1887

Abstract

The recent advances in bacterial species identification methods have led to the rapid taxonomic diversification of the genus Acinetobacter . In the present study, phenotypic and molecular methods have been used to determine the taxonomic position of a group of 12 genotypically distinct strains belonging to the Acinetobacter calcoaceticus Acinetobacter baumannii (ACB) complex, initially described by Gerner-Smidt and Tjernberg in 1993, that are closely related to Acinetobacter pittii . Strains characterized in this study originated mostly from human samples obtained in different countries over a period of 15 years. rpoB gene sequences and multilocus sequence typing were used for comparisons against 94 strains representing all species included in the ACB complex. Cluster analysis based on such sequences showed that all 12 strains grouped together in a distinct clade closest to Acinetobacter pittiithat was supported by bootstrap values of 99 %. Values of average nucleotide identity based on blast between the genome sequence of strain JVAP01 (NCBI accession no. LJPG00000000) and those of other species from the ACB complex were always <91.2 %, supporting the species status of the group. In addition, the metabolic characteristics of the group matched those of the ACB complex and the analysis of their protein signatures by matrix-assisted laser desorption ionization time-of-flight MS identified some specific peaks. Our results support the designation of these strains as representing a novel species, for which the name Acinetobacter dijkshoorniae sp. nov. is proposed. The type strain is JVAP01 (=CECT 9134=LMG 29605).

Keyword(s): ACB complex , Acinetobacter , ANIb , MLSA and rpoB
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2016-10-01
2019-10-16
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References

  1. Bouvet P. J., Grimont P. A..( 1987;). Identification and biotyping of clinical isolates of Acinetobacter. . Ann Inst Pasteur Microbiol 138: 569–578. [CrossRef] [PubMed]
    [Google Scholar]
  2. Carretto E., Barbarini D., Dijkshoorn L., van der Reijden T. J., Brisse S., Passet V., Farina C..( 2011;). Widespread carbapenem resistant Acinetobacter baumannii clones in Italian hospitals revealed by a multicenter study. . Infect Genet Evol 11: 1319–1326. [CrossRef]
    [Google Scholar]
  3. Diancourt L., Passet V., Nemec A., Dijkshoorn L., Brisse S..( 2010;). The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. . PLoS One 5: e10034. [CrossRef] [PubMed]
    [Google Scholar]
  4. Du J., Singh H., Yu H., Jin F. X., Yi T. H..( 2016;). Acinetobacter plantarum sp. nov. isolated from wheat seedlings plant. . Arch Microbiol 198: 393–398. [CrossRef] [PubMed]
    [Google Scholar]
  5. Edgar R. C..( 2004;). muscle: multiple sequence alignment with high accuracy and high throughput. . Nucleic Acids Res 32: 1792–1797. [CrossRef] [PubMed]
    [Google Scholar]
  6. Espinal P., Seifert H., Dijkshoorn L., Vila J., Roca I..( 2012;). Rapid and accurate identification of genomic species from the Acinetobacter baumannii (Ab) group by MALDI-TOF MS. . Clin Microbiol Infect 18: 1097–1103. [CrossRef] [PubMed]
    [Google Scholar]
  7. Espinal P., Mosqueda N., Telli M., van der Reijden T., Rolo D., Fernández-Orth D., Dijkshoorn L., Roca I., Vila J..( 2015;). Identification of NDM-1 in a putatively novel acinetobacter species ("NB14") closely related to Acinetobacter pittii. . Antimicrob Agents Chemother 59: 6657–6660. [CrossRef] [PubMed]
    [Google Scholar]
  8. Feng G., Yang S., Wang Y., Yao Q., Zhu H..( 2014a;). Acinetobacter refrigeratoris [corrected] sp. nov., isolated from a domestic refrigerator. . Curr Microbiol 69: 888–893. [CrossRef]
