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opencc-zeroJun 2020View details →

Data from: Home-based TB contact investigation in Uganda: a household-randomized trial

Introduction: The World Health Organization(WHO) recommends household tuberculosis(TB) contact investigation in low-income countries, but most contacts do not complete evaluation. Methods: We performed a randomized trial of home-based, SMS-facilitated, household TB contact investigation in Kampala, Uganda. Community health workers(CHWs) visited homes of index patients with pulmonary TB to screen household contacts for TB. Entire households were randomly allocated to clinic(standard-of-care) or home(intervention) evaluation. In the intervention arm, CHWs offered adults HIV testing; collected sputum from symptomatic contacts and persons living with HIV(PLWH) if ≥5 years; and transported sputum for microbiologic testing. CHWs referred PLWH, children <5, and anyone unable to complete sputum testing to clinic. Sputum-testing results and/or follow-up instructions were returned by automated SMS. The primary outcome was completion of TB evaluation within 14 days; secondary, TB and HIV diagnoses and treatments among screened contacts. Results: There were 471 contacts of 190 index patients allocated to the intervention and 448 contacts of 182 index patients allocated to the standard-of-care. CHWs identified 190/471(40%) intervention and 213/448(48%) standard-of-care contacts requiring TB evaluation. In the intervention arm, CHWs obtained sputum from 35/91(39%) sputum-eligible contacts and SMS were sent to 95/190(50%) contacts. Completion of TB evaluation in intervention and standard-of-care arms at 14 days(14% vs 15%; difference -1%, 95%CI -9% to +7%, p=0.81) and yields of confirmed TB(1.5% vs 1.1%, p=0.62) and new HIV(2.0% vs. 1.8%, p=0.90) diagnoses were similar. Conclusions: Home-based, SMS-facilitated evaluation did not improve completion or yield of household TB contact investigation, likely due to challenges delivering the intervention components.

Supplementary material 1 from: Wilson JRU, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM (2020) Frameworks used in invasion science: progress and prospects. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 1-30. https://doi.org/10.3897/neobiota.62.58738

Details of the workshop, the invitation, list of attendees, the programme, ground rules, form for highlighting case-studies, and the process for compiling the special issue

Supplementary material 1 from: Datta A, Kumschick S, Geerts S, Wilson JRU (2020) Identifying safe cultivars of invasive plants: six questions for risk assessment, management, and communication. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 81-97. https://doi.org/10.3897/neobiota.62.51635

Table S1. Plant taxa listed under South African regulations for which certain sub-specific entities are listed differently from other entities

Supplementary material 1 from: Brock KC, Daehler CC (2020) Applying an invasion and risk framework to track non-native island floras: a case study of challenges and solutions in Hawai'i. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 55-79. https://doi.org/10.3897/neobiota.62.52764

Guidance on the status confidence rating and adapting a regional checklist to track invasion statuses

Supplementary material 2 from: Kumschick S, Wilson JRU, Foxcroft LC (2020) A framework to support alien species regulation: the Risk Analysis for Alien Taxa (RAAT). In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 213-239. https://doi.org/10.3897/neobiota.62.51031

Risk Analysis for Alien Taxa framework, adapted to South African NEMBA A&IS Regulations (v.1.2) (Appendix S2)

Supplementary material 1 from: Kumschick S, Wilson JRU, Foxcroft LC (2020) A framework to support alien species regulation: the Risk Analysis for Alien Taxa (RAAT). In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 213-239. https://doi.org/10.3897/neobiota.62.51031

How the Risk Analysis Framework covers Section 6, Regulation 14-17, in the NEM:BA A&IS Regulations of 2014 (Appendix S1)

opencc-zeroDec 2017View details →

Data from: Cough frequency during treatment associated with baseline cavitary volume and proximity to the airway in pulmonary TB

