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ABSTRACT Surface waters function as ecological niches where Salmonella enterica can persist and disseminate to fresh produce production systems. We examined the genomic characteristics of S. enterica serotypes Agona (n = 86), Braenderup (n = 47), Muenchen (n = 53), and Panama (n = 69) isolates from surface waters in Chile, Mexico, and Brazil between 2019 and 2022. Mexican isolates consistently displayed a higher occurrence of genotypic antimicrobial resistance (AMR) than Chilean and Brazilian isolates. All S. Agona isolates exhibited the presence of fosA7.2, while qnrB19 emerged as the predominant AMR gene (ARG) among S. Braenderup isolates. S. Muenchen isolates from Chile displayed an absence of any ARGs, while those from Mexico and Brazil predominantly carried qnrB19. Among S. Panama isolates from Chile, aadA1, floR, sat2, and tet(B) were the most prevalent ARGs, whereas those from Mexico and Brazil harbored tet(A), and floR and tet(A) as the leading ARGs, respectively. ARG sharing among isolates and ARG co-occurrence within individual isolates were prevalent across countries and serotypes. All isolates containing integrons exhibited genotypic multidrug resistance. The principal coordinates analysis reveals distinct clustering patterns based on country, serotype, number of ARGs per isolate, and plasmid and integron presence/absence. The whole-genome phylogenetic analysis demonstrates clear clusters, each associated with their respective countries. However, a notable exception was observed with one S. Agona isolate from Brazil closely related to two isolates from Chile, differing by only 18 and 19 single-nucleotide polymorphisms, respectively.IMPORTANCEThis comprehensive study explored the intricate genomic landscapes of S. Agona, Braenderup, Muenchen, and Panama isolates from surface waters across Chile, Mexico, and Brazil. By filling important knowledge gaps related to the genomic characteristics of these serotypes, the research offers a nuanced understanding of these serotypes as potential reservoirs for multidrug resistance. Our findings emphasize the urgency of targeted interventions to mitigate the emergence and dissemination of multidrug-resistant Salmonella enterica. This work underscores the need for informed policies and collaborative efforts to address the risks posed by S. enterica in Latin American surface waters.

Quartz-rich xenoliths in lavas (basalts to andesites; 90-30 ka) from Alicudi contain abundant melt and fluid inclusions. Two generations of CO2-rich fluid inclusions are present in quartz-rich xenolith grains: early (Type I) inclusions related to partial melting of the host xenoliths, and late Type II inclusions related to the fluid trapping during xenolith ascent. Homogenisation temperatures of fluid inclusions correspond to two density intervals: 0.93-0.68 g/cm3 (Type I) and 0.47-0.26 g/cm3 (Type II). Early Type I fluid inclusions indicate trapping pressures around 6 kbar, which are representative for the levels of partial melting of crustal rocks and xenolith formation. Late Type II fluid inclusions show lower trapping pressures, between 1.7 kbar and 0.2 kbar, indicative for shallow magma rest and accumulation during ascent to the surface. Data suggest the presence of two magma reservoirs: the first is located at lower crustal depths (about 24 km), site of fractional crystallization, mixing with source derived magma, and various degrees of crustal assimilation. The second magma reservoir is located at shallow crustal depths (about 6 km), the site where magma rested for a short time before erupting.

ABSTRACTSurface 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.IMPORTANCEUnveiling the genomic landscape of S. enterica in Latin American surface waters is pivotal for ensuring public health. This investigation sheds light on the intricate genomic diversity of S. enterica in surface waters across Chile, Mexico, and Brazil. Our research also addresses critical knowledge gaps, pioneering a comprehensive understanding of surface waters as a reservoir for multidrug-resistant S. enterica. By integrating our understanding of integron carriage as biomarkers into broader MDR control strategies, we can also work toward targeted interventions that mitigate the emergence and dissemination of MDR in S. enterica in surface waters. Given its potential implications for food safety, this study emphasizes the critical need for informed policies and collaborative initiatives to address the risks associated with S. enterica in surface waters.

Late Cretaceous coastal plain deposits of the Prince Creek Formation (PCF) offer a rare glimpse into an ancient, high-latitude, arctic greenhouse ecosystem for which there is no modern analog. Here, we employ quantitative biofacies analysis to explore the spatio-temporal variability in PCF palynomorph and microbiota assemblages from nine paleosol horizons exposed along the Colville River, North Slope, Alaska. Biofacies results provide insight into paleoenvironmental controls on the coastal plain ecosystem. Cluster and ordination analyses recognize five biofacies and the following two assemblage types: (1) fern and moss dominated assemblages and (2) algae dominated assemblages. Ordination arrays biofacies along environmental gradients related to soil moisture and marine influence. Fern and moss dominated biofacies from regularly water-logged paleosols along lake and swamp margins on the lower delta plain clearly segregated from algae dominated assemblages of periodically drier levee-overbank paleosols. These results support previous interpretations from the sedimentology, paleopedology, and geochemistry of PCF paleosols that suggest that fluctuations in the water table, related to seasonal river discharge and variations in topography and drainage, controlled soil development and vegetation growth across the coastal plain. This quantitative biofacies-based approach provides an independent predictive tool and cross-check for interpreting environmental conditions along any ancient coastal ecosystem.

