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Diagnostic Microbiology Development Program

Laboratory Strengthening and the Diagnostic Microbiology Development Program

Robert Martin, MPH, DrPH President, Diagnostic Microbiology Development Program

http://dmdp.org Kathmandu, Nepal, May 2018

http://dmdp.org/

http://dmdp.org/


Global Burden of Infectious Disease

DALY = Disability Adjusted Life Year


Infectious diseases still cause ~40% of

mortality in RLC’s

Morens et al Nature, July 2004; 430, 242-249

Fauci and Morens,, N Engl J Med February 2012; 366:454-461


From: IHME Global Burden of Disease Study - Nepal


From Himalayan News Service Saturday, May 5, 2108


Laboratory Testing Supports:

• Patient Care

• Public Health Disease Reporting

• International Obligations


Value of a Diagnostic Microbiology Laboratory

• Individual case management by detection and identification of microbial agents of bloodstream infections, pneumonia, wound infections, meningitis, diarrhea, urinary tract infections

• Detection of emerging antibiotic resistance and prevention of spread of resistance

• Antimicrobic stewardship (AMS) • Hospital infection prevention and control (IPC) • Early detection of microbial pathogens with public

health importance • Support of outbreak investigations


Regulatory Agencies and

Professional Organizations

http://www.fda.gov/default.htm

http://www.cms.gov/

http://www.ascp.org/default.aspx

http://www.asm.org/index.php

http://www.cap.org/apps/cap.portal

http://www.clsi.org/

http://www.aab.org/aab/default.asp?SnID=1766579982

http://www.aacc.org/Pages/default.aspx


Complexity of a Laboratory System

Patient/Client Prep Sample Collection

Sample Receipt & preparation

Sample Transport

Quality Control Testing

Record Keeping

Reporting

Personnel Competency


LQMS model

Organization Personnel Equipment

Purchasing

&

Inventory

Process

Control

Information

Management

Documents

&

Records

Occurrence

Management

Assessment

Process

Improvement

Customer

Service

Facilities

&

Safety


• Limited or no gov’t. oversight

• Few or no national policies

• No or weak laboratory network

• No registration of labs, no accreditation of laboratories

• No process for procurement of quality laboratory reagents/kits

• Few professional organizations

• Limited testing menu

• Weak academics for lab medicine

Most Resource-Limited Countries:


CDC Quality Management Workshop


DMDP background

• Created in 2008

• Vision: To establish diagnostic microbiology laboratories in low resource settings

• Supported by DTRA since 2013

– Media production and distribution

– Diagnostic microbiology mentoring

– Broadened to other laboratory disciplines in 2015

– Clinical mentoring


DMDP-Diagnostic Microbiology Development Program

• DMDP Mission:

To build capacity for reliable laboratory testing by strengthening the infrastructure of laboratories and the technical capabilities of laboratory technicians in resource-poor countries.

• www.dmdp.org

• In-country staff: 16

• Visiting experts

http://www.dmdp.org


DMDP supported laboratories

2

1, 7, 8

4

3

6

5 Kampot

Province Implement

Microbiology

Bed

Number

1 National Pediatric

Hospital

2011 150

2 Kampong Cham 2009 260

3 Battambang 2011 240

4 Takeo 2011 270

5 Kampot 2013 150

6 Siem Reap 2014 300

7 CMML 2013 NA

8 NPHL US CDC 2010

DMDP 2016

NA


How DMDP Strengthens Diagnostic Laboratories

• 2017: Onsite mentoring- 6 laboratories • 5 diagnostic laboratories

– Kampong Cham, Takeo, Siem Reap, Battambang, NPHL

• 1 media making laboratory – Central Media Making Laboratory

• Remote assistance

• Support manager’s meetings – all government microbiology labs (NMMLN)

– 13 government microbiology laboratories

– Invite collaboration with with partners

– Leadership from Bureau of Medical Laboratory

Services


Pathogen Identification & Antibiotic Susceptibility Testing (AST)

