Cystic Fibrosis Microbiology: Away Day October 2017 Dr David Garner Consultant Microbiologist Frimley Park Hospital

Aims & Objectives Discuss current issues in CF microbiology To understand how a sputum sample is processed To know how to interpret a sputum result To understand why antibiotic sensitivities are of limited use in CF To know the problem microorganisms in CF To be aware of the infection control issues in CF To make microbiology “interesting” for all of you!

Mark 27 years old with cystic fibrosis Initial problems as a child with bacteria such as: Streptococcus pneumoniae Haemophilus influenzae Staphylococcus aureus More recent problems with: Pseudomonas aeruginosa Admitted with an exacerbation of his cystic fibrosis What are you going to do?

Mark Check what he has grown before Admit him to a side room on the CF unit Send a sputum sample to Microbiology Intensify physiotherapy Start antibiotics Review compliance with other medications

Requesting sputum cultures? In ICE select “Respiratory and AAFB Acute

Requesting sputum cultures? Top box is a drop down menu for the test, next box is for clinical details (don’t leave it blank!) This affects the tests the laboratory do

Requesting sputum cultures In ICE common tests tab select CFU tab

What tests does the lab do? Chronic Pseudomonas Biannual review sent to Ref. Lab for Typing and MIC testing Only select twice yearly (the reference laboratory will not test samples which are sent more frequently) Chronic pseudomonas NOT annual review Identification of Pseudomonas, no sensitivities NOT chronic pseudomonas Full identification and sensitivities of microorganisms

What does a lab look like?

What does a lab look like?

What does a lab look like?

Respiratory laboratory

Respiratory laboratory

Culture: how is sputum processed? Plated to mixture of selective and non-selective agar depending on clinical details E.g. Cystic Fibrosis = B. cepacia agar Incubated for 48 hours before reporting Sensitivities take a further 24-48 hours Total time 48-96 hours after receipt.

How to interpret a sputum result? Appearance Mucoid, Salivary, Purulent, Blood Stained… Microscopy Gram’s stain, Ziehl Neelsen (ZN) stain… Culture Is the organism consistent with the clinical picture?

Appearance of sputum Salivary Mucoid Purulent Blood stained Spit not phlegm, risk of contamination Mucoid Upper respiratory tract specimen, no evidence of inflammation Purulent Pus, indicates inflammation Blood stained May indicate infection

Gram’s stain

Ziehl Neelson Stain

Culture: classification of bacteria Causes of pneumonia usually originate in the upper respiratory tract

Classification of Gram-positive cocci

Bacterial Identification: Gram-negative bacilli

Normal Flora

CF “Normal” Flora Eventually also: MDR P. aeruginosa, Burkholderia spp., Stenotrophomas maltophilia, Achromobacter spp., Non-tuberculous mycobacteria…!

Factors Affecting Normal Flora Exposure to antibiotics provides a selective pressure e.g. previous antibiotics for CAP Increased antimicrobial resistant organisms in the environment e.g. Pseudomonas in critical care units Easily transmissible organisms e.g. Staphylococcus aureus Failure to clear colonising bacteria E.g. Pseudomonas aeruginosa Immunosuppressants e.g. steroids

Do patients need antibiotics? CF patients can get the same types of infection everyone gets e.g. UTI, tonsillitis, cellulitis Viruses do not respond to antibacterials! However there are antivirals e.g. aciclovir, oseltamivir The presence of bacteria does not necessarily mean there is an infection! Bacteria colonise, such as upper respiratory tract, surgical wounds, ulcers

How do you choose an antibiotic? What are the common micro-organisms causing the infection? Is the antibiotic active against the common micro-organisms? Do I need a bactericidal antibiotic rather than bacteriostatic? Does the antibiotic get into the site of infection in adequate amounts? How much antibiotic do I need to give? What route do I need to use to give the antibiotic?

…you choose what worked before… In reality… …you choose what worked before…

Why do exacerbations of cystic fibrosis occur?

