DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens?

Establishment and evaluation of an overlap extension polymerase chain reaction technique for rapid and efficient detection of drug-resistance in Mycobacterium tuberculosis

BACKGROUND

Rapid and accurate detection of drug resistance in Mycobacterium tuberculosis is critical for effective control of tuberculosis (TB). Herein, we established a novel, low cost strategy having high accuracy and speed for the detection of M. tuberculosis drug resistance, using gene splicing by overlap extension PCR (SOE PCR).

METHODS

The SOE PCR assay and Sanger sequencing are designed and constructed to detect mutations of rpoB, embB, katG, and inhA promoter, which have been considered as the major contributors to rifampicin (RFP), isoniazid (INH), and ethambutol (EMB) resistance in M. tuberculosis. One hundred and eight M. tuberculosis isolates came from mycobacterial cultures of TB cases at Chongqing Public Health Medical Center in China from December 2018 to April 2019, of which 56 isolates were tested with the GeneXpert MTB/RIF assay. Performance evaluation of the SOE PCR technique was compared with traditional mycobacterial culture and drug susceptibility testing (DST) or GeneXpert MTB/RIF among these isolates. Kappa identity test was used to analyze the consistency of the different diagnostic methods.

RESULTS

We found that the mutations of S531L, S315T and M306V were most prevalent for RFP, INH and EMB resistance, respectively, in the 108 M. tuberculosis isolates. Compared with phenotypic DST, the sensitivity and specificity of the SOE PCR assay for resistance detection were 100.00% and 88.00% for RFP, 94.64% and 94.23% for INH, and 68.97% and 79.75% for EMB, respectively. Compared with the GeneXpert MTB/RIF, the SOE PCR method was completely consistent with results of the GeneXpert MTB/RIF, with a concordance of 100% for resistance to RFP.

CONCLUSIONS

In present study, a novel SOE PCR diagnostic method was successfully developed for the accurate detection of M. tuberculosis drug resistance. Our results using this method have a high consistency with that of traditional phenotypic DST or GeneXpert MTB/RIF, and SOE PCR testing in clinical isolates can also be conducted rapidly and simultaneously for detection of drug resistance to RFP, EMB, and INH.

Cross Sectional Study and Risk Factors Analysis of Francisella tularensis in Soil Samples in Punjab Province of Pakistan

Tularemia is an endemic zoonotic disease in many parts of the world including Asia. A cross-sectional study was conducted to determine genome-based prevalence of Francisella tularensis (Ft) in soil, assess an association between its occurrence in soil and likely predictors i.e., macro and micro-nutrients and several categorical variables, and determine seroconversion in small and large ruminants. The study included a total of 2,280 soil samples representing 456 villages in eight districts of the Punjab Province of Pakistan followed by an analysis of serum antibodies in 707 ruminants. The genome of Ft was detected in 3.25% (n = 74, 95% CI: 2.60-4.06) of soil samples. Soluble salts (OR: 1.276, 95% CI: 1.043-1.562, p = 0.015), Ni (OR: 2.910, 95%CI: 0.795-10.644, p = 0.106), Mn (OR:0.733, 95% CI:0.565-0.951, p = 0.019), Zn (OR: 4.922, 95% CI:0.929-26.064, p = 0.061) and nutrients clustered together as PC-1 (OR: 4.76, 95% CI: 2.37-9.54, p = 0.000) and PC-3 (OR: 0.357, 95% CI: 0.640, p = 0.001) were found to have a positive association for the presence of Ft in soil. The odds of occurrence of Ft DNA in soil were higher at locations close to a water source, including canals, streams or drains, [χ2 = 6.7, OR = 1.19, 95% CI:1.05-3.09, p = 0.004] as well as places where animals were present [χ2 = 4.09, OR = 2.06, 95% CI: 1.05-4.05, p = 0.02]. The seroconversion was detected in 6.22% (n = 44, 95% CI: 4.67-8.25) of domestic animals. An occurrence of Ft over a wide geographical region indicates its expansion to enzootic range, and demonstrates the need for further investigation among potential disease reservoirs and at-risk populations, such as farmers and veterinarians.

Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools

The magnitude of interest in the epidemiology of transmissible human diseases is reflected in the vast number of tools and methods developed recently with the expressed purpose to characterize and track evolutionary changes that occur in agents of these diseases over time. Within the past decade a new suite of such tools has become available with the emergence of the so-called "omics" technologies. Among these, two are exponents of the ongoing genomic revolution. Firstly, high-density nucleic acid probe arrays have been proposed and developed using various chemical and physical approaches. Via hybridization-mediated detection of entire genes or genetic polymorphisms in such genes and intergenic regions these so called "DNA chips" have been successfully applied for distinguishing very closely related microbial species and strains. Second and even more phenomenal, next generation sequencing (NGS) has facilitated the assessment of the complete nucleotide sequence of entire microbial genomes. This technology currently provides the most detailed level of bacterial genotyping and hence allows for the resolution of microbial spread and short-term evolution in minute detail. We will here review the very recent history of these two technologies, sketch their usefulness in the elucidation of the spread and epidemiology of mostly hospital-acquired infections and discuss future developments.

Molecular characterization of the human microbiome from a reproductive perspective

The process of reproduction inherently poses unique microbial challenges because it requires the transfer of gametes from one individual to the other, meanwhile preserving the integrity of the gametes and individuals from harmful microbes during the process. Advances in molecular biology techniques have expanded our understanding of the natural organisms living on and in our bodies, including those inhabiting the reproductive tract. Over the past two decades accumulating evidence has shown that the human microbiome is tightly related to health and disease states involving the different body systems, including the reproductive system. Here we introduce the science involved in the study of the human microbiome. We examine common methods currently used to characterize the human microbiome as an inseparable part of the reproductive system. Finally, we consider a few limitations, clinical implications, and the critical need for additional research in the field of human fertility.

Molecular approaches to recognize relevant and emerging infectious diseases in animals

Since the introduction of the first molecular tests, there has been a continuous effort to develop new and improved assays for rapid and efficient detection of infectious agents. This has been motivated by a need for improved sensitivity as well as results that can be easily communicated. The experiences and knowledge gained at the World Organisation for Animal Health (OIE) Collaborating Centre for Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Uppsala, Sweden, will here be used to provide an overview of the different molecular approaches that can be used to diagnose and identify relevant and emerging infectious diseases in animals.

Bacterial strain typing

Over the course of the past several decades, rapid advancements in molecular technologies have revolutionized the practice of public health microbiology, and have fundamentally changed the nature, accuracy, and timeliness of laboratory data for outbreak investigation and response. Whole-genome sequencing, in particular, is becoming an increasingly feasible and cost-effective approach for near real-time high-resolution strain typing, genomic characterization, and comparative analyses. This review discusses the current state of the art in bacterial strain typing for outbreak investigation and infectious disease surveillance, and the impact of emerging genomic technologies on the field of public health microbiology.

A lateral flow assay for identification of Escherichia coli by ribosomal RNA hybridisation

Existing technologies for analysis of microbiological contaminants in food or clinical samples are often expensive and require laboratory settings and trained personnel. Here we present a lateral flow assay employing gold nanoparticle-oligodeoxynucleotide conjugates and four-component sandwich hybridisation for direct detection of specific sequences in bacterial 16S ribosomal RNA. Combined with rapid "one step" lysis the developed procedure allows detection of 5 × 10(4) colony forming units per mL Escherichia coli within less than 25 minutes. Several Escherichia coli strains were detected successfully, whereas non-related as well as closely related bacterial species produced no signal. The developed nucleic acid lateral flow assay is inexpensive, rapid to perform and requires no nucleic acid amplification step.

A system to simultaneously detect tick-borne pathogens based on the variability of the 16S ribosomal genes

BACKGROUND

DNA microarrays can be used to quickly and sensitively identify several different pathogens in one step. Our previously developed DNA microarray, based on the detection of variable regions in the 16S rDNA gene (rrs), which are specific for each selected bacterial genus, allowed the concurrent detection of Borrelia spp., Anaplasma spp., Francisella spp., Rickettsia spp. and Coxiella spp.

METHODS

In this study, we developed a comprehensive detection system consisting of a second generation DNA microarray and quantitative PCRs. New oligonucleotide capture probes specific for Borrelia burgdorferi s.l. genospecies and Candidatus Neoehrlichia mikurensis were included. This new DNA microarray system required substantial changes in solution composition, hybridization conditions and post-hybridization washes.

