Distribution of Allelic Variants of the Chromosomal Gene bla OXA-114-like in Achromobacter xylosoxidans Clinical Isolates

Traglia, Germán Matías; Almuzara, Marisa; Merkier, Andrea Karina; Papalia, Mariana Andrea; Galanternik, L.; Radice, Marcela; Vay, Carlos; Centrón, Daniela; Ramírez, María Soledad

doi:10.1007/s00284-013-0407-5

Cited by 7 publications

(9 citation statements)

References 15 publications

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“…Analysis of HiSeq Illumina data using Galaxy software revealed that isolates from patients A1-A3 were representatives of ST144, while patient A4's isolate differed at all but two of seven loci, representing a novel ST. A search for resistance genes detected a novel bla OXA gene variant. The variant, which was also present in patient A4's isolate (albeit with one base pair difference), was more closely related to the bla OXA-364 variant found in A. dolens (95.3% similarity at the nucleotide level) than to the bla OXA-243e variant found to be associated with A. insuavis 2b (92.0% similarity at the nucleotide level) [10,11].…”

Section: Whole Genome Sequencingmentioning

confidence: 67%

“…Intrinsic and acquired resistance in Achromobacter species have been documented, with various carbapenemases described, each of which contributes to the therapeutic challenges associated with these pathogens [5,[8][9][10][11][12]. The intrinsic bla OXA genes reported in the genus, which may not be expressed, are species-specific and are therefore helpful in identification studies [10,11,13,14].…”

Section: Introductionmentioning

confidence: 99%

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Use of nrdA gene sequence clustering to estimate the prevalence of different Achromobacter species among Cystic Fibrosis patients in the UK

Coward

Kenna

Perry

et al. 2016

Journal of Cystic Fibrosis

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Section: Whole Genome Sequencingmentioning

confidence: 67%

Section: Introductionmentioning

confidence: 99%

Use of nrdA gene sequence clustering to estimate the prevalence of different Achromobacter species among Cystic Fibrosis patients in the UK

Coward

Kenna

Perry

et al. 2016

Journal of Cystic Fibrosis

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“…Previous PCR-based studies, mostly because they were misguided by the incorrect classification of the genus, present different results regarding allelic variants and the presence of OXA genes in Achromobacter species, and should be treated with caution (Amoureux et al. 2013b; Traglia et al. 2013, 2014).…”

Section: Resultsmentioning

confidence: 99%

A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter

Jeukens

Freschi

Vincent

et al. 2017

Genome Biology and Evolution

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Over the past decade, there has been a rising interest in Achromobacter sp., an emerging opportunistic pathogen responsible for nosocomial and cystic fibrosis lung infections. Species of this genus are ubiquitous in the environment, can outcompete resident microbiota, and are resistant to commonly used disinfectants as well as antibiotics. Nevertheless, the Achromobacter genus suffers from difficulties in diagnosis, unresolved taxonomy and limited understanding of how it adapts to the cystic fibrosis lung, not to mention other host environments. The goals of this first genus-wide comparative genomics study were to clarify the taxonomy of this genus and identify genomic features associated with pathogenicity and host adaptation. This was done with a widely applicable approach based on pan-genome analysis. First, using all publicly available genomes, a combination of phylogenetic analysis based on 1,780 conserved genes with average nucleotide identity and accessory genome composition allowed the identification of a largely clinical lineage composed of Achromobacter xylosoxidans, Achromobacter insuavis, Achromobacter dolens, and Achromobacter ruhlandii. Within this lineage, we identified 35 positively selected genes involved in metabolism, regulation and efflux-mediated antibiotic resistance. Second, resistome analysis showed that this clinical lineage carried additional antibiotic resistance genes compared with other isolates. Finally, we identified putative mobile elements that contribute 53% of the genus’s resistome and support horizontal gene transfer between Achromobacter and other ecologically similar genera. This study provides strong phylogenetic and pan-genomic bases to motivate further research on Achromobacter, and contributes to the understanding of opportunistic pathogen evolution.

