PRJNA416915
Mannheimia varigena Genome sequencing
Mannheimia varigena is a gram negative bacillus that is pathogenic in ruminants. It has been isolated from pneumonic lungs (Harhay et al., 2015), udder and spleen (Blackall et al., 2002) of cattle. It has also been isolated from bovine meninges and was identified as the cause of fatal bovine meningitis (Catry et al., 2004). However, little is known about this pathogen and its ability to cause disease. So far, there are complete genome sequences available for only four M. varigena isolates which were all isolated from lung necroscopies taken from cattle with shipping fever and sequenced using the PacBio SMRT platform (Harhay et al., 2014). In the current study we used the Oxford Nanopore Technologies nanopore platform to sequence a bovine milk isolate that was identified by a veterinary diagnostic laboratory as Mannheimia haemolytica in March 2017. DNA was extracted and a sequencing library was generated directly (without fragmentation) from 1 µg of the extracted bacterial DNA using the 1D² Sequencing Kit (R9.5) (Oxford Nanopore Technologies). The library was run on a FLO-MIN107 SpotON flowcell on a MinION Mk1B Nanopore sequencer (Oxford Nanopore Technologies) using MinKnow (v1.7.14) software (Oxford Nanopore Technologies) on a lap top (Dell Latitude E6540, 64 bit). Approximately 200,000 sequence reads of up to 400 kb were generated. CANU was used to assemble these long reads into a single contig of 2.18 Mbp. This is the first Mannheimia varigena bovin milk isolate to be fully sequenced.Blackall PJ, Bisgaard M, Stephens CP. 2002. Phenotypic characterisation of Australian sheep and cattle isolates of Mannheimia haemolytica, Mannheimia granulomatis and Mannheimia varigena. Aust Vet J. 80:87-91.Harhay GP, Murray RW, Lubbers B,Griffin D, Koren S, Phillippy AM, Harhay DM, Bono J, Clawson ML, Heaton MP, Chitko-McKown CG, Smith TPL. 2014. Complete closed genome sequences of four Mannheimia varigena isolates from cattle with shipping fever. Genome Announc 2(1) e00088-14.Catry B, Opsomer G, Decostere A, Feyen B, de Kruif A, Haesebrouck F. 2004. Fatal meningitis in a calf caused by Mannheimia varigena. Research in Veterinary Science 77: 187-188 https://doi.org/10.1016/j.rvsc.2004.04.002