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Agyabeng-Dadzie F, Xiao R, Kissinger JC. Cryptosporidium Genomics - Current Understanding, Advances, and Applications. CURRENT TROPICAL MEDICINE REPORTS 2024; 11:92-103. [PMID: 38813571 PMCID: PMC11130048 DOI: 10.1007/s40475-024-00318-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2024] [Indexed: 05/31/2024]
Abstract
Purpose of Review Here we highlight the significant contribution that genomics-based approaches have had on the field of Cryptosporidium research and the insights these approaches have generated into Cryptosporidium biology and transmission. Recent Findings There are advances in genomics, genetic manipulation, gene expression, and single-cell technologies. New and better genome sequences have revealed variable sub-telomeric gene families and genes under selection. RNA expression data now include single-cell and post-infection time points. These data have provided insights into the Cryptosporidium life cycle and host-pathogen interactions. Antisense and ncRNA transcripts are abundant. The critical role of the dsRNA virus is becoming apparent. Summary The community's ability to identify genomic targets in the abundant, yet still lacking, collection of genomic data, combined with their increased ability to assess function via gene knock-out, is revolutionizing the field. Advances in the detection of virulence genes, surveillance, population genomics, recombination studies, and epigenetics are upon us.
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Affiliation(s)
| | - Rui Xiao
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602 USA
| | - Jessica C. Kissinger
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602 USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Coverdell Center, 107, 500 D.W. Brooks Drive, Athens, GA 30602 USA
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Carey M, Arju T, Cotton JA, Alam M, Kabir M, Faruque ASG, Haque R, Petri WA, Gilchrist CA. Genomic Heterogeneity of Cryptosporidium parvum Isolates From Children in Bangladesh: Implications for Parasite Biology and Human Infection. J Infect Dis 2023; 228:1292-1298. [PMID: 37832036 PMCID: PMC10629705 DOI: 10.1093/infdis/jiad257] [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: 08/08/2022] [Indexed: 10/15/2023] Open
Abstract
Cryptosporidium species are a major cause of diarrhea and associated with growth failure. There is currently only limited knowledge of the parasite's genomic variability. We report a genomic analysis of Cryptosporidium parvum isolated from Bangladeshi infants and reanalysis of sequences from the United Kingdom. Human isolates from both locations shared 154 variants not present in the cattle-derived reference genome, suggesting host-specific adaptation of the parasite. Remarkably 34.6% of single-nucleotide polymorphisms unique to human isolates were nonsynonymous and 8.2% of these were in secreted proteins. Linkage disequilibrium decay indicated frequent recombination. The genetic diversity of C. parvum has potential implications for vaccine and therapeutic design. Clinical Trials Registration. NCT02764918.
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Affiliation(s)
- Maureen Carey
- Departments of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Tuhinur Arju
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | | | - Masud Alam
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Mamun Kabir
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Abu S G Faruque
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Rashidul Haque
- International Centre for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - William A Petri
- Departments of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Carol A Gilchrist
- Departments of Medicine, University of Virginia, Charlottesville, Virginia, USA
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Risby H, Robinson G, Chandra N, King G, Vivancos R, Smith R, Thomas D, Fox A, McCarthy N, Chalmers RM. Application of a new multi-locus variable number tandem repeat analysis (MLVA) scheme for the seasonal investigation of Cryptosporidium parvum cases in Wales and the northwest of England, spring 2022. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2023; 4:100151. [PMID: 38021189 PMCID: PMC10665698 DOI: 10.1016/j.crpvbd.2023.100151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023]
Abstract
The protozoan Cryptosporidium parvum is an important cause of gastroenteritis in humans and livestock, and cryptosporidiosis outbreaks are common. However, a multi-locus genotyping scheme is not widely adopted. We describe the further development and application of a seven-locus multi-locus variable number of tandem repeats analysis (MLVA) scheme. From 28th March to 31st July 2022, confirmed C. parvum stools (n = 213) from cryptosporidiosis patients (cases) in Wales (n = 95) and the north west of England (n = 118) were tested by MLVA. Typability (defined as alleles identified at all seven loci in a sample) was 81.2% and discriminatory power estimated by Hunter Gaston Discriminatory Index was 0.99. A MLVA profile was constructed from the alleles, expressed in chromosomal order. Profiles were defined as simple (single allele at each locus) or mixed (more than one allele at any locus). A total of 161 MLVA profiles were identified; 13 were mixed, an additional 38 simple profiles contained null records, and 110 were complete simple profiles. A minimum spanning tree was constructed of simple MLVA profiles and those identical at all seven loci defined genetic clusters of cases (here, null records were considered as an allele); 77 cases formed 25 clusters, ranging from two to nine (mode = two) cases. The largest cluster, following epidemiological investigation, signalled a newly-identified outbreak. Two other cases with mixed profiles that contained the outbreak alleles were included in the outbreak investigation. In another epidemiologically-identified outbreak of six initial cases, MLVA detected two additional cases. In a third, small outbreak of three cases, identical MLVA profiles strengthened the microbiological evidence. Review of the performance characteristics of the individual loci and of the seven-locus scheme suggested that two loci might be candidates for review, but a larger dataset over a wider geographical area and longer timeframe will help inform decision-making about the scheme by user laboratories and stakeholders (such as public health agencies). This MLVA scheme is straightforward in use, fast and cheap compared to sequence-based methods, identifies mixed infections, provides an important tool for C. parvum surveillance, and can enhance outbreak investigations and public health action.
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Affiliation(s)
- Harriet Risby
- Cryptosporidium Reference Unit, Public Health Wales Microbiology and Health Protection, Singleton Hospital, Swansea, SA2 8QA, UK
| | - Guy Robinson
- Cryptosporidium Reference Unit, Public Health Wales Microbiology and Health Protection, Singleton Hospital, Swansea, SA2 8QA, UK
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
| | - Nastassya Chandra
- United Kingdom Health Security Agency, Field Service North West, Suite 3B, 3rd Floor, Cunard Building, Water Street, Liverpool, L3 1DS, UK
| | - Grace King
- Communicable Disease Surveillance Centre, Public Health Wales, 2 Capital Quarter, Tyndall Street, Cardiff, CF10 4BZ, UK
| | - Roberto Vivancos
- United Kingdom Health Security Agency, Field Service North West, Suite 3B, 3rd Floor, Cunard Building, Water Street, Liverpool, L3 1DS, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, L69 3GL, UK
- Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Robert Smith
- Communicable Disease Surveillance Centre, Public Health Wales, 2 Capital Quarter, Tyndall Street, Cardiff, CF10 4BZ, UK
| | - Daniel Thomas
- Communicable Disease Surveillance Centre, Public Health Wales, 2 Capital Quarter, Tyndall Street, Cardiff, CF10 4BZ, UK
| | - Andrew Fox
- United Kingdom Health Security Agency, Field Service North West, Suite 3B, 3rd Floor, Cunard Building, Water Street, Liverpool, L3 1DS, UK
| | - Noel McCarthy
- University of Warwick, Coventry, CV4 7AL, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, L69 3GL, UK
- Trinity College Dublin, Dublin, D02 PN40, Ireland
| | - Rachel M. Chalmers
- Cryptosporidium Reference Unit, Public Health Wales Microbiology and Health Protection, Singleton Hospital, Swansea, SA2 8QA, UK
- Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
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Uran-Velasquez J, Alzate JF, Farfan-Garcia AE, Gomez-Duarte OG, Martinez-Rosado LL, Dominguez-Hernandez DD, Rojas W, Galvan-Diaz AL, Garcia-Montoya GM. Multilocus Sequence Typing helps understand the genetic diversity of Cryptosporidium hominis and Cryptosporidium parvum isolated from Colombian patients. PLoS One 2022; 17:e0270995. [PMID: 35802653 PMCID: PMC9269747 DOI: 10.1371/journal.pone.0270995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/21/2022] [Indexed: 11/19/2022] Open
Abstract
Multilocus Sequence Typing has become a useful tool for the study of the genetic diversity and population structure of different organisms. In this study, a MLST approach with seven loci (CP47, MS5, MS9, MSC6-7, TP14, and gp60) was used to analyze the genetic diversity of Cryptosporidium hominis and Cryptosporidium parvum isolated from 28 Colombian patients. Five Cryptosporidium species were identified: C. hominis, C. parvum, Cryptosporidium felis, Cryptosporidium meleagridis, and Cryptosporidium suis. Unilocus gp60 analysis identified four allelic families for C. hominis (Ia, Ib, Id, and Ie) and two for C. parvum (IIa and IIc). There was polymorphic behavior of all markers evaluated for both C. hominis and C. parvum, particularly with the CP47, MS5, and gp60 markers. Phylogenetic analysis with consensus sequences (CS) of the markers showed a taxonomic agreement with the results obtained with the 18S rRNA and gp60 gene. Additionally, two monophyletic clades that clustered the species C. hominis and C. parvum were detected, with a higher number of subclades within the monophyletic groups compared to those with the gp60 gene. Thirteen MLG were identified for C. hominis and eight for C. parvum. Haplotypic and nucleotide diversity were detected, but only the latter was affected by the gp60 exclusion from the CS analysis. The gene fixation index showed an evolutionary closeness between the C. hominis samples and a less evolutionary closeness and greater sequence divergence in the C. parvum samples. Data obtained in this work support the implementation of MLST analysis in the study of the genetic diversity of Cryptosporidium, considering the more detailed information that it provides, which may explain some genetic events that with an unilocus approach could not be established. This is the first multilocus analysis of the intra-specific variability of Cryptosporidium from humans in South America.
