MicrobiologyBytes

Bacteria communicate with one another via quorum-sensing signal molecules. This paper describes the first example of quorum-sensing molecules participating in interspecies bacterial cell death. This is an interesting observation in its own right – but think about this: these peptides potentially provide the basis for a new class of antibiotics which trigger death by acting from outside the cell.

Novel Quorum-Sensing Peptides Mediating Interspecies Bacterial Cell Death. (2013) mBio 4(3): e00314-13 doi: 10.1128/mBio.00314-13
Escherichia coli mazEF is a toxin-antitoxin stress-induced module mediating cell death. It requires the quorum-sensing signal (QS) “extracellular death factor” (EDF), the penta-peptide NNWNN (EcEDF), enhancing the endoribonucleolytic activity of E. coli toxin MazF. Here we discovered that E. coli mazEF-mediated cell death could be triggered by QS peptides from the supernatants (SN) of the Gram-positive bacterium Bacillus subtilis and the Gram-negative bacterium Pseudomonas aeruginosa. In the SN of B. subtilis, we found one EDF, the hexapeptide RGQQNE, called BsEDF. In the SN of P. aeruginosa, we found three EDFs: the nonapeptide INEQTVVTK, called PaEDF-1, and two hexadecapeptides, VEVSDDGSGGNTSLSQ, called PaEDF-2, and APKLSDGAAAGYVTKA, called PaEDF-3. When added to a diluted E. coli cultures, each of these peptides acted as an interspecies EDF that triggered mazEF-mediated death. Furthermore, though their sequences are very different, each of these EDFs amplified the endoribonucleolytic activity of E. coli MazF, probably by interacting with different sites on E. coli MazF. Finally, we suggest that EDFs may become the basis for a new class of antibiotics that trigger death from outside the bacterial cells.

Microbiology Today: Getting the message out

The Society for General Microbiology (SGM) leads the way on antimicrobial resistance.

http://www.sgm.ac.uk/en/publications/microbiology-today/current-issue.cfm

Last week I got involved in an interesting “discussion” with a senior professor of physics about what makes a good pathogen. I wish I’d had this at the time to show him.

Experimental Evolution of Pathogenesis: “Patient” Research. (2013) PLoS Pathog 9(5): e1003340. doi:10.1371/journal.ppat.1003340
Laboratory passage has long been recognized as an effective means to modify the host range of pathogens, with successive passage of viruses in nonhuman hosts an early strategy for generating live attenuated vaccines. The principle behind this attenuation is that confined passage in one host species can modify the host range of a pathogen such that it no longer efficiently causes disease in the original host. Armed with modern molecular and genomic tools, several groups have revisited the basic outlines of this approach to directly test how natural host diversity and host cycling influence the evolutionary trajectory of pathogens.

Remember Koch’s Postulates? These are the four criteria designed to establish a causal relationship between a causative microbe and a disease:

1. The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.
2. The microorganism must be isolated from a diseased organism and grown in pure culture.
3. The cultured microorganism should cause disease when introduced into a healthy organism.
4. The microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

Simply finding a potentially-disease causing organism does not necessarily mean it’s up to no good!

The bacterium Mycoplasma pneumoniae is carried at high rates in the upper respiratory tracts of healthy children and usual diagnostic tests cannot differentiate between such asymptomatic carriage and actual respiratory tract infection, according to a new study. These findings are important as they suggest that clinicians may need to reconsider the clinical significance of a positive test result for the presence of this bacterium.

The researchers compared upper respiratory tract swabs and blood culture results taken from 321 children (aged 3 months to 16 years) admitted to hospital with a respiratory tract infection with those from 405 healthy children undergoing an elective surgical procedure. They found that the prevalence of M. pneumoniae (as measured using PCR tests) did not differ significantly between the asymptomatic group and the symptomatic group. There was also no difference in prevalence when diagnosed using blood tests. In addition, a high rate of other bacteria and viruses was found in both asymptomatic and symptomatic children.

