Important updates and changes in Microbiology

In line with new European reporting requirements, the microbiology laboratory report susceptibility results in three categories: S, I or R.

 For some bug-drug combinations, there is no "S" category. Susceptibilities will be reported as either "I" or "R".

·         "S" = susceptible at a standard dosing regimen.

This means there is a high likelihood of therapeutic success using standard doses and dosing intervals.

·         "I" = susceptible at increased drug exposures.

This means there is a high likelihood of therapeutic success if antibiotic exposure is optimised by using higher doses or increasing dosing frequency.
Click here for recommended doses and frequency for organisms with "I" susceptibility.

·         "R" = resistant.
This means there is a high likelihood of therapeutic failure using this antibiotic.

For paediatrics where susceptibilities are reported as "I" and a dosing range is given in the BNFc, the dose at the higher end of the range should be used.

These doses are for adults with normal renal function. For patients with renal impairment, use the maximum safe doses for the patient’s CrCl, discussing with a pharmacist if necessary.

​Organism	​Drug and Dose	​Dosing interval
​E.coli, Proteus mirabilis, Klebsiella pneumoniae and other coliforms (Enterobacterales group)	​Cefuroxime 1.5g IV	​Three times a day
​Pseudomonas aeruginosa	​Piperacillin tazobactam 4.5g IV Ceftazidime 2g IV Aztreonam 2g IV Ciprofloxacin 750mg PO Ciprofloxacin 400mg IV	​Four times a day Three times a day Four times a day Twice a day Three times a day
​ Streptococci groups A, C and G And Streptococcus pneumoniae	​Levofloxacin 500mg PO/IV	​Twice a day
​Staphylococcus aureus	​Ciprofloxacin 750mg PO Ciprofloxacin 400mg IV   Clindamycin 450-600mg PO Clindamycin 600-1200mg IV	​Twice a day Three times a day   Four times a day Four times a day
​Haemophilus influenzae	​Amoxicillin 1g TDS PO Amoxicillin 2g TDS IV   Co-amoxiclav 625mg PO prescribed with Amoxicillin 500mg PO   Co-amoxiclav 1.2g IV prescribed with Amoxicillin 1g IV	​Three times a day Three times a day   Three times a day     Three times a day

Female genital samples that are received in the department have a set of default tests performed which include; culture for Candida species and Neisseria gonorrhoea/microscopic detection for Trichomonas vaginalis and if of child bearing age microscopic detection of clue cells an indicator of bacterial vaginosis. Other bacterial pathogens will be investigated dependant on patients demographics or documented clinical details. The department separately reports on Trichomonas and clue cells and a separate report on culture is issued with a standard report “No pathogens isolated” for negative bacterial cultures.

Following a recent audit the department has decided to improve its culture reporting and now issues two negative culture reports based on the investigations performed:

• Neisseria gonorrhoea and Candida not isolated – for samples that only have the default  investigations performed
• No pathogens isolated – for samples that have had the default investigations as well as additional pathogens based on clinical information supplied.

Please note: Chlamydia testing is a separate molecular test that will be reported on a separate report if tested.

From April 2020, The Department of Microbiology will be strictly enforcing the Trust policies and procedures (Sample acceptance in Pathology laboratories procedure - CL/CGP/049 & Request and Specimen labelling policy – CL-CGP/018) on the minimum number of patient identifiers required and will reject any specimens that do not meet this requirement.

RE: Change of collection device for Chlamydia trachomatis and Neisseria gonorrhoeae molecular (NAAT) testing

The Department of Clinical Microbiology is always seeking ways to improve the services we offer.  We are in the process of implementing a new molecular NAAT’s test for Chlamydia trachomatis and Neisseria gonorrhoeae. The new system will help to improve the efficiency within our laboratory and ultimately improve the time taken to generate a patient result.  In order to take full advantage of the efficiency of the new Abbott Alinity m System, we will require you to start using a different collection kit.

From the 10^th August the specimen collection kit that will be sent out for Chlamydia trachomatis and Neisseria gonorrhoeae molecular (NAAT) testing will be the Alinity m multi-Collect Specimen Collection kit (Product number: 09N19-001), see pictures below.  

image

Kit as it will be received

Picture showing contents of kit

 

The benefit of the new kit is it is one collection kit for male and female samples. The kit contains a transfer pipette for adding approximately 2.1 ml of urine to the transport tube, urines should be added until the liquid falls within the fill window on the tube label, and an individually packaged sterile specimen collection swab that is placed into the transport tube, utilising the breakpoint on the shaft, after swab sampling. This swab can be either self-taken by the patient or taken by the clinician.  Do not place multiple swabs or a combination of swab and urine in the transport tube.  The transport tube contains 1.35 ml of specimen transport buffer and is used to stabilize DNA until sample preparation.  After collection, transport and storage conditions should be between 2°C to 30°C for up to 14 days.

Please see the product information that has been included with this communication for details on specimen collection procedures and use the new Alinity m multi-Collect Specimen Collection kit.

Please note due to this change any swabs requiring MC&S for bacterial culture MUST now be sent on a separate request form as these are no longer processed within the same laboratory as the Chlamydia/Gonorrhoea NAAT samples.

The current BD swabs (Self Taken Product code: 441122, Male urethral swab Product code: 441358, Female endocervical swab Product code: 441357) and also urine samples in plain universals will no longer be accepted for testing after the 1^st September and the new collection device must be used. If you have remaining stocks of any of the above BD swabs then please return to the Microbiology Department at QMC.

If you had previously been using the BD swabs for taking samples for Herpes Simplex Virus testing, then you will now need to use the viral transport media (VTM) kits.  The current VTM being supplied by Pathology is the green top swab kits by Medical Wire (Product code: MW951S).  This may be subject to change as all VTM is currently being nationally supplied and therefore this may be subject to change with no notice.

Thank you for your co-operation and if you have any questions regarding the transition, please do not hesitate to contact the department on Ext: 64950.

Alinity Multi-Connect Specimen Collection Kit instructions[pdf] 1010KB