A Multilocus Sequence Typing Scheme Implies Population Structure and Reveals Several Putative Novel Achromobacter Species

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Published inJournal of Clinical Microbiology Vol. 50; no. 9; pp. 3010 - 3015
Main Authors Spilker, Theodore, Vandamme, Peter, LiPuma, John J.
Format Journal Article
LanguageEnglish
Published Washington, DC American Society for Microbiology 01.09.2012
Subjects
Achromobacter - classification
Achromobacter - genetics
Achromobacter - isolation & purification
Bacteriology
Biological and medical sciences
Cluster Analysis
DNA Primers - genetics
DNA, Bacterial - genetics
Fundamental and applied biological sciences. Psychology
Genetic Variation
Gram-Negative Bacterial Infections - epidemiology
Gram-Negative Bacterial Infections - microbiology
Humans
Microbiology
Miscellaneous
Molecular Epidemiology - methods
Multilocus Sequence Typing
Bacteria
Genotype
Population structure
Achromobacter
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Abstract Article Usage Stats Services JCM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue JCM About JCM Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy JCM RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0095-1137 Online ISSN: 1098-660X Copyright © 2014 by the American Society for Microbiology.   For an alternate route to JCM .asm.org, visit: JCM       
AbstractList The genus Achromobacter currently is comprised of seven species, including Achromobacter xylosoxidans, an opportunistic and nosocomial pathogen that displays broad-spectrum antimicrobial resistance and is recognized as causing chronic respiratory tract infection in persons with cystic fibrosis (CF). To enable strain typing for global epidemiologic investigations, to clarify the taxonomy of "Achromobacter-like" strains, and to elucidate the population structure of this genus, we developed a genus-level multilocus sequence typing (MLST) scheme. We employed in silico analyses of whole-genome sequences of several phylogenetically related genera, including Bordetella, Burkholderia, Cupriavidus, Herminiimonas, Janthinobacterium, Methylibium, and Ralstonia, for selecting loci and designing PCR primers. Using this MLST scheme, we analyzed 107 genetically diverse Achromobacter isolates cultured from biologic specimens from CF and non-CF patients, 1 isolate recovered from sludge, and an additional 39 strains obtained from culture collections. Sequence data from these 147 strains, plus three recently genome-sequenced Achromobacter strains, were assigned to 129 sequence types based on seven loci. Calculation of the nucleotide divergence of concatenated locus sequences within and between MLST clusters confirmed the seven previously named Achromobacter species and revealed 14 additional genogroups. Indices of association showed significant linkage disequilibrium in all of the species/genogroups able to be tested, indicating that each group has a clonal population structure. No clear segregation of species/genogroups between CF and non-CF sources was found.
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The genus Achromobacter currently is comprised of seven species, including Achromobacter xylosoxidans, an opportunistic and nosocomial pathogen that displays broad-spectrum antimicrobial resistance and is recognized as causing chronic respiratory tract infection in persons with cystic fibrosis (CF). To enable strain typing for global epidemiologic investigations, to clarify the taxonomy of "Achromobacter-like" strains, and to elucidate the population structure of this genus, we developed a genus-level multilocus sequence typing (MLST) scheme. We employed in silico analyses of whole-genome sequences of several phylogenetically related genera, including Bordetella, Burkholderia, Cupriavidus, Herminiimonas, Janthinobacterium, Methylibium, and Ralstonia, for selecting loci and designing PCR primers. Using this MLST scheme, we analyzed 107 genetically diverse Achromobacter isolates cultured from biologic specimens from CF and non-CF patients, 1 isolate recovered from sludge, and an additional 39 strains obtained from culture collections. Sequence data from these 147 strains, plus three recently genome-sequenced Achromobacter strains, were assigned to 129 sequence types based on seven loci. Calculation of the nucleotide divergence of concatenated locus sequences within and between MLST clusters confirmed the seven previously named Achromobacter species and revealed 14 additional genogroups. Indices of association showed significant linkage disequilibrium in all of the species/genogroups able to be tested, indicating that each group has a clonal population structure. No clear segregation of species/genogroups between CF and non-CF sources was found.The genus Achromobacter currently is comprised of seven species, including Achromobacter xylosoxidans, an opportunistic and nosocomial pathogen that displays broad-spectrum antimicrobial resistance and is recognized as causing chronic respiratory tract infection in persons with cystic fibrosis (CF). To enable strain typing for global epidemiologic investigations, to clarify the taxonomy of "Achromobacter-like" strains, and to elucidate the population structure of this genus, we developed a genus-level multilocus sequence typing (MLST) scheme. We employed in silico analyses of whole-genome sequences of several phylogenetically related genera, including Bordetella, Burkholderia, Cupriavidus, Herminiimonas, Janthinobacterium, Methylibium, and Ralstonia, for selecting loci and designing PCR primers. Using this MLST scheme, we analyzed 107 genetically diverse Achromobacter isolates cultured from biologic specimens from CF and non-CF patients, 1 isolate recovered from sludge, and an additional 39 strains obtained from culture collections. Sequence data from these 147 strains, plus three recently genome-sequenced Achromobacter strains, were assigned to 129 sequence types based on seven loci. Calculation of the nucleotide divergence of concatenated locus sequences within and between MLST clusters confirmed the seven previously named Achromobacter species and revealed 14 additional genogroups. Indices of association showed significant linkage disequilibrium in all of the species/genogroups able to be tested, indicating that each group has a clonal population structure. No clear segregation of species/genogroups between CF and non-CF sources was found.
