Journal Articles

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    Effects of biochar in combination with varied N inputs on grain yield, N uptake, NH3 volatilization, and N2O emission in paddy soil
    (Frontiers Media, 12/05/2023) Yi Z; Jeyakumar P; Yin C; Sun H
    Biochar application can improve crop yield, reduce ammonia (NH3) volatilization and nitrous oxide (N2O) emission from farmland. We here conducted a pot experiment to compare the effects of biochar application on rice yield, nitrogen (N) uptake, NH3 and N2O losses in paddy soil with low, medium, and high N inputs at 160 kg/ha, 200 kg/ha and 240 kg/ha, respectively. The results showed that: (1) Biochar significantly increased the rice grain yield at medium (200 kg/ha) and high (240 kg/ha) N inputs by 56.4 and 70.5%, respectively. The way to increase yield was to increase the rice N uptake, rice panicle number per pot and 1,000 grain weight by 78.5–96.5%, 6–16% and 4.4–6.1%, respectively; (2) Under low (160 kg/ha) N input, adding biochar effectively reduced the NH3 volatilization by 31.6% in rice season. The decreases of pH value and NH4+-N content in surface water, and the increases of the abundance of NH4+-N oxidizing archaea and bacteria (AOA and AOB) communities contributed to the reduction of NH3 volatilization following the biochar application; (3) Under same N input levels, the total N2O emission in rice season decreased by 43.3–73.9% after biochar addition. The decreases of nirK and nirS gene abundances but the increases of nosZ gene abundance are the main mechanisms for biochar application to reduce N2O emissions. Based on the results of the current study, adding biochar at medium (200 kg/ha) N level (N200 + BC) is the best treatment to synchronically reduce NH3 and N2O losses, improve grain yield, and reduce fertilizer application in rice production system.
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    Comparison of the effects of 7.2% hypertonic saline and 20% mannitol on whole blood coagulation and platelet function in dogs with suspected intracranial hypertension-a pilot study
    (BioMed Central, 19/06/2017) Yozova ID; Howard J; Henke D; Dirkmann D; Adamik KN
    Hyperosmolar therapy with either mannitol or hypertonic saline (HTS) is commonly used in the treatment of intracranial hypertension (ICH). In vitro data indicate that both mannitol and HTS affect coagulation and platelet function in dogs. The aim of this study was to compare the effects of 20% mannitol and 7.2% HTS on whole blood coagulation using rotational thromboelastometry (ROTEM®) and platelet function using a platelet function analyzer (PFA®) in dogs with suspected ICH. Thirty client-owned dogs with suspected ICH needing osmotherapy were randomized to receive either 20% mannitol (5 ml/kg IV over 15 min) or 7.2% HTS (4 ml/kg IV over 5 min). ROTEM® (EXTEM® and FIBTEM® assays) and PFA® analyses (collagen/ADP cartridges) were performed before (T0), as well as 5 (T5), 60 (T60) and 120 (T120) minutes after administration of HTS or mannitol. Data at T5, T60 and T120 were analyzed as a percentage of values at T0 for comparison between groups, and as absolute values for comparison between time points, respectively.No significant difference was found between the groups for the percentage change of any parameter at any time point except for FIBTEM® clotting time. Within each group, no significant difference was found between time points for any parameter except for FIBTEM® clotting time in the HTS group, and EXTEM® and FIBTEM® maximum clot firmness in the mannitol group. Median ROTEM® values lay within institutional reference intervals in both groups at all time points, whereas median PFA® values were above the reference intervals at T5 (both groups) and T60 (HTS group).Using currently recommended doses, mannitol and HTS do not differ in their effects on whole blood coagulation and platelet function in dogs with suspected ICH. Moreover, no relevant impairment of whole blood coagulation was found following treatment with either solution, whereas a short-lived impairment of platelet function was found after both solutions.
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    Extended-spectrum β-lactamase- and AmpC β-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study
    (Elsevier Ltd on behalf of International Society for Infectious Diseases, 2023-03) Toombs-Ruane LJ; Marshall JC; Benschop J; Drinković D; Midwinter AC; Biggs PJ; Grange Z; Baker MG; Douwes J; Roberts MG; French NP; Burgess SA
    OBJECTIVES: To assess whether having a pet in the home is a risk factor for community-acquired urinary tract infections associated with extended-spectrum β-lactamase (ESBL)- or AmpC β-lactamase (ACBL)- producing Enterobacterales. METHODS: An unmatched case-control study was conducted between August 2015 and September 2017. Cases (n = 141) were people with community-acquired urinary tract infection (UTI) caused by ESBL- or ACBL-producing Enterobacterales. Controls (n = 525) were recruited from the community. A telephone questionnaire on pet ownership and other factors was administered, and associations were assessed using logistic regression. RESULTS: Pet ownership was not associated with ESBL- or ACBL-producing Enterobacterales-related human UTIs. A positive association was observed for recent antimicrobial treatment, travel to Asia in the previous year, and a doctor's visit in the last 6 months. Among isolates with an ESBL-/ACBL-producing phenotype, 126/134 (94%) were Escherichia coli, with sequence type 131 being the most common (47/126). CONCLUSIONS: Companion animals in the home were not found to be associated with ESBL- or ACBL-producing Enterobacterales-related community-acquired UTIs in New Zealand. Risk factors included overseas travel, recent antibiotic use, and doctor visits.
