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Pilling OA, Sundararaman SA, Brisson D, Beiting DP. Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment. PLoS Pathog 2024; 20:e1012418. [PMID: 39264872 PMCID: PMC11392400 DOI: 10.1371/journal.ppat.1012418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionized microbiology, but many microbes exist at low abundance in their natural environment and/or are difficult, if not impossible, to culture in the laboratory. This makes it challenging to use HTS to study the genomes of many important microbes and pathogens. In this review, we discuss the development and application of selective whole genome amplification (SWGA) to allow whole or partial genomes to be sequenced for low abundance microbes directly from complex biological samples. We highlight ways in which genomic data generated by SWGA have been used to elucidate the population dynamics of important human pathogens and monitor development of antimicrobial resistance and the emergence of potential outbreaks. We also describe the limitations of this method and propose some potential innovations that could be used to improve the quality of SWGA and lower the barriers to using this method across a wider range of infectious pathogens.
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Affiliation(s)
- Olivia A Pilling
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sesh A Sundararaman
- Department of Pediatrics, Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dustin Brisson
- Department of Biology, School of Arts & Sciences, University of Pennsylvania, Pennsylvania, United States of America
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Martín-Sánchez J, Díaz-Sáez V, Morillas-Márquez F, Corpas-López V, Ibáñez-De Haro P, Torres-Llamas A, Morales-Yuste M. Wild rabbits are Leishmania infantum reservoirs in southeastern Spain. Zoonoses Public Health 2024; 71:584-590. [PMID: 38693773 DOI: 10.1111/zph.13139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/04/2024] [Accepted: 04/20/2024] [Indexed: 05/03/2024]
Abstract
OBJECTIVE We contribute to the understanding of the transmission dynamics of Leishmania infantum suggesting the involvement of rabbits as wild reservoirs. RESULTS The prevalence of infection was 86.0% (270/314 wild rabbits) ranging from 18.2% to 100% in natural geographical regions. The estimated average parasite load was 324.8 [CI 95% 95.3-554.3] parasites per mg of ear lobe ranging from 0 to 91,597 parasites/mg per tissue section. CONCLUSIONS A positive correlation was found between skin parasite load in wild rabbits and human incidence with evidence of the presence of the same L. infantum genotypes in rabbits and humans, providing new epidemiological and biological basis for the consideration of wild rabbits as a relevant L. infantum wild reservoir. Molecular parasite surveillance reflects the great genotypic variability of the parasite population in wild rabbits. Most of these genotypes have also been found to infect humans, dogs and sandflies in the region. Our findings also highlight that direct genotyping of the parasite in host tissues should be used for molecular surveillance of the parasite instead of cultured isolates.
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Monsieurs P, Cloots K, Uranw S, Banjara MR, Ghimire P, Burza S, Hasker E, Dujardin JC, Domagalska MA. Source Tracing of Leishmania donovani in Emerging Foci of Visceral Leishmaniasis, Western Nepal. Emerg Infect Dis 2024; 30:611-613. [PMID: 38407178 PMCID: PMC10902524 DOI: 10.3201/eid3003.231160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
We sequenced Leishmania donovani genomes in blood samples collected in emerging foci of visceral leishmaniasis in western Nepal. We detected lineages very different from the preelimination main parasite population, including a new lineage and a rare one previously reported in eastern Nepal. Our findings underscore the need for genomic surveillance.
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Gritti T, Carra E, Van der Auwera G, Solana JC, Gaspari V, Trincone S, Ortalli M, Rabitti A, Reggiani A, Rugna G, Varani S. Molecular Typing of Leishmania spp. Causing Tegumentary Leishmaniasis in Northeastern Italy, 2014-2020. Pathogens 2023; 13:19. [PMID: 38251327 PMCID: PMC10820635 DOI: 10.3390/pathogens13010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/12/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
Tegumentary leishmaniasis (TL) is endemic but neglected in southern Europe. Therefore, this study aimed to analyze the Leishmania strains causing TL cases in northeastern Italy, where an upsurge of TL cases has been observed in the last decade. Sections from 109 formalin-fixed and paraffin-embedded (FFPE) biopsies of skin and mucosal tissues were collected from TL cases in the selected area. Two DNA targets were amplified and sequenced: the ribosomal internal transcribed spacer 1 (ITS1) and the heat-shock protein 70 gene (hsp70). An in silico analysis was also performed on 149 genomes belonging to the Leishmania donovani complex. A total of 88 out of 109 (80.7%) samples from 83 TL cases were successfully typed by ITS1 and/or hsp70. ITS1 analysis identified L. infantum in 67 cases (91.8%), while L. major (n = 4, 5.5%) and L. tropica (n = 2, 2.7%) were detected in the remaining cases that were categorized as imported. Further, the hsp70 typing of 75 autochthonous cases showed the presence of eight distinct sequence variants belonging to the Leishmania donovani complex, with high genetic variability when compared to known L. infantum populations. In conclusion, our findings show that peculiar L. infantum variants are emerging in the novel focus on TL in northeastern Italy.
