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Occurrence and Molecular Characterization of Cryptosporidium spp. in Dairy Cattle and Dairy Buffalo in Yunnan Province, Southwest China. Animals (Basel) 2022; 12:ani12081031. [PMID: 35454277 PMCID: PMC9025915 DOI: 10.3390/ani12081031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/02/2022] [Accepted: 04/11/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Cryptosporidium spp. are important gastrointestinal pathogens of humans and animals, causing diarrheal diseases. Cattle are considered as one of the main reservoirs of Cryptosporidium for humans. We first report the occurrence of Cryptosporidium spp. in dairy cattle (14.7%, 65/442) and dairy buffalo (1.1%, 3/258) in Yunnan Province of China. The results of this study suggest that divergent Cryptosporidium spp. (such as C. andersoni, C. bovis, C. ryanae, and C. parvum) can be found in asymptomatic dairy cattle and dairy buffalo in Yunnan, China. The IIdA18G1 subtype of C. parvum, which infects humans and other animals, was also found in this study. Thus, attention should be paid towards preventing the transmission of Cryptosporidium spp. in cattle and humans in Yunnan Province. Abstract Cryptosporidium spp. are important foodborne and waterborne pathogens in humans and animals, causing diarrheal diseases. Cattle are one of the reservoirs of Cryptosporidium infection in humans. However, data on the occurrence of Cryptosporidium spp. in cattle in Yunnan Province remains limited. A total of 700 fecal samples were collected from Holstein cows (n = 442) and dairy buffaloes (n = 258) in six counties of Yunnan Province. The occurrence and genotypes of Cryptosporidium spp. were analyzed using nested PCR and DNA sequencing. Furthermore, the C. andersoni isolates were further analyzed using multilocus sequence typing (MLST) at four gene loci (MS1, MS2, MS3, and MS16), and the C. parvum isolate was subtyped by 60-kDa glycoprotein (gp60) loci. The occurrence of Cryptosporidium spp. in Holstein cows and dairy buffaloes was 14.7% (65/442) and 1.1% (3/258), respectively. Of these positive samples, 56 Holstein cow samples represented C. andersoni, four Holstein cow samples represented C. bovis, three Holstein cow samples represented C. ryanae, and one represented C. parvum. Meanwhile, only three dairy buffalo samples represented C. ryanae. MLST analysis of subtypes of C. andersoni detected four subtypes, including A5A4A2A1 (n = 7), A4A4A4A1 (n = 7), A1A4A4A1 (n = 2), and A4A4A2A1 (n = 1). One C. parvum isolate was identified as the IIdA18G1 subtype. These results revealed the high occurrence and high genetic diversity of Cryptosporidium spp. in Holstein cows in Yunnan Province, enriching the knowledge of the population genetic structure of Cryptosporidium spp. in Yunnan Province.
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Mitochondrial cytochrome oxidase 1 reveals genetic diversity of the African Snakehead fish Parachanna obscura, Gunther, 1861 from Nigeria's freshwater environment. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2021.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Baptista RP, Cooper GW, Kissinger JC. Challenges for Cryptosporidium Population Studies. Genes (Basel) 2021; 12:894. [PMID: 34200631 PMCID: PMC8229070 DOI: 10.3390/genes12060894] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 12/31/2022] Open
Abstract
Cryptosporidiosis is ranked sixth in the list of the most important food-borne parasites globally, and it is an important contributor to mortality in infants and the immunosuppressed. Recently, the number of genome sequences available for this parasite has increased drastically. The majority of the sequences are derived from population studies of Cryptosporidium parvum and Cryptosporidium hominis, the most important species causing disease in humans. Work with this parasite is challenging since it lacks an optimal, prolonged, in vitro culture system, which accurately reproduces the in vivo life cycle. This obstacle makes the cloning of isolates nearly impossible. Thus, patient isolates that are sequenced represent a population or, at times, mixed infections. Oocysts, the lifecycle stage currently used for sequencing, must be considered a population even if the sequence is derived from single-cell sequencing of a single oocyst because each oocyst contains four haploid meiotic progeny (sporozoites). Additionally, the community does not yet have a set of universal markers for strain typing that are distributed across all chromosomes. These variables pose challenges for population studies and require careful analyses to avoid biased interpretation. This review presents an overview of existing population studies, challenges, and potential solutions to facilitate future population analyses.
