Quantifying replication slippage error in Cryptosporidium metabarcoding studies.

Genetic variation in Cryptosporidium, a common protozoan gut parasite in humans, is often based on marker genes containing trinucleotide repeats, which differentiate subtypes and track outbreaks. However, repeat regions have high replication slippage rates, making it difficult to discern biological diversity from error. Here, we synthesised Cryptosporidium DNA in clonal plasmid vectors, amplified them in different mock community ratios and sequenced them using next generation sequencing to determine the rate of replication slippage with dada2. Our results indicate that slippage rates increase with the length of the repeat region and can contribute to error rates of up to 20%.

Genomic analysis of canine pneumoviruses and canine respiratory coronavirus from New Zealand.

AIMS: To isolate canine respiratory coronavirus (CRCoV) and canine pneumovirus (CnPnV) in cell culture and to compare partial genomic sequences of CRCoV and CnPnV from New Zealand with those from other countries. METHODS: Oropharyngeal swab samples from dogs affected by canine infectious respiratory disease syndrome that were positive for CnPnV (n = 15) or CRCoV (n = 1) by virus-specific reverse transcriptase quantitative PCR (RT-qPCR) in a previous study comprised the starting material. Virus isolation was performed in HRT-18 cells for CRCoV and RAW 264.7 and Vero cells for CnPnV. The entire sequence of CnPnV G protein (1,266 nucleotides) and most (8,063/9,707 nucleotides) of the 3' region of CRCoV that codes for 10 structural and accessory proteins were amplified and sequenced. The sequences were analysed and compared with other sequences available in GenBank using standard molecular tools including phylogenetic analysis. RESULTS: Virus isolation was unsuccessful for both CRCoV and CnPnV. Pneumovirus G protein was amplified from 3/15 (20%) samples that were positive for CnPnV RNA by RT-qPCR. Two of these (NZ-048 and NZ-049) were 100% identical to each other, and 90.9% identical to the third one (NZ-007). Based on phylogenetic analysis of the G protein gene, CnPnV NZ-048 and NZ-049 clustered with sequences from the USA, Thailand and Italy in group A, and CnPnV NZ-007 clustered with sequences from the USA in group B. The characteristics of the predicted genes (length, position) and their putative protein products (size, predicted structure, presence of N- and O-glycosylation sites) of the New Zealand CRCoV sequence were consistent with those reported previously, except for the region located between open reading frame (ORF)3 (coding for S protein) and ORF6 (coding for E protein). The New Zealand virus was predicted to encode 5.9 kDa, 27 kDa and 12.7 kDa proteins, which differed from the putative coding capacity of this region reported for CRCoV from other countries. CONCLUSIONS: This report represents the first characterisation of partial genomic sequences of CRCoV and CnPnV from New Zealand. Our results suggest that the population of CnPnV circulating in New Zealand is not homogeneous, and that the viruses from two clades described overseas are also present here. Limited conclusions can be made based on only one CRCoV sequence, but the putative differences in the coding capacity of New Zealand CRCoV support the previously reported variability of this region. The reasons for such variability and its biological implications need to be further elucidated.

The prevalence of Salmonella spp. in working farm dogs and their home-kill raw meat diets in Manawatu, New Zealand.

AIMS: To investigate the prevalence of Salmonella spp. in a convenience sample of working farm dogs and their home-kill raw meat diets in Manawatu, New Zealand. METHODS: Fifty farms in the Manawatu, with at least three working/herding dogs per farm that were fed raw home-killed meat at least fortnightly, were visited. One sample of dog faeces and one sample of food were collected per farm using convenience sampling. If a dog did not defecate, a sample was obtained by digital recovery. Basic descriptive data for all dogs, meat and farm characteristics were recorded. Stomached meat samples and swabs from faecal samples were pre-enriched in buffered peptone water followed by two selective enrichments with agar subculture. Isolates were confirmed to be Salmonella spp. by serology and biochemical characterisation. RESULTS: No Salmonella spp. were isolated from dog faeces or raw meat samples, giving an observed prevalence rate of 0 (95% CI = 0.0-7.1)%. CONCLUSIONS: In this study, there was no evidence that working farm dogs and their home-kill raw meat represent likely sources of infection with Salmonella spp. CLINICAL RELEVANCE: Although this study found no evidence suggesting that farmers should change their feeding practices, it is based on a small sample, from a single region of New Zealand and involved sampling on one occasion for Salmonella spp. only. Currently, although the prevalence of Salmonella spp. carriage appears to be low, feeding raw meat-based diets to working dogs remains a risk and due to the potential zoonotic implications for humans, hygienic measures should be maintained when in contact with dogs and raw meat.

Microbial contamination in drinking water at public outdoor recreation facilities in New Zealand.

AIM: The aim of our study was to assess the presence and risk of waterborne pathogens in the drinking water of outdoor facilities in New Zealand and track potential sources of microbial contamination in water sources. METHODS AND RESULTS: A serial cross-sectional study with a risk-based sample collection strategy was conducted at 15 public campgrounds over two summer seasons (2011-2012 and 2012-2013). Drinking water supplied to these campgrounds was not compliant with national standards, based on Escherichia coli as an indicator organism, in more than half of the sampling occasions. Campylobacter contamination of drinking water at the campgrounds was likely to be of wild bird origin. Faecal samples from rails (pukeko and weka) were 35 times more likely to return a Campylobacter-positive result compared to passerines. Water treatment using ultraviolet (UV) irradiation or a combination of filtration and UV irradiation or chemicals was more likely to result in water that was compliant with the national standards than water from a tap without any treatment. The use of filters alone was not associated with the likelihood of compliance. CONCLUSIONS: Providing microbiologically safe drinking water at outdoor recreational facilities is imperative to avoid gastroenteritis outbreaks. This requires an in-depth understanding of potential sources of contamination in drinking water sources and the installation of adequate water treatment facilities. SIGNIFICANCE AND IMPACT OF THE STUDY: Our study provides evidence that drinking water without treatment or filter-only treatment in public campgrounds is unlikely to comply with national standards for human consumption and extra water treatment measures such as UV irradiation or chemical treatment are needed.

A molecular survey of canine respiratory viruses in New Zealand.

AIMS: The aim of this study was to identify viruses associated with canine infectious respiratory disease syndrome (CIRDS) among a population of New Zealand dogs. METHODS: Convenience samples of oropharyngeal swabs were collected from 116 dogs, including 56 CIRDS-affected and 60 healthy dogs from various locations in New Zealand between March 2014 and February 2016. Pooled samples from CIRDS-affected (n = 50) and from healthy (n = 50) dogs were tested for the presence of canine respiratory viruses using next generation sequencing (NGS). Individual samples (n = 116) were then tested by quantitative PCR (qPCR) and reverse transcriptase qPCR (RT-qPCR) for specific viruses. Groups were compared using Fisher's exact or χ2 tests. The effect of explanatory variables (age, sex, type of household, presence of viral infection) on the response variable (CIRDS-affected or not) was tested using RR. RESULTS: Canine pneumovirus (CnPnV), canine respiratory coronavirus (CRCoV), canine herpesvirus-1 (CHV-1), canine picornavirus and influenza C virus sequences were identified by NGS in the pooled sample from CIRDS-affected but not healthy dogs. At least one virus was detected by qPCR/RT-qPCR in 20/56 (36%) samples from CIRDS dogs and in 23/60 (38%) samples from healthy dogs (p = 0.84). CIRDS-affected dogs were most commonly positive for CnPnV (14/56, 25%) followed by canine adenovirus-2 (CAdV-2, 5/56, 9%), canine parainfluenza virus (CpiV) and CHV-1 (2/56, 4% each), and CRCoV (1/56, 2%). Only CnPnV (17/60, 28%) and CAdV-2 (14/60, 23%) were identified in samples from healthy dogs, and CAdV-2 was more likely to be detected healthy than diseased dogs (RR 0.38; 95% CI = 0.15-0.99; p = 0.045). CONCLUSIONS: The frequency of detection of viruses traditionally linked to CIRDS (CAdV-2 and CPiV) among diseased dogs was low. This suggests that other pathogens are likely to have contributed to development of CIRDS among sampled dogs. Our data represent the first detection of CnPnV in New Zealand, but the role of this virus in CIRDS remains unclear. On-going monitoring of canine respiratory pathogens by NGS would be beneficial, as it allows rapid detection of novel viruses that may be introduced to the New Zealand canine population in the future. Such monitoring could be done using pooled samples to minimise costs. CLINICAL RELEVANCE: Testing for novel respiratory viruses such as CnPnV and CRCoV should be considered in all routine laboratory investigations of CIRDS cases, particularly in dogs vaccinated with currently available kennel cough vaccines.

Insights into the Geobacillus stearothermophilus species based on phylogenomic principles.

BACKGROUND: The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species. For example, G. stearothermophilus was traditionally defined as a species that does not utilise lactose, but the ability of dairy strains of G. stearothermophilus to use lactose has now been well established. RESULTS: This study compared the genome sequences of 63 Geobacillus isolates and showed that based on two different genomic approaches (core genome comparisons and average nucleotide identity) the Geobacillus genus could be divided into sixteen taxa for those Geobacillus strains that have genome sequences available thus far. In addition, using Geobacillus stearothermophilus as an example, we show that inclusion of the accessory genome, as well as phenotypic characteristics, is not suitable for defining this species. For example, this is the first study to provide evidence of dairy adaptation in G. stearothermophilus - a phenotypic feature not typically considered standard in this species - by identifying the presence of a putative lac operon in four dairy strains. CONCLUSIONS: The traditional polyphasic approach of combining both genotypic and phenotypic characteristics to define a bacterial species could not be used for G. stearothermophilus where many phenotypic characteristics vary within this taxon. Further evidence of this discordant use of phenotypic traits was provided by analysis of the accessory genome, where the dairy strains contained a putative lac operon. Based on the findings from this study, we recommend that novel bacterial species should be defined using a core genome approach.

Seasonality of Campylobacter jejuni isolates associated with human campylobacteriosis in the Manawatu region, New Zealand.

A 9-year time-series of genotyped human campylobacteriosis cases from the Manawatu region of New Zealand was used to investigate strain-type seasonality. The data were collected from 2005 to 2013 and the samples were multi-locus sequence-typed (MLST). The four most prevalent clonal complexes (CCs), consisting of 1215 isolates, were CC48, CC21, CC45 and CC61. Seasonal decomposition and Poisson regression with autocorrelated errors, were used to display and test for seasonality of the most prevalent CCs. Of the four examined CCs, only CC45 showed a marked seasonal (summer) peak. The association of CC45 with summer peaks has been observed in other temperate countries, but has previously not been identified in New Zealand. This is the first in-depth study over a long time period employing MLST data to examine strain-type-associated seasonal patterns of C. jejuni infection in New Zealand.

Familial cylindromatosis (turban tumour syndrome) gene localised to chromosome 16q12-q13: evidence for its role as a tumour suppressor gene.

The human skin is a complex organ composed of the surface epidermis, the subjacent dermis (in which blood vessels, lymphatics and nerves are located) and the skin appendages. The latter include hair follicles, sebaceous glands (which secrete lipids that may serve as a permeability barrier, emollient or antimicrobial agent), apocrine glands (which secrete scents) and eccrine glands (which produce sweat for temperature control). Hereditary cylindromatosis (MIM 123850) is a rare autosomal dominant disease characterised by the development of multiple neoplasms originating from the skin appendages. These neoplasms have been termed cylindromas due to their characteristic microscopic architecture and are believed to exhibit apocrine or eccrine differentiation. We have carried out a genome search using two families with this disease, which has provided strong evidence for linkage of cylindromatosis to loci on chromosome 16q12-q13. Using markers close to the cylindromatosis gene, consistent loss of the wild-type allele was observed in 19 tumours from four individuals in the two families, indicating that the gene is likely to be a tumour suppressor gene.

Identification of the familial cylindromatosis tumour-suppressor gene.

Familial cylindromatosis is an autosomal dominant genetic predisposition to multiple tumours of the skin appendages. The susceptibility gene (CYLD) has previously been localized to chromosome 16q and has the genetic attributes of a tumour-suppressor gene (recessive oncogene). Here we have identified CYLD by detecting germline mutations in 21 cylindromatosis families and somatic mutations in 1 sporadic and 5 familial cylindromas. All mutations predict truncation or absence of the encoded protein. CYLD encodes three cytoskeletal-associated-protein-glycine-conserved (CAP-GLY) domains, which are found in proteins that coordinate the attachment of organelles to microtubules. CYLD also has sequence homology to the catalytic domain of ubiquitin carboxy-terminal hydrolases (UCH).

Isolation of Campylobacter spp. from Client-Owned Dogs and Cats, and Retail Raw Meat Pet Food in the Manawatu, New Zealand.

Campylobacter causes acute gastroenteritis in people worldwide and is frequently isolated from food, animals and the environment. The disease is predominately food-borne but many routes of transmission and sources of infection have been described, including contact with pets. The prevalence of Campylobacter spp. in dogs and cats varies widely, and data on New Zealand pets are limited. This study aimed to investigate the prevalence of Campylobacter spp. in dogs, cats and retail raw meat pet food products in New Zealand and to characterize Campylobacter jejuni isolates using multilocus sequence typing (MLST). Ninety dogs and 110 cats examined at the Massey University Veterinary Teaching Hospital for elective procedures, and fifty locally purchased retail raw meat pet diets were sampled. Two culture protocols combining Bolton broth enrichment and mCCDA and CAT agars in a microaerobic atmosphere at 42°C and 37°C with species identification using PCR were performed. The prevalence of Campylobacter spp., C. jejuni, Campylobacter upsaliensis and Campylobacter helveticus was 36%, 13%, 23% and 1% in dogs and 16%, 5%, 5% and 7% in cats, respectively. One dog had Campylobacter lari confirmed, and three dogs and one cat had multiple Campylobacter spp. detected. Significantly more animals tested positive using CAT than mCCDA agar (P < 0.001). Being neutered, vaccinated for Bordetella bronchiseptica, fed dry diets and brought in for neutering were protective factors for dogs, whereas attendance for dental treatment was a risk factor for cats. Campylobacter spp. were isolated from 28%, C. jejuni 22%, C. lari 6% and Campylobacter coli 6% of food samples. Six isolates positive by Campylobacter genus PCR were identified as Arcobacter butzleri. Poultry meat was more likely to be positive than non-poultry meat (P = 0.006). Of the 13 C. jejuni pet isolates with full MLST profiles, eight were of different sequence types (ST) and all nine food isolates were of different STs.

The cylindromatosis gene (cyld1) on chromosome 16q may be the only tumour suppressor gene involved in the development of cylindromas.

Hereditary cylindromatosis is a rare autosomal dominant disease characterised by the development of multiple benign neoplasms of the skin. We recently localised the gene responsible for this disease (cyld1) to chromosome 16q12-q13 and provided evidence that it is a tumour suppressor gene (Biggs et al., 1995). We have now examined polymorphic markers on every chromosome, some of which are close to known tumour suppressor genes, in 25 tumours from 4 individuals with familial cylindromatosis. No loss of heterozygosity (LOH) was detected other than at loci on chromosome 16q. This observation suggests that the cyld1 gene may be the only tumour suppressor gene implicated in the development of cylindromas. We have also demonstrated LOH using markers on chromosome 16q in 8/14 (57%) sporadic cylindromas, indicating that the cyld1 gene is likely to be involved in the genesis of both familial and sporadic cylindromas.

Theoretical shape of cavity to locate ovoid sources.

A mathematical technique is described for calculating the shape of a cavity required to position an ovoid source in its appropriate location within an applicator. This locus depends only on the assumption of a fixed angle between the source and wall that the source is touching. This technique has enabled us to avoid the problems of constructing ovoid cavities where the source sticks mid-course or does not seat properly, and has therefore resulted in a considerable saving of machine shop time and hence cost.

Effect of a femoral head prosthesis on megavoltage beam radiotherapy.

A few patients undergoing pelvic irradiation present with a prosthetic hip. The presence of this metal object often interferes with the lateral treatment fields if a four-field box irradiation technique is used. Measurements of the effect such a prosthesis may have on the dose delivered to the pelvis for beams of 60Co gamma rays and 10 MV and 25 MV X-rays, as a function of field size and depth have been made. The results show a strong variation in the dose behind the prosthesis depending on the position of the measurement, with little or no increase through the center of the head or ball, but a sharp drop either around its circumference or along the stem of the prosthesis. Measurements made with ionization chambers through the head of the prosthesis indicate an average dose decrease of approximately 2% for 25 MV X rays and average increases of approximately 2% for 10 MV X rays and 5% for 60Co. There is little variation with field size and depth except close to the prosthesis, at 25 MV. Measurements also indicate an increase in dose close to the upstream surface of the prosthesis at all energies, but in the downstream direction, only the data at 25 MV shows an increase.

A linear accelerator couch attachment for extended SSD treatments.

An attachment to an existing linear accelerator couch is described that extends the range of SSD's at which patients can be treated. This couch attachment, which is mounted on castors for ease of mobility, is attached to and locks into the rail of the accelerator couch such that the axis of the new device is normal to the existing couch. All motions of this assembly are then under the control of the existing couch. The overall size of the couch attachment is 215 cm x 90 cm, sufficiently large to treat all clinically used fields.

An intra-oral cone for an 18 MeV linear accelerator.

