Biology subjects

Clavijo, M. J.

Publications and source records attributed to Clavijo, M. J..

2 recordsLinked to original sources

bioRxiv2026

Population genomics of Actinobacillus pleuropneumoniae reveals lineage-associated K:O antigen and Apx toxin diversity

Actinobacillus pleuropneumoniae (APP) is the causative agent of porcine pleuropneumonia, causing high mortality and morbidity and substantial economic losses in the swine industry. Nineteen capsular (K) serotypes, defined by variation in capsular polysaccharide (CPS) biosynthesis loci, ten O serotypes, defined by variation in lipopolysaccharide (LPS) biosynthesis loci, characteristic Apx toxin profiles, and genomic diversity have been increasingly described; however, relationships among genomic lineage, surface antigen genotype, and Apx toxin repertoire remain incompletely resolved. Here, we analyzed 328 APP genomes, including 153 newly sequenced isolates and 175 public genomes from 21 countries. Core-genome SNP phylogeny and FastBAPS identified 23 genomic lineages. Nineteen capsular K types and 10 O-antigen types formed 26 K:O genotypes, of which 24 were restricted to a single lineage. Adjusted Wallace analysis showed greater concordance of K:O genotype with lineage than K type alone (0.881 versus 0.759), and with ApxI, ApxII and ApxIII genotype (0.949 versus 0.787). ApxIVA related sequence was detected in all genomes, while 56 complete loci revealed recurrent length variation within the N-terminus or the RTX repeat rich region and an additional divergent ApxIVA related homolog. In conclusion, our comprehensive population genomic study gives a more informative picture of APP genomics and virulence-associated diversity, providing a useful genomic basis for future diagnostic test and vaccine development.

genomics↗

bioRxiv2023

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs

The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species this can affect the health of humans as well as livestock. Here we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realised.

evolutionary biology↗