Biology subjects

Allard, S.

Publications and source records attributed to Allard, S..

5 recordsLinked to original sources

bioRxiv2026

Environmental Fungi Modulate the Vaginal Mycobiome and Cervical Disease Progression in Hispanic Women

The vaginal mycobiome, though a minor component of the cervicovaginal ecosystem, plays a crucial role in reproductive health and disease. However, its composition and interactions with bacterial communities remain poorly understood, particularly among Hispanic women, who experience disproportionately high rates of Human papillomavirus (HPV) infection and cervical cancer. We characterized the vaginal mycobiota across reproductive stages and examined its associations with cervical disease, HPV status, and bacterial community state types (CSTs) in 86 Hispanic participants from Puerto Rico using ITS1 amplicon sequencing. Amplicon sequence variants were inferred with QIIME2/DADA2 and taxonomically classified using the UNITE database, with diversity and discriminant taxa analyses applied to explore clinical and microbial associations. We detected 173 fungal Species Hypotheses, dominated by Candida albicans, Agaricomycetes sp., Scopuloides dimorpha, and Hortaea werneckii. While fungal composition did not differ significantly by reproductive stage, non-pregnant individuals exhibited greater inter-individual variability. Alpha diversity was reduced in high-grade squamous intraepithelial lesions compared with low-grade or normal cytology, and Candida parapsilosis prevalence was elevated in low-grade lesions. CST III, characterized by Lactobacillus iners dominance, showed greater dispersion variance than other CSTs. Collectively, these findings reveal a diverse vaginal mycobiome with stage- and disease-specific features, and a notable contribution of environmental fungi that may influence cervical pathogenesis. This work provides foundational insight into cervicovaginal fungal ecology in a high-risk Hispanic population and highlights the importance of integrating bacteriome-mycobiome analyses in womens health research.

microbiology↗

bioRxiv2022

Host and Water Microbiota are Differentially Linked to Potential Human Pathogen Accumulation in Oysters

Oysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering human health. For example, bacterial pathogens from both marine and terrestrial sources concentrate in oysters and can cause human illness when oysters are consumed raw. While pathogen concentrations in coastal waters are often linked to environmental conditions and runoff events, these do not always correlate with pathogen concentrations in oysters. Additional factors related to oyster hosts and the microbial ecology of pathogenic bacteria likely play a role in accumulation but are poorly understood. In this study, we investigated whether microbial communities in water and oysters were linked to accumulation of fecal indicators, Vibrio parahaemolyticus, and Vibrio vulnificus. Site-specific environmental conditions significantly influenced the composition and diversity of water microbial communities, which were linked to the highest concentrations of both Vibrio spp. and fecal indicator bacteria. Oyster microbial communities, however, were less impacted by environmental variability and exhibited less variability in microbial community diversity and accumulation of target bacteria. Instead, changes in specific microbial taxa in oyster and water samples, particularly in oyster digestive glands, were linked to elevated potential pathogens in oysters, especially V. parahaemolyticus. This included an increase in cyanobacteria in both water and oyster digestive gland microbial communities, which could represent an environmental vector for Vibrio spp. transport and decreased relative abundance of Mycoplasma and other key members of the oyster digestive gland microbiota. These findings suggest that host and microbial factors, in addition to environmental variables, may influence pathogen accumulation in oysters.

microbiology↗

bioRxiv2022

Molecular epidemiology of carbapenemase-producing Acinetobacter spp. from Israel, 2001-2006: earliest report of blaNDM predating the oldest known blaNDM-positive strains

