Tag: microbiology

CDC Recommendations for Laboratory Detection of STDs

Several months ago the CDC updated their recommendations for laboratory detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

A summary:

Chlamydia trachomatis

  • Swabs must have a plastic or wire shaft and a rayon, Dacron, or cytobrush tip.
  • Swabs must be inserted 2-3 cm into the male urethral or 1-3 cm into the endocervical canal followed by 2-3 rotations
  • Specimens should be sent to the laboratory 1) within 24 hours of collection, 2) in sucrose phosphate glutamate buffer or M4 media, and 3) at less than or equal to 4 degrees C

Neisseria gonorrhoeae

  • Gram stain of male urethral specimen that contains PMS and intracellular Gram-negative diplococcic is considered diagnostic
  • A negative Gram stain result does NOT rule out infection
  • Swabs must have a plastic or wire shaft and a rayon, Dacron, or cytobrush tip.
  • Swabs must be inserted 2-3 cm into the male urethral or 1-3 cm into the endocervical canal followed by 2-3 rotations
  • For specimen transport, culture transport systems are preferred over swab transport systems
  • Specimens should be plated and incubated in an increased CO2 environment as soon as possible
  • Culture media should include selective (such as Thayer-Martin or Martin-Lewis) and nonselective (such as chocolate) agar
  • Oxidase-positive, Gram-negative diplococcic that grow on selective media can be presumptively identified as N. gonorrhoeae

Nucleic acid amplification tests (NAATs) are superior when compared to other culture and nonculture diagnostic methods for both organisms. However, it’s important that lab professionals understand the limitations of these tests.

Microbiologists should take the time to read the report here.

 

Swails

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

CLSI Releases New Microbiology Standard for Detection of Anaerobes

Anyone who has worked in Microbiology for any length of time knows that anaerobes are finicky at best and impossible to identify at worst. Having guidelines for their identification would be helpful. Enter CLSI.

From their press release:

“The Clinical and Laboratory Standards Institute (CLSI) released a new microbiology standard, Principles and Procedures for Detection of Anaerobes in Clinical Specimens; Approved Guideline (M56-A). This document presents standardized, cost-effective, and efficient best practice processes for anaerobe bacteriology to assist clinical laboratories in selecting those methods that lead to improved patient care.”

 

It’s That Time of Year Again

It’s a few days after a major holiday (Memorial Day in the United States), and clinical microbiologists knows what that means. It’s foodborne illness season! According to the CDC, Norovirus and Salmonella are the biggest culprits, but several organisms can be implicated.

If your lab doesn’t recover Salmonella, Campylobacter, or E. coli O157:H7 often, consider brushing up on the identifying characteristics of these organisms. (Do you know which one doesn’t ferment sorbitol?) It’s also helpful to keep the patient history (in particular, their travel history) in mind when reading enteric cultures or performing a microscopic ova and parasite examination. Also, now is a good time to be sure your reporting procedures (including local public health contact information) are up to date.

Check out the CDC’s website for more information on foodborne outbreaks, including how many people are affected.

 

Swails

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

 

Your Microbiome and Your Health

The fine folks at Scientific American recently published a fascinating blog post about the diversity of one’s fecal bacteria. While it’s long been thought gut microbiomes can vary widely from day to day within the same person, the advent of direct-to-consumer microbiome testing has uncovered that variety can exist within the same specimen.

What? You’ve never heard of personal microbiome testing? Think of it as 23andMe for feces. Ubiome and American Gut provide this service for folks who aren’t squeamish about collecting their own stool swabs.

From the laboratory professional perspective, what do you think about this type of direct-to-consumer testing? Do you think testing a patient’s microbiome has a future in diagnostic or preventative medicine?

 

Swails

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

Antiobiotic Resistance Worldwide

The World Health Organization assessed worldwide antibacterial resistance and recently published their findings. The report notes that a post-antibiotic era isn’t a dystopian fantasy but, in fact, a real possibility in the 21st century. Dire? Yes, but if you’ve been following the news, unsurprising.

The press release is here.

You can download or order the report here.

You can read a summary of the report here.

