Ciencia e Ingeniería en Alimentos y Biotecnología

URI permanente para esta comunidadhttp://repositorio.uta.edu.ec/handle/123456789/412

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Evaluación de la diversidad genómica y las relaciones filogenéticas de Salmonella enterica aislada a partir de pollo comercializado en mercados de la ciudad de Ambato mediante secuenciación de Tercera Generación
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-07)
Constante Chimborazo, Sasha Carolina
;
Calero Cáceres, William Ricardo
Salmonellosis is one of the most important foodborne diseases worldwide, with S. enterica being one of the main pathogens associated with the poultry production chain. In Ecuador, the commercialization of chicken in traditional markets constitutes a potential source of exposure, especially in cities such as Ambato, where information on the genomic characterization of circulating strains is limited. The present study evaluated the genetic diversity and phylogenetic relationships of 12 S. enterica strains isolated from chicken carcasses and giblets marketed in Ambato markets. The strains were sequenced using Oxford Nanopore technology and characterized through bioinformatics tools to determine serotypes, sequence types, virulence genes, antimicrobial resistance genes, plasmids, and prophages. Phylogenetic relationships were established through comparative analysis of single nucleotide polymorphisms with reference strains. The genomes showed completeness levels ranging from 95.52 percent to 100 percent. Eleven isolates belonged to the Infantis serotype and one to the Kentucky serotype. All strains carried genes associated with resistance to aminoglycosides and sulfonamides, whereas blaCTX-M-65 was detected in seven isolates. Phylogenetic analysis revealed the circulation of a predominant clonal lineage of S. Infantis related to poultry isolates previously reported in Ecuador. The results demonstrate the presence of multidrug-resistant strains of epidemiological importance and highlight the value of third-generation sequencing for strengthening genomic surveillance under the One Health approach.
Evaluación de la diversidad genómica y las relaciones filogenéticas de Salmonella enterica aislada a partir de pollo comercializado en mercados de la ciudad de Ambato mediante secuenciación de Tercera Generación
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2026-07)
Castelo Fiallos, Yajaira Ivanova
;
Calero Cáceres, William Ricardo
Salmonellosis is one of the most important foodborne diseases worldwide, with S. enterica being one of the main pathogens associated with the poultry production chain. In Ecuador, the commercialization of chicken in traditional markets constitutes a potential source of exposure, especially in cities such as Ambato, where information on the genomic characterization of circulating strains is limited. The present study evaluated the genetic diversity and phylogenetic relationships of 12 S. enterica strains isolated from chicken carcasses and giblets marketed in Ambato markets. The strains were sequenced using Oxford Nanopore technology and characterized through bioinformatics tools to determine serotypes, sequence types, virulence genes, antimicrobial resistance genes, plasmids, and prophages. Phylogenetic relationships were established through comparative analysis of single nucleotide polymorphisms with reference strains. The genomes showed completeness levels ranging from 95.52 percent to 100 percent. Eleven isolates belonged to the Infantis serotype and one to the Kentucky serotype. All strains carried genes associated with resistance to aminoglycosides and sulfonamides, whereas blaCTX-M-65 was detected in seven isolates. Phylogenetic analysis revealed the circulation of a predominant clonal lineage of S. Infantis related to poultry isolates previously reported in Ecuador. The results demonstrate the presence of multidrug-resistant strains of epidemiological importance and highlight the value of third-generation sequencing for strengthening genomic surveillance under the One Health approach.
Análisis genómico de Escherichia coli portadoras de genes de resistencia mcr-1 y blaOXA-48 de origen ambiental ecuatoriano utilizando secuenciación de tercera generación
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2024-02)
Villacís López, Keyla Monserrath
;
Calero Cáceres, William Ricardo
The present research emphasizes the importance of analyzing antimicrobial resistance (AMR) both globally and in Ecuador, focusing on the analysis of two complete genome sequences of E. coli strains (62A and 17A) of environmental origin, which harbor resistance genes. The relevance of this work in global public health is significant, highlighting the urgency to address this issue. Using the Oxford Nanopore Technologies (ONT) sequencing technique and bioinformatics tools, a detailed characterization of the chromosomes and plasmids of the strains was achieved. The analysis was carried out on the platform of the Center for Genomic Epidemiology (CGE-DTU), allowing the identification of resistance genes, virulence factors, plasmids, sequence types, including multilocus sequence typing (MLST). Additionally, the genetic environment was studied using DiGAling and phylogeny through the cgMLST method of the Galaxy platform, using the iTOL tool for visualization. The results revealed that both strains have an approximate genomic size of 4.8 Mb, and the resistance genes are located on IncFII type plasmids. They also share phylogenetic profiles and antibiotic resistance, particularly highlighting the E. coli 17A strain, being the first in Ecuador reported with the blaOXA-48 gene. These discoveries are vital for the surveillance and control of E. coli, underscoring the importance of an integrated One Health approach, which considers the relationship between human, animal, and environmental health; allowing for coordinated strategies against the challenges of antibiotic resistance.
