Genomic insights into intrinsic and acquired drug resistance mechanisms in Achromobacter xylosoxidans

Abstract

Achromobacter xylosoxidans is an opportunistic pathogen known to be resistant to a wide range of antibiotics; however, the knowledge about the drug resistance mechanisms is limited. We used a high-throughput sequencing approach to sequence the genomes of the A. xylosoxidans type strain ATCC 27061 and a clinical isolate, A. xylosoxidans X02736, and then we used different bioinformatics tools to analyze the drug resistance genes in these bacteria. We obtained the complete genome sequence for A. xylosoxidans ATCC 27061 and the draft sequence for X02736. We predicted a total of 50 drug resistance-associated genes in the type strain, including 5 genes for β-lactamases and 17 genes for efflux pump systems; these genes are also conserved among other A. xylosoxidans genomes. In the clinical isolate, except for the conserved resistance genes, we also identified several acquired resistance genes carried by a new transposon embedded in a novel integrative and conjugative element. Our study provides new insights into the intrinsic and acquired drug resistance mechanisms in A. xylosoxidans, which will be helpful for better understanding the physiology of A. xylosoxidans and the evolution of antibiotic resistance in this bacterium.

FIG 1

Heat map of nucleotide identities for predicted drug resistance genes between the type strain ATCC 27061 and other Achromobacter species. The indicator on the top denotes the relationship between the nucleotide identity and color range. Locus tags of the antibiotic resistance genes in ATCC 27061 are listed on the right. The strains (columns) were clustered by using the MultiExperiment viewer (MeV, version 4.6) and the Pearson correlation and average linkage.

FIG 2

Multiple-sequence alignment of partial amino acid sequences containing the conserved motifs/residues in the different β-lactamase classes. The number to the right of each sequence indicates the amino acid position of the displayed region within the complete ORF. Residues identical to the consensus are shaded gray. Conserved motifs/residues in known enzymes are denoted with an asterisk. The numbers below conserved motifs/residues are based on the β-lactamase standard numbering system. (A) Sequence alignment of AX27061_5685 with representative members of β-lactamase class A. Conserved motifs/residues are ⁷⁰S-X-X-K⁷³, ¹³⁰S-N-D¹³², E¹⁶⁶, and ²³⁴K-T(S)-G²³⁶. (B) Sequence alignment of AX27061_5340 and AX27061_5469 with representative members of β-lactamase class B. Conserved motifs/residues in subclass B1 are H¹¹⁶, H¹¹⁸, D¹²⁰, H¹⁹⁶, C²²¹, and H²⁶³; in subclass B2, they are N¹¹⁶, H¹¹⁸, D¹²⁰, H¹⁹⁶, C²²¹, and H²⁶³; in subclass B3, they are H/Q¹¹⁶, H¹¹⁸, D¹²⁰, H¹⁹⁶, C²²¹, and H²⁶³. (C) Sequence alignment of AX27061_4045 with representative members of β-lactamase class C. Conserved motifs/residues are ⁷⁰S-X-X-K⁷³, ¹³⁰Y-A/S-N¹³², and ²³⁴K-T-G²³⁶. (D) Sequence alignment of AX27061_4146 with representative members of β-lactamase class D. Conserved motifs/residues are ⁷⁰S-T-F-K⁷³, ¹⁴⁴Y-G-N¹⁴⁶, and ²¹⁶K-T-G²¹⁸.

FIG 3

Detailed structure and comparative analysis of Tn6203 with the Tn402-like class 1 integron/transposon in the salmonella genomic island SGI1. Shading indicates more than 99% nucleotide sequence identity. The black line box indicates a 7-kb deletion in Tn6203. The Tn4378-like transposon, the complete mer operon, and the class 1 integrons are indicated by dashed line boxes. The inverted and/or direct repeats flanking Tn6203, Tn4378, and IS6100 are shown with their respective boundaries. The SGI1 sequence was retrieved from NCBI (accession number AF261825).

FIG 4

The locus of ICEAx02736-1 in A. xylosoxidans X02736 compared with two complete genomes. The blank rhombus indicates the 3′ end of the tRNA^Gly gene. The apparent length of ICEAx02736-1 is not to scale.

FIG 5

Detailed structure of ICEAx02736-1. attL and attR denote the two direct repeats flanking ICEAx02736-1. Dashed line boxes indicate more than 95% nucleotide identity in more than 3-kb continuous sequence in the other closest genomes. Important ICE-associated components are shown below the ORFs. Two gray-shaded regions (ORFs in black) denote Tn6203 and a type I RM system.