Characterization of Actinobacillus pleuropneumoniae biovar 2 isolates reportedly reacted with the serovar 4 antiserum, and development of a multiplex PCR for O-antigen typing.

We have analyzed the capsule (CPS) and the lipopolysaccharide O-Antigen (O-Ag) biosynthesis loci of twelve Spanish field isolates of Actinobacillus pleuropneumoniae biovar 2, eleven of them previously typed serologically as serovar 4 and one non-typable (NT) (Maldonado et al., 2009, 2011). These isolates have the common core genes of the type I CPS locus, sharing >98% identity with those of serovar 2. However, the former possesses the O-Ag locus as serovar 4, and the latter possesses the O-Ag locus as serovar 7. The main difference found between the CPS loci of the 11 isolates and that of serovar 2 reference strain S1536 are two deletions, one of an 8 bp sequence upstream of the coding sequence and one of 111 bp sequence at the 5' end of the cps2G gene. The deletion mutations mentioned lead to a defect in the production of CPS in these isolates, which contributed to their previous mis-identification. In order to complement the serotyping of A. pleuropneumoniae in diagnostics and epidemiology, we have developed a multiplex PCR for the comprehensive O-Ag typing of all A. pleuropneumoniae isolates.

Pulmonary lesions with asteroid bodies in a pig experimentally infected with Actinobacillus pleuropneumoniae serovar 15.

Five pigs experimentally infected with Actinobacillus pleuropneumoniae serovar 15 isolated in our previous study were pathologically examined. One pig died at 2 days post inoculation (dpi) and four pigs were euthanized at 7 dpi. Autopsy revealed fibrinohemorrhagic pleuropneumonia in all pigs. Histopathologically, the lesions were characterized by extensive hemorrhage and necrosis, fibrin deposition, and multifocal abscesses composed of numerous neutrophils including oat cells and numerous Gram-negative bacilli. In one survived pig, asteroid body formation was confirmed in the lung. The bacteria within the abscesses and asteroid bodies were immunohistochemically positive for antiserum raised against A. pleuropneumoniae serovar 15. This is the first report describing porcine pleuropneumonia with asteroid bodies in a pig experimentally infected with A. pleuropneumoniae serovar 15.

Characterization of nonencapsulated Actinobacillus pleuropneumoniae serovar K12:O3 isolates.

Three Actinobacillus pleuropneumoniae isolates from clinical cases of porcine pleuropneumonia were positive by capsular serovar 12-specific PCR assay, but not reactive to antiserum prepared against serovar 12 using the rapid slide agglutination (RSA) test. The isolates were positive for apxIICA, apxIIICA, apxIBD, apxIIIBD, and apxIVA in the PCR toxin gene assay, which is the profile seen in serovars 2, 4, 6, 8, and 15, and reacted with antisera against serovars 3, 6, 8, 15, and 17. Nucleotide sequence analysis revealed that genes involved in the biosynthesis of capsular polysaccharide of the 3 isolates were identical or nearly identical to those of serovar 12. However, genes involved in the biosynthesis of O-polysaccharide of the 3 isolates were highly similar to those of reference strains of serovars 3, 6, 8, 15, 17, and 19. In agreement with results from the RSA test, transmission electron microscopic analysis confirmed the absence of detectable capsular material in the 3 isolates. The existence of nonencapsulated A. pleuropneumoniae serovar K12:O3 would hamper precise serodetection.

Characterization of an atypical Actinobacillus pleuropneumoniae serovar 2 isolate with a rough-type lipopolysaccharide.

We describe phenotypic and genetic characterization of an atypical Japanese Actinobacillus pleuropneumoniae isolate OT761. Nucleotide sequence analysis revealed that gene clusters involved in capsular polysaccharide and O-polysaccharide (O-PS) biosynthesis of the isolate were nearly identical to those of serovar 2 reference strain. The main difference found between the O-PS loci is the shortening of 31 amino acids from the C terminus of WcaJ in the atypical isolate due to a 93 bp deletion at the 3' end of wcaJ gene. Immunoblot analysis revealed that this isolate could not produce O-PS. Taken together, our results showed that the C-terminal domain of the A. pleuropneumoniae WcaJ plays a critical role in enzyme function of WcaJ involved in the biosynthesis of O-PS.

