Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection

In a previous study, Multiplex-nanopore-sequencing based whole genome sequencing (WGS) allowed for accurate in silico serotype prediction of Salmonella within one day for five multiplexed isolates, using both SISTR and SeqSero2. Since only ten serotypes were tested in our previous study, the conclusions above were yet to be evaluated in a larger scale test. In the current study we evaluated this workflow with 69 Salmonella serotypes and also explored the feasibility of using multiplex-nanopore-sequencing based WGS for antimicrobial resistance gene (AMR) and virulence gene detection. We found that accurate in silico serotype prediction with nanopore-WGS data was achieved within about five hours of sequencing at a minimum of 30× Salmonella genome coverage, with SeqSero2 as the serotype prediction tool. For each tested isolate, small variations were observed between the AMR/virulence gene profiles from the Illumina and Nanopore sequencing platforms. Taking results generated using Illumina data as the benchmark, the average precision value per isolate was 0.99 for both AMR and virulence gene detection. We found that the resistance gene identifier - RGI identified AMR genes with nanopore data at a much lower accuracy compared to Abricate, possibly due to RGI's less stringent minimum similarity and coverage by default for database matching. This study is an evaluation of multiplex-nanopore-sequencing based WGS as a cost-efficient and rapid Salmonella classification method, and a starting point for future validation and verification of using it as a AMR/virulence gene profiling tool for the food industry. This study paves the way for the application of nanopore sequencing in surveillance, tracking, and risk assessment of Salmonella across the food supply chain.

Oxidative stress, activity behaviour and body mass in captive parrots

Many parrot species are kept in captivity for conservation, but often show poor reproduction, health and survival. These traits are known to be influenced by oxidative stress, the imbalance between the production of reactive oxygen species (ROS) and ability of antioxidant defences to ameliorate ROS damage. In humans, oxidative stress is linked with obesity, lack of exercise and poor nutrition, all of which are common in captive animals. Here, we tested whether small parrots (budgerigars, Melopsittacus undulatus) maintained in typical pet cages and on ad libitum food varied in oxidative profile, behaviour and body mass. Importantly, as with many birds held in captivity, they did not have enough space to engage in extensive free flight. Four types of oxidative damage, single-stranded DNA breaks (low-pH comet assay), alkali-labile sites in DNA (high-pH comet assay), sensitivity of DNA to ROS (H2O2-treated comet assay) and malondialdehyde (a byproduct of lipid peroxidation), were uncorrelated with each other and with plasma concentrations of dietary antioxidants. Without strenuous exercise over 28 days in a relatively small cage, more naturally 'active' individuals had more single-stranded DNA breaks than sedentary birds. High body mass at the start or end of the experiment, coupled with substantial mass gain, were all associated with raised sensitivity of DNA to ROS. Thus, high body mass in these captive birds was associated with oxidative damage. These birds were not lacking dietary antioxidants, because final body mass was positively related to plasma levels of retinol, zeaxanthin and α-tocopherol. Individuals varied widely in activity levels, feeding behaviour, mass gain and oxidative profile despite standardized living conditions. DNA damage is often associated with poor immunocompetence, low fertility and faster ageing. Thus, we have candidate mechanisms for the limited lifespan and fecundity common to many birds kept for conservation purposes.

Does adiposity status influence femoral cortical strength in rodent models of growth hormone deficiency?

Growth hormone (GH)-deficiency is usually associated with elevated adiposity, hyperleptinemia, and increased fracture risk. Since leptin is thought to enhance cortical bone formation, we have investigated the contribution of elevated adiposity and hyperleptinemia on femoral strength in rodent models of GH deficiency. Quantification of the transpubertal development of femoral strength in the moderately GH-deficient/hyperleptinemic Tgr rat and the profoundly GH-deficient/hypoleptinemic dw/dw rat revealed that the mechanical properties of cortical bone in these two models were similarly compromised, a 25-30% reduction in failure load being entirely due to impairment of geometric variables. In contrast, murine models of partial (GH antagonist transgenic) and complete (GH receptor-null) loss of GH signaling and elevated adiposity showed an impairment of femoral cortical strength proportionate to the reduction of GH signaling. To determine whether impaired femoral strength is exacerbated by obesity/hyperleptinemia, femoral strength was assessed in dw/dw rats following two developmental manipulations that elevate abdominal adiposity and circulating leptin, neonatal monosodium glutamate (MSG) treatment, and maintenance on an elevated fat diet. The additional impairment of femoral strength following MSG treatment is likely to have resulted from a reduction in residual activity of the hypothalamo-pituitary-GH-IGF-I axis, but consumption of elevated dietary fat, which did not reduce circulating IGF-I, failed to exacerbate the compromised femoral strength in dw/dw rats. Taken together, our data indicate that the obesity and hyperleptinemia usually associated with GH deficiency do not exert a significant influence over the strength of cortical bone.

