Publications by authors named "Fabrice Touzain"

26 Publications

  • Page 1 of 1

Molecular characterization of encephalomyocarditis virus strains isolated from an African elephant and rats in a French zoo.

J Vet Diagn Invest 2021 Mar 8;33(2):313-321. Epub 2020 Dec 8.

Animal Health Laboratory, UMR1161 Virology, INRAE, ANSES, ENVA, Paris-Est University, Maisons-Alfort, France.

In November 2013, a fatal encephalomyocarditis virus (EMCV) case in a captive African elephant () occurred at the Réserve Africaine de Sigean, a zoo in the south of France. Here we report the molecular characterization of the EMCV strains isolated from samples collected from the dead elephant and from 3 rats () captured in the zoo at the same time. The EMCV infection was confirmed by reverse-transcription real-time PCR (RT-rtPCR) and genome sequencing. Complete genome sequencing and sequence alignment indicated that the elephant's EMCV strain was 98.1-99.9% identical to the rat EMCV isolates at the nucleotide sequence level. Phylogenetic analysis of the ORF, P1, VP1, and 3D sequences revealed that the elephant and rat strains clustered into lineage A of the EMCV 1 group. To our knowledge, molecular characterization of EMCV in France and Europe has not been reported previously in a captive elephant. The full genome analyses of EMCV isolated from an elephant and rats in the same outbreak emphasizes the role of rodents in EMCV introduction and circulation in zoos.
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http://dx.doi.org/10.1177/1040638720978389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953090PMC
March 2021

Viral variant visualizer (VVV): A novel bioinformatic tool for rapid and simple visualization of viral genetic diversity.

Virus Res 2021 01 17;291:198201. Epub 2020 Oct 17.

Agence National de Sécurité Sanitaire, de l'environnement et du travail (ANSES) Laboratory of Ploufragan-Plouzané-Niort, Virology, Immunology and Parasitology in Poultry and Rabbit (VIPAC) Unit, Université Bretagne Loire (UBL), France. Electronic address:

Here a bioinformatic pipeline VVV has been developed to analyse viral populations in a given sample from Next Generation Sequencing (NGS) data. To date, handling large amounts of data from NGS requires the expertise of bioinformaticians, both for data processing and result analysis. Consequently, VVV was designed to help non-bioinformaticians to perform these tasks. By providing only the NGS data file, the developed pipeline generated consensus sequences and determined the composition of the viral population for an avian Metapneumovirus (AMPV) and three different animal coronaviruses (Porcine Epidemic Diarrhea Virus (PEDV), Turkey Coronavirus (TCoV) and Infectious Bronchitis Virus (IBV)). In all cases, the pipeline produced viral consensus genomes corresponding to known consensus sequence and made it possible to highlight the presence of viral genetic variants through a single graphic representation. The method was validated by comparing the viral populations of an AMPV field sample, and of a copy of this virus produced from a DNA clone. VVV demonstrated that the cloned virus population was homogeneous (as designed) at position 2934 where the wild-type virus demonstrated two variant populations at a ratio of almost 50:50. A total of 18, 10, 3 and 28, viral genetic variants were detected for AMPV, PEDV, TCoV and IBV respectively. The simplicity of this pipeline makes the study of viral genetic variants more accessible to a wide variety of biologists, which should ultimately increase the rate of understanding of the mechanisms of viral genetic evolution.
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http://dx.doi.org/10.1016/j.virusres.2020.198201DOI Listing
January 2021

DUGMO: tool for the detection of unknown genetically modified organisms with high-throughput sequencing data for pure bacterial samples.

BMC Bioinformatics 2020 Jul 6;21(1):284. Epub 2020 Jul 6.

ANSES, Laboratoire de Ploufragan, GVB unit, 22440, Ploufragan, France.

Background: The European Community has adopted very restrictive policies regarding the dissemination and use of genetically modified organisms (GMOs). In fact, a maximum threshold of 0.9% of contaminating GMOs is tolerated for a "GMO-free" label. In recent years, imports of undescribed GMOs have been detected. Their sequences are not described and therefore not detectable by conventional approaches, such as PCR.

