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      Chlamydia pecorum detection in aborted and stillborn lambs from Western Australia

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          Abstract

          Lamb survival is an important welfare and productivity issue for sheep industries worldwide. Lower lamb survival has been reported for primiparous ewes, but the causes of this are not well studied. The aim of this study was to determine causes of perinatal deaths for lambs born to primiparous ewes in Western Australia, and identify if infectious diseases are implicated. Lamb mortality from birth to marking were determined for 11 primiparous ewe flocks on 10 farms in Western Australia. Lamb mortality from birth to marking averaged 14% for single-born and 26% for multiple-born lambs. Lamb necropsies ( n = 298) identified starvation–mismosthering–exposure (34%), dystocia (24%) and stillbirth (15%) as the most common causes of perinatal lamb death. There was no evidence of exotic abortigenic pathogens in aborted and stillborn lambs ( n = 35). Chlamydia pecorum was detected by qPCR in 15/35 aborted and stillborn lambs on 5/6 farms. Preliminary molecular characterisation of C. pecorum detected in samples from aborted and stillborn lambs ( n = 8) using both Multilocus Sequence Typing and ompA genotyping indicated all strains were genetically identical to previously described pathogenic livestock strains, denoted ST23, and dissimilar to gastrointestinal strains. High frequency of detection of a pathogenic C. pecorum strains ST23 associated with ovine abortion and stillbirth on multiple farms located across a wide geographic area has not been previously reported. Chlamydia pecorum may contribute to reproductive wastage for primiparous sheep in Western Australia. Further investigation to understand C. pecorum epidemiology and impact on sheep reproduction is warranted.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s13567-021-00950-w.

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          FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

          Background We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability. Methodology/Principal Findings Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the “CAT” approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100–1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory. Conclusions/Significance FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.
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            MRBAYES: Bayesian inference of phylogenetic trees

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              Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications

              The PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera.  Although the PubMLST website was conceived as part of the development of the first multi-locus sequence typing (MLST) scheme in 1998 the software it uses, the Bacterial Isolate Genome Sequence database (BIGSdb, published in 2010), enables PubMLST to include all levels of sequence data, from single gene sequences up to and including complete, finished genomes.  Here we describe developments in the BIGSdb software made from publication to June 2018 and show how the platform realises microbial population genomics for a wide range of applications.  The system is based on the gene-by-gene analysis of microbial genomes, with each deposited sequence annotated and curated to identify the genes present and systematically catalogue their variation.  Originally intended as a means of characterising isolates with typing schemes, the synthesis of sequences and records of genetic variation with provenance and phenotype data permits highly scalable (whole genome sequence data for tens of thousands of isolates) means of addressing a wide range of functional questions, including: the prediction of antimicrobial resistance; likely cross-reactivity with vaccine antigens; and the functional activities of different variants that lead to key phenotypes.  There are no limitations to the number of sequences, genetic loci, allelic variants or schemes (combinations of loci) that can be included, enabling each database to represent an expanding catalogue of the genetic variation of the population in question.  In addition to providing web-accessible analyses and links to third-party analysis and visualisation tools, the BIGSdb software includes a RESTful application programming interface (API) that enables access to all the underlying data for third-party applications and data analysis pipelines.
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                Author and article information

                Contributors
                T.Clune@murdoch.edu.au
                shane.besier@dpird.wa.gov.au
                sam.hair@dpird.wa.gov.au
                S.Hancock@murdoch.edu.au
                A.Lockwood@murdoch.edu.au
                Andrew.Thompson@murdoch.edu.au
                mjelocni@usc.edu.au
                C.Jacobson@murdoch.edu.au
                Journal
                Vet Res
                Vet Res
                Veterinary Research
                BioMed Central (London )
                0928-4249
                1297-9716
                11 June 2021
                11 June 2021
                2021
                : 52
                : 84
                Affiliations
                [1 ]GRID grid.1025.6, ISNI 0000 0004 0436 6763, Centre for Animal Production and Health, , Murdoch University, ; South Street, Murdoch, WA 6150 Australia
                [2 ]GRID grid.493004.a, Department of Primary Industries and Regional Development, ; South Perth, WA 6151 Australia
                [3 ]GRID grid.1034.6, ISNI 0000 0001 1555 3415, Genecology Research Centre, , University of the Sunshine Coast, ; 90 Sippy Downs Drive, Sippy Downs, QLD 4557 Australia
                Author information
                http://orcid.org/0000-0001-9427-1941
                Article
                950
                10.1186/s13567-021-00950-w
                8196467
                34116730
                1c4abdc7-2ac5-4292-962a-9fef91c4acf0
                © The Author(s) 2021

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 4 March 2021
                : 18 May 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001054, Meat and Livestock Australia;
                Award ID: B.AHE.0318
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100003526, Department of Agriculture, Australian Government;
                Funded by: Australian Research Council Discovery Early Career Research Award
                Award ID: DE190100238
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2021

                Veterinary medicine
                chlamydia,sheep,reproduction,abortion,stillbirth,dystocia,lamb survival,necropsy
                Veterinary medicine
                chlamydia, sheep, reproduction, abortion, stillbirth, dystocia, lamb survival, necropsy

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