Corynebacterium diphtheriae spoligotyping based on combined use of two CRISPR loci

CRISPR genotyping methods: Tracing the evolution from spoligotyping to machine learning

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems provide prokaryotes with adaptive immunity defenses against foreign genetic invaders. The identification of CRISPR-Cas function is among the most impactful discoveries of recent decades that have shaped the development of genome editing in various organisms paving the way for a plethora of promising applications in biotechnology and health. Even before the discovery of CRISPR-Cas biological role, the particular structure of CRISPR loci has been explored for epidemiological genotyping of bacterial pathogens. CRISPR-Cas loci are arranged in CRISPR arrays of mostly identical direct repeats intercalated with invader-derived spacers and an operon of cas genes encoding the Cas protein components. Each small CRISPR RNA (crRNA) encoded within the CRISPR array constitutes a key functional unit of this RNA-based CRISPR-Cas defense system guiding the Cas effector proteins toward the foreign nucleic acids for their destruction. The information acquired from prior invader encounters and stored within CRISPR arrays turns out to be extremely valuable in tracing the microevolution and epidemiology of major bacterial pathogens. We review here the history of CRISPR-based typing strategies highlighting the first PCR-based methods that have set the stage for recent developments of high-throughput sequencing and machine learning-based approaches. A great amount of whole genome sequencing and metagenomic data accumulated in recent years opens up new avenues for combining experimental and computational approaches of high-resolution CRISPR-based typing.

Characteristics of subtype III-A CRISPR-Cas system in Mycobacterium tuberculosis: An overview

CRISPR-Cas systems are the only RNA- guided adaptive immunity pathways that trigger the detection and destruction of invasive phages and plasmids in bacteria and archaea. Due to its prevalence and mystery, the Class 1 CRISPR-Cas system has lately been the subject of several studies. This review highlights the specificity of CRISPR-Cas system III-A in Mycobacterium tuberculosis, the tuberculosis-causing pathogen, for over twenty years. We discuss the difference between the several subtypes of Type III and their defence mechanisms. The anti-CRISPRs (Acrs) recently described, the critical role of Reverse transcriptase (RT) and housekeeping nuclease for type III CRISPR-Cas systems, and the use of this cutting-edge technology, its impact on the search for novel anti-tuberculosis drugs.

Diphtheria

Diphtheria is a potentially fatal infection mostly caused by toxigenic Corynebacterium diphtheriae strains and occasionally by toxigenic C. ulcerans and C. pseudotuberculosis strains. Diphtheria is generally an acute respiratory infection, characterized by the formation of a pseudomembrane in the throat, but cutaneous infections are possible. Systemic effects, such as myocarditis and neuropathy, which are associated with increased fatality risk, are due to diphtheria toxin, an exotoxin produced by the pathogen that inhibits protein synthesis and causes cell death. Clinical diagnosis is confirmed by the isolation and identification of the causative Corynebacterium spp., usually by bacterial culture followed by enzymatic and toxin detection tests. Diphtheria can be treated with the timely administration of diphtheria antitoxin and antimicrobial therapy. Although effective vaccines are available, this disease has the potential to re-emerge in countries where the recommended vaccination programmes are not sustained, and increasing proportions of adults are becoming susceptible to diphtheria. Thousands of diphtheria cases are still reported annually from several countries in Asia and Africa, along with many outbreaks. Changes in the epidemiology of diphtheria have been reported worldwide. The prevalence of toxigenic Corynebacterium spp. highlights the need for proper clinical and epidemiological investigations to quickly identify and treat affected individuals, along with public health measures to prevent and contain the spread of this disease.

Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings

Corynebacterium diphtheriae (C. diphtheriae) is a relatively rare pathogen in most Western countries. While toxin producing strains can cause pharyngeal diphtheria with potentially fatal outcomes, the more common presentation is wound infections. The diphtheria toxin is encoded on a prophage and can also be carried by Corynebacterium ulcerans and Corynebacterium pseudotuberculosis. Currently, across Europe, infections are mainly diagnosed in travelers and refugees from regions where diphtheria is more endemic, patients from urban areas with poor hygiene, and intravenous drug users. About half of the cases are non-toxin producing isolates. Rapid identification of the bacterial pathogen and toxin production is a critical element of patient and outbreak management. Beside the immediate clinical management of the patient, public health agencies should be informed of toxigenic C. diphtheriae diagnoses as soon as possible. The collection of case-related epidemiological data from the patient is often challenging due to language barriers and social circumstances. However, information on patient contacts, vaccine status and travel/refugee route, where appropriate, is critical, and should be documented. In addition, isolates should be characterized using high resolution typing, in order to identify transmissions and outbreaks. In recent years, whole genome sequencing (WGS) has become the gold standard of high-resolution typing methods, allowing detailed investigations of pathogen transmissions. De-centralized sequencing strategies with redundancy in sequencing capacities, followed by data exchange may be a valuable future option, especially since WGS becomes more available and portable. In this context, the sharing of sequence data, using public available platforms, is essential. A close interaction between microbiology laboratories, treating physicians, refugee centers, social workers, and public health officials is a key element in successful management of suspected outbreaks. Analyzing bacterial isolates at reference centers may further help to provide more specialized microbiological techniques and to standardize information, but this is also more time consuming during an outbreak. Centralized communication strategies between public health agencies and laboratories helps considerably in establishing and coordinating effective surveillance and infection control. We review the current literature on high-resolution typing of C. diphtheriae and share our own experience with the coordination of a Swiss-German outbreak.

Laboratory Methods in Molecular Epidemiology: Bacterial Infections

In infectious disease epidemiology, the laboratory plays a critical role in diagnosis, outbreak investigations, surveillance, and characterizing biologic properties of microbes associated with their transmissibility, resistance to anti-infectives, and pathogenesis. The laboratory can inform and refine epidemiologic study design and data analyses. In public health, the laboratory functions to assess effect of an intervention. In addition to research laboratories, the new-generation molecular microbiology technology has been adapted into clinical and public health laboratories to simplify, accelerate, and make precise detection and identification of infectious disease pathogens. This technology is also being applied to subtype microbes to conduct investigations that advance our knowledge of epidemiology of old and emerging infectious diseases. Because of the recent explosive progress in molecular microbiology technology and the vast amount of data generated from the applications of this technology, this Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases describes these methods separately for bacteria, viruses, and parasites. This review discusses past and current advancements made in laboratory methods used to conduct epidemiologic studies of bacterial infections. It describes methods used to subtype bacterial organisms based on molecular microbiology techniques, following a discussion on what is meant by bacterial "species" and "clones." Discussions on past and new genotyping tests applied to epidemiologic investigations focus on tests that compare electrophoretic band patterns, hybridization matrices, and nucleic acid sequences. Applications of these genotyping tests to address epidemiologic issues are detailed elsewhere in other reviews of this series. *This article is part of a curated collection.

