Development of an integrative vector for the expression of antisense RNA in Clostridium difficile

Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome

Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916 is an ICE found in several Gram-positive genera, including Enterococcus, Staphylococcus, Streptococcus, and Clostridioides (previously Clostridium). In contrast to the many ICEs that preferentially integrate into a single site, Tn916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 105 independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for C. difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.

Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome

Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916 is an ICE found in several Gram-positive genera, including Enterococcus, Staphylococcus, Streptococcus, and Clostridum. In contrast to the many ICEs that preferentially integrate into a single site, Tn916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 105 independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for Clostridium difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.

Transcription termination and antitermination are critical for the fitness and function of the integrative and conjugative element Tn916

Premature expression of genes in mobile genetic elements can be detrimental to their bacterial hosts. Tn916, the founding member of a large family of integrative and conjugative elements (ICEs; aka conjugative transposons), confers tetracycline-resistance and is found in several Gram-positive bacterial species. We identified a transcription terminator near one end of Tn916 that functions as an insulator that prevents expression of element genes when Tn916 is integrated downstream from an active host promoter. The terminator blocked expression of Tn916 genes needed for unwinding and rolling circle replication of the element DNA, and loss of the terminator caused a fitness defect for the host cells. Further, we identified an element-encoded antiterminator (named canT for conjugation-associated antitermination) that is essential for transcription of Tn916 genes after excision of the element from the host chromosome. We found that the antiterminator is orientation-specific, functions with heterologous promoters and terminators, is processive and is most likely a cis-acting RNA. Insulating gene expression in conjugative elements that are integrated in the chromosome is likely a key feature of the interplay between mobile genetic elements and their hosts and appears to be critical for the function and evolution of the large family of Tn916-like elements.

Activation of the integrative and conjugative element Tn916 causes growth arrest and death of host bacteria

Integrative and conjugative elements (ICEs) serve as major drivers of bacterial evolution. These elements often confer some benefit to host cells, including antibiotic resistance, metabolic capabilities, or pathogenic determinants. ICEs can also have negative effects on host cells. Here, we investigated the effects of the ICE (conjugative transposon) Tn916 on host cells. Because Tn916 is active in a relatively small subpopulation of host cells, we developed a fluorescent reporter system for monitoring activation of Tn916 in single cells. Using this reporter, we found that cell division was arrested in cells of Bacillus subtilis and Enterococcus faecalis (a natural host for Tn916) that contained an activated (excised) Tn916. Furthermore, most of the cells with the activated Tn916 subsequently died. We also observed these phenotypes on the population level in B. subtilis utilizing a modified version of Tn916 that can be activated in the majority of cells. We identified two genes (orf17 and orf16) in Tn916 that were sufficient to cause growth defects in B. subtilis and identified a single gene, yqaR, that is in a defective phage (skin) in the B. subtilis chromosome that was required for this phenotype. These three genes were only partially responsible for the growth defect caused by Tn916, indicating that Tn916 possesses multiple mechanisms to affect growth and viability of host cells. These results highlight the complex relationships that conjugative elements have with their host cells and the interplay between mobile genetic elements.

The cwp66 Gene Affects Cell Adhesion, Stress Tolerance, and Antibiotic Resistance in Clostridioides difficile

