Drug Resistance Mechanism & Their Detection, Recent Advances ESBL MBL Beta LACTAMASES

1. Drug Resistance Mechanism & Their
Detection, Recent Advances
Dr Kanwal Deep Singh Lyall

2. History
• Sir Alexander Fleming (1929 ) Penicillin
• 1940’s Penicillin introduced → 1946 PRSA
• 1960 Methicillin introduced → late 1960’s MRSA
• 1970’s - 1990’s MRSA spread globally
• Streptomycin, Chloramphenicol and Tetracycline - late 1940s & early 1950s
• Shigella outbreaks in Japan (1953) - multiple drug resistant, resistant to
Chloramphenicol, Tetracycline, Streptomycin and Sulfanilamide.
• Neisseria Gonorrhoeae isolates in Africa and Asia (1976) - Beta lactamase
• 1970’s – 1990’s Vancomycin last effective treatment
• VRE – 1ST
isolated in vitro in 1969 - described clinically in 1988
• 1996 Japan first report of GISA (VISA)
• 1999 reports of CA-MRSA
• 2002-08 - 8 isolates of VRSA
• Today, 70% of all nosocomial pathogens are resistant to 1 or more antibiotics

3. Factors Leading To Resistance
• Antibiotics in food and water
• Indiscriminate use of antibiotics in agriculture & veterinary
practice
• Antibiotic resistance in genetically modified crops
• Inappropriate use of antibiotics in the medical environment
• Inappropriate dosage & administration
• Use of monotherapy
• Under use of microbiological testing

4. Risk Factors
• Admission in ICUs
• Recent surgery
• Instrumentation
• Prolonged hospital stay
• Antibiotic exposure

5. Risk Group
• Neutropenic
• Organ transplantation
• Premature infants
• Prolonged and intensive antibiotic therapy
• Gastrointestinal surgery

6. Definitions
• Susceptible (S)– isolates are inhibited by usually achievable conc. of AMA
when recommended dose is used for site of infection
• Intermediate – isolates with AMA MICs that approach usually attainable
blood & tissue levels & for which response rates may be lower than for
susceptible isolates
• Resistant – isolates are not inhibited by usually achevelabe conc. of agent
with normal dosage schedules , &/or that demonstrate zone diameters that
fall in range where specific microbial resistance mechanisms are likely &
clinical efficacy of agent against isolate has not been reliably shown in
treatment studies
• Drug resistance (R) – unresponsiveness of a microorganism to an AMA

7. Classification
• Natural resistance – some microbes always R to a certain AMA
• d/t lack of metabolic process or target site affected by drug
• E.g. GNB – R to penicillin G or M.TB R to tetracyclines
• Not a significant clinical problem
• Acquired – development of R (was S earlier) d/t use of an AMA over a
period of time
• Any microbe may develop, pose a significant clinical problem
• Adaptive – rapidly developing (1-2hrs) & reversible (16-24hrs) –
phenotypic alteration – no genetic change (P .aeruginosa – AGs )
• Cross-resistance – R to 1 AMA conferring R to another to which
organism is not exposed (R to 1 sulfonamide = R to all other, R to 1
tetracyc = R to all tertracy)

8. Expression
• Constitutive – resistance mechanism expressed continuously
whether an in acting challenge is present or not
• Induced – by exposure to the challenge substance before they
produce the induced gene product (staph – β – lactamase)
• Homogenous – same R pattern in all bacteria in a population
• Heterogeneous – only small fraction of bacteria express
resistance mechanism – sample errors

9. Genetic Basis Of Drug Resistance
• Plasmids – circularized pieces of DNA that act independently
of the chromosome- mobiles from 1 strain/species to another –
bulk transfer
• Chromosome – relatively stable
• Transposon -transposable genetic material –can carry portions
of plasmids, or piece of chromosome (conjugative transposon
or jumping gene)

10. • Mutation – stable & heritable genetic change that occurs
spontaneously & randomly – not induced by AMA
• Any S population may contain R mutants – selectively preserved &
proliferate when S strains eliminated – in time S strains replaced by
R strains (when ATT drug used alone)
• Single step – single gene mutation – high degree of R, emerges
rapidly ( enterococci – streptomycin, E. coli & Staph – rifam)
• Multistep – no. of gene modifications involved, S ↓ gradually, in
stepwise manner (R to erythro, tertra, CPC)

