Genomic epidemiology of extended-spectrum beta-lactamase-producing from humans and a river in Aotearoa New Zealand.

In Aotearoa New Zealand, urinary tract infections in humans are commonly caused by extended-spectrum beta-lactamase (ESBL)-producing . This group of antimicrobial-resistant bacteria are often multidrug resistant. However, there is limited information on ESBL-producing found in the environment and their link with human clinical isolates.

Impact of land-use and fecal contamination on Escherichia populations in environmental samples.

Understanding the composition of complex Escherichia coli populations from the environment is necessary for identifying strategies to reduce the impacts of fecal contamination and protect public health. Metabarcoding targeting the hypervariable gene gnd was used to reveal the complex population diversity of E. coli and phenotypically indistinct Escherichia species in water, soil, sediment, aquatic biofilm, and fecal samples from native forest and pastoral sites.

New Campylobacter Lineages in New Zealand Freshwater: Pathogenesis and Public Health Implications.

This study investigated the diversity of thermophilic Campylobacter species isolated from three New Zealand freshwater catchments affected by pastoral and urban activities. Utilising matrix-assisted laser desorption ionisation-time of flight and whole genome sequence analysis, the study identified Campylobacter jejuni (n = 46, 46.0%), C.

Heritability estimates and genetic and phenotypic correlations of skin thickness and skin temperature with key production traits in FocusPrime, Texel, Romney and Highlander sheep.

Skin thickness was found to be moderately heritable and genetically associated with lamb survival in a previous study on Romney sheep. The aims of this study were to estimate the heritabilities of skin thickness and skin temperature at around five and 11 months of age, and determine genetic and phenotypic correlations between them and with production traits such as fat depth, loin-eye muscle depth and width, live weights at weaning, scanning, and 12 months, and 12-month fleece weight, in FocusPrime (n=2,088), Texel (n=732), Romney (n=825) and Highlander (n=1,801) sheep breeds. Heritability estimates of skin thickness at 5-month old were moderate in FocusPrime (0.

Out of (the) bag-encoding categorical predictors impacts out-of-bag samples.

Performance of random forest classification models is often assessed and interpreted using out-of-bag (OOB) samples. Observations which are OOB when a tree is trained may serve as a test set for that tree and predictions from the OOB observations used to calculate OOB error and variable importance measures (VIM). OOB errors are popular because they are fast to compute and, for large samples, are a good estimate of the true prediction error.

Transcriptomic and proteomic changes associated with cobalamin-dependent propionate production by the rumen bacterium .

Unlabelled: is an abundant rumen bacterium that produces propionate in a cobalamin (vitamin B)-dependent manner via the succinate pathway. However, the extent to which this occurs across ruminal and closely related bacteria, and the effect of cobalamin supplementation on the expression of propionate pathway genes and enzymes has yet to be investigated. To assess this, we screened 14 strains and found that almost all strains produced propionate when supplemented with cobalamin.

Visual Integration of Genome-Wide Association Studies and Differential Expression Results with the Hidecan R Package.

Background/objectives: We present hidecan, an R package for generating visualisations that summarise the results of one or more genome-wide association studies (GWAS) and differential expression analyses, as well as manually curated candidate genes, e.g., extracted from the literature.

Assessing antimicrobial resistance in pasture-based dairy farms: a 15-month surveillance study in New Zealand.

Antimicrobial resistance is a global public and animal health concern. Antimicrobial resistance genes (ARGs) have been detected in dairy farm environments globally; however, few longitudinal studies have utilized shotgun metagenomics for ARG surveillance in pasture-based systems. This 15-month study aimed to undertake a baseline survey using shotgun metagenomics to assess the relative abundance and diversity of ARGs in two pasture-based dairy farm environments in New Zealand with different management practices.

Population structure and pathogen interaction of Escherichia coli in freshwater: Implications of land-use for water quality and public health in Aotearoa New Zealand.