This data indicates that the presence of M. pneumoniae in the upper respiratory tract is common in asymptomatic children. Current diagnostic tests for M. pneumoniae are unable to differentiate between asymptomatic carriage and symptomatic infection. Cinicians may need to readdress the clinical significance of a positive test result.

Carriage of Mycoplasma pneumoniae in the Upper Respiratory Tract of Symptomatic and Asymptomatic Children: An Observational Study. (2013) PLoS Med 10(5): e1001444. doi:10.1371/journal.pmed.1001444
Mycoplasma pneumoniae is thought to be a common cause of respiratory tract infections (RTIs) in children. The diagnosis of M. pneumoniae RTIs currently relies on serological methods and/or the detection of bacterial DNA in the upper respiratory tract (URT). It is conceivable, however, that these diagnostic methods also yield positive results if M. pneumoniae is carried asymptomatically in the URT. Positive results from these tests may therefore not always be indicative of a symptomatic infection. The existence of asymptomatic carriage of M. pneumoniae has not been established. We hypothesized that asymptomatic carriage in children exists and investigated whether colonization and symptomatic infection could be differentiated by current diagnostic methods. This study was conducted at the Erasmus MC–Sophia Children’s Hospital and the after-hours General Practitioners Cooperative in Rotterdam, The Netherlands. Asymptomatic children (n = 405) and children with RTI symptoms (n = 321) aged 3 mo to 16 y were enrolled in a cross-sectional study from July 1, 2008, to November 30, 2011. Clinical data, pharyngeal and nasopharyngeal specimens, and serum samples were collected. The primary objective was to differentiate between colonization and symptomatic infection with M. pneumoniae by current diagnostic methods, especially real-time PCR. M. pneumoniae DNA was detected in 21.2% (95% CI 17.2%–25.2%) of the asymptomatic children and in 16.2% (95% CI 12.2%–20.2%) of the symptomatic children (p=0.11). Neither serology nor quantitative PCR nor culture differentiated asymptomatic carriage from infection. A total of 202 children were tested for the presence of other bacterial and viral pathogens. Two or more pathogens were found in 56% (63/112) of the asymptomatic children and in 55.5% (50/90) of the symptomatic children. Finally, longitudinal sampling showed persistence of M. pneumoniae in the URT for up to 4 mo. Fifteen of the 21 asymptomatic children with M. pneumoniae and 19 of the 22 symptomatic children with M. pneumoniae in this longitudinal follow-up tested negative after 1 mo. Although our study has limitations, such as a single study site and limited sample size, our data indicate that the presence of M. pneumoniae in the URT is common in asymptomatic children. The current diagnostic tests for M. pneumoniae are unable to differentiate between asymptomatic carriage and symptomatic infection.

Ideally, invading bacteria are detected as early as possible in critically ill patients: the strain of morbific pathogens is identified rapidly, and antimicrobial sensitivity is known well before the start of new antimicrobial therapy. Bacteria have a distinct metabolism, part of which results in the production of bacteria-specific volatile organic compounds (VOCs), which might be used for diagnostic purposes. Volatile metabolites can be investigated directly in exhaled air, allowing for noninvasive monitoring.

The aim of this review is to provide an overview of VOCs produced by the six most abundant and pathogenic bacteria in sepsis, including Staphylococcus aureus, Streptococcus pneumoniae, Enterococcus faecalis, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli. Such VOCs could be used as biological markers in the diagnostic approach of critically ill patients. A systematic review of existing literature revealed 31 articles. All six bacteria of interest produce isopentanol, formaldehyde, methyl mercaptan, and trimethylamine. Since humans do not produce these VOCs, they could serve as biological markers for presence of these pathogens.

Targeted studies should be performed to identify potential sets of volatile biological markers and evaluate the diagnostic accuracy of these markers in critically ill patients.

