MicrobiologyBytes

DNA fragments encoding enzymes, transcriptional regulators and virulence factors are fluxing through bacterial taxonomic walls by horizontal gene transfer. These elements often endow environmental and clinical strains of bacteria with new properties, including an enhanced virulence. Lateral genetic exchange, particularly of drug tolerance genes has been recognized for a long time; however, our understanding of this phenomenon is limited. Ontology and phylogeny of laterally transferred genetic elements are difficult to investigate, let alone the predictions of their insertion sites in hosts chromosomes.

An outbreak of the lethal Escherichia coli in Europe in 2011 highlighted the shortcoming of our knowledge on the basic principles of evolutionary trends of new pathogens. The outbreak first occurred in Germany in May 2011 where a rare enterohemorrhagic strain Escherichia coli O104:H4 caused haemolytic-uremic syndrome. The infection spread fast through many other European countries and sickened thousands of people. The level of lethality associated with the production of Shiga toxin by the strain and its resistance against many antibiotics was significant. A number of isolates from this outbreak have been sequenced and annotated. Based on the unique combination of genomic features these strains were suggested to represent a new pathotype Entero-Aggregative-Haemorrhagic E. coli (EAHEC).

Mainstreams of Horizontal Gene Exchange in Enterobacteria: Consideration of the Outbreak of Enterohemorrhagic E. coli O104:H4 in Germany in 2011. (2011) PLoS ONE 6(10): e25702. doi:10.1371/journal.pone.0025702
Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest relatives but failed to resolve ways in which it originated and evolved. On account of the previous statement, may we expect similar upcoming outbreaks to occur recurrently or spontaneously in the future? The inability to answer these questions shows limitations of the current comparative and evolutionary genomics methods. The study revealed oscillations of gene exchange in enterobacteria, which originated from marine γ-Proteobacteria. These mobile genetic elements have become recombination hotspots and effective ‘vehicles’ ensuring a wide distribution of successful combinations of fitness and virulence genes among enterobacteria. Two remarkable peculiarities of the strain TY-2482 and its relatives were observed: i) retaining the genetic primitiveness by these strains as they somehow avoided the main fluxes of horizontal gene transfer which effectively penetrated other enetrobacteria; ii) acquisition of antibiotic resistance genes in a plasmid genomic island of β-Proteobacteria origin which ontologically is unrelated to the predominant genomic islands of enterobacteria. Oscillations of horizontal gene exchange activity were reported which result from a counterbalance between the acquired resistance of bacteria towards existing mobile vectors and the generation of new vectors in the environmental microflora. We hypothesized that TY-2482 may originate from a genetically primitive lineage of E. coli that has evolved in confined geographical areas and brought by human migration or cattle trade onto an intersection of several independent streams of horizontal gene exchange. Development of a system for monitoring the new and most active gene exchange events was proposed. Tweet

Bacteria are generally distinguished from the cells of fungi, plants, and animals (eukaryotes) not only by their much smaller size but also by the absence of certain subcellular structures such as nuclei, internal organelles, and microtubules. Using state-of-the-art microscopy, this paper shows that microtubules do exist in some bacteria. These bacterial microtubules are built from proteins that are closely related to the microtubule proteins in eukaryotes. Bacterial microtubules are smaller in diameter than their counterparts in eukaryotic cells but have the same basic architecture. This paper proposes that bacterial microtubules represent primordial structures that preceded eukaryotic microtubules evolutionarily. Because bacterial microtubules can be produced and handled in the lab more easily than their eukaryotic counterparts, they may become useful tools for microtubule research and anti-cancer drug screening.

Microtubules in Bacteria: Ancient Tubulins Build a Five-Protofilament Homolog of the Eukaryotic Cytoskeleton. (2011) PLoS Biol 9(12): e1001213. doi:10.1371/journal.pbio.1001213
Microtubules play crucial roles in cytokinesis, transport, and motility, and are therefore superb targets for anti-cancer drugs. All tubulins evolved from a common ancestor they share with the distantly related bacterial cell division protein FtsZ, but while eukaryotic tubulins evolved into highly conserved microtubule-forming heterodimers, bacterial FtsZ presumably continued to function as single homopolymeric protofilaments as it does today. Microtubules have not previously been found in bacteria, and we lack insight into their evolution from the tubulin/FtsZ ancestor. Using electron cryomicroscopy, here we show that the tubulin homologs BtubA and BtubB form microtubules in bacteria and suggest these be referred to as “bacterial microtubules” (bMTs). bMTs share important features with their eukaryotic counterparts, such as straight protofilaments and similar protofilament interactions. bMTs are composed of only five protofilaments, however, instead of the 13 typical in eukaryotes. These and other results suggest that rather than being derived from modern eukaryotic tubulin, BtubA and BtubB arose from early tubulin intermediates that formed small microtubules. Since we show that bacterial microtubules can be produced in abundance in vitro without chaperones, they should be useful tools for tubulin research and drug screening.