    [Google Scholar]
  9. Feng G. D., Yang S. Z., Wang Y. H., Deng M. R., Zhu H. H..( 2014b;). Acinetobacter guangdongensis sp. nov., isolated from abandoned lead-zinc ore. . Int J Syst Evol Microbiol 64: 3417–3421. [CrossRef]
    [Google Scholar]
  10. Gundi V. A., Dijkshoorn L., Burignat S., Raoult D., La Scola B..( 2009;). Validation of partial rpoB gene sequence analysis for the identification of clinically important and emerging Acinetobacter species. . Microbiology 155: 2333–2341. [CrossRef] [PubMed]
    [Google Scholar]
  11. Kim M., Oh H. S., Park S. C., Chun J..( 2014a;). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. . Int J Syst Evol Microbiol 64: 346–351. [CrossRef]
    [Google Scholar]
  12. Kim P. S., Shin N. R., Kim J. Y., Yun J. H., Hyun D. W., Bae J. W..( 2014b;). Acinetobacter apis sp. nov., isolated from the intestinal tract of a honey bee, Apis mellifera. . J Microbiol 52: 639–645. [CrossRef]
    [Google Scholar]
  13. Kimura M..( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16: 111–120. [CrossRef] [PubMed]
    [Google Scholar]
  14. Krizova L., Maixnerova M., Sedo O., Nemec A..( 2014;). Acinetobacter bohemicus sp. nov. widespread in natural soil and water ecosystems in the Czech Republic. . Syst Appl Microbiol 37: 467–473. [CrossRef] [PubMed]
    [Google Scholar]
  15. Krizova L., Maixnerova M., Sedo O., Nemec A..( 2015a;). Acinetobacter albensis sp. nov., isolated from natural soil and water ecosystems. . Int J Syst Evol Microbiol 65: 3905–3912. [CrossRef]
    [Google Scholar]
  16. Krizova L., McGinnis J., Maixnerova M., Nemec M., Poirel L., Mingle L., Sedo O., Wolfgang W., Nemec A..( 2015b;). Acinetobacter variabilis sp. nov. (formerly DNA group 15 sensu Tjernberg & Ursing), isolated from humans and animals. . Int J Syst Evol Microbiol 65: 1395.[CrossRef]
    [Google Scholar]
  17. La Scola B., Gundi V. A., Khamis A., Raoult D..( 2006;). Sequencing of the rpoB gene and flanking spacers for molecular identification of Acinetobacter species. . J Clin Microbiol 44: 827–832. [CrossRef] [PubMed]
    [Google Scholar]
  18. Li W., Zhang D., Huang X., Qin W..( 2014a;). Acinetobacter harbinensis sp. nov., isolated from river water. . Int J Syst Evol Microbiol 64: 1507–1513. [CrossRef]
    [Google Scholar]
  19. Li Y., He W., Wang T., Piao C. G., Guo L. M., Chang J. P., Guo M. W., Xie S. J..( 2014b;). Acinetobacter qingfengensis sp. nov., isolated from canker bark of Populus xeuramericana. . Int J Syst Evol Microbiol 64: 1043–1050.[CrossRef]
    [Google Scholar]
  20. Li Y., Chang J., Guo L. M., Wang H. M., Xie S. J., Piao C. G., He W..( 2015;). Description of Acinetobacter populi sp. nov. isolated from symptomatic bark of Populus x euramericana canker. . Int J Syst Evol Microbiol 65: 4461–4468. [CrossRef] [PubMed]
    [Google Scholar]
  21. Montealegre M. C., Maya J. J., Correa A., Espinal P., Mojica M. F., Ruiz S. J., Rosso F., Vila J., Quinn J. P. et al.( 2012;). First identification of OXA-72 carbapenemase from Acinetobacter pittii in Colombia. . Antimicrob Agents Chemother 56: 3996–3998. [CrossRef] [PubMed]
    [Google Scholar]
  22. Nemec A., Musílek M., Maixnerová M., De Baere T., van der Reijden T. J., Vaneechoutte M., Dijkshoorn L..( 2009;). Acinetobacter beijerinckii sp. nov. and Acinetobacter gyllenbergii sp. nov., haemolytic organisms isolated from humans. . Int J Syst Evol Microbiol 59: 118–124. [CrossRef] [PubMed]
    [Google Scholar]
  23. Nemec A., Musílek M., Sedo O., De Baere T., Maixnerová M., van der Reijden T. J., Zdráhal Z., Vaneechoutte M., Dijkshoorn L..( 2010;). Acinetobacter bereziniae sp. nov. and Acinetobacter guillouiae sp. nov., to accommodate Acinetobacter genomic species 10 and 11, respectively. . Int J Syst Evol Microbiol 60: 896–903. [CrossRef] [PubMed]
