Biology subjects

Olivares-Pacheco, J.

Publications and source records attributed to Olivares-Pacheco, J..

4 recordsLinked to original sources

bioRxiv2023

Widespread dissemination of ESBL-producing Salmonella enterica serovar Infantis exhibiting intermediate fluoroquinolone resistance and harboring blaCTX-M-65-positive pESI-like megaplasmids in Chile

BackgroundMultidrug-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, a better understanding of its molecular epidemiology and antimicrobial-resistance profiles are required to inform effective surveillance and control measures. MethodsWe sequenced 396 Salmonella Infantis genomes and analyzed 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 AMR profiles of Salmonella Infantis in the country. FindingsThe 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. The latter 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. InterpretationOur 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. FundingAgencia de Investigacion 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. Research in contextO_ST_ABSEvidence before the studyC_ST_ABSIn the last decade, emergent multidrug-resistant Salmonella Infantis has spread worldwide, primarily linked to poultry product consumption. However, in most countries from the Americas Region, such as Chile, the extent of the dissemination of emergent Salmonella Infantis and its molecular epidemiology remains unknown. In May and September 2023, an online search was conducted using the Google engine and the PMC database with the terms "Salmonella," "Infantis," and "Chile," with no language restrictions. We assessed the results to select those presenting antimicrobial resistance, epidemiologic, or genomic data directly associated with isolates from Chile (13 studies). The selected studies showed that the prevalence of Salmonella Infantis in poultry-meat production systems, its resistance to different antibiotics, and the number of human cases of infection caused by this serovar have increased since 2014-2016. However, these reports were limited to phenotypic data or involved the genomic analysis of a few isolates (<50) obtained from the same source. No study has assessed the genomic epidemiology of the Salmonella Infantis population at the country level. Added value of this studyHere, we present the first large-scale genomic epidemiology analysis of Salmonella Infantis in Chile, including isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. We found that Salmonella Infantis in Chile is divided into several clusters of highly related isolates and that only a single cluster, the HC20_343, was associated with multiple antimicrobial-resistance determinants and pESI-like megaplasmids. We also report that isolates from this cluster are widespread among most sources, including irrigation water, poultry, food, and human cases. Detection of AMR determinants coupled with antimicrobial- susceptibility testing indicated that most HC20_343 isolates are ESBL-producers and have intermediate resistance to ciprofloxacin. Population structure analysis of this foodborne pathogen evidenced an active transmission of MDR Salmonella Infantis between different niches. This study reveals the widespread dissemination of MDR Salmonella Infantis in Chile. Implications of all the available evidenceThe evidence indicates that emerging Salmonella Infantis from the HC20_343 cluster is spreading among various niches, including irrigation water, poultry, and food, causing human infections in Chile. Its resistance to first-line antibiotics used for treating salmonellosis in individuals with a higher risk of severe or invasive infections is concerning. Currently, most surveillance and control efforts to reduce salmonellosis in Chile are focused on the poultry industry, and the study of outbreaks does not include whole-genome sequence analyses. Our findings highlight the urgent necessity to improve the surveillance and control measures to include agricultural waters to prevent contamination of produce and the further dissemination of resistance genes in the environment. As the HC20_343 cluster is highly prevalent in the Americas, further research involving large-scale genomic population analyses would shed light on the extent of the dissemination and transmission routes of emergent Salmonella Infantis in the continent and may contribute to informing surveillance and control policies.

genomics↗

bioRxiv2023

Heavy Metal Pollution From a Major Earthquake and Tsunami in Chile Is Associated With Geographic Divergence of Clinical Isolates of Methicillin-Resistant Staphylococcus aureus in Latin America

Methicillin-resistant Staphylococcus aureus (MRSA) is a priority pathogen listed by the World Health Organization. The global spread of MRSA is characterized by successive waves of epidemic clones that predominate in specific geographical regions. The acquisition of genes encoding resistance to heavy-metals is thought to be a key feature in the divergence and geographical spread of MRSA. Increasing evidence suggests that extreme natural events, such as earthquakes and tsunamis, could release heavy-metals into the environment. However, the impact of environmental exposition to heavy-metals on the divergence and spread of MRSA clones has been insufficiently explored. We assess the association between a major earthquake and tsunami in an industrialized port in southern Chile and MRSA clone divergence in Latin America. We performed a phylogenomic reconstruction of 113 MRSA clinical isolates from seven Latin American healthcare centers, including 25 isolates collected in a geographic area affected by an earthquake and tsunami that led to high levels of heavy-metal environmental contamination. We found a divergence event strongly associated with the presence of a plasmid harboring heavy-metal resistance genes in the isolates obtained in the area where the earthquake and tsunami occurred. Moreover, clinical isolates carrying this plasmid showed increased tolerance to mercury, arsenic, and cadmium. We also observed a physiological burden in the plasmid-carrying isolates in absence of heavy-metals. Our results are the first evidence that suggests that heavy-metal contamination, in the aftermath of an environmental disaster, appears to be a key evolutionary event for the spread and dissemination of MRSA in Latin America.