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The delightful NCBI ROFL carried this item recently. Certainly something to think about over the “festive” season.

Scent Recognition of Infected Status in Humans. J Sex Med. Dec 6 2011. doi: 10.1111/j.1743-6109.2011.02562.x
There is a body of experimental evidence that mice and rats use chemical signals to avoid sexual contact with infected conspecifics. In contrast to animals, body scent of sick humans is employed only in medical diagnostics. A modification of human body odor, due to an infection, has not been studied as a potential signal for choice of a sexual partner. It might, however, be especially important for sexually transmitted infections (STI) because many such infections have no obvious external manifestations.
Aim: In this study, we have investigated odor pleasantness of young men infected with gonorrhea, Neisseria gonorrhoeae.
Methods:We collected armpit sweat and saliva from young men (17-25 years old) belonging to three groups: healthy persons (N=16), young men infected with gonorrhea, Neisseria gonorrhoeae (N=13), and persons recovered due to specific therapy (N=5). The sweat samples odor was then assessed by healthy young women (17-20 years old). Concentrations of cortisol, testosterone, immunoglobulin A (IgA), and immunoglobulin G (IgG) were measured in saliva by means of enzyme-linked immunosorbent assay.
Main Outcome Measures: Subjective rates of odor pleasantness, association of scent of armpit sweat with odor descriptors, stepwise regression of odor pleasantness and salivary cortisol, testosterone, IgA, and IgG. Results: The odor from infected individuals was reported as less pleasant in comparison with the odor of healthy and recovered young men. The scent of infected men was more frequently associated by raters with the descriptor “putrid.” Odor pleasantness of the male sweat correlated negatively with concentration of the nonspecific salivary IgA and IgG, which was measured as an indicator of current immunoenhancement.
Conclusion: Perhaps, the immune-dependent reduction of the scent pleasantness in the acute phase of STI is part of an evolutionary mechanism ensuring, unconsciously, avoidance of a risky romantic partner.

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During the past decade, there has been a striking increase in Clostridium difficile infections worldwide predominantly due to the emergence of epidemic or hypervirulent isolates, leading to an increased research focus on this bacterium. Particular interest has surrounded the two large clostridial toxins encoded by most virulent isolates, known as toxin A and toxin B. Toxin A was thought to be the major virulence factor for many years; however, it is becoming increasingly evident that toxin B plays a much more important role than anticipated. It is clear that further experiments are required to accurately determine the relative roles of each toxin in disease, especially in more clinically relevant current epidemic isolates.

The role of toxin A and toxin B in the virulence of Clostridium difficile. Trends in Microbiology, 7 December 2011

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Prematurity is the leading cause of neonatal deaths and long-term infant disability, with the rate of preterm births continuing to rise. Despite improved medical and respiratory management, the mortality rate for the most premature infants remains high. Extremely low birth weight infants are at increased risk for complications such as sepsis, meningitis, necrotizing enterocolitis and poor growth- problems, all associated with high risk for neurodevelopmental impairment, and all of which may be impacted by the microbial communities in their gut. Among premature infants, frequently used treatments, such as antibiotics and histamine-2 blockers are associated with an increased risk of necrotizing enterocolitis and may exert their influence via alternations in gut microbiota.

This paper uses molecular methods to resolve the microbial constituents of the gut-associated microbiome in premature babies. The study highlights unprecedented early fungal diversity, evidence of roundworms, human and bacterial viruses, and a bacterial community harboring many potential pathogens.

