Microbiology
The microbiology department provides a comprehensive service encompassing the diagnosis, treatment, prevention and control of bacterial, fungal and parasitological disease. With over 100 staff, including consultants, junior medical staff, biomedical scientists, clinical scientists, laboratory assistants and administrative staff, it provides a high quality and comprehensive diagnosis, monitoring and disease management service to our clinical colleagues and their patients.
Biomedical scientists in the department undertake a wide range of tests including pathogen identification and antimicrobial susceptibility. Please see the User Manual for details of the full repertoire of tests offered and sample requirements.
The medical microbiology team of consultants and specialist registrars are available 24 hours a day to provide clinical advice around patient management and result interpretation. The microbiology department collaborates closely with the infection prevention and control team, in the surveillance, control and prevention of infection in both secondary care and the local community. Teaching, training, audit, research and development are all actively pursued within the department.
There is a microbiology service provided across the Barts Health NHS Trust, Homerton Healthcare NHS Foundation Trust and Lewisham and Greenwich NHS Trust. Please see the user handbooks provided for more information on these services.
Alternatively refer to our Test A-Z.
We have also compiled a FAQ page that set outs some answers to the most frequent questions that come through to the infection team. See the accordian at the bottom of this page.
Please visit UKAS.com for information on the accredited tests or refer to the schedules of accreditation provided below for UKAS number 8285.
For quick and easy treatment guidance following local policies, visit Eolas Medical. The application can also be downloaded onto your smartphone by searching Eolas Medical and selecting the relevant trust.
The Barts Health Microbiology service can be contacted using this email address: microbiology.bartshealth@nhs.net.
Antimicrobial susceptibility
Antimicrobial susceptibility testing guides clinicians in their choice of antimicrobial therapy. Results of susceptibility testing are reported when there is a reliable correlation between the results of in vitro susceptibility tests and clinical outcome.
Since 2002, susceptibility testing reports used the terms ’susceptible’(S), ‘intermediate’ (I) and ‘resistant’ (R) to classify the likely outcome if the organism is treated with a specific antibiotic. Susceptibility tests reported as ‘intermediate’ tended to be interpreted by clinical teams to mean ‘We are not really sure if this bug is susceptible to this antibiotic, so probably safest not to use it’. In light of this ambiguity, the definitions of S, I and R have been updated to S, D and R.
The updated term ‘D’ is meant to be more directive, and indicates that the organism is susceptible , but that a higher than standard dose of antibiotic is needed.
For further information, including a list of High-dose antibiotic regimens please refer to the Barts Health MicroGuide App (EUCAST 2021 changes to antibiotic susceptibility reports and dosing recommendations). The MicroGuide App is free to download from the App Store or from GooglePlay. MicroGuide can also be accessed from the Trust Intranet in the Medicines Management Guidelines
section.
Further information around the rationale for the changes in susceptibility reporting can be found on the website of the European Committee for Antimicrobial Susceptibility Testing (EUCAST, https://www.eucast.org/newsiandr/)
Microbiology FAQs for Healthcare Professionals
Urine Samples
URINE
Why wasn’t the urine sample set up for culture?
Urine MC&S samples received from primary care are set up for culture if microscopy detects elevated numbers of white blood cells as well as bacterial cells (both must be elevated). Urine MC&S samples received from secondary care are set up for culture if microscopy detects either elevated numbers of white blood cells or bacterial cells. The cut-offs defining abnormal cell counts are as follows: white blood cells >= 30 x10^6/L, bacterial cells >=500 x10^6/L.
Urine samples will be set-up for culture, irrespective of the microscopy result, if the patient is <=3 years old, if the sample is from a nephrostomy or supra-pubic aspirate or if the clinical details indicate that the patient is pregnant.
The rationale for this testing approach takes into consideration optimal use of resources and over-sensitivity of urine culture potentially leading to unnecessary antibiotic treatment.
The white cell count and bacterial count are both expected to be elevated in a patient with a UTI. The thresholds for setting up culture are based on both published literature and local verification. As all tests and testing algorithm have limitations, some urine samples may not be cultured in the presence of a true UTI with these thresholds. In the local validation exercise, this was around 5% of samples.
