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Open Access Publications from the University of California

Scholarly Works (43 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2016)

Background: Rapid molecular diagnostics, with their ability to quickly identify genetic mutations associated with drug resistance, have great potential to curb the spread of drug-resistant tuberculosis (DR-TB). Unfortunately, the technical and diagnostic performance of these technologies has yet to be thoroughly evaluated in diverse clinical environments, and the reliability and clinical relevance of the tuberculosis (TB) resistance mutations identified by these assays has not been well characterized.

Methods: These analyses use data from a multisite, observational cohort study conducted by the Global Consortium for Drug Resistant TB Diagnostics (GCDD). Chapter 2 assesses the diagnostic performance of a pyrosequencing assay in this study and applies logistic regression to identify the variables associated with poor assay technical performance. Chapter 3 presents the frequency and distribution of all TB resistance mutations identified between clinical sites. Chapter 4 applies multivariate logistic regression to determine the associations between TB resistance mutations and patient mortality for the GCDD study cohort.

Results: Chapter 2 found pyrosequencing assay performance to be high, overall, though sensitivity fluctuated between sites. Smear negativity, culture negativity, site (Moldova), and sequencing of the rpoB, gyrA, and rrs genes were associated with poor assay technical performance. Chapter 3 found inclusion of the ahpC and eis promoter gene regions to be critical for optimal test sensitivity for isoniazid resistance detection in South Africa and kanamycin resistance detection in Moldova. Chapter 4 found that the detection of a mutation associated with high-level fluoroquinolone or kanamycin resistance was significantly associated with higher odds of patient mortality by 52 weeks.

Conclusions: A DR-TB diagnostic demonstrated excellent specificity in a large, multisite study, though performance was influenced by regional genetics and technical errors. Findings of the high prevalence of low-global frequency TB resistance mutations in specific sites emphasizes that these mutations may be important resistance markers in certain regions. The observation that patients with high-level gyrA and rrs resistance mutations had higher mortality odds provides strong evidence that certain high-level resistance mutations are clinically relevant. Together, these findings underscore the potential for molecular diagnostics to replace conventional growth-based diagnostics as predictors of phenotypic drug resistance and clinical outcome.

    Cover page: Molecular diagnostics for drug-resistant tuberculosis: Can genetic tests replace conventional diagnostics as predictors of drug resistance and clinical outcome?
    • Article
    • Peer Reviewed
    UC San Diego Previously Published Works (2019)
    Clinical phenotypic fluoroquinolone susceptibility testing of Mycobacterium tuberculosis is currently based on M. tuberculosis growth at a single critical concentration, which provides limited information for a nuanced clinical response. We propose using specific resistance-conferring M. tuberculosis mutations in gyrA together with population pharmacokinetic and pharmacodynamic modeling as a novel tool to better inform fluoroquinolone treatment decisions. We sequenced the gyrA resistance-determining region of 138 clinical M. tuberculosis isolates collected from India, Moldova, Philippines, and South Africa and then determined each strain's MIC against ofloxacin, moxifloxacin, levofloxacin, and gatifloxacin. Strains with specific gyrA single-nucleotide polymorphisms (SNPs) were grouped into high or low drug-specific resistance categories based on their empirically measured MICs. Published population pharmacokinetic models were then used to explore the pharmacokinetics and pharmacodynamics of each fluoroquinolone relative to the empirical MIC distribution for each resistance category to make predictions about the likelihood of patients achieving defined therapeutic targets. In patients infected with M. tuberculosis isolates containing SNPs associated with a fluoroquinolone-specific low-level increase in MIC, models suggest increased fluoroquinolone dosing improved the probability of achieving therapeutic targets for gatifloxacin and moxifloxacin but not for levofloxacin and ofloxacin. In contrast, among patients with isolates harboring SNPs associated with a high-level increase in MIC, increased dosing of levofloxacin, moxifloxacin, gatifloxacin, or ofloxacin did not meaningfully improve the probability of therapeutic target attainment. We demonstrated that quantifiable fluoroquinolone drug resistance phenotypes could be predicted from rapidly detectable gyrA SNPs and used to support dosing decisions based on the likelihood of patients reaching therapeutic targets. Our findings provide further supporting evidence for the moxifloxacin clinical breakpoint recently established by the World Health Organization.
      Cover page: Using Mycobacterium tuberculosis Single-Nucleotide Polymorphisms To Predict Fluoroquinolone Treatment Response
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2011)
      PURPOSE

      To describe long-term trends in TB mortality and to compare trends estimated from two different sources of public health surveillance data.

      METHODS

      Trends and changes in trend were estimated by joinpoint regression. Comparisons between datasets were made by fitting a Poisson regression model.