Clostridioides difficile is a Gram-positive, spore-forming anaerobic bacteria that is one of the leading causes of antibiotic-associated diarrhea. The cell wall protein 66 gene (cwp66) encodes a cell wall protein, which is the second major cell surface antigen of C. difficile. Although immunological approaches, such as antibodies and purified recombinant proteins, have been implemented to study the role of Cwp66 in cell adhesion, no deletion mutant of the cwp66 gene has yet been characterized. We constructed a cwp66 gene deletion mutant using Clustered Regularly Interspaced Short Palindromic Repeats Cpf1 (CRISPR-Cpf1) system. The phenotypic and transcriptomic changes of the Δcwp66 mutant compared with the wild-type (WT) strain were studied. The deletion of the cwp66 gene led to the decrease of cell adhesive capacity, cell motility, and stresses tolerance (to Triton X-100, acidic environment, and oxidative stress). Interestingly, the Δcwp66 mutant is more sensitive than the WT strain to clindamycin, ampicillin, and erythromycin but more resistant than the latter to vancomycin and metronidazole. Moreover, mannitol utilization capability in the Δcwp66 mutant was lost. Comparative transcriptomic analyses indicated that (i) 22.90-fold upregulation of cwpV gene and unable to express gpr gene were prominent in the Δcwp66 mutant; (ii) the cwp66 gene was involved in vancomycin resistance of C. difficile by influencing the expression of d-Alanine-d-Alanine ligase; and (iii) the mannose/fructose/sorbose IIC and IID components were upregulated in Δcwp66 mutant. The present work deepens our understanding of the contribution of the cwp66 gene to cell adhesion, stress tolerance, antibiotic resistance, and mannitol transportation of C. difficile. IMPORTANCE The cell wall protein 66 gene (cwp66) encodes a cell wall protein, which is the second major cell surface antigen of C. difficile. Although immunological approaches, such as antibodies and purified recombinant proteins, have been implemented to study the role of Cwp66 in cell adhesion, no deletion mutant of the cwp66 gene has yet been characterized. The current study provides direct evidence that the cwp66 gene serves as a major adhesion in C. difficile, and also suggested that deletion of the cwp66 gene led to the decrease of cell adhesive capacity, cell motility, and stresses tolerance (to Triton X-100, acidic environment, and oxidative stress). Interestingly, the antibiotic resistance and carbon source utilization profiles of the Δcwp66 mutant were significantly changed. These phenotypes were detrimental to the survival and pathogenesis of C. difficile in the human gut and may shed light on preventing C. difficile infection.

In vivo atomic force microscopy-infrared spectroscopy of bacteria

A new experimental platform for probing nanoscale molecular changes in living bacteria using atomic force microscopy-infrared (AFM-IR) spectroscopy is demonstrated. This near-field technique is eminently suited to the study of single bacterial cells. Here, we report its application to monitor dynamical changes occurring in the cell wall during cell division in Staphylococcus aureus using AFM to demonstrate the division of the cell and AFM-IR to record spectra showing the thickening of the septum. This work was followed by an investigation into single cells, with particular emphasis on cell-wall signatures, in several bacterial species. Specifically, mainly cell wall components from S. aureus and Escherichia coli containing complex carbohydrate and phosphodiester groups, including peptidoglycans and teichoic acid, could be identified and mapped at nanometre spatial resolution. Principal component analysis of AFM-IR spectra of six living bacterial species enabled the discrimination of Gram-positive from Gram-negative bacteria based on spectral bands originating mainly from the cell wall components. The ability to monitor in vivo molecular changes during cellular processes in bacteria at the nanoscale opens a new platform to study environmental influences and other factors that affect bacterial chemistry.

Plasmids can transfer to Clostridium difficile CD37 and 630Δerm both by a DNase resistant conjugation-like mechanism and a DNase sensitive mechanism

Broad host range conjugative plasmids that replicate in Escherichia coli have been widely used to mobilise smaller replicons, bearing their cognate origin of transfer (oriT) into a variety of organisms that are less tractable genetically, such as Clostridium (Clostridioides) difficile. In this work we demonstrated that the oriT region of pMTL9301 (derived from RK2) is not required for transfer between E. coli and C. difficile strains 630Δerm and CD37 and that this oriT-independent transfer is abolished in the presence of DNase when CD37 is the recipient. Transfer to the 630Δerm strain is DNase resistant even without an obvious oriT, when E. coli CA434 is used as a donor and is sensitive to DNase when E. coli HB101 is the donor.

Multiplexed CRISPR-Cpf1-Mediated Genome Editing in Clostridium difficile toward the Understanding of Pathogenesis of C. difficile Infection

Clostridium difficile is often the primary cause of nosocomial diarrhea, leading to thousands of deaths annually worldwide. The availability of an efficient genome editing tool for C. difficile is essential to understanding its pathogenic mechanism and physiological behavior. Although CRISPR-Cas9 has been extensively employed for genome engineering in various organisms, large gene deletion and multiplex genome editing is still challenging in microorganisms with underdeveloped genetic engineering tools. Here, we describe a streamlined CRISPR-Cpf1-based toolkit to achieve precise deletions of fur, tetM, and ermB1/2 in C. difficile with high efficiencies. All of these genes are relevant to important phenotypes (including iron uptake, antibiotics resistance, and toxin production) as related to the pathogenesis of C. difficile infection (CDI). Furthermore, we were able to delete an extremely large locus of 49.2-kb comprising a phage genome ( phiCD630-2) and realized multiplex genome editing in a single conjugation with high efficiencies (simultaneous deletion of cwp66 and tcdA). Our work highlighted the first application of CRISPR-Cpf1 for multiplexed genome editing and extremely large gene deletion in C. difficile, which are both crucial for understanding the pathogenic mechanism of C. difficile and developing strategies to fight against CDI. In addition, for the DNA cloning, we developed a one-step-assembly protocol along with a Python-based algorithm for automatic primer design, shortening the time for plasmid construction to half that of conventional procedures. The approaches we developed herein are easily and broadly applicable to other microorganisms. Our results provide valuable guidance for establishing CRISPR-Cpf1 as a versatile genome engineering tool in prokaryotic cells.

