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<mods:title id="99407B9F8FFE5F2B18A3886A36E5ECCA">Molecular dissection of laboratory contamination between two schistosome populations</mods:title>
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<mods:namePart id="F7CB1C5CB4733121D9179140774358A2">Platt, Roy N.</mods:namePart>
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<mods:namePart id="E0F1F7DE5E71BB92A4D3B5451ECFFA92">Li, Xue</mods:namePart>
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<mods:namePart id="3BDAA8720B2D51B33B6E015F5F4A25E6">Morales, Madison</mods:namePart>
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<mods:namePart id="EC07EFDEC7886EA4528846869B2A7985">Chevalier, Frédéric D.</mods:namePart>
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<mods:title id="7CCCE41C6844501C14A51B81A2DE031B">Parasites & Vectors</mods:title>
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<mods:date id="17A4E3B33DD915BA1463156EB59340BD">2024</mods:date>
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<mods:title id="046C8B8A95E45F2FFC7716C0C277EF46">528</mods:title>
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<mods:number id="158C8B0788413BA810BD045E77603B06">17</mods:number>
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<mods:identifier id="A5ECD85DC1D71FD80476F5AB35E5EE09" type="ISSN">1756-3305</mods:identifier>
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<treatment id="03D96E3AFFBEFFB672EAFF1DFA14FB0E" LSID="urn:lsid:plazi:treatment:03D96E3AFFBEFFB672EAFF1DFA14FB0E" httpUri="http://treatment.plazi.org/id/03D96E3AFFBEFFB672EAFF1DFA14FB0E" lastPageNumber="2" pageId="1" pageNumber="2">
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<emphasis id="B904033EFFBEFFB67369FF1DFE2AFEA5" box="[297,427,254,279]" italics="true" pageId="1" pageNumber="2">Schistosoma</emphasis>
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<taxonomicName id="4C70A4AFFFBEFFB673F0FF1DFD8BFEA5" authority=", Parasite" authorityName="Parasite" box="[432,522,254,279]" class="Gammaproteobacteria" family="Enterobacteriaceae" genus="Salmonella" kingdom="Bacteria" order="Enterobacteriales" pageId="1" pageNumber="2" phylum="Proteobacteria" rank="species" species="mansoni">
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<emphasis id="B904033EFFBEFFB673F0FF1DFD8BFEA5" box="[432,522,254,279]" italics="true" pageId="1" pageNumber="2">mansoni</emphasis>
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,
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<keyWord id="3086844BFFBEFFB67054FF1DFDE6FEA5" box="[532,615,254,279]" pageId="1" pageNumber="2">Parasite</keyWord>
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,
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<keyWord id="3086844BFFBEFFB67030FF1DFCEBFEA5" box="[624,874,254,279]" pageId="1" pageNumber="2">Laboratory populations</keyWord>
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,
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<keyWord id="3086844BFFBEFFB67133FF1DFB94FEA5" box="[883,1045,254,279]" pageId="1" pageNumber="2">Contamination</keyWord>
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,
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<keyWord id="3086844BFFBEFFB6765EFF1DFBEBFEA5" box="[1054,1130,254,279]" pageId="1" pageNumber="2">SmBRE</keyWord>
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,
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<keyWord id="3086844BFFBEFFB67632FF1DFB2EFEA5" box="[1138,1199,254,279]" pageId="1" pageNumber="2">SmLE</keyWord>
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,
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<keyWord id="3086844BFFBEFFB676F7FF1DFE94FE85" pageId="1" pageNumber="2">Population genomics</keyWord>
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,
