Biology subjects

Topp, E.

Publications and source records attributed to Topp, E..

6 recordsLinked to original sources

bioRxiv2024

Gut Microbiome Perturbation Affected Conjugative Transfer of Antimicrobial Resistance Genes

The global spread of antimicrobial resistance genes (ARGs) poses a significant threat to public health. While antibiotics effectively treat bacterial infections, they can also induce gut dysbiosis, the severity of which varies depending on the specific antibiotic treatment used. However, it remains unclear how gut dysbiosis affects the mobility and dynamics of ARGs. To address this, mice were pre-treated with streptomycin, ampicillin, or sulfamethazine, and then orally inoculated with Salmonella enterica serovar Typhimurium and S. Heidelberg carrying a multi-drug resistance IncA/C plasmid. The streptomycin pre- treatment caused severe microbiome perturbation, promoting high-density colonization of S. Heidelberg and S. Typhimurium, and enabling IncA/C transfer from S. Heidelberg to S. Typhimurium and a commensal Escherichia coli. The ampicillin pre-treatment induced moderate microbiome perturbation, supporting only S. Heidelberg colonization and IncA/C transfer to commensal E. coli. The sulfamethazine pre-treatment led to mild microbiome perturbation, favoring neither Salmonella spp. colonization nor conjugative plasmid transfer. The degree of gut dysbiosis also influenced the enrichment or depletion of ARGs associated with mobile plasmids or core commensal bacteria, respectively. These findings underscore the significance of pre-existing gut dysbiosis induced by various antibiotic treatments on ARG dissemination and may inform prudent antibiotic use practices.

microbiology↗

bioRxiv2023

Metagenomic Analysis Reveals the Transfer of Antibiotic Resistance from Manure-Fertilized Soil to Carrot Microbiome

Crops grown in manure-fertilized soil are more likely to be contaminated with antibiotic resistance genes (ARGs) than when grown in unmanured soil, and therefore more likely to represent a route of ARG exposure to consumers. Existing studies scarcely focused on the residual ARGs on the carrot peel growing in the manured soil after the careful washing. In the present study, residual microbiome and resistome on the carrots surface (Daucus carota subsp. sativus) at harvest after careful washing was investigated to reveal the impact of manure fertilization. Residual surface bacteria were recovered from the peel, and total bacterial DNA was extracted for the high-throughput sequencing-based metagenomic analysis. Despite the overall unaltered level of alpha diversity in both soil and carrot peel samples, manuring increased the resistome in soil significantly, but not on the carrot peel. The largely overlapped resistome detected on carrots grown with and without manuring, plus the pattern revealed by source tracking analysis indicated a soil-source of ARGs on carrots, whereas the beta-lactamases CTX-M-84, OXY-4, and CTX-M-122 only detected in the manured soil and on the carrot peel harvested from manured soil indicated that beta-lactamases appear to be transferred from manure to the carrot. The evident impact of soil resistome and community on carrot peel microbiome, plus the limited level of plasmid and integron mediated ARGs transfer suggested the main ARGs transfer pathway from manured soil to carrot peel was via the colonization of rhizosphere soil microbes. To further elucidate the ARG propagation within the soil-carrot system, a network was constructed to explore the pattern of nine types of concurrent ARGs genotypes carried by ten different host populations, emphasizing that the residual antibiotic resistances transfer via raw carrot represents a risk to human health even after extensive washing.

microbiology↗

bioRxiv2023

Potential selection and maintenance of manure-originated multi-drug resistant plasmids at sub-clinical antibiotic concentrations

The goal of this study was to determine minimum selection concentrations of various antibiotics using four manure-originated multi-drug resistant plasmids in a surrogate Escherichia coli host. These plasmids carried genes conferring resistance phenotypes to several antibiotic classes including {beta}-lactams, lincosamides, phenicols, macrolides, sulfonamides and tetracyclines. The minimum selection concentrations of antibiotics tested in nutrient-rich medium were determined: 14.1-28.2 mg/L for penicillin G, 0.1 mg/L for oxytetracycline, 0.45 mg/L for chlortetracycline, 2 mg/L for lincomycin, 1 mg/L for florfenicol, 1.3-4 mg/L for azithromycin, 0.13-0.25 mg/L for tetracycline, 0.004-0.01 mg/L for cefotaxime. Penicillin G, oxytetracycline, chlortetracycline, lincomycin and florfenicol had minimum selection concentrations in nutrient-defined medium slightly changed within 3.5-fold range compared to those in nutrient-rich medium. The minimum selection concentrations of antibiotics interfering folic acid synthesis in bacteria were also determined: 63 mg/L for sulfamethoxazole, 11.2 mg/L for sulfisoxazole and 0.06 mg/L for trimethoprim. Mixing two antibiotics changed minimum selection concentrations within 3.7-fold range compared to those in single antibiotic tests. Relatively high plasmid loss rates (> 90%) were observed when culturing plasmid-bearing strains in antibiotic-free nutrient-rich and nutrient-defined media. Overall results suggested that these plasmids can be maintained at concentrations environmentally relevant in waste water treatment plants, sewage, manure and manured soil although they are not stable in antibiotic-free environments. IMPORTANCEAntibiotic resistance crisis is a grave concern in healthcare systems around the world. To combat this crisis, we sought to find out how likely manure-originated multi-drug resistant plasmids are to be selected and maintained in different environment matrices. Our study showed that these plasmids conferring resistance to {beta}-lactams, lincosamides, phenicols, macrolides, sulfonamides and tetracyclines can be selected at minimum selection concentrations which are lower than minimum inhibition concentrations of the E. coli host strain. Lincomycin, oxytetracycline, chlortetracycline, tetracycline, chloramphenicol, trimethoprim had minimum selection concentrations lower than the antibiotic concentrations in several environment matrices reported previously. Our findings suggest that despite the burden and the high rate of plasmid loss, these plasmids can still be selected, maintained and circulated well in some polluted environments.

