Skip to main content

HSL Microbiology Specialities

The Microbiology service is sub-divided into eight key areas throughout the Infection Sciences department across levels 3 and 4 of the Halo building with the aim of developing highly skilled, specialist teams that process specimens according to their pathology.

Level 3

Blood cultures

Blood cultures focuses on the investigation of bacterial and fungal blood infection. Blood cultures bottles are incubated on continuous monitoring culture systems (BacTec FX) based either on site at the local SRA or at the Halo building. Bottles which ‘flag’ positive are removed and processed 24/7 to minimise time to identification and susceptibility results for patient management.

Positive cultures are gram-stained and cultured. In addition, rapid identification of bacterial pathogens direct from the positive blood bottle using MALDI-TOF, within 4 hours of blood culture positivity is performed during daytime shift and positive bottles processed at night have 8-hour rapid culture MALDI-TOF identification the following morning.

All positive blood cultures are communicated to the Microbiology doctors for management. Interim negative blood culture results are reported at 36-hours for paediatric patients, 48-hours for adult patients and final negative results are reported after 5-days incubation.

Mycobacterial and respiratory investigation

Housed in our state of the art containment level 3 laboratories, the CL3 service offers a comprehensive Mycobacterial diagnostics service.

Our service includes auramine smear microscopy, with a 24-hour turnaround from the time the sample arrives at the Halo, and rapid PCR testing to detect M. tuberculosis complex and Rifampicin resistance.

The mainstay of detection is mycobacterial culture, from specimens including blood, tissue, early morning urine (EMU; minimum 60ml) and respiratory samples. Mycobacteria isolates are first examined with MPT64 rapid antigen testing for the preliminary identification of MTB; Isolates are then referred to the Mycobacterial Reference Laboratory (MRL) for full identification and susceptibility testing.

The routine culture of specimens for Mycobacterium species is primarily carried out through MGIT liquid broth automated culture. After careful clinical review, the laboratory service has discontinued Löwenstein– Jensen (LJ) agar slope culture on all specimens.

The following lists detail the specimens which will have a LJ agar slope culture carried out in addition to the routine MGIT liquid broth automated culture:

  • Supplementary LJ slope culture at 30°C, incubated for 8 weeks:
    • All skin biopsies
    • Any specimen where clinical details indicate possible M. marinum infection
  • Supplementary LJ slope culture at 37°C, incubated for 8 weeks:
    • Any specimen which is positive on Mycobacterium tuberculosis PCR direct from specimen
    • Any specimen which is positive on auramine stain direct from specimen
    • All lung and pleural biopsies
    • On clinical request via laboratory communication or through clinical details provided with the specimen. For LJ slopes to be set up, the request needs to specify the clinical reasons why extended Mycobacterial culture is required.

Negative mycobacterial cultures are reported after 6-weeks incubation. Routine respiratory culture is performed for the detection of respiratory pathogens, and PCR for the investigation of atypical Pathogens (Legionella pneumophila, Mycoplasma pneumoniae and Chlamydia pneumoniae) is available.

If you wish to request supplementary LJ slope culture at 37°C please contact the laboratory.



Automated culture of swab specimens using twin Kiestra total laboratory systems. The automated microbiology section offers a comprehensive bacteriology service processing ENT, wound, genital, orthopaedic/ staphylococcal screen swabs and other clinical swab specimens.

The molecular service also performs PCR for the detection of the Panton Valentine Leukocidin toxin gene from Staphylococcus aureus isolates on clinical request.

Please note: culture for Trichomonas vaginalis from genital swabs has been discontinued due to unavailability of reagents. Analysis is performed by direct microscopy and is limited to swabs from non-GUM settings with appropriate clinical details including: pregnancy, STI screen or Trichomonas vaginalis infection.

In view of the low sensitivity of direct microscopy compared with culture or PCR a negative microscopy result should be interpreted with caution. Please consider TV PCR testing if clinically indicated.

Tissue, fluids and specialist microbiology

Investigation of sterile specimens including: tissue, bone, CSF fluids and prosthetic material. The specialist service offers semi-quantitative and quantitative microscopy’ synovial fluid crystal analysis and enrichment culture for all sterile fluids using BacTec broth continuous monitoring culture. Prosthetic joint specimens will undergo prolonged enrichment culture for 14 days, but only if the clinical details alert the laboratory to the presence of prosthetic material. If these details are not provided, routine 5-day enrichment culture will be applied.

Level 4


The service provides investigation of non-travel related diarrhoeal infections using the EntericBio multiplex PCR for Salmonella, Shigella, Campylobacter, STEC, Giardia and Cryptosporidium, with culture follow-up of positive Salmonella, Shigella and STEC specimens. Travel-related diarrhoeal pathogens are tested using culture techniques for bacteria and microscopy for ova, cysts and parasites, Clostridium difficile using PCR screening assay followed by toxin EIA detection on all positive PCR samples.

The enterics service also includes the detection of Helicobacter pylori antigen.


Our UK Clinical Mycology Network regional laboratory provides culture, serological and molecular diagnostics. The service offers PCR, microscopy and culture for the investigation of superficial fungal infection, identification and susceptibility testing of clinically significant yeasts, routine (7-day) and extended (21-day) fungal culture from clinical specimens. The serology service provides TDM for triazoles, Galactomannan antigen detection, 1-3-β-d- glucan detection, Cryptococcal antigen by LFD and the detection of Histoplasma antigen from urine. The molecular mycology service offers Pneumocystis jirovecii PCR, Candida PCR by T2MR and Aspergillus PCR.

Healthcare-associated infection

Processing of routine screening specimens for MRSA, carbapenemase-producing organisms (CPO) and vancomycin-resistant enterococci (VRE) as well as bespoke screening for outbreak management. The service offers rapid molecular MRSA detection for high-risk in-patients, culture screening for multi-drug resistant bacteria including: MRSA, CPO and VRE. A rapid response service is available for potential outbreak of infections via liaison with the laboratory.

Urine investigation

Routine and complex urinary pathology investigation. The service offers automated and manual microscopy, culture, identification and susceptibility testing. Urine antigen test for legionella and pneumococcal antigen is available. A specialist urine service includes the analysis of sequential urine samples and prostatic secretions in the diagnosis of prostatitis and other complex genitourinary samples including VBU specimens, and invasive urine samples such as suprapubic aspirates and ureteric urine.