11. • Gene transfer – (infectious R) – 1 org to another
1. Conjugation – sexual contact – bridge or sex pilus
• Chromosomal or extra chromosomal DNA
• Frequent in colon, amongst GNB – close contact
• CPC in typhoid, strep in E. coli, Pen in Haemophilus & gonococci
• Multi drug R
2. Transduction – transfer of gene via bacteriophage – pen, ery, CPC
3. Transformation – R bacterium – release R carrying DNA into
medium – taken up by S bacterium – becomes R- not v. significant
clinically

13. Sites OA of Various AMA

14. Mechanism Of Drug Resistance
• Altered permeability
• Production of enzymes
• Altered structural target
• Altered metabolic pathway

15. AM A MOA MOR
Sulfonamides Structural analogs of
PABA – inhibit folate
synthetase -FA not formed
•Increased production of
PABA
•Low affinity folate
synthetase enzyme
•Alternate folate
metabolism pathway
Co-trimoxazole Inhibits dihydrofolate
reductase (DHFRase)
•Low affinity DHFRase
Fluoroquinolones Inhibits bacterial enzyme
DNA gyrase or
topoisomerase IV
•Low affinity DNA gyrase
or topoisomerase IV
•↓ permeability
•↑ efflux
Beta lactams Inhibit transpeptidases
(PBPs)– crosslinking of
peptidoglycan residues
does not occur
•β- lactamases
•Altered PBPs
•Active efflux
Tetracyclines Bind to 30S ribosomes –
inhibit protein synthesis
•↓ influx
•Active efflux
•Inactivating enzymes

16. Chloramphenicol Bind to 50S ribosomes –
inhibit protein synthesis
•Acetyl transferase –
inactivates CPC
•↓ influx
•Low affinity ribosomes
Aminoglycosides STM- 30S ribosome
Others – 30S, 50S & 30S-
50S interface = inhibit
protein synthesis
•Inactivating enzymes
•↓ affinity of ribosomal
proteins
•↓ efficiency of AG
transporting mechanism
Macrolides Binds with 50S ribosome
subunits – inhibits protein
synthesis
•↓ permeability
•↑ efflux
•Erythromycin esterase
•Alteration in ribosomal
binding by methylase
enzyme

17. Antibiotic-modifying Enzymes:
The β-lactamases

18. β-Lactamases

19. The β lactams
Consist of 4 major groups-
• Penicillins, Cephalosporins, Monobactams &
Carbapenems
• All have a β-lactam ring

20. β-lactamases
1. Most common β-lactamases have a serine based MOA
2. 3 major classes (A, C & D) on bases of amino acid sequences.
3. Contain active site consisting of a narrow longitudinal groove with
a cavity on its floor which is loosely constructed in order to have
conformational flexibility in terms of substrate binding.
4. Close to this lies serine residues that irreversibly reacts with
carbonyl carbon of the β lactam ring - open ring (Inactive
β- lactam) & regenerating β-lactamases

21. Methods of detection
Detection of penicilloic acid
• Acidometric method
• Iodometric method
Chromogenic cephalosporin
(Nitrocephin)
• Rods
• Broth

22. Acidometric method
• Benzylpenicillin penicilloic acid
• Commercially available filter paper containing
penicillin+ pH indicator dye
• Bacterial growth applied on it→ if β-lactamase
produced → ↓pH → color change
β-lactamase

23. Iodometric method
• Reagents → 1% starch solution & iodine reagent (2.03g
iodine+ 5.32g KI+100ml D. water)
• Heavy suspension of overnight growth (109
cfu/ml) in PBS
containing penicillin at 6g/L conc.
• Positive & negative controls (without growth)
• 0.1ml of put in wells of microtitre plate
• Incubate x 37° C x 1hr
• Add 1 drop of starch solution
• Loss of blue color = positive
• Persistence of blue color = negative

24. Chromogenic cephalosporin method
• Above test relies on penicillinase production
• Nitrocephin more sensitive, rapid detection, but
expensive
• Nitrocephin (colorless) → β-lactam ring hydrolyzed →
red color
• Nitrocephin impregnated rods – commercially available –
touch +ve colony – turns red
or