Proposal of a subtype of serovar 4, K4b:O3, of Actinobacillus pleuropneumoniae based on serological and genotypic analysis.

The aim of this study was to investigate an isolate of Actinobacillus pleuropneumoniae, named 14-760, which was serologically not classifiable among the recognised serovars of A. pleuropneumoniae. It reacted with the antisera raised against serovars 3, 6, 8, 15 and 17 in the agar gel precipitation (AGP) test, and was positive in the capsular serovar 4-specific PCR (cps4B PCR) assay. The isolate contains a type II capsule locus similar to serovar 4 but with variations in the length of four intergeneric regions (modF-cpxA, cpxD-cpsA, cpsC-a 114 bp orf, and lysA-ydeN), and three gene sequences (modF, cpsC and ydeN). The main difference found between the K4 and K4b cps genes is the additional 35 AAs found in type 4b due to a 4 bp insert in cps4bC. The LPS O-Ag locus is highly similar to that of reference strains of serovars 3, 6, 8, 15, 17 and 19. Isolate 14-760 is biovar 1 and contains solely the structural genes required for toxin ApxII production (apxIICA), and the type I secretion system (apxIBD) for the export of ApxII. Antiserum against isolate 14-760 adsorbed with antigen prepared from serovars 8, 15 or 17 reference strains remained reactive with isolate 14-760, but not with antigens prepared from serovars 1-18. Taken together, our results indicate the existence of a subtype of A. pleuropneumoniae, serovar 4, that we called "K4b:O3″, and we propose isolate 14-760 as the reference strain.

Serovars and SpaA Types of Erysipelothrix rhusiopathiae Isolated from Pigs in Japan from 2012 to 2019.

Erysipelothrix rhusiopathiae causes swine erysipelas (SE), which results in considerable economic loss on pig farms. During SE outbreaks that occurred sporadically from 2008 to 2011 in Japan, new E. rhusiopathiae strains were isolated with a specific surface protective antigen (Spa)A protein characterized by methionine at position 203 and isoleucine at position 257 (M203/I257 SpaA type). To determine whether strains with the M203/I257 SpaA type are still prevalent in Japan, we collected 79 strains of E. rhusiopathiae from pigs showing various SE symptoms from 2012 to 2019 and classified them based on serovar typing, spaA gene sequence analysis, and lineage typing. We found that the majority of recent E. rhusiopathiae strains (59/79) belonged to the serovar 1a strain, and that the M203/I257 SpaA type (56/59) was predominant continuing from 2008 to 2011. Furthermore, serovar 1a strains with IVb-1 and IVb-2 lineages that had been isolated in specific regions of Japan were no longer local but were found across Japan. The pathogenicity of recent isolates tested in mice was not significantly changed when compared to that of previously isolated strains. Our results suggest that recent SE outbreaks were not due to changes in the SpaA protein or to altered virulence of E. rhusiopathiae but were rather caused by the persistent presence of E. rhusiopathiae with the M203/I257 SpaA type.

Characterization of nontypeable Actinobacillus pleuropneumoniae isolates.

Two Actinobacillus pleuropneumoniae isolates from clinical cases of porcine pleuropneumonia in Japan were positive in the capsular serovar 15-specific PCR assay, but nontypeable (NT) in the agar gel precipitation (AGP) test. Nucleotide sequence analysis of gene clusters involved in the biosynthesis of capsular polysaccharide (CPS) and lipopolysaccharide O-polysaccharide (O-PS) revealed that both clusters contained transposable element ISApl1 of A. pleuropneumoniae belonging to the IS30 family. Immunoblot analysis revealed that these 2 isolates could not produce O-PS. We conclude that the ISApl1 of A. pleuropneumoniae can interfere in the biosynthesis of both CPS and O-PS.

Isolation and characterization of atypical Actinobacillus pleuropneumoniae serovar 15 lacking the apxIICA genes in Japan.

