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Diagnosis of pulmonary tuberculosis (TB) relies on a sputum sample, which cannot be obtained from all symptomatic individuals. Mycobacterium tuberculosis (Mtb) transrenal DNA (trDNA) has been detected in urine, an easily obtainable, noninvasive, alternative sample type. However, reported sensitivities have been variable and likely depend on collection and assay procedures and aspects of trDNA biology. We analyzed three serial urine samples from each of 75 adults with culture-confirmed pulmonary TB disease in Lima, Peru for detection of trDNA using short-fragment real-time PCR. Additionally, we examined host, urine, and sampling factors associated with detection. Overall per-sample sensitivity was 38 % (95 % Confidence Interval [CI] 30-45 %). On an individual level (i.e., any of the three samples positive), sensitivity was 73 % (95 % CI: 62-83 %). Sensitivity was highest among samples from patients with smear-positive TB, 92 % (95 % CI: 62-100 %). Specificity from a single sample from each of 10 healthy controls was 100 % (95 % CI: 69-100 %). Adjusting our assay positivity threshold increased individual-level sensitivity to 88 % (95 % CI: 78-94 %) overall without affecting the specificity. We did not find associations between Mtb trDNA detection and individual characteristics or urine sample characteristics. Overall, our results support the potential of trDNA detection for TB diagnosis.
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Background: Loss to follow-up (LTFU) from tuberculosis (TB) treatment and care is a significant public health problem. It is important to understand what drives LTFU in children - a population whose treatment and management depend on an adult caregiver - to better provide support services to families affected by TB. Methods: We conducted a prospective cohort study of household contacts in Lima, Peru (2009-12). Using multilevel logistic regression analysis, we explored individual-level characteristics of children and their adult household members with TB disease to identify risk factors for LTFU among children initiated on treatment for TB. Results: A total of 154 child (0-14 years) household contacts were diagnosed with TB and initiated on treatment. While most (n = 133, 86.4%) had a successful outcome, 20 (13.0%) children were LTFU. Six (30.0%) children were LTFU within three months, nine (45.0%) between five to seven months, and three (15.0%) after seven months of treatment being initiated. In univariable analysis, children with index patients above 25 years of age had decreased odds of being LTFU (odds ratio = 0.26; 95% confidence interval = 0.08-0.84) compared to children with index patients 25 years or younger. Conclusions: In this cohort, more than 10% of children sick with TB who were exposed to the disease at home were LTFU. An integrated, family-centred TB prevention and management approach may reduce barriers to a child completing their course of TB treatment.
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Perdida de Seguimiento , Tuberculosis , Humanos , Niño , Estudios Prospectivos , Femenino , Masculino , Preescolar , Lactante , Adolescente , Perú/epidemiología , Tuberculosis/tratamiento farmacológico , Tuberculosis/epidemiología , Adulto , Factores de Riesgo , Recién Nacido , Antituberculosos/uso terapéuticoRESUMEN
The cultural significance of the flora used by the native Asheninka Sheremashe community in Ucayali, Peru was determined. To do this, a fieldwork of over 4 months was conducted, involving semi-structured interviews with 106 residents through non-probabilistic convenience sampling. The community utilizes 139 plant species in their daily lives, belonging to 120 genera and 52 families, with the most abundant being Fabaceae, Arecaceae, Malvaceae, Solanaceae, Poaceae, and Rutaceae. Furthermore, 25.9% of the species are of significant importance to theinhabitants according to the Cultural Index (CI), such as Manihot esculenta, Theobroma cacao, Bixa orellana, Musa paradisiaca, Ficus insipida, among others. It can be concluded that the flora plays a prominent role in the life of the community, with the categories reporting the highest number of species being: food (29.35%), medicine (28.36%), culture (9.95%), construction (9.45%), lumber (6.97%), commerce (3.48%), craftsmanship (2.49%), toxic (2.49%), and other uses (7.46%)
Se determinó la importancia cultural de la flora empleada por la comunidad nativa Asheninka Sheremashe, en Ucayali, Perú. Para ello, se realizó un trabajo de campo de más de 4 meses, donde se aplicaron entrevistas semiestructuradas a 106 habitantes mediante un muestreo no probabilístico por conveniencia. La comunidad emplea 139 especies vegetales en su día a día, pertenecientes a 120 géneros y 52 familias; siendo las más abundantes las Fabaceae, Arecaceae, Malvaceae, Solanaceae, Poaceae y Rutaceae. Además, el 25.9% de las especies tiene gran importancia para los pobladores según el Índice Cultural (IC): Manihot esculenta, Theobroma cacao, Bixa orellana, Musa paradisiaca, Ficus insipida, entre otras. Se concluye que la flora tiene un rol preponderante en la vida de la comunidad, siendo las categorías que presentaron mayor reporte de especies: alimentación (29.35%), medicina (28.36%), cultura (9.95%), construcción (9.45%), aserrío (6.97%), comercio (3.48%), artesanía (2.49%), tóxico (2.49%) y otros usos (7.46%)
