Rationally designed mariner vectors for functional genomic analysis of Actinobacillus pleuropneumoniae and other Pasteurellaceae species by transposon-directed insertion-site sequencing (TraDIS)

Comprehensive identification of conditionally essential genes requires efficient tools for generating high-density transposon libraries that, ideally, can be analysed using next-generation sequencing methods such as Transposon Directed Insertion-site Sequencing (TraDIS). The Himar1 (mariner) transposon is ideal for generating near-saturating mutant libraries, especially in AT-rich chromosomes, as the requirement for integration is a TA dinucleotide, and this transposon has been used for mutagenesis of a wide variety of bacteria. However, plasmids for mariner delivery do not necessarily work well in all bacteria. In particular, there are limited tools for functional genomic analysis of Pasteurellaceae species of major veterinary importance, such as swine and cattle pathogens, Actinobacillus pleuropneumoniae and Pasteurella multocida, respectively. Here, we developed plasmids, pTsodCPC9 and pTlacPC9 (differing only in the promoter driving expression of the transposase gene), that allow delivery of mariner into both these pathogens, but which should also be applicable to a wider range of bacteria. Using the pTlacPC9 vector, we have generated, for the first time, saturating mariner mutant libraries in both A. pleuropneumoniae and P. multocida that showed a near random distribution of insertions around the respective chromosomes as detected by TraDIS. A preliminary screen of 5000 mutants each identified 8 and 14 genes, respectively, that are required for growth under anaerobic conditions. Future high-throughput screening of the generated libraries will facilitate identification of mutants required for growth under different conditions, including in vivo, highlighting key virulence factors and pathways that can be exploited for development of novel therapeutics and vaccines.

Evaluation of the recombinant proteins RlpB and VacJ as a vaccine for protection against Glaesserella parasuis in pigs

BACKGROUND

Glaesserella parasuis, the causative agent of Glӓsser's disease, is widespread in swine globally resulting in significant economic losses to the swine industry. Prevention of Glӓsser's disease in pigs has been plagued with an inability to design broadly protective vaccines, as many bacterin based platforms generate serovar or strain specific immunity. Subunit vaccines are of interest to provide protective immunity to multiple strains of G. parasuis. Selected proteins for subunit vaccination should be widespread, highly conserved, and surface exposed.

RESULTS

Two candidate proteins for subunit vaccination (RlpB and VacJ) against G. parasuis were identified using random mutagenesis and an in vitro organ culture system. Pigs were vaccinated with recombinant RlpB and VacJ, outer membrane proteins with important contributions to cellular function and viability. Though high antibody titers to the recombinant proteins and increased interferon-γ producing cells were found in subunit vaccinated animals, the pigs were not protected from developing systemic disease.

CONCLUSIONS

It appears there may be insufficient RlpB and VacJ exposed on the bacterial surface for antibody to bind, preventing high RlpB and VacJ specific antibody titers from protecting animals from G. parasuis. Additionally, this work confirms the importance of utilizing the natural host species when assessing the efficacy of vaccine candidates.

Is e-cigarette use in non-smoking young adults associated with later smoking? A systematic review and meta-analysis

OBJECTIVE

The aim of this review was to investigate whether e-cigarette use compared with non-use in young non-smokers is associated with subsequent cigarette smoking.

DATA SOURCES

PubMed, Embase, Web of Science, Wiley Cochrane Library databases, and the 2018 Society for Research on Nicotine and Tobacco and Society for Behavioural Medicine conference abstracts.

STUDY SELECTION

All studies of young people (up to age 30 years) with a measure of e-cigarette use prior to smoking and an outcome measure of smoking where an OR could be calculated were included (excluding reviews and animal studies).

DATA EXTRACTION

Independent extraction was completed by multiple authors using a preprepared extraction form.

DATA SYNTHESIS

Of 9199 results, 17 studies were included in the meta-analysis. There was strong evidence for an association between e-cigarette use among non-smokers and later smoking (OR: 4.59, 95% CI: 3.60 to 5.85) when the results were meta-analysed in a random-effects model. However, there was high heterogeneity (I2 =88%).

CONCLUSIONS

Although the association between e-cigarette use among non-smokers and subsequent smoking appears strong, the available evidence is limited by the reliance on self-report measures of smoking history without biochemical verification. None of the studies included negative controls which would provide stronger evidence for whether the association may be causal. Much of the evidence also failed to consider the nicotine content of e-liquids used by non-smokers meaning it is difficult to make conclusions about whether nicotine is the mechanism driving this association.

Use of Proteins Identified through a Functional Genomic Screen To Develop a Protein Subunit Vaccine That Provides Significant Protection against Virulent Streptococcus suis in Pigs

Streptococcus suis is a bacterium that is commonly carried in the respiratory tract and that is also one of the most important invasive pathogens of swine, commonly causing meningitis, arthritis, and septicemia. Due to the existence of many serotypes and a wide range of immune evasion capabilities, efficacious vaccines are not readily available. The selection of S. suis protein candidates for inclusion in a vaccine was accomplished by identifying fitness genes through a functional genomics screen and selecting conserved predicted surface-associated proteins. Five candidate proteins were selected for evaluation in a vaccine trial and administered both intranasally and intramuscularly with one of two different adjuvant formulations. Clinical protection was evaluated by subsequent intranasal challenge with virulent S. suis While subunit vaccination with the S. suis proteins induced IgG antibodies to each individual protein and a cellular immune response to the pool of proteins and provided substantial protection from challenge with virulent S. suis, the immune response elicited and the degree of protection were dependent on the parenteral adjuvant given. Subunit vaccination induced IgG reactive against different S. suis serotypes, indicating a potential for cross protection.

The influence of cartilage thickness at the sigmoid notch on inclination at the distal radioulnar joint

AIMS

The aims of this study were: firstly, to investigate the influence of the thickness of cartilage at the sigmoid notch on the inclination of the distal radioulnar joint (DRUJ), and secondly, to compare the sensitivity and specificity of MRI with plain radiographs for the assessment of the inclination of the articular surface of the DRUJ in the coronal plane.

