Source: https://mbioblog.asm.org/mbiosphere/2016/07/index.html
Timestamp: 2019-04-19 08:32:08+00:00

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Recently, one of the Journal of Bacteriology Classic Spotlight series highlighted the numerous studies on bacterial spores that have been published in the journal throughout the years. Bacterial endospores, the resilient and relatively quiescent bacterial structures first identified in the 1800s, have had their genetic regulation, immunological properties, and biochemical makeup investigated for decades. The structures are incredibly resistant and produced by select members of the Gram-positive Firmicutes phylum. Despite many rigorous studies investigating these biological structures, new research published in Applied and Environmental Microbiology shows that there's always something new to learn in microbiology, including aspects that appear as straightforward as morphology.
One of the methods that has proved extremely useful in studying spore morphology is transmission electron microscopy (TEM). Some of the original research described in the Classic Spotlight utilized this technique to investigate the structural changes that occur during outgrowth, as a spore germinates to become a vegetative cell again. This is technology allowed scientists to define spore structures: the outermost, electron-dense layer called the exosporium; the laminated underlying spore coat; a thick cortex; and an inner spore coat with a cytoplasmic membrane and germ cell wall (see figure, right).
This same microscopy technique is still used fifty years later for structural studies. Marjorie Pizarro-Guajardo made her initial TEM observations, which revealed two different morphologies in spores from the same Clostridium difficile culture: one with a thick and one with a thin exosporium layer (see image, left). The spores from this original report were purified with different techniques and from different biofilm development timepoints, and so the research team set out to determine which of these factors was behind the different spore types with a follow-up study, now published in AppEnvMicro.
To minimize variables that might affect spore morphology, the team recovered purified C. difficile spores from a single culture and examined the morphology by TEM. The team observed a both thick and thin exosporium morphologies from biofilm and nonbiofilm cultures when using the same strain (hypervirulent strain R20291), but saw that the ratio of thick:thin exosporium changed when the strain was grown as a sporulating culture versus when the strain was grown as an in vitro biofilm (see figure below right).
The biofilms used for experimentation, though still an in vitro growth condition, more closely mimic what researchers have seen during C. difficile infection in a mouse. Finding that biofilm growth affects spore morphology brings up questions of how a mixed species biofilm might affect sporulation . The exosporium outer layer may affect attachment/detachment to the tissue surface or other bacterial cells, and in fact spore morphology could be regulated by biofilm formation itself. A previous Journal of Bacteriology report from a separate group found a transcriptional regulator that regulates sporulation, Spo0A, is also required for normal biofilm formation, suggesting these two processes may be related.
The ability C. difficile to resist antibiotic action through spore formation is one reason this pathogen causes such terrible illness. If scientists can better understand regulation or development of this outer spore layer, this knowledge may provide clues on how to manipulate the spore formation or germination processes. The exosporium layer is also the first layer to interact with the outside environment, and these insights introduce questions regarding its regulation and development. Spore biology, though a classic in many senses, still holds many scientific mysteries, with important applications if and when solved.
No matter the niche field a scientist pursues, there is one aspect of almost all career paths that scientists have in common: teaching. Whether lecturing a quorum of undergraduates about bacterial genetics, mentoring a research fellow as they learn the lab protocols, or presenting an invited lecture to a group of established scientists, one must consider how to present information in an understandable and absorbable manner. The American Society for Microbiology Conference for Undergraduate Education (ASMCUE) is the annual forum for science educators to discuss learning objectives, active learning exercises, and the best applications for new technologies. This year’s meeting, held July 21-24 in North Bethesda, Maryland, focused on presenting information in many styles, with an emphasis on learning by doing. Other major conference themes included assessment methods and primary literature use in the classroom.
