The Clinician and the Microbiology Laboratory

Guidelines

• Utilization of Micro Lab 2013: Baron et al. Clin Infect Dis. 2013;57(4):485-8.
• Utilization of Micro Lab 2018: Miller et al. Clin Infect Dis. 2018;67(6):e1–e94
• Micro lab testing for dx of fungal infections in pulm/crit practice guideline: Hage et al. Am J Respir Crit Care Med. 2019;200:535-550.
• CLSI: Clinical and Laboratory Standards Institute. 2014. Clinical and Laboratory Standards Institute, Wayne, PA.

Review articles

• Dx of bacterial and fungal bloodstream infections in the ICU: Murray et al. Crit Care Med. 2012 Dec;40(12):3277-82.
• Metagenomic next-generation sequencing: Simner et al. Clin Infect Dis. 2018;66(5):778-788.
• Markers of intestinal inflammation for the diagnosis of infectious gastroenteritis: Gonzalez et al. Clin Lab Med. 2015;35:333-344.
• Best practices for isolation of bacteria and fungi in IE. BC yield increases linearly with the amount of blood collected: Towns et al. Infect Dis Clin North Am. 2002;16(2):363-376. ix-x.
• EUCAST expert rules in antimicrobial susceptiblity testing: Leclercq et al. Clin Microbiol Infect. 2013;19(2):141-60.
• Need for diagnostic and antimicrobial stewardship with rapid molecular diagnostics: Messacar et al. J Clin Microbiol. 2017;55(3):715-723.
• Biomarker-guided antibiotics therapy: Nora et al. Ann Transl Med. 2017;5(10):208.
• Carroll. J Clin Microbiol. 2002;40(9):3115-20.

Systematic Reviews / Meta-analyses

• When to order blood cultures: Fabre et al. Clin Infect Dis 2020;71(5):1339-1347.

Trials

• Use of MALDI-TOFmay reduce the time to appropriate antibiotic, length of ICU stay and mortality of patients with bacteremia: Huang et al. Clin Infect Dis. 2013;57:1237-1245.
• MALDI-TOF and PCR-based rapid detection of MRSA reduced unnecessary coverage for MRSA: O’Clerc et al. Clin Microbiol Infect. 2014;20:355-360.
• Use and benefit of MALDI-TOF: Tan et al. J Clin Microbiol. 2012;50:3301-3308.
• Validation of metagenomic next-generation sequencing: Schlaberg et al. Arch Pathol Lab Med. 2017;141:776-786.
• In IE, most HACEK organisms grow within 5 days and prolonged incubation doesn’t really increase the yield: Baron et al. Clin Infect Dis. 2005;41(11):1677-1680.
• Reducing the number of BC drawn from central lines reduced the contamination rate and saved money: Boyce et al. Infect Control Hosp Epidemiol. 2013;34(10):1042-7.
• Performance characteristics of Verigene for Gm- organism and resistance identification in blood cultures: Ledeboer et al. J Clin Microbiol. 2015;53(8):2460-72.
• Verigene for identification of Gm+ organisms in blood cultures: Bhatti et al. J Clin Microbiol. 2014;52(9):3433-6.
• Verigene for identification of Gm- organisms and resistance identification in blood cultures: Mancini et al. J Clin Microbiol. 2014;52(4):1242-5.
• Single center evaluation of BioFire FilmArray for GI Panel performance characteristics: Murphy et al. Eur J Clin Microbiol Infect Dis. 2017;36(4):747-754.
• Multicenter evaulation of BioFire FilmArray for GI panel performance characteristics: Buss et al. J Clin Microbiol. 2015;53(3):915-25.

Articles

• How to obtain, process, report, interpret blood cultures: Kirn et al. Clin Microbiol Infect 2013;19:513-520
• How to use blood cultures: De et al. Arch Dis Child Educ Pract Ed 2014;99:144-151.
• How to optimize use of blood cultures: Lamy et al. Front Microbiol 2016;7:1-13.
• State of the art of blood cultures: Opota et al. Clin Microbiol Infect 2015;21:313-322.
• Does suspected bacteremia require blood cultures?: Coburn et al. J Am Med Assoc 2012;308(5):502-511.
• Interpretation of catheter tip cultures: O’Flaherty et al. Arch Dis Child Educ Pract Ed 2015;100:69-74.

Tweetorials

Mandell chapter summary

Mandell ch. 16:
Clinicians and the micro lab work closely together to make sure that appropriate tests are available on the menu, proper specimen collection is performed*, and test characteristics are communicated to allow accurate interpretation of results#IDtwitter #idmeded

— Hillary Hunsinger, DO (@DrH_flu) November 29, 2019

Antibiotic susceptibility testing

#IDDailyPearl One might assume antibiotic susceptibility testing (AST) and the reporting of results is a straightforward topic. Turns out, there is a lot of nuance to it. Given how often I find myself explaining AST to clinicians, I felt a brief review was worth the time 1/11

— Sanjat Kanjilal (@SanjatKanjilal) May 24, 2019

Use of urine antigens for lung pathogens

1/
Why do we use urine antigen tests to diagnose respiratory pathogens?

Patients admitted with pneumonia are often diagnosed with S pneumoniae or legionella based on a positive URINE test.

Let's try and figure out why we search the urine to identify lung pathogens. pic.twitter.com/H511NKYOi2

— Tony Breu (@tony_breu) December 24, 2018

Susceptibility testing

Thanks for the tag!
1/
Time for a short #IDtweetorial on Abx Susc Testing

Four major methods:

1⃣ Kirby Bauer Disk Diffusion: disks impregnanted w/ Abx ➡️circular gradient➡️zone of inhibition. ❌MIC
2⃣Broth microdilution: Abx in 2-fold dilutions in 96-well plate. ✔️MIC https://t.co/BcU5xmsQXt pic.twitter.com/es3lM1zxAA

— Infectious Disease Fellows Network (@ID_fellows) August 12, 2020

Phenotypic detection of carbapenemase producting organisms

Got to squeeze in that non-COVID learning too! Friday AM Conference today is Part 2 from @DKopeMD, reviewing resistant gram negative infections. #IDTwitter #MedTwitter #MicroRounds #MedEd
1/10 pic.twitter.com/PIiYuVR44p

— BIDMC Infectious Diseases Fellowship (@BIDMC_IDFellows) May 15, 2020

Last Updated 12/17/2020