Publications by authors named "Patrick J Biggs"

71 Publications

Complete Genome Sequences of Three R-7 Group Strains Isolated from the Bovine Rumen in New Zealand.

Microbiol Resour Announc 2021 Jul 1;10(26):e0031021. Epub 2021 Jul 1.

AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand.

Members of the R-7 group are abundant bacterial residents of the rumen microbiome; however, they are poorly characterized. We report the complete genome sequences of three members of the R-7 group, FE2010, FE2011, and XBB3002, isolated from the ruminal contents of pasture-grazed dairy cows in New Zealand.
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http://dx.doi.org/10.1128/MRA.00310-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8248865PMC
July 2021

Genome Sequences for Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Strains Isolated from Different Water Sources.

Microbiol Resour Announc 2021 Jun 17;10(24):e0032821. Epub 2021 Jun 17.

mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand.

Extended-spectrum beta-lactamase (ESBL)-producing are considered a critical priority by the World Health Organization. Presented here are two genome sequences of Escherichia coli strains isolated from New Zealand freshwater. The genome sequences' mean size was 5.2 Mb, with a mean of 4,848 coding sequences. Both genomes carried the ESBL gene.
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http://dx.doi.org/10.1128/MRA.00328-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8210700PMC
June 2021

First report of novel assemblages and mixed infections of Giardia duodenalis in human isolates from New Zealand.

Acta Trop 2021 Aug 23;220:105969. Epub 2021 May 23.

Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Private Bag, 11 222, Palmerston North 4442, New Zealand.

Giardia duodenalis (syn. G. intestinalis and G. lamblia) is a protozoan parasite that cause disease (giardiasis) in humans and other animals. The pathogen is classified into eight assemblages, further divided into sub-assemblages, based on genetic divergence and host specificities. There are two zoonotic subtypes known as assemblages A and B, whilst assemblages from C to H are mainly found in domesticated animals, rodents and marine mammals. Here, we report for the first time the presence of assemblage E and sub-assemblage AIII in human isolates from the South Island in New Zealand. We identified a > 99% nucleotide similarity of assemblage E and sub-assemblage AIII with sequences of the gdh gene available in GenBank from individual human samples collected in Dunedin and Christchurch, respectively. We also performed a deep sequencing approach to assess intra-host assemblage variation. The sample from Dunedin showed evidence of mixed assemblage E and zoonotic sub-assemblage BIV. The report of two novel assemblages and mixed infections provides insights into the genetic diversity, epidemiology and transmission dynamics of Giardia duodenalis in New Zealand.
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http://dx.doi.org/10.1016/j.actatropica.2021.105969DOI Listing
August 2021

One dog's waste is another dog's wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome.

PLoS One 2021 19;16(4):e0250344. Epub 2021 Apr 19.

Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa.

Canine acute hemorrhagic diarrhea syndrome (AHDS) has been associated in some studies with Clostridioides perfringens overgrowth and toxin-mediated necrosis of the intestinal mucosa. We aimed to determine the effect of a single fecal microbiota transplantation (FMT) on clinical scores and fecal microbiomes of 1 and 7 dogs with AHDS from New Zealand and South Africa. We hypothesized that FMT would improve AHDS clinical scores and increase microbiota alpha-diversity and short-chain fatty acid (SCFA)-producing microbial communities' abundances in dogs with AHDS after FMT. We sequenced the V3-V4 region of the 16S-rRNA gene in the feces of AHDS FMT-recipients and sham-treated control dogs, and their healthy donors at admission, discharge, and 30 days post-discharge. There were no significant differences in median AHDS clinical scores between FMT-recipients and sham-treated controls at admission or discharge (P = 0.22, P = 0.41). At admission, the Shannon diversity index (SDI) was lower in AHDS dogs than healthy donors (P = 0.002). The SDI did not change from admission to 30 days in sham-treated dogs yet increased in FMT-recipients from admission to discharge (P = 0.04) to levels not different than donors (P = 0.33) but significantly higher than sham-treated controls (P = 0.002). At 30 days, the SDI did not differ between FMT recipients, sham-treated controls, and donors (P = 0.88). Principal coordinate analysis of the Bray-Curtis index separated post-FMT and donor dogs from pre-FMT and sham-treated dogs (P = 0.009) because of increased SCFA-producing genera's abundances after FMT. A single co-abundance subnetwork contained many of the same OTUs found to be differentially abundant in FMT-recipients, and the abundance of this module was increased in FMT-recipients at discharge and 30 days, compared to sham-treated controls. We conclude in this small pilot study FMT did not have any clinical benefit. A single FMT procedure has the potential to increase bacterial communities of SCFA-producing genera important for intestinal health up to 30 days post-FMT.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0250344PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8055013PMC
April 2021

Transmission Dynamics of Shiga Toxin-Producing Escherichia coli in New Zealand Cattle from Farm to Slaughter.

Appl Environ Microbiol 2021 05 11;87(11). Epub 2021 May 11.

EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand.

Cattle are asymptomatic carriers of Shiga toxin-producing (STEC) strains that can cause serious illness or death in humans. In New Zealand, contact with cattle feces and living near cattle populations are known risk factors for human STEC infection. Contamination of fresh meat with STEC strains also leads to the potential for rejection of consignments by importing countries. We used a combination of PCR/matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) and whole-genome sequencing (WGS) to evaluate the presence and transmission of STEC on farms and in processing plants to better understand the potential pathways for human exposure and thus mitigate risk. Animal and environmental samples ( = 2,580) were collected from six farms and three meat processing plants in New Zealand during multiple sampling sessions in spring of 2015 and 2016. PCR/MALDI-TOF analysis revealed that 6.2% were positive for "Top 7" STEC. Top 7 STEC strains were identified in all sample sources ( = 17) tested. A marked increase in Top 7 STEC prevalence was observed between calf hides on farm (6.3% prevalence) and calf hides at processing plants (25.1% prevalence). Whole-genome sequencing was performed on Top 7 STEC bacterial isolates ( = 40). Analysis of STEC O26 ( = 25 isolates) revealed relatively low genetic diversity on individual farms, consistent with the presence of a resident strain disseminated within the farm environment. Public health efforts should focus on minimizing human contact with fecal material on farms and during handling, transport, and slaughter of calves. Meat processing plants should focus on minimizing cross-contamination between the hides of calves in a cohort during transport, lairage, and slaughter. Cattle are asymptomatic carriers of Shiga toxin-producing (STEC) strains, which can cause serious illness or death in humans. Contact with cattle feces and living near cattle are known risk factors for human STEC infection. This study evaluated STEC carriage in young calves and the farm environment with an in-depth evaluation of six farms and three meat processing plants over 2 years. An advanced molecular detection method and whole-genome sequencing were used to provide a detailed evaluation of the transmission of STEC both within and between farms. The study revealed widespread STEC contamination within the farm environment, but no evidence of recent spread between farms. Contamination of young dairy calf hides increased following transport and holding at meat processing plants. The elimination of STEC in farm environments may be very difficult given the multiple transmission routes; interventions should be targeted at decreasing fecal contamination of calf hides during transport, lairage, and processing.
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http://dx.doi.org/10.1128/AEM.02907-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8208155PMC
May 2021

Draft Genome Sequences of Seven Extended-Spectrum β-Lactamase-Producing Escherichia coli Strains Isolated from New Zealand Waterways.

Microbiol Resour Announc 2021 Mar 18;10(11). Epub 2021 Mar 18.

Epilab, School of Veterinary Science, Massey University, Palmerston North, New Zealand.

Draft genomes of seven extended-spectrum β-lactamase (ESBL)-producing strains recovered from New Zealand waterways are described. The mean genome size was 5.1 Mb, with 4,724 coding sequences. All genomes contained the ESBL gene , and one carried a plasmid-mediated AmpC gene, A multidrug-resistant genotype was detected in three isolates.
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http://dx.doi.org/10.1128/MRA.01445-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7975887PMC
March 2021

Genetic characterisation of Campylobacter concisus: Strategies for improved genomospecies discrimination.

Syst Appl Microbiol 2021 May 20;44(3):126187. Epub 2021 Feb 20.

Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.

Although at least two genetically distinct groups, or genomospecies, have been well documented for Campylobacter concisus, no phenotype has yet been identified for their differentiation and thus formal description as separate species. C. concisus has been isolated from a variety of sites in the human body, including saliva and stool samples from both healthy and diarrhoeic individuals. We evaluated the ability of a range of whole genome-based tools to distinguish between the two C. concisus genomospecies (GS) using a collection of 190 C. concisus genomes. Nine genomes from related Campylobacter species were included in some analyses to provide context. Analyses incorporating sequence analysis of multiple ribosomal genes generated similar levels of C. concisus GS discrimination as genome-wide comparisons. The C. concisus genomes formed two groups; GS1 represented by ATCC 33237 and GS2 by CCUG 19995. The two C. concisus GS were separated from the nine genomes of related species. GS1 and GS2 also differed in G+C content with medians of 37.56% and 39.51%, respectively. The groups are consistent with previously established GS and are supported by DNA reassociation results. Average Nucleotide Identity using MUMmer (ANIm) and Genome BLAST Distance Phylogeny generated in silico DNA-DNA hybridisation (isDDH) (against ATCC 33237 and CCUG 19995), plus G+C content provides cluster-independent GS discrimination suitable for routine use. Pan-genomic analysis identified genes specific to GS1 and GS2. WGS data and genomic species identification methods support the existence of two GS within C. concisus. These data provide genome-level metrics for strain identification to genomospecies level.
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http://dx.doi.org/10.1016/j.syapm.2021.126187DOI Listing
May 2021

Comparative Genomics of Subspecies Sheep Strains.

Front Vet Sci 2021 15;8:637637. Epub 2021 Feb 15.

