Who bit the boat? New DNA collection and genomic methods enable species identification in suspected shark-related incidents.

Species identification following shark-related incidents is critical for effective incident management and for collecting data to inform shark-bite mitigation strategies. Witness statements are not always reliable, and species identification is often ambiguous or missing. Alternative methods for species identification include morphological assessments of bite marks, analysis of collected teeth at the scene of the incident, and genetic approaches. However, access to appropriate collection media and robust genetic assays have limited the use of genetic technologies. Here, we present a case study that facilitated a unique opportunity to compare the effectiveness of medical gauze readily available in first-aid kits, and forensic-grade swabs in collecting genetic material for shark-species identification. Sterile medical gauze and forensic-grade swabs were used to collect transfer DNA from the bite margins on a bitten surf ski which were compared to a piece of shark tissue embedded along the bite margin. Witness accounts and the characteristics of the bite mark impressions inferred the involvement of a Carcharodon carcharias (white shark). The morphology of a tooth found on the boat that picked up the surf ski, however, suggested it belonged to an Orectolobus spp. (wobbegong). Genetic analysis of DNA transferred from the shark to the surf ski included the application of a broad-target nested PCR assay followed by Sanger sequencing, with white shark contribution to the 'total sample DNA' determined with a species-specific qPCR assay. The results of the genetic analyses were congruent between sampling methods with respect to species identification and the level of activity inferred by the donor-specific DNA contribution. These data also supported the inferences drawn from the bite mark morphology. DNA from the recovered tooth was PCR amplified with a wobbegong-specific primer pair designed for this study to corroborate the tooth's morphological identification. Following the confirmation of gauze used for sampling in the case study event, two additional isolated incidents occurred and were sampled in situ using gauze, as typically found in a first-aid kit, by external personnel. DNA extracted from these gauze samples resulted in the identification of a white shark as the donor of the DNA collected from the bite marks in both instances. This study, involving three incidents separated by time and location, represents the seminal application of gauze as a sampling media after critical human-shark interactions and strongly supports the practical implementation of these methods in the field.

Tips to Support the Recruitment, Retention, and Progression of Clinical Academics.

Training to become a clinical academic is a long and arduous process with many obstacles. Many potential candidates fall by the wayside both during and following completion of the combined clinical and academic training pathway with negative implications for clinical and translational research and teaching. Findings from a recent national multi-funder study, alongside clinical academic experiences and current literature, have led to the creation of this 12-tip paper. The tips are targeted at supervisors and employers of clinical academics, aiming to improve recruitment, experiences, retention, and progression through the career path.

Development and Validation of Novel PCR Assays for the Diagnosis of Bovine Stephanofilariasis and Detection of Stephanofilaria sp. Nematodes in Vector Flies.

BACKGROUND: Stephanofilaria spp. nematodes are associated with cutaneous lesions in cattle and other livestock and mammalian wildlife species. In Australia, Haematobia irritans exigua, commonly known as buffalo fly (BF) transmits a well-described but presently unnamed species of Stephanofilaria, which has been speculatively implicated in the aetiology of BF lesions. The sensitivity of current techniques for detecting Stephanofilaria spp. in skin lesions and vector species is low, and there is no genomic sequence for any member of the genus Stephanofilaria currently available in sequence databases. METHODS: To develop molecular assays for the detection of the Australian Stephanofilaria sp., skin biopsies were collected from freshly slaughtered cattle with typical lesions near the medial canthus. Adult nematodes and microfilariae were isolated from the biopsies using a saline recovery technique. The nematodes were morphologically identified as Stephanofilaria sp. by scanning electron microscopy. DNA was extracted and the internal transcribed spacer 2 (ITS2) region of rDNA, and the cytochrome c oxidase subunit 1 (cox1) region of mtDNA was amplified and sequenced. Stephanofilaria sp. specific polymerase chain reaction (PCR) and qPCR assays (SYBR Green® and TaqMan™) were developed and optimised from the novel ITS2 sequence obtained. The specificity of each assay was confirmed by testing against nematode species Onchocerca gibsoni and Dirofilaria immitis, as well as host (bovine) and BF DNA. RESULTS: Scanning electron microscopy of the anterior and posterior ends of isolated nematodes confirmed Stephanofilaria sp. A phylogenetic analysis of the cox1 sequence demonstrated that this species is most closely related to Thelazia callipaeda, a parasitic nematode that is a common cause of thelaziasis (or eyeworm infestation) in humans, dogs, and cats. Both conventional and qPCR assays specifically amplified DNA from Stephanofilaria sp. Conventional PCR, TaqMan™, and SYBR Green® assays were shown to detect 1 ng, 1 pg, and 100 fg of Stephanofilaria DNA, respectively. Both qPCR assays detected DNA from single Stephanofilaria microfilaria. CONCLUSION: Molecular diagnostic assays developed in this study showed high specificity and sensitivity for Stephanofilaria sp. DNA. The availability of an accurate and sensitive PCR assay for Stephanofilaria will assist in determining its role in the pathogenesis of cattle skin lesions, as well as in understanding its epidemiological dynamics. This assay may also have application for use in epidemiological studies with other species of Stephanofilaria, most particularly closely related S. stilesi, but this will require confirmation.

