UK Anaerobe Reference Unit (UKARU)

Pure isolates/cultures of anaerobic bacteria and putative Actinomyces spp. may be referred for identification by molecular and conventional methods.

These include phenotypic biochemical tests, MALDI-TOF MS & DNA sequencing.

Susceptibility testing of clinically relevant anaerobes including confirmation of unusual resistance phenotypes is performed via agar dilution (AD). A panel of antimicrobials is routinely tested which includes ceftriaxone, co-amoxiclav, clindamycin, meropenem, metronidazole, piperacillin-tazobactam, penicillin, vancomycin, doxycycline and rifampicin. Testing for other antimicrobials is available on request. Anaerobes not suitable for AD will be tested by gradient strip (GS).

Faeces may be submitted from patients within Wales for WGS typing. For patients outside of Wales please contact us for advice on how we can support your request before submission.

UKARU: Submission of isolates for identification and susceptibility testing request form

Please ensure that you have read the guidance notes and completed the request form before submission of isolates.

Pure anaerobes for confirmation of identity and standard AST panel = 14 working days.

For slow-growing isolates, mixed cultures or where additional tests are requested/required (e.g. further MICs) TATs may be extended.

Please note that samples that do not grow initially will be re-cultured.

Clostridium difficile isolates and faeces samples for WGS typing = 12 working days.

TATs for mixed cultures, additional tests, and non-outbreak work (e.g. commercial studies, planned surveillance) may be extended.

For referrals deemed to be outside the area of expertise of the UKARU (eg aerobic actinomycetes, certain capnophilic organisms) advice for re-referral to the appropriate reference facility will be provided.

Before referring an isolate to us, please ensure that you have excluded the possibility that it may be, or may contain, a hazard group 3 organism. Rapid growing non-tuberculous mycobacteria (NTM) and other acid/alcohol-acid fast bacilli (AFB/AAFB) should also be ruled out prior to referral of bacterial isolates.​

The UKARU has criteria in place where samples are rejected depending on the scenario as follows:

1. Mixed cultures with >2 organism with no indication of the target organism or relevant clinical history – the culture will be stored.  UKARU will not perform any further work unless contacted. Please repeat and re-submit a pure culture &/or contact ARU for further advice.
2. Mixed cultures with >2 organisms where ARU is unable to ascertain the target organism. If no relevant clinical history was stated then the culture will be stored.  UKARU will not perform any further work unless you contact us for discussion. Please repeat and re-submit a pure culture &/or contact ARU for further advice.
3. Mixed cultures with >2 organisms. If no relevant clinical history was stated only the target organism will be fully identified. The mixed sample will be stored & UKARU will not perform any further work unless you contact us for discussion.

Please ensure that all relevant identifiers including full postal address (not DX only) are included on the request form.

If submitting samples from outside the UK please consider all relevant paperwork and highlight the time sensitive nature of the request.

For anything outside of these standard referrals please discuss with Lead Scientist.

ESGAI is made up of scientists and clinicians from across the world involved in the promotion of research and education in the diagnosis and therapy of anaerobic infections. The Study Group focusses on providing education and training for less experienced scientists and encourages participation at ECCMID the European Society for Clinical Microbiology and Infectious Disease’ leading conference.

ESCMID Study Group for Anaerobic Infections – ESGAI

The Anaerobe Society of the Americas is an international organization, promoting the study and application of knowledge of anaerobic bacteriology. The primary activity of the society is organizing the biennial Anaerobe Congress for researchers, clinicians, and lab technicians from around the world to engage in presentations, exchanges, and dialogues related to anaerobes. Membership fee-includes subscription to the journal Anaerobe (6 issues per year). US-based.

Firstly, obtain a pure culture of the organism in question on a non-selective blood agar medium that yields good growth e.g. Fastidious Anaerobe Agar (FAA) preferably using a transport swab, take a sweep of the colonies and place the swab immediately in the transport medium.

Place in a sealed plastic bag.

Alternatively, inoculate a cooked meat broth and incubate until good growth is evident.

Seal the lid with parafilm and place in a sealed plastic bag.

