Comparative Genomics of Rhodococcus equi Virulence Plasmids Indicates Host-Driven Evolution of the vap Pathogenicity Island

Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi

We present the description of the new species, Rhodococcus parequi, found during phylogenomic investigations of a global collection of strains identified as Rhodococcus (Prescottella) equi. Strain PAM 2766T was isolated from horse-breeding farm soil in Normandy, France, and was indistinguishable from R. equi based on the usual identification tests. Whole-genome phylogenetic analyses located PAM 2766T in the same Rhodococcus sublineage as R. equi, together with Rhodococcus agglutinans, Rhodococcus defluvii, Rhodococcus soli, Rhodococcus subtropicus, Rhodococcus spongiicola and Rhodococcus xishaensis. PAM 2766T is most closely related to, but sufficiently distinct from, R. equi DSM 20307 T to be considered a separate species. The average nt identity (ANI) and average aa identity (AAI) values are 88.60% and 92.35, respectively, well below the species cutoff. The PAM 2766T draft genome is ~5.3 Mb in size with 68.98% G+C mol content. PAM 2766T is strictly aerobic and non-motile and produces smooth, creamy to buff-coloured colonies very similar to those of R. equi. It phenotypically differs from the latter by the ability to grow at 5 °C, a strongly positive urease test at 24 h and specificities in the carbon and nitrogen source utilization profile as determined by phenotype microarray screens. Our data indicate that PAM 2766T belongs to a novel species, for which the name Rhodococcus parequi sp. nov. is proposed. R. parequi was avirulent in macrophage infection assays and is assumed to be non-pathogenic. The type strain is PAM 2766T (=CETC 30995T=NCTC 14987T).

In vitro susceptibility pattern of Rhodococcus equi isolated from patients to antimicrobials recommended exclusively to humans, to domestic animals and to both

Rhodococcus equi is an opportunistic soil-borne bacterium that is eliminated in feces of multi-host animals. An increase in multidrug-resistant R. equi isolates has been reported in humans and domestic animals, and it has been hypothesized that the treatment of R. equi in foals could increase the selective pressure on multidrug-resistant isolates and favor human infections by resistant isolates. We investigated the in vitro antimicrobial susceptibility/resistance of 41 R. equi strains from humans, which were isolated from patients with pulmonary signs, using 19 antimicrobials from 10 distinct classes, recommended exclusively to humans, recommended exclusively to domestic animals and used in both. All isolates were subjected to mass spectrometry and identified as R. equi. Among the antimicrobials used exclusively in humans, tigecycline and vancomycin showed 100% efficacy. Amikacin, amoxicillin/clavulanic acid, imipenem, levofloxacin, clarithromycin, rifampin, ciprofloxacin, and gentamicin, used in both humans and animals, revealed high efficacy (97-100%). Conversely, a higher frequency of isolates was resistant to penicillin (87.8%) and trimethoprim/sulfamethoxazole (43.9%), which are used in both humans and animals. Among the antimicrobials used only in animals, isolates were resistant to florfenicol (46.4%), ceftiofur (17.1%), and enrofloxacin (2.5%). Multidrug resistance was observed in 34% of isolates. The identification of drug-resistant R. equi isolated from humans used exclusively in animals is circumstantial evidence of the pathogen transmission from domestic animals to humans. This study contributes to the molecular identification of Rhodococcus species from humans and to the epidemiological vigilance of the multidrug-resistant isolates.

Experimental infection of goats with pVAPN-harboring Rhodococcus equi causes latent infection in the lymph nodes

Rhodococcus equi has recently been identified in various animals, including ruminants. Several studies have highlighted the emergence of pVAPN-harboring strains, isolated from multiple abscesses, in the liver and lungs of ruminants. Epidemiological evidence strongly suggests that pVAPN-harboring strains are pathogenic in ruminants. This study aims to replicate the disease in goats through experimental infection. Intravenous administration of the pVAPN-harboring strain (Yokkaichi), pVAPA-harboring strain (ATCC33701), and pVAPN-cured strain (Yokkaichi_P-), each at 1.0 × 107 CFU/head, was conducted in 24-month-old goats (n = 1 per group). During the observation period, goats treated with Yokkaichi or ATCC33701 exhibited transient increases in body temperature and white blood cell count, alongside a decrease in body weight from the administration day. Conversely, goats treated with Yokkaichi_P- displayed no significant changes in these values. The Yokkaichi-treated goat demonstrated a >10-fold increase in anti-VapN antibody titers from 11 to 14 days postadministration, whereas the other two goats exhibited no variation in anti-VapA and VapN antibody titers. Pathological autopsy analysis of organs harvested 28 days postadministration revealed no characteristic lesions on gross examination. However, the inoculated strain (vapN-positive R. equi) was exclusively recovered from the tracheobronchial lymph node in the Yokkaichi-treated goat. Immunohistochemistry detected a VapN-positive reaction in the tracheobronchial lymph node, confirming latent infection despite the absence of dramatic suppurative lesions seen in ruminants. Overall, this study highlights the latent infection in lymph nodes induced by the pVAPN-harboring strain, despite the absence of overt pathological manifestations.

