Você está na página 1de 88

MICROBIOLOGY

&
MANAGING PATIENTS WITH
INFECTION
Dr.Partha Pratim DE
Head of Lab Medicine and Consultant Microbiologist
Tan Tock Seng Hospital
Singapore
Microbiology & The Patient
Day 1

68 yo
male, diabetic
vegetable grower
cough for past month,
increasing for last 10 days
increasing shortness of
breath last 3 days
rainy season
Day 1

68 yo

Define the problem.


Day 1

68 yo

Assess severity. C confused

U 18 mmol/L

R 35 / min

BP 110/70
Day 1

68 yo

Assess risk for MDRO’s.

Assess
immunosuppression.
Day 1

68 yo

What is the likeliest How do you know this?


pathogen(s)?
Is local data the same as
international data?

If you don’t test locally,


how do you get local
data?
Peto, Leon, et al. "The bacterial aetiology of adult community-acquired pneumonia in Asia: a systematic review." Transactions of the Royal Society of Tropical
Medicine and Hygiene 108.6 (2014): 326-337.
Results
As in western studies, Streptococcus pneumoniae, Mycoplasma
pneumoniae, Chlamydophila pneumoniae, Legionella spp. and
Haemophilus influenzae were all significant pathogens. However,
compared with western studies, S. pneumoniae was of less relative
importance. Gram-negative bacilli and Mycobacterium tuberculosis
were more important, and in northeast Thailand Burkholderia
pseudomallei was a major pathogen.

Conclusion
These data have major implications for diagnostic strategies and
empirical treatment. Narrow-spectrum antibiotics targeting S.
pneumoniae may be inappropriate in many Asian settings, and agents
active against TB may lead to partial response and delayed TB
diagnosis.
Results Different regions have different
As in western studies, Streptococcus pneumoniae, Mycoplasma
pathogens
pneumoniae, Chlamydophila pneumoniae, Legionella spp. and
Haemophilus influenzae were all significant pathogens. However,
compared with western studies, S. pneumoniae was of less relative
Guidelines
importance. Gram-negative from othertuberculosis
bacilli and Mycobacterium countries were
more important, and in northeast
need Thailand
to be Burkholderiato
modified pseudomallei
your needs
was a major pathogen.

Conclusion
You need local data to modify
These data have major implications for diagnostic strategies and
guidelinesantibiotics targeting S.
empirical treatment. Narrow-spectrum
pneumoniae may be inappropriate in many Asian settings, and agents
active against TB may lead to partial response and delayed TB
diagnosis.
What antibiotic therapy would you recommend?

A. Amoxicillin-clavulanate

B. Ceftriaxone and clarithromycin

C. Amoxicillin-clavulanate and tetracycline

D. Imipenem and clarithromycin

E. Moxifloxacin
Day 1

68 yo

Admitted to ICU C confused

U 18 mmol/L
Given imipenem and
clarithromycin R 35 / min

BP 110/70
Singapore Antimicrobial Stewardship 2017

Review

Results

Testing

Seven Steps
Review

Results

Testing

Seven Steps

DIAGNOSTIC TESTING
Encompasses:
testing, sample collection, laboratory
CULTURE SEROLOGY
aerobic culture all sorts
anaerobic culture
fungal culture
viral culture MICROSCOPY
mycobacterial culture Gram stain
other culture fungal microscopy
acid-fast stain
Immuno-fluorescence
MOLECULAR TESTING scrapings
PCR other microscopy
Probe testing parasitology
What diagnostic tests could you perform?

Blood cultures
Balance of:
Legionella urine antigen
1.Availability
Streptococcus
pneumoniae urine antigen 2.Clinical utility
Sputum cultures 3.Cost
Silver stain, broncho- 4.Test timing
alveolar lavage fluid
5.Disease severity
Influenza virus culture
Mycoplasma IgG serology
Results turn around time
Non-culture tests Culture

Blood tests Aerobic culture


1-3 days 2-5 days

Microscopy Viral culture


1-2 days 7-21 days

PCR TB culture
1-3 days 10-42 days
The diagnosis and management of CAP has hardly changed for decades.

Improved diagnostic testing (radiologic) and/or microbiologically by point-of-care


multiplex PCR, has the potential to largely influence the choice and start of antibiotic
therapy in hospitalized CAP patients.

Rapid microbiological testing will hopefully improve antibiotic de-escalation or early


pathogen-directed therapy, both potent ways of reducing broad-spectrum antibiotic
use.

