The Mycoplasma conjunctivae genome sequencing, annotation and analysis

<p>Abstract</p> <p>Background</p> <p>The mollicute <it>Mycoplasma conjunctivae </it>is the etiological agent leading to infectious keratoconjunctivitis (IKC) in domestic sheep and wild caprinae. Although this pathogen is relatively benign for domestic animals treated by antibiotics, it can lead wild animals to blindness and death. This is a major cause of death in the protected species in the Alps (e.g., <it>Capra ibex</it>, <it>Rupicapra rupicapra</it>).</p> <p>Methods</p> <p>The genome was sequenced using a combined technique of GS-FLX (454) and Sanger sequencing, and annotated by an automatic pipeline that we designed using several tools interconnected via PERL scripts. The resulting annotations are stored in a MySQL database.</p> <p>Results</p> <p>The annotated sequence is deposited in the EMBL database (<ext-link ext-link-type="embl" ext-link-id="FM864216">FM864216</ext-link>) and uploaded into the mollicutes database MolliGen <url>http://cbi.labri.fr/outils/molligen/</url> allowing for comparative genomics.</p> <p>Conclusion</p> <p>We show that our automatic pipeline allows for annotating a complete mycoplasma genome and present several examples of analysis in search for biological targets (e.g., pathogenic proteins).</p

Short Term Evolution of a Highly Transmissible Methicillin-Resistant Staphylococcus aureus Clone (ST228) in a Tertiary Care Hospital

Staphylococcus aureus is recognized as one of the major human pathogens and is by far one of the most common nosocomial organisms. The genetic basis for the emergence of highly epidemic strains remains mysterious. Studying the microevolution of the different clones of S. aureus is essential for identifying the forces driving pathogen emergence and spread. The aim of the present study was to determine the genetic changes characterizing a lineage belonging to the South German clone (ST228) that spread over ten years in a tertiary care hospital in Switzerland. For this reason, we compared the whole genome of eight isolates recovered between 2001 and 2008 at the Lausanne hospital. The genetic comparison of these isolates revealed that their genomes are extremely closely related. Yet, a few more important genetic changes, such as the replacement of a plasmid, the loss of large fragments of DNA, or the insertion of transposases, were observed. These transfers of mobile genetic elements shaped the evolution of the ST228 lineage that spread within the Lausanne hospital. Nevertheless, although the strains analyzed differed in their dynamics, we have not been able to link a particular genetic element with spreading success. Finally, the present study showed that new sequencing technologies improve considerably the quality and quantity of information obtained for a single strain; but this information is still difficult to interpret and important investments are required for the technology to become accessible for routine investigations

Draft Genome sequence of the virulent avibacterium paragallinarum serotype a strain JF4211 and identification of two toxins

Avibacterium paragallinarum is an important pathogen of chicken livestock causing infectious coryza. Here, we report the draft genome sequence of the virulent A. paragallinarum serotype A strain JF4211 (2.8 Mbp and G+C content of 41%) and the two toxin operons discovered from the annotation of the genome

Draft genome sequence of the virulent Clostridium chauvoei reference strain JF4335

Clostridium chauvoei is the etiological agent of blackleg, a disease of cattle and sheep with high mortality rates, causing severe economic losses in livestock production. Here, we report the draft genome sequence of the virulent C. chauvoei strain JF4335 (2.8 Mbp and 28% G+C content) and the annotation of the genome

Draft Genome Sequence of the Virulent Clostridium chauvoei Reference Strain JF4335

Clostridium chauvoei is the etiological agent of blackleg, a disease of cattle and sheep with high mortality rates, causing severe economic losses in livestock production. Here, we report the draft genome sequence of the virulent C. chauvoei strain JF4335 (2.8 Mbp and 28% G+C content) and the annotation of the genome

Major differences observed between the eight isolates.

<p>A difference is considered as major when it affected more than three base pairs. The position of the differences is given relative to the alignment of the eight isolates. The presence of the difference is indicated for each isolate by a cross. The type of difference (deletions, insertions or other) is described. If the difference occurred in a non-coding region it was labeled by a NC and by C when it occurred in a coding region. Finally the region or gene affected by the variation is given.</p

MRSA survey at the tertiary care hospital of Lausanne.

<p>Molecular typing was performed by Pulsed Field Gel Electrophoresis (PFGE) until 2005 and then by Double Locus Sequence Typing (DLST; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038969#pone.0038969-Kuhn1" target="_blank">[51]</a>). A. Trimestral incidence of patients with MRSA between 1999 and 2009. The four main lineages of MRSA encountered at the hospital are labeled by colors; the ST228 in red, the ST105 in violet, the ST45 in green and the ST8 in yellow. The other lineages, less common at the hospital, are in black. B. Trimestral incidence of patients with MRSA of clone ST228 at the University hospital of Lausanne between 1999 and 2009. A subset of MRSA detected between 2008 and 2009 were randomly selected for PFGE typing. The four most common pulsotypes (Da, Db,Dc and Dd) were labeled in red-like colors. C. PFGE profile of the eight isolates selected for the genome comparison. Among these eight isolates, we selected the four most common pulsotypes described in B. The eight pulsotypes were bordered by a marker (M) corresponding to the restriction of the reference strain NCTC 8325.</p

RaxML phylogeny based on the SNPs obtained after the alignment of the core genome.

<p>A. In this analysis, the strain N315 was included and used as outgroup. B. Same analysis as in A with bootstrap values given for each node. Nodes that were under the 50% majority rule were collapsed. The tree was rooted with N315 but the distance between this strain and the other was shortened to focus on the relationships between the eight isolates. C. Phylogeny based on the SNPs of the core genome based on the comparison of the eight isolates. D. Mapping of the MGEs and major differences observed between the different isolates onto the phylogenetic tree. Plasmids are represented by circle. The light blue and green circles represent the plasmids that are closely related to the published plasmid SAP064A and pUSA03, respectively. The black trait at the left side of the plasmids represents the presence of the mercuric operon whereas those on the right represent insertions of IS elements. The purple square illustrates the presence of an element of phage of about 18’500 bp. The smaller symbols describe the genetic variations described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038969#pone-0038969-t002" target="_blank">Table 2</a>. Circles were used for deletions, triangles for insertions and squares for other types of modifications. The numbers within each symbol correspond to the genetic variation described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038969#pone-0038969-t002" target="_blank">Table 2</a>. The symbols are white when the difference is unique to one isolate and colored when it is shared between different isolates.</p