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Funding: This work was supported by the Wellcome Trust (206724/Z/17/Z to NTTT and 106680/B/14/Z to GT). New tools to monitor treatment response and predict outcome from tuberculous meningitis (TBM) are urgently required. We retrospectively evaluated the 16S rRNA-based molecular bacterial load assay (MBLA) to quantify viable Mycobacterium tuberculosis in serial cerebrospinal fluid (CSF) from adults with TBM. 187 CSF samples were collected before and during the first two months of treatment from 99 adults TBM, comprising 56 definite, 43 probable or possible TBM, and 18 non-TBM and preserved at −80 °C prior to MBLA. We compared MBLA against MGIT culture, GeneXpert MTB/RIF (Xpert) and Ziehl-Neelsen (ZN) smear. Before treatment, MBLA was positive in 34/99 (34.3%), significantly lower than MGIT 47/99 (47.5%), Xpert 51/99 (51.5%) and ZN smear 55/99 (55.5%). After one month of treatment, MBLA and MGIT were positive in 3/38 (7.9%) and 4/38 (10.5%), respectively, whereas Xpert and ZN smear remained positive in 19/38 (50.0%) and 18/38 (47.4%). In summary, MBLA was less likely to detect CSF bacteria before the start of treatment compared with MGIT culture, Xpert and ZN smear. MBLA and MGIT positivity fell during treatment because of detecting only viable bacteria, whereas Xpert and ZN smear remained positive for longer because of detecting both live and dead bacteria. Sample storage and processing may have reduced MBLA-detectable viable bacteria; and sampling earlier in treatment may yield more useful results. Prospective studies with CSF sampling after 1–2 weeks are warranted. Publisher PDF

To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb. Screening for parallel evolution of Beijing lineage-associated SNPs in other Mtb lineages as a signal of positive selection, we identify an alteration in the ESX-5 type VII-secreted protein EsxW, which could potentially contribute to the enhanced transmission of Beijing lineage Mtb in Vietnamese and other host populations.

In this paper we present a printed, fast, high-sensitive and cheap wireless incontinence sensor system, which could be integrated in a common diaper for urinary detection. The system consists of a flexible screen-printed IDEs (Inter Digital Electrodes) sensor with bio compatible conducting PEDOT:PSS material, a battery, a readout electronics for sensor signal and a wireless module.

Mountainous black-bone chickens are characterized by black bones, meat and skin meat from black-bone chickens has been preferred by consumers. Conservation of mountainous black-bone chickens is one way to maintain the animal bio-diversity for H¿mong minority group in the northern mountainous provinces. From the original generation consisted of 200 females and 30 males selected from Xin Man and Dong Van, the first generation was established. From the first generation, a breeding flock consisted 773 birds in 30 households was established. The body weight of hens and cocks at 20 weeks old was 1,266 - 1,218.66 and 1,706.33 - 1,720.67 g, respectively. Selection by feather phenotypes showed that there was a difference in the growth rate among three feather phenotypes. The body weight at one day old of the black, white and striped feather chicken, which was 36.33, 32.70 and 30.07 g, respectively, was not significantly different. However, the body weight at 20 weeks old of the black, white and striped feather chicken, which was 1505.70, 1114.00, 612.10 and 1480.90 g, respectively.

Ha Giang is considered as one of provinces having the richest bio-diversity of animal resources, and was selected by BIODIVA project for a field study aiming at investigation, assessement of bio-charecteristics, bio-diversity of animal breeds, production systems. Factors including potential or hidden factors influencing bio-diversity and risks of losses of animal bio-diversity were also included in the study for seting up a plan on building microprojects, which were aimed at biodiversity protection and development, valorization of local animal genetics resources, increasing income for local people. Interviews and records were made on 1674 households of different ethnic minorities in 251 villages of 37 communes in the province. Information collected during interviews included: current status of household economics, production systems, breeding activities, origin of animals, animal feeding, diseases, vaccination programs and geography information. A total of 7427 animals including buffalos, bulls, cows, pigs, chickens, goats and ducks were used for bio-sampling and describing phenotyes of animals. Bio-samples and phenotypes of animals were further used for a monocular genetic analysis and assessments of phenotype biodiversity. The results of the field study showed that there was a remarkable diversity of phenotypic characteristics and animal¿s genetic resources by topography, ethnic groups in HaGiang province.

