Use of genomics to track bovine tuberculosis transmission.

The control of any infectious disease of livestock is made more difficult by the presence of a wildlife reservoir, as the reservoir is often poorly observed and difficult to manage. This problem is particularly acute for bovine tuberculosis (bTB) because the long duration of infection and low levels of infectiousness make tracing the sources of infection difficult. For over 30 years, the process of contact tracing has been aided by the exploitation of molecular markers in the pathogen, but this has largely only been capable of characterising broad associations between large communities of similar types. However, the recent advent of mass high-throughput 'whole-genome' sequencing (WGS) has revolutionised forensic epidemiology for other diseases, and now it has the potential to do so for bTB. In this review, the authors consider the historical context of WGS use and look at what prior molecular techniques have already achieved. They outline the key approaches to interpreting WGS data and consider both the role of advanced analytical techniques that exploit the evolutionary and epidemiological properties of the system and the problems associated with quantifying the role of hidden reservoirs of disease. Finally, they consider the particular difficulties associated with developing this technology for routine diagnostics and its potential for mass use.

Les maladies infectieuses affectant les animaux d'élevage sont plus difficiles à contrôler lorsqu'il existe un réservoir sauvage, celui-ci étant souvent difficile à observer et à gérer. Ce problème est particulièrement crucial dans le cas de la tuberculose bovine en raison de la durée prolongée de l'infection et des faibles niveaux d'infectiosité qui rendent difficile le traçage des sources d'infection. Pendant plus de 30 ans, le processus de traçage des contacts s'est appuyé sur l'exploitation de marqueurs moléculaires au sein de l'agent pathogène, mais cette technique n'a guère pu aller au-delà d'une caractérisation d'associations générales entre vastes communautés de types similaires. L'avènement récent du séquençage massif à haut débit du génome entier a toutefois révolutionné l'épidémiologie légale appliquée à d'autres maladies, et il en ira bientôt probablement de même pour la tuberculose bovine. Les auteurs de cette synthèse s'intéressent au contexte historique de la mise au point du séquençage du génome entier en relevant ce que les techniques moléculaires antérieures avaient déjà accompli. Ils soulignent les principales méthodes pour interpréter les données générées par le séquençage du génome entier et examinent aussi bien le rôle des techniques analytiques les plus avancées basées sur l'exploitation des propriétés évolutionnistes et épidémiologiques du système que les problèmes qui se posent lorsqu'on cherche à quantifier le rôle joué par les réservoirs inapparents d'une maladie. Enfin, ils exposent les difficultés particulières liées à la mise en oeuvre de cette technologie pour des applications diagnostiques de routine ainsi que son potentiel d'utilisation à grande échelle.

La presencia de un reservorio en la fauna salvaje siempre complica la lucha contra las enfermedades infecciosas del ganado, en la medida en que esos reservorios son observados con poca frecuencia y resultan difíciles de gestionar. Este problema cobra especial gravedad en el caso de la tuberculosis bovina, pues la larga duración de la infección y los bajos niveles de infecciosidad hacen difícil localizar el origen de los focos. Durante más de 30 años se han empleado marcadores moleculares del patógeno como método auxiliar en el proceso de localización de los contactos, pero ello casi siempre ha servido únicamente para caracterizar correlaciones más bien laxas entre grandes comunidades de tipos parecidos. En los últimos tiempos, sin embargo, el advenimiento de la secuenciación masiva de alto rendimiento de genomas completos ha revolucionado la epidemiología forense aplicada a otras enfermedades, y ahora puede ocurrir otro tanto con la tuberculosis bovina. Los autores, tras repasar el contexto histórico del uso de la secuenciación de genomas completos, exponen los resultados que hasta la fecha se han podido obtener con las técnicas moleculares anteriores. Asimismo, describen brevemente los principales métodos para interpretar los datos de secuenciación de genomas completos y examinan tanto la función de las técnicas analíticas avanzadas que explotan las propiedades evolutivas y epidemiológicas del sistema como los problemas que surgen para cuantificar la intervención de reservorios ocultos de enfermedad. Por último, exponen las especiales dificultades que plantea el desarrollo de esta tecnología para efectuar diagnósticos sistemáticos y las posibilidades que ofrece para una utilización generalizada.

Newly attenuated Mycobacterium bovis mutants as vaccines against bovine tuberculosis, particularly for possums.