In animal husbandry, antimicrobial agents have been administered as supplements to increase production over the last 60 years. Large-scale animal production has increased the importance of antibiotic management because it may favor the evolution of antimicrobial resistance and select resistant strains. Brazil is a significant producer and exporter of animal-derived food. Although Brazil is still preparing a national surveillance plan, several changes in legislation and timely programs have been implemented. Thus, Brazilian data on antimicrobial resistance in bacteria associated with animals come from official programs and the scientific community. This review aims to update and discuss the available Brazilian data on this topic, emphasizing legal aspects, incidence, and genetics of the resistance reported by studies published since 2009, focusing on farm animals and derived foods with the most global public health impact. Studies are related to poultry, cattle, and pigs, and mainly concentrate on non-typhoid Salmonella, Escherichia coli, and Staphylococcus aureus. We also describe legal aspects of antimicrobial use in this context; and the current occurrence of genetic elements associated with resistance to beta-lactams, colistin, and fluoroquinolones, among other antimicrobial agents. Data here presented may be useful to provide a better understanding of the Brazilian status on antimicrobial resistance related to farm animals and animal-derived food products.

Alguns microrganismos possuem a capacidade de produzir substâncias que podem influenciar no desenvolvimento de outros microrganismos. Desde os anos 50 é relatada a capacidade de várias espécies de bactérias do gênero Bacillus de produzir substâncias com atividade antimicrobiana como peptídeos, também denominados de bacteriocinas e enzimas como a subtilisina, subtilina, as proteases e as termolisinas. Muitos desses peptídeos e enzimas têm sido caracterizados bioquimicamente e geneticamente. Embora sejam conhecidas, a função estrutural, a biossíntese e modo de ação de alguns peptídeos antimicrobianos e enzimas, muitos aspectos desses compostos ainda permanecem desconhecidos. Esse artigo descreve uma revisão sobre as principais bacteriocinas e enzimas produzidas por Bacillus spp., bem como suas aplicações em alimentos. Alguns dados de segurança de bacteriocinas e enzimas produzidas por Bacillus spp. também são relatados. PALAVRAS-CHAVE: Bacteriocinas; enzimas; Bacillus spp.; alimentos.

Simple Summary: Beyond their use of treating human and animal diseases, antimicrobial agents have also been employed in animal feeding as "growth promoters", being administrated at low doses throughout the husbandry period, and leading to beneficial effects, mainly for large-scale production. However, the consequent selective pressure has helped to increase antimicrobial resistance frequencies in isolates from animals globally. Brazil is a major food producer and exporter; therefore, it is of great value to look at the panorama of bacterial resistance associated with farm animals. Since 1998, many drugs have been prohibited from being used as growth promoters in Brazil. However, neither data on the prophylactic and therapeutic use of antimicrobial agents in farms, nor results of contemporary and integrated surveillance programs regarding antimicrobial resistance associated with food production animals, are still publicly available. This review aims to update and discuss the available Brazilian data on this topic emphasizing legal aspects, occurrence, and genetics of the resistance reported by studies published since 2009, focusing on producing animals and derived foods with the most global public health impact. Data here compiled may be useful to monitor and evaluate the local situation and serve as a basis for establishing parameters for the future. In animal husbandry, antimicrobial agents have been administered as supplements to increase production over the last 60 years. Large-scale animal production has increased the importance of antibiotic management because it may favor the evolution of antimicrobial resistance and select resistant strains. Brazil is a significant producer and exporter of animal-derived food. Although Brazil is still preparing a national surveillance plan, several changes in legislation and timely programs have been implemented. Thus, Brazilian data on antimicrobial resistance in bacteria associated with animals come from official programs and the scientific community. This review aims to update and discuss the available Brazilian data on this topic, emphasizing legal aspects, incidence, and genetics of the resistance reported by studies published since 2009, focusing on farm animals and derived foods with the most global public health impact. Studies are related to poultry, cattle, and pigs, and mainly concentrate on non-typhoid Salmonella, Escherichia coli, and Staphylococcus aureus. We also describe legal aspects of antimicrobial use in this context; and the current occurrence of genetic elements associated with resistance to beta-lactams, colistin, and fluoroquinolones, among other antimicrobial agents. Data here presented may be useful to provide a better understanding of the Brazilian status on antimicrobial resistance related to farm animals and animal-derived food products. [ABSTRACT FROM AUTHOR]

