Multilocus sequence typing supports the hypothesis that cow- and human-associated Salmonella isolates represent distinct and overlapping populations

Abstract

A collection of 179 human and 156 bovine clinical Salmonella isolates obtained from across New York state over the course of 1 year was characterized using serotyping and a multilocus sequence typing (MLST) scheme based on the sequencing of three genes (fimA, manB, and mdh). The 335 isolates were differentiated into 52 serotypes and 72 sequence types (STs). Analyses of bovine isolates collected on different farms over time indicated that specific subtypes can persist over time on a given farm; in particular, a number of farms showed evidence for the persistence of a specific Salmonella enterica serotype Newport sequence type. Serotypes and STs were not randomly distributed among human and bovine isolates, and selected serotypes and STs were associated exclusively with either human or bovine sources. A number of common STs were geographically widespread. For example, ST6, which includes isolates representing serotype Typhimurium as well as the emerging serotype 4,5,12:i:-, was found among human and bovine isolates in a number of counties in New York state. Phylogenetic analyses supported the possibility that serotype 4,5,12:i:- is closely related to Salmonella serotype Typhimurium. Salmonella serotype Newport was found to represent two distinct evolutionary lineages that differ in their frequencies among human and bovine isolates. A number of Salmonella isolates carried two copies of manB (33 isolates) or showed small deletion events in fimA (nine isolates); these duplication and deletion events may provide mechanisms for the rapid diversification of Salmonella surface molecules. We conclude that the combined use of an economical three-gene MLST scheme and serotyping can provide considerable new insights into the evolution and transmission of Salmonella.

FIG. 1.

Map of New York and Vermont counties where Salmonella isolates were obtained. The map was drawn using MapViewer 4.01 (Golden Sofware, Inc., Golden, CO). County codes are as follows: Alb, Albany; Brx, Bronx; Brm, Broome; Cat, Cattaraugus; Cay, Cayuga; Cha, Chautauqua; Cmg, Chemung; Cno, Chenango; Cvt, Chittenden, VT; Cli, Clinton; Cor, Cortland; Del, Delaware; Dut, Dutchess; Eri, Erie; Fra, Franklin; Fvt, Franklin, VT; Gen, Genesee; Kin, Kings; Lvt, Lamoille, VT; Lew, Lewis; Liv, Livingston; Mon, Monroe; Nas, Nassau; New, New York; Nia, Niagara; One, Oneida; Ono, Onondaga; Ont, Ontario; Ora, Orange; Orl, Orleans; Osw, Oswego; Ots, Otsego; Put, Putnam; Ren, Rensselaer; Sar, Saratoga; Sch, Schenectady; Sen, Seneca; Stl, St. Lawrence; Ste, Steuben; Suf, Suffolk; Tom, Tompkins; Uls, Ulster; Unk, Unkown; War, Warren; Was, Washington; Way, Wayne; Wes, Westchester; and Wyo, Wyoming.

FIG. 2.

Phylogenetic trees based on Salmonella fimA (A) and mdh (B) gene sequences. Neighbor-joining trees were built in PAUP* using one representative isolate for each sequence type, including STs previously described by Sukhnanand et al. (49), which were not represented among the isolates found here (these STs are indicated by a *). ML trees (not shown) displayed similar clusterings and topologies. Bootstrap analyses were performed using 5,000 replications, and bootstrap values >50 are indicated. M indicates STs representing isolates that contain a manB gene duplication; the branch labeled as “clade 1” represents a number of related STs, including STs (ST52 to ST57, ST63, and ST67 in the mdh tree) that correspond to isolates with two manB copies, indicating a common ancestral event that was responsible for the two manB copies found in these isolates. D1, D2, and D3 indicate STs representing isolates that contain fimA deletion types D1 through D3 (Table 6). STs representing the two distinct Salmonella serotype Newport groups (designated types A and B) are marked by circles or boxes and the respective type.