Isolation of vapB-positive Rhodococcus equi from submaxillary lymph nodes with or without granulomatous lesions in growing-finishing pigs in Japan

To investigate the etiological role of vapB-positive Rhodococcus equi in pigs, R. equi was isolated from the submaxillary lymph nodes with or without macroscopically detectable lesions of apparently healthy growing-finishing pigs at a slaughterhouse in Toyama Prefecture, Japan. R. equi was isolated from 57 (24.6%) of 232 pigs with macroscopically detectable lymph node lesions, and 56 (98.2%) of the 57 isolates were vapB-positive. R. equi was isolated from 10 (2.4%) of 420 pigs without lymph node lesions, and six (60%) of the 10 isolates were vapB-positive. Plasmid DNA was isolated from the 62 vapB-positive isolates and digested with EcoRI and NsiI to obtain the plasmid profile. Fifty-two (83.9%), three (4.8%), and four (6.5%) isolates contained pVAPB subtypes 1, 2, and 3, respectively, while the remaining three isolates were of pVAPB subtypes 9, 13, and 14, respectively. Twelve specimens from lymph nodes with macroscopically detectable lesions were randomly selected for histopathological staining. Granulomatous lesions resembling tuberculosis were found in 11 of the 12 specimens, and the remaining specimen showed typical foci of malakoplakia in the lymph node. The isolation rates of R. equi and vapB-positive R. equi from lymph nodes with macroscopically detectable lesions were significantly higher (P<0.05) than those of lymph nodes without lesions, suggesting an etiologic association between vapB-positive R. equi and macroscopically detectable granulomatous lesions in porcine submaxillary lymph nodes. Previous reports on the prevalence of vapB-positive R. equi in pigs are reviewed and discussed.

Development of monoclonal antibodies against Rhodococcus equi virulence-associated protein N and their application to pathological diagnosis

IMPORTANCE

Rhodococcus equi can cause infection in ruminants, and its pathogenicity is suggested to be associated with VapN. Despite its wide distribution, no immunological diagnostic method has been developed for VapN-producing R. equi. Against this background, we attempted to develop monoclonal antibodies targeting VapN and assess their application in immunostaining. In the study, mice were immunized with recombinant VapN, and cell fusion and cloning by limiting dilution permitted the generation of three antibody-producing hybridomas. The utility of the antibodies produced from the hybridomas in immunostaining was demonstrated using an infected mouse model, and the antibodies were further applied to previously reported cases of R. equi infection in goats and cattle. Although the 4H4 antibody induced the strongest reactions, the reactivity of two other antibodies was improved by antigen retrieval. Our monoclonal antibodies will be utilized to support the definitive diagnosis of suspected R. equi infection, including cases that were previously missed.

Short review: Geographical distribution of equine-associated pVAPA plasmids in Rhodococcus equi in the world

Virulent Rhodococcus equi strains expressing virulence-associated 15-17 kDa protein (VapA) and having a large virulence plasmid (pVAPA) of 85-90 kb containing vapA gene are pathogenic for horses. In the last two decades, following pVAPA, two host-associated virulence plasmid types of R. equi have been discovered: a circular plasmid, pVAPB, associated with porcine isolates in 1995, and a recently detected linear plasmid, pVAPN, related to bovine and caprine isolates. Molecular epidemiological studies of R. equi infection in foals on horse-breeding farms in Japan and many countries around the world have been conducted in the last three decades, and the epidemiological studies using restriction enzyme digestion patterns of plasmid DNAs from virulent isolates have shown 14 distinct pVAPA subtypes and their geographical preference. This short review summarizes previous reports regarding equine-associated pVAPA subtypes in the world and discusses their geographic distribution from the standpoint of horse movements.

An Autobioluminescent Method for Evaluating In Vitro and In Vivo Growth of Rhodococcus equi

A previously reported method for evaluating the intracellular growth of Rhodococcus equi using enhanced green fluorescent protein is unsuitable for the quantitative evaluation of the entire sample because the signal can be detected only in the excitation region. Therefore, we created an autobioluminescent R. equi using luciferase (luxABCDE). First, we connected luxABCDE to the functional promoter P_aphII and introduced it into the chromosomes of ATCC33701 and ATCC33701_P-. Luminescence was detected in both transformants, and a correlation between the bacterial number and luminescence intensity in the logarithmic phase was observed, indicating that luxABCDE is functionally and quantitatively expressed in R. equi. The luminescence of ATCC33701 was significantly higher than that of ATCC33701_P- at 24 h after infection with J774A.1. Next, RNA-Seq analysis of ATCC33701 to search for endogenous high-expression promoters resulted in the upstream sequences of RS29370, RS41760, and vapA being selected as candidates. Luminescence was detected in each transformant expressing the luxABCDE using these upstream sequences. We examined the luminescence intensity by coexpressing the frp gene, an enhancer of the luciferase reaction, with luxABCDE. The luminescence intensity of the coexpressing transformant was significantly enhanced in J774A.1 compared with the non-coexpressing transformant. Finally, we examined the luminescence in vivo. The luminescence signals in the organs peaked on the third day following the administration of ATCC33701 derivatives in mice, but no luminescence signal was detected when the ATCC33701_P- derivative was administered. The autologous bioluminescent method described herein will enhance the in vitro and in vivo quantitative analysis of R. equi proliferation.

