Browsing by Author "Adell, Aiko D."

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    A 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, Magaly
    This 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.
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    Biogeographical variation in antimicrobial resistance in rivers is influenced by agriculture and is spread through bacteriophages
    (WILEY, 2022) Andersson, Tilde; Adell, Aiko D.; Moreno-Switt, Andrea I.; Spegel, Peter; Turner, Charlotta; Overballe-Petersen, Soren; Fuursted, Kurt; Lood, Rolf
    Antibiotic resistance is currently an extensive medical challenge worldwide, with global numbers increasing steadily. Recent data have highlighted wastewater treatment plants as a reservoir of resistance genes. The impact of these findings for human health can best be summarized using a One Health concept. However, the molecular mechanisms impacting resistance spread have not been carefully evaluated. Bacterial viruses, that is bacteriophages, have recently been shown to be important mediators of bacterial resistance genes in environmental milieus and are transferrable to human pathogens. Herein, we investigated the biogeographical impact on resistance spread through river-borne bacteriophages using amplicon deep sequencing of the microbiota, absolute quantification of resistance genes using ddPCR, and phage induction capacity within wastewater. Microbial biodiversity of the rivers is significantly affected by river site, surrounding milieu and time of sampling. Furthermore, areas of land associated with agriculture had a significantly higher ability to induce bacteriophages carrying antibiotic resistance genes, indicating their impact on resistance spread. It is imperative that we continue to analyse global antibiotic resistance problem from a One Health perspective to gain novel insights into mechanisms of resistance spread.
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    Development of a robust FT-IR typing system for Salmonella enterica, enhancing performance through hierarchical classification
    (American Society for Microbiology, 2025) Fredes García, Diego Antonio; Jiménez Rodríguez, Javiera Alejandra; Piña Iturbe, Luis Alejandro; Caballero Díaz, Pablo Ignacio; González Villarroel, Tamara Nicol; Dueñas, Fernando; Wozniak Banchero, Aniela; Adell, Aiko D.; Moreno Switt, Andrea Isabel; García Cañete, Patricia
    Salmonella enterica is a leading cause of foodborne illnesses globally, with significant mortality rates, especially among vulnerable populations. Traditional serotyping methods for Salmonella are accurate but expensive, resource-intensive, and time-consuming, necessitating faster and more reliable alternatives. This study evaluates the IR Biotyper, a Fourier-transform infrared spectroscopy system, in differentiating Salmonella serovars. We assessed 458 isolates of nine Salmonella serovars (Infantis, Enteritidis, Typhimurium, I,4,[5],12:i:-, Montevideo, Agona, Thompson, Panama, and Abony) from diverse sources. The IR Biotyper was used to acquire spectra from these isolates. Machine learning algorithms, including support vector machines, were trained to classify the isolates. The accuracy of classifiers was validated using a validation set to determine sensitivity, specificity, positive predictive value, and negative predictive value. Initial classifiers showed high accuracy for Abony, Agona, Enteritidis, and Infantis serovars, with sensitivities close to 100%. However, classifiers for S. Typhimurium, S. Panama, and S. Montevideo exhibited lower performance. Implementing a hierarchical classification system enhanced the accuracy of serogroup O:4 serovars, demonstrating that this approach offers a robust framework for Salmonella serovar identification. The hierarchical system enables progressive refinement of classification, minimizing misclassifications by focusing on serogroup-specific features, making it adaptable to complex data sets and diverse serovars. The IR Biotyper demonstrates high potential for rapid and accurate Salmonella serovar identification. This study supports its implementation as a cost-effective, high-throughput tool for pathogen typing, enhancing real-time epidemiological surveillance, and guiding treatment strategies for salmonellosis. This method establishes a robust and scalable framework for advancing Salmonella serotyping practices across clinical, industrial, and public health domains by leveraging hierarchical classification.IMPORTANCEEarly and accurate identification of Salmonella serovars is extremely important for epidemiological surveillance, public health, and food safety. Traditional serotyping is very successful but is laborious and costly. In this study, we demonstrate the promise of Fourier-transform infrared spectroscopy together with machine learning as a means for Salmonella serotyping. Using hierarchical classification, we attain optimal serovar identification accuracy, particularly for challenging-to-type serogroups. Our findings recognize the IR Biotyper as a high-throughput, scalable pathogen typing solution that offers real-time data that can enable enhanced outbreak response and prevention of foodborne disease. The approach bridges the gap between traditional microbiological practice and sophisticated analytical technology, the path to more effective, cost-saving interventions in the clinical, industrial, and regulatory settings. Application of these technologies can significantly improve Salmonella surveillance-control and Public Health outcomes.
