Analysis of resistance genes of clinical Pannonibacter phragmitetus strain 31801 by complete genome sequencing
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ORIGINAL PAPER
Analysis of resistance genes of clinical Pannonibacter phragmitetus strain 31801 by complete genome sequencing De‑song Ming1 · Qing‑qing Chen1 · Xiao‑tin Chen1 Received: 18 September 2017 / Revised: 13 April 2018 / Accepted: 3 May 2018 © Springer-Verlag GmbH Germany, part of Springer Nature 2018
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. Keywords Pannonibacter phragmitetus · Genome sequencing · Resistance
Introduction Although previously recognized as Achromobacter groups B and E (Holmes et al. 2006; McKinley et al. 1990), Pannonibacter phragmitetus was first described in 1998 after being isolated from a Hungarian soda lake (Borsodi et al. 2003). P. phragmitetus has since been identified in lake bed mud, waste water, and even a hot alkaline spring (Borsodi et al. 2005; Coman et al. 2013). It is a gram-negative, facultatively anaerobic, chemoorganotrophic and motile rod, with optimal growth observed at 37 °C and pH 7.0–10.0 (Bandyopadhyay et al. 2013). Several studies have confirmed its capacity to Communicated by Djamel Drider. * De‑song Ming [email protected] 1
Department of Clinical Laboratory, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou 362000, Fujian, China
reduce the heavy metal chromium, suggesting a potential application for P. phragmitetus in environmental protection (Borsodi et al. 2005; Shi et al. 2012; Wang et al. 2013; Xu et al. 2011). Pannonibacter phragmitetus has also been identified as a
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