Culture Collections are Critical in the Response to the COVID-19 Pandemic

Culture collections are critical to solving infectious disease challenges

Biological repositories including culture collections provide essential materials to researchers and clinicians around the world, allowing rapid response to outbreaks of infectious disease. These materials are used in:

·      Understanding the properties of the infectious agent

·      Developing diagnostic tests to detect and contain the outbreak

·      Developing antiviral and antibacterial therapeutics to treat infected individuals

·      Developing vaccines to prevent future outbreaks

Specific examples of biological repository contributions to the COVID-19 pandemic

The American Type Culture Collection (ATCC) is the leading biological materials resource whose mission is to acquire, authenticate, produce, preserve, develop, and distribute microorganisms, cell lines, and other materials. Specific materials relevant for the current crisis include: 

·      SARS-CoV-2 Heat-inactivated virus strain

·      Genomic RNA

·      Cell lines to grow SARS-CoV-2

·      Synthetic and quantitative standards for SARS-CoV-2 molecular assays 

·      A wide range of materials from other Coronavirus

BEI Resources (Biodefense and Emerging Infections Research Resources Repository), which is funded by the National Institute of Allergy and Infectious Diseases (NIAID) and managed by ATCC, acquires, produces, and distributes a variety of materials to support infectious disease research. These products are used by academia, government entities, private laboratories, pharmaceutical, and biotech companies to basic research and development of antiviral therapeutics. Registration for access to these materials increased 400% in the month of March, 2020. Biological materials relevant to the coronavirus pandemic are currently being distributed to registered users at a very high rate and replenished in-house under appropriate quality control to ensure the demand is met. Materials include:

·      Multiple isolates and derivatives of the SARS-CoV-2 virus

·      Genomic RNA

·      Inactivated virus

·      Plasmids with SARS-CoV-2 genes for protein expression, recombinant proteins, etc. that have been deposited by the research community

·      Polyclonal antibodies and recombinant proteins developed and produced by the community as well as being produced in-house

·      A wide range of materials from other Coronavirus, such as SARS and MERS

The International Reagent Resource (IRR), is a biological reagent repository established by the Centers for Disease Control and Prevention (CDC) and is also managed under contract by ATCC. IRR acquires, authenticates, and produces reagents, tools, information, and controls to registered users for basic research and development of improved diagnostic tests, vaccines, and detection methods. Materials currently being distributed to qualified county and state laboratories in the US in response to the current health crisis include:

·      The CDC-approved SARS-CoV-2 (previously titled “2019-nCOV”) Real-Time RT-PCR Diagnostic Panel

·      Positive controls of the SARS-CoV-2 virus

·      Human specimen controls

How these organizations were able to respond so quickly to the current crisis

Over many decades, these organizations have built a reputation for reliability among the research community. They have become the recognized repositories for researchers to deposit materials in order to make these materials quickly and broadly available to the international research community.

Lessons going forward

Biological collections including culture collections are essential not only in times of crisis, but for furthering discovery and innovation in life science every day. Many collections contain specimens that cannot be replaced because they are historic, rare, or costly. Collection personnel have in-depth knowledge that cannot be replicated. Appreciation of collections that is generated during the current crisis should be followed by appropriate support to allow them to continue to respond to future crises and life science research more broadly. 

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Sources:

https://atcc.org

https://www.beiresources.org/Home.aspx

https://www.internationalreagentresource.org/Home.aspx

Authors:

Manzour Hazbón, Senior Scientist, Bacteriology, ATCC

Kyria Boundy-Mills, curator, Phaff Yeast Culture Collection, UC Davis

Microbial culture collections can help researchers during a research hiatus

Many academic, government agency, and industry research laboratories around the world are taking a break from lab work due to the COVID-19 health crisis. Although researchers who are not involved in COVID-19 research are ordering few supplies including microbe strains, other resources offered by culture collections can be helpful for manuscript and grant writing, and planning future lines of research. Here’s some ideas gathered from several US culture collections.

1.     Culture collections can provide updated information about strains you are already using. This is especially important if you received the strain from the collection years ago. Species names change due to taxonomic revisions, and you don’t want to use an obsolete species name in your manuscript. Examples: 

• Since 2016, hundreds of yeast species names have changed due to taxonomic revisions. A large proportion of basidiomycete species have been revised, and also many former Candida species have been changed to line up with their equivalent teleomorph genus. 
• Just last week (April 15, 2020), industrially important lactic acid bacteria genus Lactobacillus was divided into 24 genera (Zheng et al. 2020, IJSEM ijsem004107). This is so recent that culture collections that distribute these species may not have updated these genus and species names in their online catalogs yet. 

