Next-generation sequencing amplicon analysis of the genetic diversity of Eimeria populations in livestock and wildlife samples from Australia

Eimeria is an important coccidian enteric parasite that infects a wide range of hosts and can cause substantial economic losses in the poultry and livestock industries. It is common for multiple Eimeria species to infect individual hosts, and this can make species identification difficult due to morphological similarities between species and mixed chromatograms when using Sanger sequencing. Relatively few studies have applied next-generation amplicon sequencing (NGS) to determining the genetic diversity of Eimeria species in different hosts. The present study screened 408 faecal samples from a range of hosts including livestock and wildlife using a previously developed quantitative polymerase chain reaction (qPCR) at the 18S locus and conducted amplicon NGS on the positives using a ~ 455-bp fragment of the 18S locus. A total of 41 positives (10.1%) were identified by qPCR from various hosts and NGS was successful for 38 of these positives. Fifteen Eimeria species and three genotypes were detected by NGS: E. ferrisi, E. kanyana, E. potoroi, E. quokka, E. setonicis, E. trichosuri, E. reichenowi, E. angustus, E. ahsata, E. auburnensis, E. bovis, E. brasiliensis, E. christenseni, E. crandallis, E. ovinoidalis, Eimeria sp. (JF419345), Eimeria sp. (JF419349) and Eimeria sp. (JF419351). Mixed infections were detected in 55.3% (21/38) of positive samples. The most striking finding was the identification of the same species in different hosts. This could be due to contamination and/or mechanical transmission or may provide support for previous studies suggesting that Eimeria species can infect not just closely related hosts but different genera and further research is required. This is also the first study to audit Eimeria populations in livestock (sheep and cattle) by NGS and could be applied in the future to determine the extent of pathogenic species and outcomes of Eimeria control strategies.

The biology and palaeontology of the Peramelemorphia: a review of current knowledge and future research directions

Bandicoots and bilbies (Marsupialia : Peramelemorphia) represent the dominant omnivorous clade of Australasian marsupials and, as ground-dwelling, small- to medium-sized mammals, have not fared well in the 200 years since European settlement. Unlike large or charismatic marsupial species, the cryptic nature of bandicoots and bilbies tends to keep them out of the public eye, at a time when public interest plays a significant role in conservation efforts. The inconspicuous ‘rat-like’ appearance of many bandicoots and a generalist ecological strategy belie a complex biology of adaptive traits and evolutionary diversity. For a few species these biological traits have enabled them to make use of urban environments. In the main, however, peramelemorphians are facing ongoing pressure from introduced predators and human impacts. Basic biological information for many species, particularly those from New Guinea, is still lacking. In this review, we examine advances in the knowledge of the biology of this group over the past 25 years including anatomical, physiological and ecological studies. We also provide a comprehensive review of the fossil records of bandicoots in order to provide an up-to-date platform for future studies. From this work, it is clear that there is still much to be done regarding the taxonomy and biology of these animals before a more detailed understanding of the evolutionary history of this group can be elucidated.

Studies on coccidian oocysts (Apicomplexa: Eucoccidiorida)

The oocysts of the coccidia are robust structures, frequently isolated from the feces or urine of their hosts, which provide resistance to mechanical damage and allow the parasites to survive and remain infective for prolonged periods. The diagnosis of coccidiosis, species description and systematics, are all dependent upon characterization of the oocyst. Therefore, this review aimed to the provide a critical overview of the methodologies, advantages and limitations of the currently available morphological, morphometrical and molecular biology based approaches that may be utilized for characterization of these important structures. It has become apparent that no single methodology is sufficient to fully characterize these structures and the majority of researchers favor the use of combinational or polyphasic approaches.