Results: We developed DUGMO, a bioinformatics pipeline for the detection of genetically modified (GM) bacteria, including unknown GM bacteria, based on Illumina paired-end sequencing data. The method is currently focused on the detection of GM bacteria with - possibly partial - transgenes in pure bacterial samples. In the preliminary steps, coding sequences (CDSs) are aligned through two successive BLASTN against the host pangenome with relevant tuned parameters to discriminate CDSs belonging to the wild type genome (wgCDS) from potential GM coding sequences (pgmCDSs). Then, Bray-Curtis distances are calculated between the wgCDS and each pgmCDS, based on the difference of genomic vocabulary. Finally, two machine learning methods, namely the Random Forest and Generalized Linear Model, are carried out to target true GM CDS(s), based on six variables including Bray-Curtis distances and GC content. Tests carried out on a GM Bacillus subtilis showed 25 positive CDSs corresponding to the chloramphenicol resistance gene and CDSs of the inserted plasmids. On a wild type B. subtilis, no false positive sequences were detected.

Conclusion: DUGMO detects exogenous CDS, truncated, fused or highly mutated wild CDSs in high-throughput sequencing data, and was shown to be efficient at detecting GM sequences, but it might also be employed for the identification of recent horizontal gene transfers.
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http://dx.doi.org/10.1186/s12859-020-03611-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7336441PMC
July 2020

Genomic polymorphism of Mycoplasma flocculare revealed by a newly developed multilocus sequence typing scheme.

Vet Microbiol 2019 Oct 16;237:108422. Epub 2019 Sep 16.

French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané-Niort Laboratory, Mycoplasmology, Bacteriology and Antimicrobial Resistance Unit, Ploufragan, France; Bretagne Loire University, Rennes, France. Electronic address:

Mycoplasma flocculare is genetically closely related to M. hyopneumoniae, the etiologic agent of porcine enzootic pneumonia, and is frequently isolated with this second species. In this article, we report on the development of the first multilocus sequence typing (MLST) scheme for M. flocculare, based on three genes (adk, rpoB and tpiA). In total, 5022 bp of sequence were analyzed. MLST was used to characterize seven M. flocculare isolates and the reference strain. Eight distinct sequence types were defined, showing the great intraspecies variability of M. flocculare, and the high discriminatory power of the new typing method. The relative contribution of recombinations to the genomic evolution of M. flocculare was revealed by calculating the index of association (I: 0.0185). This MLST scheme is now available for the acquisition of new knowledge on M. flocculare epidemiology via an online database comprising the DNA sequences of each allele, available at http://pubmlst.org/mflocculare/.
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http://dx.doi.org/10.1016/j.vetmic.2019.108422DOI Listing
October 2019

Identification of a Divergent Avian Influenza H3N2 Virus from Domestic Ducks in France.

Microbiol Resour Announc 2018 Dec 13;7(23). Epub 2018 Dec 13.

Anses, Unité VIPAC-LNR Influenza Aviaire, Ploufragan, France.

An avian influenza H3N2 virus was isolated from domestic ducks in France in 2016. Although this French H3N2 virus possesses traits of an avian virus, the genetic distances observed for hemagglutinin (HA) and neuraminidase (NA) show that these two genes most likely evolved independently from other avian influenza sequences.
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http://dx.doi.org/10.1128/MRA.00943-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298543PMC
December 2018

Characterization of plasmids harboring bla genes in Escherichia coli from French pigs.

Vet Microbiol 2018 Oct 4;224:100-106. Epub 2018 Aug 4.

ANSES, Laboratoire de Ploufragan-Plouzané, Ploufragan, France; Université Bretagne Loire, France. Electronic address:

Resistance to extended-spectrum cephalosporins is prevalent in French pig E. coli isolates. The aim of this study was to characterize the plasmids and genes present in pathogenic and commensal extended-spectrum cephalosporins -resistant isolates. The resistance plasmids of 26 strains were sequenced and then analyzed to identify resistance and virulence genes. Results showed that resistance to extended-spectrum cephalosporins in French pig E. coli isolates is-as in other food animals in France-mainly carried by highly similar bla IncI1/ST3 plasmids. These plasmids very often bear other resistance genes such as resistance to sulphonamides (sul2), trimethoprim (dfrA17) and aminoglycosides (aadA5), and occasionally to tetracycline (tet(A)), macrolides (mph(A) and erm genes), phenicols (floR) or streptomycin (strA, strB). Few virulence genes were detected, including colicins, heat-stable enterotoxins, adhesins or temperature-sensitive hemagglutinins. The other cefotaximases detected were bla and bla, the latter being on an IncF plasmid which showed very close identity to a human epidemic plasmid. Importantly, resistance genes for quinolones or polymyxins were never detected on the extended-spectrum cephalosporins resistance plasmids. These results are helpful to evidence the risk of co-selecting cephalosporins -resistance using antibiotics outside this group. They also highlight the occasional presence in pigs of human epidemic plasmids.
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http://dx.doi.org/10.1016/j.vetmic.2018.08.005DOI Listing
October 2018

Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015.

Sci Rep 2018 06 18;8(1):9305. Epub 2018 Jun 18.

Hygiene and Quality of Poultry & Pork Products Unit, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (Anses), Ploufragan, France.

Pathogen source attribution studies are a useful tool for identifying reservoirs of human infection. Based on Multilocus Sequence Typing (MLST) data, such studies have identified chicken as a major source of C. jejuni human infection. The use of whole genome sequence-based typing methods offers potential to improve the precision of attribution beyond that which is possible from 7 MLST loci. Using published data and 156 novel C. jejuni genomes sequenced in this study, we performed probabilistic host source attribution of clinical C. jejuni isolates from France using three types of genotype data: comparative genomic fingerprints; MLST genes; 15 host segregating genes previously identified by whole genome sequencing. Consistent with previous studies, chicken was an important source of campylobacteriosis in France (31-63% of clinical isolates assigned). There was also evidence that ruminants are a source (22-55% of clinical isolates assigned), suggesting that further investigation of potential transmission routes from ruminants to human would be useful. Additionally, we found evidence of environmental and pet sources. However, the relative importance as sources varied according to the year of isolation and the genotyping technique used. Annual variations in attribution emphasize the dynamic nature of zoonotic transmission and the need to perform source attribution regularly.
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http://dx.doi.org/10.1038/s41598-018-27558-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006168PMC
June 2018

Longitudinal study of Escherichia coli plasmid resistance to extended-spectrum cephalosporins in free-range broilers.

Vet Microbiol 2018 Mar 31;216:20-24. Epub 2018 Jan 31.

ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Bretagne Loire, France. Electronic address:

Resistance to extended-spectrum cephalosporins (ESCs) is mostly borne by conjugative plasmids. The aim of the present study was to evaluate the characteristics and diversity of ESC resistance plasmids in Escherichia coli from different free-range broiler flocks in France, and their persistence in flocks during rearing. Two hatcheries were selected. Faecal samples from 11 flocks were collected from before their arrival on the broiler production farm up to their slaughter at the end of the rearing period. A selection of 25 E. coli isolates obtained at different times from different flocks but all harbouring an ESC resistance gene was characterised. The plasmids coding for ESC resistance were sequenced using Mi-seq Illumina technology or the ion proton system (Ion Torrent). Ten IncI1 ST12 plasmids carried the bla gene, and most of them had no other resistance genes. All bla plasmids were obtained from day-old to 7-day-old chicks from four flocks hatched at the same hatchery and sent to three different farms. Sequence comparisons showed identity percentages higher than 99%. Fifteen IncI1 ST3 plasmids were obtained from day-old to 77-day-old broilers from seven flocks on six farms. These plasmids harboured the bla gene, and most also had the tet(A) and sul2 genes, with sequence identity higher than 99%. For both types of plasmid, very high identity percentages were also obtained with published sequences of plasmids isolated from broilers in other countries or from other animal species. Thus, unlike the IncI1 ST12 bla plasmids, the epidemic nature of the IncI1 ST3 bla plasmids in the French poultry production makes it difficult to determine the origin of a contamination which may persist for weeks in a flock.
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http://dx.doi.org/10.1016/j.vetmic.2018.01.012DOI Listing
March 2018

Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from French broilers.

PLoS One 2018 23;13(1):e0188768. Epub 2018 Jan 23.

ANSES, Ploufragan Laboratory, Ploufragan, France.

