Julie Segre – Microbial Genomics in a clinical setting. #AGBTPH

Two cases.

Genetic disorders and microbial disorders often interact.  Nearly all microbes can be uniquely identified by shotgun nucleic acid sequencing.

Topic 1.  Infectious diseases in hospitalized patients.  Sometimes can’t tell the kingdom, even.   Sample -> sequencing -> Bioinformatics ->  hopefully identifying agent.

Human genome is often considered the contamination – can’t physically extract it out.  Opening cells for fungi requires some harsh treatment.

URPI bioinformatics pipeline used.  What do you get out, and is it even in your database?

case 1: 3 hospitalization over 4 months – 44 days in ICU. over 100 inconclusive tests.  Cured 2 weeks after NGS dx with appropriate treatment.

Very clear hit found with Leptospira santarosai.   Had been travel to Puerto Rico, and Leptospira is a water-born disease.  Used appropriate treatment, and the infection resolved. (Tests were run that validated the diagnosis.)

Clia validation of these methods is required.  It’s a step by step process.  Happens over a year.  [appears to take nearly 2 years?  April 2015 to March 2017]

Asside: Nanopore sequencing  may also be a hugely exciting development for this field because it’s so fast.

Topic 2:  Unsing sequencing to inform healthcare-associated infections.

CRE – carbapenem resistant Enterobacteriacae.  We have no antibiotics left to fight these bacteria.  (Klebsiella pneumoniae)

Patient 1 – June, but several patients in August.  Either patient 1 was unrelated or transmission occurred.

Sequencing happened: patient 1 unine sample (assume as reference genome.)  3 variants in throat isolate, 3 different snps in lung.  Patient 2 and 3, identical to throat sample from first patient.  (one extra snp in patient 3).

Patient 1 and 3 overlapped in ICU.  3 and 2 overlapped in ICU.

Patient 4 had variants matching lung(?)  so separate transmission.

This data showed that transmission was happening – ultimately, a transmission map was created with other patients.  It was ultimately clear how it was transmitted.  Helped to identify which avenues needed to be tracked down by cohorting patients.

Resistance genes are generally on plasmids, so we need to be aware of the possibility of transmission of the plasmid to other organisms.

National Pathogen Reference Database – CDC, FDA and NIH.

If you have a reference, you can pretty much assemble anything.


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