Beyond Bacteria: A Study of the Enteric Microbial Consortium in Extremely Low Birth Weight Infants. (2011) PLoS ONE 6(12): e27858
Extremely low birth weight (ELBW) infants have high morbidity and mortality, frequently due to invasive infections from bacteria, fungi, and viruses. The microbial communities present in the gastrointestinal tracts of preterm infants may serve as a reservoir for invasive organisms and remain poorly characterized. We used deep pyrosequencing to examine the gut-associated microbiome of 11 ELBW infants in the first postnatal month, with a first time determination of the eukaryote microbiota such as fungi and nematodes, including bacteria and viruses that have not been previously described. Among the fungi observed, Candida sp. and Clavispora sp. dominated the sequences, but a range of environmental molds were also observed. Surprisingly, seventy-one percent of the infant fecal samples tested contained ribosomal sequences corresponding to the parasitic organism Trichinella. Ribosomal DNA sequences for the roundworm symbiont Xenorhabdus accompanied these sequences in the infant with the greatest proportion of Trichinella sequences. When examining ribosomal DNA sequences in aggregate, Enterobacteriales, Pseudomonas, Staphylococcus, and Enterococcus were the most abundant bacterial taxa in a low diversity bacterial community (mean Shannon-Weaver Index of 1.02±0.69), with relatively little change within individual infants through time. To supplement the ribosomal sequence data, shotgun sequencing was performed on DNA from multiple displacement amplification (MDA) of total fecal genomic DNA from two infants. In addition to the organisms mentioned previously, the metagenome also revealed sequences for gram positive and gram negative bacteriophages, as well as human adenovirus C. Together, these data reveal surprising eukaryotic and viral microbial diversity in ELBW enteric microbiota dominated bytypes of bacteria known to cause invasive disease in these infants.

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Salmonella enterica serotype Typhimurium (S. Typhimurium) is an important food-borne pathogen that in humans causes a self-limited gastroenteritis, characterized by fever, acute intestinal inflammation, diarrhea, and the presence of neutrophils in stool samples. In addition, S. Typhimurium is a model organism for studying bacterial genetics and microbial pathogenesis. As the frontier in bacterial pathogenesis research is moving towards understanding the complexity of host-pathogen interaction at the tissue level, studies on the pathogenesis of S. Typhimurium gastroenteritis using animal models have helped establish important new concepts that exert a strong influence on the research field. Recent studies on S. Typhimurium pathogenesis reveal how tissue-specific host factors and the presence of other bacterial species shape the outcome of host-pathogen interaction in the intestinal lumen. This review discusses these new paradigms for the interplay between the pathogen, the host and its resident microbial community.
Salmonella, the host and its microbiota. Curr Opin Microbiol. Oct 24 2011
The intestine is host to a diverse bacterial community whose structure, at the phylum level, is maintained through unknown mechanisms. Acute inflammation triggered by enteric pathogens, such as Salmonella enterica serotype Typhimurium (S. Typhimurium), is accompanied by changes in the bacterial community structure marked by an outgrowth of the pathogen. Recent studies show that S. Typhimurium can harness benefit from the host response to edge out the beneficial bacterial species that dominate in the healthy gut. The elucidation of how S. Typhimurium alters the bacterial community structure during gastroenteritis is beginning to provide insights into mechanisms that dictate the balance between the host and its microbiota.

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The introduction of rRNA-targeted fluorescence in situ hybridization (FISH) using oligonucleotide probes for the cultivation-independent identification of microbes more than 20 years ago marked the beginning of a new era for environmental and medical microbiology. When integrated into the so-called full-cycle rRNA approach, FISH enables microbiologists to decipher complete structures of microbial communities in a quantitative manner. Furthermore, this phylogenetic staining technique in its basic format is easy to apply and once probes have been designed and evaluated, the detection of their target organisms in environmental or medical samples is straightforward and can be completed in a few hours. In its original format, fluorescent monolabeled oligonucleotide probes are used for FISH, but as the signal intensity of this technique is insufficient for cells with low ribosome contents, FISH detection efficiencies in oligotrophic environments are generally rather low. For such systems, catalyzed reporter deposition (CARD)-FISH, which exploits horseradish peroxidase (HRP)-labeled oligonucleotide probes and tyramide signal amplification is the method of choice to capture most microbial community members.

rRNA-targeting FISH techniques are continuously developed further and major improvements regarding increased cell permeability, accessibility of probe target sites, probe specificity, signal intensity, and so on have been achieved. A second rapidly evolving FISH-related research area is the combination of rRNA-FISH with other techniques, which provide additional information on (i) the presence of specific genes or mRNA molecules of the target cell, (ii) its specific metabolic activity or (iii) important environmental parameters such as the concentration of chemical compounds in the vicinity of the detected cell. For this purpose rRNA-FISH or CARD-FISH have been combined with various other FISH techniques and staining procedures as well as with microautoradiography, microelectrode measurements, Raman microspectroscopy, and NanoSIMS. This review provides an overview on the most recent developments in the FISH field.

