Horizontal gene transfer in plant microbiomes: integrons as hotspots for cross-species gene exchange

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: April 29, 2024

Plant microbiomes play important roles in plant health and fitness. Bacterial horizontal gene transfer (HGT) can influence outcomes, driving the spread of both growth-promoting phytopathogenic traits. However, community dynamics, including range genetic elements bacteria involved this process are still poorly understood. Integrons recently shown to be abundant microbiomes, associated with HGT across broad phylogenetic boundaries. They facilitate cassettes, small mobile that collectively confer a diverse suite adaptive functions. Here, we analysed 5,565 plant-associated bacterial genomes investigate prevalence functional diversity integrons niche. We found particularly Pseudomonadales, Burkholderiales, Xanthomonadales. In total, detected nearly 9,000 many could growth promotion or phytopathogenicity, suggesting might role mutualistic pathogenic lifestyles. The rhizosphere was enriched cassettes transport metabolism substrates, they may aid adaptation environment, which is rich root exudates. also cross-species HGT, enhanced phyllosphere. This finding provide an ideal opportunity promote by fostering genes relevant leaf health. Together, our findings suggest drive have potential host adaptation.

Language: Английский

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The Impact Aerobic and Anaerobic Incubations of Poultry Litter Have on Class 1 Integron Resistome and Microbiome

Agriculture, Journal Year: 2025, Volume and Issue: 15(4), P. 398 - 398

Published: Feb. 13, 2025

Animal manure is a desirable fertilizer because of its rich nitrogen, but it also contains large and diverse reservoir antimicrobial resistance (AMR) genes (ARGs). To reduce this AMR reservoir, five treatments (passive aeration, forced static or anaerobic incubations, autoclaving) were assessed for their impact on the poultry litter resistome. Bacterial DNA was extracted from qPCR-estimated copy number 16S rrs, class1 integrons (intI1) associated (aadA, sul1). Then, amplicon metagenomic sequencing used to determine community diversity composition. Depending incubation conditions, class 1 ARGs reduced by 0.5 1.0 Log10/g litter. Only autoclaving three Log10. Changes in abundance reflected fluctuations bacteriome composition at family, genus, sequence variant level. There negative correlation between integron genes, with genera belonging Actinobacteria, Firmicutes, Proteobacteria phyla. While these failed abundance, aerobic taxons that contained pathogenic species. The approach remediating may be more effective if focused reducing bacterial pathogens.

Language: Английский

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The Trade-Off Between Sanitizer Resistance and Virulence Genes: Genomic Insights into E. coli Adaptation

Antibiotics, Journal Year: 2025, Volume and Issue: 14(3), P. 291 - 291

Published: March 11, 2025

Background: Escherichia coli is one of the most studied bacteria worldwide due to its genetic plasticity. Recently, in addition characterizing pathogenic potential, research has focused on understanding resistance profile inhibitory agents, whether these be antibiotics or sanitizers. Objectives: The present study aimed investigate six main serogroups foodborne infection (O26, O45, O103, O111, O121, and O157) understand dynamics heterogeneity sanitizers derived from quaternary ammonium compounds (QACs) peracetic acid (PAA) using whole-genome sequencing (WGS). Methods: Twenty-four E. strains with varied profiles QACs PAA were analyzed by WGS NovaSeq6000 (150 bp Paired End reads). Bioinformatic analyses included genome assembly (Shovill), annotation via Prokka, antimicrobial gene identification Abricate, core-genome analysis Roary. A multifactorial multiple correspondence (MCA) was conducted explore gene–sanitizer relationships. In addition, a large-scale utilizing NCBI Pathogen Detection database involved 2 × chi-square test examine associations between presence qac stx genes. Results: isolates exhibited varying profiles, O45 O157 being resistant serogroups. identified only strain (S22), while four other carried gene. Through analysis, results obtained indicated that harboring genes encoding Shiga toxin (stx) presented more likely sensitive QACs. To further confirm results, we 393,216 genomes database. Our revealed significant association (p < 0.001) absence stx1, stx2, both Conclusion: findings highlight complexity bacterial mechanisms suggest non-pathogenic may exhibit greater tolerance QAC sanitizer than those carrying pathogenicity genes, particularly

Language: Английский

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Temporal dynamics of class 1 and class 3 integron pools in treated wastewater

Water Research, Journal Year: 2025, Volume and Issue: unknown, P. 123718 - 123718

Published: May 1, 2025

Language: Английский

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Hiding in Plain Sight: Characterization of Aeromonas Species Isolated from a Recreational Estuary Reveals the Carriage and Putative Dissemination of Resistance Genes

Antibiotics, Journal Year: 2023, Volume and Issue: 12(1), P. 84 - 84

Published: Jan. 4, 2023

Antimicrobial resistance (AMR) has become one of the greatest challenges worldwide, hampering treatment a plethora infections. Indeed, AMR crisis poses threat to achievement United Nations' Sustainable Development Goals and, due its multisectoral character, holistic approach is needed tackle this issue. Thus, investigation environments beyond clinic utmost importance. Here, we investigated thirteen strains antimicrobial-resistant Aeromonas isolated from an urban estuary in Brazil. Most carried at least antimicrobial gene and 11 heavy metal gene. Noteworthy, four (30.7%) blaKPC gene, coding for carbapenemase. In particular, whole-genome sequence hydrophila strain 34SFC-3 was determined, revealing not only presence genes but also versatile virulome repertoire. Mobile genetic elements, including insertion sequences, transposons, integrative conjugative IncQ1 plasmid were detected. Considering ubiquity species, their promiscuity, pathogenicity, intrinsic features endure environmental stress, our findings reinforce concept that A. truly "Jack all trades'' should be overlooked under One Health perspective.

