Biology subjects

Clermont, O.

Publications and source records attributed to Clermont, O..

15 recordsLinked to original sources

bioRxiv2025

Influence of iron uptake systems on cefiderocol activity in Escherichia coli: at the crossroads of antibiotic resistance and virulence

Cefiderocol (FDC) is a new siderophore-conjugated cephalosporin that enters the periplasm via iron transport systems. However, the specific contribution of individual iron uptake pathways to FDC activity remains unclear. We investigated the role of 12 iron acquisition systems using several Escherichia coli strain collections. FDC MICs were determined in iron-depleted and iron-supplemented media for E. coli mutants (Keio and pathogenic island [PAI]-deleted collections) and for clinical wild-type or TEM-producing E. coli (WT/TEM-Ec) and NDM-producing (NDM-Ec) isolates. The distribution of iron uptake genes was assessed in these isolates. In addition, fec operon prevalence and genomic location were investigated in E. coli genomes from EnteroBase and RefSeq databases. Among Keio and 536-PAI-deleted mutants, only {Delta}cirA and {Delta}fiu (enterobactin system) showed increased FDC MICs (8- and 3-fold, respectively), while {Delta}fecA and {Delta}fecB had lower MICs (3-fold decrease). The fec operon, a known extraintestinal virulence factor, was significantly more prevalent in isolates with FDC MICs above median than in those with MICs below (94% vs. 38% in WT/TEM-Ec; 100% vs. 0% in NDM-Ec). According to EUCAST breakpoints, 66.7% of fec-positive NDM-Ec were resistant to FDC while none of the fec-negative were. The fec operon was found in 46.5% of E. coli genomes, including virulent clones (ST131, 77%) and was mostly chromosome-borne (99%). Plasmid-borne fec closely resembled that of Enterobacter hormaechei, suggesting interspecies transfer. Our findings highlight the role of Fec in reducing FDC susceptibility and promoting resistance in NDM-producing E. coli. They challenge the virulence-resistance trade-off demonstrating the liaisons dangereuses between iron and antibiotics.

microbiology↗

bioRxiv2024

Lessons from twenty years of the life of commensal Escherichia coli populations in a human gut

Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary commensal niche, the vertebrate gut. Using Illumina and/or Nanopore technologies, we sequenced whole genomes of 210 E. coli isolates from 22 stools sampled during a 20-year period from a healthy man (ED) living in Paris, France. All phylogroups, except C, were represented, with a predominance of B2 (34.3%), followed by A and F (19% each) phylogroups. Thirty-five clones were identified based on their haplogroup and pairwise genomic single nucleotide polymorphism distance and classified in three phenotypes according to their abundance and residence time: 25 sub-dominant/transient (52 isolates), five dominant/transient (48 isolates) and five dominant/resident (110 isolates). Four over five dominant/resident clones belonged to B2 and closely related F phylogroups, whereas sub-dominant/transient clones belonged mainly to B1, A and D phylogroups. The long residence times of B2 clones seemed to be counterbalanced by lower colonization abilities. Clones with larger within-host frequency persisted for longer in the host. By comparing ED strain genomes to a collection of commensal E. coli genomes from 359 French individuals, we identified ED-specific genomic properties including a set of genes involved in a metabolic pathway (mhp cluster) and a very rare antiviral defense island. The E. coli colonization within the gut microbiota was shaped by both the intrinsic properties of the strain lineages, in particular longer residence of phylogroup B2, and the environmental constraints such as diet or phages.

microbiology↗

bioRxiv2023

Predicting phage-bacteria interactions at the strain level from genomes

Predicting how phages can selectively infect specific bacterial strains holds promise for developing novel approaches to combat bacterial infections and better understanding microbial ecology. Experimental studies on phage-bacteria interactions have been mostly focusing on a few model organisms to understand the molecular mechanisms which makes a particular bacterial strain susceptible to a given phage. However, both bacteria and phages are extremely diverse in natural contexts. How well the concepts learned from well-established experimental models generalize to a broad diversity of what is encountered in the wild is currently unknown. Recent advances in genomics allow to identify traits involved in phage-host specificity, implying that these traits could be utilized for the prediction of such interactions. Here, we show that we could predict outcomes of most phage-bacteria interactions at the strain level in Escherichia natural isolates based solely on genomic data. First, we established a dataset of experimental outcomes of phage-bacteria interactions of 403 natural, phylogenetically diverse, Escherichia strains to 96 bacteriophages matched with fully sequenced and genomically characterized strains and phages. To predict these interactions, we set out to define genomic traits with predictive power. We show that most interactions in our dataset can be explained by adsorption factors as opposed to antiphage systems which play a marginal role. We then trained predictive algorithms to pinpoint which interactions could be accurately predicted and where future research should focus on. Finally, we show the application of such predictions by establishing a pipeline to recommend tailored phage cocktails to target pathogenic strains from their genomes only and show higher efficiency of tailored cocktails on a collection of 100 pathogenic E. coli isolates. Altogether, this work provides quantitative insights into understanding phage-host specificity at the strain level and paves the way for the use of predictive algorithms in phage therapy.