Hands-on labs and lab courses are a natural environment for students to learn through experience, but the types of experiences students acquire are changing. Jay Labov of the National Academies of Sciences presented a session on integrating discovery-based research into the undergraduate curriculum. Labov suggests lab courses should be a place of experimentation, where undergraduates participate in true discovery research instead of a prefabricated lab experience. Course-based research experiences, or CUREs, expose students to real research (and the risk of failed experiments) early in their careers and may be a more accessible starting point for students without a strong science background. Although these course types are less standardized due to the nature of different research projects and implementations, CUREs have higher student and teacher enthusiasm (compare grading 25 nearly identical reports to 25 nearly unique reports), and studies are beginning to show that genuine research experiences lead to better student retention rates.
Incorporating these research experiences into courses is important, but so is a systematic analysis of what students should be learning from these experiences. Paula Soneral of Bethel University hosted a session in which instructors detailed the processes they had taken to design and implement CUREs into the scientific curriculum. Deciding learning outcomes and discovery milestones will determine both the experimental structure and subsequent student assessments, which she walked participants through using their own CURE ideas. All lab courses and research experiences should emphasize safety, as Jeffrey Byrd presented in a session on safety assessment and instruction for lab practices. Byrd, faculty at St. Mary's College of Maryland, is also the Safety Editor for the Journal of Microbiology & Biology Education.
In addition to discussing CURE course assessment, Sara Brownell of Arizona State University addressed ethical issues surrounding this type of course. For example, students who pay tuition may be gaining similar experiences to student researchers who earn money through work-study programs, setting up conflicts between students. The relationship between the CURE research projects and the instructor’s research projects can also cause conflicts of interest, which are important to disclose and resolve, if possible. Imagining possible issues before they arise can help prevent disputes and ultimately add to a better student experience.
Many active-learning techniques used at ASMCUE sessions!
Just as CUREs and similarly run programs are designed to give students a taste of authentic research experience, reading primary literature is one way for students to get a taste of research communication. Primary literature has been used in upper-level courses for years, but several presentations concentrated on primary literature for introductory microbiology or biology students. A session led by Amy Briggs of Beloit College covered the use of primary literature to introductory biology courses, which often require textbooks but can be complemented by primary literature. She illustrated with examples from her own experiences, in which students compared news articles with the initial scientific article, an exercise designed to stress the role of responsible journalism in scientific communication. Discussing a table or data without explanatory text can also inspire students to think creatively and apply textbook concepts in their analyses.
Nancy Boury of Iowa State University addressed the challenge of holding a journal club with over one hundred students, as many state colleges and public universities have in their introductory microbiology courses. Using session participants as prospective students (one of many active learning techniques held at ASMCUE), the session held a brief journal club in a lecture hall setting, demonstrating the challenges of full student involvement in this environment. Large lectures can benefit from primary literature analyses, but the interactions should to be tailored to the setting.
Concept Inventories are a student assessment tool gaining popularity among faculty. Concept inventories (CI) are multiple-choice assessments that rigorously probe student understanding, using criterion-referenced tests around specific concepts. Three validated CI developed by faculty from around the country for microbiology-related topics (Microbiology in Health Sciences CI, General Microbiology CI, and Host Pathogen CI) were presented, with discussion centered around their use to address gaps in student knowledge and student misconceptions. The session participants used these CI as examples to create their own, based on previously collected student assessments. Student assessments are used to generate distractors – choices on a multiple-choice question that are common wrong answers. This helps to differentiate students who fully comprehend a topic from those with fuzzy comprehension, as well as pinpoint where the gaps or misunderstandings may lie.
The small sample of sessions described here also illustrate an overarching theme of ASMCUE this year: the joy of learning. It was clear that all conference goers attended the conference because of a deep-instilled love of learning, which they sought to share in a variety of ways. Kelly Gull and ASM staff had fun promoting Mikey the Microbe for president (with Gull acting as Mikey’s security, right). As part of the ArtWalk, Mark Martin of the University of Puget Sound brought bioluminescent bacteria for participants to paint glow-in-the-dark plate. The Federal Department of Agriculture's Eric Brown shared his passion for food safety in a plenary lecture on whole-genome sequencing technologies. After four intense days, conference attendees who had traveled from across the United States (and across the world!) to share their best teaching tips and tools returned, inspired, to prepare for the rapidly approaching school year.
