MicrobiologyBytes

Swarming is flagella-driven bacterial group motility over a surface, which is observed in the laboratory on media solidified with agar. The percentage of agar is critical for enabling swarming. Some bacteria like Vibrio parahaemolyticus and Proteus mirabilis can swarm readily on higher percentage agar, whereas others like Salmonella, Escherichia coli, Serratia, Pseudomonas, and Bacillus swarm only on lower percentage agar. Hard-agar swarmers differentiate into specialized swarm cells that are elongated and have increased flagella. Medium-agar swarmers generally do not display a similar differentiated morphology. In many of the latter class of swarmers (e.g. Serratia, Pseudomonas, Bacillus), movement is enabled by powerful extracellular surfactants whose synthesis is under quorum-sensing control. Surfactants lower surface tension and allow rapid colony expansion. Salmonella and E. coli do not appear to make such surfactants.

Swarming bacteria exhibit adaptive resistance to multiple antibiotics. Analysis of this phenomenon has revealed the protective power of high cell densities to withstand exposure to otherwise lethal antibiotic concentrations. This paper shows that that high cell densities promote bacterial survival, even in a nonswarming state, but that the ability to move, as well as the speed of movement, confers an added advantage, making swarming an effective strategy for prevailing against antimicrobials. There is no evidence of induced resistance pathways or quorum-sensing mechanisms controlling this group resistance, which occurs at a cost to cells directly exposed to the antibiotic. This work is relevant to the adaptive antibiotic resistance of bacterial biofilms.

Cell density and mobility protect swarming bacteria against antibiotics. PNAS USA February 2 2010 doi: 10.1073/pnas.0910934107

Related:

• Look who’s talking
• Antibiotics, your gut, and you
• MicrobiologyBytes: Antibiotics

A 21-year Michigan State University experiment that distills the essence of evolution in laboratory flasks not only demonstrates natural selection at work, but could lead to biotechnology and medical research advances. Researchers at Michigan State University started a culture of Escherichia coli bacteria in 1988. The results are in.

Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 18 October 2009 doi:10.1038/nature08480
The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.

Related:

• The continuing evolution of E. coli O157:H7
• Global functional atlas of Escherichia coli proteins

The urinary tract is among the most common sites of bacterial infection. Over half (53%) of all women and 14% of men experience at least one urinary tract infection (UTI) in their lifetime, leading to an average of 6.8 million physician office visits, 1.3 million emergency room visits, and 245,000 hospitalizations per year, with an annual cost of over US$2.4 billion in the United States alone. Escherichia coli is the infectious agent in more than 80% of uncomplicated UTIs, which occur in patients with a normal urinary tract devoid of structural abnormalities or inflammatory lesions.

In light of the recent E. coli outbreak in the UK, the news that scientists have made an important step toward what could become the first vaccine to prevent urinary tract infections is interesting. To help combat this common health issue, the scientists used a novel systematic approach combining bioinformatics, genomics and proteomics to look for key parts of the E. coli bacterium that could be used in a vaccine to elicit an effective immune response. The team screened 5,379 possible bacterial proteins and identified three strong candidates to use in a vaccine to prime the body to fight E. coli, the cause of most uncomplicated urinary tract infections. The vaccine produced prevented infection and produced key types of immunity when tested in mice.

Scientists have attempted to develop a vaccine for UTIs over the past two decades. This latest potential vaccine has features that may better its chances of success. It alerts the immune system to iron receptors on the surface of bacteria that perform a critical function allowing infection to spread. Administered via the nose rather than injected, it induces an immune response in the body’s mucosa, a first line of defense against invading pathogens. The protective immune response, which also produced in mucosal tissue in the urinary tract, should help the body fight infection where it starts. The research team is currently testing more strains of E. coli. Most of the strains produce the same iron-related proteins that the vaccine targets, an encouraging sign that the vaccine could work against many urinary tract infections.

Iron acquisition is a critical function required by bacteria in order to cause infections. In uropathogenic E. coli, this function is mediated by a repertoire of systems that scavenge iron from the host during infection. Vaccination with certain iron receptors from these systems is sufficient to elicit protective immunity from experimental urinary tract infection. Induction of an antibody response played a key role in protection from infection because antibody class-switching and the production of antibodies in urine correlated with reduced numbers of bacteria in the bladder. By targeting an entire class of molecules involved in iron acquisition instead of a single protein, it was possible to successfully identify components of a protective UTI vaccine. This strategy could be a useful approach in the development of vaccines to prevent infections caused by other pathogenic bacteria.

