Bacterial Infections

1. Bacterial Infections Professor Mark Pallen

2. Microbes and humans

3. Definitions Pathogen an organism that can cause infection in individuals with normal host defences, e.g., Salmonella enteritidis, Vibrio cholerae Commensal an organism that is found normally on those parts of the body that are exposed to, or communicate with, the external environment, eg. Bacteroides fragilis, Staphylococcus epidermidis; the 'normal flora' Opportunistic pathogen ('opportunist') an organism that can cause infection in individuals with abnormal host defences. Commensals may be opportunistic pathogens.

4. Microbes and humans Disease can come about in several overlapping ways 1. Some bacteria are entirely adapted to the pathogenic way of life in humans. They are never part of the normal flora but may cause subclinical infection, e.g. M . tuberculosis 2. Some bacteria which are part of the normal flora acquire extra virulence factors making them pathogenic, e.g. E. coli 3. Some bacteria which are part of the normal flora can cause disease if they gain access to deep tissues by trauma, surgery, lines, e.g. S. epidermidis 4. In immunocompromised patients many free-living bacteria and components of the normal flora can cause disease, especially if introduced into deep tissues, e.g. Acinetobacter

5. How do we know that a given pathogen causes a specific disease? Koch's postulates the pathogen must be present in every case of the disease the pathogen must be isolated from the diseased host & grown in pure culture the specific disease must be reproduced when a pure culture of the pathogen is inoculated into a healthy susceptible host the pathogen must be recoverable from the experimentally infected host

7. How do we know that a given pathogen causes a specific disease?

8. Microbes and humans Evidence for a potential pathogen being clinical significant (particularly for bacteria) Isolated in abundance Isolated in pure culture Isolated on more than one occasion Isolated from deep tissues Evidence of local inflammation Evidence of immune response to pathogen Fits with clinical picture

9. The Normal Flora

10. The Normal Flora Our bodies are like mobile warm-blooded coral reefs, rich in microbial biodiversity and home to vast numbers of bacterial cells there are more bacterial cells (1014) associated with the human body than there are human ones (only 1013)! composition of normal flora varies from individual to individual some bacterial species carried only transiently most fairly permanent difficult to alter composition of the normal flora ofgut in a healthy individual

11. Changes in normal flora with changes in hormal physiology and development female genital tract and lactobacilli when antibiotics select for a 'resistant flora’ Candida overgrowth in mouth, vagina Clostridium difficile (antibiotic-associated colitis) new organisms may be acquired neonate from maternal genital tract during birth Gram-negative colonisation of gut and URT in hospitalised patients Cross-infection with C. difficile, MRSA, VRE etc

12. Why care about the normal flora? it may be good for you! colonization resistance: competition for space and nutrients with pathogens release of bacteriocins and colicins (antibacterial substances) to prevent pathogen growth vitamin K production in gut continued antigenic stimulation from commensals cross-reacting protective immunity against pathogens commensal neisseriaceae and Neisseria meningitidis

13. Why care about the normal flora? commensal bacteria may cause disease at their site of carriage or nearby, e.g. Streptococcus mutans (mouth) causes dental caries Streptococcus pneumoniae (upper airways) causes otitis media, sinusitis Some members of the normal flora can become pathogenic if they acquire additional virulence factors (e.g. E. coli) or are introduced into normally sterile sites (e. g. Staphylococcus aureus)

14. Why care about the normal flora? Normal flora as contaminants To allow interpretation of Gram stains on clinical samples Culture results Skin flora in blood cultures BUT coagulase-negative staphylococci can be pathogens in device-associated sepsis, so can be hard to interpret Perineal flora in urine Take an MSU! Mixed culture=contamination Throat flora in sputum Need to assess whether Heavy pure growth Obtained repeatedly Fits clinical picture

15. The normal floramouth and throat saliva has approx. 108 bacteria/ml 'viridans streptococci' Strep. mutans, Strep. mitior, Strep. salivarius Neisseria spp. N. lactamica, N. flavescens, N. meningitidis Haemophilus influenzae Streptococcus pneumoniae Corynebacterium spp. inc. C. diphtheriae - toxigenic and non-toxigenic strains Spirochaetes Bacteroides melaninogenicus Fusobacteria anaerobic cocci Actinomyces spp.