The evolving epidemic of Clostridium difficile 630

Clostridium difficile is a major pathogen responsible for a range of diseases in humans and animals. The genetic tools used to explore C. difficile biology are a relatively recent development in comparison to those used to investigate some other pathogens. Consequently, a rapid and haphazard dispersal of strains throughout the scientific community has led to the evolution of different C. difficile lineages within strains in different geographical locations and these genotypic differences are likely to affect the phenotype of the organism. Here we review the history of C. difficile 630, the first genome-sequenced C. difficile isolate and the most widely distributed reference strain, and its derivatives. We also invite researchers to take part in a community wide genome sequencing study to trace the evolution of these strains as they have travelled between laboratories around the world.

CdtR Regulates TcdA and TcdB Production in Clostridium difficile

Clostridium difficile is a global health burden and the leading cause of antibiotic-associated diarrhoea worldwide, causing severe gastrointestinal disease and death. Three well characterised toxins are encoded by this bacterium in two genetic loci, specifically, TcdB (toxin B) and TcdA (toxin A) in the Pathogenicity Locus (PaLoc) and binary toxin (CDT) in the genomically distinct CDT locus (CdtLoc). Toxin production is controlled by regulators specific to each locus. The orphan response regulator, CdtR, encoded within the CdtLoc, up-regulates CDT production. Until now there has been no suggestion that CdtR influences TcdA and TcdB production since it is not carried by all PaLoc-containing strains and CdtLoc is not linked genetically to PaLoc. Here we show that, in addition to CDT, CdtR regulates TcdA and TcdB production but that this effect is strain dependent. Of clinical relevance, CdtR increased the production of TcdA, TcdB and CDT in two epidemic ribotype 027 human strains, modulating their virulence in a mouse infection model. Strains traditionally from animal lineages, notably ribotype 078 strains, are increasingly being isolated from humans and their genetic and phenotypic analysis is critical for future studies on this important pathogen. Here we show that CdtR-mediated toxin regulation did not occur in other strain backgrounds, including a ribotype 078 animal strain. The finding that toxin gene regulation is strain dependent highlights the regulatory diversity between C. difficile isolates and the importance of studying virulence regulation in diverse lineages and clinically relevant strains. Our work provides the first evidence that TcdA, TcdB and CDT production is linked by a common regulatory mechanism and that CdtR may act as a global regulator of virulence in epidemic 027 strains.

Clostridium difficile is the leading cause of antibiotic-associated diarrhoea. The TcdB, TcdA and binary toxins produced by C. difficile are encoded in two genomically distinct loci: TcdB and TcdA in the Pathogenicity Locus (PaLoc) and binary toxin (CDT) in the CDT locus (CdtLoc). Toxin production is primarily controlled by regulators specific to each locus. Because the presence of these loci varies amongst different strains of C. difficile, no rational link for their co-regulation has ever been proposed. Here we have shown that the regulator of CDT production, CdtR, also regulates production of TcdA and TcdB in a strain dependent manner. These results represent the first evidence that TcdA and TcdB production is linked to the production of CDT by a common regulatory mechanism. Collectively, our results establish CdtR as an important virulence regulator in two clinically important, epidemic strains of C. difficile, and further highlights the need to investigate regulatory mechanisms of important virulence factors in diverse strain backgrounds.

Mobile genetic elements in Clostridium difficile and their role in genome function

Approximately 11% the Clostridium difficile genome is made up of mobile genetic elements which have a profound effect on the biology of the organism. This includes transfer of antibiotic resistance and other factors that allow the organism to survive challenging environments, modulation of toxin gene expression, transfer of the toxin genes themselves and the conversion of non-toxigenic strains to toxin producers. Mobile genetic elements have also been adapted by investigators to probe the biology of the organism and the various ways in which these have been used are reviewed.