Resistance to extended-spectrum cephalosporins (ESC) is a global health issue. The aim of this study was to analyze and compare plasmids coding for resistance to ESC isolated from 16 avian commensal and 17 avian pathogenic Escherichia coli (APEC) strains obtained respectively at slaughterhouse or from diseased broilers in 2010-2012. Plasmid DNA was used to transform E. coli DH5alpha, and the resistances of the transformants were determined. The sequences of the ESC-resistance plasmids prepared from transformants were obtained by Illumina (33 plasmids) or PacBio (1 plasmid). Results showed that 29 of these plasmids contained the blaCTX-M-1 gene and belonged to the IncI1/ST3 type, with 27 and 20 of them carrying the sul2 or tet(A) genes respectively. Despite their diverse origins, several plasmids showed very high percentages of identity. None of the blaCTX-M-1-containing plasmid contained APEC virulence genes, although some of them were detected in the parental strains. Three plasmids had the blaCMY-2 gene, but no other resistance gene. They belonged to IncB/O/K/Z-like or IncFIA/FIB replicon types. The blaCMY-2 IncFIA/FIB plasmid was obtained from a strain isolated from a diseased broiler and also containing a blaCTX-M-1 IncI1/ST3 plasmid. Importantly APEC virulence genes (sitA-D, iucA-D, iutA, hlyF, ompT, etsA-C, iss, iroB-E, iroN, cvaA-C and cvi) were detected on the blaCMY-2 plasmid. In conclusion, our results show the dominance and high similarity of blaCTX-M-1 IncI1/ST3 plasmids, and the worrying presence of APEC virulence genes on a blaCMY-2 plasmid.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188768PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5779644PMC
February 2018

Novel Streptococcus suis Sequence Type 834 among Humans, Madagascar.

Emerg Infect Dis 2018 02;24(2):391-392

Two cases of meningitis caused by Streptococcus suis occurred in Madagascar, 1 in 2015 and 1 in 2016. We report the characterization of the novel sequence type, 834, which carried the mrp+/sly+/epf+ virulence marker and a mutation G→T at position 174, leading to a substitution mutS1 to mutS284.
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http://dx.doi.org/10.3201/eid2402.171138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5782891PMC
February 2018

Complete Mitochondrial Genome Sequence of (Coleoptera: Nitidulidae), a Beekeeping Pest.

Genome Announc 2017 Nov 2;5(44). Epub 2017 Nov 2.

Anses, Laboratory of Sophia-Antipolis, European Reference Laboratory for Honey Bee Health, Honey Bee Pathology Unit, Sophia-Antipolis, France.

We report here the full mitochondrial genome sequence of , a Nitidulidae species beetle, that is a pest of bee hives. The obtained sequence is 16,576 bp in length and contains 13 protein-coding genes, 2 rRNA genes, and 22 tRNAs.
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http://dx.doi.org/10.1128/genomeA.01165-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668533PMC
November 2017

A single amino acid change in the non-structural NV protein impacts the virulence phenotype of Viral hemorrhagic septicemia virus in trout.

J Gen Virol 2017 Jun 22;98(6):1181-1184. Epub 2017 Jun 22.

VIM, INRA, Université Paris-Saclay, Jouy-en-Josas, France.

Novirhabdoviruses like the Viral hemorrhagic septicemia virus (VHSV) are rhabdoviruses infecting fish. In the current study, RNA genomes of different VHSV field isolates classified as high, medium or low virulent phenotypes have been sequenced by next-generation sequencing and compared. Various amino acid changes, depending on the VHSV phenotype, have been identified in all the VHSV proteins. As a starting point, we focused our study on the non-virion (NV) non-structural protein in which an arginine residue (R116) is present in all the virulent isolates and replaced by a serine/asparagine residue S/N116 in the attenuated isolates. A recombinant virus derived from a virulent VHSV strain in which the NV R116 residue has been replaced by a serine, rVHSVNVR116S, was generated by reverse genetics and used to infect juvenile trout. We showed that rVHSVNVR116S was highly attenuated and that surviving fish were almost completely protected from a challenge with the wild-type VHSV.
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http://dx.doi.org/10.1099/jgv.0.000830DOI Listing
June 2017

Complete Genome Sequence of a Recombinant Porcine Reproductive and Respiratory Syndrome Virus Strain from Two Genotype 1 Modified Live Virus Vaccine Strains.

Genome Announc 2017 Jun 1;5(22). Epub 2017 Jun 1.