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<keyWord id="3086844BFFBEFFB6735EFEFDFE53FE85" box="[286,466,286,311]" pageId="1" pageNumber="2">Pool-sequencing</keyWord>
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<emphasis id="B904033EFFBEFFB672D7FE47FEADFE0F" bold="true" box="[151,300,420,445]" pageId="1" pageNumber="2">Background</emphasis>
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<paragraph id="8BCFDF2CFFBEFFB672D7FE26FD15FB2F" blockId="1.[151,775,420,1885]" pageId="1" pageNumber="2">
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Laboratory research with pathogen populations or cell lines requires rigorous safeguards to prevent contamination and to ensure repeatability of results from different laboratories. Nevertheless, a growing body of literature suggests that contamination (or mislabeling) of laboratory pathogens is surprisingly common. For example, phylogenetic studies of laboratory-adapted malaria parasite lines reveal widespread evidence for these issues [
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||||
<bibRefCitation id="EFE1A2DDFFBEFFB67373FD26FEC1FD6F" author="Mu J & Awadalla P & Duan J & McGee KM & Joy DA & McVean GAT" box="[307,320,709,733]" pageId="1" pageNumber="2" refId="ref7557" refString="1. Mu J, Awadalla P, Duan J, McGee KM, Joy DA, McVean GAT, et al. Recombination hotspots and population structure in Plasmodium falciparum. PLoS Biol. 2005; 3: e 335." type="journal volume" year="2005">1</bibRefCitation>
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–3]. Contamination from positive control samples has resulted in extensive false-positive diagnoses in hospital diagnostic laboratories working with
|
||||
<taxonomicName id="4C70A4AFFFBEFFB67291FCC6FD8CFC8F" authorityName="Lehmann & Neumann" authorityYear="1896" baseAuthorityName="Zopf" baseAuthorityYear="1883" box="[209,525,805,829]" class="Actinobacteridae" family="Mycobacteriaceae" genus="Mycobacterium" kingdom="Bacteria" order="Actinomycetales" pageId="1" pageNumber="2" phylum="Actinobacteria" rank="species" species="tuberculosis">
|
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<emphasis id="B904033EFFBEFFB67291FCC6FD8CFC8F" box="[209,525,805,829]" italics="true" pageId="1" pageNumber="2">Mycobacterium tuberculosis</emphasis>
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,
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<taxonomicName id="4C70A4AFFFBEFFB6705BFCC6FD50FC8F" box="[539,721,805,829]" class="Gammaproteobacteria" family="Enterobacteriaceae" genus="Salmonella" kingdom="Bacteria" order="Enterobacteriales" pageId="1" pageNumber="2" phylum="Proteobacteria" rank="species" species="undetermined">
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<emphasis id="B904033EFFBEFFB6705BFCC6FD18FC8F" box="[539,665,805,829]" italics="true" pageId="1" pageNumber="2">Salmonella</emphasis>
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spp.
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, and enterococci [
|
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<bibRefCitation id="EFE1A2DDFFBEFFB6736BFCA6FEB9FCEF" author="Jasmer RM & Roemer M & Hamilton J & Bunter J & Braden CR & Shinnick TM" box="[299,312,837,861]" pageId="1" pageNumber="2" pagination="1260 - 3" refId="ref7700" refString="4. Jasmer RM, Roemer M, Hamilton J, Bunter J, Braden CR, Shinnick TM, et al. A prospective, multicenter study of laboratory cross-contamination of Mycobacterium tuberculosis cultures. Emerg Infect Dis. 2002; 8: 1260 - 3." type="journal article" year="2002">4</bibRefCitation>
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–
|
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<bibRefCitation id="EFE1A2DDFFBEFFB67308FCA5FED4FCEF" author="Katz KC & McGeer A & Low DE & Willey BM" box="[328,341,838,861]" pageId="1" pageNumber="2" pagination="2686 - 8" refId="ref7849" refString="7. Katz KC, McGeer A, Low DE, Willey BM. Laboratory contamination of specimens with quality control strains of vancomycin-resistant enterococci in Ontario. J Clin Microbiol. 2002; 40: 2686 - 8." type="journal article" year="2002">7</bibRefCitation>