PATIENTS AND METHODS

Contemporaneous MRI images and radiographs of 100 wrists from 98 asymptomatic patients (mean age 43 years, (16 to 67); 52 male, 53%) with no history of a fracture involving the wrist or surgery to the wrist, were reviewed. The thickness of the cartilage at the sigmoid notch, inclination of the DRUJ and Tolat Type of each DRUJ were determined.

RESULTS

The assessment using MRI scans and cortical bone correlated well with radiographs, with a kappa value of 0.83. The mean difference between the inclination using the cortex and cartilage on MRI scans was 12°, leading to a change of Tolat type of inclination in 66% of wrists. No reverse oblique (Type 3) inclinations were found when using the cartilage to assess inclination.

CONCLUSION

These data revealed that when measuring the inclination of the DRUJ using cartilage, reverse oblique inclinations might not exist. The data suggest that performing an ulna shortening osteotomy might be reasonable even in distal radioulnar joints where the plain radiographic appearance suggests an unfavourable reverse oblique inclination in the coronal plane. We recommend using MRI to validate radiographs in those that appear to be reverse oblique (Tolat Type 3), as the true inclination might be different, thereby removing one possible contraindication to ulnar shortening. Cite this article: Bone Joint J 2017;99-B:369-75.

Expert consensus on facilitators and barriers to return-to-work following surgery for non-traumatic upper extremity conditions: a Delphi study

This Delphi study aimed to reach consensus on important facilitators and barriers for return-to-work following surgery for non-traumatic upper extremity conditions. In Round 1, experts ( n = 42) listed 134 factors, which were appraised in Rounds 2 and 3. Consensus (⩾85% agreement) was achieved for 13 facilitators (high motivation to return-to-work; high self-efficacy for return-to-work and recovery; availability of modified/alternative duties; flexible return-to-work arrangements; positive coping skills; limited heavy work exertion; supportive return-to-work policies; supportive supervisor/management; no catastrophic thinking; no fear avoidance to return-to-work; no fear avoidance to pain/activity; return to meaningful work duties; high job satisfaction) and six barriers (mood disorder diagnosis; pain/symptoms at more than one musculoskeletal site; heavy upper extremity exertions at work; lack of flexible return-to-work arrangements; lack of support from supervisor/management; high level of pain catastrophizing). Future prognostic studies are required to validate these biopsychosocial factors to further improve return-to-work outcomes.

LEVEL OF EVIDENCE

V.

A matched comparison study of hepatitis C treatment outcomes in the prison and community setting, and an analysis of the impact of prison release or transfer during therapy

Prisoners are a priority group for hepatitis C (HCV) treatment. Although treatment durations will become shorter using directly acting antivirals (DAAs), nearly half of prison sentences in Scotland are too short to allow completion of DAA therapy prior to release. The purpose of this study was to compare treatment outcomes between prison- and community-based patients and to examine the impact of prison release or transfer during therapy. A national database was used to compare treatment outcomes between prison treatment initiates and a matched community sample. Additional data were collected to investigate the impact of release or transfer on treatment outcomes. Treatment-naïve patients infected with genotype 1/2/3/4 and treated between 2009 and 2012 were eligible for inclusion. 291 prison initiates were matched with 1137 community initiates: SVRs were 61% (95% CI 55%-66%) and 63% (95% CI 60%-66%), respectively. Odds of achieving a SVR were not significantly associated with prisoner status (P=.33). SVRs were 74% (95% CI 65%-81%), 59% (95% CI 42%-75%) and 45% (95% CI 29%-62%) among those not released or transferred, transferred during treatment, or released during treatment, respectively. Odds of achieving a SVR were significantly associated with release (P<.01), but not transfer (P=.18). Prison-based HCV treatment achieves similar outcomes to community-based treatment, with those not released or transferred during treatment doing particularly well. Transfer or release during therapy should be avoided whenever possible, using anticipatory planning and medical holds where appropriate.

The essential genome of Streptococcus agalactiae

BACKGROUND

Next-generation sequencing of transposon-genome junctions from a saturated bacterial mutant library (Tn-seq) is a powerful tool that permits genome-wide determination of the contribution of genes to fitness of the organism under a wide range of experimental conditions. We report development, testing, and results from a Tn-seq system for use in Streptococcus agalactiae (group B Streptococcus; GBS), an important cause of neonatal sepsis.

METHODS

Our method uses a Himar1 mini-transposon that inserts at genomic TA dinucleotide sites, delivered to GBS on a temperature-sensitive plasmid that is subsequently cured from the bacterial population. In order to establish the GBS essential genome, we performed Tn-seq on DNA collected from three independent mutant libraries-with at least 135,000 mutants per library-at serial 24 h time points after outgrowth in rich media.

RESULTS

After statistical analysis of transposon insertion density and distribution, we identified 13.5 % of genes as essential and 1.2 % as critical, with high levels of reproducibility. Essential and critical genes are enriched for fundamental cellular housekeeping functions, such as acyl-tRNA biosynthesis, nucleotide metabolism, and glycolysis. We further validated our system by comparing fitness assignments of homologous genes in GBS and a close bacterial relative, Streptococcus pyogenes, which demonstrated 93 % concordance. Finally, we used our fitness assignments to identify signal transduction pathway components predicted to be essential or critical in GBS.

CONCLUSIONS

We believe that our baseline fitness assignments will be a valuable tool for GBS researchers and that our system has the potential to reveal key pathogenesis gene networks and potential therapeutic/preventative targets.

Whole genome investigation of a divergent clade of the pathogen Streptococcus suis

Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here, we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN, and cpn60) did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70), of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further, sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species.

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis

Background

Haemophilus parasuis is the etiologic agent of Glässer’s disease in pigs and causes devastating losses to the farming industry. Whilst some hyper-virulent isolates have been described, the relationship between genetics and disease outcome has been only partially established. In particular, there is weak correlation between serovar and disease phenotype. We sequenced the genomes of 212 isolates of H. parasuis and have used this to describe the pan-genome and to correlate this with clinical and carrier status, as well as with serotype.

