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Building Laboratory Capacity in Resource-poor Settings: Part 1
By Ellen Jo Baron, MD, PhD, Professor of Pathology and Medicine, Stanford University; Clinical Microbiology and Virology Laboratories, Stanford University Medical Center, is Associate Editor for Infectious Disease Alert.
Dr. Baron reports no financial relationships relevant to this field of study.
Physicians in the developed parts of the world have an unrealistic expectation that when they order a patient's specimen to be sent to the microbiology laboratory for culture that the results they receive in the laboratory's report are always reliable and can be used to initiate or modify the patient's therapeutic regimen. For the most part, physicians have placed their trust in a number of important events occurring in the appropriate order and in the appropriate manner. In reality, numerous roadblocks exist between clinicians' high expectations and the outcome. Many types of mistakes, or oversights, can happen, starting from the time the initial order was placed.
Common events, from my experience, serve as examples. The type of order required may not be the order placed into the system and acted on by the laboratory. For example, a respiratory secretion sample from a patient with cystic fibrosis (CF) must be inoculated onto at least two special, selective agars to have any chance of detecting two major pathogens in this population: Burkholderia cepacia selective agar and Staphylococcus aureus selective agar. If the laboratory is not aware that the patient has CF, the special media will not be used and the mucoid Pseudomonas aeruginosa, which is the hallmark of this disease, will overgrow the Petri plates and negate any possibility of recovering the other pathogens. Failure to detect one of these key pathogens can lead to severe negative consequences for the patient. If a physician obtains an endocervical swab but the swab doesn't reach the laboratory until the next day, small quantities of Neisseria gonorrhoeae may not survive. Molecular tests for N. gonorrhoeae may be more robust because viable organisms are not necessary, but if the endocervical pus was not removed before sample collection, the amplification process may be inhibited and the test will be indeterminate. Tissues are inadvertently placed in formalin when cultures are needed, tiny needle biopsies can dry out before they reach the laboratory, containers with precious samples can be diverted and then lost in a blind tunnel of the pneumatic tube (in one case for months) and, once, a group of inoculated blood culture bottles were found days after collection in a small refrigerator under a counter in the chemistry laboratory. Seth Haber, a clever pathologist who wrote a column in CAP Today for many years, created a set of laws that tried to inject a bit of humor into a devastating situation (Haber's Laws) (www.CAPToday.com), one of which I will paraphrase as "if a technologist drops a precious patient sample, it will fall on the most delicate piece of equipment in the laboratory, destroying both items."
These comments do not even begin to represent examples of problems that occur after the sample reaches the laboratory. Several years ago, in a laboratory in Southern California, a tired second-shift laboratory assistant plated an entire night's worth of urine cultures onto a selective agar plate that looked like standard blood agar but contained antibiotics and other inhibitors that killed every organism except group A streptococci, the one organism unlikely to be present in urine in the first place. These events are far from rare. In the future, we could present an entire article on common laboratory errors that result in frustrations for the physician and delays or worse for the patient. The more we realize the sorts of unwelcome incidents that can happen, the more defensive actions we can take to try to prevent these mistakes. Sadly, bad events happen too often, even in the best of laboratories staffed by professionals who have the worthiest of intentions.
Now, consider the nascent microbiology laboratories in the developing world. Although similar situations can be found in scores of countries, this report focuses on Cambodia because that is where support from World Health Organization (WHO) and the Global Health and Security Initiative of the Nuclear Threat Initiative allows our non-profit organization Diagnostic Microbiology Development Program (DMDP) to provide assistance in the form of supplies, infrastructure development, and volunteers who bring diagnostic microbiology expertise to a few primitive sites in this impoverished and devastated country.
The earthquake in Haiti, a disaster of monumental proportions, has shed a spotlight on the world's poorest countries. In one list of 194 countries ranked by gross domestic product, Haiti was 168 but Cambodia was nearby at 154. A number of African countries are at the bottom and the U.S. was #8 in this listing (www.who.int). Problems in Cambodia began with the legacy left by the despot Pol Pot. Within the lifetime of many Cambodians age 32 and older, one of the world's worst genocides occurred. Most adults today remember a time when all they had to eat were a few brown rice kernels that fell off the wagons of rice that they were forced to grow for export. As many Cambodians died from starvation and diarrheal disease, many were killed outright. Pol Pot's troops, no more than children themselves, tortured and killed anyone with an education, anyone who spoke French, anyone who could read, and even anyone who wore glasses. Most of the generation of Cambodians administering the country today have grown up without cultural, spiritual, or educational role models. They are still living in the mindset of "get whatever you can for yourself to survive." Unfortunately, that does not leave much emotional space to care for other citizens of the country beyond their circle of friends and family. Right now, the primary sources of revenue are tourism (Angkor Wat and the surrounding ancient temples) and the country's land, including some lovely seacoast, which the leaders are fast selling off to foreign developers, to the detrimental, sometimes fatal, outcomes of the locals who had lived there for generations and are now moved inland to locations with no possible means of making a living. Cambodia, even without a gigantic natural disaster, is in desperate straits. Fifty percent of the population is less than 25 years old.1 This is the only country in the world where the mortality rate among children < 5 years old is increasing. Medical care is virtually nonexistent. Almost without exception, if you become seriously ill in Cambodia, your only chance of survival is to fly to Bangkok quickly enough to get decent medicine.
