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Searching for microbes Part V. Testing of microbial susceptibility to antibacterial agents and assessment of microbial resistance factors. Ondřej Zahradníček To practical of VLLM0421c Contact to me: [email protected] Introduction & tale. Content of this slideshow.

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Ond ej zahradn ek to practical of vllm0421c contact to me zahradnicek@fnusa cz

Searching for microbesPart V.Testing of microbial susceptibility to antibacterial agents and assessment ofmicrobial resistance factors

Ondřej Zahradníček

To practical of VLLM0421c

Contact to me:

[email protected]


Content of this slideshow

Introduction & tale

Content of this slideshow

Antimicrobial agents – overview

MIC, MBC, bactericidal and bacteriostatic antibiotics

Mechanisms of action of atb-s and mechanisms of resistance

Epidemiologically important types of resistance

Methods of susceptibility testing I: Diffusion disc test

Methods of susceptibility testing II: E-test

Methods of susceptibility testing III: Microdilution test

Methods of assessment of resistance factors + phage therapy

Check-up questions


Ond ej zahradn ek to practical of vllm0421c contact to me zahradnicek fnusa cz

Tale

  • There was an antibiotic, let's call him ampicillin. And he decided to go out and to help people to fight with microbes.

  • It was a brave antibiotic, decided to destroy any microbe, that might walk around. Nevertheless…


Ampicillin meets microbes

Ampicillin meets microbes…

  • The first microbe was called Proteus mirabilis and really, it was destroyed by ampicillin. And ampicillin was pleasured by that, and continued it‘s trip.

  • But he met another microbe. Klebsiella pneumoniae, and he was disgusted. Ampicillin said: Oh, no, Klebsiella, I cannot destroy you, you are primarily resistant to me, I can do nothing… I will continue my trip, and I will send you a more effective brother to destroy you…


And the third meeting

And the third meeting

  • Ampicillin met a microbe called Escherichia coli. It is OK, it said to itself, I could destroy it. Nevertheless… Escherichia escaped, and giggled: Ha, ha, you thought you can destroy me! Well, some time ago, I was susceptible to you, but then I have developedsecondary resistance, and so you can never catch me!


Ampicillin was very sad

Ampicillin was very sad…

  • But a microbiologist came and told him: don‘t worry, be happy, ampicillin, next time it‘ll be better. Each microbe, that could be either susceptible or resistant to you, should be tested, to see the situation. And if you will be found to be no help for treatment? After susceptibility testing we will see, who of your brothers could be sent to fight the microbe!

  • So ampicillin dried his tears, and run to help people again.


What to learn from our tale

What to learn from our tale

  • Some microbes are primarily resistant to some antibiotics. It has no sense to test their antibiotic susceptibility – it is zero.

  • Other microbes may (not necessarily) get secondarily resistant. Then

    • either we test microbial antibiotic in vitro susceptibility to the given antimicrobial agent

    • or we search for a certain factor, produced by bacteria, that is responsible for the microbial resistance


Antimicrobial agents overview

Antimicrobial agents – overview


Methods of fight with microbes

Methods of „fight“ with microbes

  • Immunization – exploits natural mechanisms of a macroorganism

  • Decontamination methods – crude physical and chemical influences, action outside the organism (see last practical)

  • Antimicrobial agents – fine, targeted action inside the organism with aim of maximal effect of the microbe and minimal influence on the host macroorganism

  • And also some more methods, for example use of bacteriophages (= „biological fight“)


Types of antimicrobial agents

Types of antimicrobial agents

First antibiotic was penicillin, derived by A. Fleming

  • Agents acting to the whole body:

    • Antiparasital agents against parasites

    • Antimycotics against yeasts and molds

    • Antiviroticsagainst viruses

    • Antituberculotics against mycobacteria

    • Antibioticsagainst bacteria (natural origin)

    • Antibacterial chemotherapeutics also against bacteria, but synthetic

      In recent period, the last two groups are often put into one group called „antibiotics“

  • Locally acting agents:antiseptics


Decontamination or an antimicrobial agent

Decontamination, or an antimicrobial agent?

