1/I want to take some time to share findings from our semi-recent PETACS study. This was a wonderful collaboration between @COpedsID faculty, survey designers, and #microbiologists across the US.
@JClinMicro @ASMicrobiology #ASMClinMicro
jcm.asm.org/content/59/3/e…
2/ First, I want to emphasize that this project highlights many of the reasons I chose to pursue a #PhD in clinical & translational science. As a long-time microbiologist, I can say that the clinical lab doesn't often have a seat at the clinical effectiveness / research table.
3/ This project focuses on the tracheal aspirate culture- a diagnostic process that is greatly limited by contamination with normal respiratory flora, and which lacks consensus or standardization across labs and hospitals. @ASCLS @ASMicrobiology @ASCP_Chicago
4 / When combing through the literature, you will often find that ventilator-associated pneumonia (#VAP)(and/or tracheitis) studies rely on different laboratory methods for TAs, which makes the findings hard to interpret or apply across centers.
5/ Additionally, studies seem to make assumptions about what the lab is doing with TAs, or even go so far as to have a clinician perform testing elements such as reading Gram stains (instead of the lab). Most importantly: the lab is never really asked about their process.
6/ We wanted to dive deeper in to the TA culture process on the laboratory side. TA cultures serve as a major stewardship problem that needs to be addressed on both the clinical & lab side. If we are going to improve the process, we HAVE TO TALK TO THE LAB!
#ASMClinMicro @ASCLS
7/ We used the PHIS database to identify pediatric hospitals and assess for eligibility. We excluded any labs that did not perform microbiology in-house, or for which there was no contact information. This = 107 Adult+peds & 46 freestanding peds hospitals.
8/ An important thing to understand about labs: Not all #labs have a PhD-level director, and even if they do, that person may not be the person who can speak to the intricacies of the bench-level procedure for tracheal aspirate cultures.
9 / I personally reached out to every lab to ask for participation and ensure that we were surveying the most appropriate people. I loved this part. Microbiologists are wonderful.
@ASMicrobiology #ASMClinMicro
10 / The overall response rate was 48% (73/153), including a response rate of 69% (32/46) for freestanding pediatric hospitals. Considering this was a digital survey of (mostly) total strangers, this is great!
11 / We found a lot of interesting things from this survey, but here are the key findings:
1. There is a lot of variability across hospitals when it comes to the tracheal aspirate culture process. This is true from start to finish
12 / Only 7% of labs reported being aware of if a TA specimen has been diluted with saline when it arrives in the lab. We know that saline is frequently used during suctioning, but the lab is rarely made aware of this. This affects the results and the way things are reported.
13 / 44% of labs have rejection criteria based on how long it takes the sample to reach the lab, but those criteria varied quite a bit.

23% of labs reject TA specimens based on Gram stain criteria, but there wasn't a whole lot of agreement on the method for this either.
14 / There is a lot of variability in other Gram staining components such as which objective to use to quantify human cells - the majority use the 10x objective, but 10% use 40x and 23% use 100x.

56% of labs use minimum field review criteria, but these ranged from 5-100 fields
13/ In the culture domain of the survey, we asked about ID & reporting practices for organisms that are potential pneumonia pathogens. For each, we wanted to know: if they are ALWAYS reported (no matter what), or when other factors like predominance or Gram stain come into play.
14 / Bottom line: this varies quite a bit between labs.
Overall, nonacademic labs are more likely to always ID and report S. pneumoniae, S. aureus, P. aeruginosa, enteric GNRs and nonfermenting GNRs regardless of factors like purity, predominance, original Gram stain (P<0.05).
15 / Freestanding pediatric labs are more likely to always identify and report Group A strep and P. aeruginosa, regardless of other factors like purity, predominance in culture, or original Gram stain results (P<0.05).
16 / Important themes that emerged from the free-response section include:
1. Microbiologists find the existing process to be frustrating, challenging, and in need of formal guidance.

2. Pressure from clinicians to report certain organisms is a big issue (and drives processes)
17 / Concluding thoughts:
1. We use TA cultures in pediatrics a lot. They are less-invasive, and when collected appropriately and interpreted well, can be very helpful for the diagnosis of pneumonia or tracheitis...which are very serious conditions. BUT...
18/
2. The lack of standardization on both the clinical and laboratory side render them unhelpful (and often confusing).
3. It is really hard to determine what is a colonizing organism and what is a respiratory pathogen in each patient.
19/
4. We are all doing different things. This makes interpretation, quality improvement, and communication around these cultures challenging.

