Molecular diagnostic methods are currently being used for the early detection of many viral, bacterial, parasitic and fungal infections. Due to their high specificity and sensitivity, these methods will be inserted in the routine of the clinical laboratories to complement information provided by more conventional methods and above all, to help in the diagnosis of dubious cases. The design of specific probes, coupled to the Polymerase Chain Reaction (PCR) technique provides the required specificity and sensitivity to identify fungal species in a short time. Multicopy genes such as those of ribosomal origin are preferred by many researchers to achieve well defined results. However, because they may generate false positive results, other researchers have looked at single-copy genes of high specificity. This technology is being applied to the identification of frequently found causative agents of systemic mycoses such as Candida albicans, Aspergillus fumigatus and other species within these genera, or agents of less frequent mycoses produced by Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum, Paracoccidioides brasiliensis, among others.

Further reading: Pathogenic Fungi: Insights in Molecular Biology

Labels: diagnosis, fungi, mycology, PCR, real-time PCR

from Future Virol. (2008) 3(2): 119-123.

"The book entitled Coronaviruses: Molecular and Cellular Biology presents a comprehensive review of the field of coronavirus virology. The contributors to the book are many of the experts in coronavirus virology. The contents of the book are particularly useful for those wishing to conduct research on coronaviruses because most of the authors include in their summary or conclusion paragraphs a number of key questions or problems for which research needs to be carried out to further the understanding of coronaviruses and how to treat the infections they cause. Most of the figures are very useful in helping the reader understand the narratives provided by the authors. The few tables provided are excellent in summarizing information ...

recommended for those who want to quickly be brought up to date on coronavirus research or who want to know what research questions remain to be answered in the field of coronavirus virology."

Further reading: Coronaviruses: Molecular and Cellular Biology

Labels: book review, virology, virus

Helicobacter pylori is an important human pathogen that infects up to 50% of the human population. As the leading cause of peptic ulcers, gastritis and gastric cancer worldwide, the organism has been the subject of intensive research to unravel the mysteries of its genetics and cellular biology. In fact the number of publications in this field has risen dramatically in recent years making it extremely difficult for even the most diligent reader to stay abreast of progress.

A recent book on Helicobacter pylori distills the most important cutting-edge findings in the field to produce a timely and comprehensive review. Topics include: lipopolysaccharides, outer membrane proteins, motility and chemotaxis, type IV secretions systems, metal metabolism, molecular mechanisms of host adaptation, genomotyping, and proteonomics.

The book has been described as a "useful introduction to the subject for new researchers and an invaluable reference for the experienced researcher".

Further reading: Helicobacter pylori: Molecular Genetics and Cellular Biology

Corynebacteria are a diverse group Gram-positive bacteria found in a range of different ecological niches such as soil, vegetables, sewage, skin, and cheese smear. Some, such as Corynebacterium diphtheriae, are important pathogens while others, such as Corynebacterium glutamicum, are of immense industrial importance. In fact C. glutamicum is one of the biotechnologically most important bacterial species in use today with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine. Due to its industrial importance, C. glutamicum has been studied extensively over the years, and the publication of the C. glutamicum genome sequence in 2003 provided renewed impetus to these studies. To date, the complete genome sequences of four different species have been published, and sequencing of at least two more species is ongoing. These genomic data have enabled a dramatic improvement in our understanding of the corynebacterial genome architecture, metabolic processes, species-specific traits, industrial capabilities, and potential roles in pathogenicity of humans and animals. In addition these genome sequences, allied with newly developed genetic tools will consolidate C. glutamicum as a model organism for systems biology. Research in this area has never been more exciting.

Further reading: Corynebacteria: Genomics and Molecular Biology

Staphylococcus aureus is a major pathogen responsible for both nosocomial and community acquired infections. The severity of these infections varied from local benign wounds to severe systemic diseases. The situation is also complicated with emergence of bacterial resistance to common antibiotics, such as methicillin. Endemic strains of MRSA carrying multiple resistance determinants have become a worldwide nosocomial problem only in the early 1980's, carrying a threefold attributable cost and a threefold excess length of hospital stay when compared with methicillin-susceptible S. aureus bacteraemia. Recent genetic advances have enabled identification and characterization of clinical isolates in real-time. These tools support infection control strategies to limit bacterial spreading and ensure the appropriate use of diminishing antibiotics. They are also attractive for understanding the epidemiology of MRSA and the relationship between genome content and virulence.

Further reading: Francois, P. and Schrenzel, J. (2008) Rapid Diagnosis and Typing of Staphylococcus aureus In: Staphylococcus: Molecular Genetics

Rapid detection and identification of MRSA is an absolute prerequisite to adopt prompt isolation measures. Until recently, microbiological methods dedicated to MRSA identification were based on the utilization of selective growth media, which are timeconsuming and preclude same-day diagnosis. For more than one decade, nucleic acid-based identification assays have demonstrated their usefulness and robustness for the detection of hardly cultivable, non-cultivable and even killed microorganisms, as well as for the identification of specific pathogens against the background of a complex microflora. The current view is still that molecular methods are used to supplement, but not to replace cultures. MRSA molecular detection nicely illustrates this paradigm: it provides early warning but cultures are still required for further antimicrobial susceptibility testing or epidemiological typing. Molecular assays based on target nucleic acid amplification, and especially real-time PCR, have proven rapid, affordable and successful in terms of sensitivity and specificity. Current challenges for MRSA screening are centred on the selection of the most appropriate assay, both in terms of feasibility (costs, technical expertise) and assay performance. One has to be especially careful when embarking on detection strategies that are based on mobile and highly variable genetic regions, such as the SCCmec insertion site. Indeed, iterative changes in the detection protocol to adapt for emerging variants might not only affect the performance of the assay but also open unpredictable and systematic breaches in the infection control programme. To date, with several decades of hindsight, we can firmly state that molecular variations will continuously emerge, but it is currently impossible to predict where these changes will emerge. As the molecular epidemiology may substantially vary from country to country, and possibly also between different regions, this underlines the importance of having an epidemiologic molecular surveillance, ideally as close as possible to our own lab practice.