The effects of short-term antioxidant supplementation on oxidative stress and flight performance in adult budgerigars Melopsittacus undulatus

Antioxidants are known to play an important role in quenching reactive oxygen species (ROS), thus ameliorating oxidative stress. Since increased metabolism associated with exercise can increase oxidative stress, dietary antioxidants may be a limiting factor in determining aspects of physical performance. Here we tested whether oxidative stress associated with flight exercise of captive adult budgerigars, Melopsittacus undulatus differed after they received a diet containing either enhanced (EQ) or reduced levels (RQ) of a nutritional supplement (Nutrivit) rich in antioxidants for 4 weeks. We also assessed differences in take-off escape time, a potential fitness-determining physiological capability. Oxidative stress was measured in two ways: comet assay to measure DNA damage; and analysis of malondialdehyde (MDA), a by-product of lipid peroxidation. Flight exercise appeared to increase oxidative stress. Moreover, birds had a higher percentage of intact DNA (fewer alkali labile sites) in one comet measure and lower levels of MDA after an EQ diet than after an RQ diet. We found no difference in flight performance between the two diets. Our results suggested that birds exerted maximum effort in escape flights, regardless of diet. However, this was at a cost of increased oxidative stress post-flight when on a reduced quality diet, but not when on an enhanced, antioxidant-rich diet. We suggest that dietary antioxidants may prove important in reducing exercise-related costs through multiple physiological pathways. Further work is necessary to fully understand the effects of antioxidants and oxidative stress on exercise performance in the longer term.

Mass screening for antimicrobial resistant Escherichia coli in dairy cows in northern New South Wales

OBJECTIVE

To describe aspects of the epidemiology of antimicrobial resistance in Escherichia coli shed in the faeces of milking cows in a dairying region of New South Wales.

DESIGN

A survey based on multi-stage sampling with repeated measures made within herds for estimating within-herd correlation of resistance status, and with repeated measures made on identical specimens for estimating test-retest reliability.

PROCEDURE

From a population of 110 dairy herds, 30 were selected at random and from each herd between 5 and 10 faecal specimens were obtained from fresh manure pats. E coli from faecal specimens were grown on hydrophobic grid membrane filters (HGMF) and replicated onto chromogenic agar and agar containing antimicrobials (gentamicin, ampicillin, tetracycline and sulfamethoxazole). Image analysis was used to assess colony growth. Data were analysed descriptively, by generalised linear mixed models and by Taylor series linearisation to account for attributes of the survey design.

RESULTS

Of the 10,279 E coli isolates assessed, 91% expressed no resistance, 7.3% were resistant to sulfamethoxazole, 3.6% to tetracycline, 2.2% to ampicillin and 0.09% to gentamicin. The most common multiple resistance phenotype was ampicillin-tetracycline-sulfamethoxazole (1.8% of isolates). Most multiple resistant isolates appeared clustered within particular herds but were too rare to obtain valid estimates of variance, confidence intervals or intra-herd correlation. The estimated proportion of isolates in the population that were susceptible to all four antimicrobials was 97% (95% CI: 91% to 100%) and 55% of cows had no resistance detected in faecal E coli (95% CI: 27% to 83%). Within-herd correlation of shedding status (any resistance pattern) was absent and test-retest reliability of the measurement system was estimated to be at the lower end of good (0.40) but increased to excellent (0.89) after excluding sulfamethoxazole resistance, which had a greater measurement error.

