Proof of concept study on early forecasting of antimicrobial resistance in hospitalized patients using machine learning and simple bacterial ecology data.

Antibiotic resistance in bacterial pathogens is a major threat to global health, exacerbated by the misuse of antibiotics. In hospital practice, results of bacterial cultures and antibiograms can take several days. Meanwhile, prescribing an empirical antimicrobial treatment is challenging, as clinicians must balance the antibiotic spectrum against the expected probability of susceptibility.

Identification of Southeast Asian Anopheles mosquito species using MALDI-TOF mass spectrometry.

Malaria elimination in Southeast Asia remains a challenge, underscoring the importance of accurately identifying malaria mosquitoes to understand transmission dynamics and improve vector control. Traditional methods such as morphological identification require extensive training and cannot distinguish between sibling species, while molecular approaches are costly for extensive screening. Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and cost-effective tool for Anopheles species identification, yet its current use is limited to few specialized laboratories.

Using MALDI-ToF mass spectrometry to identify mushroom species: Proof of concept analysis of Amanita genus specimens.

Unlabelled: Food poisoning caused by toxic mushrooms, such as species in the Amanita genus, occurs frequently around the world. To properly treat these patients, it is important to rapidly and accurately identify the causal species. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry is a rapid technique that has been used in medical laboratories for the past three decades to identify bacteria, yeasts, and filamentous fungi.

Targeting Malaria Hotspots to Reduce Transmission Incidence in Senegal.

In central Senegal, malaria incidence declined in response to scaling-up of control measures from 2000 to 2010 and has since remained stable, making elimination unlikely in the short term. Additional control measures are needed to reduce transmission. We simulated chemoprophylaxis interventions targeting malaria hotspots using a metapopulation mathematical model, based on a differential-equation framework and incorporating human mobility.

Delineating and Analyzing Locality-Level Determinants of Cholera, Haiti.

Centre Department, Haiti, was the origin of a major cholera epidemic during 2010-2019. Although no fine-scale spatial delineation is officially available, we aimed to analyze determinants of cholera at the local level and identify priority localities in need of interventions. After estimating the likely boundaries of 1,730 localities by using Voronoi polygons, we mapped 5,322 suspected cholera cases reported during January 2015-September 2016 by locality alongside environmental and socioeconomic variables.

Multicentric Analysis of the Species Distribution and Antifungal Susceptibility of Cryptic Isolates from Section .

The antifungal susceptibility of cryptic species is poorly known. We assessed 51 isolates, belonging to seven cryptic species, by the EUCAST reference method and the concentration gradient strip (CGS) method. Species-specific patterns were observed, with high MICs for azole drugs, except for and , and high MICs for amphotericin B for and Essential and categorical agreements between EUCAST and CGS results were between 53.

Spatio-temporal variation of malaria hotspots in Central Senegal, 2008-2012.

Background: In malaria endemic areas, identifying spatio-temporal hotspots is becoming an important element of innovative control strategies targeting transmission bottlenecks. The aim of this work was to describe the spatio-temporal variation of malaria hotspots in central Senegal and to identify the meteorological, environmental, and preventive factors that influence this variation.

Methods: This study analysed the weekly incidence of malaria cases recorded from 2008 to 2012 in 575 villages of central Senegal (total population approximately 500,000) as part of a trial of seasonal malaria chemoprevention (SMC).

Visceral Leishmaniasis in West Africa: Clinical Characteristics, Vectors, and Reservoirs.

Visceral leishmaniasis (VL) is the most serious form of human leishmaniasis. VL is understudied in West Africa. The increasing number of patients at-risk, including persons living with HIV and other chronic immunosuppressive diseases, and likely underreporting of VL related to diagnostic challenges advocate for review of existing data to understand VL regional epidemiology.

Epidemiologic Trends in Malaria Incidence Among Travelers Returning to Metropolitan France, 1996-2016.

Importance: Despite annually adapted recommendations to prevent malaria in travelers to endemic areas, France is still the industrialized country reporting the highest number of imported cases of malaria. Better understanding of the epidemiologic context and evolution during the past 2 decades may help to define a better preventive strategy.

Objective: To study epidemiologic trends of imported cases of malaria in travelers in geographic territories of France on the European continent (metropolitan France) from 1996 through 2016 to potentially explain the persistence of high imported malaria incidence despite national preventive measures.

Dynamics of cholera epidemics from Benin to Mauritania.

Background: The countries of West Africa are largely portrayed as cholera endemic, although the dynamics of outbreaks in this region of Africa remain largely unclear.

Methodology/principal Findings: To understand the dynamics of cholera in a major portion of West Africa, we analyzed cholera epidemics from 2009 to 2015 from Benin to Mauritania. We conducted a series of field visits as well as multilocus variable tandem repeat analysis and whole-genome sequencing analysis of V.