Identifying shark species responsible for fisheries depredation off Southeast Queensland, Australia.

Anecdotal reports from fishers in Southeast Queensland, Australia suggest that shark depredation is a significant issue, however little is known about which species are responsible for depredating catches. This research aimed to identify depredating species in Southeast Queensland line based fisheries, by undertaking a genetic analysis of depredated samples collected by commercial, charter and recreational fishers. The genetic analysis successfully identified ten depredating sharks, all from the genus Carcharhinus (19.2% success). The species identified using mitochondrial DNA included five C. leucas (bull sharks), two C. plumbeus (sandbar sharks), one C. amboinensis (pigeye shark), one C. brevipinna (spinner shark) and one unconfirmed C. plumbeus/C. altimus (bignose shark). While many species of Carcharhinus have been found to depredate catches in Australia, C. leucas has not been highlighted until this research as a potential problematic species. The optimised protocol allowed for the confident identification of shark species responsible for depredation in fisheries using frozen fish samples donated by fishers.

Wolbachia: A tool for livestock ectoparasite control.

Ectoparasites and livestock-associated insects are a major concern throughout the world because of their economic and welfare impacts. Effective control is challenging and relies mainly on the use of chemical insecticides and acaricides. Wolbachia, an arthropod and nematode-infecting, maternally-transmitted endosymbiont is currently of widespread interest for use in novel strategies for the control of a range of arthropod-vectored human diseases and plant pests but to date has received only limited consideration for use in the control of diseases of veterinary concern. Here, we review the currently available information on Wolbachia in veterinary ectoparasites and disease vectors, consider the feasibility for use of Wolbachia in the control of livestock pests and diseases and highlight critical issues which need further investigation.

Molecular markers reveal diversity in composition of Megastigmus (Hymenoptera: Megastigmidae) from eucalypt galls.

Since outbreaks of the invasive blue gum chalcids Leptocybe spp. began, the genus Megastigmus (Hymenoptera: Megastigmidae) has been increasingly studied as containing potential biocontrol agents against these pests. Megastigmus species have been collected and described from Australia, the presumed origin of Leptocybe spp., with M. zvimendeli and M. lawsoni reported as Leptocybe spp. parasitoids established outside of Australia. Parasitic Megastigmus have been reported to occur locally in the Neotropics, Afrotropic, Palearctic, and Indomalaya biogeographic realms, and in many cases described as new to science. However, molecular tools have not been used in studying parasitic Megastigmus, and difficulties in morphological taxonomy have compromised further understanding of eucalypt-associated Megastigmus as well as the Megastigmus-Leptocybe association. In this study, we used molecular markers to study the species composition and phylogeny of Megastigmus collected from eucalypt galls in Australia and from Leptocybe spp. galls from South Africa, Kenya, Israel, China, and Vietnam. We record thirteen discrete species and a species complex associated with eucalypt galls. A summary of morphological characters is provided to assist morphological delimitation of the studied group. A phylogeny based on 28S rDNA identified species groups of importance to Leptocybe spp. biocontrol agents from four clades with nine species. Relationships between Megastigmus from eucalypt galls and their phytophagous congeners were unresolved. Further molecular work is needed to clarify the identity of many species.

Transinfection of buffalo flies (Haematobia irritans exigua) with Wolbachia and effect on host biology.

