Browsing by Author "Toro, Magaly"
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- ItemA multicenter genomic epidemiological investigation in Brazil, Chile, and Mexico reveals the diversity and persistence of Salmonella populations in surface waters(2024) Chen, Zhao; Moreno-Switt, Andrea I.; Reyes-Jara, Angelica; Suarez, Enrique Delgado; Adell, Aiko D.; Oliveira, Celso Jose Bruno; Bonelli, Raquel Regina; Huang, Xinyang; Brown, Eric; Allard, Marc; Grim, Christopher; Bell, Rebecca; Meng, Jianghong; Toro, MagalyThis study examined the diversity and persistence of Salmonella in the surface waters of agricultural regions of Brazil, Chile, and Mexico. Research groups (three in 2019-2020 and five in 2021-2022) conducted a long-term survey of surface water across 5-8 months annually (n = 30 monthly). On-site, each team filtered 10-L water samples with modified Moore Swabs to capture Salmonella, which were then isolated and identified using conventional microbiological techniques. Salmonella isolates were sequenced on Illumina platforms. Salmonella was present in 1,493/3,291 water samples (45.8%), with varying isolation rates across countries and years. Newport, Infantis, and Typhimurium were the most frequent among the 128 different serovars. Notably, 22 serovars were found in all three countries, representing almost half of the 1,911 different isolates collected. The resistome comprised 72 antimicrobial resistance (AMR) genes and six point mutations in three genes. At least one AMR determinant was observed in 33.8% (646/1,911) of the isolates, of which 47.4% (306/646) were potentially multidrug resistant. Phylogeny based on core genome multilocus sequence typing (cgMLST) showed that most isolates clustered according to sequence type and country of origin. Only 14 cgMLST multi-country clusters were detected among the 275 clusters. However, further analysis confirmed that close genetic relatedness occurred mostly among isolates from the same country, with three exceptions. Interestingly, isolates closely related phylogenetically were recovered over multiple years within the same country, indicating the persistence of certain Salmonella in those areas. In conclusion, surface waters in these regions are consistently contaminated with diverse Salmonella, including strains that persist over time. IMPORTANCE Salmonella is a leading foodborne pathogen responsible for millions of illnesses, hospitalizations, and deaths annually. Although Salmonella-contaminated water has now been recognized as an important contamination source in the agrifood chain, there is a lack of knowledge on the global occurrence and diversity of Salmonella in surface water. Moreover, there has been insufficient research on Salmonella in surface waters from Latin American countries that are major producers and exporters of agricultural products. Incorporating genetic profiling of Salmonella isolates from underrepresented regions, such as Latin America, enhances our understanding of the pathogen's ecology, evolution, antimicrobial resistance, and pathogenicity. Moreover, leveraging genomic data derived from pathogens isolated from diverse geographical areas is critical for assessing the potential public health risk posed by the pathogen and expediting investigations of foodborne outbreaks. Ultimately, global efforts contribute significantly to reducing the incidence of foodborne infections.
- ItemEnvironmental and anthropogenic factors associated with the likelihood of detecting Salmonella in agricultural watersheds(2022) Toro, Magaly; Weller, Daniel; Ramos, Romina; Diaz, Leonela; Alvarez, Francisca P.; Reyes-Jara, Angelica; Moreno-Switt, Andrea I.; Meng, Jianghong; Adell, Aiko D.Surface water is one of the primary sources of irrigation water for produce production; therefore, its contamination by foodborne pathogens, such as Salmonella, may substantially impact public health. In this study, we determined the presence of Salmonella in surface water and characterized the relationship between Salmonella detection and environmental and anthropogenic factors. From April 2019 to February 2020, 120 samples from 30 sites were collected monthly in four watersheds located in two different central Chile agricultural regions (N =1080). Water samples from rivers, canals, streams, and ponds linked to each watershed were obtained. Surface water (10 L) was filtrated in situ, and samples were analyzed for the presence of Salmonella. Salmonella was detected every month in all watersheds, with a mean detection percentage of 28% (0%-90%) across sampling sites, regardless of the season. Overall, similar detection percentages were observed for both regions: 29.1% for Metropolitan and 27.0% for Maule. Salmonella was most often detected in summer (39.8% of all summer samples tested positive) and least often in winter (14.4% of winter samples). Random forest analysis showed that season, water source, and month, followed by latitude and river, were the most influential factors associated with Salmonella detection. The influences of water pH and temperature (categorized as environmental factors) and factors associated with human activity (categorized as anthropogenic factors) registered at the sampling site were weakly or not associated with Salmonella detection. In conclusion, Salmonella was detected in surface water potentially used for irrigation, and its presence was linked to season and water source factors. Interventions are necessary to prevent contamination of produce, such as water treatment before irrigation.
