Publications by authors named "Pierrick Lucas"

25 Publications

  • Page 1 of 1

Identification of β-Lactamase-Encoding () Genes in Phenotypically β-Lactam-Resistant Isolated from Young Calves in Belgium.

Microb Drug Resist 2021 Apr 28. Epub 2021 Apr 28.

Bacteriology, Department of Infectious and Parasitic Diseases, FARAH and Faculty of Veterinary Medicine, ULiège, Belgium.

The genes identification present in 94 phenotypically resistant isolated from feces or intestinal contents of young calves with diarrhea or enteritis in Belgium was performed by microarrays (MA) and whole genome sequencing (WGS). According to their resistance phenotypes to 8 β-lactams at the disk diffusion assay these 94 produced a narrow-spectrum-β-lactamase (NSBL), an extended-spectrum-β-lactamase (ESBL) or a cephalosporinase (AmpC). All ESBL-encoding genes identified by MA and WGS belonged to the family, with a majority to the subfamily. Two different genes encoding an AmpC, , and were detected in isolates with an AmpC phenotype. The and the were detected alone in isolates with a NSBL phenotype or in combination with ESBL-/AmpC-encoding genes. Furthermore, the WGS identified mutations in the gene promoter at nucleotides -42 (C>T) and/or -18 (G>A) that could not be identified by MA, in several isolates with an AmpC-like resistance phenotype. No carbapenemase-encoding gene was detected. To our knowledge this is the first survey on the identification of genes in isolated from young diarrheic or septicemic calves in Belgium.
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http://dx.doi.org/10.1089/mdr.2020.0472DOI Listing
April 2021

Comparison of the Staphylococcal Chromosome Cassette (SCC) in Methicillin-Resistant (MRSA) and Non- Staphylococci (MRNAS) from Animals and Humans.

Antibiotics (Basel) 2021 Mar 4;10(3). Epub 2021 Mar 4.

Bacteriology, Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine and Institute for Fundamental and Applied Research in Animals and Health (FARAH), University of Liège, Quartier Vallée 2, Avenue de Cureghem 6, 4000 Liège, Belgium.

Methicillin-resistant (MRSA) and non- staphylococci (MRNAS) cause different infections in animals, including mastitis, in livestock and humans. This study aimed to identify and compare the staphylococcal chromosome cassette (SCC) types of MRSA or MRNAS isolated from several animal species and humans in different countries. Of 1462 and non- staphylococci, 68 grew on Chrom MRSA ID agar, were phenotypically resistant to cefoxitin and tested positive with the PCR for the gene. These 60 MRSA and 8 MRNAS were isolated in Belgium mainly from cows (livestock-associated (LA) MRS) and humans (community-acquired (CA) MRS) and in Japan from dogs and cats. The SCC cassettes were identified by multiplex PCR in 52 MRSA and 7 MRNAS and by whole genome sequencing (WGS) in 8 additional MRSA. The SCC types IV and V were the most frequent in Belgian LA-MRS and CA-MRS, while the SCC type II was identified in four of the five Japanese MRSA. The remaining isolate was a bovine in which no SCC was identified. These results confirm the high prevalence of the SCC types IV and V in LA-MRS and CA-MRS in Belgium, emphasizing the possible public health hazard of the former, and the absence of SCC in some MRNAS.
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http://dx.doi.org/10.3390/antibiotics10030256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7998684PMC
March 2021

Development and evaluation of a core genome multilocus sequence typing scheme for Paenibacillus larvae, the deadly American foulbrood pathogen of honeybees.

Environ Microbiol 2021 Feb 21. Epub 2021 Feb 21.

Anses, Sophia-Antipolis Laboratory, Unit of Honey Bee Pathology, Sophia Antipolis, France.