Online strain catalogs may have other new information about strains you received a few years ago, such as citation in other people’s publications or patents, DNA sequences, and new phenotype data. As you write your manuscripts, check in with the culture collections for updated information about the strains you are using.

• First stop: Look at the online catalog of the collection you ordered the strain from. There may be new information posted. Strain catalogs cross reference the strain ID number in other collections. 
• If the same strain is available from other collections (such as type strains and other frequently used strains), check the other collections' online catalogs too – different collections post different categories of information.
• Kyria Boundy-Mills, curator of the Phaff Yeast Culture Collection said, “We have updated about 300 species names in the last four years, but the strain ID number stays the same. One example: genus Rhodosporidium no longer exists. Look up the strain ID number in our online strain catalog (phaffcollection.ucdavis.edu) to confirm the current species name before you submit your manuscript. Also check recent taxonomy publications in case we missed an update.”
• Brandy Russell, curator of the Arbovirus Reference Collection said, “If you are having difficulty working with a viral isolate obtained from us we are always happy to consult. We may have found other cell types that work better for replication for that particular isolate. If additional sequencing of the isolate has been performed since you received it from us, we are happy to provide you with an updated product insert”

2.     Culture collections can help you select strains for your future research. Curators have extensive knowledge about the organisms in general, the specific strains held in the collection, and the associated data. If you tell them what question you are studying, or strain properties you desire, collection curators can guide you to some useful strains. For example:

• Curators can help you find strains with phenotypes or mutant genotypes related to the property you are studying.
• Collection curators can help you select strains or species whose genome has already been sequenced. 
• Inside secret: Many curators are willing to help researchers find strains in other culture collections to supplement what is not available from their own collection.
• The catalogs of over 130 culture collections around the world have been combined into one catalog: the Global Catalog of Microorganisms (http://gcm.wfcc.info). You may find a strain available from a collection you didn’t know about. Prices and distribution policies differ greatly among different collections.
• Boundy-Mills said, “Several years ago, we helped a researcher find yeasts able to perform a certain function at low pH. Based on our knowledge of the collection, we selected a variety of yeast strains that were originally isolated from low pH environments such as fruits. The best performing strain was originally isolated from citrus fruit juice. Other strains of that same species isolated from less acidic environments did not perform as well. Another example: A researcher wanted to compare fungicide resistance genes in strains of an environmental yeast species collected before vs. after agricultural pesticides were commonly used. We were able to provide several strains collected many decades ago.”
• Russell said, “We have a large number of unpublished isolates and can help you select isolates in addition to those found in the published literature.”

3.     Culture collection websites have new strains and new data, which may inspire some new research ideas. Collections preserve and distribute organisms of course, but they also act as a repository for information about those organisms. 

• Culture collections acquire new strains continually, sometimes as large sets. Last year, 13 people associated with 12 different US culture collections co-authored the publication, “Preserving US microbe collections sparks future discoveries”. (J Appl Microbiol, doi:10.1111/jam.14525). This paper lists 26 sizeable sets of strains that were deposited into 10 different culture collections. Check in with your favorite collections for newly acquired strains -- you may find some pleasant surprises.
• The genome sequences of 2,199 strains in the E. coli Reference Center are now incorporated into NCBI’s Pathogen Detection pipeline, which includes a screen for virulence and antibiotic resistance genes.  It can be accessed here: https://www.ncbi.nlm.nih.gov/pathogens/isolates#/search/PSU.  This table can be searched so researchers can identify isolates with specific combinations of genes they are interested in.  This table can also be sorted, identifying things such as the isolate with the most number of resistance genes. Current record holder: a calf isolate carrying 28 antibiotic resistance genes!
• Boundy-Mills said, “The Phaff Yeast Culture Collection online catalog recently added a searchable field for the substrate category, which may be particularly informative for microbiome analysis. You can now generate lists of yeasts in the Phaff collection that originated from certain types of buildings, dairy products, food fermentations, flower nectar, decaying wood, insects, trees, air, water, and many other categories.”