Did you attend a great session at ASMCUE? Share it in the comments! Wish you had been able to attend ASMCUE? Have a great teaching technique to share with your fellow educators? The 2017 meeting is already scheduled for July 27-30 for Denver, Colorado – get your proposals in by October 15th!
The Gram-positive bacterium Enterococcus faecium is a member of the ESKAPE pathogens for which drug resistance has been a growing problem. How E. faecium becomes drug resistant has been a long-standing question, and is the focus of a new study now available in Antimicrobial Agents and Chemotherapy. A research team led by senior scientist Louis Rice has identified chromosomal regions where homologous recombination facilitates incorporation of genes conferring beta-lactam and vancomycin resistance.
Enterococci have been problematic for many decades, particularly in the context of health care-associated infections. Many Enterococcal species have intrinsic resistance to various drugs, meaning that they are unaffected by the mechanism by which certain drugs act. Typing infections to the species level is important in clinical diagnoses to determine whether a species is inherently sensitive or resistant to a particular compound. However, Enterococci are also masters of sharing DNA, including drug-resistance genes, meaning that many infections have acquired drug resistance as well. In their study, the researchers investigated the incorporation of genetic resistant determinants in E. faecium.
The researchers investigated the transfer of genetic determinants for drug resistance, concentrating on the penicillin binding protein 5 (pbp5) operon and the vancomycin resistance cassette (vanB) from a clinical isolate. Pbp5 is a gene that encodes a transmembrane protein important for cell wall assembly and is found in all wild-type E. faecium strains. The vanB element is a complex cassette that encodes different proteins that modify the peptidoglycan precursors that are incorporated into the cell wall, effectively altering the vancomycin target in a way that renders the antibiotic ineffective. The pbp5 gene is chromosomally encoded, while vancomycin resistance is normally encoded by transposons that can be plasmid or chromosomally borne.
How is resistance to penicillins and vancomycin transferred? To find out, the researchers used two E. faecium strains: a donor strain that was vancomycin-resistant and highly resistant to penicillins and a recipient strain that was vancomycin-susceptible and less resistant to penicillins than the donor. The strains were then incubated together and transconjugants selected by their resistance profiles were further investigated by whole genome sequencing. This detailed information allowed the scientists to determine that transfer of pbp5 and the adjacent vanB operon was almost always linked, and that the strain acquiring vancomycin resistance replaced its own pbp5 allele with that of the donor strain through homologous recombination (see schematic, right).
Discovering the involvement of multiple mechanisms in E. faecium sharing or incorporating new DNA emphasizes the importance of basic genetic research. This is a successful pathogen in health care settings in part due to its ability to resist antibiotic action. As researchers look for ways to combat the spread of antibiotic resistance, one means is to inhibit the spread of resistance genes between bacteria. But when it comes to E. faecium resistance and genetic swapping, “there is not a ‘one size fits all’ mechanism this bacterium uses,” says Garcia-Solache.
The anaerobic, Gram-positive Clostridium difficile is a big problem. It causes rampant diarrhea and tissue necrosis, with more than 150,000 annual cases in the United States alone. Many of the disease manifestations of C. difficile are mediated by two exotoxins that C. difficile produces: TcdA and TcdB. Researchers have long been working at toxin inhibition as an approach to disarm C. difficile and improve treatment, and new research in Clinical and Vaccine Immunology shows promise in blocking toxin activity in vivo.
Both TcdA and TcdB toxins are glucosyltransferases that transfer sugars to several targeted host molecules, including Ras family members involved in cell signaling and actin regulation. Cells exposed to TcdA/TcdB experience a rapid change in cell shape as F-actin concentrations decrease (see figure, left). Structural damage increases tight junction permeability, and fluid secretion from epithelial cells accumulates, leading to edema. Ultimately, many of the cells die by apoptosis.
