RESUMEN
Corynebacterium striatum, present in the microbiota of human skin and nasal mucosa, has recently emerged as a causative agent of hospital-acquired infections, notable for its resistance to multiple antimicrobials. Its mobilome comprises several mobile genetic elements, such as plasmids, transposons, insertion sequences and integrons, which contribute to the acquisition of antimicrobial resistance genes. This study analyzes the contribution of the C. striatum mobilome in the transfer and dissemination of resistance genes. In addition, integrative and conjugative elements (ICEs), essential in the dissemination of resistance genes between bacterial populations, whose role in C. striatum has not yet been studied, are examined. This study examined 365 C. striatum genomes obtained from the NCBI Pathogen Detection database. Phylogenetic and pangenome analyses were performed, the resistance profile of the bacterium was recognized, and mobile elements, including putative ICE, were detected. Bioinformatic analyses identified 20 antimicrobial resistance genes in this species, with the Ermx gene being the most predominant. Resistance genes were mainly associated with plasmid sequence regions and class 1 integrons. Although an ICE was detected, no resistance genes linked to this element were found. This study provided valuable information on the geographic spread and prevalence of outbreaks observed through phylogenetic and pangenome analyses, along with identifying antimicrobial resistance genes and mobile genetic elements that carry many of the resistance genes and may be the subject of future research and therapeutic approaches.
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Corynebacterium , Filogenia , Corynebacterium/genética , Humanos , Plásmidos/genética , Genoma Bacteriano , Infecciones por Corynebacterium/microbiología , Antibacterianos/farmacología , Farmacorresistencia Bacteriana/genética , Elementos Transponibles de ADN/genética , Integrones/genética , Farmacorresistencia Bacteriana Múltiple/genética , Secuencias Repetitivas Esparcidas/genéticaRESUMEN
Background: Infections caused by antibiotic-resistant bacteria pose a major challenge to modern healthcare. This systematic review evaluates the efficacy of machine learning (ML) approaches in predicting antimicrobial resistance (AMR) in critical pathogens (CP), considering Whole Genome Sequencing (WGS) and antimicrobial susceptibility testing (AST). Methods: The search covered databases including PubMed/MEDLINE, EMBASE, Web of Science, SCOPUS, and SCIELO, from their inception until June 2024. The review protocol was officially registered on PROSPERO (CRD42024543099). Results: The review included 26 papers, analyzing data from 104,141 microbial samples. Random Forest (RF), XGBoost, and logistic regression (LR) emerged as the top-performing models, with mean Area Under the Receiver Operating Characteristic (AUC) values of 0.89, 0.87, and 0.87, respectively. RF showed superior performance with AUC values ranging from 0.66 to 0.97, while XGBoost and LR showed similar performance with AUC values ranging from 0.83 to 0.91 and 0.76 to 0.96, respectively. Most studies indicate that integrating WGS and AST data into ML models enhances predictive performance, improves antibiotic stewardship, and provides valuable clinical decision support. ML shows significant promise for predicting AMR by integrating WGS and AST data in CP. Standardized guidelines are needed to ensure consistency in future research.
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Farmacorresistencia Bacteriana , Aprendizaje Automático , Pruebas de Sensibilidad Microbiana , Secuenciación Completa del Genoma , Humanos , Farmacorresistencia Bacteriana/genética , Antibacterianos/uso terapéutico , Antibacterianos/farmacología , Bacterias/efectos de los fármacos , Bacterias/genéticaRESUMEN
Introduction. Multidrug-resistant infections present a critical public health due to scarce treatment options and high mortality. Ocimum gratissimum L. essential oil (O.geo) is a natural resource rich in eugenol known for its antimicrobial activity.Hypothesis/Gap Statement. O.geo may exert effective antimicrobial activity against polymyxin-resistant Klebsiella pneumoniae and, when combined with Polymyxin B (PMB), may exhibit a synergistic effect, enhancing treatment efficacy and reducing antimicrobial resistance.Aim. This study aims to investigate the antimicrobial activity of O.geo against polymyxin-resistant K. pneumoniae using in vitro tests and an in vivo Caenorhabditis elegans model.Methodology. The O.geo was obtained by hydrodistillation followed by gas chromatography. The MIC and antibiofilm activity were determined using broth microdilution. Checkerboard and time-kill assays evaluated the combination of O.geo and polymyxin B (PMB), whereas a protein leakage assay verified its action.Results. Eugenol (39.67%) was a major constituent identified. The MIC of the O.geo alone ranged from 128 to 512 µg ml-1. The fractional inhibitory concentration index (0.28) and time-kill assay showed a synergism. In addition, O.geo and PMB inhibited biofilm formation and increased protein leakage in the plasma membrane. The treatment was tested in vivo using a Caenorhabditis elegans model, and significantly increased survival without toxicity was observed.Conclusion. O.geo could be used as a potential therapeutic alternative to combat infections caused by multidrug-resistant bacteria, especially in combination with PMB.
