Figure - available from: Molecular Microbiology
This content is subject to copyright. Terms and conditions apply.
Whole‐genome Corynebacteriales ML tree. Nodes indicate bootstrap values. Tree constructed with five R.equi genomes, 47 non‐equi Rhodococus genomes including representatives from the major 16S rRNA gene clades (Goodfellow et al., 1998; McMinn et al., 2000; Jones and Goodfellow, 2012; Ludwig et al., 2012), and 57 genomes from 11 Corynebacteriales genera. Rooted with Streptomyces albus NBRC 1304T (outgroup). (T) indicates type strain. Genome used for R. equi type strain DSM 20307T = ATCC 6939T is assembly acc. no. LWTX00000000 (Anastasi et al., 2016). Major genera are highlighted in different colour. Black arrowheads indicate misclassifications revealed by the phylogenomic analysis. One of them is R. rhodnii NRRL B‐16535T (GenBank assembly acc. no. GCA_000720375.1); this probably represents a sequence mislabelling or strain mixup. Modified from Anastasi et al. (2016).
Source publication
Rhodococcus equi is the only 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...
Citations
... Members of the genus have a broad geographic range, and have been isolated from a variety of environments, most often soil including at contaminated sites, but also from freshwater, wastewater, sediment, air, and crude oil [2,[6][7][8]. They have also been found in host-associated systems, and while most species are benign, some can cause infections in plants [9] and animals [10], and more rarely in humans [11,12]. ...
Background
Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process.
Results
By five minutes post-infection WC1 showed upregulation of a CAS-4 family exonuclease, putative immunity repressor, an anti-restriction protein, while the host showed strong upregulation of DNA replication, SOS repair, and ribosomal protein genes. By 30 min post-infection, WC1 DNA synthesis genes were strongly upregulated while the host showed increased expression of transcriptional and translational machinery and downregulation of genes involved in carbon, energy, and lipid metabolism pathways. By 60 min WC1 strongly upregulated structural genes while the host showed a dramatic disruption of metal ion homeostasis. There was significant expression of both host and phage non-coding genes at all time points. While host gene expression declined over the course of infection, our results indicate that phage may exert more selective control, preserving the host’s regulatory mechanisms to create an environment conducive for virion production.
Conclusions
The Rhodococcus genus is well recognized for its ability to synthesize valuable compounds, particularly steroids, as well as its capacity to degrade a wide range of harmful environmental pollutants. A detailed understanding of these phage-host interactions and gene expression is not only essential for understanding the ecology of this important genus, but will also facilitate development of phage-mediated strategies for bioremediation as well as biocontrol in industrial processes and biomedical applications. Given the current lack of detailed global gene expression studies on any Rhodococcus species, our study addresses a pressing need to identify tools and genes, such as F6 and rpf, that can enhance the capacity of Rhodococcus species for bioremediation, biosynthesis and pathogen control.
... According to Ryan and Pembroke (2018), the Brevundimonas genus is a widespread pathogen thay can cause invasive and severe infections. The genus Rhodococcus is home to the species Rhodococcus equi, best known as a horse pathogen, causes severe opportunistic infections in people (Vázquez-Boland & Meijer, 2019). ...
Soil is one of the largest reservoirs of microbial diversity in nature. Although soil management is vital for agricultural purposes, intensive practices can have a significant impact on fertility, microbial community, and resistome. Thus, the aim of this study was to evaluate the effects of an intensive soil management system on the chemical attributes, composition and structure of prevalent bacterial communities, and presence and abundance of antimicrobial resistance genes (ARGs). The chemical characterization, bacterial diversity and relative abundance of ARGs were evaluated in soils from areas of intensive vegetable cultivation and forests. Results indicate that levels of nutrients and heavy metals were higher in soil samples from cultivated areas. Similarly, greater enrichment and diversity of bacterial genera was detected in agricultural areas. Of the 18 target ARGs evaluated, seven were detected in studied soils. The oprD gene exhibited the highest abundance among the studied genes and was the only one that showed a significantly different prevalence between areas. The oprD gene was identified only from soil of the cultivated areas. The blaSFO, erm(36), oprD and van genes, in addition to the pH, showed greater correlation with in soil of cultivated areas, which in turn exhibited higher contents of nutrients. Thus, in addition to changes in chemical attributes and in the microbial community of the soil, intensive agricultural cultivation systems cause a modification of its resistome, reinforcing the importance of the study of antimicrobial resistance in a One Health approach.