BackgroundCarbapenem-resistant Acinetobacter baumannii (CRAb) is a WHO priority 1 critical pathogen. Despite early emergence of elevated CRAb rates in Israel, limited molecular data from this location are available. We searched for carbapenemases among 198 clinical Acinetobacter spp. from Israel between 2001 and 2006. MethodsStrains from 3 archives underwent whole-genome sequencing (Illumina NovaSeq on all, MinION on a subset) and computational analyses: assembly (Unicycler), annotation (prokka), identification (Kraken, rpoB similarity), search for carbapenemases (ResFinder, BLDB curation). FindingsA. baumannii (Ab) represented 179 (90{middle dot}4%) Acinetobacter spp. Eighty-four Ab (46{middle dot}9%) carried a carbapenemase: 38 (45{middle dot}2%) blaOXA-72 (blaOXA-24-like); 28 (33{middle dot}3%) blaOXA-23-like (20 blaOXA-23 and 8 blaOXA-225); 18 (21{middle dot}5%) blaOXA-58 (16 from 2001-2). Carbapenemase rates increased yearly from 2002 (32%) to 2006 (67%). Eight species of non-baumannii Acinetobacter (NbA) accounted for 19 isolates (9{middle dot}6%). Two of three A. junii contained blaOXA-58, one of which, Ajun-H1-3, isolated in January 2004, also possessed blaNDM-1. The pNDM-Ajun-H1-3 plasmid matched numerous NDM-positive plasmids reported from 2005 onwards in Acinetobacter spp. as well as Enterobacterales. InterpretationWe assessed carbapenemase diversity among Acinetobacter spp. in Israel from 2001-2006. Findings in Ab predate observations elsewhere: rapidly rising carbapenemase rates, driven by blaOXA-23-like and blaOXA-24-like genes replacing blaOXA-58. Among NbA, an A. junii isolated in 2004 carried blaNDM-1, making it the earliest NDM-positive isolate reported to date, preceding those from 2005 in India. Further research into blaNDMs emergence is warranted, in order to shed light on the evolution and spread of this and other antibiotic-resistance genes. FundingCentre de recherche Charles-Le Moyne; Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Universite de Sherbrooke; Fonds de recherche du Quebec - Sante; New Frontiers in Research Fund Grant NFRFE-2019-00444; CIFAR-Azrieli Global Scholars Program.

microbiology↗

bioRxiv2020

Super-resolved live-cell imaging using Random Illumination Microscopy

Super-resolution fluorescence microscopy has been instrumental to progress in biology. Yet, the photo-induced toxicity, the loss of resolution into scattering samples or the complexity of the experimental setups curtail its general use for functional cell imaging. Here, we describe a new technology for tissue imaging reaching a 114nm/8Hz resolution at 30 {micro}m depth. Random Illumination Microscopy (RIM) consists in shining the sample with uncontrolled speckles and extracting a high-fidelity super-resolved image from the variance of the data using a reconstruction scheme accounting for the spatial correlation of the illuminations. Super-resolution unaffected by optical aberrations, undetectable phototoxicity, fast image acquisition rate and ease of use, altogether, make RIM ideally suited for functional live cell imaging in situ. RIM ability to image molecular and cellular processes in three dimensions and at high resolution is demonstrated in a wide range of biological situations such as the motion of Myosin II minifilaments in Drosophila.

bioengineering↗

bioRxiv2019

Reward timing and its expression by inhibitory interneurons in the mouse primary visual cortex

Primary sensory cortex has historically been studied as a low-level feature detector, but has more recently been implicated in many higher-level cognitive functions. For instance, after an animal learns that a light predicts water at a fixed delay, neurons in primary visual cortex (V1) can produce \"reward timing activity\" (i.e., spike modulation of various forms that relate the interval between the visual stimulus and expected reward). The manner by which V1 produces these representations is unknown. Here, we combine behavior, in vivo electrophysiology, and optogenetics to investigate the characteristics of and circuit mechanisms underlying V1 reward timing in the head-fixed mouse. We find that reward timing activity is present in mouse V1, that inhibitory interneurons participate in reward timing, and that these representations are consistent with a theorized network architecture. Together, these results deepen our understanding of V1 reward timing and the manner by which it is produced.

neuroscience↗