Volatile Metabolites of Pathogens: A Systematic Review. (2013) PLoS Pathog 9(5): e1003311. doi:10.1371/journal.ppat.1003311

Over the last few years, many microbiomes (all of the microbobes found in a particular enviromnet) have been published. Most of these long list of bugs have been purely descriptive, but this knowledge is now starting to pay off by finding out which microbes are associated with particular diseases. In many cases, it’s not as simple as a single organism causing a disease.

For example, take chronic rhinosinusitis, a disease with a significant societal burden, but despite extensive research efforts, an unknown pathophysiology. There is emerging evidence that microorganisms play an important role in the exacerbation and perpetuation of mucosal inflammation:

The microbiome of chronic rhinosinusitis: culture, molecular diagnostics and biofilm detection. (2013) BMC Infectious Diseases, 13:210 doi:10.1186/1471-2334-13-210
Bacteria and fungi are believed to influence mucosal inflammation in chronic rhinosinusitis (CRS). However their presence and relationship to disease is debated. This study used multiple detection methods to compare microbial diversity and microbial abundance in healthy and diseased sinonasal mucosa. The utility of contemporary detection methods is also examined. Sinonasal mucosa was analyzed from 38 CRS and 6 controls. Bacterial and fungal analysis was performed using conventional culture, molecular diagnostics (polymerase chain reaction coupled with electrospray ionization time-of-flight mass spectrometry) and fluorescence in situ hybridization. Microbes were detected in all samples, including controls, and were often polymicrobial. 33 different bacterial species were detected in CRS, 5 in control patients, with frequent recovery of anaerobes. Staphylococcus aureus and Propionibacterium acnes were the most common organisms in CRS and controls, respectively. Using a model organism, FISH had a sensitivity of 78%, and a specificity of 93%. Many species were detected in both CRS and controls however, microbial abundance was associated with disease manifestation. This study highlights some cornerstones of microbial variations in healthy and diseased paranasal sinuses. Whilst the healthy sinus is clearly not sterile, it appears prevalence and abundance of organisms is critical in determining disease. Evidence from high-sensitivity techniques, limits the role of fungi in CRS to a small group of patients. Comparison with molecular analysis suggests that the detection threshold of FISH and culture is related to organism abundance and, furthermore, culture tends to select for rapidly growing organisms.

Or consider the news that antibiotics may ease chronic back pain:

Antibiotic treatment in patients with chronic low back pain and vertebral bone edema (Modic type 1 changes): a double-blind randomized clinical controlled trial of efficacy. (2013) European Spine Journal, 1-11.
The study was a double-blind RCT with 162 patients whose only known illness was chronic LBP of greater than 6 months duration occurring after a previous disc herniation and who also had bone edema demonstrated as Modic type 1 changes in the vertebrae adjacent to the previous herniation. Patients were randomized to either 100 days of antibiotic treatment (Bioclavid) or placebo and were blindly evaluated at baseline, end of treatment and at 1-year follow-up. Primary outcome, disease-specific disability, lumbar pain. Secondary outcome leg pain, number of hours with pain last 4 weeks, global perceived health, EQ-5D thermometer, days with sick leave, bothersomeness, constant pain, magnetic resonance image (MRI). 144 of the 162 original patients were evaluated at 1-year follow-up. The two groups were similar at baseline. The antibiotic group improved highly statistically significantly on all outcome measures and improvement continued from 100 days follow-up until 1-year follow-up. At baseline, 100 days follow-up, 1-year follow-up the disease-specific disability-RMDQ changed: antibiotic 15, 11, 5.7; placebo 15, 14, 14. Leg pain: antibiotics 5.3, 3.0, 1.4; placebo 4.0, 4.3, 4.3. Lumbar pain: antibiotics 6.7, 5.0, 3.7; placebo 6.3, 6.3, 6.3. For the outcome measures, where a clinically important effect size was defined, improvements exceeded the thresholds, and a trend towards a dose–response relationship with double dose antibiotics being more efficacious. The antibiotic protocol in this study was significantly more effective for this group of patients (CLBP associated with Modic I) than placebo in all the primary and secondary outcomes.

