Biology subjects

de Pontual, L.

Publications and source records attributed to de Pontual, L..

3 recordsLinked to original sources

bioRxiv2026

Quantifying the mechanisms of vaccine-induced serotype replacement in Streptococcus pneumoniae using genome-informed modelling

Streptococcus pneumoniae is a colonizer of the childs nasopharynx and a leading cause of invasive pneumococcal disease (IPD). Despite widespread use of pneumococcal conjugate vaccines, recent rebounds in IPD incidence have coincided with serotype replacement. Whether this phenomenon is driven by the replacement of serotypes within lineages or the replacement of the lineages themselves is unclear. Here, we quantified the relative contribution of these two mechanisms to serotype replacement in carriage and their consequences for IPD. We combined nationwide longitudinal surveillance of carriage and IPD in children from 2002 to 2023 with whole-genome sequencing. Observed lineage-specific carriage rates across PCV-related periods were fitted with polynomial logistic regression and compared with two counterfactual scenarios, each isolating one mechanism with: (i) fixed serotype composition within varying lineages and (ii) serotype shifts within fixed lineage carriage rates over time. Carriage dynamics were consistent with an 82% contribution of serotype shifts within persistent lineages. Estimates of serotype-specific IPD incidence derived from this predominant scenario correlated with observed IPD trends. These findings quantify the dominant role of serotype replacement within persistent lineages, disentangling the vaccine-driven adaptive history of S. pneumoniae.

microbiology↗

bioRxiv2022

Performances of bioinformatics tools for the analysis of sequencing data of Mycobacterium tuberculosis complex strains

Whole genome sequencing of Mycobacterium tuberculosis complex (MTBC) strains is a new and rapidly growing tool to obtain results regarding resistance, virulence factors and phylogeny of the strains. Bioinformatics tools presented as user-friendly and easy to use are available online. The objective of this work was to evaluate the performances of two bioinformatics tools, easily accessible on the internet, for the analysis of sequencing data of MTBC strains. Two hundred and twenty-seven MTBC strains isolated at the laboratory of the Avicenne Hospital between 2015 and 2021 were sequenced using Illumina(R)(USA) MiSeq technology. An analysis of the sequencing data was performed using the two tools Mykrobe and PhyResSE. Sequencing quality, resistance or susceptibility status and phylogeny were investigated for each strain. Genotypic resistance results were compared to the results obtained by phenotypic drug susceptibility testing performed in the hospitals routine laboratory. Using the PhyResSE tool we found an average coverage of 98% against the reference strain H37Rv and an average depth of 119X. No information on sequencing quality was obtained with the Mykrobe tool. The concordance of each tool with the phenotypic method for determining susceptibility to first-line anti-tuberculosis drugs was 95%. Mykrobe and PhyResSE tools identified resistance to second-line anti-tuberculosis drugs in 5.3% and 5.7% of cases respectively. The sensitivity and specificity of each tool compared to the phenotypic method was respectively 70% and 98% for Mykrobe and 76% and 97% for PhyResSE. Finally, the two tools showed 99.5% agreement in lineage determination. The Mykrobe and PhyResSE bioinformatics tools were easy to use, fast and efficient. The Mykrobe tool had the advantage of being offline and its interface was more user-friendly. The use of these platforms depends on their accessibility and updating. However, their use is accessible to people not trained in bioinformatics and would allow a complementary approach to phenotypic methods for the study of MTBC strains.

bioinformatics↗

bioRxiv2022

Identification of a CCG-enriched expanded allele in DM1 patients using Amplification-free long-read sequencing

Myotonic dystrophy type 1 (DM1) exhibits highly heterogeneous clinical manifestations caused by an unstable CTG repeat expansion reaching up to 4,000 CTG. The clinical variability depends on CTG repeat number, CNG repeat interruptions and somatic mosaicism. Currently, none of these factors are simultaneously and accurately determined due to the limitations of gold standard methods used in clinical and research laboratories. An amplicon method for targeting DM1 locus using Single-Molecule Real-Time sequencing was recently developed to accurately analyze expanded alleles. However, amplicon-based sequencing still depends on PCR and the inherent bias towards preferential amplification of smaller repeats can be problematic in DM1. Thus, an amplification-free long-read sequencing method was developed using the CRISPR/Cas9 technology in DM1. This method was used to sequence the DM1 locus in patients with CTG repeat expansion ranging from 130 to > 1000 CTG. We showed that elimination of PCR amplification improves the accuracy of measurement of inherited repeat number and somatic repeat variations, two important key factors in the DM1 severity and age at onset. For the first time, an expansion composed of over 85% CCG repeats was identified using this innovative method in a DM1 family with an atypical clinical profile. No-Amplification targeted sequencing represents a promising method that can overcome research and diagnosis shortcomings, with translational implications for clinical and genetic counseling in DM1.

molecular biology↗