Patavino, Claudio
(2019)
Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections, [Dissertation thesis], Alma Mater Studiorum Università di Bologna.
Dottorato di ricerca in
Biologia cellulare e molecolare, 31 Ciclo. DOI 10.6092/unibo/amsdottorato/9076.
Documenti full-text disponibili:
|
Documento PDF (English)
- Richiede un lettore di PDF come Xpdf o Adobe Acrobat Reader
Disponibile con Licenza: Salvo eventuali più ampie autorizzazioni dell'autore, la tesi può essere liberamente consultata e può essere effettuato il salvataggio e la stampa di una copia per fini strettamente personali di studio, di ricerca e di insegnamento, con espresso divieto di qualunque utilizzo direttamente o indirettamente commerciale. Ogni altro diritto sul materiale è riservato.
Download (4MB)
|
Abstract
The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technologies has become a widely accepted method for microbiology laboratories in the application of molecular typing, for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome multilocus sequence typing (cgMLST) has not been explored so far. The current study developed an allele-based cgMLST method and compared its performance to that of the genome-wide SNP approach and the traditional multilocus variable-number tandem repeat analysis (MLVA) on a defined sample collection. The data set was comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 isolates with unknown epidemiological status, composed of human and animal samples collected in Italy. The cgMLST scheme generated in this study contained 2,704 targets of the B. melitensis 16M reference genome. We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be 6 loci in the cgMLST and 7 in WGS SNP analysis. Higher phylogenetic distance resolution was achieved with cgMLST and SNP analysis than with MLVA, particularly for strains belonging to the same lineage, thereby allowing diverse and unrelated genotypes to be identified with greater confidence. The application of a cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen, and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.
Abstract
The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technologies has become a widely accepted method for microbiology laboratories in the application of molecular typing, for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome multilocus sequence typing (cgMLST) has not been explored so far. The current study developed an allele-based cgMLST method and compared its performance to that of the genome-wide SNP approach and the traditional multilocus variable-number tandem repeat analysis (MLVA) on a defined sample collection. The data set was comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 isolates with unknown epidemiological status, composed of human and animal samples collected in Italy. The cgMLST scheme generated in this study contained 2,704 targets of the B. melitensis 16M reference genome. We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be 6 loci in the cgMLST and 7 in WGS SNP analysis. Higher phylogenetic distance resolution was achieved with cgMLST and SNP analysis than with MLVA, particularly for strains belonging to the same lineage, thereby allowing diverse and unrelated genotypes to be identified with greater confidence. The application of a cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen, and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.
Tipologia del documento
Tesi di dottorato
Autore
Patavino, Claudio
Supervisore
Dottorato di ricerca
Ciclo
31
Coordinatore
Settore disciplinare
Settore concorsuale
Parole chiave
Brucella melitensis, MLVA, SNP analysis, cgMLST
URN:NBN
DOI
10.6092/unibo/amsdottorato/9076
Data di discussione
3 Aprile 2019
URI
Altri metadati
Tipologia del documento
Tesi di dottorato
Autore
Patavino, Claudio
Supervisore
Dottorato di ricerca
Ciclo
31
Coordinatore
Settore disciplinare
Settore concorsuale
Parole chiave
Brucella melitensis, MLVA, SNP analysis, cgMLST
URN:NBN
DOI
10.6092/unibo/amsdottorato/9076
Data di discussione
3 Aprile 2019
URI
Statistica sui download
Gestione del documento: