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.

Accelerated telomere shortening in ataxia telangiectasia.

Ataxia telangiectasia (AT) is characterized by neurological deterioration, immunodeficiency, spontaneous chromosomal instability, hypersensitivity to ionizing radiation, predisposition to cancer, particularly T cell leukaemia and lymphoma, and premature ageing. The most commonly observed defect affecting telomeres in humans is telomeric fusions, particularly in T lymphocytes in AT patients. Rarely, some tumour cells, like senescent cells, have dicentric chromosomes that may arise as a result of telomeric sequence loss. We show that the AT mutation in the homozygous state confers a predisposition to accelerated telomere shortening with increasing age in peripheral blood lymphocytes (PBLs), which may be linked to premature senescence. We also show that telomeric fusions are associated with large (> 90%) preleukaemic translocation clones in T cells. We propose that these fusions may result from a compound effect of accelerated telomere shortening, together with a growth advantage of cells in large clones which leads to further telomere loss. Fusions are not observed in leukaemic cells in these patients. There is no evidence that either accelerated telomere loss per se or telomeric fusions are important in tumourigenesis. Telomerase is present in both normal and AT lymphocytes and so neither telomere shortening nor telomeric fusions can be explained by the absence of telomerase.

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).

Localization to Xq27 of a susceptibility gene for testicular germ-cell tumours.

Testicular germ-cell tumours (TGCT) affect 1 in 500 men and are the most common cancer in males aged 15-40 in Western European populations. The incidence of TGCT has risen dramatically over the last century. Known risk factors for TGCT include a history of undescended testis (UDT), testicular dysgenesis, infertility, previously diagnosed TGCT (ref. 7) and a family history of the disease. Brothers of men with TGCT have an 8-10-fold risk of developing TGCT (refs 8,9), whereas the relative risk to fathers and sons is fourfold (ref. 9). This familial relative risk is much higher than that for most other types of cancer. We have collected samples from 134 families with two or more cases of TGCT, 87 of which are affected sibpairs. A genome-wide linkage search yielded a heterogeneity lod (hlod) score of 2.01 on chromosome Xq27 using all families compatible with X inheritance. We obtained a hlod score of 4.7 from families with at least one bilateral case, corresponding to a genome-wide significance level of P=0.034. The proportion of families with UDT linked to this locus was 73% compared with 26% of families without UDT (P=0.03). Our results provide evidence for a TGCT susceptibility gene on chromosome Xq27 that may also predispose to UDT.

Severe reaction to radiotherapy for breast cancer as the presenting feature of ataxia telangiectasia.

BACKGROUND: Severe early and late radiation reaction to radiotherapy is extremely rare in breast cancer patients. Such a reaction prompted an investigation into a 44-year-old mother (patient A-T213). METHODS: A neurological examination was performed and blood lymphocytes and skin fibroblasts were assessed for radiosensitivity chromosomally and by colony-forming assay. The ATM gene was sequenced and ATM mutations modelled by site-directed mutagenesis. The ATM kinase activity was also assessed. RESULTS: Patient A-T213 was normally ambulant with no ataxia and minimal other neurological features. T lymphocytes and skin fibroblasts were unusually radiosensitive, although less sensitive than in classical ataxia telangiectasia (A-T). A lymphoblastoid cell line and skin fibroblasts expressed ATM protein with some retained kinase activity. One missense ATM mutation c.8672G>A (p.Gly2891Asp) and a c.1A>G substitution were identified. In the modelling system, the p.Gly2891Asp mutant protein was expressed and shown to have residual ATM kinase activity. CONCLUSION: Patient A-T213 has a milder form of A-T with biallelic ATM mutations, which may have contributed to breast cancer development, and certainly caused the severe radiation reaction. Ataxia telangiectasia should be investigated as a potential cause of untoward severe early and late radiation reactions in breast cancer patients.

Assessing functional recovery following total knee replacement surgery using objective classification of level gait data and patient-reported outcome measures.

BACKGROUND: Patient recovery can be quantified objectively, via gait analysis, or subjectively, using patient reported outcome measures. Association between these measures would explain the level of disability reported in patient reported outcome measures and could assist with therapeutic decisions. METHODS: Total knee replacement outcome was assessed using objective classification and patient-reported outcome measures (Knee Outcome Survey and Oxford Knee Scores). A classifier was trained to distinguish between healthy and osteoarthritic characteristics using knee kinematics, ground reaction force and temporal gait data, combined with anthropometric data from 32 healthy and 32 osteoarthritis knees. For the osteoarthritic cohort, classification of 20 subjects quantified changes at up to 3 timepoints post-surgery. FINDINGS: Osteoarthritic classification was reduced for 17 subjects when comparing pre- to post-operative assessments, however only 6 participants achieved non-pathological classification and only 4 of these were classified as non-pathological at 12 months. In 15 cases, the level of osteoarthritic classification did not decrease between every post-operative assessment. For an individual's recovery, classification outputs correlated (r > 0.5) with knee outcome survey for 75% of patients and oxford knee score for 78% of patients (based on 20 and 9 subjects respectively). Classifier outputs from all visits of the combined total knee replacement sample correlated moderately with knee outcome survey (r > 0.4) and strongly with oxford knee score (r > 0.6). INTERPRETATION: Biomechanical deficits existed in most subjects despite improvements in Patient Reported Outcome Measures, with larger changes reported subjectively as compared to measured objectively. Objective Classification provides additional insight alongside Patient Reported Outcomes when reporting recovered outcomes.

The effects of whole grains on nutrient digestibilities, growth performance, and cecal short-chain fatty acid concentrations in young chicks fed ground corn-soybean meal diets.

Five experiments were conducted to evaluate the effects of whole wheat, whole sorghum, or whole barley on nutrient digestibility, growth performance, and cecal short-chain fatty acid concentrations when supplemented primarily at the expense of corn in ground corn-soybean meal control diets. The first 4 experiments utilized New Hampshire x Columbian male chicks. In the first 2 experiments, feeding 5, 10, 15, or 20% whole wheat had no effect on growth performance at 21 d when compared with chicks fed the control diet. The third experiment tested 20, 35, and 50% whole wheat fed from 0 to 21 d of age and showed that a 50% whole wheat diet decreased (P<0.05) 21-d growth and feed efficiency when compared with chicks fed the control diet. In experiment 4, 10 and 20% whole sorghum reduced (P<0.05) growth at 21 d, whereas chicks fed 10 and 20% whole barley had similar weight gains to chicks fed a ground corn-soybean meal diet. The fifth experiment with commercial Ross x Ross male broiler chicks evaluated 10 and 20% whole sorghum or whole barley and 20 and 35% whole wheat. Growth at 21 d was unaffected by any dietary treatment. Feed efficiency was decreased (P<0.05) at 21 d with 20% whole wheat and improved (P<0.05) with 10% whole barley. Feeding whole grains to chicks resulted in an increase in gizzard weight, even as early as 7 d, in all experiments. Chicks fed diets containing 10 to 20% whole wheat generally had increased MEn values at 3 to 4, 7, 14, and 21 d and also had increased amino acid digestibility at 21 d in one experiment. At 21 d, cecal pH and short-chain fatty acid concentrations in all experiments were unaffected by feeding whole grains to chicks. The results of this study indicated that feeding whole wheat, sorghum, or barley increased gizzard weight, and feeding 10 to 20% whole wheat may increase ME and amino acid digestibility.

Correlations between patient-perceived outcome and objectively-measured biomechanical change following Total Knee Replacement.

