1887

Abstract

Two isolates of a non-fermenting, Gram-negative bacterial strain were cultured from two throat swabs that were taken from a pair of twins during routine microbiological surveillance screening. As these isolates could not be unambiguously identified using routine diagnostic methods, whole genome sequencing was performed followed by phylogenetic analysis based on the gene sequence and by whole genome datasets. The two strains compose a separate branch within the clade formed by the (ACB) complex with CIP 70.29 as the most closely related species. The average nucleotide identity compared to all other species of the ACB complex was below 94.2% and digital DNA–DNA hybridization values were less than 60%. Biochemical characteristics confirm affiliation to the ACB complex with some specific phenotypic differences. As a result of the described data, a new species is introduced, for which the name sp. nov. is proposed. The type strain is J00019 with a G+C DNA content of 38.8 mol% and it is deposited in the DSMZ Germany (DSM 111094) and CCUG Sweden (CCUG 74625).

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2021-10-11
2021-10-25
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References

  1. Al Atrouni A, Joly-Guillou ML, Hamze M, Kempf M. baumannii Front Microbiol 2016; 7:49 [View Article] [PubMed]
    [Google Scholar]
  2. Seifert H, Dijkshoorn L, Gerner-Smidt P, Pelzer N, Tjernberg I et al. Distribution of Acinetobacter species on human skin: comparison of phenotypic and genotypic identification methods. J Clin Microbiol 1997; 35:2819–2825 [View Article] [PubMed]
    [Google Scholar]
  3. Berlau J, Aucken H, Malnick H, Pitt T. Distribution of Acinetobacter species on skin of healthy humans. Eur J Clin Microbiol Infect Dis 1999; 18:179–183
    [Google Scholar]
  4. McConnell MJ, Actis L, Pachon J. Acinetobacter baumannii: human infections, factors contributing to pathogenesis and animal models. FEMS Microbiol Rev 2013; 37:130–155 [View Article] [PubMed]
    [Google Scholar]
  5. Jimenez-Guerra G, Heras-Canas V, Gutierrez-Soto M, Del Pilar Aznarte-Padial M, Exposito-Ruiz M et al. Urinary tract infection by Acinetobacter baumannii and Pseudomonas aeruginosa: evolution of antimicrobial resistance and therapeutic alternatives. J Med Microbiol 2018; 67:790–797 [View Article] [PubMed]
    [Google Scholar]
  6. Guerrero DM, Perez F, Conger NG, Solomkin JS, Adams MD et al. Acinetobacter baumannii-associated skin and soft tissue infections: recognizing a broadening spectrum of disease. Surg Infect (Larchmt 2010; 11:49–57 [View Article] [PubMed]
    [Google Scholar]
  7. Garnacho J, Sole-Violan J, Sa-Borges M, Diaz E, Rello J. Clinical impact of pneumonia caused by Acinetobacter baumannii in intubated patients: a matched cohort study. Crit Care Med 2003; 31:2478–2482 [View Article] [PubMed]
    [Google Scholar]
  8. Sturiale M, Corpina C, Sturiale L. Endocarditis due to Acinetobacter baumannii. Int J Cardiol 2016; 209:161–163S0167-5273(14)02035-X [View Article] [PubMed]
    [Google Scholar]
  9. Wisplinghoff H, Bischoff T, Tallent SM, Seifert H, Wenzel RP et al. Nosocomial bloodstream infections in US hospitals: analysis of 24,179 cases from a prospective nationwide surveillance study. Clin Infect Dis 2004; 39:309–317 [View Article] [PubMed]
    [Google Scholar]
  10. Spellberg B, Rex JH. The value of single-pathogen antibacterial agents. Nat Rev Drug Discov 2013; 12:963 [View Article] [PubMed]
    [Google Scholar]
  11. Wong D, Nielsen TB, Bonomo RA, Pantapalangkoor P, Luna B et al. Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges. Clin Microbiol Rev 2017; 30:409–447 [View Article] [PubMed]
    [Google Scholar]
  12. Gales AC, Seifert H, Gur D, Castanheira M, Jones RN et al. Antimicrobial susceptibility of Acinetobacter calcoaceticus-Acinetobacter baumannii complex and Stenotrophomonas maltophilia clinical isolates: results from the SENTRY Antimicrobial Surveillance Program (1997-2016). Open Forum Infect Dis 2019; 6:S46–S34