IMPORTANCE We established an autologous bioluminescent strain of R. equi and a method to evaluate its proliferation in vitro and in vivo quantitatively. This method overcomes the weakness of the fluorescence detection system that only measures the site of excitation light irradiation. It is expected to be used as an in vitro and in vivo growth evaluation method with excellent quantitative properties. In addition, it was suggested that the selection of a promoter that expresses luxABCDE could produce a luminescence with high intensity. Although this method needs further improvement, such as creating transformants that can maintain high luminescence intensity regardless of environmental changes such as temperature fluctuations, it is possible to observe bacterial growth over time in mice without killing them. Therefore, this method can be used to not only evaluate the pathogenicity of various wild and gene-deficient strains but also to screen preventive and therapeutic methods such as vaccines.

Virulence plasmids in clinical isolates of Rhodococcus equi from sick foals in the Netherlands

Clinical samples from 123 foals with suspected rhodococcosis submitted to the Veterinary Microbiological Diagnostic Centre of the Faculty of Veterinary Medicine between 1993 and 2006 were tested for the presence of the virulence gene vapA. Of the 123 samples, 120 were vapA-positive and 3 vapA-negative Rhodococcus equi were isolated. The 120 vapA-positive R. equi were isolated from 70 tracheal wash, 19 lung tissues, 7 lymph nodes, 6 synovial fluids, 13 abscesses or pus and single isolates from the uterus, gut, cerebrospinal fluid, abdomen fluid and faeces. Of the 120 isolates, 46 were from Dutch warmblood horses, 23 from Friesian horses, 14 from Trotters, 4 from Holsteiners, 3 from Arab breed, 2 from ponies, 1 from a Welsh pony and 27 from undefined breed horses. Using plasmid profile analysis of the 120 isolates, 117 isolates contained the 85-kb type I plasmid, 2 contained the 87-kb type I plasmid and 1 contained the novel 52-kb non-mobilizable virulence plasmid reported recently. These results showed that the virulent R. equi strains harbouring a virulence plasmid of 85-kb type I or 87-kb type I, which have been detected in clinical isolates from five European countries, are widespread in the Netherlands. This is the first report of plasmid types of clinical R. equi isolates in the Netherlands.

Rhodococcus equi U19 strain harbors a nonmobilizable virulence plasmid

Rhodococcus equi is the causative agent of pyogenic pneumonia in foals, and a virulence-associated protein A (VapA) encoded on the pVAPA virulence plasmid is important for its pathogenicity. In this study, we analyzed the virulence of R. equi strain U19, originally isolated in the Netherlands in 1997 and the genetic characteristics of the pVAPA_U19 plasmid. U19 expressed VapA that was regulated by temperature and pH and underwent significant intracellular proliferation in macrophages. The restriction fragment length polymorphism of pVAPA_U19 digested with EcoRI was similar to that of pREAT701 (85-kb type I) harbored by R. equi ATCC33701, although the band pattern at 10-20 kb differed. Whole-genome sequencing showed that pVAPA_U19 was 51,684 bp in length and that the vapA pathogenicity island region and the replication/participation were almost identical to those in pREAT701. In contrast, the ORF26 to ORF45 genes of pREAT701 (approximately 29,000 bp) were absent from pVAPA_U19. In this lacking region, mobility (MOB) genes, such as relaxase, which allows conjugative DNA processing, and the mating pair formation (MPF) genes, which are a form of the type IV secretion system and provides the mating channel, were present. Co-culture between U19 and five different recipient strains (two plasmid-cured strains and three cryptic plasmid-harboring strains) demonstrated that pVAPA_U19 could not support conjugation. Therefore, pVAPA_U19 does not differ significantly from the previously reported pVAPA in terms of virulence and plasmid replication and maintenance but is a nonmobilizable plasmid unable to cause conjugation because of the absence of genes related to MOB and MPF. This article is protected by copyright. All rights reserved.

Genomic Characteristics Revealed Plasmid-Mediated Pathogenicity and Ubiquitous Rifamycin Resistance of Rhodococcus equi

Rhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysis showed that all R. equi strains contained 11481 pan genes, including 3690 core genes and 602 ~ 1079 accessory genes. Functional annotation of pan genome focused on the genes related to basic lifestyle, such as the storage and expression of metabolic and genetic information. Phylogenetic analysis based on pan-genome showed that the R. equi strains were clustered into six clades, which was not directly related to the isolation location and host source. Also, a total of 84 virulence genes were predicted in 53 R. equi strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (RbpA, tetA (33), erm (46), sul1, qacEdelta 1 and aadA9) were detected, and all strains carried RbpA related to rifamycin resistance. In addition, 28 plasmids were found in the 53 R. equi strains, belonging to Type-A (n = 14), Type-B (n = 8) and Type-N (n = 6), respectively. The genetic structures of the same type of plasmid were highly similar. In conclusion, R. equi strains show different genomic characteristics, virulence-related genes, potential drug resistance and virulence plasmid structures, which may be conducive to the evolution of its pathogenesis.