BACKGROUND: Total Knee Replacement (TKR) surgery is being utilised in a younger, more active population with greater functional expectations. Understanding whether patient-perceived measures of function reflect objective biomechanical measures is critical in understanding whether functional limitations can be adequately captured within a clinical setting. RESEARCH QUESTION: Do changes in objective gait biomechanics measures reflect patient-reported outcome measures at approximately 12 months following TKR surgery? METHODS: Three-dimensional gait analysis was performed on 41 patients with OA who were scheduled for TKR surgery, 22 of which have returned for a (9-24 month) follow-up assessment. Principal Component Analysis was used to define features of variation between OA subjects and an additional 31 non-pathological control subjects. These were used to train the Cardiff Classifier, an objective classification technique, and subsequently quantify changes following TKR surgery. Patient-perceived changes were also assessed using the Oxford Knee Score (OKS), Knee Outcome Survey (KOS), and Pain Audit Collection System scores (PACS). Pearson and Spearman correlation coefficients were calculated to establish the relationship between changes in objectively-measured and perceived outcome. RESULTS: Objective measures of biomechanical change were strongly correlated to changes in OKS(r=-0.695, p < 0.001) and KOS(r=-.810, p < 0.001) assessed outcomes. Pain (PACS) was only related to biomechanical function post-operatively (r=-.623, p = 0.003). SIGNIFICANCE: In this biomechanics study, the relationship between changes in objective function and patient-reported measures pre to post TKR surgery is stronger than in studies which did not include biomechanics metrics. Quality of movement may hold more significance for a patient's perception of improvement than functional measures which consider only the time taken or distance travelled during functional activities.

The effects of several organic acids on growth performance, nutrient digestibilities, and cecal microbial populations in young chicks.

Four experiments were conducted to evaluate the effects of citric, gluconic, fumaric, and malic acids on growth and nutrient digestibility in New Hampshire x Columbian male chicks from hatch to 21 d. For growth performance, chicks fed 1 to 4% gluconic acid, 4% citric acid, or 4% malic acid in a corn-soybean meal diet generally showed reductions (P < 0.05) in growth to 21 d, whereas 3% citric acid, 2% malic acid, or 1.5 to 4.5% fumaric acid had no significant effect. In the first experiment, 2, 4, and 6% gluconic acid increased ME(n) values at 7, 14, and 21 d, but in experiment 2, 1 and 2% gluconic acid decreased ME(n) at 4 and 7 d, but had no effect at 14 and 21 d. The 4% level of citric acid increased ME(n) at 4 d. Digestibility of most amino acids (AA) was reduced by gluconic acid in some treatments, whereas citric acid (3%) increased AA digestibility at 4 d but not at 21 d. For cecal microbial populations at 21 d, bifidobacteria were reduced when 2% gluconic acid and 3% citric acid were fed to chicks in a corn-soybean meal diet, whereas 4% gluconic acid had no effect when fed in a dextrose-casein diet to chicks. In a dextrose-isolated soy protein diet, 4% gluconic acid reduced the cecal populations of Lactobacillus, Escherichia coli, and Clostridium perfringens. The results of this study indicated that feeding organic acids did not have any consistent effects on growth performance, ME(n), AA digestibility, or cecal microbial numbers.

The effects of Grobiotic-P on growth performance, nutrient digestibilities, and cecal microbial populations in young chicks.

This study was conducted to evaluate the effects of Grobiotic-P (GB), a prebiotic-type product that contains dairy and yeast fractions and dried fermentation extracts, on growth performance and nutrient digestibility at 4 and 21 d of age and cecal populations of Bifidobacterium, Lactobacillus, Escherichia coli, and Clostridium perfringens at 21 d of age. Two experiments were conducted using male New Hampshire x Columbian chicks. The first experiment evaluated GB at 2, 4, and 6% in a corn-soybean meal diet and compared these dietary treatments to a diet containing no GB (negative control) and a diet containing an antibiotic growth promoter (positive control), bacitracin methylene disalicylate. The second experiment used semi-purified dextrose-casein and dextrose-isolated soy protein diets to examine the effects of a 5% GB addition. In the first experiment, supplementing GB at 2, 4, and 6% in a corn-soybean meal diet had no effect on weight gain (P > 0.05). Feed efficiency and ME(n) were decreased (P < 0.05) by feeding 4 and 6% GB for some time periods, suggesting that the ME(n) value of GB used in diet formulation was too high. The GB had no consistent effect on apparent digestibility of amino acids. Cecal lactobacilli populations were linearly increased (P < 0.05) by GB in a corn-soybean meal diet in experiment 1. In the second experiment, the cecal populations of bifidobacteria were increased (P < 0.05) when 5% GB was supplemented to chicks fed a dextrose-casein diet, and the cecal populations of E. coli and C. perfringens were reduced (P < 0.05) when 5% GB was supplemented to chicks fed a dextrose-isolated soy protein diet. The results of this study indicate that feeding GB to chicks may promote the growth of beneficial bifidobacteria while reducing the growth of E. coli and C. perfringens in the ceca.

