Abstract
We used phylogenomic and risk factor data on isolates of Salmonella enterica serovars Mississippi and Typhimurium definitive type 160 (DT160) collected from human, animal, and environmental sources to elucidate their epidemiology and disease reservoirs in Australia and New Zealand. Sequence data suggested wild birds as a likely reservoir for DT160; animal and environmental sources varied more for Salmonella Mississippi than for Salmonella Typhimurium. Australia and New Zealand isolates sat in distinct clades for both serovars; the median single-nucleotide polymorphism distance for DT160 was 29 (range 8–66) and for Salmonella Mississippi, 619 (range 565–737). Phylogenomic data identified plausible sources of human infection from wildlife and environmental reservoirs and provided evidence supporting New Zealand–acquired DT160 in a group of travelers returning to Australia. Wider use of real-time whole-genome sequencing in new locations and for other serovars may identify sources and routes of transmission, thereby aiding prevention and control.
Highlights
We used phylogenomic and risk factor data on isolates of Salmonella enterica serovars Mississippi and Typhimurium definitive type 160 (DT160) collected from human, animal, and environmental sources to elucidate their epidemiology and disease reservoirs in Australia and New Zealand
For sequenced Salmonella Mississippi isolates, the ML tree showed that the isolates from Vanuatu, United States, and New Zealand were distinctly different from the Australia isolates (Figure 3); median single-nucleotide polymorphism (SNP) distance was 619 between Australia and New Zealand isolates (Appendix Figure 1) and 1,625 between Australia and Vanuatu or US isolates
Phylogenomic analysis revealed genetic diversity and persistence of Salmonella Mississippi strains in the environment and animals, suggesting it is endemic with a broad range of host reservoirs in Tasmania that is persisting over time
Summary
We used phylogenomic and risk factor data on isolates of Salmonella enterica serovars Mississippi and Typhimurium definitive type 160 (DT160) collected from human, animal, and environmental sources to elucidate their epidemiology and disease reservoirs in Australia and New Zealand. Sequence data suggested wild birds as a likely reservoir for DT160; animal and environmental sources varied more for Salmonella Mississippi than for Salmonella Typhimurium. A case–control study conducted in 2001 in New Zealand suggested that handling of dead wild birds, contact with persons with diarrheal illness, and ingestion of fast food were associated with illness [12], the relationship between the Tasmania and New Zealand DT160 infections and the relationship between animal and human isolates in Tasmania is unknown. We aimed to use these 2 nontyphoidal S. enterica serovars as case studies to investigate how epidemiologic and genomic data can be integrated to better understand the geographic niche and transmission pathways of these organisms to subsequently improve prevention and control strategies
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