What are the reference ranges / normal values for urine microscopy and culture?
Cut-offs for abnormal urine microscopy are as follows:
white blood cells >= 30 x10^6/L
bacterial cells >=500 x10^6/L
red cells >=40 x10^6/L
epithelial cells >=50 x10^6/L
What is considered significant bacterial growth in the urine?
In the relevant clinical context, a bacterial count of ≥10*7 CFU/L is indicative of an infection. Counts below this usually indicate contamination but may be significant in specific patient groups or clinical scenarios. A positive culture does not necessarily represent the presence of infection. Please correlate the culture result with the clinical picture.
The red cell count in the urine sample is elevated – what does this mean / what should I do?
Urine MC&S should only be requested as part of the diagnostic evaluation for urinary tract infection. There are occasions when the urine is clear of infection, but other abnormalities are detected, such as an elevated red blood cell count on urine microscopy.
There are no fixed national guidelines for the acceptable range for red blood cells (RBC) present in urine. This is primarily due to the number of factors that can cause transient haematuria that could be misleading, for example exercise trauma, anticoagulant treatment, or taking ibuprofen
The urinary red cell count does not play a role in the diagnosis of urinary tract infection. A urine dipstick should be undertaken to confirm the presence of absence of haematuria. Urine dipsticks are a rapid and relatively sensitive (>80%) method for detecting haematuria in a freshly voided sample of urine.
What does an elevated number of epithelial cells in the urine sample indicate?
This may be an indicator of contamination due to poor collection technique. Suggest repeat if clinically indicated ensuring a mid-stream sample, if possible.
There is mixed growth in the urine culture. How should this be interpreted?
If a mixture of bacteria have been identified on culture, this is most likely to represent sample contamination or urine catheter colonisation. If the patient is symptomatic or pregnant, a repeat urine sample should be sent, with strict adherence to good sample collection technique.
There is bacterial growth in a catheter urine sample. How should this be interpreted?
All urinary catheters become colonised by bacteria. A positive urine dipstick, microscopy or culture is NOT an indication for treatment in the absence of clinical suspicion of catheter-associated UTI e.g. fever, elevated CRP, raised WBC etc.
Please note that suprapubic catheters are less prone to contamination and positive results are more likely to be significant.
When antibiotics are prescribed for suspected catheter-associated UTI changing the catheter is also recommended.
A urine MC&S has come back with a positive culture, but the patient has no symptoms – what should I do?
Asymptomatic bacteriuria (ABU) is defined by a mid-stream sample of urine showing bacterial growth >10*8 cfu/L in an individual without urinary tract symptoms. ABU is common, and corresponds to a commensal colonisation, and does not cause renal disease or damage. Asymptomatic bacteriuria only requires treatment if the bacterial growth is >10*8 cfu/L and the patient is either pregnant or is due to have a urological procedure that breaches the urothelial mucosa.
Management of asymptomatic bacteriuria in pregnancy should be discussed with the patient’s midwife team. If a urine sample from a pregnant patient is reported as growing Group B streptococcus, then the patient’s midwife team should be informed, as this result should trigger the use of prophylactic antibiotics during labour, to prevent early onset neonatal sepsis.
Resources:
https://www.nice.org.uk/guidance/ng109/chapter/Recommendations#managing-asymptomatic-bacteriuria
A urine MC&S has come back with a positive culture with an organism that is resistant to all oral agents – what should I do?
Consider contacting your local microbiology team.
Examples of resistant organisms are bacteria that produce enzymes such as ‘ESBL’ and ‘AmpC’, which can break down B-lactam antibiotics such as penicillins and cephalosporins. In most cases, these bacteria will still remain susceptible to first line agents such as Nitrofurantoin.
Contact your local microbiology team to discuss options for treatment if needed. In some cases, a repeat urine sample may be suggested based on the clinical details.
A urine MC&S has detected pseudomonas. How should this be managed?