RESULTS

This second generation chip displayed high specificity and sensitivity. The specificity of the capture probes was tested by hybridizing the DNA microarrays with Cy5-labeled, PCR-generated amplicons encoding the rrs genes of both target and non-target bacteria. The detection limit was determined to be 10(3) genome copies, which corresponds to 1-2 pg of DNA. A given sample was evaluated as positive if its mean fluorescence was at least 10% of the mean fluorescence of a positive control. Those samples with fluorescence close to the threshold were further analyzed using quantitative PCRs, developed to identify Francisella spp., Rickettsia spp. and Coxiella spp. Like the DNA microarray, the qPCRs were based on the genus specific variable regions of the rrs gene. No unspecific cross-reactions were detected. The detection limit for Francisella spp. was determined to be only 1 genome copy, for Coxiella spp. 10 copies, and for Rickettsia spp., 100 copies.

CONCLUSIONS

Our detection system offers a rapid method for the comprehensive identification of tick-borne bacteria, which is applicable to clinical samples. It can also be used to identify both pathogenic and endosymbiontic bacteria in ticks for eco-epidemiological studies, tick laboratory colony testing, and many other applications.

Comparative studies on species identification of Noctuoidea moths in two nature reserve conservation zones (Beijing, China) using DNA barcodes and thin-film biosensor chips

Rapid and accurate identification of species is required for the biological control of pest Noctuoidea moths. DNA barcodes and thin-film biosensor chips are two molecular approaches that have gained wide attention. Here, we compare these two methods for the identification of a limited number of Noctuoidea moth species. Based on the commonly used mitochondrial gene cytochrome c oxidase I (the standard DNA barcode for animal species), 14 probes were designed and synthesized for 14 species shared by two national nature reserves in Beijing and Hebei, China. Probes ranged in length from 18 to 27 bp and were designed as mismatch probes to guarantee that there were at least three base differences between the probe and nontarget sequences. The results on the chip could be detected by the naked eye without needing special equipment. No cross-hybridizations were detected although we tested all probes on the 14 target and 24 nontarget Noctuoidea species. The neighbour-joining tree of the 38 species based on COI sequences gave 38 highly supported independent groups. Both DNA barcoding and thin-film biosensor chips, based on the COI gene, are able to accurately identify and discriminate the 14 targeted moth species in this study. Because of its speed, high accuracy and low cost, the thin-film biosensor chip is a very practical means of species identification. Now, a more comprehensive chip will be developed for the identification of additional Noctuoidea moths for pest control and ecological protection.

Microarray for Identification of the Chiropteran Host Species of Rabies Virus in Canada

Species identification through genetic barcoding can augment traditional taxonomic methods, which rely on morphological features of the specimen. Such approaches are especially valuable when specimens are in poor condition or comprise very limited material, a situation that often applies to chiropteran (bat) specimens submitted to the Canadian Food Inspection Agency for rabies diagnosis. Coupled with phenotypic plasticity of many species and inconclusive taxonomic keys, species identification using only morphological traits can be challenging. In this study, a microarray assay with associated PCR of the mitochondrial cytochrome c oxidase subunit I (COI) gene was developed for differentiation of 14 bat species submitted to the Canadian Food Inspection Agency from 1985–2012 for rabies diagnosis. The assay was validated with a reference collection of DNA from 153 field samples, all of which had been barcoded previously. The COI gene from 152 samples which included multiple specimens of each target species were successfully amplified by PCR and accurately identified by the microarray. One sample that was severely decomposed failed to amplify with PCR primers developed in this study, but amplified weakly after switching to alternate primers and was accurately typed by the microarray. Thus, the chiropteran microarray was able to accurately differentiate between the 14 species of Canadian bats targeted. This PCR and microarray assay would allow unequivocal identification to species of most, if not all, bat specimens submitted for rabies diagnosis in Canada.

