Evaluation of the WHO laboratory quality stepwise implementation tool.

OBJECTIVES: To introduce the Laboratory Quality Stepwise Implementation (LQSI) tool and provide data about its roll-out, usage and effectiveness in assisting laboratories with quality improvement. METHODS: The LQSI tool, a freely available stepwise guide, was developed by WHO to assist laboratories with efficiently implementing a quality management system. RESULTS: Since the tool's launch in 2014, it has been accessed by 130 986 unique users from 195 of 206 listed states. Of 35 respondents to a survey, 12 (34%) indicated that their laboratory had been able to achieve accreditation/certification/licensing as a result of using the tool. CONCLUSIONS: The LQSI tool, currently being used worldwide and available in English, French, Russian, Spanish, Arabic and Turkish, positively impacts the quality of services provided by clinical and public health laboratories, leading to improved clinical care and disease surveillance capacity as required by the IHR (2005) and envisioned by the Global Health Security Agenda.

Liquid culture for Mycobacterium tuberculosis: proceed, but with caution.

Attempts to improve the diagnosis of tuberculosis (TB) in high-burden countries has resulted in significant funding and initiatives to change the method of diagnosis of TB from light microscopy supplemented with X-ray to a sophisticated diagnostic algorithm based on the latest technological innovations. Such activities are overdue and should be welcomed, but the lack of skills and support available to interpret and use the results represents a danger. The introduction of new diagnostic methods, particularly liquid culture, should be carefully structured according to the local situation, failing which frustration and the disruption of previously underdeveloped but adequately functioning laboratories may result.

Buoyant density of Mycobacterium tuberculosis: implications for sputum processing.

SETTING: A tuberculosis (TB) research laboratory in the Netherlands. OBJECTIVE: The concentration of Mycobacterium tuberculosis cells from sputum is almost universally performed by centrifugation after chemical liquefaction. These methods are thus dependent on the effective sedimentation of mycobacterial cells, and the buoyant density of these cells relative to sputum is therefore of critical importance. DESIGN: We cultured M. tuberculosis in different systems and measured their buoyant density. We also calculated the centrifuge times and speeds needed to effectively pellet the mycobacteria. RESULTS: In contrast to earlier reports, we were unable to identify cells with a buoyant density <1 g/cm(3). The measured buoyant density of the cells ranged from 1.13 to 1.02 g/cm(3), and we suspect that the less dense cells are more likely to reflect clinically derived mycobacterial cells. CONCLUSION: Based on our results, this means that for effective sedimentation in a typical universal centrifuge, centrifugation for 22 min at 3200 x g would be required. A limitation of this study is that cultured M. tuberculosis was studied. The data from this study should be confirmed in clinical samples. However, based on our results, centrifugation at lower speed for less time is unlikely to result in effective recovery.

Development of multiplex assay for rapid characterization of Mycobacterium tuberculosis.

We have developed a multiplex assay, based on multiplex ligation-dependent probe amplification (MLPA), that allows simultaneous detection of multiple drug resistance mutations and genotype-specific mutations at any location in the Mycobacterium tuberculosis genome. The assay was validated on a reference panel of well-characterized strains, and the results show that M. tuberculosis can be accurately characterized by our assay. Eighteen discriminatory markers identifying drug resistance (rpoB, katG, inhA, embB), members of the M. tuberculosis complex (16S rRNA, IS6110, TbD1), the principal genotypic group (katG, gyrA), and Haarlem and Beijing strains (ogt, mutT2, mutT4) were targeted. A sequence specificity of 100% was reached for 16 of the 18 selected genetic targets. In addition, a panel of 47 clinical M. tuberculosis isolates was tested by MLPA in order to determine the correlation between phenotypic drug resistance and MLPA and between spoligotyping and MLPA. Again, all mutations present in these isolates that were targeted by the 16 functional probes were identified. Resistance-associated mutations were detected by MLPA in 71% of the identified rifampin-resistant strains and in 80% of the phenotypically isoniazid-resistant strains. Furthermore, there was a perfect correlation between MLPA results and spoligotypes. When MLPA is used on confirmed M. tuberculosis clinical specimens, it can be a useful and informative instrument to aid in the detection of drug resistance, especially in laboratories where drug susceptibility testing is not common practice and where the rates of multidrug-resistant and extensively drug resistant tuberculosis are high. The flexibility and specificity of MLPA, along with the ability to simultaneously genotype and detect drug resistance mutations, make MLPA a promising tool for pathogen characterization.

Light emitting diodes for auramine O fluorescence microscopic screening of Mycobacterium tuberculosis.

We describe the simple adaptation of a standard fluorescent microscope for illumination using a 'Royal Blue' Luxeon light emitting diode (LED) and demonstrate that this form of illumination is suitable for the detection of auramine O stained Mycobacterium spp. The low cost, low power consumption, safety and reliability of LEDs makes them attractive alternatives to mercury vapour lamps.

The role and performance of chest X-ray for the diagnosis of tuberculosis: a cost-effectiveness analysis in Nairobi, Kenya.

BACKGROUND: The objective of this study was to establish 1) the performance of chest X-ray (CXR) in all suspects of tuberculosis (TB), as well as smear-negative TB suspects and 2) to compare the cost-effectiveness of the routine diagnostic pathway using Ziehl-Neelsen (ZN) sputum microscopy followed by CXR if case of negative sputum result (ZN followed by CXR) with an alternative pathway using CXR as a screening tool (CXR followed by ZN). METHODS: From TB suspects attending a chest clinic in Nairobi, Kenya, three sputum specimens were examined for ZN and culture (Lowenstein Jensen). Culture was used as gold standard. From each suspect a CXR was made using a four point scoring system: i: no pathology, ii: pathology not consistent for TB, iii: pathology consistent for TB and iv: pathology highly consistent for TB. The combined score i + ii was labeled as "no TB" and the combined score iii + iv was labeled as "TB". Films were re-read by a reference radiologist. HIV test was performed on those who consented. Laboratory and CXR costs were used to compare for cost-effectiveness. RESULTS: Of the 1,389 suspects enrolled, for 998 (72%) data on smear, culture and CXR was complete. 714 films were re-read, showing a 89% agreement (kappa value = 0.75 s.e.0.037) for the combined scores "TB" or "no-TB". The sensitivity/specificity of the CXR score "TB" among smear-negative suspects was 80%/67%. Using chest CXR as a screening tool in all suspects, sensitivity/specificity of the score "any pathology" was 92%, respectively 63%. The cost per correctly diagnosed case was for the routine process 8.72 dollars, compared to 9.27 dollars using CXR as screening tool. When costs of treatment were included, CXR followed by ZN became more cost-effective. CONCLUSION: The diagnostic pathway ZN followed by CXR was more cost-effective as compared to CXR followed by ZN. When cost of treatment was also considered CXR followed by ZN became more cost-effective. The low specificity of chest X-ray remains a subject of concern. Depending whether CXR was performed on all suspects or on smear-negative suspects only, 22%-45% of patients labeled as "TB" had a negative culture. The introduction of a well-defined scoring system, clinical conferences and a system of CXR quality control can contribute to improved diagnostic performance.

Sex-specific performance of routine TB diagnostic tests.

SETTING: City Council Chest Clinic, Nairobi, Kenya. OBJECTIVE: To determine to what extent the performance of smear microscopy is responsible for sex differences in notification rates. METHODOLOGY: Three sputum samples from TB suspects were subjected to smear microscopy with Ziehl-Neelsen (ZN) and auramine (FM) staining. Lowenstein-Jensen culture was used as the gold standard. RESULTS: Of 998 suspects, 600 (60%) were men and 398 (40%) women. The odds of detecting culture-positive patients with ZN was lower for women (OR 0.67). By examining the first spot specimen, ZN detected 35% of culture-positive males and 26% of culture-positive females. These proportions increased to respectively 63% and 53% when examining three specimens, and to 79% and 74% when using FM. The sex difference reduced and became non-significant (P = 0.19) when adjusted for HIV; however, the numbers involved for HIV stratification were low. CONCLUSION: The performance of a diagnostic tool contributes to sex differences in notification rates and influences male/female ratios. Women were less likely to be diagnosed (P = 0.08), and when ZN was used they were less likely to be labelled as smear-positive TB (P < 0.01). The application of more sensitive diagnostic tools such as FM is to the advantage of women.

Direct detection of Staphylococcus aureus mRNA using a flow through microarray.

The direct detection of mRNAs from bacterial cultures on a DNA array without amplification and labelling would greatly extend the range of applications suitable for microarray analysis. Here we describe the direct detection of 23S rRNA and seven mRNA species from total Staphylococcus aureus RNA prepared using commercially available RNA purification columns followed by fluorescent detection on a flow through microarray. RNA hybridisation was detected using paired secondary labelled probes directly 5' and 3' to immobilised 60 mers. In this way, we were able to detect the effect of 30-min exposure to antimicrobials on mRNA levels within 3 h after column purification of total RNA without the need for enzymatic manipulation. Specifically the expression of mecA was confirmed in a highly resistant strain and induction of katA and ile-tRNA synthetase genes after exposure to mupirocin could be detected.

Epidemiology of leprosy on five isolated islands in the Flores Sea, Indonesia

We conducted a population-based survey on 5 small island in South Sulawesi Province (Indonesia) to collect baseline data previous to a chemoprophylactic intervention study aiming at interrrupting the transmission of Mycobacterium leprae. Here we describe the present leprosy epidemiology on these geographically isolated islands. Of the 4774 inhabitants living in the study area 4140 were screened for leprosy (coverage: 87%). We identified 96 leprosy patients (85 new and 11 old patients), representing a new case detection rate (CDR) of 205/10,000 and prevelence rate 195/10,000. CDRs were similar for males and females. Male patients were more often classified as multibacillary (MB) than women. Of the new patients, 33 (39%) were classified as MB, 16 (19%) as paucibacillary (PB) 2-5 lesions and 36 (42%) as PB single lesion. In this area of high leprosy endemicity leprosy patients were extensively clustered, i.e. not equally distributed among the islands and within the islands among the houses

Population survey to determine risk factors for Mycobacterium leprae transmission and infection

Background: Not every leprosy patient is equally effective in transmitting Mycobacterium leprae. We studied the spatial distribution of infection (using seropositivity as a marker) in the population to identifity which disease characteristics of leprosy patients are important in transmission. Methods: Clinical data and blood samples for anti-M.leprae ELISA were collected during a cross-sectional survey on five Indonesian islands highly endemic for leprosy. A geographic information system (GIS) was used to define contacts of patients. We investigated spatial clustering of patients and seropositive people and used logist regression to determine risk factors for seropositivity. Results: Of the 3986 people examined for leprosy, 3271 gave blood. Seroprevalence varied between islands (1.7-8.7%) and correlated significantly with leprosy prevalence. Five clusters of patients and two clusters of seropositives were detected. In multivariate analysis, seropositivity significantly differed to be the best discriminator of contact groups with higher seroprevalence: contacts of seropositive patients had an adjusted odds ratio (aOR) of 1.75 (95% CI: 0.92-3,31). This increased seroprevalence was strongest for contact groups living _< 75 metres of two seropositive patients (aOR:3.07;95%CI:1.74-5.42). Conclusions: In this highly endemic area for leprosy, not only household contacts of seropositive patients, but also persons living in the vicinity of seropositive patient were more likely to harbour antibodies against M.leprae. Through measuring the serological status of patients and using a broader definition of contacts, higher risk groups can be more specifically identified

Genetic, household and spatial clustering of leprosy in an island population in Indonesia

It is generally accepted that genetic factors play a role in susceptibility to both leprosy per se and leprosy type, but the strength of this effects has never been quantified. Estimating the contribution of genetic factors to clustering of leprosy within families is difficult since these persons often shave the same environment. Three correlation structures (genetic, household and spatial) were proposed for population data (n=560), collected on a geographically isolated Indonesian island highly endemic for leprosy, to explain the distribution of leprosy per se, leprosy type and Mycobacterium leprae-specific antibody. Heritability estimates and risk ratios for siblings were calculated to quantify the genetic effect. Leprosy was clinically diagnosed and specific anti-M.leprae antibodies were measured using ELISA. For leprosy per se in the total population the genetic correlation structure fitted best. In the population with relative stable household status (persons under 21 years and above 39 years) all structures were significant. For multibacillary leprosy (MB) genetic factors seemed more important than for paucibacillary leprosy. Seropositivity could be explained best by the apatial model, but the genetic model was also significant. Herediatry was 57% for leprosy per se and 31% for seropositivity. Genetic factors seem to play an important role in the clustering of leprosy patients, especially MB patients, and they could explain more then half of the toral phenotypic variance. This unique study population is very suitable to confirm the role of already known chromosome regions in controlling leprosy or to search for new susceptibility loci

Risk factores for developing leprosy -A population-based cohort study in Indonesia

This study identified risk factors for developing leprosy through yearly incidence rates in five island populations. Personal factors, like age, sex, household size and the presence of M.leprae-specific antibodies as well as contact were studied. Of the 94 index patients (patients diagnosed in 2000) 43 (46%) were classified as multibacillary (MB), 17 (19%) were seropositive and 6 (7%) presented M.leprae DNA in nasal swabs as determined by polumerase chain reaction (PCR). All PCR positive patients were also seropositive. Forty-four of the 4903 persons initially without symptoms of leprosy developed leprosy in almost four years follow-up, giving an incidence rate of 2.98 per 1000 person-years. Men had a 2.2 times higher risk (95% Confidence Interval [CI]: 1.2-4.1) to developd leprosy than women. Persons living in households of more than 7 household members. Persons who were seropositive in 2000 had a 3.7 times higher risk (95% CI:1.1-12.4) than seronegative persons. Household contacts of MB patients had an adjusted hazard ratio (aHR) of 4.6 (95% CI:1.6-12.9) and household contacts of PCR positive patients an aHR of 9.36 (95% CI: 2.5-34.9) compared to non-contacts. Patients with PCR positive nasal swabs, suggesting nasal excretion of M.leprae, are probably the patients with the highest transmission patential. Since all index patients who were PCR positive were also seropositive, serology semms an adequate tool to identify these patients. Preventing seropositive persons to become seropositive patients and thus the main source of infection may break the chain of transmission

Prevention of leprosy using rifampicin as chemoprophylaxis

An intervention study was implemented on five Indinesian island highly endemic for leprosy to determine whether rifampicin can be used as chemoprophylaxis to prevent leprosy. The population was actively screened before the intervention and subsequently once a year for three years. In the control group, no chemoprophylaxis was given. In the contact group, chemoprophylaxis was only given to contacts of leprosy patients and in the blanket group to all aligible persons. The cohort consited of 3,965 persons. The yearly incidence rate in the control group was 39/10,000; the cumulative incidence after three years was significantly lower in the blanket group (P=0.031). No difference was found between the contact and the control groups (P=0.93). Whether this apparent reduced leprosy incidence in the first three years in the blanket group is due to a delayed development of leprosy or a complete clearence of infections needs to be determined

Prospective study of serological conversion as a risk factor for development of leprosy among household contacts.

Although the prevalence of leprosy has declined over the years, there is no evidence that incidence rates are falling. A method of early detection of those people prone to develop the most infectious form of leprosy would contribute to breaking the chain of transmission. Prophylactic treatment of serologically identified high-risk contacts of incident patients should be an operationally feasible approach for routine control programs. In addition, classification of high-risk household contacts will allow control program resources to be more focused. In this prospective study, we examined the ability of serology used for the detection of antibodies to phenolic glycolipid I of Mycobacterium leprae to identify those household contacts of multibacillary leprosy patients who had the highest risk of developing leprosy. After the start of multidrug therapy for the index case, a new case of leprosy developed in one in seven of the 178 households studied. In households where new cases appeared, the seropositivity rates were significantly higher (P < 0.001) than those in households without new cases. Seropositive household contacts had a significantly higher risk of developing leprosy (relative hazard adjusted for age and sex [aRH], 7.2), notably multibacillary leprosy (aRH = 24), than seronegative contacts.

Prospective study of serological conversion as a risk factor for development of leprosy among household contacts

Although the prevalence of leprosy has decline over the years, there is no evidence that incidence rates are falling. A method of early detection of those people prone to develop the mosth infectious form of leprosy would contribute to breaking the chain of transmission. Prophylactic treatment of serologically idenfified high-risk contacts of incidend patients should be an operationally feasible approach for routine control programs. In addition, classification of high-risk household contacts will allow control program resources to be more focused. Is this prospective study, we examined the ability of serology used for the detection of antibodies to phenolic glycolipid I of Mycobacterium leprae to identify those household contacts of multibacillary leprosy patients who had the highest risk of developing leprosy. After the start of multidrug therapy for the index case, a new case of leprosy developed in one in seven of the 178 households studied. In households where new cases appeared, the seropositivity rates were significantly higher (P<0.001) than those in households without new cases. Seropositive household contacts had a significantly higher risk of developing leprosy (relative hazard adjusted for age and sex [aRH], 7.2), notably multibacillary leprosy (aRH=24), than seronegative contacts

Nasal carriage of Mycobacterium leprae DNA in healthy individuals in Lega Robi village, Ethiopia.

The number of registered leprosy patients world-wide has decreased dramatically after extensive application of WHO recommended Multiple Drug Therapy (MDT). The annual number of new cases has, however, been almost unchanged in several populations, indicating that the infection is still present at community level. Nasal carriage of Mycobacterium leprae DNA was studied in Lega Robi village in Ethiopia. MDT had been applied for more than ten years, and 718 residents over 5 years old were eligible for the study. During the first survey nasal swab samples were collected from 664 (92.5%) individuals. The results of a Peptide Nucleic Acid-ELISA test for M. leprae DNA interpreted by stringent statistical criteria were available for 589 (88.7%) subjects. Thirty-five (5.9%) individuals without clinical signs of leprosy were positive for M. leprae DNA. Seven PCR positive individuals lived in a household where one or two other members were also positive for M. leprae DNA. During a second survey 8 (46%) of 175 interpretable PNA-ELISA tests were positive. Of 137 individuals tested twice, only two were positive on both occasions whereas 10 were PCR positive only once. The study confirms the widespread distribution of M. leprae DNA in healthy individuals. The feasibility of curbing possible transmission of subclinical infection needs further consideration.

Simple and fast lateral flow test for classification of leprosy patients and identification of contacts with high risk of developing leprosy.

The interruption of leprosy transmission is one of the main challenges for leprosy control programs since no consistent evidence exists that transmission has been reduced after the introduction of multidrug therapy. Sources of infection are primarily people with high loads of bacteria with or without clinical signs of leprosy. The availability of a simple test system for the detection of antibodies to phenolic glycolipid-I (PGL-I) of Mycobacterium leprae to identify these individuals may be important in the prevention of transmission. We have developed a lateral flow assay, the ML Flow test, for the detection of antibodies to PGL-I which takes only 10 min to perform. An agreement of 91% was observed between enzyme-linked immunosorbent assay and our test; the agreement beyond chance (kappa value) was 0.77. We evaluated the use of whole blood by comparing 539 blood and serum samples from an area of high endemicity. The observed agreement was 85.9% (kappa = 0.70). Storage of the lateral flow test and the running buffer at 28 degrees C for up to 1 year did not influence the results of the assay. The sensitivity of the ML Flow test in correctly classifying MB patients was 97.4%. The specificity of the ML Flow test, based on the results of the control group, was 90.2%. The ML Flow test is a fast and easy-to-perform method for the detection of immunoglobulin M antibodies to PGL-I of M. leprae. It does not require any special equipment, and the highly stable reagents make the test robust and suitable for use in tropical countries.

