Publication – Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group

EVENT : C3BI Publication

Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group


Main speaker : , from Date : 12/09/2017 at Location : ,Institut Pasteur, Paris


Staphylococcus sciuri is considered to be one of the most ancestral species in the natural history of the Staphylococcus genus that consists of 48 validly described species. It belongs to the basal group of oxidase-positive and novobiocin-resistant staphylococci that diverged from macrococci approximately 250 million years ago. Contrary to other groups, the S. sciuri species group has not developed host-specific colonization strategies. Genome analysis of S. sciuri ATCC 29059 provides here the first genetic basis for atypical traits that would support the switch between the free-living style and the infective state in animals and humans. From among the most remarkable features, it was noticed in this extensive study that there were a number of phosphoenolpyruvate:carbohydrate phosphotransferase systems (PTS), almost twice as many as any other staphylococci, and the co-occurrence of mevalonate and non-mevalonate pathways for isoprenoid synthesis. The sequenced strain was devoid of the main virulence factors present in Staphylococcus aureus, although it exhibited numerous heme and iron acquisition systems, as well as crt and aldH genes necessary for gold pigment synthesis. The sensing and signaling networks, exemplified by a large and typical repertoire of two-component regulatory systems and a complete panel of master regulators, such as agr, rex, mgrA, rot, sarA and sarR genes, depict the background in which S. aureus virulence genes were later acquired. An additional sigma factor, a distinct set of electron transducer elements and many gene operons similar to those found in Bacillus spp. would constitute the most visible remnant links with Bacillaceae organisms.


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Publication – Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov

EVENT : C3BI Publication

Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov


Main speaker : , from Date : 01/09/2017 at Location : ,Institut Pasteur, Paris


The genus Elizabethkingia is genetically heterogeneous, and the phenotypic similarities between recognized species pose challenges in correct identification of clinically derived isolates. In addition to the type species Elizabethkingia meningoseptica, and more recently proposed Elizabethkingia miricola, Elizabethkingia anophelis and Elizabethkingia endophytica, four genomospecies have long been recognized. By comparing historic DNA-DNA hybridization results with whole genome sequences, optical maps, and MALDI-TOF mass spectra on a large and diverse set of strains, we propose a comprehensive taxonomic revision of this genus. Genomospecies 1 and 2 contain the type strains E. anophelis and E. miricola, respectively. Genomospecies 3 and 4 are herein proposed as novel species named as Elizabethkingia bruuniana sp. nov. (type strain, G0146(T) = DSM 2975(T) = CCUG 69503(T) = CIP 111191(T)) and Elizabethkingia ursingii sp. nov. (type strain, G4122(T) = DSM 2974(T) = CCUG 69496(T) = CIP 111192(T)), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070(T) = DSM 2976(T) = CCUG 69505(T) = CIP 111193(T)), is proposed.


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Publication – Psychrobacter pasteurii and Psychrobacter piechaudii sp. nov., two novel species within the genus Psychrobacter

EVENT : C3BI Publication

Psychrobacter pasteurii and Psychrobacter piechaudii sp. nov., two novel species within the genus Psychrobacter


Main speaker : , from Date : 28/08/2017 at Location : ,Institut Pasteur, Paris


Six Gram-negative, non-motile, non-spore-forming, non-pigmented, oxidase- and catalase-positive bacterial strains were deposited in 1972, in the Collection of the Institut Pasteur (CIP), Paris, France. The strains, previously identified as members of the genus Moraxella on the basis of their phenotypic and biochemical characteristics, were placed within the genus Psychrobacter based on the results from comparative 16S rRNA gene sequence studies. Their closest phylogenetic relatives were Psychrobacter sanguinis CIP 110993T, Psychrobacter phenylpyruvicus CIP 82.27T and Psychrobacter lutiphocae CIP 110018T. The DNA G+C contents were between 42.1 and 42.7 mol%. The predominant fatty acids were C18 : 1ω9c, C16 : 0, C12 : 0 3-OH, and C18 : 0. Average nucleotide identity between the six strains and their closest phylogenetic relatives, as well as their phenotypic characteristics, supported the assignment of these strains to two novel species within the genus Psychrobacter. The proposed names for these strains are Psychrobacter pasteurii sp. nov., for which the type strain is A1019T (=CIP 110853T=CECT 9184T), and Psychrobacter piechaudii sp. nov., for which the type strain is 1232T (=CIP110854T=CECT 9185T).


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Publication – Real-time whole-genome sequencing for surveillance of Listeria monocytogenes, France.

EVENT : C3BI Publication

Real-time whole-genome sequencing for surveillance of Listeria monocytogenes, France.