To exert these effects, the TcdA and TcdB toxins are released by C. difficile into the extracellular space, and must interact with host cell receptors for uptake by endocytosis. A team of scientists led by Saul Tzipori generated a molecule, based on recombinant antibody technology, that blocks TcdA and TcdB uptake. Rather than treat C. difficile infection with an entire antibody, which has been successful but is quite expensive, the team generated a VHH, which is the variable region of the immunoglobulin heavy chain (see figure, right). This small fragment can be recombinantly expressed from E. coli, decreasing cost and increasing yield. Because the molecule is based on a toxin-recognizing antibody, it can potentially neutralize these molecules.
What’s better than a single VHH? Multiple VHHs! The team had previously characterized VHHs that neutralize against TcdA and TcdB, and used this data to create a construct of two VHHs that neutralize each toxin (four total), connected by linker sequences. This tetra-specific, heteromultimeric VHH-based neutralizing agent, called VNA2-Tcd, was the molecule tested against C. difficile pathogenesis in two forms: one, as a purified protein expressed from E. coli, and one, as a gene therapeutic in an adenovirus vector.
The first proof-of-principle was to look at the ability of purified VNA2-Tcd to protect against toxin. Host cells were exposed to TcdA/TcdB, which resulted in a classic round phenotype, as the actin scaffold within the cell disintegrated. As expected, increasing doses of VNA2-Tcd protected more cells from rounding. A dose of VNA2-Tcd was also able to protect mice from subsequent toxin challenge, demonstrating in vivo efficacy.
But the toxins are a problem in the context of disease, so the researchers moved into three animal models of C. difficile infection: mouse, hamster, and pig. The rodent models were first used to test the efficacy of the purified VNA2-Tcd. Mice were challenged with C. difficile spores, and mice receiving purified VNA-Tcd2 treatment were injected at 4, 24, and 48 hours after infection. Untreated mice uniformly became sick with diarrhea, but no treated mice became moribund (although one mouse did develop diarrhea, which resolved after a day), and the treatment protected all animals from death (see figure, left). Hamsters were less well protected: treated animals were delayed in symptom onset, but all animals (except one treated hamster) developed and eventually succumbed to disease symptoms.
Pigs were then tested with both purified protein and adenovirus therapies. Just like the mice, all piglets were infected with C. difficile spores. Both the purified VNA2-Tcd and the adenovirus gene therapy treatment were able to lessen (though not prevent) disease. Histology showed that lesions were smaller in the treated groups, demonstrating the positive effect of toxin blockage on tissue damage. When looking at the adenovirus-treated animals, the research team observed a correlation between animals with a high serum VNA2-Tcd concentration and mild to moderate symptoms – more production equaled more protection.
The VNA2-Tcd treatments were administered to the animals systemically, but ideally sick human patients would take their medication orally. However, even orally-administered purified protein therapy would need to continue as long as the patient remained colonized with high levels of C. difficile bacteria, because the VHHs neutralize toxins but have no antibacterial activity. The gene therapy treatment success in piglets is a promising way to address this problem: patients’ own cells generate the VNA2-Tcd VHH constructs to mediate prolonged protection. Patients would still experience C. difficile overgrowth, which may still need addressing through other clinical treatments. But eliminating the bacterial toxins' effects through neutralization may be the first step to turn this deadly pathogen into a bothersome nuisance.
If it looks like a duck and quacks like a duck, it’s likely a duck – so goes the saying that illustrates the simplest explanation is usually the right one. But what about duck decoys used in conjunction with bird calls? Misidentification can be a deadly error – and the same goes for microbes. Misdiagnosed infectious disease etiologies can be a very dangerous mistake for sick patients. Most clinical microbiology labs are able to use sophisticated biochemical and genetic tests to differentiate microbial species and strains, but newly emerging pathogens can be misidentified if they closely mimic another. That appears to be the case with the newly emerging fungal pathogen, Candida auris.