Cellulitis-related Rhodococcus equi in a cat harboring VAPA-type plasmid pattern

Rhodococcus equi is a well-known intracellular facultative bacterium that is opportunistic in nature, and a contagious disease-causing agent of pyogranulomatous infections in humans and multihost animals. Feline rhodococcosis is an uncommon or unnoticed clinical condition, in which the organism is usually refractory to conventional antimicrobial therapy. The pathogenicity of the agent is intimately associated with plasmid-governed infectivity, which is attributed to the presence of plasmid-encoded virulence-associated proteins (Vap). Three host-adapted virulence plasmid types (VAPs) have been distinguished to date: pVAPA, pVAPB, and pVAPN, whose infections are related to equine, pig, and bovine or caprine origin, respectively, while humans are infected by all three VAP types. Most virulence studies with R. equi plasmid types in animals involve livestock species. Conversely, data on the pathogenicity and human relevance of the virulence plasmid profile of R. equi isolated from cats remains unclear. This report describes a case of cellulitis-related R. equi that harbors the pVAPA-type in a cat with cutaneous lesion. Long-term therapy of the cat using marbofloxacin, a broad-spectrum third-generation fluoroquinolone, resulted effectiveness. pVAPA is a host-adapted virulent type that has been associated predominantly with pulmonary foal infections. Our cat had a history of contact with other cats, livestock (including horses), and farm environment that could have favored the transmission of the pathogen. Besides no clear evidence of cat-to-humans transmission of the pathogen, the identification of R. equi harboring pVAPA-type in a cat with cutaneous abscessed lesion represent relevance in human health because this virulent type has been described in people worldwide with clinical rhodococcal disorders.

Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species

Under conditions of increasing environmental pollution, true saprophytes are capable of changing their survival strategies and demonstrating certain pathogenicity factors. Actinobacteria of the genus Rhodococcus, typical soil and aquatic biotope inhabitants, are characterized by high ecological plasticity and a wide range of oxidized organic substrates, including hydrocarbons and their derivatives. Their cell adaptations, such as the ability of adhering and colonizing surfaces, a complex life cycle, formation of resting cells and capsule-like structures, diauxotrophy, and a rigid cell wall, developed against the negative effects of anthropogenic pollutants are discussed and the risks of possible pathogenization of free-living saprotrophic Rhodococcus species are proposed. Due to universal adaptation features, Rhodococcus species are among the candidates, if further anthropogenic pressure increases, to move into the group of potentially pathogenic organisms with "unprofessional" parasitism, and to join an expanding list of infectious agents as facultative or occasional parasites.

Antimicrobial resistance spectrum conferred by pRErm46 of emerging macrolide (multidrug)-resistant Rhodococcus equi

Clonal multidrug resistance recently emerged in Rhodococcus equi, complicating the therapeutic management of this difficult-to-treat animal and human pathogenic actinomycete. The currently spreading multidrug-resistant (MDR) "2287" clone arose in equine farms upon acquisition, and co-selection by mass macrolide-rifampin therapy, of the pRErm46 plasmid carrying the erm(46) macrolides-lincosamides-streptogramins resistance determinant, and an rpoB^S531F mutation. Here, we screened a collection of susceptible and macrolide-rifampin-resistant R. equi from equine clinical cases using a panel of 15 antimicrobials against rapidly growing mycobacteria (RGM), nocardiae and other aerobic actinomycetes (NAA). R. equi -including MDR isolates- was generally susceptible to linezolid, minocycline, tigecycline, amikacin and tobramycin according to Staphylococcus aureus interpretive criteria, plus imipenem, cefoxitin and ceftriaxone based on Clinical & Laboratory Standards Institute (CLSI) guidelines for RGM/NAA. Ciprofloxacin and moxifloxacin were in the borderline category according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Molecular analyses linked pRErm46 to significantly increased MICs for trimethoprim-sulfamethoxazole and doxycycline in addition to clarithromycin within the RGM/NAA panel, and to streptomycin, spectinomycin and tetracycline resistance. pRErm46 variants with spontaneous deletions in the class 1 integron (C1I) region, observed in ≈30% of erm(46)-positive isolates, indicated that the newly identified resistances were attributable to C1I's sulfonamide (sul1) and aminoglycoside (aaA9) resistance cassettes and adjacent tetRA(33) determinant. Most MDR isolates carried the rpoB^S531F mutation of the 2287 clone, while different rpoB mutations (S531L, S531Y) detected in two cases suggest the emergence of novel MDR R. equi strains.

Pathogenicity and genomic features of vapN-harboring Rhodococcus equi isolated from human patients

Rhodococcus equi is a saprophytic soil bacterium and intracellular pathogen that causes refractory suppurative pneumonia in foals and has emerged as a pathogenic cause of zoonotic disease. Several studies have reported human infections caused by R. equi harboring a recently described third type of virulence plasmid, the ruminant-associated pVAPN, which carries the vapN virulence determinant. Herein, we analyzed pathogenicity and genomic features of nine vapN-harboring R. equi isolated from human patients with and without HIV/AIDS. Four of these strains showed significant VapN production and proliferation in cultured macrophages. These strains were lethally pathogenic after inoculation with 1.0 × 10⁸ CFU in mice and reproduced a necrotizing granulomatous inflammation in the liver and spleen similar to that observed in humans. Additionally, we determined entire genome sequences of all nine strains. Lengths of sequences were 5.0-5.3 Mbp, and GC contents were 68.7 %-68.8 %. All strains harbored a 120- or 125-kbp linear plasmid carrying vapN (Type I or Type II pVAPN) classified on the basis of differences in the distal sequences on the 3' side. Interestingly, VapN production differed significantly among strains harboring nearly identical types of pVAPN with variation limited to several SNPs and short base pair indels. The pVAPN sequences possessed by the VapN-producing strains did not retain any common genetic characteristics, and more detailed analyses, including chromosomal genes, are needed to further elucidate the VapN expression mechanism.