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    Environmental 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.
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    Global prevalence and molecular characterization of extended-spectrum beta-lactamase producing-Escherichia coli in dogs and cats - A scoping review and meta-analysis
    (ELSEVIER, 2021) Salgado Caxito, Marilia; Benavides, Julio A.; Adell, Aiko D.; Paes, Antonio Carlos; Moreno Switt, Andrea, I
    Antimicrobial resistance (AMR) represents a major threat to human and animal health. Part of the AMR dimension is the circulation of extended-spectrum ?-lactamases producing-Escherichia coli (ESBL-E. coli), which is now commonly reported among companion animals. However, the global perspective of the prevalence and population structure of ESBL-E. coli circulating in dogs and cats has not been estimated limiting our understanding of their role in the dissemination of ESBL-E. coli. The aim of this study was to compare the prevalence of ESBL-E. coli between dogs and cats and across countries through meta-analysis. We also performed a scoping review to summarize the current knowledge on ESBL genes and E. coli clones circulating among companion animals. A total of 128 studies published in PubMed, Web of Science, and Scopus up to April 2020 were selected and contained information on prevalence and/or molecular characterization of ESBL genes and ESBL-E. coli clones. Our review shows an increase in the number of publications between 2000 and 2019, concentrated mainly in Europe. Prevalence varied across continents, ranging from 0.63% (Oceania) to 16.56% (Africa) in dogs and from 0% (Oceania) to 16.82% (Asia) in cats. Although there were twice as many studies reporting prevalence on dogs (n = 61) than on cats (n = 32), and only 9 studies focused exclusively on cats, our meta-analysis showed no difference in the global prevalence of ESBL-E. coli between dogs (6.87% [95% CI: 4.46?10.45%]) and cats (5.04% [95% CI: 2.42?10.22%]). A considerable diversity of ESBL genes (n = 60) and sequence types (ST) (n = 171) were recovered from companion animals. ESBL-E. coli encoded by CTX-M-15 (67.5%, 77/114) and SHV-12 (21.9%, 25/114), along with resistant strains of ST38 (22.7%, 15/66) and ST131 (50%, 33/66) were widespread and detected in all continents. While presence of ESBL-E. coli is widespread, the drivers influencing the observed ESBL-E. coli prevalence and the clinical relevance in veterinary medicine and public health along with economic impact of ESBL-E. coli infections among companion animals need to be further investigated.
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    Humans and Hoofed Livestock Are the Main Sources of Fecal Contamination of Rivers Used for Crop Irrigation: A Microbial Source Tracking Approach
    (FRONTIERS MEDIA SA, 2022) Diaz-Gavidia, Constanza; Barria, Carla; Weller, Daniel L.; Salgado-Caxito, Marilia; Estrada, Erika M.; Araya, Anibal; 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.
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    Isolation of Ciprofloxacin and Ceftazidime-Resistant Enterobacterales From Vegetables and River Water Is Strongly Associated With the Season and the Sample Type
    (FRONTIERS MEDIA SA, 2021) Diaz Gavidia, Constanza; Barria, Carla; Rivas, Lina; Garcia, Patricia; Alvarez, Francisca P.; Gonzalez Rocha, Gerardo; Opazo Capurro, Andres; Araos, Rafael; Munita, Jose M.; Cortes, Sandra; Olivares Pacheco, Jorge; Adell, Aiko D.; Moreno Switt, Andrea I.; CEDEUS (Chile)
    The dissemination of antibiotic-resistant bacteria (ARB) from water used for crop irrigation to vegetables is poorly studied. During a year, five farmer markets in a city in Central Chile were visited, and 478 vegetable samples (parsleys, corianders, celeries, lettuces, chards, and beets) were collected. Simultaneously, 32 water samples were collected from two rivers which are used to irrigate the vegetables produced in the area. Resistant Enterobacterales were isolated and identified. Colistin resistance gene mcr-1 and extended spectrum beta-lactamases (ESBL) were molecularly detected. The association of environmental factors was evaluated, with the outcomes being the presence of Enterobacterales resistant to four antibiotic families and the presence of multidrug resistance (MDR) phenotypes. Parsley, coriander, and celery showed the highest prevalence of resistant Enterobacterales (41.9% for ciprofloxacin and 18.5% for ceftazidime). A total of 155 isolates were obtained, including Escherichia coli (n = 109), Citrobacter sp. (n = 20), Enterobacter cloacae complex (n = 8), Klebsiella pneumoniae (n = 8), and Klebsiella aerogenes (n = 1). Resistance to ampicillin (63.2%) and ciprofloxacin (74.2%) was most frequently found; 34.5% of the isolates showed resistance to third-generation cephalosporins, and the MDR phenotype represented 51.6% of the isolates. In two E. coli isolates (1.29%), the gene mcr-1 was found and ESBL genes were found in 23/62 isolates (37%), with bla(CTX-M) being the most frequently found in 20 isolates (32%). Resistant Enterobacterales isolated during the rainy season were less likely to be MDR as compared to the dry season. Understanding environmental associations represent the first step toward an improved understanding of the public health impact of ARB in vegetables and water.
