Archive for the “Bacteriology” Category

The term “superbug” is nothing new to the microbiology world but has only been under the spotlight for a few years, which consequently led to an increasing interest in antibiotic resistance by researchers. A superbug refers to a multidrug resistant bacterium which can therefore cause untreatable and fatal infections. This particular aspect has sparked global worry that our known antibiotics will eventually fail us.

With the interest in superbugs at its highest, scientists from Indiana University and Harvard University had their share in the investigation, using multi-colored dyes called fluorescent D-amino acids (FDAAs), aka rainbow dyes, which turned out to be just as cheerful to the researchers as actual rainbows. These dyes enabled them to visualize the detailed process of cell division, particularly the movement of the filaments FtsZ and FtsA (cytoskeletal polymers and prokaryotic homologs of the protein tubulin) that determine the site of cell division by driving peptidoglycan synthesizing enzymes to the correct sites. Cytokinesis starts with the formation of a Z-ring at the site of cell division, and both FtsZ and FtsA are required for this process.

When visualized, the filaments appeared to move in circular concentric rings, in a movement which was described as “treadmilling” in which the FtsZ filament loses a molecule at one end and gains a molecule at the other end, resulting in the circular motion. With the guidance of these rings, peptidoglycan was shown to begin forming a septum dividing the cell.

A more detailed aspect of the FtsZ and FtsA system is the lack of any means to convert chemical energy into mechanical force. However, the rearrangement is primarily dependent on FtsZ polymerization dynamics under the influence of conflicting regulation by FtsA, first, by promoting FtsZ assembly and second, by inhibiting FtsZ network organization. The result of this regulation is the formation of higher ordered structures by FtsZ as tubules, circles and sheets.

These findings might be a magnificent aid in combating superbugs by visualizing so accurately their division and offering a broader comprehension of their mechanisms.

Finally, if you ever find yourself anxious about superbugs, just remember: there always comes a RAINBOW after a rainy day.


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Infections in the teeth implants are dreaded, running a high risk of potentially affecting the jaw bones. It is actually not that uncommon. The overall number of performed teeth implantations in the US and Europe has doubled over the last decade, yet studies show that 10 percent of the implants are associated with problems, usually in the first year directly after the operation. To prevent any further deterioration, the implants sometimes have to be removed.

New methods are now being developed by researchers in the University of Zurich to keep inflammation-causing bacteria at bay. In their PLoS ONE article, they present their materials and methods, which have successfully eliminated 99% of the microbes after a 15-minute electrical treatment.

Conventional treatment methods of this sort of inflammation depend on the utilization of topical antibiotics, which is surely a burden for the patient. The aim of the study was to develop a non-invasive approach to efficiently fight off the bacteria, or, as the researchers phrase it in their paper, to develop “an in-situ decontamination of the dental implants”.

The whole idea is based on the process of water treatment, where sterile water is produced through electrolysis. In order to simulate the conditions in the jaw, an Escherichia coli bacterial film was coated onto the titanium implants, which were impregnated in a gelatinous preparation. In the experimental design, one implant functioned as the cathode and the other as the anode. The implants were subjected to a 15-minute-long electrical treatment, of an intensity ranging between 0 and 10 Milliampere. This artificially generated electrical field caused the hydroxyl ions of the water molecules to migrate to the cathode, and thus raising the pH. A color change of the indicators, used in the gelatin, prove that an alkaline environment predominates at the cathode. On the other hand, the pH value drops at the anode, forming an acidic milieu.

The numerous experimental models with various electrical intensities show that in cases, where an acidic ambience was produced around the implants, 99% of the bacteria died off after a 15-minute treatment. Therefore, the patient implants in the future will take up the role of the anode. A clip at the lip will be used as a cathode.

What at first glance might seem as a torture mechanism is in reality completely harmless. The minute amount of Milliampere, which is sufficient to conquer the bacteria, is hardly even perceived by the patient and would tops cause a mild muscle twitching.