Phylogenetic relationship of prophages is affected by CRISPR selection in Group A Streptococcus

BACKGROUND

Group A Streptococcus (GAS) is a major human pathogen, which is associated with a wide spectrum of invasive diseases, such as pharyngitis, scarlet fever, rheumatic fever, and streptococcal toxic shock syndrome (STSS). It is hypothesized that differences in GAS pathogenicity are related to the acquisition of diverse bacteriophages (phages). Nevertheless, the GAS genome also harbors clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (cas) genes, which play an important role in eliminating foreign DNA, including those of phages. However, the structure of prophages in GAS strains is mosaic, and the phylogenetic relationship between prophages and CRISPR is not clear. In this study, we analyzed CRISPR and prophage structure using 118 complete genome sequences of GAS strains to elucidate the relationship between two genomic elements. Additionally, phylogenetic and M-type analyses were performed.

RESULTS

Of the 118 GAS strains, 80 harbored type I-C and/or II-A CRISPR/cas loci. A total of 553 spacer sequences were identified from CRISPR/cas loci and sorted into 229 patterns. We identified and classified 373 prophages into 14 groups. Some prophage groups shared a common integration site, and were related to M-type. We further investigated the correlation between spacer sequences and prophages. Of the 229 spacer sequence patterns, 203 were similar to that of other GAS prophages. No spacer showed similarity with that of a specific prophage group with mutL integration site. Moreover, the average number of prophages in strains with type II-A CRISPR was significantly less than that in type I-C CRISPR and non-CRISPR strains. However, there was no statistical difference between the average number of prophages in type I-C strains and that in non-CRISPR strains.

CONCLUSIONS

Our results indicated that type II-A CRISPR may play an important role in eliminating phages and that the prophage integration site may be an important criterion for the acceptance of foreign DNA by GAS. M type, spacer sequence, and prophage group data were correlated with the phylogenetic relationships of GAS. Therefore, we hypothesize that genetic characteristics and/or phylogenetic relationships of GAS may be estimated by analyzing its spacer sequences.

Pathogenomics of Virulence Traits of Plesiomonas shigelloides That Were Deemed Inconclusive by Traditional Experimental Approaches

One of the major challenges of modern medicine includes the failure of conventional protocols to characterize the pathogenicity of emerging pathogens. This is particularly apparent in the case of Plesiomonas shigelloides. Although a number of infections have been linked to this microorganism, experimental evidence of its virulence factors (VFs), obtained by traditional approaches, is somewhat inconclusive. Hence, it remains unclear whether P. shigelloides is a true or opportunistic one. In the current study, four publicly available whole-genome sequences of P. shigelloides (GN7, NCTC10360, 302-73, and LS1) were profiled using bioinformatics platforms to determine the putative candidate VFs to characterize the bacterial pathogenicity. Overall, 134 unique open reading frames (ORFs) were identified that were homologous or orthologous to virulence genes identified in other pathogens. Of these, 52.24% (70/134) were jointly shared by the strains. The numbers of strain-specific virulence traits were 4 in LS1; 7 in NCTC10360; 10 in 302-73; and 15 in GN7. The pathogenicity islands (PAIs) common to all the strains accounted for 24.07% ORFs. The numbers of PAIs exclusive to each strain were 8 in 302-73; 11 in NCTC10360; 14 in GN7; and 18 in LS1. A PAI encoding Vibrio cholerae ToxR-activated gene d protein was specific to 302-73, GN7, and NCTC10360 strains. Out of 33 antibiotic multi-resistance genes identified, 16 (48.48%) genes were intrinsic to all strains. Further, 17 (22.08%) of 77 antibiotic resistance islands were found in all the strains. Out of 23 identified distinct insertion sequences, 13 were only harbored by strain LS1. The number of intact prophages identified in the strains was 1 in GN7; 2 in 302-73; and 2 in NCTC10360. Further, 1 CRISPR element was identified in LS1; 2 in NCTC10360; and 8 in 302-73. Fifteen (78.95%) of 19 secretion systems and secretion effector variants were identified in all the strains. In conclusion, certain P. shigelloides strains might possess VFs associated with gastroenteritis and extraintestinal infections. However, the role of host factors in the onset of infections should not be undermined.

The CRISPR-Cas system in Enterobacteriaceae

In nature, microorganisms are constantly exposed to multiple viral infections and thus have developed many strategies to survive phage attack and invasion by foreign DNA. One of such strategies is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) bacterial immunological system. This defense mechanism is widespread in prokaryotes including several families such as Enterobacteriaceae. Much knowledge about the CRISPR-Cas system has been generated, including its biological functions, transcriptional regulation, distribution, utility as a molecular marker and as a tool for specific genome editing. This review focuses on these aspects and describes the state of the art of the CRISPR-Cas system in the Enterobacteriaceae bacterial family.

Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies

Introduction

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era.

Methods

These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements. This property can be used as a tool for RNA editing in bioengineering studies.

Conclusion

The aim of this review was to survey some details about the history, nature, and potential applications of CRISPR arrays in both genetic engineering and bacterial genotyping studies.

CRISPR-Cas: biology, mechanisms and relevance

Prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes—termed spacers—into the CRISPR locus. The spacers interspaced with repeats are expressed as small guide CRISPR RNAs (crRNAs) that are employed by Cas proteins to target invaders sequence-specifically upon a reoccurring infection. The ability of the minimal CRISPR-Cas9 system to target DNA sequences using programmable RNAs has opened new avenues in genome editing in a broad range of cells and organisms with high potential in therapeutical applications. While numerous scientific studies have shed light on the biochemical processes behind CRISPR-Cas systems, several aspects of the immunity steps, however, still lack sufficient understanding. This review summarizes major discoveries in the CRISPR-Cas field, discusses the role of CRISPR-Cas in prokaryotic immunity and other physiological properties, and describes applications of the system as a DNA editing technology and antimicrobial agent.

