PRINCIPLES OF INFECTIOUS DISEASES: ANTIMICROBIAL THERAPY AND LABORATORY MONITORING

ID

• are caused by microorganisms including: viruses, bacteria, fungi, protozoa, parasites

• transmitted by various mechanisms including: physical contact, through body fluids, consuming contaminated food or water, touching contaminated objects, airborne inhalation

• Factors impacting treatment: pathogen(bugs) , antimicrobial (drug), patient (host)

Systematic approach to treating ID

1. Confirm the presence of infection : Fever

• the average normal body temperature range taken orally is 36.7 -37 ℃ (98℉ to 98.6℉)

  • Normal daily temperature variation of 0.5℃ (0.9℉) and 1℃ (1.8℉) if

    recovering from a febrile illness

• Fever is defined as a controlled elevation of body temperature above the normal range

  • Aberrations of temperature reaching >38℃ (100.4℉) or <36℃ (96.8℉) are indicative of systemic inflammation

  • Ability to develop fever in older adults is impaired and their baseline temperature is lower, thus can have clinical implications when treating the elderly

  • During fever, the hypothalamus is reset at a higher temperature

  • Elevated body temperature, unless very high (greater than 40.5℃ [105℉]), is not harmful and may be beneficial

  • Check to see if antipyretics been given as they can affect patient’s temperature reading

• How was temperature measured?

  •  Oral

  • Rectal: 0.6℃ (1℉) higher than oral

  • Axillary: 0.6℃ (1℉) lower than oral

  • Skin: less than the oral temperature but can vary depending

    on the specific measurement method

  • Tympanic membrane: more variable, unadjusted-mode

    tympanic membrane values are 0.8℃ (1.6℉) lower than

    rectal temperatures, adjusted mode similar to rectal

    temperature

  • Forehead (temporal) scanner is usually 0.5℉ (0.3℃) to 1℉

    (0.6℃) lower than an oral temperature

1. Confirm the presence of infection : Signs and symptoms of Infection

• localized

  • GI: diarrhea, n/v, abdominal pain/distention

  • Urinary: dysuria, frequency, urgency

  • CNS: headache, stiff neck, photophobia, seizures

  • Skin/skin structure: erythema (Skin redness) , swelling, warmth, pain, purulent discharge

  • Respiratory: sputum production, cough, sore throat, otalgia

  • Other: chills, rigors

• systemic

  • Hypo or hyperthermia

  • Malaise

  • Tachycardia

  • Tachypnea

  • Hypotension

  • Hypoxemia, acidosis/alkalosis

  • Mental status changes

  • Weakness

1. Confirm the presence of infection : Diagnostic Information Confirming Infection

• imaging and scans

  • x rays

  • CT scan

  • MRI

  • others

• examples

  • Chest X-ray or CT: consolidation, infiltrate, effusion, cavitary

    nodules

  • Bone X-ray or MRI: bony destruction or periosteal elevation

  • ECHO: vegetations

  • Head CT/MRI: rin- enhancing lesions

  • Abdominal ultrasound or CT: perforation, abscess

1. Confirm the presence of infection : Labs : WBC

1. Confirm the presence of infection :Use of Other Laboratory Tests

• Acute phase reactants

  • Elevated in inflammatory state; not specific for infection

  • Include: Erythrocyte sedimentation rate (ESR); C-reactive protein (CRP): shorter half-life

  • Large elevations in ESR and CRP are associated with infections such as endocarditis, osteomyelitis, and

    pyelonephritis

  • ESR can be especially useful in tracking the improvement and resolution of chronic infections such as osteomyelitis, as it has demonstrable value in determining the efficacy of therapy

•  Procalcitonin (PCT)

  • Peptide precursor of calcitonin; rises in response to a

    proinflammatory stimulus, especially bacterial; produced by the thyroid during calcitonin synthesis, resulting in low serum levels

  • During bacterial infection, PCT is produced through alternative

    pathways in the spleen, kidneys, colon, brain, and lungs in response to

    inflammatory cytokines

  • PCT levels may help determine whether to discontinue empiric

    antibiotics in possibly infected patients as well as to determine

    when antibiotics can be discontinued in patients recovering from infections (pneumonia)

