Lab Matters Spring 2022 - Page 9

FEATURE and opening a BSL-3 facility in a clinical reference laboratory .
Plan , Plan , Plan — But Don ’ t Get Too Attached
Public health laboratories are accustomed to planning for short-term outbreaks . But maintaining surge capacity during a prolonged public health emergency is a different beast , one that takes meticulous planning paired with the flexibility to scrap and rework those plans at a moment ’ s notice .
“ Coordinating and planning — that ’ s the bottom line ,” said Vanda Makris , a microbiologist in the Oregon laboratory . “ You have an action plan . And then the next day , something changes , and you have to make adjustments .”
Good communication among personnel allowed them to coordinate and triage the most pressing needs .
“ Oftentimes people may feel comfortable juggling multiple benches , so maybe they ’ re doing chlamydia , gonorrhea and our serologies at the same time and , as they have downtime , they ’ ll bounce from one instrument to the other ,” Sevey said .
It helped that laboratory personnel had to work in person throughout the pandemic , Bateman said , because that facilitated the quick communication and discussion needed to adapt to daily needs and situations .
“ We can walk down the hall and immediately touch base .”
Planning also has to happen at the instrumentation and supply level . Resource limitations sometimes necessitated some influenza samples being triaged for later analysis , said Kirsten St . George , PhD , MAppSc , director of the virology laboratory at the Wadsworth Center in New York . And in
South Dakota , a surge in syphilis — with cases rising more than 1000 % between 2019 and 2021 — prompted a new public health campaign aimed at improving healthcare for vulnerable populations that has brought an influx of specimens to the public health laboratory for sexually transmitted infection ( STI ) testing .
“ There ’ s been a mad dash for syphilis reagents of all kinds ,” Southern said . “ We have learned that we have to be very mindful of the amount of reagents and supplies that we keep . We ’ ve also brought on some new instrumentation and we ’ re really thinking about how we ’ re going to approach syphilis in the future , so that we can better accommodate a surge like what we ’ re seeing now .”
Find Efficiencies …
To stretch capacity as much as possible , Southern and others are turning to systems with higher throughput and automation wherever possible .
“ The surge in syphilis is really pushing us towards automation of some of the algorithms that we use ,” he said . Crumpler echoed this , saying that shifting STI testing from a traditional manual assay to the more automated reverse sequence screening algorithm helped the Orange County laboratory maintain syphilis testing throughout the pandemic .
The Wisconsin team has shifted a lot of their COVID-19 testing to more automated instruments as well , a move that enables anyone from the serology team to step in and help if the virology staff are needed elsewhere — which has proven especially beneficial during the first season of concurrent influenza and COVID-19 . At Wadsworth , too , St . George said , “ Significant efforts have been made in recent years to develop and implement more automated testing platforms and more multiplexed assays that provide concurrent test results for multiple respiratory agents simultaneously .”
The Oregon laboratory is similarly ramping up use of a multiplex assay , BioFire , to streamline testing for a panel of gastroenteritis-associated pathogens . In collaboration with the US Centers for Disease Control and Prevention ( CDC ) and APHL , they are also helping develop a new , next-generation sequencing assay for norovirus as a faster , higher throughput replacement for traditional Sanger sequencing .
In some cases , increased efficiency has even enabled new capabilities . Prior to the pandemic , the Orange County laboratory had started testing some clinical samples for C . auris by 16S sequencing , a multi-step , labor-intensive process . In mid-2020 , demand began to increase and despite the throes of COVID-19 testing , the laboratory added C . auris outbreak testing and PCR screening to facilitate patient transfers between facilities . In 2021 , the team switched to a MALDI platform to speed up the confirmation process . For PCR screening , they obtained an instrument , collaborated with CDC and the Washington State Public Health Laboratory to get specimens for validation of the assay , and went live in September , becoming the first local laboratory in California to offer this type of testing .
Although demand still far exceeds their capacity , Crumpler said , Orange County is hoping to receive funding through the CDC ’ s Strengthening HAI / AR Program Capacity ( SHARP ) program and is now working with the state of California to figure out how to increase capacity for resource-intensive C . auris point prevalence surveys .
Oftentimes , it ’ s more than just the testing itself that backs up . The detail-oriented ,
We can ’ t say , ‘ well , there ’ s COVID , we can ’ t do [ National Influenza Reference Center ] testing ;’ or ‘ sorry , there ’ s COVID , we can ’ t do [ Antibiotic Resistance Laboratory Network ] work .’ That ’ s just not an option .”
Allen Bateman , PhD , MPH , D ( ABMM )
Spring 2022 LAB MATTERS 7