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Humanos , Flora , Etnobotánica , Medicina Tradicional , Perú , Encuestas y CuestionariosRESUMEN
A quarter of humanity is estimated to have been exposed to Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n = 63) or did not progress to TB (controls, n = 63). Transcriptomic profiling of monocyte-derived DCs and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Four genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.
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Células Dendríticas , Macrófagos , Mycobacterium tuberculosis , Sitios de Carácter Cuantitativo , Tuberculosis , Humanos , Perú , Tuberculosis/genética , Tuberculosis/microbiología , Macrófagos/metabolismo , Macrófagos/microbiología , Mycobacterium tuberculosis/patogenicidad , Mycobacterium tuberculosis/genética , Femenino , Células Dendríticas/metabolismo , Masculino , Adulto , Predisposición Genética a la Enfermedad , Variación Genética , Regulación de la Expresión Génica , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , Perfilación de la Expresión GénicaRESUMEN
The World Health Organization's end TB strategy promotes the use of symptom and chest radiograph screening for tuberculosis (TB) disease. However, asymptomatic early states of TB beyond latent TB infection and active disease can go unrecognized using current screening criteria. We conducted a longitudinal cohort study enrolling household contacts initially free of TB disease and followed them for the occurrence of incident TB over 1 year. Among 1,747 screened contacts, 27 (52%) of the 52 persons in whom TB subsequently developed during follow-up had a baseline abnormal radiograph. Of contacts without TB symptoms, persons with an abnormal radiograph were at higher risk for subsequent TB than persons with an unremarkable radiograph (adjusted hazard ratio 15.62 [95% CI 7.74-31.54]). In young adults, we found a strong linear relationship between radiograph severity and time to TB diagnosis. Our findings suggest chest radiograph screening can extend to detecting early TB states, thereby enabling timely intervention.
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Composición Familiar , Tamizaje Masivo , Radiografía Torácica , Humanos , Perú/epidemiología , Masculino , Femenino , Adulto , Adolescente , Adulto Joven , Tamizaje Masivo/métodos , Estudios Longitudinales , Persona de Mediana Edad , Niño , Tuberculosis Pulmonar/epidemiología , Tuberculosis Pulmonar/diagnóstico , Tuberculosis Pulmonar/diagnóstico por imagen , Trazado de Contacto/métodos , Preescolar , Tuberculosis Latente/diagnóstico , Tuberculosis Latente/epidemiología , Tuberculosis Latente/diagnóstico por imagen , Lactante , Tuberculosis/epidemiología , Tuberculosis/diagnóstico , Tuberculosis/diagnóstico por imagenRESUMEN
Rationale: The persistent burden of tuberculosis (TB) disease emphasizes the need to identify individuals with TB for treatment and those at a high risk of incident TB for prevention. Targeting interventions toward those at high risk of developing and transmitting TB is a public health priority. Objectives: We aimed to identify characteristics of individuals involved in TB transmission in a community setting, which may guide the prioritization of targeted interventions. Methods: We collected clinical and sociodemographic data from a cohort of patients with TB in Lima, Peru. We used whole-genome sequencing data to assess the genetic distance between all possible pairs of patients; we considered pairs to be the result of a direct transmission event if they differed by three or fewer SNPs, and we assumed that the first diagnosed patient in a pair was the transmitter and the second was the recipient. We used logistic regression to examine the association between host factors and the likelihood of direct TB transmission. Measurements and Main Results: Analyzing data from 2,518 index patients with TB, we identified 1,447 direct transmission pairs. Regardless of recipient attributes, individuals less than 34 years old, males, and those with a history of incarceration had a higher likelihood of being transmitters in direct transmission pairs. Direct transmission was more likely when both patients were drinkers or smokers. Conclusions: This study identifies men, young adults, former prisoners, alcohol consumers, and smokers as priority groups for targeted interventions. Innovative strategies are needed to extend TB screening to social groups such as young adults and prisoners with limited access to routine preventive care.