... It has been suggested to reclas sify the relatively small genome-sized R. equi as a type species of a new genus called Prescottella (23,34), together with closely related Rhodococcus defluvii, Rhodococcus agglutinans, Rhodococcus soli, and Rhodococcus subtropica. Other studies found R. equi to be deeply embedded within the phylogenetic tree of Rhodococcus and see it as a valid member of the genus (35,36). We did see evidence for both, on the one hand, rhodo cocci with small genomes had down to only 34% of the size of the large Rhodococcus genomes, and shared a dDDH value of 19.8%, with a GC difference of 5.02%. ...
The genus Rhodococcus is recognized for its potential to degrade a large range of aromatic substances, including plant-derived phenolic compounds. We used comparative genomics in the context of the broader Rhodococcus pan-genome to study genomic traits of two newly described Rhodococcus strains (type-strain Rhodococcus pseudokoreensis R79 T and Rhodococcus koreensis R85) isolated from apple rhizosphere. Of particular interest was their ability to degrade phenolic compounds as part of an integrated approach to treat apple replant disease (ARD) syndrome. The pan-genome of the genus Rhodococcus based on 109 high-quality genomes was open with a small core (1.3%) consisting of genes assigned to basic cell functioning. The range of genome sizes in Rhodococcus was high, from 3.7 to 10.9 Mbp. Genomes from host-associated strains were generally smaller compared to environmental isolates which were characterized by exceptionally large genome sizes. Due to large genomic differences, we propose the reclassification of distinct groups of rhodococci like the Rhodococcus equi cluster to new genera. Taxonomic species affiliation was the most important factor in predicting genetic content and clustering of the genomes. Additionally, we found genes that discriminated between the strains based on habitat. All members of the genus Rhodococcus had at least one gene involved in the pathway for the degradation of benzoate, while biphenyl degradation was mainly restricted to strains in close phylogenetic relationships with our isolates. The ~40% of genes still unclassified in larger Rhodococcus genomes, particularly those of environmental isolates, need more research to explore the metabolic potential of this genus.
IMPORTANCE
Rhodococcus is a diverse, metabolically powerful genus, with high potential to adapt to different habitats due to the linear plasmids and large genome sizes. The analysis of its pan-genome allowed us to separate host-associated from environmental strains, supporting taxonomic reclassification. It was shown which genes contribute to the differentiation of the genomes based on habitat, which can possibly be used for targeted isolation and screening for desired traits. With respect to apple replant disease (ARD), our isolates showed genome traits that suggest potential for application in reducing plant-derived phenolic substances in soil, which makes them good candidates for further testing against ARD.
... In addition, R. equi has been isolated from various animal species such as pigs, dogs, cats, cattle, goats, and humans, indicating its wide host range (3)(4)(5). The pathogenicity of R. equi is associated with the presence of a virulence plasmid (pVAP) encoding a family of virulence-associated proteins (Vaps), and the virulence plasmids are associated with host tropism (6)(7)(8). In ruminants, R. equi harboring the linear virulence plasmid pVAPN (encoding VapN and multiple homologs) was isolated from bovine lung abscess and granulomatous lymphadenitis in Europe in 2015 (9). ...
Since 2015, virulence-associated protein N ( vapN )-positive Rhodococcus equi has been isolated from pyogenic lesions in ruminants in multiple countries, including Japan, supporting the widespread distribution of this pathogen in ruminants, and suggesting that VapN is responsible for the pathogenicity of this infection. However, no immunological diagnostic method has been established for this infection. In this study, we attempted to produce anti-VapN monoclonal antibodies and apply them to immunostaining methods. Mice were immunized intraperitoneally or subcutaneously with 5 µg of recombinant VapN (rVapN). After cell fusion and cloning by limiting dilution, we generated three anti-VapN antibody-producing hybridomas (4H4, 5C3, and 5G10). Next, VapN-based immunostaining was performed using a mouse model inoculated with rVapN, the JCM94-3 (VapN-producing) strain, or the JID03-27 (low-producing) strain. Positive reactions were observed in necrotic lesions in the liver and spleen, especially in the rVapN-treated and JCM94-3-treated groups. Immunostaining of goats ( n = 2) and cattle ( n = 3) presumed to be infected with vapN -positive R. equi was also positive in organs carrying necrotic lesions including the lungs, lymph nodes, abomasum, and ribs. The reactivity of immunostaining differed among the antibodies, with the 4H4 antibody exhibiting the best reactivity and allowing detection at low concentrations. However, the reactivity of the other two antibodies was improved by antigen retrieval treatment. Several known diseases cause necrotizing granuloma formation, and the immunological diagnostic method established in this study can be used to distinguish R. equi infection from similar diseases or identify infection in previously missed cases.
