plan.

RESULTS

We analyzed the choice of 17,087 medical students. ID was the first-chosen specialty with a median national rank of 526/8539, followed by plastic surgery and ophthalmology. The questionnaire was completed by 90% of the French ID residents (n = 100). The most encouraging factors to choose ID were the multi-system approach of the specialty, the importance of diagnostic medicine and having done an internship in ID during medical school. The potential deterrents were the work-life balance, the workload and the salary.

CONCLUSIONS

The recent recognition of ID as a qualifying specialty in France can be considered a success insofar as the specialty is the most popular among all medical and surgical specialties. Individuals who choose ID are attracted by the intellectual stimulation of the specialty but express concerns about the working conditions and salaries.