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1 - 6 of 6 for "Patrick J. Biggs"
Genomic epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli 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 Escherichia coli. This group of antimicrobial-resistant bacteria are often multidrug resistant. However there is limited information on ESBL-producing E. coli found in the environment and their link with human clinical isolates. In this study we examined the genetic relationship between environmental and human clinical ESBL-producing E. coli and isolates collected in parallel within the same area over 14 months. Environmental samples were collected from treated effluent stormwater and multiple locations along an Aotearoa New Zealand river. Treated effluent stormwater and river water sourced downstream of the treated effluent outlet were the main samples that were positive for ESBL-producing E. coli (7/14 samples 50.0%; 3/6 samples 50%; and 15/28 samples 54% respectively). Whole-genome sequence comparison was carried out on 307 human clinical and 45 environmental ESBL-producing E. coli isolates. Sequence type 131 was dominant for both clinical (147/307 47.9%) and environmental isolates (11/45 24.4%). Only one ESBL gene was detected in each isolate. Among the clinical isolates the most prevalent ESBL genes were bla CTX-M-27 (134/307 43.6%) and bla CTX-M-15 (134/307 43.6%). Among the environmental isolates bla CTX-M-15 (28/45 62.2%) was the most prevalent gene. A core SNP analysis of these isolates suggested that some strains were shared between humans and the local river. These results highlight the importance of understanding different transmission pathways for the spread of ESBL-producing E. coli.
Genomic diversity of Campylobacter jejuni and Campylobacter coli isolates recovered from human and poultry in Australia and New Zealand, 2017 to 2019
We used genomic and epidemiological data to assess and compare the population structure and origins of Campylobacter a major foodborne pathogen in two neighbouring countries with strong trade and cultural links similar poultry production systems and frequent movement of people and food products. The most common sequence types (STs) differed between Australia and New Zealand with many unique to each country. Over half of all STs were represented by a single isolate. Multidrug-resistant (MDR) genotypes were detected in 0.8% of all samples with no MDR isolates detected in poultry. Quinolone and tetracycline resistant ST6964 was prevalent in New Zealand (10.6% of C. jejuni). Closely related isolates suggested some similar food sources or contacts. We have shown that there is little genetic overlap in human and poultry STs of Campylobacter between the countries which highlights that this common foodborne pathogen has domestic origins in Australia and New Zealand.
Aristaeella hokkaidonensis gen. nov. sp. nov. and Aristaeella lactis sp. nov., two rumen bacterial species of a novel proposed family, Aristaeellaceae fam. nov.
Two strains of Gram-negative anaerobic rod-shaped bacteria from an abundant but uncharacterized rumen bacterial group of the order ‘Christensenellales’ were phylogenetically and phenotypically characterized. These strains designated R-7T and WTE2008T shared 98.6–99.0 % sequence identity between their 16S rRNA gene sequences. R-7T and WTE2008T clustered together on a distinct branch from other Christensenellaceae strains and had <88.1 % sequence identity to the closest type-strain sequence from Luoshenia tenuis NSJ-44T. The genome sequences of R-7T and WTE2008T had 83.6 % average nucleotide identity to each other and taxonomic assignment using the Genome Taxonomy Database indicates these are separate species within a novel family of the order ‘Christensenellales’. Cells of R-7T and WTE2008T lacked any obvious appendages and their cell wall ultra-structures were characteristic of Gram-negative bacteria. The five most abundant cellular fatty acids of both strains were C16 : 0 C16 : 0 iso C17 : 0 anteiso C18 : 0 and C15 : 0 anteiso. The strains used a wide range of the 23 soluble carbon sources tested and grew best on cellobiose but not on sugar-alcohols. Xylan and pectin were fermented by both strains but not cellulose. Acetate hydrogen ethanol and lactate were the major fermentation end products. R-7T produced considerably more hydrogen than WTE2008T which produced more lactate. Based on these analyses Aristaeellaceae fam. nov. and Aristaeella gen. nov. with type species Aristaeella hokkaidonensis sp. nov. are proposed. Strains R-7T (=DSM 112795T=JCM 34733T) and WTE2008T (=DSM 112788T=JCM 34734T) are the proposed type strains for Aristaeella hokkaidonensis sp. nov. and Aristaeella lactis sp. nov. respectively.
A large chromosomal inversion affects antimicrobial sensitivity of Escherichia coli to sodium deoxycholate
Resistance to antimicrobials is normally caused by mutations in the drug targets or genes involved in antimicrobial activation or expulsion. Here we show that an Escherichia coli strain named DOC14 selected for increased resistance to the bile salt sodium deoxycholate has no mutations in any ORF but instead has a 2.1 Mb chromosomal inversion. The breakpoints of the inversion are two inverted copies of an IS5 element. Besides lowering deoxycholate susceptibility the IS5-mediated chromosomal inversion in the DOC14 mutant was found to increase bacterial survival upon exposure to ampicillin and vancomycin and sensitize the cell to ciprofloxacin and meropenem but does not affect bacterial growth or cell morphology in a rich medium in the absence of antibacterial molecules. Overall our findings support the notion that a large chromosomal inversion can benefit bacterial cells under certain conditions contributing to genetic variability available for selection during evolution. The DOC14 mutant paired with its isogenic parental strain form a useful model as bacterial ancestors in evolution experiments to study how a large chromosomal inversion influences the evolutionary trajectory in response to various environmental stressors.
Aliarcobacter, Halarcobacter, Malaciobacter, Pseudarcobacter and Poseidonibacter are later synonyms of Arcobacter: transfer of Poseidonibacter parvus, Poseidonibacter antarcticus, ‘Halarcobacter arenosus’, and ‘Aliarcobacter vitoriensis’ to Arcobacter as Arcobacter parvus comb. nov., Arcobacter antarcticus comb. nov., Arcobacter arenosus comb. nov. and Arcobacter vitoriensis comb. nov.
This paper re-examines the taxonomic positions of recently described Poseidonibacter (P. parvum and P. antarcticus ) Aliarcobacter (‘Al. vitoriensis’) Halarcobacter (‘H. arenosus’) and Arcobacter ( A. caeni A. lacus ) species and other species proposed to represent novel genera highly related to the genus Arcobacter . Phylogenomic and several overall genome relatedness indices (OGRIs) were applied to a total of 118 representative genomes for this purpose. Phylogenomic analyses demonstrated the Arcobacter clade to be distinct from other Epsilonproteobacteria clearly defined and containing closely related species. Aliarcobacter butzleri and Malaciobacter pacificus did not cluster with other members of these proposed genera indicating incoherence of these genera. Every OGRI measure applied indicated a high level of relatedness among all Arcobacter clade species including the recently described taxa studied here and substantially lower between type species representatives for other Epsilonproteobacteria. Where published guidelines were available OGRI values for Arcobacter clade species were either unsupportive of division into other genera or were at the lowest boundary range (for average amino acid identity). We propose that Aliarcobacter Halarcobacter Malaciobacter Pseudarcobacter Poseidonibacter and Arcobacter sensu stricto be considered members of a single genus Arcobacter and subsequently transfer P. parvum P. antarcticus ‘ Al. vitoriensis ’ and ‘H. arenosus’ to Arcobacter as Arcobacter parvum comb. nov. Arcobacter antarcticus comb. nov. Arcobacter vitoriensis comb. nov. and Arcobacter arenosus comb. nov.
Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni
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.