- ItemEvaluating the Capacity of Human Gut Microorganisms to Colonize the Zebrafish Larvae (Danio rerio)(2018) Valenzuela, María José; Caruffo, Mario; Herrera, Yoani; Medina, Daniel A.; Coronado, Máximo; Feijoo, Carmen G.; Muñoz, Salomé; Garrido Cortés, Daniel; Troncoso, Miriam; Figueroa, Guillermo; Toro, Magaly; Reyes Jara, Angélica; Magne, Fabien; Navarrete, Paola
- ItemGenomic characterisation of the population structure and antibiotic resistance of Salmonella enterica serovar Infantis in Chile, 2009-2022(2024) Pina-Iturbe, Alejandro; Diaz-Gavidia, Constanza; Alvarez, Francisca P.; Barron-Montenegro, Rocio; Alvarez-Espejo, Diana M.; Garcia, Patricia; Solis, Doina; Constenla-Albornoz, Rodrigo; Toro, Magaly; Olivares-Pacheco, Jorge; Reyes-Jara, Angelica; Meng, Jianghong; Bell, Rebecca L.; Moreno-Switt, Andrea I.Background Multidrug-resistant (MDR) Salmonella Infantis has disseminated worldwide, mainly linked to the consumption of poultry products. Evidence shows dissemination of this pathogen in Chile; however, studies are primarily limited to phenotypic data or involve few isolates. As human cases of Salmonella Infantis infections have substantially increased in recent years, this study aimed to characterise the genomic epidemiology and antimicrobialresistance profiles of isolates obtained from different sources, aiming to inform effective surveillance and control measures. Methods We sequenced 396 Salmonella Infantis genomes and analysed them with all publicly available genomes of this pathogen from Chile (440 genomes in total), representing isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. Based on bioinformatic and phenotypic methods, we assessed the population structure, dissemination among different niches, and antimicrobial resistance (AMR) profiles of Salmonella Infantis in the country. Findings The genomic and phylogenetic analyses showed that Salmonella Infantis from Chile comprised several clusters of highly related isolates dominated by sequence type 32. The HC20_343 cluster grouped an important proportion of all isolates. This was the only cluster associated with pESI-like megaplasmids, and up to 12 acquired AMR genes/mutations predicted to result in an MDR phenotype. Accordingly, antimicrobial -susceptibility testing revealed a strong concordance between the AMR genetic determinants and their matching phenotypic expression, indicating that a significant proportion of HC20_343 isolates produce extended -spectrum beta-lactamases and have intermediate fluoroquinolone resistance. HC20_343 Salmonella Infantis were spread among environmental, animal, food, and human niches, showing a close relationship between isolates from different years and sources, and a low intra-source genomic diversity. Interpretation Our findings show a widespread dissemination of MDR Salmonella Infantis from the HC20_343 cluster in Chile. The high proportion of isolates with resistance to first -line antibiotics and the evidence of active transmission between the environment, animals, food, and humans highlight the urgency of improved surveillance and control measures in the country. As HC20_343 isolates predominate in the Americas, our results suggest a high prevalence of ESBL-producing Salmonella Infantis with intermediate fluoroquinolone resistance in the continent.
