Shotgun genome sequence and population diversity of Mannheimia haemolytica isolates from sheep in South Africa

Abstract

Respiratory disease caused by Mannheimia haemolytica is a major economic and welfare concern in the cattle and small stock industry worldwide. Disease occurs due to the interaction of numerous factors, including weaning stress, shipment, inclement weather, and overcrowding coupled with viral and bacterial infections. The whole genome of M. haemolytica strain Mh10517 was analyzed using an Illumina MiSeq high throughput sequencing platform. The genome size is 2.67 Mb with 2,879 predicted gene sequences. The molecular evolution and relatedness of M. haemolytica was investigated using nucleotide sequence data of seven housekeeping gene fragments from 21 ovine isolates. MEGA version 7.0 genomic workbench was used for alignment and analysis of the nucleotide data sets. For each gene fragment, the sequences were compared and isolates with identical sequences were assigned the same allele number. Results suggested that the 21 isolates belonged to six sequence types (ST) and ST 28 accounted for 33% of the isolates. Neighbour joining method was used to produce dendograms based on the concatenated sequences of the seven loci in multilocus allelic profile. There was significant variation between the number of synonymous and non-synonymous substitutions between each sequence pairs (p=0.018) based on results from the Fisher’s exact test of neutrality of sequence pairs. These preliminary data show substantial sequence variations and this supports the hypothesis that ovine isolates of M. haemolytica are more diverse that what has been reported for isolates from other species. These results will advance studies on various aspects of the biology of M. haemolytica in Africa, and the world at large.