Results

Recombination and population structure analyses identified five groups with very high rates of recombination, separated into two clades of H. parasuis with no signs of recombination between them. We used genome-wide association methods including discriminant analysis of principal components (DAPC) and generalised linear modelling (glm) to look for genetic determinants of this population partition, serovar and pathogenicity. We were able to identify genes from the accessory genome that were significantly associated with phenotypes such as potential serovar specific genes including capsule genes, and 48 putative virulence factors that were significantly different between the clinical and non-clinical isolates. We also show that the presence of many previously suggested virulence factors is not an appropriate marker of virulence.

Conclusions

These genes will inform the generation of new molecular diagnostics and vaccines, and refinement of existing typing schemes and show the importance of the accessory genome of a diverse species when investigating the relationship between genotypes and phenotypes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1179) contains supplementary material, which is available to authorized users.

Transposon mutagenesis in Mycoplasma hyopneumoniae using a novel mariner-based system for generating random mutations

Mycoplasma hyopneumoniae is the cause of enzootic pneumonia in pigs, a chronic respiratory disease associated with significant economic losses to swine producers worldwide. The molecular pathogenesis of infection is poorly understood due to the lack of genetic tools to allow manipulation of the organism and more generally for the Mycoplasma genus. The objective of this study was to develop a system for generating random transposon insertion mutants in M. hyopneumoniae that could prove a powerful tool in enabling the pathogenesis of infection to be unraveled. A novel delivery vector was constructed containing a hyperactive C9 mutant of the Himar1 transposase along with a mini transposon containing the tetracycline resistance cassette, tetM. M. hyopneumoniae strain 232 was electroporated with the construct and tetM-expressing transformants selected on agar containing tetracycline. Individual transformants contained single transposon insertions that were stable upon serial passages in broth medium. The insertion sites of 44 individual transformants were determined and confirmed disruption of several M. hyopneumoniae genes. A large pool of over 10 000 mutants was generated that should allow saturation of the M. hyopneumoniae strain 232 genome. This is the first time that transposon mutagenesis has been demonstrated in this important pathogen and could be generally applied for other Mycoplasma species that are intractable to genetic manipulation. The ability to generate random mutant libraries is a powerful tool in the further study of the pathogenesis of this important swine pathogen.

Generation of a Tn5 transposon library in Haemophilus parasuis and analysis by transposon-directed insertion-site sequencing (TraDIS)

Haemophilus parasuis is an important respiratory tract pathogen of swine and the etiological agent of Glässer's disease. The molecular pathogenesis of H. parasuis is not well studied, mainly due to the lack of efficient tools for genetic manipulation of this bacterium. In this study we describe a Tn5-based random mutagenesis method for use in H. parasuis. A novel chloramphenicol-resistant Tn5 transposome was electroporated into the virulent H. parasuis serovar 5 strain 29755. High transposition efficiency of Tn5, up to 10(4) transformants/μg of transposon DNA, was obtained by modification of the Tn5 DNA in the H. parasuis strain HS071 and establishment of optimal electrotransformation conditions, and a library of approximately 10,500 mutants was constructed. Analysis of the library using transposon-directed insertion-site sequencing (TraDIS) revealed that the insertion of Tn5 was evenly distributed throughout the genome. 10,001 individual mutants were identified, with 1561 genes being disrupted (69.4% of the genome). This newly-developed, efficient mutagenesis approach will be a powerful tool for genetic manipulation of H. parasuis in order to study its physiology and pathogenesis.

Comprehensive assignment of roles for Salmonella typhimurium genes in intestinal colonization of food-producing animals

Chickens, pigs, and cattle are key reservoirs of Salmonella enterica, a foodborne pathogen of worldwide importance. Though a decade has elapsed since publication of the first Salmonella genome, thousands of genes remain of hypothetical or unknown function, and the basis of colonization of reservoir hosts is ill-defined. Moreover, previous surveys of the role of Salmonella genes in vivo have focused on systemic virulence in murine typhoid models, and the genetic basis of intestinal persistence and thus zoonotic transmission have received little study. We therefore screened pools of random insertion mutants of S. enterica serovar Typhimurium in chickens, pigs, and cattle by transposon-directed insertion-site sequencing (TraDIS). The identity and relative fitness in each host of 7,702 mutants was simultaneously assigned by massively parallel sequencing of transposon-flanking regions. Phenotypes were assigned to 2,715 different genes, providing a phenotype–genotype map of unprecedented resolution. The data are self-consistent in that multiple independent mutations in a given gene or pathway were observed to exert a similar fitness cost. Phenotypes were further validated by screening defined null mutants in chickens. Our data indicate that a core set of genes is required for infection of all three host species, and smaller sets of genes may mediate persistence in specific hosts. By assigning roles to thousands of Salmonella genes in key reservoir hosts, our data facilitate systems approaches to understand pathogenesis and the rational design of novel cross-protective vaccines and inhibitors. Moreover, by simultaneously assigning the genotype and phenotype of over 90% of mutants screened in complex pools, our data establish TraDIS as a powerful tool to apply rich functional annotation to microbial genomes with minimal animal use.

Salmonella Typhimurium is a major cause of human diarrhoeal infections, usually acquired from chickens, pigs, cattle, or their products. To understand the basis of persistence and pathogenesis in these reservoir hosts, and to inform the design of novel vaccines and treatments, we generated a library of 7,702 S. Typhimurium mutants, each bearing an insertion at a random position in the genome. Using DNA sequencing, we identified the disrupted gene in each mutant and determined its relative abundance in a laboratory culture and after experimental infection of mice, chickens, pigs, and cattle. The method allowed large numbers of mutants to be investigated simultaneously, drastically reducing the number of animals required to perform a comprehensive screen. We identified mutants that grow in culture but do not survive in one or more of the animals. The genes disrupted in these mutants are inferred to be important for the infection process. Most of these genes were required in all three food-producing animals, but smaller subsets of genes may mediate persistence in a specific host species. The data provide the most comprehensive map of virulence-associated genes for any bacterial pathogen in natural hosts and are highly relevant for the design of control strategies.