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Affiliation(s)
- Johanna Uran-Velasquez
- Centro Nacional de Secuenciación Genómica–CNSG, Sede de Investigación Universitaria–SIU, Medellín, Antioquia, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica–CNSG, Sede de Investigación Universitaria–SIU, Medellín, Antioquia, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
- Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - Ana E. Farfan-Garcia
- Universidad de Santander, Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Bucaramanga, Colombia
| | - Oscar G. Gomez-Duarte
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, United States of America
- John R. Oishei Children’s Hospital, Buffalo, NY, United States of America
| | - Larry L. Martinez-Rosado
- Equipo Latinoamericano de Investigación en Infectología y Salud Pública (ELISAP), E.S.E. Hospital La María, Medellín, Colombia
| | - Diego D. Dominguez-Hernandez
- Equipo Latinoamericano de Investigación en Infectología y Salud Pública (ELISAP), E.S.E. Hospital La María, Medellín, Colombia
| | - Winston Rojas
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
| | - Ana Luz Galvan-Diaz
- Grupo de Microbiología Ambiental, Escuela de Microbiología, Universidad de Antioquia, Medellín, Antioquia, Colombia
- * E-mail:
| | - Gisela M. Garcia-Montoya
- Centro Nacional de Secuenciación Genómica–CNSG, Sede de Investigación Universitaria–SIU, Medellín, Antioquia, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
- Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Antioquia, Colombia
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Robinson G, Pérez-Cordón G, Hamilton C, Katzer F, Connelly L, Alexander CL, Chalmers RM. Validation of a multilocus genotyping scheme for subtyping Cryptosporidium parvum for epidemiological purposes. Food Waterborne Parasitol 2022; 27:e00151. [PMID: 35498551 PMCID: PMC9043402 DOI: 10.1016/j.fawpar.2022.e00151] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/21/2022] [Accepted: 03/27/2022] [Indexed: 11/17/2022] Open
Abstract
Subtyping Cryptosporidium parvum for outbreak investigations or epidemiological surveillance usually relies on DNA sequence analysis of a gene coding for a 60 KDa glycoprotein (gp60). Although gp60 can be useful for allelic discrimination and to help investigate sources and routes of transmission, the presence of common subtypes and recombination during the parasite's sexual life-cycle demand a multilocus-based method for more discriminatory genotyping. While whole genome sequencing would provide the ultimate approach, it is a time consuming and expensive option for faecal parasites such as Cryptosporidium that occur at low density and are difficult to propagate routinely. In this study, we selected and evaluated a panel of previously identified variable-number tandem-repeat (VNTR) markers, to establish a multilocus genotyping scheme based on fragment sizing, appropriate for inter-laboratory surveillance and outbreak investigations. Seven VNTR markers were validated in vitro and demonstrated typeability of 0.85 and discriminatory power of 0.99. The discriminatory power was much greater than the currently used gp60 sequencing (0.74), which identified 26 subtypes, compared to 100 different MLVA profiles within the same sample set. The assay was robust, with repeatable results and reproducibility across three laboratories demonstrating the scheme was suitable for inter-laboratory comparison of C. parvum subtypes. As the majority of genotypes (79%) were unique among epidemiologically unrelated samples, there was efficiency to infer linkage, and epidemiological concordance was observed in historical outbreaks. We propose that the multilocus variable number of tandem repeats analysis scheme is suitable to assist outbreak investigations.
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O'Leary JK, Blake L, Corcoran GD, Sleator RD, Lucey B. Development of a novel, high resolution melting analysis based genotyping method for Cryptosporidium parvum. Eur J Protistol 2021; 79:125799. [PMID: 34044353 DOI: 10.1016/j.ejop.2021.125799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 12/16/2022]
Abstract
This study employed the post-real-time PCR application, high resolution melting (HRM) analysis, in order to differentiate between characterised clinical and reference Cryptosporidium parvum samples obtained from Cork University Hospital (Cork, Ireland) and the Cryptosporidium Reference Unit (Swansea, Wales). A sample set composed of 18 distinct C. parvum gp60-subtypes of the IIa gp60-subtype family (an allele family accounting for over 80% of all cryptosporidiosis cases in Ireland) was employed. HRM analysis-based interrogation of the gp60, MM5 and MS9-Mallon tandem repeat loci was found to completely differentiate between 10 of the 18 studied gp60-subtypes. The remaining eight gp60-subtypes were differentiated into three distinct groupings, with the designations within these groupings resolved to two to three potential gp60-subtypes. The current study aimed to develop a novel, reproducible, real-time PCR based multi-locus genotyping method to distinguish between C. parvum gp60-subtypes. These preliminary results support the further expansion of the multi-locus panel in order to increase the discriminatory capabilities of this novel method.
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Affiliation(s)
- Jennifer K O'Leary
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland
| | - Liam Blake
- Department of Clinical Microbiology, Cork University Hospital, Wilton, Cork, Ireland
| | - Gerard D Corcoran
- Department of Clinical Microbiology, Cork University Hospital, Wilton, Cork, Ireland
| | - Roy D Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland.