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]. Finally, methods like isozyme analysis, human leukocyte antigen (HLA) identity testing, and DNA fingerprinting have exposed misidentification of lymphoma, hematopoietic, and ovarian carcinoma cell lines as a result of cross-contamination [
|
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<bibRefCitation id="EFE1A2DDFFBEFFB670DEFC26FD2AFC6F" author="Liscovitch M & Ravid D." box="[670,683,965,989]" pageId="1" pageNumber="2" pagination="350 - 2" refId="ref7889" refString="8. Liscovitch M, Ravid D. A case study in misidentification of cancer cell lines: MCF- 7 / AdrR cells (re-designated NCI / ADR-RES) are derived from OVCAR- 8 human ovarian carcinoma cells. Cancer Lett. 2007; 245: 350 - 2." type="journal article" year="2007">8</bibRefCitation>
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–
|
||||
<bibRefCitation id="EFE1A2DDFFBEFFB670FCFC26FD56FC6F" author="Drexler HG & MacLeod RA & Dirks WG" box="[700,727,965,989]" pageId="1" pageNumber="2" pagination="3495 - 6" refId="ref7970" refString="10. Drexler HG, MacLeod RA, Dirks WG. Cross-contamination: HS-Sultan is not a myeloma but a Burkitt lymphoma cell line. Blood. 2001; 98: 3495 - 6." type="journal article" year="2001">10</bibRefCitation>
|
||||
]. In many cases, the contamination may go unnoticed, particularly when no change is observed in pathogen phenotypes or when changes are subtle. As a result, the National Institutes of Health (NIH) and other funding agencies now require provision of protocols for validating the identity of the pathogens under study.
|
||||
</paragraph>
|
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<paragraph id="8BCFDF2CFFBEFFB672EDFB45FEA0FA6F" blockId="1.[151,775,420,1885]" pageId="1" pageNumber="2">
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A second process—rapid evolution—can also result in genomic and phenotypic changes in pathogen populations over a short time period [
|
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<bibRefCitation id="EFE1A2DDFFBEFFB6705DFB06FDB9FB4F" author="Messer PW & Petrov DA" box="[541,568,1253,1277]" pageId="1" pageNumber="2" pagination="659 - 69" refId="ref8005" refString="11. Messer PW, Petrov DA. Population genomics of rapid adaptation by soft selective sweeps. Trend Ecol Evol. 2013; 28: 659 - 69." type="journal article" year="2013">11</bibRefCitation>
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]. Rapid evolution of microbial populations in response to drug pressure, or to avoid immune attack, is ubiquitous. Evolution can also be surprisingly rapid in helminth parasites such as schistosomes. For example, selection for drug resistance [12,
|
||||
<bibRefCitation id="EFE1A2DDFFBEFFB67307FA66FEE3FA2F" author="Rogers SH & Bueding E." box="[327,354,1413,1437]" pageId="1" pageNumber="2" pagination="1057 - 8" refId="ref8087" refString="13. Rogers SH, Bueding E. Hycanthone resistance: development in Schistosoma mansoni. Science. 1971; 172: 1057 - 8." type="journal article" year="1971">13</bibRefCitation>
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] or cercarial shedding number [
|
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<bibRefCitation id="EFE1A2DDFFBEFFB670A3FA66FD7FFA2F" author="Gower CM & Webster JP" box="[739,766,1413,1437]" pageId="1" pageNumber="2" pagination="1178 - 84" refId="ref8113" refString="14. Gower CM, Webster JP. Fitness of indirectly transmitted pathogens: restraint and constraint. Evolution. 2004; 58: 1178 - 84." type="journal article" year="2004">14</bibRefCitation>
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] can substantially alter parasite phenotypes in <10 generations.
