1. Capacity building for laboratory strengthening and detecting antibiotic resistance: findings of a needs assessment in Uganda and Zambia Alliance for the Prudent Use of Antibiotics Antibiotic Resistance: Situation Analysis and Needs Assessment in Uganda and Zambia (AR-SANA) 1

2. AMR in Zambia: Key Findings S. pneumoniae resistance rates to penicillin rose from 14.3% resistance in 1990s to 53-67 % in 2007. Infants are most likely to have S. pneumoniae identified from their blood and spinal fluid. Co-trimoxazole resistance of S. pneumoniae is high (80-100%). Enteric infections that affected Zambian children were due to rotavirus and enteric bacteria (E. coli, V. cholerae, Salmonella spp., and Shigella spp.). Available data showed very high resistance among enteric bacteria to gentamicin, cefotaxime, nalidixic acid, ciprofloxacin, co-trimoxazole and cephalexin ranges between 70-100%. Alliance for the Prudent Use of Antibiotics

3. Antibiotic resistance by drug and selected pathogens in Zambia 3

4. Mortality from severe S. pneumoniae pneumonia of children in the University Teaching Hospital, Zambia, 2005-2007 4

5. Acute respiratory and enteric infections in Uganda are main causes of increased morbidity, mortality and costs. Streptococcus pneumoniae, and Haemophilus influenzae type b (Hib) continue to be the main bacteria responsible for Acute Respiratory Infections (ARI). Viral etiology (mainly Respiratory Syncytial Virus-RSV) in severe pneumonia among infants and children needs to be investigated.  Empirical treatment should be guided by data provided by antibiotic resistance surveillance, particularly in common pathogens.  Available information on Antibiotic Resistance (ABR) is in most cases scattered, incomplete and often unreliable. Alliance for the Prudent Use of Antibiotics AMR in Uganda: Key Findings

6. Antibiotic resistance profiles of S. pneumoniae from 2005- 2007 in Kampala Alliance for the Prudent Use of Antibiotics Data from Mulago Hospital Laboratory Data

7. Purpose of the laboratory survey To examine: I. Laboratory capacity to conduct research on antibiotic resistance. II. Ability of laboratories to deliver accurate results III. Ability of laboratories to detect pathogens and perform antimicrobial sensitivity testing IV. Availability of a system for quality control in the laboratories V. Availability of mechanisms for dissemination of laboratory/ surveillance data VI. Availability of a system for collection, analysis and transmission of the data to be used for antibiotic management decisions VII. Economic situation of the survey laboratories VIII. Availability of the WHONET software for antimicrobial resistance surveillance 7

8. Method of laboratory survey 17 and 29 laboratories across Zambia and Uganda were surveyed respectively. Structured questionnaires (adapted from the WHO assessment form) were used to conduct the interview. Training of data collectors was carried out The survey was carried out 2009 and 2010. The study obtained ethical approvals from the University of Zambia Ethical Review Board, the Ethical Review Committee of Makerere University College of Health Sciences, Kampala, and Boston Tufts University Institutional Review Board 8

9. 17 Laboratories Surveyed in Zambia 9 Monze, Livingstone, Chikankata, Mutendere Maina Soko, Lusaka Trust, Chest Disease, UTH Kasama, Mpika Mansa Lundazi Ndola, Kitwe, Tropical Dis., Nchanga, Arthur Davidson

10. 29 Surveyed Laboratories in Uganda Alliance for the Prudent Use of Antibiotics10

11. Laboratory survey Components I. Laboratory staffing and trainings II. Laboratory equipment III. Laboratory supply logistics IV. Laboratory record keeping for supplies management V. Sources of laboratory reagents VI. Specimen collection, handling and labelling VII. Laboratory specific capacity VIII. Structure of reporting laboratory results IX. Quality control procedures X. Cost of laboratory testing and sources of funding 11

12. Microbiology Laboratory University Teaching Hospital of Lusaka 12

13. Microbiology Laboratory University Teaching Hospital of Lusaka

14. Uganda: Sources and supply of bacteriological laboratory consumables Alliance for the Prudent Use of Antibiotics14 68.9% - delays in obtaining reagents from the medical stores. 51.7% - Stock outs at the supply stores 34.5% -consumables are ordered but no deliveries received 6.9% -lack of information on how to make orders 3.4% - inconsistent demands for laboratory tests, lack of response on placed orders, delivery of what was not ordered and delivery of expired reagents

15.  76.4% (13/17) of the laboratories admitted to experiencing problems in obtaining reagents from suppliers.  23% (4/17) of the laboratories experienced problems with reagent stock out at the medical stores.  58.8% (10/17), 41.2% (7/17) and, 11.8% (2/17) of the laboratories experienced delays in receiving ordered reagents from medical stores, inconsistency in the supply of laboratory consumables, and lack of knowledge on making orders, respectively. Zambia: Sources and supply of bacteriological laboratory consumables 15 Source Number of laboratories Medical Stores limited 7 National Medical Store 7 Commercial Suppliers 3

