1887

Abstract

We herein report the isolation and characterization of 21 Gram-stain-negative strains cultivated from the oropharynx of healthy children in Israel and Switzerland. Initially described as small colony variants of , phenotypic analysis, biochemical analysis, phylogenetic analysis based on sequencing of the partial 16S rRNA gene and five housekeeping genes (, , , and ), and whole genome sequencing and comparison between members of the genera and provided evidence for assigning them to the genus . Cellular fatty acids included important amounts of C, C, C and C. Digital DNA–DNA hybridization between the isolates Sch538 and ATCC 23330 revealed relatedness of 19.9 %. Comparative analysis of 16S rRNA gene sequences available in GenBank allowed matches to strains isolated in the USA, suggesting a wider geographical distribution. A novel species named sp. nov. is proposed, as most strains have been isolated in the Negev, a desert region of southern Israel. The type strain is Sch538 (=CCUG 69806=CSUR P957).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001957
2017-07-01
2019-12-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/7/2370.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001957&mimeType=html&fmt=ahah

References

  1. Henriksen SD, Bovre K. Moraxella kingii sp.nov., a haemolytic, saccharolytic species of the genus Moraxella. J Gen Microbiol 1968;51:377–385 [CrossRef][PubMed]
    [Google Scholar]
  2. Henriksen SD, Bøvre K. Transfer of Moraxella kingae Henriksen and Bøvre to the genus Kingella gen. nov. in the family Neisseriaceae. Int J Syst Evol Microbiol 1976;26:447–450
    [Google Scholar]
  3. Snell JJS, Lapage SP. Transfer of some saccharolytic Moraxella species to Kingella Henriksen and Bøvre 1976, with descriptions of Kingella indologenes sp. nov. and Kingella denitrificans sp. nov. Int J Syst Evol Microbiol 1976;26:451–458
    [Google Scholar]
  4. Hollis DG, Weaver RE, Riley PS. Emended description of Kingella denitrificans (Snell and Lapage 1976): correction of the maltose reaction. J Clin Microbiol 1983;18:1174–1176[PubMed]
    [Google Scholar]
  5. Dewhirst FE, Chen CK, Paster BJ, Zambon JJ. Phylogeny of species in the family Neisseriaceae isolated from human dental plaque and description of Kingella oralis sp. nov [corrected]. Int J Syst Bacteriol 1993;43:490–499 [CrossRef][PubMed]
    [Google Scholar]
  6. Lawson PA, Malnick H, Collins MD, Shah JJ, Chattaway MA et al. Description of Kingella potus sp. nov., an organism isolated from a wound caused by an animal bite. J Clin Microbiol 2005;43:3526–3529 [CrossRef][PubMed]
    [Google Scholar]
  7. Chambers ST, Murdoch D, Morris A, Holland D, Pappas P et al. HACEK infective endocarditis: characteristics and outcomes from a large, multi-national cohort. PLoS One 2013;8:e63181 [CrossRef][PubMed]
    [Google Scholar]
  8. Yagupsky P. Kingella kingae: from medical rarity to an emerging paediatric pathogen. Lancet Infect Dis 2004;4:358–367 [CrossRef][PubMed]
    [Google Scholar]
  9. El Houmami N, Minodier P, Dubourg G, Mirand A, Jouve JL et al. Patterns of Kingella kingae disease outbreaks. Pediatr Infect Dis J 2016;35:340–346 [CrossRef][PubMed]
    [Google Scholar]
  10. Yagupsky P, Weiss-Salz I, Fluss R, Freedman L, Peled N et al. Dissemination of Kingella kingae in the community and long-term persistence of invasive clones. Pediatr Infect Dis J 2009;28:707–710 [CrossRef][PubMed]
    [Google Scholar]
  11. Ceroni D, Dubois-Ferrière V, Anderson R, Combescure C, Lamah L et al. Small risk of osteoarticular infections in children with asymptomatic oropharyngeal carriage of Kingella kingae. Pediatr Infect Dis J 2012;31:983–985 [CrossRef][PubMed]
    [Google Scholar]
  12. Yagupsky P, Merires M, Bahar J, Dagan R. Evaluation of novel vancomycin-containing medium for primary isolation of Kingella kingae from upper respiratory tract specimens. J Clin Microbiol 1995;33:1426–1427[PubMed]
    [Google Scholar]
  13. Basmaci R, Bonacorsi S, Bidet P, Balashova NV, Lau J et al. Genotyping, local prevalence and international dissemination of β-lactamase-producing Kingella kingae strains. Clin Microbiol Infect 2014;20:O811–O817 [CrossRef][PubMed]
    [Google Scholar]
  14. Yagupsky P. Kingella kingae: carriage, transmission, and disease. Clin Microbiol Rev 2015;28:54–79 [CrossRef][PubMed]
    [Google Scholar]
  15. Maslow JN, Slutsky AM, Arbeit RD. Application of pulsed-field gel electrophoresis to molecular epidemiology. In Persing DH, Smith TF, White TJ. (editors) Diagnostic Molecular Microbiology: Principles and Applications Washington, DC: American Society for Microbiology Press; 1993; pp.563–572