Postma, Douwe F., Cornelis H. van Werkhoven, and Jan Jelrik Oosterheert. "Community-acquired pneumonia requiring hospitalization: rational decision
making and interpretation of guidelines." Current opinion in pulmonary medicine 23.3 (2017): 204-210.
There
The diagnosis and management arehas
of CAP new diagnostic
hardly tools
changed for decades.

Improved diagnostic testingTesting


(radiologic)can
and/or microbiologically
guide therapy by point-of-care
multiplex PCR, has the potential to largely influence the choice and start of antibiotic
therapy in hospitalized CAP patients.
Guided therapy reduces
Rapid microbiological testing unnecessary antibiotic
will hopefully improve usage or early
antibiotic de-escalation
pathogen-directed therapy, both potent ways of reducing broad-spectrum antibiotic
use.

Postma, Douwe F., Cornelis H. van Werkhoven, and Jan Jelrik Oosterheert. "Community-acquired pneumonia requiring hospitalization: rational decision
making and interpretation of guidelines." Current opinion in pulmonary medicine 23.3 (2017): 204-210.
Day 1 Day 2 Day 3

Sputum culture Urine

Source: Respiratory Source: Urine


Site: Sputum Site: Mid-stream

Escherichia coli Staphylococcus aureus


Enterococcus species Viable count 1,000 cfu/ml
- Pending
susceptibilities
Day 1 Day 2 Day 3

Blood culture (aerobic)

Gram-positive cocci and


pairs and short chains

Blood culture (anaerobic)

Gram-positive cocci and


pairs and short chains
Review

Results

Testing

Seven Steps

REVIEW RESULTS
What does it mean?
What is the diagnosis now?
Step 9: Review results & diagnosis
What is the infecting Escherichia coli?
organism?
Staphylococcus aureus?

Gram-positive cocci?

All three?
Sterile Sites

contamination?
infection?

diagnosis clinical features pathogen


Interpreting results

Blood culture:
contamination? (Coagulase-negative
staphylococci,
diptheroids)
growing organisms that are
not from the intended site Urine culture:
culture Mixed bacterial growth, low
viable counts

Sterile sites:
(Coagulase-negative
staphylococci, diptheroids)
Non-Sterile Sites

contamination?

colonisation?
infection?
diagnosis clinical features pathogen
Interpreting results
colonisation? Superficial swabs:
Gram-negative bacilli,
coagulase-negative staph,
diptheroids
growing organisms that are
unlikely to cause infection Urine culture:
or growing organisms without Bacterial growth from
signs of infection indwelling catheters

Respiratory tract:
(non-invasive)
[ Gram-negative bacilli ]
Day 1 Day 2 Day 3

Patient Microbiology
Pneumonia Sputum:
Community-acquired Escherichia coli
? risk factors MDRO Not likely respiratory
pathogen from SAP
Some chronic disease
Mixed with other bacteria
Day 1 Day 2 Day 3

Patient Microbiology
Pneumonia Urine:
Community-acquired Why urine?
? risk factors MDRO
Some chronic disease Blood cultures:
Streptococcus something…
Day 1 Day 2 Day 3

Sputum culture Urine

Source: Respiratory Source: Urine


Site: Sputum Site: Mid-stream

White cells: 1+ Urinary FEME: 0


Epithelial cells: 3+ Epithelial cells: 10

Escherichia coli
Scanty growth Staphylococcus aureus
Enterococcus species Viable count 10,000
Scanty growth cfu/ml
- Pending
susceptibilities
Step 9: Review the diagnosis (again)
What is the diagnosis? clinical

other investigations

microbiology

progression

time!
Review

Results

Testing

Seven Steps

REVIEW ANTIBIOTICS
Was your empirical antibiotic correct?
Can you modify your empirical antibiotic?
What antibiotic therapy would you recommend?