The genus Achromobacter currently is comprised of seven species, including Achromobacter xylosoxidans , an opportunistic and nosocomial pathogen that displays broad-spectrum antimicrobial resistance and is recognized as causing chronic respiratory tract infection in persons with cystic fibrosis (CF). To enable strain typing for global epidemiologic investigations, to clarify the taxonomy of “ Achromobacter -like” strains, and to elucidate the population structure of this genus, we developed a genus-level multilocus sequence typing (MLST) scheme. We employed in silico analyses of whole-genome sequences of several phylogenetically related genera, including Bordetella , Burkholderia , Cupriavidus , Herminiimonas , Janthinobacterium , Methylibium , and Ralstonia , for selecting loci and designing PCR primers. Using this MLST scheme, we analyzed 107 genetically diverse Achromobacter isolates cultured from biologic specimens from CF and non-CF patients, 1 isolate recovered from sludge, and an additional 39 strains obtained from culture collections. Sequence data from these 147 strains, plus three recently genome-sequenced Achromobacter strains, were assigned to 129 sequence types based on seven loci. Calculation of the nucleotide divergence of concatenated locus sequences within and between MLST clusters confirmed the seven previously named Achromobacter species and revealed 14 additional genogroups. Indices of association showed significant linkage disequilibrium in all of the species/genogroups able to be tested, indicating that each group has a clonal population structure. No clear segregation of species/genogroups between CF and non-CF sources was found.
Author John J. LiPuma
Peter Vandamme
Theodore Spilker
Author_xml – sequence: 1
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  surname: Vandamme
  fullname: Vandamme, Peter
  organization: Laboratory of Microbiology, Ghent University, Ghent, Belgium
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  surname: LiPuma
  fullname: LiPuma, John J.
  organization: Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
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The genus Achromobacter currently is comprised of seven species, including Achromobacter xylosoxidans , an opportunistic and nosocomial pathogen that displays...
The genus Achromobacter currently is comprised of seven species, including Achromobacter xylosoxidans, an opportunistic and nosocomial pathogen that displays...
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StartPage 3010
SubjectTerms Achromobacter - classification
Achromobacter - genetics
Achromobacter - isolation & purification
Bacteriology
Biological and medical sciences
Cluster Analysis
DNA Primers - genetics
DNA, Bacterial - genetics
Fundamental and applied biological sciences. Psychology
Genetic Variation
Gram-Negative Bacterial Infections - epidemiology
Gram-Negative Bacterial Infections - microbiology
Humans
Microbiology
Miscellaneous
Molecular Epidemiology - methods
Multilocus Sequence Typing
Title A Multilocus Sequence Typing Scheme Implies Population Structure and Reveals Several Putative Novel Achromobacter Species
URI http://jcm.asm.org/content/50/9/3010.abstract
https://www.ncbi.nlm.nih.gov/pubmed/22785192
https://www.proquest.com/docview/1034200586
https://pubmed.ncbi.nlm.nih.gov/PMC3421806
Volume 50
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