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Affiliation(s)
- Tommaso Gritti
- Department of Medical and Surgical Sciences, University of Bologna, 40126 Bologna, Italy; (T.G.); (M.O.); (S.V.)
| | - Elena Carra
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 25124 Brescia, Italy; (E.C.); (A.R.)
| | | | - José Carlos Solana
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28022 Madrid, Spain
- WHO Collaborating Centre for Leishmaniasis, National Center for Microbiology, Instituto de Salud Carlos III, 28022 Majadahonda, Spain
| | - Valeria Gaspari
- Unit of Dermatology, Head and Neck Department, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | - Silvana Trincone
- Unit of Dermatology, Ospedale Bufalini, Azienda Unità Sanitaria Locale della Romagna, 47521 Cesena, Italy;
| | - Margherita Ortalli
- Department of Medical and Surgical Sciences, University of Bologna, 40126 Bologna, Italy; (T.G.); (M.O.); (S.V.)
- Unit of Microbiology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | - Alice Rabitti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 25124 Brescia, Italy; (E.C.); (A.R.)
| | - Alessandro Reggiani
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 25124 Brescia, Italy; (E.C.); (A.R.)
| | - Gianluca Rugna
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, 25124 Brescia, Italy; (E.C.); (A.R.)
| | - Stefania Varani
- Department of Medical and Surgical Sciences, University of Bologna, 40126 Bologna, Italy; (T.G.); (M.O.); (S.V.)
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Jara M, Arevalo J, Llanos-Cuentas A, den Broeck FV, Domagalska MA, Dujardin JC. Unveiling drug-tolerant and persister-like cells in Leishmania braziliensis lines derived from patients with cutaneous leishmaniasis. Front Cell Infect Microbiol 2023; 13:1253033. [PMID: 37790908 PMCID: PMC10543814 DOI: 10.3389/fcimb.2023.1253033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/21/2023] [Indexed: 10/05/2023] Open
Abstract
Introduction Resistance against anti-Leishmania drugs (DR) has been studied for years, giving important insights into long-term adaptations of these parasites to drugs, through genetic modifications. However, microorganisms can also survive lethal drug exposure by entering into temporary quiescence, a phenomenon called drug tolerance (DT), which is rather unexplored in Leishmania. Methods We studied a panel of nine Leishmania braziliensis strains highly susceptible to potassium antimonyl tartrate (PAT), exposed promastigotes to lethal PAT pressure, and compared several cellular and molecular parameters distinguishing DT from DR. Results and discussion We demonstrated in vitro that a variable proportion of cells remained viable, showing all the criteria of DT and not of DR: i) signatures of quiescence, under drug pressure: reduced proliferation and significant decrease of rDNA transcription; ii) reversibility of the phenotype: return to low IC50 after removal of drug pressure; and iii) absence of significant genetic differences between exposed and unexposed lineages of each strain and absence of reported markers of DR. We found different levels of quiescence and DT among the different L. braziliensis strains. We provide here a new in-vitro model of drug-induced quiescence and DT in Leishmania. Research should be extended in vivo, but the current model could be further exploited to support R&D, for instance, to guide the screening of compounds to overcome the quiescence resilience of the parasite, thereby improving the therapy of leishmaniasis.
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Affiliation(s)
- Marlene Jara
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Jorge Arevalo
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Frederik Van den Broeck
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
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de Azevedo SLC, Catanho M, Guimarães ACR, Galvão TC. Genomic surveillance: a potential shortcut for effective Chagas disease management. Mem Inst Oswaldo Cruz 2023; 117:e220164. [PMID: 36700581 PMCID: PMC9870261 DOI: 10.1590/0074-02760220164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/29/2022] [Indexed: 01/27/2023] Open
Abstract
Chagas disease is an enduring public health issue in many Latin American countries, receiving insufficient investment in research and development. Strategies for disease control and management currently lack efficient pharmaceuticals, commercial diagnostic kits with improved sensitivity, and vaccines. Genetic heterogeneity of Trypanosoma cruzi is a key aspect for novel drug design since pharmacological technologies rely on the degree of conservation of parasite target proteins. Therefore, there is a need to expand the knowledge regarding parasite genetics which, if fulfilled, could leverage Chagas disease research and development, and improve disease control strategies. The growing capacity of whole-genome sequencing technology and its adoption as disease surveillance routine may be key for solving this long-lasting problem.