Paenibacillus larvae is the causative agent of the fatal American foulbrood disease in honeybees (Apis mellifera). Strain identification is vital for preventing the spread of the disease. To date, the most accessible and robust scheme to identify strains is the multilocus sequence typing (MLST) method. However, this approach has limited resolution, especially for epidemiological studies. As the cost of whole-genome sequencing has decreased and as it becomes increasingly available to most laboratories, an extended MLST based on the core genome (cgMLST) presents a valuable tool for high-resolution investigations. In this study, we present a standardized, robust cgMLST scheme for P. larvae typing using whole-genome sequencing. A total of 333 genomes were used to identify, validate and evaluate 2419 core genes. The cgMLST allowed fine-scale differentiation between samples that had the same profile using traditional MLST and allowed for the characterization of strains impossible by MLST. The scheme was successfully used to trace a localized Swedish outbreak, where a cluster of 38 isolates was linked to a country-wide beekeeping operation. cgMLST greatly enhances the power of a traditional typing scheme, while preserving the same stability and standardization for sharing results and methods across different laboratories.
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http://dx.doi.org/10.1111/1462-2920.15442DOI Listing
February 2021

Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018.

Viruses 2020 11 13;12(11). Epub 2020 Nov 13.

Swine Virology Immunology Unit, Ploufragan-Plouzané-Niort Laboratory, ANSES, BP53, 22440 Ploufragan, France.

This study evaluated the genetic and antigenic evolution of swine influenza A viruses (swIAV) of the two main enzootic H1 lineages, i.e., HA-1C (H1) and -1B (H1), circulating in France between 2000 and 2018. SwIAV RNAs extracted from 1220 swine nasal swabs were hemagglutinin/neuraminidase (HA/NA) subtyped by RT-qPCRs, and 293 virus isolates were sequenced. In addition, 146 H1Ny and 105 H1Ny strains were submitted to hemagglutination inhibition tests. H1N1 (66.5%) and H1N2 (25.4%) subtypes were predominant. Most H1 strains belonged to HA-1C.2.1 or -1B.1.2.3 clades, but HA-1C.2, -1C.2.2, -1C.2.3, -1B.1.1, and -1B.1.2.1 clades were also detected sporadically. Within HA-1B.1.2.3 clade, a group of strains named "Δ146-147" harbored several amino acid mutations and a double deletion in HA, that led to a marked antigenic drift. Phylogenetic analyses revealed that internal segments belonged mainly to the "Eurasian avian-like lineage", with two distinct genogroups for the M segment. In total, 17 distinct genotypes were identified within the study period. Reassortments of H1/H1 strains with H1N1pdm virus were rarely evidenced until 2018. Analysis of amino acid sequences predicted a variability in length of PB1-F2 and PA-X proteins and identified the appearance of several mutations in PB1, PB1-F2, PA, NP and NS1 proteins that could be linked to virulence, while markers for antiviral resistance were identified in N1 and N2. Altogether, diversity and evolution of swIAV recall the importance of disrupting the spreading of swIAV within and between pig herds, as well as IAV inter-species transmissions.
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http://dx.doi.org/10.3390/v12111304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7697621PMC
November 2020

Contrasted Epidemiological Patterns of West Nile Virus Lineages 1 and 2 Infections in France from 2015 to 2019.

Pathogens 2020 Oct 30;9(11). Epub 2020 Oct 30.

UMR 1161 Virology, ANSES, INRAE, ENVA, ANSES Animal Health Laboratory, EURL for Equine Diseases, 94704 Maisons-Alfort, France.

Since 2015, annual West Nile virus (WNV) outbreaks of varying intensities have been reported in France. Recent intensification of enzootic WNV circulation was observed in the South of France with most horse cases detected in 2015 ( = 49), 2018 ( = 13), and 2019 ( = 13). A WNV lineage 1 strain was isolated from a horse suffering from West Nile neuro-invasive disease (WNND) during the 2015 episode in the Camargue area. A breaking point in WNV epidemiology was achieved in 2018, when WNV lineage 2 emerged in Southeastern areas. This virus most probably originated from WNV spread from Northern Italy and caused WNND in humans and the death of diurnal raptors. WNV lineage 2 emergence was associated with the most important human WNV epidemics identified so far in France (n = 26, including seven WNND cases and two infections in blood and organ donors). Two other major findings were the detection of WNV in areas with no or limited history of WNV circulation (Alpes-Maritimes in 2018, Corsica in 2018-2019, and Var in 2019) and distinct spatial distribution of human and horse WNV cases. These new data reinforce the necessity to enhance French WNV surveillance to better anticipate future WNV epidemics and epizootics and to improve the safety of blood and organ donations.
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http://dx.doi.org/10.3390/pathogens9110908DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7692118PMC
October 2020

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

Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus Lagovirus europaeus/GI.2.

