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 realized.

Emerging Zoonotic Influenza A Virus Detection in Myanmar: Surveillance Practices and Findings.

We describe 2-season, risk-based, virological surveillance for zoonotic avian influenza in Myanmar and report the first detection of influenza A subtypes H5N6 and H9N2 in Myanmar. The study focused mainly on the live bird markets in border townships, where illegal poultry importation from China usually takes place. The objective was to enhance early warning for low pathogenic avian influenza A(H7N9) incursion. The study followed the guidelines of the Food and Agriculture Organization (FAO) of the United Nations for influenza A(H7N9) surveillance in uninfected countries. The sampling strategy was risk-based at all sampling levels. Sample collection and laboratory analysis were carried out with the government of the Union of the Republic of Myanmar. Laboratory testing was according to a previously published FAO laboratory protocol and algorithm designed to detect a range of influenza A subtypes. Challenges to implementation are outlined. The study provided evidence that the H7N9 subtype had not entered Myanmar but detected other subtypes, including H5N6 and H9N2. Although there were logistical difficulties associated with nation-related issues, the results highlight the importance and feasibility of this risk-based active surveillance, which should be urgently established in other countries, especially those located at the east-southeast influenza epicenter.