Rapid bacterial genome sequencing: methods and applications in clinical microbiology.

The recent advances in sequencing technologies have given all microbiology laboratories access to whole genome sequencing. Providing that tools for the automated analysis of sequence data and databases for associated meta-data are developed, whole genome sequencing will become a routine tool for large clinical microbiology laboratories. Indeed, the continuing reduction in sequencing costs and the shortening of the 'time to result' makes it an attractive strategy in both research and diagnostics. Here, we review how high-throughput sequencing is revolutionizing clinical microbiology and the promise that it still holds. We discuss major applications, which include: (i) identification of target DNA sequences and antigens to rapidly develop diagnostic tools; (ii) precise strain identification for epidemiological typing and pathogen monitoring during outbreaks; and (iii) investigation of strain properties, such as the presence of antibiotic resistance or virulence factors. In addition, recent developments in comparative metagenomics and single-cell sequencing offer the prospect of a better understanding of complex microbial communities at the global and individual levels, providing a new perspective for understanding host-pathogen interactions. Being a high-resolution tool, high-throughput sequencing will increasingly influence diagnostics, epidemiology, risk management, and patient care.

Next generation sequencing of pooled samples reveals new SNRNP200 mutations associated with retinitis pigmentosa.

The gene SNRNP200 is composed of 45 exons and encodes a protein essential for pre-mRNA splicing, the 200 kDa helicase hBrr2. Two mutations in SNRNP200 have recently been associated with autosomal dominant retinitis pigmentosa (adRP), a retinal degenerative disease, in two families from China. In this work we analyzed the entire 35-Kb SNRNP200 genomic region in a cohort of 96 unrelated North American patients with adRP. To complete this large-scale sequencing project, we performed ultra high-throughput sequencing of pooled, untagged PCR products. We then validated the detected DNA changes by Sanger sequencing of individual samples from this cohort and from an additional one of 95 patients. One of the two previously known mutations (p.S1087L) was identified in 3 patients, while 4 new missense changes (p.R681C, p.R681H, p.V683L, p.Y689C) affecting highly conserved codons were identified in 6 unrelated individuals, indicating that the prevalence of SNRNP200-associated adRP is relatively high. We also took advantage of this research to evaluate the pool-and-sequence method, especially with respect to the generation of false positive and negative results. We conclude that, although this strategy can be adopted for rapid discovery of new disease-associated variants, it still requires extensive validation to be used in routine DNA screenings. © 2011 Wiley-Liss, Inc.

Sequencing and identification of expressed Schistosoma mansoni genes by random selection of cDNA clones from a directional library

We have initiated a gene discovery program in Schistosoma mansoni based on the technique of Expressed Sequence Tags (ESTs), i.e. partial sequences of cDNAs obtained from single passes in automatic DNA sequencers. ESTs can be used to identify genese onf the basis of their homology whith sequences from other species deposited in DNA or protein databases. Trasncripts with sequences without matches in teh databases may represent novel parasite-specific genes. This approach has shown to be very efficient and in less than two years a broad range of novel genes has already been ascertained, more than doubling the number of known S. mansoni genes.

La depuradora de Begues: reactor biològic o aiguamolls construïts?. Estudi comparatiu dels vectors: paràmetres de l'H2O, fangs produïts, costos capitals i d'explotació, personal

L’objectiu del present estudi és comparar els vectors de paràmetres de l’aigua, producció de fangs, costos i personal entre 2 tipus d’instal·lacions EDAR al municipi de Begues; una ja existent amb tractament secundari i terciari mitjançant un reactor biològic i una potencial amb tractament secundari i terciari mitjançant aiguamolls construïts. La finalitat del projecte és determinar, gràcies a l’estudi dels principals vectors ambientals de la infraestructura i a altres estudiats per na Susana Forero Sánchez, quina de les 2 tipologies d’instal·lació s’ajusta més al territori i a les necessitats de tractament de les aigües del mateix. Els resultats de la investigació indiquen que tant els costos d’explotació com la producció de fangs i el personal donen avantatge als aiguamolls construïts, però els costos capitals i el tractament de nutrients són favorables per a la depuradora actual. Amb el projecte de Susana Forero Sánchez, les conclusions que es poden establir en referència a la decisió d’instal·lar una depuradora o una altra segons els vectors estudiats indiquen que l’EDAR sense aiguamolls té més probabilitat de ser escollida com la més adient per les necessitats del territori d’estudi.

La depuradora de Begues: reactor biològic o aiguamolls construïts?. Estudi comparatiu dels vectors: superfície, consum energètic, integració en el medi

L’objectiu del present estudi és comparar els vectors de superfície, consum energètic i integració en el medi entre 2 tipus d’instal·lacions EDAR al municipi de Begues; una ja existent amb tractament secundari i terciari mitjançant un reactor biològic i una potencial amb tractament secundari i terciari mitjançant aiguamolls construïts. La finalitat del projecte és determinar, gràcies a l’estudi dels principals vectors ambientals de la infraestructura i a altres estudiats per en Jordi Gómez Castillo, quina de les 2 tipologies d’instal·lació s’ajusta més al territori i a les necessitats de tractament de les aigües del mateix. Els resultats de la investigació indiquen que els aiguamolls construïts fan un ús més productiu del sòl però ocupen l’espai de reserva disponible amb el sistema de reactor biològic. A més, consumeixen 50kWh/dia menys que l’altra instal·lació, fet que implica un 7% menys d’emissions de CO2 anuals. Finalment, tenen una millor integració en el medi i proporcionen uns beneficis auxiliars afegits. Amb el projecte d’en Jordi Gómez Castillo, les conclusions que es poden establir en referència a la decisió d’instal·lar una depuradora o una altra indiquen que l’EDAR sense aiguamolls té més probabilitat de ser escollida com la més adient per les necessitats del territori d’estudi.

