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Bradbury R, Inagaki K, Singh G, Agana U, Patterson K, Malloch L, Rodriguez E, Qvarnstrom Y, Hobbs CV. A Pilot Comparison of Fixatives for Hookworm Real-time Polymerase Chain Reaction. Am J Trop Med Hyg 2023; 108:335-339. [PMID: 36509060 PMCID: PMC9896329 DOI: 10.4269/ajtmh.22-0406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/06/2022] [Indexed: 12/15/2022] Open
Abstract
Polymerase chain reaction (PCR) is increasingly used in the diagnosis of soil-transmitted helminth infections. Despite this, few studies have evaluated the impact of different fecal fixatives on the outcome of fecal helminth qPCR analysis, and none have evaluated the effect of commercial parasitology fixatives commonly used in diagnostic laboratories. We fixed dog feces containing Ancylostoma spp. hookworm eggs in zinc polyvinyl alcohol (Zn-PVA) and Total-Fix, and with 70% ethanol (EtOH) as a control. DNA was extracted at timepoints 11, 33, 64, and 94 days and subjected to Ancylostoma spp. quantitative PCR (qPCR). A linear regression model was created to assess the effect of preservative types on the temporal change of qPCR quantification cycle number (Cq) values, accounting for variances among individual animals. Fixation in 70% EtOH least affected Cq values over 94 days. Total-Fix preservation yielded a higher Cq overall, but there was no significant difference compared with 70% EtOH fixation. Fixation in Zn-PVA resulted in significantly (P < 0.001) higher Cq values than 70% EtOH after only 33 days and loss of amplification at 64 days. Consistent with other helminth fixation studies, 70% EtOH performed well in preserving hookworm DNA over 94 days. Total-Fix provided a comparable alternative for qPCR analysis for hookworm. Fixation in Zn-PVA resulted in loss of detectable hookworm DNA at 64 days, as determined by qPCR.
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Affiliation(s)
| | - Kengo Inagaki
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
- Department of Pediatrics, Division of Infectious Disease, Children’s of Mississippi, University of Mississippi Medical Center, Jackson, Mississippi
| | - Gurbaksh Singh
- Department of Pediatrics, Division of Infectious Disease, Children’s of Mississippi, University of Mississippi Medical Center, Jackson, Mississippi
| | - Urita Agana
- Department of Pediatrics, Division of Infectious Disease, Children’s of Mississippi, University of Mississippi Medical Center, Jackson, Mississippi
| | - Kayla Patterson
- Department of Pediatrics, Division of Infectious Disease, Children’s of Mississippi, University of Mississippi Medical Center, Jackson, Mississippi
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
| | - Lacy Malloch
- Department of Pediatrics, Division of Infectious Disease, Children’s of Mississippi, University of Mississippi Medical Center, Jackson, Mississippi
| | - Eduardo Rodriguez
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Charlotte V. Hobbs
- Department of Pediatrics, Division of Infectious Disease, Children’s of Mississippi, University of Mississippi Medical Center, Jackson, Mississippi
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Tuli MD, Li H, Li S, Zhai J, Wu Y, Huang W, Feng Y, Chen W, Yuan D. Molecular detection of a novel Ancylostoma sp. by whole mtDNA sequence from pangolin Manis javanica. Parasit Vectors 2022; 15:70. [PMID: 35236404 PMCID: PMC8889679 DOI: 10.1186/s13071-022-05191-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/03/2022] [Indexed: 12/05/2022] Open
Abstract
Background Ancylostoma species are hematophagous parasites that cause chronic hemorrhage in various animals and humans. Pangolins, also known as scaly anteaters, are mammals that live in soil environments where they are readily exposed to soil-borne parasitic nematodes. However, only a limited number of helminth species have been identified in this animal host so far. Methods Ancylostoma sp. was isolated from a wild pangolin, and the complete mitochondrial (mt) genome of Ancylostoma sp. was obtained by Illumina sequencing of total genomic DNA. Results The circular complete mt genome that was assembled had a total length of 13,757 bp and comprised 12 protein-coding genes (PCGs), 22 transfer ribosomal RNAs, two ribosomal RNAs (rRNAs), two non-coding regions and one AT-rich region, but lacked the gene coding for ATPase subunit 8 (atp8). The overall AT content of the mt genome of Ancylostoma sp. was 76%, which is similar to that of other nematodes. The PCGs used two start codons (ATT and TTG) and three