Análisis genómico de Escherichia coli portadoras de genes de resistencia mcr-1 y blaOXA-48 de origen ambiental ecuatoriano utilizando secuenciación de tercera generación
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2024-02)
Jaramillo Mariño, Vivian Arlette
;
Calero Cáceres, William Ricardo
The present research emphasizes the importance of analyzing antimicrobial resistance (AMR) both globally and in Ecuador, focusing on the analysis of two complete genome sequences of E. coli strains (62A and 17A) of environmental origin, which harbor resistance genes. The relevance of this work in global public health is significant, highlighting the urgency to address this issue. Using the Oxford Nanopore Technologies (ONT) sequencing technique and bioinformatics tools, a detailed characterization of the chromosomes and plasmids of the strains was achieved. The analysis was carried out on the platform of the Center for Genomic Epidemiology (CGE-DTU), allowing the identification of resistance genes, virulence factors, plasmids, sequence types, including multilocus sequence typing (MLST). Additionally, the genetic environment was studied using DiGAling and phylogeny through the cgMLST method of the Galaxy platform, using the iTOL tool for visualization. The results revealed that both strains have an approximate genomic size of 4.8 Mb, and the resistance genes are located on IncFII type plasmids. They also share phylogenetic profiles and antibiotic resistance, particularly highlighting the E. coli 17A strain, being the first in Ecuador reported with the blaOXA-48 gene. These discoveries are vital for the surveillance and control of E. coli, underscoring the importance of an integrated One Health approach, which considers the relationship between human, animal, and environmental health; allowing for coordinated strategies against the challenges of antibiotic resistance.
Caracterización de la resistencia a tigeciclina mediada por plásmidos en Acinetobacter baumannii de origen ecuatoriano
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2023-03)
Vayas Arcos, Patricio Alejandro
;
Calero Cáceres, William Ricardo
Antimicrobial resistance (AMR) is a threat to the world's health systems. Carbapenem-resistant Acinetobacter baumannii (CRAB) is classified as a critical priority pathogen due to its ability to acquire genetic material through mobile elements such as plasmids. The emerging resistance tet(X) genes and its homologs, tet(X3)/tet(X4), encode enzymes that break down last-line antibiotics such as tigecycline (TGC). In Ecuador, there are no studies on the detection of these genes. For this reason, the phenotypic profiles of TGC resistance were evaluated by broth microdilution and genotypic by molecular techniques in the A. baumannii collection from the period 2017-2021 from respiratory samples (sputum, induced sputum, bronchial, tracheal and tracheal aspirate) in Intensive Unit Care patients (ICU). The line of research was Microbiology and biotechnology. The results obtained indicated that the 32 TGC resistant isolates (10.9 percent), clustered in subdivisions R4, R9, R11, R13, and R14 of the total collection (n=292), did not have tet(X) genes or its homologs. Most of the isolates have different combinations of double and triple OXA carbapenemases. Even though there is a decrease of about 3 percent in the TGC resistance rate between the pre-pandemic (2017-2019) and pandemic (2020-2021) periods, the percentage of resistance to other antibiotics was maintained (CIP5, MEM10, IMP10, FEP30, TPZ110) and even increased (COL, CN10, CAZ30). Future research is essential to monitor the spread and potential reservoirs of tet(X) and its variants.