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland
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Zhang Z, Hu S, Zhao W, Guo Y, Li N, Zheng Z, Zhang L, Kváč M, Xiao L, Feng Y. Population structure and geographical segregation of Cryptosporidium parvum IId subtypes in cattle in China. Parasit Vectors 2020; 13:425. [PMID: 32811542 PMCID: PMC7437029 DOI: 10.1186/s13071-020-04303-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background Cryptosporidium parvum is a zoonotic pathogen worldwide. Extensive genetic diversity and complex population structures exist in C. parvum in different geographical regions and hosts. Unlike the IIa subtype family, which is responsible for most zoonotic C. parvum infections in industrialized countries, IId is identified as the dominant subtype family in farm animals, rodents and humans in China. Thus far, the population genetic characteristics of IId subtypes in calves in China are not clear. Methods In the present study, 46 C. parvum isolates from dairy and beef cattle in six provinces and regions in China were characterized using sequence analysis of eight genetic loci, including msc6-7, rpgr, msc6-5, dz-hrgp, chom3t, hsp70, mucin1 and gp60. They belonged to three IId subtypes in the gp60 gene, including IIdA20G1 (n = 17), IIdA19G1 (n = 24) and IIdA15G1 (n = 5). The data generated were analyzed for population genetic structures of C. parvum using DnaSP and LIAN and subpopulation structures using STRUCTURE, RAxML, Arlequin, GENALEX and Network. Results Seventeen multilocus genotypes were identified. The results of linkage disequilibrium analysis indicated the presence of an epidemic genetic structure in the C. parvum IId population. When isolates of various geographical areas were treated as individual subpopulations, maximum likelihood inference of phylogeny, pairwise genetic distance analysis, substructure analysis, principal components analysis and network analysis all provided evidence for geographical segregation of subpopulations in Heilongjiang, Hebei and Xinjiang. In contrast, isolates from Guangdong, Shanghai and Jiangsu were genetically similar to each other. Conclusions Data from the multilocus analysis have revealed a much higher genetic diversity of C. parvum than gp60 sequence analysis. Despite an epidemic population structure, there is an apparent geographical segregation in C. parvum subpopulations within China. ![]()
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Affiliation(s)
- Zhenjie Zhang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Suhui Hu
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Wentao Zhao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Na Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zezhong Zheng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Martin Kváč
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, 37005, Czech Republic
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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Morris A, Robinson G, Swain MT, Chalmers RM. Direct Sequencing of Cryptosporidium in Stool Samples for Public Health. Front Public Health 2019; 7:360. [PMID: 31921734 PMCID: PMC6917613 DOI: 10.3389/fpubh.2019.00360] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/13/2019] [Indexed: 01/24/2023] Open
Abstract
The protozoan parasite Cryptosporidium is an important cause of diarrheal disease (cryptosporidiosis) in humans and animals, with significant morbidity and mortality especially in severely immunocompromised people and in young children in low-resource settings. Due to the sexual life cycle of the parasite, transmission is complex. There are no restrictions on sexual recombination between sub-populations, meaning that large-scale genetic recombination may occur within a host, potentially confounding epidemiological analysis. To clarify the relationships between infections in different hosts, it is first necessary to correctly identify species and genotypes, but these differentiations are not made by standard diagnostic tests and more sophisticated molecular methods have been developed. For instance, multilocus genotyping has been utilized to differentiate isolates within the major human pathogens, Cryptosporidium parvum and Cryptosporidium hominis. This has allowed mixed populations with multiple alleles to be identified: recombination events are considered to be the driving force of increased variation and the emergence of new subtypes. As yet, whole genome sequencing (WGS) is having limited impact on public health investigations, due in part to insufficient numbers of oocysts and purity of DNA derived from clinical samples. Moreover, because public health agencies have not prioritized parasites, validation has not been performed on user-friendly data analysis pipelines suitable for public health practitioners. Nonetheless, since the first whole genome assembly in 2004 there are now numerous genomes of human and animal-derived cryptosporidia publically available, spanning nine species. It has also been demonstrated that WGS from very low numbers of oocysts is possible, through the use of amplification procedures. These data and approaches are providing new insights into host-adapted infectivity, the presence and frequency of multiple sub-populations of Cryptosporidium spp. within single clinical samples, and transmission of infection. Analyses show that although whole genome sequences do indeed contain many alleles, they are invariably dominated by a single highly abundant allele. These insights are helping to better understand population structures within hosts, which will be important to develop novel prevention strategies in the fight against cryptosporidiosis.
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Affiliation(s)
- Arthur Morris
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Guy Robinson
- Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, United Kingdom
- Swansea University Medical School, Swansea, United Kingdom
| | - Martin T. Swain
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Rachel M. Chalmers
- Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, United Kingdom
- Swansea University Medical School, Swansea, United Kingdom
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9
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Genetic Diversity and Population Structure of Cryptosporidium. Trends Parasitol 2018; 34:997-1011. [DOI: 10.1016/j.pt.2018.07.009] [Citation(s) in RCA: 269] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 12/14/2022]
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Chalmers RM, Pérez-Cordón G, Cacció SM, Klotz C, Robertson LJ. Cryptosporidium genotyping in Europe: The current status and processes for a harmonised multi-locus genotyping scheme. Exp Parasitol 2018; 191:25-30. [PMID: 29908140 DOI: 10.1016/j.exppara.2018.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/11/2018] [Accepted: 06/12/2018] [Indexed: 11/29/2022]
Abstract
Due to the occurrence of genetic recombination, a reliable and discriminatory method to genotype Cryptosporidium isolates at the intra-species level requires the analysis of multiple loci, but a standardised scheme is not currently available. A workshop was held at the Robert Koch Institute, Berlin in 2016 that gathered 23 scientists with appropriate expertise (in either Cryptosporidium genotyping and/or surveillance, epidemiology or outbreaks) to discuss the processes for the development of a robust, standardised, multi-locus genotyping (MLG) scheme and propose an approach. The background evidence and main conclusions were outlined in a previously published report; the objectives of this further report are to describe 1) the current use of Cryptosporidium genotyping, 2) the elicitation and synthesis of the participants' opinions, and 3) the agreed processes and criteria for the development, evaluation and validation of a standardised MLG scheme for Cryptosporidium surveillance and outbreak investigations. Cryptosporidium was characterised to the species level in 7/12 (58%) participating European countries, mostly for human outbreak investigations. Further genotyping was mostly by sequencing the gp60 gene. A ranking exercise of performance and convenience criteria found that portability, biological robustness, typeability, and discriminatory power were considered by participants as the most important attributes in developing a multilocus scheme. The major barrier to implementation was lack of funding. A structured process for marker identification, evaluation, validation, implementation, and maintenance was proposed and outlined for application to Cryptosporidium, with prioritisation of Cryptosporidium parvum to support investigation of transmission in Europe.
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Affiliation(s)
- Rachel M Chalmers
- National Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, SA2 8QA, UK; Swansea University Medical School, Grove Building, Swansea University, Singleton Park, Swansea, SA2 8PP, UK.
| | - Gregorio Pérez-Cordón
- National Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, SA2 8QA, UK
| | - Simone M Cacció
- European Reference Laboratory for Parasites, Istituto Superiore di Sanità, Viale regina Elena 299, Rome 00161 Italy
| | - Christian Klotz
- Unit for Mycotic and Parasitic Agents and Mycobacteria, Department of Infectious Diseases, Robert Koch-Institute, 13353 Berlin, Germany
| | - Lucy J Robertson
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Adamstuen Campus, Oslo, Norway
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Infection with anthroponotic Cryptosporidium parvum does not fully protect the host against a subsequent challenge with C . hominis. Microbes Infect 2018; 20:267-270. [DOI: 10.1016/j.micinf.2018.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 01/31/2023]
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12
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Xiao L, Feng Y. Molecular epidemiologic tools for waterborne pathogens Cryptosporidium spp. and Giardia duodenalis. Food Waterborne Parasitol 2017; 8-9:14-32. [PMID: 32095639 PMCID: PMC7034008 DOI: 10.1016/j.fawpar.2017.09.002] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 01/26/2023] Open
Abstract
Molecular diagnostic tools have played an important role in improving our understanding of the transmission of Cryptosporidium spp. and Giardia duodenalis, which are two of the most important waterborne parasites in industrialized nations. Genotyping tools are frequently used in the identification of host-adapted Cryptosporidium species and G. duodenalis assemblages, allowing the assessment of infection sources in humans and public health potential of parasites found in animals and the environment. In contrast, subtyping tools are more often used in case linkages, advanced tracking of infections sources, and assessment of disease burdens attributable to anthroponotic and zoonotic transmission. More recently, multilocus typing tools have been developed for population genetic characterizations of transmission dynamics and delineation of mechanisms for the emergence of virulent subtypes. With the recent development in next generation sequencing techniques, whole genome sequencing and comparative genomic analysis are increasingly used in characterizing Cryptosporidium spp. and G. duodenalis. The use of these tools in epidemiologic studies has identified significant differences in the transmission of Cryptosporidium spp. in humans between developing countries and industrialized nations, especially the role of zoonotic transmission in human infection. Geographic differences are also present in the distribution of G. duodenalis assemblages A and B in humans. In contrast, there is little evidence for widespread zoonotic transmission of giardiasis in both developing and industrialized countries. Differences in virulence have been identified among Cryptosporidium species and subtypes, and possibly between G. duodenalis assemblages A and B, and genetic recombination has been identified as one mechanism for the emergence of virulent C. hominis subtypes. These recent advances are providing insight into the epidemiology of waterborne protozoan parasites in both developing and developed countries.
