- Trudy M. Wassenaar is director of Molecular Microbiology and Genomics Consultants. For more information, see http://www.mmgc.euedit
The genus Burkholderia consists of a number of very diverse species, both in terms of lifestyle (which varies from category B pathogens to apathogenic soil bacteria and plant colonizers) and their genetic contents. We have used 56... more
The genus Burkholderia consists of a number of very diverse species, both in terms of lifestyle (which varies from category B pathogens to apathogenic soil bacteria and plant colonizers) and their genetic contents. We have used 56 publicly available genomes to explore the genomic diversity within this genus, including genome sequences that are not completely finished, but are available from the NCBI database. Defining the pan- and core genomes of species results in insights in the conserved and variable fraction of genomes, and can verify (or question) historic, taxonomic groupings. We find only several hundred genes that are conserved across all Burkholderia genomes, whilst there are more than 40,000 gene families in the Burkholderia pan-genome. A BLAST matrix visualizes the fraction of conserved genes in pairwise comparisons. A BLAST atlas shows which genes are actually conserved in a number of genomes, located and visualized with reference to a chosen genome. Genomic islands are common in many Burkholderia genomes, and most of these can be readily visualized by DNA structural properties of the chromosome. Trees that are based on relatedness of gene family content yield different results depending on what genes are analyzed. Some of the differences can be explained by errors in incomplete genome sequences, but, as our data illustrate, the outcome of phylogenetic trees depends on the type of genes that are analyzed.
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Background: Zika virus (ZIKV) is an emerging human pathogen. Since its arrival in the Western hemisphere, from Africa via Asia, it has become a serious threat to pregnant women, causing microcephaly and other neuropathies in developing... more
Background: Zika virus (ZIKV) is an emerging human pathogen. Since its arrival in the Western hemisphere, from Africa via Asia, it has become a serious threat to pregnant women, causing microcephaly and other neuropathies in developing fetuses. The mechanisms behind these teratogenic effects are unknown, although epidemiological evidence suggests that microcephaly is not associated with the original, African lineage of ZIKV. The sequences of 196 published ZIKV genomes were used to assess whether recently proposed mechanistic explanations for microcephaly are supported by molecular level changes that may have increased its virulence since the virus left Africa. For this we performed phylogenetic, recombination, adaptive evolution and tetramer frequency analyses, and compared protein sequences for the presence of protease cleavage sites, Pfam domains, glycosylation sites, signal peptides, trans-membrane protein domains, and phosphorylation sites.
Colonization of body epithelial surfaces with a highly specific microbial community is a fundamental feature of all animals, yet the underlying mechanisms by which these communities are selected and maintained are not well understood.... more
Colonization of body epithelial surfaces with a highly specific microbial community is a fundamental feature of all animals, yet the underlying mechanisms by which these communities are selected and maintained are not well understood. Here, we show that sensory and ganglion neurons in the ectodermal epithelium of the model organism hydra (a member of the animal phylum Cnidaria) secrete neuropeptides with antibacterial activity that may shape the microbiome on the body surface. In particular, a specific neuropeptide, which we call NDA-1, contributes to the reduction of Gram-positive bacteria during early development and thus to a spatial distribution of the main colonizer, the Gram-negative Curvibacter sp., along the body axis. Our findings warrant further research to test whether neuropeptides secreted by nerve cells contribute to the spatial structure of microbial communities in other organisms.