In the absence of urinary catheters/stents or abnormal urinary tract anatomy, pseudomonas is not a common a cause of urinary tract infection. Please consider whether there are significant numbers of white blood cells, bacterial cells and bacterial growth, as well as patient’s symptoms. In some cases, a repeat urine sample may be helpful. Contact your local microbiology team to discuss options for treatment if needed.
A patient’s urine sample has an elevated white cell count, but no bacterial growth – what can cause this and what should I do?
Sterile Pyuria (ie no growth on routine culture media and the persistent presence of white blood cells in the urine) may be the result of many factors including: a result of prior treatment with antimicrobial agents; catheterisation; calculi (stones); or bladder neoplasms. Other conditions which may lead to sterile pyuria include genital tract infection; sexually transmitted diseases, e.g. C. trachomatis or an infection with a fastidious organism. Renal tuberculosis may also be implicated in sterile pyuria but is uncommon, although should be considered if clinically indicated (e.g. in high risk populations). Consider testing for Chlamydia and Gonorrhoea if there is a relevant sexual history.
I have given a patient antibiotics for a UTI – do I need to send a repeat urine for MC&S to check that the infection has gone?
Routine post-treatment urinalysis or urine cultures in asymptomatic patients are not indicated. In patients whose symptoms do not resolve by end of treatment, and in those whose symptoms resolve but recur within two weeks, urine culture and antimicrobial susceptibility testing should be performed.
Where can I find advice around which antibiotics to use to treat a UTI ?
Please follow local and national guidelines
Local
National
https://www.gov.uk/government/publications/urinary-tract-infection-diagnosis
https://www.nice.org.uk/guidance/ng109
Where can I find advice around managing a patient with recurrent UTIs ?
Management of recurrent urinary tract infection can be challenging. Consider discussing with your local microbiology team; as well as relevant teams such as urology and urogynaecology. In many cases, treating recurrent UTIs will require treatment of an underlying condition such as stasis, obstruction, prolapse, atrophic vaginitis etc. Optimal control of other conditions such as diabetes is also important. Therefore, a holistic approach is needed.
I have done a dipstick test which is abnormal – do I need to send a sample for culture
If the patient does not have any symptoms suggestive of a UTI, then there is no need to send a sample for culture. For example, if a dipstick test was done as part of a regular check up for a patient with diabetes or hypertension, and it has detected nitrites and/or leucocytes, but the patient has not symptoms, then there is no need to send a sample for culture.
In patients with long-term urinary catheters, the catheter tubing invariably becomes colonised with bacteria from the perineum. A dipstick from a long-term urinary catheter will almost always be positive for leucocytes and/or nitrites. If the patient does not have any symptoms suggestive of a UTI, then there is no need to send a sample for culture.
Stool / Faeces / Enteric samples
STOOL / FAECES / ENTERIC
What faecal pathogens are tested for in the stool sample?
A standard ‘faeces MC&S’ request will test for the following bacteria by PCR: Salmonella, Shigella, Enteroinvasive E.coli, Campylobacter and E.coli/Shigella dystenteriae which produces Shigatoxins. If the PCR is positive, this will be followed up routinely by culture and sensitivity in all cases except Campylobacter. There is an extended panel that includes PCerner/iCare for other organisms such as Vibrio, Plesiomonas and Yersinia; as well a separate panel for parasite PCerner/iCare such as Cryptosporidium and Giardia. The extended panel can be tested if relevant clinical details are mentioned (e.g. travel history) or the test is specifically requested.
Please note a separate stool sample should be sent for C.diff testing, stool microscopy for ova, cysts and parasites and viral pathogens.
I have received a result reporting detection of Campylobacter – what do I need to do?
Notify your local Health Protection team by phone if any of the following:
1: the case is part of a possible outbreak
2: the patient is a food handler
Gastrointestinal infections by Campylobacter are usually self-limiting. Consider antibiotic treatment if:
1: severe symptoms - incapacitating diarrhoea, very bloody stools, high fever, systemically unwell, requiring hospital admission
2: protracted symptoms
3: extremes of age
4: immunocompromised patient
For treatment options, refer to your local antibiotic guidelines. Contact your local infection team for advice if required.
I have received a result reporting detection of Shigella – what do I need to do?
