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Item Zoonotic transmission of asymptomatic carriage Staphylococcus aureus on dairy farms in Canterbury, New Zealand.(Microbiology Society, 2024-12-04) Straub C; Taylor W; French NP; Murdoch DR; Priest P; Anderson T; Scott PZoonotic pathogen transmission is of growing concern globally, with agricultural intensification facilitating interactions between humans, livestock and wild animals. Staphylococcus aureus is a major human pathogen, but it also causes mastitis in dairy cattle, leading to an economic burden on the dairy industry. Here, we investigated transmission within and between cattle and humans, including potential zoonotic transmission of S. aureus isolated from cattle and humans from three dairy farms and an associated primary school in New Zealand. Nasal swabs (N=170) were taken from healthy humans. Inguinal and combined nasal/inguinal swabs were taken from healthy cattle (N=1163). Whole-genome sequencing was performed for 96 S. aureus isolates (44 human and 52 cattle). Multilocus sequence typing and assessments of antimicrobial resistance and virulence were carried out. Potential within- and across-species transmission events were determined based on single nucleotide polymorphisms (SNPs). Thirteen potential transmission clusters were detected, with 12 clusters restricted to within-species and one potential zoonotic transmission cluster (ST5). Potential transmission among cattle was mostly limited to single age groups, likely because different age groups are managed separately on farms. While the prevalence of antimicrobial resistance (AMR) was low among both bovine and human isolates, the discovery of an extended-spectrum beta-lactamase gene (bla TEM-116) in a bovine isolate was concerning. This study provides evidence around frequency and patterns of potential transmission of S. aureus on dairy farms and highlights the AMR and virulence profile of asymptomatic carriage S. aureus isolates.Item Changing epidemiology of Leptospirosis in New Zealand, with a focus on the novel strain of Leptospira borgpetersenii : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand(Massey University, 2024-12-25) Sokolova, MarynaIn New Zealand, leptospirosis has been a common disease in dairy cattle since the 1940s. Six pathogenic Leptospira serovars from two species have been identified as endemic to New Zealand: Leptospira borgpetersenii serovars (sv.) Hardjobovis (Hardjo), Tarassovi, Ballum, Balcanica, and Leptospira interrogans sv. Pomona and Copenhageni. From these, sv. Pomona and Hardjo are the most commonly reported in cattle, and sv. Ballum, Tarassovi, and Copenhageni are less common. The estimated 99% of the national dairy herd is vaccinated against leptospirosis by vaccines containing antigens to Pomona and Hardjobovis and sometimes vaccines also include Copenhageni antigen. Vaccines for protecting dairy cows against Tarassovi were unavailable in New Zealand before December 2023. Historically, leptospirosis due to Tarassovi infection in New Zealand cattle was considered accidental and clinically unimportant. Serosurveys of apparently healthy cattle in New Zealand showed that over the past fifty years, Tarassovi seroprevalence increased from 6% (50/300) at MAT ≥ 50 to 18% (698/3878) at MAT ≥ 48. More recently, a serology and urine shedding study from 2015- 2016 evaluated the status of 4,000 dairy cows from 200 randomly selected farms, stratified by New Zealand's geographical location and herd size. The study found that on the animal level, 17% of the study animals showed evidence of past infection with Tarassovi, as defined by at least one sample reacting at MAT ≥ 48 for the study's purposes. Moreover, 96% (90/94) of PCR-positive urine samples were sequenced, and 68% (54/80) of those were found to have a novel allele in the sequenced region at the glmU loci. Thus, the use of molecular diagnostic tools, specifically molecular typing targeting a partial region of the glmU gene, allowed New Zealand researchers to identify a novel L. borgpetersenii strain, informally called strain (str.) Pacifica, in the urine of these cows. The 2015-2016 survey reported that dairy cows with Tarassovi titres were associated with urinary shedding, as determined by microscopic agglutination test (MAT) and polymerase chain reaction (PCR) testing, respectively. Because of this association, str. Pacifica is thought to belong to the serogroup Tarassovi. Additionally, the DNA of str. Pacifica has been retrospectively detected in cattle and deer samples dating back as early as 