microbiology↗

bioRxiv2020

The analysis of the role of MexAB-OprM on quorum sensing homeostasis shows that the apparent redundancy of Pseudomonas aeruginosa multidrug efflux pumps allows keeping the robustness and the plasticity of this intercellular signaling network

Multidrug efflux pumps are key determinants for antibiotic resistance. Besides contributing to intrinsic resistance, their overexpression is frequently a cause of the increased resistance acquired during therapy. In addition to their role in resistance to antimicrobials, efflux pumps are ancient and conserved elements with relevant roles in different aspects of the bacterial physiology. It is then conceivable that their overexpression might cause a burden that will be translated into a fitness cost associated with the acquisition of resistance. In the case of Pseudomonas aeruginosa, it has been stated that overexpression of different efflux pumps is linked to the impairment of the quorum sensing (QS) response. Nevertheless, the causes of such impairment are different for each analyzed efflux pump. In this study, we performed an in-depth analysis of the QS-mediated response of a P. aeruginosa antibiotic resistant mutant that overexpresses MexAB-OprM. Although previous work claimed that this efflux pump extrudes the QS signal 3-oxo-C12-HSL, we show otherwise. Our results suggest that the observed attenuation in the QS response when overexpressing this pump is related to a reduced availability of intracellular octanoate, one of the precursors of the biosynthesis of alkyl quinolone QS signals. The overexpression of other P. aeruginosa efflux pumps has been shown to also cause a reduction in intracellular levels of QS signals or their precursors impacting on these signaling mechanisms. However, the molecules involved are distinct for each efflux pump, indicating that they can differentially contribute to the P. aeruginosa quorum sensing homeostasis. ImportanceThe success of bacterial pathogens to cause disease relies on their virulence capabilities as well as in their resistance to antibiotic interventions. In the case of the important nosocomial pathogen Pseudomonas aeruginosa, multidrug efflux pumps participate in the resistance/virulence crosstalk since, besides contributing to antibiotic resistance, they can also modulate the quorum sensing (QS) response. We show that mutants overexpressing the MexAB-OprM efflux pump, present an impaired QS response due to the reduced availability of the QS signal precursor octanoate, not because they extrude, as previously stated, the QS signal 3-oxo-C12-HSL. Together with previous studies, this indicates that, although the consequences of overexpressing efflux pumps are similar (impaired QS response), the mechanisms are different. This apparent redundancy of RND efflux systems can be understood as a P. aeruginosa strategy to keep the robustness of the QS regulatory network and modulate its output in response to different signals.

microbiology↗

bioRxiv2019

High prevalence of class 1 integrase and characterization of class 1 integron gene cassettes in multiresistant bacteria isolated from the gut microbiota of extended antibiotic treated Salmo salar fish farms

The use of antimicrobials in aquaculture is a common practice. Chile is second larger producer of salmon worldwide, but unfortunately is the first consumer of antibiotics. Tonnes of florfenicol and oxytetracycline yearly are used in the Chilean salmoniculture to control the pathogens that threaten the sustainability of the industry. This excessive use of antibiotics have selected populations of resistant bacteria from the sediments and the water column that sorround the fish farms. In a recent work, our lab described the high prevalence of multiresistant bacteria and Antibiotic Resistance Genes (ARGs) in the gut microbiota of Antlactic salmon (Salmo salar) treated with high doses of antibiotics. In this work, we revisited the analysis of the previously described gut multiresistant bacteria grouped in banks of florfenicol resistant isolates (FB) and oxytetracycline resistant isolates (OB) looking for the presence of integron-integrase elements. These elements have been described as an important players in the Antimicrobial Resistance (AMR) phenomenon and they are considered a good markers of the anthopogenic activities pollution. The results showed that the 100% of the multiresistant isolates present the class 1 intagrase. Despite this result, no isolate from FB showed the typical structure of class 1 integrons: the presence in 3-CS of qacE{Delta}1/sul1 genes. While in OB, only 23% of the isolates showed this characteristic structure. Additionally, only four isolates of OB and none of FB showed recognisable gene cassettes and no genes of resistance to florfenicol and oxytetacycline appeared in them. Of these four isolates, three of them showed a single gene cassette containing the dfrA-14 gene, which confers resistance to trimethoprim. Whilst the other isolate showed the aac(6)31-qacH-blaoxa2 genes, which confers resistance to aminoglycosides, quaternary ammonium compounds and beta-lactams, respectively. Finally, it was possible to demonstrate that the described integrons probably come from anthropogenic activities like clinical settings and/or industrial animal husbandry, since they show integrases proteins identical to those carried by human pathogens.

microbiology↗