Molecular evidence for the infection of zoo chimpanzees by pig Ascaris

Genetic diversity and identity of Ascaris worms from human and pig hosts in Thailand

Ascaris roundworms are of public health and socio-economic importance worldwide. They are conventionally attributed to two taxa - A. lumbricoides infecting principally human and A. suum infecting principally pig. Phylogenomic analysis has revealed that Ascaris worms from both human and pig are represented in Clades A and B. A recent study indicates that the Ascaris worms from human and pig in Thailand belong to Clade A. We examined adult Ascaris worms from human and pig in Thailand by means of the partial sequences of three mitochondrial genes (cox1, cox2 and nad1) and concatenation of these genes. Phylogenomic analysis indicates that two isolates (H1,H2) of A. lumbricoides from human belonged to Clade B; one isolate (H3) belonged to Clade A (based on cox1, cox2 and concatenated sequences) or as an outlier to Clades A and B (based on nad1 sequences). All the eight isolates of A. suum from pig clustered in Clade A. The partial nad1 and the concatenated sequences revealed two lineages of A. suum isolates which were distinct from the two A. lumbricoides isolates of Clade B. It is evident that greater genetic diversity, and a more robust phylogeny, could be uncovered by the application of multiple genes. In sum, the present study reveals the presence in Thailand of A. lumbricoides from human in Clades A and B which necessitates appropriate treatment and control measures; Clades A and B have been reported to contain haplotypes of Ascaris worms from both human and pig in other parts of the world. A country wide study is needed to elucidate the identity, distribution, prevalence, cross transmission, genetic diversity and phylogeny of the Ascaris worms in Thailand.

Mitochondrial phylogenomics of human-type Ascaris, pig-type Ascaris, and hybrid Ascaris populations

Ascaris lumbricoides and Ascaris suum are parasitic nematodes in human and pig intestines. The two species can cross infect and produce hybrids, which contribute to the controversy concerning the taxonomy of A. lumbricoides and A. suum. The purpose of this study was to investigate the microevolutionary process and evolutionary history of human-type Ascaris, pig-type Ascaris, and hybrid Ascaris and provide a theoretical basis for the prevention and control of human and animal ascariasis. The mitochondrial phylogenomics of human-type Ascaris (n = 5), pig-type Ascaris (n = 6), and hybrid Ascaris (n = 6) populations were analyzed using high-throughput sequencing technology. The mitochondrial genomes of human-type Ascaris, pig-type Ascaris, and hybrid Ascaris contained 36 genes (atp8 was missing), including 12 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. All genes were located on the heavy chain. The initiation codons used for protein-coding genes were ATT and TTG and the termination codons were TAA and TAG. The base distribution showed obvious AT preference. The phylogenetic tree based on the Ascaris mitochondrial genomes showed three main clusters (A, B, and C). The Ascaris populations sequenced in this study were all gathered in cluster B. The human-type and hybrid Ascaris populations belonged to different sub-clusters, but the pig-type Ascaris population was more scattered. The mitochondrial genome sequences of the 17 Ascaris individuals in this study did not differ much. The results of this study indicate that Ascaris populations were geographically isolated before host shift. In addition, the data show that there are differences between hybrid Ascaris, human-type Ascaris, and pig-type Ascaris. The information has important theoretical significance and application value.

Molecular identification of Ascaris lumbricoides and Ascaris suum recovered from humans and pigs in Thailand, Lao PDR, and Myanmar

Ascaris lumbricoides is the largest roundworm known from the human intestine while Ascaris suum is an internal parasite of pigs. Ascariasis, caused by Ascaris lumbricoides, has a worldwide distribution. Here, we have provided the first molecular identification of Ascaris eggs and adults recovered from humans and pigs in Thailand, Lao PDR, and Myanmar. We amplified and sequenced nuclear ribosomal DNA (ITS1 and ITS2 regions) and mitochondrial DNA (cox1 gene). Sequence chromatograms of PCR-amplified ITS1 region revealed a probable hybrid genotype from two human ascariasis cases from Chiang Mai Province, northern Thailand. All complete ITS2 sequences were identical and did not differ between the species. Phylogenetic trees and haplotype analysis of cox1 sequences showed three clusters with 99 haplotypes. Forty-seven samples from the present study represented 14 haplotypes, including 7 new haplotypes. To our knowledge, this is the first molecular confirmation of Ascaris species in Thailand, Lao PDR, and Myanmar. Zoonotic cross-transmission of Ascaris roundworm between pigs and humans probably occurs in these countries.