Notify your local Health Protection team by phone if any of the following.
1: a non-sonnei Shigella species (S. flexneri/boydii/dysenteri) is identified by culture
2: the case is part of a possible outbreak
3: the patient is a food handler
Gastrointestinal infections by Shigella are usually self-limiting.
Consider antibiotic treatment if:
1: severe symptoms - incapacitating diarrhoea, very bloody stools, high fever, systemically unwell, requiring hospital admission
2: protracted symptoms
3: extremes of age
4: immunocompromised patient
For treatment options, refer to your local antibiotic guidelines. Contact your local infection team for advice if required.
I have received a result reporting detection of VTEC/STEC E coli – what do I need to do?
Verotoxin (VT) is a toxin produced by some Shigellae species and some strains E.coli (including O157). VT may cause Haemolytic Uraemic Syndrome (HUS) & other complications (mostly in children < 5 years old).
Notify your local Health Protection team by phone if any of the following:
1: VT-producing E coli is isolated from culture (the initial result will be a PCR result)
2: HUS is clinically suspected (marked abdominal pain, bloody diarrhoea, acute renal failure, thrombocytopenia, anaemia)
3: there is bloody diarrhoea
4: the patient is linked to a known case of HUS
5: the patient is an in-patient or requires hospital admission
Diarrhoea caused by a VT-positive organism or confirmed E.coli O157/O104 is usually self-limiting. Anti-motility agents and antibiotics are not recommended. Antibiotics may trigger HUS. Severe bloody diarrhoea or marked abdominal pain are signs of HUS and require specialist assessment. Contact your local infection team for advice if required.
I have received a result reporting detection of Salmonella – what do I need to do?
Notify your local Health Protection team by phone if any of the following:
1: the clinical presentation is consistent with enteric fever (typhoid)
2: S. typhi or S. paratyphi is identified by culture
3: the case is part of a possible outbreak
4: the patient is a food handler
Gastrointestinal infections by non-typhoidal Salmonella are usually self-limiting. Consider antibiotic treatment if:
1: severe symptoms - incapacitating diarrhoea, very bloody stools, high fever, systemically unwell, requiring hospital admission
2: protracted symptoms
3: extremes of age
4: immunocompromised patient
For treatment options, refer to your local antibiotic guidelines. Contact your local infection team for advice if required.
Where can I get advice about interpreting a C diff result ?
Testing for Clostridium difficile is a multi-step process.
C.difficile infection (CDI) is caused by toxin produced by C.difficile bacteria. However, not all C.difficile bacteria are capable of producing toxin.
The first part of the test looks for the ‘GDH’ antigen, which is present in all C.difficile bacteria. If this is positive, then a PCR test, which looks for the presence of the toxin gene; and a toxin test, which looks for toxin production itself, are carried out.
Treatment should be given when there is evidence of toxin production (i.e. a positive toxin test). Treatment can be considered in some cases when the PCR is positive and the toxin is negative, based on clinical suspicion of CDI and/or if the patient is at high risk of getting CDI. This should be discussed with the local infection team.
The comment on the report should outline how the results should be interpreted and whether or not treatment is indicated. If questions remain, contact your local infection team for advice.
Infection control measures should be initiated straightaway on suspecting CDI and not wait until positive result.
For more information on managing C.diff, please see NICE guidance:
https://www.nice.org.uk/guidance/ng199/chapter/Recommendations
Why has the stool sample been rejected for C.diff testing?
The sample will not be processed for C.diff if a repeat sample is sent too soon – for example, if there was a stool result with a negative GDH in the last 3 days or a positive PCR or toxin result in the last 28days.
Sputum samples
SPUTUM / RESPIRATORY
I think a patient may have Whooping cough – what sample(s) should I send?
