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NTP Laboratory Network Assessment (Draft) NTP LABORATORY NETWORK ASSESSMENT (2016) Arthur B. Lagos MD Lynette P. Adorio-Arce MD Marlon L. Bayot RMT March 2017 Disclaimer: This document is a draft and is provided for information only. The information contained herein is subject to change and does not commit USAID, SIAPS, MSH and the authors. The final version of the report will be published as soon as adopted. Page 1 of65 NTP LABORATORY NETWORK ASSESSMENT (2016) Page 2 of65 Table of Contents List of Acronyms Preface Executive Summary Page 1 Introduction Page 7 Findings Page 7 I. Laboratory Services Page 7 1. TB sputum microscopy Page 13 2. Xpert MTB/RIF Assay Page 21 3. Culture and DST Page 28 4. Line Probe Assay Page 29 5. External Quality Assurance Program Page 34 II. Laboratory systems Page 34 1. Human resources Page 34 2. Training and supervision Page 36 3. Financing Page 37 4. Information management Page 38 5. Supply chain management Page 39 6. Equipment, facility (physical plant) and infrastructure Page 41 7. Monitoring and evaluation system Page 41 8. Leadership and management of the lab network Page 42 9. Biosafety Page 42 10. Infection control Page 42 11. Waste management Page 43 12. Laboratory health promotion and education Page 45 Recommendations Page 48 References Page 51 Annex A. Summary results of smear quality assessment Page 52 Annex B. Types of inconclusive test results in Xpert testing Page 53 Annex C. List of facilities included in the assessment Page 54 Annex D. List of persons interviewed Page 3 of 65 List of Acronyms Biomed Biomedical Department (RITM) BHMC Barangay Health Management Council BHS Barangay Health Station BSC Biological Safety Cabinet CHO City Health Office CTRL Cebu TB Reference Laboratory CXR Chest X-ray DOH Department of Health DSSM Direct Sputum Smear Microscopy DR drug resistant DST Drug susceptibility testing EPTB Extra-pulmonary tuberculosis EQA External Quality Assurance Program / External Quality Assessment EVRMC Eastern Visayas Regional Medical Center HC Health center HIV Human Immunodeficiency Virus IC Infection control ILW Informal laboratory worker ITR Inconclusive test result LCP Lung Center of the Philippines LED-FM Light emitting diode – Fluorescence Microscopy LNW Laboratory Network LPA Line Probe Assay LTBI Latent TB Infection MDRTB Multiple Drug-resistant Tuberculosis MTB Mycobacterium tuberculosis NGO Non-governmental organization NTM Non-tuberculous Mycobacteria NTP National TB control Program NTRL National TB Reference Laboratory NR No result (from an Xpert test) PCR Polymerase Chain Reaction PhilPACT Philippine Plan of Action to Control Tuberculosis PPE Personal Protective Equipment PTC Presumptive TB Cases RHU Rural Health Unit RITM Research Institute for Tropical Medicine RR An Xpert test result: MTB detected, Rifampicin resistant Page 4 of 65 RSS Remote Smearing Station PMDT Programmatic Management of Drug Resistant Tuberculosis PTSI Philippine Tuberculosis Society, Inc. QAC Quality Assurance Center SIAPS Systems for Improved Access to Pharmaceuticals and Services SLH San Lazaro Hospital T An Xpert test result: MTB detected, Rifampicin susceptible TAT Turnaround time TI An Xpert test result: MTB detected, Rifampicin resistance indeterminate TML TB microscopy laboratory XDRTB Extremely drug resistant tuberculosis ZN Ziehl-Neelsen Page 5 of 65 Preface Draft version - please do not quote or circulate Page 6 of 65 Executive Summary Draft version - please do not quote or circulate Page 7 of 65 Introduction I. The Philippines The Philippines is an archipelago composed of 7,107 islands located at the southeast coast of Asia with a total land area of approximately 343,448.32 km2. The country’s three major island groups and their land areas are: Luzon, covering 147,947.63 km2; Visayas with 59,873.84 km2; and Mindanao with 135,626.85 km2. The country has a diverse terrain consisting of high mountains, volcanoes and extensive valleys and plateaus that are surrounded by bodies of water such as rivers and lakes. The Philippines is a tropical country with an average temperature of 27°C. There are two seasons experienced each year: wet and dry1. The dry season can be divided into the cool dry season from December to January; and a hot dry season extending from March to May2. The highest temperatures recorded in the period of 2014 to 2016 were recorded in Tuguegarao City, Cagayan Province and in Metro Manila with temperatures exceeding 40 degrees Celsius3,4,5. The country is divided into 18 administrative regions with the addition of the newly established Negros Island Region (NIR) in mid-2016. NIR includes the provinces of Negros Occidental and Negros Oriental and Bacolod City. The population in 2015 was almost 101 million with an average annual population growth rate of 1.72% from 2010 to 2015 (Census and Housing Population, Philippine Statistics Authority). Region 4-A (CALABARZON) had the biggest population with 14.41 