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A simple online search for anti-microbial clothing and you are bound to come across an assortment of brand names, even Adidas, promoting their products, mostly sportswear. But are they really safe? To answer this question, researchers at the Hohenstein Institute tested the safety of such anti-bacterial textiles. The result: Even in cases of volunteers, who wore those clothing articles for an extended period of time, their skin flora was not affected.

Over the last years, anti-microbial textiles have gained popularity. It started off in the medical sector in an approach to cut down on cross-infection between patients and to ensure the safety of the hospital staff. Recently, the industry has managed to find potential customers, those who are interested in sport and outdoor activities, looking for ways to control bad odours. The majority of these products, found on the market, are manufactured using anti-bacterial silver strands, which help in “eliminating 99.9% of odour-causing bacteria” as one ad claims. Furthermore, one firm releases products to be used in cases of neurodermatitis. On their homepage, it is stated that, “our silver textiles provide a realistic alleviation of this agonizing skin disease” and are backed up by statements of health experts.

Despite the previous positive experiences concerning the implementation of silver, like in the purification of water, anti-bacterial clothing have raised a controversial discussion in the media. This encouraged researchers to run a 6-week-long experiment, in which 60 healthy volunteers participated. For the study, special T-shirts were manufactured, which conveyed antimicrobial activity on one side, yet a non-antibacterial placebo effect on the other. For confirmation that this model actually did exert an antibacterial effect, the T-shirts were tested in the laboratory using Staphylococcus aureus und Klebsiella pneumonia. The volunteers were instructed to wear the T-shirts for at least 8 hours each day during the course of 4 weeks. The researchers analyzed on a weekly basis several parameters concerning the skin flora. In all the participating volunteers, the skin flora, both before and after, were within the normal range. There were no threats of a skin pathogen at any time. Therefore, these clothes have been characterized as being harmless and it seems like, their market will continue to expand as more people appreciate the benefits of leading an active life style.

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Forget about the old Petri dishes and culture media! A brilliant new method for the growing of microorganisms in order to study their behavior, especially in a large community, again tracking the phenomenon of quorum sensing , has been developed and put to use.

The new invention, by Connell et al., resembles a trapping sack for microorganisms, made of bovine serum albumin covalently cross-linked by laser lithography to form a three dimensional structure. These harboring chambers are very small, with a 2 to 6 picoliter capacity, and are permeable, and thus allowing an infinite influx of nutrients and other essential small molecules for the bacteria growing inside.

Scientists have already compared the growth rates of Pseudomonas cells in “the trap sacks” to those in conventional culture media and mouse lungs and the results were promising! The new technique allows them to study patterns of antibiotic resistance, infection and biofilm formation more clearly and in earlier phases of bacterial growth…

Source: Science magazine, Vol. 330 issue 6004.

Image source: Microbiology Bytes

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So, we thought the worse was over; we thought we are done fighting the bad guys, HIV, SARS and H1N1A, but now it seems that a new menace is eminent. Our chaotic and rather foolish use of antibiotics have created this unknown danger that could add a new chapter to the history of medicine and fighting infectious diseases. This danger is called New Delhi metallo Beta-Lactamase -1, AKA NDM-1

Meet the Bug

In December 2009, a super villain appeared on the scene; he’s violent, resistant and determined to do as much damage as he could. Our super villain is the NDM-1 (New Delhi metallo beta lactamase – 1), a newly emerging beta-lactam resistance enzyme including carbapenems, which are one of few alternatives used for antibiotic-resistant bacterial infections. The NDM-1 gene is classified as a Carbapenemases . The enzyme is named after the city in which it first appeared, New Delhi, the Indian capital. In December 2009, a Swedish patient in India acquired an antibiotic resistant infection. Being unsuccessfully treated in India, the patient was further transferred to Sweden. The carbapenem-resistant Klebsiella pneumoniae was identified carrying the novel NDM-1 gene. A later study in India found that carbapenem-resistant strains from patients in India carried the NDM-1.