microbiology↗

bioRxiv2023

Inter-phylum circulation of a beta-lactamase - encoding gene: a rare but observable event

Beta-lactam degradation by beta-lactamases is the most common mechanism of beta-lactam resistance in Gram-negative bacteria. Beta-lactamase encoding genes can be transferred between closely-related bacteria, but spontaneous inter-phylum transfers (between distantly related bacteria) has never been reported. Here, we describe an extended-spectrum beta-lactamase (ESBL)-encoding gene (blaMUN-1) shared between the Peudomonadota and Bacteroidota phyla. An Escherichia coli strain was isolated from a patient in Munster (Germany). Its genome was sequenced (Illumina and Nanopore). The ESBL encoding gene was cloned and the corresponding enzyme was characterised. Distribution of the gene among bacteria was studied with BLASTN using RefSeq Genomes databases. Frequency of its closest homolog in the Global Microbial Gene Catalog (GMGC) was also analysed. The blaMUN-1 gene found in the E. coli strain, encoded for an Ambler subclass A2 beta-lactamase with 82.2% amino acid identity to TLA-1 and it was found to confer an ESBL phenotype. blaMUN-1 was found in four copies, two chromosomal copies and two located on a phage-plasmid p0111. Each copy was found on a 7.6kb genomic island associated with mobility. blaMUN-1 was found distributed among the Bacteroidales order and in Sutterella wardsworthensis (Pseudomonadota). Its closest homolog in the GMGC was found predominantly and frequently in the Human gut sub-catalog (found in 26.8% of the samples). This is the first reported case of inter-phylum transfer of an ESBL-encoding gene, between the Bacteroidota and Pseudomonadota phyla. While the gene was frequently found in the human gut, inter-phylum transfer was rare, suggesting that inter-phylum barriers are strong but not impassable.

microbiology↗

bioRxiv2023

Persistence-colonization trade-off and niche differentiation enable the coexistence of E. coli phylogroups

Despite extensive literature on the pathogenicity and virulence of the opportunistic pathogen Escherichia coli, much less is known about its ecological and evolutionary dynamics as a commensal in healthy hosts. Based on two detailed longitudinal datasets on the gut microbiota of healthy adult individuals followed over months to years in France and in the USA, we identified a robust trade-off between the ability to establish in a new host (colonization) and the ability to remain in the host (residence). Major E. coli lineages (phylogroups) exhibited similar fitness but a diversity of strategies, from strong colonizers residing for a few days in the gut, to poor colonizers residing for years. Strains with the largest number of extra-intestinal virulence associated genes and highest pathogenicity resided for longest in hosts. Moreover, the residence time of a strain was reduced more strongly when it competed with other strains of the same phylogroup than of different phylogroups, suggesting niche differentiation between them. To investigate the consequences of the trade-off and niche differentiation for coexistence between strains, we developed a discrete-state Markov model describing the dynamics of E. coli in a population of hosts. We found that the trade-off and niche differentiation acted together as equalizing and stabilizing mechanisms enabling the coexistence of phylogroups over extended periods of time. Our model predicted that a reduction in transmission (e.g. better hygiene) would not alter the balance between phylogroups, while disturbance of the microbiome (e.g. antibiotics) would hinder residents strains such as those of the extra-intestinal pathogenic phylogroup B2.3.

evolutionary biology↗

bioRxiv2023

The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans

Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostics, prevention and treatment is still lacking. We used a collection of 1282 BSI and commensal E. coli isolates collected in France over a 17-year period (2000-2017) and we compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity increased steadily from 23% in 1980 to 46% in 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.

microbiology↗

bioRxiv2022

High pathogenicity island, aer and sit operons: a "menage a trois" in Escherichia coli extra-intestinal virulence

The intrinsic virulence of extra-intestinal pathogenic Escherichia coli is attributed to numerous chromosome and/or plasmid-borne virulence associated genes (VAGs), encoding diverse functions as adhesins, toxins, protectins and iron capture systems, which occur in specific genetic backgrounds. Little is however known on their respective contribution to virulence. Here, by analyzing genomes of 232 sequence type complex (STc) 58 strains, we show that virulence quantified in a mouse model of sepsis emerged in a sub-group of STc58 due to the presence of the siderophore encoding high-pathogenicity island (HPI). When extending our analysis to 370 Escherichia strains we show that full virulence is associated with the presence of the aer or sit operons, in addition to the HPI. The prevalence of these operons, their co-occurrence and genomic location depend on the strain phylogeny. Selection of lineage-dependent specific associations of VAGs argues for strong epistatic interactions shaping the emergence of virulence in E. coli.

microbiology↗

bioRxiv2022

Variable effects on virulence of bacteriophage resistance mechanisms in extraintestinal pathogenic Escherichia coli

AO_SCPLOWBSTRACTC_SCPLOWBacteria exposed to killing agents such as antibiotics or viruses develop resistance. While phage therapy, the use of bacteriophages (phages) for treating bacterial infections, is proposed to answer the antibiotic resistance crisis, bacterial resistance to phages remains poorly characterized during phage treatment. We studied a large population of phage-resistant extra-intestinal pathogenic Escherichia coli 536 clones emerging from both in vitro (non-limited liquid medium) and in vivo (murine pneumonia) conditions. Genome sequencing revealed a mutational convergence of phage resistance mechanisms towards the modification of two cell-wall components, the K15 capsule and the LPS, whatever the condition, showing that their identification could be predicted from the in vitro conditions. The fitness cost of all phage resistant clones was broad in terms of growth rate and resistance to grazing by amoeba and could not discriminate K15 capsule to LPS mutants. By contrast, the virulence of the clones tested in mice showed that K15 capsule mutants were as virulent as the wildtype strain while LPS mutants were strongly attenuated. We also found that resistance to one phage led to the sensitization to other phages. In clinics, to control phage-resistant clones that remains virulent phage cocktail should include phages infecting both phage susceptible and future phage resistant clones. ImportanceEscherichia coli is a leading cause of life-threatening infections, including pneumonia acquired during ventilatory assistance for patients hospitalized in Intensive Care Unit, and a major multidrug resistant pathogen. A century-old concept, phage therapy (i.e. using specific anti-bacterial viruses), is being clinically re-evaluated supported with hundreds of successful compassionate phage treatments. However, along billions of years of coevolution bacteria have developed many ways to resist to phages. Phage resistance occurring during phage therapy remains often overlooked despite its critical role for a successful outcome. During this work we characterized phage resistant mutants in a virulent extra-intestinal pathogenic E coli strain and found that (1) phage resistance taking place during a phage treatment in vivo could be predicted from an in vitro assay; (2) phage resistance has, often but not always, a major fitness cost in terms of virulence; and (3) could be countered by appropriate cocktails of phages.

microbiology↗

bioRxiv2021

Chlorhexidine reduced susceptibility associated to tetracycline resistance in clinical isolates of Escherichia coli

Chlorhexidine is a widely used antiseptic in hospital and community healthcare. Decreased susceptibility to this compound has been recently described in Klebsiella pneumoniae and Pseudomonas aeruginosa, together with cross-resistance to colistin. Surprisingly, few data are available for Escherichia coli, the main species responsible for community and healthcare-associated infections. In order to decipher chlorhexidine resistance mechanisms in E. coli, we studied both in vitro derived and clinical isolates through whole-genome sequence analysis. Comparison of strains grown in vitro under chlorhexidine pressure identified mutations in the gene mlaA coding for a phospholipid transport system. Phenotypic analyses of single-gene mutant from the Keio collection confirmed the role of this mutation in the decreased susceptibility to chlorhexidine. However, mutations in mlaA were not found in isolates from large clinical collections. In contrast, genome wide association studies (GWAS) showed that, in clinical strains, chlorhexidine reduced susceptibility was associated with the presence of tetA genes of class B coding for efflux pumps and located in a Tn10 transposon. Construction of recombinant strains in E. coli K-12 confirmed the role of tetA determinant in acquired resistance to both chlorhexidine and tetracycline. Our results reveal two different evolutionary paths leading to chlorhexidine decreased susceptibility: one restricted to in vitro evolution conditions and involving a retrograde phospholipid transport system; the other observed in clinical isolates associated with efflux pump TetA. None of these mechanisms provides cross-resistance to colistin or to the cationic surfactant octenidine. This work demonstrates the GWAS power to identify new resistance mechanisms in bacterial species.

