Thursday, November 19, 2009

Biosensors, the newest way to detect a bio-terrorism attack

Here is a great article about new jellyfish sensors are being tested to rapidly detect an attack using bio-threat agents.

Leggo my Listeria!

I dont know how many of you have heard but there is an EGGO waffle shortage! GASSSPP!! I know its tragic but apparently our little friend L.monocytogenes has struck again and has crippled the marketshare of frozen delectable goodies....We wrote about listeria awhile back you can check it out here Up top is the press release

Consumption of food contaminated with Listeria monocytogenes can cause listeriosis, an uncommon but potentially serious disease. The most common manifestation of listeriosis is meningitis, which has symptoms of high fever, severe headache, neck stiffness and nausea. Listeriosis can also cause miscarriages and stillbirths, as well as serious and sometimes fatal infections to infants, the elderly and those with weakened immune systems such as persons with chronic diseases or taking chemotherapy for cancer. Below is a nice photo is a distinct umbrella shape on the motility tube which is produced by L.monoctogenes they are also small gram positive rods, and are beta hemolytic on sheeps blood agar.

NYCers get their own Flu Line!

Hey if you live at the center of the Empire, you can just call 311 and speak to a nurse about your flu symptoms....or you could just google it like everyone else!

Wednesday, November 18, 2009

Flu View

For those interested in morbid things (if you are here you probably are) or epi, Flu View by the CDC is a great tool to stay on top of what is going on during Flu Season

Switch and Swine!

Rapid EIA (enzyme immunoassay) is often used in hospital laboratories as a quick way to diagnose patients with potenially risky dieseases like influenza, so that medication may be quickly administered.
Using only the rapid EIA for the detection of Flu has always been considered a risk and was generally backed up by viral culture and/or PCR. However, with the increasing number of emergency room visits and the high strain on the healthcare system many hospitals are relying on tests that are inaccurate, and could ultimately have up to a 50% fail rate.

This is a pretty decent article on the dangers of diagnoses on rapid tests alone, but it does not get into the nitty gritty like we like here, of course the best resource is the CDC published guidelines which is presented here

Wash your hands while singing Happy Birthday!
Sneeze into your arm!


Back from a long hiatus! Why do I leave things right before they get good, my apologies out there to all the folks who waited with baited breath for when I would return, but a little squabble with a publishing platform wont stop this machine! I will be doing crazy updates and get this blog on track for the readers because we all love it!

Wednesday, July 1, 2009

Update! Microbe Meetup, Can you Dig it??

Update: Ok so we have a GNCB oxidase neg, cat pos, with some bpolar staining and raised colonies associated with an appendectomy that does not present as an enteric pathogen. I have heard screams of setting up an API 20NE, but unfortunately came out with low selectivity! So I will help out of course we were going to set up a urea slant, TSI, simmons citrate, and motility here is what we got:

TSI: Acid over acid with no gas, and no h2s
Urea: Positive
Simmons: Negative
Motility: Non Motile

So far I have heard salmonella, shigella, but the gram stain would rule that out, and someone else emailed me with: The gram stain looks like a Y.pestis and the adentitis would be in line with that, however not really an enteric like pathogen.....hmmm sounds interesting, just for that maybe we will incubate everything at 25c to see what might come, you never know with these crazy bugs, check back tommorow for the results.

Monday, June 29, 2009

Acinetobacter, that's a quite a neato bacteria

Acinetobacter baumannii is a strictly aerobic, gram-negative coccobacillus that is oxidase negative, non-motile, and non-fermentative. This organism has a high capacity for survival on environmental surfaces, and has an ability to acquire antimicrobial resistance makes it an increased concern for nosocomial (hospital acquired) infections. It has been an increasingly hot button issue as it has become known to some nurses, soldiers, and microbiologists as Iraqnobacter due to its spread throughout the military hospitals. Many times soldiers have survived hellacious trauma on the battlefield only to succumb to even more damage by an organism that has picked up antimicrobial resistance factors to the drugs primarily associated with treating them almost impossible. Many (11%) of the A.baumannii isolates submitted to the CDC have been resistant to all carbapenems (by using a carbapenemases like CfiA, IMI-1etc.), which is the last line of antimicrobial therapy available to treat these organisms. Bob Woodruff, the reporter from ABC, famously contracted an MDR A.baumannii infection after surviving the attack on his unit.
Generally Acinetobacter baumannii does not cause infection, but in a hospital or other setting can enter into the body through open wounds, catheters, and breathing tubes and can cause an infection and depending on resistance patterns and overall patient health can lead to death. Health care and hospital workers can become colonized, however, colonization poses no threat to people who aren't already ill (card carrying microbiologists like me are a regular germ lab) but colonized health care workers and hospital visitors can carry the bacteria into neighboring wards and other medical facilities.
One of the best ways to handle Acinetobacter baumannii is to have an effective infection control policy, hand washing, effective equipment decon, and even a fecal surveillance program are good ways to control the spread of this bug. There are even new, effective ways of controlling the way the infection spreads to new patients like the one in this article: The article talks about taking a compound called hCAP – 18 that is normally produced by skin and acts as an antimicrobial peptide and placing it inside of wounds to see a significant drop of infectious organisms inside of wounds. Novel technologies like this are critical for passing into the next phase of microbiology where we are seeing increasing resistance to the drugs that have once worked.