Spread of Multidrug-Resistant Rhodococcus equi, United States

Multidrug resistance has been detected in the animal and zoonotic human pathogen Rhodococcus equi after mass macrolide/rifampin antibioprophylaxis in endemically affected equine farms in the United States. Multidrug-resistant (MDR) R. equi emerged upon acquisition of pRERm46, a conjugative plasmid conferring resistance to macrolides, lincosamides, streptogramins, and, as we describe, tetracycline. Phylogenomic analyses indicate that the increasing prevalence of MDR R. equi since it was first documented in 2002 is caused by a clone, R. equi 2287, attributable to coselection of pRErm46 with a chromosomal rpoB^S531F mutation driven by macrolide/rifampin therapy. pRErm46 spillover to other R. equi genotypes has given rise to a novel MDR clone, G2016, associated with a distinct rpoB^S531Y mutation. Our findings illustrate that overuse of antimicrobial prophylaxis in animals can generate MDR pathogens with zoonotic potential. MDR R. equi and pRErm46-mediated resistance are currently disseminating in the United States and are likely to spread internationally through horse movements.

Virulence Plasmids of Rhodococcus equi Isolates From Cuban Patients With AIDS

Rhodococcus equi is an animal pathogen and zoonotic human opportunistic pathogen associated with immunosuppressive conditions. The pathogenicity of R. equi is linked to three animal host-associated virulence plasmids encoding a family of “Virulence Associated Proteins” (VAPs). Here, the PCR-based TRAVAP molecular typing system for the R. equi virulence plasmids was applied to 26 R. equi strains isolated between 2010 and 2016 at the Institute of Tropical Medicine “Pedro Kourí,” Cuba, from individuals living with HIV/AIDS. TRAVAP detects 4 gene markers, traA common to the three virulence plasmids, and vapA, vapB, and vapN specific to each of the host-associated plasmid types (equine pVAPA, porcine pVAPB, and ruminant pVAPN). Of the 26 isolates, six were positive to the vapB (porcine-type) marker, 4 (15.4%) to the vapA (equine-type) marker, and 1 (3.8%) to the vapN (ruminant-type) marker. Most of the isolates 14 (53.8%) were negative to all TRAVAP markers, suggesting they lacked a virulence plasmid. To our knowledge, this work is the first to report the molecular characterization of R. equi isolates from Cuba. Our findings provide insight into the zoonotic origin of R. equi infections in people and the potential dispensability of the virulence plasmid in immunosuppressed patients.

Reinvestigation of the virulence of Rhodococcus equi isolates from patients with and without AIDS

Rhodococcus equi emerged as a zoonotic pathogen of human immunodeficiency virus-infected patients over the last three decades. Two virulence plasmid types of R. equi, pVAPA and pVAPB associated with equine and porcine isolates, have been recognized, and more recently, pVAPN, a novel host-associated virulence plasmid in R. equi, was found in bovine and caprine isolates. We reinvestigated 39 previously reported isolates of R. equi from patients with and without acquired immunodeficiency syndrome (AIDS) by detecting vapA, vapB and vapN using PCR and plasmid profiling. After excluding one isolate that could not be cultured from frozen storage, eight isolates carried a virulence plasmid encoding vapA (pVAPA), 10 carried a virulence plasmid encoding vapB (pVAPB), seven carried a virulence plasmid encoding vapN (pVAPN) and 13 were negative for those genes. Of the 29 isolates from patients with AIDS, 7, 10 and 5 harboured pVAPA, pVAPB and pVAPN respectively. Among nine isolates from patients without AIDS, one and two harboured pVAPA and pVAPN respectively. This study demonstrated that pVAPN-positive R. equi existed in human isolates before 1994 and reaffirmed that equine-associated pVAPA-positive, porcine-associated pVAPB-positive and bovine- or caprine-associated pVAPN-positive R. equi are widely spread globally. Because domestic animals might be major sources of human infection, further research is needed to reveal the prevalence of pVAPN-positive R. equi infection in cattle and goats.

Relationship between rifampicin resistance and RpoB substitutions of Rhodococcus equi strains isolated in France

OBJECTIVES

Study of the rifampicin resistance of Rhodococcus equi strains isolated from French horses over a 20-year period.

METHODS

Rifampicin susceptibility was tested by disk diffusion (DD) and broth macrodilution methods, and rpoB gene sequencing and MLST were performed on 40 R. equi strains, 50.0% of which were non-susceptible to rifampicin.

