Examinando por Autor "Moreno Switt, Andrea I."
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Ítem Genomic characterization of salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States(BioMed Central Ltd., 2014-06) Rodriguez-Rivera, Lorraine D.; Moreno Switt, Andrea I.; Degoricija, Lovorka; Fang, Rixun; Cummings, Craig A.; Furtado, Manohar R.; Wiedmann, Martin; Den Bakker, Henk C.Background: Within the last decade, Salmonella enterica subsp. enterica serovar Cerro (S. Cerro) has become one of the most common serovars isolated from cattle and dairy farm environments in the northeastern US. The fact that this serovar is commonly isolated from subclinically infected cattle and is rarely associated with human disease, despite its frequent isolation from cattle, has led to the hypothesis that this emerging serovar may be characterized by reduced virulence. We applied comparative and population genomic approaches to (i) characterize the evolution of this recently emerged serovar and to (ii) gain a better understanding of genomic features that could explain some of the unique epidemiological features associated with this serovar. Results: In addition to generating a de novo draft genome for one Salmonella Cerro strain, we also generated whole genome sequence data for 26 additional S. Cerro isolates, including 16 from cattle operations in New York (NY) state, 2 from human clinical cases from NY in 2008, and 8 from diverse animal sources (7 from Washington state and 1 from Florida). All isolates sequenced in this study represent sequence type ST367. Population genomic analysis showed that isolates from the NY cattle operations form a well-supported clade within S. Cerro ST367 (designated here “NY bovine clade”), distinct from isolates from Washington state, Florida and the human clinical cases. A molecular clock analysis indicates that the most recent common ancestor of the NY bovine clade dates back to 1998, supporting the recent emergence of this clone. Comparative genomic analyses revealed several relevant genomic features of S. Cerro ST367, that may be responsible for reduced virulence of S. Cerro, including an insertion creating a premature stop codon in sopA. In addition, patterns of gene deletion in S. Cerro ST367 further support adaptation of this clone to a unique ecological or host related niche. Conclusions: Our results indicate that the increase in prevalence of S. Cerro ST367 is caused by a highly clonal subpopulation and that S. Cerro ST367 is characterized by unique genomic deletions that may indicate adaptation to specific ecological niches and possibly reduced virulence in some hostsÍtem Humans and Hoofed Livestock Are the Main Sources of Fecal Contamination of Rivers Used for Crop Irrigation: A Microbial Source Tracking Approach(Frontiers Media S.A., 2022-06) Díaz Gavidia, Constanza; Barría, Carla; Weller, Daniel L.; Salgado Caxito, Marilia; Estrada, Erika M.; Araya, Aníbal; Vera, Leonardo; Smith, Woutrina; Kim, Minji; Moreno Switt, Andrea I.; Olivares Pacheco, Jorge; Adell, Aiko D.Freshwater bodies receive waste, feces, and fecal microorganisms from agricultural, urban, and natural activities. In this study, the probable sources of fecal contamination were determined. Also, antibiotic resistant bacteria (ARB) were detected in the two main rivers of central Chile. Surface water samples were collected from 12 sampling sites in the Maipo (n = 8) and Maule Rivers (n = 4) every 3 months, from August 2017 until April 2019. To determine the fecal contamination level, fecal coliforms were quantified using the most probable number (MPN) method and the source of fecal contamination was determined by Microbial Source Tracking (MST) using the Cryptosporidium and Giardia genotyping method. Separately, to determine if antimicrobial resistance bacteria (AMB) were present in the rivers, Escherichia coli and environmental bacteria were isolated, and the antibiotic susceptibility profile was determined. Fecal coliform levels in the Maule and Maipo Rivers ranged between 1 and 130 MPN/100-ml, and 2 and 30,000 MPN/100-ml, respectively. Based on the MST results using Cryptosporidium and Giardia host-specific species, human, cattle, birds, and/or dogs hosts were the probable sources of fecal contamination in both rivers, with human and cattle host-specific species being more frequently detected. Conditional tree analysis indicated that coliform levels were significantly associated with the river system (Maipo versus Maule), land use, and season. Fecal coliform levels were significantly (p < 0.006) higher at urban and agricultural sites than at sites immediately downstream of treatment centers, livestock areas, or natural areas. Three out of eight (37.5%) E. coli isolates presented a multidrug-resistance (MDR) phenotype. Similarly, 6.6% (117/1768) and 5.1% (44/863) of environmental isolates, in Maipo and Maule River showed and MDR phenotype. Efforts to reduce fecal discharge into these rivers should thus focus on agriculture and urban land uses as these areas were contributing the most and more frequently to fecal contamination into the rivers, while human and cattle fecal discharges were identified as the most likely source of this fecal contamination by the MST approach. This information can be used to design better mitigation strategies, thereby reducing the burden of waterborne diseases and AMR in Central Chile. Copyright © 2022 Díaz-Gavidia, Barría, Weller, Salgado-Caxito, Estrada, Araya, Vera, Smith, Kim, Moreno-Switt, Olivares-Pacheco and Adell.