  • The borderline between decontamination methods and antimicrobial agents is not sharp.

  • Usually action on intact skin is still considered to be a decontamination.

  • Application into the wound means already use of an antimicrobial agent (antiseptic)

  • It has its legal consequences: decontamination agents are not considered „remedies“


Mic mbc bacteriostatic and bactericidal antibiotics

MIC, MBC, bacteriostatic and bactericidalantibiotics


Action of influences on microbes i

lower survival limit (bactericidal)

lower growth limit (inhibitory)

upper growth limit (inhibitory)

upper survival limit (bactericidal)

Action of influences on microbes I

  • At action of an influence like pH the axe has both upper and lower extremes

upper growth limit (inhibitory)

upper survival limit (bactericidal)

  • At action of antimicrobial agents (but also e. g. disinfectants)only right part of the axe has a logical sense


Action of influences on microbes ii

Action of influences on microbes II

  • At decontamination we insist on killing microbes (microbicidal effect)

  • At use of antimicrobial agents we can count with cooperation of patient‘s immunity, therefore even microbistatic (inhibitory) effect is usually sufficient

  • This is not valid for acute states or immunocompromised patients, where we try to ensure microbicidal action always


Mic and mbc

MIC and MBC

MIC – minimal inhibitory concentration is a term, that is used in antibiotics for growth (multiplication) limit of a microbe

MBC – minimal bactericidal concentration is a term used in antibiotics for survival limit of a microbe. (For simplicity, we talk about bacteria only. In viruses, we would use term „minimal virucidal concentration“ etc.)

Later, you will meet also terms MBIC and MBEC, that are connected with action of on antibiotic in biofilm


Primarily bactericidal and primarily bacteriostatic antibiotics

Primarily bactericidal and primarily bacteriostatic antibiotics

Primarily bactericidal are atb-s, where MIC and MBC are nearly equal

Primarily bacteriostatic are atb-s, where values over MIC, but not over MBC are exploited (they are inhibitory in substance)

In practice, we avoid using bacteriostatic antibiotics in serious acute states, imunosupressed patients etc. (This rule is not absolute – e. g. atb-s with very good effect to bone tissue are used for acute osteomyelitis treatment despite being bacteriostatic only)


Primarily bactericidal and primarily bacteriostatic atb

Primarily bactericidal and primarily bacteriostatic atb

Primarily bactericidal antibiotic

THERAPEUTICAL

CONCENTRATIONS

atb concentration

toxicity for the macroorganism

Primarily bacteriostatic antibiotic


Mechanisms of action and mechanisms of resistance

Mechanisms of action and mechanisms of resistance


Mechanisms of antibiotic action

Mechanisms of antibiotic action

  • To the cell wall (bactericidal)

    • Betalactamic antibiotics

    • Glycopeptidic antibiotics (partially)

  • To cytoplasmic membrane – polypeptids (bactericidal)

  • To nucleic acids – quinolones (bactericidal)

  • To proteosynthesis:aminoglykosides (bactericidal); makrolids, tetracyclins, linkosamids, amphenicols (bacteriostatic)

  • To metabolism – sulfonamids, bacteriostatic

  • Primarily bacteriostatic antibiotics are not recommended for treatment in acute states and immunocompromised persons!

BAKTERICIDAL

BAKTERIO- STATIC


Microbial resistance to antimicrobial agents

Microbial resistance to antimicrobial agents

  • Primary resistance: all strains of a given species are resistant. Example: betalactamic atb-s do not act on mycoplasms, that do not have any cell wall at all.

