<i>Klebsiella pneumoniae</i> as a key trafficker of drug resistance genes from environmental to clinically important bacteria

Wyres, Kelly L.; Holt, Kathryn E.

doi:10.7287/peerj.preprints.26852v1

Cited by 35 publications

(45 citation statements)

References 55 publications

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“…A much smaller number of human infections are caused by S. plymuthica (Mahlen, 2011) and the lower virulence of the isolate in this study compared to S. liquefaciens is consistent with this observation. The lack of genomic differentiation between isolates from both clinical and environmental sources observed here is consistent with a highly generalist lifestyle, as has also been found in other human pathogens such as Klebsiella pneumoniae (Wyres and Holt, 2018) and Campylobacter jejuni (Sheppard et al ., 2014).…”

Section: Discussionsupporting

confidence: 89%

Determining the prevalence, identity and possible origin of bacterial pathogens in soil

Ferraresso

Lawton

Bayliss

et al. 2020

Environmental Microbiology

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Soil biomes are vast, exceptionally diverse and crucial to the health of ecosystems and societies. Soils also contain an appreciable, but understudied, diversity of opportunistic human pathogens. With climate change and other forms of environmental degradation potentially increasing exposure risks to soilborne pathogens, it is necessary to gain a better understanding of their ecological drivers. Here we use the Galleria mellonella insect virulence model to selectively isolate pathogenic bacteria from soils in Cornwall (UK). We find a high prevalence of pathogenic soil bacteria with two genera, Providencia and Serratia, being especially common. Providencia alcalifaciens, P. rustigianii, Serratia liquefaciens and S. plymuthica strains were studied in more detail using phenotypic virulence and antibiotic resistance assays and whole-genome sequencing. Both genera displayed low levels of antibiotic resistance and antibiotic resistance gene carriage. However, Serratia isolates were found to carry the recently characterized metallo-β-lactamase blaSPR-1 that, although not conferring high levels of resistance in these strains, poses a potential risk of horizontal transfer to other pathogens where it could be fully functional. The Galleria assay can be a useful approach to uncover the distribution and identity of pathogenic bacteria in the environment, as well as uncover resistance genes with an environmental origin.

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Section: Discussionsupporting

confidence: 89%

Determining the prevalence, identity and possible origin of bacterial pathogens in soil

Ferraresso

Lawton

Bayliss

et al. 2020

Environmental Microbiology

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“…Although the genes of the sil operon cannot be expressed in gram-positive bacteria, its presence in this type of bacteria is of importance. Under stress conditions, these genes could be transmitted to bacterial strains with the ability to express them [22,23] due to horizontal gene transfer, which is increased in biofilms that are the main form of bacterial growth in infected root canals with secondary endodontic infection [24,25].…”

Section: Discussionmentioning

confidence: 99%

Detection of Genes Related to Resistance to Silver Nanoparticles in Bacteria from Secondary Endodontic Infections

Orozco

Niño-Martínez

Martínez-Castañón

et al. 2019

Journal of Nanomaterials

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Introduction. Silver nanoparticles are used in endodontics due to their antimicrobial activity, although it is considered that bacteria are unable to develop resistance to silver nanoparticles. Silver resistance genes have been related to resistance to nanoparticles and antibiotics. The presence of these resistance genes has not been studied in endodontic bacteria. The objective of this study is to report the prevalence of silver resistance genes in endodontic bacteria. Methods. The selected teeth were isolated using a rubber dam and any restoration, post, or caries was eliminated. The operative field was disinfected, and the root-filling material was removed. The samples were obtained using three sterile paper points to absorb the fluid of the root canal. The DNA from the samples and the control organism was extracted, and the detection of the silCBA resistance genes was carried out by PCR. Results. The results of this study show a high prevalence (73.3%) of silCBA silver resistance genes. The Spearman rank correlation coefficient was utilized to identify correlations between the presence of genes and clinical variables. Conclusions. This study reports a high frequency of silver resistance genes related to nanoparticle resistant from bacteria.

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“…This problem is expected to be frequent in our context because several of the bacteria involved in the HAP-VAP infections are known to resort to horizontal gene transfer to rapidly improve their fitness, e.g. P. aeruginosa [36], K. pneumoniae [37], A. baumannii [38], or S. aureus [39].…”

Section: Bioinformatics Pipelinementioning

confidence: 99%

Clinical metagenomics bioinformatics pipeline for the identification of hospital-acquired pneumonia pathogens antibiotic resistance genes from bronchoalveolar lavage samples

Tournoud

Ruppé

Perrin

et al. 2020

Preprint

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Background: Shortening the time-to-result for pathogen detection and identification and antibiotic susceptibility testing for patients with Hospital-Acquired and Ventilator-Associated pneumonia (HAP-VAP) is of great interest. For this purpose, clinical metagenomics is a promising non-hypothesis driven alternative to traditional culture-based solutions: when mature, it would allow direct sequencing all microbial genomes present in a BronchoAlveolar Lavage (BAL) sample with the purpose of simultaneously identifying pathogens and Antibiotic Resistance Genes (ARG). In this study, we describe a new bioinformatics method to detect pathogens and their ARG with good accuracy, both in mono-and polymicrobial samples.Methods: The standard approach (hereafter called TBo), that consists in taxonomic binning of metagenomic reads followed by an assembly step, suffers from lack of sensitivity for ARG detection. Thus, we propose a new bioinformatics approach (called TBwDM) with both models and databases optimized for HAP-VAP, that performs reads mapping against ARG reference database in parallel to taxonomic binning, and joint reads assembly.Results: In in-silico simulated monomicrobial samples, the recall for ARG detection increased from 51% with TBo to 97.3% with TBwDM ; in simulated polymicrobial infections, it increased from 41.8% to 82%. In real sequenced BAL samples (mono and polymicrobial), detected pathogens were also confirmed by traditional culture approaches. Moreover, both recall and precision for ARG detection were higher with TBwDM than with TBo (35 points difference for recall, and 7 points difference for precision).Conclusions: We present a new bioinformatics pipeline to identify pathogens and ARG in BAL samples from patients with HAP-VAP, with higher sensitivity for ARG recovery than standard approaches and the ability to link ARG to their host pathogens.

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Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

Cited by 35 publications

References 55 publications

Determining the prevalence, identity and possible origin of bacterial pathogens in soil

Determining the prevalence, identity and possible origin of bacterial pathogens in soil

Detection of Genes Related to Resistance to Silver Nanoparticles in Bacteria from Secondary Endodontic Infections

Clinical metagenomics bioinformatics pipeline for the identification of hospital-acquired pneumonia pathogens antibiotic resistance genes from bronchoalveolar lavage samples

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