An intraspecies Leishmania donovani hybrid from the Indian subcontinent is associated with an atypical phenotype of cutaneous disease

Lypaczewski, Patrick; Thakur, Lovlesh; Jain, Aklank; Kumari, Shikha; Paulini, Kayla; Matlashewski, Greg; Jain, Manju

doi:10.1016/j.isci.2022.103802

Cited by 16 publications

(4 citation statements)

References 38 publications

(114 reference statements)

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“…For example, Kaufer et al used a variation on the Leishmania maxicircle sequences ( ND7 gene) to design PCR–RFLP assays to discriminate nine Leishmania species [ 63 ]. A recent study identified the origin of the intra-species L. donovani hybrid from Himachal Pradesh, India, that was derived from two independent L. donovani parents of the ISC1-Yeti clade from the Nepalese highlands using maxicircle phylogenetics, suggesting the usefulness for examination of intra-species diversity [ 64 ]. Similarly, this study showed that the L. martiniquensis maxicircle was highly homologous to L. enriettii and L. arabica (Fig.…”

Section: Discussionmentioning

confidence: 99%

Identification of a conserved maxicircle and unique minicircles as part of the mitochondrial genome of Leishmania martiniquensis strain PCM3 in Thailand

et al. 2022

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Background The mitochondrial DNA of trypanosomatids, including Leishmania, is known as kinetoplast DNAs (kDNAs). The kDNAs form networks of hundreds of DNA circles that are evidently interlocked and require complex RNA editing. Previous studies showed that kDNA played a role in drug resistance, adaptation, and survival of Leishmania. Leishmania martiniquensis is one of the most frequently observed species in Thailand, and its kDNAs have not been illustrated. Methods This study aimed to extract the kDNA sequences from Illumina short-read and PacBio long-read whole-genome sequence data of L. martiniquensis strain PCM3 priorly isolated from the southern province of Thailand. A circular maxicircle DNA was reconstructed by de novo assembly using the SPAdes program, while the minicircle sequences were retrieved and assembled by the rKOMIC tool. The kDNA contigs were confirmed by blasting to the NCBI database, followed by comparative genomic and phylogenetic analysis. Results We successfully constructed the complete circular sequence of the maxicircle (19,008 bp) and 214 classes of the minicircles from L. martiniquensis strain PCM3. The genome comparison and annotation showed that the maxicircle structure of L. martiniquensis strain PCM3 was similar to those of L. enriettii strain LEM3045 (84.29%), L. arabica strain LEM1108 (82.79%), and L. tarentolae (79.2%). Phylogenetic analysis also showed unique evolution of the minicircles of L. martiniquensis strain PCM3 from other examined Leishmania species. Conclusions This was the first report of the complete maxicircle and 214 minicircles of L. martiniquensis strain PCM3 using integrated whole-genome sequencing data. The information will be helpful for further improvement of diagnosis methods and monitoring genetic diversity changes of this parasite. Graphical abstract

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Section: Discussionmentioning

confidence: 99%

Identification of a conserved maxicircle and unique minicircles as part of the mitochondrial genome of Leishmania martiniquensis strain PCM3 in Thailand

et al. 2022

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“…Sequencing of Leishmania is complicated: they have either a flagellated (promastigote) or aflagellated form (amistagote) [ 147 ]. Genomes have been sequenced in both stages [ 148 , 149 , 150 , 151 , 152 ], and differences exist in genome architecture: aneuploidy in amastigotes cultivated from Syrian golden hamsters was lower compared to in vitro promastigotes [ 153 ]. Similarly, clinical samples of L. donovani also exhibited lower levels of aneuploidy, exemplified by sequencing genomes directly from leishmaniasis specimens in India via HC, using 218,904 (120 nt) baits spanning 26 Mbp of the 32 Mbp genome [ 152 ].…”

Section: Hybrid-capture Target Enrichment For Pathogensmentioning

confidence: 99%

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Quek,

2024

Pathogens

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High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens—bacteria, fungi, parasites and viruses—including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.

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“…Furthermore, intraspecies hybridization in L. donovani has been demonstrated to cause a phenotypic reposition from visceral to cutaneous form, causing an atypical CL phenotype. The recombinant derived from a CL focus in Himachal Pradesh resulted from genomic hybridization between the two parental types of L. donovani , which belong to the Yeti ISC1 variant of the Nepalese highlands [ 87 ]. In atypical CL cases due to L. donovani in Sri Lanka, sodium stibogluconate is the opted treatment.…”

Section: Atypical Presentations Of Leishmaniasismentioning

confidence: 99%

Unusual Observations in Leishmaniasis—An Overview

et al. 2023

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Leishmaniasis significantly affects the population of the tropics and subtropics. Clinical features and infective species of Leishmania are the primary factors driving the direction of diagnosis. The rise in incidences of atypical presentations present a challenge in patient treatment. Knowledge of unusual/rare presentations can aid in having a broader perspective for including the different aspects during the examination and thus avoid misdiagnosis. A comprehensive literature survey was performed to present the array of atypical presentations confounding clinicians which have been seen in leishmaniasis. Case reports of unusual findings based on the localizations and morphology of lesions and infective species and the predominant geographical sites over almost five decades highlight such presentations in the population. Information regarding the clinical features recorded in the patient and the chosen treatment was extracted to put forward the preferred drug regimen in such cases. This comprehensive review presents various unusual observations seen in visceral leishmaniasis, post-kala-azar dermal leishmaniasis, cutaneous leishmaniasis, and mucocutaneous leishmaniasis. It highlights the need to consider such features in association with differential diagnosis to facilitate proper treatment of the patient.

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An intraspecies Leishmania donovani hybrid from the Indian subcontinent is associated with an atypical phenotype of cutaneous disease

Cited by 16 publications

References 38 publications

Identification of a conserved maxicircle and unique minicircles as part of the mitochondrial genome of Leishmania martiniquensis strain PCM3 in Thailand

Identification of a conserved maxicircle and unique minicircles as part of the mitochondrial genome of Leishmania martiniquensis strain PCM3 in Thailand

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Unusual Observations in Leishmaniasis—An Overview

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