Meiotic sex in Chagas disease parasite Trypanosoma cruzi

Schwabl, Philipp; Imamura, Hideo; Broeck, Frederik Van den; Costales, Jaime A.; Maiguashca-Sánchez, Jalil; Miles, Michael A.; Andersson, Björn; Grijalva, Mario J.; Llewellyn, Martin S.

doi:10.1038/s41467-019-11771-z

Cited by 63 publications

(109 citation statements)

References 78 publications

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“…Median read-depth was 266x across all sites. Of 403 loci targeted from the WGS dataset 1 , 97% (391) were recovered by GLST and 82 contained polymorphism outside of Ecuador. GLST recovered 80 of 87 SNPs previously identified in TBM_2795_CL2 using WGS.…”

Section: Resultsmentioning

confidence: 99%

“…The tree also contains TBM_2795_CL2_wgs (see asterisk). This control sample was genotyped at the same 556 GLST loci using whole-genome sequencing (Illumina HiSeq) data from Schwabl et al 2019 1 .…”

Section: Resultsmentioning

confidence: 99%

“…Isopropanol precipitation was also used to extract DNA from T. cruzi plate clone TBM_2795_CL2. This sample was previously analyzed by WGS 1 and served as a control for GLST method development in this study.…”

Section: Methodsmentioning

confidence: 99%

“…We began our GLST sequence target selection process by screening single-nucleotide variants previously identified in T. cruzi populations from southern Ecuador 1 . Briefly, Schwabl et al sequenced genomic DNA from 45 cloned and 14 non-cloned T. cruzi field isolates on the Illumina HiSeq 2500 platform and mapped resultant 125 nt reads to the TcI-Sylvio reference assembly using default settings in BWA-mem v0.7.3 41 .…”

Section: Methodsmentioning

confidence: 99%

“…Genome-wide single nucleotide polymorphism (SNP) analysis is a powerful and increasingly common approach in the study and surveillance of infectious disease. Understanding patterns of SNP diversity within pathogen genomes and across pathogen populations can resolve fundamental biological questions (e.g., reproductive mechanisms in T. cruzi 1 , reconstruct past 2 and present transmission networks (e.g., Staphylococcus infections within hospitals) 3 or identify the genetic bases of virulence 4,5 and resistance to drugs (see examples from Plasmodium spp. 6,7 ).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide locus sequence typing (GLST) of eukaryotic pathogens

Schwabl¹,

et al. 2020

Preprint

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20Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful 21 inference from pathogen genetic variation, however, is often restrained by limited access to representative 22 target DNA, especially in the study of obligate parasitic species for which ex vivo culture is resource-intensive 23 or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly 24 from vector/host material but are often too complex and expensive for resource-poor settings where infectious 25 diseases prevail. This study proposes a simple, cost-effective 'genome-wide locus sequence typing' (GLST) 26 tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. 27 The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a 28 single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation 29 at under 4 USD per sample. Approximately 100 libraries can be sequenced together in one Illumina MiSeq 30 run. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic 31 agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free 32 metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/µl T. cruzi DNA and further 33 elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing 34 discrete typing units (DTUs) TcI, TcIII, TcIV, and TcVI. The 780 SNP sites we identify in the sample set 35 repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and 36 geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate 37 DTUs. We discuss the advantages, limitations and prospects of our method across a spectrum of 38 epidemiological research. 40Genome-wide single nucleotide polymorphism (SNP) analysis is a powerful and increasingly common 41 approach in the study and surveillance of infectious disease. Understanding patterns of SNP diversity within 42 pathogen genomes and across pathogen populations can resolve fundamental biological questions (e.g., 43 reproductive mechanisms in T. cruzi 1 , reconstruct past 2 and present transmission networks (e.g., 44 Staphylococcus infections within hospitals) 3 or identify the genetic bases of virulence 4,5 and resistance to drugs 45 (see examples from Plasmodium spp. 6,7 ). A number of obstacles, however, complicate access to 46 representative, genome-wide SNP information using modern sequencing tools. Micro-pathogens are often 47 sampled in low quantities and together with large amounts of host/vector tissue, microbiota, or environmental 48 DNA. Sequencing is rarely viable directly from the infection source and studies have often found it necessary 49 to isolate and culture the target organism to higher densities before extracting D...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-wide locus sequence typing (GLST) of eukaryotic pathogens

Schwabl¹,

et al. 2020

Preprint

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Trypanosomiases

Gibson¹

2021

Encyclopedia of Life Sciences

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The human trypanosomiases are vector‐borne tropical diseases that occur in tropical Africa and South America and are caused by parasitic protozoa. Human African trypanosomiasis (or sleeping sickness) is caused by two subspecies of Trypanosoma brucei and is transmitted by the bite of the bloodsucking tsetse fly. Chagas disease occurs in Latin America and is caused by Trypanosoma cruzi . This parasite is transmitted by triatomine bugs, which acquire infection by feeding on infected blood, but pass the parasites on to the next host via their infected faeces. The human trypanosomiases are zoonoses and a range of wild and domestic mammals can act as reservoir hosts for the parasites. There are no vaccines for these diseases and control relies on drug treatment and limiting opportunities for transmission. Key Concepts Human African trypanosomiasis and Chagas disease are both caused by insect‐borne, parasitic trypanosomes, but the diseases and the parasite life cycles are completely different. Control of the trypanosomiases relies on treatment of human patients and reduction of transmission, largely achieved through killing the insect vectors. The human trypanosomiases are zoonotic diseases and a range of wild and domestic mammals act as reservoir hosts for the parasites. Vector‐borne diseases with animal reservoirs have complex epidemiology and are difficult to control. Elimination of Human African trypanosomiasis as a public health problem in sub‐Saharan Africa seems likely if current treatment, surveillance and tsetse control measures are maintained. Animal reservoir hosts are more important in maintaining Human African trypanosomiasis in East Africa than West and Central Africa. Eradication of Chagas disease is thwarted by the longevity of infection in humans, circulation of the parasite in a wide range of animal reservoir hosts and transmission by routes other than the insect vector.

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