title: Genotyping of Campylobacter coli strains isolated  in Brazil suggests possible contamination amongst  environmental, human, animal and food sources.
abstract: Campylobacter coli and Campylobacter jejuni are two of the most common causative agents of food-borne gastroenteritis in numerous countries worldwide. In Brazil, campylobacteriosis is under diagnosed and under-reported, and few studies have molecularly characterized Campylobacter spp. in this country. The current study genotyped 63 C. coli strains isolated from humans (n512), animals (n521), food (n510) and the environment (n520) between 1995 and 2011 in Brazil. The strains were genotyped using pulsed-field gel electrophoresis (PFGE), sequencing the short variable region (SVR) of the flaA gene ( flaA-SVR) and high-resolution melting analysis (HRMA) of the clustered regularly interspaced short palindromic repeat (CRISPR) locus to better understand C. coli genotypic diversity and compare the suitability of these three methods for genotyping this species. Additionally, the discrimination index (DI) of each of these methods was assessed. Some C. coli strains isolated from clinical and non-clinical origins presented ≥80 % genotypic similarity by PFGE and flaA-SVR sequencing. HRMA of the CRISPR locus revealed only four different melting profiles. In total, 22 different flaA-SVR alleles were detected. Of these, seven alleles, comprising gt1647–gt1653, were classified as novel. The most frequent genotypes were gt30 and gt1647. This distribution reveals the diversity of selected Brazilian isolates in comparison with the alleles described in the PubMLST database. The DIs for PFGE, flaA–SVR sequencing and CRISPR-HRMA were 0.986, 0.916 and 0.550, respectively. PFGE and flaA-SVR sequencing were suitable for subtyping C. coli strains, in contrast to CRISPR-HRMA. The high genomic similarity amongst some C. coli strains confirms the hypothesis that environmental and food sources potentially lead to human and animal contamination in Brazil.
authors.affiliation: Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Av. do Café, s/no, Campus Universitário USP, Ribeirão Preto, SP 14040-903, Brazil.
authors.forename: Carolina N
authors.initials: CN
authors.lastname: Gomes
authors.affiliation: Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Av. do Café, s/no, Campus Universitário USP, Ribeirão Preto, SP 14040-903, Brazil.
authors.forename: Roberto A
authors.initials: RA
authors.lastname: Souza
authors.affiliation: Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Av. do Café, s/no, Campus Universitário USP, Ribeirão Preto, SP 14040-903, Brazil.
authors.forename: Jaqueline
authors.initials: J
authors.lastname: Passaglia
authors.affiliation: Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz, Pavilhão Rocha Lima, sala 516, Av. Brasil, 4365, Rio de Janeiro, RJ 21040-900, Brazil.
authors.forename: Sheila S
authors.initials: SS
authors.lastname: Duque
authors.affiliation: Instituto Adolfo Lutz de Ribeirão Preto, Rua Minas, 877 Ribeirão Preto, SP 14085-410, Brazil.
authors.forename: Marta I C
authors.initials: MIC
authors.lastname: Medeiros
authors.affiliation: Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Av. do Café, s/no, Campus Universitário USP, Ribeirão Preto, SP 14040-903, Brazil.
authors.forename: Juliana P
authors.initials: JP
authors.lastname: Falcão
mesh_terms: D000483:Alleles; D000818:Animals; D015373:Bacterial Typing Techniques / Q000379:methods*; D001938:Brazil; D002169:Campylobacter Infections; D017000:Campylobacter coli / Q000145:classification* / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics; D016521:Electrophoresis, Gel, Pulsed-Field; D004783:Environmental Microbiology; D005408:Flagellin / Q000235:genetics; D005506:Food Contamination; D005516:Food Microbiology; D005517:Foodborne Diseases / Q000382:microbiology; D056426:Genetic Loci; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D005408:Flagellin; C067138:flaA protein, bacteria