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    Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites.
    (2022-10) Burgess SA; Moinet M; Brightwell G; Cookson AL
    Extended-spectrum beta lactamase (ESBL)-producing Escherichia coli are often isolated from humans with urinary tract infections and may display a multidrug-resistant phenotype. These pathogens represent a target for a One Health surveillance approach to investigate transmission between humans, animals and the environment. This study examines the multidrug-resistant phenotype and whole genome sequence data of four ESBL-producing E. coli isolated from freshwater in New Zealand. All four isolates were obtained from a catchment with a mixed urban and pastoral farming land-use. Three isolates were sequence type (ST) 131 (CTX-M-27-positive) and the other ST69 (CTX-M-15-positive); a phylogenetic comparison with other locally isolated strains demonstrated a close relationship with New Zealand clinical isolates. Genes associated with resistance to antifolates, tetracyclines, aminoglycosides and macrolides were identified in all four isolates, together with fluoroquinolone resistance in two isolates. The ST69 isolate harboured the bla CTX-M-15 gene on a IncHI2A plasmid, and two of the three ST131 isolates harboured the bla CTX-M-27 genes on IncF plasmids. The last ST131 isolate harboured bla CTX-M-27 on the chromosome in a unique site between gspC and gspD. These data highlight a probable human origin of the isolates with subsequent transmission from urban centres through wastewater to the wider environment.
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    Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion
    (Microbiology Society, 1/10/2016) Llarena AK; Zhang J; Vehkala M; Välimäki N; Hakkinen M; Hänninen M; Roasto M; Mäesaar M; Taboada E; Barker D; Garofolo G; Cammà C; Di Giannatale E; Corander J; Ross M
    The decreased costs of genome sequencing have increased the capability to apply whole-genome sequencing to epidemiological surveillance of zoonotic Campylobacter jejuni. However, knowledge of the genetic diversity of this bacteria is vital for inferring relatedness between epidemiologically linked isolates and a necessary prerequisite for correct application of this methodology. To address this issue in C. jejuni we investigated the spatial and temporal signals in the genomes of a major clonal complex and generalist lineage, ST-45 CC, by analysing the population structure and genealogy as well as applying genome-wide association analysis of 340 isolates from across Europe collected over a wide time range. The occurrence and strength of the geographical signal varied between sublineages and followed the clonal frame when present, while no evidence of a temporal signal was found. Certain sublineages of ST-45 formed discrete and genetically isolated clades containing isolates with extremely similar genomes regardless of time and location of sampling. Based on a separate data set, these monomorphic genotypes represent successful C. jejuni clones, possibly spread around the globe by rapid animal (migrating birds), food or human movement. In addition, we observed an incongruence between the genealogy of the strains and multilocus sequence typing (MLST), challenging the existing clonal complex definition and the use of whole-genome gene-by-gene hierarchical nomenclature schemes for C. jejuni.
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    Targeting the chromosome partitioning protein ParA in tuberculosis drug discovery.
    (2010-11) Nisa S; Blokpoel MCJ; Robertson BD; Tyndall JDA; Lun S; Bishai WR; O'Toole R
    OBJECTIVE: To identify inhibitors of the essential chromosome partitioning protein ParA that are active against Mycobacterium tuberculosis. METHODS: Antisense expression of the parA orthologue MSMEG_6939 was induced on the Mycobacterium smegmatis background. Screening of synthetic chemical libraries was performed to identify compounds with higher anti-mycobacterial activity in the presence of parA antisense. Differentially active compounds were validated for specific inhibition of purified ParA protein from M. tuberculosis (Rv3918c). ParA inhibitors were then characterized for their activity towards M. tuberculosis in vitro. RESULTS: Under a number of culture conditions, parA antisense expression in M. smegmatis resulted in reduced growth. This effect on growth provided a basis for the detection of compounds that increased susceptibility to expression of parA antisense. Two compounds identified from library screening, phenoxybenzamine and octoclothepin, also inhibited the in vitro ATPase activity of ParA from M. tuberculosis. Structural in silico analyses predict that phenoxybenzamine and octoclothepin undergo interactions compatible with the active site of ParA. Octoclothepin exhibited significant bacteriostatic activity towards M. tuberculosis. CONCLUSIONS: Our data support the use of whole-cell differential antisense screens for the discovery of inhibitors of specific anti-tubercular drug targets. Using this approach, we have identified an inhibitor of purified ParA and whole cells of M. tuberculosis.
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    Occurrence of genes encoding spore germination in Clostridium species that cause meat spoilage.