• Strategy: Mentoring in sustainable microbiology practices needed for health care at Provincial Hospitals

• Pathogen Identification:

– Bench-top Diagnostic Microbiology (Biosafety Level II)

– Flow charts developed by Dr. Ellen Jo Baron

– Train in the ‘art’ of recognition of Gram stain and colony morphology

• AST Method-International standard: – CLSI M100S and M02-A12

– Disc diffusion testing

– Agar diffusion with E-test to determine Minimal Inhibitory Concentration (MIC)

– Beta-Lactamase testing with Nitrocefin-based test (cefinase)


Ellen Jo Baron Visual Charts ‘On bench’ Training


Sputum Specimen

Primary pathogens: Streptococcus pneumoniae, Klebsiella species, Haemophilus

influenzae, Staphylococcus aureus, Pseudomonas aeruginosa

NOT pathogens: Yeast, viridans streptococci, coagulase negative staphylococci

Patient should rinse mouth

with water, cough from

deep in lung, do not spit

#1

• Make Gram stain to screen if

acceptable for culture

• Call significant Gram stain

results to Doctor ASAP

#2

#3

Good: Rare squamous

epithelial cells

Optochin disk

Incubate up

to 48 hours

in CO2

#4

Plate to Choc,

BAP, Mac

#5

Reject: Many

squamous

epithelial cells

Klebsiella pneumoniae

Identify & perform susceptibilities

on significant pathogens

Staph aureus

Strep. pneumo

Bile solubility +

Optochin +

Haemophilus influenzae


Implementation of international standard AST

Implementation of Antibiotic Susceptibility Testing (AST) for resistance tracking using Clinical and Laboratory Standards

Institute (CLSI) M100 and M02 in Cambodian Microbiology Laboratories S. Oeng1, J. Letchford1

1Diagnostic Microbiology Development Program (DMDP), Phnom Penh, CAMBODIA

Modified Abstract

Introduction

Background: DMDP collaborates with the Cambodian Ministry of Health (CMoH) to

build microbiology diagnostic capacity as part of the National Strategic Plan for

Laboratory Services. We introduced CLSI M100 and M02 disc diffusion to 6 Cambodian

laboratories to achieve quality AST result reporting to clinicians and to begin collection

of surveillance data by CMoH.

Methods: DMDP used a multi-strategy approach in 2014-15 which included 9 manager

meetings, the CLSI annual AST update webinar and CLSI M100 and M02 documents to

prepare AST guidelines adapted to fit Cambodia. Mentors, DMDP staff with expertise in

diagnostic microbiology, provided regular on bench training at 6 sites.

Results: 5 of 6 DMDP supported laboratories have implemented AST according to

CLSI M100 and M02. In 2015, 5 of 6 laboratories performed weekly AST Internal

Quality Control (IQC). Problems diminished from weekly to none over 12 months.

Conclusions: The multi-strategy approach strengthened Cambodian laboratory

capacity for AST. Regular on site mentoring was essential.

Results

Conclusions

Methods

Diagnostic Microbiology

Development Program

Phone: 415-722-7629

[email protected]

Table 1: Cambodian hospital

microbiology laboratories

• 5 of 6 DMDP supported laboratories implemented AST according to CLSI M100 & M02

• AST IQC failures diminished from 13% (77/598) in Jan. 2015 to 1% (9/657) in Dec. (Fig 7).

• By Nov and Dec. 2015, 3 of 5 labs recorded no AST IQC failures.

• Laboratory assessments in Dec 2015 showed that ‘AST’ was a top component (Fig 8).

• Of the 3% (273/7805) of AST IQC failures in 2015, corrective action in 45% (122/273) was not

applied (Fig 9)

• In 2015, laboratories achieved scores of 85%-95% in the pathogen ID and AST EQA.

