Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017

Pightling, Arthur W.; Pettengill, James B.; Luo, Yan; Strain, Errol; Rand, Hugh

doi:10.1099/mic.0.000895

Cited by 3 publications

(3 citation statements)

References 19 publications

(21 reference statements)

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“…Salmonella enterica is a major foodborne pathogen of global importance, and its genomic diversity has been widely studied [67][68][69][70][71][72]. Subspecies I contains more than 1,500 of the total 2,600+ serotypes in the species and is of most importance with respect to human infections [73].…”

Section: Discussionmentioning

confidence: 99%

Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species

Bhandare,

Lawal,

Colavecchio

et al. 2024

Preprint

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Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole genome sequencing data (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb with GC contents be-tween 39.9 and 50.0 %. Two of the phages SB13 and SB28 represent new species Epsep-timavirus SB13 and genera Macdonaldcampvirus, respectively as designated by the In-ternational Committee for the Taxonomy of Viruses (ICTV) as per genome based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the re-maining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I-VI toxin-antitoxin modules or lysogeny genes. Three (SB3, SB15 and SB18) out of the eight phages possessed tailspike proteins. Whole genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, C and seven subclusters (A1, A2, A3, B1, B2, C1 and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use to control the presence of S. enterica in foods.

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Section: Discussionmentioning

confidence: 99%

Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species

Bhandare,

Lawal,

Colavecchio

et al. 2024

Preprint

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“…In total, the five outbreaks resulted in 325 ill persons reported in the U.S. The epidemiologic details and the genetic diversity for some of the isolates recovered from papaya during the 2017 outbreaks have been reported elsewhere (8,24). The purpose of this report is to provide further details regarding the traceback investigation to the source of the contaminated papayas, the extensive laboratory investigation, and the environmental investigations at implicated fields and facilities; we also want to highlight the benefit of partnerships among federal, state, and international partners when investigating foodborne illness outbreaks and prevention activities enacted as a result of these outbreaks.…”

Section: Highlightsmentioning

confidence: 99%

“…A summary of the outbreak clusters with associated non-human isolates as of because in 2017 not all clinical isolates were sequenced, and conversely, there may be additional isolates in the clusters that are not necessarily outbreak-related due to subsequent updates to the database. A more detailed analysis and discussion of FDA's papaya isolates from 2017 can be found elsewhere (24).…”

Section: Traceback Investigation For Outbreaks C and Dmentioning

confidence: 99%

A Series of Papaya-Associated Salmonella Illness Outbreak Investigations in 2017 and 2019: A Focus on Traceback, Laboratory, and Collaborative Efforts

Whitney

McCLURE

Hassan

et al. 2021

Journal of Food Protection

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In 2017 and 2019, five outbreaks of infections from multiple strains of Salmonella linked to the consumption of whole, fresh Maradol papayas were reported in the United States, resulting in 325 ill persons. Traceback, laboratory, and epidemiologic evidence indicated papayas as the likely vehicle for each of these outbreaks and identified the source of papayas. State and FDA laboratories recovered Salmonella from papaya samples from various points of distribution, including at import entry, and conducted serotyping, pulsed-field gel electrophoresis (PFGE), and phylogenetic analyses of whole genome sequencing (WGS) data. Federal and state partners led traceback investigations to determine the source of papayas. Four different suppliers of papayas were linked by traceback and laboratory results to five separate outbreaks of Salmonella infections associated with papayas. In 2017, multiple states tested papaya samples collected at retail, and Maryland and Virginia investigators recovered strains of Salmonella associated with one outbreak. FDA collected 183 papaya samples in 2017, and 11 samples yielded 62 isolates of Salmonella. Eleven serotypes of Salmonella were recovered from FDA papaya samples, and nine serotypes were closely related genetically by PFGE and WGS to clinical isolates of four outbreaks, including the outbreak associated with positive state sample results. Four farms in Mexico were identified and their names were released to the general public, retailers, and foreign authorities. In 2019, FDA collected 119 papaya samples, three of which yielded Salmonella; none yielded the 2019 outbreak strain. Investigators determined that papayas of interest had been sourced from a single farm in Campeche, Mexico through traceback. This information was used to protect public health through public guidance, recalls, and import alerts and helped FDA collaborate with Mexican regulatory partners to enhance the food safety requirements for papayas imported from Mexico.

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Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species

Bhandare,

Lawal,

Colavecchio

et al. 2024

Microorganisms

View full text Add to dashboard Cite

Bacteriophages (phages) are potential alternatives to chemical antimicrobials against pathogens of public health significance. Understanding the diversity and host specificity of phages is important for developing effective phage biocontrol approaches. Here, we assessed the host range, morphology, and genetic diversity of eight Salmonella enterica phages isolated from a wastewater treatment plant. The host range analysis revealed that six out of eight phages lysed more than 81% of the 43 Salmonella enterica isolates tested. The genomic sequences of all phages were determined. Whole-genome sequencing (WGS) data revealed that phage genome sizes ranged from 41 to 114 kb, with GC contents between 39.9 and 50.0%. Two of the phages SB13 and SB28 represent new species, Epseptimavirus SB13 and genera Macdonaldcampvirus, respectively, as designated by the International Committee for the Taxonomy of Viruses (ICTV) using genome-based taxonomic classification. One phage (SB18) belonged to the Myoviridae morphotype while the remaining phages belonged to the Siphoviridae morphotype. The gene content analyses showed that none of the phages possessed virulence, toxin, antibiotic resistance, type I–VI toxin–antitoxin modules, or lysogeny genes. Three (SB3, SB15, and SB18) out of the eight phages possessed tailspike proteins. Whole-genome-based phylogeny of the eight phages with their 113 homologs revealed three clusters A, B, and C and seven subclusters (A1, A2, A3, B1, B2, C1, and C2). While cluster C1 phages were predominantly isolated from animal sources, cluster B contained phages from both wastewater and animal sources. The broad host range of these phages highlights their potential use for controlling the presence of S. enterica in foods.

show abstract

Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017

Cited by 3 publications

References 19 publications

Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species

Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species

A Series of Papaya-Associated Salmonella Illness Outbreak Investigations in 2017 and 2019: A Focus on Traceback, Laboratory, and Collaborative Efforts

Genomic and Phenotypic Analysis of Salmonella enterica Bacteriophages Identifies Two Novel Phage Species

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