This article is part of the themed issue ‘The new bacteriology’.

Genomic analysis of endemic clones of toxigenic and non-toxigenic Corynebacterium diphtheriae in Belarus during and after the major epidemic in 1990s

BACKGROUND

Diphtheria remains a major public health concern with multiple recent outbreaks around the world. Moreover, invasive non-toxigenic strains have emerged globally causing severe infections. A diphtheria epidemic in the former Soviet Union in the 1990s resulted in ~5000 deaths. In this study, we analysed the genome sequences of a collection of 93 C. diphtheriae strains collected during and after this outbreak (1996 - 2014) in a former Soviet State, Belarus to understand the evolutionary dynamics and virulence capacities of these strains.

RESULTS

C. diphtheriae strains from Belarus belong to ten sequence types (STs). Two major clones, non-toxigenic ST5 and toxigenic ST8, encompassed 76% of the isolates that are associated with sore throat and diphtheria in patients, respectively. Core genomic diversity is limited within outbreak-associated ST8 with relatively higher mutation rates (8.9 × 10-7 substitutions per strain per year) than ST5 (5.6 × 10-7 substitutions per strain per year) where most of the diversity was introduced by recombination. A variation in the virulence gene repertoire including the presence of tox gene is likely responsible for pathogenic differences between different strains. However, strains with similar virulence potential can cause disease in some individuals and remain asymptomatic in others. Eight synonymous single nucleotide polymorphisms were observed between the tox genes of the vaccine strain PW8 and other toxigenic strains of ST8, ST25, ST28, ST41 and non-toxigenic tox gene-bearing (NTTB) ST40 strains. A single nucleotide deletion at position 52 in the tox gene resulted in the frameshift in ST40 isolates, converting them into NTTB strains.

CONCLUSIONS

Non-toxigenic C. diphtheriae ST5 and toxigenic ST8 strains have been endemic in Belarus both during and after the epidemic in 1990s. A high vaccine coverage has effectively controlled diphtheria in Belarus; however, non-toxigenic strains continue to circulate in the population. Recombination is an important evolutionary force in shaping the genomic diversity in C. diphtheriae. However, the relative role of recombination and mutations in diversification varies between different clones.

Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa

BACKGROUND

Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M. viscosa strains. Matches between M. viscosa clustered, regularly interspaced, short palindromic, repeats and associated cas genes (CRISPR-Cas) were analysed to correlate CRISPR-Cas with adaptive immunity against MGEs.

RESULTS

The comparative genomic analysis of M. viscosa isolates from across the North Atlantic region and from different fish species support delineation of M. viscosa into four phylogenetic lineages. The results showed that M. viscosa carries two distinct variants of the CRISPR-Cas subtype I-F systems and that CRISPR features follow the phylogenetic lineages. A subset of the spacer content match prophage and plasmid genes dispersed among the M. viscosa strains. Further analysis revealed that prophage and plasmid-like element distribution were reflected in the content of the CRISPR-spacer profiles.

CONCLUSIONS

Our data suggests that CRISPR-Cas mediated interactions with MGEs impact genome properties among M. viscosa, and that patterns in spacer and MGE distributions are linked to strain relationships.

CRISPR technologies for bacterial systems: Current achievements and future directions

Throughout the decades of its history, the advances in bacteria-based bio-industries have coincided with great leaps in strain engineering technologies. Recently unveiled clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) systems are now revolutionizing biotechnology as well as biology. Diverse technologies have been derived from CRISPR/Cas systems in bacteria, yet the applications unfortunately have not been actively employed in bacteria as extensively as in eukaryotic organisms. A recent trend of engineering less explored strains in industrial microbiology-metabolic engineering, synthetic biology, and other related disciplines-is demanding facile yet robust tools, and various CRISPR technologies have potential to cater to the demands. Here, we briefly review the science in CRISPR/Cas systems and the milestone inventions that enabled numerous CRISPR technologies. Next, we describe CRISPR/Cas-derived technologies for bacterial strain development, including genome editing and gene expression regulation applications. Then, other CRISPR technologies possessing great potential for industrial applications are described, including typing and tracking of bacterial strains, virome identification, vaccination of bacteria, and advanced antimicrobial approaches. For each application, we note our suggestions for additional improvements as well. In the same context, replication of CRISPR/Cas-based chromosome imaging technologies developed originally in eukaryotic systems is introduced with its potential impact on studying bacterial chromosomal dynamics. Also, the current patent status of CRISPR technologies is reviewed. Finally, we provide some insights to the future of CRISPR technologies for bacterial systems by proposing complementary techniques to be developed for the use of CRISPR technologies in even wider range of applications.

Evolution, epidemiology and diversity of Corynebacterium diphtheriae: New perspectives on an old foe

Diphtheria is a debilitating disease caused by toxigenic Corynebacterium diphtheriae strains and has been effectively controlled by the toxoid vaccine, yet several recent outbreaks have been reported across the globe. Moreover, non-toxigenic C. diphtheriae strains are emerging as a major global health concern by causing severe pharyngitis and tonsillitis, endocarditis, septic arthritis and osteomyelitis. Molecular epidemiological investigations suggest the existence of outbreak-associated clones with multiple genotypes circulating around the world. Evolution and pathogenesis appears to be driven by recombination as major virulence factors, including the tox gene and pilus gene clusters, are found within genomic islands that appear to be mobile between strains. The number of pilus gene clusters and variation introduced by gain or loss of gene function correlate with the variable adhesive and invasive properties of C. diphtheriae strains. Genomic variation does not support the separation of C. diphtheriae strains into biovars which correlates well with findings of studies based on multilocus sequence typing. Genomic analyses of a relatively small number of strains also revealed a recombination driven diversification of strains within a sequence type and indicate a wider diversity among C. diphtheriae strains than previously appreciated. This suggests that there is a need for increased effort from the scientific community to study C. diphtheriae to help understand the genomic diversity and pathogenicity within the population of this important human pathogen.

