Pathogen–host–environment interplay and disease emergence

Engering, Anneke; Hogerwerf, Lenny; Slingenbergh, Jan

Horizontal gene transfer is not restricted to just bacteria but also the fungus Pyrenophora tritici-repentis that causes tan spot in wheat acquired a virulence factor from another plant fungus through gene transfer. 64 Protozoa and helminths may also acquire drug resistance. For example, Plasmodium falciparum with resistance to the malaria drug artemisin recently emerged in southeast Asia and is spreading. 65 Pathogen characteristics pertaining to the transmission ecology play a main role in disease emergence through novel traits within the same host species. Food-, water-and vector-borne transmission, enhanced environmental robustness may assist in the emergence of new disease complexes. For instance, pathogen characteristics that optimize transmission in specific food production chains or host meta-populations may be selected for, and a 'winner takes all' scenario may occur if a new pathogen is much fitter than its progenitors. In each situation, the full trait profile of a pathogen determines what the new disease complex will look like. Sometimes, the more host aggressive pathogens gain fitness through enhanced environmental survival, as transmission from immobilized or dead hosts may still be efficient. [66] [67] [68] Examples of aggressive pathogens featuring environmental robustness include the H5N1 HPAI virus, E. coli bacteria including E. coli O157:H7 and the infectious bursal disease virus. 61, [69] [70] [71] [72] Drivers of emergence of a pathogen with novel traits Drivers of the evolution of pathogens emerging with novel traits comprise the rise in food animal populations, the process of agricultural intensification and global food supply dynamics as well as the extensive use of antimicrobials and vaccines. 27, 59, 66, 73 Food animal production, processing, marketing and distribution have intensified progressively in most industrial countries since the 1950s. 16, 59, 73 Confined animal feeding operations for cattle, and largescale rearing units with poultry and pigs form patches of 'monocultures' in the host landscape mosaic. In these settings, there is a premium going to pathogens circumventing bio-exclusion and other health protection regimens. Also, mass rearing of food animals entails large numbers of genetically-similar animals of the same age (young) and sex, kept in high densities. Rapid population turnover and live animal transport support onward transmission once a pathogen with novel traits has emerged. For example, flocks of free-grazing ducks rotating in rice paddy fields and ending up in live bird markets played an important role in the transmission of H5N1 HPAI. 49, 74, 75 Pathogens with novel traits may find ready access to human hosts via the food chain, through the handling of live animals, via aerosols emitted by animals in the intensive production units, in wet markets, through ingestion of manure contaminated food commodities, or related to waste disposal. 59 One example forms a novel methicillinresistant Staphylococcus aureus strain that emerged in humans in the Netherlands in 2003 and could be traced back to an origin in pig farming. 76 Monoculture fruit, vegetable and crop production provide identical scenarios, generating bulk quantities of food, featuring very little An infectious disease emergence framework A Engering et al 4 genetic diversity and giving rise to the emergence of pathogens with novel traits. 77 One example is the fungus Cochliobolus miyabeanus that destroyed rice crops resulting in th