BACKGROUND: Buffalo flies (Haematobia irritans exigua) (BF) and closely related horn flies (Haematobia irritans irritans) (HF) are invasive haematophagous parasites with significant economic and welfare impacts on cattle production. Wolbachia are intracellular bacteria found widely in insects and currently of much interest for use in novel strategies for the area wide control of insect pests and insect-vectored diseases. In this paper, we report the transinfection of BF towards the development of area-wide controls. METHODS: Three stages of BF; embryos, pupae and adult female flies, were injected with different Wolbachia strains (wAlbB, wMel and wMelPop). The success of transinfection and infection dynamics was compared by real-time PCR and FISH and fitness effects were assessed in transinfected flies. RESULTS: BF eggs were not easily injected because of their tough outer chorion and embryos were frequently damaged with less than 1% hatch rate of microinjected eggs. No Wolbachia infection was recorded in flies successfully reared from injected eggs. Adult and pupal injection resulted in higher survival rates and somatic and germinal tissue infections, with transmission to the succeeding generations on some occasions. Investigations of infection dynamics in flies from injected pupae confirmed that Wolbachia were actively multiplying in somatic tissues. Ovarian infections were confirmed with wMel and wMelPop in a number of instances, though not with wAlbB. Measurement of fitness traits indicated reduced longevity, decreased and delayed adult emergence, and reduced fecundity in Wolbachia-infected flies compared to mock-injected flies. Effects varied with the Wolbachia strain injected with most marked changes seen in the wMelPop-injected flies and least severe effects seen with wAlbB. CONCLUSIONS: Adult and pupal injection were the most suitable methods for transinfecting BF and all three strains of Wolbachia successfully replicated in somatic tissues. The Wolbachia-induced fitness effects seen in transinfected BF suggest potential for use of the wMel or wMelPop strains in Wolbachia-based biocontrol programmes for BF.

Multivariate ratio analysis and DNA markers reveal a new Australian species and three synonymies in eucalypt-gall-associated Megastigmus (Hymenoptera: Megastigmidae).

The genus Megastigmus Dalman, 1820 (Hymenoptera: Megastigmidae) contains potential biocontrol agents of the invasive eucalypt galling chalcid Leptocybe spp. (Hymenoptera: Eulophidae), with several species reported in various parts of the world. Species discrimination is challenging due to intraspecific morphological variation, difficulty in measuring sizes of body parts, and the lack of information regarding the global distribution of parasitic Megastigmus. We used two species commonly associated with Leptocybe in its native range to review taxonomic methods and determine the most reliable morphological characters in species delimitation. We examined size variation of body characters, and conducted species discrimination using multivariate ratio analysis, mitochondrial Cytochrome c oxidase subunit 1 (COI) and nuclear 28S rDNA (28S) sequences. Morphological traits were effective in species delimitation yet revealed high variation in several characters employed in current keys. Knowledge generated on morphology and DNA justified the description of a new species, M. manonae, sp. n., the first record of M. pretorianensis in Australia, and revised diagnostic characters for M. zvimendeli. Based on these diagnostic characters and molecular data, we synonymize three species (M. judikingae, syn. n., from Australia, M. sichuanensis, syn. n., from China and M. icipeensis, syn. n., from Kenya) with M. zvimendeli. Our findings highlight the importance of molecular markers in assisting taxonomic decision-making and the need for coordinated work in identifying Megastigmus associated with Leptocybe spp.

Wolbachia successfully replicate in a newly established horn fly, Haematobia irritans irritans (L.) (Diptera: Muscidae) cell line.

BACKGROUND: Haematobia spp., horn flies (HF) and buffalo flies (BF), are economically important ectoparasites of dairy and beef cattle. Control of these flies relies mainly on treating cattle with chemical insecticides. However, the development of resistance to commonly used compounds is compromising the effectiveness of these treatments and alternative methods of control are required. Wolbachia are maternally transmitted endosymbiotic bacteria of arthropods that cause various reproductive distortions and fitness effects, making them a potential candidate for use in the biological control of pests. The first step towards this is the establishment and adaptation of xenobiotic infections of Wolbachia in target host cell lines. RESULTS: Here, we report the successful establishment of a continuous HF cell line (HIE-18) from embryonic cells and its stable transinfection with Wolbachia strains wAlbB native to mosquitoes, and wMel and wMelPop native to Drosophila melanogaster. HIE-18 cells were typically round and diploid with ten chromosomes (2n = 10) or tetraploid with 20 chromosomes (4n = 20), with a doubling time of 67.2 h. Wolbachia density decreased significantly in HIE-18 cells in the first 48 h of infection, possibly due to overexpression of antimicrobial peptides through the Imd immune signalling pathway. However, density recovered after this time and HIE-18 cell lines stably infected with the three strains of Wolbachia have now each been subcultured more than 50 times as persistently infected lines. CONCLUSION: The amenability of HF cells to infection with different strains of Wolbachia and the establishment of stable sustaining infections suggest the potential for use of Wolbachia in novel approaches for the control of Haematobia spp. Further, the availability of the HIE-18 cell line will provide an important resource for the study of genetics, host-parasite interactions and chemical resistance in Haematobia populations. © 2020 Society of Chemical Industry.

