Rapid detection and differentiation of Erysipelothrix spp. by a novel multiplex real-time PCR assay

Genomic characterization and virulence gene profiling of Erysipelothrix rhusiopathiae isolated from widespread muskox mortalities in the Canadian Arctic Archipelago

BACKGROUND

Muskoxen are important ecosystem components and provide food, economic opportunities, and cultural well-being for Indigenous communities in the Canadian Arctic. Between 2010 and 2021, Erysipelothrix rhusiopathiae was isolated from carcasses of muskoxen, caribou, a seal, and an Arctic fox during multiple large scale mortality events in the Canadian Arctic Archipelago. A single strain ('Arctic clone') of E. rhusiopathiae was associated with the mortalities on Banks, Victoria and Prince Patrick Islands, Northwest Territories and Nunavut, Canada (2010-2017). The objectives of this study were to (i) characterize the genomes of E. rhusiopathiae isolates obtained from more recent muskox mortalities in the Canadian Arctic in 2019 and 2021; (ii) identify and compare common virulence traits associated with the core genome and mobile genetic elements (i.e. pathogenicity islands and prophages) among Arctic clone versus other E. rhusiopathiae genomes; and iii) use pan-genome wide association studies (GWAS) to determine unique genetic contents of the Arctic clone that may encode virulence traits and that could be used for diagnostic purposes.

RESULTS

Phylogenetic analyses revealed that the newly sequenced E. rhusiopathiae isolates from Ellesmere Island, Nunavut (2021) also belong to the Arctic clone. Of 17 virulence genes analysed among 28 Arctic clone isolates, four genes - adhesin, rhusiopathiae surface protein-A (rspA), choline binding protein-B (cbpB) and CDP-glycerol glycerophosphotransferase (tagF) - had amino acid sequence variants unique to this clone when compared to 31 other E. rhusiopathiae genomes. These genes encode proteins that facilitate E. rhusiopathiae to attach to the host endothelial cells and form biofilms. GWAS analyses using Scoary found several unique genes to be overrepresented in the Arctic clone.

CONCLUSIONS

The Arctic clone of E. rhusiopathiae was associated with multiple muskox mortalities spanning over a decade and multiple Arctic islands with distances over 1000 km, highlighting the extent of its spatiotemporal spread. This clone possesses unique gene content, as well as amino acid variants in multiple virulence genes that are distinct from the other closely related E. rhusiopathiae isolates. This study establishes an essential foundation on which to investigate whether these differences are correlated with the apparent virulence of this specific clone through in vitro and in vivo studies.

Erysipelothrix spp. and other Erysipelotrichales detected by 16S rRNA microbial community profiling in samples from healthy conventionally reared chickens and their environment

Outbreaks of erysipelas, a disease caused by infection with Erysipelothrix rhusiopathiae (ER), is a re-emerging problem in cage-free laying hen flocks. The source of ER infection in hens is usually unknown and serological evidence has also indicated the presence of ER or other antigenically related bacteria in healthy flocks. The aim of the present study was to evaluate sample collection, culture methods and DNA-based methodology to detect ER and other Erysipelotrichales in samples from healthy chickens and their environment. We used samples from a research facility with conventionally reared chickens with no history of erysipelas outbreaks where hens with high titres of IgY recognising ER previously have been observed. Microbial DNA was extracted from samples either directly or after pre-culture in nonselective or ER-selective medium. Real-time PCR was used for detection of Erysipelothrix spp. and high-throughput amplicon sequencing of 16S rRNA sequencing was used for detection of Erysipelotrichales. A pilot serological analysis of some Erysipelotrichales members with IgY from unvaccinated and ER-vaccinated high-biosecurity chickens, as well as conventionally reared chickens, was also performed. All samples were negative for ER, E. tonsillarum and E. piscisicarius by PCR analysis. However, 16S rRNA community profiling indicated the presence of several Erysipelotrichales genera in both environmental samples and chicken intestinal samples, including Erysipelothrix spp. that were detected in environmental samples. Sequences from Erysipelothrix spp. were most frequently detected in samples pre-cultured in ER-selective medium. At species level the presence of Erysipelothrix anatis and/or Erysipelothrix aquatica was indicated. Serological results indicated that IgY raised to ER showed some cross-reactivity with E. anatis. Hence, environmental samples pre-cultured in selective medium and analysis by 16S rRNA sequencing proved a useful method for detection of Erysipelotrichales, including Erysipelothrix spp., in chicken flocks. The observation of such bacteria in environmental samples offers a possible explanation for the observation of high antibody titres to ER in flocks without a history of clinical erysipelas.