  • Secondary resistance: non-susceptible mutants raise, and under selection pressure of an antibiotic they start to be in majority. (Escherichia may be susceptible to ampicillin, although in recent period, resistant strains become very common)


Mechanisms of resistance

Mechanisms of resistance

  • Blocade of entrance of an atb into the cell

  • Active efflux of an atb from a cell

  • A false receptor is offered to an atb

  • Microbes split antibiotics enzymatically (e. g. betalactamase split betalactamic antibiotic)

    Knowledge of the resistance mechanism enable us to try to defense ourselves against such a resistances.


Betalactamase inhibitors 1

Betalactamase inhibitors – 1

Bacterium

„BELA“ The Dog

(a betalactamase)

  • When we act by a single antibiotic, it is inactivated by a bacterial betalactamase.


Betalactamase inhibitors 2

Betalactamase inhibitors – 2

  • When a beta-lactamase has a more attractive substrate to be chosen, it is used instead, and the antibiotic can act.

ACID


Examples of antibiotics potentiated by betalactamase inhibitors

Examples of antibiotics potentiated by betalactamase inhibitors

From FN USA intranet


Beta lactamase inhibitors are not always sufficiently effective

Beta-lactamase inhibitors are not always sufficiently effective

  • Unfortunately, beta-lactamase inhibitors are effective only in some „not so strong“ types of beta-lactamases

  • There exist also extended specter beta-lactamases (see later), where inhibitors are not sufficient (the treatment is not effective although we use them)

  • Nevertheless, some effect can be seen also in these beta-lactamases. This is used in diagnostics, where we observe difference in effect of certain antibiotic with : without inhibitor


Epidemio logically important types of resistance

Epidemio- logically important types of resistance


Epidemiologically important resistance pattern s 1

Epidemiologically important resistance patterns – 1

  • MRSA – methicillin resistant staphylococci. Oxacilin or other beta lactams are not able to enter their cells. Many MRSA are also resistant to more antibiotics (macrolids, lincosamids). Glycopeptids (vancomycin, teicoplanin) remain effective.

  • VISA, VRSA – staphylococci partially or fully resistant to glycopeptids, too

  • VRE – vancomycin resistant enterococci. They sperad easily – many people have enterococci in their intestine


Mrsa in europe 2008

MRSA in Europe 2008

http://upload.wikimedia.org/wikipedia/de/e/ed/EARSS_MRSA_2008.gif


Epidemiologically important resistances 2

Epidemiologically important resistances – 2

  • ESBL (Extended Spectrum Beta Lactamase)producers. G- bacteria (Klebsiella, but also E. coli and other) may produce extended specter beta-lactamase, where even inhibitor effect is not sufficient. Only carbapenems and sometimes certain non-betalactam atb-s are effective.

  • Similar are ampC betalactamases. Besides carbapenems also 4th generation cephalosporins remain effective.

  • MLS resistance is a resistance to macrolids and lincosamids (and streptogramins) in streptococci and enterococci. In S. aureus by good luck still rare.


Antibiotic politic s atb cent re s

„Antibiotic politics“, atb centres

  • Use of broad sprecter antibiotics performs a selection pressure – resistant strains of bacteria survive.

  • In countries, where atb-s are used freely, there is usually high of atb resistance

  • In Czechia there exist „free atb-s“, that can be prescribed freely, and „special atb-s“; their use should be approved by antibiotic centre.

  • Atb center is usually part of microbiological labs in big hospitals. They do advisor work, too.


Methods of susceptibility i diffusion disc test

Methods of susceptibility I: Diffusion disc test


In vitro susceptibility observation methods

In vitro susceptibility observation methods

  • Assessment of susceptibility in vitro = in the laboratory

  • No guarantee of 100% treatment effect

  • Nevertheless, useful in majority of findings of cultivable bacteria

  • In common cases, qualitative tests (susceptible – resistant)

  • In indicated cases, quantitative tests (assessment of MIC). Usually risky strains at risky patients.