Ítem Infectología en la era de la genómica(Sociedad Chilena de Infectología, 2015-10) Moreno Switt, Andrea I.; Toledo, VivianaLa nueva generación de secuenciadores (NGS) ha llegado para cambiar el modo de realizar investigación. Particularmente en Infectología, estas tecnologías modernas la han dirigido a una próxima era, denominada la "era de la genómica". En países desarrollados, las NGS se están utilizando en un gran número de aplicaciones, las que incluyen diagnóstico clínico, epidemiología y microbiología. En la actualidad, secuenciar el genoma de un microorganismo completo, ya sea bacteriano o viral, cuesta aproximadamente $100 dólares, precio bastante asequible en comparación a los precios de las tecnologías más antiguas. En esta revisión se describen algunas publicaciones recientes que han utilizado la secuenciación de genomas completos para, (i) rastrear brotes de enfermedades transmitidas por alimentos, (ii) la preparación de base de datos de genomas para los Gobiernos (iii) investigación de enfermedades nosocomiales, y (iv) en diagnóstico clínico. La era de la genómica está aquí, y llegó para quedarse, por lo cual se debe enfocar todos los esfuerzos en aprender a utilizar la gran cantidad de "datos masivos" generados por estas tecnologías, para reducir el impacto de las enfermedades infecciosas y así, mejorar la salud de personas y animales.Ítem Long-Term Interactions of Salmonella Enteritidis With a Lytic Phage for 21 Days in High Nutrients Media(Frontiers Media S.A., 2022-05) Barron Montenegro, Rocio; Rivera, Dácil; Serrano, María Jesus; García, Rodrigo; Álvarez, Diana M.; Benavides, Julio; Arredondo, Fernanda; Álvarez, Francisca P.; Bastías, Roberto; Ruiz, Soledad; Hamilton West, Christopher; Castro Nallar, Eduardo; Moreno Switt, Andrea I.Salmonella spp. is a relevant foodborne pathogen with worldwide distribution. To mitigate Salmonella infections, bacteriophages represent an alternative to antimicrobials and chemicals in food animals and food in general. Bacteriophages (phages) are viruses that infect bacteria, which interact constantly with their host. Importantly, the study of these interactions is crucial for the use of phages as a mitigation strategy. In this study, experimental coevolution of Salmonella Enteritidis (S. Enteritidis) and a lytic phage was conducted in tryptic soy broth for 21 days. Transfer to fresh media was conducted daily and every 24 hours, 2 mL of the sample was collected to quantify Salmonella OD600 and phage titter. Additionally, time-shift experiments were conducted on 20 colonies selected on days 1, 12, and 21 to evaluate the evolution of resistance to past (day 1), present (day 12), and future (day 21) phage populations. The behavior of the dynamics was modeled and simulated with mathematical mass-action models. Bacteria and phage from days 1 and 21 were sequenced to determine the emergence of mutations. We found that S. Enteritidis grew for 21 days in the presence and absence of the phage and developed resistance to the phage from day 1. Also, the phage was also able to survive in the media for 21 days, however, the phage titer decreased in approx. 3 logs PFU/mL. The stability of the lytic phage population was consistent with the leaky resistance model. The time-shift experiments showed resistance to phages from day 1 of at least 85% to the past, present, and future phages. Sequencing of S. Enteritidis showed mutations in genes involved in lipopolysaccharide biosynthesis genes rfbP and rfbN at day 21. The phage showed mutations in the tail phage proteins responsible for recognizing the cell surface receptors. These results suggest that interactions between bacteria and phage in a rich resource media generate a rapid resistance to the infective phage but a fraction of the population remains susceptible. Interactions between Salmonella and lytic phages are an important component for the rational use of phages to control this important foodborne pathogen. Copyright © 2022 Barron-Montenegro, Rivera, Serrano, García, Álvarez, Benavides, Arredondo, Álvarez, Bastías, Ruiz, Hamilton-West, Castro-Nallar and Moreno-Switt.