Language: Английский

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Carriage of antibiotic resistant bacteria in endangered and declining Australian pinniped pups

PLoS ONE, Journal Year: 2022, Volume and Issue: 17(1), P. e0258978 - e0258978

Published: Jan. 28, 2022

The rapid emergence of antimicrobial resistance (AMR) is a major concern for wildlife and ecosystem health globally. Genetic determinants AMR have become indicators anthropogenic pollution due to their greater association with humans rarer presence in environments less affected by humans. objective this study was determine the distribution frequency class 1 integron, genetic determinant AMR, both faecal microbiome Escherichia coli isolated from neonates three pinniped species. Australian sea lion (Neophoca cinerea), fur seal (Arctocephalus pusillus doriferus) long-nosed forsteri) pups eight breeding colonies along Southern coast were sampled between 2016-2019. DNA samples (n = 309) E. 795) 884 analysed integrons using PCRs targeting conserved integrase gene (intI) cassette array. Class detected A. p. doriferus N. cinerea at seven investigated 4.85% 15) 4.52% isolates 36). Integrons not any forsteri samples. sequencing integron array identified diverse genes conferring four antibiotic classes. relationship carriage concentration five trace elements heavy metals also investigated, finding no significant association. results add growing evidence extent which resistant bacteria are polluting marine environment. As frequently associated bacterial pathogens, occurrence suggests that these species vulnerable potential risks. implications individual population as consequence critical component ongoing investigations.

Language: Английский

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The biotechnological potential of Aeromonas: a bird’s eye view

Critical Reviews in Microbiology, Journal Year: 2022, Volume and Issue: 49(5), P. 543 - 555

Published: June 10, 2022

The genus Aeromonas comprises Gram-negative bacilli widely distributed in aquatic habitats that can also be found the terrestrial environment and close association with humans animals. spp. are particularly versatile bacteria, high genomic plasticity notable capacity to adapt different environments extreme conditions. On account of being mostly associated their pathogenic potential, research on biotechnological potentialities is considerably scarce when compared other bacterial groups. Nonetheless, studies over years have been hinting at several interesting hidden this group, especially recent advances whole-genome sequencing, unveiling as candidates for discovery novel industrial biocatalysts, bioremediation strategies, biopolyester production. In context, present study aims provide an overview main applications reported new insights into further exploration these frequently overlooked, yet fascinating, bacteria.

Language: Английский

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Correlation between the spread of IMP-producing bacteria and the promoter strength of blaIMP genes

The Journal of Antibiotics, Journal Year: 2024, Volume and Issue: 77(5), P. 315 - 323

Published: March 15, 2024

The first report of transmissible carbapenem resistance encoded by blaIMP-1 was discovered in Pseudomonas aeruginosa GN17203 1988, and has since been detected other bacteria, including Enterobacterales. Currently, many variants blaIMPs exist, point mutations the blaIMP promoter have shown to alter strength. For example, (Pc) blaIMP-1, reported P. GN17203, a weak (PcW) with low-level expression intensity. This study investigates whether region helped create strong promoters under antimicrobial selection pressure. Using bioinformatic approaches, we retrieved 115 from 14,529 genome data Pseudomonadota performed multiple alignment analyses. results analysis showed that most them used Pc located class 1 integrons (n = 112, 97.4%). year revealed population promoter, PcS, transient. In contrast, PcW-TG population, which had acquired TGn-extended -10 motif PcW an intermediate strength, gradually spread throughout world. An inverse correlation between strength Intl1 integrase excision efficiency previously [1]. Because this trade-off, it is unlikely will increase rapidly, but possibility use cannot be ruled out. Monitoring genes, analysis, necessary for global surveillance carbapenem-resistant bacteria.

Language: Английский

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Mobile Integrons Encode Phage Defense Systems

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 2, 2024

Abstract Integrons are bacterial genetic elements that capture, stockpile and modulate the expression of genes encoded in integron cassettes. Mobile (MI) borne on plasmids, acting as a vehicle for hundreds antimicrobial resistance among key pathogens. These also carry g ene c assettes u nknown function ( gcu s) whose role adaptive value remains unexplored. Here we show s encode phage systems, many which novel. B acteriophage r esistance i ntegron (BRiCs) can be combined mixed with cassettes to produce multiphage or drug/phage-resistance. The fitness costs BRiCs variable, dependent context, modulated by changing order array. Hence, MIs act highly mobile, low-cost defense islands. Figure Summary Novel systems identified Integrons. We confronted unknown from mobile integrons against panel phage. characterized 13 Bacteriophage Resistance Cassettes confirmed their Klebsiella pneumoniae Pseudomonas aeruginosa . Combined other cassettes, multi-phage/antibiotic resistance. Additionally, cost reduced an

Language: Английский

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Cross-environmental cycling of antimicrobial resistance in agricultural areas fertilized with poultry litter: a one health approach

Environmental Pollution, Journal Year: 2024, Volume and Issue: 363, P. 125177 - 125177

Published: Oct. 22, 2024

Language: Английский

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