Biology subjects

Leclercq, A.

Publications and source records attributed to Leclercq, A..

4 recordsLinked to original sources

bioRxiv2026

ATLAS: a scverse-compatible package for multi-omic single-cell trajectory inference integration

Single-cell trajectory inference is widely used to study cellular differentiation and fate decisions, yet most methods rely solely on transcriptomic data and therefore capture only part of the regulatory processes underlying cell-state transitions. Here we present ATLAS (Advanced Trajectory Learning from multi-omics At Single-cell resolution), a scverse-compatible Python package for trajectory inference from paired single-cell RNA-seq and ATAC-seq data. ATLAS integrates transcriptomic and chromatin accessibility information through Weighted Nearest Neighbor graphs, enabling both modalities to jointly inform pseudotime estimation, terminal-state identification, and fate probability inference within a unified multi-omic representation. Across synthetic and real datasets, ATLAS reconstructs coherent developmental trajectories, captures progressive fate commitment, and resolves biologically meaningful lineage structures, highlighting the value of multi-omic integration for characterizing cellular developmental dynamics. In addition, ATLAS enables joint analysis of transcription factor expression and accessibility-derived target-gene activity along pseudotime, providing insights into regulatory programs spanning transcriptomic and epigenomic layers that are not readily detectable from unimodal data. As a proof of concept, ATLAS recapitulates known hair follicle regulatory programs and reveals coherent multi-omic trajectories in which Lef1-associated regulatory patterns are linked to hair shaft differentiation. Overall, ATLAS provides an interoperable and biologically informative framework for studying cellular differentiation and regulatory dynamics in single-cell multi-omics experiments.

bioinformatics↗

bioRxiv2023

First genome-based characterization of Listeria monocytogenes in Costa Rica

Genomic data on the foodborne pathogen Listeria monocytogenes from Central America are scarse. We analysed 92 isolates collected in Costa Rica over a decade from different regions, compared them to publicly available genomes and identified unnoticed outbreaks. This study calls for mandatory reporting of listeriosis to improve pathogen surveillance.

genomics↗

bioRxiv2021

Ruminant-associated Listeria monocytogenes isolates belong preferentially to dairy-related hypervirulent clones: a longitudinal study in 19 farms

The increasing prevalence of Listeria monocytogenes infections is a public health issue. Although studies have shown that ruminants constitute reservoirs of this foodborne pathogen, little is known about its epidemiology and genetic diversity within ruminant farms. Here we conducted a large-scale genomic and epidemiologic longitudinal study of Listeria spp. in dairy ruminants and their environments, comprising 19 farms monitored for three consecutive seasons (N=3251 samples). L. innocua was the most prevalent Listeria spp, followed by L. monocytogenes. L. monocytogenes was detected in 52.6% of farms (prevalence in feces samples 3.8%, in farm environment samples 2.5%) and more frequently in cattle (4.1%) and sheep (4.5%) than in goat farms (0.2%). Lineage I accounted for 69% of L. monocytogenes isolates. Among animal samples, the most prevalent sublineages (SL) and clonal complexes (CC) were SL1/CC1, SL219/CC4, SL26/CC26 and SL87/CC87, whereas SL666/CC666 was prevalent in environmental samples. 61 different L. monocytogenes CTs (cgMLST sequence types) were found, 17 of them (27.9%) common to different animals and/or surfaces within the same farms. L. monocytogenes prevalence was not affected by farm hygiene but by season: the overall prevalence of L. monocytogenes in cattle farms was higher during winter, and in sheep farms was higher during winter and spring. Cows in their second lactation had a higher probability of L. monocytogenes fecal shedding than other lactating cows. This study highlights that dairy farms constitute a reservoir for hypervirulent L. monocytogenes and the importance of continuous animal surveillance to reduce the burden of human listeriosis. IMPORTANCEListeria monocytogenes is a bacterial pathogen responsible for listeriosis, the foodborne disease with the highest hospitalization and case-fatality rate. Despite increasing evidence that dairy products and ruminant farms are important reservoirs of L. monocytogenes, little is known about the epidemiology and genetic diversity of Listeria spp. within dairy ruminant farms. We report the largest Listeria spp. longitudinal study in individual domestic animals, and the first using whole-genome sequencing for a deep isolate characterization. Here, we show that domestic ruminants can be asymptomatic carriers of pathogenic Listeria, that L. monocytogenes fecal shedding is often intermittent, and that hypervirulent L. monocytogenes clones are overrepresented in dairy farms. Moreover, we uncover the effect of seasons and lactation number on the prevalence of L. monocytogenes in ruminants. Our study highlights the need for Listeria spp. monitoring in farm animals to control the spread of hypervirulent L. monocytogenes and reduce the burden of human listeriosis.

microbiology↗

bioRxiv2020

Emergence and global spread of Listeria monocytogenes main clinical clonal complex

Retracing microbial emergence and spread is essential to understanding the evolution and dynamics of pathogens. The bacterial foodborne pathogen Listeria monocytogenes clonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with listeriosis, and is strongly associated with cattle and dairy products. Here we analysed 2,021 Lm-CC1 isolates collected from 40 countries, since the first Lm isolation to the present day, to define its evolutionary history and population dynamics. Our results suggest that Lm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19th century and the rapid growth of cattle farming in the 20th century. Lm-CC1 then firmly established at a local level, with limited inter-country spread. This study provides an unprecedented insight into Lm-CC1 phylogeography and dynamics and can contribute to effective disease surveillance to reduce the burden of listeriosis.

genomics↗