microbiology↗

bioRxiv2021

The population genomics of increased virulence and antibiotic resistance in human commensal Escherichia coli over 30 years in France

Escherichia coli is a commensal species of the lower intestine, but also a major pathogen causing intestinal and extra-intestinal infections, increasingly prevalent and resistant to antibiotics. Most studies on genomic evolution of E. coli used isolates from infections. Here instead, we whole-genome sequenced a collection of 403 commensal E. coli isolated from fecal samples of healthy adult volunteers in France (1980-2010). These isolates were distributed mainly in phylogroups A and B2 (30% each) and belonged to 152 sequence types (STs), the five most frequent being ST10 (phylogroup A) (16.3%), ST73 and ST95 (phylogroup B2) (6.3 and 5.0%, respectively), ST69 (phylogroup D) (4.2%) and ST59 (phylogroup F) (3.9%), and 224 O:H serotypes. ST and serotype diversity increased over time. The O1, O2, O6 and O25-groups used in bioconjugate O-antigen vaccine against extra-intestinal infections were found in 23% of the strains of our collection. The increase in frequency of virulence-associated genes and antibiotic resistances was driven by two evolutionary mechanisms. Evolution of virulence gene frequency was driven by both clonal expansion of STs with more virulence genes ("ST-driven") and increases in gene frequency within STs independently of changes in ST frequencies ("gene-driven"). In contrast, the evolution of resistance was dominated by increases in frequency within STs ("gene-driven"). This study provides a unique picture of the phylogenomic evolution of E. coli in its human commensal habitat over 30 years and will have implications for the development of preventive strategies. IMPORTANCEEscherichia coli is an opportunistic pathogen with the greatest burden of antibiotic resistance, one of the main causes of bacterial infections and an increasing concern in an ageing population. Deciphering the evolutionary dynamics of virulence and antibiotic resistance in commensal E. coli is important to understand adaptation and anticipate future changes. The gut of vertebrates is the primary habitat of E. coli and probably where selection for virulence and resistance take place. Unfortunately, most whole-genome sequenced strains are isolated from pathogenic conditions. Here, we whole genome sequenced 403 E. coli commensals isolated from healthy French subjects on a 30-year period. Virulence genes increased in frequency by both clonal expansion of clones carrying them and increases in frequency within clones whereas resistance genes increased by within clone increased frequency. Prospective studies of E. coli commensals should be performed worldwide to have a broader picture of evolution and adaptation of this species.

genomics↗

bioRxiv2021

Interplay between bacterial clone and plasmid in the spread of antibiotic resistance genes in the gut: lessons from a temporal study in veal calves

Intestinal carriage of extended spectrum {beta}-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over six months. We characterized the bacterial clones and plasmids carrying blaESBL genes with a combination of genotyping methods, whole genome sequencing and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [blaCTX-M-1 (64.7%), blaCTX-M-14 (33.5%) or blaCTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and blaCTX-M-carrying plasmids, few blaCTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario clone vs. plasmid spread depended on the farm. Thus, epistatic interactions between resistance genes, plasmids and bacterial clones contribute to optimize fitness in specific environments.

microbiology↗

bioRxiv2020

The impact of genetic diversity on gene essentiality within the E. coli species

Bacteria from the same species can differ widely in their gene content. In E. coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. While recent advances in bacterial genomics have enabled to unravel genes required for fitness in various experimental conditions at the genome scale, most studies have focused on model strains. As a result, the impact of this genetic diversity on core processes of the bacterial cell largely remains to be investigated. Here, we developed a new CRISPR interference platform for high-throughput gene repression that is compatible with most E. coli isolates and closely-related species. We applied it to assess the importance of [~]3,400 nearly ubiquitous genes in 3 growth media in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens highlighted extensive variations in gene essentiality between strains and conditions. Unlike variations in gene expression level, variations in gene essentiality do not recapitulate the strains phylogeny. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we showed how mobile genetic elements can trigger the essentiality of core genes that are usually nonessential. This study provides new insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species in bacterial genomics.

genomics↗

bioRxiv2019

Success of Escherichia coli O25b:H4 ST131 clade C associated with a decrease in virulence