Biological and physicochemical wastewater treatment processes reduce the prevalence of virulent Escherichia coli

Effluents discharged from wastewater treatment plants are possible sources of pathogenic bacteria, including Escherichia coli, in the freshwater environment, and determining the possible selection of pathogens is important. This study evaluated the impact of activated sludge and physicochemical wastewater treatment processes on the prevalence of potentially virulent E. coli. A total of 719 E. coli isolates collected from four municipal plants in Québec before and after treatment were characterized by using a customized DNA microarray to determine the impact of treatment processes on the frequency of specific pathotypes and virulence genes. The percentages of potentially pathogenic E. coli isolates in the plant influents varied between 26 and 51%, and in the effluents, the percentages were 14 to 31%, for a reduction observed at all plants ranging between 14 and 45%. Pathotypes associated with extraintestinal pathogenic E. coli (ExPEC) were the most abundant at three of the four plants and represented 24% of all isolates, while intestinal pathogenic E. coli pathotypes (IPEC) represented 10% of the isolates. At the plant where ExPEC isolates were not the most abundant, a large number of isolates were classified as both ExPEC and IPEC; overall, 6% of the isolates were classified in both groups, with the majority being from the same plant. The reduction of the proportion of pathogenic E. coli could not be explained by the preferential loss of one virulence gene or one type of virulence factor; however, the quinolone resistance gene (qnrS) appears to enhance the loss of virulence genes, suggesting a mechanism involving the loss of pathogenicity islands.

Methods for genotyping verotoxin-producing Escherichia coli

Verotoxin-producing Escherichia coli (VTEC) is annually incriminated in more than 100,000 cases of enteric foodborne human disease and in losses amounting to $US 2.5 billion every year. A number of genotyping methods have been developed to track VTEC infections and determine diversity and evolutionary relationships among these microorganisms. These methods have facilitated monitoring and surveillance of foodborne VTEC outbreaks and early identification of outbreaks or clusters of outbreaks. Pulsed-field gel electrophoresis (PFGE) has been used extensively to track and differentiate VTEC because of its high discriminatory power, reproducibility and ease of standardization. Multiple-locus variable-number tandem-repeats analysis (MLVA) and microarrays are the latest genotyping methods that have been applied to discriminate VTEC. MLVA, a simpler and less expensive method, is proving to have a discriminatory power comparable to that of PFGE. Microarrays are successfully being applied to differentiate VTEC and make inferences on genome diversification. Novel methods that are being evaluated for subtyping VTEC include the detection of single nucleotide polymorphisms and optical mapping. This review discusses the principles, applications, advantages and disadvantages of genotyping methods that have been used to differentiate VTEC strains. These methods have been mainly used to differentiate strains of O157:H7 VTEC and to a lesser extent non-O157 VTEC.

Advances in subtyping methods of foodborne disease pathogens

Current subtyping methods for the detection of foodborne disease outbreaks have limitations that reduce their use by public health laboratories. Recent advances in subtyping of foodborne disease pathogens utilize techniques that identify nucleic acid polymorphisms. Recent methods of nucleic acid characterization such as microarrays and mass spectrometry (MS) may provide improvements such as increasing speed and data portability while decreasing labor compared to current methods. This article discusses multiple-locus variable-number tandem-repeat analysis, single-nucleotide polymorphisms, nucleic acid sequencing, whole genome sequencing, variable absent or present loci, microarrays and MS as potential subtyping methods to enhance our ability to detect foodborne disease outbreaks.

Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti

Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among 10 natural strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti, using pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45-7.01 Mbp, with the greatest variation arising from the pSymA replicon, followed by pSymB; no size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2% of open reading frames (ORFs) on pSymA were variably absent/present, followed by 12.7% on pSymB and 3.7% on the chromosome. However, the ORFs that were variably duplicated were more evenly distributed among the three replicons: 11.0%, 16.5%, and 15.3% of ORFs on pSymA, pSymB, and the chromosome, respectively. Among the 10 strains, the percentage of ORFs that were absent ranged from 1.51% to 6.35%, and the percentage of ORFs that were duplicated ranged from 0.27% to 8.56%. Our analyses showed that host plants, geographic origins, multilocus enzyme electrophoretic types, and replicon sizes had little influence on the distribution patterns of absent or duplicated ORFs. The proportions of ORFs that were either variably absent/present or variably duplicated differed greatly among the functional categories, for each of the three replicons as well as for the whole genome. Interestingly, we observed positive correlations among the three replicons in the number of absent ORFs as well as the number of duplicated ORFs, consistent with coordinated gene gains and losses in this important bacterium in nature.

Laboratory-Guided Detection of Disease Outbreaks: Three Generations of Surveillance Systems

Context.—Traditional biothreat surveillance systems are vulnerable to incomplete and delayed reporting of public health threats.

