matrix-based-dna-extraction-for-targeted-next-generation-sequencing

Matrix-based DNA Extraction for Targeted Next-Generation Sequencing on Decontaminated Sputum Samples

Next-generation sequencing (NGS) is now recognized as a powerful tool for timely and accurate drug-resistant tuberculosis (DR-TB) diagnosis. Targeted NGS ...

University of California, San Diego, School of Medicine

Campus Biotech

The epidemiology of tuberculosis (TB) in the United States is changing as the incidence of disease becomes more concentrated in foreign-born persons. Mycobacterium bovis appears to be contributing substantially to the TB incidence in some binational communities with ties to Mexico. We conducted a retrospective analysis of TB case surveillance data from the San Diego, California, region from 1994 through 2005 to estimate incidence trends, identify correlates of M. bovis disease, and evaluate risk factors for deaths during treatment. M. bovis accounted for 45% (62/138) of all culture-positive TB cases in children (<15 years of age) and 6% (203/3,153) of adult cases. M. bovis incidence increased significantly (p = 0.002) while M. tuberculosis incidence declined (p<0.001). Almost all M. bovis cases from 2001 through 2005 were in persons of Hispanic ethnicity. Persons with M. bovis were 2.55x (p = 0.01) as likely to die during treatment than those with M. tuberculosis.

Tuberculosis from Mycobacterium bovis in binational communities, United States.

We sought to understand tuberculosis (TB) and HIV coinfection trends in San Diego County, California, and to identify associations between sociodemographic risk factors and TB and HIV coinfection.

HIV-tuberculosis coinfection in Southern California: evaluating disparities in disease burden.

Because there is little routine tuberculosis (TB) screening in Mexico, the prevalence of latent TB infection (LTBI) is unknown. In the context of an increasing HIV epidemic in Tijuana, Mexico, understanding prevalence of LTBI to anticipate emergence of increased LTBI reactivation is critical. Therefore, we recruited injection drug users, noninjection drug users, female sex workers, and homeless persons for a study involving risk assessment, rapid HIV testing, and TB screening. Of 503 participants, the overall prevalences of TB infection, HIV infection, and TB/HIV co-infection were 57%, 4.2%, and 2.2%, respectively; no significant differences by risk group (p>0.05) were observed. Two participants had TB (prevalence 398/100,000). Incarceration in Mexico (odds ratio [OR] 2.28), age (OR 1.03 per year), and years lived in Tijuana (OR 1.02 per year) were independently associated with TB infection (p<0.05). Frequent LTBI in marginalized persons may lead to increases in TB as HIV spreads.

Latent tuberculosis among persons at risk for infection with HIV, Tijuana, Mexico.

Resettled refugees often arrive in their host country with little knowledge of nutrition or available food choices. We explored nutrition-related issues of recent refugee arrivals to San Diego County-the second largest California resettlement site. In-depth interviews (n = 40) were conducted with refugees, health care practitioners, and refugee service organizations. Content analysis identified nutrition-related themes. Unhealthy weight gain after arrival was the most common concern and was attributed to social pressures among adolescents, food choices and a more sedentary lifestyle. Conversely, undernutrition remained a concern due to poor diets. Factors influencing nutritional problems included continuation of past habits, acculturation, unfamiliarity with available foods and socio-economic influences. The nutritional concerns encountered by resettled refugees in San Diego are not unique to this group but are aggravated by their past experiences, and abrupt changes to food choices and behavior. Addressing contextual factors of poor food choices may prevent some of the long term health consequences of poor nutrition.

Under- and over-nutrition among refugees in San Diego County, California.

Mycobacterium tuberculosis (Mtb) isolates with identical genotypes, found in different patients, are most likely the result of recent transmission. Mtb strains with closely related genotypes, called clonal complexes, are most likely derived from one another. We examined Mtb genotypes from southern California TB patients from 2005 through 2008 to complete the first comprehensive molecular epidemiology analysis of this complicated and ethnically diverse region. Mtb genotypes were characterized with spoligotype and MIRU-12 typing. MIRU-VNTRplus was utilized to assign genotypes to global lineages and complete cluster analyses. Associations between patient characteristics and genotype clustering and clonal complexes were evaluated using logistic regression and frequency analysis. Of 832 Mtb isolates analyzed, 480 (58%) fell into 94 strain clusters. The majority of isolates were identified as being in the EA1 (31%), LAM (17%) and Haarlem (15%) lineages, but 13 different lineages were found in this region. TB patients with clustered isolates were more likely to be homeless (AOR 3.44, 95% CI 1.65, 7.18) and male (AOR 1.57, 95% CI 1.17, 2.10). Of the 480 clustered strains, 388 aggregated into six clonal complexes. Over 45% of reported TB cases were clustered and likely resulted from recent transmission events. Patients with clustered Mtb isolates that were grouped into clonal complexes had unique socio-demographic characteristics. These data suggest that TB is being transmitted in relatively insular community networks defined by race/ethnicity and country of origin. The addition of clonal complex analysis to simple cluster analysis provides important public health insights into the local transmission of TB in ethnically diverse regions with diverse Mtb genotypes.

Factors associated with genotype clustering of Mycobacterium tuberculosis isolates in an ethnically diverse region of southern California, United States.

The detection of mutations in the gyrA and gyrB genes in the Mycobacterium tuberculosis genome that have been demonstrated to confer phenotypic resistance to fluoroquinolones is the most promising technology for rapid diagnosis of fluoroquinolone resistance.

Frequency and geographic distribution of gyrA and gyrB mutations associated with fluoroquinolone resistance in clinical Mycobacterium tuberculosis isolates: a systematic review.

A new multi-national study of the non-commercial MODS assay shows excellent performance in detecting M/XDR-tuberculosis

Evaluation of the microscopic observation drug susceptibility assay for the detection of first- and second-line drug susceptibility for .

Mobile health (mHealth) interventions have the potential to improve health through patient education and provider engagement while increasing efficiency and lowering costs. This raises the question of whether disparities in access to mobile technology could accentuate disparities in mHealth mediated care. This study addresses whether programs planning to implement mHealth interventions risk creating or perpetuating health disparities based on inequalities in smartphone ownership.

Article	Year
Tuberculosis from Mycobacterium bovis in binational communities, United States. Emerging infectious diseases\| PubMed ID: 18507901	2008
HIV-tuberculosis coinfection in Southern California: evaluating disparities in disease burden. American journal of public health\| PubMed ID: 20147681	2010
Latent tuberculosis among persons at risk for infection with HIV, Tijuana, Mexico. Emerging infectious diseases\| PubMed ID: 20409363	2010
Under- and over-nutrition among refugees in San Diego County, California. Journal of immigrant and minority health\| PubMed ID: 20505992	2011
Factors associated with genotype clustering of Mycobacterium tuberculosis isolates in an ethnically diverse region of southern California, United States. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases\| PubMed ID: 22982156	2012
Frequency and geographic distribution of gyrA and gyrB mutations associated with fluoroquinolone resistance in clinical Mycobacterium tuberculosis isolates: a systematic review. PloS one\| PubMed ID: 25816236	2015
Evaluation of the microscopic observation drug susceptibility assay for the detection of first- and second-line drug susceptibility for . The European respiratory journal\| PubMed ID: 28381434	2017
Requiring smartphone ownership for mHealth interventions: who could be left out? BMC public health\| PubMed ID: 31959145	2020

Timothy Rodwell

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