Skip to main content

Research group for anaerobic bacteria

Anaerobic from Greek: an = ”not” + aer = ”air”

Anaerobic bacteria ”hates” air

Anaerobic bacteria constitutes the majority of the human normal microbiota, including 99% of the gut microbiota. However, the normal microbiota can also cause severe disease. The research group for anaerobic bacteria are developing and testing new methods for identification and susceptibility testing of anaerobic bacteria. We are also working with the epidemiology of resistance in anaerobic bacteria and association with cancer. Developing and testing new methods will help to improve treatment of anaerobic infections, to monitor and understand the development of resistance in the normal microbiota and to diagnose patients at risk of colorectal cancer. 


Research projects

Bacteraemia with anaerobic bacteria and association with colorectal cancer?

Bacteraemia with specific anaerobic bacteria is believed to be associated with colorectal cancer. This is being investigated in a large cohort study. Anaerobic bacteria from patients with colorectal cancer will be evaluated for special characteristics.

The cohort study, “Bacteraemia – a new diagnostic biomarker for colorectal cancer”, including national data on bacteraemia with anaerobic bacteria and colorectal cancer is supported by the NEYE-Foundation (370.650,- DKK):

Antimicrobial susceptibility testing of anaerobic bacteria – development of a disk diffusion method

Antimicrobial susceptibility testing, using disk diffusion, for anaerobic bacteria is being evaluated to develop a EUCAST method. Collaboration with the EUCAST Laboratory for Antimicrobial Susceptibility Testing, Centrallasarettet, Växjö, Sverige (Gunnar Kahlmeter and Erika Matuschek).

Typing of the Bacteroides fragilis group with whole genome sequencing

A typing scheme, MLST and cgMLST, is being developed for the Bacteroides fragilis group to be able to establish possible associations with resistance and colorectal cancer.

Research network


  • Several clinical departments at Odense University Hospital
  • Department og Biochemistry and Molecular Biology, University of Southern Denmark (SDU)


  • Several departments of clinical microbiology
  • Microbiology & Infection Control, Statens Serum Institut (SSI)
  • The Microbial Genomics and Antimicrobial Resistance Group, National Food Institute
  • Department of Pediatrics, Rigshospitalet, Copenhagen


  • EUCAST Laboratory for Antimicrobial Susceptibility Testing, Centrallasarettet, Växjö, Sweden
  • UK Anaerobe Reference Unit (UKARU), Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, Wales.
  • Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
  • Department of Medical Microbiology, University Medical Centre Groningen, Groningen, The Netherlands
  • Department of Microbiology, Université de Caen, Normandie, Caen, France
  • Department of Medical Microbiology, Marmara University, Istanbul, Turkey 

Research publications

  1. Stubhaug TT, Giske CG, Justesen US, Kahlmeter G, Matuschek E, Sundsfjord A, Skaare D; Nordic Bacteroides AST Study Group. Antimicrobial susceptibility testing of Bacteroides species by disk diffusion: The NordicAST Bacteroides study. Anaerobe. 2023 May 28:102743. DOI: 10.1016/j.anaerobe.2023.102743. Online ahead of print

  2. Justesen US, Åhman J, Matuschek E, Kahlmeter G. Assessing the quality of the anaerobic environment - a method developed to support EUCAST disk diffusion of anaerobic bacteria. Eur J Clin Microbiol Infect Dis. 2023 May 12. DOI: 10.1007/s10096-023-04622-9. Online ahead of print

  3. Nielsen FD, Skov MN, Sydenham TV, Justesen US. Development and Clinical Application of a Multilocus Sequence Typing Scheme for Bacteroides fragilis Based on Whole-Genome Sequencing Data. Microbiol Spectr. 2023;11:e0511122. DOI: 10.1128/spectrum.05111-22.
  4.  Justesen US, Nielsen SL, Jensen TG, Dessau RB, Møller JK, Coia JE, Andersen SL, Pedersen C, Gradel KO. Bacteremia With Anaerobic Bacteria and Association With Colorectal Cancer: A Population-based Cohort Study. Clin Infect Dis. 2022;75:1747-53. DOI: 10.1093/cid/ciac259.