Candida auris was first described in 2009 from a 70-year-old patient in Japan. The species is unable to form hyphae or pseudohyphae, differentiating it from Candida species such as C. albicans or C. tropicalis, and molecular tests can differentiate the isolate from C. glabrata but often misidentify it as C. haemulonii. This is a dangerous mix-up, as C. auris is resistant to fluconazole and has lower susceptibility to voriconazole, amphotericin B, and caspofungin. The basis of C. auris’ higher basal resistance isn’t yet fully understood, but the draft genome of two isolates will help scientists investigate this question, including the identification of many potential transporter homologs that may play a role.
The emergence of several outbreaks of C. auris in health-care settings, originally misdiagnosed, suggests person-to-person transmission is possible and emphasizes the importance of a simple diagnostic test to differentiate C. auris infection. Commercial identification systems such as the Vitek AST-YS07 card have misidentified 90% of C. auris as C. haemulonii, and this misidentification can lead to inaccurate treatment. A C. auris infection requires higher antifungal doses, due to its higher MICs, to ensure effective therapy. Until automatic ID systems are improved, MALDI-TOF mass spectrometry, as described in a recent Journal of Clinical Microbiology report, has most accurately differentiated between unique Candida species infections.
Tracking C. auris infections is also an issue with misdiagnosis: just as Zika infection was likely misdiagnosed as dengue due to poor diagnostics, C. auris infection may be more common than previously thought. Mass spectrometry may be accurate, but many clinical labs don’t have the capability to run this assay. An accessible diagnostic tool is therefore needed to help clinicians address this problem.
Thus far, C. auris has been reported only in Asian countries, but there’s no reason to think it won’t spread. The dispersal of Zika via globalized travel has demonstrated that infectious disease has no respect for geography, and microbes can quickly become endemic under the right conditions. Furthermore, the identification of E. coli harboring mcr-1 plasmids in U.S. patients demonstrates that the problem could already be among us, lurking quietly until detected. Waiting to address this problem will only lead to further misdiagnosis, a deadly but ultimately avoidable outcome.
As we highlighted in our previous blog, antibiotic stewardship – the careful use of appropriate antibiotic administration – can have positive effects. A small change from a difference in clinical lab reporting led to less drug use, which led to fewer drug-resistant infections. When we think of antibiotic stewardship, the onus is often thought to be on those that work in the clinic – the scientists who determine isolate susceptibility, or the clinicians who decide which antibiotic should be prescribed to a patient. These individuals certainly have an essential role to play in proper antimicrobial drug use in a health-care setting.
But the general public also has an important role to play in antibiotic stewardship, as illustrated by a new study in Antimicrobial Agents and Chemotherapy. In the report, Roger Zoorob and the team of physician scientists conducted a survey of 400 individuals, asking them about their antibiotic use. 5% of respondents said they had used non-prescription antibiotics within the past year, some multiple times, and 25% said they would be willing to use antibiotics without talking to a health-care professional. Though acquiring antibiotics without a prescription is illegal, those that had used off-prescription antibiotics had access due to leftover stocks from previous prescriptions, purchase outside of the U.S., and even within the U.S., which accounted for a whopping 40% of off-prescription antibiotics.
Who uses drugs without a prescription? The survey was given to patients waiting in one of three primary care clinics (two public and one private), with diversity in income, ethnicity, and insurance status; those who would be willing to use non-prescription antibiotics were more likely to be surveyed from one of the public clinics, with less education and lower annual incomes. There was no correlation between antibiotic self-treatment and race or ethnicity.
The reason antibiotics were self-administered varied, but several patterns emerged among respondents. Those that had used non-prescribed antibiotics were treating including respiratory symptoms, urinary tract infection symptoms, tooth pain, and stomach pain (see chart, right). Unfortunately, many of the antibiotics used may not successfully treat the microbial source of the infection. “When people self-diagnose and self-prescribe antibiotics, it is likely that the therapy is unnecessary because most often these are upper respiratory infections that are mostly caused by viruses,” said corresponding author Larissa Grigoryan.