What tests to send
The recommended test(s) for pertussis vary according to the length of time since cough onset:
· less than 2 weeks from cough onset – PCR
· between 2 and 3 weeks from cough onset – PCR and either oral fluid kit (if aged 2 to <17 years) or serology
· more than 3 weeks from cough onset – either oral fluid kit (if aged 2 to <17 years) or serology
How to request
· PCR – CERNER/ICARE request is ‘Bordetella pertussis DNA detection”
· Serology – CERNER/ICARE request is “Bordetella Pertussis Antibody” or “Whooping cough Serology”
· Oral fluid - kit supplied by local Health Protection Team following notification and discussion of the case (no need to request on CERNER/ICARE)
When making the request, please include information including symptoms duration and pertussis vaccine history in the clinical details
Details of swabs for PCR testing
Throat swab
Collect using a bacterial swab with liquid transport medium (purple-topped swab containers), or use a viral swab (green or red-topped tubes)in universal or viral transport medium (Figure 1). Please DO NOT use swabs with gel or charcoal in the swab container.
Please note that which a throat swab is an easier sample to take, the sensitivity is lower compared to when a pernasal / nasopharyngeal swab is used. See below for information re pernasal / nasopharyngeal swabs.
Resources:
UKHSA guidance re management of cases
https://www.gov.uk/government/publications/pertussis-guidelines-for-public-health-management
UKHSA guidance re testing
Bacteria have been cultured from a sputum sample – is treatment required?
The purpose of sputum culture is to identify bacteria causing pneumonia or lower respiratory tract infection. However, when collecting sputum, bacteria that are normally found in the throat or mouth may contaminate the sample. The presence of some bacteria such as coliforms/gram negative bacteria in sputum may represent oral, or upper airway contamination. Antibiotic therapy is only indicated in the presence of clinical signs of pneumonia, including exacerbations of COPD/ bronchiectasis, in bacterial infection is felt clinically likely .
The presence of Staphylococcus aureus, including MRSA, may represent upper airway contamination. Antibiotic therapy is only indicated in the presence of clinical signs of pneumonia.
Candida has been cultured from a sputum sample – is treatment required?
If candida is found in the sputum sample, this usually means that the sputum sample has been contaminated by bacteria normally found in the mouth or upper respiratory tract. True candida lower respiratory tract infection is rare and requires histopathologic evidence to confirm a diagnosis. Antifungal therapy based solely on this result is not recommended.
Skin/ Wound / Swab Samples
SKIN / WOUNDS / SWABS
Bacteria have been cultured from a wound swab or skin swab – is treatment required?
Wound infection or skin & soft tissue infection is a clinical diagnosis and should not be based on microbial growth from a surface swab. Wound swabs are poorly predictive of the underlying microbial aetiology of infection. Bacteria cultured from the surface of the skin or wound usually reflect contamination of skin surfaces; either picking up normal skin bacteria or bacteria that replace the normal skin flora after antibiotic treatment. Often, these organisms are not the ones causing infection in deeper layers of tissue. For more accurate diagnosis, please send tissue or pus samples.
Staphylococcus aureus may be part of normal flora. Antibiotics should only be prescribed if clinically indicated (for example, a clinical diagnosis of skin/soft tissue infection). If MRSA is isolated, then consider prescribing MRSA decolonisation as per local guidelines.
Treatment is recommended if Group A Strep (Streptococcus pyogenes) is isolated as it can cause invasive infection and treatment is recommended. Please refer to local guidance. Please note that scarlet fever is a clinical diagnosis which requires notification, by the assessing clinician, to your local Health Protection Team.
Pseudomonas aeruginosa is widespread in moist environments and its isolation from wound swabs often represents colonisation only.
What is the relevance of PVL toxin
Staphylococcus aureus can produce an array of toxins, including Panton Valentine Leukocidin (PVL). Production of PVL is epidemiologically associated with a clinical pattern of recurrent boils and abscesses. However, other toxins can also produce the same clinical picture. Decision-making around antibiotic use and/or decolonisation should be made on the basis of the clinical presentation, and not the presence or absence of a single toxin.
Patients with recurrent or severe skin and soft tissue infections should be treated as if they are infected with a virulent, toxin-producing strain of Staphylococcus aureus. They should receive antibiotic that interfere with toxin production. Optimal treatment (including decolonisation of the patient and their household contacts) will depend on the type of infection and on any microbiology results – please consider discussing patients presenting with recurrent skin & soft tissue infection with your local infection team. If decolonisation therapy is clinical indicated then refer to local MRSA decolonisation guidelines (even if the isolate is methicillin-susceptible).
