Specialist and reference microbiology: laboratory tests and services

Acanthamoeba For keratitis/ophthalmic samples only Contact the Diagnostic Parasitology Laboratory at the London School of Hygiene and Tropical Medicine LSHTM Achromobacter Species identification, molecular typing and antimicrobial resistance H1, H2 AMRHAI Acinetobacter Species identification, molecular typing and antimicrobial resistance H1, H2 AMRHAI Actinomycetes (Aerobic) Antimicrobial susceptibility H1, H2 AMRHAI Actinomycetes (Aerobic) Identification and confirmation M1, H2 AMRHAI Adenoviruses (enteric) PCR E1 EVU Adenoviruses (respiratory) PCR E27 RVU Amoebae (excluding Acanthamoeba keratitis) Detection, identification and confirmation, serodiagnosis Contact National parasitology reference laboratory (NPRL) NPRL Anaerobes (bacteroides, clostridia, fusobacteria, actinomyces spp., other closely related genera) Identification Contact ARU ARU Anthrax See Bacillus anthracis     Antibiotic resistance surveys European antibiotic resistance surveillance scheme (EARSS) and surveillance of resistance H1 AMRHAI Antibiotic susceptibility testing New antimicrobials, susceptibility testing service, beta-lactamases, endocarditis H1, H2 AMRHAI Arboviruses (bunyaviridae, flaviviridae, togaviridae) Isolation, serology, PCR P1 RIPL Aspergillus Identification and confirmation Y1 or Y2 Mycology RL Astrovirus RT-PCR E1 EVU Astrovirus Genotyping Contact EVU EVU Bacillus anthracis Identification and confirmation, PCR, serology, characterisation (phage, penicillin sensitivity) Contact RIPL lab RIPL Bacillus (other than B.anthracis) Identification L4 GBRU Bacillus (other than B.anthracis) Molecular typing L4 GBRU Bacillus (other than B.anthracis) Detection of emetic toxin gene by PCR L4 GBRU Bacillus (other than B.anthracis) Antimicrobial susceptibility H1, H2 AMRHAI Bacterial Identification Service (BIDS) – isolates Isolate identification (unknown, atypical, fastidious, emerging bacteria) M1 AMRHAI Bacterial Identification Service (BIDS) – clinical samples Bacterial detection and species identification for culture-negative, unknown clinical samples from normally sterile sites M1 AMRHAI Blastomyces dermatidis Serology, identification and confirmation Y1 or Y2 MRL Bordetella spp. Identification R3 RVPBRU Bordetella spp. Antimicrobial susceptibility H1, H2 AMRHAI Bordetella pertussis Serology: anti-PT IgG antibodiesNot suitable for immune status R3 RVPBRU Bordetella pertussis Oral fluid: anti-PT IgG antibodies. NOT suitable for immune status Form distributed with kit RVPBRU Bordetella pertussis qPCR R3 RVPBRU Brucella spp. Serodiagnosis Y3 BRU Brucella spp. Speciation and characterisation Contact AHVLA laboratory, Weybridge BRU Burkholderia spp. Species identification, molecular typing and antimicrobial resistance H1, H2 AMRHAI Burkholderia pseudomallei Identification and antimicrobial resistance H1, H2 AMRHAI Candida spp. Identification and confirmation Y1 or Y2 Mycology RL Campylobacter Antibiotic susceptibility testing for gram negative GI pathogens L4 GBRU Campylobacter Identification L4 GBRU Chikungunya virus Serology, PCR P1 RIPL Chlamydia (respiratory) Only available after discussion and prior agreement with RVPBRU C. pneumoniae, C. psittacci, C. abortus: PCR assay For urgent enquiries, contact RVPBRU RVPBRU Chlamydia trachomatis C. trachomatis: LGV multiplex PCR B7 CSU Clostridium difficile 16S/23S PCR ribotyping, antibiotic susceptibility testing and toxin A and B assay on isolates Contact ARU ARU Clostridium botulinum Detection and identification of C. botulinum from clinical, food or environmental samples by PCR and culture L4 GBRU Clostridium botulinum Detection of botulinum neurotoxins in clinical specimens or food L4, L7 GBRU Clostridium perfringens Identification of enterotoxigenic C. perfringens