Farm Animal Health Group, Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia.

subspecies (MAP) is the aetiological agent of Johne's disease (JD), a chronic enteritis that causes major losses to the global livestock industry. Further, it has been associated with human Crohn's disease. Several strains of MAP have been identified, the two major groups being sheep strain MAP, which includes the Type I and Type III sub-lineages, and the cattle strain or Type II MAP lineage, of which bison strains are a sub-grouping. Major genotypic, phenotypic and pathogenic variations have been identified in prior comparisons, but the research has predominately focused on cattle strains of MAP. In countries where the sheep industries are more prevalent, however, such as Australia and New Zealand, ovine JD is a substantial burden. An information gap exists regarding the genomic differences between sheep strain sub-lineages and the relevance of Type I and Type III MAP in terms of epidemiology and/or pathogenicity. We therefore investigated sheep MAP isolates from Australia and New Zealand using whole genome sequencing. For additional context, sheep MAP genome datasets were downloaded from the Sequence Read Archive and GenBank. The final dataset contained 18 Type III and 16 Type I isolates and the K10 cattle strain MAP reference genome. Using a pan-genome approach, an updated global phylogeny for sheep MAP from assemblies was produced. When rooted with the K10 cattle reference strain, two distinct clades representing the lineages were apparent. The Australian and New Zealand isolates formed a distinct sub-clade within the type I lineage, while the European type I isolates formed another less closely related group. Within the type III lineage, isolates appeared more genetically diverse and were from a greater number of continents. Querying of the pan-genome and verification using BLAST analysis revealed lineage-specific variations ( = 13) including genes responsible for metabolism and stress responses. The genetic differences identified may represent important epidemiological and virulence traits specific to sheep MAP. This knowledge will potentially contribute to improved vaccine development and control measures for these strains.
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http://dx.doi.org/10.3389/fvets.2021.637637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7917049PMC
February 2021

Carriage of Extended-Spectrum-Beta-Lactamase- and AmpC Beta-Lactamase-Producing Escherichia coli Strains from Humans and Pets in the Same Households.

Appl Environ Microbiol 2020 11 24;86(24). Epub 2020 Nov 24.

EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand

Extended-spectrum-beta-lactamase (ESBL)- or AmpC beta-lactamase (ACBL)-producing bacteria are the most common cause of community-acquired multidrug-resistant urinary tract infections (UTIs) in New Zealand. The carriage of antimicrobial-resistant bacteria has been found in both people and pets from the same household; thus, the home environment may be a place where antimicrobial-resistant bacteria are shared between humans and pets. In this study, we sought to determine whether members (pets and people) of the households of human index cases with a UTI caused by an ESBL- or ACBL-producing strain also carried an ESBL- or ACBL-producing strain and, if so, whether it was a clonal match to the index case clinical strain. Index cases with a community-acquired UTI were recruited based on antimicrobial susceptibility testing of urine isolates. Fecal samples were collected from 18 non-index case people and 36 pets across 27 households. Eleven of the 27 households screened had non-index case household members (8/18 people and 5/36 animals) positive for ESBL- and/or ACBL-producing strains. Whole-genome sequence analysis of 125 isolates (including the clinical urine isolates) from these 11 households showed that within seven households, the same strain of ESBL-/ACBL-producing was cultured from both the index case and another person (5/11 households) or pet dog (2/11 households). These results suggest that transmission within the household may contribute to the community spread of ESBL- or ACBL-producing that produce extended-spectrum beta-lactamases (ESBLs) and AmpC beta-lactamases (ACBLs) are important pathogens and can cause community-acquired illnesses, such as urinary tract infections (UTIs). Fecal carriage of these resistant bacteria by companion animals may pose a risk for transmission to humans. Our work evaluated the sharing of ESBL- and ACBL-producing isolates between humans and companion animals. We found that in some households, dogs carried the same strain of ESBL-producing as the household member with a UTI. This suggests that transmission events between humans and animals (or vice versa) are likely occurring within the home environment and, therefore, the community as a whole. This is significant from a health perspective, when considering measures to minimize community transmission, and highlights that in order to manage community spread, we need to consider interventions at the household level.
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http://dx.doi.org/10.1128/AEM.01613-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7688229PMC
November 2020

Comparison of the Pathogenic Potential of , and and Limitations of Using Larvae of as an Infection Model.

Pathogens 2020 Aug 29;9(9). Epub 2020 Aug 29.

mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand.

enteritis in humans is primarily associated with infection. Other species cause campylobacteriosis relatively infrequently; while this could be attributed to bias in diagnostic methods, the pathogenicity of non- spp. such as and (isolated from dogs and cats) is uncertain. larvae are suitable models of the mammalian innate immune system and have been applied to studies. This study compared the pathogenicity of , , and isolates. Larvae inoculated with either or showed significantly higher survival than those inoculated with . All three species induced indistinguishable histopathological changes in the larvae. could be isolated from inoculated larvae up to eight days post-inoculation whereas and could only be isolated in the first two days. There was a significant variation in the hazard rate between batches of larvae, in strains, and in biological replicates as random effects, and in species and bacterial dose as fixed effects. The model is applicable to other spp. as well as but may be subject to significant variation with all species. While and cannot be considered non-pathogenic, they are significantly less pathogenic than .
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http://dx.doi.org/10.3390/pathogens9090713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7560178PMC
August 2020

A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic, phylogenetic, and phenotypic criteria.

