Genomic Characterization of a Nalidixic Acid-Resistant Salmonella Enteritidis Strain Causing Persistent Infections in Broiler Chickens.

Grayson K Walker,M Mitsu Suyemoto,Fernando Jimenez,Siddhartha Thakur,Rocio Crespo,Luke B Borst,Laura R Chen,Sesny Gall,Dawn M Hull

doi:10.3389/fvets.2021.725737

Grayson K Walker, M Mitsu Suyemoto + Show 7 more

Open Access

https://doi.org/10.3389/fvets.2021.725737

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Abstract

Virulent strains of Salmonella enterica subsp. enterica serovar Enteritidis (SE) harbored by poultry can cause disease in poultry flocks and potentially result in human foodborne illness. Two broiler flocks grown a year apart on the same premises experienced mortality throughout the growing period due to septicemic disease caused by SE. Gross lesions predominantly consisted of polyserositis followed by yolk sacculitis, arthritis, osteomyelitis, and spondylitis. Tissues with lesions were cultured yielding 59 SE isolates. These were genotyped by Rep-PCR followed by whole-genome sequencing (WGS) of 15 isolates which were clonal. The strain, SE_TAU19, was further characterized for antimicrobial susceptibility and virulence in a broiler embryo lethality assay. SE_TAU19 was resistant to nalidixic acid and sulfadimethoxine and was virulent to embryos with 100% mortality of all challenged broiler embryos within 3.5 days. Screening the SE_TAU19 whole-genome sequence revealed seven antimicrobial resistance (AMR) genes, 120 virulence genes, and two IncF plasmid replicons corresponding to a single, serovar-specific pSEV virulence plasmid. The pef, spv, and rck virulence genes localized to the plasmid sequence assembly. We report phenotypic and genomic features of a virulent SE strain from persistently infected broiler flocks and present a workflow for SE characterization from isolate collection to genome assembly and sequence analysis. Further SE surveillance and investigation of SE virulence in broiler chickens is warranted.

Highlights

Salmonella enterica subsp. enterica is comprised of over 2,500 serovars, including the pathogenic Salmonella enterica subsp. enterica serovar Enteritidis (SE) [1]
All isolates had identical banding patterns, suggesting clonality. This was confirmed for 15 selected isolates from broiler flock A by single nucleotide polymorphism (SNP) phylogenetic analysis using whole-genome sequencing (WGS) of sequenced isolates
Based on culture results from daily necropsy, it was estimated that 37/357 (10%) and 42/274 (15%) of total mortality for flocks A and B was attributable to SE infection and a total of 59 isolates were collected from the flocks

Summary

Introduction

Salmonella enterica subsp. enterica is comprised of over 2,500 serovars, including the pathogenic Salmonella enterica subsp. enterica serovar Enteritidis (SE) [1]. Enterica is comprised of over 2,500 serovars, including the pathogenic Salmonella enterica subsp. Enterica serovar Enteritidis (SE) [1] As it relates to poultry production, SE is best known for its ability to survive on and within eggs despite causing no discernable disease in infected layers [2, 3]. Because of these adaptations, SE is likely the most frequent cause of human salmonellosis globally [4], and investigations of SE today are largely focused on reducing foodborne illness. A fundamental understanding of SE genotypes and virulence mechanisms is essential to developing surveillance, treatment, and control approaches for broiler flocks.

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