Differential single nucleotide polymorphism-based analysis of an outbreak caused by Salmonella enterica serovar Manhattan reveals epidemiological details missed by standard pulsed-field gel electrophoresis.
Erika ScaltritiDavide SasseraFrancesco ComandatoreMarina MorgantiCarmen MandalariStefano GaiarsaClaudio BandiGianguglielmo ZehenderLuca BolzoniGabriele CasadeiStefano PongoliniPublished in: Journal of clinical microbiology (2015)
We retrospectively analyzed a rare Salmonella enterica serovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients (n=15) and food, feed, animal, and environmental sources (n=24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB_BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system.
Keyphrases
- genetic diversity
- genome wide
- endothelial cells
- human health
- machine learning
- dna methylation
- ejection fraction
- public health
- newly diagnosed
- genome wide association
- deep learning
- copy number
- risk assessment
- induced pluripotent stem cells
- high throughput
- wound healing
- hyaluronic acid
- patient reported outcomes
- drug induced
- life cycle