Infections and Opportunistic Infections PDF

Usage of Microbiology Laboratory and Opportunistic Infections Dr Neelam Maheshwari Associate Professor Clinical Consultant Microbiologist  Session aims or Learning objectives 1. Recognise barriers agains...

Usage of Microbiology Laboratory and Opportunistic Infections Dr Neelam Maheshwari Associate Professor Clinical Consultant Microbiologist  Session aims or Learning objectives 1. Recognise barriers against infections 2. To understand the basics of infections I. Definition II. Classification of microorganisms III. Commensal vs. Pathogens IV. Host Microbe Interactions V. Stages of Infection 3. Usage of microbiology laboratory -Choose wisely 4. Opportunistic infections I. Definition II. Risk factors and pathogenesis III. Opportunist pathogens IV. Prevention: Infection Prevention and Control measures V. Brief management: Investigations and Treatment Using Clinical cases studies  2(I) Infection: Definition Inflammation + Pathogen = Infection  1. Barriers against Infections Inborn No prior stimulus required Secretions Non-specific-Non immunologic Acquired Prior stimulus required Specific-Immunologic Lotti Forum = Natural barriers or Body defences  2.(II) Classification of microorganisms 4  Basis of bacterial classification Phenotypic Morphology –shape, size and motility. Staining - colour on (gram) stain Growth requirements-O2 requirement: aerobic, anaerobic Biochemical tests Genotypic 16s ribosomal RNA genes –Bacteria 18s-Fungi Ecology Pathogens vs. Commensal International Committee on Systematic Bacteriology-Nomenclature  Phenotypic classification –Based on Gram stain Purple Pink e.g., Staphylococci, e.g. Neisseria, Coliforms Streptococci, Clostridium Virulence: Mainly endotoxins Virulence: Exotoxins, mainly Bacterial Classification based on staining and shape 1. Gram positive cocci Gram positive bacilli StaphylococciAerobic: Corynebacterium, Listeria spp. , Bacillus Streptococci Anaerobic: Clostridium, Lactobacillus Enterococci-Group D Streptoccoci 2. Gram negative cocci Gram negative bacilli-GUT Neissseria Aerobic: E.coli, Klebsiella ,Proteus ,Salmonella Pseudomonas Anaerobic: Bacteroides 3. Gram negative –spiral: Vibrios, Campylobacter, Helicobacter 4. Not gram stainable. Need special microcopy/stains/PCR Spirochetes: Treponema, Leptospira, Borrelia Mycoplasma: Has no cell wall Filamentous bacteria: Actinomyces, Mycobacterium, Nocardia Rickettsia and Chlamydiae  2.( III) Commensals vs. Pathogens Commensals Normal human flora Co-habitat and are harmless Depend on host for survival Friends normally Can become Pathogenic when find an Opportunity ! Breach in Host Defences Surface barriers : trauma, burns, exfoliative skin conditions, IV lines Foreign location- e.g. Streptococcus viridians (from Nasopharynx to Heart valves) Immunosuppression-Cell mediated Immunity/ Humoral  2.( IV) Host microbe environment Interaction What decides the extent of damage by a micro-organism? Triangle Age Host defences: Barriers/Immunity Concomitant diseases=Comorbidities Site and severity Host Antimicrobial exposure Environment Microbe Invasive procedures and foreign body Commensal/Pathogen Infection Control Practises Infectivity=Pathogenicity Hand hygiene, Isolation, PPE Virulence factors Antibiotic pressure (prescribing practises) – Adherence Hospital/Nursing home – Cell wall Humid environments – Invasion Overcrowding, Poor ventilation – Toxin/Secretions Water and sanitation – Evasion of host defences Endemicity – Spread Antimicrobial resistance  2.