Significance and Impact of the Study: We have analysed five resistance genes in Staphylococcus aureus that are positioned between the replication elements of rolling-circle plasmids. For three of these genes, evidence was obtained... more
Significance and Impact of the Study: We have analysed five resistance genes in Staphylococcus aureus that are positioned between the replication elements of rolling-circle plasmids. For three of these genes, evidence was obtained indicative of recent mobilization. The historical use of the antibiotics to which the genes produce resistance could be related to the number of mutations collected in these genes. However, two other resistance genes have not collected any mutations over time, and the reasons for this are discussed. The analyses presented provide insights into the spread and evolution of antibiotic resistance genes. Abstract The qacC and lnuA genes of Staphylococcus species were recently proposed to comprise a mobile element when residing on rolling-circle plasmids. Here we present other examples of resistance genes on staphylococcal rolling-circle plasmids, including fosB producing resistance to fosfomycin, cat resulting in resistance to chloramphenicol and cadB for resistance to the toxic heavy metal cadmium. For three of these genes (qacC, lnuA and fosB), evidence was obtained that the genes have spread between different plasmid backgrounds. The lack of mutations in qacC suggests that the spread occurred relatively recently, while the build up of mutations in lnuA and fosB suggests their mobilization occurred in the more distant past. These observations can be explained by the use of the respective antibiotics over time. However, the cat and cadB genes sequences analysed had not collected any mutations, an observation that is not completely understood but possible explanations are discussed.
We present here the complete genome sequences of three mumps virus (MuV) strains isolated from patients who tested positive for the mumps virus during a mumps outbreak in Springdale, AR (USA), in 2016. The virus genomes, se-quenced with... more
We present here the complete genome sequences of three mumps virus (MuV) strains isolated from patients who tested positive for the mumps virus during a mumps outbreak in Springdale, AR (USA), in 2016. The virus genomes, se-quenced with Oxford Nanopore technology, belong to genotype G and have an average length of 15,342 nucleotides (nt).
The aim of this study was to determine if commercially available strains of probiotic bacteria belonging to the species Ent. faecalis and E. coli were able to survive passage through the human stomach and colonise the gastrointestinal... more
The aim of this study was to determine if commercially available strains of probiotic bacteria belonging to the species Ent. faecalis and E. coli were able to survive passage through the human stomach and colonise the gastrointestinal tract (GIT). Survival of bacteria following exposure to gastric pH levels was assessed using a dynamic in vitro model resembling conditions in the stomach as well as the SHIME® model more closely mimicking the upper GIT environment (stomach and small intestine) during fed conditions.
Viability of both Ent. faecalis DSM 16431 and E. coli DSM 17257 decreased during acid exposure. However, subsequent exposure to simulated small intestine conditions resulted in no further decrease. A human volunteer took a single dose of probiotic Ent. faecalis, after which live bacteria were determined for 6 days in faeces by means of targeted cultivation and identification of colonies using species- and strain-specific PCR primers. Detection of the strain’s DNA by PCR in stool samples was positive for 4 days. This duration of colonisation was much shorter compared to previously determined human colonisation by E. coli DSM 17257.
In conclusion, probiotic E. coli and Ent. faecalis are susceptible to gastric pH, which reduces their viability with several logs. However, sufficient numbers survive to colonise the gut, so that the bacteria are detected in the stool for several days (Ent. faecalis) and multiple weeks (E. coli) following a single dose.
Viability of both Ent. faecalis DSM 16431 and E. coli DSM 17257 decreased during acid exposure. However, subsequent exposure to simulated small intestine conditions resulted in no further decrease. A human volunteer took a single dose of probiotic Ent. faecalis, after which live bacteria were determined for 6 days in faeces by means of targeted cultivation and identification of colonies using species- and strain-specific PCR primers. Detection of the strain’s DNA by PCR in stool samples was positive for 4 days. This duration of colonisation was much shorter compared to previously determined human colonisation by E. coli DSM 17257.
In conclusion, probiotic E. coli and Ent. faecalis are susceptible to gastric pH, which reduces their viability with several logs. However, sufficient numbers survive to colonise the gut, so that the bacteria are detected in the stool for several days (Ent. faecalis) and multiple weeks (E. coli) following a single dose.
Background: Guidelines for the control of hospital-acquired MRSA include decolonization measures to end MRSA carrier status in colonized and infected patients. Successful decolonization typically requires up to 22 days of treatment, which... more
Background: Guidelines for the control of hospital-acquired MRSA include decolonization measures to end MRSA carrier status in colonized and infected patients. Successful decolonization typically requires up to 22 days of treatment, which is longer than the average hospital length of stay (LOS). Incomplete decolonization is therefore common, with long-term MRSA carriage as a consequence. To overcome this, we developed an integrated MRSA Management (IMM) by extending MRSA decolonization to the outpatient and domestic setting. The protocol makes use of polyhexanide-based products, in view of reported qac-mediated resistance to chlorhexidine in S. aureus and MRSA.
