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Analysis of resistance genes of clinical Pannonibacter phragmitetus strain 31801 by complete genome sequencing

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A Correction to this article was published on 27 September 2018

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Abstract

To clarify the resistance mechanisms of Pannonibacter phragmitetus 31801, isolated from the blood of a liver abscess patient, at the genomic level, we performed whole genomic sequencing using a PacBio RS II single-molecule real-time long-read sequencer. Bioinformatic analysis of the resulting sequence was then carried out to identify any possible resistance genes. Analyses included Basic Local Alignment Search Tool searches against the Antibiotic Resistance Genes Database, ResFinder analysis of the genome sequence, and Resistance Gene Identifier analysis within the Comprehensive Antibiotic Resistance Database. Prophages, clustered regularly interspaced short palindromic repeats (CRISPR), and other putative virulence factors were also identified using PHAST, CRISPRfinder, and the Virulence Factors Database, respectively. The circular chromosome and single plasmid of P. phragmitetus 31801 contained multiple antibiotic resistance genes, including those coding for three different types of β-lactamase [NPS β-lactamase (EC 3.5.2.6), β-lactamase class C, and a metal-dependent hydrolase of β-lactamase superfamily I]. In addition, genes coding for subunits of several multidrug-resistance efflux pumps were identified, including those targeting macrolides (adeJ, cmeB), tetracycline (acrB, adeAB), fluoroquinolones (acrF, ceoB), and aminoglycosides (acrD, amrB, ceoB, mexY, smeB). However, apart from the tripartite macrolide efflux pump macAB-tolC, the genome did not appear to contain the complete complement of subunit genes required for production of most of the major multidrug-resistance efflux pumps.

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  • 27 September 2018

    Subsequent to publication it has been noticed that the below listed text parts, figures and tables of the above paper were taken from paper

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Acknowledgements

We thank the staff of the Yun Leung Laboratory for Molecular Diagnostics, School of Biomedical Sciences, Huaqiao University, Xiamen, for their providing bioinformatic analysis, especially Dr. Mingxi Wang for his kind assistance. This work was supported by the Fujian Province Science and Technology Planning Foundations (2015J01514), the Quanzhou high level talent innovation and Entrepreneurship Project (2017Z36).

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  1. Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, 362000, Fujian, China

    De-song Ming, Qing-qing Chen & Xiao-tin Chen

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  1. De-song Ming
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  2. Qing-qing Chen
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Correspondence to De-song Ming.

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Ming, Ds., Chen, Qq. & Chen, Xt. Analysis of resistance genes of clinical Pannonibacter phragmitetus strain 31801 by complete genome sequencing. Arch Microbiol 200, 1101–1109 (2018). https://doi.org/10.1007/s00203-018-1522-2

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