Erysipelothrix amsterdamensis sp. nov., associated with mortalities among endangered seabirds

Infectious diseases threaten endangered species, particularly in small isolated populations. Seabird populations on the remote Amsterdam Island in the Indian Ocean have been in decline for the past three decades, with avian cholera caused by Pasteurella multocida proposed as the primary driver. However, Erysipelothrix species have also been sporadically detected from albatrosses on Amsterdam Island and may be contributing to some of the observed mortality. In this study, we genomically characterized 16 Erysipelothrix species isolates obtained from three Indian yellow-nosed albatross (Thalassarche carteri) chick carcasses in 2019. Histological analyses suggest that they died of bacterial septicaemia. Two isolates were sequenced using both Illumina short-read and MinION long-read approaches, which - following hybrid assembly - resulted in closed circular genomes. Mapping of Illumina reads from the remaining isolates to one of these new reference genomes revealed that all 16 isolates were closely related, with a maximum of 13 nucleotide differences distinguishing any pair of isolates. The nucleotide diversity of isolates obtained from the same or different carcasses was similar, suggesting all three chicks were likely infected from a common source. These genomes were compared with a global collection of genomes from Erysipelothrix rhusiopathiae and other species from the same genus. The isolates from albatrosses were phylogenetically distinct, sharing a most recent common ancestor with E. rhusiopathiae. Based on phylogenomic analysis and standard thresholds for average nucleotide identity and digital DNA-DNA hybridization, these isolates represent a novel Erysipelothrix species, for which we propose the name Erysipelothrix amsterdamensis sp. nov. The type strain is A18Y020dT (=CIP 112216T=DSM 115297T). The implications of this bacterium for albatross conservation will require further study.

Development of a multiplex qRT-PCR assay for detection of classical swine fever virus, African swine fever virus, and Erysipelothrix rhusiopathiae

Classical swine fever virus (CSFV), African swine fever virus (ASFV), and Erysipelothrix rhusiopathiae (E. rhusiopathiae) remain endemic in many parts of China. Co-infections make distinguishing their clinical symptoms and pathological changes difficult. This study developed a multiplex real-time quantitative reverse transcription polymerase chain reaction (multiplex qRT-PCR) that can simultaneously detect CSFV, ASFV, and E. rhusiopathiae. Three sets of primers and probes were designed to target the CSFV 5΄ untranslated region, ASFV p72 gene, and E. rhusiopathiae 16sRNA gene. Multiplex qRT-PCR for simultaneous differential detection of these three pathogens was developed after optimizing reaction parameters such as annealing temperature, primer and probe concentrations, amplification cycles, etc. The multiplex qRT-PCR could detect CSFV, ASFV, and E. rhusiopathiae simultaneously but could not amplify other porcine pathogens. The assay's limit of detection (LOD) was 2.89 × 10² copies/μL for CSFV, ASFV, and E. rhusiopathiae. All correlation coefficients (R²) at higher than 0.99, and the amplification efficiency was 98, 90, and 84%, respectively. All correlation coefficients (R2) were higher than 0.99, and the efficacy of amplification was 84%. In a repeatability test utilizing standard recombinant plasmids, the intra- and inter-assay coefficients of variation (CVs) were less than 2.27 and 3.79 percent, respectively. Lastly, 150 clinical samples were used to evaluate the assay's applicability in the field. The positive rates of CSFV, ASFV, and E. rhusiopathiae were 1.33%, 0, and 3.33%, respectively. And no co-infection among the three pathogens was found. The concordance rate between the multiplex qRT-PCR and single-plex commercial PCR kits reached 100%. This study's multiplex qRT-PCR could provide a rapid, sensitive, and specific method for the simultaneous and differential detection of CSFV, ASFV, and E. rhusiopathiae.

Human Erysipelothrix rhusiopathiae infection via bath water – case report and genome announcement

Erysipelothrix rhusiopathiae is a facultative anaerobic, environmentally stable, Gram-positive rod that causes swine and avian erysipelas as a zoonotic pathogen. In humans, the main manifestations described are circumscribed erysipeloid, generalized erysipeloid, and endocarditis. Here, we report a 46-year-old female patient who presented to the physician because of redness and marked functio laesa of the hand, in terms of a pain-related restricted range of motion, and was treated surgically. E. rhusopathiae was detected in tissue biopsy. The source of infection was considered to be a pond in which both swine and, later, her dog bathed. The genome of the isolate was completely sequenced and especially the presumptive virulence associated factors as well as the presumptive antimicrobial resistance genes, in particular a predicted homologue to the multiple sugar metabolism regulator (MsmR), several predicted two-component signal transduction systems, three predicted hemolysins, two predicted neuraminidases, three predicted hyaluronate lyases, the surface protective antigen SpaA, a subset of predicted enzymes that potentially confer resistance to reactive oxygen species (ROS), several predicted phospholipases that could play a role in the escape from phagolysosomes into host cell cytoplasm as well as a predicted vancomycin resistance locus (vex23-vncRS) and three predicted MATE efflux transporters were investigated in more detail.

Gut microbiome diversity of porcine peritonitis model of sepsis

Animal models are essential in understanding of the mechanisms of sepsis moreover the development and the assessment of emerging therapies. In clinically relevant porcine model, however, a significant variability in the host response has been observed among animals. Thus, there is a strong demand to better understand the potential sources of this heterogeneity. In this study, we compared faecal microbiome composition of 12 animals. Three samples were collected at different time points from each animal. Bacteriome was subjected to 16S rDNA profiling. A significant difference in bacterial composition was associated with the season (p < 0.001) but not with the sex of the pig (p = 0.28), the timing of sample collection (p = 0.59), or interactions thereof (all p > 0.3). The season batch explained 55% of the total variance in the bacteriome diversity. The season term was highly significant from the high-resolution level of the bacterial amplicon sequencing variants up to the level of phylum. The diversity of the microbiome composition could significantly influence experimental model of sepsis, and studies are warranted to demonstrate the effects of gut microbiome diversity on the host-response. If confirmed, control of the gut microbiome should become a standard part of the pre-clinical sepsis experiments.