RESULTS

Consistency of results was observed between rifampicin susceptibility testing and rpoB sequencing. Strains non-susceptible to rifampicin by DD had a substitution at one of the sites (Asp516, His526 and Ser531) frequently encountered and conferring rifampicin resistance. High-level resistance was correlated with His526Asp or Ser531Leu substitutions; low-level resistance was correlated with Asp516Tyr substitution, a novel substitution for R. equi. Strains susceptible to rifampicin by DD showed no substitution in the three sites, except for two strains carrying, respectively, the His526Asn and Asp516Val substitutions (previously correlated with low-level rifampicin resistance). Both strains were isolated from an animal from which ten other strains were also isolated and found to be rifampicin-non-susceptible by DD. MLST showed the presence of 10 STs (including the novel ST43), but no association was observed with rifampicin resistance.

CONCLUSIONS

This study confirms that certain substitutions in RpoB are more likely to confer high- or low-level rifampicin resistance, describes a new substitution conferring rifampicin resistance in R. equi and suggests non-clonal dissemination of rifampicin-resistant strains in France. Standard DD may miss strains with a low-level rifampicin-resistant substitution; further studies are needed to remedy the absence of R. equi-specific clinical breakpoints.

Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Rhodococcus hoagii (Morse 1912) Kämpfer et al. 2014

A recent taxonomic study confirmed the synonymy of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and Corynebacterium hoagii (Morse 1912) Eberson 1918. As a result, both R. equi and C. hoagii were reclassified as Rhodococcus hoagii comb. nov. in application of the principle of priority of the Prokaryotic Code. Because R. equi is a well-known animal and zoonotic human pathogen, and a bacterial name solidly established in the veterinary and medical literature, we and others argued that the nomenclatural change may cause error and confusion and be potentially perilous. We have now additionally found that the nomenclatural type of the basonym C. hoagii, ATCC 7005T, does not correspond with the original description of the species C. hoagii in the early literature. Its inclusion as the C. hoagii type on the Approved Lists 1980 results in a change in the characters of the taxon and in C. hoagii designating two different bacteria. Moreover, ATCC 7005, the only strain in circulation under the name C. hoagii, does not have a well documented history; it is unclear why it was deposited as C. hoagii and a possible mix-up with a Corynebacterium (Rhodococcus) equi isolate is a reasonable assumption. We therefore request the rejection of Rhodococcus hoagii as a nomen ambiguum, nomen dubium and nomen perplexum in addition to nomen periculosum, and conservation of the name Rhodococcus equi, according to Rules 56ab of the Code.

Horizontal Spread of Rhodococcus equi Macrolide Resistance Plasmid pRErm46 across Environmental Actinobacteria

Conjugation is one of the main mechanisms involved in the spread and maintenance of antibiotic resistance in bacterial populations. We recently showed that the emerging macrolide resistance in the soilborne equine and zoonotic pathogen Rhodococcus equi is conferred by the erm(46) gene carried on the 87-kb conjugative plasmid pRErm46. Here, we investigated the conjugal transferability of pRErm46 to 14 representative bacteria likely encountered by R. equi in the environmental habitat. In vitro mating experiments demonstrated conjugation to different members of the genus Rhodococcus as well as to Nocardia and Arthrobacter spp. at frequencies ranging from ∼10^-2 to 10^-6 pRErm46 transfer was also observed in mating experiments in soil and horse manure, albeit at a low frequency and after prolonged incubation at 22 to 30°C (environmental temperatures), not 37°C. All transconjugants were able to transfer pRErm46 back to R. equi Conjugation could not be detected with Mycobacterium or Corynebacterium spp. or several members of the more distant phylum Firmicutes such as Enterococcus, Streptococcus, or Staphylococcus Thus, the pRErm46 host range appears to span several actinobacterial orders with certain host restriction within the Corynebacteriales All bacterial species that acquired pRErm46 expressed increased macrolide resistance with no significant deleterious impact on fitness, except in the case of Rhodococcus rhodnii Our results indicate that actinobacterial members of the environmental microbiota can both acquire and transmit the R. equi pRErm46 plasmid and thus potentially contribute to the maintenance and spread of erm(46)-mediated macrolide resistance in equine farms.IMPORTANCE This study demonstrates the efficient horizontal transfer of the Rhodococcus equi conjugative plasmid pRErm46, recently identified as the cause of the emerging macrolide resistance among equine isolates of this pathogen, to and from different environmental Actinobacteria, including a variety of rhodococci as well as Nocardia and Arthrobacter spp. The reported data support the notion that environmental microbiotas may act as reservoirs for the endemic maintenance of antimicrobial resistance in an antibiotic pressurized farm habitat.

Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.

Clonal Confinement of a Highly Mobile Resistance Element Driven by Combination Therapy in Rhodococcus equi

MDR clades arise upon acquisition of resistance traits, but the determinants of their clonal expansion remain largely undefined. Taking advantage of the unique features of Rhodococcus equi infection control in equine farms, involving the same dual antibiotic treatment since the 1980s (a macrolide and rifampin), this study sheds light into the determinants of multiresistance clonality and the importance of combination therapy in limiting the dissemination of mobile resistance elements. Clinically effective therapeutic alternatives against R. equi foal pneumonia are currently lacking, and the identified macrolide-rifampin MDR clone 2287 has serious implications. Still at early stages of evolution and local spread, R. equi 2287 may disseminate globally, posing a significant threat to the equine industry and, also, public health due to the risk of zoonotic transmission. The characterization of the 2287 clone and its resistance determinants will enable targeted surveillance and control interventions to tackle the emergence of MDR R. equi.