by PCR L4 GBRU Clostridium perfringens Molecular typing L4 GBRU Clostridium perfringens Detection of C. perfringens enterotoxin in faeces by ELISA L4 GBRU Clostridium perfringens C. perfringens Toxin (lethal toxins) typing by PCR L4 GBRU Clostridium tetani Detection and identification of C. tetani by PCR and culture L4 GBRU Clostridium tetani Detection of C. tetani neurotoxin in serum (note: serum will be first tested for tetanus antibody levels by RVPBRU) L4 GBRU Clostridium tetani Tetanus immunity: serum antibodies R3 RVPBRU Coccidioides immitis Serology, identification and confirmation Y1 or Y2 Mycology RL Coronavirus Virus detection by PCR (sequencing) E16 RVU Coronavirus (SARS) Contact laboratory prior to collection of samples E16 RVU Coronavirus (SARS-CoV-2) Confirmatory testing V30 regional PHE Coronavirus (MERS-CoV) Contact laboratory prior to collection of samples E16 RVU Corynebacterium Molecular typing and antimicrobial resistance H1, H2 AMRHAI Corynebacterium diphtheriae C. diphtheriae and other potentially toxigenic corynebacteria: identification and toxin testing by PCR and Elek R3 RVPBRU Corynebacterium diphtheriae Diphtheria immunity: serum antibodies R3 RVPBRU Corynebacterium jeikeium C. jeikeium antimicrobial sensitivity H2 AMRHAI Crimean-Congo haemorrhagic fever Serology, PCR. Please contact lab before sending samples. P1 RIPL Cronobacter C. sakazakii: confirmation of identification, molecular typing and antimicrobial resistance H1, H2 AMRHAI Cystic Fibrosis (CF) pathogens Identification and molecular typing H2 AMRHAI Cystic Fibrosis (CF) pathogens Antimicrobial susceptibility H1, H2 AMRHAI Cryptococcus spp. Identification and confirmation Y1 or Y2 Mycology RL Cryptosporidium spp. Detection, identification and confirmation, typing Contact CRU CRU Dengue virus Serology, PCR P1 RIPL Dermatophytes Identification, confirmation Y1 or Y2 Mycology RL Diphtheria (see Corynebacterium diphtheriae)       Ebola virus Serology, PCR. Please contact lab before sending samples. P1 RIPL Elizabethkingia.spp Identification, molecular typing and antimicrobial resistance H1, H2 AMRHAI Enterobacter spp. Molecular typing and antimicrobial resistance H1, H2 AMRHAI Enterococcus spp. Species identification, molecular typing and antimicrobial resistance H1, H2 AMRHAI Enterovirus RT-PCR E1 EVU Enterovirus Virus culture Contact EVU EVU Enterovirus Typing E1 EVU Escherichia Antibiotic susceptibility testing for gram negative GI pathogens L4 GBRU Escherichia E. coli (ACDP HG 2 only): molecular typing and antimicrobial resistance H1, H2 AMRHAI Escherichia Identification and typing L4 GBRU Escherichia E. coli O157: serodiagnostic service L5 GBRU Escherichia Detection and isolation from faeces L5 GBRU Francisella spp., including tularensis PCR, serology, isolation P1 RIPL Gram-negative bacteria non fermenter and fastidious organisms Molecular typing and antimicrobial resistance H1, H2 AMRHAI Gram-positive bacteria (except C.diphtheriae) Molecular typing and antimicrobial resistance H1, H2 AMRHAI Haemophilus Haemophilus spp. (excluding H. ducreyi): identification R3 RVPBRU Haemophilus H. influenzae: sero typing and capsular genotyping of H.influenzae R3 RVPBRU Haemophilus spp. and Aggregatibacter spp. Antimicrobial susceptibility H1, H2 AMRHAI Haemorrhagic fever viruses (filoviridae, arenaviridae, Bunyaviridae) Serology, PCR. Please contact lab before sending samples. P1 RIPL Hantavirus Serology, PCR. P1 RIPL Hendra virus Serology, PCR. Please contact lab before sending samples. P1 RIPL Helicobacter Antibiotic susceptibility testing for gram negative GI pathogens L4 GBRU Helicobacter H. pylori identification and antibiotic susceptibility L4,L5 GBRU Hepatitis A virus (HAV) RNA S1 BBVU Hepatitis A virus (HAV) Genotyping and phylogenetics S1 BBVU Hepatitis A virus (HAV) Anti-HAV IgG and IgM S1 CSU Hepatitis B virus (HBV) HBsAg detection S1 CSU Hepatitis B virus (HBV) HBsAg quantification S1 CSU Hepatitis B virus (HBV) HBsAg neutralisation S1 CSU Hepatitis B virus (HBV) HBeAg S1 CSU Hepatitis B virus (HBV) Anti-HBc S1 CSU Hepatitis B virus (HBV) Anti-HBc IgM S1 CSU Hepatitis B virus (HBV) Anti-HBs S1 CSU Hepatitis B virus (HBV) Anti-HBe S1 CSU Hepatitis B virus (HBV) DNA viral load S1 CSU Hepatitis B virus (HBV) Pre-core and BCP mutation screen S10 BBVU Hepatitis B virus (HBV) Surface mutation screen S10 BBVU Hepatitis B virus (HBV) Antiviral resistance S10 BBVU Hepatitis B virus (HBV) Genotyping and phylogenetics S10 BBVU Hepatitis C virus (HCV) Antibody confirmation and viral load S1 CSU Hepatitis C virus (HCV) Antibody confirmation (dried blood spots and oral fluid samples) S1 BBVU Hepatitis C virus (HCV) Viral load S1 CSU Hepatitis C virus (HCV) Viral load (sensitivity >15 IU/ml) Please contact lab prior to sample referral S1 CSU Hepatitis C virus (HCV) Qualitative RNA detection S1 BBVU Hepatitis C virus (HCV) Genotyping (NS5B sequencing): EDTA plasma S1 CSU Hepatitis C virus (HCV) Genotyping (NS5B sequencing): dried blood spots S1 BBVU Hepatitis C virus (HCV) Phylogenetics S1 BBVU Hepatitis C virus (HCV) HCV DAA genotypic resistance Contact AVU AVU Hepatitis Delta virus (HDV) Anti-HDV IgG S1 CSU Hepatitis Delta virus (HDV) Anti-HDV IgM S1 CSU Hepatitis Delta virus (HDV) RNA S1 BBVU Hepatitis E virus (HEV) Anti-HEV IgG S1 CSU Hepatitis E virus (HEV) Anti-HEV IgM S1 CSU Hepatitis E virus (HEV) RNA S1 BBVU Hepatitis E virus (HEV) Genotyping, phylogenetics S1 BBVU Herpes simplex virus (HSV 1 and 2) Phenotypic drug resistance Contact AVU AVU Herpes simplex virus (HSV 1 and 2) Intrathecal antibody testing S4 IDU Histoplasma capsulatum Serology, identification and confirmation Y1 or Y2 Mycology RL Histology slides Examination for the presence of fungi Y1 or Y2 Mycology RL HIV-1 and HIV-2 HIV 1, HIV-2 antibody screen, confirmation, typing S3 CSU HIV-1 and HIV-2 HIV 1, HIV-2 antibody screen, confirmation, typing (dried blood spots) S3 CSU HIV-1 and HIV-2 HIV 1, HIV-2 antibody screen, confirmation, typing, oral fluid (OraSure) S3 CSU HIV-1 and HIV-2 HIV-1 proviral DNA S3 CSU HIV-1 and HIV-2 HIV-1 RNA quantification (viral load) S3 CSU HIV-1 and HIV-2 HIV-1 p24 antigen with neutralisation S3 CSU HIV-1 and HIV-2 HIV-1 incidence testing (avidity) S3 CSU HIV-1 and HIV-2 HIV-1 genotypic resistance S9 AVU HIV-1 and HIV-2 HIV-1 proviral tropism testing S9 AVU HIV-1 and HIV-2 Detection of minority drug resistance mutants S9 AVU HIV-1 and HIV-2 HIV-1 sequencing and sequence comparison Contact AVU AVU Human T-lymphotropic virus type I and Human T-lymphotropic virus type II (HTLV-I and II) HTLV antibody screen, confirmation, typing S5 CSU Human T-lymphotropic virus type I and Human T-lymphotropic virus type II (HTLV-I and II) HTLV type-specific PCR S5 CSU Human herpesvirus 6 (HHV-6) Antibody testing E18 IDU Human herpesvirus 6 (HHV-6) PCR and genotyping E18 IDU Human herpesvirus 7 (HHV-7) Antibody testing E18 IDU Human herpesvirus 7 (HHV-7) PCR and genotyping E18 IDU Human herpesvirus 8 (HHV-8) Quantitative DNA PCR S19 CSU Human metapneumovirus Virus detection by PCR andsequencing Contact RVU RVU Hydatid disease or Echinococcosis Serology Contact NPRL NPRL Identification of bacterial isolates with no national reference facility (unknowns, atypical, fastidious, emerging MALDI-TOF-MS, 16s ribosomal sequence analysis M1 AMRHAI Infection prevention and control testing Contact AMRHAI AMRHAI Influenza Virus detection by multiplex PCR E3 RVU Influenza Strain typing HAI E3 RVU Influenza Antibody response HAI E2 RVU Influenza Phenotypic drug resistance Contact RVU RVU Influenza Genotypic drug resistance by pyrosequencing and SNP PCR Contact RVU