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    Qualitative Risk Assessment for Antimicrobial Resistance among Humans from Salmon Fillet Consumption Due to the High Use of Antibiotics against Bacterial Infections in Farmed Salmon
    (MDPI, 2022) Salgado-Caxito, Marilia; Zimin-Veselkoff, Natalia; Adell, Aiko D.; Olivares-Pacheco, Jorge; Mardones, Fernando O.
    Background: Worldwide, aquaculture is considered as a hotspot environment for antimicrobial resistance (AMR) due to the intense use of antibiotics in its productive systems. Chile is the second largest producer of farmed salmon worldwide, and tons of antibiotics are used to control bacterial diseases, such as Salmon Rickettsial Syndrome (SRS) and Bacterial Kidney Disease (BKD). However, studies determining the risk of consuming salmon fillets that have been treated with antibiotics during the salmon production are limited. Consulting leading experts in the field could provide a knowledge base to identify and address this question and research gaps. Methods: Multisectoral risk perception of AMR through salmon fillet consumption was evaluated by eliciting expert data obtained through discussions during a workshop and from questionnaires given to experts from academia (n = 15, 63%), the public sector (n = 5, 21%), and the salmon industry (n = 4, 17%). Results: The qualitative risk analysis suggested an overall 'low' probability of AMR acquisition by consumption of salmon fillet that had been treated during the production cycle. The risk perception varied slightly between production stages in freshwater and seawater. In consensus with all sectors, this overall 'low', but existing, risk was probably associated with bacterial infections and the use of antibiotics. Conclusions: As it is essential to reduce the use of antibiotics in the Chilean salmon industry, this intersectoral approach and consensual results could favor effective implementation of targeted initiatives for the control and prevention of major bacterial diseases.
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    Unveiling 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, Jianghong
    Surface 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.
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    Widespread Environmental Presence of Multidrug-Resistant Salmonella in an Equine Veterinary Hospital That Received Local and International Horses
    (2020) Soza-Ossandon, Paula; Rivera, Dacil; Tardone, Rodolfo; Riquelme-Neira, Roberto; Garcia, Patricia; Hamilton-West, Christopher; Adell, Aiko D.; Gonzalez-Rocha, Gerardo; Moreno-Switt, Andrea, I
    Salmonella entericais a highly infectious microorganism responsible for many outbreaks reported in equine hospitals. Outbreaks are characterized by high morbidity and mortality rates, nosocomial transmission to other patients, zoonotic transmission to hospital personnel, and even closure of facilities. In this study, 545 samples (environmental and hospitalized patients) were collected monthly during a 1-year period from human and animal contact surfaces in an equine hospital that received local and international horses. A total of 22Salmonellaisolates were obtained from human contact surfaces (e.g., offices and pharmacy) and animal contact surfaces (e.g., stalls, surgery room, and waterers), and one isolate from a horse. Molecular serotyping revealed 18 isolates asSalmonellaTyphimurium and three asSalmonellaInfantis. Nineteen isolates were resistant to at least one antimicrobial class, and only two isolates were susceptible to all antimicrobials tested. In addition, we identified nine multidrug-resistant (MDR) isolates inS. Typhimurium, which displayed resistance to up to eight antimicrobials (i.e., amoxicillin/clavulanate, ampicillin, ciprofloxacin, chloramphenicol, streptomycin, gentamicin, trimethoprim/sulfamethoxazole, and tetracycline). Pulsed-field gel electrophoresis (PFGE) revealed the presence of three PFGE patterns permanently present in the environment of the hospital during our study. The persistent environmental presence of MDRSalmonellaisolates, along with the fact that local and international horses are attended in this hospital, highlights the importance of improving biosecurity programs to prevent disease in horses and the hospital personnel and also for the global dissemination and acquisition of MDRSalmonella.