A century ago, Alfred Nissle discovered that intentional intake of particular strains of Escherichia coli could treat patients suffering from infectious diseases. Since then, one of these strains became the most frequently used probiotic... more
A century ago, Alfred Nissle discovered that intentional intake of particular strains of Escherichia coli could treat patients suffering from infectious diseases. Since then, one of these strains became the most frequently used probiotic E. coli in research and was applied to a variety of human conditions. Here, properties of that E. coli Nissle 1917 strain are compared with other commercially available E. coli probiotic strains, with emphasis on their human applications. A literature search formed the basis of a summary of research findings reported for the probiotics Mutaflor, Symbioflor 2, and Colinfant. The closest relatives of the strains in these products are presented, and their genetic content, including the presence of virulence, genes is discussed. A similarity to pathogenic strains causing urinary tract infections is noticeable. Historic trends in research of probiotics treatment for particular human conditions are identified. The future of probiotic E. coli may lay in what Alfred Nissle originally discovered: to treat gastrointestinal infections, which nowadays are often caused by antibiotic-resistant pathogens.
Resistance of Staphylococcus species to quaternary ammonium compounds, frequently used as disinfectants and biocides, can be attributed to qac genes. Most qac gene products belong to the Small Multidrug Resistant (SMR) protein family, and... more
Resistance of Staphylococcus species to quaternary ammonium compounds, frequently used as disinfectants and biocides, can be attributed to qac genes. Most qac gene products belong to the Small Multidrug Resistant (SMR) protein family, and are often encoded by rolling-circle (RC) replicating plasmids. Four classes of SMR-type qac gene families have been described in Staphylococcus species: qacC, qacG, qacJ, and qacH. Within their class, these genes are highly conserved, but qacC genes are extremely conserved, although they are found in variable plasmid backgrounds. The lower degree of sequence identity of these plasmids compared to the strict nucleotide conservation of their qacC means that this gene has recently spread. In the absence of insertion sequences or other genetic elements explaining the mobility, we sought for an explanation of mobilization by sequence comparison. Publically available sequences of qac genes, their flanking genes and the replication gene that is invariably present in RC-plasmids were compared to reconstruct the evolutionary history of these plasmids and to explain the recent spread of qacC. Here we propose a new model that explains how qacC is mobilized and transferred to acceptor RC-plasmids without assistance of other genes, by means of its location in between the Double Strand replication Origin (DSO) and the Single-Strand replication Origin (SSO). The proposed mobilization model of this DSO-qacC-SSO element represents a novel mechanism of gene mobilization in RC-plasmids, which has also been employed by other genes, such as lnuA (conferring lincomycin resistance). The proposed gene mobility has aided to the wide spread of clinically relevant resistance genes in Staphylococcus populations.
The probiotic product Symbioflor2 (DSM 17252) is a bacterial concentrate of six different Escherichia coli genotypes, whose complete genome sequences are compared here, between each other as well as to other E. coli genomes. The genome... more
The probiotic product Symbioflor2 (DSM 17252) is a bacterial concentrate of six different Escherichia coli genotypes, whose complete genome sequences are compared here, between each other as well as to other E. coli genomes. The genome sequences of Symbioflor2 E. coli components contained a number of virulence-associated genes. Their presence seems to be in conflict with a recorded history of safe use, and with the observed low frequency of adverse effects over a period of more than 6 years. The genome sequences were used to identify unique sequences for each component, for which strain-specific hybridization probes were designed. A colonization study was conducted whereby five volunteers were exposed to an exceptionally high single dose. The results showed that the probiotic E. coli could be detected for 3 months or longer in their stools, and this was in particular the case for those components containing higher numbers of virulence-associated genes. Adverse effects from this long-term colonization were absent. Thus, the presence of the identified virulence genes does not result in a pathogenic phenotype in the genetic background of these probiotic E. coli.