The Spread

In May 2010, an E. coli expressing the NDM-1 gene was isolated from a patient in the UK, the patient was of Indian origin and had visited India 18 months ago where he had been undergoing dialysis. According to CDC Morbidity and Mortality Weekly Report (MMWR) , as of June 2010, three Enterobacteriaceae isolates carrying the NDM-1 gene were discovered in the U.S., which were E. coli, Klebsiella pneumoniae, and Enterobacter cloacae, NDM-1 provided the three isolates with resistance to all antibiotics except for Aztreonam. Fortunately to the bacteria but unfortunately to our patient, the isolates conferred resistance even to Aztreonam by different mechanism other than the NDM-1, and the MMWR established that all the three U.S. isolates were related to patients who had medical care in India.

Furthermore, a team in India in July 2010, reported cases of Acinetobacter baumannii carrying the NDM-1 in India. A recent study by a multinational team published in “The Lancet Infectious Diseases, September 2010” reported that the isolation of 44 isolates with NDM-1 in Chennai, 26 in Haryana, 37 in the UK, and 73 in other sites in India and Pakistan. NDM-1 was mostly found among E. coli (36) and Klebsiella pneumoniae (111), which were highly resistant to all antibiotics. Luckily, all the studies have confirmed that all NDM-1 isolates were susceptible to the antibiotics tigecycline (the FDA-approved glycylcycline antibiotic developed by Francis Tally and marketed by Wyeth under the brand name Tygacil®), and colistin (polymyxin E antibiotic, which causes nephrotoxicity and neurotoxicity at high dose IV). Some unconfirmed reports indicate the NDM-1 appearing in Canada and Japan earlier this month (Sep 2010).

First Victim

In June 2010, patient zero –the first reported death– was a Belgian man who had a car accident in Pakistan, first being treated in a hospital in Pakistan and he became infected with the Bug carrying the NDM-1. He was further transferred to Belgium where he was hospitalized with major leg injury, and despite being administered colistin, the patient died!

We now face a new challenge. Could this superbug mean the end of the beta-lactam antibiotics era?!


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The pursuit of renewable sources of energy just hit a crucial breakthrough. Since the stores of fossil fuel are diminishing as we speak, researchers are trying to exploit the machinery of microorganisms for the production of diverse chemical compounds, which can be consumed by themselves or later channeled into some form of combustible fuel. One major group of those compounds are alkanes, those saturated organic compounds abundantly found in gasolline.

The study started off when ten out of the eleven strains of Cyanobacteria, that were photoautotrophically cultured, produced forms of alkanes, mostly those with 15 & 17 carbons atoms “termed penatdecane and heptadecane respectively”. Logically, that indicates that the ‘alkane-producing gene’ is shared in all ten of them, yet absent in that unlucky 11th strain. So the search was launched.

Trying to pinpoint the gene responsible for the production of alkanes through using a method referred to as subtractive genome analysis, the study authors compared ten genomes of the alkane-producing strains to figure out which genes they have in common. Next, any of those shared genes was immediately eliminated if it had additionally showed up in the genome of the NON-alkane producing strain. Eventually, the researchers were left with 17 genes found in common and the function of 10 of them had already been previously assigned. Through careful scrutiny of the families to which proteins of those remaining 7 genes probably belong to, two of them particularly stood out, being likely participants in the pathway of the alkane synthesis.

And as always, there is no better way to test the hypothesis than to consult a microbiologist’s favorite lab microbe. To our pleasant surprise, extracts from the colonies of Escherichia coli engineered to express both genes did in fact contain alkanes. So, although we are still not fully aboard the track heading the way towards large scale production of alkanes using such microbes, this is definitely a gigantic leap in the right direction!