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Affiliation(s)
- Lihua Xiao
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Yaoyu Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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Evolutionary processes in populations of Cryptosporidium inferred from gp60 sequence data. Parasitol Res 2017; 116:1855-1861. [PMID: 28502018 DOI: 10.1007/s00436-017-5459-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/24/2017] [Indexed: 10/19/2022]
Abstract
Cryptosporidiosis is one of the most common human infectious diseases globally. The gp60 gene has been adopted as a key marker for molecular epidemiological investigations into this protozoan disease because of the capability to characterize genotypes and detect variants within Cryptosporidium species infecting humans. However, we know relatively little about the potential spatial and temporal variation in population demography that can be inferred from this gene beyond that it is recognized to be under selective pressure. Here, we analyzed the genetic variation in time and space within two putative populations of Cryptosporidium in New Zealand to infer the processes behind the patterns of sequence polymorphism. Analyses using Tajima's D, Fu, and Li's D* and F* tests show significant departures from neutrality in some populations and indicate the selective maintenance of alleles within some populations. Demographic analyses showed distortions in the pattern of the genetic variability caused by high recombination rates and population expansion, which was observed in case notification data. Our results showed that processes acting on populations that have similar effects can be distinguished from one another and multiple processes can be detected acting at the same time. These results are significant for prediction of the parasite dynamics and potential mechanisms of long-term changes in the risk of cryptosporidiosis in humans.
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Chalmers RM, Cacciò S. Towards a consensus on genotyping schemes for surveillance and outbreak investigations of Cryptosporidium, Berlin, June 2016. ACTA ACUST UNITED AC 2017; 21:30338. [PMID: 27685759 PMCID: PMC5032853 DOI: 10.2807/1560-7917.es.2016.21.37.30338] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/09/2016] [Indexed: 11/25/2022]
Affiliation(s)
- R M Chalmers
- Cryptosporidium Reference Unit, Public Health Wales Microbiology and Health Protection, Singleton Hospital, Swansea, United Kingdom
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Comparative genomic analysis of the IId subtype family of Cryptosporidium parvum. Int J Parasitol 2017; 47:281-290. [PMID: 28192123 DOI: 10.1016/j.ijpara.2016.12.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 12/19/2016] [Accepted: 12/22/2016] [Indexed: 11/20/2022]
Abstract
Host adaptation is known to occur in Cryptosporidium parvum, with IIa and IId subtype families preferentially infecting calves and lambs, respectively. To improve our understanding of the genetic basis of host adaptation in Cryptosporidium parvum, we sequenced the genomes of two IId specimens and one IIa specimen from China and Egypt using the Illumina technique and compared them with the published IIa IOWA genome. Sequence data were obtained for >99.3% of the expected genome. Comparative genomic analysis identified differences in numbers of three subtelomeric gene families between sequenced genomes and the reference genome, including those encoding SKSR secretory proteins, the MEDLE family of secretory proteins, and insulinase-like proteases. These gene gains and losses compared with the reference genome were confirmed by PCR analysis. Altogether, 5,191-5,766 single nucleotide variants were seen between genomes sequenced in this study and the reference genome, with most SNVs occurring in subtelomeric regions of chromosomes 1, 4, and 6. The most highly polymorphic genes between IIa and IId encode mainly invasion-associated and immunodominant mucin proteins, and other families of secretory proteins. Further studies are needed to verify the biological significance of these genomic differences.
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Pérez-Cordón G, Robinson G, Nader J, Chalmers RM. Discovery of new variable number tandem repeat loci in multiple Cryptosporidium parvum genomes for the surveillance and investigation of outbreaks of cryptosporidiosis. Exp Parasitol 2016; 169:119-28. [PMID: 27523797 DOI: 10.1016/j.exppara.2016.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 01/28/2023]
Abstract
Cryptosporidium parvum is a protozoan parasite causing gastro-intestinal disease (cryptosporidiosis) in humans and animals. The ability to investigate sources of contamination and routes of transmission by characterization and comparison of isolates in a cost- and time-efficient manner will help surveillance and epidemiological investigations, but as yet there is no standardised multi-locus typing scheme. To systematically identify variable number tandem repeat (VNTR) loci, which have been shown to provide differentiation in moderately conserved species, we interrogated the reference C. parvum Iowa II genome and seven other C. parvum genomes using a tandem repeat finder software. We identified 28 loci that met criteria defined previously for robust typing schemes for inter-laboratory surveillance, that had potential for generating PCR amplicons analysable on most fragment sizing platforms: repeats ≥6 bp, occurring in tandem in a single repeat region, and providing a total amplicon size of <300 bp including 50 bp for the location of the forward and reverse primers. The qualifying loci will be further investigated in vitro for consideration as preferred loci in the development of a robust VNTR scheme.
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Affiliation(s)
- Gregorio Pérez-Cordón
- Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, SA2 8QA, UK
| | - Guy Robinson
- Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, SA2 8QA, UK; Swansea University Medical School, Grove Building, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | - Johanna Nader
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rachel M Chalmers
- Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, SA2 8QA, UK; Swansea University Medical School, Grove Building, Swansea University, Singleton Park, Swansea, SA2 8PP, UK.
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17
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Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections. Clin Microbiol Rev 2016; 27:371-418. [PMID: 24696439 DOI: 10.1128/cmr.00122-13] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies.
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Cryptosporidium within-host genetic diversity: systematic bibliographical search and narrative overview. Int J Parasitol 2016; 46:465-71. [PMID: 27021167 DOI: 10.1016/j.ijpara.2016.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/29/2016] [Accepted: 03/06/2016] [Indexed: 11/21/2022]
Abstract
Knowledge of the within-host genetic diversity of a pathogen often has broad implications for disease management. Cryptosporidium protozoan parasites are among the most common causative agents of infectious diarrhoea. Current limitations of in vitro culture impose the use of uncultured isolates obtained directly from the hosts as operational units of Cryptosporidium genotyping. The validity of this practice is centred on the assumption of genetic homogeneity of the parasite within the host, and genetic studies often take little account of the within-host genetic diversity of Cryptosporidium. Yet, theory and experimental evidence contemplate genetic diversity of Cryptosporidium at the within-host scale, but this diversity is not easily identified by genotyping methods ill-suited for the resolution of DNA mixtures. We performed a systematic bibliographical search of the occurrence of within-host genetic diversity of Cryptosporidium parasites in epidemiological samples, between 2005 and 2015. Our results indicate that genetic diversity at the within-host scale, in the form of mixed species or intra-species diversity, has been identified in a large number (n=55) of epidemiological surveys of cryptosporidiosis in variable proportions, but has often been treated as a secondary finding and not analysed. As in malaria, there are indications that the scale of this diversity varies between geographical regions, perhaps depending on the prevailing transmission pathways. These results provide a significant knowledge base from which to draw alternative population genetic structure models, some of which are discussed in this paper.
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Abstract
Simple sequence repeat markers have played an important role in elucidating the epidemiology of human and animal cryptosporidiosis. The drawback of sequence length polymorphisms is that nucleotide substitutions remain undetected. As some laboratories have opted for using length polymorphisms, while others have relied on sequencing, there is a need to compare both methods. We used a diversified set of unique length polymorphisms and matching nucleotide sequences to assess the ability of each genotyping protocol to discern clusters of related Cryptosporidium parvum isolates. We found a weak correlation between the two distance measures for individual markers. This analysis was extended to four-locus genotypes based on sequence length data or concatenated sequences from the same loci. We interrogated these data to assess whether one would reach the same conclusions regardless of the genotyping method. Clusters of isolates generated with the concatenated sequences were not observed with amplicon length, indicating that inferences on the structure of a Cryptosporidium population depend on the genotyping method. Moreover, isolate clusters derived from concatenated sequences were dependent on the algorithm used to calculate distances. These results emphasize the need for harmonizing genotyping tools, not only by selecting informative markers, but also by standardizing the entire genotyping method.