The effects of several oligosaccharides on true amino acid digestibility and true metabolizable energy in cecectomized and conventional roosters.

Prebiotics, such as indigestible oligosaccharides, are considered to be possible dietary alternatives to antibiotic growth promoters in poultry. The effects of indigestible oligosaccharides on nutrient digestibility in poultry are largely unknown. Therefore, an experiment was conducted to evaluate the effects of several oligosaccharides on amino acid digestibility and TMEn in roosters. The dietary treatments consisted of a corn-isolated soy protein control diet or that diet supplemented with 4 or 8 g/kg of inulin, oligofructose, mannanoligosaccharide (MOS), short-chain fructooligosaccharide, or transgalactooligosaccharide (TOS). Each of the 11 diets was tube-fed (30 g) to 4 cecectomized and 4 intact Single Comb White Leghorn roosters that had been fasted for 24 h. Excreta were then collected for the following 48 h, freeze-dried, and analyzed for amino acid content. The true digestibility of lysine and valine was increased (P<0.05) in cecectomized roosters fed 8 g/kg of MOS or TOS when compared with roosters fed the control diet. In addition, methionine digestibility was improved (P<0.05) in cecectomized roosters fed 4 g/kg of MOS or short-chain fructooligosaccharide and by 8 g/kg of oligofructose or TOS. The true digestibility of isoleucine was increased (P<0.05) in cecectomized roosters fed 8 g/kg of MOS or 4 or 8 g/kg of TOS. The magnitude of the increases in amino acid digestibility coefficients for cecectomized roosters ranged from 3 to 9 percentage units. Feeding either 4 or 8 g/kg of inulin to intact roosters decreased (P<0.05) the true digestibility of methionine. The oligosaccharides generally had no significant effect on TMEn. The results of this study indicated that the indigestible oligosaccharides had no significant effect on the digestibility of most amino acids in a corn-isolated soy protein diet. The digestibility of a few amino acids, however, was increased by some oligosaccharides in cecectomized roosters but not in intact roosters.

The effects of several oligosaccharides on growth performance, nutrient digestibilities, and cecal microbial populations in young chicks.

Two experiments were conducted with New Hampshire x Columbian chicks fed a corn-soybean meal diet and 1 experiment was conducted with chicks fed a dextrose-isolated soy protein diet to examine the effects of inulin, oligofructose, mannanoligosaccharide (MOS), short-chain fructooligosaccharide (SCFOS), and transgalactooligosaccharide on growth performance, ME(n), digestibility of amino acids (AA), and cecal microbial populations. Each diet was fed to chicks from 0 to 21 d of age, and excreta were collected at 3-4, 7, 14, and 21 d of age in both experiments. Neither 4 nor 8 g of oligosaccharides/kg had a significant effect on growth performance. The ME(n) and AA digestibility values increased with increasing age. Feeding 8 g/kg of inulin and SCFOS had a negative effect (P <0.05) on ME(n) at most ages, and 8 g/kg of most of the oligosaccharides reduced (P <0.05) digestibility of AA at various ages. In experiment 2, 4 g/kg of SCFOS, MOS, and transgalactooligosaccharide significantly reduced ME(n) at 3 to 4 d, but most oligosaccharides increased (P <0.05) ME(n) values at 7, 14, and 21 d. The effects of oligosaccharides (4 g/kg) on AA digestibility were generally small and inconsistent. Feeding corn-soybean meal diets containing 4 g/kg of oligosaccharides had no significant effect on cecal Bifidobacterium, Lactobacillius, Clostridium perfringens, or Escherichia coli populations in 21-d-old chicks. In a third experiment, cecal populations of C. perfringens were reduced when SCFOS and MOS were supplemented at 4 g/kg into a dextrose-isolated soy protein diet. These results indicate that a low concentration (4 g/kg) of an indigestible, prebiotic oligosaccharide can be fed with no deleterious effects on ME(n) and AA digestibility. Feeding a higher level of an oligosaccharide (8 g/kg), however, may depress ME(n) and AA digestibility.

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.