Syst Appl Microbiol 2020 Sep 30;43(5):126108. Epub 2020 Jun 30.

Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.

The proposal to restructure the genus Arcobacter into six distinct genera was critically examined using: comparative analyses of up to 80 Epsilonproteobacterial genome sequences (including 26 arcobacters); phylogenetic analyses of three housekeeping genes and also 342 core genes; and phenotypic criteria. Genome sequences were analysed with tools to calculate Percentage of Conserved Proteins, Average Amino-acid Identity, BLAST-based Average Nucleotide Identity, in silico DNA-DNA hybridisation values, genome-wide Average Nucleotide Identity, Alignment Fractions and G+C percentages. Genome analyses revealed the genus Arcobacter sensu lato to be relatively homogenous, and phylogenetic analyses clearly distinguished the group from other Epsilonproteobacteria. Genomic distinction of the genera proposed by Pérez-Cataluña et al. [2018] was not supported by any of the measures used and a subsequent risk of strain misidentification clearly identified. Similarly, phenotypic analyses supported the delineation of Arcobacter sensu lato but did not justify the position of the proposed novel genera. The present polyphasic taxonomic study strongly supports the continuance of the classification of "aerotolerant campylobacters" as Arcobacter and refutes the proposed genus-level subdivision of Pérez-Cataluña et al. [2018].
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http://dx.doi.org/10.1016/j.syapm.2020.126108DOI Listing
September 2020

Does land use affect pathogen presence in New Zealand drinking water supplies?

Water Res 2020 Oct 27;185:116229. Epub 2020 Jul 27.

Innovative River Solutions, School of Agriculture and Environment, Massey University, Private Bag, 11 222, Palmerston North 4442, New Zealand. Electronic address:

Four microbes (Campylobacter spp., Escherichia coli, Cryptosporidium spp. and Giardia spp.) were monitored in 16 waterways that supply public drinking water for 13 New Zealand towns and cities. Over 500 samples were collected from the abstraction point at each study site every three months between 2009 and 2019. The waterways represent a range from small to large, free flowing to reservoir impoundments, draining catchments of entirely native vegetation to those dominated by pastoral agriculture. We used machine learning algorithms to explore the relative contribution of land use, catchment geology, vegetation, topography, and water quality characteristics of the catchment to determining the abundance and/or presence of each microbe. Sites on rivers draining predominantly agricultural catchments, the Waikato River, Oroua River and Waiorohi Stream had all four microbes present, often in high numbers, throughout the sampling interval. Other sites, such as the Hutt River and Big Huia Creek in Wellington which drain catchments of native vegetation, never had pathogenic microbes detected, or unsafe levels of E. coli. Boosted Regression Tree models could predict abundances and presence/absence of all four microbes with good precision using a wide range of potential environmental predictors covering land use, geology, vegetation, topography, and nutrient concentrations. Models were more accurate for protozoa than bacteria but did not differ markedly in their ability to predict abundance or presence/absence. Environmental drivers of microbe abundance or presence/absence also differed depending on whether the microbe was protozoan or bacterial. Protozoa were more prevalent in waterways with lower water quality, higher numbers of ruminants in the catchment, and in September and December. Bacteria were more abundant with higher rainfall, saturated soils, and catchments with greater than 35% of the land in agriculture. Although modern water treatment protocols will usually remove many pathogens from drinking water, several recent outbreaks of waterborne disease due to treatment failures, have highlighted the need to manage water supplies on multiple fronts. This research has identified potential catchment level variables, and thresholds, that could be better managed to reduce the potential for pathogens to enter drinking water supplies.
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http://dx.doi.org/10.1016/j.watres.2020.116229DOI Listing
October 2020

A large scale waterborne Campylobacteriosis outbreak, Havelock North, New Zealand.

J Infect 2020 09 29;81(3):390-395. Epub 2020 Jun 29.

Hawke's Bay District Health Board, New Zealand.

Background: We describe the investigation of a Campylobacter outbreak linked to contamination of an untreated, groundwater derived drinking water supply.

Methods: We analysed epidemiological data collected from clinician-confirmed diarrheal cases and estimated the total burden of Havelock North cases using an age-adjusted cross-sectional telephone survey. Campylobacter isolates from case fecal specimens, groundwater samples, and sheep fecal specimens from paddocks adjacent to the drinking water source were whole genome sequenced.