In treating chronic diseases such as these, those long lists of organisms associated with certain diseases states is going to start paying off over the next few years.

Polyphosphate (polyP) is a linear polymer of a few to many hundreds of phosphate (Pi) residues linked by high-energy phosphoanhydride bonds. This ubiquitous polymer is found in bacteria, protists, and mammalian cells, and probably predates living cells. In bacteria, polyP accumulates in volutin or metachromatic granules, which are equivalent to acidocalcisomes. In eukaryotic cells, polyP is present in different compartments, including the cytosol, nucleus, lysosomes, and mitochondria, but is preferentially accumulated in acidic vacuoles such as the yeast vacuole and acidocalcisomes.

Acidocalcisomes were first described in trypanosomes and later found in Apicomplexan parasites, algae, slime molds, fungi, eggs of different origins, and human cells. These organelles were originally described as acidic compartments storing high concentrations of calcium, and later work found that they are highly enriched in polyP. As the description of acidocalcisomes progressed over the years, it was found that they are similar to the volutin or metachromic granules described in bacteria and are now considered to be the only organelles maintained over evolutionary time from bacteria to human cells.

The function of polyP has been studied mainly in prokaryotes: as a Pi store, an energy source to replace ATP, in cation sequestration and storage, in cell membrane formation and function, in gene transcription control, in regulation of enzyme activities, in response to stress and stationary phase, and in the structure of channels and pumps. PolyP is also important in the physiological adjustments of bacteria to growth, development, stress, and deprivation; its role in biofilm development, quorum sensing, and virulence, as well as in long-term survival and expression of virulence factors.

PolyP, which in bacteria is mainly of long-chain type (>300 and up to 1,000 Pi residues), has been reported to be important for virulence of different bacteria, such as Salmonella spp., Shigella flexneri, Vibrio cholerae, Neisseria meningitidis, Pseudomonas aeruginosa, and Mycobacterium tuberculosis, but the mechanism involved is not known. It has also been reported that conditions that decrease the levels of polyP in parasites such as T. brucei, T. gondii, or L. major reduce their pathogenicity. Whether this is due to osmotic fragility of the parasites as a result of changes in polyP levels that impact their ability to grow in vivo, making the immune response against them more successful, or to a role of polyP in modulating the immune response is not yet known.

PolyP has been found in bacterial to human cells and has been reported to be important for virulence of different bacteria and a number of parasites, including those that cause toxoplasmosis, African trypanosomiasis, and leishmaniasis. Even more exciting are the findings about the role of polyP in cancer metastasis, blood coagulation, inflammation, and innate immunity. For example, a significant finding is that enzymes involved in polyP metabolism could be excellent targets for drug design not only against bacteria and parasites but also for regulation of important physiological and pathological processes such as coagulation, inflammation, innate immunity, and thrombosis.

Polyphosphate and Its Diverse Functions in Host Cells and Pathogens. (2013) PLoS Pathog 9(5): e1003230. doi:10.1371/journal.ppat.1003230

Welcome to the Weekend!

World Malaria Day recognises global efforts being made in the fight against malaria. First established in 2007 by the World Health Assembly, it falls on 25 April every year.

Measles outbreak: In graphics
Great use of data by BBC News – students take note – this is how you do it.

Strain of measles possible cause of dolphin deaths [Audio]
Scientists think that more than a hundred dead dolphins found washed up on the Italian coast, may have been infected with a killer strain of “measles”. [Human measles, or another Paramyxovirus?]

Mapping the H7N9 avian flu outbreaks
Where are the 104 human cases reported so far and where might the virus go next?

Promising Treatment for New Human Coronavirus
A new report says that two antiviral drugs, ribavirin and interferon-alpha 2b, will stop nCoV from replicating in cells grown in the lab.