Background: Cough frequency, and its duration, is a lab-free biomarker that can be used in low-resource settings and has been associated with transmission and treatment response. Radiological characteristics associated with increased cough frequency may be important in understanding transmission. The relationship between cough frequency and cavitary lung disease has never been studied. Methods: We analyzed 41 human immunodeficiency virus-negative adults with culture-confirmed, drug-susceptible pulmonary tuberculosis throughout treatment. Cough recordings were based on the Cayetano Cough Monitor and sputum samples were evaluated using microscopic-observation drug susceptibility broth culture, among culture-positive samples bacillary burden was assessed by time to positivity. Computerized tomography scans were analyzed by a U.S. board-certified radiologist and an automated-computer algorithm. The algorithm evaluates cavity volume and cavitary proximity to the airway. Computerized tomography scans were taken within one month of treatment initiation. We compared small cavities (≤7-mL) versus large cavities (>7-mL) and cavities located closer to (≤10-mm) and farther (>10-mm) from the airway to cough frequency and cough cessation until treatment day 62. Results: Cough frequency during treatment was two-fold higher in participants with large cavity volumes (Rate Ratio [RR]=1.98, p=0.01) and cavities located closer to the airway (RR=2.44, p=0.001). Comparably, cough ceased three times faster in smaller cavities (adjusted hazard ratio [HR]=2.89, p=0.06) and those farther from the airway (adjusted HR=3.61, p=0.02). Similar results are found for bacillary burden and culture conversion during treatment. Conclusions: Cough frequency during treatment is greater and lasts for longer in patients with larger cavities, especially those closer to the airway.

opencc-zeroDec 2016View details →

Data from: Delays and loss to follow up before treatment of drug-resistant TB following implementation of Xpert MTB/RIF in South Africa: a retrospective cohort study

Background: South Africa has a large burden of rifampicin-resistant tuberculosis (RR-TB), with 18,734 patients diagnosed in 2014. The number of diagnosed patients has increased substantially with the introduction of the Xpert MTB/RIF test, used for TB diagnosis for all patients with presumptive TB. Routine aggregate data suggest a large treatment gap (pre-treatment loss to follow up) between the numbers of laboratory confirmed RR-TB patients and those reported to have started second-line treatment. We aimed to assess the impact of Xpert MTB/RIF implementation on the delay to treatment initiation and loss to follow-up before second-line treatment for RR-TB across South Africa. Methods and findings: A nationwide retrospective cohort study was conducted to assess second-line treatment initiation and treatment delay among laboratory diagnosed RR-TB patients. Cohorts, including approximately 300 sequentially diagnosed RR-TB patients per South African province, were drawn from 2011 and 2013, before and after Xpert implementation. Patients with prior laboratory RR-TB diagnoses within 6 months and currently treated patients were excluded. Treatment initiation was determined through data linkage with national and local treatment registers, medical record review, interviews with healthcare staff, and direct contact with patients or household members. Additional laboratory data were used to track cases. National estimates of percentage treatment initiation and time to treatment were weighted to account for the sampling design. There were 2,508 and 2,528 eligible patients in the 2011 and 2013 cohorts respectively; 92% were newly diagnosed with RR-TB (new RR-TB, no prior RR-TB diagnoses). Nationally, among 2,340 and 2,311 new RR-TB patients in the 2011 and 2013 cohorts, 55% (95% CI 53-57) and 63% (95% CI 61-65) respectively started treatment within 6 months of their diagnostic specimen being sent (p<0.001). However, in 2013, there was no difference in the percentage of patients who initiated treatment at six months between the 1,368174 new RR-TB patients diagnosed by Xpert (62%, 95% CI 59-65) and the 943ose diagnosed by other methods (64%, 95% CI 61-67) (p=0.39). The median time to treatment decreased from 44 (IQR 20-69) days in 2011 to 22 (IQR 2-43) days in 2013 (p<0.001). In 2013, across the nine provinces, there were substantial variations in both treatment initiation (range 51-73% by six months) and median time to treatment (range 15-36 days, N=1,450), and only 53% of 1,448 new RR-TB who received treatmented patients were recorded on the national RR-TB register. This retrospective study is limited by the lack of information to assess reasons for non-initiation of treatment, particularly pre-treatment mortality data. Other limitations include the use of names and dates of birth to locate patient-level data, potentially resulting in missed treatment initiation among some patients. Conclusions: In 2013, there was a large treatment gap for RR-TB in South Africa which varied significantly across provinces. Xpert implementation, while reducing treatment delay, had not contributed substantially to reducing the treatment gap in 2013. However, given improved case detection with Xpert, overall a larger proportion of the total RR-TB burden has received treatment, with reduced delays. Nonetheless, strategies to further improve linkage to treatment for all diagnosed RR-TB patients are urgently required.