2007. Moreover, the 19-year (1999-2007) average annual incidence of notified human cases of Tarassovi leptospirosis was estimated at 12.59/100,000 in dairy farmers, compared to an overall annual average incidence of 2.01/100,000. These coincidental findings raised public health concerns. Therefore, at least some cases of Tarassovi seropositivity, as identified by MAT and reported before 2021, could partially be attributed to str. Pacifica. To confirm str. Pacifica's serogroup, isolation by culture and complete genetic characterisation of an isolate are required. Since str. Pacifica was only recently detected, its epidemiology, morphology, maintenance, and pathogenicity in the host population, as well as its impact on animal and human health, were not well understood. In this study, we investigated the possibility of isolating str. Pacifica from cow's urine by running a series of laboratory experiments where laboratory-adapted strains were used as a proxy for L. borgpetersenii str. Pacifica in the absence of an isolate to better understand its growth requirements. Laboratory-adapted Leptospira borgpetersenii strains were seeded into different types of media, and Leptospira growth rates were evaluated (Chapter 3). As a result, we ruled out unsuitable media and growth conditions, and this work helped to select the best media and growth conditions for a follow-up field investigation, where freshly collected cow's urine was seeded into selected media. Str. Pacifica was isolated from the urine of a shedding cow using HAN medium at 37°C and 5% CO2. However, this medium failed to sustain str. Pacifica and the culture was lost (Chapter 4). In addition, over the 2020-2021-2022 milking seasons, we collected and tested blood and urine samples from dairy farms, identified as str. Pacifica positive from the 2016 survey. Our results revealed that str. Pacifica was still maintained in the same dairy herds six years after initial detection. Moreover, we reported an estimated prevalence ratio (PR) of 7, indicating that the prevalence of shedders was seven times as high at the beginning than at the end of lactation in primiparous cows (Chapter 4). These findings provide evidence that str. Pacifica is adapted to dairy cows in New Zealand, and the peak shedding in primiparous heifers occurs in early lactation. Since the highest levels of str. Pacifica shedding were detected at the start of the milking season during peak milk production, which also coincides with a relatively short 3-month mating period, the associations between str. Pacifica and milk production and reproductive performance of milking cows were also investigated using herd test data and serological and PCR test results of the 2016 survey. Statistical models, including linear, logistic, and generalised mixed models with fixed and random effects, as well as a shared frailty survival model, were used to evaluate the associations between str. Pacifica positivity and reproduction (Chapter 5) and milk reproduction (Chapter 6) in dairy cows. Results of the statistical analysis of the association between str. Pacifica positivity and reproduction (Chapter 5) of dairy herds showed that str. Pacifica delayed the time from calving to conception (HR = 0.84; 95%: CI 0.74-0.96), although there was no effect on the pregnancy rate (Chapter 5). An analysis of milk production data did not reveal any associations with str. Pacifica at either animal or herd level (Chapter 6). The absence of clinical signs and the lack of association with milk production and reproduction at both the animal and herd levels provides further evidence towards str. Pacifica being well adapted to dairy cows. Therefore, evidence from this thesis suggests that dairy cattle are the maintenance host for str. Pacifica in New Zealand. It is also important to note that str. Pacifica shedders can infect people, especially dairy farmers, milkers, and farm workers who are in regular contact with str. Pacifica-shedding animals. Therefore, the prevention of str. Pacifica transmission via vaccination or the use of appropriate personal protective gear should be prioritised.Item Study Protocol for a Randomized Controlled Trial Investigating the Effects of the Daily Consumption of Ruminant Milk on Digestive Comfort and Nutrition in Older Women: The YUMMI Study.