RVU Influenza Genotypic drug resistance by gene sequencing Contact RVU RVU Influenza (avian) Confirmation of regional laboratory H9 virus detection Contact RVU RVU Influenza (avian) Antibody response Contact RVU RVU JC virus (see Polyomavirus) Serology, PCR E13 IDU Klebsiella spp. Molecular typing and antimicrobial resistance H1, H2 AMRHAI Lassa virus Serology, PCR. Please contact lab before sending samples. P1 RIPL Legionella L.pneumophila: in-house urinary antigen EIA assay (confirmation of sending lab testing results only) R1 RVPBRU Legionella L pneumophila PCR (from urinary antigen positive patients only) R1 RVPBRU Legionella Identification and epidemiological typing of clinical or outbreak associated isolates R1 RVPBRU Leuconostoc spp. Antimicrobial susceptibility H1, H2 AMRHAI Leptospira spp Isolation and confirmation, identification, serology Leptospirosis: request form NLS Listeria spp. Identification, serotyping and molecular typing of L.monocytogenes L4 GBRU Listeria spp. Species identification of Listeria L4 GBRU Listeria spp. Antimicrobial susceptibility H1, H2 AMRHAI Lyme disease Serology, PCR P2 RIPL Malaria Blood film diagnosis, antigen detection, PCR, drug resistance markers Malaria report form Malaria RL Marburg virus Serology, PCR. Please contact lab before sending samples. P1 RIPL Measles IgG and IgM serology for recent infection E8 IDU Measles IgG antibody status E8 IDU Measles Intrathecal antibody testing E8 IDU Measles PCR E8 IDU Measles Same day testing E8 IDU Measles Plaque reduction neutralisation assay E8 IDU Measles Virus culture E8 IDU Middle East respiratory syndrome coronavirus (MERS-CoV) Contact laboratory prior to collection of specimens E16 RVU Molluscum contagiosum Electron microscopy E17 HPU Moulds Identification and confirmation, susceptibility testing Y1 or Y2 Mycology RL Methicillin-resistant staphylococcus aureus (MRSA) (see Staphylococcus)       Mumps IgG and IgM serology for recent infection E8 IDU Mumps IgG antibody status E8 IDU Mumps PCR E8 IDU Mumps Virus culture E8 IDU Mycobacterium spp. Identification, genotyping, drug susceptibility, molecular diagnosis (eg PCR for rapid species identification and detection of resistance genes), molecular epidemiological studies, QuantiFERON®-TB Gold test N1, N4 NMRS-South Mycoplasma M.hominis and Ureaplasma spp.: PCR and/or culture R1 RVPBRU Mycoplasma Mycoplasma and ureaplasma: biochemical characterisation and molecular methods R1 RVPBRU Mycoplasma M. pneumoniae: PCR R1 RVPBRU Mycoplasma M. genitalium: molecular detection of the adhesion MgPa gene B7 AMRHAI Mycoplasma Other species: culture, PCR and sequencing when relevant R1 RVPBRU Neisseria spp. N.gonorrhoeae: confirmation of identification by phenotypic and molecular methods B7 AMRHAI Neisseria spp. Susceptibility testing for third-generation cephalosporin and azithromycin antibiotics B2 AMRHAI Neisseria spp. Molecular confirmation of GC NAAT result B2 CSU Neisseria spp. Programme: Gonococcal resistance to antimicrobials surveillance programme (GRASP) Contact AMRHAI before sending samples AMRHAI Neisseria meningitidis Culture identification, molecular epidemiological studies, PCR, serology Meningococcal reference unit request form MRU Nipah and Hendra viruses PCR, isolation P1 RIPL Nocardia spp. Antimicrobial susceptibility H1, H2 AMRHAI Noroviruses RT-PCR E6 EVU Noroviruses Genotyping E6 EVU Opportunistic Pathogens Molecular typing and antimicrobial resistance H1, H2 AMRHAI Orf Electron microscopy E17 HPU Pandoraea spp. Molecular typing and antimicrobial resistance H1, H2 AMRHAI Parainfluenza virus Virus detection by PCR (sequencing) Contact RVU RVU Parasites, intestinal protozoa and helminths, blood and tissue protozoa and helminths   Contact NPRL NPRL Parvovirus B19 Serology (IgG and IgM) E9 IDU Parvovirus B19 PCR and genotyping E9 IDU Penicillium marneffei   Y1 or Y2 Mycology RL Plasmodium spp.   Malaria report form Malaria RL Polioviruses RT-PCR, genotyping, virus culture E1 EVU Polioviruses Intratypic neutralisation E1 EVU