An unusual outbreak of erysipelas on a goat farm in Pennsylvania

Erysipelothrix rhusiopathiae infection and septicemia occurred in a 5-d old Boer goat found dead on a farm in western Pennsylvania. On autopsy, there was moderate, focally extensive hemorrhage along the remnants of the urachus and umbilical arteries and the apex of the urinary bladder. Microscopic examination of immunohistochemical stained tissues revealed abundant intracellular and extracellular E. rhusiopathiae antigen-positive bacilli in all tissues stained, including lung, heart, liver, skeletal muscle, kidney, and thymus. Bacteria isolated from liver and urachus were identified as E. rhusiopathiae by MALDI-TOF mass spectrometry and further confirmed by a PCR assay. An epidemiologic investigation was conducted via an on-farm questionnaire after the owners noted a 70% mortality rate from the 2019 kidding season. The epidemiologic investigation showed that E. rhusiopathiae, an opportunistic zoonotic organism, was introduced to the farm through a breach in biosecurity and was likely perpetuated among the resident poultry species.

Characterization of Erysipelothrix rhusiopathiae Isolates from Diseased Pigs in 15 Chinese Provinces from 2012 to 2018

Erysipelothrix rhusiopathiae can cause erysipelas in animals and erysipeloid in humans. Since its recurrence in 2012, swine erysipelas has caused serious losses within the pig industry in China. The aim of this study was to perform multilocus sequence typing and understand the virulence and antimicrobial susceptibility of E. rhusiopathiae isolates in China. Multilocus sequence typing (MLST) of a total of 120 strains was performed, and as a result, three different sequence types were identified, of which ST48 was the main one. Five isolates of each MLST type were randomly selected to be used to challenge mice. ST48 was associated with a higher virulence. Antimicrobial susceptibility was tested using a microdilution technique and, to analyze the resistance mechanism, six strains were selected for genome sequencing. A comparison of the six genomes indicated the presence of a suspected macrolide resistance gene, namely, Erm(A)-like, in erythromycin-resistant strains, which increased the minimum inhibitory concentration (MIC) of erythromycin against E. coli C600 at least four-fold. In addition, three mutations (gyrA86T-I, gyrA90D-N, and parC81S-I) were observed in the quinolone resistance-determining regions (QRDRs) of gyrA and parC in quinolone-resistant strains. After the gyrA gene with the 86T-I mutation or the parC gene with the 81S-I mutation was transfected into E. coli C600, the MIC of enrofloxacin against this strain increased at least two-fold. Our findings provide a theoretical basis for developing antibacterial drugs and may contribute to the clinical prevention and control of E. rhusiopathiae.

Influence of Anthropic Environmental-Related Factors on Erysipelas in Wild Boar

Erysipelothrix rhusiopathiae (ER) is an old but still emerging zoonotic infection that is not yet completely understood. ER infects a wide range of species and wild boar is of significant interest because of their similarities to pigs, a known ER reservoir. Moreover, the increase of its densities and the limited data available about ER in this species should be considered. The need is to investigate whether wild boar could represent a risk of erysipelas at the wildlife-domestic-human interface. Here, 1067 sera and 149 tonsils of wild boar from five hunting districts in Northwest Italy were tested using ELISA and bacteriological culture, respectively. Using generalized linear models, we evaluated host and environmental factors influencing ER spread and dynamics. We found an ER seroprevalence of 69.4% among wild boar. Increased human density and pig farm density lead to an increase of ER seropositivity highlighting its association with anthropic environmental-related factors. The high ER percentage of isolation (34.2%) found in healthy wild boar suggests that this species can serve as a healthy carrier. This fact, together with the high seroprevalence, supports a role of wild boar as an ER reservoir. Potential zoonotic and economic risks should be considered in light of these data.

Exposure of the Gulf of St. Lawrence grey seal Halichoerus grypus population to potentially zoonotic infectious agents

The population of grey seals Halichoerus grypus in Canadian waters is currently used as a commercial source of meat for human consumption. As with domestic livestock, it is important to understand the occurrence in these seals of infectious agents that may be of public health significance and thus ensure appropriate measures are in place to avoid zoonotic transmission. This study examined the prevalence of antibodies against Brucella spp., Erysipelothrix rhusiopathiae, 6 serovars of Leptospira interrogans, and Toxoplasma gondii in 59 grey seals and determined by polymerase chain reaction (PCR) the presence of these potentially zoonotic agents in specific organs and tissues of seropositive animals. The presence of encysted Trichinella spp. larvae was also investigated by digestion of tongue, diaphragm and other muscle samples, but none were detected. Seroprevalence against Brucella spp. and E. rhusiopathiae was low (5 and 3%, respectively). All 59 seals tested had antibodies against L. interrogans, but no carrier of this bacterium was detected by PCR. Seroprevalence against T. gondii was 53%, and DNA of this protozoan was detected by PCR in 11/30 (37%) seropositive animals. Standard sanitary measures mandatory for commercialization of meat products for human consumption should greatly reduce the potential for exposure to these infectious agents. However, special consideration should be given to freezing seal meat for at least 3 d to ensure destruction of tissue cysts of T. gondii.

