Skip to main content

Advertisement

SpringerLink
Log in

Characterization of sixteen Achromobacter xylosoxidans phages from Abidjan, Côte d’Ivoire, isolated on a single clinical strain

  • Brief Report
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Sixteen bacteriophages of Achromobacter xylosoxidans distributed into four genera have been isolated from sewage water in Abidjan, Côte d’Ivoire, using a single clinical strain, and their genomes have been sequenced. Three podoviruses belonged to the genus Phikmvvirus, and these represent the first A. xylosoxidans phages of this genus. Seven podoviruses, distributed into three groups, belonged to the genus Jwalphavirus. Among the siphoviruses, three revealed similarities to Pseudomonas phage 73 and members of the genus Septimatrevirus, and three were YuA-like phages. The virulence of these phages toward a panel of 10 genetically diverse strains was tested, with the phiKMV-like phages showing the broadest host range.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Data availability

The genome sequences of the sixteen phages are available at GenBank under the following accession numbers: Axy04 (MK962626), Axy06 (MK962627), Axy09 (MK962628), Axy10 (MK962629), Axy11 (MK962630), Axy12 (MK962631), Axy13 (MK962632), Axy14 (MK962633), Axy16 (MK962634), Axy18 (MK962635), Axy19 (MK962636), Axy20 (MK962637), Axy21 (MK962638), Axy22 (MK962639), Axy23 (MK962640), Axy24 (MK962641). The raw read archives were deposited in bioproject PRJEB33638 together with raw sequencing data from A. xylosoxidans strain 19-32. The project can be accessed at https://www.ebi.ac.uk/ena/data/view/PRJEB33638.

References

  1. Dupont C, Jumas-Bilak E, Doisy C, Aujoulat F, Chiron R, Marchandin H (2018) Chronic airway colonization by Achromobacter xylosoxidans in cystic fibrosis patients is not sustained by their domestic environment. Appl Environ Microbiol. https://doi.org/10.1128/aem.01739-18

    Article  PubMed  PubMed Central  Google Scholar 

  2. Perez Barragan E, Sandino Perez J, Corbella L, Orellana MA, Fernandez-Ruiz M (2018) Achromobacter xylosoxidans bacteremia: clinical and microbiological features in a 10-year case series. Rev Esp Quimioter 31(3):268–273

    CAS  PubMed  Google Scholar 

  3. Habib S, Fuca N, Azam M, Siddiqui AH, Rajdev K, Chalhoub M (2018) Achromobacter xylosoxidans/denitrificans bacteremia and subsequent fatal Escherichia coli/Streptococcus anginosus pleural empyema. Respir Med Case Rep 25:311–313. https://doi.org/10.1016/j.rmcr.2018.10.010

    Article  PubMed  PubMed Central  Google Scholar 

  4. Tokuyasu H, Fukushima T, Nakazaki H, Shimizu E (2012) Infective endocarditis caused by Achromobacter xylosoxidans: a case report and review of the literature. Intern Med 51(9):1133–1138

    Article  Google Scholar 

  5. Lee B, Cai CX, Srikumaran D, Woreta FA (2018) Severe Achromobacter xylosoxidans keratitis with deep corneal involvement. Am J Ophthalmol Case Rep 11:128–130. https://doi.org/10.1016/j.ajoc.2018.06.006

    Article  PubMed  PubMed Central  Google Scholar 

  6. Jeukens J, Freschi L, Vincent AT, Emond-Rheault JG, Kukavica-Ibrulj I, Charette SJ, Levesque RC (2017) A pan-genomic approach to understand the basis of host adaptation in Achromobacter. Genome Biol Evol. https://doi.org/10.1093/gbe/evx061

    Article  PubMed  PubMed Central  Google Scholar 

  7. Traglia GM, Almuzara M, Merkier AK, Adams C, Galanternik L, Vay C, Centron D, Ramirez MS (2012) Achromobacter xylosoxidans: an emerging pathogen carrying different elements involved in horizontal genetic transfer. Curr Microbiol 65(6):673–678. https://doi.org/10.1007/s00284-012-0213-5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Hoyle N, Zhvaniya P, Balarjishvili N, Bolkvadze D, Nadareishvili L, Nizharadze D, Wittmann J, Rohde C, Kutateladze M (2018) Phage therapy against Achromobacter xylosoxidans lung infection in a patient with cystic fibrosis: a case report. Res Microbiol 169(9):540–542. https://doi.org/10.1016/j.resmic.2018.05.001

