A novel molecular strategy for surveillance of multidrug resistant tuberculosis in high burden settings

BACKGROUND In South Africa and other high prevalence countries, transmission is a significant contributor to rising rates of multidrug resistant tuberculosis (MDR-TB). Thus, there is a need to develop an early detection system for transmission clusters suitable for high burden settings. We have evaluated the discriminatory power and clustering concordance of a novel and simple genotyping approach, combining spoligotyping with pncA sequencing (SpoNC), against two well-established methods: IS6110-RFLP and 24-loci MIRU-VNTR. METHODS A total of 216 MDR-TB isolates collected from January to June 2010 from the NHLS Central TB referral laboratory in Braamfontein, Johannesburg, representing a diversity of strains from South Africa, were included. The isolates were submitted for genotyping, pncA sequencing and analysis to the Centre for Tuberculosis in South Africa and the Public Health Research Institute Tuberculosis Center at Rutgers University in the United States. Clustering rates, Hunter-Gaston Discriminatory Indexes (HGI) and Wallace coefficients were compared between the methods. RESULTS Overall clustering rates were high by both IS6110-RFLP (52.8%) and MIRU-VNTR (45.8%), indicative of on-going transmission. Both 24-loci MIRU-VNTR and IS6110-RFLP had similar HGI (0.972 and 0.973, respectively), with close numbers of unique profiles (87 vs. 70), clustered isolates (129 vs. 146), and cluster sizes (2 to 26 vs. 2 to 25 isolates). Spoligotyping alone was the least discriminatory (80.1% clustering, HGI 0.903), with 28 unique types. However, the discriminatory power of spoligotyping was improved when combined with pncA sequencing using the SpoNC approach (61.8% clustering, HGI 0.958). A high proportion of MDR-TB isolates had mutations in pncA (68%, n = 145), and pncA mutations were significantly associated with clustering (p = 0.007 and p = 0.0013 by 24-loci MIRU-VNTR and IS6110-RFLP, respectively), suggesting high rates of resistance to pyrazinamide among all MDR-TB cases and particularly among clustered cases. CONCLUSION We conclude that SpoNC provides good discrimination for MDR-TB surveillance and early identification of outbreaks in South Africa, with 24-loci MIRU-VNTR applied for pncA wildtype strains as needed.Supporting Information. S1 File. (XLSX)http://www.plosone.orgam2016Medical Microbiolog

A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings.

In South Africa and other high prevalence countries, transmission is a significant contributor to rising rates of multidrug resistant tuberculosis (MDR-TB). Thus, there is a need to develop an early detection system for transmission clusters suitable for high burden settings. We have evaluated the discriminatory power and clustering concordance of a novel and simple genotyping approach, combining spoligotyping with pncA sequencing (SpoNC), against two well-established methods: IS6110-RFLP and 24-loci MIRU-VNTR.A total of 216 MDR-TB isolates collected from January to June 2010 from the NHLS Central TB referral laboratory in Braamfontein, Johannesburg, representing a diversity of strains from South Africa, were included. The isolates were submitted for genotyping, pncA sequencing and analysis to the Centre for Tuberculosis in South Africa and the Public Health Research Institute Tuberculosis Center at Rutgers University in the United States. Clustering rates, Hunter-Gaston Discriminatory Indexes (HGI) and Wallace coefficients were compared between the methods.Overall clustering rates were high by both IS6110-RFLP (52.8%) and MIRU-VNTR (45.8%), indicative of on-going transmission. Both 24-loci MIRU-VNTR and IS6110-RFLP had similar HGI (0.972 and 0.973, respectively), with close numbers of unique profiles (87 vs. 70), clustered isolates (129 vs. 146), and cluster sizes (2 to 26 vs. 2 to 25 isolates). Spoligotyping alone was the least discriminatory (80.1% clustering, HGI 0.903), with 28 unique types. However, the discriminatory power of spoligotyping was improved when combined with pncA sequencing using the SpoNC approach (61.8% clustering, HGI 0.958). A high proportion of MDR-TB isolates had mutations in pncA (68%, n = 145), and pncA mutations were significantly associated with clustering (p = 0.007 and p = 0.0013 by 24-loci MIRU-VNTR and IS6110-RFLP, respectively), suggesting high rates of resistance to pyrazinamide among all MDR-TB cases and particularly among clustered cases.We conclude that SpoNC provides good discrimination for MDR-TB surveillance and early identification of outbreaks in South Africa, with 24-loci MIRU-VNTR applied for pncA wild-type strains as needed

Revisiting the Protest Paradigm: the Tea Party as Filtered through Prime-Time Cable News

The emergence of a national Tea Party movement in the United States stimulated much media commentary regarding the movement\u27s origins, goals, participants, and even temperament. Unlike political movements of the recent past, the Tea Party stands starkly to the right. This study examines nightly cable news coverage of this movement by using key frames associated with the protest paradigm —the tendency for media to marginalize movements by drawing attention away from core concerns raised by such movements. We ask whether the protest paradigm can be applied to a right-wing movement and whether such application varies by the ideological leaning of a given source. That is, do cable news channels use frames in ways consistent with their respective ideological hues? We draw on a representative sample of stories regarding the national movement from the most viewed nightly news programs on Fox News, MSNBC, and CNN, with the Associated Press as a reference point. Results show significant differences across sources in issue and marginalization frame use. Although utilization of marginalization frames is popular among ideological channels, traditional news sources are not immune from using these devices

A systematic conservation plan identifying critical areas for improved chondrichthyan protection in South Africa

The International Union for Conservation of Nature (IUCN) estimates that over a third of all chondrichthyan species (sharks, rays and chimaeras) are threatened with extinction, primarily by overfishing (as target or bycatch species). Owing to the wide-ranging distributions of many chondrichthyans, they are often overlooked in marine protected area (MPA) design. South Africa is a biodiversity hotspot for chondrichthyan species diversity, and to improve the conservation status of these species in the country's continental exclusive economic zone (EEZ), we collaborated widely to collate existing occurrence data. Ensemble models were developed for 87 species' distributions, which informed a systematic conservation planning analysis for 64 threatened and endemic species. We assessed the current representation of these species in South Africa's MPA network and identified priority areas for protection, avoiding fishing pressure where possible. Results show that many MPAs are well placed to protect chondrichthyans, especially along the east coast (KwaZulu-Natal province). Unfortunately, permissive fishing regulations within many MPA zones reduces their effectiveness at protecting chondrichthyans. Improved regulations designed to protect chondrichthyans within all MPAs should be considered a high priority. Priority areas for increased spatial protection were identified along the west coast continental shelf, the Agulhas Bank off the south coast, and south coast embayments. We found that supplementing the current MPA network by an additional 5 % of the EEZ would be sufficient to protect >30 % of the range of all 64 species, provided there is adequate enforcement. As South Africa prepares to expand its MPA estate to meet international targets, these findings can ensure that chondrichthyans are well represented. •We collaborated widely to collate occurrence data on 164 chondrichthyan species in South Africa.•Distribution models were developed for 87 chondrichthyan species.•Priority areas for protection were identified using systematic conservation planning.•Priority areas included the shelf offshore of the west and south coast.•South Africa's MPA regulations require better management to protect chondrichthyans