However, this is still early clinical research and this candidate vaccine has not yet undegone even a phase 1 safety trial in humans. And even if that were successful, the vaccine would take several more years to reach the market, even if manufacturers decided they could make a profit from producing it. So the next time you’re down on the farm, wash your hands – and make sure that burger is properly cooked through.

Mucosal Immunization with Iron Receptor Antigens Protects against Urinary Tract Infection. 2009PLoS Pathog 5(9): e1000586 doi:10.1371/journal.ppat.1000586
Uncomplicated infections of the urinary tract, caused by uropathogenic Escherichia coli, are among the most common diseases requiring medical intervention. A preventive vaccine to reduce the morbidity and fiscal burden these infections have upon the healthcare system would be beneficial. Here, we describe the results of a large-scale selection process that incorporates bioinformatic, genomic, transcriptomic, and proteomic screens to identify six vaccine candidates from the 5379 predicted proteins encoded by uropathogenic E. coli strain CFT073. The vaccine candidates, ChuA, Hma, Iha, IreA, IroN, and IutA, all belong to a functional class of molecules that is involved in iron acquisition, a process critical for pathogenesis in all microbes. Intranasal immunization of CBA/J mice with these outer membrane iron receptors elicited a systemic and mucosal immune response that included the production of antigen-specific IgM, IgG, and IgA antibodies. The cellular response to vaccination was characterized by the induction and secretion of IFN-c and IL-17. Of the six potential vaccine candidates, IreA, Hma, and IutA provided significant protection from experimental infection. In immunized animals, class-switching from IgM to IgG and production of antigen-specific IgA in the urine represent immunological correlates of protection from E. coli bladder colonization. These findings are an important first step toward the development of a subunit vaccine to prevent urinary tract infections and demonstrate how targeting an entire class of molecules that are collectively required for pathogenesis may represent a fundamental strategy to combat infections.

Related:

• Microbiology Video Library: Escherichia coli
• E. coli O157:H7 – getting to the bottom of the burger bug
• The continuing evolution of E. coli O157:H7
• Bacterial toxins

Despite improvements in agricultural practices, leafy greens, tomatoes, salad crops and nuts were among the foods linked to recent outbreaks of gastrointestinal illnesses caused by Escherichia coli O157:H7 and non-typhoidal Salmonella (Human enteric pathogens in produce: un-answered ecological questions with direct implications for food safety. Curr Opin Biotechnol. April 4 2009). Because plants are not traditionally considered as hosts for human enteric pathogens, recent produce-associated outbreaks highlight important deficiencies in our understanding of the ecology of enteric pathogens outside of their human and animal hosts. The ongoing food safety debate focuses on answering the question whether plants are true alternate hosts for Salmonella or E. coli, or whether they are simply matrices where these organisms persist.

In a survey of several farms, up to 43% of produce sampled in the field was positive for Salmonella enterica, and the pathogen was found in the soil, irrigation water and on the hands of agricultural laborers. Following the 2006 E. coli O157:H7 spinach outbreak in the United States, the pathogen was isolated from cattle and feral swine faeces, river sediment, pasture soil, and surface water near the implicated fields. Human enteric pathogens are often recovered from surface water and untreated waste water used for irrigation. These reports establish that enteric pathogens in various environmental reservoirs may lead to food-associated outbreaks. Once deposited in soils, enteric bacteria persist for periods of time that range from a few weeks to several years. In field studies, both E. coli and Salmonella from raw manure were capable of colonizing the root zone and above ground parts of plants, supporting the hypothesis that pre-harvest contamination in the field could be a plausible route of produce contamination.

Subscribe to podcasts (free):
[iTunes] Enhanced podcasts & videos
[RSS] mp3 podcasts (audio only)
Play this episode: Enhanced version | Audio only

For an enteric bacterium, it may make evolutionary sense to colonize vegetative and reproductive parts of plants that are then eaten by animals. If so, then enteric bacteria should have sophisticated, co-evolved mechanisms for getting into plants, spreading and multiplying in edible plant tissues to levels capable of populating guts of their herbivorous hosts. Salmonella enterica and enterovirulent E. coli are able to colonize tissues of plants quite effectively. This suggests that under favorable conditions enterics can exist as epi- or endophytes. If endophytic growth is truly a part of the life cycle of enterics, then this explains why current surface salad crop decontamination procedures may not be very effective. Conversely, if endo- or epiphytic growth is an important part of the life cycle of enterics, then we should be able to uncover evidence of specificity in the bacterial attachment, colonization and avoidance of plant defenses.

