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Volume 7, Issue 8

Genomics of (newly named ) reveals a new subgroup Open Access

Abstract

(newly named ) is an emerging pathogen in immunodeficient and immunocompetent patients. Most documented cases associated with are frequently catheter-related and exhibit wide-spectrum β-lactam resistance. Misidentification of this pathogen using commercial bacterial identification kits is common. We identified a case of infection associated with cholelithiasis. The genome was sequenced and reconstructed using a Nanopore and Illumina hybrid strategy. A novel divergent from existing OXA members was identified and subsequent analysis revealed its existence in all available genomes, which forms a new phylogenetic subgroup distinct from other OXA clusters. Further analysis demonstrated the presence of the novel in the chromosome of several other species. Our study indicated that chromosomes may be a reservoir of β-lactamases.

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  • Accepted:
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Keyword(s): Brucella pseudogrignonensis , Ochrobactrum pseudogrignonense , OXA and β-lactamases
Funding
This study was supported by the:
  • Taichung Veteran General Hospital (Award TCVGH-NK1109004)
    • Principal Award Recipient: LiuPo-Yu
  • Taichung Veterans General Hospital (Award TCVGH-1103901C)
    • Principal Award Recipient: Po-YuLiu
  • Taichung Veterans General Hospital (Award TCVGH-1103901D)
    • Principal Award Recipient: Po-YuLiu
  • Ministry of Science and Technology, Taiwan (Award 109-2314-B-075A-009)
    • Principal Award Recipient: Po-YuLiu
  • Ministry of Science and Technology, Taiwan (Award 109-2221-E-194 -038 -MY3)
    • Principal Award Recipient: Yao-TingHuang
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2021-08-27
2026-03-05