microbiology↗

bioRxiv2023

Genetic characterization of extended-beta-lactamase (ESBL) plasmids captured from dairy manures

This study was to assess the gene diversity and characterize a large set of plasmids harboring extended {beta}-lactamase (ESBL) genes from raw and digested dairy manure. A total of eighty-four plasmids that were captured in this E. coli recipient were sequenced using Illumina MiSeq sequencing technology. Twenty-four plasmids of interest were subsequently sequenced using MinION technology in order that a hybrid assembly could be performed on short-and long-read sequences to circularize and complete these plasmids. The size of sequenced plasmids ranged between 40 and 260 kb with various incompatibility groups: IncC, IncI1, IncN, IncY, IncB/O/K/Z, IncX1, IncHI2, IncHI2A, IncFIB(K), IncFII. A variety of extended {beta}-lactamase genes were identified: blaCTXM -1, blaCTXM -14, blaCTXM -15, blaCTXM-27, blaCTXM-55, blaCTXM-61, blaPER-1, blaIMP-27. Interestingly, the blaIMP-27 gene, a novel metallo-{beta}-lactamase discovered in the last decade, was found located on an integrated region in the host chromosome. And one plasmid carrying the blaCMY-2 gene, an AmpC gene, also expressed ESBL phenotype. Four virulence factors, including cia, cib, traT and terC, were detected on some of these plasmids. In addition, six type-2 toxin-antitoxin systems were detected: MazF/E, PemK/I, HipA/B, YdcE/D, RelB/E and HigB/A. Twenty-two out of twenty-four complete plasmids carried putative prophage regions; and most of prophage hits were marked as incomplete, except that the largest plasmid pT525A and the IncY plasmid pT415A had prophage hits with higher scores. IMPORTANCEThe widespread of antibiotic resistant bacteria is largely due to the exchange of mobile genetic elements such as plasmids. Plasmids harboring extended {beta}-lactamase (ESBL) genes originated from dairy manure potentially become entrained in manured soil, which subsequently enter the human food chain. Currently there is a lack of detailed information on these plasmids in the environment, specifically in dairy manure. This study unveils the abundance and diversity of ESBL-carrying plasmids from both raw and digested manures which were captured in gfp-labelled E. coli CV601. In addition, the study provides insightful information of plasmid characteristics including incompatibility groups, ESBL genes combined with other resistance genes, mobile genetic elements (transposons, insertion sequence), toxin-antitoxin systems, virulence factors and prophage sequences.

microbiology↗

bioRxiv2019

Choosing Your Battles: Which Resistance Genes Warrant Global Action?

The increasing accumulation of antibiotic resistance genes (ARGs) in pathogens poses a severe threat to the treatment of bacterial infections. However, not all ARGs do not pose the same threats to human health. Here, we present a framework to rank the risk of ARGs based on three factors: \"anthropogenic enrichment\", \"mobility\", and \"host pathogenicity\". The framework is informed by all available bacterial genomes (55,000), plasmids (16,000), integrons (3,000), and 850 metagenomes covering diverse global eco-habitats. The framework prioritizes 3% of all known ARGs in Rank I (the most at risk of dissemination amongst pathogens) and 0.3% of ARGs in Rank II (high potential emergence of new resistance in pathogens). We further validated the framework using a list of 38 ARG families previously identified as high risk by the World Health Organization and published literature, and found that 36 of them were properly identified as top risk (Rank I) in our approach. Furthermore, we identified 43 unreported Rank I ARG families that should be prioritized for public health interventions. Within the same gene family, homologous genes pose different risks, host range, and ecological distributions, indicating the need for high resolution surveillance into their sequence variants. Finally, to help strategize the policy interventions, we studied the impact of industrialization on high risk ARGs in 1,120 human gut microbiome metagenomes of 36 diverse global populations. Our findings suggest that current policies on controlling the clinical antimicrobial consumptions could effectively control Rank I, while greater antibiotic stewardship in veterinary settings could help control Rank II. Overall, our framework offered a straightforward evaluation of the risk posed by ARGs, and prioritized a shortlist of current and emerging threats for global action to fight ARGs.

microbiology↗

bioRxiv2018

CaptureSeq: Capture-based enrichment of cpn60 gene fragments empowers pan-Domain profiling of microbial communities without universal PCR

BackgroundMolecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with universal PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. MethodsWe present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. ResultsThe CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three Domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health.

microbiology↗