Antibiotic use has been linked to changes in the population structure of human pathogens and the clonal expansion of multidrug-resistant (MDR) strains among healthcare- and community-acquired infections. Here we present a compelling example in a veterinary pathogen, Rhodococcus equi, the causative agent of a severe pulmonary infection affecting foals worldwide. We show that the erm(46) gene responsible for emerging macrolide resistance among equine R. equi isolates in the United States is part of a 6.9-kb transposable element, TnRErm46, actively mobilized by an IS481 family transposase. TnRErm46 is carried on an 87-kb conjugative plasmid, pRErm46, transferable between R. equi strains at frequencies up to 10⁻³. The erm(46) gene becomes stabilized in R. equi by pRErm46’s apparent fitness neutrality and wholesale TnRErm46 transposition onto the host genome. This includes the conjugally exchangeable pVAPA virulence plasmid, enabling the possibility of cotransfer of two essential traits for survival in macrolide-treated foals in a single mating event. Despite its high horizontal transfer potential, phylogenomic analyses show that erm(46) is paradoxically confined to a specific R. equi clone, 2287. R. equi 2287 also carries a unique rpoB^S531F mutation conferring high-level resistance to rifampin, systematically administered together with macrolides against rhodococcal pneumonia on equine farms. Our data illustrate that under sustained combination therapy, several independent “founder” genetic events are concurrently required for resistance, limiting not only its emergence but also, crucially, horizontal spread, ultimately determining multiresistance clonality.

Ulcerative, granulomatous glossitis and enteritis caused by Rhodococcus equi in a heifer

Rhodococcus equi infection in horses is common and is characterized by pyogranulomatous pneumonia and ulcerative enterocolitis. R. equi clinical disease in cattle, however, is rare and typically manifests as granulomatous lymphadenitis discovered in the abattoir. A 19-mo-old female Santa Gertrudis had a history of intermittent inappetence and weight loss for a 3-mo period before euthanasia. Gross and histologic examination revealed severe, chronic, ulcerative, and granulomatous inflammation in the tongue, pharynx, and small intestine. Also, the heifer had severe, granulomatous pharyngeal and mesenteric lymphadenitis. Bacterial cultures from the ileum, tongue, and liver yielded numerous-to-moderate numbers of R. equi. PCR analysis of the isolate detected the linear virulence plasmid vapN, which is often identified in bovine isolates (traA- and vapN-positive). The bacteria also lack the circular plasmids vapA and vapB that are associated with virulence in horses and swine, respectively. We report herein an atypical and unusual clinical presentation of R. equi infection in cattle, which has zoonotic potential.

Genomic analysis of a novel Rhodococcus (Prescottella) equi isolate from a bovine host

Rhodococcus (Prescottella) equi causes pneumonia-like infections in foals with high mortality rates and can also infect a number of other animals. R. equi is also emerging as an opportunistic human pathogen. In this study, we have sequenced the genome of a novel R. equi isolate, B0269, isolated from the faeces of a bovine host. Comparative genomic analyses with seven other published R. equi genomes, including those from equine or human sources, revealed a pangenome comprising of 6876 genes with 4141 genes in the core genome. Two hundred and 75 genes were specific to the bovine isolate, mostly encoding hypothetical proteins of unknown function. However, these genes include four copies of terA and five copies of terD genes that may be involved in responding to chemical stress. Virulence characteristics in R. equi are associated with the presence of large plasmids carrying a pathogenicity island, including genes from the vap multigene family. A BLAST search of the protein sequences from known virulence-associated plasmids (pVAPA, pVAPB and pVAPN) revealed a similar plasmid backbone on two contigs in bovine isolate B0269; however, no homologues of the main virulence-associated genes, vapA, vapB or vapN, were identified. In summary, this study confirms that R. equi genomes are highly conserved and reports the presence of an apparently novel plasmid in the bovine isolate B0269 that needs further characterisation to understand its potential involvement in virulence properties.

The pathogenic actinobacterium Rhodococcus equi: what's in a name?

Rhodococcus equi is the only recognized animal pathogenic species within an extended genus of metabolically versatile Actinobacteria of considerable biotechnological interest. Best known as a horse pathogen, R. equi is commonly isolated from other animal species, particularly pigs and ruminants, and causes severe opportunistic infections in people. As typical in the rhodococci, R. equi niche specialization is extrachromosomally determined, via a conjugative virulence plasmid that promotes intramacrophage survival. Progress in the molecular understanding of R. equi and its recent rise as a novel paradigm of multihost adaptation has been accompanied by an unusual nomenclatural instability, with a confusing succession of names: "Prescottia equi", "Prescotella equi", Corynebacterium hoagii and Rhodococcus hoagii. This article reviews current advances in the genomics, biology and virulence of this pathogenic actinobacterium with a unique mechanism of plasmid-transferable animal host tropism. It also discusses the taxonomic and nomenclatural issues around R. equi in the light of recent phylogenomic evidence that confirms its membership as a bona fide Rhodococcus.