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Antibacterianos , Biopelículas , Caenorhabditis elegans , Sinergismo Farmacológico , Klebsiella pneumoniae , Pruebas de Sensibilidad Microbiana , Ocimum , Aceites Volátiles , Polimixina B , Klebsiella pneumoniae/efectos de los fármacos , Caenorhabditis elegans/efectos de los fármacos , Animales , Antibacterianos/farmacología , Aceites Volátiles/farmacología , Aceites Volátiles/química , Ocimum/química , Biopelículas/efectos de los fármacos , Polimixina B/farmacología , Infecciones por Klebsiella/tratamiento farmacológico , Infecciones por Klebsiella/microbiología , Farmacorresistencia Bacteriana , Polimixinas/farmacología , Farmacorresistencia Bacteriana MúltipleRESUMEN
Thermotolerant Campylobacter is an important zoonotic pathogen known for causing gastroenteritis in humans, with poultry as its primary reservoir. A total of 468 samples were collected, of which 335 were chicken carcass samples (representing the food component), and 133 were chicken caeca samples (representing the animal component). These samples underwent culture, with colonies examined under a microscope. Species identification was achieved through multiplex PCR. Additionally, antimicrobial susceptibility profiles were determined using the Kirby-Bauer method, testing for sensitivity to gentamicin, ciprofloxacin, tetracycline, and erythromycin. Additionally, 55 C. jejuni (62.5%) and 33 C. coli (37.5%) isolates were selected for whole genome sequencing (WGS). A High prevalence of Campylobacter was observed, with rates of 95.5% (n = 127, CI95%: 92.5% - 98.5%) in the animal component and 72.5% (n = 243, CI95%: 69.9% - 75.1%) in the food component. Specifically, C. jejuni was detected in 33.1% (n = 42) of poultry farms and 38.3% (n = 93) of chicken carcasses, while C. coli was found in 64.6% (n = 82) of poultry farms and 60.5% (n = 147) of chicken carcasses. Antimicrobials with the highest rates of resistance (67%-100%) were ciprofloxacin and tetracycline, in both animal and food component isolates. Erythromycin resistance was notable, ranging from 22% to 33%, with only two C. jejuni isolates from retail were resistant to gentamicin. Furthermore, multidrug resistance was identified in 23% (20 isolates) of the Campylobacter isolates. Genetic analysis revealed the presence of fourteen resistance genes in both C. jejuni and C. coli isolates, including tet(O), blaOXA-460, blaOXA-184, blaOXA-489, blaOXA-193, blaOXA-784, blaOXA-603, aph(3')-IIIa, aad9, aph(2'')-If, aadE-Cc, sat4, and ant(6)-Ia. Additionally, twenty-five plasmids were detected in the 88 Campylobacter isolates examined. Interestingly, most isolates also harbored genes encoding putative virulence factors associated with pathogenicity, invasion, adherence, and production of cytolethal distending toxin (cdt): cheV, cheA, cheW, cheY, flaA, flgR, flaC, flaD, flgB, flgC, ciaB, ciaC. The WGS analysis showed the presence of several cgSTs in both animal and food components, with nine of them widely disseminated between components. Moreover, C. coli and C. jejuni isolates from different sources presented less than 11 single nucleotide polymorphisms (SNPs), suggesting clonality (16 isolates). Further analysis using SNP tree demonstrated widespread distribution of certain C. jejuni and C. coli clones across multiple farms and retail stores. This study presents, for the first-time, insights into the clonality, plasmid diversity, virulence, and antimicrobial resistance (AMR) of thermotolerant Campylobacter strains originating from the Ecuadorian poultry industry. The identification of AMR genes associated with the main antibiotics used in the treatment of campylobacteriosis in humans, highlights the importance of the prudent use of antimicrobials in the poultry industry. Additionally, this research remarks the need for regional studies to understand the epidemiology of this pathogen.
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Antibacterianos , Infecciones por Campylobacter , Campylobacter coli , Campylobacter jejuni , Pollos , Granjas , Variación Genética , Campylobacter coli/genética , Campylobacter coli/efectos de los fármacos , Campylobacter coli/aislamiento & purificación , Animales , Campylobacter jejuni/genética , Campylobacter jejuni/efectos de los fármacos , Campylobacter jejuni/aislamiento & purificación , Pollos/microbiología , Antibacterianos/farmacología , Infecciones por Campylobacter/microbiología , Infecciones por Campylobacter/epidemiología , Infecciones por Campylobacter/veterinaria , Farmacorresistencia Bacteriana/genética , Ecuador/epidemiología , Pruebas de Sensibilidad Microbiana , Humanos , Microbiología de Alimentos , Secuenciación Completa del Genoma , Tetraciclina/farmacologíaRESUMEN
BACKGROUND: Helicobacter pylori infects the stomach and/or small intestines in more than half of the human population. Infection with H. pylori is the most common cause of chronic gastritis, which can lead to more severe gastroduodenal pathologies such as peptic ulcer, mucosa-associated lymphoid tissue lymphoma, and gastric cancer. H. pylori infection is particularly concerning in Colombia in South America, where > 80% of the population is estimated to be infected with H. pylori and the rate of stomach cancer is one of the highest in the continent. RESULTS: We compared the antimicrobial susceptibility profiles and short-read genome sequences of five H. pylori isolates obtained from patients diagnosed with gastritis of varying severity (chronic gastritis, antral erosive gastritis, superficial gastritis) in Pereira, Colombia sampled in 2015. Antimicrobial susceptibility tests revealed the isolates to be resistant to at least one of the five antimicrobials tested: four isolates were resistant to metronidazole, two to clarithromycin, two to levofloxacin, and one to rifampin. All isolates were susceptible to tetracycline and amoxicillin. Comparative genome analyses revealed the presence of genes associated with efflux pump, restriction modification systems, phages and insertion sequences, and virulence genes including the cytotoxin genes cagA and vacA. The five genomes represent three novel sequence types. In the context of the Colombian and global populations, the five H. pylori isolates from Pereira were phylogenetically distant to each other but were closely related to other lineages circulating in the country. CONCLUSIONS: H. pylori from gastritis of different severity varied in their antimicrobial susceptibility profiles and genome content. This knowledge will be useful in implementing appropriate eradication treatment regimens for specific types of gastritis. Understanding the genetic and phenotypic heterogeneity in H. pylori across the geographical landscape is critical in informing health policies for effective disease prevention and management that is most effective at local and country-wide scales. This is especially important in Colombia and other South American countries that are poorly represented in global genomic surveillance studies of bacterial pathogens.