Complete genome sequence of BS49 and draft genome sequence of BS34A, Bacillus subtilis strains carrying Tn916

Bacillus subtilis strains BS49 and BS34A, both derived from a common ancestor, carry one or more copies of Tn916, an extremely common mobile genetic element capable of transfer to and from a broad range of microorganisms. Here, we report the complete genome sequence of BS49 and the draft genome sequence of BS34A, which have repeatedly been used as donors to transfer Tn916, Tn916 derivatives or oriTTn916-containing plasmids to clinically important pathogens.

Spo0A differentially regulates toxin production in evolutionarily diverse strains of Clostridium difficile

Clostridium difficile is an important pathogen of humans and animals, representing a significant global healthcare problem. The last decade has seen the emergence of epidemic BI/NAP1/027 and ribotype 078 isolates, associated with the onset of more severe disease and higher rates of morbidity and mortality. However, little is known about these isolates at the molecular level, partly due to difficulties in the genetic manipulation of these strains. Here we report the development of an optimised Tn916-mediated plasmid transfer system, and the use of this system to construct and complement spo0A mutants in a number of different C. difficile strain backgrounds. Spo0A is a global regulator known to control sporulation, but may also be involved in the regulation of potential virulence factors and other phenotypes. Recent studies have failed to elucidate the role of Spo0A in toxin A and toxin B production by C. difficile, with conflicting data published to date. In this study, we aimed to clarify the role of Spo0A in production of the major toxins by C. difficile. Through the construction and complementation of spo0A mutants in two ribotype 027 isolates, we demonstrate that Spo0A acts as a negative regulator of toxin A and toxin B production in this strain background. In addition, spo0A was disrupted and subsequently complemented in strain 630Δerm and, for the first time, in a ribotype 078 isolate, JGS6133. In contrast to the ribotype 027 strains, Spo0A does not appear to regulate toxin production in strain 630Δerm. In strain JGS6133, Spo0A appears to negatively regulate toxin production during early stationary phase, but has little effect on toxin expression during late stationary phase. These data suggest that Spo0A may differentially regulate toxin production in phylogenetically distinct C. difficile strain types. In addition, Spo0A may be involved in regulating some aspects of C. difficile motility.

Effect of subinhibitory concentrations of four commonly used biocides on the conjugative transfer of Tn916 in Bacillus subtilis

Objectives

Large amounts of biocides are used to reduce and control bacterial growth in the healthcare sector, food production and agriculture. This work explores the effect of subinhibitory concentrations of four commonly used biocides (ethanol, hydrogen peroxide, chlorhexidine digluconate and sodium hypochlorite) on the conjugative transposition of the mobile genetic element Tn916.

Methods

Conjugation assays were carried out between Bacillus subtilis strains. The donor containing Tn916 was pre-exposed to subinhibitory concentrations of each biocide for a defined length of time, which was determined by an analysis of the transcriptional response of the promoter upstream of tet(M) using β-glucuronidase reporter assays.

Results

Ethanol significantly (P = 0.01) increased the transfer of Tn916 by 5-fold, whereas hydrogen peroxide, chlorhexidine digluconate and sodium hypochlorite did not significantly affect the transfer frequency.

Conclusions

These results suggest that exposure to subinhibitory concentrations of ethanol may induce the transfer of Tn916-like elements and any resistance genes they contain.

Fitness costs of various mobile genetic elements in Enterococcus faecium and Enterococcus faecalis

Objectives

To determine the fitness effects of various mobile genetic elements (MGEs) in Enterococcus faecium and Enterococcus faecalis when newly acquired. We also tested the hypothesis that the biological cost of vancomycin resistance plasmids could be mitigated during continuous growth in the laboratory.

Methods

Different MGEs, including two conjugative transposons (CTns) of the Tn916 family (18 and 33 kb), a pathogenicity island (PAI) of 200 kb and vancomycin-resistance (vanA) plasmids (80–200 kb) of various origins and classes, were transferred into common ancestral E. faecium and E. faecalis strains by conjugation assays and experimentally evolved (vanA plasmids only). Transconjugants were characterized by PFGE, S1 nuclease assays and Southern blotting hybridization analyses. Single specific primer PCR was performed to determine the target sites for the insertion of the CTns. The fitness costs of various MGEs in E. faecium and E. faecalis were estimated in head-to-head competition experiments, and evolved populations were generated in serial transfer assays.

Results

The biological cost of a newly acquired PAI and two CTns were both host- and insertion-locus-dependent. Newly acquired vanA plasmids may severely reduce host fitness (25%–27%), but these costs were rapidly mitigated after only 400 generations of continuous growth in the absence of antibiotic selection.

