Journal Articles
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Item New Campylobacter Lineages in New Zealand Freshwater: Pathogenesis and Public Health Implications(John Wiley and Sons, 2024-12) Cookson AL; Burgess S; Midwinter AC; Marshall JC; Moinet M; Rogers L; Fayaz A; Biggs PJ; Brightwell GThis 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. coli (n = 39, 39%), C. lari (n = 4, 4.0%), and two novel Campylobacter species lineages (n = 11, 11%). Core genome sequence analysis provided evidence of prolonged persistence or continuous faecal shedding of closely related strains. The C. jejuni isolates displayed distinct sequence types (STs) associated with human, ruminant, and environmental sources, whereas the C. coli STs included waterborne ST3302 and ST7774. Recombination events affecting loci implicated in human pathogenesis and environmental persistence were observed, particularly in the cdtABC operon (encoding the cytolethal distending toxin) of non-human C. jejuni STs. A low diversity of antimicrobial resistance genes (aadE-Cc in C. coli), with genotype/phenotype concordance for tetracycline resistance (tetO) in three ST177 isolates, was noted. The data suggest the existence of two types of naturalised waterborne Campylobacter: environmentally persistent strains originating from waterbirds and new environmental species not linked to human campylobacteriosis. Identifying and understanding naturalised Campylobacter species is crucial for accurate waterborne public health risk assessments and the effective allocation of resources for water quality management.Item Assessing antimicrobial resistance in pasture-based dairy farms: a 15-month surveillance study in New Zealand.(American Society for Microbiology, 2024-10-23) Collis RM; Biggs PJ; Burgess SA; Midwinter AC; Liu J; Brightwell G; Cookson ALAntimicrobial 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. There was no statistically significant difference in overall ARG relative abundance between the two dairy farms (P = 0.321) during the study period. Compared with overseas data, the relative abundance of ARG copies per 16S rRNA gene in feces (0.08-0.17), effluent (0.03-0.37), soil (0.20-0.63), and bulk tank milk (0.0-0.12) samples was low. Models comparing the presence or absence of resistance classes found in >10% of all feces, effluent, and soil samples demonstrated no statistically significant associations (P > 0.05) with "season," and only multi-metal (P = 0.020) and tetracycline (P = 0.0003) resistance were significant at the "farm" level. Effluent samples harbored the most diverse ARGs, some with a recognized public health risk, whereas soil samples had the highest ARG relative abundance but without recognized health risks. This highlights the importance of considering the genomic context and risk of ARGs in metagenomic data sets. This study suggests that antimicrobial resistance on pasture-based dairy farms is low and provides essential baseline ARG surveillance data for such farming systems. IMPORTANCE: Antimicrobial resistance is a global threat to human and animal health. Despite the detection of antimicrobial resistance genes (ARGs) in dairy farm environments globally, longitudinal surveillance in pasture-based systems remains limited. This study assessed the relative abundance and diversity of ARGs in two New Zealand dairy farms with different management practices and provided important baseline ARG surveillance data on pasture-based dairy farms. The overall ARG relative abundance on these two farms was low, which provides further evidence for consumers of the safety of New Zealand's export products. Effluent samples harbored the most diverse range of ARGs, some of which were classified with a recognized risk to public health, whereas soil samples had the highest ARG relative abundance; however, the soil ARGs were not classified with a recognized public health risk. This emphasizes the need to consider genomic context and risk as well as ARG relative abundance in resistome studies.Item Whole-Genome Sequencing of Clostridium sp. Strain FP2, Isolated from Spoiled Venison.(American Society for Microbiology, 2020-04-30) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Cuomo CAClostridium sp. strain FP2 was isolated from vacuum-packaged refrigerated spoiled venison in New Zealand. This report describes the generation and annotation of the 5.6-Mb draft genome sequence of Clostridium sp. FP2, which will facilitate future functional genomic studies to improve our understanding of premature spoilage of red meats.Item Draft Genome Sequence of Clostridium bowmanii DSM 14206T, Isolated from an Antarctic Microbial Mat.