Abundance and diversity of resistomes differ between healthy human oral cavities and gut

Carr, Victoria R.; Witherden, Elizabeth A.; Lee, Sunjae; Shoaie, Saeed; Mullany, Peter; Proctor, Gordon; Gomez-Cabrero, David; Moyes, David L.

doi:10.1038/s41467-020-14422-w

Cited by 66 publications

(87 citation statements)

References 55 publications

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“…In our study, we found the APH(3')-IIb gene belonging to the APH gene family, most probably originated from L. mesenteroides. Similarly, Carr et al 18 found a strong co-occurrence between APH(3')-Ia and L. mesenteroides in China saliva samples. Further similarity between our and Carr et al 18 results is the Lc.…”

Section: Discussionmentioning

confidence: 78%

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A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

Tóth

Csabai

Maróti

et al. 2020

Preprint

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Antimicrobial resistance (AMR) is a global threat gaining more and more practical significance every year. The protection of bacteria against antimicrobials based on antimicrobial resistance genes (ARGs) developed in evolution. One of the essential clinical questions is the origin of ARGs of pathogen bacteria. Since the bacteria can share genetic components by horizontal gene transfer (HGT), all even non-pathogen bacteria may provide ARG to any pathogens when they became close physically. The bacteria of the human gut may make contact with bacteria entered into the body by food. The fermented food contains bacteria in high amount by its nature. Here we studied the diversity of ARG content by a unified metagenomic approach in various kefir and yoghurt products, in grain and isolated bacterial strains. We found numerous ARGs of commonly used fermenting bacteria with diversity characteristics in kefir and yoghurt samples. Even with the strictest filter restrictions we identified ARGs undermining the efficacy of aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, diaminopyrimidine, elfamycin, fluoroquinolone, fosfomycin, glycylcycline, lincosamides, macrolide, monobactam, nitrofuran, nitroimidazole, penam, penem, peptide, phenicol, rifamycin, tetracycline and triclosan. In the case of gene lmrD, we detected genetic environment providing mobility of this ARG. Our findings support that theory during the fermentation process the food ARG content can grow by the bacteria multiplication. Results presented suggest that starting culture strains of fermented food should be monitored and selected to decrease the ARG amount intake by nutrition.

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Section: Discussionmentioning

confidence: 78%

“…Similarly, Carr et al 18 found a strong co-occurrence between APH(3')-Ia and L. mesenteroides in China saliva samples. Further similarity between our and Carr et al 18 results is the Lc. lactis origin of lmrD.…”

Section: Discussionmentioning

confidence: 78%

A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

Tóth

Csabai

Maróti

et al. 2020

Preprint

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“…As reviewed by Moraes et al [5], few reports are available in the scientific literature on the occurrence of AR genes in specific oral environments, including saliva, supragingival biofilm, and acute endodontic infections. The importance of characterizing the still poorly explored resistome at the human oral cavity has been very recently pointed out by Carr et al [30]. Even in this latter study, deriving and comparing the oral and gut resistomes from 788 and 386 shotgun metagenomes, respectively, just 72 saliva samples were analyzed, including just 18 samples from Western Europe.…”

Section: Discussionmentioning

confidence: 99%

“…The present research represents a follow-up of a previous study aimed at evaluating the effects of long-term omnivore, ovo-lacto vegetarian, and vegan diets on the occurrence of the same 12 target genes in the human gut of the same cohort of subjects herein considered [29]. In this regard, Carr et al [30] have very recently pointed out the necessity for extensive AR surveillance studies across different body sites, including the gut and the oral cavity. Interestingly, the analyses done on the feces showed a low effect of diet and a high impact of the geographical location on the AR gene distribution [29].…”

Section: Introductionmentioning

confidence: 92%

Distribution of Antibiotic Resistance Genes in the Saliva of Healthy Omnivores, Ovo-Lacto-Vegetarians, and Vegans