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Bacterial pathogens are being sequenced at an increasing rate. To many microbiologists, it appears that there simply is not enough time to digest all the information suddenly available. In this chapter we present several tools for... more
Bacterial pathogens are being sequenced at an increasing rate. To many microbiologists, it appears that there simply is not enough time to digest all the information suddenly available. In this chapter we present several tools for comparison of sequenced pathogenic genomes, and discuss differences between pathogens and non-pathogens. The presented tools allow comparison of large numbers of genomes in a hypothesis-driven manner. Visualization of the results is very important for clear presentation of the results and various ways of graphical representation are introduced.
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The role of a dprA ortholog (Cj0634) in Campylobacter jejuni transformation was phenotypically assessed using two strains. C. jejuni strain 11168 was naturally competent for transformation by chromosomal DNA, while efficiency decreased... more
The role of a dprA ortholog (Cj0634) in Campylobacter jejuni transformation was phenotypically assessed using two strains. C. jejuni strain 11168 was naturally competent for transformation by chromosomal DNA, while efficiency decreased 100-fold in a Cj0634::aphA mutant, whereas C. jejuni strain 480 was not naturally competent. C. jejuni strain 480 but not 11168 could be elec-tro-transformed by shuttle plasmid pRY111, an effect completely abolished by Cj0634 interruption. Complementation of the Cj0634 mutation in C. jejuni strain 480 in trans with vectors containing the dprA homologs from C. jejuni, Helicobacter pylori, or Haemophilus influenzae, completely (for Cj0634) or partially (H. pylori > H. influenzae) restored electro-transformation. Thus, C. jejuni expresses a DprA ortholog that functionally most closely resembles that of H. pylori and is involved in DNA transformation.
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Production of a single cysteine substitution mutant, S177C, allowed Escherichia coli hemolysin (HlyA) to be radioactively labeled with N-ethylmaleimide without affecting biological activity. It thus became possible to study the binding... more
Production of a single cysteine substitution mutant, S177C, allowed Escherichia coli hemolysin (HlyA) to be radioactively labeled with N-ethylmaleimide without affecting biological activity. It thus became possible to study the binding characteristics of HlyA as well as of toxin mutants in which one or both acylation sites were deleted. All toxins bound to erythrocytes and granulocytes in a non-saturable manner. Only wild-type toxin and the lytic monoacylated mutant stimulated production of superoxide anions in granulo-cytes. An oxidative burst coincided with elevation of intracellular Ca 2 , which was likely because of passive influx of Ca 2 through the toxin pores. Competition experiments showed that binding to the cells was receptor-independent, and preloading of cells with a non-lytic HlyA mutant did not abrogate the respiratory burst provoked by a subsequent application of wild-type HlyA. In contrast to a previous report, expression or activation of the 2 integrin lymphocyte function-associated antigen-1 did not affect binding of HlyA. We conclude that HlyA binds nonspecifically to target cells and a receptor is involved neither in causing hemolysis nor in triggering cellular reactions.
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For most bacteria it is essential to secrete particular proteins, and there are several methods available for predicting which proteins will be secreted and how. This genome update deals with characterization of secretion systems in... more
For most bacteria it is essential to secrete particular proteins, and there are several methods available for predicting which proteins will be secreted and how. This genome update deals with characterization of secretion systems in bacterial genomes.