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Tuberculosis , Humanos , Perú/epidemiología , Masculino , Femenino , Adulto , Estudios Transversales , Persona de Mediana Edad , Adulto Joven , Estudios de Cohortes , Tuberculosis/transmisión , Tuberculosis/epidemiología , Adolescente , Factores de Riesgo , Secuenciación Completa del Genoma , AncianoRESUMEN
OBJECTIVE: To develop a framework to estimate the practical costs incurred from, and programmatic impact related to, tuberculosis (TB) infection testing-tuberculin skin tests (TST) versus interferon gamma release assay (IGRA)-in a densely populated high-burden TB area. METHODS: We developed a seven-step framework that can be tailored to individual TB programmes seeking to compare TB infection (TBI) diagnostics to inform decision-making. We present methodology to estimate (1) the prevalence of TBI, (2) true and false positives and negatives for each test, (3) the cost of test administration, (4) the cost of false negatives, (5) the cost of treating all that test positive, (6) the per-test cost incurred due to treatment and misdiagnosis and (7) the threshold at which laboratory infrastructure investments for IGRA are outweighed by system-wide savings incurred due to IGRA utilisation. We then applied this framework in a densely populated, peri-urban district in Lima, Peru with high rates of Bacillus Calmette-Guérin (BCG) vaccination. FINDINGS: The lower sensitivity of TST compared with IGRA is a major cost driver, leading to health system and societal costs due to misdiagnosis. Additionally, patient and staff productivity costs were greater for TST because it requires two patient visits compared with only one for IGRA testing. When the framework was applied to the Lima setting, we estimate that IGRA-associated benefits outweigh infrastructural costs after performing 672 tests. CONCLUSIONS: Given global shortages of TST and concerns about costs of IGRA testing and laboratory capacity building, this costing framework can provide public health officials and TB programmes guidance for decision-making about TBI testing locally. This framework was designed to be adaptable for use in different settings with available data. Diagnostics that increase accuracy or mitigate time to treatment should be thought of as an investment instead of an expenditure.
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Tuberculosis Latente , Tuberculosis , Humanos , Tuberculosis/diagnóstico , Tuberculosis/epidemiología , Tuberculosis Latente/diagnóstico , Tuberculosis Latente/epidemiología , Ensayos de Liberación de Interferón gamma/métodos , Prueba de Tuberculina/métodos , Gastos en SaludRESUMEN
We explored the utility of brief Mycobacterium tuberculosis whole-genome sequencing (WGS) "snapshots" at a sentinel site within Lima, Peru for evaluating local transmission dynamics over time. Within a 17 km2 area, 15/70 (21%) isolates with WGS collected during 2011-2012 and 22/81 (27%) collected during 2020-2021 were clustered (p = 0.414), and additional isolates clustered with those from outside the area. Isolates from the later period were disproportionately related to large historic clusters in Lima from the earlier period. WGS snapshots at a sentinel site may not be useful for monitoring transmission, but monitoring the persistence of large transmission clusters might be.