A set of intra-oral cones has been constructed for electron beam therapy from a linear accelerator. We have modified the 4 cm X 4 cm treatment accessory provided with this machine by simply removing the lower collimator and replacing it with a brass plate into which all the cones can fit, so that they are easily interchangeable. Six circular cones, with diameters ranging from 27 mm and to 45 mm, plus two elliptical cones are currently in use. A light field system has been built that fits into the acrylic compartment directly above the base, and provides a clear, well-illuminated view of the treatment field. The dosimetry for these cones shows that the percent depth dose curve for a 41 mm diameter field is the same as that obtained with the 4 cm X 4 cm treatment accessory, and that the isodose curves are very similar. This intra-oral cone system has been in operation for over two years and we have found it very useful in boosting the dose to specific primary lesions in the oral cavity, for example, oral tongue, floor of mouth, retromolar trigone, and soft palate.

Breakaway safety feature for an intra-oral cone system.

With an increasing number of high energy accelerators in operation, intra-oral electron radiotherapy is likely to become a more widely-used modality in the treatment of lesions of the oral cavity. However, there is one potential problem associated with this modality which concerns patient safety. There must never be any uncontrolled movement of the couch or gantry while the cone is in the patient's mouth, otherwise serious consequences could occur. In an effort to overcome this problem, a set of cones previously constructed by us for use in intra-oral electron radiotherapy has been modified to include a breakaway safety feature. This modification consists of separating the plate into which each of the treatment cones screws, into two pieces, the dividing line being in the shape of a cone frustum flaring out in the upward direction. A set of four spring plungers projecting into a notch on the inner ring prevents the cone from being pushed upwards without the application of an upward force. The amount of force required to push the cone upwards can be changed by adjusting the pressure of the spring plungers.

A beam width improving device for a 25 MV X ray beam.

We have made a device that improves the dose distributions of X ray fields from a 25 MV accelerator by increasing the width of the 95% dose relative to the 50%. This device, called a beam width improving device, is a specially designed "compensator," consisting of two lead sheets taped onto a plastic blocking tray and is tailored for each field so that it can accommodate square fields, rectangular fields and fields with corner cuts. Comparison of profiles with and without this compensator indicates an increase in the width of the 95% dose of approximately 8 mm for small fields to approximately 14 mm for large fields.

A diagnostic X ray field verification device for a 10 MV linear accelerator.

The quality of portal films taken at megavoltage energies is frequently poor, despite the use of various techniques such as lead screens to improve the image. When critical structures, such as the spinal cord, are to be blocked out of the treatment field, it is frequently difficult to determine whether the block is correctly placed. To solve this problem, a diagnostic X ray source has been mounted on the side of a 10 MV linear accelerator to provide accurate verification of patient positioning and location of shielding blocks. The coincidence between the mechanical, 10 MV and diagnostic X ray isocenters is about 1 mm. The system has been designed so that procedures to monitor this coincidence, and adjustment procedures to maintain it, are easily performed.

An afterloading vaginal applicator.

An afterloading vaginal applicator has been built that incorporates two ovoid sources and two tandem sources arranged in the shape of a T, the tandems forming the upright and the ovoids, orthogonal to the tandems, located at the ends of the crossbar. The body of the applicator was designed and constructed to correspond to the 90 cGy/hr contour for a source loading of 10 mg Ra Eq 137Cs for the ovoids and 15 mg Ra Eq 137Cs for the tandems. TLD measurements made at various points located around the applicator in the AP and lateral planes indicate agreement with the dose calculated by computer to within +/- 1%.

Intra-oral cone radiation therapy for selected carcinomas of the oral cavity.

A study of 101 patients with early carcinomas of the oral cavity, T1 and T2, treated by external cobalt 60 beam and/or intra-oral cone (IOC) radiation therapy between 1964 through 1980 was made. The two year disease-free survival rate, including surgical salvage, was 88% and the local control rate was 85%. The incidence of radiation complications, i.e. soft tissue ulceration and/or osteoradionecrosis, was 14% and varied with various tumor sites and radiation doses delivered. The present review shows that local control and radiation complications are closely related to radiation doses and varies with different tumor sites of the oral cavity. Radiation therapy dosages expressed in terms of TDF values for these lesions are herein recommended. With proper selections of lesions arising from the oral cavity, combined external beam and IOC radiation therapy has been found extremely efficacious in achieving good local tumor control and high survival rates with excellent cosmetic and functional results and minimum radiation sequelae.