Wolbachia Endosymbiont of the Horn Fly (Haematobia irritans irritans): a Supergroup A Strain with Multiple Horizontally Acquired Cytoplasmic Incompatibility Genes.

The horn fly, Haematobia irritansirritans, is a hematophagous parasite of livestock distributed throughout Europe, Africa, Asia, and the Americas. Welfare losses on livestock due to horn fly infestation are estimated to cost between $1 billion and $2.5 billion (U.S. dollars) annually in North America and Brazil. The endosymbiotic bacterium Wolbachia pipientis is a maternally inherited manipulator of reproductive biology in arthropods and naturally infects laboratory colonies of horn flies from Kerrville, TX, and Alberta, Canada, but it has also been identified in wild-caught samples from Canada, the United States, Mexico, and Hungary. Reassembly of PacBio long-read and Illumina genomic DNA libraries from the Kerrville H. i. irritans genome project allowed for a complete and circularized 1.3-Mb Wolbachia genome (wIrr). Annotation of wIrr yielded 1,249 coding genes, 34 tRNAs, 3 rRNAs, and 5 prophage regions. Comparative genomics and whole-genome Bayesian evolutionary analysis of wIrr compared to published Wolbachia genomes suggested that wIrr is most closely related to and diverged from Wolbachia supergroup A strains known to infect Drosophila spp. Whole-genome synteny analyses between wIrr and closely related genomes indicated that wIrr has undergone significant genome rearrangements while maintaining high nucleotide identity. Comparative analysis of the cytoplasmic incompatibility (CI) genes of wIrr suggested two phylogenetically distinct CI loci and acquisition of another cifB homolog from phylogenetically distant supergroup A Wolbachia strains, suggesting horizontal acquisition of these loci. The wIrr genome provides a resource for future examination of the impact Wolbachia may have in both biocontrol and potential insecticide resistance of horn flies.IMPORTANCE Horn flies, Haematobia irritans irritans, are obligate hematophagous parasites of cattle having significant effects on production and animal welfare. Control of horn flies mainly relies on the use of insecticides, but issues with resistance have increased interest in development of alternative means of control. Wolbachia pipientis is an endosymbiont bacterium known to have a range of effects on host reproduction, such as induction of cytoplasmic incompatibility, feminization, male killing, and also impacts vector transmission. These characteristics of Wolbachia have been exploited in biological control approaches for a range of insect pests. Here we report the assembly and annotation of the circular genome of the Wolbachia strain of the Kerrville, TX, horn fly (wIrr). Annotation of wIrr suggests its unique features, including the horizontal acquisition of additional transcriptionally active cytoplasmic incompatibility loci. This study provides the foundation for future studies of Wolbachia-induced biological effects for control of horn flies.

What do families want to improve in the management of paediatric febrile neutropenia during anti-cancer treatment? Report of a patient/public involvement group.

BACKGROUND: This study reports how parents and young people who had an experience offebrile neutropenia (FN) improved the design of a trial to inform the management of this condition. Five parents, a young person who had completed treatment and three clinician-researchers contributed. METHODS: The group was formed after an invitation on social media and met via video conference. Many participants were from an existing childhood-cancer parent-involvement group. The initial questions asked during discussion were about the importance of the topic, the views on the need for a trial, which important outcomes should be measured and the practical aspects which would make it easier or more difficult for people to take part in it. The conversation occurred for an entire afternoon, was audio and video recorded, transcribed, analysed and checked by those involved. The fifth parent added to this via email. RESULTS: The group altered the trial structure by proposing randomising of each child to one of the two management methods through the whole of their anti-cancer treatment, rather than randomising the study sites or the child at each visit. They felt that even if people declined taking part in the study in the first weeks of diagnosis, their views might change and they should be allowed to consent later. They also proposed methods of collecting important patient and family data, enriching the medical information gained in the study. Active follow-up, negotiated for each individual family, was also suggested. CONCLUSION: Trials for improving the management of FN in children and young people who are undergoing anti-cancer treatments should consider individual-patient randomisation, collection of 'quality of life' and 'experience of care' aspects using digital and paper-based methods, engage families in shared decision-making about management options and ensure adequate supportive information is available and accessible to all patients regardless of background, geographical location or age.