25. Nitrocephin solution (500mg/L)
1. 50 µl heavy sus. Into well – add 10 µl nitrocephin – red
in 30 mins - +ve
2. Place drop of solution on colony on solid media – red
color - +ve
3. Add few drops of solution to broth culture – immediate
red color production - +ve
• Negatives incubated for 30 mins

26. Inducible β-lactamases
• Induction system = potent inducer (cefoxitin) + weak
inducer (cefotaxime)
• Lawn culture of test organism on MHA
• 2 Discs containing 30µg of each drug placed on it at a
suitable distance
• After overnight incubation – flattening of zone of
inhibition on side of cefoxitin disc = +ve

27. Cefoxitin
30µg
Cefotaxime
30µg

28. Extended Spectrum Beta-lactamases
ESBLs

29. Definition
• Enzymes that hydrolyze 3rd
generation cephalosporins
(e.g. Ceftazidime, cefotaxime) & monobactams
(aztreonam)
• Produced by members of the family enterobacteriaceae,
(E.coli, klebsiella) & other gram-negative organisms
(pseudomonas, acinetobacter etc.)
• Mainly plasmid mediated

30. Detection of ESBLs
Screening
• AST by Kirby-Bauer’s
disc diffusion method
• MIC
Confirmatory
• Double disc method
• 3 dimensional test
• MIC
• E-test
• Automated systems

31. Screening Methods

32. Kirby-Baur’s disc diffusion test
• AST on MHA by Kirby-Baur’s disc diffusion test using
followings antibiotic discs
• If zone of inhibition is less than above mentioned zones –
labeled as probable ESBL producers
Antibiotic Potency Zone size (S)
Ceftazidime 30 µg 22 mm
Cefotaxime 30 µg 27 mm
Ceftriaxone 30 µg 25 mm
Cefpodoxime 10 µg 17 mm
Aztreonam 30 µg 27 mm

33. MIC
• Done using broth microdilution method using following
antibiotics
• If MIC is more than above mentioned MIC – probable
ESBL producer
Antibiotic MIC
Ceftazidime 1 µg/ml
Cefotaxime 1 µg/ml
Ceftriaxone 1 µg/ml
Cefpodoxime 4 µg/ml
Aztreonam 1 µg/ml

34. Confirmatory Tests

35. Double disc diffusion method
• Lawn culture of test organism on MHA
• β-lactam disc placed on it
• Another disc containing β-lactam + clavulanic acid is
placed at a distance of 30mm
• An expansion of zone of inhibition ≥5mm around
combination disc is indicative of ESBL production

36. Red circle inhibition zone around disk on left, & at top.
Disks: centre, amoxycillin+clavulanate 20 + 10 μg; right, cefepime 30 μg; left,
aztreonam 30 μg; top, ceftazidime 30 μg; bottom ,ceftriaxone 30 μg.

37. Detection of ESBL production by double disk test on DSM-ES agar.
Disks: centre, amoxycillin+clavulanate 20 + 10 μg; right , cefepime 30 μg;
left, ceftriaxone 30 μg; top, ceftazidime 30 μg; bottom, aztreonam 30 μg.

38. MIC
• Comparison of MIC in presence & absence of β-
lactamase inhibitor (clavulanic acid)
• ↓ in MIC > 8 folds in presence of β-lactamase inhibitor =
positive

39. 3-dimensional test
• Lawn culture of E. coli ATCC 25922 on MHA plate
• β-lactam disc (3rd
gen. cephalosporin) placed in the centre of plate
• A well of 4mm diameter punched at a distance of 2mm from it
• 30 µl of test strain in BHI broth (5.0 McFarland’s) seeded into
the well
• Incubation x 37º C x 24hrs
• Heart shape distortion of zone of inhibition around β-lactam
disc = ESBL producer

40. E-test
• Done with E-test strips with graded MIC values
• At one end is β-lactam antibiotic
• At other β-lactam + clavulanic acid
• Points where zones of inhibitions intersects strips, gives the
MIC value
• > 8folds reduction in MIC, in presence of β-lactamase
inhibitor = ESBL producer