(V) Stages of infection Encounter: Triangle interaction Enter Establish (multiply) Damage Spread Outcome  3: Investigations: Choose wisely How to best use the diagnostic laboratory Full blood count (FBC): White cell count and differential Acute phase reactants: C-Reactive Protein (C-RP)/ESR Sample: Microbiology, Culture and Sensitivity (MCS) Depends on the site of infection e.g.: Blood cultures, Wound swabs, Pus, Tissue, Bone, Sputum, Stool, Urine, IV-line tip, Nasopharyngeal swab, Tracheal aspirate Interventional radiology guided sampling, if deep seated infection Coagulation profile Renal and Liver function tests Molecular: Serology (Antigens/antibodies/complements), PCR, WGS  Things to remember when taking samples 1. Assess the need for samples (Choose wisely): Is it going to make difference in the patient management 1. If yes, then 2. Send right sample, at the right time, in the right laboratory container ( Healthcare Pathology test manual) with prefect and matching clinical and sample details on labels a. Sample type b. Collection time c. Site 3. Provide adequate clinical details on request form a. Clinical diagnosis-Reason for testing b. Ward/place where the patient is ? c. Right patient Id details ( full name/DOB/hosp number) d. Is patient on any antimicrobials 4. Contact details of who has collected, the test requestor with name, phone number and ward to contact (legible). 5. Indicate high risk samples by labelling them (BBV/Communicable diseases samples) 5. Contact seniors or lab or microbiologist if still struggling to find test/result details  4. (I) Opportunistic Infections Definition An infection caused by a microbe that takes advantage of an opportunity in the host and its environment which is not normally available: e.g.:  Weak immune system  Breached barriers  Altered microbiome Incidence Long life span Advances in medical management  Host microbe Interaction-Opportunistic Infection Triangle Age Commensals /Pathogen Host defences: barriers/Immunity Virulence factors Host Concomitant diseases – Adherence Site and severity – Invasion Antimicrobial exposure – Toxin production – Evasion of host defences Antimicrobial resistance Infectivity Environment Microbe Invasive procedures and foreign body Infection Control Practises breach Hand hygiene, Isolation, PPE Antibiotic pressure (prescribing practises) Immunosuppressants Susceptible Environments: Hospital/Nursing home Overcrowding, Poor ventilation, Humid Poor water and sanitation  3.(II) Risk factors and Opportunists NB: Long but not an exhaustive list Risk factors = Opportunity Pathophysiological Opportunist (Organism) mechanism Burns / Trauma Breach in barrier Skin flora: Staphylococci spp. Necrotic tissue and exudate Pseudomonas: Burns Loss of plasma proteins Surgery Invasive procedures Foreign bodies/Invasive devices e.g. Breach and sticky material, Septic Staphylococci spp. IV lines, Tubes, Catheters, Prosthesis, technique, Biofilm formation Pseudomonas Pacemaker, grafts Candida spp.( fungi) Co-morbidities: Diabetes mellitus, Altered phagocytic functions Staphylococci spp., Enterococci Chronic renal failure, Peripheral Abnormal/Impaired Immunity Pseudomonas vascular disease, Skin diseases, Vascular insufficiency Liver failure Metabolic derangements Fungi: Candida, Mucor Drugs : e.g. Steroids, Chemotherapy Anti inflammatory Viral : Herpes family like Immuno-suppressants, Irradiation Low WBC esp. agranulocytes HSV/VZV/EBV/CMV Depressed antibody formation Mycobacterium TB /Atypical TB Altered Phagocytosis Fungi: Candida, Pneumocystis (PCP) Cell injury-necrosis Immunosuppressive disorders e.g. Suppressed Adaptive Immunity Skin flora: Staphylococci spp. Myelo-proliferative disorders Gram negatives Enterobacteriaceae Lympho-proliferative disorders Mycobacterium TB/Atypical TB Cancers Depressed Cell mediated Immunity Fungi: Pneumocystis carinii, AIDS Cryptococcus in HIV patients Post Splenectomy Loss of opsonisation, altered Encapsulated bacteria e.g. phagocytosis and graveyard absent Pneumococci  3(III) When to suspect Opportunistic Infection Opportunities/Risk factors 1. Immunocompromised /Comorbid patients/Long- term healthcare contact/High risk wards like ICU/AIDS/Haem-oncology /Transplants/NICU/Endocrine/ Plastic Surgery/Renal patients 2. Patients with invasive devices and repeated antimicrobial exposure How will they present: Presence of opportunity + following 2. Unexplained temperatures (PUO) / Rise in inflammatory markers (White cell count, C-RP) 3. Deterioration in health despite being on antimicrobials : Increased respiratory secretions in ventilated patients, Diarrhoea , high grade fevers 4. Not responding to appropriate antimicrobials 5. Repeat positive cultures from same site with PUO 6. Positive routine surveillance cultures in immunocompromised patients 7. Rejection of grafts or transplants Examples Intravenous line infections Clinical cases  Case Scenario 1-Short term IV lines Day 0 A patient is being treated for severe chest infection via intravenous antibiotics. He gets high grade fever and redness with swelling at the IV-line site, on day 7. 