First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico

Abstract

Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading all over the world, causing economic losses in the agricultural sector and sporadically infecting humans. Six C. pseudotuberculosis strains were isolated from goats, sheep, and horses with distinct abscess locations. For the first time, Mexican genomes of this bacterium were sequenced and studied in silico. All strains were sequenced using Ion Personal Genome Machine sequencer, assembled using Newbler and SPAdes software. The automatic genome annotation was done using the software RAST and in-house scripts for transference, followed by manual curation using Artemis software and BLAST against NCBI and UniProt databases. The six genomes are publicly available in NCBI database. The analysis of nucleotide sequence similarity and the generated phylogenetic tree led to the observation that the Mexican strains are more similar between strains from the same host, but the genetic structure is probably more influenced by transportation of animals between farms than host preference. Also, a putative drug target was predicted and in silico analysis of 46 strains showed two gene clusters capable of differentiating the biovars equi and ovis: Restriction Modification system and CRISPR-Cas cluster.Electronic supplementary materialThe online version of this article (10.1186/s40793-018-0325-z) contains supplementary material, which is available to authorized users.

Bacteriological, cytological, and molecular investigation of Corynebacterium pseudotuberculosis, mycobacteria, and other bacteria in caseous lymphadenitis and healthy lymph nodes of slaughtered sheep

“…, PLD-F (5′ -ATAA GCGTAAGCAGGGAGCA-3′), and PLD-R2 (5′-ATCA GCGGTGATTGTCTTCCAGG-3′) [8,17,25]. The C. pseudotuberculosis standard strain 1002 was used as positive control.…”

“…Although C. pseudotuberculosis is a primary cause of CL [1,[7][8][9], a group of pyogenic microorganisms, including of zoonotic impact, have also been isolated from sheep with abscess formation on peripheral lymph nodes, e.g., staphylococci (Staphylococcus aureus), Trueperella pyogenes, Pasteurella multocida, and streptococci [5,9]. These organisms are opportunistic in nature, inhabit the skin and mucous membranes, and are transmitted mainly by traumatic skin inoculation or cutaneous wounds, causing lymph nodes aspect that resembles C. pseudotuberculosis-induced infections [5,10], reinforcing the importance of proper diagnosis of the agents that cause lymph node abnormalities in sheep or flocks.…”

“…Caseous lymphadenitis remains a source of significant economic losses in many countries, including reduced yields of meat, milk, and wool, carcass, and skin condemnation; early disposal or culling of infected animals; and death caused by systemic spread of bacteria [1,7,8].…”

“…Traditionally, routine diagnosis of CL in small ruminants has focused on clinical signs, bacteriological cultures, serological approaches, and postmortem examination [5,9], although serological approaches show drawbacks, particularly to orient individual animals for culling programs due to the inability to distinguish between early exposed and sick animals [5,17]. In the last decades, different molecular methods (conventional, real-time, and multiplex PCR, sequencing, DNA-DNA hybridization, matrix-assisted laser desorption-ionization timeoff flight mass spectrometry-MALDI-TOF MS) have been used to confirm conventional diagnosis methods, in addition to investigate the virulence profile, genetic diversity, and geographical distribution of C. pseudotuberculosis strains worldwide [1,2,7,8].…”

CoryneRegNet 7, the reference database and analysis platform for corynebacterial gene regulatory networks

“…CoryneRegNet has served as the reference database of the genus Corynebacterium since 2006 23 . This genus includes organisms with medical, veterinary and biotechnological relevance [24][25][26][27] . While the National Center for Biotechnology Information (NCBI) database contains more than 60 corynebacterial species with fully sequenced and annotated genomes, there are TRNs of only eight of these species available in online databases.…”