Ears/ Nose/ Throat Samples
EARS , NOSE & THROAT
Bacteria have been cultured from an ear swab– is treatment required?
Organisms isolated from external ear swabs may just reflect colonising flora.
Many cases of otitis externa recover after thorough cleansing of the external ear canal by suction, or dry mopping. Acetic acid 2% acts as an antifungal and antibacterial in the external ear canal & is used to treat otitis externa. In severe cases a topical anti-inflammatory preparation +/- a topical infective drug is required.
If malignant / necrotising otitis externa is suspected then URGENT referral to ENT is recommended.
Group A strep has been isolated from a throat swab – do I need to treat and/or notify?
Streptococcus pyogenes (Group A strep) has the potential to cause severe infection and to transmit from person-to-person, so isolation of Group A strep from a throat swab usually warrants treatment. If treating with penicillin (or amoxicillin), a 10-day course is usually advised, to maximise the chance of eradication of pharyngeal carriage.
Streptococcal pharyngitis is not a notifiable infection, but Scarlet Fever is. If there is clinical suspicion of Scarlet Fever, please notify the patient’s local Health Protection Team.
GUM and Vaginal Samples
GUM / VAGINAL
Candida has been cultured from a vaginal swab – is treatment required?
Candidal vulvovaginitis is a clinical diagnosis. Candida is part of normal vaginal flora and isolation of Candida species from a vaginal swab does not necessarily mean that the patient has an infection. Please interpret the growth of Candida in light of clinical symptoms and signs.
Management of recurrent or recalcitrant candidal vulvovaginitis can be a challenge, consider referral to a Genito-urinary medicine service.
Hair and Nail Samples
HAIR & NAIL
A fungus has been cultured from a nail clipping sample – is it relevant?
Pathogenic fungi commonly known to be associated with oncychomycosis include:
Trichophyton species (e.g. rubrum, interdigitale, mentagrophytes
Epidermophyton floccosum and Microsporum species.
Examples of nondermatophyte moulds found in ο ո уϲhοmусοѕiѕ include Fusarium, Aspergillus, Alternaria, Acremonium, Scytalidium/ Neoscytalidium, and Scopulariopsis brevicaulis.
Candida species can cause onychomycosis, including Candida albicans, guilliermondii, parapsilosis tropicalis.
This list is not exhaustive, and other fungal species may cause infection.
Some fungal species, including Aspergillus and Penicillium, can colonise abnormal nails, and can cause contamination of fungal cultures in the laboratory, and so growth from a nail clipping does not necessarily mean that the organism that has been isolated is causing the problem.
Agents causing tinea capitis and tinea corporis / cruris may also be encountered in the fingernails of individuals with scalp or skin infection – for example including M. audouinii, M. canis, T. mentagrophytes, T. rubrum, T. tonsurans, T. soudanense, T. violaceum.
Mycology microscopy and culture has limited sensitivity, and so absence of fungal elements on microscopic examination and lack of fungal growth on culture does not preclude the diagnosis of fungal infection, and antifungal should be considered if the clinical presentation suggests fungal infection, even if the mycological work-up is negative.
Useful references
British Association of Dermatologists: clinical guideline: https://pubmed.ncbi.nlm.nih.gov/25409999/
British Association of Dermatologists: patient information leaflet: https://cdn.bad.org.uk/uploads/2021/11/19174043/Fungal-nail-infections-June-2023.pdf
A fungus has been cultured from a hair sample – is it relevant?
Pathogenic fungi commonly known to be associated with tinea capitis include:
Microsporum canis, Microsporum audoinii, Trichophyton tonsurans, Trichophyton soudanense, Trichophyton verrucosum, Trichophyton violaceum
This list is not exhaustive, and other fungal species may cause infection.
Some fungal species, including Aspergillus and Penicillium, can cause contamination of fungal cultures in the laboratory, and so fungal growth from a hair sample does not necessarily mean that the organism that has been isolated is causing the problem.