When in vitro does not correspond with in vivo

When „in vitro“ does not correspond with „in vivo“

  • At urinary infections we should use a breakpoint derived from urinary concentrations, not serum concentrations. (In majority of UTI infections, MIC is not measured)

  • In abscesses, processes in bones and mostly in meningitis: breakpoints are derived from serum concentrations, but in various parts of body the concentration they may be much lower

  • It is necessary to count that microbes may exist in a biofilm form– so, MBIC and MBEC values (biofilm inhibitory/eradication concentrations) should be assessed rather than MIC values


Diffusion disc test 1

Diffusion disc test – 1

  • To MH agar (or another one) a bacterium is inoculated from a saline suspensionusing a cotton swab

  • After that, antibiotic discs are added – round bits of papers with antibiotic

  • Atb diffuses from disc through the agar

  • In a standard Petri dish we use mostly six discs, sometimes the seventh to the middle


How to prepare a diffusion disc test

How to prepare a diffusion disc test

  • Prepare a bacterial suspension in physiological saline with glucose

  • Suspension should be distributed regularly onto the MH agar surface

  • After drying of the suspension, place carefully and uniformly the atb discs onto the agar surface


Diffusion disc test 2

Diffusion disc test – 2

  • Concentration of atb(and its inhibitory properties)decrease with distance from the disc

  • When a microbe growth to a disc, or its inhibition zone is very small, it is resistant (not susceptible, not sensitive)

  • When a zone large enough is present around the disc (more than a limit for the given antibiotic), it is susceptible (sensitive).

  • The reference zones are usually available at the disc producer, or at EUCAST:

http://www.eucast.org


Results of the diffusion disc test

Results of the diffusion disc test

CITLIVÝ

REZISTENTNÍ

1 Bacteria are affraid of antibiotics. Large zone (sometimes so large that it is impossible to measure it)

2 Bacteria are not affraid of antibiotics, they are resistant.A small zone around the disc, or no zone.


Sets of discs

Sets of discs

  • Usually we use sets of atb discs. Some sets are suitable for G+ or G– bacteria, but it is also possible to construct a set of relativelly „universal“ antibiotics (but because of polyresitstant strains, no „universal“ antibiotics are really universal)


Diffusion disk test in practice zones are measured and compared with given reference limits

Diffusion disk test in practice:Zones are measured and compared with given reference limits

No zone at all: Microbe is resistant.

www.medmicro.info

Zone is larger that the limit: Microbe is susceptible

Zone exists, but it is smaller than the reference limit: Microbe is resistant.


Diffusion disc test performed with a pigmented microbe pseudomonas aeruginosa

Diffusion disc test performed with a pigmented microbe (Pseudomonas aeruginosa)

www.medmicro.info


Sometimes the zones are too large

Sometimes the zones are too large

When zones are so large that it is impossible to measure them, do not measure them and just write, that the strain is susceptible to a given atb. In green, you have theoretical margins of zones – as you can see, majority of them are confluent or they go through the margin of the dish

Photo O. Z.


Methods of susceptibility ii e test

Methods of susceptibility II: E-test


E tests

E-tests

  • Principially simillar to diffusion disc test

  • Instead of a disc, a stripis used

  • The strip has raising atb concentration from one end to another ( grace to a special technology – that is why they are expensive)

  • The zone is not round, but egg-shaped

  • The test is quantitative

  • The strip has a scale – sipmle reeding (see image on the next screen)


E tests reading

E-tests – reading

www.uniklinik-ulm.de

We can read the MIC value directly on the strip – in place, where the margins cross the strip


Somewhere special large dishes are used

Somewhere, special large dishes are used

www.unifesp.b


Methods of susceptibility iii microdi lution test

Methods of susceptibility III: Microdi-lution test


Microdillution test

Microdillution test

  • Atb-s are in a row of wells in a plastic microtitration plate, concentration decreases

  • The lowest concentration, that inhibits the growth, is the MIC value

  • For interpretation, we need breakpointvalues for each antibiotic. MIC < breakpoint => the strain is susceptible. MIC > breakpoint => resistance