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Recently, I have been working on an essay for my last year in college.  I titled it: “Parkinsonism: Disease and Treatment”, scary enough? NO!!??  I turned it in, anyway. In it, I identified the neurodegenerative disease that targets the basal ganglia and deprives it of the inhibitory neurotransmitter (NT), dopamine. No dopamine means no balance between the excitatory action of the NT, Acetylcholine, and the inhibitory action of dopamine, leading to the well-known clinical picture of parkinsonism that Jankovic (2007) gave the acronym TRAP: Tremor at rest, Rigidity, Akinesia/bradykinesia and Postural instability.

Parkinsonism can be classified into:

  1. Primary/idiopathic “of unknown cause” which is mostly due to degeneration of dopaminergic neurons (a.k.a Parkinson’s disease)
  2. Secondary to viral infection as encephalitis & meningitis; drug-induced, e.g., antipsychotics; or due to brain damage caused by trauma, anesthetics,  or toxins as MPTP (a contaminant of street-drugs).
Arvid Carlsson

Arvid Carlsson

You may know that the Nobel Prize associated with Parkinson’s disease didn’t go to Dr. James Parkinson who described it in an essay he wrote back in 1817 calling it “The Shaking Palsy”.  It went jointly to Arvid Carlsson, Paul Greengard, and Eric R. Kandel in 2000 (To find out more about the story, here’s the Nobel lecture by Dr. Carlsson). Carlsson and colleagues discovered dopamine as a potential NT in 1957. After that, in 1960, Hornykiewicz and his postdoctoral fellow, then, Ehringer observed the decrease of dopamine levels in Parkinson’s disease patients, and levodopa successful trials started after that, in 1961.

J. Robin Warren

J. Robin Warren

What does Dr. Warren, the scientist whose discoveries led to a paradigm shift in physiology, who said out loud that peptic ulcer is an infectious disease caused by Helicobacter pylori, the gut bacteria? What does he have to do with parkinsonism? Note that: J. Robin Warren and Barry J. Marshall also won Nobel prize in medicine for 2005 for their discovery.

Helicobacter-induced parkinsonism!!

What I am trying to say here—and didn’t say in my essay—is that there is a hypothesis, Helicobacter-hypothesis, that strongly provides another cause of idiopathic parkinsonism, which will not be idiopathic any more, and this cause is H. pylori (Altschuler, 1996). Or to be more accurate, I will say parkinsonism associated with H. pylori. Dobbs and colleagues have carried out well-controlled studies and observed a significant conversion in patients with Parkinson’s disease from malignant into benign parkinsonism after successful eradication of their H. pylori, even with no levodopa administration. The rationale behind this theory is that: H. pylori induces an autoimmune reaction against mitochondria, then a systemic inflammatory response with the whole gang of inflammatory mediators and antibodies reaching and crossing the deficient areas or areas with increased permeability of the blood-brain barrier, causing parkinsonism. And the blood profile can prove the Helicobacter-hypothesis.

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“Get me more, mummy!” demands one youngster bacterium, pointing to the drops of antibiotic reaching the colony headquarters.

Come on! FOR REAL?

Sadly very true and it is not even that infrequent either! I only became aware of this after reading about a study, where researchers in HMS, led by Dr. George M. Church, collected soil samples in an experiment, attempting to search for more bio-diversity and were stunned to see that as they added antibiotics to these bacterial cultures, the bacteria didn’t seem to mind at all!

Unlike human beings, bacteria tend to like sharing. The more they share their strategic defenses, the more prosperity they end up living in. Again, to our dismay, such fear was translated into reality, as this has already extended to the pathogenic minorities of the bacterial world in a new study, published in January in the International Journal of Tuberculosis and Lung Disease. Scientists, in China, have stumbled upon a strain of tuberculosis-causing bacteria, called Mycobacterium tuberculosis, INCAPABLE of growing adequately in the absence of rifampicin. This is as ominous as such news can get.