ANSES, Ploufragan-Plouzané Laboratory, Swine Virology and Immunology Unit, Zoopôle, Ploufragan, France

This paper provides information on the complete genome sequence of a porcine reproductive and respiratory syndrome virus (PRRSV) strain isolated on a French pig farm which was identified as a recombinant strain from two commercial modified live virus vaccine strains of genotype 1 (VP-046BIS and DV strains).
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http://dx.doi.org/10.1128/genomeA.00454-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454209PMC
June 2017

Emerging highly pathogenic H5 avian influenza viruses in France during winter 2015/16: phylogenetic analyses and markers for zoonotic potential.

Euro Surveill 2017 Mar;22(9)

Anses, Unité VIPAC - LNR influenza aviaire, Ploufragan, France.

Several new highly pathogenic (HP) H5 avian influenza virus (AIV) have been detected in poultry farms from south-western France since November 2015, among which an HP H5N1. The zoonotic potential and origin of these AIVs immediately became matters of concern. One virus of each subtype H5N1 (150169a), H5N2 (150233) and H5N9 (150236) was characterised. All proved highly pathogenic for poultry as demonstrated molecularly by the presence of a polybasic cleavage site in their HA protein - with a sequence (HQRRKR/GLF) previously unknown among avian H5 HPAI viruses - or experimentally by the in vivo demonstration of an intravenous pathogenicity index of 2.9 for the H5N1 HP isolate. Phylogenetic analyses based on the full genomes obtained by NGS confirmed that the eight viral segments of the three isolates were all part of avian Eurasian phylogenetic lineage but differed from the Gs/Gd/1/96-like lineage. The study of the genetic characteristics at specific amino acid positions relevant for modulating the adaptation to and the virulence for mammals showed that presently, these viruses possess most molecular features characteristic of AIV and lack some major characteristics required for efficient respiratory transmission to or between humans. The three isolates are therefore predicted to have no significant pandemic potential.
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http://dx.doi.org/10.2807/1560-7917.ES.2017.22.9.30473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5356430PMC
March 2017

Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni.

Appl Environ Microbiol 2017 Apr 17;83(7). Epub 2017 Mar 17.

The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom

is among the most common worldwide causes of bacterial gastroenteritis. This organism is part of the commensal microbiota of numerous host species, including livestock, and these animals constitute potential sources of human infection. Molecular typing approaches, especially multilocus sequence typing (MLST), have been used to attribute the source of human campylobacteriosis by quantifying the relative abundance of alleles at seven MLST loci among isolates from animal reservoirs and human infection, implicating chicken as a major infection source. The increasing availability of bacterial genomes provides data on allelic variation at loci across the genome, providing the potential to improve the discriminatory power of data for source attribution. Here we present a source attribution approach based on the identification of novel epidemiological markers among a reference pan-genome list of 1,810 genes identified by gene-by-gene comparison of 884 genomes of isolates from animal reservoirs, the environment, and clinical cases. Fifteen loci involved in metabolic activities, protein modification, signal transduction, and stress response or coding for hypothetical proteins were selected as host-segregating markers and used to attribute the source of 42 French and 281 United Kingdom clinical isolates. Consistent with previous studies of British campylobacteriosis, analyses performed using STRUCTURE software attributed 56.8% of British clinical cases to chicken, emphasizing the importance of this host reservoir as an infection source in the United Kingdom. However, among French clinical isolates, approximately equal proportions of isolates were attributed to chicken and ruminant reservoirs, suggesting possible differences in the relative importance of animal host reservoirs and indicating a benefit for further national-scale attribution modeling to account for differences in production, behavior, and food consumption. Accurately quantifying the relative contribution of different host reservoirs to human infection is an ongoing challenge. This study, based on the development of a novel source attribution approach, provides the first results of source attribution in in France. A systematic analysis using gene-by-gene comparison of 884 genomes of isolates, with a pan-genome list of genes, identified 15 novel epidemiological markers for source attribution. The different proportions of French and United Kingdom clinical isolates attributed to each host reservoir illustrate a potential role for local/national variations in transmission dynamics.
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http://dx.doi.org/10.1128/AEM.03085-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5359498PMC
April 2017

Rare Spontaneous Loss of Multiresistance Gene Carrying IncI/ST12 Plasmid in Escherichia coli in Pig Microbiota.