 

 

Haemophilus influenzae Infections in Pregnant Women

The Journal of the American Medical Association recently published a paper about the association of invasive Haemophilus influenzae infections in pregnant women and fetal outcomes. The researchers studied British women who had an invasive H. influenzae infection (defined as recovery of said organism from a normally sterile site). The researchers concluded that pregnant women had a greater risk of invasive infection than non-pregnant women, and these infections resulted in poor pregnancy outcomes.
H. influenzae is a fastidious organism that grows on chocolate agar. Normally associated with respiratory infections, if the organism is an encapsulated strain, it can spread to other parts of the body and cause meningitis, septicemia, pericarditis, and even urinary tract infections.
In terms of identification, H. influenzae are small, gram-negative coccobacilli on microscopic examination. The opaque colonies appear grayish on chocolate agar. Because it requires X and V factors to grow, the organism will appear on blood agar only in the presence of an organism that hemolyzes the blood (like Staphylococcus aureus). In addition to the X and V requirements, H. influenzae ferments glucose and is catalase positive.

Want to learn more? The CDC has great information on this organism.

 

Swails

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

Antibacterial Resistance in Pediatric Patients

A recent paper in the Journal of the Pediatric Infectious Diseases Society discusses the rising rates of antibacterial resistance in pediatric patients. It’s an alarming (but not surprising) paper that serves as yet another call to action. Modern medicine is in jeopardy; my hope is that it’s not to late to stop the oncoming catastrophe.

As always, Maryn McKenna over at Superbug has an excellent write-up.

If you’d like to read the paper, it’s here.

 

Swails

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

 

Listeria monocytogenes

The FDA is currently reporting an outbreak of Listeria monocytogenes in some Hispanic-style cheeses. While Listeria isn’t listed in the top five pathogens that cause food poisoning, it’s number four on the list of foodborne pathogens that cause death. It also causes meningitis, encephalitis, and septicemia; in pregnant women, it can cross the placenta and cause abortion, stillbirth, or premature birth. Perhaps now would be a good time for a refresher course in this bacterium.

Listeria grows on blood agar; this growth can be enhanced by cold enrichment. Selective enrichment–inhibiting other organisms while bolstering the growth of Listeria–is recommended if the specimen is food or environmental in nature. Other characteristics include:

  • Short gram-positive rods
  • motile
  • Beta-hemolytic
  • Smooth, light gray, 1-2 mm colonies after 24-48 hours of incubation at 37 degrees C
  • Will grow at 4 degrees C
  • facilitative anaerobe
  • catalase positive
  • oxidase negative

Listeria can be hard to identify, not because it’s fastidious, but because it can be confused with organisms such as Group B Streptococcus, Erysipelothrix, and corynebacterium. Don’t let that happen to you!

 

Swails

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

 

 

 

 

Gut Flora and Chron’s Disease

I’m fascinated by the connection between gut flora and overall health. I just stumbled onto this article that discusses the connection between gut flora and Chron’s Disease. It’s based on this paper published in Cell. Recent articles about antibiotic’s role in obesity and papers on gut flora’s influence on the immune system  keep raising the issue: how much do common organisms like E. coli, Clostridium perfringes, and Bacteroides fragilis affect us? How can we use them to diagnose, prevent, or cure disease? I’ll be keeping my eye on future research.

 

Swails

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

 

Antibiotic Stewardship

The draft of the federal budget released Tuesday allocates $30 million dollars in CDC funding in order to combat antibiotic resistance. Obviously the 2015 budget isn’t finalized, but even so, it’s encouraging that the Department of Health and Human Services recognizes the need for antibiotic stewardship.

What is antibiotic stewardship, you ask? Basically, it’s a program within a healthcare community that dictates the best practices for prescribing antibiotics. Such programs would be tailored for each setting based on population demographics and antibiograms. Perhaps a program would prohibit prescribing, say, ciprofloxacin for urinary tract infections because a rise in the percentage of strains of E. coli resistant to fluoroquinolones has been noted. Maybe the program would discourage prescribing more than two antibiotics at once to a patient, or suggest antibiotics other than vancomycin (such as levoquin) when treating MRSA.

Creating a stewardship program requires input from several departments (Infectious Disease, Pharmacy, Epidemiology, and the Microbiology Laboratory) as well as acceptance by the clinician population at large. In my experience, this has been the limiting factor. Physicians don’t like being told what they can and can’t do for their patients or the insinuation that they might lack the proper knowledge about antimicrobials and microbiology to provide good patient care. This is a hurdle that hospitals will have to overcome in order to make stewardship programs a success. (Mentioning that such programs can save money and shorten hospital stays could help tip the scales.)

If you’d like to institute a stewardship program at your institution, here are a few links to get you started:

CDC’s Vital Signs about prescribing practices
Antibiotic management guidelines at John Hopkins
Professional practice resources from the Association for Professionals in Infection Control and Epidemiology
The ever-insightful Maryn McKenna over at Superbug discusses the topic at length

Does your institution have an antibiotic stewardship program? If so, what steps did you have to take in order to implement it?

Swails

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