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Mathematical models have suggested that spatially-targeted screening interventions for tuberculosis may efficiently accelerate disease control, but empirical data supporting these findings are limited. Previous models demonstrating substantial impacts of these interventions have typically simulated large-scale screening efforts and have not attempted to capture the spatial distribution of tuberculosis in households and communities at a high resolution. Here, we calibrate an individual-based model to the locations of case notifications in one district of Lima, Peru. We estimate the incremental efficiency and impact of a spatially-targeted interventions used in combination with household contact tracing (HHCT). Our analysis reveals that HHCT is relatively efficient with a median of 40 (Interquartile Range: 31.7 to 49.9) household contacts required to be screened to detect a single case of active tuberculosis. However, HHCT has limited population impact, producing a median incidence reduction of only 3.7% (Interquartile Range: 5.8% to 1.9%) over 5 years. In comparison, spatially targeted screening (which we modeled as active case finding within high tuberculosis prevalence areas 100 m2 grid cell) is far less efficient, requiring evaluation of ≈12 times the number of individuals as HHCT to find a single individual with active tuberculosis. Furthermore, the addition of the spatially targeted screening effort produced only modest additional reductions in tuberculosis incidence over the 5 year period (≈1.3%) in tuberculosis incidence. In summary, we found that HHCT is an efficient approach for tuberculosis case finding, but has limited population impact. Other screening approaches which target areas of high tuberculosis prevalence are less efficient, and may have limited impact unless very large numbers of individuals can be screened.
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Bivalvos , Tuberculosis Pulmonar , Tuberculosis , Humanos , Animales , Trazado de Contacto , Tuberculosis Pulmonar/epidemiología , Perú/epidemiología , Tuberculosis/diagnóstico , Tuberculosis/epidemiología , Composición FamiliarRESUMEN
Diagnosis of tuberculosis (TB) relies on a sputum sample, which cannot be obtained from all symptomatic patients. Mycobacterium tuberculosis (Mtb) transrenal DNA (trDNA) has been detected in urine, an easily obtainable, noninvasive, alternative sample type. However, reported sensitivities have been variable and likely depend on collection/assay procedures and aspects of trDNA biology. We analyzed three serial urine samples from each of 75 adults with culture-confirmed pulmonary TB disease in Lima, Peru for detection of trDNA using short-fragment real-time PCR. Additionally, we examined host, urine, and sampling factors associated with detection. Overall sample sensitivity was 38% (95% Confidence Interval [CI] 30-45%). On a patient level (i.e., any of three samples positive), sensitivity was 73% (95% CI: 62-83%). Sensitivity was highest among samples from patients with smear-positive TB, 92% (95% CI: 62-100%). Specificity from a single sample from each of 10 healthy controls was 100% (95% CI: 69-100%). Adjusting our assay positivity threshold increased patient-level sensitivity to 88% (95% CI: 78-94%) overall without affecting the specificity. We did not find associations between Mtb trDNA detection and either patient characteristics or urine sample characteristics. Overall, our results support the potential of trDNA detection for TB diagnosis.
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A quarter of humanity is estimated to be latently infected with Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n=63) or did not progress to TB (controls, n=63). Transcriptomic profiling of monocyte-derived dendritic cells (DCs) and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Five genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.
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OBJECTIVE.: To evaluate the association between overweight/obesity and multidrug resistance in patients with and without a history of tuberculosis treatment. MATERIALS AND METHODS.: Cross-sectional study of secondary data from a tuberculosis cohort, which included anthropometric and drug-sensitivity testing data at the baseline visit of patients with and without previous tuberculosis treatment. RESULTS.: We evaluated 3,734 new cases and 766 with a history of having received treatment for tuberculosis. Overweight/obesity was not associated with multidrug resistance in patients with a history of tuberculosis treatment, with a prevalence ratio of 0.97 and a 95% confidence interval of 0.68-1.38. CONCLUSIONS.: Overweight/obesity is not associated with multidrug resistance in tuberculosis. Overweight/obesity is a dynamic process that may influence the relationship between the immune system and the metabolic system.