Microbe Meetup Can You Dig It?

A 12 year old child has been admitted to the ER with severe stomach pain, diarrhea, right side pain, fever, and slight adentitis. The doctors diagnosed with an appendicitis, and proceeded to remove the appendix of the patient. However, 48 hours after the surgery the patient's symptoms still had not subsided the blood cultures, and cultured appendix from the surgery still had not yielded results, and the stool cultures had no yield in terms of enteric pathogens. After 72 hours there was light to medium growth on Blood agar, chocolate agar, and maconkey agar, the colonies are non hemolytic, white, and look like a bulls eye on blood agar, and non-lactose fermenters on maconkey. The gram stain produces gram negative cocco bacilli with some stain retention at the polar ends of the organisms.

They are catalase positive, and oxidase negative.

Where do we go from here? Shout out some steps I will accept the top 3 suitable ones and give you a result in the incubator by wednesday (it is a slow growing organism, I swear I am not lazy!) But remember the famous quote "the devil is in the details!"

Summertime and the livin's easy part deux! Roundup

Another week, another batch of recalls due to E.coli O157:H7 you can check out the CDC report here:

At the bottom it gives some information that may look familiar to some of you who read my first post in relation to the Nestle' outbreak its here:

You can keep coming back to find your updates on 0157 here and check back a little later for an expanded discussion on not only E.coli O157, but also the Shiga toxin producing E.coli's that cause similar disease.

Updated Quick Microbe Meetup

Update to this original post:

Check it out so you can get the skinny on the question before you see the answer!

Result: Upon careful examination of the gram stain you will see Gram negative diplococci that are kidney bean shaped, strongly indicative of the organism Neisseria meningitidis. Neisseria meningitidis usually appears as Gram (-) diplococci that sometimes may display considerable size variation, resist decolorization, and a distinct pink halo around the cells. The physician should be notified immediately so the antibiotic care can be administered.
After 18 to 24 hours the culture should be ready and growth on chocolate agar shows colonies that are generally larger than other gonococcal species, usually attaining a diameter of 1mm or more. Colonies are also low and convex, with a smooth, moist entire edge and a glistening surface. Sheep’s blood may present some alpha hemolysis and are grey, heavily encapsulated strains appear mucoid and are oxidase positive. N.meningitidis can be identified by acid production tests or by chromogeneic enzyme substrate tests. It acidifies glucose and maltose, but not sucrose fructose, or lactose. Serotyping is generally done to obtain epidemiological data on the organism and is done through a simple slide agglutination, also PCR, PFGE, and DNA fingerprinting.
All in all, N.meningitidis is an extremely pathogenic organism that can cause rapid death so stat diagnosis is key.

Saturday, June 27, 2009

More saturday coffee! Bot Fly larvae video

If you are squemish dont watch this, and it has some language, but when you see the things, you will understand!

Dont dry your swimsuit in the sun in Kenya!

Check out this really gross story about a traveler who gets the nasty little tumbu fly larvae in her skin!

Saturday Morning Coffee, My Very Own Symbiote

Ok so I officially think Saturdays are going to be for the parasitologists.....they are a funny bunch anyway lol! To me it is one of the more fascinating aspects of micro where you can know so much and have get that wonderful feeling when you spot a fantastic slide with some beautiful identifying features on it. So without further ado, I am going to try and get some of you going with another mini-microbe meetup! (O btw, the pics from now on will remain as named unk!HAHAHA Thanks for the tip you know who!)
A 42 year old male, has come to the ER after having a seizure, seems dazed, and extremely fatigued. After ruling out heart attack, and a stroke doctors draw a blood culture for stat screening and culture, after interviewing the patients wife, she described a notable weight loss, and change in attitude in her husband since their recent return from their trek around the world. She attributed it mainly to the stress coming down from the trip.
The cultures were received by you and after a gram stain and 96 hour blood culture there were no organisms seen. After several other tests have come back negative a thin blood smear stained with giemsa was ordered and this is the results:

Ok so hit the books, and study up on your parasites because this should be good!