  • ATS/IDSA Guidelines recommend that empiric antibiotic therapy

    should be initiated in adults with clinically suspected/radiographically

    confirmed CAP regardless of initial serum procalcitonin level

  • PCT level < 0.25 ng/mL associated with low risk of infection and can

    help justify the discontinuation of antibiotics, while while levels >0.5

    ng/mL may indicate antibiotics should be continued

2.Identification of the pathogen: Approach to Identifying Organism Causing Infection:

Where We Are Going

2.Identification of the pathogen: Use of the Laboratory Tests

• Rapid Bacterial Detection

  • Helps in determining empiric antimicrobial therapy

  • Gram Staining

    • Color: positive (purple), negative (pink), variable

  • Morphology (shape): spherical, rod, oval, spiral

  • Aggregation/Colony Clustering: pairs, clusters, chains

  • Review Dr. Munson’s slides on this and learn the basic classification of bacteria

    • Why do Gram-positive vs. Gram-negative bacteria stain the colors

      that they do? from dr munsons

• Other Bacterial Detection

  • Biochemistry

    • Rapid catalase test: catalase enzyme neutralizes the bactericidal effects of hydrogen peroxide and protects the bacteria (anaerobes generally lack the catalase enzyme)

      • Helps differentiate Staphylococci from Streptococci

    • Coagulase test: coagulase is an enzyme produced by Staphylococcus aureus that converts (soluble) fibrinogen in plasma to (insoluble) fibrin

      • Helps differentiate species of Staphylococci

      • Staphylococcus aureus (coagulase positive) which is more virulent vs.Staphylococcus epidermidis (coagulase negative) which is often a contaminant

    • Fermentation: ability of bacteria to metabolize sugars (glucose/lactose) to use for energy

      • Glucose/Lactose Fermenters: Enterobacteriaceae (E. Coli, Klebsiella, Serratia, Enterobacter)

      • Nonfermenting: Pseudomonas, Acinetobacter, Stenotrophonmonas, Burholderia

    • Oxidase test: used to identify bacteria that produce cytochrome c oxidase, an enzyme of the bacterial electron transport chain (and can

      use oxygen for energy production by converting O2 to H2O2 or H2O with an electron transfer chain)

      • Oxidase positive: Pseudomonas, Pasteurella , Moraxella, others

      • Oxidase negative: Enterobacteriaceae, others

• Appearance on agar

  •  Hemolysis: Some bacteria produce exoenzymes (called hemolysins) that lyse red blood cells and degrade hemoglobin (Beta-hemolysin breaks down the red blood cells and hemoglobin completely (clear zone); Alpha-hemolysin partially breaks down

    the red blood cells (green color due to biliverdin)

    • Helps differentiate species of Streptococci

    • ⍺-hemolytic: Streptococcus pneumoniae, viridans Streptococci

    • Β-hemolytic: Group A Streptococcus (pyogenes), Streptococcus

      agalactiae, Streptococcus Groups C, F, G

    • Nonhemolytic: Enterococci

2.Identification of the pathogen : Use of Laboratory Tests

• Slow Bacterial Detection

  • Fastidious Organisms: grow slowly (few days to weeks) and often require special media and nutrients

  • Examples: Mycobacterium, Haemophilus, Campylobacter, Helicobacter, Neisseria, Bartonella, Listeria, Legionella, Chlamydia, HACEK organisms (Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, Kingella)

• Other staining

  • Ziehl–Neelsen stain

    • Detect acid-fast bacilli, which is used for the identification of mycobacteria species by making them appear bright red against a blue or green background

• India ink, potassium hydroxide (KOH), Grocott’s Methenamine Silver (GMS), others

  • Detect fungi

Gram Stain

2.Identification of the pathogen :Use of Laboratory Tests: Rapid Diagnostic Testing (RDT)

• Traditional diagnostic testing for identification/susceptibility can take at least 48-72h, whereas RDT’s can significantly reduce time by at least 24h

• Use techniques such as polymerase chain reactions (PCR) or matrix-associated laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry that don’t relay on culturing

  • Common types include antigen, antibody, and nucleic acid amplification tests

• Have been shown to:

  • Decrease: time to effective and optimal therapy, antibiotic utilization, length of stay, mortality, costs

  • Increase: clinical cure rates, likelihood of ID consult

• Target microorganisms associated with increased morbidity and mortality including: Candida, Clostridioides difficile, MRSA nasal swabs, viruses (HIV,influenza, COVID), malaria, Group A Streptococcus (Rapid Strep Test), gram negative and gram positive bacteremias, meningitis, others

2.Identification of the pathogen :Use of Laboratory Tests: Culture and Susceptibility

• (24-72 hours)

  • Most definitive method for diagnosis and treatment of an

    infection

  • Sites tested determined by suspected site of infection (urine, blood, CSF, sputum, etc.)