(MDPI (Basel, Switzerland), 2024-12-06) Ong SP; Miller JC; McNabb WC; Gearry RB; Ware LM; Mullaney JA; Fraser K; Hort J; Bayer SB; Frampton CMA; Roy NC; Miranda JMBACKGROUND: Age-related changes can lead to dietary insufficiency in older adults. The inclusion of high-quality, nutrient-dense foods such as ruminant milks can significantly improve health outcomes. However, many older adults worldwide do not meet daily milk intake recommendations because of digestive discomfort and health concerns. Ovine and caprine milks are increasingly popular for their perceived digestive and nutritional benefits. While preclinical studies suggest differences in milk digestion, human studies investigating acute postprandial responses remain inconclusive, and the impacts of sustained milk consumption remain uncertain. OBJECTIVES: Hence, we present a randomized controlled trial investigating how the sustained consumption of bovine, caprine, or ovine milk influences digestion, nutrition, and metabolism in older women. METHODS: A total of 165 healthy older women were randomized to receive bovine, caprine, or ovine milk, or no milk, twice daily for 12 weeks. The primary outcome is the impact of milk consumption on digestive comfort assessed via the Gastrointestinal Syndrome Rating Scale (GSRS). Secondary outcomes include changes in nutrient intake, plasma amino acid and lipid appearance, bowel habits, the gut microbiota, cardiometabolic health, physical function, physical activity, sleep, mood, sensory perception, and emotional response. CONCLUSIONS: The findings could inform dietary recommendations for older women and facilitate the development of targeted functional food products.Item Invited review: Bovine colostrum, a promising ingredient for humans and animals-Properties, processing technologies, and uses(Elsevier, 2023-08) Costa A; Sneddon NW; Goi A; Visentin G; Mammi LME; Savarino EV; Zingone F; Formigoni A; Penasa M; De Marchi MMammalian colostrum, known as "liquid gold," is considered a valuable source of essential nutrients, growth factors, probiotics, prebiotics, antibodies, and other bioactive compounds. Precisely for this reason, bovine colostrum (BC) is an emerging ingredient for the feed, food, and pharmaceutical industries, being nowadays commercially available in a variety of forms in several countries. Moreover, quite a large number of functional foods and supplements for athletes, human medicines, pet nutrition plans, and complementary feed for some livestock categories, such as piglets and calves, contain BC. The amount of BC yielded by a cow after calving represents approximately 0.5% of the yearly output in dairy breeds. For its nutritional properties and low availability, BC is characterized by a greater market value and an increasing demand compared with other by-products of the dairy sector. However, information regarding the market size of BC for the food and pharmaceutical industries, as well as future developments and perspectives, is scarcely available in the scientific literature. This lack can be attributed to industrial secrecy as well as to the relatively small scale of the BC business when compared with other dairy products, which makes the BC market limited, specific, and intended for a restricted audience. From a legal perspective, regulations assign BC to the large family of milk-derived powders; thus, collecting specific production data, as well as import-export trend information, is not straightforward and can result in unprecise estimates. Given that the interest in BC is increasing in different fields, it is important to have an overview of the production steps and of pros and cons of this emerging ingredient. The present narrative review discloses why BC has started to be considered a product rather than a by-product of the dairy industry. Moreover, the present document aims to summarize the existing methodologies used to assess BC quality in terms of immunoglobulin concentration, the different applications of BC in the industry, and the BC processing technologies. Finally, a panoramic view of the current international market is provided for the first time for this dairy product.Item Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana.(PLOS, 2019-03-04) Otchere ID; van Tonder AJ; Asante-Poku A; Sánchez-Busó L; Coscollá M; Osei-Wusu S; Asare P; Aboagye SY; Ekuban SA; Yahayah AI; Forson A; Baddoo A; Laryea C; Parkhill J; Harris SR; Gagneux S; Yeboah-Manu D; Spigelman MBackground Bovine tuberculosis (bTB) caused by Mycobacterium bovis is a re-emerging problem in both livestock and humans. The association of some M. bovis strains with hyper-virulence, MDR-TB and disseminated disease makes it imperative to understand the biology of the pathogen. Methods Mycobacterium bovis (15) among 1755 M. tuberculosis complex (MTBC) isolated between 2012 and 2014 were characterized and analyzed for associated patient demography and other risk factors. Five of the M. bovis isolates were whole-genome sequenced and comparatively analyzed against a global collection of published M. bovis genomes. Results Mycobacterium bovis was isolated from 3/560(0.5%) females and 12/1195(1.0%) males with pulmonary TB. The average age of M. bovis infected cases was 46.8 years (7-72years). TB patients from the Northern region of Ghana (1.9%;4/212) had a higher rate of infection with M. bovis (OR = 2.7,p = 0.0968) compared to those from the Greater Accra region (0.7%;11/1543). Among TB patients with available HIV status, the odds of isolating M. bovis from HIV patients (2/119) was 3.3 higher relative to non-HIV patients (4/774). Direct contact with livestock or their unpasteurized products was significantly associated with bTB (p<0.0001, OR = 124.4,95% CI = 30.1–508.3). Two (13.3%) of the M. bovis isolates were INH resistant due to the S315T mutation in katG whereas one (6.7%) was RIF resistant with Q432P and I1491S mutations in rpoB. M. bovis from Ghana resolved as mono-phyletic branch among mostly M. bovis from Africa irrespective of the host and were closest to the root of the global M. bovis phylogeny. M. bovis-specific amino acid mutations were detected among MTBC core genes such as mce1A, mmpL1, pks6, phoT, pstB, glgP and Rv2955c. Additional mutations P6T in chaA, G187E in mgtC, T35A in Rv1979c, S387A in narK1, L400F in fas and A563T in eccA1 were restricted to the 5 clinical M. bovis from Ghana. Conclusion Our data indicate potential zoonotic transmission of bTB in Ghana and hence calls for intensified public education on bTB, especially among risk groups..Item Animal factors that affect enteric methane production measured using the GreenFeed monitoring system in grazing dairy cows.(Elsevier B.V., 2024-04-16) Starsmore K; Lopez-Villalobos N; Shalloo L; Egan M; Burke J; Lahart BSimilar to all dairy systems internationally, pasture-based dairy systems are under increasing pressure to reduce their greenhouse gas (GHG) emissions. Ireland and New Zealand are 2 countries operating predominantly pasture-based dairy production systems where enteric CH4 contributes 23% and 36% of total national emissions, respectively. Ireland currently has a national commitment to reduce 51% of total GHG emissions by 2030 and 25% from agriculture by 2030, as well as striving to achieve climate neutrality by 2050. New Zealand's national commitment is to reduce 10% of methane emissions by 2030 and between 24% and 47% reduction in methane emissions by 2050. To achieve these reductions, factors that affect enteric methane (CH4) production in a pasture-based system need to be investigated. The objective of this study was to assess the relationship between enteric CH4 and other animal traits (feed intake, metabolic liveweight, energy corrected milk yield, milk urea concentration, and body condition score [BCS]) in a grazing dairy system. Enteric CH4 emissions were measured on 45 late lactation (213.8 ± 29 d after calving) grazing Holstein-Friesian and Holstein-Friesian × Jersey crossbred cows (lactation number 3.01 ± 1.65, 538.64 ± 59.37 kg live weight, and 3.14 ± 0.26 BCS) using GreenFeed monitoring equipment for 10 wk. There was a training period for the cows to use the GreenFeed of 3 wk before the 10-wk study period. The average enteric CH4 produced in the study was 352 g ± 45.7 g per day with an animal to animal coefficient of variation of 13%. Dry matter intake averaged 16.6 kg ± 2.23 kg per day, while milk solids (fat plus protein) averaged 1.62 kg ± 0.29 kg per day. A multiple linear regression model indicated that each one unit increase in energy corrected milk yield, metabolic liveweight and milk urea concentration, resulted in an increase in enteric CH4 production per day by 3.9, 1.74, and 1.38 g, respectively. Although each one unit increase in BCS resulted in a decrease in 39.03 g CH4 produced per day. When combined, these factors explained 47% of the variation in CH4 production, indicating that there is a large proportion of variation not included in the model. The repeatability of the CH4 measurements was 0.66 indicating that cows are relatively consistently exhibiting the same level of CH4 throughout the study. Therefore, enteric CH4 production is suitable for phenotyping.Item Lactation curves of Montbéliarde-sired and Viking Red-sired crossbred cows and their Holstein herdmates in commercial dairies(Elsevier Inc. on behalf of the American Dairy Science Association, 2024-06) Houdek ES; Hazel