• AST Workshop Pre / Post test scores showed 13% improvement from mean 72% (range

43-90) to mean 85% (range 67-97) t-test p value= 0.0004

• A multi-strategy approach strengthened Cambodian government microbiology capacity.

• Regular on site mentoring was essential.

• Practice, encouragement and cultural awareness were key components to success.

• Access to CLSI M100S and M02 and American Type Culture Collection organisms was

essential-DMDP & World Health Organization purchased CLSI M100S & M02. Now, CLSI

M100S FREE is available.

• This activity provided stimulation and opportunity for Cambodia CMoH to collect National

AMR surveillance data and enroll in Global AMR Surveillance System (GLASS).

• Surveillance for priority pathogens, Typhoidal Salmonella, Burkholderia pseudomallei and

Streptococcus suis highlights the importance of continued laboratory support in Cambodia.

• Mentoring in “on bench” diagnostic microbiology

• Bi-monthly microbiology manager meetings

• Interactive AST and pathogen identification workshops

• Review and feedback of Microbiology Activity Reports and clinician reports

• DMDP developed & implemented:

• AST guidelines adapted for Cambodia

• AST workshop practical exercise book

• Electronic tool for monitoring & troubleshooting AST IQC performance

• Monthly Microbiology Activity Reports

Figure 6: Follow up workshop training

December 2015

Support; consulting

James McLaughlin- Ph.D.; D(ABMM), Prof. Emerita Univ. of New Mexico SOM, President

DMDP, Ellen Jo Baron- Ph.D., D(ABMM), Prof. Emerita, Stanford Univ., Janet A. Hindler-

MCLS, MT (ASCP), Em Rattanak- DMDP Laboratory mentor, Morn Sineang- DMDP

Laboratory mentor, Angelo Caon- DMDP Expert mentor.

MONDAY-142

Table 2: DMDP AST guidelines 2015

Fig 4: AST workshop 2015

Table 4: Monthly microbiology activity report Province Implement Microbiology Bed Number

1 National Pediatric Hospital Oct 2008 150

2 Kampong cham Jan 2009 260

3 Battambang Jan 2011 240

4 Takeo May 2011 270

5 Kampot Dec 2013 150

6 Siem Reap June 2014 300

1

2

3

4

5

6

DMDP have been strengthening microbiology diagnostic capacity in Cambodia since 2008

(Fig 1, Table 1), using sustainable diagnostics according to Professor Ellen Jo Baron’s

diagnostic flow charts (Fig 2 & Fig 3). In 2013, DMDP developed and implemented AST

guidelines adapted for Cambodia (Table 2). In 2014, DMDP chose to implement a training

of CLSI M02 and CLSI M100 (Fig 4), review of the AST guidelines and mentoring at 6

government hospitals. Laboratories were encouraged to perform weekly AST IQC. Sites

electronically submitted AST IQC (Table 3) and a monthly Microbiology Activity Report

(Table 4) for review. Mentors worked side by side with government staff (Fig 5). DMDP

included AST in the agenda of training workshops and meetings (Fig 6).

Fig 3: Salmonella Paratyphi A

Disc diffusion & biochemical testing Fig 2: Dr Ellen Jo Baron Chart

Disc Diffusion testing

Figure1: Cambodia Ref - http://www.asiavipa.com/cambodia-map

Figure 5: DMDP mentor training

Table 3: AST IQC-October 2015, week 2, all labs

87%

81%

80%

80%

75%

74%

70%

67%

65%

60%

ANTIBIOTIC

SENSITIVITY TESTING

(AST)

