1 Microbiology Nuts & Bolts Session 4 Dr David GarnerConsultant Microbiologist
2 Aims & ObjectivesTo discuss 3 common clinical scenarios from a microbiology perspectiveTo understand how to interpret basic microbiology resultsTo consider the benefits and potential pitfalls of prescribing antibioticsTo look to the future of microbiology and how this will impact primary care
4 Mary70 years oldPresents with cough, increasing shortness of breath, increasingly purulent sputumPast Medical HistoryHypertension, Type 2 Diabetes, Chronic Obstructive Pulmonary DiseaseOn examinationTemperature 37.5 oCCrepitations at the right baseB.P. 140/85, H.R. 98 bpmHow should Mary be managed?
5 Questions to ask yourself… What urgent care does she need?Does she have an infection?What is the likely source of infection?What are the likely causes of the infection?Does she need secondary care?Does she need further investigation?Does she require antibiotic treatment?
6 Differential Diagnosis British Thoracic Society Guidelines for Community Acquired Pneumonia (CAP)Cough PLUS one other respiratory tract symptomShortness of breathPurulent sputumChest painNew focal chest signsReduced expansionBronchial breathingDull percussion Vocal resonanceSystemic symptomsFever, sweats, shivers, aches & painsNo other explanationExacerbation of COPDShortness of breathPurulent sputum Amount of sputum
7 Diagnosed with Exacerbation of COPD SputumPrescribed Amoxicillin POPlanned Chest X-ray if not improving
8 How to interpret a sputum result? AppearanceMucoid, Salivary, Purulent, Blood Stained…MicroscopyGram’s stain, Ziehl Nielsen (ZN) stain…CultureIs the organism consistent with the clinical picture?
9 Appearance of sputum Salivary Mucoid Purulent Blood stained Spit not phlegm, risk of contaminationMucoidUpper respiratory tract specimen, no evidence of inflammationBeware neutropaenic patientsPurulentPus, indicates inflammation not infectionBlood stainedMay indicate infection but not pathognomic
10 Causes of Respiratory Infections Community Acquired PneumoniaViruses:RSVInfluenzaParainfluenzaAdenovirusBacteria:S. pneumoniaeH. influenzaeS. aureusM. pneumoniaC. pneumoniaeL. pneumophilaP. aeruginosa (if COPD)M. tuberculosisExacerbation of COPDViruses:RSVRhinovirusInfluenzaParainfluenzaAdenovirusBacteria:S. pneumoniaeH. influenzaeS. aureusM. catarrhalis
11 Culture: classification of bacteria Causes of LRTI usually originate in the upper respiratory tract
12 Culture: how is sputum processed? Plated to mixture of selective and non-selective agar depending on clinical detailsE.g. Cystic Fibrosis = B. cepacia agarIncubated for 48 hours before reportingSensitivities take a further hoursTotal time hours after receipt.
16 Back to Mary… Sputum How would you manage Mary now? PurulentCulture Heavy Growth of Moraxella catarrhalisResistant to Amoxicillin & ClarithromycinSensitive to Co-amoxiclav & DoxycyclineHow would you manage Mary now?Call to Mary, she was feeling much better and finished 7 days of AmoxicillinShould she be given prophylactic antibiotics?
17 Prophylactic Antibiotics Benefits frequency of exacerbationsPreservation of lung function use of steroidsPotential DrawbacksCautions and contraindicationse.g. macrolides and quinolones with myasthenia gravisAllergies to antibiotics choice for treatmentSide effects of the antibiotic?e.g. Azithromycin and bone marrow and renal impairmentWhat monitoring of your patient do you have to do?e.g. Azithromycin and FBC and U&Es↑ Antibiotic resistanceProblem: most studies on antibiotic prophylaxis do not look at long-term consequences
20 Jack 45 years old Presents with small pre-tibial laceration Ignored for few days now has slightly green sloughType 2 DiabeticNormal temperature, heart rate and blood pressureHow should Jack be managed?
21 Started empirically PO Flucloxacillin 500mg QDS Wound swab takenStarted empirically PO Flucloxacillin 500mg QDSAdvised to have daily dressing of wound with practice nurse48 hours later not much change, switched to Erythromycin96 hours after first consultation swab shows:Mixed faecal floraChanged to PO Co-amoxiclav 625mg TDSWound swab repeatedWould you have done anything different?
22 1 week later reviewed wound still sloughy Repeat wound swab Heavy growth of Pseudomonas sp. sensitive to CiprofloxacinPatient changed to PO Ciprofloxacin 500mg BDWould you do anything different?
23 2 weeks after initial injury Wound painful, surrounding erythema and increasingly purulent dischargeHow are you going to manage Jack now?
24 Culture: how are wound swabs processed? Cannot do a Gram-stainPus is always better!Mixture of selective and non-selective agar platesCulture hoursSensitivities hoursSwab total time hoursA swab cannot diagnose an infection, that is a clinical judgement, it tells you what might be causing the infection
25 How to interpret a wound swab result? AppearanceNot availableMicroscopyCultureIs the organism consistent with the clinical picture?