AR; Lopez-Villalobos N; Hansen LB; Heins BJLactation curves were estimated for Montbéliarde (MO) × Holstein (HO) and Viking Red (VR) × HO 2-breed crossbred cows and for MO × VR/HO and VR × MO/HO 3-breed crossbred cows and their HO herdmates from test-day observations in 7 high-performance herds that participated in a designed study. Cows calved from 2010 to 2017. Test-day observations from milk recording were used to fit the lactation curves of cows in their first 3 lactations. Lactations of cows were required to have at least 250 DIM and to have at least 6 test days ≤265 DIM. Lactation curves from random regression (RR) were compared for 305-d production (kg), peak production (kg), peak day of production, and production from 4 to 103 DIM (kg), from 104 to 205 DIM (kg), and from 206 to 305 DIM (kg) for milk, fat, and protein. Also, the persistency of production was compared. First-lactation versus second- and third-lactation cows were analyzed separately for both the 2-breed and 3-breed crossbred cows and their respective HO herdmates. Legendre polynomial RR had the best goodness of fit for the lactation curves compared with Ali-Schaeffer and Wilmink RR from the test-day observations of milk, fat, and protein production. For fluid milk production of first-lactation cows, the MO × HO 2-breed crossbreds were not different from their HO herdmates for any of the lactation-curve characteristics, except persistency. However, the VR × HO 2-breed crossbreds had less fluid milk production compared with their HO herdmates. For first lactation, the MO × HO 2-breed crossbreds had more persistency of milk, fat, and protein production compared with their HO herdmates. The first-lactation MO × VR/HO 3-breed crossbreds had more persistency of fluid milk production compared with their HO herdmates. For second and third lactations, both the MO × HO and the VR × HO 2-breed crossbreds had higher fat production compared with their HO herdmates. Furthermore, the MO × HO 2-breed crossbreds had more protein production (kg) in all 3 periods of lactation compared with their HO herdmates. Crossbred cows may have advantages over HO cows for persistency of production in high-performance herds.Item Fertility and survival of Swedish Red and White × Holstein crossbred cows and purebred Holstein cows(y Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association, 2023-04) Pipino DF; Piccardi M; Lopez-Villalobos N; Hickson RE; Vázquez MISwedish Red and White × Holstein (S×H) cows were compared with pure Holstein (HOL) cows for fertility and survival traits in 2 commercial dairy farms in central-southern Córdoba province, Argentina, over 6 years (2008-2013). The following traits were evaluated: first service conception rate (FSCR), overall conception rate (CR), number of services per conception (SC), days open (DO), mortality rate, culling rate, survival to subsequent calvings, and length of productive life (LPL). The data set consisted of 506 lactations from 240 S×H crossbred cows and 1,331 lactations from 576 HOL cows. The FSCR and CR were analyzed using logistic regression, DO and LPL were analyzed using a Cox's proportional hazards regression model, and differences of proportions were calculated for mortality rate, culling rate, and survival to subsequent calvings. The S×H cows were superior to HOL cows in overall lactations for all the fertility traits (+10.5% FSCR, +7.7% CR, -0.5 SC, and 35 fewer DO). During the first lactation, S×H cows were superior to HOL cows for all fertility traits (+12.8% FSCR, +8.0% CR, -0.4 SC, and 34 fewer DO). In the second lactation, S×H cows exhibited lower SC (-0.5) and 21 fewer DO than HOL cows. In the third or greater lactations, S×H cows showed higher FSCR (+11.0%) and CR (+12.2%), lower SC (-0.8), and 44 fewer DO than pure HOL cows. In addition, S×H cows had a lower mortality rate (-4.7%) and a lower culling rate (-13.7%) than HOL cows. Due to the higher fertility and lower mortality and culling rates, the S×H cows had higher survival to the second (+9.2%), third (+16.9%), and fourth (+18.7%) calvings than HOL cows. Because of these results, S×H cows had longer LPL (+10.3 mo) than HOL cows. These results indicate that S×H cows had higher fertility and survival than HOL cows on commercial dairy farms in Argentina.Item β-Casein A1 and A2: Effects of polymorphism on the cheese-making process(Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association, 2023-08) Vigolo V; Visentin E; Ballancin E; Lopez-Villalobos N; Penasa M; De Marchi MOf late, "A2 milk" has gained prominence in the dairy sector due