Use of AFLP for the study of eukaryotic pathogens affecting humans

Amplified fragment length polymorphism (AFLP) is a genotyping technique based on PCR amplification of specific restriction fragments from a particular genome. The methodology has been extensively used in plant biology to solve a variety of scientific questions, including taxonomy, molecular epidemiology, systematics, population genetics, among many others. The AFLP share advantages and disadvantages with other types of molecular markers, being particularly useful in organisms with no previous DNA sequence knowledge. In eukaryotic pathogens, the technique has not been extensively used, although it has the potential to solve many important issues as it allows the simultaneous examination of hundreds or even thousands of polymorphic sites in the genome of the organism. Here we describe the main applications published on the use of AFLP in eukaryotic pathogens, with emphasis in species of the groups fungi, protozoa and helminths, and discuss the role of this methodology in the context of new techniques derived from the advances of the next generation sequencing.

Discordant population histories of host and its parasite: A role for ecological permeability of extreme environment?

Biogeographical and ecological barriers strongly affect the course of micro-evolutionary processes in free living organisms. Here we assess the impact of a recently emerged barrier on populations of limnic fauna. Genetic diversity and population structure in a host-parasite system (Wenyonia virilis tapeworm, Synodontis schall catfish) are analyzed in the recently divided Turkana and Nile basins. The two basins, were repeatedly connected during the Holocene wet/dry climatic oscillations, following late Pleistocene dessication of the Turkana basin. Mitochondrial DNA sequences for cytochrome oxidase I gene (cox I) and a whole genome scanning method—amplified fragment length polymorphism (AFLP) were employed. A total of 347 cox I sequences (representing 209 haplotypes) and 716 AFLP fragments, as well as 120 cox I sequences (20 haplotypes) and 532 AFLP fragments were obtained from parasites and hosts, respectively. Although results indicate that host and parasite populations share some formative traits (bottlenecks, Nilotic origin), their population histories/patterns differ markedly. Mitochondrial analysis revealed that parasite populations evolve significantly faster and show remarkably higher genetic variability. Analyses of both markers confirmed that the parasites undergo lineage fission, forming new clusters specific for either freshwater or saline parts of Lake Turkana. In congruence with the geological history, these clusters apparently indicate multiple colonisations of Lake Turkana from the Nile. In contrast, the host population pattern indicates fusion of different colonisation waves. Although fish host populations remain connected, saline habitats in Lake Turkana (absent in the Nile), apparently pose a barrier to the gene flow in the parasite, possibly due to its multihost lifecycle, which involves freshwater annelids. Despite partially corroborating mitochondrial results, AFLP data was not sufficiently informative for analyzing populations with recently mixed biogeographic histories.

Whipworms in humans and pigs: origins and demography

Background

Trichuris suis and T. trichiura are two different whipworm species that infect pigs and humans, respectively. T. suis is found in pigs worldwide while T. trichiura is responsible for nearly 460 million infections in people, mainly in areas of poor sanitation in tropical and subtropical areas. The evolutionary relationship and the historical factors responsible for this worldwide distribution are poorly understood. In this study, we aimed to reconstruct the demographic history of Trichuris in humans and pigs, the evolutionary origin of Trichuris in these hosts and factors responsible for parasite dispersal globally.

Methods

Parts of the mitochondrial nad1 and rrnL genes were sequenced followed by population genetic and phylogenetic analyses. Populations of Trichuris examined were recovered from humans (n = 31), pigs (n = 58) and non-human primates (n = 49) in different countries on different continents, namely Denmark, USA, Uganda, Ecuador, China and St. Kitts (Caribbean). Additional sequences available from GenBank were incorporated into the analyses.

Results

We found no differentiation between human-derived Trichuris in Uganda and the majority of the Trichuris samples from non-human primates suggesting a common African origin of the parasite, which then was transmitted to Asia and further to South America. On the other hand, there was no differentiation between pig-derived Trichuris from Europe and the New World suggesting dispersal relates to human activities by transporting pigs and their parasites through colonisation and trade. Evidence for recent pig transport from China to Ecuador and from Europe to Uganda was also observed from their parasites. In contrast, there was high genetic differentiation between the pig Trichuris in Denmark and China in concordance with the host genetics.

Conclusions

We found evidence for an African origin of T. trichiura which were then transmitted with human ancestors to Asia and further to South America. A host shift to pigs may have occurred in Asia from where T. suis seems to have been transmitted globally by a combination of natural host dispersal and anthropogenic factors.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1325-8) contains supplementary material, which is available to authorized users.