      RESULTS

      Since 1900, TB mortality rates estimated from death certificates have declined steeply, except for a period of no change in the 1980s. This decade had long-term consequences resulting in more TB deaths in later years than would have occurred had there been no flattening of the trend. Recent trends in TB mortality estimated from National Tuberculosis Surveillance System (NTSS) data, which record all-cause mortality, differed from trends based on death certificates. In particular, NTSS data showed TB mortality rates flattening since 2002.

      CONCLUSIONS

      Estimates of trends in TB mortality vary by data source, and therefore interpretation of the success of control efforts will depend upon the surveillance dataset used. The datasets may be subject to different biases that vary with time. One dataset showed a sustained improvement in the control of TB since the early 1990s while the other indicated that the rate of TB mortality was no longer declining.

        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2018)
        Directly observed therapy (DOT) is a cornerstone of tuberculosis (TB) control. DOT has been criticised as paternalistic, but it has also been argued that the interaction with healthcare workers (HWs) can be a source of support for patients. We explored the experience of patients in antituberculosis treatment, with the aim of understanding the balance between surveillance and support from the recipient's point of view. We interviewed 27 patients in Tijuana, Mexico, employing narrative analysis to understand how participants made sense of their illness and their experience of DOT. We found a core narrative of biographic disruption and self-reconstruction, in which HWs helped participants to attribute a less negative meaning to TB. Interviewees accepted DOT's as necessary for other people to avoid treatment abandonment, but felt that in their case it was unnecessary. Only a few felt that DOT represented mistrust on the part of the HWs. We conclude that DOT can be a source of support when it is enacted in a patient-centred way. We discuss whether participants' lack of criticism of DOT is a case of adaptive preference, in the context of a power differential between patient and health system.
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2017)

          Background

          Previous retrospective and in vitro studies suggest that use of later-generation fluoroquinolones may reduce mortality risk and improve treatment outcomes for drug-resistant tuberculosis (TB) patients, including individuals resistant to a fluoroquinolone. Meta-analysis results are mixed and few studies have examined this relationship prospectively.

          Methods

          As part of a comparative diagnostic study, we conducted a prospective cohort study with 834 Mycobacterium tuberculosis-infected patients from selected hospitals and clinics with high prevalence of drug-resistant TB in India, Moldova, and South Africa. We used Cox proportional hazards regression models to assess the association between later-generation fluoroquinolone (moxifloxacin or levofloxacin) use and patient mortality, adjusting for risk factors typically associated with poor treatment outcomes.

          Results

          After adjusting for phenotypic resistance profile, low body mass index (<18.5 kg/m2), human immunodeficiency virus status, and study site, participants treated with a later-generation fluoroquinolone had half the risk of mortality compared with participants either not treated with any fluoroquinolone or treated only with an earlier-generation fluoroquinolone (adjusted hazard ratio, 0.46 [95% confidence interval, .26-.80]) during follow-up.

          Conclusions

          Use of later-generation fluoroquinolones significantly reduced patient mortality risk in our cohort, suggesting that removal of a later-generation fluoroquinolone from a treatment regimen because of demonstrated resistance to an earlier-generation fluoroquinolone might increase mortality risk. Further studies should evaluate the effectiveness of later-generation fluoroquinolones among patients with and without resistance to early-generation fluoroquinolones.

          Clinical trials registration

          NCT02170441.
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2017)
            Rapid molecular diagnostics have great potential to limit the spread of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) (M/XDR-TB). These technologies detect mutations in the Mycobacterium tuberculosis genome that confer phenotypic drug resistance. However, there have been few data published regarding the relationships between the detected M. tuberculosis resistance mutations and M/XDR-TB treatment outcomes, limiting our current ability to exploit the full potential of molecular diagnostics. We analyzed clinical, microbiological, and sequencing data for 451 patients and their clinical isolates collected in a multinational, observational cohort study to determine if there was an association between M. tuberculosis resistance mutations and patient mortality. The presence of an rrs 1401G mutation was associated with significantly higher odds of patient mortality (adjusted odds ratio [OR] = 5.72; 95% confidence interval [CI], 1.65 to 19.84]) after adjusting for relevant patient clinical characteristics and all other resistance mutations. Further analysis of mutations, categorized by the associated resistance level, indicated that the detection of mutations associated with high-level fluoroquinolone (OR, 3.99 [95% CI, 1.10 to 14.40]) and kanamycin (OR, 5.47 [95% CI, 1.64 to 18.24]) resistance was also significantly associated with higher odds of patient mortality, even after accounting for clinical site, patient age, reported smoking history, body mass index (BMI), diabetes, HIV, and all other resistance mutations. Specific gyrA and rrs resistance mutations, associated with high-level resistance, were associated with patient mortality as identified in clinical M. tuberculosis isolates from a diverse M/XDR-TB patient population at three high-burden clinical sites. These results have important implications for the interpretation of molecular diagnostics, including identifying patients at increased risk for mortality during treatment. (This study has been registered at ClinicalTrials.gov under registration no. NCT02170441.).
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2021)
              Outside of the ongoing COVID-19 pandemic, tuberculosis is the leading cause of infectious disease mortality globally. Currently, there is no commercially available point-of-care diagnostic that is rapid, inexpensive, and highly sensitive for the diagnosis of active tuberculosis disease. Here we describe the development and optimization of a novel, highly sensitive prototype bioelectronic tuberculosis antigen (BETA) assay to detect tuberculosis-specific antigen, CFP10, in small-volume serum and urine samples. In this proof-of-concept study we evaluated the performance of the BETA assay using clinical specimens collected from presumptive tuberculosis patients from three independent cohorts. Circulating CFP10 antigen was detected in ALL serum (n = 19) and urine (n = 3) samples from bacteriologically confirmed tuberculosis patients who were untreated or had less than one week of treatment at time of serum collection, successfully identifying all culture positive tuberculosis patients. No CFP10 antigen was detected in serum (n = 7) or urine (n = 6) samples from individuals who were determined to be negative for tuberculosis disease. Additionally, antigen quantification using the BETA assay of paired serum samples collected from tuberculosis patients (n = 8) both before and after treatment initiation, indicate consistently declining within-person levels of CFP10 antigen during treatment. This novel, low-cost assay demonstrates potential as a rapid, non-sputum-based, point-of-care tool for the diagnosis of tuberculosis disease.
                Cover page: Detection and quantification of Mycobacterium tuberculosis antigen CFP10 in serum and urine for the rapid diagnosis of active tuberculosis disease
                • Article
                • Peer Reviewed
                California HIV/AIDS Research Program Funded Publications (2008)
                The incidence in San Diego is increasing and is concentrated mostly in persons of Mexican origin.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 2.55× (p = 0.01) as likely to die during treatment than those with M. tuberculosis.
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2012)

                  Background

                  Rapid molecular diagnostics for detecting multidrug-resistant and extensively drug-resistant tuberculosis (M/XDR-TB) primarily identify mutations in Mycobacterium tuberculosis (Mtb) genes associated with drug resistance. Their accuracy, however, is dependent largely on the strength of the association between a specific mutation and the phenotypic resistance of the isolate with that mutation, which is not always 100%. While this relationship is well established and reliable for first-line anti-TB drugs, rifampin and isoniazid, it is less well-studied and understood for second-line, injectable drugs, amikacin (AMK), kanamycin (KAN) and capreomycin (CAP).

                  Methodology/principal findings

                  We conducted a systematic review of all published studies evaluating Mtb mutations associated with resistance to AMK, KAN, CAP in order to characterize the diversity and frequency of mutations as well as describe the strength of the association between specific mutations and phenotypic resistance in global populations. Our objective was to determine the potential utility and reliability of these mutations as diagnostic markers for detecting AMK, KAN and CAP resistance. Mutation data was reviewed for 1,585 unique clinical isolates from four continents and over 18 countries. Mutations in the rrs, tlyA, eis promoter and gidB genes were associated with AMK, KAN and/or CAP resistance.

                  Conclusions/significance

                  The rrs A1401G mutation was present in the majority of AMK, KAN and CAP resistant Mtb strains reviewed, but was also found in 7% of CAP susceptible strains. The 1401 mutation alone, however, was not found with sufficient frequency to detect more than 70-80% of global Mtb strains resistant to AMK and CAP, and 60% of strains resistant to KAN. Additional mutations in the rrs, eis promoter, tlyA and gidB genes appear to be associated with resistance and could improve sensitivity and specificity of future diagnostics.
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2010)
                    Objectives. 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.Methods. We analyzed TB surveillance data from 1993 through 2007. TB cases were grouped by HIV status: positive, negative, or unknown. We used Poisson regression to estimate trends and tested associations between TB and HIV coinfection and sociodemographic risk factors with polychotomous logistic regression.Results. Of 5172 TB cases, 8.8% were also infected with HIV. Incidence of coinfected cases did not change significantly over the period studied, but the proportion of cases among Hispanics increased significantly, whereas cases among non-Hispanic Whites and Blacks decreased. TB cases with HIV coinfection were significantly more likely to be Hispanic, male, injection drugs users, and aged 30 to 49 years, relative to cases with TB disease only.Conclusions. The burden of TB and HIV in San Diego has shifted to Hispanics in the last decade. To address this health disparity, binational TB and HIV prevention efforts are needed.
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