Antimicrob Agents Chemother 2016 10 23;60(10):6046-9. Epub 2016 Sep 23.

Laboratoire de Ploufragan-Plouzané, Agence Nationale de Sécurité Sanitaire (Anses), Université Bretagne Loire, Ploufragan, France

Resistance to extended-spectrum cephalosporins (ESCs) is a matter of considerable concern for public health. Here, we studied the spontaneous loss of an extended-spectrum beta-lactamase (ESBL)-encoding plasmid from a rifampin-resistant Escherichia coli isolate orally inoculated into pigs under controlled conditions. Fecal samples were collected and cultured on rifampin-supplemented medium, and the resistance of the E. coli isolates to ESCs was studied by phenotypic tests, PCR detection of plasmid genes, and complete sequencing. The results showed that only 3 out of 353 rifampin-resistant E. coli isolates were ESC susceptible, and PCR and bioinformatics analysis confirmed the loss of the plasmid. These in vivo experiments indicate that the loss of an ESBL-encoding plasmid seems a rare event in gut microbiota.
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http://dx.doi.org/10.1128/AAC.00864-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5038322PMC
October 2016

Complete Genome Sequence of Bluetongue Virus Serotype 8, Which Reemerged in France in August 2015.

Genome Announc 2016 Apr 14;4(2). Epub 2016 Apr 14.

Anses, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France.

We announce here the complete genome sequence (coding and noncoding) of the bluetongue virus (BTV) serotype 8, isolated from a ram in Allier department, France, 2015. Sequence analysis confirms the reemergence of the BTV-8 strain that previously circulated in France until 2009 and other European countries until 2010.
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http://dx.doi.org/10.1128/genomeA.00163-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832148PMC
April 2016

Impact of the administration of a third-generation cephalosporin (3GC) to one-day-old chicks on the persistence of 3GC-resistant Escherichia coli in intestinal flora: An in vivo experiment.

Vet Microbiol 2016 Mar 2;185:29-33. Epub 2016 Feb 2.

ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; European University of Brittany, 35000 Rennes, France. Electronic address:

The aim of the experiment was to evaluate under controlled conditions the impact on the excretion of 3GC-resistant Escherichia coli of the injection of one-day-old chicks with ceftiofur, a third-generation cephalosporin (3GC). Three isolators containing specific-pathogen-free chicks were used. In the first one, 20 birds were injected with ceftiofur then ten of them were orally inoculated with a weak inoculum of a 3GC-resistant E. coli field isolate containing an IncI1/ST3 plasmid encoding a blaCTX-M-1 beta-lactamase. The other chicks were kept as contact birds. None of the 20 birds in the second isolator were injected with ceftiofur, but ten of them were similarly inoculated with the 3GC-resistant strain and the others kept as contact birds. A third isolator contained ten non-injected, non-inoculated chicks. Fecal samples were collected regularly over one month and the E. coli isolated on non-supplemented media were characterized by antimicrobial agar dilution, detection of selected resistance genes and determination of phylogenetic group by PCR. The titers of 3GC-resistant E. coli in individual fecal samples were evaluated by culturing on 3GC-supplemented media. Results showed that the inoculated strain rapidly and abundantly colonized the inoculated and contact birds. The ceftiofur injection resulted in significantly higher percentages of 3GC-resistant E. coli isolates among the analyzed E. coli. No transfer of the 3GC-encoding plasmid to other isolates could be evidenced. In conclusion, these results highlight the dramatic capacity of 3GC-resistant E. coli to colonize and persist in chicks, and the selecting pressure imposed by the off-label use of ceftiofur.
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http://dx.doi.org/10.1016/j.vetmic.2016.01.020DOI Listing
March 2016

Complete genome sequence of a porcine epidemic diarrhea s gene indel strain isolated in france in december 2014.

Genome Announc 2015 Jun 4;3(3). Epub 2015 Jun 4.

Anses, Laboratory of Ploufragan/Plouzané, Unit of Viral Genetics and Biosafety, Ploufragan, France.

