Clinical micro-biology lecture note

1. BAHIR DAR UNIVERSITY
COLLEGE OF MEDICINE
AND HEALTH SCIENCES
8/17/2020 1
Topic:- Blood stream infections
- Sepsis and endocarditis
- Pyrexia of unknown origin
By;- Addisu Tesfaye JULY, 2020
BDU, Ethiopia

2. Outline
 Introduction
 Definition and Predisposing factors
 Epidemiology and Causative agents
 Pathogenesis and Laboratory diagnosis
 Treatment and prevention
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3. Introduction
 Blood stream infection (BSI) is one of the most devastating
preventable complications in Critical Care Units.
 It has far-reaching consequences resulting in prolonged length of
hospital-stay
 Sepsis is a life threatening condition that develops from
 Blood poisoning or
 Host immune response
 Sepsis is a global healthcare issue
 The leading cause of death from infection
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4. Intro Cont……
 Early recognition and diagnosis of sepsis is required to prevent
the transition into septic shock
 Endocarditis caused by intravenous foreign bodies from
prosthetic valves pacemaker leads and conduits
 Pyrexia of unknown origin (PUO) also known as fever of
unknown origin (FUO) is a grouping of many unrelated medical
conditions that share the feature of persistent unexplained fever
despite basic investigation
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5. 1. Blood Stream Infections
Definition
 Bloodstream infection is an infection causes by
microorganism in the bloodstream that are alive and
capable of reproducing
Predisposing factors
 Blood stream infection from
Health care-associated
Community acquired
Maternally acquired
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6. Table 1. Predisposing factors of BSI
Preconditions factors
Health care-associated  IV and urinary catheter
 Surgical site associated
 Cardiac, orthopedic devices
 Patients in ICU
Community acquired  When the episode is not health care associated
 Manifest with in 48 hrs admission
Maternally acquired  Infection of neonate
 Acquired from mother during delivery
 Infection appears with less than 48 hrs of birth
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7. Epidemiology
 Exact rates of BSI differ markedly worldwide
 BSI most frequent in intensive care units
 There are 2 major sources of IVDR BSI:
A. Catheter-related infection, are responsible for most endemic
BSIs
B. Contamination of the fluid administered through the device is
the cause of most epidemic BSIs
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8. Causative agents
 A blood stream infection must meet following conditions
1. Recognized pathogens
 Isolation of one or more recognized bacterial or
fungal pathogen from one/more blood culture like
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 S. aureus,
 S. pneumoniae,
E.coli,
 Proteus
Corynebacterium,
Klebsiella,
 Salmonella
 Candida

9. Cont… … Caus
Corynebacterium
CONS
Bacillus
α-hemolytic Strept
Non-pathogenic Neisseria
Environmental G-ve bacteria eg: Pseudomonas
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2. potential contaminants
 The patient has at least one of the following a positive culture
being collected

10. Pathogenesis
 BSI causes by dissemination pathogens from other site of infection
 Organisms are carried from hospital environment
A. Central Line Associated Blood Stream Infection (CLABSI)
B. Catheter Related Blood Stream Infection (CRBSI)
 Examples :- Catheter-related infection
 First gain organisms access to surface of the device
 They can adhere and become incorporated into a biofilm
 Sustained infection and hematogenous dissemination
 Microorganisms gain access by different mechanism
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11. Sources of intravascular catheter infection
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Intraluminal
from tubes and hubs
Extra luminal
from skin
Haematogen
from distant sites