CONCLUSION

Antimicrobial resistance was uncommon in E coli in the population of dairy cows studied. HGMF and image analysis is an effective tool for detecting rare forms of resistant E coli that are not uniformly distributed in livestock populations.

The relationship between concentration of a dual marker strain of Salmonella Typhimurium in bovine faeces and its probability of detection by immunomagnetic separation and culture

AIMS

To modify a strain of Salmonella serotype Typhimurium to express unique marker traits and then define how the concentration of the marker in bovine faeces affects the probability of its detection by culture preceded by immunomagnetic separation (IMS).

METHODS AND RESULTS

DNA encoding for the production of green fluorescent protein (gfp) and resistance to kanamycin was inserted into the bacterial chromosome of Salm. Typhimurium. Transposon insertion was demonstrated by Southern blot hybridization. Varying amounts of one electroporant (gfpSal-1) were inoculated into suspensions of bovine faeces and attempts made to isolate gfpSal-1 using a protocol based on pre-enrichment incubation, IMS and enrichment in selective media. Isolates of gfpSal-1 were differentiated from wild strains of Salmonella using fluorescence under u.v. light and expression of kanamycin resistance. A logistic and Gompertz function each derived from the dose-response data partially explained the observations with the fit of the Gompertz function judged to be superior. The 10, 50 and 90% limits of detection from the Gompertz function were estimated to be 1.92, 2.03 and 2.27 CFU g(-1) respectively.

CONCLUSIONS

Reliance on the traditional concept of 'limit of detection' could introduce unacceptable errors in the interpretation of test findings when the concentration of Salm. Typhimurium in bovine faeces (pooled or individual) is below ca 3 CFU g(-1) of faeces.

SIGNIFICANCE AND IMPACT OF THE STUDY

The dose-response curve can be used to aid the design of protocols for detecting Salmonella in individual and pooled faecal specimens. The experiments demonstrate that both reporter genes in tandem are useful for studying the performance of culture-based methods for detecting pathogens in faeces.

Nutrient intake and urine composition in calcium oxalate stone-forming dogs: comparison with healthy dogs and impact of dietary modification

Nutrient intake and urine composition were analyzed in calcium oxalate (CaOx)stone-forming and healthy control dogs to identify factors that contribute to CaOx urolithiasis. Stone-forming dogs had significantly lower intake of sodium, calcium, potassium, and phosphorus and significantly higher urinary calcium and oxalate concentrations, calcium excretion, and CaOx relative supersaturation (RSS). Feeding a diet used in the treatment of canine lower urinary tract disease for 1 month was associated with increased intake of moisture, sodium, and fat; reduced intake of potassium and calcium; and decreased urinary calcium and oxalate concentrations, calcium excretion, and CaOx RSS. No clinical signs of disease recurrence were observed in the stone-forming dogs when the diet was fed for an additional 11 months. The results suggest that hypercalciuria and hyperoxaluria contribute to the formation of CaOx uroliths in dogs and show that dietary modifications can alter this process.

Risk factor analysis and relative supersaturation as tools for identifying calcium oxalate stone-forming dogs

Twenty-four hour urine samples were collected from 17 calcium oxalate (CaOx) stone-forming (SF) dogs and 17 normal (N), age-, breed- and sex-matched dogs. Urinary CaOx relative supersaturation (RSS) was calculated and found to be significantly higher in the SF group than the N group. RSS measurement is not readily applicable to veterinary practice; thus, alternatives were explored. Discriminant analysis failed to identify key factors differentiating most SF from N dogs. Urinary calcium, oxalate and uric acid, which differed between the SF and N animals, were combined into a measure of relative probability of CaOx stone formation (PSF) to establish whether this approach could be used to assess the risk of CaOx stone formation in dogs. Although there was good correlation between the techniques, RSS more clearly discriminated between SF and N dogs. These data suggest that neither PSF nor discriminant analysis is preferable to RSS for assessing the risk of CaOx stone formation in dogs.