Erysipelothrix Spp.: Past, Present, and Future Directions in Vaccine Research

Erysipelothrix spp. comprise a group of small Gram-positive bacteria that can infect a variety of hosts including mammals, fish, birds, reptiles and insects. Among the eight Erysipelothrix species that have been described to date, only Erysipelothrix rhusiopathiae plays a major role in farmed livestock where it is the causative agent of erysipelas. E. rhusiopathiae also has zoonotic potential and can cause erysipeloid in humans with a clear occupational link to meat and fish industries. While there are 28 known Erysipelothrix serovars, over 80% of identified isolates belong to serovars 1 or 2. Vaccines to protect pigs against E. rhusiopathiae first became available in 1883 as a response to an epizootic of swine erysipelas in southern France. The overall vaccine repertoire was notably enlarged between the 1940s and 1960s following major outbreaks of swine erysipelas in the Midwest USA and has changed little since. Traditionally, E. rhusiopathiae serovar 1a or 2 isolates were inactivated (bacterins) or attenuated and these types of vaccines are still used today on a global basis. E. rhusiopathiae vaccines are most commonly used in pigs, poultry, and sheep where the bacterium can cause considerable economic losses. In addition, erysipelas vaccination is also utilized in selected vulnerable susceptible populations, such as marine mammals in aquariums, which are commonly vaccinated at regular intervals. While commercially produced erysipelas vaccines appear to provide good protection against clinical disease, in recent years there has been an increase in perceived vaccine failures in farmed animals, especially in organic outdoor operations. Moreover, clinical erysipelas outbreaks have been reported in animal populations not previously considered at risk. This has raised concerns over a possible lack of vaccine protection across various production species. This review focuses on summarizing the history and the present status of E. rhusiopathiae vaccines, the current knowledge on protection including surface antigens, and also provides an outlook into future directions for vaccine development.

Detection and quantification of Erysipelothrix rhusiopathiae in blood from infected chickens - addressing challenges with detection of DNA from infectious agents in host species with nucleated red blood cells

PURPOSE

The present study aimed to establish pretreatment protocols as well as real-time and droplet digital polymerase chain reaction (PCR) methodologies to detect and quantify Erysipelothrix rhusiopathiae (ER) DNA in blood samples from infected chickens, as tools for routine diagnostics and monitoring of experimental infections. Chicken blood is a problematic matrix for PCR analysis because nucleated erythrocytes contribute large amounts of host DNA that inhibit amplification.

METHODOLOGY

Using artificially spiked samples of fresh chicken blood, as well as blood samples from three experimental infection studies, the performance of pretreatment protocols, including choice of blood stabilization agent, centrifugation speeds and Ficoll gradient separation, was evaluated. The results were compared with those from traditional culture-based protocols combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).Results/Key findings. Simple preparations producing cell-free samples performed well on artificial spike-in samples, providing high sensitivity. However, performance was poor in clinical samples or artificial samples where the bacteria were incubated for 4 h or more in fresh blood prior to DNA extraction. In these samples, a Ficoll separation protocol that creates samples rich in lymphocytes, monocytes and thrombocytes prior to DNA extraction was far more effective.

CONCLUSIONS

Our results indicate that ER bacteria undergo rapid phagocytosis in chicken blood and that analysis of a blood fraction enriched for phagocytic cells is necessary for reliable detection and quantification. The presented results explain the poor performance of PCR detection reported in previously published experimental ER infection studies, and the proposed solutions are likely to have broader implications for PCR-based veterinary diagnostics in non-mammalian host species such as poultry and fish.

Erysipelothrix rhusiopathiae serotype 5-associated metritis in a Norwegian Red heifer

This report summarized the findings of a case of Erysipelothrix rhusiopathiae infection in a farmed Norwegian Red heifer located in the south‐east of Norway. The 2.5‐year‐old pregnant heifer was found dead after a short episode of inappetence. On gross exam, the heifer was severely dehydrated with uterine torsion. Microscopically, necrosis of the endometrium was present throughout the uterus along with presence of intralesional Gram‐positive bacteria, interstitial nephritis, and pyelonephritis. E. rhusiopathiae was isolated from the uterus and placenta and was also demonstrated by immunohistochemistry (IHC) in the uterus, placenta, and kidney. The E. rhusiopathiae isolate was further characterized as serotype 5. To the authors’ knowledge, this is the first report of bacterial metritis associated with E. rhusiopathiae serotype 5 infection. The etiology of the infection is unknown but the E. rhusiopathiae could have been a primary or opportunistic pathogen. Serotype 5 of E. rhusiopathiae has been identified in several mammalian species in recent years and could be emerging.

Isolation and Detection of Erysipelothrix rhusiopathiae and Its Distribution in Humans and Animals by Phenotypical and Molecular Methods in Ahvaz-Iran in 2015

BACKGROUND

Erysipelothrix rhusiopathiae (E. rhusiopathiae) is generally transmitted into the gastrointestinal tract of animals by the intake of contaminated food or water and causes great economic loss in agriculture worldwide. Some of the Erysipelothrix spp. are the causative agents of erysipeloid, which is an occupational infection in humans. The aim of the present study was to isolate E. rhusiopathiae from animals as well as the hands of the butchers working in Ahvaz, Iran, and to determine their susceptibility to antibiotics.

