Microbiology (Lecture Notes)

Microbiology and Infectious Diseases • Discuss the procedures to be followed in the event of a needlestick injury Immediate action: Squeeze wound to encourage bleeding, wash thoroughly, plaster if required Report incident to ward manager Report to occupational health (or microbiology lab out of hours). Be ready to give them: Patient details – known infections, reason for admission Injury details – nature (splash, stick) and time Your details – vaccination status Interventions available Hep C – none Hep B – immunoglobulins if not immune (booster if are immune) HIV – assess patient’s likelihood of being affected. Start antiretrovirals (PEP) NB: you can only do a HIV test with the patient’s consent Precautions to take after Not entitled to any time of work – surgeons can still operate Cannot give blood No elective surgery (as a patient) Use barrier contraception Follow up Baseline serum for reference range Samples at 3 months and 6 months (+ 1 yr for HIV) to follow up Risk of transmission Hep B – 30% if eAg +ve (and recipient is not immune) Hep C – 3% HIV – 0.3% for needlestick (0.1% for splash on mucous membrane) • Discuss SIRS, sepsis, severe sepsis and septic shock SIRS = systemic inflammatory response syndrome Patients must have 2 or more of the following; Temperature > 38oC or < 36oC Pulse > 90 bpm RR > 20 / min WCC > 12 or < 4 (or > 10% immature forms) Sepsis = SIRS + evidence of infection Severe sepsis = sepsis + organ dysfunction Patients are usually > 60yrs / low birth weight infants, 80% are inpatients Mortality 18-28% Septic shock = hypotension not reversed by fluid resuscitation & associated with organ dysfunction or hypoperfusion abnormalities Sepsis with organ dysfunction Hypotension (systolic < 90mmHg) Lactic acidosis Oliguria Confusion Micro 1 Liver dysfunction MANAGEMENT Initial resuscitation Vascular access & aggressive fluid resuscitation During 1st 6 hours aim for CVP of 8-12 mmHg MAP > 65mmHg Urine Output > 0.5 ml / kg / hr Diagnosis Minimum 2 sets of blood cultures before starting Abx therapy (1 set percutaneously + 1 set from each indwelling device) Other sites images / cultured (e.g. US, urine, stool etc) Antibiotic therapy Should be started within 1 hr of recognition of severe sepsis AFTER cultures Convert from empirical therapy to narrow spectrum ASAP ALWAYS monitor renal & hepatic function as these can be affected by sepsis If fluids are not helping consider… vasopressors Ionotropic therapy IV corticosteroids (hydrocortisone for 7 days) Recombiant activated protein C if High risk of death Sepsis induced multiple organ failure Septic shock ARDS AND no contraindications Always remember… DVT prophylaxis Stress ulcer prophylaxis – H2 antagonist Tight glycaemic control • Lung abscess A cavitating area of localised suppurative infection within the lung Causes: inadequately treated pneumonia, aspiration (alcoholism, bulbar palsy, oesophageal obstruction), bronchial obstruction (foreign body, tumour), pulmonary infarct, septic emboli Features: swinging fever, cough, purulent foul smelling sputum, pleuritic chest pain, haemoptysis, malaise, weight loss. Look for clubbing, anaemia, creps Ix – FBC (anaemia, neurtrophilia), ESR, CRP, Blood cultures, sputum microscopy & culture, CXR (walled cavity often with air:fluid level), consider CT to exclude obstruction & bronchoscopy to obtain specimins Rx: Ax until healed (4-6 wks). Postural drainage, repeated aspiration, antibiotic instillation or surgical excision may be required Septicaemia – due to haematological spread --> metastatic infection • Acute pharyngitis Viral Most commonly the adenovirus group à sore throat, reddening of oropharynx & soft palate & inflamed, swollen tonsils. With 1-2 days à swollen tonsillar LN. self limiting and no/only supportive treatment required Micro 2 Bacterial Previously 1/3 of pharyngitis but now falling Persistent tonsillitis requires Abx but avoid amoxycillin & ampicillin incase EBV • Infectious mononucleosis (glandular fever) Caused by EBV infection of B-lymphocytes --> proliferation of T cells (atypical mononuclear