stop codons (TAA, TAG, and T). The nucleotide identity of the 12 PCGs ranged from 83.1% to 89.7% and had the highest sequence identity with Ancylostoma caninum among species in the Ancylostomatidae family. Also, the pangolin-derived Ancylostoma sp. lacked repeat sequences in the non-coding regions and in the unique sequence of the short non-coding regions, which differentiated it from other Ancylostoma species. In addition, phylogenetic analyses of 18S rRNA and mtDNA sequences revealed that the Ancylostoma sp. was positioned in a separate branch in the subfamily Ancylostomatinae along with other Ancylostoma species. Conclusions The Ancylostoma sp. isolated from a pangolin in this study was identified as a possible new Ancylostoma species. The identification of this Ancylostoma sp. from pangolin enriches our knowledge of the species in the Ancylostomatidae family and provides information that will lead to a better understanding of the taxonomy, diagnostics, and biology of hookworms. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05191-0.
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Affiliation(s)
- Merga Daba Tuli
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Hongyi Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Song Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Junqiong Zhai
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Yajiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China
| | - Wanyi Huang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, 510070, China.
| | - Dongjuan Yuan
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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Rothmann-Meyer W, Naidoo K, de Waal PJ. Comparative mitogenomics of Spirocerca lupi from South Africa and China: Variation and possible heteroplasmy. Vet Parasitol 2021; 300:109595. [PMID: 34678674 DOI: 10.1016/j.vetpar.2021.109595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/21/2022]
Abstract
The complete mitochondrial genome of Spirocerca lupi isolated from a dog in South Africa was sequenced using next generation sequencing (NGS) technology and the 12 protein coding genes along with the two rRNA genes were compared to 18 other nematode species as well as S. lupi from China. The mitochondrial genome of S. lupi South Africa had a mean genetic diversity of 6.1 % compared to S. lupi China with some variation in nucleotide composition, gene positioning and size. Pairwise distance results indicated slightly higher variation when compared to the pairwise distances of other closely related species, however, this variation was not high enough for it to be considered a cryptic species. Phylogenetic analysis indicated that S. lupi from the two continents are very similar. In addition, single nucleotide polymorphisms were detected in the nad2 gene with ten sequence variants identified from 10 clones from a single nematode, suggesting possible heteroplasmy. The origin of the heteroplasmy is currently unknown but it is speculated to have arisen from accumulated mutations in the mitochondria during somatic replication.
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Xie Y, Xu Z, Zheng Y, Li Y, Liu Y, Wang L, Zhou X, Zuo Z, Gu X, Yang G. The mitochondrial genome of the dog hookworm Ancylostoma caninum (Nematoda, Ancylostomatidae) from Southwest China. Mitochondrial DNA B Resour 2019; 4:3002-3004. [PMID: 33365829 PMCID: PMC7706842 DOI: 10.1080/23802359.2019.1666048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 08/16/2019] [Indexed: 10/28/2022] Open
Abstract
The dog hookworm Ancylostoma caninum (Nematoda, Ancylostomatidae) is a blood-feeding intestinal parasitic nematode and can cause ancylostomiasis in humans. In this study, the complete mitochondrial genome of this anthropozoonotic hookworm was sequenced through Illumina deep sequencing technology. The whole genome was 13,721 bp in length and encoded 36 genes including 12 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. Phylogeny revealed that A. caninum grouped with species from Ancylostomatinae and separated from species of Bunostominae in the family Ancylostomatidae. Amongst the subfamily Ancylostomatinae, three dog-originated A. caninum, regardless of isolate origins, clustered together and were more closely related to the cat hookworm A. tubaeforme and the human hookworm A. duodenale than to the dog/cat hookworm A. ceylanicum and the sea lion hookworm Uncinaria sanguinis. Taken together, the cumulative mitochondrial DNA data provides insights into phylogenetic studies among Ancylostomatidae nematodes.