    [Google Scholar]
  13. Bouvet PJM, Grimont PAD. Taxonomy of the genus Acinetobacter with the recognition of Acinetobacter baumannii sp. nov, Acinetobacter haemolyticus sp nov, Acinetobacter johnsonii sp nov, and Acinetobacter junii sp nov and emended descriptions of Acinetobacter calcoaceticus and Acinetobacter lwoffii. Int J Syst Evol Microbiol 1986; 36:228–240
    [Google Scholar]
  14. Tjernberg I, Ursing J. Clinical strains of Acinetobacter classified by DNA-DNA hybridization. APMIS 1989; 97:595–605 [View Article] [PubMed]
    [Google Scholar]
  15. Touchon M, Cury J, Yoon EJ, Krizova L, Cerqueira GC et al. The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Genome Biol Evol 2014; 6:2866–2882 [View Article] [PubMed]
    [Google Scholar]
  16. Nemec A, Krizova L, Maixnerova M, Sedo O, Brisse S et al. Acinetobacter seifertii sp. nov., a member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex isolated from human clinical specimens. Int J Syst Evol Microbiol 2015; 65:934–942 [View Article] [PubMed]
    [Google Scholar]
  17. Dijkshoorn L, van der Toorn J. Acinetobacter species: which do we mean. Clin Infect Dis 1992; 15:748–749 [View Article] [PubMed]
    [Google Scholar]
  18. Chusri S, Chongsuvivatwong V, Rivera JI, Silpapojakul K, Singkhamanan K et al. Clinical outcomes of hospital-acquired infection with Acinetobacter nosocomialis and Acinetobacter pittii. Antimicrob Agents Chemother 2014; 58:4172–4179 [View Article]
    [Google Scholar]
  19. Peleg AY, Seifert H, Paterson DL. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev 2008; 21:538–582 [View Article] [PubMed]
    [Google Scholar]
  20. Gerner-Smidt P, Tjernberg I, Ursing J. Reliability of phenotypic tests for identification of Acinetobacter species. J Clin Microbiol 1991; 29:277–282 [View Article] [PubMed]
    [Google Scholar]
  21. Nemec A, Krizova L, Maixnerova M, van der Reijden TJ, Deschaght P et al. 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 2011; 162:393–404 [View Article] [PubMed]
    [Google Scholar]
  22. Howard A, O’Donoghue M, Feeney A, Sleator RD. Acinetobacter baumannii: an emerging opportunistic pathogen. Virulence 2012; 3:243–250 [View Article] [PubMed]
    [Google Scholar]
  23. Brisou J, Prevot AR. Studies on bacterial taxonomy. X. The revision of species under Acromobacter group. Ann Inst Pasteur 1954; 86:722–728 [PubMed]
    [Google Scholar]
  24. Baumann P, Doudoroff M, Stanier RY. A study of the Moraxella group. II. Oxidative-negative species (genus Acinetobacter). J Bacteriol 1968; 95:1520–1541 [View Article] [PubMed]
    [Google Scholar]
  25. Kang YS, Jung J, Jeon CO, Park W. Acinetobacter oleivorans sp. nov. is capable of adhering to and growing on diesel-oil. J Microbiol 2011; 49:29–34 [View Article] [PubMed]
    [Google Scholar]
  26. Rooney AP, Dunlap CA, Flor-Weiler LB. Acinetobacter lactucae sp. nov., isolated from iceberg lettuce (Asteraceae: Lactuca sativa). Int J Syst Evol Microbiol 2016; 66:3566–3572 [View Article] [PubMed]
    [Google Scholar]
  27. Committee of Hospital Hygiene and Infection Prevention of the Robert Koch Institute Recommendation for the prevention of nosocomial infections in neonatal intensive care patients with a birth weight less than 1,500 g. Report by the committee of hospital hygiene and infection prevention of the Robert Koch Institute. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2007; 50:1265–1303 [PubMed]
    [Google Scholar]
  28. Ruiz de Alegria-Puig C, De-Malet-Pintos-Fonseca A, Angulo-Lopez I, Aguero-Balbin J, Marco F et al. Evaluation of Vitek-MS and Microflex LT commercial systems for identification of Acinetobacter calcoaceticus-baumannii complex. Enferm Infecc Microbiol Clin 2020
    [Google Scholar]
