In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens

Algarni, Suad; Han, Jing; Gudeta, Dereje Dadi; Khajanchi, Bijay K.; Ricke, Steven C.; Kwon, Young Min; Rhoads, David B.; Foley, Steven L.

doi:10.3389/fmicb.2022.1095128

Cited by 7 publications

(11 citation statements)

References 64 publications

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“…The Plasmid Transfer Factor Comparison tool is highlighted in Figure 2 and facilitates the comparison of multiple different FASTA files simultaneously to provide a presence/absence matrix for the comparison of the transfer gene profiles among multiple strains. To assess this tool, two sets of data including the cohort of IncA/C, IncB/O/K, IncFIB, IncHI1, and IncI1 plasmids previously described ( Algarni et al, 2022a ), as well as WGS data from the 159 Salmonella strains that were previously sequenced, were analyzed.…”

Section: Resultsmentioning

confidence: 99%

“…This set of analysis allows for evaluation of whether factors for one plasmid type are identified as present, even though the particular plasmid type was not identified in the strain with PlasmidFinder. In addition, the sets of previously characterized IncA/C, IncB/O/K, IncFIB, IncHI1, and IncI1 plasmids (100 each) that were analyzed previously ( Algarni et al, 2022a ) were tested to compare the diversity of transfer genes within a particular group of plasmids and determine the congruence between the identified plasmid types and the predicted transfer genes for these groups.…”

Section: Methodsmentioning

confidence: 99%

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Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria

Algarni,

Foley,

Tang

et al. 2023

Front. Bioinform.

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Introduction: Type IV secretion systems (T4SSs) are integral parts of the conjugation process in enteric bacteria. These secretion systems are encoded within the transfer (tra) regions of plasmids, including those that harbor antimicrobial resistance (AMR) genes. The conjugal transfer of resistance plasmids can lead to the dissemination of AMR among bacterial populations.Methods: To facilitate the analyses of the conjugation-associated genes, transfer related genes associated with key groups of AMR plasmids were identified, extracted from GenBank and used to generate a plasmid transfer gene dataset that is part of the Virulence and Plasmid Transfer Factor Database at FDA, serving as the foundation for computational tools for the comparison of the conjugal transfer genes. To assess the genetic feature of the transfer gene database, genes/proteins of the same name (e.g., traI/TraI) or predicted function (VirD4 ATPase homologs) were compared across the different plasmid types to assess sequence diversity. Two analyses tools, the Plasmid Transfer Factor Profile Assessment and Plasmid Transfer Factor Comparison tools, were developed to evaluate the transfer genes located on plasmids and to facilitate the comparison of plasmids from multiple sequence files. To assess the database and associated tools, plasmid, and whole genome sequencing (WGS) data were extracted from GenBank and previous WGS experiments in our lab and assessed using the analysis tools.Results: Overall, the plasmid transfer database and associated tools proved to be very useful for evaluating the different plasmid types, their association with T4SSs, and increased our understanding how conjugative plasmids contribute to the dissemination of AMR genes.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria

Algarni,

Foley,

Tang

et al. 2023

Front. Bioinform.

Self Cite

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“…The FASTA files for plasmids noted above were analyzed using AMRFinderPlus database V3.2.1 36 with the AMRFinderPlus plugin within the GalaxyTrakr ( https://account.galaxytrakr.org ) operating environment as described previously 37 . AMRFinderPlus is a comprehensive database with 983 unique AMR genes, 82 unique HMR genes and 30 DBR genes.…”

Section: Methodsmentioning

confidence: 99%

“…Computational programs such as PlasmidFinder, PubMLST, ResFinder, AMRFinderPlus, and IntegronFinder can identify and subtype plasmids and identify different genes associated with AMR phenotypes 33 – 36 . In addition, with the increasing access to long-read sequencing technologies, there is an enhanced ability to close plasmid sequences and determine the locations of resistance determinants and mobile genetic elements (MGEs), such as transposons, insertion sequences and integrons that make up the AMR mobilome that can facilitate the spread of genes among different plasmids and bacterial populations 37 . Understanding the genetic composition of plasmids is important to aid in epidemiological investigations and identifying measures to limit the spread of AMR.…”

Section: Introductionmentioning

confidence: 99%

“…The data allowed for evaluation of the distribution of resistance genes among the assembled plasmids from different bacteria taxa, and exploration of geographical and temporal sources. Understanding the epidemiology of the resistance mobilome can help with the development of strategies to limit the spread of multidrug and HMR carrying plasmids among bacterial pathogens in the environment, food animals and humans 37 , 38 .…”

Section: Introductionmentioning

confidence: 99%

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Genotypic analyses of IncHI2 plasmids from enteric bacteria