Escherichia coli of sequence type (ST) 131 resistant to fluoroquinolones and producer of CTX-M-15 is globally one of the major extraintestinal pathogenic E. coli (ExPEC). ST131 phylogenesis showed that multidrug-resistant ST131 strains belong to a clade called C, descending from an ancestral clade called B, comprising mostly antibiotic-susceptible strains. Antibiotic resistance could appear as one of the keys of the clade C global success. We hypothesized that other features of ST131 clade C could contribute to this success since other major global ExPEC clones (ST73, ST95) are mostly antibiotic-susceptible. To test this hypothesis, we measured the growth abilities, early biofilm formation and virulence-factor content of a collection of clade B and clade C strains. Moreover, using competition assays, we measured the capacity of selected representative strains of clades B and C to colonize the mouse intestine and urinary tract, and to kill mice in a septicemia model. Clade B and C strains had similar growth ability. However, clade B strains were more frequently early biofilm producers, expressed mostly faster their type 1 fimbriae and displayed more virulence factor-encoding genes than clade C strains. Clade B outcompeted clade C in the gut and/or urinary tract colonization models and in the septicemia model. These results strongly suggest that clade C strain evolution includes a loss of virulence, i.e. a process that could enhance micro-organism persistence in a given host and thus optimize transmission. This process, associated with acquired antibiotic-resistance, could ensure clade C strain survival in environments under antibiotic pressure.\n\nImportanceExtraintestinal pathogen Escherichia coli (ExPEC) are virulent but mostly antibiotic-susceptible. One worrying exception is ST131, a major multidrug resistant ExPEC clone that has spread worldwide since the 2000s. To contain the emergence of this threatening clone, we need to understand what factors favored its emergence and dissemination. Here, we investigated whether multidrug-resistant ST131 had advantageous phenotypic properties beyond multidrug resistance. To this end, we competed the emergent multidrug-resistant ST131 with its antibiotic-susceptible ancestor in different conditions: biofilm production, in vivo colonization and virulence experiments. In all in vivo competitions, we found that multidrug-resistant ST131 was losing to its ancestor, suggesting a lesser virulence of multidrug-resistant ST131. It was previously described that losing virulence can increase micro-organism persistence in some populations and subsequently its level of transmissibility. Thus, a decreased level of virulence, associated with multidrug resistance, could explain the global success of ST131.

microbiology↗

bioRxiv2019

Major role of the high-pathogenicity island (HPI) in the intrinsic extra-intestinal virulence of Escherichia coli revealed by a genome-wide association study

The genus Escherichia is composed of several species and cryptic clades, including E. coli, which behave as a vertebrate gut commensal, but also as an opportunistic pathogen involved in both diarrheic and extra-intestinal diseases. To characterize the genetic determinants of extra-intestinal virulence within the genus, we carried out an unbiased genome-wide association study (GWAS) on 370 commensal, pathogenic and environmental strains representative of the Escherichia genus phylogenetic diversity and including E. albertii (n=7), E. fergusonii (n=5), Escherichia clades (n=32) and E. coli (n=326), tested in a mouse model of sepsis. We found that the high-pathogenicity island (HPI), a [~]35 kbp gene island encoding the yersiniabactin siderophore, is highly associated with death in mice, surpassing other associated genetic factors also related to iron uptake, such as the aerobactin and the sitABCD operons. We validated the association in vivo by deleting key components of the HPI in E. coli strains in two phylogenetic backgrounds, and found that virulence is correlated in E. coli with growth in the presence of various stressors including several antimicrobials, which hints at collateral sensitivities associated with intrinsic virulence. This study points to the major role of iron capture systems in the extra-intestinal virulence of the genus Escherichia and the collateral effects on cell growth of such systems.

microbiology↗

bioRxiv2017

Phenotype prediction in an Escherichia coli strain panel

Understanding how genetic variation contributes to phenotypic differences is a fundamental question in biology. Here, we set to predict fitness defects of an individual using mechanistic models of the impact of genetic variants combined with prior knowledge of gene function. We assembled a diverse panel of 696 Escherichia coli strains for which we obtained genomes and measured growth phenotypes in 214 conditions. We integrated variant effect predictors to derive gene-level probabilities of loss of function for every gene across strains. We combined these probabilities with information on conditional gene essentiality in the reference K-12 strain to predict the strains growth defects, providing significant predictions for up to 38% of tested conditions. The putative causal variants were validated in complementation assays highlighting commonly perturbed pathways in evolution for the emergence of growth phenotypes. Altogether, our work illustrates the power of integrating high-throughput gene function assays to predict the phenotypes of individuals.\n\nHighlightsO_LIAssembled a reference panel of E. coli strains\nC_LIO_LIGenotyped and high-throughput phenotyped the E. coli reference strain panel\nC_LIO_LIReliably predicted the impact of genetic variants in up to 38% of tested conditions\nC_LIO_LIHighlighted common genetic pathways for the emergence of deleterious phenotypes\nC_LI

systems biology↗