Bovine tuberculosis costs New Zealand more than $80 million per year, mostly because extensive areas of the country are occupied by brushtail possums infected with Mycobacterium bovis. AgResearch has a major programme to produce new live tuberculosis vaccines that can be delivered to possums. Primary work involved development of molecular biological methods to enable genetic manipulation of M. bovis, including the production of random and specific mutants. Many avirulent mutants of M. bovis have been produced and their vaccine efficacy has been compared to BCG in guinea pigs. Selected mutants that perform at least as well as BCG are retested in guinea pigs using an extended vaccination protocol in which animals are pre-sensitized to environmental mycobacteria to mimic natural exposure. Ten candidate vaccines that have induced good protection in guinea pigs have been subsequently tested as vaccines in possums. While the protective efficacy of an M. bovis mutant inoculated into guinea pigs reliably indicated that some protection would be induced in possums, the most protective mutant in guinea pigs was different from that in possums. This illustrates the importance of testing in the target species as part of new vaccine development. An important outcome of this work was the identification of an operon in M. bovis whose inactivation produced an avirulent M. bovis vaccine candidate that was better than BCG in protecting possums from experimental tuberculosis. Allelic exchange methods are now being used to produce vaccine strains with multiple specific mutations to improve safety and immunological characteristics.

The evolution and distribution of phage ST160 within Salmonella enterica serotype Typhimurium.

Salmonellosis is an internationally important disease of mammals and birds. Unique epidemics in New Zealand in the recent past include two Salmonella serovars: Salmonella enterica subsp. enterica serovar Typhimurium definitive type (DT) 160 (S. Typhimurium DT160) and S. Brandenburg. Although not a major threat internationally, in New Zealand S. Typhimurium DT160 has been the most common serovar isolated from humans, and continues to cause significant losses in wildlife. We have identified DNA differences between the first New Zealand isolate of S. Typhimurium DT160 and the genome-sequenced strain, S. Typhimurium LT2. All the differences could be accounted for in one cryptic phage ST64B, and one novel P22-like phage, ST160. The majority of the ST160 genome is almost identical to phage SE1 but has two regions not found in SE1 which are identical to the P22-like phage ST64T, suggesting that ST160 evolved from SE1 via two recombination events with ST64T. All of the New Zealand isolates of DT160 were identical indicating the clonal spread of this particular Salmonella. Some overseas isolates of S. Typhimurium DT160 differed from the New Zealand strain and contained SE1 phage rather than ST160. ST160 was also identified in New Zealand isolates of S. Typhimurium DT74 and S. Typhimurium RDNC-April06 and in S. Typhimurium DT160 isolates from the USA. The emergence of S. Typhimurium DT160 as a significant pathogen in New Zealand is postulated to have occurred due to the sensitivity of the Salmonella strains to the ST160 phage when S. Typhimurium DT160 first arrived.

The alternative electron acceptor tetrathionate supports B12-dependent anaerobic growth of Salmonella enterica serovar typhimurium on ethanolamine or 1,2-propanediol.

Synthesis of cobalamin de novo by Salmonella enterica serovar Typhimurium strain LT2 and the absence of this ability in Escherichia coli present several problems. This large synthetic pathway is shared by virtually all salmonellae and must be maintained by selection, yet no conditions are known under which growth depends on endogenous B12. The cofactor is required for degradation of 1,2-propanediol and ethanolamine. However, cofactor synthesis occurs only anaerobically, and neither of these carbon sources supports anaerobic growth with any of the alternative electron acceptors tested thus far. This paradox is resolved by the electron acceptor tetrathionate, which allows Salmonella to grow anaerobically on ethanolamine or 1,2-propanediol by using endogenously synthesized B12. Tetrathionate provides the only known conditions under which simple cob mutants (unable to make B12) show a growth defect. Genes involved in this metabolism include the ttr operon, which encodes tetrathionate reductase. This operon is globally regulated by OxrA (Fnr) and induced anaerobically by a two-component system in response to tetrathionate. Salmonella reduces tetrathionate to thiosulfate, which it can further reduce to H2S, by using enzymes encoded by the genes phs and asr. The genes for 1,2-propanediol degradation (pdu) and B12 synthesis (cob), along with the genes for sulfur reduction (ttr, phs, and asr), constitute more than 1% of the Salmonella genome and are all absent from E. coli. In diverging from E. coli, Salmonella acquired some of these genes unilaterally and maintained others that are ancestral but have been lost from the E. coli lineage.

Roles of individual disulfide bonds in the stability and folding of an omega-conotoxin.