cells) which are cytotoxic to the EBV infected cells Spread: salive / droplet Incubation: 4-5 weeks Sx: sore throat, fever, anorexia, malaise, lymphadenopathy, palatal petechiae, splenomegaly, hepatitis, hameolysis Complications: meningitis, encephalitis, ataxia, CN lesions (usually 7), guillain barre syn, neuropathy, depression, fatigue. RARE: thrombocytopenia, risk of splenic rupture, upper airways obstruction, hepatitis, 2o infections, renal failure Blood film: lymphocytosis (20%) & atypical lymphocytes (but also occur with CMV, HIV, parvovirus, toxoplasmosis, leukaemia, lymphoma) Monospot / Paul-Bunnell (antibody tests): Ab develop by week 3 and disappear after 3 months. False +ves can occur with hepatitis, parvovirus, lymphoma, leukaemia, rubella, malaria, Ca Pancreas & SLE Differentials: strep sore throat, CMV, viral hepatitis, HIV seroconversion illness, toxoplasmosis, leukaemia, diphtheria Rx: avoid alcohol (to protect liver), prednisolone if Sx severe or complications. NEVER give ampicillin / amoxicillin even if sore throat as --> severe rash Oncogenicity – linked to lymphoma, nasopharyngeal ca, leiomyosarcoma and oral hairy leucoplakia • Gastroenteritis and food poisoning An acute inflammation of the lining of the stomach and intestines, characterised by anorexia, nausea, diarrhoea, abdominal pain and weakness. Commonly caused by ingestion of bacteria, viruses or toxins. Ask about details of food & fluid intake, if other diners are well. Also ask about swimming / water sports. NB: food poisoning is a notifiable disease Causes S.Aureus – 1-6 hrs. D&V, abdo pain & hypotension. Common from meat Bacillus cereus – 1-5hrs. D&V. reheated rice Salmonella – 12-48hrs. D&V, pain, fever, septicaemia. Meat, eggs, poultry C.Perfingens – 8-24hrs. D, abdo pain. Meat C.Botulinum – 12-36hrs. V & paralysis. Meat C.Difficile – 1-7 days. Bloody D, pain, GI perf, toxic megacolon. Abx assoc Cholera (vibrio cholerae) – 2h-5d. profuse “rice water” diarrhoea & V, fever --> rapid dehydration. Water (faeco-oral spread) Campylobacter – 2-5d. Bloody D, pain, fever. From milk, poultry, water Listeria – meningoencephalitis, flu like syndrome, miscarriage. From uncooked pate, cheeses etc E.Coli 0157 – 12-72hrs. Cholera / thyphoid like. NB: --> HUS Cryptosporidium – 4-12d. Diarrhoea in HIV. Water Giardia Lamblia – 1-4 wks. Bloating, flatulence, abdo pain, loose stools --> explosive diarrhoea. Chronic --> malabsorption, weight loss, lactose intolerance. From water / faeces Micro 3 Entamoeba Histiolytica (amoebiasis / amoebic dysentry). 1-4 wks. Diarrhoea (slow --> bloody & profuse). Water Rotavirus. 1-7 days. D&V, fever & malaise. Water Shigella – 2-3d. Bloody D, pain, fever. Any food Ix: stool microscopy / culture if from abroad, an institution or outbreak suspected Prevention: hygiene. Avoid tap water (inc ice) while abroad. Reheat food thoroughly Management: supportive of Sx. Maintain oral fluids (ORT). Antiemetic+/- antidiarrhoeal if severe. Abx only if systemically unwell, immunosupressed or elderly Specific therapy: cholera (tetracycline), Salmonella, shigella and campylobacter (ciprofloxacin) • Traveller's diarrhoea E.coli is most common Consider salmonella, shigella, campylobacter, giardia, cholera If prolonged suspect protozoa or tropical sprue If HIV suspect cyrptosporidia, microsporidia • Enteric fever Typhoid (salmonella typhi) & paratyphoid (s.parathypi) Incubation: 3-21 d Spread: faeco-oral Presentation: malaise, headache, high fever, bradycardia, cough, constipation (or diarrhoea – usually after the 1st week), CNS signs (coma, delirium, meningism), rose spots (on trunk in 40%). Rarely epistaxis, bruising, abdominal pain, splenomegaly Ix: Blood culture. Later do urine / stool culture. Bone marrow culture has highest yield Rx: fluid replacement & good nutrition. Fluoroquinolones (e.g. ciprofloxacin) if unavailable use chloramphenicol. If encephalopathy give dexamethasone Complications: osteomyelitis (esp if sickle cell), DVT, GI bleed / perf, cholesystitis, myocarditis, pyelonephritis, meningitis, abscess. Dx cure: “clear” once 6 consecutive –ve urine & stool cultures • Brain abscess Suspect in any patient with raised ICP esp if fever / raised WCC May follow ear, sinus, dental or periodontal infection, skull #, congenital heart disease (L --> R shunts), endocarditis (septic emboli), bronchiectasis NB: may be no signs of systemic involvement Signs: seizures, fever, localising signs, signs of raised ICP, coma, signs of source sepsis (dental etc) Ix: CT/MRI (ring enhancing lesion), raised WCC, raised ESR --> biopsy Rx: urgent neurosurgical referral. Treat raised ICP. Organisms: dental / sinus (strep milleri or oropharyngeal anaerobes), ear (B.fragilis / anaerobes) Consider immunosupression • Travel-associated fever including malaria. In every ill traveller consider: Malaria – fever, rigors, headaches, dizziness, flu sx, diarrhoea, thrombocytopenia (see more below) Micro 4 Typhoid – fever, bradycardia, abdo pains, dry cough, constipation, lymphadenopathy, headache, splenomegaly, rose spots Dengue fever – fever, headache, myalgia, rash, thrombocytopenia, leucopenia Amoebic liver abscess – fever, jaundice, RUQ paid • Malaria Plasmodium falciparum (= protozoa)– 7-10 day incubation (present within 2 months) P. vivax – 10-17 d, P.ovale 10-17 d, P.malariae – 18-40d Carrier: female anopheles mosquito Course – protozoa multiply in RBCs --> haemolyisis, RBC sequestration, cytokine release. Protective factors – sickle cell, G6PD deficiency Sx – non specific flu-like prodrome, headache, malaise, myalgia, anorexia --> fever & chills + faints (fever spikes every 3 days). Anaemia, jaundice, hepatosplenomegally Complications Cerebral malaria – confusion, coma, fits but without focal signs. 20% mortality Metabolic (lactic) acidosis – kussmaul breathing Anaemia – common due to haemolysis of infected cells Hypoglycaemia – in severe malaria (25% children, 8% adults) Acute renal failure – ATN due to free Hb Pulmonary oedema Dx – serial thick and thin blood films. FBC (anaemia, thrombocytopenia), clotting (DIC), glucose, ABG (lactate), U&E & Creat, Urinalysis, Blood culture Prognostic factors - <3yrs, pregnancy, resp distress, fits, coma, absent corneal reflex, papilloedema, pul oedema, high lactate, low glucose, high creat Rx: most falciparium is now resistant to chloroquine Falciparum – combination therapy to avoid resistance Benign malarias – chloroquine Supportive – tepid sponges & paracetamol for fever, transfuse if severe anaemia, exchange transfusion if very ill Prophylaxis Based on area visiting (chloroquine, doxycycline, mefloquine) Long sleeved clothes, repellents, mosquito nets at night • Fever of unknown origin. Most fevers are due to immune response to viral infections --> interferons & cytokines PUO = fever > 3 weeks (e.g. resisting diagnosis after 1 wk in hospital) Causes: Infections – abscess (lung, liver, subphrenic, pelvic, perinephric), empyema, bacteria (salmonella, brucella, borrelia, leptospira, RF, SBE / IE, TB), granuloma (toxoplasmosis), parasites (amoebic liver abscess, malaria, schistosomiasis, tryptanosomiasis), fungi, HIV, typhus Neoplasms – esp lymphoma Connective tissue diseases – RA, PMR, Giant cell arteritis, SLE Others – drugs (usually short lived, PE, stroke, crohns, UC, sarcoid, amyloid Ix Stage 1 – FBC, ESR, U&E, LFT, CRP, Cultures, baseline viral serology, HIV, sputum MC&S, MSU, stools, CXR. If culture –ve consider malaria & typhus Stage 2 – recheck Sx, travel history, assess new Sx, protein electrophoresis, CT (chest & abdo), Rheumatoid factor, ANA, antistreptolysin titre, mantoux, ECG, marrow, LP. Consider trial withdrawal of each drug in turn Micro 5 Stage 3 – follow any possible leads. Repeat serology to assess changes Stage 4 – treat for ? TB / endocarditis / vasculitis if possibilities. Trial aspirin / steroids • Infection in the neutropaenic patient. Neutropenic regime – Full barrier nurse in a side room Avoid IM injections – risk of an infected haematoma Wash perineum post defecation, swab skin with chlorhexidine, avoid PRs where possible 2 hrly mouth washes with hydrogen peroxide, give candida prophylaxis TPR with high calories, avoid foods with risk of bacterial