41. Automated System
• Panel of wells containing β-lactam ( 3rd
gen.
cephalosporin) alone & in combination with
clavulanic acid
• Growth assessed by optical scanner
• ↓ in growth in wells containing cephalosporins+
clavulanic acid as compared to cephalosporin alone =
ESBL producer

42. Amp C beta lactamases

43. Amp C beta lactamases
• Cephalosporinases that confer resistance to wide variety of
β-lactam drugs
• Hydrolyse all β-lactam drugs except carbapenem & cefepime
• penicillins
• Cephamycins(cefoxitin,cefotatan,cefmetazole)
• Cephalosporins(narrow,expanded and broad spectrum)
• β-lactam-β-lactamase inhibitor combination
• Aztreonam

44. Production
Chromosomal
 Inducible
Serratia
Providencia, P.aeruginsosa
Aeromonas
C.freundii
Enterobacter, Hafnia
 Derepression
c.freundii
Enterobacter
 Basal
e.coli
Plasmid mediated
E.Coli
klebsiella
P.Mirabilis
salmonella

45. Inducer Potential
Good Variable Poor
Cefoxitin Clavulanate sulbactam
Cefmatazole Desacetyl
cefotaxime
tazobactam
Imipenem Cefamandole aztreonam
ampicillin cephalothin 3rd
gen ceph
cefonocid 4th
gen ceph

46. Methods of Detection

47. Amp C disk test
• Principle - tris edta permeablize a bacterial cell and release β
lactamases into external environment
Amp c disk preparation
• 20µl of 1:1 mixture of saline and tris EDTA
• Applied to sterile filter paper discs
• Discs dried
• Stored at 2-8°c

48. E.coli ATCC 25922 inoculated on mueller hinton
Amp C disc rehydrated with 20µl saline
Colonies of test org applied to disk
30µg cefoxitin disk placed
Inoculated amp C disk placed almost touching the antibiotic disk
with inoculated disk face in contact with agar
Incubated overnight

49. Positive result
amp C will be released from bacterial cell inoculated on disk
Inactivation of cefoxitin
Indentation or flattening of zone of inhibition

50. Three Dimensional Test
Fresh overnight growth of test org from MHA transferred to
preweighed microcentrifuge tube
Tube weighed again to determine the weight of bacterial mass
10-15 mg of bacterial wet weight
Suspended in peptone water
Centrifuge at 3000 rpm for 15 mins
Crude enzyme extract prepared by repeated freeze thawing of bacterial
suspension(10cycles)

51. Lawn culture of E. coli ATCC 25922 on MHA
Cefoxitin disk
Linear slit cut using sterile blade 3mm away from disc
25-30µl of enzyme suspension loaded in slit
Incubated overnight
Enhanced growth at slit

52. +VE +VE
-VE
2 3
1

53. Disc test using phenyl boronic acid
• 2 disks taken
• 1ST
-30µg of cefoxitin
• 2nd
-30µg of cefoxitin+400µg of boronic acid
• Zone around combined disk ≥5mm than zone around
cefoxitin disc
• Amp c producer

54. Metallo beta lactamase

55. Metallo beta lactamase
• Group of beta lactamase
• Requiring divalent cation of zinc as cofactor
• Having potent hydrolysing activity against carbapenems as
well as other commercially available β lactam antibiotics
Can hydrolyze
Penicillin
Early cephalosporins
Extended spectrum cephalosporins
Carbapenems
Not Aztreonam

56. Mbl Screening
• IMP-EDTA combined disc test
• IMP- EDTA ddst
• EDTA disc potentiation using cephalosporins discs
• Mbl E test
• Principle- MBLs require Zn ion for their activity & EDTA as
chelating agent counteract effect of MBL by inhibiting Zn

57. IMP EDTA combined disc test
Org inoculated on Mueller Hinton plate
Two 10µg Imipenem discs placed on plate
10µl of 0.5 mEDTA sol added to one disc
Incubated overnight at 35° C
Inhibition zone compared

58. • Increase in inhibition zone with IMP+EDTA ≥7mm than IMP
alone
• Mbl positive

59. IMP-EDTA DDST
Test org inoculated on Mueller Hinton
IMP disc placed 20mm centre to centre from a blank
disc containing 10µl of 0.5m EDTA
Incubated overnight at 37°c

