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Highlights • A. hippocoleae was identified from the genital swabs of 15 apparently healthy mares. • Mares were of 8 breeds and from 11 farms in the French region of Brittany. • MALDI-TOF MS and 16S rRNA gene sequencing confirmed identification of the species. • Genotypic and phenotypic differences were observed within A. hippocoleae. Abstract The present study reports the isolation of A. hippocoleae from genital swabs of 15 apparently healthy mares (at least one had an abortion one month earlier) and describes the genotypic and phenotypic characterisation of these strains. The mares were of eight different breeds with a thoroughbred dominance and came from 11 breeding farms located in the French region of Brittany. 16S rRNA gene sequencing confirmed the species' identification by comparing it with reference strain A. hippocoleae CIP 106850T. Some degree of natural divergence within A. hippocoleae was observed by 16S rRNA sequencing (two 1,002-pb sequences), MALDI-TOF MS typing (two groups), a CAMP test (three different intensities of haemolysis from CAMP-positive results) and API® Coryne system (five profiles). The strains were all susceptible to the antimicrobials tested. A national prevalence survey would be required to estimate the frequency of A. hippocoleae carriage in mares and stallions and to verify the presence of A. hippocoleae outside the French region of Brittany, which is the only one found to be affected in the current study, probably because the isolates were recovered from a single field laboratory in this region. [ABSTRACT FROM AUTHOR]

Rhodococcus equi causes pulmonary and extrapulmonary infections in animals and humans, with endemic situations and significant young foal mortality in stud farms worldwide. Despite its economic impact in the horse-breeding industry, the broad geographic and host distribution, global diversity and population structure of R. equi remain poorly characterised. In this context, we developed a multilocus sequence typing (MLST) scheme using 89 clinical and environmental R. equi of various origins and eight Rhodococcus sp. Data can be accessed at http://pubmlst.org/rhodococcus/ . A clonal R. equi population was observed with 16 out of 37 sequence types (STs) grouped into six clonal complexes (CC) based on single-locus variants. One of the six CCs (CC3) is not host-specific, suggesting potential exchanges between different R. equi reservoirs. Most of the virulent equine R. equi CCs/unlinked STs were plasmid-type-specific. Despite this, marked genetic variability with the circulation of multiple R. equi genotypes was generally observed even within the same animal. Focusing on outbreaks, data indicated (i) the potential contagious transmission of R. equi during the 2012-Mayotte equine outbreak because of the poor genotype diversity of clinical strains; (ii) a potential porcine outbreak among the 30 Belgian farms investigated in 2013. This first Rhodococcus equi MLST is a powerful tool for further epidemiological investigations and population biology studies of R. equi isolates. [ABSTRACT FROM AUTHOR]

Abstract: We describe here the development of a multilocus sequence typing (MLST) scheme for Taylorella equigenitalis, the causative agent of contagious equine metritis (CEM), and Taylorella asinigenitalis, a nonpathogenic bacterium. MLST was performed on a set of 163 strains collected in several countries over 35 years (1977–2012). The MLST data were analyzed using START2, MEGA 5.05 and eBURST, and can be accessed at http://pubmlst.org/taylorella/. Our results revealed a clonal population with 39 sequence types (ST) and no common ST between the two Taylorella species. The eBURST analysis grouped the 27 T. equigenitalis STs into four clonal complexes (CC1–4) and five unlinked STs. The 12 T. asinigenitalis STs were grouped into three clonal complexes (CC5–7) and five unlinked STs, among which CC1 (68.1% of the 113 T. equigenitalis) and CC5 (58.0% of the 50 T. asinigenitalis) were dominants. The CC1, still in circulation in France, contains isolates from the first CEM outbreaks that simultaneously emerged in several countries in the late 1970s. The emergence in different countries (e.g. France, Japan, and United Arab Emirates) of STs without any genetic relationship to CC1 suggests the existence of a natural worldwide reservoir that remains to be identified. T. asinigenitalis appears to behave same way since the American, Swedish and French isolates have unrelated STs. This first Taylorella sp. MLST is a powerful tool for further epidemiological investigations and population biology studies of the Taylorella genus. [Copyright &y& Elsevier]