Conclusions

Newly acquired MGEs may impose an immediate biological cost in E. faecium. However, as demonstrated for vanA plasmids, the initial costs of MGE carriage may be mitigated during growth and beneficial plasmid–host association can rapidly emerge.

Novel system for efficient isolation of Clostridium double-crossover allelic exchange mutants enabling markerless chromosomal gene deletions and DNA integration

Isolation of Clostridium mutants based on gene replacement via allelic exchange remains a major limitation for this important genus. Use of a heterologous counterselection marker can facilitate the identification of the generally rare allelic exchange events. We report on the development of an inducible counterselection marker and describe its utility and broad potential in quickly and efficiently generating markerless DNA deletions and integrations at any genomic locus without the need for auxotrophic mutants or the use of the mobile group II introns. This system is based on a codon-optimized mazF toxin gene from Escherichia coli under the control of a lactose-inducible promoter from Clostridium perfringens. This system is potentially applicable to almost all members of the genus Clostridium due to their similarly low genomic GC content and comparable codon usage. We isolated all allelic-exchange-based gene deletions (ca_p0167, sigF, and sigK) or disruptions (ca_p0157 and sigF) we attempted and integrated a 3.6-kb heterologous DNA sequence (made up of a Clostridium ljungdahlii 2.1-kb formate dehydrogenase [fdh] gene plus a FLP recombination target [FRT]-flanked thiamphenicol resistance marker) into the Clostridium acetobutylicum chromosome. Furthermore, we report on the development of a plasmid system with inducible segregational instability, thus enabling efficient deployment of the FLP-FRT system to generate markerless deletion or integration mutants. This enabled expeditious deletion of the thiamphenicol resistance marker from the fdh integrant strain as well as the sigK deletion strain. More generally, our system can potentially be applied to other organisms with underdeveloped genetic tools.

Behavior and target site selection of conjugative transposon Tn916 in two different strains of toxigenic Clostridium difficile

The insertion sites of the conjugative transposon Tn916 in the anaerobic pathogen Clostridium difficile were determined using Illumina Solexa high-throughput DNA sequencing of Tn916 insertion libraries in two different clinical isolates: 630ΔE, an erythromycin-sensitive derivative of 630 (ribotype 012), and the ribotype 027 isolate R20291, which was responsible for a severe outbreak of C. difficile disease. A consensus 15-bp Tn916 insertion sequence was identified which was similar in both strains, although an extended consensus sequence was observed in R20291. A search of the C. difficile 630 genome showed that the Tn916 insertion motif was present 100,987 times, with approximately 63,000 of these motifs located in genes and 35,000 in intergenic regions. To test the usefulness of Tn916 as a mutagen, a functional screen allowed the isolation of a mutant. This mutant contained Tn916 inserted into a gene involved in flagellar biosynthesis.

Antibiotic and antiseptic resistance genes are linked on a novel mobile genetic element: Tn6087

Objectives

Tn916-like elements are one of the most common types of integrative and conjugative element (ICE). In this study we aimed to determine whether novel accessory genes, i.e. genes whose products are not involved in mobility or regulation, were present on a Tn916-like element (Tn6087) isolated from Streptococcus oralis from the human oral cavity.

Methods

A minocycline-resistant isolate was analysed using restriction fragment length polymorphism (RFLP) analysis on amplicons derived from Tn916 and DNA sequencing to determine whether there were genetic differences in Tn6087 compared with Tn916. Mutational analysis was used to determine whether the novel accessory gene found was responsible for an observed extra phenotype.

Results

A novel Tn916-like element, Tn6087, is described that encodes both antibiotic and antiseptic resistance. The antiseptic resistance protein is encoded by a novel small multidrug resistance gene, designated qrg, that was shown to encode resistance to cetyltrimethylammonium bromide (CTAB), also known as cetrimide bromide.

Conclusions

This is the first Tn916-like element described that confers both antibiotic and antiseptic resistance, suggesting that selection of either antibiotic or antiseptic resistance will also select for the other and further highlights the need for prudent use of both types of compound.

Tn916-like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance

Antibiotic-resistant Gram-positive bacteria are responsible for morbidity and mortality in healthcare environments. Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus and Streptococcus pneumoniae can all exhibit clinically relevant multidrug resistance phenotypes due to acquired resistance genes on mobile genetic elements. It is possible that clinically relevant multidrug-resistant Clostridium difficile strains will appear in the future, as the organism is adept at acquiring mobile genetic elements (plasmids and transposons). Conjugative transposons of the Tn916/Tn1545 family, which carry major antibiotic resistance determinants, are transmissible between these different bacteria by a conjugative mechanism during which the elements are excised by a staggered cut from donor cells, converted to a circular form, transferred by cell-cell contact and inserted into recipient cells by a site-specific recombinase. The ability of these conjugative transposons to acquire additional, clinically relevant antibiotic resistance genes importantly contributes to the emergence of multidrug resistance.