Friday, June 26, 2009

Update to MRSA, with some VRSA!

Great dispatch report on VRSA cases in Michigan in this months edition of Emerging Infectious Diseases, check it out here:

What is your favorite bug? For me nothing beats Pseudomonas aeruginosa

What is everybody's favorite bug? Mine is Pseudomonas aeruginosa, who doesn't love the pseudo smell in the morning? One of the main reasons it is my favorite is that it is such a versatile organism that thrives in many locations. Also, fact that it secretes a wide variety of pigments like Pyocyanin. Pyocyanin is a redox-active virulence factor produced by Pseudomonas aeruginosa that allows it to kill cells, disrupts cilia actions, inhibit lymphocyte proliferation, and alter phagocytic function. (P.aeruginosa can also preoduce fluorescein, and pyorubin.) The following pic shows growth on BHI with a pyocyanin producing P.aeruginosa on the left and a negative control on the right.One of the other coolest features about P.aeruginosa is that it is capable of growing in diesel fuel and jet fuel, which is known as a hydrocarbon-utilizing microrganism. Definately has some future applications as we take a steer towards a greener society! So let everyone know what your favorite bug is!

What is this? Quick Microbe Meetup!

Stat culture comes in, it is a CSF so you make a gram stain, which looks like this: I know it is easy but what you do think you have? Course of action and what do you expect for culture tommorow!

Result: Upon careful examination of the gram stain you will see Gram negative diplococci that are kidney bean shaped, strongly indicative of the organism Neisseria meningitidis. Neisseria meningitidis usually appears as Gram (-) diplococci that sometimes may display considerable size variation, resist decolorization, and a distinct pink halo around the cells. The physician should be notified immediately so the antibiotic care can be administered.
After 18 to 24 hours the culture should be ready and growth on chocolate agar shows colonies that are generally larger than other gonococcal species, usually attaining a diameter of 1mm or more. Colonies are also low and convex, with a smooth, moist entire edge and a glistening surface. Sheep’s blood may present some alpha hemolysis and are grey, heavily encapsulated strains appear mucoid and are oxidase positive. N.meningitidis can be identified by acid production tests or by chromogeneic enzyme substrate tests. It acidifies glucose and maltose, but not sucrose fructose, or lactose. Serotyping is generally done to obtain epidemiological data on the organism and is done through a simple slide agglutination, also PCR, PFGE, and DNA fingerprinting.
All in all, N.meningitidis is an extremely pathogenic organism that can cause rapid death so stat diagnosis is key.

New Rapid Detection of B.anthracis spores

There has been a growing concern in our society about terrorism, and among chief concerns with microbiologists is bio-terrorism. The preparedness and response associated with this topic is a critical issue to all city and state governments. So it is no surprise that there is a high demand for the rapid detection of the causative agents associated with this form of terrorism. The principle agent of concern is B.anthracis because of use against civilian populations in 2001, and its previous military research into weaponization. There is currently a new rapid detection method for first responders that focuses on the detection of B.anthracis spores, and the article can be found here: Also, if you are interested in the product the insert can be found here:

It looks as if this is by no means a replacement for the microbiology of identifying B.anthracis, (even with advent of RT-PCR and other rapid detection methods, the microbiology still remains the “gold standard”), however it seems to provide a handy tool for first responders to a scene of a potential attack.
Being a microbiology blog I figured we could go over some of the principle sentinel identification over this fascinating bug, and delve into a little bit of history.
B.anthracis is the causative agent of anthrax and is primarily a disease of domestic and wild animals. There are generally three types of clinical presentations with B.anthracis: Inhalational, cutaneous, and gastro-intestinal. Prior to the 2001 terrorist attacks 18 cases of natural inhalational anthrax had been recorded in the US since 1900 (ie not many!), with 99% of naturally occurring cases due to cutaneous.
In the micro-lab, B.anthracis is a gram positive, non-motile rod. The main characteristics of sentinel rule out of B.anthracis are related to its gram stain: Long chains of thin, gram positive rods, with possible spore formations.

Colony morphology: colonies on TSA 5% sheeps blood have an irregular rough shape (sometimes described as ground glass), have a white/grey pigment, and are non hemolytic (which is key). The colonies tend to have a tenacity on the plate when teased with a loop that stand up like a beaten egg white.