Improved traceability of Shiga-toxin-producing Escherichia coli using CRISPRs for detection and typing

Among strains of Shiga-toxin-producing Escherichia coli (STEC), seven serogroups (O26, O45, O103, O111, O121, O145, and O157) are frequently associated with severe clinical illness in humans. The development of methods for their reliable detection from complex samples such as food has been challenging thus far, and is currently based on the PCR detection of the major virulence genes stx1, stx2, and eae, and O-serogroup-specific genes. However, this approach lacks resolution. Moreover, new STEC serotypes are continuously emerging worldwide. For example, in May 2011, strains belonging to the hitherto rarely detected STEC serotype O104:H4 were identified as causative agents of one of the world's largest outbreak of disease with a high incidence of hemorrhagic colitis and hemolytic uremic syndrome in the infected patients. Discriminant typing of pathogens is crucial for epidemiological surveillance and investigations of outbreaks, and especially for tracking and tracing in case of accidental and deliberate contamination of food and water samples. Clustered regularly interspaced short palindromic repeats (CRISPRs) are composed of short, highly conserved DNA repeats separated by unique sequences of similar length. This distinctive sequence signature of CRISPRs can be used for strain typing in several bacterial species including STEC. This review discusses how CRISPRs have recently been used for STEC identification and typing.

CRISPR-Based Typing and Next-Generation Tracking Technologies

Bacteria occur ubiquitously in nature and are broadly relevant throughout the food supply chain, with diverse and variable tolerance levels depending on their origin, biological role, and impact on the quality and safety of the product as well as on the health of the consumer. With increasing knowledge of and accessibility to the microbial composition of our environments, food supply, and host-associated microbiota, our understanding of and appreciation for the ratio of beneficial to undesirable bacteria are rapidly evolving. Therefore, there is a need for tools and technologies that allow definite, accurate, and high-resolution identification and typing of various groups of bacteria that include beneficial microbes such as starter cultures and probiotics, innocuous commensals, and undesirable pathogens and spoilage organisms. During the transition from the current molecular biology-based PFGE (pulsed-field gel electrophoresis) gold standard to the increasingly accessible omics-level whole-genome sequencing (WGS) N-gen standard, high-resolution technologies such as CRISPR-based genotyping constitute practical and powerful alternatives that provide valuable insights into genome microevolution and evolutionary trajectories. Indeed, several studies have shown potential for CRISPR-based typing of industrial starter cultures, health-promoting probiotic strains, animal commensal species, and problematic pathogens. Emerging CRISPR-based typing methods open new avenues for high-resolution typing of a broad range of bacteria and constitute a practical means for rapid tracking of a diversity of food-associated microbes.

Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates.

IMPORTANCE

P. aeruginosa is both an antibiotic-refractory pathogen and an important model system for type I CRISPR-Cas bacterial immune systems. By combining the genome sequences of 672 newly and previously sequenced genomes, we were able to provide a global view of the phylogenetic distribution, conservation, and potential targets of these systems. This analysis identified a new and putatively mobile P. aeruginosa CRISPR-Cas subtype, characterized the diverse distribution of known CRISPR-inhibiting genes, and provided a potential new use for CRISPR spacer libraries in accessory genome analysis. Our data demonstrated the importance of CRISPR-Cas systems in modulating the accessory genomes of globally distributed strains while also providing substantial data for subsequent genomic and experimental studies in multiple fields. Understanding why certain genotypes of P. aeruginosa are clinically prevalent and adept at horizontally acquiring virulence and antibiotic resistance elements is of major clinical and economic importance.

CRISPR Diversity in E. coli Isolates from Australian Animals, Humans and Environmental Waters

Seventy four SNP genotypes and 54 E. coli genomes from kangaroo, Tasmanian devil, reptile, cattle, dog, horse, duck, bird, fish, rodent, human and environmental water sources were screened for the presence of the CRISPR 2.1 loci flanked by cas2 and iap genes. CRISPR 2.1 regions were found in 49% of the strains analysed. The majority of human E. coli isolates lacked the CRISPR 2.1 locus. We described 76 CRISPR 2.1 positive isolates originating from Australian animals and humans, which contained a total of 764 spacer sequences. CRISPR arrays demonstrated a long history of phage attacks especially in isolates from birds (up to 40 spacers). The most prevalent spacer (1.6%) was an ancient spacer found mainly in human, horse, duck, rodent, reptile and environmental water sources. The sequence of this spacer matched the intestinal P7 phage and the pO111 plasmid of E. coli.

Spacer-Based Macroarrays for CRISPR Genotyping

Macroarray-based analysis is a powerful and economic format to study variations in "clustered regularly interspaced short palindromic repeat (CRISPR)" loci in bacteria. To date, it was used almost exclusively for Mycobacterium tuberculosis and was named spoligotyping (spacer oligonucleotides typing). Here, we describe the pipeline of this approach that includes search of loci and selection of spacers, preparation of the membrane with immobilized probes and spoligotyping itself (PCR and reverse hybridization).

Validation of a microbead-based format for spoligotyping of Legionella pneumophila

A 42-plex clustered regularly interspaced short palindromic repeat (CRISPR)-based typing technique (spoligotyping) was recently developed at the French National Reference Center for Legionella. It allows the subtyping of the Legionella pneumophila sequence type 1/Paris pulsotype. In this report, we present the transfer of the membrane-based spoligotyping technique to a microbead-based multiplexed format. This microbead-based high-throughput assay uses devices such as Luminex 200 or the recently launched Magpix system (Luminex Corp., Austin, TX). We designated this new technique LP-SPOL (for L. pneumophila spoligotyping). We used two sets of samples previously subtyped by the membrane-based spoligotyping method to set up and validate the transfer on the two microbead-based systems. The first set of isolates (n = 56) represented the whole diversity of the CRISPR patterns known to date. These isolates were used for transfer setup (determination of spacer cutoffs for both devices). The second set of isolates (n = 245) was used to validate the transfer to the two microbead-based systems. The results obtained by the Luminex 200 system were 100% concordant with those obtained by the Magpix system for the 2 sets of isolates. In total, 10 discrepant results were observed when comparing the membrane-based method to the microbead-based method. These discrepancies were further resolved by repeating either the membrane-based or the microbead-based assay. This new assay is expected to play an emerging role for surveillance of L. pneumophila, starting with one of the most frequent genotypes, the sequence type 1/Paris pulsotype. However, the generalization of this typing method to all L. pneumophila strains is not feasible, since not all L. pneumophila strains contain CRISPRs.