METHODS

Totally, 150 samples were taken from slaughterhouse workers, fishermen, and livers and hearts of sheep and calves by the swabbing method. Phenotypical methods and polymerase chain reaction (PCR) were used for the isolation and identification of E. rhusiopathiae. The isolates were tested for their susceptibility to commonly used antimicrobial agents using the disk diffusion protocol described by the Clinical and Laboratory Standards Institute.

RESULTS

Out of the 150 samples examined via phenotypical and biochemical tests, 16 samples were positive as putative Erysipelothrix spp. twelve cases out of the 16 putative Erysipelothrix spp. were confirmed by PCR. The tested isolates were highly sensitive to the antibiotics used. The results of the sensitivity and specificity of PCR revealed that the sensitivity and specificity of indirect PCR were higher than those of direct PCR.

CONCLUSION

E. rhusiopathiae is widely distributed on seafood and presents as a commensal pathogen in nature and animals. Infection with this microorganism should be emphasized because it is a rare organism causing severe infections such as infectious endocarditis and polyarthritis following localized infections.

Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates

Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors.

Shaggy Lame Fox Syndrome in Pribilof Island Arctic Foxes ( Alopex lagopus pribilofensis), Alaska

A previously unrecognized condition is described in wild free-ranging Pribilof arctic foxes ( Alopex lagopus pribilofensis) from the Pribilof Islands, Alaska, USA. This condition is called shaggy lame fox syndrome (SLFS) denoting the primary clinical signs first observed. Criteria used to suspect SLFS on gross examination included emaciation, failure to shed winter pelage and moderate to severe polyarthritis. Criteria used to confirm SLFS histologically included polyarthritis (characterized by lymphoplasmacytic synovitis, tenosynovitis, bursitis, periosteal bony proliferation, and periarticular lymphoplasmacytic vasculitis) and systemic leukocytoclastic vasculitis. Other histological lesions often found included renal cortical infarcts, myocarditis with myocardial infarcts, lymphoplasmacytic meningitis, lymphoplasmacytic cuffing of meningeal and a few cerebral vessels, and cavitating infarcts of the brainstem and thalamus. The cause of SLFS is not known at this time; however, the gross and histological lesions suggest that the cause of SLFS may be a bacterial polyarthritis with a secondary immune-mediated vasculitis. These lesions are consistent with changes described with Erysipelothrix rhusiopathiae in domestic dogs; E. rhusiopathiae was identified from the synovial membrane of a swollen stifle joint and the kidney from one fox using real-time polymerase chain reaction and with culture from a fox that had gross and histological lesions of SLFS. Therefore, E. rhusiopathiae is a possible etiological agent for SLFS.

Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution

Background

Knowledge about how bacterial populations are structured is an important prerequisite for studying their ecology and evolutionary history and facilitates inquiry into host specificity, pathogenicity, geographic dispersal and molecular epidemiology. Erysipelothrix rhusiopathiae is an opportunistic pathogen that is currently reemerging in both the swine and poultry industries globally. This bacterium sporadically causes mortalities in captive marine mammals, and has recently been implicated in large-scale wildlife die-offs. However, despite its economic relevance and broad geographic and host distribution, including zoonotic potential, the global diversity, recombination rates, and population structure of this bacterium remain poorly characterized. In this study, we conducted a broad-scale genomic comparison of E. rhusiopathiae based on a diverse collection of isolates in order to address these knowledge gaps.

Results

Eighty-three E. rhusiopathiae isolates from a range of host species and geographic origins, isolated between 1958 and 2014, were sequenced and assembled using both reference-based mapping and de novo assembly. We found that a high proportion of the core genome (58 %) had undergone recombination. Therefore, we used three independent methods robust to the presence of recombination to define the population structure of this species: a phylogenetic tree based on a set of conserved protein sequences, in silico chromosome painting, and network analysis. All three methods were broadly concordant and supported the existence of three distinct clades within the species E. rhusiopathiae. Although we found some evidence of host and geographical clustering, each clade included isolates from diverse host species and from multiple continents.

Conclusions

Using whole genome sequence data, we confirm recent suggestions that E. rhusiopathiae is a weakly clonal species that has been shaped extensively by homologous recombination. Despite frequent recombination, we can reliably identify three distinct clades that do not clearly segregate by host species or geographic origin. Our results provide an essential baseline for future molecular epidemiological, ecological and evolutionary studies of E. rhusiopathiae and facilitate comparisons to other recombinogenic, multi-host bacteria.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2643-0) contains supplementary material, which is available to authorized users.

