Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi. Salmonella enterica subsp. enterica serovar Bovismorbificans str. 3114

Background Non-typhoidal Salmonella (NTS) are an important cause of invasive disease in children and HIV-infected adults in sub-Saharan Africa, causing bacteraemia, neonatal meningitis and septic arthritis. Our NTS collection from Malawi, spanning a six year period (1998 to 2004), showed that amongst isolates of NTS associated with invasive bacteraemia, Salmonella Bovismorbificans (antigen profile 6,8:r:1,5) was the third most common serovar after Typhimurium and Enteritidis. S. Bovismorbificans is an important veterinary pathogen causing salmonellosis in cattle, sheep and horses. It also poses a problem as a zoonotic agent sporadically infecting humans. Methodology Using Next Generation Sequencing technology, the genome of S. Bovismorbificans strain 3114, a paediatric bacteraemia isolate from Malawi, was sequenced. We further investigated the genomes of 13 additional Malawian bacteraemia isolates and four veterinary isolates from the UK, to identify genomic variations. Principal Findings The core genome of S. Bovismorbificans is highly stable, sharing high similarity and co-linearity with that of S. Typhimurium. Three prophage-related regions of difference (RODs), define the major regions of genetic variation between S. Bovismorbificans human bacteraemia isolates from Malawi and veterinary isolates from the UK. Isolates differed further in the carriage of a S. Bovismorbificans virulence plasmid (pVIRBov), which was present in all bacteraemia isolates but absent from three of the four veterinary isolates investigated. Although genome degradation through pseudogene formation was observed in S. Bovismorbificans isolates, the identity of the pseudogenes was different from those identified previously in genome sequenced S. Typhimurium isolates, and there was no clear distinction between Malawi and UK isolates. In contrast to S. Typhimurium, where a distinct MLST type is associated with invasive disease in sub-Saharan Africa, we found that S. Bovismorbificans isolates from Malawi belong to the most common international S. Bovismorbificans Sequence Type, ST-142. Conclusions Differences in the accessory genome of S. Bovismorbificans isolates from Malawi may have contributed to the development of a more specialized pathotype of S. Bovismorbificans ST142 in sub-Saharan Africa.