Catalase: Positive
And Motility: Non-motile
Overall, the likelihood of encountering B.anthracis in the lab are slim at best, however it is good to be prepared, and all clinical laboratorians should be prepared and understand what their procedures are for the rapid reporting to the local health authorities. Of course this blog by no means is a reference point for the identification of this organism, it is meant to simply convey interesting news about the development of technology associated with an interesting and newsworthy microorganism. Any thoughts out there? I am sure that in the coming years with more techniques and developments encountered that the world can be a little bit safer thanks to all us microbiologists. More information can be found on the CDC website and at your local health authorities.

Thursday, June 25, 2009

Sci-blogs or Sblogs? The Taxonomy of the Interwebs

What do we call the science related blogs? Are they Sci-blogs? Sblogs (which I think are spam blogs so that rules that out)? There are probably a million cool ways to say it, but is it the right way? Are they all about the Sbliences, Sbloginces? Who knows, these things generally progress into whatever catches on in the public domain. I feel there should be a classification system now for naming the specific types of blogs, twitters, and other networking sites, with a full on nomenclature structure and everything, someone just has to figure it out!

Suck it! All about pipettes

We hear it time and time again about pipette calibration and the correct use of a pipette, but think about back when there used to be only mouth pipetting. In some countries mouth pipetting is still in practice, and I am sure that some of the old school laboratorians out there probably have a few stories about mouth pipetting! Here is a pretty cool youtube video on mouth pipetting:

Wrap Up of First Microbe Meetup

Ok so the first Microbe Meetup, possibly not a roaring success, but definitely not a failure. A few comments and some emails got close but no cigars, however this was a particularly hard identification and if you want to try and still guess then skip the rest of this post and go down to the microbe meetup.
Well lets look at what we have:
1.) The gram stain (although small) is a gram negative curved rod suggesting that it might be Vibrio spp.
2.) The colony morphology on maconkey suggests that the organism is a lactose fermenter. (Lactose fermenters on maconkey are pink, non-lactose fermenters are whitish-yellow) Most vibrio spp (cholera, alignolyticus) are NLF (non lactose ferementers) where as Vibrio vulnificus is a lactose fermenter and is commonly associated with MARINE trauma and puncture wounds, ding ding ding!
3.) Vibrio spp are also oxidase positive, H2S negative, and produce acid from TSI.

The main factors that we look at here are our gram stain, colony morphology on mac, subsequent confirmation of lactose fermentation, and patient history. We can ultimately deduce that Vibrio vulnificus is the organism of infection based on these strong identification parameters.

A little bit of background on V.vulnificus:

Vibrio vulnificus is a bacterium that causes a disease with over a 50 percent mortality rate, and it causes 95 percent of all seafood-related deaths.
Vibrio vulnificus (as we know) is a Gram-negative, motile curved bacterium found in warm water marine environments (in the Gulf of Mexico, the Atlantic Coast as far north as Cape Cod, and the U.S. West Coast). The bacterium thrives in warm seawater and is part of a group of vibrios that are "moderate halophiles", meaning they require salt for growth. It has been isolated from seawater, sediments, plankton and shellfish (oysters, clams and crabs). Vibrios are frequently isolated from oysters and other shellfish in warm coastal waters during the summer months. This correlates with the peak incidence of disease caused by the bacterium. In January of 2007 Vibrio vulnificus became a CDC nationally notifiable organism and has undergone an effort to reduce underreporting of culture results within the clinical setting.
Another aspect of Vibrio vulnificus is the rate of infections after a natural disaster such as a hurricane. Wound care is essential because contaminated sea water (as we saw with our case) can enter the wound and rapidly (12-24 hours) cause extreme infection. More information can be found here:

Wednesday, June 24, 2009

Microbe Meetup

Dont forget to check out the microbe meet up weekly quiz with updates! Please comment or email with your answers!

Dog bites can transmit MRSA
This article by the BBC is a pretty interesting view on the spread of MRSA from people to pets and back. One of the worse aspects of dogbites is the bacteria that can cause an infection after the bite (we're looking at you Pasteurella multocida). This is due to the puncture wound penetrating down the deep layers of skin. It has been widely known and reported that MRSA is increasingly encountered in the lab so this should come as no surprise to see that when up to 33% of people in the U.S. are colonized with MRSA when a dog bite breaks the skin and introduces potential pathogens that they could infact cause an infection.

For those of you who don't know the CDC recently revised its MRSA testing algorithm and it can be found here . This is an extremely helpful tool for laboratorians in the potential detection of something a little scarier VRSA which is potentially resistant to all drugs availible to treat it. Any thoughts? Is your lab following the alogrithm?

The Title Pic

Can anyone guess what the title pic image is? A gold star for the one who gets it!

Summertime and the livin's easy!