One study with the objective of accessing the genetic diversity of pig populations in Ha Gang province was undertaken. Nineteen microsatellites (FAO) were used to genotype 1053 pig individuals. A total 221 alleles were observed. The mean number of alleles per locus was 11.63 ± 3.18 (maximum in locus Sw2410 and minimum in locus Sw2008). In total population, the average observed heterozygote frequency (Ho) was 0,629 (ranged from 0.473 to 0.737) and expected heterozygote frequency (He) was 0.814 (ranged from 0.730 to 0.914). Inbreeding was indicated by heterozygosity deficiency with mean Fis = 0.228. The genetic differentiation between 4 different groups (white, black, brown and black-white pig) was small with a mean Fst = 0.017. The genetic distance was highest between white pig and three other pig groups (black, brown and black-white). There was no significant genetic variation between black and brown pig group (P>0.05). Among 10 district black pig populations, the average allele per population ranged from 7.62 (Meo Vac) to 10.68 (Xin Man), the Fis value was in a range from 0.215 to 0.323. The phylogenetic tree showed that black pig population formed 3 branches: I (Yen Minh, Quan Ba, Dong Van, Meo Vac and Bac Me district), II (Ha Giang, Vi Xuyen and Quang Binh district), III (Xin Man, Hoang Su Phi district).

This study, which covered 352 villages, 44 communes and 11 districts of Hagiang province with 2.914 chicken and lasted from March 2005 to September 2006, was aimed at evaluating the phenotype diversity of local chicken population in Hagiang province. The results showed that chicken in Hagiang had diversified appearances and were distributed in different ecological conditions. The average mature body weight of chicken was around 1.58 kg and 1.76 kg. All phenotypes were obsevered in high soil mountain and high rocky mountain areas (Dongvan, Meovac, Quangba, Yenminh, Hoangsuphi and Ximan). Feather phenotypes included fuzzy feather, smooth feather and striped feather. Fuzzy feather chicken concentrated on high rock mountain areas. Percentage of fuzzy feather and smooth feather chickens was 16.38 and 17.72% in Dongvan, respectively (the average of Hagiang province was only 4.26% and 3.32% respectively). The special black chicken breed reared by HMong ethnic group (black skin, bone, meat) occupied 4.56% and mainly concentrated in Dongvan and Xinman. There were four types of crest: single, rose, pea and strawberry crests. The percentage of chicken with orange, brown and black eyes was 81.45; 16.90, and 1.65%, respectively. Estimated allele frequencies at locus C for C and c+ were 0.753 and 0.247, respectively. Estimated allele frequencies at locus I for I and i+ were 0.041 and 0.959, respectively. Estimated allele frequencies at locus F for F and f+ were 0.753 and 0.247; at locus H for H and h+ were 0.194 and 0.806 and at locus Pg for Pg and pg+ were 0.883 and 0.117, respectively.

The current study aiming at accessing genetic diversity of 11 chicken populations (2305 samples in 11 districts) in Ha Giang province was undertaken. Twenty-two micro satellites were genotyped for chickens, which were randomly selected from 11 populations (11districts), including: Bac Me (284), Bac Quang (178), Dong Van (176), Hà Giang town (125), Hoang Su Phi (217), Meo Vac (237), Quan Ba (244), Quang Binh (171), Vi Xuyen (199), Xi Man (238), Yen Minh (236). A total of 190 alleles were observed in the 11 populations. The average number (±SD) of alleles/locus was 8.48 ± 4.71. Mean observed and expected heterozygote across all populations was 0.564 and 0.636. Overall average inbreeding coefficient (Fis) was 0.114. The overall genetic variation was low (0.01). Small Nei¿s (1972) standard genetic distances ranging from 0.007 to 0.044 were observed between 11 populations in Ha Giang. Genetic distance was small in phenotypic populations but large between phenotypic populations and Ho population. This study showed a low genetic variation and genetic distance but a high genetic diversity within the Ha Giang chicken population where scavenging method have been practicing.