60. Enhancement of zone of inhibition b/w IMP and EDTA as
compared with zone of inhibition on far side of drug is
interpreted as positive

61. EDTA disc potentiation using cephalosporin disc
Discs used are ceftazidime, ceftizoxime, cefepime, cefotaxime
Org inoculated on MHA
EDTA disc placed in centre
Cephalosporin disc placed 25 mm centre to centre from EDTA
disc
Incubated overnight at35°C

62. Enhancement of zone of inhibition in area b/w EDTA disc and
any one of cephalosporin disc in comparison of inhibition on
far side of drug is considered positive

63. Mbl E-test
• Strip containing double sided seven dilution range of
IMP(4to256µg/ml) and IMP+EDTA(1to 64µg/ml)
• MIC ratio of IMP/IMP+EDTA>8 or >log2 dilution indicate
mbl production

64. Carbapenemases

65. Mechanisms of Carbapenem Resistance
1. Carbapenemase hydrolyzing enzymes
2. Porin loss “OprD”
3. ESBL or AmpC + porin loss
• 2 major gps based on hydrolytic mechanism at active site
– Serine at active site: class A and D
– Zinc at active site: class B
• All carbapenemases hydrolyze penicillins, extended spectrum
cephalosporins, and carbapenems

66. Carbapenemase Classification
Molecular Class A B D
Functional Group 2f 3 2d
Aztreonam Hydrolysis + - -
EDTA Inhibition - + -
Clavulanate Inhibition + - ±

67. Carbapenemases Class A
• Chromosomally encoded
– Serratia marcescens enzyme (SME)
– Not metalloenzyme carbapenemases (NMC)
– Imipenem-hydrolyzing β-lactamases (IMI)
• Plasmid encoded
– Klebsiella pneumoniae carabapenemases (KPC)
– Guiana Extended-Spectrum (GES)

68. KPC
• Molecular class A and functional group 2f
• Inhibited by clavulanic acid but not by EDTA
• Confers resistance to all β-lactamases
• Plasmid-encoded
– Associated with other resistant genes
(aminoglycosides, fluoroquinolones)
– Transferable

69. Suspected KPC Producer
• Enterobacteriaceae
• Resistance to extended spectrum cephalosporins
(cefotaxime, ceftazidime, and ceftriaxone)
• Variable susceptibility to cephamycins (cefoxitin,
cefotetan)
• Carbapenem MICs ≥ 2 µg/ml

70. Screening
Antimicrobial susceptibility tests (ASTs)
• Carbapenem MIC ≥ 2 µg/ml
• Carbapenem: “I” or “R” – in DDT
• Among carbapenems, ertapenem Most S , less specific

71. Confirmation
• Modified Hodge test
– 100% sensitivity to detect KPC
1. E. coli ATCC 25922 lawn - Imipenem disk in center.
2. Streak test isolates from edge of disk to end of plate x incubate
overnight.
3. Look for growth of E. coli around test isolate streak - indicates
Carbapenem-hydrolyzing enzyme
• PCR

72. Meropenem
Ertapenem
Imipenem
++
--
--
--++
++

73. High Level Aminoglycoside Resistance
• MHA- Lawn culture
• Gentamycin disc (120µg) & streptomycin disc (300µg)
• Zone size < 7mm = HLAR positive (R)
• Zone size > 10mm = HLAR negative (S)
• Intermediate zone size inconclusive – test by broth or agar
dilution MIC
• Don’t test other aminoglycosides, their activity against
enterococci not superior

74. MRSA
• Staphylococcus aureus with mic ≥ 4µg/ml
• Altered PBPs, methicillinase & hyperproduction of penicillinase
Detection
• Methicillin Strip test (25µg) resistance
• Disc tests (oxacillin 1µg, methicillin 5µg or cefoxitin 30µg)
• Methicillin salt agar (MHA +4% NaCl + methicillin10µg/ml)
• Oxacillin salt agar (MHA +4% NaCl + oxacillin 6µg/ml)
• E - test
• Breakpoint test
• PCR for mecA gene
• Latex agglutination test

75. VRSA
Definition
Vancomycin MIC(µg/ml)
Susceptible Intermediate Resistant
≤ 4 8-16 ≥ 32
Teicoplanin MIC(µg/ml)
≤ 8 µg 16 ≥ 32