Objective.—To review current and emerging approaches to detection and monitoring of biothreats enabled by laboratory methods of diagnosis and to identify trends in the biosurveillance research.

Data Sources.—PubMed (1995 to December 2007) was searched with the combined search terms “surveillance” and “infectious diseases.” Additional articles were identified by hand searching the bibliographies of selected papers. Additional search terms were “public health,” “disease monitoring,” “cluster,” “outbreak,” “laboratory notification,” “molecular,” “detection,” “evaluation,” “genomics,” “communicable diseases,” “geographic information systems,” “bioterrorism,” “genotyping,” and “informatics.” Publication language was restricted to English. The bibliographies of key references were later hand searched to identify articles missing in the database search. Three approaches to infectious disease surveillance that involve clinical laboratories are contrasted: (1) laboratory-initiated infectious disease notifications, (2) syndromic surveillance based on health indicators, and (3) genotyping based surveillance of biothreats. Advances in molecular diagnostics enable rapid genotyping of biothreats and investigations of genes that were not previously identifiable by traditional methods. There is a need for coordination between syndromic and laboratory-based surveillance. Insufficient and delayed decision support and inadequate integration of surveillance signals into action plans remain the 2 main barriers to efficient public health monitoring and response. Decision support for public health users of biosurveillance alerts is often lacking.

Conclusions.—The merger of the 3 scientific fields of surveillance, genomics, and informatics offers an opportunity for the development of effective and rapid biosurveillance methods and tools.

Interstitial inflammatory lesions of the pulmonary allograft: a retrospective analysis of 2697 transbronchial biopsies

BACKGROUND

Parenchymal and bronchial inflammatory and fibrotic lesions other than acute cellular rejection (ACR) and lymphocytic bronchiolitis are prevalent; however, the context in which they appear is unknown, and often no specific treatment is instigated.

OBJECTIVES

To describe the prevalence, incidence and possible associations between commonly identified inflammatory and fibrotic lesions in the pulmonary allograft.

METHODS

Retrospective chart review of all transbronchial biopsies performed within the first 2 years of 299 lung-transplanted patients in the period 1996 to 2006.

RESULTS

A total of 2697 biopsies were evaluated corresponding to a mean of 6+/-2 (median 8) completed schedules per patient. Diffuse alveolar damage (DAD) was the second most common histological finding within the first 2 weeks after transplantation. The peak prevalence of bronchiolitis obliterans organizing pneumonia (BOOP) and interstitial pneumonitis occurred at 4 to 6 weeks, and 6 to 12 weeks, respectively. There was a steady increase in the cumulative proportion of patients with fibrosis and bronchiolitis obliterans, at each successive scheduled surveillance time point beyond 3 months posttransplantation. The strongest histological correlations were between ACR and lymphocytic bronchiolitis (OR 5.1, P<0.0001) or interstitial fibrosis (OR 3.2, P<0.0001). Patients with interstitial pneumonitis and pulmonary hemosiderosis were also more likely to demonstrate the finding of interstitial fibrosis (OR 3.0 and 3.7, P<0.0001, respectively). Acute cellular rejection was not associated with DAD, and patients with lymphocytic bronchiolitis were not more likely to demonstrate features of organizing pneumonia (DAD or BOOP).

CONCLUSIONS

Histologic findings of ACR, lymphocytic bronchiolitis, BOOP, and interstitial pneumonitis were directly associated with the development of interstitial fibrosis and bronchiolitis obliterans.

Recent developments and future prospects in subtyping of foodborne bacterial pathogens

Infections caused by foodborne bacterial pathogens continue to be a major public health issue around the world. During the past decade, pulsed-field gel electrophoresis (PFGE) has become the gold standard for molecular subtyping and source tracking of most foodborne bacteria. Owing to problems inherent in PFGE technology, new methods have been developed focusing on DNA sequence-based subtyping. This review discusses the feasibility of using multilocus sequence typing, multiple-locus variable-number tandem repeat analysis, single nucleotide polymorphisms, microarrays, whole genome sequencing and mass spectrometry for subtyping foodborne bacterial pathogens.

