Molecular characterization of antimicrobial resistance in Brachyspira species isolated from UK chickens: Identification of novel variants of pleuromutilin and beta-lactam resistance genes.

Brachyspira species are Gram negative, anaerobic bacteria that colonise the gut of many animals, including poultry. In poultry, Brachyspira species can be commensal (B. innocens, B.

A genomic epidemiological study shows that prevalence of antimicrobial resistance in is associated with the livestock host, as well as antimicrobial usage.

Enterobacterales from livestock are potentially important reservoirs for antimicrobial resistance (AMR) to pass through the food chain to humans, thereby increasing the AMR burden and affecting our ability to tackle infections. In this study 168 isolates from four genera of the order , primarily , were purified from livestock (cattle, pigs and sheep) faeces from 14 farms in the United Kingdom. Their genomes were resolved using long- and short-read sequencing to analyse AMR genes and their genetic context, as well as to explore the relationship between AMR burden and on-farm antimicrobial usage (AMU), in the three months prior to sampling.

Whole-Genome Sequencing of Isolates From England and Wales Reveals Similarities to European Isolates and Mutations Associated With Reduced Sensitivity to Antimicrobials.

Brachyspira hyodysenteriae is the principal cause of swine dysentery, a disease that threatens economic productivity of pigs in many countries as it can spread readily within and between farms, and only a small number of antimicrobials are authorized for treatment of pigs. In this study, we performed whole-genome sequencing (WGS) of 81 archived at the Animal and Plant Health Agency (APHA) from diagnostic submissions and herd monitoring in England and Wales between 2004 and 2015. The resulting genome sequences were analyzed alongside 34 genomes we previously published.

Corrigendum: Characterizing Antimicrobial Resistant and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain.

[This corrects the article DOI: 10.3389/fmicb.2020.

Brachyspira hyodysenteriae isolate multilocus sequence type dashboard.

This focus article has been prepared by Susanna Williamson, Emma Stubberfield and Anna Brzozowska of the APHA and Jill Thomson of SRUC - Veterinary Consulting Services, Edinburgh.

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.

and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes.

Retrospective analysis of necrotizing typhlitis cases associated with spp. in British rheas.

This paper describes a retrospective analysis of necrotizing typhlitis in common rheas () diagnosed in the United Kingdom by the Animal & Plant Health Agency (APHA). From January 2008 to January 2020, seven cases of spirochaetal typhlitis associated with spp. were identified using the Veterinary Investigation Diagnosis Analysis database.

Characterizing Antimicrobial Resistant and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain.

Combatting antimicrobial resistant (AMR) using a One-Health approach is essential as various bacteria, including , a common bacteria, are becoming increasingly resistant and livestock may be a reservoir. The AMR gene content of 492 , isolated from 56 pig farms across Great Britain in 2014-2015, and purified on antibiotic selective and non-selective plates, was determined using whole genome sequencing (WGS). The were phylogenetically diverse harboring a variety of AMR profiles with widespread resistance to "old" antibiotics; isolates harbored up to seven plasmid Inc-types.

Use of whole genome sequencing of commensal in pigs for antimicrobial resistance surveillance, United Kingdom, 2018.

BackgroundSurveillance of commensal , a possible reservoir of antimicrobial resistance (AMR) genes, is important as they pose a risk to human and animal health. Most surveillance activities rely on phenotypic characterisation, but whole genome sequencing (WGS) presents an alternative.AimIn this retrospective study, we tested 515 isolated from pigs to evaluate the use of WGS to predict resistance phenotype.

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.

Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy.

Identification of a New Antimicrobial Resistance Gene Provides Fresh Insights Into Pleuromutilin Resistance in , Aetiological Agent of Swine Dysentery.

is the aetiological agent of swine dysentery, a globally distributed disease that causes profound economic loss, impedes the free trade and movement of animals, and has significant impact on pig health. Infection is generally treated with antibiotics of which pleuromutilins, such as tiamulin, are widely used for this purpose, but reports of resistance worldwide threaten continued effective control. In pleuromutilin resistance has been associated with mutations in chromosomal genes encoding ribosome-associated functions, however the dynamics of resistance acquisition are poorly understood, compromising stewardship efforts to preserve pleuromutilin effectiveness.

mcr-1 and mcr-2 variant genes identified in Moraxella species isolated from pigs in Great Britain from 2014 to 2015.

Objectives: To determine the occurrence of mcr-1 and mcr-2 genes in Gram-negative bacteria isolated from healthy pigs in Great Britain.

Methods: Gram-negative bacteria (n = 657) isolated from pigs between 2014 and 2015 were examined by WGS.

Results: Variants of mcr-1 and mcr-2 were identified in Moraxella spp.

Characterisation of North American Brucella isolates from marine mammals.

Extension of known ecological niches of Brucella has included the description of two novel species from marine mammals. Brucella pinnipedialis is associated predominantly with seals, while two major Brucella ceti clades, most commonly associated with porpoises or dolphins respectively, have been identified. To date there has been limited characterisation of Brucella isolates obtained from marine mammals outside Northern European waters, including North American waters.

Exposure of harbour seals Phoca vitulina to Brucella in declining populations across Scotland.

Since 2000 there has been a major decline in the abundance of Scottish harbour seals Phoca vitulina. The causes of the decline remain uncertain. The aim of this study was to establish the extent to which the seals in the regions of greatest decline have been exposed to Brucella, a bacterial pathogen that causes reproductive failure in terrestrial mammalian hosts.

Isolation of Brucella ceti from a Long-finned Pilot Whale (Globicephala melas) and a Sowerby's Beaked Whale (Mesoploden bidens).

Brucella ceti is an emerging zoonotic pathogen that has been recovered from several species of cetaceans in the world's oceans over the past 20 yr. We report the recovery of B. ceti from a Sowerby's beaked whale (Mesoploden bidens) and a long-finned pilot whale (Globicehala melas).

Examination of taxonomic uncertainties surrounding Brucella abortus bv. 7 by phenotypic and molecular approaches.

Brucella taxonomy is perpetually being reshuffled, at both the species and intraspecies levels. Biovar 7 of Brucella abortus was suspended from the Approved Lists of Bacterial Names Brucella classification in 1988, because of unpublished evidence that the reference strain 63/75 was a mixture of B. abortus biovars 3 and 5.

Phenotypic and molecular characterisation of Brucella isolates from marine mammals.

Background: Bacteria of the genus Brucella are the causative organisms of brucellosis in animals and man. Previous characterisation of Brucella strains originating from marine mammals showed them to be distinct from the terrestrial species and likely to comprise one or more new taxa. Recently two new species comprising Brucella isolates from marine mammals, B.