Category Archives: Lab

Some Holiday spirit for the class

In searching through the Internet this morning, I found some microbiology art to help us get into the season!

Staphylococcus and Serratia; Author(s):Tasha Sturm, Cabrillo College

Staphylococcus and Serratia; Author(s):Tasha Sturm, Cabrillo College

Another Christmas tree!

fungal-christmas; via Stephanie Mounaud, JCVI

Star: Talaromyces stipitatus; Tree: Aspergillus nidulans Ornaments: Penicillium marneffei; Trunk: Aspergillus terreus – via Stephanie Mounaud, JCVI

Some yummy cookies!

Not OK to eat in lab, via Ms. Humble

Not OK to eat in lab, via Ms. Humble

Uh, Ebola and MRSA!

Lots of yuckier examples if you click the picture, via Wendy Staples

Lots of yuckier examples if you click the picture, via Wendy Staples


Notes from the Field: Salmonella from Microbiology lab

CaptureWe have a two-fer in this week’s CDC Morbidity and Mortality Weekly Report; several “Notes from the Field,” and an outbreak of Salmonella. Imagine my surprise to see that the Salmonella outbreak was from a college microbiology laboratory.  Actually, I wasn’t surprised at all, and BIO230 students will recall that I warned of these dangers in our very first class meeting this semester. The CDC reports that a case of salmonellosis was verified by the Maine Center for Disease Control in May 2013, and a second case was additionally reported shortly thereafter. Both patients complained of diarrhea, fever, and nausea, after attending Microbiology lab at a local community college. Molecular characterization of the patient isolates were identical, and further matched the isolate used in the class laboratory exercises.

Members of the Maine state testing laboratory visited the community college lab, and interviewed faculty and students to determine what infection control practices were in place. Survey results indicated that erratic personal protection methods were in place, including inconsistent and improper use of gloves, as well as inconsistent hand washing. Examination of control practices in the laboratory were unable to pinpoint the source of the infection, which may have resulted from direct handling of Salmonella cultures, a spill, or lab equipment that may have become contaminated. Recommendations from review of policies were much in line with the recommendations from the prior Salmonella outbreak. First, personal protective equipment including gloves, proper clothing, lab coats, and safety goggles should be used under all conditions where infection risk exists. Second, lab coats must remain in the laboratory, and can only leave the laboratory after being autoclaved. Third, all personal items such as cell phones must remain outside of the laboratory. Infectious agents may remain viable for extended periods of time, and are easily removed from the controlled laboratory setting on these items. Forth, hand hygiene remains one of the most effective methods for controlling infection in and out of the lab. Adherence to these rules of Microbiology Club will ensure that we have happy students, and happy instructors!

Happy Birthday, Julius Petri!

GoogleIf you were like me, you probably got up today and said “It’s about time that Google recognize the great science of Microbiology with a Google Doodle!”

The last day of May is the birthday of Julius Richard Petri (1852-1921), who is generally acknowledged as the inventor of the Petri dish. This little device enabled microbiologists to easily culture and subculture microorganisms in the laboratory, which in turn allowed microorganisms to be easily isolated in pure culture for the purposes of identification. Petri was trained as a physician, and while on active duty as a military physician, was assigned to the Imperial Health Office in Berlin to work as an assistant to Robert Koch. Just prior to this, the Koch laboratory had begun to culture bacteria on solid media containing the solidifying agent agar. Petri’s innovative dishes allowed microbiologists to utilize aseptic technique during the transfer of microorganisms, greatly decreasing the chances of contamination of samples and thereby making the process much more effective. Petri’s original dishes were made out of glass, and were decontaminated by autoclaving after use and carefully cleaned for reuse. In the disposable BIO230 generation, our Petri dishes are made out of plastic and go out with the trash after decontamination. Although students might be able to save tens of dollars on their college tuition by going back to the reusable glass Petri dishes, I suspect that the busy life of the college student would make it a difficult proposition to require them to wash all of their own dishware to save a buck.

Riddle me this!