Six atypical Actinobacillus pleuropneumoniae serovar 15 strains were isolated from pneumonic lesions of naturally infected dead pigs from the same farm in Japan. Genetic analyses of apx genes revealed that the atypical isolates contained the toxin-associated genes apxIBD, apxIIICA, apxIIIBD, and apxIVA, but not apxIICA. Coinciding with the result of the atypical gene profile, analyses of toxin protein production revealed that these atypical isolates expressed only ApxIII but not ApxII. A mouse pathogenicity test showed that the atypical isolate tested seemed to be less virulent than the typical isolates. This is the first report describing the emergence of atypical A. pleuropneumoniae serovar 15, which does not produce ApxII due to the absence of apxIICA genes, in Japan.

Pattern to Knowledge: Deep Knowledge-Directed Machine Learning for Residue-Residue Interaction Prediction.

Residue-residue close contact (R2R-C) data procured from three-dimensional protein-protein interaction (PPI) experiments is currently used for predicting residue-residue interaction (R2R-I) in PPI. However, due to complex physiochemical environments, R2R-I incidences, facilitated by multiple factors, are usually entangled in the source environment and masked in the acquired data. Here we present a novel method, P2K (Pattern to Knowledge), to disentangle R2R-I patterns and render much succinct discriminative information expressed in different specific R2R-I statistical/functional spaces. Since such knowledge is not visible in the data acquired, we refer to it as deep knowledge. Leveraging the deep knowledge discovered to construct machine learning models for sequence-based R2R-I prediction, without trial-and-error combination of the features over external knowledge of sequences, our R2R-I predictor was validated for its effectiveness under stringent leave-one-complex-out-alone cross-validation in a benchmark dataset, and was surprisingly demonstrated to perform better than an existing sequence-based R2R-I predictor by 28% (p: 1.9E-08). P2K is accessible via our web server on https://p2k.uwaterloo.ca .

Characterization of Actinobacillus pleuropneumoniae field strains antigenically related to the 3-6-8-15 group from diseased pigs in Japan and Argentina.

The objectives of this study were to determine the serovar of a collection of Actinobacillus pleuropneumoniae strains within the 3-6-8-15 cross-reacting group and to analyze their phenotypic and genetic properties. Based on the serological tests, forty-seven field strains of Actinobacillus pleuropneumoniae isolated from lungs with pleuropneumonia lesions in Japan and Argentina were found to be serovars belonging to the 3-6-8-15 cross-reacting group. By using a capsule loci-based PCR, twenty-nine (96.7%) and one (3.3%) from Japan were identified as serovars 15 and 8, respectively, whereas seventeen (100%) from Argentina were identified as serovar 8. The findings suggested that serovars 8 and 15 were prevalent within the 3-6-8-15 cross-reacting group, in Argentina and Japan, respectively. Phenotypic analyses revealed that the protein patterns observed on SDS-PAGE and the lipopolysaccharide antigen detected by immunoblotting of the reference and field strains of serovars 8 and 15 were similar to each other. Genetic (16S rDNA, apxIIA, apxIIIA, cps, cpx genes, apx and omlA patterns) analyses revealed that the apxIIA and apxIIIA genes of the field strains of serovars 8 and 15 were similar to those of the reference strains of serovars 3, 4, 6, 8 and 15. The results obtained in the present study may be useful for the development of more effective vaccines against disease caused by A. pleuropneumoniae by including the homologous antigens to the most prevalent serovars in specific geographical areas.

Application of an enzyme-linked immunosorbent assay for detection of antibodies to Actinobacillus pleuropneumoniae serovar 15 in pig sera.

An indirect enzyme-linked immunosorbent assay (ELISA) using lipopolysaccharide extract as antigen was evaluated for detection of antibodies to Actinobacillus pleuropneumoniae serovar 15. The serovar 15 ELISA had a higher sensitivity and specificity than latex agglutination test for 63 and 80 sera from pigs experimentally infected and not infected with A. pleuropneumoniae, respectively. When the serovar 15 ELISA was applied to 454 field sera, high rates of seropositivity were found in pigs from farms infected with A. pleuropneumoniae serovar 15, but not in those from farms free of A. pleuropneumoniae serovar 15. The results suggest that the serovar 15 ELISA may be useful for the serological surveillance of infection with A. pleuropneumoniae serovar 15.

Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering.