|
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</paragraph>
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Te life cycle of schistosome parasites can be maintained in the laboratory using freshwater snail intermediate hosts and rodents as definitive hosts. Our laboratory maintains several populations of
|
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<emphasis id="B904033EFFBEFFB670EFF9A6FEC5F9CF" italics="true" pageId="1" pageNumber="2">
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Schistosoma
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, including two parasite populations originating from
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, SmLE and SmBRE. We have previously investigated these two populations in great detail, and we have reported striking differences in virulence, sporocyst growth, cercarial shedding, and immunopathology between them [
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<bibRefCitation id="EFE1A2DDFFBEFFB67008F8E6FDE2F8AF" author="Jutzeler KS & Le Clec'h W & Chevalier FD & Anderson TJC" box="[584,611,1797,1821]" pageId="1" pageNumber="2" refId="ref8141" refString="15 Jutzeler KS, Le Clec'h W, Chevalier FD, Anderson TJC. Contribution of parasite and host genotype to immunopathology of Schistosome infections. Parasit Vector. 2024; 17: 203." type="journal volume" year="2024">15</bibRefCitation>
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–
|
||||
<bibRefCitation id="EFE1A2DDFFBEFFB67033F8E6FD0FF8AF" author="Le Clec'h W & Chevalier FD & Jutzeler K & Anderson TJC" box="[627,654,1797,1821]" pageId="1" pageNumber="2" refId="ref8260" refString="18 Le Clec'h W, Chevalier FD, Jutzeler K, Anderson TJC. No evidence for Schistosome parasite fitness trade-offs in the intermediate and definitive host. Parasit Vector. 2023; 16: 132." type="journal volume" year="2023">18</bibRefCitation>
|
||||
]. SmBRE exhibited lower fitness than SmLE for multiple life history traits in both the intermediate and definitive host. However, we noticed a drastic change in phenotypes typical for the SmBRE population starting in 2021. Over time, we noticed increased snail infectivity, higher cercarial shedding, and increased worm burden in SmBRE, while SmLE phenotypes remained relatively unchanged. Tese observations led us to speculate that the changes observed in the low-fitness SmBRE parasites could have resulted from two processes: (i) laboratory contamination with the more efficient SmLE population or (ii) selection of de novo mutations within the SmBRE population leading to increased fitness.
|
||||
</paragraph>
|
||||
<paragraph id="8BCFDF2CFFBEFFB67102FCE7FA14FB0E" blockId="1.[813,1437,420,1212]" pageId="1" pageNumber="2">To evaluate these alternative scenarios, we sequenced pools of male and female worms from SmBRE and SmLE parasites collected at 10 time intervals over a 7-year period (2016–2023). We monitored allele frequency changes across the genome over time, both within and between the SmBRE and SmLE populations, to answer the following questions: (i) How stable are allele frequencies in laboratory schistosome populations? (ii) Do phenotypic changes in SmBRE reflect the selection of de novo mutations or laboratory contamination? (iii) If contamination occurred, what can we learn about the dynamics of genomic changes following admixture? (iv) Can we develop molecular approaches to verify laboratory schistosome populations and detect contamination?</paragraph>
|
||||
</subSubSection>
|
||||
</treatment>
|
||||
</document>
|
||||
201
data/03/F2/87/03F287BA895FFFF4FCD20B39FD5FEF19.xml
Normal file
201
data/03/F2/87/03F287BA895FFFF4FCD20B39FD5FEF19.xml
Normal file
|
|
@ -0,0 +1,201 @@
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<mods:title id="64C34E7D39976E303EB3C769C989F9AB">Population genetics and molecular xenomonitoring of Biomphalaria freshwater snails along the southern shoreline of Lake Malawi, Malawi</mods:title>
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<mods:namePart id="3BD45DEC5F926AABC408CC2FDCDAE6D5">Chammudzi, Priscilla</mods:namePart>
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<mods:affiliation id="D64FC49AB5624EA97E8DADCA08669B1D">6,7 & 6,7</mods:affiliation>
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<mods:namePart id="84FD0037FBE5F34DDCDC491358A38707">Lally, David</mods:namePart>
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<mods:affiliation id="1DC8B1D3CEDD49CA342AA38C69AA2798">6,7 & 6,7</mods:affiliation>
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<mods:namePart id="C58B02180EDF8A665EC84A8BA92AE9C8">Namacha, Gladys</mods:namePart>
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<mods:affiliation id="BA03BB262D91E803C750AA29620DBFA5">6,7 & 6,7</mods:affiliation>
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<mods:namePart id="F33C67CEC2877B2FD62912DAC687100E">LaCourse, James E.</mods:namePart>