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Antibacterianos , Farmacorresistencia Bacteriana , Gastritis , Genoma Bacteriano , Infecciones por Helicobacter , Helicobacter pylori , Humanos , Helicobacter pylori/genética , Helicobacter pylori/efectos de los fármacos , Helicobacter pylori/patogenicidad , Helicobacter pylori/aislamiento & purificación , Gastritis/microbiología , Colombia , Infecciones por Helicobacter/microbiología , Antibacterianos/farmacología , Virulencia/genética , Farmacorresistencia Bacteriana/genética , Genómica , Pruebas de Sensibilidad Microbiana , Filogenia , Persona de Mediana Edad , Masculino , FemeninoRESUMEN
Antibiotic resistance, driven by the proliferation of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARBs), has emerged as a pressing global health concern. Antimicrobial resistance is exacerbated by the widespread use of antibiotics in agriculture, aquaculture, and human medicine, leading to their accumulation in various environmental compartments such as soil, water, and sediments. The presence of ARGs in the environment, particularly in municipal water, animal husbandry, and hospital environments, poses significant risks to human health, as they can be transferred to potential human pathogens. Current remediation strategies, including the use of pyroligneous acid, coagulants, advanced oxidation, and bioelectrochemical systems, have shown promising results in reducing ARGs and ARBs from soil and water. However, these methods come with their own set of challenges, such as the need for elevated base levels in UV-activated persulfate and the long residence period required for photocatalysts. The future of combating antibiotic resistance lies in the development of standardized monitoring techniques, global collaboration, and the exploration of innovative remediation methods. Emphasis on combination therapies, advanced oxidation processes, and monitoring horizontal gene transfer can pave the way for a comprehensive approach to mitigate the spread of antibiotic resistance in the environment.
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Antibacterianos , Bacterias , Bacterias/genética , Bacterias/efectos de los fármacos , Farmacorresistencia Bacteriana/genética , Farmacorresistencia Microbiana/genética , Genes Bacterianos , Monitoreo del Ambiente , Restauración y Remediación Ambiental/métodosRESUMEN
Antibiotic resistance constitutes a significant public health challenge, with diverse reservoirs of resistant bacteria playing pivotal roles in their dissemination. Among these reservoirs, pets are carrying antibiotic-resistant strains. The objective of this study was to assess the resistance profiles of Escherichia coli, and the prevalence of extended-spectrum ß-lactamase (ESBL) producing E. coli strains in dogs and cats from Tamaulipas, Mexico. A total of 300 stool samples (150 dogs and 150 cats) from healthy pets were subjected to analysis. Antibiotic susceptibility testing and the identification of ESBLs were carried out by disc diffusion method. The presence of resistance genes, class 1, 2, and 3 integrons (intI1, intI2, and intI3) and phylogroups was determined by PCR analysis. The findings reveal that 42.6% (128/300) of the strains exhibited resistance to at least one of the eight antibiotics assessed, and 18.6% (56/300) demonstrated multidrug resistance (MDR), that distributed across 69 distinct resistance patterns. Altogether 2.6% of E. coli strains (8/300) were confirmed as TEM and CTX-M type ESBL producers. These outcomes underscore the roles of dogs and cats in Tamaulipas as reservoirs for the dissemination of MDR and/or ESBL strains. The results underscore the necessity for conducting prevalence studies on ESBL-producing E. coli, forming a foundation for comprehending the present scenario and formulating strategies for the control and mitigation of this issue.
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Antibacterianos , Escherichia coli , Heces , Pruebas de Sensibilidad Microbiana , Mascotas , beta-Lactamasas , Animales , Perros/microbiología , México , Escherichia coli/genética , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Gatos/microbiología , Antibacterianos/farmacología , Mascotas/microbiología , beta-Lactamasas/genética , Heces/microbiología , Infecciones por Escherichia coli/veterinaria , Infecciones por Escherichia coli/microbiología , Farmacorresistencia Bacteriana Múltiple , Farmacorresistencia Bacteriana , Integrones , Enfermedades de los Gatos/microbiología , Enfermedades de los Perros/microbiología , PrevalenciaRESUMEN
Colistin resistance poses a major therapeutic challenge and resistant strains have now been reported worldwide. However, the occurrence of such bacteria in aquatic environments is considerably less understood. This study aimed to isolate and characterize colistin-resistant strains from water and plastic litter collected in an urban recreational estuary. Altogether, 64 strains with acquired colistin resistance were identified, mainly Acinetobacter spp. and Enterobacter spp. From these, 40.6% were positive for at least one mcr variant (1-9), 26.5% harbored, extended-spectrum beta-lactamases, 23.4% harbored, sulfonamide resistance genes, and 9.3% harbored, quinolone resistance genes. merA, encoding mercury resistance, was detected in 10.5% of these strains, most of which were also strong biofilm producers. The minimum inhibitory concentration toward colistin was determined for the mcr-positive strains and ranged from 2 to ≥512 µg ml-1. Our findings suggest that Gram-negative bacteria highly resistant to a last-resort antimicrobial can be found in recreational waters and plastic litter, thereby evidencing the urgency of the One Health approach to mitigate the antimicrobial resistance crisis.
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Antibacterianos , Colistina , Farmacorresistencia Bacteriana , Estuarios , Pruebas de Sensibilidad Microbiana , Plásticos , Colistina/farmacología , Antibacterianos/farmacología , Microbiología del Agua , Bacterias/genética , Bacterias/efectos de los fármacos , Bacterias/aislamiento & purificación , Bacterias/clasificación , Bacterias Gramnegativas/efectos de los fármacos , Bacterias Gramnegativas/genética , Bacterias Gramnegativas/aislamiento & purificaciónRESUMEN
Coastal water quality is facing increasing threats due to human activities. Their contamination by sewage discharges poses significant risks to the environment and public health. We aimed to investigate the presence of antibiotic-resistant Enterococcus in beach waters. Over a 10-month period, samples were collected from four beaches in the State of São Paulo (Brazil). Enterococcus isolates underwent matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) and molecular analysis for accurate genus and species identification. The antimicrobial susceptibility for 14 antibiotics was evaluated using the disc diffusion method followed by a multidrug-resistance (MDR) classification. PCR amplification method was used to detect antimicrobial resistance genes (ARGs). Our findings revealed the prevalence of Enterococcus faecalis, E. faecium and E. hirae. Out of 130 isolates, 118 were resistant to multiple antibiotics. The detection of resistance genes provided evidence of the potential transfer of antibiotic resistance within the environment. Our findings underscore the necessity for continuous research and surveillance to enhance understanding of the pathogenicity and antimicrobial resistance mechanisms of Enterococcus, which is crucial to implement effective measures to preserve the integrity of coastal ecosystems.
