Biology subjects

Ailloud, F.

Publications and source records attributed to Ailloud, F..

5 recordsLinked to original sources

bioRxiv2025

Decoding Helicobacter pylori Resistance: Machine Learning Enhanced Prediction of Antibiotic Susceptibility using Whole-Genome Sequencing

BackgroundHelicobacter pylori is a significant risk factor for gastric cancer, peptic ulcers, and MALT lymphoma. Rising antibiotic resistance rates complicate treatment strategies. While nucleotide sequence based assays are reliable in predicting clarithromycin and levofloxacin resistance, predicting metronidazole resistance is more challenging due to diverse metabolic pathways contributing to resistance, and high genomic variability. MethodsWe assembled a cohort of 483 H. pylori clinical isolates, combining whole-genome sequencing with phenotypic susceptibility testing. Machine learning models (SVM, XGBoost, FNN) were trained on genomic variants to predict resistance phenotypes. A sliding-window approach and SHAP-based importance scoring were used for feature selection to identify biologically relevant mutations, improving prediction accuracy, particularly for metronidazole resistance. ResultsThe best-performing FNN model improved metronidazole resistance prediction by 16% compared to conventional (non-ML, single polymorphisms) sequence-based detection methods applied to the same strain collection. Feature selection identified 32 feature sets, with 11 sets significantly improving F1-scores over the baseline. Combining 2-4 feature sets revealed 53 synergistic combinations across all models. Validation showed that 87% of these combinations significantly outperformed non-ML molecular testing, with 16 combinations achieving F1-scores above 0.65. ConclusionMachine-learning can significantly improve the performance of sequence-based susceptibility testing for metronidazole in H. pylori. Novel candidate predictive markers identified from whole-genome data offer testable hypotheses about yet unexplored mechanisms of metronidazole resistance. These findings support the potential for ML-based approaches to enable more accurate susceptibility-guided therapies.

microbiology↗

bioRxiv2024

The Helicobacter pylori orphan ATTAAT-specific methyltransferase M.Hpy99XIX plays a central role in the coordinated regulation of genes involved in iron metabolism

H. pylori genomes contain a large and variable portfolio of methyltransferases (MTases), creating a highly diverse methylome. Here, we characterize a highly conserved ATTAAT-specific MTase, M.Hpy99XIX, the only H. pylori MTase never associated with an endonuclease ("orphan" MTase). Inactivation of M.Hpy99XIX resulted in a significant change in the transcription of >100 genes, despite the fact that only a small subset of their promoter regions contained an ATTAAT target motif. Patterns of transcriptional change showed significant correlations with changes reported for H. pylori mutants in the ArsRS regulators involved in iron regulation. The MTase inactivation also caused a higher susceptibility to diverse metal ions as well as iron chelation and oxidative stress. These phenotypes could be traced back to the methylation of single motifs in the promoter regions of iron transporters frpB1 and fecA1. Altogether, methylation of individual motifs in promoters can have a large downstream effect causing major changes to metabolic pathways. These findings suggest that the methylome represents a universal and dynamic interface connecting genome diversity and transcriptional regulation. Very recently, a new ecospecies Hardy of H. pylori has been reported. M.Hpy99XIX is present in the majority of "normal" (Ubiquitous) H. pylori strains, whereas no single Hardy strain contained this gene, consistent with other reported differences between Hardy and Ubiquitous strains related to iron/metal homeostasis. ATTAAT methylation is intricately connected with the bacterial transcriptional network, highlighting the important role of bacterial epigenetic modifications in bacterial physiology and pathogenesis.

microbiology↗

bioRxiv2023

Methylome evolution through lineage-dependent selection in the gastric pathogen Helicobacter pylori