Self-prescribed drugs are not only possibly ineffective, but also add to the growing antibiotic resistance problem. Exposing one’s microbiome to antibiotics increases the possible selection for drug-resistant strains, especially if the drug dosing or timing isn’t properly determined. Stemming the use of non-prescription antimicrobials is the type of antibiotic stewardship effort that belongs to all community members. These results demonstrate a necessary role for public health communication and education to inform all citizens how their actions may impact their and others’ future health. The small gains from stewardship programs can accumulate to prolonged drug efficacy if we all work together toward this common goal.
There’s no way to avoid the news of a growing concern for drug-resistant infections. In both life-threatening and relatively superficial infections, the ability to successfully treat microbial infections with antimicrobials is decreasing. Our only recourse is to use the drugs we have carefully while researchers hunt for new drugs that must pass the stringent FDA guidelines before they can be used clinically. But here comes a bit of good news among all the doom-and-gloom: meticulous drug management programs can have a positive effect on drug-resistant infections.
Support for the decrease in drug-resistant infections comes from a study performed at St. Joseph’s Health Center Hospital in Toronto, Ontario. A team of clinical scientists led by Larissa Matukas studied the effects of antibiotic stewardship surrounding the use of ciprofloxacin, a fluoroquinolone that interferes with DNA topoisomerases, to treat bacterial infections caused by Esherichia coli or Pseudomonas aeruginosa. Their results are now available in the Journal of Clinical Microbiology.
The Infectious Disease Society of America (IDSA) suggests cascade reporting of drug susceptibility, which is the practice of reporting susceptibility for the least expensive drug to which the microbe is susceptible. If three drugs A, B, and C are all tested in order of drug cost, and the isolate is susceptible to A, only that measurement is reported, because it is the cheapest. There are several controversial issues surrounding this practice and the team in this study hoped to find an alternate reporting system targeting fluoroquinolones, with a goal to reduce their use.
To attempt this, the microbiology lab at the hospital changed their susceptibility reporting for infectious isolates. Previously, ciprofloxacin susceptibility was reported regardless of other drug susceptibilities. The policy was changed such that ciprofloxacin susceptibility was reported only if no other susceptibilities were found when testing isolates against a drug panel that included cefazolin, amoxicillin-clavulanate, trimethoprim-sulfamethoxazole, gentamicin, nitrofurantoin, tobramycin, and ciprofloxacin. This selective reporting emphasized susceptibility without immediate concern of drug cost.
After implementing this new reporting strategy, the scientific team saw a drop in ciprofloxacin use, as might be expected if ciprofloxacin susceptibility isn’t reported. The defined daily dose dropped from 87 to 39 per 1000 inpatient days, demonstrating a strong reduction in use of this particular antibiotic. However, the use of amoxicillin-clavulanate increased from 3.1 to 29.8 DDD per 1000 inpatient days, which may represent compensatory usage as clinicians look for an effective drug to treat infections. This would be an important aspect to consider if broadening the scope of reporting to multiple drugs or drug classes.
In addition to measuring drug use, the team tested E. coli and P. aeruginosa isolates for ciprofloxacin susceptibility before and after the reporting change. The drop in ciprofloxacin use correlated with a change in predicted isolate susceptibility. There was no significant change to the level of P. aeruginosa susceptibility throughout the study. Importantly, the rate of drug-resistant E. coli isolates, which had been steadily increasing prior to the new selective reporting strategy, leveled off and showed a trend toward increasing susceptibility (see figure, right).
The change was small and relatively slow, but this small silver lining shows that our behavior concerning antimicrobials can have an effect. In the midst of ‘superbug’ stories and emerging resistance genes, we will need to employ many small gains, such as those observed in this study, to prolong the efficacy of the drugs we have in hand.