Milanović

Aquilanti

Tavoletti

et al. 2020

Genes

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Food consumption allows the entrance of bacteria and their antibiotic resistance (AR) genes into the human oral cavity. To date, very few studies have examined the influence of diet on the composition of the salivary microbiota, and even fewer investigations have specifically aimed to assess the impact of different long-term diets on the salivary resistome. In this study, the saliva of 144 healthy omnivores, ovo-lacto-vegetarians, and vegans were screened by nested PCR for the occurrence of 12 genes conferring resistance to tetracyclines, macrolide-lincosamide-streptogramin B, vancomycin, and β-lactams. The tet(W), tet(M), and erm(B) genes occurred with the highest frequencies. Overall, no effect of diet on AR gene distribution was seen. Some differences emerged at the recruiting site level, such as the higher frequency of erm(C) in the saliva of the ovo-lacto-vegetarians and omnivores from Bologna and Turin, respectively, and the higher occurrence of tet(K) in the saliva of the omnivores from Bologna. A correlation of the intake of milk and cheese with the abundance of tet(K) and erm(C) genes was seen. Finally, when the occurrence of the 12 AR genes was evaluated along with geographical location, age, and sex as sources of variability, high similarity among the 144 volunteers was seen.

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“…AMR++ Shiny [18] is one option of web or locally installable application with a graphical user interface. More recently, resistomeAnalysis [64] R package also provides the possibility for simplified visual exploration and downstream analysis of resistome abundance profile. Based on the detailed comparisons among those tools (Table 1), it is clear that…”

Section: Comparison With Other Toolsmentioning

confidence: 99%

ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data

Dhariwal

Junges

Chen

et al. 2020

Preprint

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Background The study of resistomes using whole metagenomic sequencing enables access to the large repertoire of resistance genes usually found in complex microbial communities, such as the human microbiome. Over recent years, sophisticated and diverse pipelines have been established to facilitate raw data processing and annotation. Despite the progress, there are no easy-to-use tools for comprehensive visual, statistical, and functional analysis of resistome data. Thus, exploration of the resulting large complex datasets remains a key bottleneck requiring robust computational resources and technical expertise, which creates a significant hurdle for advancements in the field. Results Here, we introduce ResistoXplorer, a user-friendly tool that integrates recent advancements in statistics and visualization, coupled with extensive functional annotations and phenotype collection, to enable high-throughput analysis of common outputs generated from resistome studies. ResistoXplorer contains three modules- the Antimicrobial Resistance Gene Table module offers various options for composition profiling, functional profiling and comparative analysis of resistome data; the Integration module supports integrative exploratory analysis of resistome and microbiome abundance profiles in metagenomic samples; finally, the Antimicrobial Resistance Gene List module enables users to explore antimicrobial resistance genes according to function and potential microbial hosts using visual analytics to gain biological insights. Within these three modules, ResistoXplorer offers comprehensive assistance for ARG functional annotations along with their microbe and phenotype associations based on data collected from >10 reference databases. In addition, it provides support for a variety of methods for composition profiling, visualization and exploratory data analysis, as well as extensive support for various data normalization methods and machine learning algorithms for identification of resistome signatures.Finally, ResistoXplorer offers also network visualization for intuitive exploration of associations between antimicrobial resistance genes and the microbial hosts, incorporated with functional enrichment analysis support. Conclusions ResistoXplorer is a web-based tool with a user-friendly interface that enables comprehensive and real-time downstream analysis of resistome data. As such, it allows for in-depth exploration of metagenomic datasets focusing on the intrinsic networks and correlations of antimicrobial resistance genes and their underlying microbial determinants. ResistoXplorer will assist researchers and clinicians in the field of AMR to facilitate discovery in large-scale and multi-dimensional metagenomic datasets. ResistoXplorer is publicly available at http://resistoxplorer.no/ResistoXplorer/.

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Abundance and diversity of resistomes differ between healthy human oral cavities and gut

Cited by 66 publications

References 55 publications

A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

Distribution of Antibiotic Resistance Genes in the Saliva of Healthy Omnivores, Ovo-Lacto-Vegetarians, and Vegans

ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data

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