Salmonella and Campylobacter in broilers at slaughter age : a possible source for carcasses contamination in Ecuador

Salmonella and Campylobacter are major foodborne pathogens worldwide and are especially prevalent in the poultry meat chain. Although poultry meat is a principal component of the diet in Ecuador, little is known about the presence of these pathogens in this food chain. The aim of this thesis was to collect data about Campylobacter and Salmonella in the broiler meat chain in Ecuador. To fulfill this objective, we assessed the prevalence and characterized these pathogens in broiler batches at slaughter age and studied the contamination dynamics during the slaughter of Campylobacter positive batches in commercial slaughterhouses. Chapter 1 and Chapter 2 focus on Salmonella and Campylobacter, for which samples from 388 and 379 broiler batches respectively were collected and analyzed by genotypic and phenotypic techniques. Salmonella prevalence at batch level was 16.0%. The most common serotype was S. Infantis (83.9%). S. Infantis isolates showed high resistance rates to 12 antibiotics ranging from 57.7% (kanamycin) up to 98.1% (nalidixic acid and sulfamethoxazole). The prevalence of Campylobacter at batch level was 64.1% and C. coli (68.7%) was the most common species. MIC values showed resistance rates above 67% for tetracycline, ciprofloxacin and nalidixic acid. Genotypic characterization of both pathogens demonstrated that they are widely distributed in farms. In Chapter 3, the dynamics of Campylobacter contamination were studied in three slaughterhouses. The impact of evisceration, final washing and water chilling was evaluated by quantifying Campylobacter contamination. No significant differences were found between Campylobacter counts after evisceration and after final washing, denoting a lack of efficiency of this step. In all slaughterhouses, a significant reduction of Campylobacter counts was found after the chilling step. We reported that S. Infantis and C. coli were the most prevalent ones, which differs from what is reported in other Latin American countries. High resistance rates to antibiotics used in human medicine were found in these pathogens. This could be provoked by the extensive use of antimicrobials in poultry production and might pose a human health concern. The attribution of S. Infantis and C. coli to human infections need further research. Evaluation of Campylobacter counts at slaughterhouses showed that final washing and addition of chlorine in chilling water may be used to decrease Campylobacter numbers on carcasses. This thesis represents the first study on the epidemiology of Campylobacter and Salmonella in the poultry meat chain in Ecuador

Molecular characterization of infectious bronchitis virus in laying hen farms located in Tungurahua province, Ecuador

La bronquitis infecciosa aviar genera importantes pérdidas económicas y, si bien la vacunación disminuye dichas mermas, el surgimiento continuo de nuevas cepas virales complica el control de la infección. El objetivo de esta investigación fue caracterizar, mediante técnicas moleculares, las cepas del virus de la bronquitis infecciosa aviar circulantes en explotaciones de gallinas ponedoras de la provincia de Tungurahua, Ecuador. Se trabajó con muestras de hisopados y de órganos de 47 granjas y las secuencias obtenidas fueron comparadas con las correspondientes a 17 vacunas a virus vivo empleadas en la zona. Se encontraron 16 granjas positivas al amplificar la región 5’UTR y un segmento de S1. La construcción de un árbol filogenético mostró que cinco de las secuencias se ubicaron en el mismo clado de las cepas de tipo Massachusetts, linaje GI-1; siete se encontraron en el clado del linaje GI-13 o cepas tipo 793B y cuatro secuencias se agruparon en un clado de cepas tipo Q1, linaje G1-16. Si bien se requieren estudios moleculares más completos en los que se amplifique la totalidad del gen S a fin de obtener datos más concluyentes, se logró determinar que existen tres tipos de cepas circulando en la provincia de Tungurahua, dos posiblemente vacunales y otra de origen desconocido.Avian infectious bronchitis (IBV) generates significant economic losses. While vaccination decreases these losses, new viral strains are continually emerging. The objective of this research was to perform molecular characterization of IBV strains circulating in laying hen farms in Tungurahua province, Ecuador. Swabs and organ samples from 47 farms were collected and sequenced, and results were compared to 17 live vaccines used in the area Sixteen farms were positive for IBV as determined by amplification of the 5'UTR region and a S1 segment. The construction of a phylogenetic tree showed that 5 samples were in the same clade as the Massachusetts-type strains, linage GI-1; 7 samples were in the GI-13 lineage clade of vaccine type 793B strains, and 4 samples were into a clade of Q1 type strains. In conclusion, although studies that include the entire protein S sequence are necessary, we were able to detect three types of strains circulating in the province of Tungurahua, two of which are probably vaccine-derived and one has an unknown origin.Facultad de Ciencias Veterinaria

Molecular characterization of infectious bronchitis virus in laying hen farms located in Tungurahua province, Ecuador

La bronquitis infecciosa aviar genera importantes pérdidas económicas y, si bien la vacunación disminuye dichas mermas, el surgimiento continuo de nuevas cepas virales complica el control de la infección. El objetivo de esta investigación fue caracterizar, mediante técnicas moleculares, las cepas del virus de la bronquitis infecciosa aviar circulantes en explotaciones de gallinas ponedoras de la provincia de Tungurahua, Ecuador. Se trabajó con muestras de hisopados y de órganos de 47 granjas y las secuencias obtenidas fueron comparadas con las correspondientes a 17 vacunas a virus vivo empleadas en la zona. Se encontraron 16 granjas positivas al amplificar la región 5’UTR y un segmento de S1. La construcción de un árbol filogenético mostró que cinco de las secuencias se ubicaron en el mismo clado de las cepas de tipo Massachusetts, linaje GI-1; siete se encontraron en el clado del linaje GI-13 o cepas tipo 793B y cuatro secuencias se agruparon en un clado de cepas tipo Q1, linaje G1-16. Si bien se requieren estudios moleculares más completos en los que se amplifique la totalidad del gen S a fin de obtener datos más concluyentes, se logró determinar que existen tres tipos de cepas circulando en la provincia de Tungurahua, dos posiblemente vacunales y otra de origen desconocido.Avian infectious bronchitis (IBV) generates significant economic losses. While vaccination decreases these losses, new viral strains are continually emerging. The objective of this research was to perform molecular characterization of IBV strains circulating in laying hen farms in Tungurahua province, Ecuador. Swabs and organ samples from 47 farms were collected and sequenced, and results were compared to 17 live vaccines used in the area Sixteen farms were positive for IBV as determined by amplification of the 5'UTR region and a S1 segment. The construction of a phylogenetic tree showed that 5 samples were in the same clade as the Massachusetts-type strains, linage GI-1; 7 samples were in the GI-13 lineage clade of vaccine type 793B strains, and 4 samples were into a clade of Q1 type strains. In conclusion, although studies that include the entire protein S sequence are necessary, we were able to detect three types of strains circulating in the province of Tungurahua, two of which are probably vaccine-derived and one has an unknown origin.Fil: Revelo Cueva, María Del Carmen. Universidad Central del Ecuador; EcuadorFil: Vinueza Burgos, Christian Vinicio. Universidad Central del Ecuador; EcuadorFil: Metz, German Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Microbiología. Cátedra de Virología; Argentina. Centro de Microbiologia Basica y Aplicada (cemiba) ; Facultad de Cs.veterinarias ; Universidad Nacional de la Plata;Fil: Toapanta, Ricardo Lenin. Universidad Central del Ecuador; EcuadorFil: Echeverria, Maria Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Departamento de Microbiología. Cátedra de Virología; Argentina. Centro de Microbiologia Basica y Aplicada (cemiba) ; Facultad de Cs.veterinarias ; Universidad Nacional de la Plata