A. Why change?

B. Continue ceftriaxone, stop clarithromycin

C. Change to imipenem and vancomycin, stop


others
D. Change to high-dose IV penicillin, stop
clarithromycin
E. Continue antibiotics and start vancomycin
48-72hr
review

EMPIRICAL

Microbiology
data
Clinical data
ANTIBIOTIC SUSCEPTIBILITY TESTING
Susceptibility testing
Qualitative Quantitative

Susceptible Susceptible
How susceptible?
Intermediate
Resistant
Resistant How resistant?
Method
Phenotypic
Disc testing
Minimum inhibitory concentration (MIC)

Special tests

Genotypic
Standardised methods
important to ensure results are
consistent
reproducible
reliable

variables:
inoculum, testing media, methodology,
interpretation, breakpoints, quality control
Advantages
cheap
flexible
widely available
easily understood
reliable (if done properly)

Disadvantages
Source: http://www.cdc.gov/

not automated
technique dependant
quality control important
needs training to read and interpret
qualitative results
Source: http://www.cdc.gov/

Disk Diffusion
Minimum inhibitory concentration
compares efficacy of different
antibiotics against a particular
organism

certain clinical conditions benefit from


a quantitative MIC to guide optimal
therapy
meningitis
infective endocarditis
pneumonia?
particular organisms? (MRSA, P. aeruginosa)

MIC methods
Advantages
quantitative results
may assist antibiotic dosing

Disadvantages
expensive
less flexibility
quality control important
time consuming
limited availability

MIC methods
in-vivo
isolates are not inhibited by the usually achievable
concentrations of the agent with normal dosage
resistant schedules and/or demonstrate MICs/zone diameters
that fall in the range where specific microbial
resistance mechanisms (e.g., β-lactamases) are likely
and that clinical efficacy against the isolate has not
been shown reliably in treatment studies

microorganism falls into a range of susceptibility in


which the MIC approaches or exceeds the level of
antibiotic that can ordinarily be achieved and for
intermediate which clinical response is likely to be less than with a
susceptible strain. Exceptions can occur if the
antibiotic is highly concentrated in a body fluid such
as urine, or if higher than normal dosages of the
antibiotic can be safely administered (eg, some
penicillins and cephalosporins)
isolates are inhibited by the
susceptible usually achievable concentrations of antimicrobial
agent
when the recommended dosage (dosage regimen) is
used for that site of infection.
Day 4

Blood culture (aerobic)

Streptococcus pneumoniae
Antibiotic
susceptibilities to
follow
What antibiotic therapy would you recommend?

A. I’m getting tired of this question..

B. Continue Ceftriaxone, stop clarithromycin

C. Change to Imipenem and vancomycin, stop


others
D. Change to high-dose IV penicillin, stop
clarithromycin
E. Continue antibiotics and start vancomycin
Day 5

Blood culture (aerobic) S I R


Streptococcus pneumoniae Penicillin (Oral) ≤0.06 0.12- >1.0
Penicillin (PO) I 1.0
(pneumonia)
Penicillin (IV) S Penicillin (IV, ≤2 2-4 >4
(pneumonia) non-CNS
Penicillin (IV) R
infection)
(meningitis)
Ceftriaxone S Penicillin (IV, ≤0.06 >0.06
Levofloxacin S CNS infection)
Vancomycin S

MIC penicillin 0.25 mg/L


EUCAST.
Gunnar Kahlmeter..
How drug is given Body sites
Oral drug: Urine:
must be absorbed high levels of some drugs
liver metabolism
Lung:
Intravenous drug: some drugs do not reach
higher levels
faster action Brain/CSF/Eye:
Poor penetration
McKinnon PS, Davis SL. Pharmacokinetic and pharmacodynamic issues in the treatment of bacterial infectious diseases.
European Journal of Clinical Microbiology and Infectious Diseases. 2004 Apr 1;23(4):271-88.
Consider
susceptibility test
PK / PD
site of infection
clinical outcome studies
human factors

Turnidge J and Peterson DL. 2007.


Setting and Revising Antibacterial Susceptibility Breakpoints. Clinical Microbiology Reviews 20(3):391-408.
What antibiotic therapy would you recommend?

OK, ok, only joking….


Review

Results

Testing

Seven Steps

REVIEW ANTIBIOTICS
Was your empirical antibiotic correct?
Can you modify your empirical antibiotic?
Step 10: Review the antibiotics
Continue same antibiotic

Change antibiotics
resistant organism
different body site
susceptible organism

Stop antibiotics
48-72hr 3-5 days
review review

EMPIRICAL DIRECTED

Microbiology Pathogen
data directed?
Clinical data IV-PO?
Duration?
Microbiology &
Infectious Diseases
SUSCEPTIBILITY DATA
Antibiogram
annual summary
of susceptibility
rates