Advancements in molecular epidemiology of implant infections and future perspectives

Implant infection remains the major and often irreducible complication in clinical use of biomaterials, demanding new therapeutic and preventive strategies. Etio-pathogenesis of biomaterials-related infections is being more and more studied, and various virulence bacterial factors have progressively been identified, but little is still known about the weight of the distinct molecules in the context of specific peri-implant infection sites. Molecular epidemiology has become recently integrated into the research on implant infections. What distinguishes molecular epidemiology from the simple molecular biology is that the use of molecular techniques is applied to the study of the distribution and prevalence of virulence and resistance genes in collections of bacterial clinical isolates from implant infections. Here, the authors comment on the range of molecular techniques available, reviewing the various applications of molecular epidemiology to the study of implant infections and providing some experimental examples related to the field of orthopaedic implant infections. They highlight the new opportunities arising from molecular epidemiology of designing measures useful to prevent and treat implant infections. The knowledge of the relative weight of virulence factors and of their regulatory mechanisms at molecular level can open the way to new strategies also including gene therapies aimed at silencing or knocking out crucial genes responsible for the aggressive tools (adhesins, biofilm production, antibiotic resistance) of the aetiological agents of implant-related infections.

Molecular diagnostics for the detection and characterization of microbial pathogens

New and advanced methods of molecular diagnostics are changing the way we practice clinical microbiology, which affects the practice of medicine. Signal amplification and real-time nucleic acid amplification technologies offer a sensitive and specific result with a more rapid turnaround time than has ever before been possible. Numerous methods of postamplification analysis afford the simultaneous detection and differentiation of numerous microbial pathogens, their mechanisms of resistance, and the construction of disease-specific assays. The technical feasibility of these assays has already been demonstrated. How these new, often more expensive tests will be incorporated into routine practice and the impact they will have on patient care remain to be determined. One of the most attractive uses for such techniques is to achieve a more rapid characterization of the infectious agent so that a narrower-spectrum antimicrobial agent may be used, which should have an impact on resistance patterns.

Identification of 8 Foodborne Pathogens by Multicolor Combinational Probe Coding Technology in a Single Real-Time PCR

Background: Real-time PCR assays have been widely used for detecting foodborne pathogens but have been much less frequently applied in species identification, mainly because of the low number of species they can distinguish in 1 reaction. The present study used a new probe coding/labeling strategy, termed multicolor combinational probe coding (MCPC), to increase the number of targets that can be distinguished in a single real-time PCR for rapid and reliable species identification.

Methods: With MCPC, 8 pairs of species-specific tagged primers, 1 pair of universal primers, and 8 unilabeled or mix-labeled molecular beacon probes were included in a single reaction tube. Real-time PCR was performed, and the identity of each of the 8 pathogens was determined by amplification profile comparison. The method was validated via blind assessment of 118 bacterial strains, including clinical isolates and isolates from food products.

Results: The blind test with 118 samples gave no false-positive or -negative results for the target genes. The template DNA suitable for MCPC analysis was simply prepared by heating lysis, and the total PCR analysis was finished within 2.5 h, excluding template preparation.

Conclusions: MCPC is suitable for rapid and reliable identification of foodborne pathogens at the species level.

From proteomics to systems biology of bacterial pathogens: approaches, tools, and applications

The hallmark of a systems biology approach is the integration of computational tools with experimental data encompassing multiple classes of biomolecules across different functional levels. Equally important as the availability of reasonably comprehensive information at the gene, protein, and metabolite levels is the development of adequate analysis and visualization tools to reduce the inherent complexity to interpretable dimensions. In this paper, we describe the integration of a 2-D gel-based proteome map of Staphylococcus aureus Mu50 with genomic and transcriptomic information through a customized data integration and user interface built on the Ensembl genome browser. We illustrate its application and potential through the analysis of a defined system perturbation caused by a mutation in the formyltransferase gene. We envision that this software package, which we called Insieme, can support the development of novel antibiotics by allowing a systems-based view of the bacterial response pathways.