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References

  1. Ryan MP, Pembroke JT. The genus ochrobactrum as major opportunistic pathogens. In Microorganisms Vol 8 2020 2020 p 1797 [View Article]
     [Google Scholar]
  2. Higgins CS, Avison MB, Jamieson L, Simm AM, Bennett PM et al. Characterization, cloning and sequence analysis of the inducible Ochrobactrum anthropi AmpC beta-lactamase. J Antimicrob Chemother 2001; 47:745–754 [View Article] [PubMed]
     [Google Scholar]
  3. Kampfer P, Scholz HC, Huber B, Falsen E, Busse HJ. Ochrobactrum haematophilum sp. nov. and Ochrobactrum pseudogrignonense sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol 2007; 57:2513–2518 [View Article] [PubMed]
     [Google Scholar]
  4. Kettaneh A, Weill FX, Poilane I, Fain O, Thomas M et al. Septic shock caused by Ochrobactrum anthropi in an otherwise healthy host. J Clin Microbiol 2003; 41:1339–1341 [View Article] [PubMed]
     [Google Scholar]
  5. Wu Z, Peng W, He X, Wang B, Gan B et al. Mushroom tumor: a new disease on Flammulina velutipes caused by Ochrobactrum pseudogrignonense. FEMS Microbiol Lett 2016; 363:fnv226 [View Article] [PubMed]
     [Google Scholar]
  6. Cho HW, Byun JH, Kim D, Lee H, Yong D et al. The first case of Ochrobactrum pseudogrignonense bacteremia in Korea. Ann Lab Med 2020; 40:331–333 [View Article] [PubMed]
     [Google Scholar]
  7. Teyssier C, Marchandin H, Jean-Pierre H, Diego I, Darbas H et al. Molecular and phenotypic features for identification of the opportunistic pathogens Ochrobactrum spp. J Med Microbiol 2005; 54:945–953 [View Article] [PubMed]
     [Google Scholar]
  8. Mrozek S, Dupuy M, Hoarau L, Lourtet J, Martin-Blondel G et al. Brain empyema due to Ochrobactrum anthropi. Med Mal Infect 2014; 44:128–129 [View Article] [PubMed]
     [Google Scholar]
  9. Chiu LQ, Wang W. A case of unusual Gram-negative bacilli septic arthritis in an immunocompetent patient. Singapore Med J 2013; 54:e164–8 [View Article] [PubMed]
     [Google Scholar]
  10. Gigi R, Flusser G, Kadar A, Salai M, Elias S. Ochrobactrum anthropi-caused Osteomyelitis in the foot mimicking a bone tumor. J Foot Ankle Surg 2017; 56:851–853 [View Article] [PubMed]
     [Google Scholar]
  11. Christenson JC, Pavia AT, Seskin K, Brockmeyer D, Korgenski EK et al. Meningitis due to Ochrobactrum anthropi: an emerging nosocomial pathogen. A report of 3 cases. Pediatr Neurosurg 1997; 27:218–221 [View Article] [PubMed]
     [Google Scholar]
  12. Mattos FB, Saraiva FP, Angotti-Neto H, Passos AF. Outbreak of Ochrobactrum anthropi endophthalmitis following cataract surgery. J Hosp Infect 2013; 83:337–340 [View Article] [PubMed]
     [Google Scholar]
  13. Haviari S, Cassier P, Dananche C, Hulin M, Dauwalder O et al. Outbreak of Achromobacter xylosoxidans and Ochrobactrum anthropi Infections after Prostate Biopsies, France, 2014. Emerg Infect Dis 2016; 22:1412–1419 [View Article] [PubMed]
     [Google Scholar]
  14. Romero Gomez MP, Peinado Esteban AM, Sobrino Daza JA, Saez Nieto JA, Alvarez D et al. Prosthetic mitral valve endocarditis due to Ochrobactrum anthropi: case report. J Clin Microbiol 2004; 42:3371–3373 [View Article] [PubMed]
     [Google Scholar]
  15. Ozdemir D, Soypacaci Z, Sahin I, Bicik Z, Sencan I. Ochrobactrum anthropi endocarditis and septic shock in a patient with no prosthetic valve or rheumatic heart disease: case report and review of the literature. Jpn J Infect Dis 2006; 59:264–265 [PubMed]
     [Google Scholar]
  16. Ashraf F. 2016. A case of Ochrobactrum anthropi-induced septic shock and infective endocarditis. R I Med J 2013; 99:27–28
     [Google Scholar]
  17. Sepe V, Esposito P, Sacco L, Ceci A, Magrassi A et al. Peritonitis in type 2 diabetes mellitus due to Ochrobactrum anthropi complicating automated peritoneal dialysis. Acta Diabetol 2010; 47:341–344 [View Article] [PubMed]
     [Google Scholar]
  18. YM W, Peck KR. Biliary sepsis caused by Ochrobactrum anthropi. Jpn J Infect Dis 2010; 63:444–446
     [Google Scholar]
  19. Song S, Ahn JK, Lee GH, Park YG. An epidemic of chronic pseudophakic endophthalmitis due to Ochrobactrum anthropi: clinical findings and managements of nine consecutive cases. Ocul Immunol Inflamm 2007; 15:429–434 [View Article] [PubMed]
     [Google Scholar]
  20. Qasimyar H, Hoffman MA, Simonsen KA. Late-onset Ochrobactrum anthropi sepsis in a preterm neonate with congenital urinary tract abnormalities. J Perinatol 2014; 34:489–491 [View Article] [PubMed]