New trends in fluorescence in situ hybridization for identification and functional analyses of microbes. Curr Opin Biotechnol. Nov 11 2011
Fluorescence in situ hybridization (FISH) has become an indispensable tool for rapid and direct single-cell identification of microbes by detecting signature regions in their rRNA molecules. Recent advances in this field include new web-based tools for assisting probe design and optimization of experimental conditions, easy-to-implement signal amplification strategies, innovative multiplexing approaches, and the combination of FISH with transmission electron microscopy or extracellular staining techniques. Further emerging developments focus on sorting FISH-identified cells for subsequent single-cell genomics and on the direct detection of specific genes within single microbial cells by advanced FISH techniques employing various strategies for massive signal amplification.

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Gathering and sharing of information is extremely important in human society. Especially in times of war, the difference between victory and defeat can depend on the ability to obtain, encrypt, and share information, and sophisticated systems have been developed for exactly this purpose. Similarly, in their constant battles with competitors and the host immune system, (opportunistic) microbial pathogens have developed sophisticated cell–cell communication systems termed quorum sensing (QS) that allow exchange of critical information. In return, competing microbes, as well as the host immune system, have developed means to intercept and decode these messages. The information obtained by this molecular espionage is used for their benefit, either to win the war (microbe against microbe), or to prepare for an upcoming battle (microbe against immune system).

QS is a system that enables microbes to monitor population cell density through the production, secretion, and sensing of small diffusible molecules. When such molecules reach a threshold concentration, microbial cells in the vicinity detect the signal and coordinately respond by modifying their gene expression; often these genes are associated with virulence and pathogenesis. Several different types of QS molecules have been described for a wide variety of microbial species.

To illustrate the clinical importance of this microbial spy game, this short review focuses on the biological activity of a single bacterial QS molecule on surrounding microbes and the host immune system and its diverse “meaning” to different receivers. Infections related to burn wounds, cystic fibrosis, and periodontal diseases consist most commonly of the bacteria Pseudomonas aeruginosa and Staphylococcus aureus and the fungus Candida albicans, and represent niches with an active host response. This short review provides five facts about how the P. aeruginosa QS molecule plays a pivotal role in this triangle of interspecies interactions and how microbial behavior elicited by this small signalling molecule has consequences for the host response.

Microbial Spy Games and Host Response: Roles of a Pseudomonas aeruginosa Small Molecule in Communication with Other Species. (2011) PLoS Pathog 7(11): e1002312. doi:10.1371/journal.ppat.1002312

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Carbapenems were the last β-lactams retaining near-universal anti-Gram-negative activity, but carbapenemases are spreading, conferring resistance. New Delhi metallo-β-lactamase (NDM) enzymes are the latest carbapenemases to be recognized and since 2008 have been reported worldwide, mostly in bacteria from patients epidemiologically linked to the Indian subcontinent, where they occur widely in hospital and community infections, and also in contaminated urban water. The main type is NDM-1, but minor variants occur. NDM enzymes are present largely in Enterobacteriaceae, but also in non-fermenters and Vibrionaceae. Dissemination predominantly involves transfer of the bla(NDM-1) gene among promiscuous plasmids and clonal outbreaks. Bacteria with NDM-1 are typically resistant to nearly all antibiotics, and reliable detection and surveillance are crucial.

E. coli is one of the most prevalent human pathogens, and the window of opportunity to control it from becoming widely resistant is rapidly closing. No vaccine is likely to become available and one that affects commensal gut strains would probably be undesirable, even though these might act as vectors of potent resistance, including NDM-1. Therefore, everything must be done now to prevent infections due to bacteria with NDM-1, otherwise infections as common as pyelonephritis might soon become life-threatening owing to the lack of effective treatment.

The emerging NDM carbapenemases. Trends Microbiol. Nov 9 2011

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