Protocol for a systematic review of time to antibiotics (TTA) in patients with fever and neutropenia during chemotherapy for cancer (FN) and interventions aiming to reduce TTA.

BACKGROUND: Fever and neutropenia (FN) is a common complication of chemotherapy for cancer. Prompt empiric broad-spectrum antibiotic therapy in FN is typically considered standard of care, but the definition of prompt is not clear. We seek to systematically review the available data on the association between time to antibiotics (TTA) administration and clinical outcomes in patients with FN being treated with chemotherapy. There have been several efforts to reduce TTA in patients with FN, by implementing specific interventions, presuming there will be a beneficial effect on patient-important outcomes. This systematic review will also collect data on such interventions and their effect to reduce TTA and potentially change clinical outcomes. METHODS/DESIGN: The search will cover MEDLINE, MEDLINE In-Process & Other Non-Indexed Citations, EMBASE, CINAHL, CDSR, CENTRAL, and LILACS. A full-search strategy is provided. Lists of studies identified by references cited and forward citation searching of included articles will also be reviewed. Studies will be screened, and data extracted by one researcher and independently checked by a second. Confounding biases and quality of studies will be assessed with the risk of bias in non-randomised studies-of interventions (ROBINS-I) tool. Data will be presented in narrative and tabular forms; in addition, if appropriate data is available, random effects meta-analysis will be used to examine TTA. A detailed analysis plan, including an assessment of heterogeneity and publication bias, is provided. DISCUSSION: This study aims to evaluate the association between TTA and patient-important clinical outcomes. Additionally, it will identify, critically appraise, and synthesise information on performed interventions and its effect to reduce TTA as a way of gaining insight into the potential use of these approaches. This will provide better knowledge for an adjusted treatment approach of FN. SYSTEMATIC REVIEW REGISTRATION: PROSPERO [ CRD42018092948 ].

A Redescription of Serrasentis sagittifer (Rhadinorhynchidae: Serrasentinae) from Rachycentron canadum (Rachycentridae) with Comments on its Biology and its Relationship to Other Species of Serrasentis.

Adult and cystacanth forms of the acanthocephalan Serrasentis sagittifer from Australian coastal waters are redescribed and verified as the same species using both molecular and morphological data. This study provides the baseline 18S rDNA, 28S rDNA, and cox1 sequence data to serve as genetic barcode for S. sagittifer. The validity of the currently recognized species of Serrasentis is discussed. The most recently described species are junior synonyms of either Serrasentis nadakali or S. sagittifer, and a number of species are species inquirenda. When using morphological characters to distinguish the species of Serrasentis, consideration needs to be given to the maturity of the specimens, since the trunk elongates and the number and distribution of the ventral combs changes as worms mature, although the proboscis armature itself does not change. A simple key to assist in the identification of species of Serrasentis is provided. Adult S. sagittifer appear to be highly host specific to the cobia, Rachycentron canadum, in northern Australian waters, whereas cystacanths have been reported from a wide range of fish species. The relationship between host length and number of cystacanths shows that most paratenic infections are acquired as young fish, most likely via a crustacean intermediate host.

Mitochondrial genomes of Australian chicken Eimeria support the presence of ten species with low genetic diversity among strains.

Modern molecular approaches have vastly improved diagnostic capabilities for differentiating among species of chicken infecting Eimeria. Consolidating information from multiple genetic markers, adding additional poultry Eimeria species and increasing the size of available data-sets is improving the resolving power of the DNA, and consequently our understanding of the genus. This study adds information from 25 complete mitochondrial DNA genomes from Australian chicken Eimeria isolates representing all 10 species known to occur in Australia, including OTU-X, -Y and -Z. The resulting phylogeny provides a comprehensive view of species relatedness highlighting where the OTUs align with respect to others members of the genus. All three OTUs fall within the Eimeria clade that contains only chicken-infecting species with close affinities to E. maxima, E. brunetti and E. mitis. Mitochondrial genetic diversity was low among Australian isolates likely reflecting their recent introduction to the country post-European settlement. The lack of observed genetic diversity is a promising outcome as it suggests that the currently used live vaccines should continue to offer widespread protection against Eimeria outbreaks in all states and territories. Flocks were frequently found to host multiple strains of the same species, a factor that should be considered when studying disease epidemiology in the field.

A morphological and genetic description of pentastomid infective nymphs belonging to the family Sebekidae Sambon, 1922 in fish in Australian waters.