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.
... However, echoing some low-resolution studies in the 1980s-1990s that failed to pinpoint its position in the Nocardia/Rhodococcus radiation (26)(27)(28)(29), transfer of the species to a separate genus was (unsuccessfully) attempted in 2013, first as "Prescottia equi," then "Prescottella equi" (https://lpsn.dsmz.de/genus/prescottella). Despite R. equi sharing evident physiological and genetic features with the other rhodococci (30), and its differentiation from the genus Rhodococcus being unsupported by compelling phylochemotaxonomic (31) and phylogenomic evidence (32), the transfer was proposed again and validly published in 2022 (22). The creation of the genus Prescottella for the rhodococcal sublineage comprising R. equi renders the Rhodococcus genus paraphyletic, theoretically entailing the need to create new genera for every of the other major rhodococcal sublineages of equal rank (30). ...
... Despite R. equi sharing evident physiological and genetic features with the other rhodococci (30), and its differentiation from the genus Rhodococcus being unsupported by compelling phylochemotaxonomic (31) and phylogenomic evidence (32), the transfer was proposed again and validly published in 2022 (22). The creation of the genus Prescottella for the rhodococcal sublineage comprising R. equi renders the Rhodococcus genus paraphyletic, theoretically entailing the need to create new genera for every of the other major rhodococcal sublineages of equal rank (30). ...
Genomics allows accurately pinpointing microbial ancestry for taxonomic purposes, yet there is currently no consensus to genus definition based on genome data. Different metrics and criteria are used, with an increasing trend toward genera over-splitting. Here, we report a method for prokaryotic genus assignment that combines normalized tree clustering and network analysis of several genomic relatedness indices. Objectivity is maximized by linear application of the same partitioning thresholds across an entire middle/high taxonomic rank context (order level), with the classical (“pre-genomic”) genera as demarcation reference, ensuring continuity in taxonomy and nomenclature. We tested the method with the Mycobacteriales , where recent examples of genus fragmentation divided Mycobacterium into five genera, or made Rhodococcus paraphyletic by creating the genus Prescottella for the sublineage containing the animal and human pathogen, Rhodococcus equi . Our approach did not support the mycobacterial five-genus split or the Prescottella nested genus, but identified a basal branch in each of the mycobacterial and rhodococcal radiations warranting genus status ( Mycobacteroides , and novel genus Rhodococcoides for the Rhodococcus fascians clade, respectively). The median average amino acid identity (AAI) between the demarcated genera was 56% to 59%, consistent with the <65% AAI genus boundary standard. Shifting the demarcation threshold to the Prescottella /mycobacterial five-genus level systematically elevated the intrageneric sublineages to genus rank, leading to taxonomic atomization (≈threefold increase in potential Mycobacteriales genera). The proposed approach provides a standardizable methodological framework for non-subjective prokaryotic genus delineation.
IMPORTANCE
A robust taxonomy is essential for the organized study of prokaryotes and the effective communication of microbial knowledge. The genus rank is the mainstay of biological classification as it brings together under a common name a group of closely related organisms sharing the same recent ancestry and similar characteristics. Despite the unprecedented resolution afforded by whole-genome sequencing in defining evolutionary relationships, a consensus approach for phylogenomics-based prokaryotic genus delineation remains elusive. Taxonomists use different demarcation criteria, sometimes leading to genus rank over-splitting and the creation of multiple new genera. This work reports a simple, reliable, and standardizable method that seeks to minimize subjectivity in genomics-based demarcation of prokaryotic genera, exemplified through application to the order Mycobacteriales . Formal descriptions of proposed taxonomic changes based on our study are included.
