Antigen-specific polyclonal immunoglobulins derived from the serum, colostrum, or milk of immunized ruminant animals have potential as scalable therapeutics for the control of viral diseases including COVID-19. Here we show that the immunization of sheep with fusions of the SARS-CoV-2 receptor binding domain (RBD) to ovine IgG2a Fc domains promotes significantly higher levels of antigen-specific antibodies compared to native RBD or full-length spike antigens. This antibody population contained elevated levels of neutralizing antibodies that suppressed binding between the RBD and hACE2 receptors in vitro. A second immune-stimulating fusion candidate, Granulocyte-macrophage colony-stimulating factor (GM-CSF), induced high neutralizing responses in select animals but narrowly missed achieving significance. We further demonstrated that the antibodies induced by these fusion antigens were transferred into colostrum/milk and possessed cross-neutralizing activity against diverse SARS-CoV-2 variants. Our findings highlight a new pathway for recombinant antigen design in ruminant animals with applications in immune milk production and animal health.

We report here the complete genome sequence of Mycobacterium tuberculosis strain Colonial S-type 1 (CS1), which has been responsible for ongoing outbreaks of tuberculosis in New Zealand over the past 30 years. CS1 appears to be highly transmissible, with greater rates of progression to active disease, compared to other circulating M. tuberculosis strains; therefore, comparison of its genomic content is of interest.

The equine disease strangles, which is characterized by the formation of abscesses in the lymph nodes of the head and neck, is one of the most frequently diagnosed infectious diseases of horses around the world. The causal agent, Streptococcus equi subspecies equi, establishes a persistent infection in approximately 10 % of animals that recover from the acute disease. Such 'carrier' animals appear healthy and are rarely identified during routine veterinary examinations pre-purchase or transit, but can transmit S. equi to naïve animals initiating new episodes of disease. Here, we report the analysis and visualization of phylogenomic and epidemiological data for 670 isolates of S. equi recovered from 19 different countries using a new core-genome multilocus sequence typing (cgMLST) web bioresource. Genetic relationships among all 670 S. equi isolates were determined at high resolution, revealing national and international transmission events that drive this endemic disease in horse populations throughout the world. Our data argue for the recognition of the international importance of strangles by the Office International des Épizooties to highlight the health, welfare and economic cost of this disease. The Pathogenwatch cgMLST web bioresource described herein is available for tailored genomic analysis of populations of S. equi and its close relative S. equi subspecies zooepidemicus that are recovered from horses and other animals, including humans, throughout the world. This article contains data hosted by Microreact.

The Mycobacterium tuberculosis complex lineage 4 (L4), also known as the “Euro-American” lineage, is the most widely dispersed of the seven human adapted lineages. L4 is comprised of ten sublineages including L4.4, which has a moderate global distribution and is the most common L4 sublineage in New Zealand. We have used a phylodynamics approach and a dataset of 236 global M. tuberculosis genomes to trace the origins and dispersal of L4.4 strains in New Zealand that are predominantly found in Māori and Pacific people. We identify an L4.4.1.1 sublineage clade of European origin, likely French, that is prevalent in indigenous populations in both New Zealand and Canada. Molecular dating suggests that expansion of European trade networks in the early 19th century led to dispersal of this clade to the South Pacific. We also identify historical and social factors within the region that have contributed to the local spread and expansion of these strains, including recent Pacific migrations to New Zealand and the rapid urbanization of Māori in the 20th century. Our results offer new insight into the dispersal of M. tuberculosis in the South Pacific region and provide a striking example of the role of historical European migrations in the dispersal of M. tuberculosis . Author Summary Tuberculosis kills more people worldwide than any other infectious disease and indigenous populations are disproportionately affected by the disease. Here, we have used a large global dataset of Mycobacterium tuberculosis bacterial genomes to trace the historical origins of tuberculosis strains in New Zealand that are most frequently found in Māori and Pacific people. These strains are locally known as the ‘Rangipo’ and ‘Otara’ strains (both Māori place names) and belong to the “Euro-American” lineage of M. tuberculosis . Via genome analysis, we find that these strains are closely related to M. tuberculosis strains found in indigenous populations in Canada that have a European origin. We used a molecular dating approach (a molecular clock) to infer the ages of these strains and date divergence events. The timing we infer corresponds to the introduction of these strains to Polynesia via expanding European trade networks in the South Pacific in the early 19th century and suggests that the Otara strain has migrated to New Zealand from the Pacific Islands multiple times. Our results provide insight into human social phenomena underlying the expansion and dispersal of M. tuberculosis and reassert the important role of European colonial migrations in the global dispersal of the M. tuberculosis Euro-American lineage. This work also highlights the pejorative and stigmatizing mislabelling of the New Zealand strains with indigenous Māori place names, suggesting that these strains should be renamed.