OBJETIVO.: Evaluar la asociación entre el sobrepeso/obesidad y la multidrogoresistencia en pacientes con y sin antecedentes de tratamiento para tuberculosis. MATERIALES Y MÉTODOS.: Estudio transversal realizado a través de un análisis secundario de la base de datos de una cohorte de tuberculosis, que incluyó datos de pruebas antropométricas y pruebas de sensibilidad a drogas en la visita basal de pacientes con y sin tratamiento previo para tuberculosis. RESULTADOS.: Se evaluaron 3,734 casos nuevos y 766 con antecedente de haber recibido tratamiento para tuberculosis. El sobrepeso/obesidad no se asoció a la multidrogoresistencia en pacientes con antecedente de tratamiento para tuberculosis, mostrando una razón de prevalencia de 0,97 con un intervalo de confianza al 95% de 0,68-1,38. CONCLUSIONES.: El sobrepeso/obesidad no está asociado a la multidrogoresistencia en tuberculosis; siendo el sobrepeso/obesidad un proceso dinámico que puede influir en las relaciones entre el sistema inmune y el sistema metabólico.
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Mycobacterium tuberculosis , Tuberculosis Resistente a Múltiples Medicamentos , Humanos , Antituberculosos/uso terapéutico , Sobrepeso/epidemiología , Estudios Transversales , Tuberculosis Resistente a Múltiples Medicamentos/epidemiología , Tuberculosis Resistente a Múltiples Medicamentos/tratamiento farmacológico , Obesidad/complicaciones , Obesidad/epidemiología , Obesidad/tratamiento farmacológico , Pruebas de Sensibilidad MicrobianaRESUMEN
BACKGROUND: Rapid IgM/IgG antibody tests were largely used in lieu of RT-PCR tests as part of COVID-19 public health response activities in Lima, Peru. To assess their utility, we explored the relationship between the time since onset of several COVID-19-related symptoms and the sensitivity of a rapid combined IgM/IgG antibody test. METHODS: We collected data from a community sample of individuals (n = 492) who received concurrent RT-PCR and rapid IgM/IgG antibody testing between May 2020 and March 2021. We estimated the sensitivity of the antibody test, against the RT-PCR test, by weeks since symptom onset via segmented regression analysis. RESULTS: The overall sensitivity of the rapid IgM/IgG antibody test was 46.7% (95% CI, 42.4-51.2%). Among 372 (75.6%) participants who reported COVID-19-related symptoms, sensitivity increased from 30.4% (95% CI, 24.7-36.6%) in week 1 after symptom onset to 83.3% (95% CI, 41.6-98.4%) in week 4. The test sensitivity increased by 31.9% (95% CI, 24.8-39.0%) per week until week 2 to 3, then decreased by - 6.0% (95% CI, - 25.7-13.7%) per week thereafter. CONCLUSION: Rapid antibody tests are a poor substitute for RT-PCR testing, regardless of presenting symptoms. This highlights the need for future pandemic planning to include timely and equitable access to gold-standard diagnostics, treatment, and vaccination.
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COVID-19 , Humanos , COVID-19/diagnóstico , SARS-CoV-2/genética , Inmunoglobulina G/análisis , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Perú/epidemiología , Sensibilidad y Especificidad , Inmunoglobulina M/análisis , Anticuerpos Antivirales/análisis , Prueba de COVID-19RESUMEN
Objetivo. Evaluar la asociación entre el sobrepeso/obesidad y la multidrogoresistencia en pacientes con y sin antecedentes de tratamiento para tuberculosis. Materiales y métodos. Estudio transversal realizado a través de un análisis secundario de la base de datos de una cohorte de tuberculosis, que incluyó datos de pruebas antropométricas y pruebas de sensibilidad a drogas en la visita basal de pacientes con y sin tratamiento previo para tuberculosis. Resultados. Se evaluaron 3,734 casos nuevos y 766 con antecedente de haber recibido tratamiento para tuberculosis. El sobrepeso/obesidad no se asoció a la multidrogoresistencia en pacientes con antecedente de tratamiento para tuberculosis, mostrando una razón de prevalencia de 0,97 con un intervalo de confianza al 95% de 0,68-1,38. Conclusiones. El sobrepeso/obesidad no está asociado a la multidrogoresistencia en tuberculosis; siendo el sobrepeso/obesidad un proceso dinámico que puede influir en las relaciones entre el sistema inmune y el sistema metabólico.