... Other nomenclatures were also previously used, including Nocardia restricted, Corynebacterium equi, Bacillus hoagii, Corynebacterium purulentus, Mycobacterium equi, Mycobacterium restricted and Proactinomyces restricted 8,9. According to Vázquez-Boland & Meijer (2019) 10 and Vázquez-Boland et al., 2020 11, the recent rise of R. equi as a new paradigm of multi-host adaptation has been accompanied by an unusual instability in nomenclature with a confusing succession of names: "Prescottia equi", "Prescottella equi", Corynebacterium hoagii and Rhodococcus hoagii. These researchers reviewed current advances in the genomics, biology, and virulence of these actinobacteria, confirming their pathogenesis due to a unique mechanism of plasmiddetermined animal host tropism. ...
... Rhodococcus equi (R. equi) is a gram-positive, aerobic, facultative intracellular actinobacterium that causes severe pulmonary and extrapulmonary pyogranulomatous infections in different animal species and humans [1]. R. equi shows a worldwide distribution and a high incidence, and long-term treatment and nursing costs and high mortality rates have led to considerable economic losses at farms where R. equi is endemic. ...
Rhodococcus equi (R. equi) is a zoonotic opportunistic pathogen that can cause life-threatening infections. The rapid evolution of multidrug-resistant R. equi and the fact that there is no currently licensed effective vaccine against R. equi warrant the need for vaccine development. Reverse vaccinology (RV), which involves screening a pathogen's entire genome and proteome using various web-based prediction tools, is considered one of the most effective approaches for identifying vaccine candidates. Here, we performed a pangenome analysis to determine the core proteins of R. equi. We then used the RV approach to examine the subcellular localization, host and gut flora homology, antigenicity, transmembrane helices, physicochemical properties, and immunogenicity of the core proteins to select potential vaccine candidates. The vaccine candidates were then subjected to epitope mapping to predict the exposed antigenic epitopes that possess the ability to bind with major histocompatibility complex I/II (MHC I/II) molecules. These vaccine candidates and epitopes will form a library of elements for the development of a polyvalent or universal vaccine against R. equi. Sixteen R. equi complete proteomes were found to contain 6,238 protein families, and the core proteins consisted of 3,969 protein families (∼63.63% of the pangenome), reflecting a low degree of intraspecies genomic variability. From the pool of core proteins, 483 nonhost homologous membrane and extracellular proteins were screened, and 12 vaccine candidates were finally identified according to their antigenicity, physicochemical properties and other factors. These included four cell wall/membrane/envelope biogenesis proteins; four amino acid transport and metabolism proteins; one cell cycle control, cell division and chromosome partitioning protein; one carbohydrate transport and metabolism protein; one secondary metabolite biosynthesis, transport and catabolism protein; and one defense mechanism protein. All 12 vaccine candidates have an experimentally validated 3D structure available in the protein data bank (PDB). Epitope mapping of the candidates showed that 16 MHC I epitopes and 13 MHC II epitopes with the strongest immunogenicity were exposed on the protein surface, indicating that they could be used to develop a polypeptide vaccine. Thus, we utilized an analytical strategy that combines pangenome analysis and RV to generate a peptide antigen library that simplifies the development of multivalent or universal vaccines against R. equi and can be applied to the development of other vaccines.
... Accordingly, exposure to farm animals is a relevant factor in transmitting the infection to humans. [2][3][4][5][6][7] Here, we describe an immunocompromised patient with advanced HIV who presented bloodstream infection by R. hoagie despite residing in an urban setting and having undertaken no trips to the countryside or elsewhere during the COVID-19 pandemic. This case shows the importance of recognizing severe infection, discerning the failure of antibiotic therapy, and changing to more appropriate antimicrobials to ensure survival. ...
Rhodococcus hoagie, previously referred to as R. equi, is a Gram-positive intracellular coccobacillus that belongs to the Nocardiaceae family. This multi-host pathogen causes infections in farm animals, particularly foals, but also in immunosuppressed patients, mainly individuals treated with high doses of corticosteroids, subjected to organ transplant, or infected with human immunodeficiency virus Objectives of the study are to report a bloodstream infection in an immunocompromised patient. Immunocompromised patients with advanced HIV who presented bloodstream infection, residing in an urban setting and having undertaken no trips to the countryside or elsewhere during the COVID-19 pandemic. Blood culture by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was done in order to identify the bacteria. The immunocompromised female patient presented bloodstream infection by Rhodococcus hoagie, which was identified using MALDI-TOF-MS. R. hoagie can cause a severe infection with a high mortality rate if prompt treatment with a combination of antibiotics is not established. A high level of suspicion is required to establish the diagnosis, as it may be misdiagnosed as pulmonary tuberculosis. On gram stain, R. hoagie may appear as beaded to solid staining coccobacilli, which can be dismissed as a "diphtheroid" contaminant. The infection was identified using MALDI-TOF-MS.