Polyomavirus JC Serology E13 IDU Polyomavirus JC PCR E13 IDU Polyomavirus JC Intrathecal antibody testing E13 IDU Pseudomonas spp. Molecular typing and antimicrobial susceptibility H1, H2 AMRHAI PVL (see staphylococcus)       Q fever (Coxiella burnetii)   P1 RIPL Rabies exposure Contact rabies clerk on 020 8327 6204     Rabies diagnosis Contact rabies clerk on 020 8327 6204     Ralstonia spp. Molecular typing and antimicrobial resistance H1, H2 AMRHAI Respiratory syncytial virus (RSV) Virus detection by multiplex PCR Contact RVU RVU Resistance mechanisms Molecular detection and confirmation H1, H2 AMRHAI Rickettsiae (typhus and spotted fever groups, scrub typhus group)   P1 RIPL Rhinovirus Virus detection by PCR Contact RVU RVU Rotavirus RT-PCR E1 EVU Rotavirus VP6 and NSP4 genotyping E1 EVU Rubella IgG and IgM serology for recent infection E8 IDU Rubella IgG antibody status E8 IDU Rubella PCR E8 IDU Rubella Virus culture E8 IDU Salmonella Antibiotic susceptibility testing for gram negative GI pathogens L4 GBRU Salmonella Identification and typing L4 GBRU Sapovirus RT-PCR E1 EVU Severe acute respiratory syndrome (SARS) See coronavirus. Contact laboratory prior to collection of specimens E16 RVU Serratia Molecular typing and antimicrobial resistance H1, H2 AMRHAI Shigella Antibiotic susceptibility testing for gram negative GI pathogens L4 GBRU Shigella Identification and typing L4 GBRU Staphylococcus S.aureus: molecular typing H1, H2 AMRHAI Staphylococcus Staphylococcus coagulase negative: species identification and molecular typing H1, H2 AMRHAI Staphylococcus Antimicrobial susceptibility testing H1, H2 AMRHAI Staphylococcus Resistance gene detection H1, H2 AMRHAI Staphylococcus Toxin gene detection (including PVL) H1, H2 AMRHAI Staphylococcus Detection of staphylococcal enterotoxins A, B, C, D or E in foods or beverages. Contact laboratory GBRU Stenotrophomonas S.maltophilia: molecular typing and antimicrobial resistance H1, H2 AMRHAI Streptococcus Streptococcus spp. and related genera or Gram positive cocci: identification R1 RVPBRU Streptococcus S.pyogenes (Lancefield Group A) typing R1 RVPBRU Streptococcus S.agalactiae (Lancefield Group B) typing R1 RVPBRU Streptococcus Lancefield Group C and G typing R1 RVPBRU Streptococcus S. pneumoniae: serological typing R3 RVPBRU Streptococcus Antimicrobial susceptibility H1, H2 AMRHAI Tetanus Tetanus immunity: serum antibodies R3 RVPBRU Toxoplasma gondii Isolation, identification, culture collection, serology (for active infection) molecular diagnostics by PCR Contact toxoplasma reference laboratory, Swansea TRL Treponema T. pallidum (syphilis): serological B3 CSU Treponema T.pallidum, Haemophilus ducreyi, Herpes Simplex Virus (HSV) complex (Genital ulcer disease): PCR B3 CSU Unknown haemadsorbing agents Virus detection by PCR Contact RVU RVU Ureaplasma Refer to mycoplasma R1 RVPBRU Varicella-zoster virus (VZV) IgG serology E11 IDU Varicella-zoster virus (VZV) Intrathecal antibody testing E11 IDU Vibrio (including Plesiomonas shigelloides) Antibiotic susceptibility testing for gram negative GI pathogens L4 GBRU Vibrio (including Plesiomonas shigelloides) Identification and typing L4 GBRU Viral haemorrhagic fever (filoviridae, arenaviridae, Bunyaviridae) Serology, PCR, isolation. Please contact lab before sending samples. P1 RIPL VTEC O157 (See Escherichia coli)       West Nile virus Serology, PCR P1 RIPL Yeasts Serodiagnosis Y1 or Y2 Mycology RL Yellow fever virus Serology, PCR P1 RIPL Yersinia Antibiotic susceptibility testing for gram negative GI pathogens L4 GBRU Yersinia Identification L4 GBRU