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Antibacterianos , Enterococcus faecalis , Enterococcus faecium , Enterococcus hirae , Brasil , Enterococcus faecalis/efectos de los fármacos , Enterococcus faecalis/genética , Enterococcus faecalis/aislamiento & purificación , Enterococcus faecium/efectos de los fármacos , Enterococcus faecium/genética , Enterococcus faecium/aislamiento & purificación , Antibacterianos/farmacología , Enterococcus hirae/efectos de los fármacos , Enterococcus hirae/genética , Enterococcus hirae/aislamiento & purificación , Farmacorresistencia Bacteriana , Playas , Pruebas de Sensibilidad Microbiana , Agua de Mar/microbiologíaRESUMEN
Although diphtheria is a vaccine-preventable disease, numerous cases are still reported around the world, as well as outbreaks in countries, including European ones. Species of the Corynebacterium diphtheriae complex are potentially toxigenic and, therefore, must be considered given the possible consequences, such as the circulation of clones and transmission of antimicrobial resistance and virulence genes. Recently, Corynebacterium rouxii was characterized and included among the valid species of the complex. Therefore, two cases of C. rouxii infection arising from infections in domestic animals are presented here. We provide molecular characterization, phylogenetic analyses, genome sequencing, and CRISPR-Cas analyses to contribute to a better understanding of the molecular bases, pathogenesis, and epidemiological monitoring of this species, which is still little studied. We confirmed its taxonomic position with genome sequencing and in silico analysis and identified the ST-918 for both strains. The clinical isolates were sensitive resistance to benzylpenicillin and rifampin. Antimicrobial resistance genes, including tetB, rpoB2, and rbpA genes, were predicted. The bla and ampC genes were not found. Several virulence factors were also detected, including adhesion, iron uptake systems, gene regulation (dtxR), and post-translational modification (MdbA). Finally, one prophage and the Type I-E CRISPR-Cas system were identified.
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Antibacterianos , Infecciones por Corynebacterium , Corynebacterium , Enfermedades de los Perros , Filogenia , Rifampin , Animales , Corynebacterium/genética , Corynebacterium/efectos de los fármacos , Enfermedades de los Perros/microbiología , Perros , Rifampin/farmacología , Infecciones por Corynebacterium/veterinaria , Infecciones por Corynebacterium/microbiología , Antibacterianos/farmacología , Genoma Bacteriano , Farmacorresistencia Bacteriana/genética , Penicilinas/farmacologíaRESUMEN
Neisseria gonorrhoeae is a global threat to public health due to the accumulation of antimicrobial resistance mechanisms. ST-1901 is an internationally important sequence type (ST) because of its high incidence and the usual occurrence of chromosomally determined resistance. In this study, we describe the evolution of the ST-1901 and its single locus variants in Rio de Janeiro from 2006 to 2022. We analyzed 82 N. gonorrhoeae isolates according to antimicrobial susceptibility profile, resistance mechanisms, molecular typing, and phylogenetics. Six different single locus variants were detected. Phylogenetic analysis identified five clades, which share similar characteristics. Resistance rates for penicillin and tetracycline decreased due to the lower occurrence of resistance plasmids, but intermediary resistance to penicillin rose. Resistance to ciprofloxacin remained high throughout all clades and the years of the study. Regarding resistance to azithromycin, alterations in mtrR promoter and gene, and 23S rRNA encoding gene rrl were detected, with a notable rise in the incidence of C2611T mutations in more recent years occurring in four of five clades. In contrast, ß-lactam resistance associated penA 34 mosaic was found only in one persisting clade (Clade D), and unique G45D and A39T mutations in mtrR gene and its promoter (Nm-Like) were found only in Clade B. Taken together, these data suggest that ST-1901, a persistently circulating lineage of N. gonorrhoeae in Rio de Janeiro, has undergone changes over the years and may evolve to develop resistance to the current recommended dual therapy adopted in Brazil, namely, ceftriaxone and azithromycin.
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Antibacterianos , Gonorrea , Pruebas de Sensibilidad Microbiana , Neisseria gonorrhoeae , Filogenia , Neisseria gonorrhoeae/genética , Neisseria gonorrhoeae/efectos de los fármacos , Neisseria gonorrhoeae/clasificación , Brasil , Antibacterianos/farmacología , Humanos , Gonorrea/microbiología , Gonorrea/epidemiología , Gonorrea/tratamiento farmacológico , Farmacorresistencia Bacteriana/genética , Proteínas Bacterianas/genética , Azitromicina/farmacología , Ciprofloxacina/farmacología , ARN Ribosómico 23S/genética , Proteínas Represoras/genética , Plásmidos/genética , Mutación , Penicilinas/farmacologíaRESUMEN
Motivation for the study. The presence of antibiotic resistance genes in bacteria isolated from common flies is a potential public health hazard because it facilitates the presence and spread of antibiotic resistance genes in the environment. Main findings. Thirty-eight bacterial strains identified in 14 species were isolated from within the fly bodies, of which 31 strains showed resistance to carbapenems and 26 strains showed resistance to colistin. Seven bacterial strains showed carbapenem resistance genes and one Escherichia coli strain had resistance to KPC, OXA-48 and mcr-1. Implications. This is the first report of antibiotic resistance genes in bacteria carried by common flies in Peru. The objective was to determine the presence of carbapenem resistance genes and plasmid resistance to colistin (mcr-1) in bacteria isolated from Musca domestica in a garbage dump near a hospital in Lima, Peru. Bacteria with phenotypic resistance to carbapenemics were isolated on CHROMagar mSuperCARBATM medium and colistin resistance profiling was performed using the colistin disk elution method. Detection of blaKPC, blaNDM, blaIMP, blaOXA-48, blaVIM and mcr-1 genes was performed by conventional PCR. The antimicrobial susceptibility profile was determined using the automated MicroScan system. We found that 31/38 strains had phenotypic resistance to carbapenemics and 26/38 strains had phenotypic resistance to colistin with a minimum inhibitory concentration ≥ 4 µg/ml. Finally, we identified seven bacterial strains with carbapenem resistance genes (OXA-48 and KPC) and one bacterial strain with plasmid resistance to colistin (mcr-1). One Escherichia coli strain had three resistance genes: KPC, OXA-48 and mcr-1.