Ítem Lysis profiles of salmonella phages on salmonella isolates from various sources and efficiency of a phage cocktail against s. Enteritidis and s. typhimurium(MDPI, 2019-04) Petsong, Kantiya; Benjakul, Soottawat; Chaturongakul, Soraya; Moreno Switt, Andrea I.; Vongkamjan, KitiyaSalmonella enterica serovar Enteritidis and Salmonella enterica serovar Typhimurium are major foodborne pathogens of concern worldwide. Bacteriophage applications have gained more interest for biocontrol in foods. This study isolated 36 Salmonella phages from several animal farms in Thailand and tested them on 47 Salmonella strains from several sources, including farms, seafood processing plant and humans in Thailand and USA. Phages were classified into three major groups. The estimated phage genome size showed the range from 50 ± 2 to 200 ± 2 kb. An effective phage cocktail consisting of three phages was developed. Approximately 4 log CFU/mL of S. Enteritidis and S. Typhimurium could be reduced. These phages revealed a burst size of up to 97.7 on S. Enteritidis and 173.7 PFU/cell on S. Typhimurium. Our phage cocktail could decrease S. Enteritidis on chicken meat and sunflower sprouts by 0.66 log CFU/cm2 and 1.27 log CFU/g, respectively. S. Typhimurium on chicken meat and sunflower sprouts were decreased by 1.73 log CFU/cm2 and 1.17 log CFU/g, respectively. Overall, animal farms in Thailand provided high abundance and diversity of Salmonella phages with the lysis ability on Salmonella hosts from various environments and continents. A developed phage cocktail suggests a potential biocontrol against Salmonella in fresh foods. © MDPI AG. All rights reserved.Ítem Novel Salmonella Phage, vB_Sen_STGO-35-1, Characterization and Evaluation in Chicken Meat(MDPI, 2022-03) Rivera, Dácil; Moreno Switt, Andrea I.; Denes, Thomas G.; Hudson, Lauren K.; Peters, Tracey L.; Samir, Reham; Aziz, Ramy K.; Noben, Jean-Paul; Wagemans, Jeroen; Dueñas, FernandoSalmonellosis is one of the most frequently reported zoonotic foodborne diseases world-wide, and poultry is the most important reservoir of Salmonella enterica serovar Enteritidis. The use of lytic bacteriophages (phages) to reduce foodborne pathogens has emerged as a promising bio-control intervention for Salmonella spp. Here, we describe and evaluate the newly isolated Salmonella phage STGO-35-1, including: (i) genomic and phenotypic characterization, (ii) an analysis of the reduction of Salmonella in chicken meat, and (iii) genome plasticity testing. Phage STGO-35-1 repre-sents an unclassified siphovirus, with a length of 47,483 bp, a G + C content of 46.5%, a headful strategy of packaging, and a virulent lifestyle. Phage STGO-35-1 reduced S. Enteritidis counts in chicken meat by 2.5 orders of magnitude at 4 °C. We identified two receptor-binding proteins with affinity to LPS, and their encoding genes showed plasticity during an exposure assay. Phenotypic, proteomic, and genomic characteristics of STGO-35-1, as well as the Salmonella reduction in chicken meat, support the potential use of STGO-35-1 as a targeted biocontrol agent against S. Enteritidis in chicken meat. Additionally, computational analysis and a short exposure time assay allowed us to predict the plasticity of genes encoding putative receptor-binding proteins. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.Ítem Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee(Springer-Verlag Wien, 2018-04) Adriaenssens, Evelien M.; Wittmann, Johannes; Kuhn, Jens H.; Turner, Dann; Sullivan, Matthew B.; Dutilh, Bas E.; Jang, Ho Bin; van Zyl, Leonardo J.; Klumpp, Jochen; Lobocka, Malgorzata; Moreno Switt, Andrea I.; Rumnieks, Janis; Edwards, Robert A.; Uchiyama, Jumpei; Alfenas-Zerbini, Poliane; Petty, Nicola K.; Kropinski, Andrew M.; Barylski, Jakub; Gillis, Annika; Clokie, Martha R. C.; Prangishvili, David; Lavigne, Rob; Aziz, Ramy Karam; Duffy, Siobain; Krupovic, Mart; Poranen, Minna M.; Knezevic, Petar; Enault, Francois; Tong, Yigang; ksanen, Hanna M.; Rodney Brister J.The prokaryotic virus community is represented at the International Committee on Taxonomy of Viruses (ICTV) by the Bacterial and Archaeal Viruses Subcommittee. Since our last report [5], the committee composition has changed, and a large number of taxonomic proposals (TaxoProps) were submitted to the ICTV Executive Committee (EC) for approval.Ítem Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee(Springer, 2020-05-01) Adriaenssens, Evelien M.; Sullivan, Matthew B.; Knezevic, Petar; van Zyl, Leonardo J.; Sarkar B.L.; Dutilh, Bas E.; Alfenas-Zerbini, Poliane; Łobocka, Małgorzata; Tong, Yigang; Brister, James Rodney; Moreno Switt, Andrea I.; Klumpp, Jochen; Aziz, Ramy Karam; Barylski, Jakub; Uchiyama, Jumpei; Edwards, Rob A.; Kropinski, Andrew M.; Petty, Nicola K.; Clokie, Martha R. J.; Kushkina, Alla I.; Morozova, Vera V.; Duffy, Siobain; Gillis, Annika; Rumnieks, Janis; Kurtböke, Ipek; Chanishvili, Nina; Goodridge, Lawrence; Wittmann, Johannes; Lavigne, Rob; Jang, Ho Bin; Prangishvili, David; Enault, Francois; Turner, Dann; Poranen, Minna M.; Oksanen, Hanna M.; Krupovic, MartThis article is a summary of the activities of the ICTV’s Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV’s ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.