Main speaker : , from Date : 19/07/2017 at Location : ,Institut Pasteur, Paris


During 2015-2016, we evaluated the performance of whole-genome sequencing (WGS) as a routine typing tool. Its added value for microbiological and epidemiologic surveillance of listeriosis was compared with that for pulsed-field gel electrophoresis (PFGE), the current standard method. A total of 2,743 Listeria monocytogenes isolates collected as part of routine surveillance were characterized in parallel by PFGE and core genome multilocus sequence typing (cgMLST) extracted from WGS. We investigated PFGE and cgMLST clusters containing human isolates. Discrimination of isolates was significantly higher by cgMLST than by PFGE (p<0.001). cgMLST discriminated unrelated isolates that shared identical PFGE profiles and phylogenetically closely related isolates with distinct PFGE profiles. This procedure also refined epidemiologic investigations to include only phylogenetically closely related isolates, improved source identification, and facilitated epidemiologic investigations, enabling identification of more outbreaks at earlier stages. WGS-based typing should replace PFGE as the primary typing method for L. monocytogenes.


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Training – C3BI Hands-on NGS course Hong-Kong 2017

EVENT : C3BI Training

C3BI Hands-on NGS course Hong-Kong 2017


Main speaker : C3BI Training, from Institut Pasteur Date : 06/11/2017 at 09:00 am Location : Other – HKU-Pasteur Research Pole


This theoretical and practical course is aimed at researchers who would like to get the most out of their Next Generation Sequencing datasets. We will tackle several topics, encompassing theoretical NGS approaches and statistical analysis of NGS data. Ultimately, we want this course to be of immediate value to the students. The first week of this course (Nov 6th – 10th) will be devoted to theory and practical examples for a broad audience, while the second week (Nov 13th – 17th) will be dedicated to practical analysis and hands-on for a selected group of participants. Prospective students when registering can apply for the first theoretical week only or for both weeks. Students applying for the hands-on section will be selected based on their data and the analyses they wish to perform. The course will be free for participants coming from the Institut Pasteur International Network, whereas all other students will pay 1000HKD if they assist to the first week and, 2000HKD if they take the whole course. The course will be held at the University of Hong-Kong. The official language for the theoretical and hands-on session will be English. This hands-on NGS course is open to the whole Pasteur International Network, Hong- Kong Universities and Research Centers.

Please fill the application form HERE, and send your CV and 1-2 letters of recommendation to hku-pasteur@hku.hk

Deadline for applications: September 1st, 2017 (midnight Paris time) For more information, please contact the course secretariat at hku-pasteur@hku.hk
Course Documents

Publication – Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain.

EVENT : C3BI Publication

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain.


Main speaker : , from Date : 01/05/2017 at Location : ,Institut Pasteur, Paris


An atypically large outbreak of Elizabethkingia anophelis infections occurred in Wisconsin. Here we show that it was caused by a single strain with thirteen characteristic genomic regions. Strikingly, the outbreak isolates show an accelerated evolutionary rate and an atypical mutational spectrum. Six phylogenetic sub-clusters with distinctive temporal and geographic dynamics are revealed, and their last common ancestor existed approximately one year before the first recognized human infection. Unlike other E. anophelis, the outbreak strain had a disrupted DNA repair mutY gene caused by insertion of an integrative and conjugative element. This genomic change probably contributed to the high evolutionary rate of the outbreak strain and may have increased its adaptability, as many mutations in protein-coding genes occurred during the outbreak. This unique discovery of an outbreak caused by a naturally occurring mutator bacterial pathogen provides a dramatic example of the potential impact of pathogen evolutionary dynamics on infectious disease epidemiology.


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Publication – Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation

EVENT : C3BI Publication

Proteome remodelling by the stress sigma factor RpoS/σS in Salmonella: identification of small proteins and evidence for post-transcriptional regulation


Main speaker : , from Date : 01/05/2016 at Location : ,Institut Pasteur, Paris


The RpoS/σS sigma subunit of RNA polymerase is the master regulator of the general stress response in many Gram-negative bacteria. Extensive studies have been conducted on σS-regulated gene expression at the transcriptional level. In contrast, very limited information regarding the impact of σS on global protein production is available. In this study, we used a mass spectrometry-based proteomics approach to explore the wide σS-dependent proteome of the human pathogen Salmonella enterica serovar Typhimurium. Our present goals were twofold: (1) to survey the protein changes associated with the ΔrpoS mutation and (2) to assess the coding capacity of σS-dependent small RNAs. Our proteomics data, and complementary assays, unravelled the large impact of σS on the Salmonella proteome, and validated expression and σS regulation of twenty uncharacterized small proteins of 27 to 96 amino acids. Furthermore, a large number of genes regulated at the protein level only were identified, suggesting that post-transcriptional regulation is an important component of the σS response. Novel aspects of σS in the control of important catabolic pathways such as myo-inositol, L-fucose, propanediol, and ethanolamine were illuminated by this work, providing new insights into the physiological remodelling involved in bacterial adaptation to a non-actively growing state.