There are possibly as many as 20 hospitals in this country of 14,250,000 people, most run by non-governmental aid organizations (NGOs) from around the world.1 A few small hospitals in Phnom Penh, notably the Pasteur Institute facility, have the capability of performing a microbiological culture and delivering relatively accurate results. But, such services come at a pretty high cost only the wealthy (here you may substitute "foreigners" or "corrupt officials") can afford them. In another model, exemplified by the hospitals built with foreign donations by Dr. Beat Richter, facilities are staffed mostly by foreign volunteers or missionaries, and Cambodians work primarily in unskilled jobs. In these NGO hospitals, some locals learn skills through on-the-job training, as there are very few schools of higher learning, and none with adequate general laboratory or microbiology training programs. In the bulk of the country, government-run hospitals get by with minimal support, but laboratory services are virtually non-existent. Patients are expected to pay for whatever care or medicines they receive when they visit the clinic or enter the hospital. In a country where the average annual income is $2,000, this is not easy, and laboratory tests are not high on their list of necessities.
With regard to microbiology laboratory training, there is one governmental laboratory technical school but the microbiology portion of the curriculum is rudimentary or nonexistent. And practical laboratory skills are not taught at all. The Merieux Foundation supports a pharmacy school with at least one microbiology class; this school (still taught in French, which is not spoken anywhere else in the country) turns out almost all of the laboratory directors in Cambodia, and the graduates know more microbiology than anyone else (which is not much and certainly not enough to perform a simple urine culture). These people are paid $30 a month by the Ministry of Health to work in and manage the government hospital laboratories, but the pharmacists actually make their living by owning and running a private pharmacy (which also performs microbiology culture studies) on the side. This causes conflict of interest, as the work in the hospital laboratory is hurriedly finished each day to allow time to go to the private pharmacy/laboratory and make money. Supplies are "transferred" off site, and worst of all, the most promising young technicians are hired to work in the private laboratory for wages that cannot be turned down. Samples from patients who have the ability to pay for laboratory tests are diverted to the private laboratory. Motivation to work hard for the hospital patients, who usually have barely enough money to pay for minimal services, is lacking. It is this environment in which we try to motivate technicians to upgrade their knowledge and abilities and perform quality diagnostic work. How do you convince such workers to perform daily quality control activities? How do you cajole them to come in on a weekend to read susceptibility results on an important culture? The environment of caring for the patient's well being is not there.
Equally as daunting as the challenges posed by the economic and educational environment are challenges involved in obtaining the resources needed to perform reliable microbiology. In the United States, we take for granted that we will have sufficient components for the media used in agar plates. Sheep and horses are plentiful in the developed world, and it is not technically difficult to bleed the animals and collect their blood aseptically, defibrinate it to remove clots, and use that blood to pour the plates. We depend on the growth characteristics on blood agar of the organisms we recover in cultures to begin the identification steps needed to determine the genus and species. For more than a century, microbiologists have used key colony morphology and the nature of red cell hemolytic activity on sheep and horse blood to name the pathogens. There are no sheep in Cambodia. It is too hot, there are too many parasites, and the local population would not know how to care for or manage sheep. Horses are out of the question, being too expensive, requiring too much land and support, and being also rare in Cambodia and many developing countries.
So Cambodian technicians as well as microbiologists everywhere else in the developing regions of the tropics with insufficient resources to purchase blood from out of country use outdated human blood bank blood to make their media. This poses two problems: human blood is unsafe, often carrying hepatitis or HIV; and human blood does not grow pathogens or other human microbes either very well or with recognizable colony morphologies, negative characteristics that degrade even more after storage. In other words, human blood doesn't work. We have purchased a few scrawny sheep and found another NGO willing to husband and to bleed them, but it is not the most satisfactory arrangement, and the sheep are not thriving. There will be more on a potential solution for the problem of obtaining the blood component of media in a future column.