Infective nymphal stages of the family Sebekidae Sambon, 1922 are reported from four species of fish in Australian waters for the first time. Infected fish were collected from locations in Western Australia, the Northern Territory and north Queensland. The infective nymphs of Alofia merki Giglioli in Sambon, 1922 and Sebekia purdieae Riley, Spratt et Winch, 1990 are reported and described for the first time. The remaining specimens were identified as belonging to the genus Sebekia Sambon, 1922 based on the combination of buccal cadre shape, shape and size of hooks, and overall body size, but could not be attributed to any of the other species of Sebekia already reported due to missing required morphological features. DNA sequences of members of the family Sebekidae are presented for the first time. The lack of knowledge on the pentastome fauna of wild crocodiles, and any potential intermediate hosts, in northern Australia, is also outlined.

The complete validated mitochondrial genome of the black marlin Istiompax indica (Cuvier, 1832).

Two complete mitochondrial genomes of the black marlin Istiompax indica were assembled from approximately 3.5 and 2.5 million reads produced by Ion Torrent next generation sequencing. The complete genomes were 16,531 bp and 16,532 bp in length consisting of 2 rRNA, 13 protein-coding genes, 22tRNA and 2 coding regions. They demonstrated a similar A + T base (52.6%) to other teleosts. Intraspecific sequence variation was 99.5% for three I. indica mitogenomes and 99.7% for X. gladius. A lower value (85%) was found for the I. platypterus mitogenomes from genbank and accredited to inadvertent inclusion of gene regions from a con-familial species in one record, highlighting the need for cautious downstream use of genbank data.

An Evaluation of Quantitative PCR Assays (TaqMan® and SYBR Green) for the Detection of Babesia bigemina and Babesia bovis, and a Novel Fluorescent-ITS1-PCR Capillary Electrophoresis Method for Genotyping B. bovis Isolates.

Babesia spp. are tick-transmitted haemoparasites causing tick fever in cattle. In Australia, economic losses to the cattle industry from tick fever are estimated at AUD$26 Million per annum. If animals recover from these infections, they become immune carriers. Here we describe a novel multiplex TaqMan qPCR targeting cytochrome b genes for the identification of Babesia spp. The assay shows high sensitivity, specificity and reproducibility, and allows quantification of parasite DNA from Babesia bovis and B. bigemina compared to standard PCR assays. A previously published cytochrome b SYBR Green qPCR was also tested in this study, showing slightly higher sensitivity than the Taqman qPCRs but requires melting curve analysis post-PCR to confirm specificity. The SYBR Green assays were further evaluated using both diagnostic submissions and vaccinated cattle (at 7, 9, 11 and 14 days post-inoculation) showed that B. bigemina can be detected more frequently than B. bovis. Due to fewer circulating parasites, B. bovis detection in carrier animals requires higher DNA input. Preliminary data for a novel fluorescent PCR genotyping based on the Internal Transcribed Spacer 1 region to detect vaccine and field alleles of B. bovis are described. This assay is capable of detecting vaccine and novel field isolate alleles in a single sample.

A molecular survey of Eimeria in chickens across Australia.

Coccidiosis is a costly enteric disease of chickens caused by protozoan parasites of the genus Eimeria. Disease diagnosis and management is complicated since there are multiple Eimeria species infecting chickens and mixed species infections are common. Current control measures are only partially effective and this, combined with concerns over vaccine efficacy and increasing drug resistance, demonstrates a need for improved coccidiosis diagnosis and control. Before improvements can be made, it is important to understand the species commonly infecting poultry flocks in both backyard and commercial enterprises. The aim of this project was to conduct a survey and assessment of poultry Eimeria across Australia using genetic markers, and create a collection of isolates for each Eimeria species. A total of 260 samples (faecal or caecal) was obtained, and survey results showed that Eimeria taxa were present in 98% of commercial and 81% of backyard flocks. The distribution of each Eimeria species was widespread across Australia, with representatives of all species being found in every state and territory, and the Eimeria species predominating in commercial flocks differed from those in backyard flocks. Three operational taxonomic units also occurred frequently in commercial flocks highlighting the need to understand the impact of these uncharacterised species on poultry production. As Eimeria infections were also frequent in backyard flocks, there is a potential for backyard flocks to act as reservoirs for disease, especially as the industry moves towards free range production systems. This Eimeria collection will be an important genetic resource which is the crucial first step in the development of more sophisticated diagnostic tools and the development of new live vaccines which ultimately will provide savings to the industry in terms of more efficient coccidiosis management.