opencc-by-4.0Dec 2021View details →

Article experimental infection TB foxes

supplementary data article Experimental infection of captive red foxes (Vulpes vulpes) with Mycobacterium bovis

opencc-zeroDec 2017View details →

Data from: Type 1 interferon-inducible gene expression in QuantiFERON Gold TB-positive uveitis: a tool to stratify a high versus low risk of active tuberculosis?

QuantiFERON-Gold TB (QFT)-positive patients with undetermined cause of uveitis are problematic in terms of whether to diagnose and treat them for tuberculosis (TB). Here, we investigated whether peripheral blood expression of type 1 interferon (IFN)-inducible genes may be of use to stratify QFT-positive patients with uveitis into groups of high versus low risk of having active TB-associated uveitis. We recruited all new uveitis patients in Cipto Mangunkusumo Hospital, Jakarta, Indonesia for one year. We included 12 patients with uveitis and clinically diagnosed active pulmonary TB, 58 QFT-positive patients with uveitis of unknown cause, 10 newly diagnosed sputum-positive active pulmonary TB patients without uveitis and 23 QFT-negative healthy controls. Expression of 35 type 1 IFN-inducible genes was measured in peripheral blood cells from active pulmonary TB patients without uveitis and healthy controls. Differentially expressed genes were identified and used for further clustering analyses of the uveitis groups. A type-1 IFN gene signature score was calculated and the optimal cut-off value for this score to differentiate active pulmonary TB from healthy controls was determined and applied to QFT-positive patients with uveitis of unknown cause. Ten type 1 IFN-inducible genes were differentially expressed between active pulmonary TB and healthy controls. Expression of these 10 genes in QFT-positive patients with uveitis of unknown cause revealed three groups: 1); patients resembling active pulmonary TB, 2); patients resembling healthy controls, and 3); patients displaying an in-between gene expression pattern. A type 1 IFN gene signature score ≥5.61 displayed high sensitivity (100%) and specificity (91%) for identification of active TB. Application of this score to QFT-positive patients with uveitis of unknown cause yielded two groups with expected different likelihood (high vs. low) of having active-TB uveitis, and therefore may be useful in clinical management decisions.

opencc-zeroSep 2022View details →

Viet Nam: Private pharmacy TB referrals acceptability survey data

Pharmacies represent a key health system entry point for people with TB in Viet Nam, but high fragmentation hinders their broader engagement. Professional networking apps may be able to facilitate pharmacy engagement for systematic TB screening and referral. Between September and December 2019, we piloted the use of a social networking app, SwipeRx, to recruit pharmacists for a TB referral scheme across four districts of Ho Chi Minh City, Viet Nam. We measured chest X-ray (CXR) referrals and TB detection yields at participating pharmacies and fielded 100 acceptability surveys, divided into pharmacists who did and did not make a CXR referral. We then fitted mixed-effect odds proportional models to explore acceptability factors that were associated with making a CXR referral.1,816 push notifications were sent to pharmacists via the SwipeRx app and 78 indicated their interest in participating; however, only one was within the pilot's intervention area. Additional in-person outreach resulted in the recruitment of 146 pharmacists, with 54 (37.0%) making at least one CXR referral. A total of 182 pharmacy customers were referred, resulting in a total of 64 (35.2%) CXR screens and seven people being diagnosed with TB. Compared to pharmacists who did not make any CXR referrals, pharmacists making at least one CXR referral understood the pilot's objectives more clearly (aOR=2.6, 95% CI: 1.2-5.8) and they believed that TB screening increased customer trust (aOR=2.7, 95% CI: 1.2-5.8), benefited their business (aOR=2.8, 95% CI: 1.3-6.2) and constituted a competitive advantage (aOR=4.4, 95% CI: 1.9-9.9). They were also more confident in using mHealth apps (aOR=3.1, 95 CI%: 1.4-6.8). Pharmacies can play an important role in early and increased TB case finding. It is critical to highlight the value proposition of TB referral schemes to their business during recruitment. Digital networking platforms, such as SwipeRx, can facilitate referrals for TB screening by pharmacists, but their ability to identify and recruit pharmacists requires optimization, particularly when targeting specific segments of a nation-wide digital network.