million, followed by the National Capital Region (NCR) with 12.88 million, and Region 3 (Central Luzon) with 11.22 million. The combined population of these three regions accounted for about 38.1 percent of the Philippine population in 2015. The Philippines is composed of 81 provinces and 144 cities, 1,490 municipalities and 42,036 barangays6. The country has 33 highly urbanized cities (HUCs), 4 of which have a population of over 1 million, these are Quezon City (2.94 million), City of Manila (1.78 million), Davao City (1.63 million), and Caloocan City (1.58 million)7. There are 1,489 municipalities in the Philippines. Cavite province (Region 4-A) is the most populous province in 2015 with a population of 3.68 million; followed by Bulacan in Region 3 (3.29 million); and Laguna in Region 4A (3.04 million). Batanes province has the smallest population size with 17,246 persons. Two other provinces had a population of less than 100,000 namely, Siquijor (95,984) and Camiguin (88,478). 1 Philippine Statistics Authority (PSA). A view of the Philippines. Geography. 2010. 2 Philippine Atmospheric, Geophysical and Astronomical Services Administration (PAGASA). Climate of the Philippines. 2016. 3 Corrales, N. Inquirer.Net. Tuguegarao City records hottest temperature–Pagasa. 2014 4 Locsin, J. GMA News. PAGASA: Highest temperature of 2015 so far recorded in Cagayan on Sunday. 2015. 5 Santos, E. PAGASA: Election day records hottest temperature of 2016 so far. 2016. 6 Philippine Standard Geographic Codes (PSGC). List of regions. 2016. 7 Philippine Statistics Authority (PSA). Highlights of the Philippine Population 2015 Census of Population. 2016 Page 8 of 65 There are three municipalities with big populations, namely: Rodriquez (pop: 369,222); Cainta (pop: 332,128); and Taytay (pop: 319,104), these are all located in Rizal province (Region 4A). The municipality of Kalayaan in Palawan province (Region 4B) has the smallest population with 184 persons. The population in urban areas is 41.9 million, while the rural population is 50.5 million which translates to an urban to rural population ratio of 0.83 (2013). The Philippine population is characterized by the rapid growth of the working age groups, and the slowly but steadily increasing elderly population. From 1970 to 2010, the proportion of the older age group (65 years and older) had increased faster than the younger age group (0-14 years and 15-64 years age group). However, the younger age group still has the bigger part of the population8. There were more males than females in the age groups 0 to 54 years (2010), but there were more females than males in the older age groups of 55 years and over9. The gender proportions are 50.4% males and 49.6% females. This pattern of age and gender distribution is also observed for 2016 based on population estimates. Life expectancy of Filipinos in 2015 is lower in males (65 years) than in females (72 10 years). In 2013, the literacy rate among Filipinos aged 15 to 24 remained high at 98.1% with women having a slightly higher literacy rate than men. One of every 10 Filipinos aged 6 to 24 years were out-of-school, which translates to about 24 million Filipinos in the country (2010). ARMM had the highest out-of-school population at 14.4% which is higher than the national average of 10.6%.11 The country is classified as a lower middle income country. The poverty incidence is 26.3% and the proportion of Filipino families in 12 extreme poverty was estimated at 9.2% in the first half of 2015. The country has a developed transport infrastructure but services are still inadequate due to lack of sustainable financing. There were modest improvements in the country’s transport services but large parts of the road network remain in poor which is largely due to poor and inadequate maintenance and is linked closely to weak transport sector governance. Significant developments were made in water transport with the upgraded Roll on – Roll off (ro-ro) ferry services as an alternative to the traditional inter-island shipping services. However, serious capacity limitation for air transport is anticipated as domestic and international air traffic grows. The urban transport system is mainly composed of buses, mass transport system (trains in Metro Manila), jeepneys, taxis, tricycles and pedicabs.13 From 2007 to 2013, motorcycles and tricycles 8 Castro, L.V. Efforts of the Philippine Statistical System (PSS) in Compiling Statistics on Population Ageing. 2015. 9 Philippine Statistics Authority (PSA). The Age and Sex Structure of the Philippine Population. 2012. 10 World Health Organization (WHO). Philippines Statistics. 2016. 11 Rodriguez, F. In numbers: #PHvote and PH education. 2016. 12 Philippine Statistics Authoriry (PSA). Poverty incidence among Filipinos registered at 26.3%, as of first semester of 2015 – PSA. 2016. 13 Asian Development Bank. Philippines: Transport Sector Assessment, Strategy and Road Map. 2012.
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