12. Laboratory diagnosis
1. Blood culture
2.MALDI-TOF (Matrix-assisted laser desorption/ ionization time-of-
flight mass spectrometry) analyte molecules
Can provide genus and species level identification
Significant time saving over conventional methods
3.Modified PCR/ESI-MS (electrospray ionization mass spectrometry)
provide
Genotyping, virulence marker and resistance mechanism
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13. Cont … …Lab
4 . Diagnostic tools for early detection of candidemia
 Clinical and radiological signs are non specific
 Traditional culture-based tools suffer from low sensitivity
 Generated interest include combined detection
 Mannan antigen
 Anti-mannan antibodies,
𝛽-1, 3, D-glucan
Molecular techniques
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14. Treatment and prevention
 Multidrug resistant bacteria in hospitals cause therapeutic
challenges therefore
 Develop strategies to prevent BSI infections
 Education and training of health-care workers,
 Use of maximum sterile barrier precautions
 Appropriate skin antisepsis during central venous catheter
insertions
 Rx:  Based on AST of isolate
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15. 2. Sepsis
 Definition
 Sepsis is a life threatening condition from blood poisoning
 Can be systemic inflammatory response syndrome
 Can be bacterial, viral, fungal, and parasitic infection
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16. Table 2. Three stages of sepsis
stages of sepsis Symptoms and severity
Sepsis Sepsis syndrome
High fever, rapid breathing and high pulse
Sever sepsis sepsis syndrome
complication of organ dysfunction,
 hypotension,
oliguria, hypoxia, confusion, slurred speech and dizziness
Septic shock sepsis syndrome
organ dysfunction
Hypotension
unresponsive to adequate fluid replacement
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17. Predisposing factors
 Organisms vary with several factors such as
 Low immunity due to
 HIV/AIDS,
 Cirrhosis,
 Autoimmune disease
 Solid organ transplantation
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Pregnant women
Newborns
Elderly
Low immunity
Diabetes
Life support devices
Surgery
Chronic kidney disease
Neutropenia
Cancer
 Inflammatory disorder

18. Epidemiology
 Over the past 40 years the incidence of severe sepsis has
substantially increased,
 Common (More than 200,000 cases per year in US)
 Women have a lower incidence of severe sepsis
 Older patients are far more likely to develop sepsis
 Only AIDS, neutropenia and cancer
 Were idependent risk factors for 28 day
 mortality
 Genetic variants like polymorphisms in Toll-like receptor (TLR4)
and TLR1 have been associated with increased susceptibility to
sepsis
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19. Table 3. Genetic variants and sepsis
TLR4 polymorphism Mechanism
Asp299Gly variants and Protection against cerebral malaria
Related to ethnic deferences in incidence and
severity of sepsis
SVEP1 allele frequency Which encodes a cell adhesion molecule
 Capable of interacting with complement,
growth factors, integrins, and cytokines
FER gene  (Fps/FES related tyrosine kinase,
 Cytosolic protein
Involved in leukocyte recruitment
 Associated with increased survival from sepsis
patients with pneumonia
NOD2 were additive in increasing the risk of
bacteremia
and hospital mortality
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20. Causative agents
A. Non-infectious
 Patients who develop a clinical picture of sepsis without an
identifiable infection
 Several sterile inflammatory conditions can also progress to shock
and multiorgan failure these include
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 Pancreatitis
 Tissue ischemia
 Trauma
Surgical tissue injury
Thromboembolism
 Vasculitis
Drug reactions
 Burns

21. Cont… …Cau
2. Infectious
 The infectious causes of sepsis
Gram-positive bacteria-cocci
 Gram-negative bacteria-bacilli
fungi (Candida),parasites and viruses
 The site of infection mainly
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 Lungs
 An infected insect bite
 Abdominal infection
 Wound infection
 Genitourinary tract
 Central line infection

22. Pathogenesis
Sepsis
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Pathogenic
products and
components
Activation of
coagulation and
complement system
Tissue factor release
fibrinolytic activity
Macrophage
and other
immune cell
TNF –a
IL-1
IL-6
Neutrophil
activation
aggregation and
Degranulation
Release ROS and
protease
Platelet
activation and
degranulation
Endothelial damage
Tissue injury
Organ dysfunction
T-cell release
IL-1 and INF-ý