El objetivo fue determinar la presencia de genes de resistencia a carbapenémicos y resistencia plasmídica a colistina (mcr-1) en bacterias aisladas de Musca domestica en un basural cercano a un hospital de Lima, Perú. Las bacterias con resistencia fenotípica a los carbapénemicos se aislaron en medio CHROMagar mSuperCARBATM y el perfil de resistencia a colistina se realizó mediante el método de elución de discos de colistina. La detección de genes blaKPC, blaNDM, blaIMP, blaOXA-48, blaVIM y mcr-1 se realizó mediante PCR convencional. El perfil de susceptibilidad antimicrobiana se determinó mediante el sistema automatizado MicroScan. Las bacterias con resistencia fenotípica a carbapenémicos fueron 31/38 cepas y a colistina fueron 26/38 cepas con una concentración inhibitoria mínima ≥ 4 µg/ml. Finalmente, se identificaron siete cepas bacterianas con genes de resistencia a carbapenémicos (OXA-48 Y KPC) y una cepa bacteriana con resistencia plasmídica a colistina (mcr-1). Una cepa de Escherichia coli presentó tres genes de resistencia: KPC, OXA-48 y mcr-1. Motivación para realizar el estudio. La presencia de genes de resistencia a antibióticos en bacterias aisladas de moscas comunes es un peligro potencial para la salud pública debido a que facilita la presencia y dispersión de genes de resistencia a antibióticos en el medio ambiente. Principales hallazgos. Se aislaron 38 cepas bacterianas identificadas en 14 especies dentro del cuerpo de las moscas, de las cuales 31 cepas mostraron resistencia a los carbapenémicos y 26 cepas mostraron resistencia a colistina. Siete cepas bacterianas presentaron genes de resistencia a carbapenémicos y una cepa de Escherichia coli con resistencia a KPC, OXA-48 y mcr-1. Implicancias. Se realiza el primer reporte en el Perú de genes de resistencia a antibióticos en bacterias movilizadas por moscas comunes.
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Antibacterianos , Carbapenémicos , Colistina , Farmacorresistencia Bacteriana , Moscas Domésticas , Colistina/farmacología , Moscas Domésticas/genética , Moscas Domésticas/microbiología , Animales , Perú , Carbapenémicos/farmacología , Antibacterianos/farmacología , Farmacorresistencia Bacteriana/genética , Hospitales , Pruebas de Sensibilidad Microbiana , Genes BacterianosRESUMEN
OBJECTIVES.: To evaluate the presence and sensitivity to antimicrobials of Escherichia coli strains isolated from 24 irrigation water samples from the Rimac river of East Lima, Peru. MATERIALS AND METHODS.: The E. coli strains were identified by PCR. Antibiotic susceptibility was processed by the disk diffusion method. Genes involved in extended spectrum beta-lactamases (BLEE), quinolones and virulence were determined by PCR. RESULTS.: All samples exceeded the acceptable limits established in the Environmental Quality Standards for vegetable irrigation. Of the 94 isolates, 72.3% showed resistance to at least one antibiotic, 24.5% were multidrug resistant (MDR) and 2.1% were extremely resistant. The highest percentages of resistance were observed for ampicillin-sulbactam (57.1%), nalidixic acid (50%), trimethoprim-sulfamethoxazole (35.5%) and ciprofloxacin (20.4%). Among the isolates, 3.2% had a BLEE phenotype related to the bla CTX-M-15 gene. qnrB (20.4%) was the most frequent transferable mechanism of resistance to quinolones, and 2.04% had qnrS. It was estimated that 5.3% were diarrheagenic E. coli and of these, 60% were enterotoxigenic E. coli, 20% were enteropathogenic E. coli and 20% were enteroaggregative E. coli. CONCLUSIONS.: The results show the existence of diarrheogenic pathotypes in the water used for irrigation of fresh produce and highlight the presence of BLEE- and MDR-producing E. coli, demonstrating the role played by irrigation water in the dissemination of resistance genes in Peru.Motivation for the study. Aquatic systems, including irrigation water, have been identified as reservoirs of antimicrobial resistance, with few studies in Peru on the presence of Escherichia coli and their levels of virulence and antimicrobial resistance. Main findings. Our results show the presence of E. coli above the established standard for vegetable irrigation water, some with very high levels of antimicrobial resistance. Implications. The presence of ESBL-producing strains of extended-spectrum beta-lactamases and multidrug-resistant E. coli in irrigation water could contribute to the dissemination of resistance genes in Peru, posing a significant threat to public health.
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Riego Agrícola , Cefalosporinas , Escherichia coli , Quinolonas , Ríos , Microbiología del Agua , Perú , Escherichia coli/efectos de los fármacos , Escherichia coli/genética , Escherichia coli/aislamiento & purificación , Ríos/microbiología , Quinolonas/farmacología , Cefalosporinas/farmacología , Farmacorresistencia Bacteriana , Antibacterianos/farmacología , Pruebas de Sensibilidad MicrobianaRESUMEN
BACKGROUND: Marmosets (Callithrix sp.), including black-tuffed marmosets (C. penicillata), are neotropical primates that can be highly adapted to urban environments, especially parks and forested areas near cities. Staphylococcus spp. are part of the microbiota of many different hosts and lead to opportunistic severe infection. Isolates from wild animals can be resistant to antimicrobial drugs. However, there are a few studies that evaluated Staphylococcus spp. in neotropical primates. The goal of this study was to evaluate Staphylococcus spp. isolated from free-ranging black-tuffed marmosets. METHODS: Marmosets were captured in six urban parks. After sedation, skin and rectal swabs and feces were sampled. Staphylococcus spp. isolates were identified by MALDI-ToF and their antimicrobial susceptibility was determined. RESULTS: Over 30% of captured individuals were positive for Staphylococcus spp., and S. aureus was the most isolated species followed by Mammaliicoccus (Staphylococcus) sciuri. With the exception of the marmoset subjected to necropsy, none of the other had lesions, which supports that notion that Staphylococcus spp. are members of the microbiota, but also opportunistic pathogens. Most isolates were susceptible to all antimicrobials tested; however, one isolate of S. epidermidis was resistant to multiple antimicrobials (penicillin, cefoxitin, ciprofloxacin, clindamycin, and erythromycin). We considered S. aureus as the main staphylococci to colonize black-tuffed marmosets. CONCLUSIONS: Black-tuffed marmosets can be colonized by several Staphylococcus species, most frequently by S. aureus, and the majority of isolates were sensible to the antimicrobials tested. One S. epidermidis isolate was considered multidrug resistant.