A rapid multiplexed chemiluminescent immunoassay for the detection of Escherichia coli O157:H7, Yersinia enterocolitica, Salmonella typhimurium, and Listeria monocytogenes pathogen bacteria

A simple and rapid multiplexed sandwich chemiluminescent enzyme immunoassay has been developed for the simultaneous detection of Escherichia coli O157:H7, Yersinia enterocolitica, Salmonella typhimurium, and Listeria monocytogenes. To achieve the multiplexed detection of the four pathogens, a new polystyrene 96 well microtiter plate format has been designed, in which each main well contains four subwells in the bottom. The monoclonal antibodies specific for each bacteria were separately immobilized in each subwell. When the samples were added to the main wells, the bacteria able to specifically bind to the corresponding monoclonal antibody were captured in one of the four subwells. Subsequently, a mixture of peroxidase-labeled polyclonal antibodies against the four bacteria was added and the peroxidase activity of the bound polyclonal labeled antibodies in each well was measured by an enhanced luminol-based chemiluminescent cocktail using a low-light charge-coupled imaging device. The assay was simple and fast, and the limit of quantification was in the order of 104-105 CFU/mL for all bacterial species. The accuracy of the method, evaluated by comparison of the results with a conventional culturing methodology, was satisfactory, with recovery values ranging from 90 to 120%. This method can be used as a screening test to evaluate the presence of these pathogen bacteria in different foodstuffs.

Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring

BACKGROUND

The rapid and accurate identification of species is a critical component of large-scale biodiversity monitoring programs. DNA arrays (micro and macro) and DNA barcodes are two molecular approaches that have recently garnered much attention. Here, we compare these two platforms for identification of an important group, the mammals.

RESULTS

Our analyses, based on the two commonly used mitochondrial genes cytochrome c oxidase I (the standard DNA barcode for animal species) and cytochrome b (a common species-level marker), suggest that both arrays and barcodes are capable of discriminating mammalian species with high accuracy. We used three different datasets of mammalian species, comprising different sampling strategies. For DNA arrays we designed three probes for each species to address intraspecific variation. As for DNA barcoding, our analyses show that both cytochrome c oxidase I and cytochrome b genes, and even smaller fragments of them (mini-barcodes) can successfully discriminate species in a wide variety of specimens.

CONCLUSION

This study showed that DNA arrays and DNA barcodes are valuable molecular methods for biodiversity monitoring programs. Both approaches were capable of discriminating among mammalian species in our test assemblages. However, because designing DNA arrays require advance knowledge of target sequences, the use of this approach could be limited in large scale monitoring programs where unknown haplotypes might be encountered. DNA barcodes, by contrast, are sequencing-based and therefore could provide more flexibility in large-scale studies.

Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing

Traditional microbial typing technologies for the characterization of pathogenic microorganisms and monitoring of their global spread are often difficult to standardize and poorly portable, and they lack sufficient ease of use, throughput, and automation. To overcome these problems, we introduce the use of comparative sequencing by MALDI-TOF MS for automated high-throughput microbial DNA sequence analysis. Data derived from the public multilocus sequence typing (MLST) database (http://pubmlst.org/neisseria) established a reference set of expected peak patterns. A model pathogen, Neisseria meningitidis, was used to validate the technology and explore its applicability as an alternative to dideoxy sequencing. One hundred N. meningitidis samples were typed by comparing MALDI-TOF MS fingerprints of the standard MLST loci to reference sequences available in the public MLST database. Identification results can be obtained in 2 working days. Results were in concordance with classical dideoxy sequencing with 98% correct automatic identification. Sequence types (STs) of 89 samples were represented in the database, seven samples revealed new STs, including three new alleles, and four samples contained mixed populations of multiple STs. The approach shows interlaboratory reproducibility and allows for the exchange of mass spectrometric fingerprints to study the geographic spread of epidemic N. meningitidis strains or other microbes of clinical importance.

Use of DNA microarray technology and gene expression profiles to investigate the pathogenesis, cell biology, antifungal susceptibility and diagnosis of Candida albicans

The use of DNA microarrays is becoming the method of choice for assaying gene expression, particularly as costs and complexity are being reduced as the technology becomes more widespread and better standardized. A DNA array is nothing but a collection of probes fixed on a solid support. The probes can be PCR products of ORFs or short intragenic oligonucleotides deposited or synthesized in situ by photolithographic methods. To date, sequencing projects for fungal genomes have yielded 10 complete genomes and 21 whole shotgun sequences, including Candida albicans strain SC5314. Sequencing of the C. albicans genome has led to the construction of whole-genome DNA microarrays for in vitro transcription profiling by several universities and companies. The use of microarray or DNA chip techniques for Candida research has started recently but the number of studies using this technology is increasing rapidly, in order to address important remaining questions about pathogenesis, cell biology, antifungal susceptibility, and diagnosis.