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“…Most Achromobacter clinical isolates are designated as Achromobacter xylosoxidans; however, the commonly used phenotypic tests are not reliable (1)(2)(3). Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis is used in clinical microbiology laboratories as an emerging technology for bacterial species identification (4)(5)(6)(7)(8).…”

mentioning

confidence: 99%

Characterization of Achromobacter Species in Cystic Fibrosis Patients: Comparison of bla _OXA-114 PCR Amplification, Multilocus Sequence Typing, and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

et al. 2015

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A chromobacter is an emerging pathogen in cystic fibrosis (CF) patients, but accurate species identification of isolates is difficult. Most Achromobacter clinical isolates are designated as Achromobacter xylosoxidans; however, the commonly used phenotypic tests are not reliable (1-3). Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis is used in clinical microbiology laboratories as an emerging technology for bacterial species identification (4-8). Genotypic methods have also been developed for Achromobacter species. The amplification of an inner fragment of the bla OXA-114 gene has been proposed for A. xylosoxidans identification (9). Furthermore, the presence of bla , bla , and bla OXA-243 has been detected in Achromobacter ruhlandii, Achromobacter dolens, and Achromobacter insuavis, respectively (2, 3). Multilocus sequence typing (MLST) schemes that increase the accuracy of the characterization and identification of Achromobacter strains and species have also been developed (10,11). This study compares the identification of Achromobacter species from CF patients by bla OXA-114 gene sequencing, MLST, and MALDI-TOF MS.Twenty-eight archived isolates that had been collected between 2003 and 2008 from 16 CF patients attending two reference centers in Rio de Janeiro, Brazil, were included. The isolates were identified as A. xylosoxidans by 16S rRNA gene sequencing (12, 13); bla OXA-114-like gene amplification and sequencing were performed as described by Turton et al. (9). MLST analysis by sequencing of seven housekeeping genes (nusA, rpoB, eno, gltB, lepA, nuoL, and nrdA) was performed as described previously (11). Allelic profiles and sequence types (STs) were analyzed according to the PubMLST databases (http://pubmlst.org/achromobacter). MALDI-TOF MS identification was performed with a Microflex LT instrument (Bruker Daltonics, GmbH, Germany) using FlexControl 3.0 software (Bruker Daltonics). Scores of Ն2.0 indicated species-level identification, scores of 1.7 to 1.9 indicated genuslevel identification, and scores of Ͻ1.7 indicated no reliable identification (14, 15).Positive bla OXA-114 amplification was obtained for 26 isolates. In 17 isolates, amplicons showed 99 to 100% identity with the bla OXA-114 reference sequence. In 9 isolates, identified as A. ruhlandii, sequences displayed 99% identity with bla OXA-258 . Two isolates (isolates 4530 and 7393) were negative for bla OXA . As observed by Papalia et al. (2), in our study not only A. xylosoxidans but also A. ruhlandii yielded positive amplification for the A. xylosoxidans species-specific marker bla . Amplification of the inner fragment without sequence analysis, as initially described by Turton et al. (9), thus may result in the misidentification of some Achromobacter species; by this criterion, we would have identified 26 isolates instead of 17 as A. xylosoxidans. MALDI-TOF MS identified 89% of the isolates (25/28 isolates) as A. xylosoxidans, while 7% (2/28 isolates) were identified at the probable ge...

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Distribution of Allelic Variants of the Chromosomal Gene bla OXA-114-like in Achromobacter xylosoxidans Clinical Isolates

Cited by 7 publications

References 15 publications

Use of nrdA gene sequence clustering to estimate the prevalence of different Achromobacter species among Cystic Fibrosis patients in the UK

Use of nrdA gene sequence clustering to estimate the prevalence of different Achromobacter species among Cystic Fibrosis patients in the UK

A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter

Characterization of Achromobacter Species in Cystic Fibrosis Patients: Comparison of bla _OXA-114 PCR Amplification, Multilocus Sequence Typing, and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

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Distribution of Allelic Variants of the Chromosomal Gene bla OXA-114-like in Achromobacter xylosoxidans Clinical Isolates

Cited by 7 publications

References 15 publications

Use of nrdA gene sequence clustering to estimate the prevalence of different Achromobacter species among Cystic Fibrosis patients in the UK

Use of nrdA gene sequence clustering to estimate the prevalence of different Achromobacter species among Cystic Fibrosis patients in the UK

A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter

Characterization of Achromobacter Species in Cystic Fibrosis Patients: Comparison of bla OXA-114 PCR Amplification, Multilocus Sequence Typing, and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

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Characterization of Achromobacter Species in Cystic Fibrosis Patients: Comparison of bla _OXA-114 PCR Amplification, Multilocus Sequence Typing, and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry