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Test agreement between GeneXpert and urine lipoarabinomannan test for tuberculosis diagnosis among children in Ethiopia

BMC Pediatrics volume 25, Article number: 254 (2025) Cite this article

Abstract

Background

Tuberculosis (TB) is one of the leading public health problems in children mainly due to difficulties in the diagnosis of disease in children. It has been reported that the commercial urine lipoarabinomannan (LAM) assays used in patients with confirmed pulmonary TB have low sensitivity. This raises the need for alternative tests to screen for M. tuberculosis infection using easily collectable samples, such as urine, in host samples. This study aimed to detect the diagnostic agreement between GeneXpert MTB/RIF and WHO-recommended LAM antigen test for the detection of TB in children using urine samples.

Methods

An institutional-based cross-sectional study was conducted on 337 children in Wolaita Sodo University comprehensive Hospital. LAM antigen and GeneXpert methods were used to detect TB from urine samples. The agreement between the two tests was assessed using Kappa statistics with the standard error (SE), concordance, and disagreements statistics. Logistic regression was used to determine factors associated with TB and P-values less than 0.05 were considered as having a statistically significant association.

Results

M. tuberculosis was detected in 26 using TB LAM giving an overall prevalence of 7.7% (5.0-10.7%) and 8.6%; CI 5.6–11.6) using GeneXpert. The two tests had an almost perfect agreement (Concordance of 99.1% and kappa value of 0.94 with a standard error of 0.034) for the detection of TB in urine samples. Co-infections with other diseases [AOR = 4.00: 95% CI, 1.428, 11.203], cough for the previous two weeks [AOR = 3.700: 95% CI, 1.039, 13.183], night sweat [AOR = 4.255: 95% CI, 1.453, 12.463] and loss of appetite [AOR = 3.994: 95% CI, 1.444, 11.045] had significant associations with pulmonary TB among children in the study area.

Conclusion

Tuberculosis was still a public health concern among children under five years old in the study area. The GeneXpert had almost perfect test agreement with WHO recommended TB LAM antigen test for the diagnosis of TB among under-five children, however, it needs further confirmation study with a large sample size to use as a diagnostic test.

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Introduction

Tuberculosis (TB) due to M.tuberculosis is one of the leading public health problems in which human beings are the only reservoir and occurs all around the world [1, 2]. In 2020, the COVID-19 pandemic dislodged TB from the top infectious disease cause of mortality globally [3]. However, the disease remains a major public health problem that affects all age groups globally [4]. It is a public health concern among children causing considerable mortality in resource-limited settings due to challenges associated with difficulties in diagnosis and treatment of the disease [5,6,7]. Childhood TB in recent years has been given less public health priority although TB is an important cause of childhood morbidity and mortality globally [8].

Ethiopia is one of the high-burden countries for TB, TB/HIV, and multidrug-resistant (MDR) TB in the world; ranking 10th among the world’s 22 high-burden countries for TB, and 4th in Sub-Saharan Africa [9]. TB kills an estimated 32,000 individuals per year (more than 80 people per day) and it has a long-term impact on the economy of the country since it mainly affects young adults and children [9]. Even though TB remains a major cause of disease and death among children, is often unrecognized in disease endemic setting of Ethiopia [10, 11].

Childhood TB has been relatively neglected for several years, mainly due to difficulties in diagnosis of the disease that resulted from difficulties in expelling of sputum [12]. Due to the paucibacillary nature of pediatric TB, together with challenges in obtaining clinical samples, microbiologically confirmed TB is obtained in less than 30% of children with radiological/clinical evidence of intra-thoracic disease, even when sputum induction and a referral laboratory are available. The diagnosis of TB relies on a constellation of history, examination, immunology, radiology, and bacteriology, all with limited sensitivity and specificity. Culture-based diagnostics remain the gold standard for TB diagnosis; however, it is time-consuming and unavailable in many TB endemic settings. TB diagnoses by symptom-based screening, chest x-ray, and sputum smear microscopy for Acid Fast Bacilli (AFB) have demonstrated limited performance.

Early accurate diagnosis of active TB disease is important to stop transmission but the current widely used diagnostic test, microscopic detection, has poor sensitivity and is restricted to live bacilli in the sample [13, 14]. A recently developed LAM test is recommended by WHO for immunocompromised patients but a meta-analysis of studies using commercial urine LAM assays in patients with microbiologically confirmed pulmonary TB reported that sensitivity ranged from 13 to 93% with good specificity ranged from 87–99% [15]. Therefore, the need for the best alternative tests in this study is raised from the lack of suitable screening tests for M. tuberculosis infection using easily collectible samples like urine in host samples.

In Ethiopia, there were several studies done among different study groups with varying findings among the adult population living with HIV and others [16,17,18,19]. Despite this, there is a lack of data on the detection of TB using urine LAM antigen and comparing it with GeneXpert methods among under-five children in Ethiopia in general and in the study area in particular. To our knowledge, the prevalence and associated risk factors of pulmonary TB among children in the present study area are also unknown. Therefore, the present study aims to determine the prevalence of TB in the Wolaita area using the LAM antigen test, to compare its test agreement with GeneXpert, and to find out factors associated with TB infection.

Methods and materials

Study setting, study design, and period

An institutional-based cross-sectional study was conducted in Wolaita Sodo University Comprehensive Specialized Hospital (WSUCSH) from February 1, 2022, to April 30, 2022. Wolaita Sodo University Comprehensive Specialized Hospital (WSUCSH), is located in Sodo town southern Ethiopia. It is 329 km from Addis Ababa, the capital of Ethiopia.

Sample size and sampling technique

The sample size for prevalence was calculated using a single proportional formula with the assumption of a 95% level of confidence, 13% prevalence of TB among children [5], and a margin of error 5% (d = 0.05) which gives a sample size of 174. The sample size for risk factors was calculated using Open Epi-3.5 by considering odds of 14.8 for TB contact, 5.5 for HIV infection, and 4.12 for malnutrition from previous study in Ethiopia [20]. For TB contact, the sample size was 191, for HIV infection, the sample size was 377, and for malnutrition, it was 133. The largest sample size which is 337 taken as sample size for this study. According to hospital records, approximately 12 children presumptive TB cases attended WSUCSH per day, resulting in a total of 720 in three months of working days. Study participants were selected using systematic random sampling after detecting kth –value (720/337 = 2.1). One child was chosen from the two children by lottery method, the followings were selected in every 2nd individuals until the required sample size was fulfilled.

Data collection

Socio-demographic data collection

A structured questionnaire was used to collect socio-demographic data about the child (sex, age, body mass index, and residence). The other risk factors of TB like contact history with TB patient, family size, family occupation, raw milk consumption, BCG vaccine history, and co-morbidity were collected by interviewing the parents or guardians. The BCG vaccination was confirmed by inspecting for scars associated with BCG vaccination on the upper arm of the children. Clinical presentation associated with TB was assessed by a physician and the laboratory diagnosis was performed by a laboratory technologist. The specimens were processed immediately in the central laboratory of WSUCH.

Laboratory data collection and processing

Presumptive TB cases were included in the study and a urine sample was obtained from each child for the LAM Alere Determine test (Alere Determine TB-LAM, Waltham, MA, USA) [21] and GeneXpert method. Caretakers or parents were oriented on how to collect the child’s midstream urine samples by trained data collectors. The collected urine specimens were kept unprocessed at 2–8 °C and testing was carried out on the same day. A sixty microliter (60µL) was added to the sample pad, and the specimen released the colloidal gold conjugated antibodies attached to the LAM antigen from the conjugate pad. This immunological complex was then captured by anti-LAM antibodies immobilized on the nitrocellulose membrane and made visible after 25 min under standard indoor lighting due to the presence of the colloidal gold label. A positive result (a visible purple/gray line) indicates that the LAM antigen of M. tuberculosis is present in the sample at or above the detection limit of the test; whereas a negative result (no visible purple/gray line) indicates not present or below the detection limit. The test result was read between 25 and 35 min later and graded by comparing the test strip with a reference card. The original 2012 reference scale card that consisted of 5 color intensity grades was used. The test band was graded as zero if no visual band appeared and graded 1 through 5 for a visualized band of equal intensity as those on the reference card. If a faint band was observed with intensity lower than the grade 1 cut-point it was recorded as “faint”.

The GeneXpert MTB-RIF assay was performed from a fresh urine sample according to the manufacturer’s specifications (Cepheid, CA, USA) to confirm TB, and results were obtained. Xpert MTB/RIF was an automated molecular test that makes use of the molecular beacons to identify DNA sequences amplified in a hemi-nested real time-PCR to detect the presence of M.tuberculosis and simultaneously of rifampicin resistance in clinical specimen in less than two hours. Five overlapping nucleic acid hybridization probes, labeled with colored fluorophores, are used for binding to an 81-base pair core region of the wild-type rpoB gene. The Xpert MTB/RIF diagnostic system integrates and automates sample processing, nucleic acid amplification, and detection of the target sequences in samples using semi-nested, real-time PCR. The only manual step is the addition of a bactericidal buffer to the sputum specimen before transferring a defined volume to the cartridge. The cartridges are pre-loaded with all reagents necessary for sample processing, DNA extraction, amplification, and laser detection of target amplicon binding to the molecular beacons [22].

Operational definitions

Kappa agreement interpretation

values less zero(0), it shows no agreement; 0.01–0.20 shows none to a slight agreement; 0.21–0.4 shows fair agreement;0.41–0.60 shows moderate;0.61–0.80 shows substantial and 0.81-1.0 shows perfect agreement [23].

Quality control

The questionnaire was translated into Amharic languages and back-translated to the English language by another person who knows both languages to check for any inconsistencies or distortions in the meaning. Two days of orientation was given for data collectors on the objective of the study and the art of interviewing. The specimens were processed immediately. The data collection process was supervised and the collected data was reviewed and checked for completeness by the principal investigator. Standardized operational procedures and manufacturer’s instructions were strictly followed. Data was entered and checked for completeness using epi info version 3.5 and exported to SPSS version 24 for analysis. After the complete entry of all the questionnaires, a soft copy was checked with its hard copy to see the consistency. After cross-checking, cleaning was done to avoid missing values, outliers, and inconsistencies before analysis.

Methods of data analysis

Descriptive analysis was used to characterize the study population. Kappa statistics, concordance, and disagreement assessments were used to determine the inter-rater agreement between the LAM test and GeneXpert. Accuracy measures (sensitivity, specificity, positive predictive values (PPV), negative predictive values (NPV), and likelihood ratio (LR)) were calculated with a 95% Confidence Interval (CI) by considering the urine LAM test as a reference since the test is recommended by WHO for detection of TB in immunocompromised patients including children. The factors associated with TB detection would also be determined using logistic regression. Finally, every variable with P-values less than 0.05 at a 95% confidence interval was considered as having a statistically significant association.

Ethical consideration

The study was ethically approved by the Institutional Review Board of the College of Health Sciences and Medicine, Woliata Sodo University. Informed written assent was obtained from primary caregivers of all children. Information about the study such as the purpose of the study, sample collection procedure, potential risks, and benefit of the study were explained. All study records of the study participants were kept confidential. All information collected in this study was treated anonymously. All the investigations done for participants of this study were free of charge but hospital care and treatments were paid according to the rule of the hospital. The positive results of the urine analysis were promptly given to the treating physician to assist in patient management.

Results

Socio-demographic data

Data was collected from all 337 under five children giving a response rate of 100%. Of the total of 337 study participants, 62.3% were males and 66.5% belonged to the age range of 3–5 years. The majority of the children’s families (38.3%) had primary educational level and 53.7% were urban dwellers. About 50% of children’s families were private workers, and 67.4% had 4–6 family size (Table 1).

Table 1 Socio-demographic and clinical characteristics of TB suspected children of under five years old, WSUCSH, 2022
Full size table

Clinical characteristics

A total of 337 study participants’ families were interviewed for TB-related clinical data using a pre-structured questionnaire. All of the children were HIV-negative. As presented in Tables 1 and 92.6% of total children had no contact history with TB patients. Of 337 participants, 53.7% were vaccinated with BCG, 15.4% were co-infected with any other infection, 6.2% had had cough for the previous 2 weeks, 5.9% showed weight loss, 10.4% had night sweat and 29.1% were malnourished.

Prevalence of TB among TB-suspected children under five years in WSUCSH, from February 1, 2022 to April 30, 2022

A urine specimen was collected from all 337 children with presumptive TB. From the total urine specimens collected, 26 (7.7%; 95 CI = 5.0-10.6) were LAM-TB test positive and 29 (8.6%; 95% CI = 5.6–11.6) were GeneXpert positive. Among 29 TB positives by GeneXpert, 19 (65.5%) were males and 24 (82.8%) belonged to the age group of 3–5 years. Children from private working families were more infected with TB (48.3%) as compared to others. Of the total TB-infected children, 25(82.3%) had no contact history with TB patients, 44.8% had a family size of more than 6 families, 15 (51.7%) were rural dwellers, 13 (44.8%) were not vaccinated with BCG and only 6(20.7%) and 11(37.9%) had a cough and night sweat respectively. The prevalence of TB is slightly high in males as compared to females, in the age of 3–5 years as compared to other age groups and rural Dowler’s as compared to urban but not statistically significant (P > 0.05) However, the prevalence is high among the family size of ≥ six (14.8%), children co-infected with other diseases (25% vs. 5.6%; X2 = 21.014; P < 0.001), children having cough of ≥ two weeks (42.9% vs. 6.3%; x2 = 33.407; P < 0.001), weight loss (30% vs. 7.3%; x2 = 12.374; P = 0.004), night sweat (31.4% vs. 6%; x2 = 25.868; P < 0.001), and loss of appetites (21.7% vs. 5.8%; x2 = 15.834; P < 0.001) (Table 2).

Table 2 Distribution of TB with socio-demographic and clinical characteristics among TB suspected children under five years old in WSUCSH, 2022
Full size table

Comparison of GeneXpert and TB-LAM test in diagnosis of TB

The comparison of both GeneXpert and TB-LAM tests showed that GeneXpert detected more mycobacterial isolates 29 (8.61%) than TB-LAM 26 (7.71%). However, the diagnosis agreement of GeneXpert and TB-LAM was almost perfect agreement (kappa = 0.941, SE = 0.034; Concordance = 99.1%; and disagreement = 0.9%) Considering the LAM Ag test as a baseline, the test accuracy of GeneXpert was performed and the results were presented in Table 3.

Table 3 Comparison of diagnostic yield GeneXpert and LAM test for diagnosis of pulmonary TB among TB suspected children from urine specimen in WSUCSH, 2022
Full size table

Risk factors associated with Mycobacterium tuberculosis in children aged under five in WSURCSH, 2023

Both bivariate and multivariate were computed to assess the association of expiatory variables with the dependent variable. Family size, other co-infection, cough for the previous 2 weeks, weight loss, night seat, loss of appetite, and nutritional status were independent factors with pulmonary TB in bivariate analysis (p < 0.05).

After excluding the confounding factors, the presence of other co-infection [AOR = 4.00: 95% CI, 1.428, 11.203)], cough for previous 2 weeks [AOR = 3.700: 95% CI, 1.039, 13.183], night sweat [AOR = 4.255: 95% CI, 1.453, 12.463] and loss of appetite [AOR = 3.994: 95% CI, 1.444, 11.045] showed significant association with pulmonary TB in children (Table 4).

Table 4 Bivariate and multivariate analysis of pulmonary tuberculosis among TB suspected children under five years old in WSUCSH, 2022
Full size table

Discussion

The purpose of this study was to detect pulmonary TB and associated factors among under-five-year-old children and to evaluate the test agreement between GeneXpert and TB-LAM antigen diagnostic methods in the detection of pulmonary TB from urine samples. This study revealed that the overall prevalence of pulmonary TB among under-five-year-old children with presumptive TB case was 8.6% (5.6–11.6%) and 7.7% (5.0-10.7%) by GeneXpert and TB-LAM antigen, respectively. The two tests showed almost perfect agreement for the detection of TB in urine samples. The presence of other co-infections, cough for the previous 2 weeks, night sweats, and loss of appetite showed a significant association with pulmonary TB in children in the study area.

The overall prevalence of PTB among children in this finding is in agreement with other studies conducted in Northwest, Ethiopia 5.73% [20], Jimma, Ethiopia 11.5% [24], Tigray, Ethiopia 8.1% [25], Zimbabwe 8.7% [26], Greenland 8.5% [27], and Uganda 10% [28]. However, the finding was higher than the findings reported in India 2.3% [29], Zambia 1.58% [30], Mozambique 1.65% [31], south Africa 1.3% [32] and Tanzania 5.4% [33]. On the contrary, in this study, the prevalence was lower than that of India at 20% [34], Nigeria at 32% [35], and Bangladesh at 32.97% [36]. The variation in the prevalence of Pediatric TB could be due to the difference in socio-demographic characteristics, HIV status of study participants. Co-infection with other diseases may affect TB protection status.

The second objective of this study was to compare the test agreement of GeneXpert and LAM Ag test from urine samples to recommend GeneXpert from urine since it has two advantages; parallel detection of drug resistance and cost effectiveness. The accuracy of the urine GeneXpert test was assessed against the TB-LAM antigen test and the overall sensitivity, specificity, PPV, and NPV of GeneXpert in this study was 89.7%, 100%, 100%, and 99%, respectively. This study detected the test agreement of GeneXpert and TB-LAM diagnostics methods with almost perfect agreement. This finding is supported by other studies that reported high test agreement in Mozambique (kappa = 0.91) 95%CI 0.96–0.99 [37], South Africa (kappa = 0.937) [38], and Ghana (Kappa = 0.94; SE = 0.05) [39]. However. the study conducted in Jimma, Ethiopia to evaluate the test accuracy of GeneXpert and TB-LAM reported less test agreement of the methods than our finding (Kappa = 0.722) [40] and Uganda (kappa = 0.888) [41].

In our study, co-infection with other diseases was identified as an independent risk factor for TB. This finding is in agreement with the report from a previous study in India [38], and the finding was also supported by studies conducted elsewhere in the globe [36, 38, 40]. These strengthen the nation that household contacts are at high risk of getting TB infection from their index patient and co-infection with another infectious disease like HIV (42). The prevalence of pulmonary TB among children with coughs for previous 2 weeks had almost four times higher than those without coughs for the previous 2 weeks. This report was in agreement with a study conducted in Ethiopia that reported a history of TB contact [20] and duration of cough greater than 3 weeks were risk factors of TB [42].

Surprisingly, in our study, those children who had BCG vaccinated had a slightly high prevalence of TB as compared to non-BCG vaccinated children. This finding strengthens the notion that the co-infection with helminths in developing countries polarizes the immune system toward the anti-inflammatory Th2 pathway through activation of the immune regulatory pathway that alters pathogenesis and may reduce the development of immunity or response to vaccines in Mycobacterium tuberculosis and Mycobacterium leprae and decrease BCG vaccine efficacy [43].

Limitation of the study

It’s important to note that although urine LAM has a known level of sensitivity and specificity compared to LJ culture, the GeneXpert result should ideally be compared to the gold standard technique (LJ culture). However, in this particular study, due to resource shortages, the agreement between GeneXpert and the TB-LAM test was compared without using the gold standard technique (LJ culture). Instead, it was assumed that urine LAM has a known level of sensitivity and specificity compared to LJ culture.

Conclusions and recommendations

The prevalence of pulmonary TB in the study area was considerably high. The detection rate of GeneXpert was slightly higher than the TB-LAM method, however, GeneXpert and TB-LAM antigen test methods showed very high test agreement for the diagnosis of TB in children from urine samples. Co-infection, cough for 2 weeks, night sweats, and loss of appetite were factors significantly associated with pulmonary TB in children under five years old. Based on the findings, we recommended GeneXpert for diagnosing TB in under five children using urine samples because urine can easily be collected from children and GeneXpert is widely used throughout the country. However, a large sample size of a different population would be required to confirm the results.

Data availability

The datasets used and analyzed during the current study available from the corresponding author on reasonable request.

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Acknowledgements

We acknowledge all clinicians particularly pathologists involved in this study for their support during patient recruitment, data, and sample collection. The authors would like to thank all the study participants who volunteered to participate in this study.

Funding

No any funding source.

Author information

Authors and Affiliations

  1. Departement of Medical Laboratory Science, Wolaita Sodo University Comprehensive Specialized Hospital, Wolaita Sodo, Ethiopia

    Daniel Derese & Temesgen Anjulo

  2. School of Medical Laboratory Science, College of Health Sciences and Medicine, Wolaita Sodo University, Wolaita Sodo, Ethiopia

    Takele Teklu, Abera Kumalo & Tariku Chinasho

  3. 11700 Old Columbia pike, Silver Spring MD 20904 #1411, Maryland, United States of America

    Tariku Chinasho

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Contributions

Daniel Derese., Takele Teklu., Abera Kumalo. Tariku Chinasho and Temesgen Anjulo. conceived and designed the study, analyzed, and interpreted the data. Danieal Derese. performed data collection and the laboratory culture. Takele Teklu wrote the manuscript. All authors contributed to the revision of the manuscript. All authors reviewed and approved the final manuscript.

Corresponding author

Correspondence to Takele Teklu.

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Ethics approval and consent to participate

The study was ethically approved by the Institutional Review Board of the College of Health Sciences and Medicine, Woliata Sodo University. Informed written assent was obtained from primary caregivers of all children. Information about the study such as the purpose of the study, sample collection procedure, potential risks and benefits of the study was explained. All study records of the study participants were kept confidential. All information collected in this study was treated anonymously. All the investigations done for participants of this study were free of charge but hospital care and treatments were paid according to the rule of the hospital. The positive results of the urine analysis were promptly given to the treating physician to assist in patient management.

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Not applicable.

Conflict of interest

I declare that the authors have no competing interests as defined by BMC, or other interests that might be perceived to influence the results and/or discussion reported in this paper.

Competing interests

The authors declare no competing interests.

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Derese, D., Teklu, T., Kumalo, A. et al. Test agreement between GeneXpert and urine lipoarabinomannan test for tuberculosis diagnosis among children in Ethiopia. BMC Pediatr 25, 254 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12887-024-05344-3

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  • DOI: https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12887-024-05344-3

Keywords

BMC Pediatrics

ISSN: 1471-2431

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