BIOSAFETY

MICROSCOPY/GRAM STAIN

PATHOGEN

IDENTIFICATION

OTHER

SPECIMEN PROCESSING

MAKING MEDIA

QUALITY ASSURANCE

CULTURE INTERPRETATION

REPORTING/URGENT RESULTS

13%

4%

2%

4%

2% 2% 2%

4%

5%

2% 1% 1%

0%

2%

4%

6%

8%

10%

12%

14%

Jan Feb Mar Apr May Jun Jul Aug Sept Oct Nov Dec

Fig 7: Percentage failed AST IQC, 2015 in 5

Cambodian Microbiology laboratory Fig 8: 9 components of lab assessment

Average result from 5 microbiology in Cambodia 2015

No problem

(97%, 7532)

Problem

(3%, 273)

No C

orr

ective

actio

n (

45

%,

12

2)

Co

rre

ctiv

e a

ctio

n (

55

%,

15

1)

Fig 9: AST IQC result (7805 tests) from 5

Microbiology labs in 2015

Implementation of CLSI M100S and M02 • On site mentoring • Development of Pathogen AST guidelines, updated annually • Development SOPs and job aids • Managers meetings, workshops (networking 13 microbiology laboratories)


National Public Health Laboratory (NPHL)

• Strengthen NPHL microbiology • Assessment February 2016

• Placement of expat mentors at NPHL

• Activities: • Establish National Reference Laboratory-

beginning with national AMR surveillance

• Assist NPHL to develop a national microbiology EQA program 2017-2018

NPHL AST guideline training


Microbiology meetings Agenda topics

March 2016 2 days

Culture interpretation Antibiotic Susceptibility Testing (AST) Guideline

Sept/Oct 2016 3 days

Bioterrorism agents Pathogen identification CLSI update and orientation to use revised AST Guideline Specimen processing and culture interpretation

January 2017 2 days Takeo UHS NIPH

Case presentations-lab presentation Peter H Gilligan, PhD • Clinical case presentations • Pathogen identification interactive quiz • Antimicrobial Resistance


Central Media-Making Laboratory


• Human blood is readily available (outdated human

bank blood or volunteers)

• It is free

• Wool sheep too hard

to maintain & bleed

Why are Resource poor Micro Lab results often wrong?

One reason - use of human blood in blood agar

Staph aureus Strep. pyogenes


DMDP supporting and strengthening production and distribution of quality media

Brain Heart Infusion Adult 50ml Pediatric 25ml

MacConkey agar Mueller Hinton II Sheep Blood MH II

Biochemical tube media: Urea, Citrate, SIM, LIA, KIA

Sheep Blood Agar Plates

Central Media Making Laboratory

•Internal Quality Control •External Quality Control Sihanouk Hospital Centre of Hope

Ashdowns agar


Kossamak NPH Kampot Battambang TakeoKampong

ChamSiem Reap

Privateclient

Tubes 0 0 0 0 160 160 480 0

Bottles 200 1300 250 1001 2063 990 1630 3240

Plates 520 0 1120 6160 5680 7177 8470 290

0

2000

4000

6000

8000

10000

12000

Un

its

of

me

dia

Media distribution 2016*, 40891 media units Media plate 29417, Blood culture bottle 10674, tube 800


Benefit of blood culture: Detect pathogens in Cambodia

Burkholderia pseudomallei Streptococcus suis

You can gain valuable information from observation and simple initial tests


Streptococcus suis


Burkholderia pseudomallei

Blood culture isolate Sheep blood agar, Day 3

Blood culture isolate MacConkey agar, Day 3


Burkholderia pseudomallei

B. pseudomallei on sheep blood agar, Day 1

PB: Polymixin B resistant AMC: Amoxicillin Clavulanic acid susceptible CN: Gentamicin resistant

Sheep blood agar


Major gaps and challenges

• Lack of quality pre-service training for Health Care Workers lab tech, clinician, nurse, pharmacist….

• Lack of clinician understanding of appropriate use of the microbiology service

• Lack of patient information and quality specimens to provide good data

• Lack of quality microbiology lab supply procurement

• Lack of capacity in data management and data analysis

• Limited dissemination of data to range of stakeholders


Thank you


Mt Baker National Park Washington State