Further reading: Francois, P. and Schrenzel, J. (2008) Rapid Diagnosis and Typing of Staphylococcus aureus In: Staphylococcus: Molecular Genetics

The staphylococci are important pathogenic bacteria responsible for a variety of diseases in humans and other animals. They are the most common cause of hospital acquired infection and antibiotic resistant strains (MRSA) have become endemic in hospitals in most countries causing major public health issues. In addition, the incidence of new strains that cause severe community-acquired infections in healthy people is increasing and MRSA strains are emerging in agricultural and domestic animals. In the race to understand staphylococcal pathogenesis the focus has been on genetics, as a bacterium can only do what its genes allow. The publication of the first staphylococcal whole genome sequence in 2001 paved the way for a greater understanding of the molecular basis of its virulence, evolution, epidemiology and drug resistance. Since then the available genomic data has mushroomed and this, coupled with the major advances in genetic know-how and the availability of better genetic tools, has allowed significant advances to be made.

Further reading: Staphylococcus: Molecular Genetics

Whole genome sequences for twelve diverse Staphylococcus aureus isolates are available and their annotation provides enormous insight into S. aureus physiology, capabilities and virulence. Whole genome microarrays, built using the sequences, have enabled whole genome regulatory responses to environmental conditions or global regulators to be investigated. Comparative genomics by sequencing and by multi-strain microarrays have identified the S. aureus population structure and how genomes vary, as well as suggesting that invasive isolates do not carry more virulence genes than carriage isolates.

A large amount of genetic information is available on several examples of this species and this, together with multilocus sequence typing (MLST) data on >1400 isolates from many countries has provided unique insights into the biology of the species and in particular, its ability to exploit a wide variety of niches. These studies show that although the great majority of S. aureus genes share a high degree of homology, virulence and antibiotic resistance genes carried on mobile genetic elements can drastically alter strain characteristics in the short-term giving the species a high degree of adaptability. These allow it to survive in many different human and animal tissues and provide the adaptability necessary to evolve resistance to new antibiotics.

Further reading: Staphylococcus: Molecular Genetics

See also: Plasmids

There is enormous variation between strains of S. aureus. Evolution occurs when genomes vary and the fittest bacteria are selected. Variation occurs in three major ways: single nucleotide polymorphisms (SNP) and other minor changes in conserved core genes; variation in hundreds of genes (particularly those encoding proteins that interact with host) that are associated with lineages of S. aureus; and acquisition and loss of mobile genetic elements (MGE) which often encode virulence and resistance genes. Barriers that block horizontal transfer of DNA, such as restriction modification, influence lineages and MGE. S. aureus MGE have their own complex life-cycles that control their spread and survival. Selection of the fittest bacteria is likely being driven by mammalian host factors and antibiotic use, and new strains of S. aureus are emerging that are increasingly virulent and resistant to antibiotics, causing novel healthcare issues.

Recommended reading: Staphylococcus: Molecular Genetics

Leishmania is a vector-borne pathogenic parasite found in 88 countries worldwide and is the causative agent of leishmaniasis. The different Leishmania species infect macrophages and dendritic cells of the host immune system, causing symptoms that range from disfiguring cutaneous and mucocutaneous lesions, widespread destruction of mucous membranes, or visceral disease affecting the haemopoetic organs. The recent publication of the complete genome sequences of three different Leishmania species provides new insights into this important pathogen and presents scientists with a vital resource to increase the understanding of Leishmania molecular and cellular biology.

A new book, Leishmania: After The Genome, has been published recently reviewing the most important aspects of current Leishmania research, providing the first coherent picture of the organism's molecular and cellular biology since the publication of the genome sequence. The book covers a range of Leishmania-specific aspects of trypanosomatid biology and pathology. Topics include: diagnosis and epidemiology, genome structure and content, regulation of gene expression, the proteome, the metabolome, differentiation, interaction with the sand fly vector, drug discovery and drug resistance.

Further reading Leishmania: After The Genome

Peptide or protein antibiotics have been discovered in all three domains of life, and their production is nearly universal. Bacteriocin and eucaryocin research is well established, while research on archaeocins is still in its infancy. To date, only eight archaeocins (seven halocins and one sulfolobicin) have been partially or fully characterized, but hundreds of archaeocins are believed to exist, especially within the haloarchaea. The prevalence of archaeocins from other members of this domain is unknown simply because no one has looked for them. The discovery of new halocins hinges on recovery and cultivation of haloarchaeal organisms from the environment. For example, samples from a novel hypersaline field site, Wilson Hot Springs, recovered 350 halophilic organisms; preliminary analysis of 75 isolates showed that 48 were archaeal and 27 were bacterial. Significantly, 77% inhibited the growth of at least one other isolate. Inter-domain antagonisms were also present with 43 haloarchaeons inhibiting halophilic members of the domain Bacteria and 7 Bacteria antagonized haloarchaeons. Finally, archaeocin research provides excellent opportunities for discovery of novel antibiotics that may have clinical applications in addition to unique models for training students both in and outside the classroom.

More information: Archaea: New Models for Prokaryotic Biology