Salmonella enterica serovar Typhimurium mutants completely lacking the F(0)F(1) ATPase are novel live attenuated vaccine strains

The F₀F₁ ATPase plays a central role in both the generation of ATP and the utilisation of ATP for cellular processes such as rotation of bacterial flagella. We have deleted the entire operon encoding the F₀F₁ ATPase, as well as genes encoding individual F₀ or F₁ subunits, in Salmonella enteric serovar Typhimurium. These mutants were attenuated for virulence, as assessed by bacterial counts in the livers and spleens of intravenously infected mice. The attenuated in vivo growth of the entire atp operon mutant was complemented by the insertion of the atp operon into the malXY pseudogene region. Following clearance of the attenuated mutants from the organs, mice were protected against challenge with the virulent wild type parent strain. We have shown that the F₀F₁ ATPase is important for bacterial growth in vivo and that atp mutants are effective live attenuated vaccines against Salmonella infection.

Multiple redundant stress resistance mechanisms are induced in Salmonella enterica serovar Typhimurium in response to alteration of the intracellular environment via TLR4 signalling

Toll-like receptor 4 (TLR4) senses bacterial LPS and is required for the control of systemic Salmonella enterica serovar Typhimurium infection in mice. The mechanisms of TLR4 activation and its downstream signalling cascades are well described, yet the direct effects on the pathogen of signalling via this receptor remain unknown. To investigate this we used microarray-based transcriptome profiling of intracellular S. Typhimurium during infection of primary bone marrow-derived macrophages from wild-type and TLR4-deficient mice. We identified 17 S. Typhimurium genes that were upregulated in the presence of functional TLR4. Nine of these genes have putative functions in oxidative stress resistance. We therefore examined S. Typhimurium gene expression during infection of NADPH oxidase-deficient macrophages, which lack normal oxidative killing mechanisms. We identified significant overlap between the 'TLR4-responsive' and 'NADPH oxidase-responsive' genes. This is new evidence for a link between TLR4 signalling and NADPH oxidase activity. Interestingly, with the exception of a dps mutant, S. Typhimurium strains lacking individual TLR4- and/or oxidative stress-responsive genes were not attenuated during intravenous murine infections. Our study shows that TLR4 activity, either directly or indirectly, induces the expression of multiple stress resistance genes during the intracellular life of S. Typhimurium.

Comprehensive identification of Salmonella enterica serovar typhimurium genes required for infection of BALB/c mice

Genes required for infection of mice by Salmonella Typhimurium can be identified by the interrogation of random transposon mutant libraries for mutants that cannot survive in vivo. Inactivation of such genes produces attenuated S. Typhimurium strains that have potential for use as live attenuated vaccines. A quantitative screen, Transposon Mediated Differential Hybridisation (TMDH), has been developed that identifies those members of a large library of transposon mutants that are attenuated. TMDH employs custom transposons with outward-facing T7 and SP6 promoters. Fluorescently-labelled transcripts from the promoters are hybridised to whole-genome tiling microarrays, to allow the position of the transposon insertions to be determined. Comparison of microarray data from the mutant library grown in vitro (input) with equivalent data produced after passage of the library through mice (output) enables an attenuation score to be determined for each transposon mutant. These scores are significantly correlated with bacterial counts obtained during infection of mice using mutants with individual defined deletions of the same genes. Defined deletion mutants of several novel targets identified in the TMDH screen are effective live vaccines.

The enzyme phosphoglucomutase (Pgm) is required by Salmonella enterica serovar Typhimurium for O-antigen production, resistance to antimicrobial peptides and in vivo fitness

The enzyme phosphoglucomutase (Pgm) catalyses the interconversion of glucose 1-phosphate and glucose 6-phosphate and contributes to glycolysis and the generation of sugar nucleotides for biosynthesis. To assess the role of this enzyme in the biology of the pathogen Salmonella enterica serovar Typhimurium we have characterized a pgm deletion mutant in strain SL1344. Compared to SL1344, SL1344 pgm had impaired growth in vitro, was deficient in the ability to utilize galactose as a carbon source and displayed reduced O-antigen polymer length. The mutant was also more susceptible to antimicrobial peptides and showed decreased fitness in the mouse typhoid model. The in vivo phenotype of SL1344 pgm indicated a role for pgm in the early stages of infection, most likely through deficient O-antigen production. Although pgm mutants in other pathogens have potential as live attenuated vaccine strains, SL1344 pgm was not sufficiently attenuated for such use.

Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)

Background

In recent years there has been an increasing problem with Staphylococcus aureus strains that are resistant to treatment with existing antibiotics. An important starting point for the development of new antimicrobial drugs is the identification of "essential" genes that are important for bacterial survival and growth.

Results

We have developed a robust microarray and PCR-based method, Transposon-Mediated Differential Hybridisation (TMDH), that uses novel bioinformatics to identify transposon inserts in genome-wide libraries. Following a microarray-based screen, genes lacking transposon inserts are re-tested using a PCR and sequencing-based approach. We carried out a TMDH analysis of the S. aureus genome using a large random mariner transposon library of around a million mutants, and identified a total of 351 S. aureus genes important for survival and growth in culture. A comparison with the essential gene list experimentally derived for Bacillus subtilis highlighted interesting differences in both pathways and individual genes.

Conclusion

We have determined the first comprehensive list of S. aureus essential genes. This should act as a useful starting point for the identification of potential targets for novel antimicrobial compounds. The TMDH methodology we have developed is generic and could be applied to identify essential genes in other bacterial pathogens.