    (2022-02) Burgess SA; Palevich FP; Gardner A; Mills J; Brightwell G; Palevich N
    Members of the genus Clostridium are frequently associated with meat spoilage. The ability for low numbers of spores of certain Clostridium species to germinate in cold-stored vacuum-packed meat can result in blown pack spoilage. However, little is known about the germination process of these clostridia, despite this characteristic being important for their ability to cause spoilage. This study sought to determine the genomic conditions for germination of 37 representative Clostridium strains from seven species (C. estertheticum, C. tagluense, C. frigoris, C. gasigenes, C. putrefaciens, C. aligidicarnis and C. frigdicarnis) by comparison with previously characterized germination genes from C. perfringens, C. sporogenes and C. botulinum. All the genomes analysed contained at least one gerX operon. Seven different gerX operon configuration types were identified across genomes from C. estertheticum, C. tagluense and C. gasigenes. Differences arose between the C. gasigenes genomes and those belonging to C. tagluense/C. estertheticum in the number and type of genes coding for cortex lytic enzymes, suggesting the germination pathway of C. gasigenes is different. However, the core components of the germination pathway were conserved in all the Clostridium genomes analysed, suggesting that these species undergo the same major steps as Bacillus subtilis for germination to occur.
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    Engineering Bacillus megaterium for production of functional intracellular materials
    (BioMed Central, 22/11/2017) Grage K; McDermott P; Rehm BHA
    Background: Over the last 10-15 years, a technology has been developed to engineer bacterial polyhydroxybutyrate (PHB) inclusions as functionalized beads, for applications such as vaccines, diagnostics and enzyme immobilization. This has been achieved by translational fusion of foreign proteins to the PHB synthase (PhaC). The respective fusion protein mediates self-assembly of PHB inclusions displaying the desired protein function. So far, beads have mainly been produced in recombinant Escherichia coli which is problematic for some applications as the lipopolysaccharides (LPS) co-purified with such inclusions are toxic to humans and animals. Results: In this study, we have engineered the formation of functional PHB inclusions in the Gram-positive bacterium Bacillus megaterium, an LPS-free and established industrial production host. As B. megaterium is a natural PHB producer, the PHB-negative strain PHA05 was used to avoid any background PHB production. Plasmid-mediated T7 promoter-driven expression of the genes encoding β-ketothiolase (phaA), acetoacetyl-CoA-reductase (phaB) and PHB synthase (phaC) enabled/effected PHB production by B. megaterium PHA05. To produce functionalized PHB inclusions, the N- and C-terminus of PhaC was fused to four and two IgG binding Z-domains from Staphylococcus aureus, respectively. The ZZ-domain PhaC fusion protein was strongly overproduced at the surface of the PHB inclusions and the corresponding isolated ZZ-domain displaying PHB beads were found to purify IgG with a binding capacity of 40-50 mg IgG/g beads. As B. megaterium has the ability to sporulate and respective endospores could co-purify with cellular inclusions, a sporulation negative production strain was generated by disrupting the spoIIE gene in PHA05. This strain did not produce spores when tested under sporulation inducing conditions and it was still able to synthesize ZZ-domain displaying PHB beads. Conclusions: This study provides proof of concept for the successful genetic engineering of B. megaterium as a host for the production of functionalized PHB beads. Disruption of the spoIIE gene rendered B. megaterium incapable of sporulation but particularly suitable for production of functionalized PHB beads. This sporulation-negative mutant represents an improved industrial production strain for biotechnological processes otherwise impaired by the possibility of endospore formation.
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    Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments.
    (2022) Collis RM; Biggs PJ; Burgess SA; Midwinter AC; Brightwell G; Cookson AL
    Antimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, the role antimicrobial usage on pasture-based dairy farms, such as those in NZ, plays in driving the spread of AMR within the dairy farm environment remains equivocal. Culture-based methods were used to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli from farm environmental samples collected over a 15-month period from two NZ dairy farms with contrasting management practices. Whole genome sequencing was utilised to understand the genomic epidemiology and antimicrobial resistance gene repertoire of a subset of third-generation cephalosporin resistant E. coli isolated in this study. There was a low sample level prevalence of ESBL-producing E. coli (faeces 1.7%; farm dairy effluent, 6.7% from Dairy 4 and none from Dairy 1) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3% and 8.3%; farm dairy effluent 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). ESBL- and AmpC-producing E. coli were isolated from faeces and farm dairy effluent in spring and summer, during months with varying levels of antimicrobial use, but no ESBL- or AmpC-producing E. coli were isolated from bulk tank milk or soil from recently grazed paddocks. Hybrid assemblies using short- and long-read sequence data from a subset of ESBL- and AmpC-producing E. coli enabled the assembly and annotation of nine plasmids from six E. coli, including one plasmid co-harbouring 12 antimicrobial resistance genes. ESBL-producing E. coli were infrequently identified from faeces and farm dairy effluent on the two NZ dairy farms, suggesting they are present at a low prevalence on these farms. Plasmids harbouring several antimicrobial resistance genes were identified, and bacteria carrying such plasmids are a concern for both animal and public health. AMR is a burden for human, animal and environmental health and requires a holistic "One Health" approach to address.