Transposon mutagenesis in Clostridium difficile

Genetic manipulation of Clostridium difficile is notoriously difficult, currently there is only one reliable method for generating random mutations in the organism and that is to use the conjugative transposon Tn916. Tn916 enters the genome of most strains of C. difficile with no obvious target site preference. In order to use the genome strain C. difficile 630 for transposon mutagenesis a erythromycin-sensitive derivative C. difficile 630Deltaerm was constructed and the Tn916 derivative, Tn916DeltaE, was shown to enter the genome at multiple sites enabling the construction of a Tn916 insertion library.

A modular master on the move: the Tn916 family of mobile genetic elements

The Tn916 family is a group of mobile genetic elements that are widespread among many commensal and pathogenic bacteria. These elements are found primarily, but not exclusively, in the Firmicutes. They are integrated into the bacterial genome and are capable of conjugative transfer to a new host and, often, intracellular transposition to a different genomic site - hence their name: 'conjugative transposons', or 'integrative conjugative elements'. An increasing variety of Tn916 relatives are being reported from different bacteria, harbouring genes coding for resistance to various antibiotics and the potential to encode other functions, such as lantibiotic immunity. This family of mobile genetic elements has an extraordinary ability to acquire accessory genes, making them important vectors in the dissemination of various traits among environmental, commensal and clinical bacteria. These elements are also responsible for genome rearrangements, providing considerable raw material on which natural selection can act. Therefore, the study of this family of mobile genetic elements is essential for a better understanding and control of the current rise of antibiotic resistance among pathogenic bacteria.

Characterization of tet(32) genes from the oral metagenome

tet(32) Was identified in three bacterial isolates and in metagenomic DNA from the human oral cavity. The regions immediately flanking the gene were found to have similarities to the mobile elements TnB1230 from Butyrivibrio fibrisolvens, ATE-3 from Arcanobacterium pyogenes, and CTn5 from Clostridium difficile.

Diversity of putative Tn5253-like elements in Streptococcus pneumoniae

Pneumococcal resistance to tetracycline, chloramphenicol, erythromycin and clindamycin is often attributed to carriage of conjugative transposons of the Tn916 family. The less well studied conjugative transposon Tn5253 is a composite transposon consisting of a Tn916-like element inserted within the unrelated Tn5252 element, which has also been associated with chloramphenicol and tetracycline resistance. Here, carriage of the Tn5252 integrase (int(5252)), Tn5252-encoded umuC and umuD homologues and Tn916 integrase (int(916)) was examined among 55 clinical isolates of Streptococcus pneumoniae resistant to one or more of the above mentioned antibiotics. Tn5253-associated genes were common among the antibiotic-resistant S. pneumoniae examined, including members of international clones, although the spectrum of genes and resistances carried was diverse. Analysis of five isolates demonstrated insertion of a Tn5253-related element at the same chromosomal locus but sequence and restriction site diversity. This study shows for the first time a high degree of variability of Tn5253-related elements within clinical isolates of pneumococci. The fact that these elements are prevalent among internationally recognised pandemic clones warrants a more intensive investigation.

Evaluation of the metS and murB loci for antibiotic discovery using targeted antisense RNA expression analysis in Bacillus anthracis

The biowarfare-relevant bacterial pathogen Bacillus anthracis contains two paralogs each of the metS and murB genes, which encode the important antibiotic target functions methionyl-tRNA synthetase and UDP-N-acetylenolpyruvoylglucosamine reductase, respectively. Empirical screens were conducted to detect and characterize gene fragments of each of these four genes that could cause growth reduction of B. anthracis when inducibly expressed from a plasmid-borne promoter. Numerous such gene fragments that were overwhelmingly in the antisense orientation were identified for the metS1 and murB2 alleles, while no such orientation bias was seen for the metS2 and murB1 alleles. Gene replacement mutagenesis was used to confirm the essentiality of the metS1 and murB2 alleles, and the nonessentiality of the metS2 and murB1 alleles, for vegetative growth. Induced transcription of RNA from metS1 and murB2 antisense-oriented gene fragments resulted in specific reduction of mRNA of their cognate genes. Attenuation of MetS1 enzyme expression hypersensitized B. anthracis cells to a MetS-specific antimicrobial compound but not to other antibiotics that affect cell wall assembly, fatty acid biosynthesis, protein translation, or DNA replication. Antisense-dependent reduction of MurB2 enzyme expression caused hypersensitivity to beta-lactam antibiotics, a synergistic response that has also been noted for the MurA-specific antibiotic fosfomycin. These experiments form the basis of mode-of-action detection assays that can be used in the discovery of novel MetS- or MurB-specific antibiotic drugs that are effective against B. anthracis or other gram-positive bacterial pathogens.