Exacerbation of CF Caused by: New bacteria New strain of bacteria or change in phenotype Non-cultured bacteria or viruses Increased exacerbations  decreased survival Decreased symptoms  increased FEV1 Risk factors for treatment failure: Female Low BMI Cepacia Time delay to starting treatment

Treatment of Exacerbation High doses of Beta-lactam PLUS aminoglycoside Choice of antibiotic Identification of organism Previous successful therapy Allergies Susceptibility testing not helpful Too variable Not predictive of clinical response No value in synergy testing Duration Good lung function = 7-14 days Poor lung function = longer (guided by response)

Why sensitivities don’t help At least 4 different appearances of P. aeruginosa

Why sensitivities don’t help At least 3 different sensitivity patterns for each appearance of P. aeruginosa Is this 12 different bacteria?

Why sensitivities don’t help Genetic finger printing shows only 1 P. aeruginosa = clever bug!!!!

Problem microorganisms

Mycobacterium abscessus

Decreased macrophage activity Who gets M. abscessus? Rates are increasing: highest in 11-20 year olds Transmission Indirect patient to patient Surface contamination Airborne? Pseudomonas detectable in air 3 hours after room vacated Vitamin B12 deficiency Azithromycin Decreased autophagy Decreased macrophage activity Increased M. abscessus

Why does it matter? Faster rate of decline in lung function (FEV1) 2.5% vs. 1.6% per year Absolute contraindication to transplant (unless able to eradicate?) Infection control restrictions Stigmatisation? Difficult to diagnose in patients on antibiotics that interfere with culture e.g. macrolides, aminoglycosides

Combination therapy Approx. 20% response (off Abx and culture negative) Intensive phase (1-3 months) Clarithromycin (if sensitive) PLUS IV Amikacin PLUS Tigecycline AND Imipenem Continuation phase (until culture negative for 12 months on therapy!) PLUS nebulised Amikacin PLUS 1-3 of Minocycline OR Clofazamine OR Linezolid OR Moxifloxacin OR Cotrimoxazole

Rhinovirus

Rhinovirus 1 in 3 patients have a virus in an exacerbation Two fold increased risk of exacerbation Less effect on FEV1 than other causes Associated with increased Abx use Mainly found in summer and autumn Increase bacterial release from biofilms Individual response to Rhinovirus Immune mediated? Worse with type A than B or C Persists for ≥ 2 months in some patients

Burkholderia cepacia complex

B. cepacia complex 2010 = 17 species 2014 = 18 species (B. pseudomultivorans) Previous Genomovars now have distinct names Most important B. cepacia B. multivorans B. cenocepacia (contraindication to transplant) Mortality 2003 >50% at 5 years (Manchester, Vancouver) 2010 <10% at 5 years (Prague) – Why? Not part of the normal human flora

Epidemiology Infection control precautions work Prevent spread from patient-to-patient Global epidemic B. cepacia strains How do they spread internationally? B. multivorans Increasingly common Rare patient-to-patient transmission Can be replaced by B. cepacia (but not the reverse)

Non B. cepacia complex strains B. gladioli 3rd most common strain in USA Clinical significance unclear

Infection Control

Transmission Main problems P. aeruginosa and B. cepacia complex Routes Environment-to-patient Patient-to-patient Mainly droplet spread Within few metres Potential droplet nuclei spread Remain suspended in air up to 3 hours after patient leaves

Recommendations Surveillance Standard precautions Identify organisms Refer for PFGE Standard precautions For patients as well as staff Consider H2O2 but no evidence Segregate ALL patients No common areas Only patients from same household can share No B. cepacia complex or M. abscessus patients in CF wards or outpatient clinics

M. abscessus CF Trust UK and American CF Guidelines Separate clinic in different building No shared equipment AT ALL! No admission to CF unit Negative pressure side-room Sporicidal cleaning then leave room empty for 24 hours

Recommendations Gloves and aprons for contact with patient and their environment (UK CF Trust) 20% of HCW contamination from environment No routine use of masks for inpatients Ventilation Wait 60 minutes before final disinfection of room after patient discharged Negative pressure room

After all that… Mark Previous results checked Admitted to CF unit No epidemic P. aeruginosa, B. cepacia complex, M. abscessus Admitted to CF unit Sputum sample sent (requested as exacerbation of CF not chronic Pseud) Started on Meropenem PLUS Tobramycin Sputum result confirmed P. aeruginosa sensitive to Meropenem and Tobramycin Mark improved quickly and went home after a week in hospital

Conclusion Infections in cystic fibrosis are very difficult to manage Multiple factors cause problems: Patient factors Allergies Antibiotic resistance Laboratory issues Odd bacteria! Successful management requires team work!

Any Questions? Available to buy on