Colony collapse disorder (CCD) has caused such a profound drop in honeybee populations that even the U.S. Congress is addressing the issue: Senator Jeff Merkley (D-Oregon) has proposed the Pollinator Recovery Act to preserve pollinator habitat. The rapid decline in these important pollinators affects the economy and agriculture of bee-deprived regions. Hive disappearances have been described by beekeepers before, but the large number of countries affected, and the duration of the phenomenon, have motivated scientists to concentrate on this apiary anomaly.
While there is no universally-accepted cause of CCD, a number of pathogenic viruses have been associated with the death of entire colonies, with geographically distinct picorna-like viruses from the Dicistroviridae and Iflaviridae families playing a large role. In the United States, the non-enveloped, RNA virus, Israeli acute paralysis virus (IAPV), infects every stage and caste of honeybees and is strongly associated with CCD. New research now available in the Journal of Virology investigates the structure of IAPV.
Knowing the virus structure can provide valuable information such as what are the size limitations of the virus, where are the receptors for attachment, or how does the virus uncoat its genome. First author Edukondalu Mullapudi and senior author Pavel Plevka hoped to learn some of these biological aspects from determining the structure of IAPV.
To begin their studies, the scientists propagated the virus in honeybee larvae to generate native structures. The crystal structure of the purified virus showed the viral capsid, composed of VP1, VP2, VP3, and VP4 capsid proteins, has icosahedral symmetry. The IAPV surface topology differs quite a bit from the previously crystallized dicistrovirus, CrPV, and somewhat from the dicistrovirus TrV (see figure, right). IAPV shares only about 25% sequence similarity with each of these viruses, which are more closely related to each other, demonstrating the importance of determining the structure independent from sequence homology.
Although native virions were purified for crystallization, some of the crystals formed were from capsid protomers, the repeating capsid subunit consisting of several capsid proteins, rather than intact capsid. These protomers lacked VP4, which is released along with the viral genome during mammalian picornavirus uncoating. The authors speculate that the crystallized protomers represent the remnant capsid particles of uncoated virions, and that VP4 may play a similar role in IAPV uncoating. This adds a valuable clue to the dicistrovirus genome delivery mechanism, which has previously remained unstudied.
The IAPV structure is similar to vertebrate picornaviruses, which includes enteroviruses, hepatoviruses, and rhinoviruses. Some picornaviruses can be treated with compounds that inhibit their uncoating; the compound interacts with a hydrophobic pocket in the V1 capsid protein. Comparing the IAPV VP1 structure to that of PV-1 reveals no hydrophobic pocket in the IAPV structure (see figure, left), suggesting IAPV is unlikely to inhibited by similar compounds.
Defining the IAPV structure and life cycle may help scientists design inhibitors for these CCD-associated pathogens. While this may not answer all aspects of these mysterious events (such as: why are there no bee carcasses from collapsed colonies?), protecting these hives remains the current top priority. Learning the IAPV structure may have ruled out one class of inhibitors, but it will also allow scientists to examine new methods to manipulate viral biology and stem the spread of IAPV.
Imitation may be the sincerest form of flattery, but it can also be the easiest way to make a buck. That’s the primary motivation for camouflaging within an already-established brand: Sunbucks, McDowell’s, and Mountain Lightening all rely on brand recognition – of a brand that isn’t their own. While ASM Journals are by no means the only imitated journals, the well-established credibility of the journals published by ASM makes them an easy target for unscrupulous publishers.
An invitation to submit to the Journal of Bacteriology, for example, may have a subscript or footnote clarifying the full journal title to be “Academic Journal of Bacteriology and Advanced Sciences Online,” as illustrated in an article from the June Microbe Magazine by Robert Hunziker, Jr, of Dunner Law PLLC. A busy reader might skim over the footnote and take the invitation at face value – and believe themselves to be submitting to a century-old credible publisher.
The term predatory publishing comes in part from the use of tricky titles meant to deceive authors and readers alike, and in part from the high-throughput, low-quality manuscripts produced by these outlets. Such publishers hope to issue large numbers of manuscripts without strong consideration of scientific quality, and therefore use minimal peer review standards. They are also willing to publish duplicate data sets, directly plagiarized content, or add non-involved authors, which act in direct opposition to scientific publishing ethics. Those most at risk for falling prey to these tactics are young scientists at the onset of their careers, or scientists publishing in a field tangential to their own, where the author may not be familiar with well-reputed journal titles.
