title: 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.
abstract: 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.
authors: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Sezione di Parma, Parma, Italy.
authors: Erika
authors: E
authors: Scaltriti
authors: Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy.
authors: Davide
authors: D
authors: Sassera
authors: Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy Dipartimento di Scienze Veterinarie e Sanità Pubblica (DIVET), Università degli Studi di Milano, Milan, Italy.
authors: Francesco
authors: F
authors: Comandatore
authors: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Sezione di Parma, Parma, Italy.
authors: Marina
authors: M
authors: Morganti
authors: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Sezione di Parma, Parma, Italy.
authors: Carmen
authors: C
authors: Mandalari
authors: Dipartimento di Scienze Veterinarie e Sanità Pubblica (DIVET), Università degli Studi di Milano, Milan, Italy Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
authors: Stefano
authors: S
authors: Gaiarsa
authors: Dipartimento di Scienze Veterinarie e Sanità Pubblica (DIVET), Università degli Studi di Milano, Milan, Italy.
authors: Claudio
authors: C
authors: Bandi
authors: Dipartimento di Scienze Cliniche L. Sacco, Università degli Studi di Milano, Milan, Italy.
authors: Gianguglielmo
authors: G
authors: Zehender
authors: Direzione Sanitaria - Servizio di Analisi del Rischio, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Parma, Italy.
authors: Luca
authors: L
authors: Bolzoni
authors: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Sezione di Parma, Parma, Italy.
authors: Gabriele
authors: G
authors: Casadei
authors: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Sezione di Parma, Parma, Italy Direzione Sanitaria - Servizio di Analisi del Rischio, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Parma, Italy stefano.pongolini@izsler.it.
authors: Stefano
authors: http://orcid.org/0000-0002-4823-3562
authors: S
authors: Pongolini
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004196:Disease Outbreaks; D016521:Electrophoresis, Gel, Pulsed-Field; D005516:Food Microbiology; D005838:Genotype; D006801:Humans; D007558:Italy / Q000453:epidemiology; D017720:Molecular Epidemiology; D058889:Molecular Typing / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D012189:Retrospective Studies; D012480:Salmonella Infections / Q000453:epidemiology* / Q000382:microbiology; D012481:Salmonella Infections, Animal / Q000453:epidemiology* / Q000382:microbiology; D019779:Salmonella enterica / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification
chemical_list: D004269:DNA, Bacterial
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