  • Provides initial identification of organism by:

    • Gram stain

    • Growth on selective media

    • Presence or absence of enzymes

    • Chemical characteristics

  • Definitive identification of organism follows

  • Susceptibility (sensitivity) of organism to antimicrobial agent

2.Identification of the pathogen :Use of Laboratory Tests: MIC and MBC

• Minimum Inhibitory Concentration (MIC): Lowest concentration

  of drug that will inhibit visible growth

  • Organism is isolated and drug added in vitro to determine

• Minimum Bactericidal Concentration (MBC): Lowest

  concentration of drug that kills the bacteria or results in 99.9% reduction of the initial inoculum

  • Organism is isolated and drug added in vitro to determine

  • Subculture of tubes showing inhibition of growth

  • More difficult to perform and not usually done in clinical practice

2.Identification of the pathogen :Use of Laboratory Tests

• Sensitivity Testing Methods

  • Disk Diffusion (Kirby-Bauer)

  • Tube-dilution

  • Automated

    •  Vitek System

    • Microscan Walkaway System

    • BD Phoenix Automated Microbiology System

  • Epsilometer test (E test)

• Interpretative Guidelines (based on breakpoints set by Clinical and Laboratory Standards Institute [CLSI])

  • Sensitive (susceptible)

  • Intermediate (moderately susceptible)

  • Resistant

Use of Laboratory Tests

• Bactericidal:

  • Antibiotic kills the bacteria without needing help from the patient’s immune system (preferred for endocarditis, meningitis, osteomyelitis, neutropenic patients)

• Bacteriostatic:

  • Antibiotic inhibits growth of the bacteria without killing it, but is usually successful in treating infection because the immune system of the patient can kill the bacteria

Microdilution MIC Testing: commonly used in micro labs

and in automated systems

Sensitivity Testing Methods: Epsilometer Test (Etest)

• Plastic strip with fixed concentration gradient of an antibiotic placed on an agar plate streaked with bacteria

• Bottom of ellipse crossing strip is the MIC

• Employed for Streptococcus pneumoniae, some gram negatives

Antibiotic Susceptibility : MIC Breakpoints

• MIC Breakpoint: concentration at which antibiotic and

  bacteria is considered susceptible, intermediate, resistant

  • Standards published by Clinical and Laboratory Standards Institute (CLSI) and set by FDA upon drug approval process

  • Breakpoints established by achievable serum concentrations of the antibiotic after normal dosing, inherent susceptibility of the organism to the antibiotic, site of infection, and results of efficacy trial

  • Breakpoints vary for an antibiotic based on the particular bacteria and site of the infection

  • Done to help predict the probable response of an infection to an antibiotic

MIC Breakpoints. : Susceptible

bacteria tested has a low MIC (very sensitive) will most likely be eradicated since concentrations (represented by the MIC) are easily achievable by standard doses employed

MIC Breakpoints: Intermediate

bacteria tested has a higher MIC and thussuccessful treatment may or may not occur or might possibly employ a higher dose

MIC Breakpoints:Resistant

bacteria tested has an extremely high MIC (not sensitive) that exceeds the achievable serum concentration of the antibiotic even if high doses are

used, and the strain would not be inhibited and poor patient response would be expected

Antibiotic Susceptibility Breakpoints

Antibiotic Susceptibility Testing

Clinical Pearls

• Just because an antibiotic has the lowest MIC for an organism does not mean it’s the best antibiotic to use because different antibiotics achieve different concentrations in the body depending on the site of infection: MIC’s are specific to the microorganism and antimicrobial

• Remember that the in vitro efficacy of the susceptibility tests may not translate into in vivo efficacy in the patient due to multiple factors

• Other factors need to be considered—make sure always make the clinical correlation

  • Site of infection

  • Severity of infection

  • Pharmacokinetics

  • Concomitant disease states, allergies, etc.