Construction and analysis of chromosomal Clostridium difficile mutants

Clostridium difficile is an emerging nosocomial pathogen of increasing importance and virulence but our ability to study the molecular mechanisms underlying the pathogenesis of C. difficile-associated disease has been limited because of a lack of tools for its genetic manipulation. We have now developed a reproducible method for the targeted insertional inactivation of chromosomal C. difficile genes. The approach relies on the observation that an Escherichia coli-Clostridium perfringens shuttle vector is unstable in C. difficile and can be used as a form of conditional lethal vector to deliver gene constructs to the chromosome. We have used this methodology to insertionally inactivate two putative response regulator genes, rgaR and rgbR, which encode proteins with similarity to the toxin gene regulator, VirR, from C. perfringens. Transcriptomic analysis demonstrated that the C. difficile RgaR protein positively regulated four genes, including a putative agrBD operon. The RgaR protein was also purified and shown to bind specifically to sites that contained two consensus VirR boxes located just upstream of the putative promoters of these genes. The development of this methodology will significantly enhance our ability to use molecular approaches to develop a greater understanding of the ability of C. difficile to cause disease.

Incidence and behaviour of Tn916-like elements within tetracycline-resistant bacteria isolated from root canals

INTRODUCTION

Tetracycline resistance is commonly found in endodontic bacteria. One of the most common tetracycline-resistance genes is tet(M), which is often encoded on the broad-host-range conjugative transposon Tn916. This study aimed to determine whether tet(M) was present in bacteria isolated from endodontic patients at the Eastman Dental Institute and whether this gene was carried on the transferable conjugative transposon Tn916.

METHODS

The cultivable microflora isolated from 15 endodontic patients was screened for resistance to tetracycline. Polymerase chain reactions for tet(M) and for unique regions of Tn916 were carried out on the DNA of all tetracycline-resistant bacteria. Filter-mating experiments were used to see if transfer of any Tn916-like elements could occur.

RESULTS

Eight out of 15 tetracycline-resistant bacteria isolated were shown to possess tet(M). Furthermore, four of these eight were shown to possess the Tn916-unique regions linked to the tet(M) gene. Transfer experiments demonstrated that a Neisseria sp. donor could transfer an extremely unstable Tn916-like element to Enterococcus faecalis.

CONCLUSIONS

The tet(M) gene is present in the majority of tetracycline-resistant bacteria isolated in this study and the conjugative transposon Tn916 has been shown to be responsible for the support and transfer of this gene in some of the bacteria isolated.

The maintenance in the oral cavity of children of tetracycline-resistant bacteria and the genes encoding such resistance

OBJECTIVES

To investigate the maintenance of tetracycline-resistant oral bacteria and the genes encoding tetracycline resistance in these bacteria in children (aged 4--6 years) over a period of 12 months.

METHODS

Plaque and saliva samples were taken from 26 children. Tetracycline-resistant bacteria were isolated and identified. The types of resistance genes and their genetic locations were also determined.

RESULTS

Fifteen out of 18 children harboured tetracycline-resistant (defined as having a MIC>or=8 mg/L) oral bacteria at all three time points. The median percentage of tetracycline-resistant bacteria at 0, 6 and 12 months was 1.37, 1.37 and 0.85%, respectively; these were not significantly different. The MIC(50) of the group was 64 mg/L at all three time points compared with the MIC(90), which was 64 mg/L at 0 months, and 128 mg/L at 6 and 12 months. The most prevalent resistant species were streptococci (68%), which were isolated at all three time points in 13 children. The most prevalent gene encoding tetracycline resistance was tet(M) and this was found in different species at all three time points. For the first time, tet(32) was found in Streptococcus parasanguinis and Eubacterium saburreum. PCR and Southern-blot analysis (on isolates from three of the children) showed that the tet(M) gene was located on a Tn916-like element and could be detected at all three time points, in four different genera, Streptococcus, Granulicatella, Veillonella and Neisseria.