  29. Peter S, Bezdan D, Oberhettinger P, Vogel W, Dörfel D et al. Whole-genome sequencing enabling the detection of a colistin-resistant hypermutating Citrobacter werkmanii strain harbouring a novel metallo-β-lactamase VIM-48. Int J Antimicrob Agents 2018; 51:867–874S0924-8579(18)30018-9 [View Article] [PubMed]
    [Google Scholar]
  30. Liese J, Schule L, Oberhettinger P, Tschorner L, Nguyen T et al. Expansion of vancomycin-resistant Enterococcus faecium in an academic tertiary hospital in southwest Germany: a large-scale whole-genome-based outbreak investigation. Antimicrob Agents Chemother (Bethesda) 2019; 63:
    [Google Scholar]
  31. Oberhettinger P, Schule L, Marschal M, Bezdan D, Ossowski S et al. Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples. Int J Syst Evol Microbiol 2020; 70:2998–3003 [View Article] [PubMed]
    [Google Scholar]
  32. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 2013; 20:714–737 [View Article] [PubMed]
    [Google Scholar]
  33. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PloS one 2010; 5:e11147 [View Article] [PubMed]
    [Google Scholar]
  34. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article]
    [Google Scholar]
  35. Clermont D, Motreff L, Passet V, Fernandez JC, Bizet C et al. Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov. Int J Syst Evol Microbiol 2015; 65:1486–1490 [View Article] [PubMed]
    [Google Scholar]
  36. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
    [Google Scholar]
  37. Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  38. Richter M, Rossello-Mora R, Oliver Glockner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  39. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  40. Nemec A, Musilek M, Maixnerova M, De Baere T, van der Reijden TJ et al. Acinetobacter beijerinckii sp. nov. and Acinetobacter gyllenbergii sp. nov., haemolytic organisms isolated from humans. Int J Syst Evol Microbiol 2009; 59:118–124 [View Article] [PubMed]
    [Google Scholar]
  41. Krizova L, Maixnerova M, Sedo O, Nemec A. Acinetobacter albensis sp. nov., isolated from natural soil and water ecosystems. Int J Syst Evol Microbiol 2015; 65:3905–3912 [View Article] [PubMed]
    [Google Scholar]
  42. Qin J, Hu Y, Feng Y, Lv X, Zong Z. Acinetobacter sichuanensis sp. nov., recovered from hospital sewage in China. Int J Syst Evol Microbiol 2018; 68:3897–3901 [View Article] [PubMed]
    [Google Scholar]
  43. Clemmer KM, Bonomo RA, Rather PN. Genetic analysis of surface motility in Acinetobacter baumannii. Microbiology (Reading) 2011; 157:2534–2544 [View Article] [PubMed]
    [Google Scholar]
  44. Kilic A, Li H, Mellmann A, Basustaoglu AC, Kul M et al. Acinetobacter septicus sp. nov. association with a nosocomial outbreak of bacteremia in a neonatal intensive care unit. J Clin Microbiol 2008; 46:902–908 [View Article] [PubMed]
    [Google Scholar]
  45. Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 2007; 45:2761–2764 [View Article] [PubMed]
    [Google Scholar]
  46. Nemec A, Radolfova-Krizova L, Maixnerova M, Vrestiakova E, Jezek P et al. 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 2016; 66:1673
    [Google Scholar]
  47. Gundi V, Dijkshoorn L, Burignat S, Raoult D, La Scola B. Validation of partial rpoB gene sequence analysis for the identification of clinically important and emerging Acinetobacter species. Microbiology (Reading) 2009; 155:2333–2341 [View Article] [PubMed]
    [Google Scholar]
  48. Chen L, Yuan J, Xu Y, Zhang F, Chen Z. Comparison of clinical manifestations and antibiotic resistances among three genospecies of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex. PloS one 2018; 13:e0191748
    [Google Scholar]
  49. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  50. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
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