16. Alliance for the Prudent Use of Antibiotics16 Score Range 0-49%Score Range 50%-74%Score Range >75% Lundazi District Hospital Mutendere Mission Hospital Livingstone General Hospital Maina Soko Military Hospital Mansa General Hospital Chikankata Mission Hospital Mpika General Hospital Kasama General Hospital Kitwe Central Hospital Ndola Central Hospital Monze Mission Hospital Nchanga South Hospital Lusaka Trust Hospital University of Zambia Teaching Hospital * Tropical Disease Research Center * (research facility) Arthur Davidson (Pediatric) Hospital Laboratory* Chest Disease Laboratory * (national laboratory) Scores of Zambian Laboratories

17. Scores of Ugandan Laboratories 17 Score Range 0-49%Score Range 50%-74%Score Range >75% Kibuli Hospital Kisubi Hospital Lira Regional Referral Hospital Cure Hospital Jinja Regional Referral Hospital Soroti Hospital Kuluva Hospital Masaka Regional Referral Hospital Arua Regional Referral hospital Lacor Hospital Kiwoko Hospital Kagando hospital Nsambya Hospital Kitovu Hospital Tororo Hospital Entebbe Hospital Kibuli Hospital Gulu Independent Hospital Rubaga Hospital Mbarara Regional Referral Hospital * Kitovu Hospital * Mulago National Referral Hospital * Mengo Hospital * Mbale Hospital* International Hospital Kampala * Butabika Regional Referral Hospital

18. Zambia: Quality assurance in isolation, characterization of microorganisms and antibiotic susceptibility testing 4/17 laboratories (23.5%) had external quality control procedures for antibiotic susceptibility testing, performed by: Acid-fast bacilli (AFB) microscopy National TB reference Laboratory National Institute for Communicable Diseases (NICD)/WHO, South Africa 18

19. Zambia: Availability and use of the WHONET software Only the University Teaching Hospital, Lusaka laboratory is currently using WHONET software (version 5.1 installed in May 2009) There is no national policy on antibiotic resistance surveillance 19

20. Uganda: Quality assurance in isolation, characterization of microorganisms and antibiotic susceptibility testing  Only 6.6% have external quality control procedures for Antibiotic Susceptibility, performed by:  Center for Public Health Laboratories (CPHL) Alliance for the Prudent Use of Antibiotics20 None (0/29) of the surveyed laboratories installed or used the WHONET software to monitor AMR. Availability and use of the WHONET software

21. Availability of Laboratory Equipment The survey of laboratory equipment examined the following: I. Availability of the essential equipment required to provide routine clinical diagnostics II. Functioning of equipment III. Equipment operation and maintenance standards IV. Equipment storage conditions, and the records of equipment calibration Bactec at the Lusaka University Teaching Hospital Microbiology Laboratory, 2009 21

22. Availability of Laboratory Equipment  Most of the surveyed laboratories had the essential equipment needed to perform clinical diagnostics  Some of this equipment was not in working condition.  Most of the laboratory equipment was not regularly calibrated and maintained. 22

23. Mulago National Referral Hospital & Makerere School of Medicine, Kampala Alliance for the Prudent Use of Antibiotics23

24. Charges of tests (US$) performed by Zambian laboratories 11/17 laboratories charged user fees for clinical tests Average costs for performing blood smear for malaria, urinalysis, sputum, blood, CSF, and stool cultures by different laboratories 24

25. Charges of tests (US$) performed by Ugandan laboratories 55.2 % (16/29) of the laboratories surveyed charged fees for each laboratory test. The highest cost was of CSF and blood cultures Average costs for performing blood smear for malaria, urinalysis, Sputum, blood culture, CSF cultures, and stool cultures by different laboratories Alliance for the Prudent Use of Antibiotics25

26. Specimen handling Alliance for the Prudent Use of Antibiotics Some laboratories discarded specimens a few days after testing. Most of the laboratories had no criteria for sample disposal. 26

27. Conclusions and Major Constraints 1. Limited antibiotics susceptibility testing capabilities. 2. Essential equipment is available in most laboratories, but often, the equipment is not maintained, calibrated, or in working condition 3. No standard specimen handling procedures 4. No sample disposal procedures 5. No antibiotic resistance surveillance systems in place in most hospitals 27

28. 6. Lack of adequate funding for laboratory equipment, reagents, staff, stationery, and consumables 7. No standard procedures on antibiotic susceptibility testing 8. Problems with reagent stock-outs from suppliers and medical stores 9. Delays in receiving laboratory supplies 10. Inconsistent reporting of notable diseases to national and district health authorities Conclusion and major constrains (continued) 28

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