Category: microbiology

To Test or Not to Test

Recently the editors of Lab Medicine received a request for information regarding referral of sensitivities from one site to another or to the same site within three days. Here are a few examples of what I mean so we’re all on the same page:

  1. A pan-sensitive Staphylococcus aureus is recovered from a left ankle wound on 1/28; the same organism is recovered from the same site on 1/31.
  2. An E. coli with a typical susceptibility pattern is recovered from a right knee incision on 2/3; the same organism is recovered from the right ankle on the same date.

Referring sensitivities can streamline processes; thereby saving time and money (for the lab as well as the patient). According to the CLSI guideline M100-S23 (January 2013), Enterobacter, Citrobacter, and Serratia may develop resistance within three to four days of treatment with third-generation cephalosporin; Staphylococcus spp. may develop resistance to during prolonged therapy with quinolones. Since resistance can develop over the course of the same disease occurrence, it’s advisable to retest the susceptibility after three days so therapy can be adjusted if needed.

As for referring one site to another—such a left ankle to a left knee—I couldn’t find any source that advocated this practice. However, I am aware of facilities that have implemented such policies. What policies does your microbiology department follow when referring one sensitivity result to another?

 

Swails

–Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.

Why I Love Microbiology

I’ve been off the bench for almost a year, and while I don’t miss clocking in at 7:00 am or shoveling my driveway at 5 in the morning so I can get to work, I do miss actually working in a microbiology lab. Here are a few reasons why.

1. Making something out of nothing. For me, growing microorganisms on an agar plate is the closest thing to magic a laboratory scientist can do. Today, the plate is sterile; tomorrow, teeming with bacteria!

2. Learning more about a patient’s personal habits than you wanted to. Gram negative bacteria in a throat culture, oral flora in a necrotic toe, a forty-something with a UTI caused by S. saprophyticus or isolating Pasturella canis from a buttock incision site. Microbiologists know everyone’s dirty little secrets.

3. The technologist becomes the patient. When my husband and I adopted kittens, I immediately broke out in an itchy, scaly rash. Of course I performed a calcofluor white stain on a skin scraping that … just happened … to find itself on a glass slide. Diagnosing my own ringworm infection was equal parts exciting and dismaying. And since some of my flaky skin also made its way to an agar plate, we had a great fungus for our students.  (For the record, we identified Mycosporum gypsem.)

4. Finding the occasional zebra. I’ll never forget the feeling the first time I recovered Malessezia furfur or the day I found an H2S-producing E. coli.

5. Learning something new everyday. Whether it was a new process at the bench, a new organism I hadn’t seen before, or attending an infectious disease lecture given by a resident, I was constantly learning about the exciting world of bacteria.

And last, but certainly not least:

6. Using my unique skill set to make a difference in patient’s lives every day.

What are some of the reasons you love your job?

Swails

–Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.

Procalcitonin: Sepsis Marker Extraordinaire?

Sepsis is one of the most common causes of significant morbidity and mortality in hospitalized patients as well as the most common cause of death in ICU patients.  In addition, the earlier sepsis is identified and treated, the better the prognosis for the patient. We actually do not have a biochemical marker which can be used to effectively diagnose sepsis. Sepsis diagnosis depends on finding microbial infection by culture, and while PCR methods do exist to quickly identify bacteremia, in most institutions cultures take at least 24 hours to grow.  To aid in the diagnosis, clinicians can check three biomarkers commonly considered “sepsis” markers: C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and procalcitonin (PCT).

Despite being very different tests, these three assays are ultimately indicators of inflammation or the inflammatory response. ESR is a simple manual test that measures how far red cells sediment out of a blood sample in one hour. It is used as a marker of inflammation but is quite unspecific; several conditions can cause inflammation. The ESR can tell a clinician that inflammation exists but not the cause of that inflammation CRP is an acute phase reactant protein. Its production by the liver increases in acute inflammation. However, its levels will be affected by liver dysfunction. PCT is a pro-hormone produced by extra-thyroidal immune cells within 2-4 hours of a bacterial insult or an inflammatory response.

Deciding whether a biomarker is a good indicator of sepsis is made difficult by its complex pathology. Studies that show one marker performs better are contradicted by other studies that show it does not. The utility of PCT for predicting sepsis remains controversial for this reason. However PCT has shown to be useful for predicting prognosis in sepsis. Increasing PCT concentrations correlate with increasing severity and a poor prognosis. Decreasing or low concentrations indicate a good prognosis. PCT is also being used to guide antibiotic therapy, although this use should be limited to non-surgical/trauma ICU patients, which is where the studies have been done. Thus although PCT proponents consider it to be the best available biomarker indicator of sepsis, none of the three tests have been shown to be good at diagnosing sepsis. Unfortunately, all three of these biomarkers are indicative of an inflammatory response and not specific for sepsis itself. However, once sepsis is known, all three biomarkers can be used to monitor its progression and response to therapy.

