Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important pathogenic phenotypes

Abstract

Achromobacter xylosoxidans is an environmental opportunistic pathogen, which infects an increasing number of immunocompromised patients. In this study we combined genomic analysis of a clinical isolated A. xylosoxidans strain with phenotypic investigations of its important pathogenic features. We present a complete assembly of the genome of A. xylosoxidans NH44784-1996, an isolate from a cystic fibrosis patient obtained in 1996. The genome of A. xylosoxidans NH44784-1996 contains approximately 7 million base pairs with 6390 potential protein-coding sequences. We identified several features that render it an opportunistic human pathogen, We found genes involved in anaerobic growth and the pgaABCD operon encoding the biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamin. Furthermore, the genome contains a range of antibiotic resistance genes coding efflux pump systems and antibiotic modifying enzymes. In vitro studies of A. xylosoxidans NH44784-1996 confirmed the genomic evidence for its ability to form biofilms, anaerobic growth via denitrification, and resistance to a broad range of antibiotics. Our investigation enables further studies of the functionality of important identified genes contributing to the pathogenicity of A. xylosoxidans and thereby improves our understanding and ability to treat this emerging pathogen.

Figure 1. A circular view of the genome of A. xylosoxidans NH44784-1996.

Including CDS and RNA features, GC content and skew. The figure was prepared using CGView [97]. A genome-genome comparison with A. xylosoxidans A8 (CP002287 [40]) was created using MegaBlast with default parameters.

Figure 2. The 11 most related bacterial strains to A. xylosoxidans NH44784-1996 investigated by BLASTP search.

The numbers are referring to open reading frames.

Figure 3. Phylogenetic tree.

Neighbor-joining dendrogram showing the relationship of NH44784-1996 and 77 Achromobacter strains, using B . petrii DSM 12804 as an outgroup. The comparison was based on the concatenated sequences of MLSA genes atpD, icd, recA, rpoB and tyrB (2,098 nt). MLSA clusters I–V are shown. Bootstrap support of clusters is indicated to the left of the node. Scale bar, 0.01 substitutions per site.

Figure 4. Comparison of the amount of genes connected to subsystems.

Number of genes of A. xylosoxidans NH44784-1996, E. coli K-12 and P. aeruginosa PAO1 connected to the different subsystems in The RAST software.

Figure 5. Drug resistance systems.

A comparison of drug resistance systems as annotated by RAST between A. xylosoxidans NH44784-1996 and 10 other pathogens. The classification is divided in following groups: ‘antibiotic resistance’, ‘metal resistance’ and ‘other resistance’ according to RAST.

Figure 6. Biofilm formation of A. xylosoxidans NH44784-1996.

A: 3 day old biofilm grown in flow cell system and visualized by scanning confocal laser microscopy. Syto 9 was injected 15 min. before examination to stain for the presence of living cells. B: 2 day old biofilm grown under static condition investigated with SEM.