Slide1I picked up one of the two remaining unknowns from the mystery rack, after all BIO230 students chose their unknowns. I have conducted a series of biochemical tests on unknown #3, but will not reveal its identity quite yet. Here is an opportunity for you to test our your Dichotomous Key, and to earn a bonus point.

Each test was inoculated for 24 hours at 37 °C, and various reagents were added to cultures where appropriate. The appearance of each test at this point is presented below:

IND -> no reaction

MR -> red color

VP -> yellow color

CIT -> green color

PHE -> green color

LYS -> brown color

GEL -> liquid

SUL -> black color

URE -> pink color

You may infer results to Carbohydrate Fermentation tests by the following:

MacConkey’s Agar -> white colonies

Triple Sugar Iron Agar -> red slant, yellow butt, no cracking of agar

Here is the Bonus opportunity; using your dichotomous key and the above results, determine what Unknown number 3 is. To preserve the fun, email me your answer! Note that this special Bonus opportunity is only available until the end of Spring Break on Monday evening April 1st at 6PM.
UPDATE! Unknown #3 was Proteus mirabilis. The combination of the urea and indole tests would have been a good tipoff. Thanks to all who played!

Scrubbing Bubbles, take me away!

Not the way we want our floors to look!

Students in the Thursday 11 AM BIO230 lab last week may have noticed a couple of “OOPS” events from the earlier lab sections. My dire warnings about the tendency of dyes to end up in unwanted locations were apparently disregarded, and consequently a number of locations throughout the lab were festively decorated with Malachite Green. Faced with the possibility of a permanently disfigured Microbiology lab, I pulled out the box of cleaning supplies stowed away for our lab on microbial control.

Fortunately, the cleaning supply cabinet is well-stocked and gave me the opportunity to find just the right reagent. Here is a summary of my results:

  • soapunsuccessful
  • Fantasticunsuccessful
  • an orange oil based cleaner–unsuccessful, however the lab smelled delicious
  • Gram’s alcoholunsuccessful, although it did appear to eat away at the floor a bit
  • Dow Scrubbing Bubbles–SUCCESS!!!!!!

Scrubbing Bubbles (not actual size)

The trained scientist in me was pleased with the results, however the lazy person in me should have done just a bit of sleuthing before randomly trying out toxic chemicals. A brief Google search (documented below) indicated that this is the sort of lab mishap that happens regularly. Amazingly enough, it turned up over 82,000 results that could potentially be of help. The best advice appears to apply a dilute solution (0.3%) of hydrogen peroxide, which as we have learned in class recently is a strong oxidizing agent for which aerobic organisms have powerful defensive protections against. Malachite green however has no catalase, and so quickly succumbs to the power of reactive oxygen! Bonus points this week in lab for anyone who can spill additional malachite green, allowing me to test this amazing reagent.

Proper reading of cultures: still important

As I cannot stay away from the Micro lab, even on the weekend, I made my Saturday morning pilgrimage to make sure nothing was amiss. I did find two things of note: first, even though there was a practical question dealing with the proper discarding of cultures that essentially everyone got correct, in practice people seem to miss what the proper procedure is. All to-be-discarded culture tube need to go in the appropriate rack, with all tape removed prior to discard. Second, I found about a dozen cultures in the incubator. Those of you who left cultures in the incubator for the weekend will need to run them again. I do feel somewhat like a broken record in this regard, as I did specifically state it to everyone repeatedly on Wednesday and Thursday, and wrote about it here previously, but perhaps it is time to reemphasize things that are important for success in a lab.

Names blurred, since this is on teh interwebs! One culture appears to belong to Lord Voldemort, He Who Must Not Be Named!

All of our cultures need to be run, incubated, and interpreted according to specific guidelines, or else the interpretation of the culture is completely invalid. The Clinical and Laboratory Standards Institute is a national organization that establishes guidelines for the proper way to set up and read clinical assays in laboratories. If a test is run for too short of an interval, there is a significant possibility of obtaining a false negative result, and if a test is run for too long of an interval, there is a possibility of obtaining a false positive result. Either case represents the possibility of a poor patient outcome: for the false negative, they might not receive notice that they have a given infection, and for the false positive, they might be started on an inappropriate treatment regimen.

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