Mycology microscopy and culture has limited sensitivity, and so absence of fungal elements on microscopic examination and lack of fungal growth on culture does not preclude the diagnosis of fungal infection, and antifungal should be considered if the clinical presentation suggests fungal infection, even if the mycological work-up is negative.
Useful references
British Association of Dermatologists: clinical guideline: https://pubmed.ncbi.nlm.nih.gov/25234064/
British Association of Dermatologists: patient information leaflet:
https://cdn.bad.org.uk/uploads/2023/05/19174107/TINEA-CAPITIS-MAY-2023.pdf
A fungus has been cultured from a skin scraping – is it relevant?
Pathogenic fungi commonly known to be associated with fungal skin infection include::
Trichophyton. mentagrophytes, Trichophyton erinacei, Trichophyton verrucosum, Trichophyton rubrum, Trichophyton tonsurans, Trichophyton soudanense, Trichophyton violaceum, Microsporum audouinii, Microsporum canis, Microsporum persicolor, Epidermophyton floccosum.
This list is not exhaustive, and other fungal species may cause infection. There is some association between the anatomical location of the skin lesions and the likely causative fungal pathogen. For example, tinea of the palms and soles (manuum and pedis respectively) is more likely to be due to T. rubrum, whereas tinea affecting the beard area is more likely to be due to T. mentagrophytes,
Some fungal species, including Aspergillus and Penicillium, can cause contamination of fungal cultures in the laboratory, and so fungal growth from a hair sample does not necessarily mean that the organism that has been isolated is causing the problem.
Mycology microscopy and culture has limited sensitivity, and so absence of fungal elements on microscopic examination and lack of fungal growth on culture does not preclude the diagnosis of fungal infection, and antifungal should be considered if the clinical presentation suggests fungal infection, even if the mycological work-up is negative.
There is an epidemic of tinea infection due to Trichophyton species that are resistant to terbinafine. Please discuss all cases of recurrent, recalcitrant or refractory tinea infection with your local dermatology team and local infection team.
How to obtain Dermatophyte Collection Kits
Dermatophyte Collection Kits (e.g. MycoTrans) are helpful for sampling and transport of samples for mycological investigation, including skin scrapings, hair sample and nail clippings. Collection kits can be ordered from Pathology Reception at the Royal London Hospital using the GP pathology stock order form (the same form is used for blood tubes, urine containers etc) and write on the form the number of MycoTrans collection kits required.
Lyme Disease
Lyme disease
For questions related to Lyme disease, please see the following useful references
UKHSA: https://www.gov.uk/government/collections/lyme-disease-guidance-data-and-analysis
NICE: https://www.nice.org.uk/guidance/ng95
In addition, please contact your local infection team (See ‘Who to Contact’ section).
Who to contact
Please see the Microbiology User Guide on the ESEL Pathology Partnership website https://www.eselpathology.nhs.uk/microbiology
Operations leads e.g. for queries re pending results & requesting additional tests
Phone 020 324 60308 or 60307
Email microbiology.bartshealth@nhs.net
The microbiology.bartshealth@nhs.net includes scientific and operation leads: Susan Benson, David Ball, Natalie Marshall and Nathan North
Other useful numbers - microbiology
Duty senior mobile: 07709 523 438 (in-hours and out of hours)
RLH switchboard 0207 377 7000
Microbiology clinical teams by borough (in-hours)
Tower Hamlets & City of London 07710 920866
Newham 07887 856 174
Waltham Forest 07756 882 796
City & Hackney HUH duty microbiologist: 07623 986 285, 0208 510 7181 or 4736
Lewisham & Greenwich QEH site clinical queries: 0208 836 6000 Ext 65697
UHL site clinical queries: 0208 836 6000 Ext 33256
Virology
Email results.virology@nhs.net (Mon-Fri, 9 a.m-5 p.m)
Phone 0203 246 0364 (Mon-Fri, 9 a.m-5 p.m)
For out of hours queries, go through the hospital switchboard
For any comments, corrections or suggestions regarding the content of this page, please email Jonathan.lambourne@nhs.net (Consultant Microbiologist, Barts Health NHS Trust)