(American Society for Microbiology, 2022-01-20) Palevich FP; Palevich N; Maclean PH; Altermann E; Mills J; Brightwell G; Gill SRClostridium bowmanii type strain DSM 14206 (ATCC BAA-581) was isolated from a microbial mat sample retrieved from Lake Fryxell, Antarctica. This report describes the generation and annotation of the 4.9-Mb draft genome sequence of C. bowmanii DSM 14206T.Item Draft Genome Sequence of Clostridium sp. Strain FP1, with Similarity to Clostridium tagluense, Isolated from Spoiled Lamb.(American Society for Microbiology, 2020-04-30) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Hotopp JCDClostridium sp. strain FP1 was isolated from vacuum-packaged refrigerated spoiled lamb, and this article describes its 5.4-Mb draft genome sequence. The FP1 genome was sequenced to facilitate source tracking and attribution studies, adding to our understanding of the role of Clostridium species in premature spoilage of red meats.Item Draft Genome Sequence of Clostridium estertheticum-like Strain FP4, Isolated from Spoiled Uncooked Lamb.(American Society for Microbiology, 2020-05-07) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Rasco DIn order to improve the phylogenetic resolution of the genus Clostridium and our limited knowledge of meat spoilage caused by Clostridium estertheticum, the genome of C. estertheticum-like strain FP4 was sequenced. Here, we describe the 4.1-Mb draft genome sequence of C. estertheticum-like strain FP4, isolated from vacuum-packaged refrigerated spoiled lamb.Item Draft Genome Sequence of Clostridium estertheticum-Like Strain FP3, Isolated from Spoiled Uncooked Lamb.(American Society for Microbiology, 2020-05-14) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Gill SRClostridium estertheticum-like strain FP3 was isolated from vacuum-packaged refrigerated spoiled lamb. This bacterium is psychrotrophic, Gram positive, spore-forming, and a strict anaerobe. Here, we report the generation and annotation of the 5.6-Mb draft genome sequence of C. estertheticum-like strain FP3.Item Draft Genome Sequence of Clostridium estertheticum subsp. laramiense DSM 14864T, Isolated from Spoiled Uncooked Beef.(American Society for Microbiology, 2019-11-21) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Newton ILGClostridium estertheticum subsp. laramiense type strain DSM 14864 (ATCC 51254) was isolated from vacuum-packaged refrigerated spoiled beef. This report describes the generation and annotation of the 5.0-Mb draft genome sequence of C. estertheticum subsp. laramiense DSM 14864T.Item Non-Targeted Metabolomic Profiling Identifies Metabolites with Potential Antimicrobial Activity from an Anaerobic Bacterium Closely Related to Terrisporobacter Species.(MDPI (Basel, Switzerland), 2023-02-09) Pahalagedara ASNW; Flint S; Palmer J; Brightwell G; Luo X; Li L; Gupta TB; Eisenreich WThis work focused on the metabolomic profiling of the conditioned medium (FS03CM) produced by an anaerobic bacterium closely related to Terrisporobacter spp. to identify potential antimicrobial metabolites. The metabolome of the conditioned medium was profiled by two-channel Chemical Isotope Labelling (CIL) LC-MS. The detected metabolites were identified or matched by conducting a library search using different confidence levels. Forty-eight significantly changed metabolites were identified with high confidence after the growth of isolate FS03 in cooked meat glucose starch (CMGS) medium. Some of the secondary metabolites identified with known antimicrobial activities were 4-hydroxyphenyllactate, 3-hydroxyphenylacetic acid, acetic acid, isobutyric acid, valeric acid, and tryptamine. Our findings revealed the presence of different secondary metabolites with previously reported antimicrobial activities and suggested the capability of producing antimicrobial metabolites by the anaerobic bacterium FS03.Item Draft Genome Sequence of Psychrotolerant Clostridium sp. Strain M14, Isolated from Spoiled Uncooked Venison.(American Society for Microbiology, 2020-04-16) Palevich N; Palevich FP; Maclean PH; Jauregui R; Altermann E; Mills J; Brightwell G; Hotopp JCDClostridium sp. strain M14 was isolated from vacuum-packaged refrigerated spoiled venison, and this report describes the generation and annotation of its 3.9-Mb draft genome sequence.