  • One plate is usually used for one strain, e. g. 12 antibiotics, each in 8 concentrations (more precisely: the 12th one in 7 concentrations only, the well in right upper corner = growth control)


Practical reading a microdilution test

Practical reading a microdilution test

  • Find and write MIC values for twelfve tested antibiotics

  • Turbid well = it grows

  • Clear well = no growth

  • No growth = it is inhibited

  • The lowest inhibitory concentration = minimal inhibitory concentration

  • MIC  breakpoint  strain susceptible

  • MIC > breakpoint  strain resistant


Microdilution test an example

Microdilution test – an example

Photo: O. Z.


Microdilution test reading

Microdilution test – reading

Sometimes, bubbles may appear in wells – do not take any regard to them when reading results

  • In case of columns 1, 3, 4 & 5, MIC value is too high and cannot be measured using this test. Nevertheless, it is possible to write „MIC > x“, where „x“ is the value in the top well.


Example of reading

Example of reading

E F G H

  • E: MIC >32, breakpoint =16, conclusion: resistant

  • F: MIC = 32, breakpoint = 16, conclusion: resistant

  • G: MIC = 8, breakpoint = 32 conclusion: susceptible

  • H: MIC £1, breakpoint = 8, conclusion: susceptible


Methods of assessment of resistance factors

Methods of assessment of resistance factors


Assessment of resistance factors

Assessment of resistance factors

  • Sometimes, instead of susceptibility testing, we should rather assess the presence of individual resistance factors by special methods, e. g. betalactamases

  • The reason for this may be following:

    • susceptibility testing does not give sure results (bad diffusion in diffusion test, antibiotic does not work directly, but as a metabolite…)

    • we want to know, whether the resistance belongs to a specific type (ESBL, ampC)


Nitrocephine test for presence of common betalactamase

Nitrocephine test for presence of common betalactamase

  • It is used in situations, where the result of a diffusion disc test, but even microdilution test, is not clear

  • Mostly we speak about

    • Neisseria (instead of penicillin susceptibility testing)

    • Moraxella catarrhalis (replaces ampicillin)

    • Haemophilus influenzae (replaces ampicillin)

  • In practice, it is a strip test similar to biochemical identification tests (oxidase test)

  • It gives good results for fresh strains only, therefore it is not performed practically in the practical sessions (results were not always good)


  • Two ways of nitrocephin test use

    Two ways of nitrocephin test use

    Testing by touching the colonies

    Testing in a liquid

    +

    -

    +

    -


    Detection of esbl type broad specter beta lactamases

    Detection of ESBL-type broad specter beta-lactamases

    • Broad spectre beta-lactamases are worse than „common“ beta-lactamases (those tested by nitrocephin test). One important type is „ESBL“ beta-lactamase. There exist two tests for it. Both tests are based on comparison of an effect of the same antibiotic (cefotaxime, ceftazidime) without/with clavulanic acid. (The effect of added clavulanic acid would not be sufficient for being used for treatment, but it is sufficient to be used in diagnostics)

    • In double disk synergy (DDS) test,(not in recent version of practical sessions)diffusion of clavulanic acid from co-amoxicilin disc (amoxicilin + clavulanic acid) is used

    • In the CLSI test we have directly discs of the same antibiotic (1) alone and (2) in combination with clavulanic acid. We compare their zones.


    Clsi test

    CLSI test

    When the difference of zone diameter of cefotaximewith inhibitor : cefotaxime without inhibitoris more than five milimeters, the strain is considered to be a (broad specter) b-lactamase producer. The same for ceftazidime.

    Difference = 9 mm

    ESBL positive

    Photo O. Z.