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Multilocus typing and population structure of Cryptosporidium from children in Zaragoza, Spain. INFECTION GENETICS AND EVOLUTION 2015; 31:190-7. [DOI: 10.1016/j.meegid.2015.01.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/16/2015] [Accepted: 01/21/2015] [Indexed: 11/19/2022]
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Ichikawa-Seki M, Aita J, Masatani T, Suzuki M, Nitta Y, Tamayose G, Iso T, Suganuma K, Fujiwara T, Matsuyama K, Niikura T, Yokoyama N, Suzuki H, Yamakawa K, Inokuma H, Itagaki T, Zakimi S, Nishikawa Y. Molecular characterization of Cryptosporidium parvum from two different Japanese prefectures, Okinawa and Hokkaido. Parasitol Int 2014; 64:161-6. [PMID: 25481361 PMCID: PMC7108262 DOI: 10.1016/j.parint.2014.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/07/2014] [Accepted: 11/13/2014] [Indexed: 11/21/2022]
Abstract
Infectious diarrhea is the most frequent cause of morbidity and mortality in neonatal calves. Cryptosporidium parvum is one of the main pathogens associated with calf diarrhea. Although diarrhea is a symptom of infection with various pathogens, investigations to detect the types of pathogens have never been performed in Japan. This study investigated the prevalence of four major diarrhea-causing pathogens in calves: C. parvum, rotavirus, coronavirus, and enterotoxigenic Escherichia coli (E. coli K99). Commercial immunochromatography testing of all four pathogens and molecular analysis of C. parvum with diarrhea in calves from southernmost Okinawa and northernmost Hokkaido, Japan, were conducted. The frequencies of C. parvum, rotavirus, coronavirus, and E. coli (K99) in Okinawa were 50%, 28%, 2.3%, and 4.7%, respectively. Watery fecal stools were significantly correlated with C. parvum (p < 0.05). In oocyst calculations for C. parvum, no significant difference was observed between the single-infection cases and the mixed-infection cases with rotavirus. Interestingly, molecular analyses targeting small subunit ribosomal RNA as well as glycoprotein 60 (GP60) genes revealed that the C. parvum nucleotide sequences from the two prefectures were identical, indicating that C. parvum with a uniform characteristic is distributed throughout Japan. GP60 subtyping analysis identified C. parvum from Okinawa and Hokkaido as belonging to the IIaA15G2R1 subtype, a known zoonotic subtype. Hence, control of cryptosporidiosis is important not only for pre-weaned calves, but also for human health. ICT strips were used for calf diarrhea to detect four major enteric pathogens. C. parvum showed the highest frequency in the southernmost Okinawa prefecture, Japan. C. parvum from the northernmost Hokkaido prefecture was used for a comparative study. C. parvum from the two prefectures had a uniform character in SSUrRNA and GP60 genes. GP60 subtyping revealed that IIaA15G2R1, a known zoonotic subtype, was predominant.
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Affiliation(s)
- Madoka Ichikawa-Seki
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka 020-8550, Japan; National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-13 Inada-cho, Obihiro 080-8555, Japan
| | - Junya Aita
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka 020-8550, Japan
| | - Tatsunori Masatani
- Transboundary Animal Diseases Center, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-13 Inada-cho, Obihiro 080-8555, Japan
| | - Moemi Suzuki
- Yaeyama Livestock Hygiene Service Center, 1-2 Miyara, Ishigaki, Okinawa 907-0243, Japan
| | - Yoshiki Nitta
- Yaeyama Livestock Hygiene Service Center, 1-2 Miyara, Ishigaki, Okinawa 907-0243, Japan
| | - Genta Tamayose
- Tamayose Veterinary Hospital, 204-332 Maezato, Ishigaki, Okinawa 907-0002, Japan
| | - Takehiro Iso
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka 020-8550, Japan
| | - Keisuke Suganuma
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-13 Inada-cho, Obihiro 080-8555, Japan
| | - Takashi Fujiwara
- Honbetsu Veterinary Clinical Center, Tokachi Agricultural Mutual Aid Association, Honbetsu 089-3324, Japan
| | - Keita Matsuyama
- Hokubu Veterinary Clinical Center, Tokachi Agricultural Mutual Aid Association, Asyoro 089-3708, Japan
| | - Tadamasa Niikura
- Hokubu Veterinary Clinical Center, Tokachi Agricultural Mutual Aid Association, Asyoro 089-3708, Japan
| | - Naoaki Yokoyama
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-13 Inada-cho, Obihiro 080-8555, Japan
| | - Hiroshi Suzuki
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-13 Inada-cho, Obihiro 080-8555, Japan
| | - Kazuhiro Yamakawa
- Yubetsu Herd Management Service, Baro, Yubetsu-cho, Hokkaido 093-0731, Japan
| | - Hisashi Inokuma
- Department of Clinical Veterinary Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada-cho, Obihiro 080-8555, Japan
| | - Tadashi Itagaki
- Laboratory of Veterinary Parasitology, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka 020-8550, Japan
| | - Satoshi Zakimi
- Yaeyama Livestock Hygiene Service Center, 1-2 Miyara, Ishigaki, Okinawa 907-0243, Japan
| | - Yoshifumi Nishikawa
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-13 Inada-cho, Obihiro 080-8555, Japan.
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Cryptosporidiumspecies in humans and animals: current understanding and research needs. Parasitology 2014; 141:1667-85. [DOI: 10.1017/s0031182014001085] [Citation(s) in RCA: 402] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SUMMARYCryptosporidiumis increasingly recognized as one of the major causes of moderate to severe diarrhoea in developing countries. With treatment options limited, control relies on knowledge of the biology and transmission of the members of the genus responsible for disease. Currently, 26 species are recognized as valid on the basis of morphological, biological and molecular data. Of the nearly 20Cryptosporidiumspecies and genotypes that have been reported in humans,Cryptosporidium hominisandCryptosporidium parvumare responsible for the majority of infections. Livestock, particularly cattle, are one of the most important reservoirs of zoonotic infections. Domesticated and wild animals can each be infected with severalCryptosporidiumspecies or genotypes that have only a narrow host range and therefore have no major public health significance. Recent advances in next-generation sequencing techniques will significantly improve our understanding of the taxonomy and transmission ofCryptosporidiumspecies, and the investigation of outbreaks and monitoring of emerging and virulent subtypes. Important research gaps remain including a lack of subtyping tools for manyCryptosporidiumspecies of public and veterinary health importance, and poor understanding of the genetic determinants of host specificity ofCryptosporidiumspecies and impact of climate change on the transmission ofCryptosporidium.
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Valenzuela O, González-Díaz M, Garibay-Escobar A, Burgara-Estrella A, Cano M, Durazo M, Bernal RM, Hernandez J, Xiao L. Molecular characterization of Cryptosporidium spp. in children from Mexico. PLoS One 2014; 9:e96128. [PMID: 24755606 PMCID: PMC3996000 DOI: 10.1371/journal.pone.0096128] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 04/02/2014] [Indexed: 11/19/2022] Open
Abstract
Cryptosporidiosis is a parasitic disease caused by Cryptosporidium spp. In immunocompetent individuals, it usually causes an acute and self-limited diarrhea; in infants, infection with Cryptosporidium spp. can cause malnutrition and growth retardation, and declined cognitive ability. In this study, we described for the first time the distribution of C. parvum and C. hominis subtypes in 12 children in Mexico by sequence characterization of the 60-kDa glycoprotein (GP60) gene of Cryptosporidium. Altogether, 7 subtypes belonging to 4 subtype families of C. hominis (Ia, Ib, Id and Ie) and 1 subtype family of C. parvum (IIa) were detected, including IaA14R3, IaA15R3, IbA10G2, IdA17, IeA11G3T3, IIaA15G2R1 and IIaA16G1R1. The frequency of the subtype families and subtypes in the samples analyzed in this study differed from what was observed in other countries.
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Affiliation(s)
- Olivia Valenzuela
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
- * E-mail:
| | - Mariana González-Díaz
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Adriana Garibay-Escobar
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Alexel Burgara-Estrella
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | - Manuel Cano
- Servicio de Infectología, Hospital Infantil del Estado de Sonora, Hermosillo, Sonora, México
| | - María Durazo
- Servicio de Infectología, Hospital Infantil del Estado de Sonora, Hermosillo, Sonora, México
| | - Rosa M. Bernal
- Laboratorio de Parasitología y Micología, Hospital Infantil de México Federico Gómez, México Distrito Federal, México
| | - Jesús Hernandez
- Laboratorio de Inmunologia, Centro de Investigación en Alimentación y Desarrollo A. C., Hermosillo, Sonora, México
| | - Lihua Xiao
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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Tibayrenc M, Ayala FJ. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades? PLoS Pathog 2014; 10:e1003908. [PMID: 24722548 PMCID: PMC3983055 DOI: 10.1371/journal.ppat.1003908] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE) recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination), are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately (“Russian doll pattern”). Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections (“starving sex hypothesis”). We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi. Micropathogen species definition is extremely difficult, since concepts applied to higher organisms (the biological species concept) are inadequate. In particular, the pathogens here surveyed have given rise to long-lasting controversies about their species status and that of the genotypes that subdivide them. The population genetic approach based on the predominant clonal evolution (PCE) concept proposed by us could bring simple solutions to these controversies, since it permits the description of clearly defined evolutionary entities (clonal multilocus genotypes and near-clades [incompletely isolated clades]) that could be the basis for species description, if the concerned specialists find it justified for applied research. The PCE model also provides a convenient framework for applied studies (molecular epidemiology, vaccine and drug design, clinical research) dealing with these pathogens and others.