  5. Bavelaar H, Justesen US, Morris TE, Anderson B, Copsey-Mawer S, Stubhaug TT, Kahlmeter G, Matuschek E. Development of a EUCAST disk diffusion method for the susceptibility testing of rapidly growing anaerobic bacteria using Fastidious Anaerobe Agar (FAA): a development study using Bacteroides species. Clin Microbiol Infect. 2021;27:1695.e1-1695.e6. DOI: 10.1016/j.cmi.2021.03.028        

  6. Kjær Hansen S, Løfberg SV, Nielsen DK, Kobberø H, Justesen US. Bacteraemia with Moryella indoligenes and Fastidiosipila sanguinis: a case report. Access Microbiol. 2020;2:acmi000108. DOI: 10.1099/acmi.0.000108


  7. Tiltnes TS, Kehrer M, Hughes H, Morris TE, Justesen US. Ceftriaxone treatment of spondylodiscitis and other serious infections with Cutibacterium acnes. J Antimicrob Chemother. J Antimicrob Chemother. 2020;75:3046-8. DOI: 10.1093/jac/dkaa259


  8. Toprak NU, Veloo ACM, Urban E, Wybo I, Jean-Pierre H, Morris T, Justesen US, Tripkovic V, Jeverica S, Soyletir G, Nagy E; ESCMID Study Group for Anaerobic Infections (ESGAI)**. Comparing identification of clinically relevant Prevotella species by VITEK MS and MALDI biotyper. Acta Microbiol Immunol Hung. 2019;67:6-13. DOI: 10.1556/030.66.2019.022


  9. Sydenham TV, Overballe-Petersen S, Hasman H, Wexler H, Kemp M, Justesen US. Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids. Microb Genom. 2019;5. DOI: 10.1099/mgen.0.000312


  10. Veloo ACM, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, Kostrzewa M, Friedrich AW, On Behalf Of The Enria Workgroup. An overview of the data obtained during the validation of an optimized MALDI-TOF MS Biotyper database for the identification of anaerobic bacteria. Data Brief. 2018;18:1484-96. DOI: 10.1016/j.dib.2018.04.070


  11. Ulger Toprak N, Alida C M V, Urban E, Wybo I, Justesen US, Jean-Pierre H, Morris T, Akgul O, Kulekci G, Soyletir G, Nagy E; ESCMID Study Group for Anaerobic Infections (ESGAI). Performance of mass spectrometric identification of clinical Prevotella species using the VITEK MS system: A prospective multi-center study. Anaerobe. 2018;54:205-9. DOI: 10.1016/j.anaerobe.2018.05.016


  12. Ulger Toprak N, Veloo ACM, Urban E, Wybo I, Justesen US, Jean-Pierre H, Morris T, Akgul O, Kulekci G, Soyletir G, Nagy E; ESCMID Study Group for Anaerobic Infections (ESGAI). A multicenter survey of antimicrobial susceptibility of Prevotella species as determined by Etest methodology. Anaerobe. 2018;52:9-15. DOI: 10.1016/j.anaerobe.2018.05.005


  13. Veloo ACM, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, Kostrzewa M, Friedrich AW; ENRIA workgroup. Validation of MALDI-TOF MS Biotyper database optimized for anaerobic bacteria: The ENRIA project. Anaerobe. 2018;54:224-30. DOI: 10.1016/j.anaerobe.2018.03.007


  14. Justesen US, Acar Z, Sydenham TV, Johansson Å; ESGAI (ESCMID Study Group on Anaerobic Infections). Antimicrobial susceptibility testing of Bacteroides fragilis using the MALDI Biotyper antibiotic susceptibility test rapid assay (MBT-ASTRA). Anaerobe. 2018;54:236-9. DOI: 10.1016/j.anaerobe.2018.02.007


  15. Nagy E, Boyanova L, Justesen US; ESCMID Study Group of Anaerobic Infections. How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories. Clin Microbiol Infect. 2018;24:1139-48. DOI: 10.1016/j.cmi.2018.02.008


  16. Veloo ACM, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, Shah HN, Friedrich AW; ENRIA workgroup, Morris T, Shah HN, Jean-Pierre H, Justesen US, Nagy E, Urban E, Kostrzewa M, Veloo A, Friedrich AW. A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS. Anaerobe. 2017;48:94-7. DOI: 10.1016/j.anaerobe.2017.07.004


