Whole-Genome Sequencing ofSalmonellaMississippi and Typhimurium Definitive Type 160, Australia and New Zealand

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.

Phylogeographic Clustering Suggests that Distinct Clades of Salmonella enterica Serovar Mississippi Are Endemic in Australia, the United Kingdom, and the United States

“…Similar phylogeographic relationships have been observed among other Salmonella serovars isolated from different geographic locations within the same country, including S. Typhimurium ( 33 ), S. Cerro ( 34 ), and S. Dublin ( 35 ), as well as between countries (e.g., S. Kentucky [ 36 ], S. Dublin [ 37 ], S. Typhi [ 38 ], and S. Typhimurium [ 39 ]). Ford and colleagues ( 16 ) also observed that S. Mississippi isolates from New Zealand (excluded from our analyses) represented a distinct phylogenetic clade separate from all Australian isolates, suggesting that there are likely additional phylogenetic clades of S. Mississippi outside those characterized here. Similarly, clade Bii S. Mississippi, which contained just 7 isolates from the United Kingdom, may also represent a distinct, geographically isolated clade representing a different region within the United Kingdom.…”

“…In this study, we describe the diversity of the geographically associated clades of S. Mississippi, which evolved from two separate MRCAs from serovars in clade B and clade A section Typhi. While infections with S. Mississippi are common in regions in the United States ( 14 , 18 ) and Australia ( 16 , 17 ), there were few reports about S. Mississippi in the United Kingdom ( 25 ). Gene presence/absence comparisons suggested that differentiation among isolates within the major clades is driven by the acquisition/loss of mobile elements such as prophage (clades Ai and Aii) and integration/conjugation elements (clade Bii).…”

“…Similarly, some clades of the polyphyletic serovar S. Montevideo are associated with cattle, while other S. Montevideo clades include isolates from a broader range of hosts ( 30 ). In a recent phylogenetic study characterizing S. Mississippi isolates from Australia, human clinical isolates clustered closely with isolates from livestock (e.g., ovine, avian, caprine, and bovine), water, and domestic (e.g., feline, canine, and alpaca) and wild (e.g., platypus, lizard, kangaroo, and wombat) animals, suggesting that clade Aii Mississippi isolates have a broad host range ( 16 ). Conversely, only three nonhuman S. Mississippi isolates were classified into clades Ai, Bi, and Bii; these isolates were from a horse, a dog, and an unidentified environmental source (all clade Ai) (see Data Set S2 in the supplemental material).…”

“… S. enterica serovar Mississippi was first isolated from a stool sample collected from a food handler in the state of Mississippi in the United States and was confirmed as a new serovar in 1943 ( 13 ). S. Mississippi continues to be an important cause of human salmonellosis, particularly in the southern United States ( 14 , 15 ) as well as Tasmania, Australia ( 16 , 17 ). In the United States, S. Mississippi is the 14th most commonly isolated serovar from human clinical cases ( 18 ), while in Tasmania, S. Mississippi represents the 2nd most commonly isolated serovar, accounting for 37% of all nontyphoidal salmonellosis cases in that state ( 17 ).…”

“…In the United States, S. Mississippi is the 14th most commonly isolated serovar from human clinical cases ( 18 ), while in Tasmania, S. Mississippi represents the 2nd most commonly isolated serovar, accounting for 37% of all nontyphoidal salmonellosis cases in that state ( 17 ). Although an environmental source or reservoir has not been definitively described for S. Mississippi, consumption of contaminated drinking water and contact with wild animals have been reported as risk factors for infection with S. Mississippi in Australia ( 16 , 19 ), while in the United States, infection with S. Mississippi is associated with animal exposure ( 15 ). We previously suggested that S. Mississippi is likely a polyphyletic serovar ( 20 , 21 ), although the overall population structure of isolates within this serovar was unknown.…”