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), IRD Center, BP 64501, Montpellier, France
- * E-mail:
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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Widmer G, Ras R, Chalmers RM, Elwin K, Desoky E, Badawy A. Population structure of natural and propagated isolates of Cryptosporidium parvum, C. hominis and C. meleagridis. Environ Microbiol 2014; 17:984-93. [PMID: 24593863 DOI: 10.1111/1462-2920.12447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 02/25/2014] [Accepted: 02/26/2014] [Indexed: 11/28/2022]
Abstract
The three protozoan species Cryptosporidium parvum, C. meleagridis and C. hominis (phylum Apicomplexa) are enteric pathogens of humans. The former two species are zoonotic and the latter is thought to infect only humans. To better characterize the structure and transmission of natural and laboratory-propagated isolates, we analyzed a collection of archived human and animal isolates of these three species by deep-sequencing polymerase chain reaction products amplified from a polymorphic sequence on chromosome 1. Thousands of screened 200-nucleotide sequences were analyzed to compare the diversity among samples, to assess the impact of laboratory propagation on population complexity and to identify taxonomically mixed isolates. Contrary to our expectation, repeated propagation in animals did not reduce intra-isolate diversity nor was diversity associated with host species. Significantly, in most samples, sequences characteristic of a different species were identified. The presence of C. hominis alleles in C. parvum and C. meleagridis isolates confirms earlier reports of mixed isolates and raises the possibility that the host range of C. hominis is broader than typically assumed. In a genetically divergent isolate of C. parvum, a majority of sequences was found to be recombinant, suggesting that this genotype originated from a C. parvum × C. hominis recombination event.
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Affiliation(s)
- Giovanni Widmer
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, USA
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Abstract
SUMMARYCryptosporidiumhost cell interaction remains fairly obscure compared with other apicomplexans such asPlasmodiumorToxoplasma. The reason for this is probably the inability of this parasite to complete its life cyclein vitroand the lack of a system to genetically modifyCryptosporidium. However, there is a substantial set of data about the molecules involved in attachment and invasion and about the host cell pathways involved in actin arrangement that are altered by the parasite. Here we summarize the recent advances in research on host cell infection regarding the excystation process, attachment and invasion, survival in the cell, egress and the available data on omics.
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Jenkins MC, Widmer G, O'Brien C, Bauchan G, Murphy C, Santin M, Fayer R. A highly divergent 33 kDa Cryptosporidium parvum antigen. J Parasitol 2014; 100:527-31. [PMID: 24601821 DOI: 10.1645/13-433.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Previous studies comparing the genome sequences of Cryptosporidium parvum with Cryptosporidium hominis identified a number of highly divergent genes that might reflect positive selection for host specificity. In the present study, the C. parvum DNA sequence cgd8-5370, which encodes a protein whose amino acid sequence differs appreciably from its homologue in C. hominis , was cloned by PCR and expressed as a recombinant protein in Escherichia coli . Antisera raised against the recombinant cgd8-5370 antigen strongly recognized a unique 33 kDa protein in immunoblots from reducing and non-reducing SDS-PAGE of native C. parvum protein. However, anti-Cp33 sera did not recognize the native 33 kDa homologue in C. hominis . In an immunofluorescence assay (IFA), anti-Cp33 serum recognized an antigen in the anterior end of air-dried C. parvum sporozoites but failed to bind at any sites in C. hominis sporozoites, indicating its specificity for C. parvum . IFA staining of live C. parvum sporozoites with anti-Cp33 serum failed to bind to the parasite, indicating that the CP33 antigen is not on the sporozoite surface, which is consistent with topology predictions based on the encoded amino acid sequence. RT-PCR analysis of cgd8-5370 mRNA before or during C. parvum oocyst excystation revealed transcripts only in excysting sporozoites. Thus, Cp33 represents one of a small number of proteins shown to differentiate C. parvum from C. hominis sporozoites and oocysts.
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Affiliation(s)
- Mark C Jenkins
- Environmental, Microbial, and Food Safety Laboratory, ARS, USDA, Beltsville, Maryland 20705
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High-throughput genotyping assay for the large-scale genetic characterization of Cryptosporidium parasites from human and bovine samples. Parasitology 2013; 141:491-500. [PMID: 24238396 DOI: 10.1017/s0031182013001807] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The epidemiological study of human cryptosporidiosis requires the characterization of species and subtypes involved in human disease in large sample collections. Molecular genotyping is costly and time-consuming, making the implementation of low-cost, highly efficient technologies increasingly necessary. Here, we designed a protocol based on MALDI-TOF mass spectrometry for the high-throughput genotyping of a panel of 55 single nucleotide variants (SNVs) selected as markers for the identification of common gp60 subtypes of four Cryptosporidium species that infect humans. The method was applied to a panel of 608 human and 63 bovine isolates and the results were compared with control samples typed by Sanger sequencing. The method allowed the identification of species in 610 specimens (90·9%) and gp60 subtype in 605 (90·2%). It displayed excellent performance, with sensitivity and specificity values of 87·3 and 98·0%, respectively. Up to nine genotypes from four different Cryptosporidium species (C. hominis, C. parvum, C. meleagridis and C. felis) were detected in humans; the most common ones were C. hominis subtype Ib, and C. parvum IIa (61·3 and 28·3%, respectively). 96·5% of the bovine samples were typed as IIa. The method performs as well as the widely used Sanger sequencing and is more cost-effective and less time consuming.
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Abal-Fabeiro JL, Maside X, Bello X, Llovo J, Bartolomé C. Multilocus patterns of genetic variation across Cryptosporidium species suggest balancing selection at the gp60 locus. Mol Ecol 2013; 22:4723-32. [PMID: 23915002 DOI: 10.1111/mec.12425] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/08/2013] [Accepted: 06/18/2013] [Indexed: 11/27/2022]
Abstract
Cryptosporidium is an apicomplexan protozoan that lives in most vertebrates, including humans. Its gp60 gene is functionally involved in its attachment to host cells, and its high level of genetic variation has made it the reference marker for sample typing in epidemiological studies. To understand the origin of such high diversity and to determine the extent to which this classification applies to the rest of the genome, we analysed the patterns of variation at gp60 and nine other nuclear loci in isolates of three Cryptosporidium species. Most loci showed low genetic polymorphism (πS <1%) and similar levels of between-species divergence. Contrastingly, gp60 exhibited very different characteristics: (i) it was nearly ten times more variable than the other loci; (ii) it displayed a significant excess of polymorphisms relative to between-species differences in a maximum-likelihood Hudson-Kreitman-Aguadé test; (iii) gp60 subtypes turned out to be much older than the species they were found in; and (iv) showed a significant excess of polymorphic variants shared across species from random expectations. These observations suggest that this locus evolves under balancing selection and specifically under negative frequency-dependent selection (FDS). Interestingly, genetic variation at the other loci clusters very well within the groups of isolates defined by gp60 subtypes, which may provide new tools to understand the genome-wide patterns of genetic variation of the parasite in the wild. These results suggest that gp60 plays an active and essential role in the life cycle of the parasite and that genetic variation at this locus might be essential for the parasite's long-term success.