  17. Ferløv-Schwensen SA, Sydenham TV, Hansen KCM, Hoegh SV, Justesen US. Prevalence of antimicrobial resistance and the cfiA resistance gene in Danish Bacteroides fragilis group isolates since 1973. Int J Antimicrob Agents. 2017;50:552–6. DOI: 10.1016/j.ijantimicag.2017.05.007


  18. Hansen KC, Schwensen SA, Henriksen DP, Justesen US, Sydenham TV. Antimicrobial resistance in the Bacteroides fragilis group in faecal samples from patients receiving broad-spectrum antibiotics. Anaerobe. 2017;47:79-85. DOI: 10.1016/j.anaerobe.2017.04.013


  19. Sydenham TV, Jensen BH, Petersen AM, Krogfelt KA, Justesen US. Antimicrobial resistance in the Bacteroides fragilis group in faecal microbiota from healthy Danish children. Int J Antimicrob Agents. 2017; 49:573-8. DOI: 10.1016/j.ijantimicag.2017.01.011


  20. Justesen US. Design af artificial foetor flatus ved hjælp af flygtige bakterielle produkter. Ugeskrift for Læger. 2016;178:V68707. 


  21. Schwensen SA, Acar Z, Sydenham TV, Johansson ÅC, Justesen US. Phenotypic detection of the cfiA metallo-β-lactamase in Bacteroides fragilis with the meropenem-EDTA double-ended Etest and the ROSCO KPC/MBL Confirm Kit. J Antimicrob Chemother. 2017;72:437-40. DOI: 10.1093/jac/dkw436


  22. Kvich L, Jensen PØ, Justesen US, Bjarnsholt T. Incidence of Propionibacterium acnes in initially culture-negative thioglycollate broths-a prospective cohort study at a Danish University Hospital. Clin Microbiol Infect. 2016;22:941-5. DOI: 10.1016/j.cmi.2016.07.036


  23. Veloo AC, de Vries ED, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, van Winkelhoff AJ; ENRIA workgroup. The optimization and validation of the Biotyper MALDI-TOF MS database for the identification of Gram-positive anaerobic cocci. Clin Microbiol Infect. 2016;22:793-798. DOI: 10.1016/j.cmi.2016.06.016


  24. Agergaard CN, Hoegh SV, Holt HM, Justesen US. Two Serious Cases of Infection with Clostridium celatum after 40 Years in Hiding? J Clin Microbiol. 2016;54:236-8. DOI: 10.1128/JCM.01938-15


  25. Holt HM, Danielsen TK, Justesen US. Routine disc diffusion antimicrobial susceptibility testing of Clostridium difficile and association with PCR ribotype 027. Eur J Clin Microbiol Infect Dis. 2015;34:2243-6. DOI: 10.1007/s10096-015-2475-x


  26. Krogh TJ, Agergaard CN, Møller-Jensen J, Justesen US. Draft genome sequence of Parabacteroides goldsteinii with putative novel metallo-β-lactamases isolated from a blood culture from a human patient. Genome Announc. 2015;3:e00937-15. DOI: 10.1128/genomeA.00937-15


  27. Ank N, Sydenham TV, Iversen LH, Justesen US, Wang M. Characterisation of a multidrug-resistant Bacteroides fragilis isolate recovered from blood of a patient in Denmark using whole-genome sequencing. Int J Antimicrob Agents. 2015;46:117-20. DOI: 10.1016/j.ijantimicag.2015.02.024

  28. Sydenham TV, Hasman H, Justesen US. Draft genome sequences of Sanguibacteroides justesenii, gen. nov., sp. nov., strains OUH 308042T (= ATCC BAA-2681T) and OUH 334697 (= ATCC BAA-2682), isolated from blood cultures from two different patients. Genome Announc. 2015;3:e00005-15. DOI: 10.1128/genomeA.00005-15


  29. Lund LC, Sydenham TV, Høgh SV, Skov M, Kemp M, Justesen US. Draft genome sequence of “Terrisporobacter othiniensis” isolated from a blood culture from a human patient. Genome Announc. 2015;3:e00042-15. DOI: 10.1128/genomeA.00042-15