To characterize the potential epidemiological relationship between the origin of Rhodococcus equi strains and the type of their virulence plasmids, we performed a comparative analysis of virulence plasmid types encountered in 96 R. equi strains isolated from (1) autopsied horses, (2) organic samples (horse faeces, manure and straw) and (3) environmental samples. Our results revealed no clear epidemiological link between virulence plasmid type and the origin of R. equi strains isolated from horse-related environments. To understand this result, we determined the nucleotide sequence of the second most frequently isolated virulence plasmid type: a 87-kb type I (pVAPA116) plasmid and compared it with the previously sequenced (and most commonly encountered) 85-kb type I (pVAPA1037) plasmid. Our results show that the divergence between these two plasmids is mainly due to the presence of three allelic exchange loci, resulting in the deletion of two genes and the insertion of three genes in pVAPA116 compared with pVAPA1037. In conclusion, it appears that the divergence between the two sequenced rhodococcal virulence plasmids is not associated with the vap pathogenicity island and may result from an evolutionary process driven by a mobility-related invertase/resolvase invA-like gene. [ABSTRACT FROM AUTHOR]

• T. equigenitalis (Te) viability was assessed in 11 commercial transport systems. • Viability at ambient temperature was inferior to refrigeration at 1–2 days. • Four of 11 swab systems were superior for viability but qPCR results were similar. • A liquid transport medium for mycoplasmas and viruses (UTM) was assessed. • UTM was superior to Amies charcoal gel for Te viability during 10-day refrigeration. The cultural diagnosis of the causal agent of contagious equine metritis (Taylorella equigenitalis) using transport swabs is challenging. Swabs must be placed in Amies charcoal medium, refrigerated during transport, and plated out at the laboratory no later than 48 h after sampling. In this study, the viability of T. equigenitalis strain CIP 79.7T in 11 commercial swab transport systems was initially compared at 1 day and 2 days of storage at ambient (20 ± 3 °C) or refrigerated (5 ± 3 °C) temperature. The four best swab transport systems, systems B, E, F (used as the reference) and K, were then compared at 0, 2, 3, 4, 7 and 10 days at refrigerated temperatures. Statistically significant differences were observed after 10 days only for system K compared to the reference, with approximately 95% viable T. equigenitalis recovered in system K compared to approximately 77% in system F. System K is thus promising for preservation and transport of viable T. equigenitalis for culture. [ABSTRACT FROM AUTHOR]

• Identification of three major and three minor clonal complexes and 11 singletons in European T. equigenitalis population. • Emergence of several STs with cross-border circulation, in particular ST16 and ST46 from the major complexes CC2 and CC8. The accurate identification of Taylorella equigenitalis strains is essential to improve worldwide prevention and control strategies for contagious equine metritis (CEM). This study compared 367 worldwide equine strains using multilocus sequence typing according to the geographical origin, isolation year and equine breed. The strains were divided into 49 sequence types (STs), including 10 described for the first time. Three major and three minor clonal complexes (CCs), and 11 singletons, were identified. The genetic heterogeneity was low (0.13 STs/strain) despite the wide diversity of geographical origins (n = 16), isolation years (1977–2018) and equine breeds (n = 18). It was highest outside Europe and in the 1977–1997 period; current major STs and CCs already existed before 1998. Previous data associated the major CC1 with the first CEM outbreaks in 1977–1978 in the United Kingdom, Australia and the United States, and revealed its circulation in France. Our study confirms its circulation in France over a longer period of time (1992–2018) and its distribution in Spain and Germany but not throughout Europe. In addition to CC1, relationships between non-European and European countries were observed only through ST4, ST17 and ST30. Within Europe, several STs emerged with cross-border circulation, in particular ST16 and ST46 from the major complexes CC2 and CC8. These results constitute a baseline for monitoring the spread of CEM outbreaks. A retrospective analysis of a higher number of strains isolated worldwide between 1977 and the early 2000s would be helpful to obtain an exhaustive picture of the original CEM situation. [ABSTRACT FROM AUTHOR]