23. Cont … … path
 Among bacteria inflammatory and coagulation pathways may
be complex interactions
 Malfunction of the regulatory mechanisms during sepsis
 Loss of control inflammation due to the excessive activation
of the inflammatory response
 Widespread tissue factor expression, fibrin deposition, and
impaired anticoagulant mechanisms
 Can produce and disseminated intravascular coagulation (DIC)
 Widespread immunothrombosis can result in DIC
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24. Cont… … path
 Impaired microvascular function and organ injury
 Asyndrome associated with increased organ dysfunction
 Bleeding and mortality
 pathogenesis in different level
A. Organ and tissue level
 A sepsis progresses from a localized infection to mild systemic
inflammation and on to septic shock, disseminated to different
organ
 The endothelial changes in severe sepsis are associated with altered
barrier function in other organs
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25. Tabel 4. sepsis in different Organ
Organ pathogenesis in sepsis
Lung Permeable lung capillaries and accumulation of protein-rich edema fluid
Alveolar epithelial barrier dysfunction and edema fluid floods into alveoli
Mismatch arterial hypoxemia and reduced lung compliance
Breakdown endothelial and epithelial barriers lethal organ dysfunction
Gastro intestinal Gut epithelium permeable in hypercytokinemia
Gut injury by pancreatic enzymes (autodigestion)
Bacterial translocation
Worsening systemic inflammation and multiple organ dysfunction
Liver Impairs hepatocyte and loss crucial hepatic functions
Loss clearance of bilirubin
Loss transport and processing of enteric pathogen lipids
Acute kidney
injury (AKI)
Is common in severe sepsis and increases the risk of death
Cytokine and immune mediated microvascular tubular dysfunction
Nervous system Endothelial dysfunction compromises the blood-brain barrier
 Cytokines and cells to enter the brain causing encephalopathy
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26. Cont… …path
B. Cellular and molecular level
 Asingle inflammatory macrophage derived cytokine can produce a
clinical picture of septic shock
 Proteins such as complement and fibrinogen cause neutrophils to
release extracellular traps (NETs),
 Inflammatory cytokine production response is rapid control
localized infections but response exceeds systemic injury occurs
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27. Table 5. Cellular and molecular level
Pathophysiologic
processes
Mechanism
Inflammatory
signaling
Inet immune cell to detect PAMPs, DAMPs and receptors in the cytosol
Transcription type I interferons , TNF-a IL-1 and IL-6
NOD assemble in to inflammasomes
Maturation and secretion IL-18 and IL-1ß,
Can trigger highly inflammatory and programmed cell death by caspase
Early damage
pathways
Inflammatory cytokine production
Reactive oxygen species (ROS) production
Damage cellular proteins lipids, and DNA
Impair mitochondrial function
Metabolic dysfunction ATP levels drop at the cellular level
Catabolism
Rapid breakdown of muscle tissue
Proliferation of innate immune cells
Resolution pathways Anti-inflammatory cytokine pathways are activated
Produced IL-10 suppresses production of IL-6 and interferon ý
Production receptors anti TNF-a and IL-1 signaling to neutralize
Subcellular level autophagy provides to eliminate DAMPs and PAMPs
Lysosomal degradation of pathogens, damaged organelles and proteins
Reducing inflammasome activation8/17/2020 27

28. Cont… … path
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29. Clinical feature
 Generalized body swelling
 Faster heart rate
 Reduced urine output
 Fever and chills
 Decrease in platelet count
 Difficulty In breathing
 Mental confusion
 Hyperventilation
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30. Cont… … Cli
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31. Diagnosis
 It’s difficult to self- diagnose blood poisoning because its
symptoms mimic those of other conditions
 First perform a physical exam
 Lab dx
 Imaging scan :- Detect infection in body’s organs
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 Blood culture and PCR
 Blood oxgen levels
 Blood count
Clotting factor
Urine tests including urine culture
Electrolyte and kidney function tests
X-ray
CT scan
Mri Scan
Ultrasound

32. Treatment and Prevention
 Treatment of blood poisning is essential because the
infection can quickly spread to tissues or heart valves
 Showing symptoms of shock admitted to the ICU
 Sepsis is usually treated with
 Mechanically ventilated
 Dialysis
 Vasopressor resuscitation
Prevention
• Source control should be considered
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Hydration
Use of blood products
Intravenous antibiotic therapy

