Research Note: Repetitive element–based polymerase chain reaction genotyping improves efficiency of Salmonella surveillance in a model broiler production system

Abstract

The genetic relatedness and antimicrobial susceptibility profiles of Salmonella isolated from poultry and their environment were determined. One broiler breeder flock ( BBF1 ) and 2 broiler flocks ( BF1 and BF2 ) were reared over a 1.75-year period on the same poultry research farm. Hatching eggs were obtained from BBF1 to produce BF1 chicks, while BF2 chicks were progeny of a separate, unsampled broiler breeder flock. BF1 and BF2 were reared in the same housing facilities but 6 mo apart. Salmonella isolates were collected via litter sock sampling (BF1), cecal excision (BF1 and BF2), or cloacal swabs (BBF1). Serotyping identified Salmonella enterica subsp. enterica serovar Altona ( SA ) in BBF1 and S. enterica subsp. enterica serovar Senftenberg ( SS ) in BF1 and BF2. Genotypic fingerprinting was achieved with Rep-PCR using the ( GTG ) 5 primer and revealed sequence homology among Senftenberg isolates from BF1 and BF2. For each isolate, the minimum inhibitory concentration was determined for 27 antimicrobial agents using Sensititre plates with formularies specific to antimicrobials used in poultry production or those used to control gram negative pathogens. Isolates from the 3 flocks were resistant to clindamycin, erythromycin, novobiocin, penicillin, and tylosin tartrate and demonstrated intermediate resistance to azithromycin, florfenicol, and spectinomycin. These data demonstrated that serovar Altona and Senftenberg were harbored by poultry, the latter appeared to persist in broiler flocks, and both serotypes shared similar patterns of antimicrobial susceptibility in an integrated research operation. In the case of multiple Salmonella isolates, combining genotypic fingerprinting methods with serotyping of representative isolates would reduce the number of samples required for serotyping and more clearly identify relatedness of isolates. These methods facilitate effective surveillance in poultry production systems, thus allowing for implementation of precise Salmonella control measures.

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

“…Additional genomic analyses of pathogens can be used to improve the identification, prevention, and research of infectious agents that diminish food animal production and threaten public health. In this case, the characterization of SE_TAU19 could aid in the detection of clones in the broiler supply chain ( 26 ) or the development of SE autogenous vaccines ( 57 ). At the time of publication, there were over 29,000 SE genome assemblies available in the NCBI Sequencing Read Archive (SRA) database ( 58 ).…”

“…was confirmed by either the Biolog GenIII Microplate™ microbial identification system as described by Borst et al ( 24 ) or PCR for the Salmonella -specific invA gene sequence ( 25 ). All isolates were then genotyped using repetitive element-based PCR methods using the (GTG) 5 primer as described by Walker et al ( 26 ). All isolates had identical banding patterns, suggesting clonality.…”

“…A representative clone, SE_TAU19, that was isolated from the yolk sac of a chick from broiler flock A, was used for all downstream experiments. The minimum inhibitory concentration of 27 antimicrobial drugs was determined by microbroth dilution methods according to guidelines defined by the National Antimicrobial Susceptibility Monitoring System (NARMS) ( 26 ). These drugs included 14 antimicrobials tested by NARMS for Gram-negative pathogens (ThermoFisher CMV3AGNF) and 13 drugs specific for treatment of poultry (ThermoFisher AVIAN1F).…”

DNA Extraction- and Amplification-Free Nucleic Acid Biosensor for the Detection of Foodborne Pathogens Based on CRISPR/Cas12a and Argonaute Protein-Mediated Cascade Signal Amplification

“…Therefore, the accurate and early detection of foodborne pathogens plays a key role in averting or reducing the risk of infection. Currently, a variety of methods are used to detect foodborne pathogens, including polymerase chain reaction (PCR), which is considered the gold standard, 3 real-time quantitative PCR (qPCR), 4 lowcost recombinant polymerase amplification, 5 and cyclically mediated isothermal amplification. 6 Unfortunately, these methods rely on the preamplification of upstream targets, and nonspecific amplification signals may result in false positives.…”