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Antibacterianos , Callithrix , Enfermedades de los Monos , Infecciones Estafilocócicas , Staphylococcus , Animales , Callithrix/microbiología , Staphylococcus/efectos de los fármacos , Staphylococcus/aislamiento & purificación , Enfermedades de los Monos/microbiología , Enfermedades de los Monos/epidemiología , Infecciones Estafilocócicas/veterinaria , Infecciones Estafilocócicas/microbiología , Infecciones Estafilocócicas/epidemiología , Antibacterianos/farmacología , Femenino , Farmacorresistencia Bacteriana , Masculino , Microbiota/efectos de los fármacos , Ciudades , Brasil/epidemiología , Heces/microbiologíaRESUMEN
Yersiniosis, caused by Yersinia ruckeri, has become the most common disease in farmed rainbow trout Oncorhynchus mykiss in Peru, affecting Puno and Junín Regions, important aquaculture areas in the country. Florfenicol (FLO) and oxytetracycline (OXY) are the antimicrobials most frequently used to mitigate losses attributed to this pathogen. This study presents an analysis of the susceptibility patterns of 60 Y. ruckeri isolates (30 isolates each from Puno and Junín), including the type strain CECT 4319T and the strains CECT 955 and CECT 956, against FLO and OXY. Minimum inhibitory concentrations (MICs) were determined following the guideline for standard broth dilution method published by the Clinical and Laboratory Standards Institute. MIC results ranged from 4.0 to 8.0 µg ml-1 for FLO and 0.5 to 4.0 µg ml-1 for OXY. Normalized resistance interpretation (NRI) analysis identified epidemiological cut-off values of ≤16.0 µg ml-1 for FLO and ≤4.0 µg ml-1 for OXY. All Peruvian isolates, including the collection strains, were categorized as wild-type for both antimicrobials. Even though the number of Y. ruckeri isolates with MIC values of 8 µg ml-1 for FLO is more than double in Puno than in Junín (15 vs. 7 isolates), the NRI analysis showed the same epidemiological cutoff of 16 µg ml-1; while for OXY, it was 4.0 µg ml-1 for Puno and 2.0 µg ml-1 for Junín. This study establishes the basis for monitoring susceptibility to FLO and OXY in new Y. ruckeri isolates in Peruvian rainbow trout farming.
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Antibacterianos , Enfermedades de los Peces , Pruebas de Sensibilidad Microbiana , Oxitetraciclina , Tianfenicol , Yersinia ruckeri , Antibacterianos/farmacología , Tianfenicol/análogos & derivados , Tianfenicol/farmacología , Yersinia ruckeri/efectos de los fármacos , Perú/epidemiología , Oxitetraciclina/farmacología , Animales , Enfermedades de los Peces/microbiología , Farmacorresistencia Bacteriana , Yersiniosis/veterinaria , Yersiniosis/microbiología , Oncorhynchus mykissRESUMEN
The collective involvement of virulence markers of Escherichia coli as an emerging pathogen associated with periodontitis remains unexplained. This study aimed to implement an in vitro model of infection using a human epithelial cell line to determine the virulome expression related to the antibiotic and disinfectant resistance genotype and pulse field gel electrophoresis (PFGE) type in E. coli strains isolated from patients with periodontal diseases. We studied 100 strains of E. coli isolated from patients with gingivitis (n = 12), moderate periodontitis (n = 59), and chronic periodontitis (n = 29). The identification of E. coli and antibiotic and disinfectant resistance genes was performed through PCR. To promote the expression of virulence genes in the strains, an in vitro infection model was used in the human epithelial cell line A549. RNA was extracted using the QIAcube robotic equipment and reverse transcription to cDNA was performed using the QuantiTect reverse transcription kit (Qiagen). The determination of virulence gene expression was performed through real-time PCR. Overall, the most frequently expressed adhesion genes among the isolated strains of gingivitis, moderate periodontitis, and chronic periodontitis were fimH (48%), iha (37%), and papA (18%); those for toxins were usp (33%); those for iron acquisition were feoB (84%), fyuA (62%), irp-2 (61%), and iroN (35%); those for protectins were traT (50%), KpsMT (35%), and ompT (28%); and those for pathogenicity islands were malX (45%). The most common antibiotic and disinfectant resistance genes among gingivitis, moderate periodontitis, and chronic periodontitis strains were sul-2 (43%), blaSHV (47%), blaTEM (45%), tet(A) (41%), dfrA1 (32%), marR-marO (57%), and qacEA1 (79%). The findings revealed the existence of a wide distribution of virulome expression profiles related to the antibiotic and disinfectant resistance genotype and PFGE type in periodontal strains of E. coli. These findings may contribute toward improving the prevention and treatment measures for periodontal diseases associated with E. coli.