Ensure all cultures are labelled and packed separately and surrounded by absorbent material and sent in a crush-proof container according to the current postal regulations for infectious materials.

Leaking cultures will be rejected.

Please note: viability of some anaerobes is reduced if strong pigment or acid is produced.

Please consider using fresh cultures of these isolates in order to allow maximum recovery for processing at the UKARU.

Complete the UKARU ID Request Form

Should we send it to the UKARU for confirmation?

Yes. Although some organisms that only grow anaerobically are intrinsically resistant to metronidazole, such as Propionibacterium/Cutibacterium spp and Actinomyces spp, others, such as the Bacteroides fragilis group and some clostridia may develop resistance. We need to closely monitor the evolution of any resistance within these groups.

Yes, most antimicrobials can be tested.  Requests for agents additional to the panel which is routinely tested (see Core Services) requires consultation with the Lead Scientist.  Some antimicrobials e.g. Gentamicin are unsuitable for testing under anaerobic conditions.

A different ID result could be due to the enhanced performance of our reference level methods or simply due to a change in the nomenclature of the organism. For the latter instance we will direct you to the appropriate published literature.

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 Apr 2:S1198-743X(21)00163-4. doi: 10.1016/j.cmi.2021.03.028. Online ahead of print.PMID: 33813129

Perry MD, White PL, Morris TE. Impact of the introduction of nucleic acid amplification testing on Clostridioides difficile detection and ribotype distribution in Wales. Anaerobe. 2020 Dec 9;67:102313. doi: 10.1016/j.anaerobe.2020.102313. Epub ahead of print. PMID: 33309680.

Tiltnes TS, Kehrer M, Hughes H, Morris TE, Justesen US. Ceftriaxone treatment of spondylodiscitis and other serious infections with Cutibacterium acnes. J Antimicrob Chemother. 2020 Oct 1;75(10):3046-3048. doi: 10.1093/jac/dkaa259. PMID: 32591800.

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 Dec 9;67(1):6-13. doi: 10.1556/030.66.2019.022. PMID: 31813262.

Eyre DW, Shaw R, Adams H, Cooper T, Crook DW, Griffin RM, Mannion P, Morgan M, Morris T, Perry M, Jones S, Peto TEA, Sutton J, Walker AS, Williams D, Craine N. WGS to determine the extent of Clostridioides difficile transmission in a high incidence setting in North Wales in 2015. J Antimicrob Chemother. 2019 Apr 1;74(4):1092-1100. doi: 10.1093/jac/dky523. PMID: 30561656.

Alexeyev OA, Dekio I, Layton AM, Li H, Hughes H, Morris T, Zouboulis CC, Patrick S. Why we continue to use the name Propionibacterium acnes. Br J Dermatol. 2018 Nov;179(5):1227. doi: 10.1111/bjd.17085. Epub 2018 Sep 19. PMID: 30101491.

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 Apr 23;18:1484-1496. doi: 10.1016/j.dib.2018.04.070. PMID: 29904651; PMCID: PMC5998164.

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 Dec;54:205-209. doi: 10.1016/j.anaerobe.2018.05.016. Epub 2018 May 30. PMID: 29880448.

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 Aug;52:9-15. doi: 10.1016/j.anaerobe.2018.05.005. Epub 2018 May 17. PMID: 29860038.

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 Dec;54:224-230. doi: 10.1016/j.anaerobe.2018.03.007. Epub 2018 Mar 12. PMID: 29545163.

Krutova M, Kinross P, Barbut F, Hajdu A, Wilcox MH, Kuijper EJ; survey contributors. How to: Surveillance of Clostridium difficile infections. Clin Microbiol Infect. 2018 May;24(5):469-475. doi: 10.1016/j.cmi.2017.12.008. Epub 2017 Dec 20. PMID: 29274463.

Knetsch CW, Kumar N, Forster SC, Connor TR, Browne HP, Harmanus C, Sanders IM, Harris SR, Turner L, Morris T, Perry M, Miyajima F, Roberts P, Pirmohamed M, Songer JG, Weese JS, Indra A, Corver J, Rupnik M, Wren BW, Riley TV, Kuijper EJ, Lawley TD. Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans. J Clin Microbiol. 2018 Feb 22;56(3):e01384-17. doi: 10.1128/JCM.01384-17. PMID: 29237792; PMCID: PMC5824051.