Development of a loop-mediated isothermal amplification assay for rapid and simple detection of Erysipelothrix rhusiopathiae

Erysipelothrix rhusiopathiae is a causative agent of swine erysipelas. We developed a novel and highly specific loop-mediated isothermal amplification (LAMP) assay for sensitive and rapid detection of E. rhusiopathiae. The LAMP assay correctly detected 39 E. rhusiopathiae strains. No LAMP products were detected from 14 non-rhusiopathiae Erysipelothrix and 16 non-Erysipelothrix strains, including E. tonsillarum serovar 10 strains, which are difficult to be discriminated from E. rhusiopathiae strains. These results were consistent with those obtained by a conventional E. rhusiopathiae-specific PCR assay. Starting with DNA extraction from a single colony, the gel-based PCR assay took 4 h to provide a result, but the LAMP assay was faster, requiring only 37-80 min. The conventional culture test required more than 3-4 days to isolate and identify E. rhusiopathiae in the enrichment cultures. In contrast, the LAMP assay required less than 22 h from the beginning of the enrichment culture to final determination. These results suggest that the LAMP assay is useful as an adjunct to facilitate early diagnosis of swine erysipelas.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of a loop-mediated isothermal amplification (LAMP) assay for simple and cost-effective detection of E. rhusiopathiae from swine samples. The LAMP assay provided more rapid detection of the bacterium than conventional PCR and biochemical-based assays, and it may potentially facilitate surveillance and early diagnosis of swine erysipelas in the field.

Improving ante mortem diagnosis of Erysipelothrix rhusiopathiae infection by use of oral fluids for bacterial, nucleic acid, and antibody detection

Swine erysipelas is an economically important disease caused by Erysipelothrix rhusiopathiae. Pen-based collection of oral fluids has recently been utilized for monitoring infection dynamics in swine operations. The diagnostic performance of bacterial isolation, real-time PCR, and antibody detection by enzyme-linked immunosorbent assay (ELISA) and fluorescent microbead-based immunoassay (FMIA) methods were evaluated on pen-based oral fluid samples from pigs experimentally infected with E. rhusiopathiae (n=112) and from negative controls (n=32). While real-time PCR was a sensitive method with an overall detection rate of 100% (7/7 pens) one day post inoculation (dpi), E. rhusiopathiae was successfully isolated in only 28.6% (2/7 pens). Anti-Erysipelothrix IgM and IgG antibodies in pen-based oral fluids were detected at 4 to 5 dpi by FMIA and at 5 and 8 dpi by ELISA. The number of infected animals per pen, and in particular the timing of antimicrobial treatment administration impacted bacterial isolation and ELISA results. In oral fluid field samples, E. rhusiopathiae DNA was found in 23.3% of the samples while anti-E. rhusiopathiae IgG and IgM antibodies were found in 59.6% and 5.5% of the samples, respectively. The results suggest that an algorithm integrating oral fluids as specimen and real-time PCR and FMIA as detection methods is effective for earlier detection of an erysipelas outbreak thereby allowing for a more effective treatment outcome.

Erysipelothrix rhusiopathiae isolates recovered from fish, a harbour seal (Phoca vitulina) and the marine environment are capable of inducing characteristic cutaneous lesions in pigs

In order to determine the diversity and pathogenicity of Erysipelothrix spp. isolates recovered from marine fish, a harbour seal (Phoca vitulina) and the marine environment, 14 isolates were characterized by genotyping, serotyping, determination of the surface protective antigen (spa) gene type and assessment of virulence in a pig bioassay. All 14 isolates were Erysipelothrix rhusiopathiae. Isolates were determined to be of serotypes 2 (n = 3), 3 (n = 1), 4 (n = 1), 12 (n = 1), 15 (n = 1) or 21 (n = 6), and one isolate cross-reacted with serotypes 5 and 21. The spa gene analysis determined that 64.3% (n = 9) were spaA and 35.7% (n = 5) were spaB1. In pigs, 10/14 isolates induced small plaques to diamond-shaped cutaneous lesions consistent with Erysipelothrix spp. infection. The results of this study indicate that the marine E. rhusiopathiae isolates have greater genetic and antigenic diversity than pig isolates and are capable of inducing classical skin lesions in pigs.

Rickets

Rickets can be attributed to nutritional, genetic, hormonal, or toxic disturbances and is classified as a metabolic bone disease. Rickets is most often associated with inappropriate dietary levels of calcium, phosphorus, and/or vitamin D. During a 27-month period (January 2010 through March 2012), the Iowa State University Veterinary Diagnostic Laboratory investigated causes of sudden, unexpected death and lameness in growing pigs throughout the Midwestern United States. Clinical observations from 17 growing pig cases included weakness, lameness, reluctance to move, muscle fasciculations and/or tremors, tetany, and death. Ribs were weak, soft, and bent prior to breaking; rachitic lesions were apparent at costochondral junctions in multiple cases. Acute and/or chronic bone fractures were also noted in multiple bones. Failure of endochondral ossification, expanded physes, infractions, thin trabeculae, and increased osteoclasts were noted microscopically. Decreased bone ash and serum 25(OH)D3, combined with clinical and microscopic evaluation, confirmed a diagnosis of vitamin D–dependent rickets in all cases. In 3 cases, disease was linked to a specific nutrient supplier that ultimately resulted in a voluntary feed recall; however, most cases in the current investigation were not associated with a particular feed company. The present report describes vitamin D–associated rickets and its importance as a potential cause of weakness, lameness, muscle fasciculations, recumbency or sudden unexpected death in swine, and describes appropriate samples and tests for disease diagnosis.