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Affiliation(s)
- J L Abal-Fabeiro
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain; Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain; Xenómica Comparada de Parásitos Humanos, IDIS, 15782, Santiago de Compostela, Spain
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Chalmers RM, Katzer F. Looking for Cryptosporidium: the application of advances in detection and diagnosis. Trends Parasitol 2013; 29:237-51. [PMID: 23566713 PMCID: PMC7106352 DOI: 10.1016/j.pt.2013.03.001] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 02/27/2013] [Accepted: 03/01/2013] [Indexed: 01/18/2023]
Abstract
The protozoan Cryptosporidium is a major public and animal health concern. Young children, immunocompromised people, and pre-weaning animals are especially vulnerable, but treatment options are limited and there is no vaccine. A laboratory diagnosis is required to confirm cases of cryptosporidiosis, and species and genotype determination is essential in distinguishing human from non-human sources, understanding transmission, and strengthening the epidemiological evidence for causative links in outbreaks. However, testing is not consistent, as demonstrated by investigation of a significant increase in cases in some European countries during 2012. Many methods employed are laborious and time-consuming; recent advances, translated into diagnostic assays, can improve testing and facilitate typing to support clinical and environmental investigations.
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Affiliation(s)
- Rachel M Chalmers
- Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea, UK.
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Nolan MJ, Jex AR, Koehler AV, Haydon SR, Stevens MA, Gasser RB. Molecular-based investigation of Cryptosporidium and Giardia from animals in water catchments in southeastern Australia. WATER RESEARCH 2013; 47:1726-1740. [PMID: 23357792 DOI: 10.1016/j.watres.2012.12.027] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/10/2012] [Accepted: 12/14/2012] [Indexed: 06/01/2023]
Abstract
There has been no large-scale systematic molecular epidemiological investigation of the waterborne protozoans, Cryptosporidium or Giardia, in southeastern Australia. Here, we explored, for the first time, the genetic composition of these genera in faecal samples from animals in nine Melbourne Water reservoir areas, collected over a period of two-years. We employed PCR-based single-strand conformation polymorphism (SSCP) and phylogenetic analyses of loci (pSSU and pgp60) in the small subunit (SSU) of ribosomal RNA and 60-kDa glycoprotein (gp60) genes to detect and characterise Cryptosporidium, and another locus (ptpi) in the triose-phosphate isomerase (tpi) gene to identify and characterise Giardia. Cryptosporidium was detected in 2.8% of the 2009 samples examined; the analysis of all amplicons defined 14 distinct sequence types for each of pSSU and pgp60, representing Cryptosporidium hominis (genotype Ib - subgenotype IbA10G2R2), Cryptosporidium parvum (genotype IIa - subgenotypes IIaA15G2R1, IIaA19G2R1, IIaA19G3R1, IIaA19G4R1, IIaA20G3R1, IIaA20G4R1, IIaA20G3R2 and IIaA21G3R1), Cryptosporidium cuniculus (genotype Vb - subgenotypes VbA22R4, VbA23R3, VbA24R3, VbA25R4 and VbA26R4), and Cryptosporidium canis, Cryptosporidium fayeri, Cryptosporidium macropodum and Cryptosporidium ubiquitum as well as six new pSSU sequence types. In addition, Giardia was identified in 3.4% of the samples; all 28 distinct ptpi sequence types defined were linked to assemblage A of Giardia duodenalis. Of all 56 sequence types characterised, eight and one have been recorded previously in Cryptosporidium and Giardia, respectively, from humans. In contrast, nothing is known about the zoonotic potential of 35 new genotypes of Cryptosporidium and Giardia recorded here for the first time. Future work aims to focus on estimating the prevalence of Cryptosporidium and Giardia genotypes in humans and a wide range of animals in Victoria and elsewhere in Australia. (Nucleotide sequences reported in this paper are available in the GenBank database under accession nos. KC282952-KC283005).
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Affiliation(s)
- Matthew J Nolan
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Grinberg A, Biggs P, Dukkipati V, George T. Extensive intra-host genetic diversity uncovered in Cryptosporidium parvum using Next Generation Sequencing. INFECTION GENETICS AND EVOLUTION 2013; 15:18-24. [DOI: 10.1016/j.meegid.2012.08.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 08/28/2012] [Accepted: 08/28/2012] [Indexed: 11/28/2022]
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Abeywardena H, Jex AR, Nolan MJ, Haydon SR, Stevens MA, McAnulty RW, Gasser RB. Genetic characterisation of Cryptosporidium and Giardia from dairy calves: discovery of species/genotypes consistent with those found in humans. INFECTION GENETICS AND EVOLUTION 2012; 12:1984-93. [PMID: 22981927 DOI: 10.1016/j.meegid.2012.08.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 10/27/2022]
Abstract
Cryptosporidium and Giardia are important genera of parasitic protists that can cause significant diarrhoeal diseases in humans and other animals. Depending on the species/genotype of parasite, human infection may be acquired via anthroponotic or zoonotic transmission routes. Here, we undertook a molecular epidemiological investigation of these two genera of parasites in pre- and post-weaned calves from eight locations in Canterbury, New Zealand, by PCR-coupled sequencing and phylogenetic analysis of sequence data for regions in the 60 kDa glycoprotein (pgp60) gene of Cryptosporidium and/or the triose-phosphate isomerase (ptpi) gene of Giardia. The pgp60 and ptpi regions were specifically amplified from 15 (8.3%) and 11 (6.1%) of the 180 individual faecal samples, respectively. The sequences derived from all of the amplicons were aligned with homologous reference sequences and subjected to phylogenetic analysis by Bayesian inference. For Cryptosporidium, three samples contained Cryptosporidium parvum genotype IIa, subgenotypes IIaA15G3R1, IIaA19G3R1 and IIaA23G4. Twelve samples contained Cryptosporidium hominis genotype Ib, subgenotype IbA10G2R2. While subgenotypes IIaA15G3R1 and IIaA23G4 are new records, IIaA19G3R1 and IbA10G2R2 are commonly found in humans in various countries. For Giardia, two samples contained Giardia duodenalis assemblage A, also common in humans. In contrast, nine samples contained G. duodenalis assemblage E, which is the first report of this assemblage in cattle in New Zealand. Therefore, the present results indicate that dairy calves on the South Island of New Zealand harbour 'zoonotic' genotypes of Cryptosporidium and Giardia, which is likely to have significant public health implications.
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Affiliation(s)
- Harshanie Abeywardena
- Faculty of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia
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Widmer G, Lee Y, Hunt P, Martinelli A, Tolkoff M, Bodi K. Comparative genome analysis of two Cryptosporidium parvum isolates with different host range. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2012; 12:1213-21. [PMID: 22522000 PMCID: PMC3372781 DOI: 10.1016/j.meegid.2012.03.027] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 03/27/2012] [Accepted: 03/29/2012] [Indexed: 11/15/2022]
Abstract
Parasites of the genus Cryptosporidium infect the intestinal and gastric epithelium of different vertebrate species. Some of the many Cryptosporidium species described to date differ with respect to host range; whereas some species' host range appears to be narrow, others have been isolated from taxonomically unrelated vertebrates. To begin to investigate the genetic basis of Cryptosporidium host specificity, the genome of a Cryptosporidium parvum isolate belonging to a sub-specific group found exclusively in humans was sequenced and compared to the reference C. parvum genome representative of the zoonotic group. Over 12,000 single-nucleotide polymorphisms (SNPs), or 1.4 SNP per kilobase, were identified. The genome distribution of SNPs was highly heterogeneous, but non-synonymous and silent SNPs were similarly distributed. On many chromosomes, the most highly divergent regions were located near the ends. Genes in the most diverged regions were almost twice as large as the genome-wide average. Transporters, and ABC transporters in particular, were over-represented among these genes, as were proteins with predicted signal peptide. Possibly reflecting the presence of regulatory sequences, the distribution of intergenic SNPs differed according to the function of the downstream open reading frame. A 3-way comparison of the newly sequenced anthroponotic C. parvum, the reference zoonotic C. parvum and the human parasite Cryptosporidium hominis identified genetic loci where the anthroponotic C. parvum sequence is more similar to C. hominis than to the zoonotic C. parvum reference. Because C. hominis and anthroponotic C. parvum share a similar host range, this unexpected observation suggests that proteins encoded by these genes may influence the host range.
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Affiliation(s)
- Giovanni Widmer
- Tufts Cummings School of Veterinary Medicine, Division of Infectious Diseases, North Grafton, MA 01536, USA.