    Article  CAS  PubMed  Google Scholar 

  9. Wittmann J, Dreiseikelmann B, Rohde C, Rohde M, Sikorski J (2014) Isolation and characterization of numerous novel phages targeting diverse strains of the ubiquitous and opportunistic pathogen Achromobacter xylosoxidans. PLoS One 9(1):e86935. https://doi.org/10.1371/journal.pone.0086935

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Dreiseikelmann B, Bunk B, Sproer C, Rohde M, Nimtz M, Wittmann J (2017) Characterization and genome comparisons of three Achromobacter phages of the family Siphoviridae. Arch Virol 162(8):2191–2201. https://doi.org/10.1007/s00705-017-3347-8

    Article  CAS  PubMed  Google Scholar 

  11. Wittmann J, Dreiseikelmann B, Rohde M, Meier-Kolthoff JP, Bunk B, Rohde C (2014) First genome sequences of Achromobacter phages reveal new members of the N4 family. Virol J 11:14. https://doi.org/10.1186/1743-422X-11-14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ma Y, Li E, Qi Z, Li H, Wei X, Lin W, Zhao R, Jiang A, Yang H, Yin Z, Yuan J, Zhao X (2016) Isolation and molecular characterisation of Achromobacter phage phiAxp-3, an N4-like bacteriophage. Sci Rep 6:24776. https://doi.org/10.1038/srep24776

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Li E, Yin Z, Ma Y, Li H, Lin W, Wei X, Zhao R, Jiang A, Yuan J, Zhao X (2016) Identification and molecular characterization of bacteriophage phiAxp-2 of Achromobacter xylosoxidans. Sci Rep 6:34300. https://doi.org/10.1038/srep34300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Li E, Zhao J, Ma Y, Wei X, Li H, Lin W, Wang X, Li C, Shen Z, Zhao R, Jiang A, Yang H, Yuan J, Zhao X (2016) Characterization of a novel Achromobacter xylosoxidans specific siphoviruse: phiAxp-1. Sci Rep 6:21943. https://doi.org/10.1038/srep21943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ceyssens PJ, Lavigne R, Mattheus W, Chibeu A, Hertveldt K, Mast J, Robben J, Volckaert G (2006) Genomic analysis of Pseudomonas aeruginosa phages LKD16 and LKA1: establishment of the phiKMV subgroup within the T7 supergroup. J Bacteriol 188(19):6924–6931. https://doi.org/10.1128/JB.00831-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Spilker T, Vandamme P, Lipuma JJ (2012) A multilocus sequence typing scheme implies population structure and reveals several putative novel Achromobacter species. J Clin Microbiol 50(9):3010–3015. https://doi.org/10.1128/JCM.00814-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75. https://doi.org/10.1186/1471-2164-9-75

    Article  CAS  Google Scholar 

  18. Wittmann J, Klumpp J, Moreno Switt AI, Yagubi A, Ackermann HW, Wiedmann M, Svircev A, Nash JH, Kropinski AM (2015) Taxonomic reassessment of N4-like viruses using comparative genomics and proteomics suggests a new subfamily—”Enquartavirinae”. Arch Virol 160(12):3053–3062. https://doi.org/10.1007/s00705-015-2609-6

    Article  CAS  PubMed  Google Scholar 

  19. Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–W689. https://doi.org/10.1093/nar/gki366(Web Server issue)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Bailly-Bechet M, Vergassola M, Rocha E (2007) Causes for the intriguing presence of tRNAs in phages. Genome Res 17(10):1486–1495. https://doi.org/10.1101/gr.6649807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Kawasaki T, Narulita E, Matsunami M, Ishikawa H, Shimizu M, Fujie M, Bhunchoth A, Phironrit N, Chatchawankanphanich O, Yamada T (2016) Genomic diversity of large-plaque-forming podoviruses infecting the phytopathogen Ralstonia solanacearum. Virology 492:73–81. https://doi.org/10.1016/j.virol.2016.02.011