opencc-zeroOct 2022View details →

Aggregate TB diagnosis and treatment data, Uganda 2017 and 2019

To accelerate tuberculosis (TB) control and elimination, reliable data is needed to improve the quality of TB care. We assessed agreement between a surveillance dataset routinely collected for Uganda's national TB program and a high-fidelity dataset collected from the same source documents for a research study from 32 health facilities in 2017 and 2019 for six measurements: 1) Smear-positive and 2) GeneXpert-positive diagnoses, 3) bacteriologically confirmed and 4) clinically diagnosed treatment initiations, and the number of people initiating TB treatment who were also 5) living with HIV or 6) taking antiretroviral therapy. We measured agreement as the average difference between the two methods, expressed as the average ratio of the surveillance counts to the research data counts, its 95% limits of agreement (LOA), and the concordance correlation coefficient. We used linear mixed models to investigate whether agreement changed over time or was associated with facility characteristics. We found good overall agreement with some variation in the expected facility-level agreement for the number of smear-positive diagnoses (average ratio [95% LOA]: 1.04 [0.38-2.82]; CCC: 0.78), bacteriologically confirmed treatment initiations (1.07 [0.67-1.70]; 0.82), and people living with HIV (1.11 [0.51-2.41]; 0.82). The agreement was poor for Xpert positives, with surveillance data undercounting relative to research data (0.45 [0.099-2.07]; 0.36). Although surveillance data overcounted relative to research data for clinically diagnosed treatment initiations (1.52 [0.71-3.26]) and the number of people taking antiretroviral therapy (1.71 [0.71-4.12]), their agreement as assessed by CCC was not poor (0.82 and 0.62, respectively). The average agreement was similar across study years for all six measurements, but facility-level agreement varied yearly and was not explained by facility characteristics. In conclusion, the agreement of TB surveillance data with high-fidelity research data was highly variable across measurements and facilities. To advance the use of routine TB data as a quality improvement tool, future research should elucidate and address reasons for variability in its quality.

opencc-zeroNov 2019View details →

Supplementary material 1 from: Bannikova AA, Jenkins PD, Solovyeva EN, Pavlova SV, Demidova TB, Simanovsky SA, Sheftel BI, Lebedev VS, Fang Y, Dalen L, Abramov AV (2019) Who are you, Griselda? A replacement name for a new genus of the Asiatic short-tailed shrews (Mammalia, Eulipotyphla, Soricidae): molecular and morphological analyses with the discussion of tribal affinities. ZooKeys 888: 133-158. https://doi.org/10.3897/zookeys.888.37982

: Explanation note: Figure S1. The phylogenetic relationships in Blarinella as reconstructed in MrBayes based on the extended alignment of cytb. Figure S2. The phylogenetic relationships in Blarinella as reconstructed in MrBayes based on the alignment of ApoB. Table S1. GenBank accession numbers of sequences retrieved from GenBank and newly collected sequences used in the study (marked in bold). Table S2. Primers for cytb amplification and sequencing. Table S3. The best-fit substitution models employed for each of the five partitions found by IQTREE.

opencc-zeroNov 2022View details →

Supplementary material 14 from: Gloria-Soria A, Shragai T, Ciota AT, Duval TB, Alto BW, Martins AJ, Westby KM, Medley KA, Unlu I, Campbell SR, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham PT, Caccone A, Armstrong PM (2022) Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NeoBiota 78: 99-127. https://doi.org/10.3897/neobiota.78.84986

Population structure on Aedes albopictus samples from all Connecticut samples (no temporal series) based on 15 microsatellite markers