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<mods:affiliation id="11877D9CA2DEF6E1136E1B8ED4A2D003">6,7</mods:affiliation>
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<mods:namePart id="7DF72DD598BB3C58490D675D0510A7EB">Kayuni, Sekeleghe A.</mods:namePart>
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<mods:namePart id="318886DCB7D1BD1B90CA86473561029A">Webster, Bonnie L.</mods:namePart>
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<mods:affiliation id="AD61C398ADDD46D85459B578FEC6F6CF">6,7 & 6,7 & 1,2 & * & †</mods:affiliation>
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<mods:namePart id="86ECA51539AF4D05C33AE983A1B34DEA">Musaya, Janelisa</mods:namePart>
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<mods:namePart id="71C492351B2439093833E3CA9206B5D2">Stothard, J. Russell</mods:namePart>
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<mods:title id="BA418089FCB847B487A71E9644061DD5">Parasites & Vectors</mods:title>
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<mods:part id="F7E7F5FBFF519BD84E32318857B36B44">
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<mods:date id="206B830E259593C603DCCDB3EE724E77">2024</mods:date>
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<mods:number id="294FD1C7EFBF8A61CA43D1AD49465342">17</mods:number>
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<treatment id="03F287BA895FFFF4FCD20B39FD5FEF19" LSID="urn:lsid:plazi:treatment:03F287BA895FFFF4FCD20B39FD5FEF19" httpUri="http://treatment.plazi.org/id/03F287BA895FFFF4FCD20B39FD5FEF19" lastPageId="6" lastPageNumber="7" pageId="5" pageNumber="6">
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<subSubSection id="C3416527895FFFF7FCD20B39FA14EBEA" pageId="5" pageNumber="6" type="nomenclature">
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<heading id="D0AC81C0895FFFF7FCD20B39FB5FEB2A" bold="true" box="[813,1239,1849,1872]" fontSize="9" level="2" pageId="5" pageNumber="6" reason="7">
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<emphasis id="B92FEABE895FFFF7FCD20B39FB5FEB2A" bold="true" box="[813,1239,1849,1872]" italics="true" pageId="5" pageNumber="6">
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Confirmatory
|
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<taxonomicName id="4C5B4D2F895FFFF7FC440B39FBC7EB2A" ID-CoL="9GTQC" authority="ND" authorityName="ND" box="[955,1103,1849,1872]" class="Trematoda" family="Schistosomatidae" genus="Schistosoma" kingdom="Animalia" order="Diplostomida" pageId="5" pageNumber="6" phylum="Platyhelminthes" rank="species" species="mansoni">S. mansoni ND</taxonomicName>
|
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5 genotyping
|
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</emphasis>
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</heading>
|
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</paragraph>
|
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<paragraph id="8BE436AC895FFFF7FCD20B58FA14EBEA" blockId="5.[813,1437,1849,1936]" pageId="5" pageNumber="6">All samples that successfully amplified all three target loci were subjected to a secondary singleplex PCR</paragraph>
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</subSubSection>
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<subSubSection id="C3416527895CFFF4FF680CECFD5FEF19" pageId="6" pageNumber="7" type="description">
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<paragraph id="8BE436AC895CFFF4FF680CECFD8FED99" blockId="6.[151,775,235,483]" pageId="6" pageNumber="7">
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to amplify only the
|
||||
<taxonomicName id="4C5B4D2F895CFFF4FE7D0CECFDBCED79" authority="ND" authorityName="ND" box="[386,564,235,259]" class="Trematoda" family="Schistosomatidae" genus="Schistosoma" kingdom="Animalia" order="Diplostomida" pageId="6" pageNumber="7" phylum="Platyhelminthes" rank="species" species="mansoni">
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<emphasis id="B92FEABE895CFFF4FE7D0CECFE76ED79" box="[386,510,236,259]" italics="true" pageId="6" pageNumber="7">S. mansoni</emphasis>
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ND
|
||||
</taxonomicName>
|
||||
5 locus for Sanger sequencing [
|
||||
<bibRefCitation id="EFCA4B5D895CFFF4FEDB0D0BFEB6ED59" author="Archer J & Yeo SM & Gadd G & Pennance T & Cunningham LJ & Juhasz A" box="[292,318,267,291]" pageId="6" pageNumber="7" refId="ref10764" refString="24. Archer J, Yeo SM, Gadd G, Pennance T, Cunningham LJ, Juhasz A, et al. Development, validation, and pilot application of a high throughput molecular xenomonitoring assay to detect Schistosoma mansoni and other trematode species within Biomphalaria freshwater snail hosts. Curr Res Parasitol Vector-Borne Dis. 2024; 5: 100174." type="journal volume" year="2024">24</bibRefCitation>
|
||||
]. Amplicons were visualised in the same manner as for the multiplex molecular xenomonitoring PCRs.