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Affiliation(s)
- Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ziyi Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Youle Zheng
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yingxin Li
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunjian Liu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lu Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xuan Zhou
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhicai Zuo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Monteiro KJL, Jaeger LH, Nunes BC, Calegar DA, Reis ERCD, Bacelar PAA, Santos JPD, Bóia MN, Carvalho-Costa FA. Mitochondrial DNA reveals species composition and phylogenetic relationships of hookworms in northeastern Brazil. Infect Genet Evol 2018; 68:105-112. [PMID: 30508686 DOI: 10.1016/j.meegid.2018.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/24/2018] [Accepted: 11/26/2018] [Indexed: 11/17/2022]
Abstract
Hookworm infection persists focally in rural communities in Brazil. In this study, we analyze the mitochondrial nucleotide sequences obtained from hookworms infecting humans in order to characterize species composition and assess their genetic diversity and phylogenetic relationships. Field expeditions and cross-sectional surveys were carried out in three Brazilian municipalities from 2013 to 2017: Nossa Senhora de Nazaré (n = 605) and Teresina (n = 297), in the state of Piauí, and Russas (n = 213) in the State of Ceará. Parasitological methods were used to evaluate fecal samples. Hookworm-positive samples had a partial mtDNA cox1 amplified and sequenced. Maximum-likelihood and Bayesian analysis demonstrated two strongly-supported clades, including Group A, corresponding to Necator americanus, and Groups B and C, corresponding to Necator sp. Group A was divided into three main clusters: A1 grouped with Asian sequences, A2 grouped with African sequences, and A3 had only Asian sequences. Group B was closely related to Necator sp., showing a sequence similarity of 98%-99% with African samples circulating zoonotically among humans and non-human primates. Twenty three N. americanus haplotypes were identified. N. americanus Median-Joining network revealed three distinct groups, designated again as A1, A2, and A3. Group A1 presented a star-like shape, with one dominant haplotype. The molecular dating suggested that the two clades dividing N. americanus and Necator sp. began to diverge during the middle Pleistocene. The most recent common ancestor among N. americanus groups was dated to the late Pleistocene. Hookworms circulating in the studied communities are structured in well-defined subpopulations presenting both Asian and African genetic backgrounds. This reveals a double origin for hookworms in northeastern Brazil and opens up new possibilities in phylogeographic, evolutionary, and molecular epidemiological studies in regions where hookworms persists focally, despite control efforts. The presence of potentially zoonotic species and the specific identification of Necator sp. should be further investigated.
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Affiliation(s)
- Kerla Joeline Lima Monteiro
- Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Oswaldo Cruz Foundation, Teresina, Piauí, Brazil
| | - Lauren Hubert Jaeger
- Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Beatriz Coronato Nunes
- Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Deiviane Aparecida Calegar
- Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Elis Regina Chaves Dos Reis
- Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Polyanna Araújo Alves Bacelar
- Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Oswaldo Cruz Foundation, Teresina, Piauí, Brazil
| | - Jéssica Pereira Dos Santos
- Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Oswaldo Cruz Foundation, Teresina, Piauí, Brazil
| | - Márcio Neves Bóia
- Laboratory of Biology and Parasitology of Wild Reservoir Mammals, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Filipe Anibal Carvalho-Costa
- Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Oswaldo Cruz Foundation, Teresina, Piauí, Brazil.
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