The participating collections in the US Culture Collection Network (USCCN.org) hope these ideas help researchers continue their innovative studies using microbial culture collections, now and for years to come. Now is a good time to reach out to culture collection curators to explore ideas.

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Authors:

Kyria Boundy-Mills, Phaff Yeast Culture Collection, University of California Davis

Brandy Russell, Arbovirus Reference Collection, Centers for Disease Control and Prevention, Division of Vector-Borne Diseases, Arboviral Diseases Branch

Edward Dudley, E. coli Reference Center, Pennsylvania State University

Why do we need so many different collections of E. coli?

Public microbe collections acquire, characterize, preserve and distribute strains for research. There are several public collections of the bacteria E. coli, because it is both an important model organism for studying cellular functions, and because it is an environmental species that impacts human and animal health. Collections of E. coli in the U.S. have similar names, and similar holdings, but different uses. 

The E. Coli Genetic Stock Center (CGSC) at Yale University (https://cgsc.biology.yale.edu/) contains 12,000 strains, primarily genetically modified strains of E. coli, most derived from lab strain K-12. Strains are used for research in medicine, microbiology, biochemistry, chemical engineering, biotechnology, cell biology, genetics, pharmacology, agriculture, physics, and much more.

The E. coli Reference Collection (STEC) at Michigan State University (http://www.shigatox.net/new/) contains (>10,000 strains) from patients with infections, livestock and environmental sources as well as genetically modified strains of different E. coli isolates.  These collections are used in studies of whole genome phylogeny, animal health, animal gut microbiome, and food safety. 

The E. Coli Reference Center (ECRC) at Pennsylvania State University (https://foodscience.psu.edu/research/centers/ecoli/services) contains 90,000 strains of wild-type, non-genetically modified E. coli isolated from humans, food, environment including soil and waterways, and other habitats. The genomes of about 4,000 of these strains have been fully sequenced. Strains with specific properties are used by academic and government agency researchers for many different studies. Some recent examples:

·       Porcine enterotoxigenic E. coli strains, which cause diarrhea in piglets; for vaccine development

·       Shiga toxin-producing strains for commercial assay development

·       Sets for developing bacteriophage therapies

·       Strains that carry the pks gene cluster, which is associated with colon cancer

ECRC is one of the few laboratories that performs agglutination-based serotyping, because it requires maintaining antibodies for over 180 O-groups. They also perform PCR screens for customers to assess potential virulence of isolates. They are also leading a panel to coordinate serogroups identified by the traditional method with genome sequence data. 

SEM of E. coli cells

Image provided by Ed Dudley

From Ed Dudley, director of ECRC: “Some notable things we’ve done recently – We participated with a vaccine company in a multi-year study identifying the O groups for E. coli most associated with septic diseases among geriatric populations, and we worked with ThermoFisher to help them develop a DNA-based method of identifying O groups by sequencing.  We also lead an international group (https://sites.psu.edu/ecolishigella/ ) to identify and name new E. coli O types identified by large sequencing efforts, and to propose the merging of E. coli and Shigella into a single genus.”

QUESTION: We have heard of E. coli O157:H7, a strain that is a foodborne pathogen that causes severe diarrhea. What do those numbers mean? 

ANSWER: For nearly 80 years, E. coli strains have been distinguished by agglutination-based serotyping, meaning ability to bind to antibodies to slightly different antigens in the lipopolysaccharide (O group), capsule (K group) or flagella (H group). There are 187 different O groups, 53 different H groups, and 60 K groups. So, the infamous foodborne pathogen strain of E. coli has O antigen number 157 in its lipopolysaccharide, and H antigen number 7 in its flagellum. Only a few labs in the world still maintain the hundreds of different antibodies needed to run the traditional panel of tests, and one of them is the E. coli Reference Center at Penn State. ECRC is leading efforts to standardize the numbering of these groups.

By: 

Kyria Boundy-Mills, Curator, Phaff Yeast Culture Collection (UCDFST), University of California Davis

Edward Dudley, Director, E. Coli Reference Center (ECRC), Pennsylvania State University

Shannon Manning, Associate Professor, E. Coli Reference Collection (STEC), Michigan State University

John Wertz, Curator, E. coli Genetic Stock Center (CGSC), Yale University

Sources:

https://sites.psu.edu/ecolishigella/

https://www.ifsh.iit.edu/sites/ifsh/files/departments/Edward_Dudley_HTS_2018.pdf