“cumulative
antibiogram
report”
trimethoprim/sulfamethoxazole
Number of isolates (2011)

amoxycillin / clavulanate

piperacillin/tazobactam
ampicillin/sulbactam
GRAM NEGATIVE

ciprofloxacin

meropenem
minocycline
ceftazidime
ceftriaxone

ertapenem
gentamicin
aztreonam
cephalexin

tigecycline
imipenem
cefepime
amikacin
Gram-negative
Acinetobacter baumannii 225 45 34 21 25 21 40 22 23 34 37 susceptibility > 80%
Enterobacter spp. 200 97 51 82 51 51 71 80 74 97 100 61 68
Escherichia coli 2050 98 75 75 37 74 74 74 57 99 83 100 100 95 97 58 susceptibility 50-79%
Klebsiella spp. 1050 96 68 69 60 71 70 69 69 92 79 100 99 77 93 61
Pseudomonas aeruginosa 750 93 76 88 86 85 86 91 91 92 susceptibility < 50%
Proteus spp. 280 94 85 86 71 87 87 87 63 99 70 95 100 99 50
not applicable

trimethoprim/sulfamethoxazole
Number of isolates (2011)

GRAM POSITIVE
erythromycin
ciprofloxacin

moxifloxacin
daptomycin

vancomycin
clindamycin

tetracycline
fusidic acid
cloxacillin
ampicillin

penicillin
linezolid

Staphylococcus aureus 1700 70 88 70 100 71 19 72 87 100


Staphylococcus aureus (MRSA) 500 0 69 20 100 16 0 53 70 100
Staphylococcus aureus (MSSA) 1200 100 95 90 100 93 27 79 94 100
Enterococcus faecalis 50 100 55 100 57 83 100
Enterococcus faecium 65 3 3 100 3 3 38
Streptococcus pneumoniae 45 100 55 100 96 100 41 49 100
Resistance to imipenem - Acinetobacter spp.
Organism No. Q2-05 Q3-05 Q4-05 Q1-06 Q2-06 Q3-06 Q4-06 Q1-07 Q2-07 Q3-07 Q4-07 Q1-08 Q2-08 Q3-08 Q4-08 Q1-09 Q2-09 Q3-09 Q4-09 Q1-10 Q2-10 Q3-10 Q4-10 Q1-11 Q2-11 Q3-11 Q4-11 Q1-12
Acinetobacter baumannii [ALL] 1560 51 60 48 34 49 30 27 40 41 29 23 36 27 45 42 41 61 49 51 52 76 80 53 83 79 61 49 49
imipenem non-susceptible 882 25 35 26 17 25 12 11 31 27 17 11 27 18 32 31 18 46 34 35 40 63 69 44 72 68 54 30 35
% imipenem resistant 49% 58% 54% 50% 51% 40% 41% 78% 66% 59% 48% 75% 67% 71% 74% 44% 75% 69% 69% 77% 83% 86% 83% 87% 86% 89% 61% 71%
inpatient-days 54669 57760 53916 53041 53403 52243 52224 54296 55325 55479 56180 56555 57515 56960 56231 56373 58525 56231 56501 58894 61253 59888 58848 59633 61260 61137 60544 63567
incidence per 1,000-inpatient days 0.46 0.61 0.48 0.32 0.47 0.23 0.21 0.57 0.49 0.31 0.20 0.48 0.31 0.56 0.55 0.32 0.79 0.60 0.62 0.68 1.03 1.15 0.75 1.21 1.11 0.88 0.50 0.55

Imipenem resistance - Acinetobacter spp.


100% 1.40
+3SD

90%
% imipenem resistant 1.20
incidence per 1,000-inpatient days
80%
+2SD
1.00
70%

60%

per 1,000 inpatient days


0.80
n resistant

50%

0.60
40%

30%
0.40

20% isolate selection:


exclude other hospitals
data in hatched bars represent a period exclude outpatients, nursing home, 0.20
before a change in laboratory reporting laboratory
10% protocols, thus the data may not be exclude duplicates: by time period, 90
equivalent days

0% 0.00
Q2-05 Q3-05 Q4-05 Q1-06 Q2-06 Q3-06 Q4-06 Q1-07 Q2-07 Q3-07 Q4-07 Q1-08 Q2-08 Q3-08 Q4-08 Q1-09 Q2-09 Q3-09 Q4-09 Q1-10 Q2-10 Q3-10 Q4-10 Q1-11 Q2-11 Q3-11 Q4-11 Q1-12
linked to disease
real-time

stratified by patient type

take account risk factors

predictive
EPIDEMIOLOGY OF DISEASE
local pathogens
local risk factors

availability of
local patient tests
types
GUIDE PATIENT MANAGEMENT
Antibiotic Patient Antibiogram
Prescribing has an infection
what is the likeliest
organism?
The way it should be
based on risk factors,
severity of infection, etc

what’s the best-guess


susceptibility?
based on risk factors,
severity of infection,
local epidemiology

any modifying factors?