Recent laboratory studies identified a few of the genes and mechanisms that enterics use to colonize external surfaces of host plants. It appears that bacterial polymers and aggregative fimbriae were involved in the attachment of E. coli and/or Salmonella to plant seedlings. In their reliance on cellulose for attachment to plant surfaces, enteric pathogens are similar to plant symbiotic and pathogenic bacteria that also use cellulose fibrils to anchor themselves to plant surfaces.

Most plant pathogens and endophytes also produce hemicellulases and pectinases, enzymes that degrade polymers in plant cell walls. Unlike closely related members of the Enterobacteriaceae, Salmonella and E. coli do not seem to produce such enzymes and their genomes do not encode homologs of these enzymes. It is not yet clear whether Salmonella has unknown classes of cell wall degrading enzymes, whether it manages to gain entry and spread in plant tissues without such enzymes by moving intercellularly, or whether it relies on enzymes from the host or from other endophytes or plant pathogens to degrade plant cell walls. Regardless of their route of entry, enteric bacteria that were present inside plant seedlings were found in the intercellular spaces between host cell walls.

Although recent research has established that Salmonella and enterovirulent E. coli are capable of spending at least a part of their life cycle as plant-associated endo- or epiphytes, several important questions about the genetics and physiology of these interactions still need to be answered before plants are designated as true alternate hosts for these bacteria. Because there is evidence of specificity in the interactions of plant genotypes with enterics, defining the genetic basis and molecular markers associated with resistance to enterics may help identify crop cultivars that are less conducive to supporting growth of human pathogens. Further characterization of the attachment to plant surfaces and interactions with the resident microbiota will likely help improve pre- and post-harvest treatments to ensure safety of produce for human consumption.

Related:

• Pathogens in raw foods
• E. coli O157:H7 Spinach Outbreak

Because of its central position in the microbial research community, the Gram-negative bacterium Escherichia coli plays a leading role in investigations of the fundamental molecular biology of bacteria. This experimentally tractable microbe is a workhorse in basic and applied research aimed at elucidating the mechanistic basis of prokaryotic processes and traits, including those of pathogens. The ever-expanding availability of genomic resources makes E. coli particularly well-suited to systematic investigations of microbial protein components and functional relationships on a global scale. These include a genome-wide collection of single-gene deletion strains along with extensive knowledge of regulatory circuits and metabolic pathways. Yet despite being the most highly studied model bacterium, a recent comprehensive community annotation effort for the fully sequenced reference K-12 laboratory strains indicated that only half (54%) of the protein-coding gene products of E. coli currently have experimental evidence indicative of a biological role. The remaining genes have either only generic, homology-derived functional attributes (e.g. “predicted DNA-binding”) or no discernable physiological significance. Some of these functional “orphans” may have eluded characterization in part because they exhibit mild mutant phenotypes, are expressed at low or undetectable levels, or have limited homology to annotated genes.

One goal of modern biology is to chart groups of proteins that act together to perform biological processes via direct and indirect interactions. Such groupings are sometimes called functional modules. The types of protein interaction within modules include physical interactions that generate protein complexes and biochemical associations that make up metabolic pathways. Researchers have combined proteomic and bioinformatic tools and used them to decipher a large number of protein interactions, complexes and functional modules with high confidence. In addition, exploring the topology of the resulting interaction networks, they successfully predicted specific biological roles for a number of proteins with previously unknown functions, and identified some potential drug targets. Although their work is focused on E. coli, their phylogenetic projections suggest that a considerable fraction of observations and predictions can be extrapolated to many other bacterial taxa. As all the data derived from this study are publicly available (at eNet), others may build on this work for further hypothesis-driven studies of gene function discovery.

Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 7(4): e1000096
One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans’ biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a ‘‘systems-wide’’ functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.

Related:

• An introduction to genomics (video)
• Digitizing Life (video)
• The end of the world? Dr Franken-Venter? Nope