33. Management of sepsis in pediatric patients
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Maternally
acquired

34. 3. Endocarditis
 Definition:
 Is an infection of the endocardium, which is the inner lining of
heart chambers especially heart valves
 Risk factors
 Intravenous foreign bodies from
 prosthetic valves pacemaker leads and conduits and also
 Bacteremia
 Hematogenous infection
 Intravenous drug abusers
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Urinary catheterization
Small injuries to skin
 Mucosal surfaces injuries

35. Epidemiology
 Infective endocarditis is uncommon but not rare infection
 Affecting 10,000 to 20,000 persons annually in the United States
 Accounts for approximately1 in every 1,000 hospital admissions
 Causative agent
 Generally occurs when bacteria, fungi or other germs from another
part of the body spread through bloodstream and attach to damaged
areas
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36. Pathogenesis
 Infective endocarditis begins when germs enter the bloodstream
and then travel to the heart
 The path physiology of infective endocarditis comprises at least
three critical elements:
Preparation of the cardiac valve for bacterial adherence
Adhesion of circulating bacteria to the prepared valvular
surface
Survival of the adherent bacteria on the surface
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37. Cont… …path
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38. Clinical feature
 Non specific symptoms, low grade fever , headache, fatigue…
 CHF
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39. Diagnosis
 Blood culture and PCR,
 Serological tests and BFA
 Electrocardiogram (ECG) for myocardial status
 Treatment:
 Antibiotics IV for 2-8 weeks and Surgery to replace valves
 Prophylaxis in high risk pts. like tonsillectomy, infections of
the GI or GU and urinary tract manipulation
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40. 4. Pyrexia of Unknown Origin
 Definition:
 Pyrexia of unknown origin refers to a condition in which the
patient has an elevated temperature but despite investigations by
a physician no explanation has been found
 Risk factors
 Infection
 Noninfectious inflammatory diseases
 Neoplasm
 Thermoregulatory disorders
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41. Pathogenesis
 The majority of febrile episodes probably due to infection
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42. Clinical features
 Death is rare but can occur due to
Respiratory obstruction
Haemorrhage (splenic rupture or thrombocytopenia
Encephalitis
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43. Table 6. Classification of Fever of Unknown Origin (FUO)
Category of
FUO
Definition Common etiologies
Classic Temperature >38.3°C (100.9°F) Infection,
Malignancy,
COllagen vascular disease
Duration of >3 weeks
Evaluation of at least 3 outpatient
visits or 3 days in hospital
Nosocomial Temperature >38.3°C Clostridium difficile enterocolitis,
Drug-induced,
Pulmonary embolism,
Septic thrombophlebitis,
Sinusitis
Patient hospitalized ≥24 hours but
no fever or incubating on admission
Evaluation of at least 3 days
Immune
deficient
(neutropenic)
Temperature >38.3°C Opportunistic bacterial infections,
Aspergillosis,
Candidiasis,
 Herpes virus
Neutrophil count ≤ 500 per mm3
Evaluation of at least 3 days
HIV-
associated
Temperature >38.3°C Cytomegalovirus,
Mycobacterium avium-intracellulare
complex,
Pneumocystis carinii pneumonia,
Drug-induced,
Kaposi's sarcoma,
Lymphoma
Duration of >4 weeks for
outpatients, >3 days for inpatients
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44. Lab Diagnosis
 General Lab indicators: CBC, ESR, CRP, BF and BFA
 Blood, Urine culture
 Serology
 Treatment
 Generally avoid empirical treatment
 Since it can mask / delay diagnosis
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45. Summary
 Improving the methodologies for detection, prevention, and
management of blood stream infections so that we can reach a
stage of “zero” morbidity and mortality from this infection
 Sepsis is a severe blood infection, introduces a large number of
bacteria into the bloodstream and affected organ.
 The number of bacteria in the bloodstream is large enough
endocarditis can develop, even in people who have normal heart
valves
 Endocarditis occur mitral valve or the aortic valve is infected.8/17/2020 45

46. Thank you!
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