The relative effects of supplemental dietary calcium and oxalate on urine composition and calcium oxalate relative supersaturation in healthy adult dogs

The aim of this study was to establish the relative effects of dietary calcium and oxalate (in the form of oxalic acid) on the composition of urine produced by healthy adult Cairn Terriers and Miniature Schnauzers. A nutritionally complete dry dog food was fed to 7 dogs (4 Cairn terriers and 3 Miniature schnauzers) for 24 weeks. The dogs were fed the diet alone, or supplemented with six different combinations of dietary calcium (as carbonate and sulphate) and oxalate (as oxalic acid) commonly found in dry commercially prepared dog foods. Urine pH, volume, specific gravity, and concentrations of 12 analytes were measured for each dog; urinary relative supersaturation (RSS) with calcium oxalate (CaOx) was calculated from these values. The effects of supplemental calcium and oxalate were established using two-way analysis of variance and multiple range tests (least significant difference); P<0.05 was considered significant. The lowest level of dietary calcium and oxalate resulted in the lowest CaOx RSS. The high calcium, low oxalate diet resulted in the highest CaOx RSS, a low calcium diet with increased dietary oxalate also tended to increase CaOx RSS although results were highly variable. Urinary calcium concentration increased significantly with dietary calcium; urinary oxalate increased, although inconsistently, with dietary oxalic acid only when dietary calcium was low. Measures to reduce both calcium and oxalate should be considered when implementing dietary changes to reduce the risk of calcium oxalate formation in dogs. A reduction in dietary calcium without a concomitant decrease in dietary oxalate may increase the risk of CaOx crystallisation in susceptible dogs.

Effect of dietary moisture and sodium content on urine composition and calcium oxalate relative supersaturation in healthy miniature schnauzers and labrador retrievers

The aim of this series of studies was to evaluate two possible feeding strategies as methods for reducing the risk of calcium oxalate (CaOx) formation in two breeds of healthy dog. The studies compared the effect of dietary moisture (Study 1) and dietary sodium (Na), (Study 2) on urine composition of labrador retrievers (LR) and miniature schnauzers (MS). A nutritionally complete dry dog food was fed to 16 dogs (eight LR, eight MS; Study 1) and 15 dogs (seven LR, eight MS; Study 2) for 24 days (Study 1), or 36 days (Study 2). The dogs were fed the diet alone (7% moisture, 0.06 g Na/100 kcal), or supplemented with deionised water to 73% moisture (Study 1), or dietary Na, to deliver 0.20 or 0.30 g Na per 100 kcal (Study 2). Urine pH, volume, specific gravity, and concentrations of 12 analytes were measured for each dog. Urinary relative supersaturations (RSS) with CaOx were calculated from these values. The effects of supplemental Na or water were established using t tests (Study 1) or analysis of variance, and multiple range tests (least significant difference) (Study 2); P<0.05 was considered significant. Increasing dietary moisture significantly increased total moisture intake (P=0.001), and reduced urine specific gravity (P=0.003), urinary oxalate concentration (P=0.04), and CaOx relative supersaturation (P=0.04) in the MS. Urinary parameters remained unchanged in the LR, indicating that feeding a high moisture diet may reduce the risk of CaOx formation in high-risk breeds. Increasing dietary Na led to production of urine with a significantly lower CaOx RSS in both breeds, indicating that sodium supplementation to dry diet formats may reduce the risk of CaOx formation. These feeding strategies should be considered when evaluating methods for preventing CaOx formation within high-risk groups.

Predicting the crystallization potential of urine from cats and dogs with respect to calcium oxalate and magnesium ammonium phosphate (struvite)