Sci Rep 2020 09 2;10(1):14502. Epub 2020 Sep 2.

Unité de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzané-Niort, Agence nationale de sécurité sanitaire, de l'alimentation, de l'environnement et du travail (Anses), Ploufragan, France.

Rabbit haemorrhagic disease is a viral disease that emerged in the 1980s and causes high mortality and morbidity in the European rabbit (Oryctolagus cuniculus). In 2010, a new genotype of the rabbit haemorrhagic disease virus emerged and replaced the former circulating Lagovirus europaeus/GI.1 strains. Several recombination events have been reported for the new genotype Lagovirus europaeus/GI.2, with pathogenic (variants GI.1a and GI.1b) and benign (genotype GI.4) strains that served as donors for the non-structural part while GI.2 composed the structural part; another recombination event has also been described at the p16/p23 junction involving GI.4 strains. In this study, we analysed new complete coding sequences of four benign GI.3 strains and four GI.2 strains. Phylogenetic and recombination detection analyses revealed that the first GI.2 strains, considered as non-recombinant, resulted from a recombination event between GI.3 and GI.2, with GI.3 as the major donor for the non-structural part and GI.2 for the structural part. Our results indicate that recombination contributed to the emergence, persistence and dissemination of GI.2 as a pathogenic form and that all described GI.2 strains so far are the product of recombination. This highlights the need to study full-genomic sequences of lagoviruses to understand their emergence and evolution.
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http://dx.doi.org/10.1038/s41598-020-71303-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7468141PMC
September 2020

Evaluation of un-methylated DNA enrichment in sequencing of African swine fever virus complete genome.

J Virol Methods 2020 11 21;285:113959. Epub 2020 Aug 21.

Viral Genetic and Biosecurity Unit, Ploufragan-Plouzané-Niort Laboratory, ANSES, Ploufragan, France. Electronic address:

African swine fever is a febrile hemorrhagic fever disease that is caused by the African swine fever virus (ASFV) and is lethal for domestic pigs and wild boar. ASFV also infects soft ticks of the genus Ornithodoros, some species of which can act as a vector for ASFV. Whole genome sequencing of ASFV is a challenge because, due to the size difference of the host genome versus the viral genome, the higher proportion of host versus virus DNA fragments renders the virus sequencing poorly efficient. A novel approach of DNA enrichment, based on the separation of methylated and un-methylated DNA, has been reported but without an evaluation of its efficacy. In this study, the efficiency of the un-methylated DNA enrichment protocol was evaluated for pig and tick samples infected by ASFV. As expected, fewer reads corresponding to ASFV were found in the methylated fraction compared to the un-methylated fraction. However, the sequencing coverage of the un-methylated fraction was not improved compared to the untreated DNA. In our hands, the ASFV DNA enrichment was inefficient for tick samples and very limited for pig samples. This enrichment process represents extra work and cost without a significant improvement of ASFV genome coverage. The efficiency of this enrichment approach and the cost/benefit ratio are discussed.
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http://dx.doi.org/10.1016/j.jviromet.2020.113959DOI Listing
November 2020

Coding-Complete Genome Sequence of an African Swine Fever Virus Strain Liv13/33 Isolate from Experimental Transmission between Pigs and Ornithodoros moubata Ticks.

Microbiol Resour Announc 2020 Apr 23;9(17). Epub 2020 Apr 23.

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

Here, we report the coding-complete genome sequence of African swine fever (ASF) virus strain Liv13/33, isolated from experimentally infected pigs and ticks. The 11 sequences that we obtained harbored no notable differences to each other, and all of them were closely related to the genome sequence of the Mkuzi 1979 strain of genotype I.
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http://dx.doi.org/10.1128/MRA.00185-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7180279PMC
April 2020

Characterization of viruses in a tapeworm: phylogenetic position, vertical transmission, and transmission to the parasitized host.