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Genotyping methods have been developed and applied to differentiate Campylobacter jejuni isolates over the last two decades. Although a wealth of information was generated, the data are disappointingly complex and do not support simple... more
Genotyping methods have been developed and applied to differentiate Campylobacter jejuni isolates over the last two decades. Although a wealth of information was generated, the data are disappointingly complex and do not support simple models of transmission. Several observations have apparently weakened the value and complicated the interpretation of genotyping methods. For several methods, instability of genotype has been demonstrated, due to recombinations with or without transformation. C. jejuni is partly non-clonal, as demonstrated by multi-locus sequence typing, which is explained by a natural abilitycompetence to take up DNA. Plasticity of the genome, allowing for
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Thirty-two genome sequences of various Vibrio-naceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed ; this fraction roughly... more
Thirty-two genome sequences of various Vibrio-naceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed ; this fraction roughly doubles for gene families conserved within the species V. cholerae. Of these, approximately 200 gene families that cluster on various locations of the genome are not found in other sequenced Vibrionaceae; these are possibly unique to the V. cholerae species. By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes. Conversely, two genomes presumably belonging to the same species have suspiciously dissimilar gene family content. We are able to identify a number of genes that are conserved in, and unique to, V. cholerae. Some of these genes may be crucial to the niche adaptation of this species.
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The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity... more
The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. Based on average amino acid identity, comparative genome analysis of over one thousand Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoids (Eastern Cottonwood tree), resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All P. aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups based on pan and core genome analysis. In contrast, the genomes of P. fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supp...
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The number of cases of salmonellosis has steadily increased during the last decade. Until the end of the 70s, the serotype Salmonella typhimurium was most commonly isolated, but since 1986 the serotype S. enteritidis has become more... more
The number of cases of salmonellosis has steadily increased during the last decade. Until the end of the 70s, the serotype Salmonella typhimurium was most commonly isolated, but since 1986 the serotype S. enteritidis has become more common. Recent research has shown that the colon is more frequently infected than was earlier recognized, but most common is still an acute enterocolitis during an infection with salmonella. In severe cases, salmonella can spread from the gut, the site of infection, to cause a systemic disease. As in vitro studies have shown, gastroenteritic salmonellae seem to possess a number of so-called virulence factors that help them to evade the host's defenses against bacterial infection. Colonisation in the gut seems to be dependent on a 66 kD heat shock protein (HSP), which binds to a 15 kD glycoprotein present in gut mucus. For penetration into the mucosa, by invasion of the epithelial cells, bacterial invasions are newly synthesized. These proteins distort the epithelial membrane and induce a port of entrance. Macrophages will attack and engulf the bacteria, but salmonella can withstand these professional killers, and even grow intracellularly in them. In order to do so, not only LPS is required, but also specific outer membrane proteins (OMP), porins. Moreover, during their intracellular survival the bacteria need to adapt to the new microenvironment, and in reaction to stress, new HSPs are expressed. Finally, the O-specific sugar chains prevent the otherwise lytic action of complement in blood serum.(ABSTRACT TRUNCATED AT 250 WORDS)
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Molecular typing and fingerprinting of bacterial pathogens has become a major part of epidemiology, disease monitoring, intervention and food safety research. This treatise will briefly address the aims of molecular typing and the... more
Molecular typing and fingerprinting of bacterial pathogens has become a major part of epidemiology, disease monitoring, intervention and food safety research. This treatise will briefly address the aims of molecular typing and the criteria that are important to choose the optimal method of typing. However, since the method of choice will depend on a number of factors, including available facilities and research goals, no particular methods are recommended; instead, theoretical considerations are presented as a guide line for the best decision. Since molecular typing is examining the nature of the population genetics of a particular organism, it is important to understand how the degree of clonality of that particular organism will influence outcome and interpretation of results. The mechanisms that lead to non-clonality are briefly outlined. The problems with typing of clonal, non-clonal, and weakly clonal populations are briefly treated. The merits and myths of multilocus sequence typing (MLST) are discussed.
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The application of bacterial genomics opens new avenues of research on foodborne pathogens. Foodborne pathogens must be able to colonize their hosts and survive transmission from host to host. Different groups of genes are involved in the... more
The application of bacterial genomics opens new avenues of research on foodborne pathogens. Foodborne pathogens must be able to colonize their hosts and survive transmission from host to host. Different groups of genes are involved in the processes of survival, colonization, and virulence, and such genes are potential targets for risk assessment and intervention strategies. Filtering from genome sequences the genes relevant to these processes is a major challenge, and although many tools are already available for analyses, this type of data mining is just beginning. For the simplest application, gene comparison, it is important to know how gene function, for instance in virulence, is being defined and tested. In other genomic applications, reserachers look for specific properties or characteristics of (virulence) genes to identify novel gene candidates. Each approach has pitfalls, and gene candidates must be tested in the lab to confirm their function. Models for colonization and virulence are available for most although not all pathogens. Models for survival and stress responses are needed to increase the utilization of genomic approaches to risk assessment. Here, I discuss how genome sequences are likely to help in microbial risk assessment of foodborne pathogens and how dreams may become promises.