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Affiliation(s)
- Rodrigo P. Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA;
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Garrett W. Cooper
- Department of Genetics, University of Georgia, Athens, GA 30602, USA;
| | - Jessica C. Kissinger
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA;
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA;
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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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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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Next Generation Sequencing uncovers within-host differences in the genetic diversity of Cryptosporidium gp60 subtypes. Int J Parasitol 2017; 47:601-607. [DOI: 10.1016/j.ijpara.2017.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/23/2017] [Accepted: 03/31/2017] [Indexed: 12/21/2022]
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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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Ramo A, Monteagudo LV, Del Cacho E, Sánchez-Acedo C, Quílez J. Intra-Species Genetic Diversity and Clonal Structure of Cryptosporidium parvum in Sheep Farms in a Confined Geographical Area in Northeastern Spain. PLoS One 2016; 11:e0155336. [PMID: 27176718 PMCID: PMC4866762 DOI: 10.1371/journal.pone.0155336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/27/2016] [Indexed: 01/21/2023] Open
Abstract
A multilocus fragment typing approach including eleven variable-number tandem-repeat (VNTR) loci and the GP60 gene was used to investigate the intra-farm and intra-host genetic diversity of Cryptosporidium parvum in sheep farms in a confined area in northeastern Spain. Genomic DNA samples of 113 C. parvum isolates from diarrheic pre-weaned lambs collected in 49 meat-type sheep farms were analyzed. Loci exhibited various degrees of polymorphism, the finding of 7–9 alleles in the four most variable and discriminatory markers (ML2, Cgd6_5400, Cgd6_3940, and GP60) being remarkable. The combination of alleles at the twelve loci identified a total of 74 multilocus subtypes (MLTs) and provided a Hunter-Gaston discriminatory index of 0.988 (95% CI, 0.979−0.996). The finding that most MLTs (n = 64) were unique to individual farms evidenced that cryptosporidial infection is mainly transmitted within sheep flocks, with herd-to-herd transmission playing a secondary role. Limited intra- host variability was found, since only five isolates were genotypically mixed. In contrast, a significant intra-farm genetic diversity was seen, with the presence of multiple MLTs on more than a half of the farms (28/46), suggesting frequent mutations or genetic exchange through recombination. Comparison with a previous study in calves in northern Spain using the same 12-loci typing approach showed differences in the identity of major alleles at most loci, with a single MLT being shared between lambs and calves. Analysis of evolutionary descent by the algorithm eBURST indicated a high degree of genetic divergence, with over 41% MLTs appearing as singletons along with a high number of clonal complexes, most of them linking only two MLTs. Bayesian Structure analysis and F statistics also revealed the genetic remoteness of most C. parvum isolates and no ancestral population size was chosen. Linkage analysis evidenced a prevalent pattern of clonality within the parasite population.
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Affiliation(s)
- Ana Ramo
- Department of Animal Pathology, Faculty of Veterinary Sciences, University of Zaragoza, Zaragoza, Spain
| | - Luis V. Monteagudo
- Department of Anatomy, Embryology and Genetics, Faculty of Veterinary Sciences, University of Zaragoza, Zaragoza, Spain
| | - Emilio Del Cacho
- Department of Animal Pathology, Faculty of Veterinary Sciences, University of Zaragoza, Zaragoza, Spain
| | - Caridad Sánchez-Acedo
- Department of Animal Pathology, Faculty of Veterinary Sciences, University of Zaragoza, Zaragoza, Spain
| | - Joaquín Quílez
- Department of Animal Pathology, Faculty of Veterinary Sciences, University of Zaragoza, Zaragoza, Spain
- * E-mail:
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