The bacterial pathogen Helicobacter pylori, the leading cause of gastric cancer, is genetically highly diverse and harbours a large and variable portfolio of restriction-modification systems. Our understanding of the evolution and function of DNA methylation in bacteria is limited. Here, we performed a comprehensive analysis of the methylome diversity in H. pylori, using a dataset of 541 genomes that included all known phylogeographic populations. The frequency of 96 methyltransferases and the abundance of their cognate recognition sequences were strongly influenced by phylogeographic structure and were inter-correlated, positively or negatively, for 20% of type II methyltransferases. Low density motifs were more likely to be affected by natural selection, as reflected by higher genomic instability and compositional bias. Importantly, direct correlation showed that methylation patterns can be actively enriched by positive selection and suggests that specific sites have important functions in methylation-dependent phenotypes. Finally, we identified lineage-specific selective pressures modulating the contraction and expansion of the motif ACGT, revealing that the genetic load of methylation could be dependent on local ecological factors. Taken together, natural selection shapes both the abundance and distribution of methyltransferases and their specific recognition sequences, likely permitting a fine-tuning of genome-encoded functions not achievable by genetic variation alone.

microbiology↗

bioRxiv2022

Plant pathogenic Ralstonia phylotypes evolved divergent respiratory strategies and behaviors to thrive in xylem

Bacterial pathogens in the Ralstonia solanacearum species complex (RSSC) infect the water-transporting xylem vessels of plants, causing bacterial wilt disease. Strains in RSSC phylotypes I and III can reduce nitrate to dinitrogen via complete denitrification. The four-step denitrification pathway enables bacteria to use inorganic nitrogen species as terminal electron acceptors, supporting their growth in oxygen-limited environments like biofilms or plant xylem. Reduction of nitrate, nitrite, and nitric oxide all contribute to virulence of a model phylotype I strain. However, little is known about the physiological role of the last denitrification step, the reduction of nitrous oxide to dinitrogen by NosZ. We found that phylotypes I and III need NosZ for full virulence. However, strains in phylotypes II and IV are highly virulent despite lacking NosZ. The ability to respire by reducing nitrate to nitrous oxide does not greatly enhance growth of phylotype II and IV strains. These partial denitrifying strains reach high cell densities during plant infection and cause typical wilt disease. However, unlike phylotype I and III strains, partial denitrifiers cannot grow well under anaerobic conditions or form thick biofilms in culture or in tomato xylem vessels. Furthermore, aerotaxis assays show that strains from different phylotypes have different oxygen and nitrate preferences. Together, these results indicate that the RSSC contains two subgroups that occupy the same habitat but have evolved divergent energy metabolism strategies to exploit distinct metabolic niches in the xylem. IMPORTANCEPlant pathogenic Ralstonia spp. are a heterogeneous globally distributed group of bacteria that colonize plant xylem vessels. Ralstonia cells multiply rapidly in plants and obstruct water transport, causing fatal wilting and serious economic losses of many key food security crops. Virulence of these pathogens depends on their ability to grow to high cell densities in the low-oxygen xylem environment. Plant pathogenic Ralstonia can use denitrifying respiration to generate ATP. The last denitrification step, nitrous oxide reduction by NosZ, contributes to energy production and virulence for only one of the three phytopathogenic Ralstonia species. These complete denitrifiers form thicker biofilms in culture and in tomato xylem, suggesting they are better adapted to hypoxic niches. Strains with partial denitrification physiology form less biofilm and are more often planktonic. They are nonetheless highly virulent. Thus, these closely related bacteria have adapted their core metabolic functions to exploit distinct micro-niches in the same habitat.

microbiology↗

bioRxiv2018

The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori

Helicobacter pylori encodes a large number of Restriction-Modification (R-M) systems despite its small genome.R-M systems have been described as \"primitive immune systems\" in bacteria, but the role of methylation in bacterial gene regulation and other processes is increasingly accepted. Every H.pylori strain harbours a unique set of R-M systems resulting in a highly diverse methylome. We identified a highly conserved GCGC-specific m5C MTase (JHP1050) that was predicted to be active in all of 459 H.pylori genome sequences analyzed. Transcriptome analysis of two H.pylori strains and their respective MTase mutants showed that inactivation of the MTase led to changes in the expression of 225 genes in strain J99, and 29 genes in strain BCM-300.10 genes were differentially expressed in both mutated strains. Combining bioinformatic analysis and site-directed mutagenesis, we demonstrated that motifs overlapping the promoter influence the expression of genes directly, while methylation of other motifs might cause secondary effects.Thus, m5C methylation modifies the transcription of multiple genes, affecting important phenotypic traits that include adherence to host cells, natural competence for DNA uptake, bacterial cell shape, and susceptibility to copper.

microbiology↗