1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 9

Taxonomic considerations on with proposal of subdivision into , sp. nov., sp. nov., and sp. nov No Access

Abstract

Average nucleotide identity analysis, based on whole genome sequences of 115 strains previously identified as , an emerging uropathogen, discriminates at least six unique genomic taxa. The whole genome analysis affords clearer species boundaries over 16S rRNA gene sequencing and traditional phenotypic approaches for the identification and phylogenetic organization of species. The newly described species can be differentiated by matrix-assisted laser desorption ionization time-of-flight analysis of protein signatures. We propose the emendation of the description of (type strain ATCC 51268 = CCUG 34223=NCFB 2893) and the names of sp. nov. (ATCC TSD-302 = DSM 115700 = CCUG 76531=NR-58630) sp. nov. (ATCC TSD-301 = DSM 115699 = CCUG 76532=NR-58629) and sp. nov. (ATCC TSD-300 = DSM 115698 = CCUG 76533=NR-58628) for three of the newly identified genomic taxa.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Aerococcus loyolae , Aerococcus mictus , Aerococcus tenax , Aerococcus urinae , MALDI-TOF MS and whole genome sequencing
Funding
This study was supported by the:
  • National Institute of Diabetes and Digestive and Kidney Diseases (Award R01 DK10718)
    • Principle Award Recipient: AlanJ. Wolfe
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006066
2023-09-27
2024-05-03
Loading full text...

Full text loading...