76. NCCLS
Vancomycin MIC(µg/ml)
Susceptible Intermediate Resistant
≤ 4 8-16 ≥ 32
BSAC
≤ 4 - ≥ 32
CLSI
4-8 - ≥ 16

77. Mechanism Of Resistance
• CONS
• Vancomycin - binds
irreversibly to the terminal
D- alanyl –D alanine of cell
wall
• Inhibits bacterial cell wall
synthesis
• In VRCONS- altered cross
links inhibit binding to
peptides
• Exact mechanism
not known
• S. aureus
• True mechanism not known
• Emission of sex pheromone
by S. aureus that are in
proximity to VRE that
contain plasmids encoding
van genes could result in
transfer of these genes
(Showsh et al)
• Van genes not recovered till
date

78. Screening of VRSA strains
Hiramatshu method CDC method Tenover et al
Overnight grown
cultures adjusted to
0.5 McFarland
10 μl spot
inoculated on BHI
agar (4 μg/ml) of
vancomycin
incubated at 35°C
for 24-48 hours
Overnight grown
cultures adjusted to
0.5 McFarland
diluted 100 times
Spots 10 μl of the
cultures inoculated
on BHI agar (6
μg/ml) of
vancomycin.
Incubated at 35°C
for 24-48 hours.
Overnight grown
cultures adjusted to
0.5 McFarland
diluted 100 times
Spot 10μL of both
the inoculums
inoculated on
MHA agar
containing 5μg/ml
of vancomycin.
Incubated at 35°C
for 24-48 hours.

79. Confirmation
• MIC by broth or agar dilution
• E-test
• Agar based methods
More sensitive
 Detect resistant subpopulations
Single colonies visualized

80. • Broth microdilution vancomycin MIC of 8-16μg/ml
• E-test vancomycin MIC of >6μg/ml
• growth on BHI agar containing 6μg/ml vancomycin
within 24 hours.
CDC criteria to identify VISA

81. VRE
• BHIA + 6µg/ml van
• Enterococcal broth + Na azide + 6µg/ml van
• M-enterococcal broth + triphenyl tetrazolium Na azide + 6µg/ml van
• Mic by agar dilution, broth dilution
• E-test
• VITEK
High level Intermediate Low level
≥256 32-128 8-16

82. Drug Resistant Mycobacteria
• MDR-TB - resistant to at least Isoniazid & Rifampicin
• XDR-TB – MDR-TB + R to
- any fluoroquinolone
- at least 1 of 3 injectable 2nd
line drugs
(Capreomycin, Kanamycin, Amikacin)

83. Drug Susceptibility Testing
Conventional methods
• Absolute concentration methods
• Resistance ratio method
• Proportion method
Newer methods
• E -test
• Microwell alamar blue assay
• Microplate tetrazolium reduction assay(colorimetric)
• Microscopic observation drug susceptibility (MODS)
• Mycolic acid index susceptibility testing
• Microcolony detection on 7h 11 agar plate
• Phage b assay
• Luciferase reporter phage assay

84. Genotypic methods
• Automated DNA sequencing
• PCR
• Line probe assay
• Ligase chain reaction
• Microarrays
• Hybridisation protection assay
• DNA strain typing

85. Prevention Of Spread
• Private room
• Gloves
• Gowns to enter room
• Gowns for patient contact
• Antibacterial hand washing agent
• Record of all health care workers entering room
• Mask and/or eye protection from aerosol
• Mupirocin for nasal colonization
• Limit number of health care workers caring for patient

86. THANK YOU

87. E test

88. AST anaerobes
Method Medium Inoculum Incubation Advantages Disadvantages
Agar
dilution
Brucella
blood agar
103
cfu/spot 48 h Reff method,
multiple
isolates tested
per
antibiotics
Labour intensive,
expensive
Broth
microdiluti
on
Supplement
ed brucella
broth
106
cfu/ml 48 h Econoical,
commercial
pannels
available,
multiple
isolates tested
per antibiotic
Limited shelf life
of frozen pannel,
poor growth by
some strains
E- test Brucella
blood aga r
0.5
McFarland,
swab plate
24-48 h Precise MIC
value,
convenient
for patient
isolates
Expensive for
surveillance
purpose