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Affiliation(s)
- Sophia Lincoln Cardoso de Azevedo
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brasil,Universidade Federal Fluminense, Niterói, RJ, Brasil
| | - Marcos Catanho
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Ana Carolina Ramos Guimarães
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brasil
| | - Teca Calcagno Galvão
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genômica Funcional e Bioinformática, Rio de Janeiro, RJ, Brasil,+ Corresponding author:
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Reimão JQ, Coser EM, Lee MR, Coelho AC. Laboratory Diagnosis of Cutaneous and Visceral Leishmaniasis: Current and Future Methods. Microorganisms 2020; 8:E1632. [PMID: 33105784 PMCID: PMC7690623 DOI: 10.3390/microorganisms8111632] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 02/03/2023] Open
Abstract
Leishmaniasis is a neglected tropical disease with two main clinical forms: cutaneous and visceral leishmaniasis. Diagnosis of leishmaniasis is still a challenge, concerning the detection and correct identification of the species of the parasite, mainly in endemic areas where the absence of appropriate resources is still a problem. Most accessible methods for diagnosis, particularly in these areas, do not include the identification of each one of more than 20 species responsible for the disease. Here, we summarize the main methods used for the detection and identification of leishmaniasis that can be performed by demonstration of the parasite in biological samples from the patient through microscopic examination, by in vitro culture or animal inoculation; by molecular methods through the detection of parasite DNA; or by immunological methods through the detection of parasite antigens that may be present in urine or through the detection of specific antibodies against the parasite. Potential new methods that can be applied for laboratory diagnosis of leishmaniasis are also discussed.
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Affiliation(s)
- Juliana Quero Reimão
- Departamento de Morfologia e Patologia Básica, Faculdade de Medicina de Jundiaí, Jundiaí 13202-550, Brazil; (J.Q.R.); (M.R.L.)
| | - Elizabeth Magiolo Coser
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, Brazil;
| | - Monica Ran Lee
- Departamento de Morfologia e Patologia Básica, Faculdade de Medicina de Jundiaí, Jundiaí 13202-550, Brazil; (J.Q.R.); (M.R.L.)
| | - Adriano Cappellazzo Coelho
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, Brazil;
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Martinez SJ, Romano PS, Engman DM. Precision Health for Chagas Disease: Integrating Parasite and Host Factors to Predict Outcome of Infection and Response to Therapy. Front Cell Infect Microbiol 2020; 10:210. [PMID: 32457849 PMCID: PMC7225773 DOI: 10.3389/fcimb.2020.00210] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/16/2020] [Indexed: 01/01/2023] Open
Abstract
Chagas disease, caused by the infection with the protozoan parasite Trypanosoma cruzi, is clinically manifested in approximately one-third of infected people by inflammatory heart disease (cardiomyopathy) and, to a minor degree, gastrointestinal tract disorders (megaesophagus or megacolon). Chagas disease is a zoonosis transmitted among animals and people through the contact with triatomine bugs, which are found in much of the western hemisphere, including most countries of North, Central and South America, between parallels 45° north (Minneapolis, USA) and south (Chubut Province, Argentina). Despite much research on drug discovery for T. cruzi, there remain only two related agents in widespread use. Likewise, treatment is not always indicated due to the serious side effects of these drugs. On the other hand, the epidemiology and pathogenesis of Chagas disease are both highly complex, and much is known about both. However, it is still impossible to predict what will happen in an individual person infected with T. cruzi, because of the highly variability of parasite virulence and human susceptibility to infection, with no definitive molecular predictors of outcome from either side of the host-parasite equation. In this Minireview we briefly discuss the current state of T. cruzi infection and prognosis and look forward to the day when it will be possible to employ precision health to predict disease outcome and determine whether and when treatment of infection may be necessary.
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Affiliation(s)
- Santiago J Martinez
- Laboratorio de Biología de Trypanosoma cruzi y la célula hospedadora-Instituto de Histología y Embriología "Dr. Mario H. Burgos," (IHEM-CONICET- Universidad Nacional de Cuyo), Mendoza, Argentina.,Department of Pathology and Laboratory Medicine, Cedars Sinai Medical Center, Los Angeles, CA, United States
| | - Patricia S Romano
- Laboratorio de Biología de Trypanosoma cruzi y la célula hospedadora-Instituto de Histología y Embriología "Dr. Mario H. Burgos," (IHEM-CONICET- Universidad Nacional de Cuyo), Mendoza, Argentina
| | - David M Engman
- Department of Pathology and Laboratory Medicine, Cedars Sinai Medical Center, Los Angeles, CA, United States.,Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Departments of Pathology and Microbiology-Immunology, Northwestern University, Chicago, IL, United States
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