CONCLUSIONS

The results of this study show that tetracycline-resistant bacteria and tet(M) are maintained within the indigenous oral microbiota of children, even though they are unlikely to have been directly exposed to tetracycline.

Acd, a peptidoglycan hydrolase of Clostridium difficile with N-acetylglucosaminidase activity

A gene encoding a putative peptidoglycan hydrolase was identified by sequence similarity searching in the Clostridium difficile 630 genome sequence, and the corresponding protein, named Acd (autolysin of C. difficile) was expressed in Escherichia coli. The deduced amino acid sequence of Acd shows a modular structure with two main domains: an N-terminal domain exhibiting repeated sequences and a C-terminal catalytic domain. The C-terminal domain exhibits sequence similarity with the glucosaminidase domains of Staphylococcus aureus Atl and Bacillus subtilis LytD autolysins. Purified recombinant Acd produced in E. coli was confirmed to be a cell-wall hydrolase with lytic activity on the peptidoglycan of several Gram-positive bacteria, including C. difficile. The hydrolytic specificity of Acd was studied by RP-HPLC analysis and MALDI-TOF MS using B. subtilis cell-wall extracts. Muropeptides generated by Acd hydrolysis demonstrated that Acd hydrolyses peptidoglycan bonds between N-acetylglucosamine and N-acetylmuramic acid, confirming that Acd is an N-acetylglucosaminidase. The transcription of the acd gene increased during vegetative cellular growth of C. difficile 630. The sequence of the acd gene appears highly conserved in C. difficile strains. Regarding deduced amino acid sequences, the C-terminal domain with enzymic function appears to be the most conserved of the two main domains. Acd is the first known autolysin involved in peptidoglycan hydrolysis of C. difficile.

Generation of an erythromycin-sensitive derivative of Clostridium difficile strain 630 (630Δerm) and demonstration that the conjugative transposon Tn916ΔE enters the genome of this strain at multiple sites

Erythromycin resistance in Clostridium difficile strain 630 is conferred by a genetic element termed Tn5398 which contains two erm(B) genes: erm1(B) and erm2(B). An erythromycin-sensitive derivative of strain 630 (designated 630Deltaerm) was generated by spontaneous mutation after continuous subculture for 30 days. This strain had lost the erm2(B) gene from within Tn5398 but retained erm1(B). However, the strain could revert to erythromycin resistance at a frequency of 2.79 x 10(-8), although it still contained the deletion of erm2(B). The availability of C. difficile 630Deltaerm allowed the behaviour of Tn916DeltaE to be investigated in this strain. This element entered the genome at multiple sites indicating that it could be useful as an insertional mutagen.

Genetic basis of erythromycin resistance in oral bacteria

We determined the prevalence of erythromycin-resistant bacteria in the oral cavity and identified mef and erm(B) as the most common resistance determinants. In addition, we demonstrate the genetic linkage, on various Tn1545-like conjugative transposons, between erythromycin and tetracycline resistance in a number of isolates.

Characterization of Tn916S, a Tn916-like element containing the tetracycline resistance determinant tet(S)

We have characterized a transferable tetracycline resistance (Tcr) element from a Streptococcus intermedius isolate. The gene responsible for this resistance was identified by PCR and Southern hybridization as tet(S). Furthermore, the genetic support for this determinant was shown to be a conjugative transposon closely related to Tn916. This element has been designated Tn916S.

The development of Clostridium difficile genetic systems

Clostridum difficile is a major cause of healthcare-associated disease in the western world, and is particularly prominent in the elderly. Its incidence is rising concomitant with increasing longevity. More effective countermeasures are required. However, the pathogenesis of C. difficile infection is poorly understood. The lack of effective genetic tools is a principal reason for this ignorance. For many years, the only tools available for the transfer of genes into C. difficile have been conjugative transposons, such as Tn916, delivered via filter mating from Bacillus subtilis donors. They insert into a preferred site within the genome. Therefore, they may not be employed for classical mutagenesis studies, but can be employed to modulate gene function through the delivery of antisense RNA. Attempts to develop transformation procedures have so far met with little success. However, in recent years the situation has been dramatically improved through the demonstration of efficient conjugative transfer of both replication-proficient and replication-deficient plasmids from Escherichia coli donors. This efficient transfer can only be achieved in certain strains through negation of the indigenous restriction barrier, and is generally most effective when the plasmid employed is based on the replicon of the C. difficile plasmid, pCD6.