Deletion of the gene encoding the glycolytic enzyme triosephosphate isomerase (tpi) alters morphology of Salmonella enterica serovar Typhimurium and decreases fitness in mice

The glycolytic enzyme triosephosphate isomerase (tpi) (EC 5.3.1.1) plays a key role in central carbon metabolism yet few studies have characterized isogenic bacterial mutants lacking this enzyme and none have examined its role in the in vivo fitness of a bacterial pathogen. Here we have deleted tpiA in Salmonella enterica serovar Typhimurium and found that the mutant had an altered morphology, displaying an elongated shape compared with the wild type. In a mouse model of typhoid fever the tpiA mutant was attenuated for growth as assessed by bacterial counts in the livers and spleens of infected mice. However, this attenuation was not deemed sufficient for consideration of a tpiA mutant as a live attenuated vaccine strain. These phenotypes were complemented by provision of tpiA on pBR322. We therefore provide the first demonstration that tpiA is required for full in vivo fitness of a bacterial pathogen, and that it has a discernable impact on cell morphology.

Redundancy in the requirement for the glycolytic enzymes phosphofructokinase (Pfk) 1 and 2 in the in vivo fitness of Salmonella enterica serovar Typhimurium

To assess the role of the glycolytic enzyme phosphofructokinase (Pfk) in the in vivo fitness of the pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) we have generated single and double gene deletion mutants of the two known isoforms of this enzyme, pfkA and pfkB. In a mouse model of typhoid fever, bacterial counts in the spleen and liver were similar between wild type and single pfkA and pfkB mutant-infected mice. However, a double pfkAB mutant was significantly attenuated for growth in vivo. This defect was complemented by provision of either pfkA or pfkB on pBR322. Together these data show that Pfk activity is required for the full in vivo fitness of S. Typhimurium with functional redundancy between pfkA and pfkB. The level of attenuation of the pfkAB double mutant was not sufficient for its consideration as a live attenuated vaccine strain.

Single, double and triple mutants of Salmonella enterica serovar Typhimurium degP (htrA), degQ (hhoA) and degS (hhoB) have diverse phenotypes on exposure to elevated temperature and their growth in vivo is attenuated to different extents

DegP (HtrA) is a well-studied protease involved in survival of bacteria under stress conditions in vitro and in vivo. There are two paralogues of DegP in the Salmonella enterica serovar Typhimurium genome, DegQ and DegS. In order to understand more about the biological significance of this gene family, a series of deg-deletion mutants was generated in S. Typhimurium strain SL3261 by allelic replacement. At elevated temperature in vitro, the viability of degP and degS mutants was reduced when compared with the parent strain whereas the viability of a degQ mutant was not significantly affected. The viability of a double degP-degS mutant at elevated temperature was severely decreased when compared with the respective single mutants or, interestingly, with a triple degP-degQ-degS mutant. All the deg deletions were transduced into the mouse-virulent strain SL1344 and the resultant mutants were injected intravenously into BALB/c mice to test virulence. degP and degS single mutants and all combinations of double and triple mutants were attenuated to different degrees, whereas the single degQ mutant was as virulent as the wild-type strain. Thus, within this gene family, degP and degS appear important for survival at elevated temperature and are necessary for full virulence, whereas a single degQ deletion appears to have no clear role in survival and growth at elevated temperature or in mice.

Identification and characterisation of hyaluronate lyase from Streptococcus suis

Hyaluronate lyase, which catalyses the degradation of hyaluronic acid (HA), has been described from several pathogenic streptococcal species. We describe, for the first time, identification and purification of hyaluronate lyase from the zoonotic pig pathogen Streptococcus suis. We have cloned the hyaluronate lyase gene from S. suis and used it to generate an allelic replacement knock-out mutant of S. suis serotype 7 that can no longer biosynthesise the enzyme. Interestingly, a limited strain survey indicates that hyaluronate lyase activity is not present in all disease isolates of S. suis. Polyclonal anti-hyaluronate lyase anti-serum raised against our recombinant hyaluronate lyase has been used in Western blots, showing that hyaluronate lyase activity is always associated with the presence of protein of the expected size, whereas lack of hyaluronate lyase activity is due to truncation or absence of the enzyme. We show that hyaluronate lyase activity is required for S. suis to use HA polymer as a carbon source and that supplying exogenous recombinant hyaluronate lyase to all S. suis strains tested allowed fermentation of the resultant HA breakdown products.

Sexual dimorphism in forelimb muscles of the bullfrog, Rana catesbeiana: a functional analysis of isometric contractile properties

In many species of frog, the forelimb muscles important in amplexus are known to be much larger in males than in females. We studied this dimorphism in three forelimb muscles in the bullfrog [abductor indicus longus (AIL), flexor carpi radialis (FCR) and extensor carpi radialis (ECR)] by testing their isometric contractile properties. One muscle that is not dimorphic, the extensor carpi ulnaris (ECU), was also studied as a control. In addition to being greater in wet mass and in cross-sectional area in the males, our data show that the dimorphic muscles also produce significantly larger isometric forces in males than in females. The tetanic force per cm(2) of muscle cross-sectional area did not differ between the sexes, so that force within a muscle varies directly with muscle size. However, a number of the contractile variables we measured show that male muscles differ functionally from those of females. The male twitch contraction times were significantly longer in the AIL, and the male half-relaxation times were longer in both the AIL and FCR. These two dimorphic muscles were also significantly less fatiguable in males than were the corresponding female muscles. Their higher endurance resulted from the maintenance of high levels of unrelaxed force sustained between trains of stimuli during the fatigue test. This sustained force is much less pronounced in the female muscles, suggesting that high levels of sustained force may be a key functional feature that enables males to maintain amplexus economically for prolonged periods.