Objective. To evaluate the association between overweight/obesity and multidrug resistance in patients with and without a history of tuberculosis treatment. Materials and methods. Cross-sectional study of secondary data from a tuberculosis cohort, which included anthropometric and drug-sensitivity testing data at the baseline visit of patients with and without previous tuberculosis treatment. Results. We evaluated 3,734 new cases and 766 with a history of having received treatment for tuberculosis. Overweight/obesity was not associated with multidrug resistance in patients with a history of tuberculosis treatment, with a prevalence ratio of 0.97 and a 95% confidence interval of 0.68-1.38. Conclusions. Overweight/obesity is not associated with multidrug resistance in tuberculosis. Overweight/obesity is a dynamic process that may influence the relationship between the immune system and the metabolic system.
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Humanos , Masculino , Femenino , Adulto , Persona de Mediana EdadRESUMEN
Using data from 388 people diagnosed with tuberculosis through a community-based screening program in Lima, Peru, we estimated that cough screening followed by sputum smear microscopy would have detected only 23% of cases found using an algorithm of radiographic screening followed by rapid nucleic acid amplification testing and clinical evaluation.
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Mycobacterium tuberculosis , Tuberculosis , Humanos , Tuberculosis/diagnóstico , Tamizaje Masivo , Técnicas de Amplificación de Ácido Nucleico , Algoritmos , Perú/epidemiología , Esputo , Mycobacterium tuberculosis/genética , Sensibilidad y EspecificidadRESUMEN
Introduction: Dietary patterns (DPs) are associated with overall nutritional status and may alter the clinical prognosis of tuberculosis. This interaction can be further intricated by dysglycemia (i.e., diabetes or prediabetes). Here, we identified DPs that are more common with tuberculosis-dysglycemia and depicted their association with tuberculosis treatment outcomes. Methods: A prospective cohort study of persons with tuberculosis and their contacts was conducted in Peru. A food frequency questionnaire and a multidimensional systems biology-based analytical approach were employed to identify DPs associated with these clinical groups. Potential independent associations between clinical features and DPs were analyzed. Results: Three major DPs were identified. TB-dysglycemia cases more often had a high intake of carbohydrates (DP1). Furthermore, DP1 was found to be associated with an increased risk of unfavorable TB outcomes independent of other factors, including dysglycemia. Conclusion: Our findings suggest that the evaluation of nutritional status through DPs in comorbidities such as dysglycemia is a fundamental action to predict TB treatment outcomes. The mechanisms underlying the association between high intake of carbohydrates, dysglycemia, and unfavorable tuberculosis treatment outcomes warrant further investigation.
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Spatially targeted interventions may be effective alternatives to individual or population-based prevention strategies against tuberculosis (TB). However, their efficacy may depend on the mechanisms that lead to geographically constrained hotspots. Local TB incidence may reflect high levels of local transmission; conversely, they may point to frequent travel of community members to high-risk areas. We used whole-genome sequencing to explore patterns of TB incidence and transmission in Lima, Peru. Between 2009 and 2012, we recruited incident pulmonary TB patients and their household contacts, whom we followed for the occurrence of TB disease. We used whole-genome sequences of 2,712 Mycobacterial tuberculosis isolates from 2,440 patients to estimate pariwise genomic distances and compared these to the spatial distance between patients' residences. Genomic distances increased rapidly as spatial distances increased and remained high beyond 2 km of separation. Next, we divided the study catchment area into 1 × 1 km grid-cell surface units and used household spatial coordinates to locate each TB patient to a specific cell. We estimated cell-specific transmission by calculating the proportion of patients in each cell with a pairwise genomic distance of 10 or fewer single-nucleotide polymorphisms. We found that cell-specific TB incidence and local transmission varied widely but that cell-specific TB incidence did not correlate closely with our estimates of local transmission (Cohen's k = 0.27). These findings indicate that an understanding of the spatial heterogeneity in the relative proportion of TB due to local transmission may help guide the implementation of spatially targeted interventions.