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The application of living bacteria as probiotics in food or food supplements requires a careful safety assessment. This review summarizes key issues concerning the safety aspects of bacteria added to particular products marketed for... more
The application of living bacteria as probiotics in food or food supplements requires a careful safety assessment. This review summarizes key issues concerning the safety aspects of bacteria added to particular products marketed for improvement of general health or treatment of (post)infectious symptoms. The bacteria used in such products should be completely safe; however, it can be challenging to provide evidence for absence of all virulence properties. In some cases, virulence factors have been detected in probiotic bacterial strains, and the implications of these traits for safety assessments are discussed. Horizontal gene transfer can result in acquisition of virulence genes or antimicrobial resistance in probiotic bacteria. Antimicrobial resistance in these bacteria can possibly aid the spread of undesired resistance in intestinal bacterial populations. The relative risk of such gene transfers is considered. The generation of complete bacterial genome sequences can both resolv...
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Of all the virulence factors that were proposed for Campylobacter jejuni and related species to cause disease in humans, the discovery of toxin production was the most promising but led to a rather confusing and even disappointing stream... more
Of all the virulence factors that were proposed for Campylobacter jejuni and related species to cause disease in humans, the discovery of toxin production was the most promising but led to a rather confusing and even disappointing stream of data. The discussion of whether proteinaceous exotoxins are relevant in disease remains open. One important reason for this lack of consensus is the anecdotal nature of the literature reports. To provide a basis for an unbiased opinion, this review compiles all described exotoxins, compares their reported properties, and provides a summary of animal model studies and clinical data. The toxins are divided into enterotoxins and cytotoxins and are sorted according to their biochemical properties. Since many Campylobacter toxins have been compared with toxins of other species, some key examples of the latter are also discussed. Future directions of toxin research that appear promising are defined.
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The complete genome of probiotic Escherichia coli strain G3/10 is presented here. In addition, the probiotic E. coli strains G1/2, G4/9, G5, G6/7, and G8 are presented in draft form. These six strains together comprise the probiotic... more
The complete genome of probiotic Escherichia coli strain G3/10 is presented here. In addition, the probiotic E. coli strains G1/2, G4/9, G5, G6/7, and G8 are presented in draft form. These six strains together comprise the probiotic product Symbioflor 2 (DSM 17252).
Virus taxonomy is based on morphologic characteristics, as there are no widely used non-phenotypic measures for comparison among virus families. We examined whether there is phylogenetic signal in virus nucleotide usage patterns that can... more
Virus taxonomy is based on morphologic characteristics, as there are no widely used non-phenotypic measures for comparison among virus families. We examined whether there is phylogenetic signal in virus nucleotide usage patterns that can be used to determine ancestral relationships. The well-studied model of tail morphology in bacteriophage classification was used for comparison with nucleotide usage patterns. Tetranucleotide usage deviation (TUD) patterns were chosen since they have previously been shown to contain phylogenetic signal similar to that of 16S rRNA. We found that bacteriophages have unique TUD patterns, representing genomic signatures that are relatively conserved among those with similar host range. Analysis of TUD-based phylogeny indicates that host influences are important in bacteriophage evolution, and phylogenies containing both phages and their hosts support their co-evolution. TUD-based phylogeny of eukaryotic viruses indicates that they cluster largely based ...