Findings: We estimate between 6260 and 8320 cases of illness including up to 2230 who lived outside the reticulation area, were linked to the contaminated water supply. Of these, 953 cases were physician reported, 42 were hospitalized, three developed Guillain-Barré syndrome, and Campylobacter infection contributed to at least four deaths. Of the 12 genotypes observed in cases, four were also observed in water, three were also observed in sheep and one was also observed in both water and sheep.

Interpretation: The contamination of the untreated reticulated water supply occurred following a very heavy rainfall event which caused drainage of sheep feces into a shallow aquifer. The existence of a routine clinical surveillance system for campylobacteriosis facilitated identification of the outbreak, recovery of clinical isolates, and early testing of the water for pathogens. Genotyping of the Campylobacter jejuni helped define the source of the outbreak and confirm outbreak periods and cases. Expected increases in heavy rainfall events and intensification of agriculture mean that additional safeguards are needed to protect populations from such drinking water outbreaks.

Funding: NZ Ministry of Health, Health Research Council, ESR SSIF, Royal Society.
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http://dx.doi.org/10.1016/j.jinf.2020.06.065DOI Listing
September 2020

Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies.

PLoS One 2020 25;15(6):e0235066. Epub 2020 Jun 25.

AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand.

Shiga toxin-producing Escherichia coli (STEC) are a leading cause of foodborne outbreaks of human disease, but they reside harmlessly as an asymptomatic commensal in the ruminant gut. STEC serogroup O145 are difficult to isolate as routine diagnostic methods are unable to distinguish non-O157 serogroups due to their heterogeneous metabolic characteristics, resulting in under-reporting which is likely to conceal their true prevalence. In light of these deficiencies, the purpose of this study was a twofold approach to investigate enhanced STEC O145 diagnostic culture-based methods: firstly, to use a genomic epidemiology approach to understand the genetic diversity and population structure of serogroup O145 at both a local (New Zealand) (n = 47) and global scale (n = 75) and, secondly, to identify metabolic characteristics that will help the development of a differential media for this serogroup. Analysis of a subset of E. coli serogroup O145 strains demonstrated considerable diversity in carbon utilisation, which varied in association with eae subtype and sequence type. Several carbon substrates, such as D-serine and D-malic acid, were utilised by the majority of serogroup O145 strains, which, when coupled with current molecular and culture-based methods, could aid in the identification of presumptive E. coli serogroup O145 isolates. These carbon substrates warrant subsequent testing with additional serogroup O145 strains and non-O145 strains. Serogroup O145 strains displayed extensive genetic heterogeneity that was correlated with sequence type and eae subtype, suggesting these genetic markers are good indicators for distinct E. coli phylogenetic lineages. Pangenome analysis identified a core of 3,036 genes and an open pangenome of >14,000 genes, which is consistent with the identification of distinct phylogenetic lineages. Overall, this study highlighted the phenotypic and genotypic heterogeneity within E. coli serogroup O145, suggesting that the development of a differential media targeting this serogroup will be challenging.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0235066PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7316241PMC
August 2020

Novel mechanisms of TolC-independent decreased bile-salt susceptibility in Escherichia coli.

FEMS Microbiol Lett 2020 05;367(10)

School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

Bile salts, including sodium deoxycholate (DOC), are secreted into the intestine to aid fat digestion and contribute to antimicrobial protection. Gram-negative pathogens such as Escherichia coli, however, are highly resistant to DOC, using multiple mechanisms of which the multidrug efflux pump AcrAB-TolC is the dominant one. Given that TolC-mediated efflux masks the interaction of DOC with potential targets, we sought to identify those targets by identifying genes whose mutations cause an increase in the MIC to DOC relative to the ∆tolC parental strain, that lacks TolC-associated functional efflux pumps. Using a mutant screen, we isolated twenty independent spontaneous mutants that had a higher MICDOC than the E. coli parental ∆tolC strain. Whole genome sequencing of these mutants mapped most mutations to the ptsI or cyaA gene. Analysis of knock-out mutants and complementation showed that elimination of PtsI, a component of the carbohydrate phosphotransferase system, or one of the two key proteins involved in cAMP synthesis and signaling, adenylate cyclase (CyaA) or cAMP receptor protein (Crp) causes low-level increased resistance of a ∆tolC E. coli strain to DOC.
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http://dx.doi.org/10.1093/femsle/fnaa083DOI Listing
May 2020

Draft Genome Sequences of Eight Strains of Campylobacter helveticus Isolated from Cats and a Dog in New Zealand.

Microbiol Resour Announc 2020 Jan 30;9(5). Epub 2020 Jan 30.

School of Veterinary Science, Massey University, Palmerston North, New Zealand

The draft genome sequences for eight isolates of isolated from companion animals are described and compared with that of the type strain. On average, the genomes are 1,825,025 bp long and have a GC content of 34.4% and 1,885 coding DNA sequences (CDSs). CRISPRs were detected in only one isolate and phages in none.
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http://dx.doi.org/10.1128/MRA.01244-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6992862PMC
January 2020

sismonr: simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R.