ABSTRACT: Objectives: In contrast to other qnr families, qnrVC has been reported mainly in Vibrio spp. and inserted in class 1 integrons. This study aimed to identify the variants of qnrVC genes detected in Klebsiella pneumoniae carbapenemase-2-producing Enterobacter and Klebsiella strains isolated from Brazilian coastal waters and the genetic contexts associated with their occurrence. Methods: qnrVC variants were identified by Sanger sequencing. Stains were typified by pulsed-field gel electrophoresis. Antimicrobial susceptibility testing, conjugation assays, and whole genome sequencing (WGS) were applied to identify the strains’ antimicrobial resistance profile, qnrVC and blaKPC-2 co-transference, and qnrVC genetic context. Results: qnrVC1 was identified in 15 Enterobacter and 3 Klebsiella, and qnrVC4 in 2 Enterobacter strains. Pulsed-field gel electrophoresis revealed 12 clonal profiles of Enterobacter and one of Klebsiella. Strains were resistant to aminoglycosides, beta-lactams, fosfomycin, quinolones, and sulfamethoxazole-trimethoprim. Co-transference of qnrVC and blaKPC-2 were obtained from five representative Enterobacter strains, which showed resistance to ampicillin and amoxicillin-clavulanate, and reduced susceptibility to extended-spectrum cephalosporins, meropenem, and ciprofloxacin. WGS analysis from representative strains revealed one K. quasipneumoniae subsp. similipneumoniae, one E. soli, four E. kobei, and seven isolates belonging to Enterobacter Taxon 3. Long-read WGS showed qnrVC and blaKPC-2 were carried by the same replicon on Klebsiella and Enterobacter strains, and the qnrVC association with not previously described genetic environments composed of insertion sequences and truncated genes. These contexts occurred in small- and high-molecular-weight plasmids belonging to IncFII, IncP6, pKPC-CAV1321, and IncU groups. Conclusion: Our results suggest that the dissemination of qnrVC among Enterobacterales in Brazilian coastal waters is associated with several genetic recombination events.

ABSTRACT The dissemination of carbapenem-resistant and third generation cephalosporin-resistant pathogens is a critical issue that is no longer restricted to hospital settings. The rapid spread of critical priority pathogens in Brazil is notably worrying, considering its continental dimension, the diversity of international trade, livestock production, and human travel. We conducted a nationwide genomic investigation under a One Health perspective that included Escherichia coli strains isolated from humans and nonhuman sources, over 45 years (1974–2019). One hundred sixty-seven genomes were analyzed extracting clinically relevant information (i.e., resistome, virulome, mobilome, sequence types [STs], and phylogenomic). The endemic status of extended-spectrum β-lactamase (ESBL)-positive strains carrying a wide diversity of blaCTX-M variants, and the growing number of colistin-resistant isolates carrying mcr-type genes was associated with the successful expansion of international ST10, ST38, ST115, ST131, ST354, ST410, ST648, ST517, and ST711 clones; phylogenetically related and shared between human and nonhuman hosts, and polluted aquatic environments. Otherwise, carbapenem-resistant ST48, ST90, ST155, ST167, ST224, ST349, ST457, ST648, ST707, ST744, ST774, and ST2509 clones from human host harbored blaKPC-2 and blaNDM-1 genes. A broad resistome to other clinically relevant antibiotics, hazardous heavy metals, disinfectants, and pesticides was further predicted. Wide virulome associated with invasion/adherence, exotoxin and siderophore production was related to phylogroup B2. The convergence of wide resistome and virulome has contributed to the persistence and rapid spread of international high-risk clones of critical priority E. coli at the human-animal-environmental interface, which must be considered a One Health challenge for a post-pandemic scenario. IMPORTANCE A One Health approach for antimicrobial resistance must integrate whole-genome sequencing surveillance data of critical priority pathogens from human, animal and environmental sources to track hot spots and routes of transmission and developing effective prevention and control strategies. As part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we present genomic data of WHO critical priority carbapenemase-resistant, ESBL-producing, and/or colistin-resistant Escherichia coli strains isolated from humans and nonhuman sources in Brazil, a country with continental proportions and high levels of antimicrobial resistance. The present study provided evidence of epidemiological and clinical interest, highlighting that the convergence of wide virulome and resistome has contributed to the persistence and rapid spread of international high-risk clones of E. coli at the human-animal-environmental interface, which must be considered a One Health threat that requires coordinated actions to reduce its incidence in humans and nonhuman hosts.