Complete mitochondrial genomes of chimpanzee- and gibbon-derived Ascaris isolated from a zoological garden in southwest China

Roundworms (Ascaridida: Nematoda), one of the most common soil-transmitted helminths (STHs), can cause ascariasis in various hosts worldwide, ranging from wild to domestic animals and humans. Despite the veterinary and health importance of the Ascaridida species, little or no attention has been paid to roundworms infecting wild animals including non-human primates due to the current taxon sampling and survey bias in this order. Importantly, there has been considerable controversy over the years as to whether Ascaris species infecting non-human primates are the same as or distinct from Ascaris lumbricoides infecting humans. Herein, we first characterized the complete mitochondrial genomes of two representative Ascaris isolates derived from two non-human primates, namely, chimpanzees (Pan troglodytes) and gibbons (Hylobates hoolock), in a zoological garden of southwest China and compared them with those of A. lumbricoides and the congeneric Ascaris suum as well as other related species in the same order, and then used comparative mitogenomics, genome-wide nucleotide sequence identity analysis, and phylogeny to determine whether the parasites from chimpanzees and gibbons represent a single species and share genetic similarity with A. lumbricoides. Taken together, our results yielded strong statistical support for the hypothesis that the chimpanzee- and gibbon-derived Ascaris represent a single species that is genetically similar to A. lumbricoides, consistent with the results of previous morphological and molecular studies. Our finding should enhance public alertness to roundworms originating from chimpanzees and gibbons and the mtDNA data presented here also serves to enrich the resource of markers that can be used in molecular diagnostic, systematic, population genetic, and evolutionary biological studies of parasitic nematodes from either wild or domestic hosts.

Molecular characterization and phylogenetic analysis of ascarid nematodes from twenty-one species of captive wild mammals based on mitochondrial and nuclear sequences

Although ascarid nematodes are important parasites of wild animals of public health concern, few species of ascarids from wild animals have been studied at the molecular level so far. Here, the classification and phylogenetic relationships of roundworms from 21 species of captive wild animals have been studied by sequencing and analysis of parts of the ribosomal 18S and 28S genes and the mitochondrial (mt) 12S gene. Phylogenetic relationships were inferred by 3 methods (NJ/MP/ML) based on the data of single gene sequences and concatenated sequences. Homology analysis indicated that the 18S sequences were conserved among roundworms from all 21 species and that 28S showed interspecies variability. Divergence levels displayed in 12S suggested that 12S appears to be either intra- or interspecifically variable. Evolutionary trees indicated that the ascarids split into 2 families, 4 genera and 7 species, with high bootstrap support for each clade. Combined trees suggested that Baylisascaris ailuri is more closely related to B. transfuga than to B. schroederi. This study provides useful molecular markers for the classification, phylogenetic analysis and epidemiological investigation of roundworms from wild animals.

Phylogeography of Ascaris lumbricoides and A. suum from China

In order to obtain further understanding of genetic structure and evolutionary relationship of Ascaris from humans and pigs, phylogeography study on 12 populations from six endemic regions in China was conducted using mitochondrial DNA markers (cytochrome c oxidase subunit 1 (COX1) and NAD1) and the software programs of DnaSP 5.0, Arlequin 3.0, MEGA 4.0, and NETWORK 4.5.1.6. Results showed that (a) genetic diversity of Ascaris varied with hosts and locations, but no distinct geographical distribution pattern was found, (b) a higher level of genetic diversity and differentiation was found in pig-derived populations in contrast to human-derived ones, and in populations of human-derived Ascaris from the southern regions in comparison to that from the middle and northern locations, but similar geographical difference was not observed within pig-derived populations, (c) historical population expanding was detected from a large part of human-derived Ascaris populations but not in pig-derived Ascaris, (d) a high level of gene flow was detected between human- and pig-derived Ascaris and also among human-derived populations, and (e) network analysis from haplotype of COX1 indicated an ancestral haplotype from human-derived Ascaris. In conclusion, the present study revealed new information on Ascaris on the aspects of genetic diversity, population differentiation and historical demographic patterns, gene flow, phylogenesis reconstruction, and haplotype network, discussed the results with historical demographic migration of humans and domestication of wild boar in China, and raised a different assumption about the evolutionary relationship of the two roundworms. This study should have certain enlightenment for the epidemiology and the evolutionary and taxonomy relationship of Ascaris from humans and pigs.