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 Dec;48:94-97. doi: 10.1016/j.anaerobe.2017.07.004. Epub 2017 Aug 7. PMID: 28797803.

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 Sep;22(9):793-798. doi: 10.1016/j.cmi.2016.06.016. Epub 2016 Jul 9. PMID: 27404365.

Bing AU, Loh SF, Morris T, Hughes H, Dixon JM, Helgason KO. Actinomyces Species Isolated from Breast Infections. J Clin Microbiol. 2015 Oct;53(10):3247-55. doi: 10.1128/JCM.01030-15. Epub 2015 Jul 29. PMID: 26224846; PMCID: PMC4572534.

Mac Aogáin M, Kilkenny S, Walsh C, Lindsay S, Moloney G, Morris T, Jones S, Rogers TR. Identification of a novel mutation at the primary dimer interface of GyrA conferring fluoroquinolone resistance in Clostridium difficile. J Glob Antimicrob Resist. 2015 Dec;3(4):295-299. doi: 10.1016/j.jgar.2015.09.007. Epub 2015 Nov 3. PMID: 27842877.

Fawley WN, Davies KA, Morris T, Parnell P, Howe R, Wilcox MH; Clostridium difficile Ribotyping Network (CDRN) Working Group. Enhanced surveillance of Clostridium difficile infection occurring outside hospital, England, 2011 to 2013. Euro Surveill. 2016 Jul 21;21(29). doi: 10.2807/1560-7917.ES.2016.21.29.30295. PMID: 27487436.

van Dorp SM, Notermans DW, Alblas J, Gastmeier P, Mentula S, Nagy E, Spigaglia P, Ivanova K, Fitzpatrick F, Barbut F, Morris T, Wilcox MH, Kinross P, Suetens C, Kuijper EJ; European Clostridium difficile Infection Surveillance Network (ECDIS-Net) project on behalf of all participants. Survey of diagnostic and typing capacity for Clostridium difficile infection in Europe, 2011 and 2014. Euro Surveill. 2016 Jul 21;21(29). doi: 10.2807/1560-7917.ES.2016.21.29.30292. PMID: 27469624.

Tierney D, Copsey SD, Morris T, Perry JD. A new chromogenic medium for isolation of Bacteroides fragilis suitable for screening for strains with antimicrobial resistance. Anaerobe. 2016 Jun;39:168-72. doi: 10.1016/j.anaerobe.2016.04.003. Epub 2016 Apr 6. PMID: 27060277.

Haddad N, Morris T, Dhillon R, Gibbon F. Unusual neurological presentation of Fusobacterium necrophorum disease. BMJ Case Rep. 2016 Jan 12;2016:bcr2015210710. doi: 10.1136/bcr-2015-210710. PMID: 26759436; PMCID: PMC4716438.

Moore K, Hall V, Paull A, Morris T, Brown S, McCulloch D, Richardson MC, Harding KG. Surface bacteriology of venous leg ulcers and healing outcome. J Clin Pathol. 2010 Sep;63(9):830-4. doi: 10.1136/jcp.2010.077032. Epub 2010 Jul 29. PMID: 20671048.

Brazier JS, Gal M, Hall V, Morris TE. Outbreak of Clostridium histolyticum infections in injecting drug users in England and Scotland. Euro Surveill. 2004 Sep;9(9):15-6. PMID: 15381836.

Brazier JS, Morris TE, Duerden BI. Heat and acid tolerance of Clostridium novyi Type A spores and their survival prior to preparation of heroin for injection. Anaerobe. 2003 Jun;9(3):141-4. doi: 10.1016/S1075-9964(03)00068-4. PMID: 16887701.

Brazier JS, Hall V, Morris TE, Gal M, Duerden BI. Antibiotic susceptibilities of Gram-positive anaerobic cocci: results of a sentinel study in England and Wales. J Antimicrob Chemother. 2003 Aug;52(2):224-8. doi: 10.1093/jac/dkg316. Epub 2003 Jul 1. PMID: 12837734.