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The consumption of poultry meat contaminated with Campylobacter jejuni is considered to be a risk factor for human campylobacteriosis. The development of targeted strategies to control campylobacters in broilers would benefit from... more
The consumption of poultry meat contaminated with Campylobacter jejuni is considered to be a risk factor for human campylobacteriosis. The development of targeted strategies to control campylobacters in broilers would benefit from knowledge of those bacterial factors important in colonization of the avian gut. During preliminary studies it was noted that C. jejuni NCTC 11168 was a poorer colonizer of chickens than strain 81116. This poor colonization could not be fully restored by in vivo passage, suggesting that it was a genetically endowed property of strain 11168. As the genome sequence is available for this strain, the technique of subtractive hybridization was used to identify gene fragments of strain 81116 not present in strain 11168. After two screening cycles, 24 out of 42 clones were identified as having DNA inserts specific for strain 81116. Six of these 24 clones contained gene fragment inserts with similarities to restriction-modification enzymes found in other bacteria....
Research Interests: Genetics, Microbiology, Arsenic, Multidisciplinary, Humans, and 16 moreSequence alignment, Animals, Nucleic acid hybridization, Meat, Oxidoreductases, Cytochrome c oxidase, Restriction-Modification Systems, Risk factors, Enzyme, Poultry, Chickens, Risk Factors, Genome sequence, Species Specificity, Amino Acid Sequence, and Campylobacter jejuni
Campylobacter jejuni O:41 strains are found in association with Guillain-Barré syndrome in South Africa. Strains of this serotype collected over 17 years were characterized by amplified fragment length polymorphism and flagellin typing to... more
Campylobacter jejuni O:41 strains are found in association with Guillain-Barré syndrome in South Africa. Strains of this serotype collected over 17 years were characterized by amplified fragment length polymorphism and flagellin typing to determine their clonal nature. Despite minor variation in GM1 expression, all of the strains were genetically indistinguishable, indicating that they are representative of a genetically stable clone.
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For epidemiological studies of Campylobacter infections, molecular typing methods that can differentiate campylobacters at the strain level are needed. In this study we used a recently developed genotyping method, amplified fragment... more
For epidemiological studies of Campylobacter infections, molecular typing methods that can differentiate campylobacters at the strain level are needed. In this study we used a recently developed genotyping method, amplified fragment length polymorphism (AFLP), which is based on selective amplification of restriction fragments of chromosomal DNA, for genetic typing of Campylobacter jejuni and Campylobacter coli strains derived from humans and poultry. We developed an automated AFLP fingerprinting method in which restriction endonucleases HindIII and HhaI were used in combination with one set of selective PCR primers. This method resulted in evenly distributed band patterns for amplified fragments ranging from 50 to 500 bp long. The discriminatory power of AFLP was assessed with a C. jejuni strain, an isogenic flagellin mutant, and distinct C. jejuni strains having known pulsed-field gel electrophoresis and fla PCR-restriction fragment length polymorphism genotypes. Unrelated C. jejun...
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... Introduction The genus Campylobacter comprises a diverse group of Gram-negative bacteria, which colonize the mucosal surfaces of the intestinal tracts, oral cavities, or urogenital tracts ofa wide range of bird and animal hosts. ... A... more
... Introduction The genus Campylobacter comprises a diverse group of Gram-negative bacteria, which colonize the mucosal surfaces of the intestinal tracts, oral cavities, or urogenital tracts ofa wide range of bird and animal hosts. ... A further problem is that different culture tech-Fig. ...
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When most people hear the word “bacteria” they think of food poisoning, infections, and acute, debilitating, or fatal diseases. Yet, while bacterial pathogens certainly cause their share of misery in the world, they are only a tiny... more
When most people hear the word “bacteria” they think of food poisoning, infections, and acute, debilitating, or fatal diseases. Yet, while bacterial pathogens certainly cause their share of misery in the world, they are only a tiny portion of a vast universe of prokaryotes—the most basic of life forms. Without them, nothing else could live or grow on Planet Earth. This book introduces this diverse, microscopic world and explains the fundamental microbiological concepts needed to explore the life and behavior of bacteria. The book’s clear, jargon-free language informs the reader, without the need of a background in microbiology, about a wide variety of bacterial subjects.