Modelització i control d'un reactor de producció d'hidrogen per a l'alimentació de piles de combustible

Les piles de combustible permeten la transformació eficient de l’energia química de certs combustibles a energia elèctrica a través d’un procés electroquímic. De les diferents tecnologies de piles de combustible, les piles de combustible de tipus PEM són les més competitives i tenen una gran varietat d’aplicacions. No obstant, han de ser alimentades únicament per hidrogen. Per altra banda, l’etanol, un combustible interessant en el marc dels combustibles renovables, és una possible font d’hidrogen. Aquest treball estudia la reformació d’etanol per a l’obtenció d’hidrogen per a alimentar piles de combustible PEM. Només existeixen algunes publicacions que tractin l’obtenció d’hidrogen a partir d’etanol, i aquestes no inclouen l’estudi dinàmic del sistema. Els objectius del treball són el modelat i l’estudi dinàmic de reformadors d’etanol de baixa temperatura. Concretament, proposa un model dinàmic d’un reformador catalític d’etanol amb vapor basat en un catalitzador de cobalt. Aquesta reformació permet obtenir valors alts d’eficiència i valors òptims de monòxid de carboni que evitaran l’enverinament d’una la pila de combustible de tipus PEM. El model, no lineal, es basa en la cinètica obtinguda de diferents assaigs de laboratori. El reformador modelat opera en tres etapes: deshidrogenació d’etanol a acetaldehid i hidrogen, reformat amb vapor d’acetaldehid, i la reacció WGS (Water Gas Shift). El treball també estudia la sensibilitat i controlabilitat del sistema, caracteritzant així el sistema que caldrà controlar. L’anàlisi de controlabilitat es realitza sobre la resposta de dinàmica ràpida obtinguda del balanç de massa del reformador. El model no lineal és linealitzat amb la finalitat d’aplicar eines d’anàlisi com RGA, CN i MRI. El treball ofereix la informació necessària per a avaluar la possible implementació en un laboratori de piles de combustibles PEM alimentades per hidrogen provinent d’un reformador d’etanol.

Development and testing of novel chloroplast microsatellite markers for Lolium perenne and other grasses (Poaceae) from de novo sequencing and in silico sequences

Twelve primers to amplify microsatellite markers from the chloroplast genome of Lolium perenne were designed and optimized using de novo sequencing and in silico sequences. With one exception, each locus was polymorphic with a range from two to nine alleles in L. perenne. The newly developed primer pairs cross-amplified in different species of Lolium and in 50 other grass species representing nine grass subfamilies.

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.

In Bacillus subtilis W23, the duet sigmaXsigmaM, two sigma factors of the extracytoplasmic function subfamily, are required for septum and wall synthesis under batch culture conditions.

The synthesis of poly(RboP), the main Bacillus subtilis W23 teichoic acid, is encoded by tarDF-tarABIJKL operons, the latter being controlled by two promoters designated PtarA-int and PtarA-ext. Analysis by lacZ fusions reveals that PtarA-int activity exhibits sharp increases at the beginning and end of the transition between exponential and stationary growth phase. As confirmed by mRNA quantification, these increases are mediated by ECF sigma factors sigmaX and sigmaM respectively. In liquid media, strain W23 sigX sigM double mutants experience serious difficulties in the transition and stationary growth phases. Inactivation of sigmaX- and sigmaM-controlled regulons, which precludes transcription from PtarA-int, leads to (i) delays in chromosome segregation and septation and (ii) a transient loss of up to 30% of the culture OD or lysis. However, specific inactivation of PtarA-int, leading mainly to a shortage of poly(RboP), does not affect growth while, nevertheless, interfering with normal septation, as revealed by electron microscopy. The different sigM transcription in strains W23 and 168 is discussed. In W23, expression of tarA and sigM, which is shown to control divIC, is inversely correlated with growth rate, suggesting that the sigM regulon is involved in the control of cell division.

Sequencing of simple sequence repeat anchored polymerase chain reaction amplification products of Biomphalaria glabrata

Simple sequence repeat anchored polymerase chain reaction amplification (SSR-PCR) is a genetic typing technique based on primers anchored at the 5' or 3' ends of microsatellites, at high primer annealing temperatures. This technique has already been used in studies of genetic variability of several organisms, using different primer designs. In order to conduct a detailed study of the SSR-PCR genomic targets, we cloned and sequenced 20 unique amplification products of two commonly used primers, CAA(CT)6 and (CA)8RY, using Biomphalaria glabrata genomic DNA as template. The sequences obtained were novel B. glabrata genomic sequences. It was observed that 15 clones contained microsatellites between priming sites. Out of 40 clones, seven contained complex sequence repetitions. One of the repeats that appeared in six of the amplified fragments generated a single band in Southern analysis, indicating that the sequence was not widespread in the genome. Most of the annealing sites for the CAA(CT)6 primer contained only the six repeats found within the primer sequence. In conclusion, SSR-PCR is a useful genotyping technique. However, the premise of the SSR-PCR technique, verified with the CAA(CT)6 primer, could not be supported since the amplification products did not result necessarily from microsatellite loci amplification.