In 2018, a T. asinigenitalis strain (MCE663) was isolated in a Persian onager tested for contagious equine metritis (CEM) in a United Kingdom (UK) zoo. This bacterium had never been reported in the UK and Multilocus Sequence Typing described a new atypically divergent ST (ST60). Although the causative agent of CEM is the bacterium Taylorella equigenitalis , a first natural outbreak of endometritis caused by T. asinigenitalis ST70 was reported in 2019, putting its pathogenic potential into question. In this context, we aimed to further sequence the T. asinigenitalis MCE663 genome and characterize the strain using phenotypical and genetic approaches. Results showed that it gathered all identification characteristics of T. asinigenitalis with smaller colonies and it was susceptible to all tested antibiotics. Genome-level phylogeny showed that the genome MCE663 formed a distinct phylogroup, and only shared ≈ 96.1% of average nucleotide identity (ANI) with the three published T. asinigenitalis genomes, which together shared ≈ 98.3% ANI. According to current cut-offs consensus for species and subspecies delineation (95% and 98%, respectively), our results support the first insights of a sublineage delineation within the T. asinigenitalis species. • Genome of a T. asinigenitalis isolated from a Persian onager in 2018 was sequenced. • This genome (MCE663) showed atypical genetic distance from those already published. • MCE663 genome analysis suggests sublineages within the T. asinigenitalis species. [ABSTRACT FROM AUTHOR]

Misidentification between Taylorella equigenitalis , the causative agent of contagious equine metritis (CEM), and Taylorella asinigenitalis is observed by the gold standard culture method. The performance of matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS) for Taylorella species identification was evaluated using 85 T. equigenitalis and 28 T. asinigenitalis strains selected on the basis of multilocus sequence typing data. Seven of the T. equigenitalis and 9 of the T. asinigenitalis strains were used to generate in-house reference spectra to expand the existing commercial Bruker database. Two bacterial incubation times and 3 different sample preparation procedures were compared. Overall, we demonstrated the usefulness of MALDI-TOF MS as a differential diagnostic tool for CEM; however, commercial spectra databases should be expanded with T. asinigenitalis reference spectra to achieve the expected performance. Moreover, direct spotting of 48-h colonies was not only the most efficient protocol but also the easiest to implement in a clinical setting. • An assessment of the reliability of MALDI-TOF MS for the identification of Taylorella species is presented. • Different bacterial incubation times and sample preparation procedures are compared. • Species-level identification of Taylorella equigenitalis is demonstrated. • Species-level identification of Taylorella asinigenitalis is demonstrated when the Bruker database is expanded with in-house T. asinigenitalis reference spectra. [ABSTRACT FROM AUTHOR]

Taylorella equigenitalis is the causative agent of contagious equine metritis (CEM), a sexually transmitted infection of horses. We herein report the genome sequence of T. equigenitalis strain MCE9, isolated in 2005 from the urethral fossa of a 4-year-old stallion in France. [ABSTRACT FROM AUTHOR]

The Taylorella genus comprises two species: Taylorella equigenitalis, which causes contagious equine metritis, and Taylorella asinigenitalis, a closely-related species mainly found in donkeys. We herein report on the first genome sequence of T. asinigenitalis, analyzing and comparing it with the recently-sequenced T. equigenitalis genome. The T. asinigenitalis genome contains a single circular chromosome of 1,638,559 bp with a 38.3% GC content and 1,534 coding sequences (CDS). While 212 CDSs were T. asinigenitalis-specific, 1,322 had orthologs in T. equigenitalis. Two hundred and thirty-four T. equigenitalis CDSs had no orthologs in T. asinigenitalis. Analysis of the basic nutrition metabolism of both Taylorella species showed that malate, glutamate and alpha-ketoglutarate may be their main carbon and energy sources. For both species, we identified four different secretion systems and several proteins potentially involved in binding and colonization of host cells, suggesting a strong potential for interaction with their host. T. equigenitalis seems better-equipped than T. asinigenitalis in terms of virulence since we identified numerous proteins potentially involved in pathogenicity, including hemagluttininrelated proteins, a type IV secretion system, TonB-dependent lactoferrin and transferrin receptors, and YadA and Hep•Hag domains containing proteins. This is the first molecular characterization of Taylorella genus members, and the first molecular identification of factors potentially involved in T. asinigenitalis and T. equigenitalis pathogenicity and host colonization. This study facilitates a genetic understanding of growth phenotypes, animal host preference and pathogenic capacity, paving the way for future functional investigations into this largely unknown genus. [ABSTRACT FROM AUTHOR]