We report the first and only case of a porcine epidemic diarrhea (PED) outbreak occurring in December 2014 in northern France, and we show using the full-length genome sequence of the French PED virus (PEDV) isolate that it was a PEDV indel strain close to German PEDV strains recently isolated.
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http://dx.doi.org/10.1128/genomeA.00535-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457056PMC
June 2015

Draft Genome Sequence of Taylorella equigenitalis Strain MCE529, Isolated from a Belgian Warmblood Horse.

Genome Announc 2014 Nov 26;2(6). Epub 2014 Nov 26.

ANSES, Dozulé Laboratory for Equine Diseases, Bacteriology and Parasitology Unit, Goustranville, France

Taylorella equigenitalis is the causative agent of contagious equine metritis (CEM), a sexually transmitted infection of horses. We herein report the genome sequence of T. equigenitalis strain MCE529, isolated in 2009 from the urethral fossa of a 15-year-old Belgian Warmblood horse in France.
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http://dx.doi.org/10.1128/genomeA.01214-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246161PMC
November 2014

The spatiotemporal program of replication in the genome of Lachancea kluyveri.

Genome Biol Evol 2013 ;5(2):370-88

UPMC, UMR7238, Génomique des Microorganismes, Paris, France.

We generated a genome-wide replication profile in the genome of Lachancea kluyveri and assessed the relationship between replication and base composition. This species diverged from Saccharomyces cerevisiae before the ancestral whole genome duplication. The genome comprises eight chromosomes among which a chromosomal arm of 1 Mb has a G + C-content much higher than the rest of the genome. We identified 252 active replication origins in L. kluyveri and found considerable divergence in origin location with S. cerevisiae and with Lachancea waltii. Although some global features of S. cerevisiae replication are conserved: Centromeres replicate early, whereas telomeres replicate late, we found that replication origins both in L. kluyveri and L. waltii do not behave as evolutionary fragile sites. In L. kluyveri, replication timing along chromosomes alternates between regions of early and late activating origins, except for the 1 Mb GC-rich chromosomal arm. This chromosomal arm contains an origin consensus motif different from other chromosomes and is replicated early during S-phase. We showed that precocious replication results from the specific absence of late firing origins in this chromosomal arm. In addition, we found a correlation between GC-content and distance from replication origins as well as a lack of replication-associated compositional skew between leading and lagging strands specifically in this GC-rich chromosomal arm. These findings suggest that the unusual base composition in the genome of L. kluyveri could be linked to replication.
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http://dx.doi.org/10.1093/gbe/evt014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590768PMC
September 2013

Co-evolution of segregation guide DNA motifs and the FtsK translocase in bacteria: identification of the atypical Lactococcus lactis KOPS motif.

Nucleic Acids Res 2012 Jul 28;40(12):5535-45. Epub 2012 Feb 28.

Laboratoire de Microbiologie et de Génétique Moléculaire, CNRS, Université de Toulouse, Université Paul Sabatier, F-31000, Toulouse, France.

Bacteria use the global bipolarization of their chromosomes into replichores to control the dynamics and segregation of their genome during the cell cycle. This involves the control of protein activities by recognition of specific short DNA motifs whose orientation along the chromosome is highly skewed. The KOPS motifs act in chromosome segregation by orienting the activity of the FtsK DNA translocase towards the terminal replichore junction. KOPS motifs have been identified in γ-Proteobacteria and in Bacillus subtilis as closely related G-rich octamers. We have identified the KOPS motif of Lactococcus lactis, a model bacteria of the Streptococcaceae family harbouring a compact and low GC% genome. This motif, 5'-GAAGAAG-3, was predicted in silico using the occurrence and skew characteristics of known KOPS motifs. We show that it is specifically recognized by L. lactis FtsK in vitro and controls its activity in vivo. L. lactis KOPS is thus an A-rich heptamer motif. Our results show that KOPS-controlled chromosome segregation is conserved in Streptococcaceae but that KOPS may show important variation in sequence and length between bacterial families. This suggests that FtsK adapts to its host genome by selecting motifs with convenient occurrence frequencies and orientation skews to orient its activity.
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http://dx.doi.org/10.1093/nar/gks171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384302PMC
July 2012

DNA motifs that sculpt the bacterial chromosome.

Nat Rev Microbiol 2011 Jan;9(1):15-26

INRA, UMR 1319, Institut Micalis, FR-78352, Jouy-en-Josas, France.