ISME J 2020 07 14;14(7):1755-1767. Epub 2020 Apr 14.

School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.

Parasitic flatworms (Neodermata) infect all vertebrates and represent a significant health and economic burden worldwide due to the debilitating diseases they cause. This study sheds light for the first time into the virome of a tapeworm by describing six novel RNA virus candidate species associated with Schistocephalus solidus, including three negative-strand RNA viruses (order Jingchuvirales, Mononegavirales, and Bunyavirales) and three double-stranded RNA viruses. Using in vitro culture of S. solidus, controlled experimental infections and field sampling, we demonstrate that five of these viruses are vertically transmitted, and persist throughout the S. solidus complex life cycle. Moreover, we show that one of the viruses, named Schistocephalus solidus rhabdovirus (SsRV1), is excreted by the parasite and transmitted to parasitized hosts indicating that it may impact S. solidus-host interactions. In addition, SsRV1 has a basal phylogenetic position relative to vertebrate rhabdoviruses suggesting that parasitic flatworms could have contributed to virus emergence. Viruses similar to four of the S. solidus viruses identified here were found in geographically distant S. solidus populations through data mining. Further studies are necessary to determine if flatworm viruses can replicate in parasitized hosts, how they contribute to parasite infection dynamics and if these viruses could be targeted for treatment of parasitic disease.
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http://dx.doi.org/10.1038/s41396-020-0642-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7305300PMC
July 2020

Characterisation of plasmids harbouring extended-spectrum cephalosporin resistance genes in Escherichia coli from French rivers.

Vet Microbiol 2020 Apr 28;243:108619. Epub 2020 Feb 28.

ANSES, Ploufragan-Plouzané-Niort Laboratory, 22440 Ploufragan, France. Electronic address:

Antimicrobial resistance is a "One Health" issue that requires improved knowledge of the presence and abundance of resistant bacteria in the environment. Extended-spectrum cephalosporins (ESCs) are critically important antibiotics (CIAs), and resistance to these CIAs is often encoded by beta-lactamase genes borne on conjugative plasmids. We thus decided to characterise 21 plasmids of ESC-resistant Escherichia coli randomly selected from isolates previously obtained from river water collected in a rural area in western France. The plasmids encoding ESC resistance were sequenced to investigate the diversity of the genes encoding ESC resistance and their genetic context. Sequences revealed that eleven IncI1 pMLST3 plasmids carried the bla and sul2 genes, and some of them also had the tet(A), aadA5 or dfrA17 genes. The bla gene was also detected on an IncN plasmid. Five plasmids obtained from four rivers contained bla, either on IncI1 or on IncFII plasmids. Two strains from two rivers contained bla on IncN pMLST7 plasmids, with qnrS1 and dfrA14 genes. One plasmid contained the bla, a bla-like, and fosA genes. One plasmid contained the bla gene. The diversity of the genes and plasmids of the resistant bacteria isolated from French rivers is probably related to the various animal and human origins of the isolated bacteria.
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http://dx.doi.org/10.1016/j.vetmic.2020.108619DOI Listing
April 2020

Sequencing of animal viruses: quality data assurance for NGS bioinformatics.

Virol J 2019 11 21;16(1):140. Epub 2019 Nov 21.

Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), viale dell'Università 10, 35120, Legnaro (PD), Italy.

Background: Next generation sequencing (NGS) is becoming widely used among diagnostics and research laboratories, and nowadays it is applied to a variety of disciplines, including veterinary virology. The NGS workflow comprises several steps, namely sample processing, library preparation, sequencing and primary/secondary/tertiary bioinformatics (BI) analyses. The latter is constituted by a complex process extremely difficult to standardize, due to the variety of tools and metrics available. Thus, it is of the utmost importance to assess the comparability of results obtained through different methods and in different laboratories. To achieve this goal, we have organized a proficiency test focused on the bioinformatics components for the generation of complete genome sequences of salmonid rhabdoviruses.