Identification of Leishmania by Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) Mass Spectrometry Using a Free Web-Based Application and a Dedicated Mass-Spectral Library.

Human leishmaniases are widespread diseases with different clinical forms caused by about 20 species within the genus. species identification is relevant for therapeutic management and prognosis, especially for cutaneous and mucocutaneous forms. Several methods are available to identify species from culture, but they have not been standardized for the majority of the currently described species, with the exception of multilocus enzyme electrophoresis.

Validation of a New Web Application for Identification of Fungi by Use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has emerged as a reliable technique to identify molds involved in human diseases, including dermatophytes, provided that exhaustive reference databases are available. This study assessed an online identification application based on original algorithms and an extensive in-house reference database comprising 11,851 spectra (938 fungal species and 246 fungal genera). Validation criteria were established using an initial panel of 422 molds, including dermatophytes, previously identified via DNA sequencing (126 species).

[Targeting abattoirs to control cystic echinococcosis in Algeria].

Cystic echinococcosis (CE) is an important anthropozoonotic parasitic common in Algeria. The predominant life cycle of E. granulosus is a synanthropic cycle with domestic dogs as definitive hosts and livestock animals as intermediate hosts.

Landscape and climatic characteristics associated with human alveolar echinococcosis in France, 1982 to 2007.

Human alveolar echinococcosis (AE) is a severe hepatic disease caused by Echinococcus multilocularis. In France, the definitive and intermediate hosts of E. multilocularis (foxes and rodents, respectively) have a broader geographical distribution than that of human AE.

Populations at risk for alveolar echinococcosis, France.

During 1982-2007, alveolar echinococcosis (AE) was diagnosed in 407 patients in France, a country previously known to register half of all European patients. To better define high-risk groups in France, we conducted a national registry-based study to identify areas where persons were at risk and spatial clusters of cases. We interviewed 180 AE patients about their way of life and compared responses to those of 517 controls.

Spatio-temporal dynamics of cholera during the first year of the epidemic in Haiti.

Background: In October 2010, cholera importation in Haiti triggered an epidemic that rapidly proved to be the world's largest epidemic of the seventh cholera pandemic. To establish effective control and elimination policies, strategies rely on the analysis of cholera dynamics. In this report, we describe the spatio-temporal dynamics of cholera and the associated environmental factors.

The 2009 A(H1N1) influenza pandemic in the French Armed Forces: evaluation of three surveillance systems.

Background: The French military forces had to modify their epidemiological surveillance systems at the time of the 2009 A(H1N1) influenza pandemic. The aim of this article was to present an evaluation of the different systems used.

Methods: Two influenza surveillance systems are usually used in the French forces: one permanent (Surveillance épidémiologique des armées or SEA) and one seasonal (Système militaire d'observation de la grippe or SMOG).

Increase in reported adverse events following seasonal influenza vaccination among the French armed forces, 2008-2009: possible role of stimulated reporting and background cases of influenza-like infection.

Objectives: In September 2009, an increase in seasonal influenza vaccine adverse events (VAE), compared with reports for previous years, was detected among the French armed forces in the setting of an extended immunization campaign. This work presents the results of this investigation.

Study Design: VAE were surveyed among all French military personnel from 2008 to 2009 by Epidemiological Departments of the French Military Health Service.

Dynamics of cholera outbreaks in Great Lakes region of Africa, 1978-2008.

Cholera outbreaks have occurred in Burundi, Rwanda, Democratic Republic of Congo, Tanzania, Uganda, and Kenya almost every year since 1977-1978, when the disease emerged in these countries. We used a multiscale, geographic information system-based approach to assess the link between cholera outbreaks, climate, and environmental variables. We performed time-series analyses and field investigations in the main affected areas.

Novel influenza A(H1N1) outbreak among French armed forces in 2009: results of Military Influenza Surveillance System.

Objectives: An outbreak of novel A(H1N1) virus influenza, detected in Mexico in April 2009, spread worldwide in 9 weeks. The aim of this paper is to present the monitoring results of this influenza outbreak among French armed forces.

Study Design: The period of monitoring by the Military Influenza Surveillance System (MISS) was 9 months, from May 2009 to April 2010.

Understanding the cholera epidemic, Haiti.

After onset of a cholera epidemic in Haiti in mid-October 2010, a team of researchers from France and Haiti implemented field investigations and built a database of daily cases to facilitate identification of communes most affected. Several models were used to identify spatiotemporal clusters, assess relative risk associated with the epidemic's spread, and investigate causes of its rapid expansion in Artibonite Department. Spatiotemporal analyses highlighted 5 significant clusters (p<0.