Algarni,

Gudeta,

Han

et al. 2024

Sci Rep

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Incompatibility (Inc) HI2 plasmids are large (typically > 200 kb), transmissible plasmids that encode antimicrobial resistance (AMR), heavy metal resistance (HMR) and disinfectants/biocide resistance (DBR). To better understand the distribution and diversity of resistance-encoding genes among IncHI2 plasmids, computational approaches were used to evaluate resistance and transfer-associated genes among the plasmids. Complete IncHI2 plasmid (N = 667) sequences were extracted from GenBank and analyzed using AMRFinderPlus, IntegronFinder and Plasmid Transfer Factor database. The most common IncHI2-carrying genera included Enterobacter (N = 209), Escherichia (N = 208), and Salmonella (N = 204). Resistance genes distribution was diverse, with plasmids from Escherichia and Salmonella showing general similarity in comparison to Enterobacter and other taxa, which grouped together. Plasmids from Enterobacter and other taxa had a higher prevalence of multiple mercury resistance genes and arsenic resistance gene, arsC, compared to Escherichia and Salmonella. For sulfonamide resistance, sul1 was more common among Enterobacter and other taxa, compared to sul2 and sul3 for Escherichia and Salmonella. Similar gene diversity trends were also observed for tetracyclines, quinolones, β-lactams, and colistin. Over 99% of plasmids carried at least 25 IncHI2-associated conjugal transfer genes. These findings highlight the diversity and dissemination potential for resistance across different enteric bacteria and value of computational-based approaches for the resistance-gene assessment.

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Coupling antitoxins and blue/white screening with parAB /resolvase mutation as a strategy for Salmonella spp. plasmid curing

Gudeta,

Zhao,

Aljahdali

et al. 2024

Microbiol Spectr

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Despite the dissemination of multidrug resistance plasmids, including those carrying virulence genes in Salmonella spp., efficient plasmid curing tools are lacking. Plasmid partitioning and multimer resolution systems are attractive targets for plasmid cure. However, plasmid curing strategies targeting these systems are often hindered by the host addiction system through a process known as post-segregation killing. Here, we developed vector tools that can mutate the above systems while replenishing short-lived antitoxins. Cloning was performed using Gibson assembly. parAB or resolvase ( res ) genes on Incompatibility Group (Inc)FIB, IncA/C, IncX4, and plasmids carried by Salmonella species were deleted by first knocking in the N-terminal ß-galactosidase encoding gene ( bgaB ), followed by in-frame insertion of its C-terminal region using pDG1 and pDG2 vectors, respectively. pDG1 was used as a backbone to develop a vector, designated as pDG-At, expressing 13 antitoxins driven by strong promoters. Plasmid curing was achieved by transforming pDG-At to parAB or res mutants followed by blue-white screening and PCR; however, parAB mutant isolation with this method was low and often non-reproducible. To elucidate whether the prior presence of pDG-At in cells improves viable mutant isolation, we re-constructed pDG-At, designated as pDG-Atπ, using a vector with the R6K ϒ origin of replication with its π-factor required for replication under araBAD promoter. Results showed that pDG-Atπ can replicate in the absence of arabinose but can be cured by growing cells in glucose-rich media. Next, we repeated IncFIB’s parAB deletion using pDG1 but in cells carrying pDG-Atπ. Many white colonies were detected on X-Gal-supplemented media but none of them carried the target parA mutation; however, ~80% of the white colonies lost IncFIB plasmid, while the others retained the wild-type plasmid. Similar results were obtained for IncX4 plasmid curing but also found that this method was not reproducible as the white colonies obtained after allelic replacement did not always result in plasmid curing or mutant isolation. This is the first report describing a simple blue/white screening method for plasmid curing that can avoid laborious screening procedures. IMPORTANCE Plasmids play an important role in bacterial physiology, adaptation, evolution, virulence, and antibiotic resistance. An in-depth study of these roles partly depends on the generation of plasmid-free cells. This study shows that vector tools that target genes required for plasmid stability in the presence of an antitoxin-expressing helper plasmid are a viable approach to cure specific plasmids. Expression of bgaB from target plasmids can greatly facilitate visual detection of plasmid cured colonies avoiding time-consuming screening procedures. This approach can be refined for the development of a universal plasmid curing system that can be used to generate plasmid-free cells in other human bacterial pathogens including Gram positives and Gram negatives.

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In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens

Cited by 7 publications

References 64 publications

Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria

Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria

Genotypic analyses of IncHI2 plasmids from enteric bacteria

Coupling antitoxins and blue/white screening with parAB /resolvase mutation as a strategy for Salmonella spp. plasmid curing

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