Caracterización de la resistencia a tigeciclina mediada por plásmidos en Acinetobacter baumannii de origen ecuatoriano
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2023-03)
López Cajamarca, Rosa Nayely
;
Calero Cáceres, William Ricardo
resistant Acinetobacter baumannii (CRAB) is classified as a critical priority pathogen due to its ability to acquire genetic material through mobile elements such as plasmids. The emerging resistance tet(X) genes and its homologs, tet(X3)/tet(X4), encode enzymes that break down last-line antibiotics such as tigecycline (TGC). In Ecuador, there are no studies on the detection of these genes. For this reason, the phenotypic profiles of TGC resistance were evaluated by broth microdilution and genotypic by molecular techniques in the A. baumannii collection from the period 2017-2021 from respiratory samples (sputum, induced sputum, bronchial, tracheal and tracheal aspirate) in Intensive Unit Care patients (ICU). The line of research was Microbiology and biotechnology. The results obtained indicated that the 32 TGC resistant isolates (10.9 percent), clustered in subdivisions R4, R9, R11, R13, and R14 of the total collection (n=292), did not have tet(X) genes or its homologs. Most of the isolates have different combinations of double and triple OXA carbapenemases. Even though there is a decrease of about 3 percent in the TGC resistance rate between the pre-pandemic (2017-2019) and pandemic (2020-2021) periods, the percentage of resistance to other antibiotics was maintained (CIP5, MEM10, IMP10, FEP30, TPZ110) and even increased (COL, CN10, CAZ30). Future research is essential to monitor the spread and potential reservoirs of tet(X) and its variants.
Caracterización de los perfiles de resistencia antimicrobiana de Escherichia coli aislada de mamíferos en cautiverio del EcoZoológico San Martín – Baños de Agua Santa
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología, 2022-09)
Medina Pujos, Anabell Yessenia
;
Calero Cáceres, William Ricardo
Antimicrobial resistance (AMR) has become a public health problem around the world; therefore, to prevent the emergence and spread of pathogenic bacteria, measures should be taken by adopting a One Health perspective. Around the world, one of the factors for the emergence of resistant pathogens has been the zoonotic exchange between animals and humans, and its association with the use of different antimicrobials in human and veterinary medicine. For this reason, the study of wild or captive species is essential. This research focuses on characterizing antimicrobial resistance profiles in E. coli isolates from captive mammals at the San Martín Eco Zoo in Baños de Agua Santa. From a total of 27 faecal samples collected, 90 strains were isolated. 32 strains presented resistance to more than three families of antibiotics; however, only strains E57 and E75 isolated from ocelots (Leopardus pardalis) showed resistance to six families of antibiotics. The antibiotics with the highest percentage of resistance were ampicillin (97.5), ceftriaxone (95), cefuroxime (95), trimethoprim/sulfamethoxazole (52.5), ceftazidime (47.5) and ciprofloxacin (37.5). The generated profiles showed the relationship between resistance to antimicrobials and the diet of the mammals studied, observing that those isolated from mammals with a meat-based diet were multi-resistant E. coli; In addition, the antibiotic treatment received helped with the presence of more resistant isolates. The results obtained indicate that captive species can be potential reservoirs of multi-resistant bacteria to antibiotics.
Caracterización in silico de una secuencia de genoma completo de Escherichia coli mcr-1 positiva de origen animal de Ecuador
(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Ingeniería Bioquímica, 2022-09)
Rodríguez Gando, Kerly Tatiana
;
Calero Cáceres, William Ricardo
Antimicrobial resistance (AMR) has been one of the causes of major morbidity in humans, produced by resistant bacteria that acquire their pathogenicity by transmission mechanisms, such as horizontal transmission of mobile genetic elements. mcr-1 is a gene that generates resistance to colistin, a polymyxin antibiotic used for the treatment of multidrug-resistant bacterial infections, where its global dissemination has become a health threat. Escherichia coli is a species with a major presence of mcr-1 in various reservoirs such as food, animals, environment, and humans. Ecuador has presented few studies on Escherichia coli mcr-1 in different hosts; however, its dissemination in the country remains unknown. For this reason, we intend to characterize in silico the Escherichia coli mcr-1 positive strain (UTA069) of animal origin, using its genome sequence to evaluate the phylogenetic distance by comparing it with 124 strains of E. coli carrying the mcr-1 gene from 25 countries using bioinformatics tools. UTA069 belonged to sequence type ST1196, virulence genes, plasmids and antibiotic resistance gene profiles were detected. Phylogenetic distances showed a close relationship between UTA069 and its analogues from Spain, whereas the remaining Ecuadorian strains are mainly related to isolates of Asian and European origin. Finally, Ecuadorian isolates showed co-resistance to different classes of antibiotics such as aminoglycosides, sulfonamides, tetracyclines, and in greater proportion to beta-lactams, whose presence has increased in recent years in microorganisms belonging to the Enterobacteriaceae family.

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