References

  1. Aguirre M, Collins MD. Phylogenetic analysis of some Aerococcus-like organisms from urinary tract infections: description of Aerococcus urinae sp. nov. J Gen Microbiol 1992; 138:401–405 [View Article] [PubMed]
     [Google Scholar]
  2. Rasmussen M. Aerococcus: an increasingly acknowledged human pathogen. Clin Microbiol Infect 2016; 22:22–27 [View Article] [PubMed]
     [Google Scholar]
  3. Rasmussen M. Aerococci and aerococcal infections. J Infect 2013; 66:467–474 [View Article] [PubMed]
     [Google Scholar]
  4. Christensen JJ, Korner B, Kjaergaard H. Aerococcus-like organism--an unnoticed urinary tract pathogen. APMIS 1989; 97:539–546 [View Article] [PubMed]
     [Google Scholar]
  5. Christensen JJ, Vibits H, Ursing J, Korner B. Aerococcus-like organism, a newly recognized potential urinary tract pathogen. J Clin Microbiol 1991; 29:1049–1053 [View Article] [PubMed]
     [Google Scholar]
  6. Christensen JJ, Whitney AM, Teixeira LM, Steigerwalt AG, Facklam RR et al. Aerococcus urinae: intraspecies genetic and phenotypic relatedness. Int J Syst Bacteriol 1997; 47:28–32 [View Article] [PubMed]
     [Google Scholar]
  7. Christensen JJ, Kilian M, Fussing V, Andresen K, Blom J et al. Aerococcus urinae: polyphasic characterization of the species. APMIS 2005; 113:517–525 [View Article] [PubMed]
     [Google Scholar]
  8. Felis GE, Torriani S, Dellaglio F. Reclassification of Pediococcus urinaeequi (ex Mees 1934) Garvie 1988 as Aerococcus urinaeequi comb. nov. Int J Syst Evol Microbiol 2005; 55:1325–1327 [View Article] [PubMed]
     [Google Scholar]
  9. Carkaci D, Dargis R, Nielsen XC, Skovgaard O, Fuursted K et al. Complete genome sequences of Aerococcus christensenii CCUG 28831T, Aerococcus sanguinicola CCUG 43001T, Aerococcus urinae CCUG 36881T, Aerococcus urinaeequi CCUG 28094T, Aerococcus urinaehominis CCUG 42038 BT, and Aerococcus viridans CCUG 4311T. Genome Announc 2016; 4:e00302-16 [View Article]
     [Google Scholar]
  10. Zhou W, Gao S, Zheng J, Zhang Y, Zhou H et al. Identification of an Aerococcus urinaeequi isolate by whole genome sequencing and average nucleotide identity analysis. J Glob Antimicrob Resist 2022; 29:353–359 [View Article] [PubMed]
     [Google Scholar]
  11. Carkaci D, Højholt K, Nielsen XC, Dargis R, Rasmussen S et al. Genomic characterization, phylogenetic analysis, and identification of virulence factors in Aerococcus sanguinicola and Aerococcus urinae strains isolated from infection episodes. Microb Pathog 2017; 112:327–340 [View Article] [PubMed]
     [Google Scholar]
  12. Facklam R, Lovgren M, Shewmaker PL, Tyrrell G. Phenotypic description and antimicrobial susceptibilities of Aerococcus sanguinicola isolates from human clinical samples. J Clin Microbiol 2003; 41:2587–2592 [View Article] [PubMed]
     [Google Scholar]
  13. Senneby E, Nilson B, Petersson A-C, Rasmussen M. Matrix-assisted laser desorption ionization-time of flight mass spectrometry is a sensitive and specific method for identification of aerococci. J Clin Microbiol 2013; 51:1303–1304 [View Article] [PubMed]
     [Google Scholar]
  14. Christensen JJ, Dargis R, Hammer M, Justesen US, Nielsen XC et al. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis of Gram-positive, catalase-negative cocci not belonging to the Streptococcus or Enterococcus genus and benefits of database extension. J Clin Microbiol 2012; 50:1787–1791 [View Article] [PubMed]
     [Google Scholar]
  15. Price TK, Dune T, Hilt EE, Thomas-White KJ, Kliethermes S et al. The clinical urine culture: enhanced techniques improve detection of clinically relevant microorganisms. J Clin Microbiol 2016; 54:1216–1222 [View Article] [PubMed]
     [Google Scholar]
  16. Hilt EE, Putonti C, Thomas-White K, Lewis AL, Visick KL et al. Aerococcus urinae Isolated from women with lower urinary tract symptoms: In Vitro aggregation and genome analysis. J Bacteriol 2020; 202:e00170-20 [View Article] [PubMed]
     [Google Scholar]
  17. Gilbert NM, Choi B, Du J, Collins C, Lewis AL et al. A mouse model displays host and bacterial strain differences in Aerococcus urinae urinary tract infection. Biol Open 2021; 10:bio058931 [View Article] [PubMed]
     [Google Scholar]
  18. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  19. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article] [PubMed]
     [Google Scholar]
  20. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
     [Google Scholar]
  21. Hoang DT, Vinh LS, Flouri T, Stamatakis A, von Haeseler A et al. MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol Biol 2018; 18:11 [View Article] [PubMed]
     [Google Scholar]
  22. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
     [Google Scholar]
  23. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  24. Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG et al. Anvi’o: an advanced analysis and visualization platform for omics data. PeerJ 2015; 3:e1319 [View Article] [PubMed]
     [Google Scholar]
  25. Galperin MY, Wolf YI, Makarova KS, Vera Alvarez R, Landsman D et al. COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res 2021; 49:D274–D281 [View Article] [PubMed]
     [Google Scholar]
  26. Treangen TJ, Ondov BD, Koren S, Phillippy AM. The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 2014; 15:524 [View Article] [PubMed]
     [Google Scholar]
  27. Estaki M, Jiang L, Bokulich NA, McDonald D, González A et al. QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data. Curr Protoc Bioinformatics 2020; 70:e100 [View Article] [PubMed]
     [Google Scholar]
  28. Tai DBG, Go JR, Fida M, Saleh OA. Management and treatment of Aerococcus bacteremia and endocarditis. Int J Infect Dis 2021; 102:584–589 [View Article] [PubMed]
     [Google Scholar]
  29. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  30. Tohno M, Kitahara M, Matsuyama S, Kimura K, Ohkuma M et al. Aerococcus vaginalis sp. nov., isolated from the vaginal mucosa of a beef cow, and emended descriptions of Aerococcus suis, Aerococcus viridans, Aerococcus urinaeequi, Aerococcus urinaehominis, Aerococcus urinae, Aerococcus christensenii and Aerococcus sanguinicola. Int J Syst Evol Microbiol 2014; 64:1229–1236 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006066
Loading
Taxonomic considerations on Aerococcus urinae with proposal of subdivision into Aerococcus urinae, Aerococcus tenax sp. nov., Aerococcus mictus sp. nov., and Aerococcus loyolae sp. nov
Int J Syst Evol Microbiol 73, 006066 (2023); https://doi.org/10.1099/ijsem.0.006066
/content/journal/ijsem/10.1099/ijsem.0.006066
/content/journal/ijsem/10.1099/ijsem.0.006066
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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