  • Spectrum of activity (narrow preferred)

  • Efficacy from clinical trials/drug of choice

  • Cost

Sensitivity Testing: Other Microorganisms

• Historically, mycobacteria, fungal, and viral sensitivity testing

  has not been well defined

• More recent advances have improved this

  • Radiometric techniques (BACTEC TB460 with results within 1 week, BACTEC Mycobacteria Growth Indicator Tube [MGIT 960]) for M. tuberculosis and other slow growing mycobacteria

  • Fungal sensitivities much more reliable and reproducible and now CLSI guidelines for

Hospital Antibiograms

• Cumulative report of the antimicrobial susceptibility profiles of

  the organism isolated with a hospital and surrounding

  community

• Reports the percent of isolated organisms that were susceptible

  to different antibiotics over a certain time frame (yearly, twice

  yearly, etc.)

• Useful for selecting the most appropriate empiric antibiotic

• May be done in different areas of hospital as well

use

use of laboratory tests : Serum Antibiotic Assay

• Can be done with any drug

• Various methods to perform in lab:

  • Fluorescence-Polarization Immunoassay (TDx system)— most common

  • Radioimmunoassay (RIA)

  • High-Pressure Liquid Chromatography (HPLC)

• Most useful for drugs with narrow therapeutic index to

  maximize efficacy and minimize toxicity

  • Examples: aminoglycosides, vancomycin

• Types of levels: peak, trough, random levels

Pharmacokinetic/Pharmacodynamic

Parameters and Dose Optimization

• Peak/MIC ratio (concentration-dependent)

  • Need to optimize dose to produce higher drug concentrations

  • Aminoglycosides, quinolones, daptomycin

  • Goal: high peak (increased bacterial killing), low trough (decreased toxicity)

  • Dosing: large dose, long dosing interval

• AUC/MIC ratio (exposure-dependent)

  • Need to optimize dose and exposure to unbound drug concentrations

  • Vancomycin (AUC/MIC>400-600), macrolides, tetracyclines, polymyxins

  • Goal: exposure over time

  • Dosing: variable

• Time above MIC (time-dependent)

  • Optimize duration unbound concentration at or above the MIC

  • Beta lactams (penicillins, cephalosporins, carbapenems)

  • Goal is to have drug levels above the MIC for most of the dosing interval

  • Dosing: shorter dosing interval, extended or continued infusions

use of laboratory tests:  Postantibiotic Effect (PAE)

• Continued suppression of bacterial growth after the antibiotic serum levels fall below the MIC

• Can be tested in lab by exposing bacteria to the antibiotic, and then removing/inactivating the antibiotic, and then time recorded on how long takes bacteria to regrow; quantified as time takes for organism to demonstrate 10-fold increase in viable cells (not usually tested in clinical practice)

• Clinically applied for extended interval aminoglycosides and some other antibiotics to allow for less frequent administration

3. Selection of presumptive therapy:Types of Infection

• Community-Acquired Infection

  • Infection originating in the outpatient or community setting or is present on admission

  • No recent hospitalization or invasive medical procedure

• Hospital-acquired (or nosocomial) Infection

  • Infection occurs 48 hours or more after admission and did not appear to be incubating at the time of admission

3. Selection of presumptive therapy:Describing ID States:

   Colonization

microorganisms do not invade the host and are part of the normal flora of the site without host inflammatory responses

3. Selection of presumptive therapy:Describing ID States:  Contamination

the presence of microorganisms typically acquired during acquisition or processing of specimens without host inflammatory response

3. Selection of presumptive therapy:Describing ID States: Infection

microorganisms invade the host and with host inflammatory response (signs/symptoms of infectious process)

Sterile anatomical sites: 

• CSF, blood, lungs, urinary tract, biliary

  tract

  • Microorganisms if found usually pathogenic, although could be colonization or contamination

  • Clinical correlation is important

Non-sterile anatomical sites:

• sputum, pus, skin, GI tract, vagina

  • Microorganisms expected to grow

  • Clinical correlation still important

Rational

Antibiotic

Selection

Types of ID Treatment: Empiric

Initial broad antimicrobial spectrum before identification of the organisms directed against the organisms know to cause the infection in question based on patient’s presentation