Mycobacterium tuberculosis (Mtb) is a globally distributed bacterial pathogen whose population structure has largely been shaped by the activities of its obligate human host. Oceania was the last major global region to be reached by Europeans and is the last region for which the dispersal and evolution of Mtb remains largely unexplored. Here, we investigated the evolutionary history of the Euro-American L4.4 sublineage and its dispersal to the South Pacific. Using a phylodynamics approach and a dataset of 236 global Mtb L4.4 genomes we have traced the origins and dispersal of L4.4 strains to New Zealand. These strains are predominantly found in indigenous Māori and Pacific people and we identify a clade of European, likely French, origin that is prevalent in indigenous populations in both New Zealand and Canada. Molecular dating suggests the expansion of European trade networks in the early 19th century drove the dispersal of this clade to the South Pacific. We also identify historical and social factors within the region that have contributed to the local spread and expansion of these strains, including recent Pacific migrations to New Zealand and the rapid urbanization of Māori in the 20th century. Our results offer new insight into the expansion and dispersal of Mtb in the South Pacific and provide a striking example of the role of historical European migrations in the global dispersal of Mtb.

Selenium, a trace element with anticancer properties, can reduce harmful toxicities of chemotherapy and radiotherapy without compromising efficacy. However, the dose-response relationship in normal versus malignant human cells is unclear. We evaluated how methylseleninic acid (MSA) modulates the toxicity and efficacy of chemotherapy and radiation on malignant and non-malignant human mononuclear blood cells in vitro. We specifically investigated its effects on endoplasmic reticulum stress induction, intracellular glutathione concentration, DNA damage and viability of peripheral blood mononuclear cells and THP1 monocytic leukaemia cells in response to radiation, cytosine arabinoside or doxorubicin chemotherapy. MSA, at lower concentrations, induced protective responses in normal cells but cytotoxic effects in malignant cells, alone and in conjunction with chemotherapy or radiation. However, in normal cells higher concentrations of MSA were directly toxic and increased the cytotoxicity of radiation but not chemotherapy. In malignant cells higher MSA concentrations were generally more effective in combination with cancer treatments. Thus, optimal MSA concentrations differed between normal and malignant cells and treatments. This work supports clinical reports that selenium can significantly reduce dose-limiting toxicities of anticancer therapies and potentially improve efficacy of anticancer treatments. The optimal selenium compound and dose is not yet determined.

Vitamin D supplementation prevents acute respiratory infections and, through modulating innate and adaptive immunity, could have a potential role in bronchiectasis management. The primary aims of this pilot study were to assess serum 25-hydroxyvitamin D (25(OH)D) levels in New Zealand adults with bronchiectasis, and their 25(OH)D levels after vitamin D3 supplementation. Adults with bronchiectasis received an initial 2.5 mg vitamin D3 oral loading dose and 0.625 mg vitamin D3 weekly for 24 weeks. The primary outcome was serum 25(OH)D levels before and after vitamin D3 supplementation. Secondary outcomes (time to first infective exacerbation, exacerbation frequency, spirometry, health-related quality of life measures, sputum bacteriology and cell counts and chronic rhinosinusitis) were also assessed. This study is registered with the Australian New Zealand Clinical Trials Registry (ACTRN 12612001222831). The initial, average 25(OH)D level was 71 nmol/L (95% confidence interval (CI): [58, 84]), rising to 218 nmol/L (95% CI: [199, 237]) at 12 weeks and 205 nmol/L (95% CI: [186, 224]) at 24 weeks. The initial serum cathelicidin level was 25 nmol/L (95% CI: [17, 33]), rising to 102 nmol/L (95% CI: [48, 156]) at 12 weeks and 151 nmol/L (95% CI: [97, 205]) at 24 weeks. Over the 24-week study period, we observed statistically significant changes of 1.11 (95% CI: [0.08, 2.14]) in the Leicester Cough Questionnaire and −1.97 (95% CI: [−3.71, −0.23]) in the Dartmouth COOP charts score. No significant adverse effects were recorded. Many New Zealand adults with bronchiectasis have adequate 25(OH)D levels. Weekly vitamin D3 supplementation significantly improved 25(OH)D levels.

Despite New Zealand being a low-tuberculosis (TB) burden country, there are disproportionately high rates of TB in particular populations. Here, we report a rapid molecular diagnosis of the Mycobacterium tuberculosis Rangipo strain responsible for the largest recurring TB cluster in New Zealand.