- ItemIntegrative genome-centric metagenomics for surface water surveillance: Elucidating microbiomes, antimicrobial resistance, and their associations(2024) Huang, Xinyang; Toro, Magaly; Reyes-Jara, Angelica; Moreno-Switt, Andrea, I; Adell, Aiko; Oliveira, Celso J. B.; Bonelli, Raquel R.; Gutierrez, Sebastian; Alvarez, Francisca P.; Rocha, Alan Douglas de Lima; Kraychete, Gabriela B.; Chen, Zhao; Grim, Christopher; Brown, Eric; Bell, Rebecca; Meng, JianghongSurface water ecosystems are intimately intertwined with anthropogenic activities and have significant public health implications as primary sources of irrigation water in agricultural production. Our extensive metagenomic analysis examined 404 surface water samples from four different geological regions in Chile and Brazil, spanning irrigation canals (n = 135), rivers (n = 121), creeks (n = 74), reservoirs (n = 66), and ponds (n = 8). Overall, 50.25 % of the surface water samples contained at least one of the pathogenic or contaminant bacterial genera (Salmonella: 29.21 %; Listeria: 6.19 %; Escherichia: 35.64 %). Furthermore, a total of 1,582 antimicrobial resistance (AMR) gene clusters encoding resistance to 25 antimicrobial classes were identified, with samples from Brazil exhibiting an elevated AMR burden. Samples from stagnant water sources were characterized by dominant Cyanobacteriota populations, resulting in significantly reduced biodiversity and more uniform community compositions. A significant association between taxonomic composition and the resistome was supported by a Procrustes analysis (p < 0.001). Notably, regional signatures were observed regarding the taxonomic and resistome profiles, as samples from the same region clustered together on both ordinates. Additionally, network analysis illuminated the intricate links between taxonomy and AMR at the contig level. Our deep sequencing efforts not only mapped the microbial landscape but also expanded the genomic catalog with newly characterized metagenome-assembled genomes (MAGs), boosting the classification of reads by 12.85%. In conclusion, this study underscores the value of metagenomic approaches in surveillance of surface waters, enhancing our understanding of microbial and AMR dynamics with far-reaching public health and ecological ramifications.
- ItemRevisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health(FRONTIERS MEDIA SA, 2022) Rocha, Alan Douglas de Lima; Ferrari, Rafaela Gomes; Pereira, Walter Esfrain; de Lima, Laiorayne Araujo; Givisiez, Patricia Emilia Naves; Moreno-Switt, Andrea Isabel; Toro, Magaly; Suarez, Enrique Jesus Delgado; Meng, Jianghong; de Oliveira, Celso Jose BrunoThe increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.
- ItemSalmonella enterica Serovar Abony Outbreak Caused by Clone of Reference Strain WDCM 00029, Chile, 2024(Centers Disease Control & Prevention, 2025) Piña Iturbe, Luis Alejandro; Fredes García, Diego Antonio; García Cañete, Patricia; Porte, Lorena; Johnson, Timothy J.; Singer, Randall S.; Toro, Magaly; Munita, Jose M.; Moreno Switt, Andrea IsabelA Salmonella enterica serovar Abony outbreak occurred during January–April 2024 in Chile. Genomic evidence indicated that the outbreak strain was a clone of reference strain WDCM 00029, which is routinely used in microbiological quality control tests. When rare or unreported serovars cause human infections, clinicians and health authorities should request strain characterization.
- ItemUnveiling the genomic landscape of Salmonella enterica serotypes Typhimurium, Newport, and Infantis in Latin American surface waters: a comparative analysis(2024) Chen, Zhao; Toro, Magaly; Moreno-Switt, Andrea I.; Adell, Aiko D.; Delgado-Suarez, Enrique J.; Bonelli, Raquel R.; Oliveira, Celso J. B.; Reyes-Jara, Angelica; Huang, Xinyang; Albee, Brett; Grim, Christopher J.; Allard, Marc; Tallent, Sandra M.; Brown, Eric W.; Bell, Rebecca L.; Meng, JianghongSurface waters are considered ecological habitats where Salmonella enterica can persist and disseminate to fresh produce production systems. This study aimed to explore the genomic profiles of S. enterica serotypes Typhimurium, Newport, and Infantis from surface waters in Chile, Mexico, and Brazil collected between 2019 and 2022. We analyzed the whole genomes of 106 S. Typhimurium, 161 S. Newport, and 113 S. Infantis isolates. Our phylogenetic analysis exhibited distinct groupings of isolates by their respective countries except for a notable case involving a Chilean S. Newport isolate closely related to two Mexican isolates, showing 4 and 13 single nucleotide polymorphisms of difference, respectively. The patterns of the most frequently detected antimicrobial resistance genes varied across countries and serotypes. A strong correlation existed between integron carriage and genotypic multidrug resistance (MDR) across serotypes in Chile and Mexico (R > 0.90, P < 0.01), while integron(s) were not detected in any of the Brazilian isolates. By contrast, we did not identify any strong correlation between plasmid carriage and genotypic MDR across diverse countries and serotypes.