    Article  CAS  PubMed  Google Scholar 

  22. Ceyssens PJ, Mesyanzhinov V, Sykilinda N, Briers Y, Roucourt B, Lavigne R, Robben J, Domashin A, Miroshnikov K, Volckaert G, Hertveldt K (2008) The genome and structural proteome of YuA, a new Pseudomonas aeruginosa phage resembling M6. J Bacteriol 190(4):1429–1435. https://doi.org/10.1128/JB.01441-07

    Article  CAS  PubMed  Google Scholar 

  23. Essoh C, Latino L, Midoux C, Blouin Y, Loukou G, Nguetta SP, Lathro S, Cablanmian A, Kouassi AK, Vergnaud G, Pourcel C (2015) Investigation of a large collection of Pseudomonas aeruginosa bacteriophages collected from a single environmental source in Abidjan, Côte d’Ivoire. PLoS One 10(6):e0130548. https://doi.org/10.1371/journal.pone.0130548

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kutter E (2009) Phage host range and efficiency of plating. Methods Mol Biol 501:141–149. https://doi.org/10.1007/978-1-60327-164-6_14

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank Pr. Sylvain Godreuil from the CHU de Montpellier, France, for providing the Achromobacter xylosoxidans isolates. This research was funded by a grant from Direction Générale de l’Armement (DGA) and Agence Nationale de la Recherche (ANR, France) “Resisphage” ANR-13-ASTRID-0011-01. This work was also supported by Programme d’Appui Statégique à la Recherche Scientifique (PASRES) of Côte d’Ivoire. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. This work has benefited from facilities and expertise of the high-throughput sequencing core facility of I2BC (Centre de Recherche de Gif—http://www.i2bc.paris-saclay.fr/) and of Imagerie‐Gif core facility supported by l’Agence Nationale de la Recherche (ANR-11-EQPX-0029/Morphoscope, ANR-10-INBS-04/FranceBioImaging; ANR‐11‐IDEX‐0003‐02/ Saclay Plant Sciences. This publication made use of the PubMLST website (https://pubmlst.org/) developed by Keith Jolley (Jolley et al. Wellcome Open Res 2018, 3:124), funded by the Wellcome Trust and located at the University of Oxford.

Author information

Authors and Affiliations

  1. Département de Biochimie-Génétique, UFR des Sciences Biologiques, Université Peleforo Gon- Coulibaly, Korhogo, Côte d’Ivoire

    Christiane Essoh & Adama Coulibaly

  2. Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France

    Jean-Philippe Vernadet, Gilles Vergnaud & Christine Pourcel

  3. Laboratoire de Bactériologie-Virologie, Département de Microbiologie, UFR des Sciences Médicales, Université Félix Houphouët-Boigny, Abidjan, Côte d’Ivoire

    Adèle Kakou-N’Douba

  4. Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët-Boigny, Abidjan, Côte d’Ivoire

    Assavo S.-P. N’Guetta

  5. Laboratoire de Microbiologie, UFR des Sciences Pharmaceutiques et Biologiques, Université Félix Houphouët-Boigny, Abidjan, Côte d’Ivoire

    Thimotée Ouassa

  6. Université Paris-Sud, I2BC, Bât 400, 91405, Orsay cedex, France

    Christine Pourcel

Authors
  1. Christiane Essoh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jean-Philippe Vernadet
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gilles Vergnaud
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Adama Coulibaly
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Adèle Kakou-N’Douba
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Assavo S.-P. N’Guetta
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Thimotée Ouassa
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Christine Pourcel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Christine Pourcel.

Additional information

Handling Editor: Johannes Wittmann.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 1989 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Essoh, C., Vernadet, JP., Vergnaud, G. et al. Characterization of sixteen Achromobacter xylosoxidans phages from Abidjan, Côte d’Ivoire, isolated on a single clinical strain. Arch Virol 165, 725–730 (2020). https://doi.org/10.1007/s00705-019-04511-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-019-04511-7

Search

Navigation