Comparison of isometric contractile properties of the tongue muscles in three species of frogs, Litoria caerulea, Dyscophus guinetti, and Bufo marinus

Previous studies show that anurans feed in at least three different ways. Basal frogs have a broad tongue that shortens during protraction and emerges only a short distance from the mouth. Some frogs have long, narrow tongues that elongate dramatically due primarily to inertia from mouth opening, which is transferred to the tongue. A few species have a hydrostatic mechanism that produces tongue elongation during protraction. This functional diversity occurs among frogs that share the same two pairs of tongue muscles. Our study compares the isometric contractile properties of these tongue muscles among three frog species that represent each feeding mechanism. Nerves to the paired protractors and retractors were stimulated electrically in each species to record the force properties, contraction speeds, and fatigabilites of these muscles. Few differences were found in the isometric contractile properties of tongue muscles, and the greatest differences were found in the retractors, not the protractors. We propose that the unique arrangement of the tongue muscles in frogs results in a retractor that may also be coactivated with the protractor in order to produce normal tongue protraction. Inertial effects from body, head, and jaw movements, along with clear differences that we found in passive resistance of the tongues to elongation, may explain much of the behavioral variation in tongue use among species.

Pneumocystis carinii infection in young non-immunosuppressed rabbits. Kinetics of infection and of the primary specific immune response

The aim of this study was to determine the kinetics, the dissemination of the infection and the immunological response to Pneumocystis carinii primary infection in a non-immunosuppressed rabbit model. For this purpose, we developed a nested PCR that amplified a portion of the mitochondrial large-subunit rRNA gene of rabbit-derived P. carinii. The PCR detected P. carinii DNA in lung and bronchoalveolar lavage fluids from 14- to 45-day-old rabbits but not in their serum. No P. carinii DNA was detected in extrapulmonary organs from 28-day-old rabbits with P. carinii pneumonia. ELISA and immunoblotting analysis showed that 5-day-old pups had elevated specific IgG. The IgG concentration sharply decreased, reaching a trough on day 21, and from then onwards progressively increased as the infection cleared. Conversely, the specific IgM concentration increased during the infection and peaked on day 28. IgG mainly recognized a 50-kDa subunit of P. carinii organisms; IgM recognized first a 45-kDa subunit on day 21, whereas from day 28 onwards it also recognized the 50-kDa subunit. A P. carinii-specific splenocyte proliferative response was observed on day 45. These findings suggest that P. carinii primary infection is a time-limited and a lung-limited event and contribute new information on the relationship between the kinetics of primary P. carinii infection and the immunological response in a model that mimics the primary infections in humans.

The role of Saccharomyces cerevisiae Met1p and Met8p in sirohaem and cobalamin biosynthesis

MET1 and MET8 mutants of Saccharomyces cerevisiae can be complemented by Salmonella typhimurium cysG, indicating that the genes are involved in the transformation of uroporphyrinogen III into sirohaem. In the present study, we have demonstrated complementation of defined cysG mutants of Sal. typhimurium and Escherichia coli, with either MET1 or MET8 cloned in tandem with Pseudomonas denitrificans cobA. The conclusion drawn from these experiments is that MET1 encodes the S-adenosyl-l-methionine uroporphyrinogen III transmethylase activity, and MET8 encodes the dehydrogenase and chelatase activities (all three functions are encoded by Sal. typhimurium and E. coli cysG). MET8 was further cloned into pET14b to allow expression of the protein with an N-terminal His-tag. After purification, the functions of the His-tagged Met8p were studied in vitro by assay with precorrin-2 in the presence of NAD+ and Co2+. The results demonstrated that Met8p acts as a dehydrogenase and chelatase in the biosynthesis of sirohaem. Moreover, despite the fact that S. cerevisiae does not make cobalamins de novo, we have shown also that MET8 is able to complement cobalamin cobaltochelatase mutants and have revealed a subtle difference in the early stages of the anaerobic cobalamin biosynthetic pathways between Sal. typhimurium and Bacillus megaterium.

Identification of porcine Pneumocystis carinii as a genetically distinct organism by DNA amplification

DNA was amplified from lung samples from three piglets infected with Pneumocystis carinii, using oligonucleotide primers designed to the P. carinii mitochondrial large subunit ribosomal RNA gene. The nucleotide sequence of the amplification product was determined and indicated lack of sequence variation among these pig-derived P. carinii samples at this locus. The data showed that porcine P. carinii was genetically distinct from P. carinii isolated from other mammalian host species.

Hopping and swimming in the leopard frog, Rana pipiens: II. A comparison of muscle activities

Electromyography (EMG) was used to examine muscle activity of the major hip, knee, and ankle extensors during both hopping and swimming in leopard frogs. Chronic EMG electrodes were implanted for periods of 7-10 days. This permitted us to record EMG activities during both hopping and swimming from the same electrode, allowing a direct comparison of the timing and amplitudes of muscle activity between the two behaviors. We could then relate these activities to the kinematics of locomotion. In both behaviors, all three extensors were synchronously activated 30-50 ms before limb extension began. However, the hip extensor turned on relatively earlier in hopping than in swimming when on time was expressed as percent of stride. The hip and knee extensors were activated relatively longer in hopping and the ankle extensor relatively longer in swimming. The amplitudes of the rectified, integrated EMG signals were roughly twice as large in hopping as in swimming for all three muscles, supporting the notion that propulsion in hopping requires more force than in swimming. The EMG burst durations differed little between the muscles or, in relative duration, between the behaviors. As has been found in other quadrupeds, the EMG bursts began before visible movement and ceased at or before hindlimb extension was completed. In our animals, however, we found a consistent, low level (10-30% of maximum amplitude) of EMG activity that continued 60-200 ms past the end of the burst and into the suspension periods in both hopping and swimming. We hypothesize that this unusual activity may be present in frogs so that the hind limb remains aero(hydro)dynamically stable as the frog arches through its leap or glides in swimming following completed limb extension. Thus, the timing and pattern of the EMG bursts are consistent with those present in other tetrapods and support conservatism of neural control. However, the prolonged low-level activity suggests flexibility in the control pattern and variation according to specific behaviors.