Development and evaluation of an enzyme-linked immunosorbent assay based on a recombinant SpaA protein (rSpaA415) for detection of anti-Erysipelothrix spp. IgG antibodies in pigs

The aim of this study was to develop an enzyme-linked immunosorbent assay (ELISA) for detection of anti-Erysipelothrix spp. IgG in pig sera by utilizing recombinant polypeptide SpaA415 (rSpaA415) based on surface protective antigen (Spa) A (SpaA) of Erysipelothrix spp. The sensitivity of the rSpaA415 ELISA was evaluated on sera from pigs experimentally infected with E. rhusiopathiae serotype 1a (n=72), serotype 19 (n=12), or experimentally vaccinated with a commercial attenuated-live vaccine based on serotype 1a (n=12), a commercial bacterin based on serotype 2 (n=12), or an experimental bacterin based on serotype 2 (n=300). Specificity was tested using 221 negative control samples. The earliest antibody response was detected at 7 days post-inoculation (dpi) and 14 days post-vaccination (dpv). At the cutoff of 0.9 sample optical density, the sensitivity was 96.5% and the specificity was 100%. In experimentally infected pigs, the sensitivity of the rSpaA415 ELISA ranged from 5.5 to 100% which improved as dpi increased. Antimicrobial treatment, administered prior to appearance of clinical signs, decreased assay sensitivity. In vaccinated pigs, the rSpaA415 ELISA had a sensitivity of 48.3-100%. Serum samples from rabbits each hyperimmunized with one of the 28 Erysipelothrix spp. serotypes were used to determine cross-reactivity with strains expressing SpaB, SpaC or no currently recognized Spa protein and antibodies against E. tonsillarum were not detected. These data suggest that the novel rSpaA415 ELISA test is a useful tool to detect anti-IgG antibodies against different serotypes of E. rhusiopathiae in infected or vaccinated pigs without cross-reacting with the economically less important E. tonsillarum strains.

Outbreak of Mortality in Psittacine Birds in a Mixed-Species Aviary Associated With Erysipelothrix rhusiopathiae Infection

Erysipelothrix rhusiopathiae septicemia, associated with an increased mortality of captive psittacines in a mixed-species aviary, was diagnosed by histopathology, Gram staining, bacterial culture and sequencing, immunohistochemistry, and real-time polymerase chain reaction (PCR). Over a period of 23 days with no premonitory signs, 2 rainbow lorikeets and an eclectus parrot died. Of these birds, one lorikeet and the eclectus were submitted for necropsy. The main pathologic findings were thrombosis (2/2), bacterial embolism/thromboembolism (2/2), necrotizing hepatitis (2/2), necrohemorrhagic myocarditis (1/2), fibrinohemorrhagic and heterophilic visceral coelomitis (1/2), submandibular necrosuppurative dermatitis with necrotizing vasculitis and bacterial and fungal thromboembolism (1/2), and locally extensive rhabdomyonecrosis with bacterial embolism (1/2). Intralesional bacteria were positive by Gram staining and immunohistochemistry in both cases. E. rhusiopathiae was isolated by routine bacterial culture from the liver of the lorikeet, which was also positive by real-time PCR. This report is one of the rare descriptions of erysipelas in psittacines, and to the authors’ knowledge, it appears to be the first in the described species using immunohistochemistry and real-time PCR on avian paraffin-embedded tissues for the diagnosis.

Erysipelothrix Spp. Genotypes, Serotypes, and Surface Protective Antigen Types Associated with Abattoir Condemnations

The objective of the current study was to investigate characteristics of Erysipelothrix spp. from slaughter condemnations. Specimens from 70 carcasses with lesions suspect for swine erysipelas were collected at an abattoir in Iowa from October 2007 to February 2009. Erysipelothrix spp. were isolated from 59 of 70 carcasses (84.3%). Abattoir inspectors classified lesions as acute, subacute, or chronic; 8 of 8 (100%) were acute cases, 31 of 32 (96.9%) were subacute cases, and 20 of 30 (66.6%) were chronic cases that were isolation positive. The following serotypes were identified: 1a (40.7%; 24/59), 2 (49.2%; 29/59), 7 (1/59), 10 (1/59), 11 (1/59), and untypeable (5.1%; 3/59). Serotypes 1a and 2 were identified in pigs with acute, subacute, or chronic clinical manifestations, whereas serotypes 7, 10, and 11 were only present in chronic cases. Fifty-seven of the 59 isolates were determined to belong to E. rhusiopathiae, and 2 of 59 of the isolates were determined to be E. tonsillarum by multiplex real-time polymerase chain reaction. Surface protective antigen (spa) A was detected in all E. rhusiopathiae isolates but not in E. tonsillarum serotypes 7 and 10. The results of the present study indicate that E. rhusiopathiae serotypes 1a and 2 continue to be commonly isolated from condemned pig carcasses and that spaA is the exclusive spa type in U.S. abattoir isolates. Interestingly, E. tonsillarum, thought to be avirulent for swine, was isolated from systemic sites from 3.4% of the carcasses that were negative for E. rhusiopathiae, indicating the potential importance of this genotype in erysipelas pathogenesis.