     [Google Scholar]
  21. Cieslak TJ, Drabick CJ, Robb ML. Pyogenic infections due to Ochrobactrum anthropi. Clin Infect Dis 1996; 22:845–847 [View Article] [PubMed]
     [Google Scholar]
  22. Appelbaum PC, Campbell DB. Pancreatic abscess associated with Achromobacter group Vd biovar 1. J Clin Microbiol 1980; 12:282–283 [View Article] [PubMed]
     [Google Scholar]
  23. Naik C, Kulkarni H, Darabi A, Bhanot N. Ochrobactrum anthropi: a rare cause of pneumonia. J Infect Chemother 2013; 19:162–165 [View Article] [PubMed]
     [Google Scholar]
  24. Moller LV, Arends JP, Harmsen HJ, Talens A, Terpstra P et al. Ochrobactrum intermedium infection after liver transplantation. J Clin Microbiol 1999; 37:241–244 [View Article] [PubMed]
     [Google Scholar]
  25. Dharne MS, Misra SP, Misra V, Dwivedi M, Patole MS et al. Isolation of urease-positive Ochrobactrum intermedium in the stomach of a non-ulcer dyspeptic patient from north India. J Microbiol Immunol Infect 2008; 41:183–186 [PubMed]
     [Google Scholar]
  26. Vaidya SA, Citron DM, Fine MB, Murakami G, Goldstein EJ. Pelvic abscess due to Ochrobactrum intermedium [corrected] in an immunocompetent host: case report and review of the literature. J Clin Microbiol 2006; 44:1184–1186 [View Article] [PubMed]
     [Google Scholar]
  27. Vila A, Pagella H, Vera Bello G, Vicente A. Brucella suis bacteremia misidentified as Ochrobactrum anthropi by the VITEK 2 system. J Infect Dev Ctries 2016; 10:432–436 [View Article] [PubMed]
     [Google Scholar]
  28. Poonawala H, Marrs Conner T, Peaper DR. Closing the brief case: Misidentification of Brucella melitensis as Ochrobactrum anthropi by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF ms. J Clin Microbiol 2018; 56: [View Article] [PubMed]
     [Google Scholar]
  29. Scholz HC, Tomaso H, Al Dahouk S, Witte A, Schloter M et al. Genotyping of Ochrobactrum anthropi by recA-based comparative sequence, PCR-RFLP, and 16S rRNA gene analysis. FEMS Microbiol Lett 2006; 257:7–16 [View Article] [PubMed]
     [Google Scholar]
  30. Thoma B, Straube E, Scholz HC, Al Dahouk S, Zoller L et al. Identification and antimicrobial susceptibilities of Ochrobactrum spp. Int J Med Microbiol 2009; 299:209–220 [View Article] [PubMed]
     [Google Scholar]
  31. Nadjar D, Labia R, Cerceau C, Bizet C, Philippon A et al. Molecular characterization of chromosomal class C beta-lactamase and its regulatory gene in Ochrobactrum anthropi. Antimicrob Agents Chemother 2001; 45:2324–2330 [View Article] [PubMed]
     [Google Scholar]
  32. Alonso CA, Kwabugge YA, Anyanwu MU, Torres C, Chah KF. Diversity of Ochrobactrum species in food animals, antibiotic resistance phenotypes and polymorphisms in the blaOCH gene. FEMS Microbiol Lett 2017; 364: [View Article]
     [Google Scholar]
  33. Brown S, Amyes S. OXA (beta)-lactamases in Acinetobacter: the story so far. J Antimicrob Chemother 2006; 57:1–3 [View Article] [PubMed]
     [Google Scholar]
  34. Heritier C, Poirel L, Fournier PE, Claverie JM, Raoult D et al. Characterization of the naturally occurring oxacillinase of Acinetobacter baumannii. Antimicrob Agents Chemother 2005; 49:4174–4179 [View Article] [PubMed]
     [Google Scholar]
  35. Figueiredo S, Poirel L, Seifert H, Mugnier P, Benhamou D et al. OXA-134, a naturally occurring carbapenem-hydrolyzing class D beta-lactamase from Acinetobacter lwoffii. Antimicrob Agents Chemother 2010; 54:5372–5375 [View Article] [PubMed]
     [Google Scholar]
  36. Hong JS, Kim JO, Kim JO, Hong JS, Jeong SH et al. First case report of human infection with Ochrobactrum tritici causing bacteremia and cholecystitis. Ann Lab Med 2016; 36:278–280 [View Article] [PubMed]
     [Google Scholar]
  37. Apisarnthanarak A, Kiratisin P, Mundy LM. Evaluation of Ochrobactrum intermedium bacteremia in a patient with bladder cancer. Diagn Microbiol Infect Dis 2005; 53:153–155 [View Article] [PubMed]
     [Google Scholar]
  38. Cieslak TJ, Drabick CJ, Robb ML. Pyogenic infections due to Ochrobactrum anthropi. Clin Infect Dis 1996; 22:845–847 [View Article]
     [Google Scholar]
/content/journal/mgen/10.1099/mgen.0.000626
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Genomics of Ochrobactrum pseudogrignonense (newly named Brucella pseudogrignonensis) reveals a new blaOXA subgroup
M Gen 7, 000626 (2021); https://doi.org/10.1099/mgen.0.000626
/content/journal/mgen/10.1099/mgen.0.000626
/content/journal/mgen/10.1099/mgen.0.000626
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