Types of ID Treatment:  Definitive:

Antimicrobials selected based on clear identification of the organism(s) and proven sensitivity of the organism(s)

Types of ID Treatment:  Prophylactic:

Antimicrobial directed against a single pathogen or multiple pathogens to prevent an infection from occurring; is usually short-term (before surgery, dental procedures) but can be long-term (AIDS)

Combination Antimicrobial Therapy

Advantages

• Broadening the spectrum of coverage : Necessary in mixed infections where multiple organisms expected (ex. intraabdominal infections)

• Synergism: Certain infections such as Enterococcus endocarditis

  (penicillin or ampicillin + gentamicin or streptomycin)

•  Prevent development of resistance

  • Used in tuberculosis

  • Other infections: data not as convincing

Antibiotic Combinations :Antimicrobial Combination Effect Test

• Done by microtiter fractional inhibitory concentration (“checkerboard” method) or timed-kill curves

• Not routinely done in clinical practice

• Categories

  • Synergy: Greater activity than the sum of activity of either agent alone

  • Antagonism: Activity that is worse than either agent alone

  • Additive/Indifferent: Activity that is neither synergistic or antagonistic

• Enterococcus—susceptibility to high concentrations of aminoglycosides (gentamicin 500 mg/mL) is evaluated in the lab because it correlates closely with synergy when combined with beta lactam antibiotics (endocarditis treatment)

Combination Antimicrobial Therapy

Disadvantages

• Increased costs

• Increased risk of toxicity

• Superinfection with resistant organisms

• Antagonism

4. Monitor therapeutic response: ID Monitoring

• After antimicrobial therapy has been started, monitoring of therapeutic response important

• Culture and sensitivity reports should be reviewed and therapy adjusted accordingly

  • Antimicrobials with narrowest spectrum of activity against identified pathogens recommended (streamlining therapy)

  • If anaerobes are suspected even if not identified, anaerobic therapy should be continued

• Patient monitoring should include many of the same parameters used to diagnose the infection

  • WBC and temperature should start to normalize

  • Physical complaints from the patient also should diminish (decreased pain, shortness of breath, cough, or sputum production)

  • Appetite should improve

  • Radiologic improvement can lag behind clinical improvement

• Monitor serum (or other fluid) levels of antimicrobials to ensure outcome, preventing toxicity, or both (aminoglycosides, vancomycin, others)

  • Monitor for changes in Vd, clearance

• Streamline route of administration (IV to PO switch) if possible

  • Overall clinical improvement, lack of fever for 8 to 24 hours, decreased WBC, functioning GI tract

  • Drugs with good BA

• Antimicrobial failure

  • If fail to respond over 2 to 3 days, then reevaluate

  • Disease may not be infectious or is nonbacterial in origin or there is an undetected pathogen

  • Other factors: drug selection, the host, microorganism (resistance), laboratory error in identification or susceptibility testing or both (presence of inoculum effect or resistant subpopulations)

• Antimicrobial Stewardship Programs (ASP’s) designed to promote effective use of antimicrobials

Antibiotic Resistance

• Ability of bacteria to grow in the presence of an antibiotic that

  normally limits its growth or kills it

• Significant problem resulting in antibiotic failure and significant

  morbidity and mortality

• Mechanisms of resistance:

  • Intrinsic: natural to the bacteria (ex. vancomycin resistance to gram negative bacteria because is too large to penetrate cell wall)

  • Selection Pressure: antibiotics eliminate susceptible bacteria leaving behind more resistance bacterial strains to grow

  • Acquired: bacterial DNA containing resistant genes can be transferred between different species or obtained from dead environmental bacterial fragments

  • Enzyme Inactivation: bacteria produce enzymes that inactivate the antibiotic (examples include beta lactamases, extended-spectrum beta- lactamases (ESBLs), carbapenem-resistant Enterobacteriaceae (CRE)

Common Resistant Bacteria

• Klebsiella pnuemoniae (ESBL, CRE)

• Escherichia coli (ESBL, CRE)

• Acinetobacter baumannii

• Enterococcus faecalis, Enterococcus faecium (VRE)

• Staphylococcus aureus (MRSA)

• Pseudomonas aeruginosa

  Pneumonic: Kill Each and Every Strong Pathogen

Antibiotic Resistance Mechanisms