to its potential implications in human health. Consequently, the frequency of A2 homozygous animals has considerably increased in many countries. To elucidate the potential implications that beta casein (β-CN) A1 and A2 may have on cheese-making traits, it is fundamental to investigate the relationships between the genetic polymorphisms and cheese-making traits at the dairy plant level. Thus, the aim of the present study was to evaluate the relevance of the β-CN A1/A2 polymorphism on detailed protein profile and cheese-making process in bulk milk. Based on the β-CN genotype of individual cows, 5 milk pools diverging for presence of the 2 β-CN variants were obtained: (1) 100% A1; (2) 75% A1 and 25% A2; (3) 50% A1 and 50% A2; (4) 25% A1 and 75% A2; and (5) 100% A2. For each cheese-making day (n = 6), 25 L of milk (divided into 5 pools, 5 L each) were processed, for a total of 30 cheese-making processes. Cheese yield, curd nutrient recovery, whey composition, and cheese composition were assessed. For every cheese-making process, detailed milk protein fractions were determined through reversed-phase HPLC. Data were analyzed by fitting a mixed model, which included the fixed effects of the 5 different pools, the protein and fat content as a covariate, and the random effect of the cheese-making sessions. Results showed that the percentage of κ-CN significantly decreased up to 2% when the proportion of β-CN A2 in the pool was ≥25%. An increase in the relative content of β-CN A2 (≥50% of total milk processed) was also associated with a significantly lower cheese yield both 1 and 48 h after cheese production, whereas no effects were observed after 7 d of ripening. Concordantly, recovery of nutrients reflected a more efficient process when the inclusion of β-CN A2 was ≤75%. Finally, no differences in the final cheese composition obtained by the different β-CN pools were observed.Item Heritabilities and genetic and phenotypic correlations for milk production and fertility traits of spring-calved once-daily or twice-daily milking cows in New Zealand(Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association, 2023-03) Jayawardana JMDR; Lopez-Villalobos N; McNaughton LR; Hickson REThe objectives of this study were to estimate the genetic and phenotypic correlations and heritabilities for milk production and fertility traits in spring-calved once-daily (OAD) milking cows for the whole season in New Zealand and compare those estimates with twice-daily (TAD) milking cows. Data used in the study consisted of 69,252 first parity cows from the calving seasons 2015-2016 to 2017-2018 in 113 OAD and 531 TAD milking herds. Heritability estimates for production and fertility traits were obtained through single-trait animal models, and estimates of genetic and phenotypic correlations were obtained through bivariate animal models. Heritability estimates of production traits varied from 0.26 to 0.61 in OAD and from 0.13 to 0.63 in TAD. Heritability estimates for fertility traits were low in both OAD and TAD milking cow populations, and estimates were consistent (OAD: 0.01 to 0.10 and TAD: 0.01 to 0.08) across milking regimens. Estimates of phenotypic and genetic correlations among production traits were consistent across populations. In both populations, phenotypic correlations between milk production and fertility traits were close to zero, and most of the genetic correlations were antagonistic. In OAD milking cows, genetic correlations of milk and lactose yields with the start of mating to conception, 6-wk in-calf, not-in-calf, and 6-wk calving rate were close to zero. Interval from first service to conception was negatively genetically correlated with milk and lactose yields in OAD milking cows. Protein percentage was positively genetically correlated with 3-wk and 6-wk submission, 3-wk in-calf, 6-wk in-calf, first service to conception, 3-wk calving, and 6-wk calving rate in the TAD milking cow population, but these correlations were low in the OAD milking cow population. Further studies are needed to understand the relationship of protein percentage and fertility traits in the OAD milking system. The phenotypic correlations between fertility traits were similar in OAD and TAD milking populations. Genetic correlations between fertility traits were strong (≥0.70) in cows milked TAD, but genetic correlations varied from weak to strong in cows milked OAD. Further research is required to evaluate the interaction between genotype by milking regimen for fertility traits in terms of sire selection in the OAD milking cow population.