Hopping and swimming in the leopard frog, Rana pipiens: I. Step cycles and kinematics

This study presents a model for the step cycle patterns used during both hopping and swimming by the leopard frog, Rana pipiens. The two behaviors are essentially similar in movement pattern and in the ways they are modified from quadrupedal gaits. In hopping, there is marked hind limb extension throughout stance. The swing begins with a suspension equivalent to the leap that occurs in a galloping or bounding quadruped. Following suspension, as the frog descends from the apex of its leap, the hind limbs remain posterior and in line with the spine while they flex. Near the end of flexion, there is a rapid downward rotation of the hindquarters to bring the hind feet underneath the body. This movement utilizes the planted forelimb as a pivot. A similar pattern of movement occurs in swimming; the stance (propulsion) phase involves extension at all hind limb joints. The swing (recovery) phase begins with the hind feet fully extended and includes a protracted gliding phase, equivalent to the suspension in the hop. The hind limb then recovers to its initial position during a flexion phase. Since there is no landing and the hind limbs remain lateral rather than ventral to the pelvis, less flexion occurs in the spine or the limb joints. In both behaviors, the extensor muscles of hip (M. semimembranosus), knee (M. cruralis), and ankle (M. plantaris longus) achieve their longest lengths, when they likely can produce near maximal force, at the beginning of extension. All three muscles shorten during extension, but, because they are multiple-joint muscles, the amount of shortening is relatively small (approximately 15%). Hopping and swimming in frogs are comparable asymmetrical gaits with the same relative contact intervals (25% of stride). The step cycles in both gaits are modified from quadrupedal locomotion in the same ways: by 1) loss of knee and ankle extension toward the ground prior to landing (or end of flexion in swimming), 2) loss of a yield phase on landing (or end of flexion in swimming), and 3) inclusion of extended suspensions in both gaits.

Non specific PCR products using rat-derived Pneumocystis carinii dihydrofolate reductase gene-specific primers in DNA amplification of human respiratory samples

DNA amplification using dihydrofolate reductase (DHFR) primers in bronchoalveolar lavage fluids (BALFs) from patients with Pneumocystis carinii (PC) pneumonia yielded low sensitivity and specificity. Amplified products of BALFs from an AIDS patient without PC pneumonia and five patients with PC pneumonia were cloned and sequenced. All samples showed the same sequence without any homology with DHFR cDNA of rat PC, or with any DHFR sequences in databases at the DNA or amino acid level. The data demonstrate that these DHFR primers amplify a non-specific region of DNA with a sequence unrelated to the human PC DHFR gene both in PC positive and in PC negative samples. This finding precludes the use of these DHFR primers for the diagnosis of PC pneumonia in respiratory specimens.

Properties of twitch motor units of the ankle extensor muscles in the bullfrog Rana catesbeiana

A study of the mechanical properties of the twitch motor units in the ankle extensor muscles of bullfrogs was undertaken to expand our view of the diversity of motor unit properties among vertebrates. Two muscles were chosen that represent a wide range of extensor function: the plantaris longus (PL) is a large muscle providing most of the force for ankle extension in hopping and swimming, and the tibialis posticus (TP) is relatively small and may act as an ankle stabilizer or be primarily postural in function. Both muscles have highly fatigable motor units, but also some (especially in TP) low or non-fatigable ones. Mean tetanic tensions of motor units in both muscles are relatively large as compared with those of mammals but are especially large in PL. No clear correlations were found between contraction times and either motor unit tetanic tensions or fatigability, nor did the motor units fall into clearly defined types based on any functional parameters. Overall contraction and relaxation times are slow compared with those of mammals and are somewhat slow compared to those of other frogs; unlike results from earlier studies, the large units of PL are slower than the small units of TP. This results in PL units reaching fused tetani at lower stimulus frequencies. The twitch/tetanus and force/frequency ratios in PL motor units are much larger than those of TP, giving PL units greater relative forces at lower stimulus rates. These results are discussed in the context of motor unit function.

Analysis of the membrane-anchoring properties of the putative amphiphilic alpha-helical anchor at the C-terminus of Escherichia coli PBP 6

Penicillin-binding protein (PBP) 6 is anchored to the periplasmic face of the Escherichia coli inner membrane. Analysis of the C-terminal 20 amino acids of PBP 6 implies the presence of a C-terminal amphiphilic alpha-helical anchor comparable to that of PBP 5. A C-terminal deletion of PBP 6 was constructed; it resulted in the release of the protein from the inner membrane into the periplasm, thus confirming that this region is essential for anchoring. Treatment of E. coli K12 membrane vesicles with various reagents was used to probe the membrane-binding characteristics of both PBP 5 and PBP 6. The results indicate that, although the strength of membrane anchoring of PBP 6 is weaker than that of PBP 5, both modes of anchoring involve a large hydrophobic element and have similar membrane-binding characteristics. This is in agreement with the hypothesis that both proteins exhibit the same novel method of anchoring.

Pneumocystis carinii pneumonia in thoroughbred foals: identification of a genetically distinct organism by DNA amplification

Genetically distinct forms of Pneumocystis carinii infect several mammalian hosts. We report the amplification of P. carinii DNA from samples of two infected thoroughbred foal lungs by using primers designed from the sequence of a P. carinii mitochondrial rRNA gene; these primers also prime the amplification of P. carinii DNA from other hosts. The nucleotide sequence of part of the mitochondrial rRNA gene amplified from P. carinii infecting one of the foals was determined and found to be distinct from that of published rat-, rabbit-, ferret-, and human-derived P. carinii sequences.

The cloning and characterization of the arom gene of Pneumocystis carinii

The arom gene, encoding a single polypeptide that catalyses five consecutive steps of the pre-chorismate aromatic amino acid biosynthetic pathway, has been cloned from the opportunistic pathogen Pneumocystis carinii. There is a single open reading frame of 4788 bp which includes an intron of 45 bp that does not introduce a stop codon into the sequence. Thus, the derived amino acid sequence consists of 1581 residues, which is highly homologous to all fungal AROM proteins studied to date. These data support the view that P. carinii is a fungus and imply that its aromatic amino acid biosynthesis is conventionally organized.