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Antibacterianos , Desinfectantes , Farmacorresistencia Bacteriana , Infecciones por Escherichia coli , Escherichia coli , Factores de Virulencia , Humanos , Escherichia coli/genética , Escherichia coli/efectos de los fármacos , Escherichia coli/patogenicidad , Factores de Virulencia/genética , Antibacterianos/farmacología , Infecciones por Escherichia coli/microbiología , Farmacorresistencia Bacteriana/genética , Desinfectantes/farmacología , Periodontitis/microbiología , Virulencia/genética , Células A549 , Células Epiteliales/microbiología , Genotipo , Adulto , Femenino , Masculino , Persona de Mediana Edad , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Electroforesis en Gel de Campo PulsadoRESUMEN
AIMS: Characterize global genomic features of 86 genomes of Salmonella Gallinarum (SG) and Pullorum (SP), which are important pathogens causing systemic infections in poultry. METHODS AND RESULTS: All genomes harbored efflux pump encoding gene mdsA and gold tolerance genes golS and golT. Aminoglycoside (aac(6')-Ib, aadA5, aph(6)-Id, aph(3'')-Ib, ant(2'')-Ia), beta-lactam (blaTEM-1, blaTEM-135), efflux pump (mdsB), fosfomycin (fosA3), sulfonamide (sul1, sul2), tetracycline [tet(A)], trimethoprim (dfrA17), acid (asr), and disinfectant (qacEdelta1) resistance genes, gyrA, gyrB, and parC quinolone resistance point mutations, and mercury tolerance genes (mer) were found in different frequencies. Additionally, 310 virulence genes, pathogenicity islands (including SPI-1, 2, 3, 4, 5, 6, 9, 10, 12, 13, and 14), plasmids [IncFII(S), ColpVC, IncX1, IncN, IncX2, and IncC], and prophages (Fels-2, ST104, 500465-1, pro483, Gifsy-2, 103 203_sal5, Fels-1, RE-2010, vB_SenS-Ent2, and L-413C) were detected. MLST showed biovar-specific sequence types, and core genome MLST showed country-specific and global-related clusters. CONCLUSION: SG and SP global strains carry many virulence factors and important antimicrobial resistance genes. The diverse plasmids and prophages suggest genetic variability. MLST and cgMLST differentiated biovars and showed profiles occurring locally or worldwide.
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Genoma Bacteriano , Enfermedades de las Aves de Corral , Salmonella enterica , Serogrupo , Salmonella enterica/genética , Salmonella enterica/efectos de los fármacos , Animales , Enfermedades de las Aves de Corral/microbiología , Antibacterianos/farmacología , Islas Genómicas/genética , Salmonelosis Animal/microbiología , Farmacorresistencia Bacteriana Múltiple/genética , Factores de Virulencia/genética , Plásmidos/genética , Pollos/microbiología , Genómica , Pruebas de Sensibilidad Microbiana , Farmacorresistencia Bacteriana/genéticaRESUMEN
Introduction: The Mycobacterium chelonae species and the M. avium and M. abscessus complexes are emerging pathogens that cause mycobacteriosis. Treatment depends on the species and subspecies identified. The drugs of choice are macrolides and aminoglycosides. However, due to the resistance identified to these drugs, determining the microbe's sensitivity profile will allow clinicians to improve the understanding of the prognosis and evolution of these pathologies. Objective: To describe the macrolide and aminoglycoside susceptibility profile of cultures identified by Colombia's Laboratorio Nacional de Referencia de Mycobacteria from 2018 to 2022, as Mycobacterium avium complex, M. abscessus complex, and M. chelonae. Materials and methods. This descriptive study exposes the susceptibility profile to macrolides and aminoglycosides of cultures identified as M. avium complex, M. abscessus complex, and M. chelonae using the GenoType® NTM-DR method. Materials and methods: This descriptive study exposes the susceptibility profile to macrolides and aminoglycosides of cultures identified as M. avium complex, M. abscessus complex, and M. chelonae using the GenoType® NTM-DR method. Results: We identified 159 (47.3 %) cultures as M. avium complex, of which 154 (96.9 %) were sensitive to macrolides, and 5 (3.1 %) were resistant; all were sensitive to aminoglycosides. From the 125 (37.2 %) cultures identified as M. abscessus complex, 68 (54.4 %) were sensitive to macrolides, 57 (45.6 %) were resistant to aminoglycosides, and just one (0.8 %) showed resistance to aminoglycosides. The 52 cultures (15.5 %) identified as M. chelonae were sensitive to macrolides and aminoglycosides. Conclusions: The three studied species of mycobacteria have the least resistance to Amikacin. Subspecies identification and their susceptibility profiles allow the establishment of appropriate treatment schemes, especially against M. abscessus.
Introducción. Mycobacterium chelonae y los complejos Mycobacterium avium y M. abscessus, son agentes patógenos emergentes causantes de micobacteriosis. El tratamiento de esta infección depende de la especie y la subespecie identificadas. Los fármacos de elección son los macrólidos y aminoglucósidos, contra los cuales se ha reportado resistencia; por esta razón, el determinar el perfil de sensibilidad le permite al médico tratante comprender mejor el pronóstico y la evolución de estas infecciones. Objetivo. Describir los perfiles de sensibilidad ante macrólidos y aminoglucósidos, de los cultivos identificados como complejo Mycobacterium avium, complejo M. abscessus o especie M. chelonae, en el Laboratorio Nacional de Referencia de Micobacterias durante los años 2018 a 2022. Materiales y métodos. Se llevó a cabo un estudio descriptivo del perfil de sensibilidad a macrólidos y aminoglucósidos, de los cultivos identificados como complejo M. avium, complejo M. abscessus o M. chelonae, mediante la metodología GenoType® NTM-DR. Resultados. Los cultivos del complejo M. avium fueron 159 (47,3 %), de los cuales, 154 (96,9 %) fueron sensibles y 5 (3,1 %) resistentes a los macrólidos; todos fueron sensibles a los aminoglucósidos. Del complejo M. abscessus se estudiaron 125 (37,2 %) cultivos, 68 (54,4 %) resultaron sensibles y 57 (45,6 %) resistentes a los macrólidos; solo un cultivo (0,8 %) fue resistente a los aminoglucósidos. De M. chelonae se analizaron 52 cultivos (15,5 %), todos sensibles a los macrólidos y aminoglucósidos. Conclusiones. En las tres especies de micobacterias estudiadas, la resistencia contra la amikacina fue la menos frecuente. La identificación de las subespecies y los perfiles de sensibilidad permiten instaurar esquemas de tratamiento adecuados, especialmente en las micobacteriosis causadas por M. abscessus.