1. What can you see here, day 0 &7 ? 2. What is the likely mechanism of clinical Day 7 presentation shown in picture? 3. What are the likely pathogens and its virulence factors 4. What is the clinical impression? 5. How do you investigate this infection? 6. How do you treat? Pathogenesis: Mechanism for developing pathology or clinical presentaion  Likely pathogens for abscess/cellulitis associated with IV lines 1. Staphylococcus aureus 2. Staphylococcus epidermidis (albus) Bacterial colonies on Blood agar Bunch of grapes Bacteria on gram stain  Cell wall structures o Enterotoxins – food poisoning o Deoxyribonuclease –destroys DNA  How to differentiate between two Staphylococci Coagulase test Staphylococcus Staphylococcus aureus Principle: epidermidis The clumping factor=coagulase enzyme in S.aureus reacts with fibrinogen in the plasma to convert it into fibrin clot=clumps  Treatment for all IV lines Remove the IV line, if possible Send line tip for culture growth Commence on anti-microbials Treat the underlying condition/co-morbidity ANTT (Aseptic no touch technique) if patient needs another IV line Case Scenario 2-Burns 45 male Burns Oozing yellow green pus (=discharge) from burns wound after few days What is the opportunity here ? What is the pathophysiological mechanism for developing Opportunistic infection, in this case? What sample will you send to the laboratory? Which organism/s would you suspect? 27  Case 2 Pus grows Culture growth Gram stain Gram negative bacilli Acquired from moist environment, soil and water Resistant to many disinfectants and antibiotics-Nosocomial bacteria Virulence factor: Lipo-polysaccharide LPS, pilli, flagella, Exotoxin A and S, proteases and exo-polysaccharide called pyocyanin pigment/alginate hence green pus and colonies growth on culture plate  Czech Parasitologist Otto Jirovec Case scenario 3 A patient who is known HIV, presents with low grade fever, lethargy, shortness of breath and pink frothy sputum. His WCC count is 2000 cells/mm3 ( RR: …..) with CD4 count of 50 cells/cmm (RR: 500-1200 cells/ mm3). His Chest X ray is shown. The special silver stain of his deep respiratory specimen (Bronchioalveolar lavage=BAL), is shown BAL Silver stain Chest X ray: Normal lungs PJP lungs  Pneumocystits jirovecii - yeast ( before called as Pneumocystits carinii=PCP) Normal CD4 count in blood is 500-1500 cells/cmm (or mm 3) PJP occurs when CD4 count is less than 200 cells/mm3 in AIDS patients Patient is SOB but Xray image changes are out of proportion in a background of immunosuppression – Steroids high dose for long time – Anticancer agents – Immune modulators – Immunosuppressive disease: AIDS – Autoimmune diseases PCR on Broncho alveolar lavage (BAL) Treatment: Cotrimoxazole high dose 3 ( IV) Prevention of Opportunistic infection 1. Strict Infection control measures Hand hygiene/ ANTT (aseptic no touch technique) / Isolation- or Barrier nursing/Personnel protective equipment (PPE) 2. Review the need of devices and good care of them 3. Follow local Antimicrobial policies (Antimicrobial stewardship) 4. Education: Staff, patients, relatives, students to look for warning signs of infection Multi-disciplinary team approach Wash your hands OR Gel them …………. Bare below elbow uniform Single rooms-isolation/barrier nursing  Thanks Bed time read: 1. BMJ 14 April 1973 ,pg 107-110 , Hillas Smith et al 2. A new look at Infectious Disease- Opportunistic Infection. 3. Personal experiences