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Bayona-Vásquez NJ, Sullivan AH, Beaudry MS, Khan A, Baptista RP, Petersen KN, Bhuiyan M, Brunelle B, Robinson G, Chalmers RM, Alves-Ferreira E, Grigg ME, Kissinger JC, Glenn TC. WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp. RESEARCH SQUARE 2024:rs.3.rs-4294842. [PMID: 38798642 PMCID: PMC11118713 DOI: 10.21203/rs.3.rs-4294842/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. (C. cuniculus, C. hominis, C. meleagridis, C. parvum, C. tyzzeri, and C. viatorum) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.
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Affiliation(s)
- N J Bayona-Vásquez
- Division of Natural Science and Mathematics, Oxford College of Emory University, Oxford, GA, 30054, USA
| | - A H Sullivan
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - M S Beaudry
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
- Daicel Arbor Biosciences, Ann Arbor, MI, 48103, USA
| | - A Khan
- Animal Parasitic Disease Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - R P Baptista
- Infectious Diseases, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - K N Petersen
- Odum School of Ecology, University of Georgia, University of Georgia, Athens, GA, 30602, USA
| | - Miu Bhuiyan
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, 30602, USA
| | - B Brunelle
- Daicel Arbor Biosciences, Ann Arbor, MI, 48103, USA
| | - G 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
| | - R 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
| | - Evc Alves-Ferreira
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M E Grigg
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J C Kissinger
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA
| | - T C Glenn
- Department of Environmental Health Science, College of Public Health, 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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Jangid H, Garg S, Kashyap P, Karnwal A, Shidiki A, Kumar G. Bioprospecting of Aspergillus sp. as a promising repository for anti-cancer agents: a comprehensive bibliometric investigation. Front Microbiol 2024; 15:1379602. [PMID: 38812679 PMCID: PMC11133633 DOI: 10.3389/fmicb.2024.1379602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
Cancer remains a significant global health challenge, claiming nearly 10 million lives in 2020 according to the World Health Organization. In the quest for novel treatments, fungi, especially Aspergillus species, have emerged as a valuable source of bioactive compounds with promising anticancer properties. This study conducts a comprehensive bibliometric analysis to map the research landscape of Aspergillus in oncology, examining publications from 1982 to the present. We observed a marked increase in research activity starting in 2000, with a notable peak from 2005 onwards. The analysis identifies key contributors, including Mohamed GG, who has authored 15 papers with 322 citations, and El-Sayed Asa, with 14 papers and 264 citations. Leading countries in this research field include India, Egypt, and China, with King Saud University and Cairo University as the leading institutions. Prominent research themes identified are "endophyte," "green synthesis," "antimicrobial," "anti-cancer," and "biological activities," indicating a shift towards environmentally sustainable drug development. Our findings highlight the considerable potential of Aspergillus for developing new anticancer therapies and underscore the necessity for further research to harness these natural compounds for clinical use.
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Affiliation(s)
- Himanshu Jangid
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar, Punjab, India
| | - Sonu Garg
- Department of Biotechnology, Mahatma Jyoti Rao Phoole University, Jaipur, Rajasthan, India
| | - Piyush Kashyap
- School of Agriculture, Lovely Professional University, Jalandhar, Punjab, India
| | - Arun Karnwal
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar, Punjab, India
| | - Amrullah Shidiki
- Department of Microbiology, National Medical College & Teaching Hospital, Birgunj, Nepal
| | - Gaurav Kumar
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar, Punjab, India
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Bayona-Vásquez NJ, Sullivan AH, Beaudry MS, Khan A, Baptista RP, Petersen KN, Bhuiyan M, Brunelle B, Robinson G, Chalmers RM, Alves-Ferreira E, Grigg ME, AlvesFerreira Kissinger JC, Glenn TC. WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.586458. [PMID: 38585809 PMCID: PMC10996700 DOI: 10.1101/2024.03.29.586458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. ( C. cuniculus , C. hominis , C. meleagridis , C. parvum , C. tyzzeri , and C. viatorum ) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.
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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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Zhao L, Wang M, Wang L, Wang Y, Zhang S, Zhang Z, Chai H, Fan W, Yi C, Ding Y, Wang J, Sulijid J, Liu Y. Prevalence and molecular characterization of Cryptosporidium spp. in dairy and beef cattle in Shanxi, China. Parasitol Res 2023; 123:8. [PMID: 38052995 DOI: 10.1007/s00436-023-08058-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/27/2023] [Indexed: 12/07/2023]
Abstract
Cryptosporidium spp. are key gastrointestinal protists in humans and animals worldwide. Infected cattle are considered the main source of cryptosporidiosis outbreaks in humans. However, little is known about the genetic makeup of Cryptosporidium populations in Shanxi province, China. We analyzed 858 fecal samples collected from farms in Shanxi. The presence of Cryptosporidium spp. was determined via polymerase chain reaction and subsequent sequence analysis of the small subunit rRNA gene as well as restriction fragment length polymorphism analysis. Cryptosporidium parvum was subtyped following sequence analysis of the 60 kDa glycoprotein gene (gp60). The overall prevalence of Cryptosporidium in cattle was 11.19%, with a prevalence of 13.30% and 8.67% in Lingqiu and Yingxian, respectively. The overall prevalence of Cryptosporidium in dairy and beef cattle was 10.78% and 11.50%, respectively. Cryptosporidium infection was detected across all analyzed age groups. The overall prevalence of Cryptosporidium in diarrhea and nondiarrhea samples was 18.24% and 9.72%, respectively, whereas that in intensively farmed and free-range cattle was 17.40% and 3.41%, respectively. We identified five Cryptosporidium species, with C. andersoni being the dominant species. Further, two cases of mixed infections of Cryptosporidium species were detected. All identified C. parvum isolates belonged to the subtype IIdA17G1.
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Affiliation(s)
- Li Zhao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Mingyuan Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Lifeng Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Shan Zhang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhansheng Zhang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Hailiang Chai
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Wenjun Fan
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Chao Yi
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Yulin Ding
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Jinling Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Jirintai Sulijid
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China
| | - Yonghong Liu
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China.
- Key Laboratory of Clinical Diagnosis and Treatment Technology in Animal Disease, Ministry of Agriculture and Rural Affairs, Hohhot, China.
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