contamination If any sign if illness à check FBC, plts, INR, U&E, LFT, 3x peripheral blood cultures + any other body fluids, request CXR Use of antibiotics If T > 38 (or 37.5 on 2 readings 1 hr apart), or patient is unwell assume septicaemia & start blind, broad spectrum Abx (check local preferences) Continue Abx until afebrile for 72 hrs or a 5 day course with neutrophil recovery. If fever persists suspect CMV or fungus (candida or aspergillus) May need to consider Rx for pneumocystis or consider TB Recombinant granulocyte colong stimulating factor may help – ask expert advice • Hospital acquired infection Sources Lines – peripheral or central – blood cultures through lines Urinary catheters – culture urine Lower respiratory tract infections (HAP) - examine & CXR Wound infections Abdominal sepsis Instrumentation – ERCP, TURP Management IV fluids IV Abx – in line with the hospital policy and likely cause / site of infection Micro 6 Human immunodeficiency virus-associated conditions. 0.1% prevalence in the UK (approx 30% of those are undiagnosed) Immunology HIV binds to CD4 receptors on T-lymphocytes, monocytes, macrophages and neural cells The CD4 cells migrate to the lymphoid tissue à repilication of virus New viruses infect more CD4 cells à immune dysfunction Virology HIV is a RNA-retrovirus After entry, reverse transcriptase makes a DNA copy of the RNA genome which is integrated into the host DNA. Core proteins are then produced à new virions released by budding Acute HIV infection 2-6 weeks approx 50% are asymptomatic Diagnosis at this point requires a high index of suspicion Persistent generalised lymphadenopathy (PGL) (30%) Nodes > 1 cm at > 2 extra-inguinal sites persisting for > 3 months Aids related complex (ARC) - very non-specific – fever, lethargy, skin rash, myalgia, headache, sore throat, etc Mean duration of Sx is 7-10 days Due to T lymphocytes(CD8) cells attacking the virus Tests at this stage are based on –ve antibodies but +ve active virus titre NB: Viral load is very high at this stage so patient is highly infectious Chronic infection Approx 1/3 present late (when CD4 < 200) – although many can retrospectively identify acute symptom period Many late presenters have respiratory / neurological infection. Recommendations say ALL people with TB should have HIV test Micro 7 AIDS A stage in HIV illness characterised by the presence of an indicator disease CD4 count usually < 200 x 106 / l 2 yr prognosis at this stage if untreated Pneumocystis Pneumonia (PCP) = AIDS defining illness Sub-acute presentation with progressive exertional dyspnoea with dry cough and fever CXR signs are variable (can show lobar pneumonia, cavitation or pneumothorax) Often have had other signs of immunocompromise (e.g. oral candidiasis) Dx - immunofluorescence from bronchioalveolar lavage or deep sputum Rx – cotrimoxazole +/- steroids (with caution as will worsen bacterial illness) TB At any CD4 count but the count will predict the pattern (high = cavitation, low = diffuse) Increased incidence of extrapulmonary disease Sputum smears often negative so have to wait on cultures More likely to be drug resistant (although treatment regime is same) HIV testing – who? Anyone with TB / other HIV linked condition Lymphoma Suspected acute infection Illness comparable with HIV related illness Anyone at high risk All women attending for antenatal care When to treat HIV If AIDS diagnosed Any patient with CD4 < 2000 Asymptomatic with CD4 of 200-350, or rapidly falling Treatments Anti-retroviral work in 2 ways: Reverse transcriptase inhibitors block the RNA à DNA process Protease inhibitors slow cell to cell spread Micro 8 Surgical infection A surgical site or wound infection is defined by having pus, exuding from it or a painful spreading erythema indicative of cellulitis Other surgery associated infections include Ventilator associated pneumonia Hospital acquired pneumonia Central venous catheter infection and related bacteraemia Urinary tract infection (from catheter) • List the factors that contribute to infection following a surgical procedure. Wound Classification (clean, dirty etc) CLEAN – usually elective surgery CLEAN/CONTAMINATED – usually elective on the GI tract with no spill eg. elective Hartmann’s. CONTAMINATED – major lapse in technique eg. Open heart massage or a fresh stabbing in the GI tract. DIRTY – pus present eg. Perforated appendix Co-existing disease eg. Diabetes & steroids Obesity & malnutrition Elective vs emergency surgery Duration of surgery Peri-operative shaving • Discuss the different types of skin disinfectants used in theatres and surgical wards The first surgical hand scrub should be for 5 minutes with chlorhexidine and then 2 minutes between cases. • List the types of surgical infections. In general 56% due to Gram-positive bacteria: Micro 9 – Staphylococcus aureus – Beta-haemolytic streptococcI - Coagulase negative staphs 38% due to Gram-negative bacteria 4% due to Candida spp For abdominal wounds Superficial SSI infections usually Staph. aureus. Deep SSI organisms may have come from the bowel. Anaerobes such as Bacteroides & Clostridia and Coliforms can cause intra-abdominal abscesses that can dehisce • Discuss the principles used to reduce infections including the use of prophylactic antibiotics in surgery. Patient factors Minimise the pre-operative stay to reduce the risk of colonisation of the patient with resistant bacteria. Pre-operative screening for MRSA in those having prosthetic surgery and urine in those men having trans urethral resection of the prostate. Erradicate skin carriage and optomise antibiotic prophylaxis. Ensure diabetics are well under control Theatre factors To avoid theatre contamination after dirty cases, put dirty cases at the end of a list. Clean the theatre after a dirty case. Ensure that there are at least 20 clean-air changes per hour in theatres. There will need to be 40 for certain types of surgery. Theatres should be at a positive air pressure c/w corridors and scrub rooms. For orthopaedic prosthetic surgery and cardiac valve replacements use ‘Ultra-Clean-Air (UCA)’ laminar-flow ventilation through high particular air (HPA) filters. Ensure the minimum number of personnel are present at the operating field. Antibiotic use Usually a single dose of antibiotic at induction for: All contaminated and dirty surgery. Orthopaedic and vascular prosthetic surgery. Cardiac surgery Rx of infections May need to drain pus and debride devitalised tissue. ANTIBIOTICS: flucloxacillin usually for 5 days If known to be colonised with MRSA or an in-patient for a couple of weeks use vancomycin empirically and await swab results. If an amputation use metronidazole empirically in case of Clostridial gangrene • Describe the clinical features and treatment of anaerobic and synergistic gangrene Gangrene is death of tissue from poor vascular supply and is a sign of critical ischaemia. Tissues are black and skin sloughs. There should be a line of demarcation Wet gangrene is tissue death with infection Dry gangrene means no infection Pregangrene is a term used to describe tissue that is on the brink of gangrene Micro 10 Management Take cultures. Look for B-haemolytic strep (will rapidly à necrotising fascitis) Radical debridement is needed (+/- amputation) 5 days of benzylpenicillin IV to prevent gas gangrene (+ clindamycin) Gas Gangrene – clostridium perfingens myositis. Risk factors – DM, trauma, malignancy, Features – early toxaemia, delirium, haemolytic jaundice. At the site look for oedema, crepitus (from surgical emphysema) and bubbly brown pus Rx – remove all dead tissue (e.g. amputation). Benzylpenicillin, hyperbaric O2 ( bacteria is anaerobe), clindamycin & metronidazole • Describe the basis on which antibiotics are chosen for varying infections. Empirical use based on the most likely causative organism until cultures come back If serious (for patient or in severity) then give broad spectrum to cover all organisms • Describe the diagnostic evaluation of an intra-abdominal abscess. Patients with intra-abdominal abscesses have: Fever Abdominal tenderness sometimes peritonism Bowel stasis Palpable mass Diagnosis by USS Treat with cefalosporin and metronidazole Micro 11