    [Google Scholar]
  16. Amit U, Porat N, Basmaci R, Bidet P, Bonacorsi S et al. Genotyping of invasive Kingella kingae isolates reveals predominant clones and association with specific clinical syndromes. Clin Infect Dis 2012;55:1074–1079 [CrossRef][PubMed]
    [Google Scholar]
  17. Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE et al. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 1995;33:2233–2239[PubMed]
    [Google Scholar]
  18. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009;49:543–551 [CrossRef][PubMed]
    [Google Scholar]
  19. Seng P, Abat C, Rolain JM, Colson P, Lagier JC et al. Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2013;51:2182–2194 [CrossRef][PubMed]
    [Google Scholar]
  20. Sasser M, Kunitsky C, Jackoway G, Ezzell JW, Teska JD et al. Identification of Bacillus anthracis from culture using gas chromatographic analysis of fatty acid methyl esters. J AOAC Int 2005;88:178–181[PubMed]
    [Google Scholar]
  21. Dione N, Sankar SA, Lagier JC, Khelaifia S, Michele C et al. Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 2016;10:66–76 [CrossRef][PubMed]
    [Google Scholar]
  22. Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP et al. 16s ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 2000;38:3623–3630[PubMed]
    [Google Scholar]
  23. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002;30:3059–3066 [CrossRef][PubMed]
    [Google Scholar]
  24. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  25. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346–351 [CrossRef][PubMed]
    [Google Scholar]
  26. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014;12:635–645 [CrossRef][PubMed]
    [Google Scholar]
  27. Bennett JS, Jolley KA, Maiden MC. Genome sequence analyses show that Neisseria oralis is the same species as 'Neisseria mucosa var. heidelbergensis'. Int J Syst Evol Microbiol 2013;63:3920–3926 [CrossRef][PubMed]
    [Google Scholar]
  28. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010;11:119 [CrossRef][PubMed]
    [Google Scholar]
  29. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007;35:3100–3108 [CrossRef][PubMed]
    [Google Scholar]
  30. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997;25:955–964 [CrossRef][PubMed]
    [Google Scholar]
  31. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004;340:783–795 [CrossRef][PubMed]
    [Google Scholar]
  32. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001;305:567–580 [CrossRef][PubMed]
    [Google Scholar]
  33. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75 [CrossRef][PubMed]
    [Google Scholar]
  34. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011;39:W347–W352 [CrossRef][PubMed]
    [Google Scholar]
  35. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009;25:119–120 [CrossRef][PubMed]
    [Google Scholar]
  36. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P et al. Artemis: sequence visualization and annotation. Bioinformatics 2000;16:944–945 [CrossRef][PubMed]
    [Google Scholar]
  37. Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004;14:1394–1403 [CrossRef][PubMed]
    [Google Scholar]
  38. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M et al. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 2014;64:384–391 [CrossRef][PubMed]
    [Google Scholar]
  39. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome- to-genome sequence comparison. Stand Genomic Sci 2010;2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  40. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef][PubMed]
    [Google Scholar]
  41. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [Google Scholar]
  42. Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. New York, NY: Springer-Verlag; 2005
    [Google Scholar]
  43. Grant PE, Brenner DJ, Steigerwalt AG, Hollis DG, Weaver RE, Subsp N. Neisseria elongata subsp. nitroreducens subsp. nov., formerly CDC group M-6, a gram-negative bacterium associated with endocarditis. J Clin Microbiol 1990;28:2591–2596[PubMed]
    [Google Scholar]
  44. Andersen BM, Steigerwalt AG, O'Connor SP, Hollis DG, Weyant RS et al. Neisseria weaveri sp. nov., formerly CDC group M-5, a gram-negative bacterium associated with dog bite wounds. J Clin Microbiol 1993;31:2456–2466[PubMed]
    [Google Scholar]
  45. Holmes B, Costas M, On SL, Vandamme P, Falsen E et al. Neisseria weaveri sp. nov. (formerly CDC group M-5), from dog bite wounds of humans. Int J Syst Bacteriol 1993;43:687–693 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001957
Loading
/content/journal/ijsem/10.1099/ijsem.0.001957
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error