    Testing for some other betalactamase types

    Testing for some other betalactamase types

    • In constitutive ampC detection we compare sizes of susceptibility zones of four betalactamic antibiotics on common MH medium and medium with oxacilin

    • Besides constitutive ampC betalactamase also induced ampC betalactamase exists. The betalactamase is only produced when the bacterium is challenged by clavulanic acid or another activator

    • In recent period, new types of betalactamases occur: metalobetalactamases (mostly in G– non-fermenters) and carbapenemases (is various G– bacteria)


    Abcd test

    „ABCD“ test

    In this test we can detect two types of beta-lactamase in one test. The difference between individual discs (with various types of inhibitors) is typical for either ESBL type beta-lactamase, or constitutive type of ampC beta-lactamase (as shown on the picture)

    httpjmm.sgmjournals.orgcontent606715F1.expansion.gif


    Screening for mrsa and vre

    Screening for MRSA and VRE

    • In screening for MRSA and VRE strains (but also ESBL producers) we use special screening media.

    • They are usually chromogenic, specific for the genus and species of bacterium, and they contain the „incriminated“ antibiotic (e. g. vancomycin for VRE), so susceptible strains are not able to grow there.


    Mrsa left and vre right on their specific chromogenic media

    MRSA (left) and VRE (right) on their specific chromogenic media


    Bacteriophage therapy

    Bacteriophage therapy

    • As antibiotics become often non-effective (bacteria are resistant), alternative variants of therapycome again to the focus.

    • It is also possible to check the effect of bacteriophages, or bacteriophage lysate (mixture of proteins produced by a phage) on the culture (a strain either does or does not grow in the place where bacteriophage lysate was applied to the culture)

    • Later (in J14 and P04) we will also try the effect bacteriophages to the biofilm, and their use of so called phagotypisation (one special type of identification of bacteria)


    Bacteriphage terapy in practice

    Bacteriphage terapy in practice

    On that picture you can see a strain of Staphylococcus inoculated so that it covered the complete surface of the medium. But phage lysate caused the presence of inhibitory zones – that means that the strain is susceptible to the phage lysate. Absence of zones would mean resistance of the strain.


    The end

    The end

    Photo O. Z.


    Sir alexander fleming

    Sir Alexander Fleming

    http://cs.wikipedia.org/wiki/Alexander_Fleming

    • Sir Alexander Fleming was born at Lochfield near Darvel in Ayrshire, Scotland on August 6th, 1881.

    http://nobelprize.org/nobel_prizes/medicine/laureates/1945/fleming-bio.html

    • In 1921, he discovered in «tissues and secretions» an important bacteriolytic substance which he named Lysozyme. In 1928, while working on influenza virus, he observed that mould had developed accidentally on a staphylococcus culture plate and that the mould had created a bacteria-free circle around itself. Isolation was only possible in 1940 by other scientists. Dr Fleming died on March 11th in 1955 and is buried in St. Paul's Cathedral.

    http://nobelprize.org/nobel_prizes/medicine/laureates/1945/fleming-bio.html


    Check up questions

    Check-up questions

    • What is the main difference between use of disinfectants and use of antibiotics?

    • What type of drugs are used for treatment of mycoses?

    • What type of drugs are used for treatment of (heavy) viroses?

    • What type of drugs are used for treatment of tuberculosis?

    • How do we call the antimicrobial drugs for local use?

    • What does the term „breakpoint“ mean?

    • What groups of antibiotics belong to beta-lactam antibiotics?

    • In what type of antibiotics MIC and MBC values are nearly identical?

    • What is the meaning of abbreviations ESBL, MRSA, VRE and MLS(B)?

    • Which tests for antibiotic susceptibility testing are quantitative?

    • What feature is hidden under the abbreviation „ampC“?

    • What can be used as alternative of antibiotic therapy?


    Double synergy test

    Double synergy test

    On a picture, the result is positive – the zone is enlarged to the left side (presence of co-amoxicillin disc)


    An example of a positive result

    An example of a positive result

    The area labelled blue is the important one

    Photo O. Z.


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