Radioactive Listeria cures cancer – or does it?
This report just appeared in PNAS. Let’s hope it’s a generalisable method, but for the present this is one small scale study – still a long way to go before this is a routine treatment.

The Truth About Why Microbes Make You Sick
Between fevers, congestion and diarrhea, there are numerous ways that microbes can make us feel sick. But just how do microorganisms cause these symptoms?

Gonorrhea could be untreatable by 2015 [Audio]
There’s been a sharp increase in the number of cases of the sexually transmitted infection gonorrhoea – up 25% in 2011. It is also becoming harder to find antibiotics that treat it, which has raised the prospect that it could soon become untreatable.

Holy Virus Treasure Trove, Batman!
Think about the type of animal that would make an ideal host for a virus. It would gather in large dense groups, making it easier for the virus to jump into fresh hosts. It should have a relatively long lifespan, so any single individual has many chances of becoming infected. It would certainly travel over long distances to spread the infection far and wide. Humans certainly fit the bill. So do bats.

tldr; = your armpits = lunch for bacteria

The human skin exhibits a diversity of ecological niches varying in moisture, the availability of nutrients, and the presence of host- and bacteria-derived antimicrobial peptides. In general, skin regions can be classified as dry, sebaceous, or moist environments with specifically adapted organisms establishing a distinct microbial profile characteristic for each topographical region. 16S rDNA profiling of the skin microbiota in the course of the Human Microbiome Project shed the first light on the community structure at different skin sites independent of microbial culture.

In moist areas such as the armpit (in medispeak, the “axilla”), Corynebacterium and Staphylococcus dominate the bacterial flora, which was demonstrated by culture-based approaches. The axillary region is a specific habitat and differs significantly from other body parts because it harbors hair follicles with sebaceous glands and a high density of sweat glands. In this environment nutrients are readily available, which allows for dense bacterial colonization reaching up to 10⁶ cells per cm². Different types of sweat glands are present including eccrine and apoeccrine glands which are responsible for sweating when you’re hot. Apocrine glands, so-called scent glands, contribute to the high density of nutrients. They secret a milky odorless fluid consisting of electrolytes, steroids, proteins, vitamins, and a variety of lipid compounds. Despite the fact that the exact composition of apocrine sweat is currently unknown due to insufficient availability of pure samples, the microbial biotransformation of these secreted nutrients in the human axilla undoubtedly leads to the development of characteristic and individual odor profiles. Perception and pleasantness of specific odor compounds have been reported to correlate with gender, sexual orientation, and the use of oral contraceptives.

It is of particular interest for the cosmetic industry to understand body-odor formation mechanisms to be able to design deodorants which specifically target them. The classic functional mechanism of deodorants is the depletion of cutaneous bacteria employing unspecific antimicrobial agents. This can cause skin irritations upon very frequent usage not only due to the direct topical action of alcoholic or organic substances. Also, disruption of the integrity of the skin microbiota may have negative effects on the host in terms of health because symbiotic and commensal bacteria participate in immune defense against pathogens. This article gives an overview of the biochemical origin of human axillary odor and the taxonomic composition of the axillary microbiota based on recent data generated with next-generation sequencing techniques.

Daily battle against body odor: towards the activity of the axillary microbiota. Trends in Microbiology. 05 April 2013 doi: 10.1016/j.tim.2013.03.002
The microbial community of the human axilla plays a key role in the formation of axillary odor by biotransformation of odorless natural secretions into volatile odorous molecules. Culture-based microbiological and biochemical studies have allowed the characterization of the axillary microbiota, but the advent of next-generation culture-independent DNA sequencing approaches has provided an unprecedented depth of data regarding the taxonomic composition of the axillary microbiota and intra- and interindividual variation. However, the physiological activity of the microbiota of an individual and its variation under different environmental conditions remains largely unknown. Thus, metatranscriptomics represents a promising technique to identify specific metabolic activities in the axillary microbiota linked to individual differences in body odor.