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

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.

Genome-Based Assessment of Antimicrobial Resistance and Virulence Potential of Isolates of Non-Pullorum/Gallinarum Salmonella Serovars Recovered from Dead Poultry in China

“…According to newly available data, more than 60 billion chickens are consumed annually ( 23 ), highlighting the importance of chicken consumption in the diet of populations across the world. At the same time, poultry farms are considered a favorable biotope for the development of many pathogens like Salmonella , causing huge economic losses for producers ( 6 , 8 , 18 , 24 ). Hence, to provide in-depth data about the AMR and virulence of Salmonella isolates causing poultry death, we used WGS combined with accurate phenotypic assays to analyze a collection of 105 Salmonella isolates recovered from dead poultry between 2008 and 2019, in 95 farms representing all 17 cities of Shandong province.…”

“…Additionally, Wang et al reported the dominance of S. Enteritidis in isolates recovered from dead-in-shell chicken embryos in Northern China ( 25 ). Furthermore, a study performed by the Walker group demonstrated the implication of S. Enteritidis in persistent infections in broiler chickens in North Carolina ( 24 ). Generally, avian salmonellosis has been linked for decades to isolates of S .…”

“…Gallinarum (biovars Gallinarum and Pullorum), which have been eradicated in many developed countries after the establishment of different mitigation strategies ( 26 ). Thus, paratyphoid diseases caused by zoonotic Salmonella serovars, especially S. Enteritidis, have taken place among a major form of salmonellosis in poultry ( 24 ). The traditional S .…”

“…Additionally, we reported high rates of resistance to nalidixic acid (97.14%) and ciprofloxacin (91.43%). In fact, quinolone resistance, especially to the first generation (nalidixic acid), has become a common issue in China and elsewhere ( 24 , 25 , 28 ). It has been noted that feed supplemented with quinolones has been widely used in poultry farms in China ( 29 ), which might exert selective pressure on pathogens, allowing the development of quinolone resistance in many Salmonella serovars.…”

Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: a review

“…A clonal group of S. enteritidis known as SE86, a frequently identified poultry Salmonella isolate in Brazil associated with foodborne outbreaks, has been reported to be resistant to ciprofloxacin (41.9%) and sulfafurazole (75%) [ 121 ]. A persistent septicemia causing S. enteritidis (SE_TAU19) resistant to nalidixic acid and sulfadimethaxine was reported [ 162 ]. Quesada et al [ 130 ] found the mcr-1 gene (colistin resistance) in E. coli and S. enterica from poultry and swine.…”