    [Google Scholar]
  24. Nemec A., Krizova L., Maixnerova M., van der Reijden T. J., Deschaght P., Passet V., Vaneechoutte M., Brisse S., Dijkshoorn L..( 2011;). Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp. nov. (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp. nov. (formerly Acinetobacter genomic species 13TU). . Res Microbiol 162: 393–404. [CrossRef] [PubMed]
    [Google Scholar]
  25. Nemec A., Krizova L., Maixnerova M., Sedo O., Brisse S., Higgins P. G..( 2015;). Acinetobacter seifertii sp. nov., a member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex isolated from human clinical specimens. . Int J Syst Evol Microbiol 65: 934–942. [CrossRef] [PubMed]
    [Google Scholar]
  26. Nemec A., Radolfova-Krizova L., Maixnerova M., Vrestiakova E., Jezek P., Sedo O..( 2016;). Taxonomy of haemolytic and/or proteolytic strains of the genus Acinetobacter with the proposal of Acinetobacter courvalinii sp. nov. (genomic species 14 sensu Bouvet & Jeanjean), Acinetobacter dispersus sp. nov. (genomic species 17), Acinetobacter modestus sp. nov., Acinetobacter proteolyticus sp. nov. and Acinetobacter vivianii sp. nov. . Int J Syst Evol Microbiol 66: 1673–1685. [CrossRef] [PubMed]
    [Google Scholar]
  27. Poppel M. T., Skiebe E., Laue M., Bergmann H., Ebersberger I., Garn T., Fruth A., Baumgardt S., Busse H. J. et al.( 2015;). Acinetobacter equi sp. nov. isolated from horse faeces. . Int J Syst Evol Microbiol. [CrossRef] [PubMed]
    [Google Scholar]
  28. Richter M., Rosselló-Móra R..( 2009;). Shifting the genomic gold standard for the prokaryotic species definition. . Proc Natl Acad Sci USA 106: 19126–19131. [CrossRef] [PubMed]
    [Google Scholar]
  29. Roca I., Marti S., Espinal P., Martínez P., Gibert I., Vila J..( 2009;). CraA, a major facilitator superfamily efflux pump associated with chloramphenicol resistance in Acinetobacter baumannii. . Antimicrob Agents Chemother 53: 4013–4014. [CrossRef] [PubMed]
    [Google Scholar]
  30. Roca I., Mosqueda N., Altun B., Espinal P., Akova M., Vila J..( 2014;). Molecular characterization of NDM-1-producing Acinetobacter pittii isolated from Turkey in 2006. . J Antimicrob Chemother 69: 3437–3438. [CrossRef] [PubMed]
    [Google Scholar]
  31. Seifert H., Dolzani L., Bressan R., van der Reijden T., van Strijen B., Stefanik D., Heersma H., Dijkshoorn L..( 2005;). Standardization and interlaboratory reproducibility assessment of pulsed-field gel electrophoresis-generated fingerprints of Acinetobacter baumannii. . J Clin Microbiol 43: 4328–4335. [CrossRef] [PubMed]
    [Google Scholar]
  32. Smet A., Cools P., Krizova L., Maixnerova M., Sedo O., Haesebrouck F., Kempf M., Nemec A., Vaneechoutte M..( 2014;). Acinetobacter gandensis sp. nov. isolated from horse and cattle. . Int J Syst Evol Microbiol 64: 4007–4015. [CrossRef] [PubMed]
    [Google Scholar]
  33. Sousa C., Botelho J., Silva L., Grosso F., Nemec A., Lopes J., Peixe L..( 2014;). MALDI-TOF MS and chemometric based identification of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex species. . Int J Med Microbiol 304: 669–677. [CrossRef] [PubMed]
    [Google Scholar]
  34. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S..( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28: 2731–2739. [CrossRef] [PubMed]
    [Google Scholar]
  35. Wisplinghoff H., Bischoff T., Tallent S. M., Seifert H., Wenzel R. P., Edmond M. B..( 2004;). Nosocomial bloodstream infections in US hospitals: analysis of 24,179 cases from a prospective nationwide surveillance study. . Clin Infect Dis 39: 309–317. [CrossRef] [PubMed]
    [Google Scholar]
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