We mapped the distribution and diversity of mitochondrial D-loop haplotypes among 502 New Zealand house mice (Mus musculus). By widespread sampling from 74 sites, we identified 14 new haplotypes. We used Bayesian phylogenetic reconstructions to estimate the genetic relationships between the New Zealand representatives of Mus musculus domesticus (all six known clades) and M. m. castaneus (clade HG2), and mice from other locales. We defined four distinct geographic regions of New Zealand with differing haplotype diversity indices. Our Results suggest (a) two independent pre-1840 invasions by mice of different origin (domesticus clade E and castaneus clade HG2) at opposite ends of the country; (b) multiple later invasions by domesticus clades E and F accompanying the post-1840 development of New Zealand port facilities in the central regions, plus limited local incursions by domesticus clades A, B, C and D1; (c) a separate invasion of Chatham I. by castaneus clade HG2; (d) previously undescribed New Zealand haplotypes, potentially the products of localised indigenous mutation, and (e) hybridisation between different lineages.

Background: Inflammatory response to cardiopulmonary bypass (CPB) can range from subclinical organ dysfunction to severe multi organ failure. Interleukin 6 (IL-6), interleukin 10 (IL-10) and free active transforming growth factor beta 1 (TGF-â1) were used as inflammatory markers to asses benefits of haemofilter and off-pump surgery.

DNA damage quantitation assays such as the comet assay have focused on the measurement of total nuclear damage per cell. The adoption of PCR-based techniques to quantify DNA damage has enabled sequence- and organelle-specific assessment of DNA lesions. Here we report on an adaptation of a qPCR technique to assess DNA damage in nuclear and mitochondrial targets relative to control. Novel aspects of this assay include application of the assay to the Rotor-Gene platform with optimized DNA polymerase/fluorophore/primer set combination in a touchdown PCR protocol. Assay validation was performed using ultraviolet C radiation in A549 and THP1 cancer cell lines. A comparison was made to the comet assay applied to peripheral blood mononuclear cells, and an estimation of the effects of cryopreservation on ultraviolet C-induced DNA damage was carried out. Finally, dose responses for DNA damage were measured in peripheral blood mononuclear cells following exposure to the cytotoxic agents bleomycin and cisplatin. We show reproducible experimental outputs across the tested conditions and concordance with published findings with respect to mitochondrial and nuclear genotoxic susceptibilities. The application of this DNA damage assay to a wide range of clinical and laboratory-derived samples is both feasible and resource-efficient.

Andisols, developed from late-Quaternary tephra (volcanic ash) deposits and dominated by the nanocrystalline aluminosilicate, allophane, contain large stores of organic matter and are potential reservoirs for DNA. However, DNA recovery from Andisols and other allophane-bearing soils has been difficult and inefficient because of strong chemical bonding between DNA and both allophane and organic matter, and also because much DNA can be encased and physically protected in nanopores in allophane nano/microaggregates. We have therefore developed a new two-step DNA isolation method for allophanic soils and buried paleosols, including those low in clay, which circumvents these problems. The method centres on (1) releasing mainly microbial DNA, and extracellular (unbound) DNA, using an alkaline phosphate buffer (“Rai's lysis buffer”) that blocks re-adsorption sites on the allophanic materials, and (2) the novel application of acidified ammonium oxalate (Tamm's reagent) to dissolve the allophane and to release DNA which had been chemically-bound and also which had been protected within nanopores. Ammonium oxalate has not previously been applied to soil DNA extraction. DNA yields up to 44.5μgg−1 soil (oven-dry basis) were obtained from three field-moist natural allophanic soil samples from northern New Zealand using this two-step method. Following extraction, we evaluated different DNA purification methods. Gel electrophoresis of the extracted DNA followed by gel purification of the DNA from the agarose gel, despite some DNA loss, was the only purification method that removed sufficient humic material for successful DNA amplification using the polymerase chain reaction (PCR) of multiple gene regions. Sequencing of PCR products obtained from a buried allophanic paleosol at 2.2-m depth on a sandy Holocene tephra yielded endemic and exotic plants that differed from the European grasses growing currently on the soil's surface. This difference suggests that the DNA extraction method is able to access (paleo)environmental DNA derived from previous vegetation cover. Our DNA extraction and purification method hence may be applied to Andisols and allophane-bearing paleosols, potentially offering a means to isolate paleoenvironmental DNA and thus facilitate reconstruction of past environments in volcanic landscapes, datable using tephrochronology, and also aid biodiversity understanding of andic soils and paleosols.