Bioinformatics 2020 05;36(9):2938-2940

School of Fundamental Sciences.

Summary: We present sismonr, an R package for an integral generation and simulation of in silico biological systems. The package generates gene regulatory networks, which include protein-coding and non-coding genes along with different transcriptional and post-transcriptional regulations. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals. The ploidy of the system is not restricted to the usual haploid or diploid situations but can be defined by the user to higher ploidies. A choice of stochastic simulation algorithms allows us to simulate the expression profiles of the genes in the in silico system. We illustrate the use of sismonr by simulating the anthocyanin biosynthesis regulation pathway for three genetically distinct in silico plants.

Availability And Implementation: The sismonr package is implemented in R and Julia and is publicly available on the CRAN repository (https://CRAN.R-project.org/package=sismonr). A detailed tutorial is available from GitHub at https://oliviaab.github.io/sismonr/.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btaa002DOI Listing
May 2020

The effect of carbohydrate sources: Sucrose, invert sugar and components of mānuka honey, on core bacteria in the digestive tract of adult honey bees (Apis mellifera).

PLoS One 2019 4;14(12):e0225845. Epub 2019 Dec 4.

Microbiome & Metabolism, Food Nutrition & Health, The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand.

Bacteria within the digestive tract of adult honey bees are likely to play a key role in the digestion of sugar-rich foods. However, the influence of diet on honey bee gut bacteria is not well understood. During periods of low floral abundance, beekeepers often supplement the natural sources of carbohydrate that honey bees collect, such as nectar, with various forms of carbohydrates such as sucrose (a disaccharide) and invert sugar (a mixture of the monosaccharides glucose and fructose). We compared the effect of these sugar supplements on the relative abundance of bacteria in the gut of bees by feeding bees from a single colony, two natural diets: mānuka honey, a monofloral honey with known antibacterial properties, and a hive diet; and artificial diets of invert sugar, sucrose solution, and sucrose solutions containing synthesised compounds associated with the antibacterial properties of mānuka honey. 16S ribosomal RNA (rRNA)-based sequencing showed that dietary regimes containing mānuka honey, sucrose and invert sugar did not alter the relative abundance of dominant core bacteria after 6 days of being fed these diets. However, sucrose-rich diets increased the relative abundances of three sub-dominant core bacteria, Rhizobiaceae, Acetobacteraceae, and Lactobacillus kunkeei, and decreased the relative abundance of Frischella perrara, all which significantly altered the bacterial composition. Acetogenic bacteria from the Rhizobiaceae and Acetobacteraceae families increased two- to five-fold when bees were fed sucrose. These results suggest that sucrose fuels the proliferation of specific low abundance primary sucrose-feeders, which metabolise sugars into monosaccharides, and then to acetate.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0225845PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892475PMC
March 2020

Draft Whole-Genome Sequences of Campylobacter Strains Isolated from Brushtail Possums in New Zealand.

Microbiol Resour Announc 2019 Nov 21;8(47). Epub 2019 Nov 21.

EpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, New Zealand.

Draft genomes of five isolates recovered from New Zealand brushtail possums are described. Genome sizes ranged from 1.591 Mbp to 1.594 Mbp, with G+C contents of 29.9% to 29.95%. Comparison to Australian 16S rRNA gene sequences suggests that the species may be common to possums.
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http://dx.doi.org/10.1128/MRA.01276-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872890PMC
November 2019

Genomic Analysis of Fluoroquinolone- and Tetracycline-Resistant Campylobacter jejuni Sequence Type 6964 in Humans and Poultry, New Zealand, 2014-2016.

Emerg Infect Dis 2019 12;25(12):2226-2234

In 2014, antimicrobial drug-resistant Campylobacter jejuni sequence type 6964 emerged contemporaneously in poultry from 3 supply companies in the North Island of New Zealand and as a major cause of campylobacteriosis in humans in New Zealand. This lineage, not previously identified in New Zealand, was resistant to tetracycline and fluoroquinolones. Genomic analysis revealed divergence into 2 major clades; both clades were associated with human infection, 1 with poultry companies A and B and the other with company C. Accessory genome evolution was associated with a plasmid, phage insertions, and natural transformation. We hypothesize that the tetO gene and a phage were inserted into the chromosome after conjugation, leaving a remnant plasmid that was lost from isolates from company C. The emergence and rapid spread of a resistant clone of C. jejuni in New Zealand, coupled with evolutionary change in the accessory genome, demonstrate the need for ongoing Campylobacter surveillance among poultry and humans.
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http://dx.doi.org/10.3201/eid2512.190267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874264PMC
December 2019

The Pacific Biosciences assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Neumann, 1901.

Data Brief 2019 Dec 4;27:104602. Epub 2019 Oct 4.

Department of Zoology, University of Otago, Dunedin, New Zealand.

