RESUMEN
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 antimicrobial-resistance 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 ß-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. Funding: Partially supported by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services as part of an award, FDU001818, with 30% percent funded by FDA/HHS; and by Agencia de Investigación y Desarrollo de Chile (ANID) through FONDECYT de Postdoctorado Folio 3230796 and Folio 3210317, FONDECYT Regular Folio 1231082, and ANID-Millennium Science Initiative Program-ICN2021_044.
RESUMEN
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.
RESUMEN
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 ß-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.