... Such preadaptations include the predilection for fatty acid-like compounds and short organic acid nutrients, particularly acetate and lactate (Hughes & Sulaiman, 1987;Letek et al., 2010;Vázquez-Boland & Meijer, 2019). Furthermore, the possession of a thick and partly hydrophobic cell wall (Sutcliffe, 1997) which likely supports the resistance of the bacteria to lysosome contents even at acidic pH as seen here. ...
Gram‐positive Rhodococcus equi (Prescotella equi) is a lung pathogen of foals and immunocompromised humans. Intra‐macrophage multiplication requires production of the bacterial Virulence‐associated protein A (VapA) which is released into the phagosome lumen. VapA pH‐neutralizes intracellular compartments allowing R. equi to multiply in an atypical macrophage phagolysosome. Here, we show that VapA does not support intra‐macrophage growth of several other bacterial species demonstrating that only few bacteria have the specific preadaptations needed to profit from VapA. We show that the closest relative of R. equi, environmental Rhodococcus defluvii (Prescotella defluvii), does not multiply in macrophages at 37°C even when VapA is present because of its thermosensitivity but it does so once the infection temperature is lowered providing rare experimental evidence for ‘thermal restriction’. Using growth experiments with isolated macrophage lysosomes and modified infection schemes we provide evidence that R. equi resists the attack by phagolysosome contents at low pH for several hours. During this time, R. equi produces and secretes VapA which enables it to grow at the expense of lysosome constituents. We present arguments that, under natural infection conditions, R. equi is VapA‐less during the initial encounter with the host. This has important implications for vaccine development. Rhodococcus equi bacteria entering macrophages can face different fates: Avirulent R. equi are delivered to a phagolysosome and killed. When virulent R. equi are cultivated at 30°C, they do not express the major virulence factor VapA (yellow), and they spend hours in an acidified phagolysosome before they have produced enough VapA to pH‐neutralize the phagosome and grow. 37°C‐grown virulent R. equi produce VapA to start with and find themselves immediately in a privileged compartment.
... Rhodococcus (2.5%) the second most abundant genus in A. scalpturatum/A. ovale has the ability to metabolize a large number of substrates and cause pulmonary infections, especially in immunocompromised people [38]. ...
Background
Ticks are arthropods that can host and transmit pathogens to wild animals, domestic animals, and even humans. The microbiome in ticks is an endosymbiotic, pathogenic and is yet to be fully understood.
Results
Adult male Amblyomma scalpturatum ( A. scalpturatum ) and Amblyomma ovale ( A. ovale ) ticks were collected from Tapirus terrestris ( T. terrestris ) captured in the rural area of San Lorenzo Village, and males Amblyomma sabanerae were collected from Chelonoidis denticulate ( C. denticulate ) of the Gamita Farm in the Amazon region of Madre de Dios, Peru. The Chao1 and Shannon–Weaver analyses indicated a greater bacterial richness and diversity in male A. sabanerae ( Amblyomma sabanerae ; 613.65–2.03) compared to male A. scalpturatum and A. ovale ( A. scalpturatum and A. ovale ; 102.17–0.40). Taxonomic analyses identified 478 operational taxonomic units representing 220 bacterial genera in A. sabanerae and 86 operational taxonomic units representing 28 bacterial genera in A. scalpturatum and A. ovale . Of the most prevalent genera was Francisella (73.2%) in A. sabanerae , and Acinetobacter (96.8%) in A. scalpturatum and A. ovale to be considered as the core microbiome of A. sabanerae and A. scalpturatum / A. ovale respectively.
Conclusions
We found a high bacterial diversity in male of A. sabanerae collected from C. denticulata showed prevalence of Francisella and prevalence of Acinetobacter in male A. scalpturatum and A. ovale collected from T. terrestris . The greatest bacterial diversity and richness was found in males A. sabanerae . This is the first bacterial metagenomic study performed in A. scalpturatum/A. ovale and A. sabanerae collected from T. terrestris and C. denticulata in the Peruvian jungle.