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This book is part of the series Computing for Comparative Microbial Genomics. The book is written for microbiologists needing an introduction to genomics as well as for bioinformaticists who need to be introduced to microbiology. First, a... more
This book is part of the series Computing for Comparative Microbial Genomics. The book is written for microbiologists needing an introduction to genomics as well as for bioinformaticists who need to be introduced to microbiology. First, a brief overview of molecular biology and of the concept of sequences as biological information are given. There are four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and Microbial Communities. "It is a very well-written review of genomics and proteomics of microbes, and makes convincing arguments for the practicality of applying bioinformatics to the study of communities of these species. The references are well chosen. The writing style is superb. … There is an amazing amount of interesting material… The book is probably more suitable as an introduction to contemporary applications of bioinformatics and microbiology for computational scientists." (Anthony J. Duben, ACM Computing Reviews,
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'An unusual job' is the first work of fication by Trudy Wassenaar. Sue Swanson, a self-employed scientific consultant living in Germany, is frustrated with her life. For lack of work, she seeks an occupation to keep herself busy, and applies... more
'An unusual job' is the first work of fication by Trudy Wassenaar.
Sue Swanson, a self-employed scientific consultant living in Germany, is frustrated with her life. For lack of work, she seeks an occupation to keep herself busy, and applies for an unusual job at a pharmaceutical company. When she discovers that some of the medicines produced on site appear to be faulty, she loses the job, but the director demands her services back in an even more unusual manner. Not knowing whether she can trust him, she decides to accept his request to investigate under cover. Soon, more irregularities become apparent, and when the first victim presents itself, Sue is determined to get to the bottom of it.
Sue Swanson, a self-employed scientific consultant living in Germany, is frustrated with her life. For lack of work, she seeks an occupation to keep herself busy, and applies for an unusual job at a pharmaceutical company. When she discovers that some of the medicines produced on site appear to be faulty, she loses the job, but the director demands her services back in an even more unusual manner. Not knowing whether she can trust him, she decides to accept his request to investigate under cover. Soon, more irregularities become apparent, and when the first victim presents itself, Sue is determined to get to the bottom of it.
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Sue Swanson, a self-employed scientific consultant living in Germany, is happy to work on her latest project: she received an invitation to write a book about laboratory methods in forensic investigations. However, two recent local murder... more
Sue Swanson, a self-employed scientific consultant living in Germany, is happy to work on her latest project: she received an invitation to write a book about laboratory methods in forensic investigations. However, two recent local murder cases draw her attention, as there seems to be something wrong with the DNA evidence related to those cases. Reluctantly, she starts her own investigations, while her marriage gets seriously shaken up and the impact of the murders increases steadily. Eventually, her life becomes frustratingly complicated.
This is the second Sue Swanson novel, where science meets the world of crime. The first is entitled An unusual job.
This is the second Sue Swanson novel, where science meets the world of crime. The first is entitled An unusual job.
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... Thus, your DNA finger-print doesn't reveal your genes. Fig. 7.1 Variation in the length of genomes for Archaea, Bacteria, and Eukaryotes (the latter grouped in four kingdoms) plotted on a logarithmic scale ... Fern Moss... more
... Thus, your DNA finger-print doesn't reveal your genes. Fig. 7.1 Variation in the length of genomes for Archaea, Bacteria, and Eukaryotes (the latter grouped in four kingdoms) plotted on a logarithmic scale ... Fern Moss Arabidopsis Plants S. pombe Bulgaria Scutellospora Fungi ...
Research Interests:
Research Interests:
Research Interests:
... At the time enzymes were known to consist of proteins, and proteins were still assumed to be the basis of genetic material. However, a few years later, Oswald Avery, Maclyn McCarty, and Colin MacLeod demonstrated experimentally that... more
... At the time enzymes were known to consist of proteins, and proteins were still assumed to be the basis of genetic material. However, a few years later, Oswald Avery, Maclyn McCarty, and Colin MacLeod demonstrated experimentally that DNA was the material of inheritance. ...