renal dysfunction,
allergies, PK/PD,
infection severity

antibiotic prescribed
GOOD MICROBIOLOGY
appropriate testing
appropriate testing Specimen quality
urine culture (epithelial cells)
sputum culture (epithelial cells)
tissues v.s. swabs
tips of superficial drains

Specimen transport
conditions, transport, viability
appropriate reporting
appropriate testing Guidelines for reporting organisms

appropriate reporting clinically appropriate


guided in interpretative statements
evidence based
concurrent with literature
appropriate reporting
appropriate testing Guidelines for reporting organisms

appropriate reporting Respiratory Urine

sample adequacy sample type (MSU v.s. CSU)


semi-quantitation sample transport
(attempt to differentiate sample adequacy
colonisation from infection) semi-quantitation
asymptomatic bacteriuria

Baron EJ, et al. A guide to utilization of


the microbiology laboratory for diagnosis
of infectious diseases: 2013
recommendations by the Infectious
Diseases Society of America (IDSA) and
the American Society for Microbiology
(ASM)(a). Clinical Infectious Diseases.
2013 Aug;57(4):e22-e121.
appropriate reporting
appropriate testing

appropriate reporting
rapid diagnosis
appropriate testing 24 hour microbiology laboratories
“direct” susceptibility testing
appropriate reporting
rapid identification technologies
rapid diagnosis Vitek automated systems
MALDI-TOF
fluorescent hybridisation
PCR identification
improved workflows
rapid diagnostics
appropriate testing

appropriate reporting Infection markers Non-culture based

CRP “On-demand” PCR


rapid diagnosis Pro-calcitonin viral, bacterial, fungal

soluble urokinase Antigen testing


rapid diagnostics plasminogen activator Immuno-assays
receptor (suPAR) Point of care
interleukin-6
ESR
Day 1
Day 1

Markers procalcitonin 40 mg/l

Blood cultures

Urine antigen legionella antigen neg, pneumococcal antigen POS

N&T swab
Day 1

Markers procalcitonin 40 mg/l

Blood cultures

Urine antigen legionella antigen neg, pneumococcal antigen POS

N&T swab influenza virus POS


c. pneumoniae neg, mycoplasma neg

what antibiotic would you prescribe?


Imipenem & clarithromycin?
Ceftriaxone & clarithromycin?
Imipenem?
Ceftriaxone?
Penicillin

+ Anti-TB therapy?
+ Influenza therapy?
Day 1 Day 2

microscopy AFB negative

PCR Mycobacterium tuberculosis PCR: not detected


Burkholderia pseudomallei PCR: not detected

Blood cultures

what antibiotic would you prescribe?


Imipenem?
Ceftriaxone?
Penicillin?

+ Anti-TB therapy?
Day 1 Day 2

microscopy AFB negative

PCR Mycobacterium tuberculosis PCR: not detected


Burkholderia pseudomallei PCR: not detected

Blood cultures s. pneumoniae

what antibiotic would you prescribe?


100%
90%
80%
70%
60% All patients
50% <18 y
40% 18-64 y
30%
≥65 y
20%
10%
0%
Penicillin (IV) Penicillin (oral)
Day 2

Blood cultures s. pneumoniae


penicillin IV (non-mening) S
penicillin IV (mening)

what antibiotic would you prescribe?

Ceftriaxone?
Penicillin?
PATIENT

• define the problem


Diagnostics
• identify the pathogen

• interpret the result


Results
• review the diagnosis

• refine the antibiotic


Antibiotics de-escalate, change,
stop
Micro-
• understand local disease pathogens
biology

Epide- • formulate guidelines &


miology recommendations

Antibiotic • choose empirical


data treatment
Singapore Antimicrobial Stewardship 2016
The best two words in the English language..
Singapore Antimicrobial Stewardship 2017

The current diagnostic flow

Relatively Relatively Gaps in diagnostic


cheap tests slow results coverage
empiric slow to de- don’t trust
broad abx escalate results
Singapore Antimicrobial Stewardship 2017

The diagnostic paradigm shift

Relatively Faster Broader diagnostic


expensive tests results coverage
More expensive total bills?
Still slow to de-escalate?
Still don’t trust results?

Você também pode gostar