Methods: Three partners, that performed virus sequencing using different commercial library preparation kits and NGS platforms, gathered together and shared with each other 75 raw datasets which were analyzed separately by the participants to produce a consensus sequence according to their own bioinformatics pipeline. Results were then compared to highlight discrepancies, and a subset of inconsistencies were investigated more in detail.

Results: In total, we observed 526 discrepancies, of which 39.5% were located at genome termini, 14.1% at intergenic regions and 46.4% at coding regions. Among these, 10 SNPs and 99 indels caused changes in the protein products. Overall reproducibility was 99.94%. Based on the analysis of a subset of inconsistencies investigated more in-depth, manual curation appeared the most critical step affecting sequence comparability, suggesting that the harmonization of this phase is crucial to obtain comparable results. The analysis of a calibrator sample allowed assessing BI accuracy, being 99.983%.

Conclusions: We demonstrated the applicability and the usefulness of BI proficiency testing to assure the quality of NGS data, and recommend a wider implementation of such exercises to guarantee sequence data uniformity among different virology laboratories.
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http://dx.doi.org/10.1186/s12985-019-1223-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868765PMC
November 2019

Virus persistence in pig herds led to successive reassortment events between swine and human influenza A viruses, resulting in the emergence of a novel triple-reassortant swine influenza virus.

Vet Res 2019 Oct 7;50(1):77. Epub 2019 Oct 7.

Swine Virology Immunology Unit, Ploufragan-Plouzané-Niort Laboratory, ANSES, BP53, 22440, Ploufragan, France.

This report describes the detection of a triple reassortant swine influenza A virus of H1N2 subtype. It evolved from an avian-like swine H1N1 that first acquired the N2 segment from a seasonal H3N2, then the M segment from a 2009 pandemic H1N1, in two reassortments estimated to have occurred 10 years apart. This study illustrates how recurrent influenza infections increase the co-infection risk and facilitate evolutionary jumps by successive gene exchanges. It recalls the importance of appropriate biosecurity measures inside holdings to limit virus persistence and interspecies transmissions, which both contribute to the emergence of new potentially zoonotic viruses.
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http://dx.doi.org/10.1186/s13567-019-0699-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6781375PMC
October 2019

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

Bidirectional Human-Swine Transmission of Seasonal Influenza A(H1N1)pdm09 Virus in Pig Herd, France, 2018.

Emerg Infect Dis 2019 10;25(10):1940-1943

In 2018, a veterinarian became sick shortly after swabbing sows exhibiting respiratory syndrome on a farm in France. Epidemiologic data and genetic analyses revealed consecutive human-to-swine and swine-to-human influenza A(H1N1)pdm09 virus transmission, which occurred despite some biosecurity measures. Providing pig industry workers the annual influenza vaccine might reduce transmission risk.
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http://dx.doi.org/10.3201/eid2510.190068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6759248PMC
October 2019

Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated High-Throughput Sequencing Data Sets.

J Clin Microbiol 2019 08 26;57(8). Epub 2019 Jul 26.

Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany.

Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [llaborative anagement latform for Detection and nalyses of (e-)emerging and Foodborne Outbreaks in urope] virus proficiency test. An artificial, simulated data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.
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http://dx.doi.org/10.1128/JCM.00466-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6663916PMC
August 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

Development of a pig infection model with colistin-resistant Escherichia coli.

Vet Microbiol 2018 Nov 13;226:81-88. Epub 2018 Oct 13.

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

Colistin-resistant Escherichia coli are isolated from pigs suffering from post-weaning diarrhea (PWD). This study was designed to develop an experimental model of PWD using mcr-1-carrying shiga toxin-producing E. coli (STEC) or enterotoxigenic E. coli (ETEC), for the future evaluation of control measures. Three groups of eight piglets, kept in high biosecurity units, were orally inoculated with mcr-1-positive STEC or ETEC, and one unchallenged group was used as a control. Clinical signs were recorded. Regularly-collected fecal samples and samples obtained from the digestive tract of animals sacrificed one month after inoculation were cultured in selective media and isolates were characterized. Blood samples were used to genotype the polymorphisms of the pigs' intestinal receptors for F4 and F18 E. coli adhesins. Diarrhea was more frequent and more fecal samples contained the inoculated strain in the group inoculated with the O149-F4 ETEC strain than with the O141-F18 or O139-F18 STEC strains. However, fewer positive samples were obtained from the two pigs with the F4 resistant genotype. The three inoculated strains could be re-isolated up to the end of the experiment. Excretion peaked on the first week after inoculation with the O149-F4 ETEC strain, and later for the other two. An mcr-1 gene transfer to other commensal isolates was observed only for O139-F18 STEC, while the loss of mcr-1 from the inoculated strain occurred in all groups. The O149-F4 ETEC challenge may be used to evaluate alternative solutions to combat PWD caused by colistin-resistant E. coli in pigs.
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http://dx.doi.org/10.1016/j.vetmic.2018.10.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7126850PMC
November 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