The basic microbiology procedures advocated by our program result in identifying a pathogenic isolate only enough to allow the clinician to make an informed decision and then performing simple disk--diffusion antimicrobial susceptibilities. No automated methods, no multi-well biochemical panels, no expensive additional tests. The identification of isolates depends on colony and Gram stain morphology, rapid spot tests (catalase, coagulase, indole, oxidase, and pyrrolidonyl aminopeptidase), and a few typing sera. If an important organism from a patient requires a definitive identification beyond the local laboratory's capability or resources, it is sent to the U.S. Naval Army Medical Research Unit Laboratory in Phnom Penh, which does an excellent job for free, albeit with delayed results. But the reagents and supplies needed even for the very minimal rapid spot tests are difficult to obtain. One can order them from a supplier from another country, but the price becomes exorbitant. In fact, one spot reagent kit used in the Stanford laboratory that costs us $18 to purchase, ended up costing the Cambodian laboratory $200 (paid for by WHO, of course). What contributes to this enormous price inflation? The only factor is the amount of taxes, fees, and gratuities extracted from stakeholders along the way as the product moves through official importation channels. We would like to purchase our supplies in the U.S. and carry or mail them directly into Cambodia, but the head of WHO in country does not want to flout the official government process. Unfortunately a lot of the official process is unofficial. So having enough supplies on hand is challenging, and many times the laboratory has to improvise. Also regrettably, improvisation is not a skill either inherent in most technicians in the developing world, nor is it taught in the schools. The Cambodians are a wonderful, generally cheerful, group of people, but with major traits of fatalism and inertia in the face of decades of obstacles. They deserve a better future.
Given this scenario, there doesn't seem to be a lot of cause for optimism on the laboratory scene. The objective of the DMDP is to have four laboratories in Cambodia capable of performing basic microbiology, starting with a Gram stain, then moving to tasks such as a urine culture, CSF culture, blood culture, sputum or wound culture, and finally performing antimicrobial susceptibility tests on the appropriate organisms recovered in culture. One year into the work, we have a pretty good laboratory in Kampong Cham, approximately two hours up the Mekong River from Phnom Penh. Our success there is largely due to Madame Somary, a very motivated and enthusiastic pharmacist who wants to learn as much as possible and perform high-quality microbiology. We have to live with the fact that the best work is done in her private pharmacy laboratory; nevertheless, her leadership in the hospital laboratory has been superb. They identified a Streptococcus pneumoniae from a CSF last week, and they have recovered and identified Shigella, Salmonella, Acinetobacter, Haemophilus influenzae, and Staphylococcus aureus, among others. The susceptibility QC is being done weekly, and physicians are beginning to send samples as they develop more trust in the laboratory. The WHO liaison for the program project has proudly taken visitors up to Kampong Cham Hospital to showcase this laboratory. Recently an Australian volunteer arrived in Kampong Cham to live and work in the laboratory for more than a year, and she is continuing to enforce our program. This is the kind of support these laboratories need, and we hope other agencies will also come into the system.
A space has been identified for a microbiology laboratory in Battambang, the second largest city in Cambodia, located about five hours by bus northwest of Phnom Penh, and our group has contracted for renovation and building of the laboratory space. This summer we will move our next volunteer there to spend a more extended time (up to 6 months) to try to get that laboratory up and running. Our great good luck was to find a current Stanford Clinical Laboratory Science student willing to go there when she graduates this summer, but the best part is that she is ethnic Cambodian, speaks Khmer, and has an uncle living in Battambang. This extraordinarily fortunate situation must be celebrated. A third laboratory is slated for Takeo (in southern Cambodia), but the plan is not complete yet. The fourth laboratory, the National Pediatric Hospital in Phnom Penh, has major problems with laboratory staff motivation and interest. The director of the hospital laboratory also has his private laboratory, where all of the promising technicians' work is done, so there is no authority from above advocating dedication to the hospital patients' cultures. Even after four months of constant volunteer support, the laboratory won't do its quality control, cultures are left for days without examination, workbenches are dirty and supplies are disorganized, but worst of all results are unreliable. Without better leadership, volunteers cannot be effective, so we will not spend our precious resources placing them there. There is hope that the most promising technician, who won a scholarship to study microbiology in Thailand for six months, will return to the laboratory and provide the skills and leadership needed to motivate the others. Since she also has her private business nearby in downtown Phnom Penh, there is hope that she will stay in the laboratory.
This article covered some of the aspects and obstacles encountered in trying to enhance microbiology diagnostic capability in a developing world venue. If nothing else, it should cause you to appreciate the laboratory you use now. Despite a few failures and shortcomings, realize that results are generally reasonable and helpful and that the information delivered to you is timely and relevant to your patients. Some day we hope that at least a few laboratories in Cambodia can deliver the same results.