The role of CRISPR-Cas systems in virulence of pathogenic bacteria

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. The discovery that CRISPR spacers are often identical to sequence fragments of mobile genetic elements was a major breakthrough that eventually led to the elucidation of CRISPR-Cas as an adaptive immunity system. Key elements of this unique prokaryotic defense system are small CRISPR RNAs that guide nucleases to complementary target nucleic acids of invading viruses and plasmids, generally followed by the degradation of the invader. In addition, several recent studies have pointed at direct links of CRISPR-Cas to regulation of a range of stress-related phenomena. An interesting example concerns a pathogenic bacterium that possesses a CRISPR-associated ribonucleoprotein complex that may play a dual role in defense and/or virulence. In this review, we describe recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular.

Bacterial genome instability

Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.

CRISPRs: molecular signatures used for pathogen subtyping

Rapid and accurate strain identification is paramount in the battle against microbial outbreaks, and several subtyping approaches have been developed. One such method uses clustered regular interspaced short palindromic repeats (CRISPRs), DNA repeat elements that are present in approximately half of all bacteria. Though their signature function is as an adaptive immune system against invading DNA such as bacteriophages and plasmids, CRISPRs also provide an excellent framework for pathogen tracking and evolutionary studies. Analysis of the spacer DNA sequences that reside between the repeats has been tremendously useful for bacterial subtyping during molecular epidemiological investigations. Subtyping, or strain identification, using CRISPRs has been employed in diverse Gram-positive and Gram-negative bacteria, including Mycobacterium tuberculosis, Salmonella enterica, and the plant pathogen Erwinia amylovora. This review discusses the several ways in which CRISPR sequences are exploited for subtyping. This includes the well-established spoligotyping methodologies that have been used for 2 decades to type Mycobacterium species, as well as in-depth consideration of newer, higher-throughput CRISPR-based protocols.

The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition

The Shiga toxin-producing Escherichia coli (STEC) strains, including those of O157:H7 and the "big six" serogroups (i.e., serogroups O26, O45, O103, O111, O121, and O145), are a group of pathogens designated food adulterants in the United States. The relatively conserved nature of clustered regularly interspaced short palindromic repeats (CRISPRs) in phylogenetically related E. coli strains makes them potential subtyping markers for STEC detection, and a quantitative PCR (qPCR)-based assay was previously developed for O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 isolates. To better evaluate the sensitivity and specificity of this qPCR method, the CRISPR loci of 252 O157 and big-six STEC isolates were sequenced and analyzed along with 563 CRISPR1 and 624 CRISPR2 sequences available in GenBank. General conservation of spacer content and order was observed within each O157 and big-six serogroup, validating the qPCR method. Meanwhile, it was found that spacer deletion, the presence of an insertion sequence, and distinct alleles within a serogroup are sources of false-negative reactions. Conservation of CRISPR arrays among isolates expressing the same flagellar antigen, specifically, H7, H2, and H11, suggested that these isolates share an ancestor and provided an explanation for the false positives previously observed in the qPCR results. An analysis of spacer distribution across E. coli strains provided limited evidence for temporal spacer acquisition. Conversely, comparison of CRISPR sequences between strains along the stepwise evolution of O157:H7 from its O55:H7 ancestor revealed that, over this ∼7,000-year span, spacer deletion was the primary force generating CRISPR diversity.

Comparative genomic structures of Mycobacterium CRISPR-Cas

Clustered regularly interspaced short palindromic repeats (CRISPR) are inheritable genetic elements of many archaea and bacteria, conferring acquired immunity against invading nucleic acids. CRISPR might be indicative of the bacterial niche adaptation and evolutionary. Mycobacterium is an important genus occupying diverse niches with profound medical and environmental significance. To present a comparative genomic landscape of the Mycobacterium CRISPR, the feature of mycobacterium CRISPR structures with sequenced complete genomes were bioinformatically analyzed. The results show that CRISPR structures can be found among 14 mycobacteria, and all loci are chromosomally located. Long CRISPRs present in three species, namely M. tuberculosis, M. bovis, and M. avium. Integrated CRISPR-Cas system can only be found in M. tuberculosis and M. bovis, with highly conserved repeat sequences, very short leaders, and promoterless. M. tuberculosis and M. bovis repeat sequences cannot form stable RNA secondary structure, consistent with a Cas6-binding sequence. M. avium repeat sequences can form classical stem-loop structure. A three-step model of M. tuberculosis CRISPR-Cas system action was put forward based on the composition and function of cas genes cluster. M. tuberculosis and M. bovis CRISPRs might interfere with the invading nucleic acids, but have somehow lost the capacity to incorporate new spacers and co-evolve with corresponding mycobacteriophages.

CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections

Laboratory surveillance systems for salmonellosis should ideally be based on the rapid serotyping and subtyping of isolates. However, current typing methods are limited in both speed and precision. Using 783 strains and isolates belonging to 130 serotypes, we show here that a new family of DNA repeats named CRISPR (clustered regularly interspaced short palindromic repeats) is highly polymorphic in Salmonella. We found that CRISPR polymorphism was strongly correlated with both serotype and multilocus sequence type. Furthermore, spacer microevolution discriminated between subtypes within prevalent serotypes, making it possible to carry out typing and subtyping in a single step. We developed a high-throughput subtyping assay for the most prevalent serotype, Typhimurium. An open web-accessible database was set up, providing a serotype/spacer dictionary and an international tool for strain tracking based on this innovative, powerful typing and subtyping tool.

Diphtheria in Europe: current problems and new challenges

Diphtheria, caused by toxigenic strains of Corynebacterium diphtheriae, is an ancient disease with high incidence and mortality that has always been characterized by epidemic waves of occurrence. Whilst towards the beginning of the 1980s, many European countries were progressing towards the elimination of diphtheria, an epidemic re-emergence of diphtheria in the Russian Federation and the Newly Independent States of the former Soviet Union demonstrated a continuous threat of the disease into the 1990s. At present, the epidemic is under control and only sporadic cases are observed in Europe. However, the circulation of toxigenic strains is still observed in all parts of the world, posing a constant threat to the population with low levels of seroprotection. More recently, Corynebacterium ulcerans has been increasingly isolated as emerging zoonotic agent of diphtheria from companion animals such as cats or dogs, indicating the enduring threat of this thought-to-be controlled disease.

Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia

Corynebacterium diphtheriae is one of the most prominent human pathogens and the causative agent of the communicable disease diphtheria. The genomes of 12 strains isolated from patients with classical diphtheria, endocarditis, and pneumonia were completely sequenced and annotated. Including the genome of C. diphtheriae NCTC 13129, we herewith present a comprehensive comparative analysis of 13 strains and the first characterization of the pangenome of the species C. diphtheriae. Comparative genomics showed extensive synteny and revealed a core genome consisting of 1,632 conserved genes. The pangenome currently comprises 4,786 protein-coding regions and increases at an average of 65 unique genes per newly sequenced strain. Analysis of prophages carrying the diphtheria toxin gene tox revealed that the toxoid vaccine producer C. diphtheriae Park-Williams no. 8 has been lysogenized by two copies of the ω(tox)(+) phage, whereas C. diphtheriae 31A harbors a hitherto-unknown tox(+) corynephage. DNA binding sites of the tox-controlling regulator DtxR were detected by genome-wide motif searches. Comparative content analysis showed that the DtxR regulons exhibit marked differences due to gene gain, gene loss, partial gene deletion, and DtxR binding site depletion. Most predicted pathogenicity islands of C. diphtheriae revealed characteristics of horizontal gene transfer. The majority of these islands encode subunits of adhesive pili, which can play important roles in adhesion of C. diphtheriae to different host tissues. All sequenced isolates contain at least two pilus gene clusters. It appears that variation in the distributed genome is a common strategy of C. diphtheriae to establish differences in host-pathogen interactions.

CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation

Bacteria and archaea have evolved defense and regulatory mechanisms to cope with various environmental stressors, including virus attack. This arsenal has been expanded by the recent discovery of the versatile CRISPR-Cas system, which has two novel features. First, the host can specifically incorporate short sequences from invading genetic elements (virus or plasmid) into a region of its genome that is distinguished by clustered regularly interspaced short palindromic repeats (CRISPRs). Second, when these sequences are transcribed and precisely processed into small RNAs, they guide a multifunctional protein complex (Cas proteins) to recognize and cleave incoming foreign genetic material. This adaptive immunity system, which uses a library of small noncoding RNAs as a potent weapon against fast-evolving viruses, is also used as a regulatory system by the host. Exciting breakthroughs in understanding the mechanisms of the CRISPR-Cas system and its potential for biotechnological applications and understanding evolutionary dynamics are discussed.

RNA-guided genetic silencing systems in bacteria and archaea

Clustered regularly interspaced short palindromic repeat (CRISPR) are essential components of nucleic-acid-based adaptive immune systems that are widespread in bacteria and archaea. Similar to RNA interference (RNAi) pathways in eukaryotes, CRISPR-mediated immune systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids, including viruses and plasmids. However, the mechanism of RNA-based bacterial immunity is distinct from RNAi. Understanding how small RNAs are used to find and destroy foreign nucleic acids will provide new insights into the diverse mechanisms of RNA-controlled genetic silencing systems.

Role of CRISPR/cas system in the development of bacteriophage resistance

Acquisition of foreign DNA can be of advantage or disadvantage to the host cell. New DNAs can increase the fitness of an organism to certain environmental conditions; however, replication and maintenance of incorporated nucleotide sequences can be a burden for the host cell. These circumstances have resulted in the development of certain cellular mechanisms limiting horizontal gene transfer, including the immune system of vertebrates or RNA interference mechanisms in eukaryotes. Also, in prokaryotes, specific systems have been characterized, which are aimed especially at limiting the invasion of bacteriophage DNA, for example, adsorption inhibition, injection blocking, restriction/modification, or abortive infection. Quite recently, another distinct mechanism limiting horizontal transfer of genetic elements has been identified in procaryotes and shown to protect microbial cells against exogenous nucleic acids of phage or plasmid origin. This system has been termed CRISPR/cas and consists of two main components: (i) the CRISPR (clustered, regularly interspaced short palindromic regions) locus and (ii) cas genes, encoding CRISPR-associated (Cas) proteins. In simplest words, the mechanism of CRISPR/cas activity is based on the active integration of small fragments (proto-spacers) of the invading DNAs (phage or plasmids) into microbial genomes, which are subsequently transcribed into short RNAs that direct the degradation of foreign invading DNA elements. In this way, the host organism acquires immunity toward mobile elements carrying matching sequences. The CRISPR/cas system is regarded as one of the earliest defense system that has evolved in prokaryotic organisms. It is inheritable, but at the same time is unstable when regarding the evolutionary scale. Comparative sequence analyses indicate that CRISPR/cas systems play an important role in the evolution of microbial genomes and their predators, bacteriophages.

CRISPR: new horizons in phage resistance and strain identification

Bacteria have been widely used as starter cultures in the food industry, notably for the fermentation of milk into dairy products such as cheese and yogurt. Lactic acid bacteria used in food manufacturing, such as lactobacilli, lactococci, streptococci, Leuconostoc, pediococci, and bifidobacteria, are selectively formulated based on functional characteristics that provide idiosyncratic flavor and texture attributes, as well as their ability to withstand processing and manufacturing conditions. Unfortunately, given frequent viral exposure in industrial environments, starter culture selection and development rely on defense systems that provide resistance against bacteriophage predation, including restriction-modification, abortive infection, and recently discovered CRISPRs (clustered regularly interspaced short palindromic repeats). CRISPRs, together with CRISPR-associated genes (cas), form the CRISPR/Cas immune system, which provides adaptive immunity against phages and invasive genetic elements. The immunization process is based on the incorporation of short DNA sequences from virulent phages into the CRISPR locus. Subsequently, CRISPR transcripts are processed into small interfering RNAs that guide a multifunctional protein complex to recognize and cleave matching foreign DNA. Hypervariable CRISPR loci provide insights into the phage and host population dynamics, and new avenues for enhanced phage resistance and genetic typing and tagging of industrial strains.