Understanding binding cores is of fundamental importance in deciphering Protein-DNA (TF-TFBS) binding and gene regulation. Limited by expensive experiments, it is promising to discover them with variations directly from sequence data. Although existing computational methods have produced satisfactory results, they are one-to-one mappings with no site-specific information on residue/nucleotide variations, where these variations in binding cores may impact binding specificity. This study presents a new representation for modeling binding cores by incorporating variations and an algorithm to discover them from only sequence data. Our algorithm takes protein and DNA sequences from TRANSFAC (a Protein-DNA Binding Database) as input; discovers from both sets of sequences conserved regions in Aligned Pattern Clusters (APCs); associates them as Protein-DNA Co-Occurring APCs; ranks the Protein-DNA Co-Occurring APCs according to their co-occurrence, and among the top ones, finds three-dimensional structures to support each binding core candidate. If successful, candidates are verified as binding cores. Otherwise, homology modeling is applied to their close matches in PDB to attain new chemically feasible binding cores. Our algorithm obtains binding cores with higher precision and much faster runtime ( ≥ 1,600x) than that of its contemporaries, discovering candidates that do not co-occur as one-to-one associated patterns in the raw data. AVAILABILITY: http://www.pami.uwaterloo.ca/~ealee/files/tcbbPnDna2015/Release.zip.

Experimental induction of necrotic enteritis in chickens by a netB-positive Japanese isolate of Clostridium perfringens.

Necrotic enteritis (NE) is one of the most important bacterial diseases in terms of economic losses. Clostridium perfringens necrotic enteritis toxin B, NetB, was recently proposed as a new key virulent factor for the development of NE. The goal of this work was to develop a necrotic enteritis model in chickens by using a Japanese isolate of C. perfringens. The Japanese isolate has been found to contain netB gene, which had the same nucleotide and deduced amino acid sequences as those of prototype gene characterized in Australian strain EHE-NE18, and also expressed in vitro a 33-kDa protein identified as NetB toxin by nano-scale liquid chromatographic tandem mass spectrometry. In the challenge experiment, broiler chickens fed a commercial chicken starter diet for 14 days post-hatch were changed to a high protein feed mixed 50:50 with fishmeal for 6 days. At day 21 of age, feed was withheld for 24 hr, and each chicken was orally challenged twice daily with 2 ml each of C. perfringens culture (109 to 1010 CFU) on 5 consecutive days. The gross necrotic lesions were observed in 90 and 12.5% of challenged and control chickens, respectively. To our knowledge, this is the first study that demonstrated that a netB-positive Japanese isolate of C. perfringens is able to induce the clinical signs and lesions characteristic of NE in the experimental model, which may be useful for evaluating the pathogenicity of field isolates, the efficacy of a vaccine or a specific drug against NE.

Genetic and antigenic characteristics of ApxIIA and ApxIIIA from Actinobacillus pleuropneumoniae serovars 2, 3, 4, 6, 8 and 15.

Apx toxins produced by Actinobacillus pleuropneumoniae are essential components of new generation vaccines. In this study, apxIIA and apxIIIA genes of serovars 2, 3, 4, 6, 8 and 15 were cloned and sequenced. Amino acid sequences of ApxIIA proteins of serovars 2, 3, 4, 6, 8 and 15 were almost identical to those of serovars 1, 5, 7, 9 and 11-13. Immunoblot analysis showed that rApxIIA from serovars 2 and 15 reacts strongly with sera from animals infected with various serovars. Sequence analysis revealed that ApxIIIA proteins has two variants, one in strains of serovar 2 and the other in strains of serovars 3, 4, 6, 8 and 15. A mouse cross-protection study showed that mice actively immunized with rApxIIIA/2 or rApxIIIA/15 are protected against challenge with A. pleuropneumoniae strains of serovars 3, 4, 6, 8, 15, and 2 expressing ApxIII/15 and ApxIII/2, respectively. Similarly, mice passively immunized with rabbit anti-rApxIIIA/2 or anti-rApxIIIA/15 sera were found to be protected against challenge with strains of serovars 2 and 15. Our study revealed antigenic and sequence similarities within ApxIIA and ApxIIIA proteins, which may help in the development of effective vaccines against disease caused by A. pleuropneumoniae.