Hunziker explains the best defense is a good offense and advises ASM members and scientists alike to be vigilant against such practices. And though the number of predatory journal articles has increased nearly eightfold in four years, authors need not avoid open-access journals altogether. Many established publishers are creating freely available options under Creative Commons licensure, such as mBio, mSphere, and mSystems here at ASM; these journals demonstrate that open-access and high-caliber science can go hand-in-hand to benefit both science and scientists.
Although the Gram-negative bacterium Vibrio cholerae (right) is normally associated with human pathogenic disease, most V. cholerae cells spend their lives in an aquatic environment, and only a few of the many serotypes are able to cause disease. When strains acquire the right genetic makeup – such as the cholera toxin and toxin coregulated pilus associated with pathogenesis - they can cause cholera outbreaks through contamination of human food and water sources. The pandemic O1/O139 serogroups are the best-known of this species, responsible for worldwide pandemic cholera outbreaks (including the recent outbreak in Haiti), but non-O1/O139 serogroups can cause smaller outbreaks of diarrheal disease. These strains coexist in acquatic environments with other, nonpathogenic strains; what does this coexistence mean for population structure?
That was the question that a team of scientists led by Yan Boucher set out to answer. First author Paul Kirchberger and his coauthors collected 100-ml samples of water from brackish water near the coast of Massachusetts on two collection days separated by three weeks. Samples were filtered and plated on media selective for Vibrio species, after which the 480 isolates underwent multi-locus sequence typing (MLST) analysis. The authors used a large number of isolates from this single location to gain detailed understanding of the mixed populations, rather than a broad overview of a large geographic area. Their results are now available in Applied and Environmental Microbiology.
The team selected seven housekeeping genes for MLST analysis. Isolates with the same seven sequences were defined as the same sequence type (ST), and a difference in only one of seven loci was defined as the same clonal complex (CC). These parameters allowed the team to define 72 V. cholerae STs that could be grouped into 17 CCs (see figure, left).
Though their sample number was larger, the scientists observed less diversity than previous, similar studies had. A prior Mediterranean lagoon study of 109 isolates found 78 STs, only 14 of which grouped into 5 CCs, while a coastal California study of 156 isolates found 113 STs grouped into 8 CCs. The differences in diversity observed could be due to the smaller geographic range or timeframe of the current study, but may also provide a better ‘snapshot’ of the V. cholerae population is in a given waterway.
Collecting their samples at two different time points allowed the scientists to observe a population shift in the three-week separated samples. Only five of the 17 CCs were found in both samplings, while the remaining 12 were found in one or the other. The proportion of the five CCs identified in both samples changed from one sampling to another, suggesting that a new V. cholerae population, when present, can become dominant in a very short time frame (see figure, right). How does this happen? Vibrio populations are influenced by local phage and copepod populations, so a change in one of these populations, or another local condition, may quickly have repercussions in the dominant local bacteria.
The researchers looked at greater detail at some of the isolates’ genomic sequences. Sequencing from representatives of the five consistently-identified clades revealed differences in gene content, including clades with genes encoding a pilus and an ADP-ribosyltransferase toxin, which showed more similarity to the heat-labile enterotoxin LT-A of Escherichia coli than to the cholera toxin of the pandemic O1/O139 V. cholerae strains. The ability of Vibrio to exchange genes via plasmid transfer, phage or bacterial compentency means all V. cholerae are potential pathogens, given the right genetic combination.
The results show that diverse V. cholerae living together can rapidly change population proportions; in this report, the changes between the populations were among relatively harmless strains. Were a pathogenic strain lurking in low numbers, these data suggest it could become a major proportion of the local population in as short as a few weeks. The results emphasize the importance of understanding the population dynamics of local water environments, with real public health implications.

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