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. The importance of such pathways is highlighted by the extensive study of RNA interference (RNAi) and related processes in eukaryotes. In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. CRISPR sequences provide an adaptive, heritable record of past infections and express CRISPR RNAs - small RNAs that target invasive nucleic acids. Here, we review the mechanisms of CRISPR interference and its roles in microbial physiology and evolution. We also discuss potential applications of this novel interference pathway.

The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional method: providing guidelines for Quality Assurance when working on membranes

Background

The classical spoligotyping technique, relying on membrane reverse line-blot hybridization of the spacers of the Mycobacterium tuberculosis CRISPR locus, is used world-wide (598 references in Pubmed on April 8th, 2011). However, until now no inter-laboratory quality control study had been undertaken to validate this technique. We analyzed the quality of membrane-based spoligotyping by comparing it to the recently introduced and highly robust microbead-based spoligotyping. Nine hundred and twenty-seven isolates were analyzed totaling 39,861 data points. Samples were received from 11 international laboratories with a worldwide distribution.

Methods

The high-throughput microbead-based Spoligotyping was performed on CTAB and thermolyzate DNA extracted from isolated Mycobacterium tuberculosis complex (MTC) strains coming from the genotyping participating centers. Information regarding how the classical Spoligotyping method was performed by center was available. Genotype discriminatory analyses were carried out by comparing the spoligotypes obtained by both methods. The non parametric U-Mann Whitney homogeneity test and the Spearman rank correlation test were performed to validate the observed results.

Results

Seven out of the 11 laboratories (63 %), perfectly typed more than 90% of isolates, 3 scored between 80-90% and a single center was under 80% reaching 51% concordance only. However, this was mainly due to discordance in a single spacer, likely having a non-functional probe on the membrane used. The centers using thermolyzate DNA performed as well as centers using the more extended CTAB extraction procedure. Few centers shared the same problematic spacers and these problematic spacers were scattered over the whole CRISPR locus (Mostly spacers 15, 14, 18, 37, 39, 40).

Conclusions

We confirm that classical spoligotyping is a robust method with generally a high reliability in most centers. The applied DNA extraction procedure (CTAB or thermolyzate) did not affect the results in this study. However performance was center-dependent, suggesting that training is a key component in quality assurance of spoligotyping. Overall, no particular spacer yielded a higher degree of deviating results, suggesting that errors occur randomly either in the process of re-using membranes, or during the reading of the results and transferring of data from the film to a digital file. Last, the performance of the microbead-based method was excellent as previously shown by Cowan et al. (J. Clin. Microbiol. 2004) and Zhang et al. (J. Med. Microbiol. 2009) and demonstrated the proper detection of spacer 15 that is known to occasionally give weak signals in the classical spoligotyping.

Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage

The CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) found in prokaryotic genomes confer small RNA-mediated protection against viruses and other invaders. CRISPR loci contain iterations of a short repeat sequence alternating with small segments of varying invader-derived sequences. Distinct families of CRISPR-associated Cas proteins function to cleave within the repeat sequence of CRISPR transcripts and produce the individual invader-targeting crRNAs. Here, we report the crystal structure of Pyrococcus furiosus Cas6 bound with a repeat RNA at 3.2 Å resolution. In contrast to other Cas families of endonucleases, Cas6 clasps nucleotides 2-9 of the repeat RNA using its two ferredoxin-like domains, and the enzyme-anchored 5' end tethers the distal cleavage site of the RNA between nucleotides 22 and 23 to the predicted enzyme active site on the opposite side of the ferrodoxin-like domains. Our findings suggest a wrap-around mechanism for CRISPR RNA recognition and cleavage by Cas6 and related processing endonucleases.

CRISPR/Cas system and its role in phage-bacteria interactions

Clustered regularly interspaced short palindromic repeats (CRISPRs) along with Cas proteins is a widespread system across bacteria and archaea that causes interference against foreign nucleic acids. The CRISPR/Cas system acts in at least two general stages: the adaptation stage, where the cell acquires new spacer sequences derived from foreign DNA, and the interference stage, which uses the recently acquired spacers to target and cleave invasive nucleic acid. The CRISPR/Cas system participates in a constant evolutionary battle between phages and bacteria through addition or deletion of spacers in host cells and mutations or deletion in phage genomes. This review describes the recent progress made in this fast-expanding field.

Replacing reverse line blot hybridization spoligotyping of the Mycobacterium tuberculosis complex

Spoligotyping is a tool for the molecular characterization/typing of Mycobacterium tuberculosis complex (MTBC) strains based on target sequences (spacers) in the direct repeat (DR) region (14). The standard spoligotyping assay involves the hybridization of amplified sample DNA to nylon membrane-immobilized oligonucleotides whose sequences are representative of 43 spacer regions. Variations in the number of spacers as a result of deletions of adjacent blocks of repetitive units allow the differentiation of clinical isolates. In the present study, we developed a new multiplexed primer extension-based spoligotyping assay using automated matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) that improves the classical reverse line blot hybridization assay with respect to reproducibility, throughput, process flow, ease of use, and data analysis. Validation of the MALDI-TOF MS-based spoligotyping assay with two sample sets with a total of 326 samples resulted in 96.6% concordance (315/326) when the full spoligotype patterns were compared with the results of standard spoligotyping and 99.9% concordance when the results were compared with those of individual primer extension assays. Ten strains (including two Mycobacterium canettii strains) showed discordant results with one or two spacer differences from the membrane-based spoligotyping result. Most discordant samples were identified to be the result of ambiguities in the interpretation of weak hybridization signals in the reverse line blot assay and sequence variations in the spacer regions. We established a new automated primer extension assay and successfully validated it for use for the routine typing of MTBC strains in the research and public health laboratory environments. The present multiplex levels of up to 30 are extendable and allow the additional incorporation of controls and antibiotic resistance markers.

Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of 'spoligotyping' with new spacers and a microbead-based hybridization assay

The aims of the present study were to implement a microbead-based 'spoligotyping' technique and to evaluate improvements by the addition of a panel of 25 extra spacers that we expected to provide an increased resolution on principal genetic group 1 (PGG 1) strains. We confirmed the high sensitivity and reproducibility of the classical technique using the 43 spacer panel and we obtained perfect agreement between the membrane-based and the microbead-based techniques. We further demonstrated an increase in the discriminative power of an extended 68 spacer format for differentiation of PGG 1 clinical isolates, in particular for the East African-Indian clade. Finally, we define a limited yet highly informative reduced 10 spacer panel set which could offer a more cost-effective option for implementation in resource-limited countries and that could decrease the need for additional VNTR (variable number of tandem repeats) genotyping work in molecular epidemiological studies. We also present an economic analysis comparing membrane-based and microbead-based techniques.

Clustered regularly interspaced short palindromic repeats (CRISPRs) for the genotyping of bacterial pathogens

Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences composed of a succession of repeats (23- to 47-bp long) separated by unique sequences called spacers. Polymorphism can be observed in different strains of a species and may be used for genotyping. We describe protocols and bioinformatics tools that allow the identification of CRISPRs from sequenced genomes, their comparison, and their component determination (the direct repeats and the spacers). A schematic representation of the spacer organization can be produced, allowing an easy comparison between strains.

Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes

BACKGROUND

Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable data. A popular approach for analyzing such data is to construct graphs, including phylogenies. Inferences from graph representations of data assist in understanding the patterns of transmission of bacterial pathogens, and basing these graph constructs on biological models of evolution of the molecular marker helps make these inferences. Spoligotyping is a widely used method for genotyping isolates of Mycobacterium tuberculosis that exploits polymorphism in the direct repeat region. Our goal was to examine a range of models describing the evolution of spoligotypes in order to develop a visualization method to represent likely relationships among M. tuberculosis isolates.

RESULTS

We found that inferred mutations of spoligotypes frequently involve the loss of a single or very few adjacent spacers. Using a second-order variant of Akaike's Information Criterion, we selected the Zipf model as the basis for resolving ambiguities in the ancestry of spoligotypes. We developed a method to construct graphs of spoligotypes (which we call spoligoforests). To demonstrate this method, we applied it to a tuberculosis data set from Cuba and compared the method to some existing methods.

CONCLUSION

We propose a new approach in analyzing relationships of M. tuberculosis isolates using spoligotypes. The spoligoforest recovers a plausible history of transmission and mutation events based on the selected deletion model. The method may be suitable to study markers based on loci of similar structure from other bacteria. The groupings and relationships in the spoligoforest can be analyzed along with the clinical features of strains to provide an understanding of the evolution of spoligotypes.

Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats

BACKGROUND

Yersinia pestis, the pathogen of plague, has greatly influenced human history on a global scale. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), an element participating in immunity against phages' invasion, is composed of short repeated sequences separated by unique spacers and provides the basis of the spoligotyping technology. In the present research, three CRISPR loci were analyzed in 125 strains of Y. pestis from 26 natural plague foci of China, the former Soviet Union and Mongolia were analyzed, for validating CRISPR-based genotyping method and better understanding adaptive microevolution of Y. pestis.

METHODOLOGY/PRINCIPAL FINDINGS

Using PCR amplification, sequencing and online data processing, a high degree of genetic diversity was revealed in all three CRISPR elements. The distribution of spacers and their arrays in Y. pestis strains is strongly region and focus-specific, allowing the construction of a hypothetic evolutionary model of Y. pestis. This model suggests transmission route of microtus strains that encircled Takla Makan Desert and ZhunGer Basin. Starting from Tadjikistan, one branch passed through the Kunlun Mountains, and moved to the Qinghai-Tibet Plateau. Another branch went north via the Pamirs Plateau, the Tianshan Mountains, the Altai Mountains and the Inner Mongolian Plateau. Other Y. pestis lineages might be originated from certain areas along those routes.

CONCLUSIONS/SIGNIFICANCE

CRISPR can provide important information for genotyping and evolutionary research of bacteria, which will help to trace the source of outbreaks. The resulting data will make possible the development of very low cost and high-resolution assays for the systematic typing of any new isolate.

CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats

Clustered regularly interspaced short palindromic repeat (CRISPR) elements are a particular family of tandem repeats present in prokaryotic genomes, in almost all archaea and in about half of bacteria, and which participate in a mechanism of acquired resistance against phages. They consist in a succession of direct repeats (DR) of 24–47 bp separated by similar sized unique sequences (spacers). In the large majority of cases, the direct repeats are highly conserved, while the number and nature of the spacers are often quite diverse, even among strains of a same species. Furthermore, the acquisition of new units (DR + spacer) was shown to happen almost exclusively on one side of the locus. Therefore, the CRISPR presents an interesting genetic marker for comparative and evolutionary analysis of closely related bacterial strains. CRISPRcompar is a web service created to assist biologists in the CRISPR typing process. Two tools facilitates the in silico investigation: CRISPRcomparison and CRISPRtionary. This website is freely accessible at http://crispr.u-psud.fr/CRISPRcompar/.

On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing

The control of bacterial pathogens requires the development of tools allowing the precise identification of strains at the subspecies level. It is now widely accepted that these tools will need to be DNA-based assays (in contrast to identification at the species level, where biochemical based assays are still widely used, even though very powerful 16S DNA sequence databases exist). Typing assays need to be cheap and amenable to the designing of international databases. The success of such subspecies typing tools will eventually be measured by the size of the associated reference databases accessible over the internet. Three methods have shown some potential in this direction, the so-called spoligotyping assay (Mycobacterium tuberculosis, 40,000 entries database), Multiple Loci Sequence Typing (MLST; up to a few thousands entries for the more than 20 bacterial species), and more recently Multiple Loci VNTR Analysis (MLVA; up to a few hundred entries, assays available for more than 20 pathogens). In the present report we will review the current status of the tools and resources we have developed along the past seven years to help in the setting-up or the use of MLVA assays or lately for analysing Clustered Regularly Interspaced Short Palindromic Repeats called CRISPRs which are the basis for spoligotyping assays.

CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea

Arrays of clustered, regularly interspaced short palindromic repeats (CRISPRs) are widespread in the genomes of many bacteria and almost all archaea. These arrays are composed of direct repeats that are separated by similarly sized non-repetitive spacers. CRISPR arrays, together with a group of associated proteins, confer resistance to phages, possibly by an RNA-interference-like mechanism. This Progress discusses the structure and function of this newly recognized antiviral mechanism.