If you’d like to read more about PCT and sepsis, you can do so here:

http://www.nlm.nih.gov/medlineplus/ency/article/000666.htm

http://www.webmd.com/a-to-z-guides/sepsis-septicemia-blood-infection

http://www.medscape.com/viewarticle/720621_1

https://www.aacc.org/members/nacb/NACBBlog/lists/posts/post.aspx?ID=16#

 

???????????????????????????????????????????????????????????????????????????????????

-Patti Jones PhD, DABCC, FACB, is the Clinical Director of the Chemistry and Metabolic Disease Laboratories at Children’s Medical Center in Dallas, TX and a Professor of Pathology at University of Texas Southwestern Medical Center in Dallas.

Dangerous Beauty

Potentially deadly pathogens have never looked so good. A false-color electron-microscope slideshow on Discover depicts organisms such as Campylobacter and Streptococcus pyogenes in a whole new light. Apparently actresses and models aren’t the only ones who benefit from Photoshop.

 

Swails

–Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.

Are Antibacterial Soaps Effective?

The FDA is asking manufacturers to prove the effectiveness of their antibacterial products that use triclosan or triclocarban as the active ingredient. (See the press release here.) This comes on the heels of last week’s announcement of their plan to help phase out the use of medically important antibiotics in food animals.

When I became a microbiologist I stopped using products with triclosan in an effort to curb antibiotic resistance. While I like to see the FDA’s efforts, I wonder if they’re doing too little, too late, and I’m not the only one.

Some additional reading on the topic:

1. Mechanism of triclosan resistance study, published 1999.

2. Another triclosan resistance study, published 2006.

Edited to add: Maryn McKenna’s excellent write-up on the topic.

Swails

-Kelly Swails is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.

‘Tis the Season

The holiday season is rife with celebrations. Tree Trimmings! Presents! Gatherings! And let’s not forget the food. Turkey! Dressing (with or without oysters)! Cookies and its glorious dough! An unfortunate side effect of holiday celebrations is food poisoning, specifically those caused by, Salmonella, Campylobacter, and Vibrio.

According to the CDC, Salmonella and Campylobacter are in the top five pathogens with Salmonella being the biggest culprit in hospitalization. If you want to prevent Salmonella poisoning—or think you might already have it—here’s a handy guide to causes, symptoms, and treatment.

Raw eggs and mishandled poultry aren’t the only causes of food poisoning, though. Shellfish can be a concern, as is undercooked beef and unpasteurized dairy products. The Mayo Clinic has a wonderful chart describing the major food poisoning pathogens. A noticeable omission is Bacillus cereus, which breeds quite nicely in leftover rice.

For laboratory professionals, foodborne illnesses are a common cause of laboratory-acquired hospital infections. Be vigilant when handling enteric specimens and enteric cultures. Observe basic lab safety—use personal protective equipment, don’t use personal electronics in the lab, and be obsessive about washing your hands. Don’t let Salmonella or one of his buddies ruin your holiday season.

 

Swails

–Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.

Dirty Winds

Over at Body Horrors, Rebecca Kreston writes about public health concerns of infectious disease and parasites. In this thought-provoking post, she discussions musicians (specifically, those who play wind instruments) and lung infections. She cites several small studies that found pathogens (Mycobacterium, Stenotrophomonas, and Cryptococcus) in instruments such as saxophones and trumpets.

The moral of the story: horn musicians, clean your instruments. And don’t ignore a persistent cough.

Swails

–Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.

The Post-Antibiotic Era, Part 2

Linking to a few articles by Maryn McKenna because you need to read them.

In this blog post, Ms. McKenna writes about a man from New Zealand who died from a bacteria completely resistant to all antibiotics.

In this article, she imagines the post-antibiotic world. In a nutshell: it’s a scary place.

-Kelly Swails

 

 

A Possible Method to Diagnose Invasive Meningococcal Infection

Saying the word “meningitis” is a sure-fire way to scare parents of young children or college students. Invasive infections caused by Neisseria meningitidis are rare but serious. Mortality rates can run around 15%; complications include amputations due to tissue necrosis and hearing loss. In short, N. meningitidis infections are nothing to mess around with.

In order to avoid death and extremity loss, the infection needs to be diagnosed early. Trouble is, the early symptoms can be similar to those of a run-of-the-mill viral infection. Some patients do not exhibit the elevated white blood cell count so common in bacterial infections. Without clear signposts to guide the way, how can clinicians catch this fast-moving infection early in its course? A handful of esoteric hematology parameters might hold the key.

Demissie et al recently published this paper in The Pediatric Infectious Disease Journal about using neutrophil counts to diagnose meningococcal infection in children. It’s behind a paywall, but here’s the gist:

-Your automated hematology analyzer needs to report immature white blood cells.

-Using total white blood cell (WBC) counts or total neutrophil counts alone is insufficient.

-The parameters to check are absolute neutrophil count (ANC), immature neutrophil count (INC), and immature-to-total neutrophil ratio (ITR).

-Patients with invasive meningococcal infection (or, the authors also say, a serious bacterial infection) display abnormalities in at least one of the three parameters.

What do you think about these guidelines? Do you think they’d be effective in diagnosing invasive meningococcal infections?

-Kelly Swails