16. The normal floraskin & nose Staphylococcus aureus Staphylococcus epidermidis “diphtheroids”

17. The normal floraadult female genital tract Lactobacilli Diphtheroids Staphylococcus epidermidis Streptococci enterobacteriaceae

18. The normal floralarge bowel Density Upper: Medium 108 - 1010/g Lower: High >1010/g Organisms Bacteroides spp. Enterobacteriaceae, esp E. coli Enterococci Clostridium spp. Candida spp.

19. Harmful effects of gut bacteria escape of normal flora to abnormal sites perforated appendix leads to peritonitis with Bacteroides spp. and facultative aerobes inc. E. coli cholecystitis and cholangitis often mixed infection, E. coli predominant, also including enterococci urinary tract infection most frequent organism in normal urinary tract is E. coli vaginal candiosis

20. Harmful effects of alterations in normal gut flora antibiotic use leads to sensitive gut flora killed leads to overgrowth with resistant flora inc. Clostridium difficile leads to C. difficile toxin production leads to Diarrhoea, pseudomembraneous colitis Treatment stop precipitating antibiotic give oral metronidazole or vancomycin recovery requires re-establishment of normal flora ? probiotics

21. Bacterial infections & clinical syndromes Syndromes caused by bacterial infection can be classified into two basic types: those defined on basis of pathogen, where a given species of bacterium causes a clearly defined syndrome those defined on the basis of anatomical site of infection caused by many different sorts of bacteria, individually or even in combination. There is overlap between these types of syndrome because some bacteria cause characteristic infections at several sites (e.g. Haemophilus influenzae meningitis and epiglotitis).

22. Some syndromes defined by pathogen typhoid fever legionnaires disease tuberculosis diphtheria

23. Some syndromes defined by site urinary tract infection pharyngitis pneumonia septicaemia endocarditis meningitis osteomyelitis

24. Urinary tract infection Definitions infection of urinary tract lower UTI (cystitis) of bladder alone upper UTI (pyelonephritis) of kidney & bladder Signs & Symptoms Dysuria Frequency Tender bladder and/or kidneys Samples Mid-stream urine (MSU)

25. Meningitis Definition Infection of meninges & adjacent brain Signs & Symptoms Headache Photophobia Malaise Neck stiffness Coma Samples Cerebrospinal fluid, Blood cultures

26. Septicaemia Definition Infection of the blood ("blood poisoning") Bacteria multiply in the blood Signs & Symptoms Fever Malaise Hypotension ( "septic shock") Tachycardia Samples Blood cultures

27. Endocarditis Definition Infection of the heart valves Signs & Symptoms Fever Malaise Weight loss Heart failure Samples Blood cultures

28. Osteomyelitis Definition Infection of bone Signs & Symptoms Fever Malaise Local pain & tenderness Samples Blood culture Bone chippings

29. Gastroenteritis Definition Infection of gut Signs & Symptoms Nausea Vomiting Diarrhoea Samples faeces

30. Pneumonia Definition Infection of lungs Signs & Symptoms Dyspnoea Cough Chest pain Samples sputum

31. Pharyngitis Definition throat infection Signs & Symptoms sore throat malaise Samples throat swab

32. Pyrexia of unknown origin Definition varies - a common definition is that of a fever of more than 2-3 weeks duration, with no cause that be ascertained from initial tests. Signs & Symptoms various Samples many & varied

33. Diagnosis of Bacterial Infection

34. Diagnosis of Bacterial Infection

35. Microscopy Unstained preparations “Wet prep” Dark-ground illumination for syphilis

36. Microscopy Stained preparations Gram-stain Acid-fast stain Ziehl-Neelsen Fluorescence Direct, e.g. auramine Immunofluorescence

37. Culture of Bacteria Solid media Agar plates For Identification For Enumeration Slopes For safe long-term culture, e.g. Lowenstein-Jensen media for TB Liquid media (broth) For enrichment or maximum sensitivity

38. Advantages of Solid Media isolation of single clonal colonies get bacterium in pure culture identify by colonial morphology quantification by colony-forming units

39. Identification of Bacteria Morphology Growth requirements Biochemistry Enzymes Antigens

40. Non-cultural diagnostic methods Antigen detection e.g. latex agglutination Antibody detection e. g. agglutination tests, complement fixation tests, indirect immunofluorescence Molecular methods Polymerase Chain Reaction

41. Sensitivity tests on solid media disc diffusion technique in liquid media minimum inhibitory concentration (MIC) test Breakpoint methods E-test

42. Summary Bacteria and humans Normal Flora Bacterial infection syndromes Diagnosis of bacterial infection