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Publication – Molecular characterization of Chlamydia pneumoniae associated to atherosclerosis.

EVENT : C3BI Publication

Molecular characterization of Chlamydia pneumoniae associated to atherosclerosis.


Main speaker : , from Date : 13/04/2017 at Location : ,Institut Pasteur, Paris


Chlamydia pneumoniae is a respiratory pathogen associated with chronic inflammatory diseases such as asthma and atherosclerosis, and its detection in human carotid and coronary atheroma suggests some support for its involvement in atherogenesis. The main objective of our study was to evaluate the association between Chlamydia pneumoniae and atherosclerosis in Moroccan patients through a case/control approach and detected strain genotyping. A total of 137 cases and 124 controls were enrolled, nested PCR was performed for Chlamydia pneumoniae screening of the peripheral blood mononuclear cells (PBMCs) of both cases and controls as well as atheroma plaques from 37 cases, and positive samples were subjected to sequencing for genotyping and phylogenetic analysis. The results showed 54% and 18%, respectively, for positivity in cases and control PBMCs and 86.5% in atheroma plaques, the difference being significant between the two groups (p<0.001, ORa = 8.580, CI, 95% [3.273-22.491]). Strain sequence analyses showed more than 98% similarity with human reference strains, and revealed various genotypes. This study supports the involvement of Chlamydia pneumoniae in atherosclerosis in the studied population and genotyping revealed that detected strains were identical to human strains circulating worldwide.


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Publication – Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes

EVENT : C3BI Publication

Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes


Main speaker : , from Date : 11/10/2016 at Location : ,Institut Pasteur, Paris


Listeria monocytogenes (Lm) is a major human foodborne pathogen. Numerous Lm outbreaks have been reported worldwide and associated with a high case fatality rate, reinforcing the need for strongly coordinated surveillance and outbreak control. We developed a universally applicable genome-wide strain genotyping approach and investigated the population diversity of Lm using 1,696 isolates from diverse sources and geographical locations. We define, with unprecedented precision, the population structure of Lm, demonstrate the occurrence of international circulation of strains and reveal the extent of heterogeneity in virulence and stress resistance genomic features among clinical and food isolates. Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is low (∼2.5 × 10−7 substitutions per site per year, as inferred from the core genome) and that major sublineages (corresponding to so-called ‘epidemic clones’) are estimated to be at least 50–150 years old. This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology.


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Protein superfamily evolution: algorithms and applications

Kimmen Sjölander will present “Protein superfamily evolution: algorithms and applications” in Institut Pasteur, Paris #C3BISeminars 22 Oct15

EVENT : C3BI Seminars – Large audience

Protein superfamily evolution: algorithms and applications


Speaker : Kimmen Sjölander, Professor from Department of Bioengineering, University of California, Berkeley  Time : 02:00 pm Starting Date : 22/10/2015

Location : Retrovirus room – LWOFF (22) ,Institut Pasteur, Paris


Protein superfamilies evolve through diverse mechanisms, including insertions, deletions, point mutations, gene duplications and domain architecture rearrangements.   Each of these events can modify the function or structure of the encoded protein. It is not surprising, therefore, that bioinformatics algorithms for virtually every conceivable task depend on accurately reconstructed phylogenetic trees.    In this talk, I will present the SATCHMO (Simultaneous Alignment and Tree Construction using Hidden Markov mOdels) algorithm. SATCHMO is designed to handle extreme levels of sequence and structural divergence, using Hidden Markov Models and other statistical modeling techniques to model the conserved structure within nested subgroups, and HMM-HMM scoring and alignment to construct a hierarchical tree and output a multiple sequence alignment. On benchmark datasets of structurally aligned proteins, SATCHMO outperforms MUSCLE, MAFFT, and ClustalW algorithms.    In the second half of this talk, I will present phylogenomic methods for ortholog identification. Ortholog identification is fundamental to phylogenetic tree estimation as well as automatic function prediction. While most standard orthology prediction methods employ computationally efficient graph-based approaches, their accuracy is generally lower than phylogenomic approaches.   Benchmark experiments using the TreeFam dataset show the superior performance of our methods, particularly in cases where proteins contain “promiscuous” domains.


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