Genotyping of Brazilian Erysipelothrix spp. strains by amplified fragment length polymorphism

One hundred and fifty-one Erysipelothrix spp. isolates from diseased and carrier swine from Brazil were identified by PCR, submitted to serotyping and analyzed by amplified fragment length polymorphism with a single enzyme (AFLP). Reference strains from Australia and the United Kingdom were also examined. The 151 strains were classified into 18 different serotypes (1a, 1b, 2a, 2b, 4, 5, 6, 7, 8, 10, 11, 12, 15, 17, 19, 21, 24 and 25), being serotype 2b the most frequent (39.7%). By associating serotyping and PCR results, it was possible to identify 146 strains as E. rhusiopathiae and five strains as E. tonsillarum. Despite the fact that for this genus AFLP did not cluster all isolates according to serotype, origin, disease or isolation data, the execution of the technique was easy and fast, demonstrating high discriminatory power. The results produced by the AFLP analysis of Erysipelothrix spp. could also support its use as a discriminatory tool for E. rhusiopathiae and E. tonsillarum species.

Identification of surface protective antigen (spa) types in Erysipelothrix reference strains and diagnostic samples by spa multiplex real-time and conventional PCR assays

AIM

To develop spa multiplex real-time and conventional PCR assays to detect and differentiate between spaA, spaB and spaC genes within Erysipelothrix spp.

METHODS AND RESULTS

For evaluation of the assays, 28 Erysipelothrix spp. reference strains, 25 tissues from pigs inoculated with reference strains of serotypes 1, 2, 5, 10 or 18, and 15 diagnostic samples were used. SpaA was found to be present in Erysipelothrix rhusiopathiae serotypes 1a, 1b, 2, 5, 9, 12, 15, 16, 17, 23 and N; spaB was detected in E. rhusiopathiae serotypes 4, 6, 8, 11, 19 and 21 and spaC was detected in E. sp. strain 2 serotype 18. Spa-related genes were not detected in E. tonsillarum strains (serotypes 3, 7, 10, 14, 20, 22, 24, 25, 26) or E. sp. strain 1 (serotype 13). With the spa multiplex real-time PCR assay, it was also possible to further differentiate spaB into spaB1 (serotypes 4, 6, 8, 19 and 21) and spaB2 (serotype 11). Overall, spaA was detected in seven experimental tissue samples and six diagnostic tissue samples, and spaC in two experimental tissue samples. The detection limits were determined to be five colony-forming units (CFU) per reaction for the spa multiplex real-time PCR assay and 4000 CFU per reaction for the conventional PCR assay.

CONCLUSIONS

Both spa PCR assays were specific and reproducible in the identification of spa types in Erysipelothrix spp.

SIGNIFICANCE AND IMPACT OF THE STUDY

The described spa PCR assays may be useful tools for investigating spa prevalence among strains isolated from field tissues and to determine the role of the Spa proteins in vaccine protection and pathogenesis.

Characterization of Erysipelothrix species isolates from clinically affected pigs, environmental samples, and vaccine strains from six recent swine erysipelas outbreaks in the United States

The aim of this study was to characterize Erysipelothrix sp. isolates from clinically affected pigs and their environment and compare them to the Erysipelothrix sp. vaccines used at the sites. Samples were collected during swine erysipelas outbreaks in vaccinated pigs in six Midwest United States swine operations from 2007 to 2009. Pig tissue samples were collected from 1 to 3 pigs from each site. Environmental samples (manure, feed, central-line water, oral fluids, and swabs collected from walls, feed lines, air inlets, exhaust fans, and nipple drinkers) and live vaccine samples were collected following the isolation of Erysipelothrix spp. from clinically affected pigs. All Erysipelothrix sp. isolates obtained were further characterized by serotyping. Selected isolates were further characterized by PCR assays for genotype (E. rhusiopathiae, E. tonsillarum, Erysipelothrix sp. strain 1, and Erysipelothrix sp. strain 2) and surface protective antigen (spa) type (A, B1, B2, and C). All 26 isolates obtained from affected pigs were E. rhusiopathiae, specifically, serotypes 1a, 1b, 2, and 21. From environmental samples, 56 isolates were obtained and 52/56 were E. rhusiopathiae (serotypes 1a, 1b, 2, 6, 9, 12, and 21), 3/56 were Erysipelothrix sp. strain 1 (serotypes 13 and untypeable), and one was a novel species designated Erysipelothrix sp. strain 3 (serotype untypeable). Four of six vaccines used at the sites were commercially available products and contained live E. rhusiopathiae serotype 1a. Of the remaining two vaccines, one was an autogenous live vaccine and contained live E. rhusiopathiae serotype 2 and one was a commercially produced inactivated vaccine and was described by the manufacturer to contain serotype 2 antigen. All E. rhusiopathiae isolates were positive for spaA. All Erysipelothrix sp. strain 1 isolates and the novel Erysipelothrix sp. strain 3 isolate were negative for all currently known spa types (A, B1, B2, and C). These results indicate that Erysipelothrix spp. can be isolated from the environment of clinically affected pigs; however, the identified serotypes in pigs differ from those in the environment at the selected sites. At one of the six affected sites, the vaccine strain and the isolates from clinically affected pigs were of homologous serotype; however, vaccinal and clinical isolates were of heterologous serotype at the remaining five sites, suggesting that reevaluation of vaccine efficacy using recent field strains may be warranted.