This strain was discovered as physicians attempted to treat a TB-infected patient with a regimen which included rifampicin. Unexpectedly, his condition worsened and only upon the removal of rifampicin did he start feeling better, until eventually full recovery. Already, reports of multidrug-resistant TB “MDR” have been around for some time. Normally, the treatment course includes more than 1 drug to be able to effectively kill the bacteria. Apparently, the bacteria have found a way to get around that!

We can only wonder: which antibiotic is next?

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Is it a luxury to “think like a microbe” and to publish blogs such as “Adopt a Microbe and books like “The Other End of the Microscope: the Bacteria Tell Their Own Story (find it on Google Books)? Is it just about understanding or “getting to know” bacteria, or is it a necessity to be “microbe-oriented” for better understanding of pathogenesis and for developing the appropriate eradication and prevention strategies (I can’t think of better examples other than Reverse Vaccinology and H. pylori)?

When I first read this commentary “The Case for Biocentric Microbiology”* by Dr. Ramy Aziz, published by the journal “Gut Pathogens, I was shocked! The article was presenting a very different perspective, at least different from what I always dreamed of as a pharmacy student, to kill the bad bugs by designing an effective, highly selective chemotherapeutic! Plus it was my first time to read an opinion article, and I used to take the microbiology courses for granted; “this is a bad microorganism, causing this bad infectious disease with serious manifestations including these, diagnosed by the following and the antibiotic of choice is this.” And then Dr. Aziz came with this article with the cool, simple and exciting writing style that keeps one alerted the entire article, gathering all those thoughts and examples of our human-centered/self-centered view of microbiology.

Four parts I enjoyed the most in the commentary:

  • The tabular form of “differences between the anthropocentric and biocentric views of microbes.”
  • The final balancing paragraph –the conclusion.
  • The “competing interests” part, which is funny.
  • The questions part, which is an excellent idea to open up discussions, especially for those who are not-natural-born brain stormers like me!

Even though microbiology is a new science, it suffers from anthropocentric view that Galileo suffered from; starting with the field’s name itself, “microbiology” -liked what Dr. Elio Schaechter mentioned: “Small,” says who? Not the microbes… till the funding agencies that give priority to studying bad microbes (i.e., pathogens), and good microbes (i.e., fuel-producing and yogurt-making bacteria) nothing else!

Bacteria conversation -

Bacteria convention -

We, in our human-centered view; automatically classify any newly-discovered bacterium to fall into one of three categories: the good, the bad and the ugly… no, not that one! They are: the useful guys, the harmful guys and the just-existing guys. Now, let’s take a look at the biocentric view of microbes: Humans and microbes share many ecosystems. To microbes, humans are just an ecosystem that is a “relatively safe” habitat with a source of nutrition.

As victims, we think about pathogenesis/infection as it’s shedding from the immune system, invasion and toxin production; but microbe-oriented microbiologists/bacteria whisperers know that, to bacteria, pathogenesis is  just defense, seeking nutrition, and excretion of metabolic byproducts. Being pathogenic or opportunistic is not their reason of existence, it’s just a form of adaptation to survive in this hostile environment (aka the human body).

You do not believe me!? OK, bacteria lived –happily- thousands of millennia before mammals and humans, so their reason of existence can’t be to harm humans, like what Dr. Aziz is mentioning: “Who attacks whom”, are the bacteria the “one” that start the fight, or is it the human immune system that starts the war against them?  A very interesting example to understand adaptation is Legionella pathogenesis, and how they adapted to human macrophages because they used to survive in amebas, which are similar to our macrophages.

Back to the basic question, is it a luxury or a necessity?

Studying “all” bacteria from their perspective will help us in understanding pathogenesis and subsequently developing strategies to combat infectious diseases (immunization and design highly selective chemotherapeutics), will give us a better idea of the tree of life and the metabolic map, and studying environmental microbiology will allow us to meet new “useful” microbes like what happened with the PCR Taq-polymerase, we knew how to make use of this bacterial polymerase that can work at those very high temperatures required for the PCR steps.

