Project description:Several members of the Gram-negative environmental bacterial genus Achromobacter are associated with serious infections, with Achromobacter xylosoxidans being the most common. Despite their pathogenic potential, little is understood about these intrinsically drug-resistant bacteria and their role in disease, leading to suboptimal diagnosis and management. Here, we performed comparative genomics for 158 Achromobacter spp. genomes to robustly identify species boundaries, reassign several incorrectly speciated taxa and identify genetic sequences specific for the genus Achromobacter and for A. xylosoxidans. Next, we developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the rapid and simultaneous detection of Achromobacter spp. and A. xylosoxidans from both purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates identified as Achromobacter spp. using phenotypic or genotypic methods. In comparison to these routine diagnostic methods, the duplex assay showed superior identification of Achromobacter spp. and A. xylosoxidans, with five Achromobacter isolates failing to amplify with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax quantified both Achromobacter spp. and A. xylosoxidans down to ~110 genome equivalents and detected down to ~12 and ~1 genome equivalent(s), respectively. Extensive in silico analysis, and laboratory testing of 34 non-Achromobacter isolates and 38 adult cystic fibrosis sputa, confirmed duplex assay specificity and sensitivity. We demonstrate that the Ac-Ax duplex assay provides a robust, sensitive and cost-effective method for the simultaneous detection of all Achromobacter spp. and A. xylosoxidans and will facilitate the rapid and accurate diagnosis of this important group of pathogens.
Project description:Achromobacter piechaudii strain HLE is a betaproteobacterium (previously known as Alcaligenes faecalis) that was an early isolate with arsenite oxidase activity. This draft genome of 6.89 Mb is the second available genome for this species in the opportunistic pathogen Alcaligenaceae family.
Project description:<i>Achromobacter</i> species are increasingly being detected in patients with cystic fibrosis (CF), and this emerging pathogen is associated with antibiotic resistance and more-severe disease outcomes. Nonetheless, little is known about the extent of transmission and antibiotic resistance development in <i>Achromobacter</i> infections. We sequenced the genomes of 101 <i>Achromobacter</i> clinical isolates (identified as <i>Achromobacter xylosoxidans</i> based on matrix-assister laser desorption ionization-time of flight [MALDI-TOF] or API N20 typing) collected from 51 patients with CF-the largest longitudinal data set to date. We performed phylogenetic analysis on the genomes and combined this with epidemiological and antibiotic resistance data to identify patient-to-patient transmission and the development of antibiotic resistance. We confirmed that the MALDI-TOF or API N20 method was not sufficient for <i>Achromobacter</i> species-level typing and that the population of <i>Achromobacter</i> isolates was composed of five different species, among which <i>A. xylosoxidans</i> accounted for 52% of infections. Most patients were infected by unique <i>Achromobacter</i> clone types; nonetheless, suspected patient-to-patient transmission cases identified by shared clone types were observed in 35% (<i>n</i> = 18) of patients. In 15 of 16 cases, the suspected transmissions were further supported by genome- or clinic visit-based epidemiological analysis. Finally, we found that resistance developed over time. We show that whole-genome sequencing (WGS) is essential for <i>Achromobacter</i> species typing and identification of patient-to-patient transmission, which was revealed for <i>Achromobacter ruhlandii</i>, <i>A. xylosoxidans</i>, and, for the first time, <i>Achromobacter insuavis</i> Furthermore, we show that the development of antibiotic resistance is associated with chronic <i>Achromobacter</i> infections. Our findings emphasize that transmission and antibiotic resistance should be considered in future treatment strategies.
Project description:The genome of Achromobacter xylosoxidans MN001, a strain isolated from sputum derived from an adult cystic fibrosis patient, was sequenced using combined single-molecule real-time and Illumina sequencing. Assembly of the complete genome resulted in a 5,876,039-bp chromosome, representing the smallest A. xylosoxidans genome sequenced to date.
Project description:Achromobacter sp. strain B7 (= CCUG 72081) was isolated from a diesel-polluted soil from the Valparaiso Region, Chile, subjected to bioremediation with a hydrocarbon-degrading enrichment. The complete genome sequence of Achromobacter sp. B7 has been determined to have a size of 6.24?Mb, 5,578 coding sequences, 57 tRNAs, and a G+C content of 64.8%.
Project description:Achromobacter spanius UQ283 is a soilborne bacterium found to exhibit plant growth-promoting and disease-suppressing attributes in several plant species. Accordingly, we used long-read sequencing to determine its complete genome sequence. The assembled genome will aid in understanding the multifaceted interactions between plant growth-promoting rhizobacteria, pathogens, and plants.