Prevalence of extra-intestinal porcine helminth infections and assessment of sanitary conditions of pig slaughter slabs in Dar es Salaam city, Tanzania

A study was carried out to establish the prevalence of extra-intestinal porcine helminth infections and to assess the pig slaughter slab sanitary conditions in Dar es Salaam city, Tanzania. A total of 24 privately owned pig slaughter slabs were assessed. All slaughter slabs were sub-standard; wrongly located, poorly designed and constructed and lacked most basic requirements for a slaughter house. Because of inadequate slaughtering, disposal and cleaning facilities, the slaughter slabs were under unhygienic condition with questionable safety, soundness and wholesomeness of the pork produced. Routine meat inspection procedures were used to detect extra-intestinal porcine helminth infections. Of the 731 examined pigs; 8.1%, 5.9% and 0.4% were infected with ascariosis, porcine cysticercosis and hydatidosis, respectively. It was noted that almost all slaughter pigs in Dar es Salaam originated from different regions. Based on the region of origin, the status of porcine cysticercosis was 8.2% for Dodoma (n = 98), 8.2% for Manyara (n = 260) and 6.9% for Mbeya (n = 116). This study disclosed the unhygienic sanitary condition prevailing in Dar es Salaam pig slaughter slabs and recommends that strategies should be devised to improve the situation. Porcine ascariosis and cysticercosis were widely prevalent and caused economic losses due to condemnations. Because of their zoonotic nature, the observed extra-intestinal porcine helminth infections in pig pose a public health risk among consumers. Thus, there is a need to introduce appropriate control measures of parasitic infections in pigs.

Gastrointestinal parasites of the chimpanzee population introduced onto Rubondo Island National Park, Tanzania

The release of any species into a novel environment can evoke transmission of parasites that do not normally parasitize the host as well as potentially introducing new parasites into the environment. Species introductions potentially incur such risks, yet little is currently known about the parasite fauna of introduced primate species over the long term. We describe the results of long-term monitoring of the intestinal parasite fauna of an unprovisioned, reproducing population of chimpanzees introduced 40 years earlier (1966-1969) onto Rubondo Island in Lake Victoria, Tanzania, a non-native habitat for chimpanzees. Two parasitological surveys (March 1997-October 1998 and October 2002-December 2005) identified Entamoeba spp. including E. coli, Iodamoeba buetschlii, Troglodytella abrassarti, Chilomastix mesnili, Trichuris sp., Anatrichosoma sp., Strongyloides spp., Strongylida fam. gen. sp., Enterobius anthropopitheci, Subulura sp., Ascarididae gen. sp., and Protospirura muricola. The parasite fauna of the Rubondo chimpanzees is similar to wild chimpanzees living in their natural habitats, but Rubondo chimpanzees have a lower prevalence of strongylids (9%, 3.8%) and a higher prevalence of E. anthropopitheci (8.6%, 17.9%) than reported elsewhere. Species prevalence was similar between our two surveys, with the exception of Strongyloides spp. being higher in the first survey. None of these species are considered to pose a serious health risk to chimpanzees, but continued monitoring of the population and surveys of the parasitic fauna of the two coinhabitant primate species and other animals, natural reservoir hosts of some of the same parasites, is important to better understand the dynamics of host-parasite ecology and potential long-term implications for chimpanzees introduced into a new habitat.

Molecular evidence for sustained transmission of zoonotic Ascaris suum among zoo chimpanzees (Pan troglodytes)

Chimpanzees in the Copenhagen Zoo frequently excrete ascarid worms onto the cage floor in spite of a regular anthelmintic treatment program. Previously it had been shown that the source of the infections was of pig origin. However, it was unknown whether the recurrence of the infection was due to reintroduction of eggs from an external source or to a sustained transmission cycle within the zoo. We found that isolated eggs were able to embryonate to the infective J3 stage and PCR-RFLP analysis on the ITS region amplified from single embryonated eggs suggest these to be Ascaris suum. In addition, sequence analysis of the cox1 gene ('barcoding') on expelled worms followed by cluster analysis revealed that the chimpanzees are infected with pig A. suum which now, in spite of control efforts, has stabilized into a permanent transmission cycle in the zoo's chimpanzee troop.

Disentangling hybridization and host colonization in parasitic roundworms of humans and pigs

Knowledge of cross-transmission and hybridization between parasites of humans and reservoir hosts is critical for understanding the evolution of the parasite and for implementing control programmes. There is now a consensus that populations of pig and human Ascaris (roundworms) show significant genetic subdivision. However, it is unclear whether this has resulted from a single or multiple host shift(s). Furthermore, previous molecular data have not been sufficient to determine whether sympatric populations of human and pig Ascaris can exchange genes. To disentangle patterns of host colonization and hybridization, we used 23 microsatellite loci to conduct Bayesian clustering analyses of individual worms collected from pigs and humans. We observed strong differentiation between populations which was primarily driven by geography, with secondary differentiation resulting from host affiliation within locations. This pattern is consistent with multiple host colonization events. However, there is low support for the short internal branches of the dendrograms. In part, the relationships among clusters may result from current hybridization among sympatric human and pig roundworms. Indeed, congruence in three Bayesian methods indicated that 4 and 7% of roundworms sampled from Guatemala and China, respectively, were hybrids. These results indicate that there is contemporary cross-transmission between populations of human and pig Ascaris.