The longhorned tick, , feeds upon a wide range of bird and mammalian hosts. Mammalian hosts include cattle, deer, sheep, goats, humans, and horses. This tick is known to transmit a number of pathogens causing tick-borne diseases, and was the vector of a recent serious outbreak of oriental theileriosis in New Zealand. A New Zealand-USA consortium was established to sequence, assemble, and annotate the genome of this tick, using ticks obtained from New Zealand's North Island. In New Zealand, the tick is considered exclusively parthenogenetic and this trait was deemed useful for genome assembly. Very high molecular weight genomic DNA was sequenced on the Illumina HiSeq4000 and the long-read Pac Bio Sequel platforms. Twenty-eight SMRT cells produced a total of 21.3 million reads which were assembled with Canu on a reserved supercomputer node with access to 12 TB of RAM, running continuously for over 24 days. The final assembly dataset consisted of 34,211 contigs with an average contig length of 215,205 bp. The quality of the annotated genome was assessed by BUSCO analysis, an approach that provides quantitative measures for the quality of an assembled genome. Over 95% of the BUSCO gene set was found in the assembled genome. Only 48 of the 1066 BUSCO genes were missing and only 9 were present in a fragmented condition. The raw sequencing reads and the assembled contigs/scaffolds are archived at the National Center for Biotechnology Information.
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http://dx.doi.org/10.1016/j.dib.2019.104602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6806438PMC
December 2019

Novel 5-Nitrofuran-Activating Reductase in Escherichia coli.

Antimicrob Agents Chemother 2019 11 22;63(11). Epub 2019 Oct 22.

School of Fundamental Sciences, Massey University, Palmerston North, New Zealand

The global spread of multidrug-resistant enterobacteria warrants new strategies to combat these pathogens. One possible approach is the reconsideration of "old" antimicrobials, which remain effective after decades of use. Synthetic 5-nitrofurans such as furazolidone, nitrofurantoin, and nitrofurazone are such a class of antimicrobial drugs. Recent epidemiological data showed a very low prevalence of resistance to this antimicrobial class among clinical isolates in various parts of the world, forecasting the increasing importance of its uses to battle antibiotic-resistant enterobacteria. However, although they have had a long history of clinical use, a detailed understanding of the 5-nitrofurans' mechanisms of action remains limited. Nitrofurans are known as prodrugs that are activated in by reduction catalyzed by two redundant nitroreductases, NfsA and NfsB. Furazolidone, nevertheless, retains relatively significant antibacterial activity in the nitroreductase-deficient Δ Δ strain, indicating the presence of additional activating enzymes and/or antibacterial activity of the unreduced form. Using genome sequencing, genetic, biochemical, and bioinformatic approaches, we discovered a novel 5-nitrofuran-activating enzyme, AhpF, in The discovery of a new nitrofuran-reducing enzyme opens new avenues for overcoming 5-nitrofuran resistance, such as designing nitrofuran analogues with higher affinity for AhpF or screening for adjuvants that enhance AhpF expression.
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http://dx.doi.org/10.1128/AAC.00868-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811407PMC
November 2019

gndDb, a Database of Partial Sequences To Assist with Analysis of Escherichia coli Communities Using High-Throughput Sequencing.

Microbiol Resour Announc 2019 Aug 15;8(33). Epub 2019 Aug 15.

AgResearch Limited, Hopkirk Research Institute, Palmerston North, New Zealand.

The use of culture methods to detect diversity does not provide sufficient resolution to identify strains present at low levels. Here, we target the hypervariable gene and describe a database containing 534 distinct partial sequences and associated O groups for use with culture-independent community analysis.
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http://dx.doi.org/10.1128/MRA.00476-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6696633PMC
August 2019

Metagenomics and transcriptomics data from human colorectal cancer.

Sci Data 2019 07 5;6(1):116. Epub 2019 Jul 5.

Department of Surgery, University of Otago, Christchurch, New Zealand.

Colorectal cancer is a heterogenous and mostly sporadic disease, the development of which is associated with microbial dysbiosis. Recent advances in subtype classification have successfully stratified the disease using molecular profiling. To understand potential relationships between molecular mechanisms differentiating the subtypes of colorectal cancer and composition of gut microbial community, we classified a set of 34 tumour samples into molecular subtypes using RNA-sequencing gene expression profiles and determined relative abundances of bacterial taxonomic groups. To identify bacterial community composition, 16S rRNA amplicon metabarcoding was used as well as whole genome metagenomics of the non-human part of RNA-sequencing data. The generated data expands the collection of the data sources related to the disease and connects molecular aspects of the cancer with environmental impact of microbial community.
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http://dx.doi.org/10.1038/s41597-019-0117-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611873PMC
July 2019

Draft Whole-Genome Sequences of Three Isolates of a Novel Strain of a sp. Isolated from New Zealand Birds and Water.

Microbiol Resour Announc 2019 May 2;8(18). Epub 2019 May 2.