26 Types & Causes of Bacterial Skin Infections UlcersStaphylococcus aureus, b-haemolytic StreptococciiBecome colonised with bacteria, especially Enterobacteriaceae that DO NOT need treating in most patientsTake samples from “healthy” base after debriding sloughOnly treat if increasing pain, erythema or purulent dischargeCellulitis
27 Culture: classification of bacteria Skin infections are usually from direct inoculation or haematogenous spread
41 Back to Jack…Admitted to secondary care with established infection with MRSA cellulitisBlood cultures positive for MRSA20% mortalityNational target ZERO preventable MRSA bacteraemiasFortunately made a full recovery after treatment with IV Teicoplanin for 2 weeksDid Jack actually have an infection to begin with?Could his later infection have been prevented?
44 Betty 87 years old nursing home resident Presents with confusion and new incontinenceOn examinationTemperature 37.5 oCCrackles throughout precordiumCardiovascularly stableHow should Betty be managed?
45 Likely urinary tract infection No systemic signs of evolving sepsisTreated for simple UTI with 3 days of Trimethoprim
46 2 days later not much better Still no systemic signs of evolving sepsisCheck of recent bloodseGFR >60ml/minUrineDipstickLeucocytes ++, Nitrites ++MSU (How do you take a proper MSU?) sent to labMicroscopyHow would you manage Betty now?Started on second line Nitrofurantoin
47 How to interpret a urine result? Urine dipstickPoor PPV, Good NPVMicroscopyWhite blood cells, red blood cells, epithelial cellsCulture resultIs the organism consistent with the clinical picture?
48 Microscopy of urine White blood cells Red Blood Cells Epithelial cells >100 x106/L definitely significant>10 x106/L significant if properly taken MSU (rare!)Red Blood CellsPoor correlation with UTI, used by urologist and renal physiciansEpithelial cellsIndicator of contact with, and therefore contamination from, the perineum
49 Culture: how is urine processed? Day 1 Automated MicroscopyIf values not significant reported as negativeIf values significant or specific patient group cultured with direct sensitivitiesDay 2Reported with identification and sensitivitiesPatient groups always culturedCancer and haematologyPregnantUrologyChildren < 5 years old
50 2 days later Much more confused, still incontinent Very distressed Vomiting, diarrhoeaUrine resultMicroscopy >100 x106/L WBC, no epithelial cellsCulture E. coliResistant to Amoxicillin, Co-amoxiclav, Trimethoprim, Cephradine, CiprofloxacinSensitive to NitrofurantoinFurther results to followHow would you manage Betty?What further results are to follow?
51 Admitted to secondary care for IV antibiotics Started on Piptazobactam for sepsis, probably UTIFurther result on MSUE. coli ESBL positiveWhat is an ESBL?What should Betty be treated with?Why didn’t Nitrofurantoin work?
52 Antibiotic dosing in renal failure Many antibiotics require dose reduction in renal failureeGFR is not an accurate predictor of renal functionUse Cockcroft Gault equationActual body weight or Ideal Body Weight (IBW) if weight > 20% above IBWAlso use IBW for patients with oedema & ascites
53 How might weight effect Betty’s GFR (ml/min) Female, Age 87, Creatinine 75Weight (kg)eGFRCalculated GFRVariance456333-305037-265540-236044-196547-167051-1275-88059-4
54 How might weight effect Betty’s GFR (ml/min) Female, Age 87, Creatinine 75Weight (kg)eGFRCalculated GFRVariance456333-305037-265540-236044-196547-167051-1275-88059-4
55 Back to Betty… Started IV Meropenem 500mg BD 55kg, Creatinine 77 Calculated GFR = 39 ml/min
56 48 hours later Much improved, diarrhoea and vomiting settled Bloods WBC 19 x 109/LCRP 198U&Es – Urea 12, Creat 150Blood CultureEscherichia coli, resistant to Amoxycillin, Co-amoxiclav, Gentamicin, Trimethoprim, Ciprofloxacin, Piptazobactam, Ceftriaxone (ESBL positive)Sensitive to Meropenem, AmikacinWhat should we do for Betty now?
57 Continued IV Meropenem as no oral alternatives Given 7 days of antibiotics in total for severe UTI?Made a full recovery and went back to her nursing homeWarning – Betty is now known to be colonised with a Antibiotic-resistant E. coli so her future UTIs are likely to be resistant as well (it is part of her normal flora!)
58 Caution: Extended Spectrum Beta-lactamase Enzyme excreted into periplasmic space which inactivates antimicrobials by cleaving the b-lactam bond.Cause resistance to almost all b-lactams including 3rd-generation cephalosporinsAssociated with multiple antibiotic resistancesCan be chromosome, plasmid or transposon encodedCan be constitutive or inducibleIdeally patients with ESBLs should be managed in side-rooms with contact precautions
60 Caution: Extended Spectrum Beta-lactamase Source:European Centre for Disease Prevention and Control Antimicrobial resistance surveillance in Europe 2011
61 The Future is BleakIncreasing numbers of Meropenem resistant Enterobacteriaceae in the UK from overseasNDM-1 = New Delhi Metallo-beta-lactamaseKPC = Klebsiella pneumoniae carbapenemaseNow starting to see Amikacin resistance as wellOnly antibiotic left is Colistin60+ years oldSome bacteria are known to be inherently resistant (Proteus sp., Serratia sp.)May become transferable and then have a real “superbug” for the post-antibiotic era…
62 Conclusions3 clinical scenarios showing some of the pitfalls in managing apparently simple infectionsLook at microbiology results in orderAppearance, Microscopy and CultureThere are significant benefits to antibiotics but increasingly there are also dangersConflict of medicine moving to 1o care but infections moving to 2o care – need for OPATThe future is looking bleak, we need to try and preserve what we have for as long as we can…