Although it contains only 25 amino acid residues, omega-conotoxin MVIIA folds into a well-defined three-dimensional structure that is stabilized by 3 disulfide bonds. To assess the contributions of the disulfides to folding and stability, three analogues, each with one pair of disulfide-bonded Cys residues replaced with Ala, were prepared and characterized. The analogues also contained a C-terminal Gly residue that is believed to be present when the peptide folds in vivo and has been shown previously to stabilize the native structure. Circular dichroism spectra and biological assays of the analogues indicated that removing any one of the disulfides greatly destabilized the native conformation. The two disulfides in each analogue were also reduced much more rapidly than in the native form with three disulfides. When the analogues were fully reduced and allowed to form disulfides in the presence of oxidized and reduced glutathione, the native disulfides were not formed in preference to non-native disulfides, further indicating that the forms with two-native disulfides are not significantly stabilized by noncovalent interactions. However, the measured equilibrium constants for disulfide formation indicate that forming any two of the three native disulfides leads to an effective concentration of approximately 25-50 M for the two remaining thiols. The two-disulfide analogues thus appear to represent a stage of folding in which the polypeptide is constrained to a distribution of relatively compact conformations that greatly favor formation of the third disulfide and the final folded structure.

Folding of omega-conotoxins. 1. Efficient disulfide-coupled folding of mature sequences in vitro.

Disulfide-coupled refolding reactions of five omega-conotoxins, Ca2+ channel antagonists derived from marine snails of the genus Conus, were examined. These peptides are 23-26 amino acid residues long, and the native conformation of each is stabilized by three disulfide bonds. Although the primary structures of the peptides show only limited sequence similarity, the patterns of disulfides and three-dimensional conformations are very similar. Refolding of the reduced proteins was promoted by the disulfide form of glutathione (GSSG) in the presence of reduced glutathione (GSH). All five of the peptides examined were able to refold to the native conformation, as judged by reversed-phase HPLC behavior, with efficiencies of 16% for omega-MVIIC, 28% for omega-MVIID, and 50% for omega-MVIIA, omega-GVIA, and omega-SVIA. The refolded form of omega-MVIIA was further shown to have biological activity indistinguishable from that of the native form, as well as the same rate of reductive unfolding in the presence of dithiothreitol. The overall folding rate and efficiency of omega-MVIIA was found to be quite sensitive to the thiol-disulfide redox potential, with optimum rates and yields obtained in the presence of GSSG and GSH at concentrations similar to those believed to be present in the endoplasmic reticulum. The folding efficiency of this peptide was greatly reduced by the addition of 8 M urea, indicating that formation of the correct disulfides is determined largely by noncovalent interactions, as opposed to steric constraints arising from the spacing between Cys residues. These results demonstrate that the mature forms of at least some omega-conotoxins contain sufficient information to direct correct folding and disulfide formation, in spite of their small size and limited sequence conservation.

Folding of omega-conotoxins. 2. Influence of precursor sequences and protein disulfide isomerase.

The peptide Ca2+ channel antagonists found in the venoms of Conus snails, omega-conotoxins, are synthesized as precursors that include a leader peptide, presumed to direct the polypeptide to the endoplasmic reticulum, and a propeptide of unknown function. In addition, the precursors are synthesized with a C-terminal Gly residue that is posttranslationally converted to a terminal amide group. In order to determine whether the precursor sequences contain information that helps direct folding of the mature sequences, the disulfide-coupled folding of mature omega-conotoxin MVIIA was compared with that of two putative precursor forms: pro-omega-MVIIA-Gly, which contains the propeptide and the C-terminal Gly residue, and omega-MVIIA-Gly, which differs from the mature form only at the C-terminus. The three forms folded with similar kinetics, but the folding efficiency of omega-MVIIA-Gly was greater than 80%, versus approximately 50% for both mature omega-MVIIA and the form containing the propeptide. The enzyme protein disulfide isomerase was found to catalyze disulfide formation and folding of all three forms similarly. The affinity of omega-MVIIA-Gly for receptors in chick brain synaptosomes was approximately 10-fold lower than that of the mature peptide, and the N-terminal propeptide of pro-omega-MVIIA-Gly was found to decrease binding further, by approximately 100-fold. These results suggest that the omega-conotoxins do not rely on the propeptide region of their precursors to facilitate folding. Rather, the mature sequence contains most of the information required to specify the native disulfide pairings and three-dimensional conformation. The C-terminal Gly may enhance the folding efficiency by forming interactions that stabilize the native conformation with respect to other disulfide-bonded forms.