It is that time of the year again summer cookouts, burgers, hot dogs, cold drinks, friends, hot weather (unless you live on the east coast this year, which it is more like Seattle!) mayo left outside, multi state outbreaks of bug x, wait what?
We all love it its the time of the year when we shine as microbiologists! This is the time when our friends come to us with the pertinent questions about why their tummies are upset and we can look like the heroes.
All of this of course is in relation to the multi-state outbreak of E.coli O157:H7 in Nestle Cookie Dough, which of course is interesting because it is not, although not commonl. We all know our normal Escherichia coli the lovable muti-faceted organism that is highly adaptable and has contributed so much to science over the years. So a little background on this bug for those of you who dont know.....

O157 is a Shiga toxin producing E.coli (STEC) which causes hemorrhagic diarrhea and the H7 serotype include extreme abdominal cramps, and non-fever. Each year an estimated 73,000 cases are reported with 60 deaths associated usually caused by HUS, which leads to renal failure. The number can be skewed however, as most clinical laboratories do not screen for O157 and therefore may be underreported.
The traditional screening method for E.coli 0157 is____________ come on all you microbiologists out there this is your chance to shine lets see it. Comment, tell all about how your lab isolates 0157! End of today I will continue on with an update for this article, for now im going streaking!!!!! (microbiologist humor laugh its ok!)

Monday, June 22, 2009

Listeria possibly used as a drug delivery system!

A new study that uses genetically altered L.monocytogenes to deliver drug compounds, sounds promising, unless it turns everyone into zombies!
But seriously a very aggressive organism with the right amount of change can be used to help, which is something we are seeing all across the microbe world, even though one of the most prominent and commercially successful has been, botulism toxin matter what your views are there are ways to use these bugs for the greater good!
Here is a great picture of the classic umbrella motility present with l.monocytogenes compared with a negative control

Microbe Meetup

First microbe meetup.....I am so excited! So we can start this any way but I am going with the patient history followed by initial culture results with pics then let the comments flow (hopefully)!
A 32 year old patient was admitted to the ER with severe left leg pain, hemorrhagic bullae on the left leg, vomiting, and fever. The patient just returned from a summer holiday in the Florida Keys where he had hit his leg on a rock while snorkeling 2 days before. The initial impact did not visibly penetrate the skin so the patient thought it was just sore from the impact. The bullae were opened, swabbed, and the patient was put on doxycycline and a cephalosporin.
The technician plated on BAP, CHOC, and MAC, and also did a gram stain. Here are your results:
BAP: Mac:

Gram Stain: Gram Negative Rods (slightly curved)
Ok so you can just shout out what you think, email me what you think, what should the next diagnostic steps be (I dont want to hear Vitek, Phoenix, Microscan, API, etc.!!!) and you can solve this, tommorow I will check back give you some more clues and by friday we have a positive ID!
Update: Ok so were back, sorry for the delay, lab audits as you know are hell!!!!

So our one poster...come on people this is interesting! Recommended that we do a TSI and UREA, and a wet mount for motility

Urea - Negative
Motility - Motile
TSI - No H2S, Acid over Acid
That is what we have so lets review our results, Gram Negative -Curved Rods, Lactose Fermenters on Maconkey, Urea -Neg, Motile, No H2S with Acid Production, Oxidase Positive

It doesn't get any easier!!! Lets hear it if you come check out the page chat it up!

My First Post Goals and Whatnot

Hey all you microbiologists, interested parties, scientists and people who think they might be smart (just kidding!) I just wanted to start this blog so us nerds of the world have somewhere cool that we can go to talk about bugs, infectious disease, and all kinds of fun stuff that affects our lives and enables us to cure the sick and sound awesome in the process. Feel free to comment, feel free to hang out and have fun, but most of all participate and interact you will get something out of it.....and feel free to click on the ads hahahaha!!!

This blog will bascially start with something that I am tentatively calling the Microbe Meet, which will be a weekly (or whatever develops) practicum which will call upon you, the users, to identify the mystery bug or bugs that are posted. It will be in a variety of cool formats, but the one that I feel is most interesting is I will post a brief patient history or background story, followed up by initial culture results, maybe a stain or two and then the users (again you guys) hit it with all that micro knowledge. The end game being you have to identify and solve the mystery*(small disclaimer at the end). I know you are all thinking (all 2 of you who read this) why would I do work on my free time, well you are probably doing this at work anyway so why not make it legit and learn something.

So I thank you for stopping by, and don't forget to continue to drop by for all of your microbe world needs.

*(small disclaimer so I don't get sued) All practicums and Microbe Meets are completely fictional situations, all work ups, pics etc are from non clinical cultures, and all information presented is directly from literature, not from patient cases....there I hope that clears that up!