5. Without data to support the microbiology lab, it is hard to implement changes to the process due to clinician preferences.
20/ So, what to do next?
✔️Demonstrate that weeding out the contaminated, poorly collected, unhelpful TA cultures =better patient care.
✔️Use these data to help support labs make appropriate changes to their process.
✔️No more siloed diagnostics work! Involve all parties.
21/Optimize and utilize dissemination and implementation science techniques to better understand the context around this diagnostic tool. Involve EVERYONE -- pulmonary, microbiology, infectious diseases, critical care, etc. Implement something that is sustainable.
#TeamScience
23/ Finally, I am so thankful to all of the microbiologists who took the time to share their process and opinion(s). The #IDTwitter world functions well because of your added expertise. You play an enormous role in #diagnostic and antimicrobial #stewardship. Also, I love you.

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More from @andreaprinzi

30 Mar
1/Dr. Lewis Roberts is giving a really interesting talk at @ACTScience #TS21 that walks us through the art of reviewing and questioning a scientific talk.

We are all pretty familiar with reviewing manuscripts, but I think this is a fresh take!
@EdgeforScholars #phdlife #PhD
2/
This is like a dynamic (real-time) manuscript review. The corollary:
* One key for presenters: strategically repeat yourself
*Tell them what you're going to say (abstract)
*Tell them (introduction, methods, results)
*Tell them what you told them (discussion)
#TS21 @ACTScience
3/
The 40,000 ft view:
*What is the main aim of the study? Should be in the first few minutes of a presentation
*When you are listening, pick out:
-What is the problem they are trying to solve?
-What is the overall hypothesis?
#TS21
Read 7 tweets
30 Mar
1/ Dr. Stephen Ekker (@scekker) is speaking my language in his talk about the importance of #scicomm and how effective @Twitter can be for scientists.
#TS21 @EdgeforScholars @ACTScience
2/ Good science communication IS good science ethics!
Effectively communicating our science literally has life-saving implications, and it is VERY important.
#scicomm #TS21 @ACTScience @EdgeforScholars
#phdlife #PhD @CCTSI
3/ Making your own "Scientist Oath" using social media:
If you were making your own platform, what rules would YOU write?
-Be deliberate in thinking about what you share and how you share it
Read 10 tweets
30 Mar
1/Listening to an amazing plenary talk by @DrCHWilkins on racism, disparities, and the role of race/ethnicity in medicine and research. AMAZING talk!
#TS21 @EdgeforScholars @ACTScience
2/Our focus always seems to be on race alone, and not on other social scenarios. We focus so much on personal choices and access to care-- but we focus less on disparities the way we should (and race as a fully sociopolitical concept).
#TS21 @ACTScience
3/*Racism in medicine is =responsible for minorities having the worst healthcare & outcomes in the US
*Many famous physicians & scientists were involved in creating and perpetuating inferiority stereotypes
*Many continue to conflate race with biology & physiology
#TS21
Read 15 tweets
3 Dec 20
I have a few things to say this morning. A small but mighty 🧵.
First , I can't say thank you enough to @KatherineJWu for writing this amazing piece highlighting the crucial work of clinical laboratory scientists/medical technologists. Please read it: nytimes.com/2020/12/03/hea…
The article captures a piece of the talent, expertise, and dedication of these healthcare workers. This is especially true of my dear friend @darcyavelasquez, who works relentlessly day in and day out at @ChildrensColo to provide the best care possible to Colorado's children.
Sometimes it feels like the @KatherineJWu's, @kmess44's, and @jesscataldi's of the world are one-in-a-million. The failure to recognize the clinical laboratory (and people within it) for its importance in how healthcare works is not just a #COVIDー19 issue.
Read 22 tweets
17 Aug 20
Ok, sort of weird to say...but today I'm dedicating some time to SPIT (formally known as #Saliva). It's the super hot topic this week in the ever-changing #COVID19 diagnostic landscape we are living in, so let's take a quick peek at some of the evidence out there (thread)
I completely understand the importance of testing saliva, particularly as it relates to lack of supplies and resources. It can be a feasible option that basically eliminates HCW risk of infxn during collection. It can also save supplies: no swabs, media, possibly fewer reagents.
First paper is here: DOI: 10.1128/JCM.01659-20
-53 paired samples from OP and/or NP swabs, and saliva were collected
-Standard RNA extraction methods were used for the swab samples, a quick extraction method was used for saliva. Handling high-viscosity samples is discussed.
Read 20 tweets
26 Jul 20
I just want to be clear: while I understand and have similar frustrations with turnaround times for #COVIDー19 testing, I'm afraid the angst is falling on the laboratories...and I do not feel that is fair or appropriate. (Small thread)
The clinical laboratory is full of living, breathing, intelligent human beings. The work takes skill and time. Often, labs are understaffed and there has been a shortage of trained clinical lab scientists FOR A WHILE. There are only so many tests a person can crank out in a day.
Even if a lab has all the staff they need, there's only so much testing that can be done when a) your instruments are full b) you cannot get the supplies you need to run these tests. Seems like many people think labs have unlimited access to very expensive instruments...nope.
Read 8 tweets

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