Freshwater samples (n = 199) were obtained from 41 sites with contrasting land-uses (avian, low impact, dairy, urban, sheep and beef, and mixed sheep, beef and dairy) and the E. coli phylotype of 3980 isolates (20 per water sample enrichment) was determined. Eight phylotypes were identified with B1 (48.

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 synthesized 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.

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.

Development of a multiplex droplet digital PCR assay for simultaneous detection and quantification of Escherichia coli, E. marmotae, and E. ruysiae in water samples.

Escherichia coli are widely used by water quality managers as Fecal Indicator Bacteria, but current quantification methods do not differentiate them from benign, environmental Escherichia species such as E. marmotae (formerly named cryptic clade V) or E. ruysiae (cryptic clades III and IV).

Draft genome sequences of spp. isolates from New Zealand environmental sources.

is often used as a fecal indicator bacterium for water quality monitoring. We report the draft genome sequences of 500 isolates including newly described species, namely , and , obtained from diverse environmental sources to assist with improved public health risk assessments.

High-resolution genomic analysis to investigate the impact of the invasive brushtail possum (Trichosurus vulpecula) and other wildlife on microbial water quality assessments.

Escherichia coli are routine indicators of fecal contamination in water quality assessments. Contrary to livestock and human activities, brushtail possums (Trichosurus vulpecula), common invasive marsupials in Aotearoa/New Zealand, have not been thoroughly studied as a source of fecal contamination in freshwater. To investigate their potential role, Escherichia spp.

Impact of systemic antimicrobial therapy on the faecal microbiome in symptomatic dairy cows.

Antimicrobial resistance is a global threat to human and animal health, with the misuse and overuse of antimicrobials suggested as the main drivers of resistance. Antimicrobial therapy can alter the bacterial community composition and the faecal resistome in cattle. Little is known about the impact of systemic antimicrobial therapy on the faecal microbiome in dairy cows in the presence of disease.

Species-wide genomics of kākāpō provides tools to accelerate recovery.

The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations.

Generic Platform for the Multiplexed Targeted Electrochemical Detection of Osteoporosis-Associated Single Nucleotide Polymorphisms Using Recombinase Polymerase Solid-Phase Primer Elongation and Ferrocene-Modified Nucleoside Triphosphates.

Osteoporosis is a multifactorial disease influenced by genetic and environmental factors, which contributes to an increased risk of bone fracture, but early diagnosis of this disease cannot be achieved using current techniques. We describe a generic platform for the targeted electrochemical genotyping of SNPs identified by genome-wide association studies to be associated with a genetic predisposition to osteoporosis. The platform exploits isothermal solid-phase primer elongation with ferrocene-labeled nucleoside triphosphates.

Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of leveraging Oxford Nanopore long reads.

Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations.

A novel, stain-free, natural auto-fluorescent signal, Sig M, identified from cytometric and transcriptomic analysis of infectivity of and .

Cryptosporidiosis is a worldwide diarrheal disease caused by the protozoan . The primary symptom is diarrhea, but patients may exhibit different symptoms based on the species of the parasite they are infected with. Furthermore, some genotypes within species are more transmissible and apparently virulent than others.

Abundant dsRNA picobirnaviruses show little geographic or host association in terrestrial systems.

Picobirnaviruses are double-stranded RNA viruses known from a wide range of host species and locations but with unknown pathogenicity and host relationships. Here, we examined the diversity of picobirnaviruses from cattle and gorillas within and around Bwindi Impenetrable Forest National Park (BIFNP), Uganda, where wild and domesticated animals and humans live in relatively close contact. We use metagenomic sequencing with bioinformatic analyses to examine genetic diversity.

gen. nov. sp. nov. and sp. nov., two rumen bacterial species of a novel proposed family, fam. nov.

Two strains of Gram-negative, anaerobic, rod-shaped bacteria, from an abundant but uncharacterized rumen bacterial group of the order ', were phylogenetically and phenotypically characterized. These strains, designated R-7 and WTE2008, shared 98.6-99.

Investigating the genetic components of tuber bruising in a breeding population of tetraploid potatoes.

Background: Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economic importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still much to learn about this complex phenotype.