Emergence of bluetongue virus serotype 4 in mainland France in November 2017.

Transbound Emerg Dis 2018 Oct 8;65(5):1158-1162. Epub 2018 Jun 8.

UMR 1161 ANSES/INRA/ENVA, Université Paris-Est ANSES Maisons-Alfort, Maisons-Alfort, France.

In November 2017, a 15-day-old calf located in France (Haute-Savoie department) was found positive for bluetongue virus (BTV) RNA by RT-PCR. Laboratory investigations allowed the isolation and identification of the serotype: BTV-4. The analysis of the full viral genome showed that all the 10 genome segments were closely related to BTV-4 strains involved in a large BT outbreak in the Balkan Peninsula, in Italy since 2014 and in Corsica since the end of October 2016. These results together with epidemiological data suggest that BTV-4 has been introduced to mainland France from Corsica or Italy where BTV-4 outbreaks have been reported in summer and autumn 2016. This is the first report of the introduction of BTV-4 in mainland France.
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http://dx.doi.org/10.1111/tbed.12919DOI Listing
October 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

Infectious bursal disease virus in Algeria: Detection of highly pathogenic reassortant viruses.

Infect Genet Evol 2018 06 1;60:48-57. Epub 2018 Feb 1.

Avian and Rabbit Virology Immunology and Parasitology Unit (VIPAC), French Agency for Food, Environmental and Occupational Heath Safety (ANSES), Zoopole - rue des Fusillés BP 53, 22440 Ploufragan, France. Electronic address:

Infectious bursal disease (IBD) is an immunosuppressive viral disease, present worldwide, which causes mortality and immunosuppression in young chickens. The causative agent, the Avibirnavirus IBDV, is a non-enveloped virus whose genome consists of two segments (A and B) of double-stranded RNA. Different pathotypes of IBDV exist, ranging from attenuated vaccine strains to very virulent viruses (vvIBDV). In Algeria, despite the prophylactic measures implemented, cases of IBD are still often diagnosed clinically and the current molecular epidemiology of IBDV remains unknown. The presence of the virus and especially of strains genetically close to vvIBDV was confirmed in 2000 by an unpublished OIE report. In this study, nineteen IBDV isolates were collected in Algeria between September 2014 and September 2015 during clinical outbreaks. These isolates were analyzed at the genetic, antigenic and pathogenic levels. Our results reveal a broad genetic and phenotypic diversity of pathogenic IBDV strains in Algeria, with, i) the circulation of viruses with both genome segments related to European vvIBDV, which proved as pathogenic for specific pathogen-free chickens as vvIBDV reference strain, ii) the circulation of viruses closely related - yet with a specific segment B - to European vvIBDV, their pathogenicity being lower than reference vvIBDV, iii) the detection of reassortant viruses whose segment A was related to vvIBDV whereas their segment B did not appear closely related to any reference sequence. Interestingly, the pathogenicity of these potentially reassortant strains was comparable to that of reference vvIBDV. All strains characterized in this study exhibited an antigenicity similar to the cognate reference IBDV strains. These data reveal the continuous genetic evolution of IBDV strains in Algerian poultry through reassortment and acquisition of genetic material of unidentified origin. Continuous surveillance of the situation as well as good vaccination practice associated with appropriate biosecurity measures are necessary for disease control.
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http://dx.doi.org/10.1016/j.meegid.2018.01.029DOI Listing
June 2018

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