|
||||
<taxonomicName id="4C5B4D2F895CFFF4FF180D4BFD85ED19" authority="ND" authorityName="ND" box="[231,525,331,355]" class="Trematoda" family="Schistosomatidae" genus="Schistosoma" kingdom="Animalia" order="Diplostomida" pageId="6" pageNumber="7" phylum="Platyhelminthes" rank="species" species="mansoni">
|
||||
<emphasis id="B92FEABE895CFFF4FF180D4BFE5EED19" box="[231,470,331,355]" italics="true" pageId="6" pageNumber="7">Schistosoma mansoni</emphasis>
|
||||
ND
|
||||
</taxonomicName>
|
||||
5 PCR products were purified as described above and Sanger sequenced in the forward direction using a dilution of the ND52 forward primer. Sequence data were visualised, trimmed, edited and identified as described above.
|
||||
</paragraph>
|
||||
<paragraph id="8BE436AC895CFFF4FF680E0BFD5FEF19" blockId="6.[151,777,523,868]" pageId="6" pageNumber="7">
|
||||
<emphasis id="B92FEABE895CFFF4FF680E0BFD59EE59" box="[151,721,523,547]" italics="true" pageId="6" pageNumber="7">Templeton Crandall and Sing haplotype network</emphasis>
|
||||
To assess
|
||||
<taxonomicName id="4C5B4D2F895CFFF4FF1E0E2CFE03EE39" authority="ND" authorityName="ND" box="[225,395,555,579]" class="Trematoda" family="Schistosomatidae" genus="Schistosoma" kingdom="Animalia" order="Diplostomida" pageId="6" pageNumber="7" phylum="Platyhelminthes" rank="species" species="mansoni">
|
||||
<emphasis id="B92FEABE895CFFF4FF1E0E2CFED1EE39" box="[225,345,556,579]" italics="true" pageId="6" pageNumber="7">S. mansoni</emphasis>
|
||||
ND
|
||||
</taxonomicName>
|
||||
5 diversity, we performed a haplotype analysis using all generated
|
||||
<taxonomicName id="4C5B4D2F895CFFF4FE0E0E4CFD1AEE19" authority="ND" authorityName="ND" box="[497,658,587,611]" class="Trematoda" family="Schistosomatidae" genus="Schistosoma" kingdom="Animalia" order="Diplostomida" pageId="6" pageNumber="7" phylum="Platyhelminthes" rank="species" species="mansoni">
|
||||
<emphasis id="B92FEABE895CFFF4FE0E0E4CFDEDEE19" box="[497,613,588,611]" italics="true" pageId="6" pageNumber="7">S. mansoni</emphasis>
|
||||
ND
|
||||
</taxonomicName>
|
||||
5 sequence data. To do this, a MAFFT alignment was performed using sequence data within Geneious Prime (default MAFFT parameter settings). Te MAFFT alignment was then visualised, examined and edited as described above. Te alignment was then exported from Geneious Prime in Nexus file format and imported into PopART version 1.7. Within PopART, a TCS haplotype network was generated to allow examination of haplotype group structuring.
|
||||
</paragraph>
|
||||
</subSubSection>
|
||||
</treatment>
|
||||
</document>
|
||||
Loading…
Reference in a new issue