  30. Sydenham TV, Sóki J, Hasman H, Wang M, Justesen US; ESGAI (ESCMID Study Group on Anaerobic Infections). Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing. Anaerobe. 2015;31:59-64. DOI: 10.1016/j.anaerobe.2014.10.009


  31. Nagy E, Justesen US, Eitel Z, Urbán E; ESCMID Study Group on Anaerobic Infection. Development of EUCAST disk diffusion method for susceptibility testing of the Bacteroides fragilis group isolates. Anaerobe. 2015;31:65-71. DOI: 10.1016/j.anaerobe.2014.10.008


  32. Sydenham TV, Arpi M, Klein K, Justesen US. Four cases of bacteremia with Oscillibacter ruminantium-- a newly described species. J Clin Microbiol. 2014;52:1304 7. DOI: 10.1128/JCM.03128-13


  33. Pedersen RM, Marmolin ES, Justesen US. Species differentiation of Bacteroides dorei from Bacteroides vulgatus and Bacteroides ovatus from Bacteroides xylanisolvens - back to basics. Anaerobe. 2013;24:1-3. DOI: 10.1016/j.anaerobe.2013.08.004


  34. Justesen US, Hansen F, Østergaard C, Schønheyder HC, Hansen DS, Lemming LE, Schumacher H, Heltberg O, Knudsen JD, Dzajic E, Arpi M, Hammerum AM. High rates of reduced susceptibility in the Bacteroides fragilis group isolated from blood cultures – the first national survey in Denmark. Int J Antimicrob Agents. 2013;42:188-90. DOI: 10.1016/j.ijantimicag.2013.04.025


  35. Justesen T, Justesen US. A simple and sensitive quality control method of the anaerobic atmosphere for identification and antimicrobial susceptibility testing of anaerobic bacteria. Diagn Microbiol Infect Dis. 2013;76:138-40. DOI: 10.1016/j.diagmicrobio.2013.02.014


  36. Hansen SG, Skov MN, Justesen US. Two cases of Ruminococcus gnavus bacteremia associated with diverticulitis. J Clin Microbiol. 2013;51:1334-6. DOI: 10.1128/JCM.03382-12


  37. Hartmeyer GN, Sóki J, Nagy E, Justesen US. Multidrug-resistant Bacteroides fragilis group on the rise in Europe? J Med Microbiol. 2012;61:1784-8. DOI: 10.1099/jmm.0.049825-0 


  38. Erikstrup LT, Danielsen TK, Hall V, Olsen KE, Kristensen B, Kahlmeter G, Fuursted K, Justesen US. Antimicrobial susceptibility testing of Clostridium difficile using EUCAST epidemiological cut-off values and disk diffusion correlates. Clin Microbiol Infect. 2012;18:E266-72. DOI: 10.1111/j.1469-0691.2012.03907.x


  39. Justesen US, Holm A, Knudsen E, Andersen LB, Jensen TG, Kemp M, Skov MN, Gahrn-Hansen B, Møller JK. Species identification of clinical isolates of anaerobic bacteria: a comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems. J Clin Microbiol. 2011;49:4314-8. DOI: 10.1128/JCM.05788-11


  40. Madsen IR, Justesen US. Bacteremia with Bacteroides pyogenes after a cat bite. J Clin Microbiol. 2011;49:3092-3. DOI: 10.1128/JCM.00250-11


  41. Pedersen RM, Holt HM, Justesen US. Solobacterium moorei bacteremia: identification, antimicrobial susceptibility, and clinical characteristics. J Clin Microbiol. 2011;49:2766-8. DOI: 10.1128/JCM.02525-10


  42. Justesen US, Skov MN, Knudsen E, Holt HM, Søgaard P, Justesen T. 16S rRNA gene sequencing in routine identification of anaerobic bacteria isolated from blood cultures. J Clin Microbiol. 2010;48:946-8. DOI: 10.1128/JCM.02075-09




Ulrik Stenz Justesen
senior consultant,

Ulrik Stenz Justesen

Flemming Damgaard Nielsen
Ph.D. student


Last Updated 20.11.2023