School of Veterinary Science, Massey University, Palmerston North, New Zealand.

spp. are frequently found associated with the avian intestinal tract. Most are commensals, but some can cause human campylobacteriosis. Here, we report the draft genome sequences of three strains of a novel sp. isolated from urban birds and a rural river in New Zealand.
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http://dx.doi.org/10.1128/MRA.00258-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498231PMC
May 2019

Draft Genome Sequence of a Canine Uropathogenic Escherichia coli Strain Isolated in New Zealand.

Microbiol Resour Announc 2019 Mar 7;8(10). Epub 2019 Mar 7.

School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

Escherichia coli P50 is a canine uropathogenic isolate sampled in the Wellington region of New Zealand. We report the draft genome sequence of this isolate, which contains characteristic virulence genes for urinary tract infections and is predicted to be capable of causing human infections.
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http://dx.doi.org/10.1128/MRA.01665-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6406116PMC
March 2019

Use of Genomics to Investigate Historical Importation of Shiga Toxin-Producing Escherichia coli Serogroup O26 and Nontoxigenic Variants into New Zealand.

Emerg Infect Dis 2019 03;25(3):489-500

Shiga toxin-producing Escherichia coli serogroup O26 is an important public health pathogen. Phylogenetic bacterial lineages in a country can be associated with the level and timing of international imports of live cattle, the main reservoir. We sequenced the genomes of 152 E. coli O26 isolates from New Zealand and compared them with 252 E. coli O26 genomes from 14 other countries. Gene variation among isolates from humans, animals, and food was strongly associated with country of origin and stx toxin profile but not isolation source. Time of origin estimates indicate serogroup O26 sequence type 21 was introduced at least 3 times into New Zealand from the 1920s to the 1980s, whereas nonvirulent O26 sequence type 29 strains were introduced during the early 2000s. New Zealand's remarkably fewer introductions of Shiga toxin-producing Escherichia coli O26 compared with other countries (such as Japan) might be related to patterns of trade in live cattle.
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http://dx.doi.org/10.3201/eid2503.180899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390770PMC
March 2019

Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni.

Microb Genom 2019 02 19;5(2). Epub 2019 Feb 19.

5​EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand.

Campylobacter jejuni is the most common cause of bacterial diarrheal disease in the world. Clinical outcomes of infection can range from asymptomatic infection to life-threatening extraintestinal infections. This variability in outcomes for infected patients has raised questions as to whether genetic differences between C. jejuni isolates contribute to their likelihood of causing severe disease. In this study, we compare the genomes of ten C. jejuni isolates that were implicated in extraintestinal infections with reference gastrointestinal isolates, in order to identify unusual patterns of sequence variation associated with infection outcome. We identified a collection of genes that display a higher burden of uncommon mutations in invasive isolates compared with gastrointestinal close relatives, including some that have been previously linked to virulence and invasiveness in C. jejuni. Among the top genes identified were mreB and pgp1, which are both involved in determining cell shape. Electron microscopy confirmed morphological differences in isolates carrying unusual sequence variants of these genes, indicating a possible relationship between extraintestinal infection and changes in cell morphology.
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http://dx.doi.org/10.1099/mgen.0.000251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421344PMC
February 2019

Isolation of emerging Campylobacter species in working farm dogs and their frozen home-killed raw meat diets.

J Vet Diagn Invest 2019 Jan 21;31(1):23-32. Epub 2018 Dec 21.

mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand (Bojanić, Midwinter, Marshall, Biggs).

We applied 7 culture methods to 50 working farm dog fecal samples and 6 methods to 50 frozen home-killed raw meat diet samples to optimize recovery of a wide range of Campylobacter spp. Culture methods combined filtration, enrichment broths, and agars at 37°C and 42°C in conventional and hydrogen-enriched microaerobic atmospheres. Overall, a prevalence of 62% (31 of 50) and 6% (3 of 50) was detected in dog and meat samples, respectively, based on Campylobacter genus PCR. A total of 356 Campylobacter spp. isolates were recovered from dogs, with successful isolation by individual methods ranging from 2 to 25 dogs. The species detected most commonly were C. upsaliensis and C. jejuni, and less commonly C. coli and C. lari. Species isolated that are rarely reported from dogs included C. rectus, C. lari subsp. concheus, C. volucris, and Helicobacter winghamensis. Six isolates from dogs positive by Campylobacter genus PCR were confirmed, using 16S rRNA sequencing, as Arcobacter cryaerophilus (1) and Arcobacter butzleri (5). C. jejuni multi-locus sequence typing results revealed a diversity of sequence types in working dogs, with several uncommonly reported from other C. jejuni sources in New Zealand. Overall, 20 isolates from 3 meat samples were positive by Campylobacter genus PCR; 1 meat sample was positive for C. jejuni, 1 for C. rectus, and 1 isolate was subsequently identified as A. butzleri. The method using Campylobacter enrichment broth in a hydrogen-enriched environment on nonselective agar resulted in significantly reduced recovery of Campylobacter spp. from both sample types.
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http://dx.doi.org/10.1177/1040638718820082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505760PMC
January 2019
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