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Mycobacterium tuberculosis , Tuberculosis Pulmonar , Tuberculosis , Humanos , Perú/epidemiología , Tuberculosis/epidemiología , Mycobacterium tuberculosis/genética , Tuberculosis Pulmonar/epidemiología , Secuenciación Completa del GenomaRESUMEN
We investigated whether ancestry-specific genetic factors affect tuberculosis (TB) progression risk in a cohort of admixed Peruvians. We genotyped 2,105 patients with TB and 1,320 household contacts (HHCs) who were infected with Mycobacterium tuberculosis (M. tb) but did not develop TB and inferred each individual's proportion of native Peruvian genetic ancestry. Our HHC study design and our data on potential confounders allowed us to demonstrate increased risk independent of socioeconomic factors. A 10% increase in individual-level native Peruvian genetic ancestry proportion corresponded to a 25% increased TB progression risk. This corresponds to a 3-fold increased risk for individuals in the highest decile of native Peruvian genetic ancestry versus the lowest decile, making native Peruvian genetic ancestry comparable in effect to clinical factors such as diabetes. Our results suggest that genetic ancestry is a major contributor to TB progression risk and highlight the value of including diverse populations in host genetic studies.
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Widely available and reliable testing for SARS-CoV-2 is essential for the public health response to the COVID-19 pandemic. We estimated the diagnostic performance of reverse transcription PCR (RT-PCR) performed on saliva and the SD Biosensor STANDARD Q antigen test performed on nasopharyngeal swab compared to the reference standard, nasopharyngeal swab (NP) RT-PCR. We enrolled participants living and/or seeking care in health facilities in North Lima, Peru from November 2020 to January 2021. Consenting participants underwent same-day RT-PCR on both saliva and nasopharyngeal swab specimens, antigen testing on a nasopharyngeal swab specimen, pulse oximetry, and standardized symptom assessment. We calculated sensitivity, specificity, and predictive values for the nasopharyngeal antigen and saliva RT-PCR compared to nasopharyngeal RT-PCR. Of 896 participants analyzed, 567 (63.3%) had acute signs/symptoms of COVID-19. The overall sensitivity and specificity of saliva RT-PCR were 85.8% and 98.1%, respectively. Among participants with and without acute signs/symptoms of COVID-19, saliva sensitivity was 87.3% and 37.5%, respectively. Saliva sensitivity was 97.4% and 56.0% among participants with cycle threshold (CT) values of ≤30 and >30 on nasopharyngeal RT-PCR, respectively. The overall sensitivity and specificity of nasopharyngeal antigen were 73.2% and 99.4%, respectively. The sensitivity of the nasopharyngeal antigen test was 75.1% and 12.5% among participants with and without acute signs/symptoms of COVID-19, and 91.2% and 26.7% among participants with CT values of ≤30 and >30 on nasopharyngeal RT-PCR, respectively. Saliva RT-PCR achieved the WHO-recommended threshold of >80% for sensitivity for the detection of SARS-CoV-2, while the SD Biosensor nasopharyngeal antigen test did not. IMPORTANCE In this diagnostic validation study of 896 participants in Peru, saliva reverse transcription PCR (RT-PCR) had >80% sensitivity for the detection of SARS-CoV-2 among all-comers and symptomatic individuals, while the SD Biosensor STANDARD Q antigen test performed on nasopharyngeal swab had <80% sensitivity, except for participants whose same-day nasopharyngeal RT-PCR results showed cycle threshold values of <30, consistent with a high viral load in the nasopharynx. The specificity was high for both tests. Our results demonstrate that saliva sampling could serve as an alternative noninvasive technique for RT-PCR diagnosis of SARS-CoV-2. The role of nasopharyngeal antigen testing is more limited; when community transmission is low, it may be used for mass screenings among asymptomatic individuals with high testing frequency. Among symptomatic individuals, the nasopharyngeal antigen test may be relied upon for 4 to 8 days after symptom onset, or in those likely to have high viral load, whereupon it showed >80% sensitivity.