During the bacterial cell cycle, the processes of chromosome replication, DNA segregation, DNA repair and cell division are coordinated by precisely defined events. Tremendous progress has been made in recent years in identifying the mechanisms that underlie these processes. A striking feature common to these processes is that non-coding DNA motifs play a central part, thus 'sculpting' the bacterial chromosome. Here, we review the roles of these motifs in the mechanisms that ensure faithful transmission of genetic information to daughter cells. We show how their chromosomal distribution is crucial for their function and how it can be analysed quantitatively. Finally, the potential roles of these motifs in bacterial chromosome evolution are discussed.
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http://dx.doi.org/10.1038/nrmicro2477DOI Listing
January 2011

Small variable segments constitute a major type of diversity of bacterial genomes at the species level.

Genome Biol 2010 30;11(4):R45. Epub 2010 Apr 30.

INRA, UMR1319, Micalis, Bat 222, Jouy en Josas, 78350, France.

Background: Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller DNA segments, 20 to 500 bp in size, which we call microdiversity.

Results: We performed a systematic analysis of the variable segments detected by multiple whole genome alignments at the DNA level on three species for which the greatest number of genomes have been sequenced: Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Among the numerous sites of variability, 62 to 73% were loci of microdiversity, many of which were located within genes. They contribute to phenotypic variations, as 3 to 6% of all genes harbor microdiversity, and 1 to 9% of total genes are located downstream from a microdiversity locus. Microdiversity loci are particularly abundant in genes encoding membrane proteins. In-depth analysis of the E. coli alignments shows that most of the diversity does not correspond to known mobile or repeated elements, and it is likely that they were generated by illegitimate recombination. An intriguing class of microdiversity includes small blocks of highly diverged sequences, whose origin is discussed.

Conclusions: This analysis uncovers the importance of this small-sized genome diversity, which we expect to be present in a wide range of bacteria, and possibly also in many eukaryotic genomes.
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http://dx.doi.org/10.1186/gb-2010-11-4-r45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884548PMC
October 2010

SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics.

BMC Bioinformatics 2008 Jan 31;9:73. Epub 2008 Jan 31.

Laboratoire Lorrain de Recherche en Informatique et ses Applications, Campus Scientifique, B,P, 239, UMR CNRS-INPL-INRIA-Nancy 2-UHP 7503, 54506 Vandoeuvre-lès-Nancy, France.

Background: Many programs have been developed to identify transcription factor binding sites. However, most of them are not able to infer two-word motifs with variable spacer lengths. This case is encountered for RNA polymerase Sigma (sigma) Factor Binding Sites (SFBSs) usually composed of two boxes, called -35 and -10 in reference to the transcription initiation point. Our goal is to design an algorithm detecting SFBS by using combinational and statistical constraints deduced from biological observations.

Results: We describe a new approach to identify SFBSs by comparing two related bacterial genomes. The method, named SIGffRid (SIGma Factor binding sites Finder using R'MES to select Input Data), performs a simultaneous analysis of pairs of promoter regions of orthologous genes. SIGffRid uses a prior identification of over-represented patterns in whole genomes as selection criteria for potential -35 and -10 boxes. These patterns are then grouped using pairs of short seeds (of which one is possibly gapped), allowing a variable-length spacer between them. Next, the motifs are extended guided by statistical considerations, a feature that ensures a selection of motifs with statistically relevant properties. We applied our method to the pair of related bacterial genomes of Streptomyces coelicolor and Streptomyces avermitilis. Cross-check with the well-defined SFBSs of the SigR regulon in S. coelicolor is detailed, validating the algorithm. SFBSs for HrdB and BldN were also found; and the results suggested some new targets for these sigma factors. In addition, consensus motifs for BldD and new SFBSs binding sites were defined, overlapping previously proposed consensuses. Relevant tests were carried out also on bacteria with moderate GC content (i.e. Escherichia coli/Salmonella typhimurium and Bacillus subtilis/Bacillus licheniformis pairs). Motifs of house-keeping sigma factors were found as well as other SFBSs such as that of SigW in Bacillus strains.

Conclusion: We demonstrate that our approach combining statistical and biological criteria was successful to predict SFBSs. The method versatility authorizes the recognition of other kinds of two-box regulatory sites.
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http://dx.doi.org/10.1186/1471-2105-9-73DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375139PMC
January 2008