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Aminoglicósidos , Macrólidos , Pruebas de Sensibilidad Microbiana , Infecciones por Mycobacterium no Tuberculosas , Mycobacterium abscessus , Complejo Mycobacterium avium , Mycobacterium chelonae , Macrólidos/farmacología , Mycobacterium abscessus/efectos de los fármacos , Mycobacterium abscessus/genética , Mycobacterium abscessus/aislamiento & purificación , Colombia/epidemiología , Mycobacterium chelonae/efectos de los fármacos , Mycobacterium chelonae/genética , Mycobacterium chelonae/aislamiento & purificación , Aminoglicósidos/farmacología , Humanos , Complejo Mycobacterium avium/efectos de los fármacos , Complejo Mycobacterium avium/genética , Complejo Mycobacterium avium/aislamiento & purificación , Infecciones por Mycobacterium no Tuberculosas/microbiología , Infecciones por Mycobacterium no Tuberculosas/epidemiología , Infecciones por Mycobacterium no Tuberculosas/tratamiento farmacológico , Antibacterianos/farmacología , Farmacorresistencia Bacteriana , Prevalencia , Farmacorresistencia Bacteriana MúltipleRESUMEN
Ciprofloxacin is a critically important antibiotic for human health. The increase of Escherichia coli resistance to ciprofloxacin is a global public health problem due to its importance in the treatment of complicated urinary tract infections and other serious infections; however, its prescription is high in the Colombian Caribbean. The objective was to determine the resistance trend of E. coli to ciprofloxacin in a Colombian hospital of high complexity. From antibiogram reports, isolates were categorized according to Clinical and Laboratory Standards Institute criteria for each year studied; proportions were calculated and differences in sensitivity were explored using the χ2 test. The Cochran-Armitage test was used to evaluate the resistance trend. Significance was considered when p-value ≤ 0.05. In total, 6,848 isolates were analyzed, and 49.31% resistance was found. According to origin, the highest resistance was in community samples (51.96% - 95%CI: 50.51; 53.41), and by type of sample, in skin and tissues (61.76% - 95%CI: 56.96; 66.35) and urine (48.97% - 95%CI: 47.71; 50.23). Increasing trends were observed for resistance per year (p < 0.0001), community samples (p = 0.0002) and urine (p < 0.0001). Resistance to ciprofloxacin is high and tends to increase in the community and in urine, exceeding the limit established for its use at the ambulatory level, which is of concern due to the high prescription of fluoroquinolones in the locality.
La ciprofloxacina es un antibiótico de importancia crítica para la salud humana. El aumento de la resistencia de Escherichia coli a ciprofloxacina es un problema de salud pública global por su importancia en el tratamiento de infecciones urinarias complicadas y otras infecciones graves; sin embargo, su prescripción es alta en el caribe colombiano. El objetivo fue determinar la tendencia de resistencia de E. coli a ciprofloxacina en un hospital colombiano de alta complejidad. A partir de reportes de antibiogramas, los aislados fueron categorizados según los criterios del Instituto de Normas Clínicas y de Laboratorio de los Estados Unidos para cada año estudiado; se calcularon proporciones y se exploraron diferencias en la sensibilidad con pruebas χ2. Se utilizó la prueba de Cochran-Armitage para evaluar la tendencia de la resistencia. Valores de p ≤ 0,05 se consideraron significativos. Se analizaron 6.848 aislados, encontrándose una resistencia de 49,31%. Según el origen, la resistencia más alta fue en muestras comunitarias (51,96% - IC95%: 50,51; 53,41), y por tipo de muestra, en piel y tejidos (61,76% - IC95%: 56,96; 66,35) y orina (48,97% - IC95%: 47,71; 50,23). Se halló una tendencia al aumento en la resistencia por año (p < 0,0001), en muestras comunitarias (p = 0,0002) y en orina (p < 0,0001). La resistencia a ciprofloxacina es alta y tiende al aumento en comunidad y en orina, superando el límite establecido para su uso a nivel ambulatorio, lo que es preocupante por la alta prescripción de fluoroquinolonas en la localidad.
A ciprofloxacina é um antibiótico extremamente importante para a saúde humana. O aumento da resistência da Escherichia coli à ciprofloxacina é um problema de saúde pública global devido à sua importância no tratamento de infecções complicadas do trato urinário e outras infecções graves; no entanto, sua prescrição é alta no caribe colombiano. O objetivo foi determinar a tendência de resistência da E. coli à ciprofloxacina em um hospital colombiano de alta complexidade. A partir de relatórios de antibiogramas, os isolados foram categorizados de acordo com os critérios do Instituto de Padrões Clínicos e Laboratoriais dos Estados Unidos para cada ano estudado; as proporções foram calculadas e as diferenças de sensibilidade foram exploradas com os testes χ2. O teste de Cochran-Armitage foi usado para avaliar a tendência de resistência. Os valores de p ≤ 0,05 foram considerados significativos. Um total de 6.848 isolados foi testado e foi encontrada uma taxa de resistência de 49,31%. Por origem, a resistência foi mais alta em amostras comunitárias (51,96% - IC95%: 50,51; 53,41) e, por tipo de amostra, em pele e tecidos (61,76% - IC95%: 56,96; 66,35) e urina (48,97% - IC95%: 47,71; 50,23). Foi encontrada uma tendência de aumento na resistência por ano (p < 0,0001), em amostras da comunidade (p = 0,0002) e na urina (p < 0,0001). A resistência à ciprofloxacina é alta e tende a aumentar na comunidade e na urina, excedendo o limite estabelecido para uso ambulatorial, o que é preocupante, dada a alta prescrição de fluoroquinolonas na localidade.
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Antibacterianos , Ciprofloxacina , Farmacorresistencia Bacteriana , Escherichia coli , Pruebas de Sensibilidad Microbiana , Ciprofloxacina/farmacología , Humanos , Colombia/epidemiología , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Estudios Transversales , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Infecciones por Escherichia coli/tratamiento farmacológico , Infecciones por Escherichia coli/epidemiología , Infecciones por Escherichia coli/microbiología , Infecciones Urinarias/microbiología , Infecciones Urinarias/tratamiento farmacológicoRESUMEN
Surface 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.