Identification of Mycobacterium species and Rhodococcus equi in peccary lymph nodes

Mycobacterium species and the virulence-associated proteins (vapA, vapB, and vapN genes) of Rhodococcus equi isolated from 330 lymph nodes of collared peccaries (Tayassu tajacu) and white-lipped peccaries (Tayassu pecari) intended for human consumption were investigated. Thirty-six (10.9%) R. equi strains were isolated; 3.3% (n = 11/330) were from white-lipped peccary lymph nodes, and 7.6% (25/330) were from collared peccary lymph nodes. Among the 11 isolates of R. equi from the white-lipped peccaries, 90.9% (n = 10/11) were obtained from the mesenteric lymph nodes, and only 9.1% (n = 1/10) were obtained from the mediastinal lymph nodes. In the 25 isolates of R. equi obtained from the collared peccaries, 40.0% (n = 10/25) were recovered from the mesenteric lymph nodes, 36% (n = 9/25) from the submandibular lymph nodes, and 24.0% (n = 6/25) from the mediastinal lymph nodes. No vapA, vapB, or vapN genes (plasmidless) or three host-associated types (pVAPA, pVAPB, and pVAPN) were identified among the R. equi isolates. Mycobacterium species were isolated in 3.03% (n = 10/330) of all the lymph nodes analyzed. Among the 10 mycobacterial isolates, 60% (n = 6/10) were from the white-lipped peccary lymph nodes, and 40% (n = 4/10) were from the collared peccary lymph nodes. Ten Mycobacterium species were detected by PCR-PRA with a predominance of M. avium type 1. Sequencing of the hsp65 and rpob genes revealed mycobacteria that were saprophytic (M. sinense and M. kumamotonense) and potentially pathogenic (M. colombiense and M. intracellulare) to humans and animals. To our knowledge, this is the first description of R. equi and/or mycobacterial species identified in the lymph nodes of peccary specimens. R. equi (plasmidless) and the mycobacterial species described here have been reported as causes of pulmonary and extrapulmonary infections in both immunocompetent and immunocompromised humans.

Detection of vapN in Rhodococcus equi isolates cultured from humans

Rhodococcus equi can cause severe infections in people, particularly in immunocompromised individuals. The R. equi virulence plasmids (vap) encoding vapA and vapB are linked to development of infections in domestic animals. Recently, a novel virulence plasmid, vapN, was identified in isolates cultured from cattle, but its prevalence or significance in human R. equi infections has not been extensively studied. To determine the prevalence of vapN in a diverse collection of human-derived isolates from different countries, 65 R. equi isolates collected by various institutions from 1984 to 2002 were screened for the presence of vapN and other virulence plasmids through polymerase chain reaction (PCR) using redesigned primer sets. Of the isolates that carried plasmids, 43% (16/37) were vapN-positive and fewer were vapB or vapA-positive (30 and 16%, respectively). This is the first report of vapN carriage in R. equi isolated from human infections. One isolate (H-30) carried vapN but did not amplify the conjugal plasmid transfer gene traA associated with carriage of vap, which could be explained by sequence variation within the traA gene. Another isolate (H-55) amplified traA, but did not amplify vapA, B, or N (traA⁺vapABN^-) with previously described primer sets or those developed for this study. The H-55 traA sequence had 98% identity to traA sequences in vapA plasmids, which suggests that it may carry a variant of previously characterized virulence plasmids or a novel virulence plasmid. Carriage of vapN in R. equi isolates derived from people is not uncommon and more research is needed to determine its significance in the epidemiology and pathogenesis of human R. equi infections.

Novel bovine-associated pVAPN plasmid type in Rhodococcus equi identified from lymph nodes of slaughtered cattle and lungs of people living with HIV/AIDS

Rhodococcus equi is a well-recognized Gram-positive intracellular facultative bacterium that is opportunistic in nature, which causes pyogranulomatous infections in humans and multiple host animals. The pathogenicity of the microorganism has been attributed to the presence of plasmid-encoded virulence-associated proteins (Vap). To date, three host-associated virulence plasmid types of R. equi have been identified as follows: the circular pVAPA and pVAPB, related, respectively, to equine and porcine isolates, and a recently described linear pVAPN plasmid associated with bovine strains, although these three types are found in human isolates. Recent phylogenomic studies support the evidence that human R. equi infection is zoonotically acquired. Nevertheless, data regarding distribution and prevalence of the host-adapted virulence plasmid types of R. equi isolated from meat animals are scarce or unnoticed. Here, the three host-associated virulence plasmid types (pVAPA, pVAPB, and pVAPN) were investigated in 154 R. equi isolates recovered from lymph nodes of cattle with lymphadenitis (n = 31), faeces of cattle without enteric signs (n = 49), as well as different clinical specimens from human patients (n = 74). The analysis of virulence profile of 74 R. equi from humans revealed six (8.1%) isolates pVAPB (type 8), two (2.7%) pVAPN, and one (1.3%) pVAPB (type 11), all of which were from lung samples from people living with HIV/AIDS. From the lymph node samples of cattle, 41.9% (13 of 31) isolates revealed pVAPN type, whereas all isolates from faecal samples were negative for three host-associated types. Here, recently described bovine-associated pVAPN type was detected in R. equi isolates recovered from the lungs of people living with HIV/AIDS and lymph nodes from slaughtered cattle intended for human consumption; a finding that represents a public health concern, mainly in countries where undercooked or raw meat are traditionally consumed.