Effect of secondary structure on single nucleotide polymorphism detection with a porous microarray matrix; implications for probe selection.

Oligonucleotide arrays capable of detecting single nucleotide polymorphisms (SNPs) from amplified nucleic acid have many applications. The expected SNP is usually placed approximately in the center of the probe to ensure the maximum shift in Tm between complementary and SNP sequences. Unfortunately, different short probes (< 30 bases) selected using widely accepted criteria do not perform consistently in this type of assay. Here we present a systematic study on the effect of secondary structure on the ability of oligonucleotide probes to detect an SNP, using real-time array monitoring of a porous microarray substrate that incorporates a novel intra-array mixing system. These results demonstrate that, although positioning of an SNP in the middle of the probe is highly destabilizing, the effect of stable secondary structure on the signal obtained is so dramatic that such probes may be very insensitive. Therefore, if the SNP flanking sequence contains significant secondary structure, then more sensitive probes with good specificity may be obtained by positioning the mutation towards one end of the probe.

A comprehensive study of the efficiency of the routine pulmonary tuberculosis diagnostic process in Nairobi.

Tuberculosis (TB) suspects from Rhodes Chest Clinic, Nairobi, Kenya, were subjected to three sputum smear microscopy (Ziehl-Neelsen) examinations and a chest X-ray (CXR). Results were compared with Löwenstein-Jensen culture as the gold standard to establish the efficiency of the routine diagnostic process. All laboratory tests and the CXR were available for 993 (71%) of the 1,398 enrolled suspects. Of these, 554 (56%) were culture-positive. The routine diagnostic process was very sensitive, able to detect 92% of culture-positive cases but missing 8%. The specificity was low (66%), and 23% of the patients started on treatment were culture-negative, mainly due to the low specificity of the CXR. It may be possible to increase the efficiency of the diagnostic process by specifying better criteria for CXR examination, improving the quality of CXR reading and counselling patients to return when complaints persist.

Simple and fast lateral flow test for classification of leprosy patients and identification of contacts with high risk of developing leprosy

The interruption of leprosy transmission is one of the main challenges for leprosy control programs since no consistent evidence exists that transmission has been reduced after the introduction of multidrug therapy. Sources of infection are primarily people with high loads of bacteria with or without clinical signs of leprosy. The availability of a simple test system for the detection of antibodies to phenolic glycolipid-I (PGL-I) of Mycobacterium leprae to identify these individuals may be important in the prevention of transmission. We have developed a lateral flow assay, the ML Flow test, for the detection of antibodies to PGL-I which takes only 10 min to perform. An agreement of 91% was observed between enzyme-linked immunosorbent assay and our test; the agreement beyond chance (kappa value) was 0.77. We evaluated the use of whole blood by comparing 539 blood and serum samples from an area of high endemicity. The observed agreement was 85.9% (kappa = 0.70). Storage of the lateral flow test and the running buffer at 28 degrees C for up to 1 year did not influence the results of the assay. The sensitivity of the ML Flow test in correctly classifying MB patients was 97.4%. The specificity of the ML Flow test, based on the results of the control group, was 90.2%. The ML Flow test is a fast and easy-to-perform method for the detection of immunoglobulin M antibodies to PGL-I of M. leprae. It does not require any special equipment, and the highly stable reagents make the test robust and suitable for use in tropical countries.