This study provides fundamental knowledge about the interaction of allophane, deoxyribonucleic acid (DNA), and organic matter in soils, and how allophane sequesters DNA. The adsorption capacities of salmon-sperm DNA on pure synthetic allophane (characterised morphologically and chemically) and on humic-acid-rich synthetic allophane were determined, and the resultant DNA–allophane complexes were characterised using synchrotron-radiation-derived P X-ray absorption near-edge fine structure (XANES) spectroscopy and infrared (IR) spectroscopy. The synthetic allophane adsorbed up to 34μgmg−1 of salmon-sperm DNA. However, the presence of humic acid significantly lowered the DNA uptake on the synthetic allophane to 3.5μgmg−1 by occupying the active sites on allophane so that DNA was repulsed. Both allophane and humic acid adsorbed DNA chemically through its phosphate groups. IR spectra for the allophane–DNA complex showed a chemical change of the Si–O–Al stretching of allophane after DNA adsorption, possibly because of the alteration of the steric distance of the allophane outer wall, or because of the precipitation of aluminium phosphate on allophane after DNA adsorption on it, or both. The aluminol groups of synthetic allophane almost completely reacted with additions of small amounts of DNA (~2–6μgmg−1), but the chemical adsorption of DNA on allophane simultaneously led to the formation of very porous allophane aggregates up to ~500μm in diameter. The formation of the allophane nano- and microaggregates enabled up to 28μgmg−1 of DNA to be adsorbed (~80% of total) within spaces (pores) between allophane spherules and allophane nanoaggregates (as “physical adsorption”), giving a total of 34μgmg−1 of DNA adsorbed by the allophane. The stability of the allophane–DNA nano- and microaggregates likely prevents encapsulated DNA from exposure to oxidants, and DNA within small pores between allophane spherules and nanoaggregates may not be accessible to enzymes or microbes, hence enabling DNA protection and preservation in such materials. By implication, substantial organic carbon is therefore likely to be sequestered and protected in allophanic soils (Andisols) in the same way as demonstrated here for DNA, that is, predominantly by encapsulation within a tortuous network of nanopores and submicropores amidst stable nanoaggregates and microaggregates, rather than by chemisorption alone.

The differentiation of live attenuated vaccine strains from their progenitor and wild-type counterparts is important for ongoing surveillance of product safety and improved guidelines on their use. We utilised a genome sequencing approach to confirm that two cases of strangles in previously healthy horses that had received the Pinnacle I. N. vaccine (Zoetis) were caused by the vaccine strain. Our data shed new light on the safety of this vaccine and suggest that factors beyond the maturity of the animal's immune system influence the development of adverse reactions.

The bovine teat canal provides the first-line of defence against pathogenic bacteria infecting the mammary gland, yet the protein composition and host-defence functionality of the teat canal lining (TCL) are not well characterised. In this study, TCL collected from six healthy lactating dairy cows was subjected to two-dimensional electrophoresis (2-DE) and mass spectrometry. The abundance and location of selected identified proteins were determined by western blotting and fluorescence immunohistochemistry. The variability of abundance among individual cows was also investigated. Two dominant clusters of proteins were detected in the TCL, comprising members of the keratin and S100 families of proteins. The S100 proteins were localised to the teat canal keratinocytes and were particularly predominant in the cornified outermost layer of the teat canal epithelium. Significant between-animal variation in the abundance of the S100 proteins in the TCL was demonstrated. Four of the six identified S100 proteins have been reported to have antimicrobial activity, suggesting that the TCL has additional functionality beyond being a physical barrier to invading microorganisms. These findings provide new insights into understanding host-defence of the teat canal and resistance of cows to mastitis.

Very little is known about the growth and mutation rates of Mycobacterium tuberculosis during latent infection in humans. However, studies in rhesus macaques have suggested that latent infections have mutation rates that are higher than that observed during active tuberculosis disease. Elevated mutation rates are presumed risk factors for the development of drug resistance. Therefore, the investigation of mutation rates during human latency is of high importance. We performed whole genome mutation analysis of M. tuberculosis isolates from a multi-decade tuberculosis outbreak of the New Zealand Rangipo strain. We used epidemiological and phylogenetic analysis to identify four cases of tuberculosis acquired from the same index case. Two of the tuberculosis cases occurred within two years of exposure and were classified as recently transmitted tuberculosis. Two other cases occurred more than 20 years after exposure and were classified as reactivation of latent M. tuberculosis infections. Mutation rates were compared between the two recently transmitted pairs versus the two latent pairs. Mean mutation rates assuming 20 hour generation times were 5.5 X 10(-10) mutations/bp/generation for recently transmitted tuberculosis and 7.3 X 10(-11) mutations/bp/generation for latent tuberculosis. Generation time versus mutation rate curves were also significantly higher for recently transmitted tuberculosis across all replication rates (p = 0.006). Assuming identical replication and mutation rates among all isolates in the final two years before disease reactivation, the u 20 hr mutation rate attributable to the remaining latent period was 1.6 × 10(-11) mutations/bp/generation, or approximately 30 fold less than that calculated during the two years immediately before disease. Mutations attributable to oxidative stress as might be caused by bacterial exposure to the host immune system were not increased in latent infections. In conclusion, we did not find any evidence to suggest elevated mutation rates during tuberculosis latency in humans, unlike the situation in rhesus macaques.