Isolation of Salmonella enterica serovar Agona strains and their similarities to strains derived from a clone caused a serovar shift in broilers

Abstract

Salmonella enterica serovar Agona strains isolated from human cases were compared to strains that were derived from a clone caused a serovar shift in broilers. Pulsed field gel electrophoresis (PFGE) analysis with XbaI or BlnI digestion showed that three of seven strains from human case strains and most of the 81 strains from broilers were clustered in single complex in a minimum spanning tree (MST) reconstructed from the PFGE data. All the strains from human cases and 22 randomly selected strains from broilers were also analyzed by whole genome sequencing (WGS). Analysis of single nucleotide polymorphism (SNP) in the S. Agona core genes showed that four strains from human cases and all the strains from broilers were clustered in a maximum likelihood phylogenetic tree (ML tree) and an MST. These results indicated that the strains derived from the clone caused the serovar shift had already spread to humans. PFGE analysis with XbaI showed that four strains from broilers did not cluster with the other strains in an MST, though all those strains clustered in an ML tree and an MST reconstructed from SNP data. Moreover, three strains from broilers did not cluster in an MST reconstructed from PFGE with BlnI digestion, though those strains clustered in an ML tree and an MST reconstructed from SNP data. Therefore, it was suggested that S. Agona strains derived from a particular clone could not be traced by PFGE analysis but can be investigated by WGS analysis.

Characterization of Salmonella Isolates from Wastewater Treatment Plant Influents to Estimate Unreported Cases and Infection Sources of Salmonellosis

“…Here, all isolates from two each of sewage and human samples, belonging to this serotype, were concurrently identified in June 2019 (Table 3), and their PFGE patterns were indistinguishable from each other (Figure 1c). Moreover, serovar Agona strain 14-8, which was isolated from human and clustered with the isolates from broilers in the Yamanashi Prefecture using whole-genome sequencing [24], was closely related to the isolates from two sewage and four human samples (Figure 1a). Murakami et al [36] and Torii et al [25] pointed out that the strains clustered with strain 14-8 were rarely obtained from broilers, other retail poultry, or humans in other regions.…”

“…To estimate the sources of the isolates from sewage, the serovar Agona strain, designated as 14-8, which was isolated from a human in 2014 and clustered with strains isolated from broilers using PFGE analysis and whole-genome sequencing [24,25], was also analyzed. The PFGE pattern of the 14-8 strain was closely related to those of two and four isolates from sewage and humans, respectively, and the antimicrobial resistance pattern was consistent with these six isolates (Figure 1a).…”

Genetic characteristics of emerging <i>Salmonella enterica</i> serovar Agona strains isolated from humans in the prior period to occurrence of the serovar shift in broilers

“…In addition, in another study, we showed that S . Agona strains isolated from broiler chickens had highly similar genetic profiles, as determined by pulsed field gel electrophoresis (PFGE) analyses and whole genome sequence (WGS) analyses [12]. These results suggested that the serovar shift clone had emerged in the broiler-raising farms, and such a shift could change the incidence of Salmonella infections in humans [12].…”

“…Two strains isolated from sporadic human cases in Yamanashi prefecture were also investigated (Supplementary Table 1). The molecular epidemiological analysis of the strains in this study was done by PFGE analyses with XbaI or BlnI DNA digests as previously described [12]. Minimum spanning tree (MST) analysis was carried out using the PFGE pattern data obtained in this study and the PFGE data of the serovar shift clone in our previous study [12] using BioNumerics Ver.…”

“…The molecular epidemiological analysis of the strains in this study was done by PFGE analyses with XbaI or BlnI DNA digests as previously described [12]. Minimum spanning tree (MST) analysis was carried out using the PFGE pattern data obtained in this study and the PFGE data of the serovar shift clone in our previous study [12] using BioNumerics Ver. 5.1 (Applied Maths, Saint-Martens-Latem, Belgium) and the same conditions as previously described [12].…”