Comparison of DNA amplification and immunofluorescence for detecting Pneumocystis carinii in patients receiving immunosuppressive therapy

Two studies were performed to compare the sensitivity of DNA amplification with immunofluorescence for the detection of Pneumocystis carinii in asymptomatic normal and immunosuppressed subjects receiving no anti-Pneumocystis chemoprophylaxis. In the first study, immunofluorescence and silver stains were used to examine 12 induced sputa and 12 bronchoalveolar lavage specimens from 24 normal control subjects; induced sputa from 20 renal transplant recipients; and induced sputa from 11 patients with fibrosing alveolitis. All specimens were negative for P carinii using both stains, apart from one renal patient in whom 2 P carinii cysts were seen by immunofluorescence alone. In the second study, DNA amplification and immunofluorescence were used to examine induced sputa from 3 groups of 10 control, renal, and heart/lung transplant recipients. All 30 specimens were negative for P carinii by immunofluorescence. However, 3 renal and 2 heart/lung patients were positive for P carinii by DNA amplification alone. One of these patients developed P carinii pneumonia 6 weeks after sputum induction. DNA amplification is a more sensitive technique than immunofluorescence for detecting P carinii. P carinii colonization occurs in asymptomatic organ transplant recipients, but not in normal individuals.

Pneumocystis carinii shows DNA homology with the ustomycetous red yeast fungi

Pneumocystis carinii causes life-threatening pneumonia in T-lymphocyte-immunodeficient subjects in transplant and oncology units or with acquired immune deficiency syndrome (AIDS). Recent DNA homology studies show P. carinii to be a fungus. To investigate the biology and epidemiology of this parasite further, we elected to determine for it a more precise taxonomic assignment within the fungal kingdom. We screened a wide range of organisms representing the major orders of fungi using DNA amplification and subsequently sequenced a portion of the mitochondrial gene encoding the large subunit ribosomal RNA. Our data show that the opportunistic pulmonary pathogen P. carinii is closely related to the ustomycetous red yeast fungi, a group which includes organisms that are extensively distributed throughout the environment and which release many widely dispersed airborne spores.

A search for Pneumocystis carinii in post-mortem lungs by DNA amplification

DNA amplification of specific sequences and subsequent oligonucleotide hybridization were used to search for Pneumocystis carinii in post-mortem lung samplings from non-immunosuppressed individuals ranging from 15 to 70 years of age. No P. carinii-specific DNA was detected in 45 DNA amplification reactions from 15 lungs.

Quantification of the detection of Pneumocystis carinii by DNA amplification

We have developed a highly specific and sensitive technique for the detection of Pneumocystis carinii DNA using DNA amplification by the polymerase chain reaction (PCR). PCR products are detected by agarose gel electrophoresis and Southern hybridization to an oligonucleotide probe. Here we report the calibration of parasite numbers with amplification and hybridization signals and show that we can detect P. carinii to a lower limit of one to two organisms. The quantification of this diagnostic technique allows us to establish the number of organisms in a clinical sample which correspond to pneumocystis pneumonia or to sub-clinical pulmonary colonization.

Novel mercury resistance determinants carried by IncJ plasmids pMERPH and R391

HgCl2 resistance (Hgr) in a strain of Pseudomonas putrefaciens isolated from the River Mersey was identified as plasmid-borne by its transfer to Escherichia coli in conjugative matings. This plasmid, pMERPH, could not be isolated and was incompatible with the chromosomally integrated IncJ Hgr plasmid R391. pMERPH and R391 both express inducible, narrow-spectrum mercury resistance and detoxify HgCl2 by volatilization. The cloned mer determinants from pMERPH (pSP100) and R391 (pSP200) have very similar restriction maps and express identical polypeptide products. However, these features show distinct differences from those of the Tn501 family of mer determinants. pSP100 and pSP200 failed to hybridize at moderate stringency to merRTPA and merC probes from Tn501 and Tn21, respectively. We conclude that the IncJ mer determinants are only distantly related to that from Tn501 and its closely homologous relatives and that it identifies a novel sequence which is relatively rare in bacteria isolated from natural environments.

Restriction pattern and polypeptide homology among plasmid-borne mercury resistance determinants

The structural and functional properties of mercury resistance determinants cloned from a series of independently isolated conjugative plasmids were compared with those of the prototype HgR determinants from Tn501 and plasmid R100 (containing Tn21). Restriction endonuclease mapping classified the HgR determinants into at least three different but related structural groups which are distantly related to those from Tn501 and R100. These relationships were confirmed by the functional analysis of sub-clones and gamma delta insertion mutations and from the polypeptides specified by the cloned HgR determinants. Each mercury resistance clone synthesized polypeptides equivalent in size to the merA, merT, and merP gene products. However, those for merA and merT showed considerable size variation. No polypeptide equivalent to merD or merC of R100 was detected.

Motor units of the primary ankle extensor muscles of the opossum (Didelphis virginiana): functional properties and fiber types

Motor units of the medial gastrocnemius (MG) and the single lateral gastrocnemius/soleus (LG/S) muscles of the opossum (Didelphis virginiana) were found to have uniformly slow contraction times relative to homologous muscles of the cat. Though a broad range of peak tetanic tensions was found among motor units from both muscles, most of the motor units were quite large relative to tension of the whole muscle. Comparison of the relative sizes of motor units showed that those of LG/S are significantly larger and slower than the units of MG. This suggests that the motor units of the two muscles may be differentially recruited during different behaviors. All of the MG and LG/S motor units were highly or moderately resistant to fatigue. Histochemical staining for NADH-diaphorase activity indicated consistently high levels of the enzyme in all of the fibers of both muscles. Apparently, all of the fast motor units consist of fast oxidative/glycolytic (FOG)-type muscle fibers. Our data provide functional evidence that the types of myofibrillar ATPase demonstrated by Brooke and Kaiser ('70), are not necessarily correlated to physiological classification of fiber types as slow oxidative (SO), fast oxidative/glycolytic (FOG), and fast glycolytic (FG) (Peter et al., '72). Perhaps compartmentalization of muscle fiber types may be a first step in the separation of muscles into multiple heads during the evolution of specialization to diverse locomotor habits among the mammals.