Prevalence and species distribution of Achromobacter sp. cultured from cystic fibrosis patients attending the Aarhus centre in Denmark

Gade, Sinne Søberg; Nørskov‐Lauritsen, Niels; Ridderberg, Winnie

doi:10.1099/jmm.0.000499

Cited by 37 publications

(40 citation statements)

References 20 publications

(16 reference statements)

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“…Our study detected one apparent case of clinical species mis-identification: in both patients CFR06 [43,44,[46][47][48] or at least accounted for a considerable fraction of Achromobacter infections [42]. A. insuavis is also one of the few Achromobacter species capable of chronic infection [44,47,48], and our observations in patient CFR11 are in line with previous findings.…”

Section: Discussionsupporting

confidence: 91%

Strain-resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis

Dmitrijeva

Kahlert

Feigelman

et al. 2020

Preprint

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Background In cystic fibrosis, dynamic and complex communities of microbial pathogens and commensals colonize the lung. Cultured isolates from lung sputum reveal high inter- and intraindividual variability in pathogen strains, sequence variants, and phenotypes; disease progression likely depends on the precise combination of infecting strains. Routine clinical protocols, however, provide limited overview of the colonizer populations. A more comprehensive and precise identification and characterization of infecting strains could therefore assist in making corresponding decisions on treatment. Results Here, we propose a minimally invasive and culture-independent way to monitor microbial lung content. We describe longitudinal tracking of four patients with cystic fibrosis over several months, including repeated sampling and bulk DNA sequencing of sputum. We find that the taxonomic identity of individual lineages can be easily established. Crucially, even superficially clonal pathogens can be subdivided into multiple sub-strains at the sequence level. By tracking individual allelic differences over time, an assembly-free clustering approach allows us to reconstruct multiple strain-specific genomes with clear structural differences. Conclusions We emphasize the advantages of metagenomics sequencing of longitudinal data for taxonomic identification of microbial colonizers in cystic fibrosis lungs. Our study is the first to track sub-strain pathogen dynamics using a culture-independent approach, with a perspective of high-resolution routine characterization of disease progression that may allow to more accurately monitor treatment outcomes and tailor treatment.

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Section: Discussionsupporting

confidence: 91%

Strain-resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis

Dmitrijeva

Kahlert

Feigelman

et al. 2020

Preprint

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“…Pseudomonas aeruginosa and Staphylococcus aureus , are studied extensively, little is known about the extent within- and between-patient genetic adaptation has in Achromobacter infections, particularly A. ruhlandii , A. insuavis and A. xylosoxidans as they mainly cause chronic, long-term infections in patients with CF. (5–7) Furthermore, genetic features could be used for successful resistance profile predictions as conventional methods are both time consuming and occasionally do not reflect the in vivo susceptibility profiles. (8–10) Knowledge of within-host Achromobacter adaptation and genetic factors leading to antibiotic resistance development are key for urgently needed new treatment strategy development and pathogen elimination.…”

Section: Introductionmentioning

confidence: 99%

Achromobactergenetic adaptation in cystic fibrosis

Gabrielaitė

Johansen

Nielsen

et al. 2021

Preprint

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Achromobacter is an emerging pathogen in patients with cystic fibrosis (CF) and Achromobacter caused infections are associated with more severe disease outcomes and high intrinsic antibiotic resistance. While conventional CF pathogens are studied extensively, little is known about the genetic determinants leading to antibiotic resistance and the genetic adaptation in Achromobacter infections.Here, we analyzed 101 Achromobacter genomes from 51 patients with CF isolated during the course of up to 20 years of infection to identify within-host adaptation, mutational signatures, and genetic variation associated with increased antibiotic resistance.We found that the same regulatory and inorganic ion transport genes were frequently mutated in persisting clone types within and between Achromobacter species indicating convergent genetic adaptation. Genome-wide association study (GWAS) of six antibiotic resistance phenotypes revealed the enrichment of associated genes involved in inorganic ion transport genes, transcription gene enrichment in β-lactams, and energy production and translation gene enrichment in the trimethoprim/sulfonamide group.Overall, we provide insights into the pathogenomics of Achromobacter infections in patients with CF airways. Since emerging pathogens are increasingly recognised as an important healthcare issue, our findings on evolution of antibiotic resistance and genetic adaptation can facilitate better understanding of disease progression and how mutational changes have implications for patients with CF.

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“…The recent review of genetic divergence within the Achromobacter genus resulted in an increase in the number of recorded strains of A. marplatensis , owing to the reclassification of A. spiritinus as A. marplatensis [ 15 , 16 ]. A. marplatensis now carries a newly recognised importance in CF patients, being isolated from more than 10% of patients in a French CF Centre [ 12 ], as well as in CF patients in Argentina [ 17 ], Serbia [ 18 ], Denmark [ 19 ] and the UK [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

Characterization of Novel Lytic Bacteriophages of Achromobacter marplantensis Isolated from a Pneumonia Patient

Chan

Low

et al. 2020

Viruses

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Achromobacter spp. are becoming increasingly associated with lung infections in patients suffering from cystic fibrosis (CF). A. marplatensis, which is closely related to A. xylosoxidans, has been isolated from the lungs of CF patients and other human infections. This article describes the isolation, morphology and characterization of two lytic bacteriophages specific for an A. marplatensis strain isolated from a pneumonia patient. This host strain was the causal agent of hospital acquired pneumonia–the first clinical report of such an occurrence. Full genome sequencing revealed bacteriophage genomes ranging in size from 45901 to 46,328 bp. Transmission electron microscopy revealed that the two bacteriophages AMA1 and AMA2 belonged to the Siphoviridae family. Host range analysis showed that their host range did not extend to A. xylosoxidans. The possibility exists for future testing of such bacteriophages in the control of Achromobacter infections such as those seen in CF and other infections of the lungs. The incidence of antibiotic resistance in this genus highlights the importance of seeking adjuncts and alternatives in CF and other lung infections.

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Prevalence and species distribution of Achromobacter sp. cultured from cystic fibrosis patients attending the Aarhus centre in Denmark

Cited by 37 publications

References 20 publications

Strain-resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis

Strain-resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis

Achromobactergenetic adaptation in cystic fibrosis

Characterization of Novel Lytic Bacteriophages of Achromobacter marplantensis Isolated from a Pneumonia Patient

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