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Robinson G, Chalmers RM. Assessment of polymorphic genetic markers for multi-locus typing of Cryptosporidium parvum and Cryptosporidium hominis. Exp Parasitol 2012; 132:200-15. [PMID: 22781277 DOI: 10.1016/j.exppara.2012.06.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 06/26/2012] [Accepted: 06/29/2012] [Indexed: 11/29/2022]
Abstract
The use of high resolution molecular tools to study Cryptosporidium parvum and Cryptosporidium hominis intra-species variation is becoming common practice, but there is currently no consensus in the methods used. The most commonly applied tool is partial gp60 gene sequence analysis. However, multi-locus schemes are acknowledged to improve resolution over analysis of a single locus, which neglects potential re-assortment of genes during the sexual phase of the Cryptosporidium life-cycle. Multi-locus markers have been investigated in isolates from a variety of sampling frames, in varying combinations and using different assays and methods of analysis. To identify the most informative markers as candidates for the development of a standardised multi-locus fragment size-based typing (MLFT) scheme to integrate with epidemiological analyses, we examined the published literature. A total of 31 MLFT studies were found, employing 55 markers of which 45 were applied to both C. parvum and C. hominis. Of the studies, 11 had sufficient raw data, from three or more markers, and a sampling frame containing at least 50 samples, for meaningful in-depth analysis using assessment criteria based on the sampling frame, study size, number of markers investigated in each study, marker characteristics (>2 nucleotide repeats) and the combinations of markers generating all possible multi-locus genotypes. Markers investigated differed between C. hominis and C. parvum. When each scheme was analysed for the fewest markers required to identify 95% of all MLFTs, some redundancy was identified in all schemes; an average redundancy of 40% for C. hominis and 27% for C. parvum. Ranking markers, based on the most productive combinations, identified two different sets of potentially most informative candidate markers, one for each species. These will be subjected to technical evaluation including typability (percentage of samples generating a complete multi-locus type) and discriminatory power by direct fragment size analysis and analysed for correlation with epidemiological data in suitable sampling frames. The establishment of a group of users and agreed subtyping scheme for improved epidemiological and public health investigations of C. parvum and C. hominis will facilitate further developments and consideration of technological advances in a harmonised manner.
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Affiliation(s)
- Guy Robinson
- Cryptosporidium Reference Unit, Public Health Wales Microbiology, Singleton Hospital, Swansea SA2 8QA, UK
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Bouzid M, Hunter PR, McDonald V, Elwin K, Chalmers RM, Tyler KM. A new heterogeneous family of telomerically encoded Cryptosporidium proteins. Evol Appl 2012; 6:207-17. [PMID: 23467513 PMCID: PMC3586618 DOI: 10.1111/j.1752-4571.2012.00277.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 05/02/2012] [Indexed: 12/16/2022] Open
Abstract
Cryptosporidiosis is predominantly caused by two closely related species of protozoan parasites the zoonotic Cryptosporidium parvum and anthroponotic Cryptosporidium hominis which diverge phenotypically in respect to host range and virulence. Using comparative genomics we identified two genes displaying overt heterogeneity between species. Although initial work suggested both were species specific, Cops-1 for C. parvum and Chos-1 for C. hominis, subsequent study identified an abridged ortholog of Cops-1 in C. hominis. Cops-1 and Chos-1 showed limited, but significant, similarity to each other and share common features: (i) telomeric location: Cops-1 is the last gene on chromosome 2, whilst Chos-1 is the first gene on chromosome 5, (ii) encode circa 50-kDa secreted proteins with isoelectric points above 10, (iii) are serine rich, and (iv) contain internal nucleotide repeats. Importantly, Cops-1 sequence contains specific SNPs with good discriminatory power useful epidemiologically. C. parvum-infected patient sera recognized a 50-kDa protein in antigen preparations of C. parvum but not C. hominis, consistent with Cops-1 being antigenic for patients. Interestingly, anti-Cops-1 monoclonal antibody (9E1) stained oocyst content and sporozoite surface of C. parvum only. This study provides a new example of protozoan telomeres as rapidly evolving contingency loci encoding putative virulence factors.
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Affiliation(s)
- Maha Bouzid
- Biomedical Research Centre, Norwich Medical School, University of East Anglia Norwich, UK
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Evidence of host-associated populations of Cryptosporidium parvum in Italy. Appl Environ Microbiol 2012; 78:3523-9. [PMID: 22389374 DOI: 10.1128/aem.07686-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent studies have revealed extensive genetic variation among isolates of Cryptosporidium parvum, an Apicomplexan parasite that causes gastroenteritis in both humans and animals worldwide. The parasite's population structure is influenced by the intensity of transmission, the host-parasite interaction, and husbandry practices. As a result, C. parvum populations can be panmictic, clonal, or even epidemic on both a local scale and a larger geographical scale. To extend the study of C. parvum populations to an unexplored region, 173 isolates of C. parvum collected in Italy from humans and livestock (calf, sheep, and goat) over a 10-year period were genotyped using a multilocus scheme based on 7 mini- and microsatellite loci. In agreement with other studies, extensive polymorphism was observed, with 102 distinct multilocus genotypes (MLGs) identified among 173 isolates. The presence of linkage disequilibrium, the confinement of MLGs to individual farms, and the relationship of many MLGs inferred using network analysis (eBURST) suggest a predominantly clonal population structure, but there is also evidence that part of the diversity can be explained by genetic exchange. MLGs from goats were found to differ from bovine and sheep MLGs, supporting the existence of C. parvum subpopulations. Finally, MLGs from isolates collected between 1997 and 1999 were also identified as a distinct subgroup in principal-component analysis and eBURST analysis, suggesting a continuous introduction of novel genotypes in the parasite population.
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Abstract
We describe recent advances in the genomics and population biology of Cryptosporidium parvum and C. hominis, the causative agents of cryptosporidiosis in humans and animals. Many basic aspects of the biology of Cryptosporidium species remain to be investigated and effective drugs to control cryptosporidiosis are not available. Sequencing and annotation of the genome of C. parvum and C. hominis has uncovered unique features of the metabolism of these species. The recently sequenced genome of the gastric species C. muris is providing new insights into the evolution of the genus. Cryptosporidian sequence information has facilitated the identification of polymorphic genetic markers. Genotyping of oocysts excreted by human and animal hosts using such markers has revealed many new species and genotypes, and is leading to a better understanding of the epidemiology of cryptosporidiosis.
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Affiliation(s)
- G Widmer
- Division of Infectious Diseases, Tufts Cummins School of Veterinary Medicine, North Grafton, MA 01536, USA.
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Multilocus fragment typing and genetic structure of Cryptosporidium parvum Isolates from diarrheic preweaned calves in Spain. Appl Environ Microbiol 2011; 77:7779-86. [PMID: 21908632 DOI: 10.1128/aem.00751-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A collection of 140 Cryptosporidium parvum isolates previously analyzed by PCR-restriction fragment length polymorphism (PCR-RFLP) and sequence analyses of the small-subunit (SSU) rRNA and 60-kDa glycoprotein (GP60) genes was further characterized by multilocus fragment typing of six minisatellite (MSB and MS5) and microsatellite (ML1, ML2, TP14, and 5B12) loci. Isolates were collected from diarrheic preweaned calves originating from 61 dairy cattle farms in northern Spain. A capillary electrophoresis-based tool combining three different fluorescent tags was used to analyze all six satellites in one capillary. Fragment sizes were adjusted after comparison with sizes obtained by sequence analysis of a selection of isolates for every allele. Size discrepancies at all but the 5B12 locus were found for those isolates that were typed by both techniques, although identical size differences were reported for every allele within each locus. A total of eight alleles were seen at the ML2 marker, which contributed the most to the discriminatory power of the multilocus approach. Multilocus fragment typing clearly improved the discriminatory power of GP60 sequencing, since a total of 59 multilocus subtypes were identified based on the combination of alleles at the six satellite loci, in contrast to the 7 GP60 subtypes previously reported. The majority of farms (38) displayed a unique multilocus subtype, and individual isolates with mixed multilocus subtypes were seen at 22 farms. Bayesian structure analysis based on combined data for both satellite and GP60 loci suggested the presence of two major clusters among the C. parvum isolates from cattle farms in this geographical area.
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