Here are two interviews about the commentary covering two segments of readers, the first one is with Dr. Betsey Dyer, Professor of Biology at Wheaton College, and the second one is made with Radwa Raed, a micro-writer and a final-year FOPCU student:

1- What is your opinion about (the commentary)? To what extent do you find it compatible with your bacteriocentric view of bacteriology? How strong are the arguments?

Dr. Betsey D. Dyer, Professor of Biology at Wheaton College.

“I thoroughly enjoyed Ramy Karam Aziz’s article “The Case for Biocentric Microbiology.” I think he is absolutely right that some old fashion thinking about the divisions of microbiology and anthropocentrism in general have hindered a more complete understanding of the microbial world. I also think Dr Aziz is quite bold and daring. I’m not sure I could have gotten such forceful statements accepted for publication! Good for “Gut Pathogens” to print it! I hope Dr Aziz gets lots of readers and citations.”

2- How did (the commentary) change your point of view? Are you with or against the biocentric view for microbiology? Do you think about it as a view against, or at least far from, your beliefs as a pharmacy student dreaming of fighting diseases? What are your opinions regarding studying environmental microbiology in pharmacy school?

Radwa Raed, Pharmacy student, Faculty of Pharmacy, Cairo University – Egypt.

“From my humble point of view, I would have to agree (with the biocentric view of microbiology). It goes without saying that studying more about certain bacteria “the ones some would consider to be of the least priority” will definitely expand our knowledge about the overall, and in many cases analogous or even similar, methods of survival, adaptation to existing conditions, etc.., which all pretty much ultimately serve medical microbiology. Plus, leaving a whole chunk, simply unexplored, can only raise several “what if” questions; one of which, that comes to mind, is what if the simplicity and less dramatic forms of life could help researchers better grasp the machinery behind these fascinating little creatures 🙂

As for studying environmental microbiology in pharmacy schools, I would have to oppose the idea, because the field of pharmaceutical science is taught so the future students can come to understand, and hopefully later suggest, treatment methods against pathogenic microorganisms, prophylaxis, and so studying the harmless ones would not point in this direction. It can only lead them to drift away from the pharmaceutical science branch of study into a more microbiology-oriented career.”

You can read the paper, share your comments and debate the arguments here, and you can also vote for it on BioWizard.


*Full Citation:

Aziz, R. (2009). The case for biocentric microbiology Gut Pathogens, 1 (1) DOI: 10.1186/1757-4749-1-16

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Did you see some one before who can fly without wings or move without legs? You will answer : definitely no, but I know someone, or better yet some living thing, who can do just both and it is called Borrelia burgdorferi; let’s share its story. It is a loosely coiled bacterium belonging to a class called spirochetes (moving bacteria).

Borrelia burgdorferi

Borrelia burgdorferi

Borrelia burgdorferi is motile through the undulation of its axial filaments. It is transmitted to humans by the bite of infected ticks (Ixodes scapularis and Ixodes pacificus) and cause a serious progressive disease called lyme disease.

The story of lyme disease began in 1975 when a mother, with her children in lyme city in the United States, was admitted to a hospital with signs of rheumatoid arthritis. It was a mysterious case until the discovery of Borrelia burgdorferi and that is how the disease got its name, when it was discovered in 1982. Symptoms and signs of lyme disease can be categorized into three phases:

Phase (1): An early localized skin rash, characterized by inflamed red edges with a clear white center at the site of insect bite, appears and is called “erythema migrans“.


Erythema migrans

Phase (2): The rash resolves as the bacteria begin to move into the blood stream towards their target organs like large joints, heart, and nervous system.

Phase (3): Inflammation of heart muscle leads to abnormal rhythm, meningitis, confusion and finally arthritis.

Treatment in the early phase is an easy mission by amoxicillin or doxycycline, orally for few weeks. However, the recommended regimen in late stages include parenteral ceftriaxone, analgesics to control the severe pain, and anti-inflammatory drugs, usually required for months .

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Borrelia burgdorferi:
Erythema migrans:

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