The objective of this study was to validate two programs (SUPERSAT and EQUIL 2) for calculation of calcium oxalate (CaOx) and magnesium ammonium phosphate (struvite; MAP) relative supersaturation (RSS) in dog and cat urine. Healthy adult cats (n = 10) and dogs (n = 9) were fed standard diets for a 3-wk period. Urine was collected (24 h, dogs; 48 h, cats) and filtered, and the pH was measured. A 20-mL aliquot was titrated to pH 2 and frozen for analysis. Additional aliquots were incubated with 1 g seed crystals at 38 degrees C; CaOx for 24 h (cat) and 2, 6 and 9 d (dog); MAP for 48 h (dog) and 6 d (cat). Samples were analyzed for 10 substances. RSS was calculated using EQUIL 2 and SUPERSAT. CaOx RSS (SUPERSAT): dog urine was initially supersaturated, whereas cat urine was undersaturated with the diets used. Cat urine reached the solubility product (K(sp)), (RSS = 1) after 24-h incubation, whereas dog urine was still approaching K(sp) at 9 d. MAP RSS (SUPERSAT): urine from both species was undersaturated and increased toward K(sp) during incubation. Final RSS values were compared for both programs. SUPERSAT resulted in values close to 1 for both CaOx and MAP; EQUIL 2 gave similar values for CaOx RSS, although MAP RSS values were considerably higher than 1. In conclusion, EQUIL 2 and SUPERSAT both calculated reasonably accurate RSS values for CaOx, whereas only SUPERSAT provided an accurate measure of MAP RSS.

Comparison of urine composition of healthy Labrador retrievers and miniature schnauzers

OBJECTIVE

To compare urine composition in Labrador Retrievers (LR) and Miniature Schnauzers (MS) fed the same dog food.

ANIMALS

8 healthy LR (mean [+/- SD] age, 3.1+/-1.7 years) and 8 healthy MS (mean age, 3.7+/-1.3 years).

PROCEDURE

A nutritionally complete dry dog food was fed to the dogs for 24 days. Urinary pH, volume, specific gravity, frequency of urination, and urinary concentrations of 12 analytes were measured for each dog; urinary relative supersaturation (RSS) with calcium oxalate and brushite (calcium hydrogen phosphate dihydrate) were calculated from these values.

RESULTS

MS urinated significantly less often and had a lower urine volume (ml/kg of body weight per d) and a significantly higher urine pH, compared with LR. Urinary calcium concentration and brushite RSS were significantly higher in the urine of MS. As a result of a high calorie requirement, primarily as a result of high surface area to volume ratio, MS had significantly higher intake (per kg body weight) of dietary minerals, compared with LR.

CONCLUSIONS AND CLINICAL RELEVANCE

Differences in urine composition exist between breeds fed the same diet, some of which, including lower urine volume, higher calcium concentration, and higher brushite RSS, may contribute to the high prevalence of calcium oxalate uroliths observed in MS. Differences between breeds should be considered when evaluating strategies for controlling calcium oxalate stone formation.

Effects of dietary potassium citrate supplementation on urine pH and urinary relative supersaturation of calcium oxalate and struvite in healthy dogs

OBJECTIVE

To assess the effect of dietary potassium citrate supplementation on the urinary pH, relative supersaturation of calcium oxalate and struvite (defined as the activity product/solubility product of the substance), and concentrations of magnesium, ammonium, phosphate, citrate, calcium, and oxalate in dogs.

ANIMALS

12 healthy adult dogs.

PROCEDURE

Canned dog food was fed to dogs for 37 days. Dogs were randomly allocated to 3 groups and fed test diets for a period of 8 days. Study periods were separated by 6-day intervals. During each study period the dogs were fed either standard diet solus (control) or standard diet plus 1 of 2 types of potassium citrate supplements (150 mg potassium citrate/kg of body weight/d) twice daily. Urinary pH, volume and specific gravity, relative supersaturation of calcium oxalate and struvite, and concentrations of magnesium, ammonium, phosphate, calcium, oxalate, and citrate were assessed for each treatment.

RESULTS

Mean urine pH was not significantly affected by dietary potassium citrate supplementation, although urine pH did increase by 0.2 pH units with supplementation. Diets containing potassium citrate maintained a higher urine pH for a longer part of the day than control diet. Three Miniature Schnauzers had a significantly lower urinary relative calcium oxalate supersaturation when fed a diet supplemented with potassium citrate, compared with control diet.

CONCLUSIONS AND CLINICAL RELEVANCE

Dietary potassium citrate supplementation has limited effects on urinary variables in most healthy dogs, although supplementation results in maintenance of a higher urine pH later in the day. Consequently, if supplementation is introduced, dogs should be fed twice daily and potassium citrate should be given with both meals or with the evening meal only.