Discovering Binding Cores in Protein-DNA Binding Using Association Rule Mining with Statistical Measures.

Understanding binding cores is of fundamental importance in deciphering Protein-DNA (TF-TFBS) binding and for the deep understanding of gene regulation. Traditionally, binding cores are identified in resolved high-resolution 3D structures. However, it is expensive, labor-intensive and time-consuming to obtain these structures. Hence, it is promising to discover binding cores computationally on a large scale. Previous studies successfully applied association rule mining to discover binding cores from TF-TFBS binding sequence data only. Despite the successful results, there are limitations such as the use of tight support and confidence thresholds, the distortion by statistical bias in counting pattern occurrences, and the lack of a unified scheme to rank TF-TFBS associated patterns. In this study, we proposed an association rule mining algorithm incorporating statistical measures and ranking to address these limitations. Experimental results demonstrated that, even when the threshold on support was lowered to one-tenth of the value used in previous studies, a satisfactory verification ratio was consistently observed under different confidence levels. Moreover, we proposed a novel ranking scheme for TF-TFBS associated patterns based on p-values and co-support values. By comparing with other discovery approaches, the effectiveness of our algorithm was demonstrated. Eighty-four binding cores with PDB support are uniquely identified.

Discovering co-occurring patterns and their biological significance in protein families.

BACKGROUND: The large influx of biological sequences poses the importance of identifying and correlating conserved regions in homologous sequences to acquire valuable biological knowledge. These conserved regions contain statistically significant residue associations as sequence patterns. Thus, patterns from two conserved regions co-occurring frequently on the same sequences are inferred to have joint functionality. A method for finding conserved regions in protein families with frequent co-occurrence patterns is proposed. The biological significance of the discovered clusters of conserved regions with co-occurrences patterns can be validated by their three-dimensional closeness of amino acids and the biological functionality found in those regions as supported by published work. METHODS: Using existing algorithms, we discovered statistically significant amino acid associations as sequence patterns. We then aligned and clustered them into Aligned Pattern Clusters (APCs) corresponding to conserved regions with amino acid conservation and variation. When one APC frequently co-occurred with another APC, the two APCs have high co-occurrence. We then clustered APCs with high co-occurrence into what we refer to as Co-occurrence APC Clusters (Co-occurrence Clusters). RESULTS: Our results show that for Co-occurrence Clusters, the three-dimensional distance between their amino acids is closer than average amino acid distances. For the Co-occurrence Clusters of the ubiquitin and the cytochrome c families, we observed biological significance among the residing amino acids of the APCs within the same cluster. In ubiquitin, the residues are responsible for ubiquitination as well as conventional and unconventional ubiquitin-bindings. In cytochrome c, amino acids in the first co-occurrence cluster contribute to binding of other proteins in the electron transport chain, and amino acids in the second co-occurrence cluster contribute to the stability of the axial heme ligand. CONCLUSIONS: Thus, our co-occurrence clustering algorithm can efficiently find and rank conserved regions that contain patterns that frequently co-occurring on the same proteins. Co-occurring patterns are biologically significant due to their three-dimensional closeness and other evidences reported in literature. These results play an important role in drug discovery as biologists can quickly identify the target for drugs to conduct detailed preclinical studies.

Modeling associated protein-DNA pattern discovery with unified scores.

Understanding protein-DNA interactions, specifically transcription factor (TF) and transcription factor binding site (TFBS) bindings, is crucial in deciphering gene regulation. The recent associated TF-TFBS pattern discovery combines one-sided motif discovery on both the TF and the TFBS sides. Using sequences only, it identifies the short protein-DNA binding cores available only in high-resolution 3D structures. The discovered patterns lead to promising subtype and disease analysis applications. While the related studies use either association rule mining or existing TFBS annotations, none has proposed any formal unified (both-sided) model to prioritize the top verifiable associated patterns. We propose the unified scores and develop an effective pipeline for associated TF-TFBS pattern discovery. Our stringent instance-level evaluations show that the patterns with the top unified scores match with the binding cores in 3D structures considerably better than the previous works, where up to 90 percent of the top 20 scored patterns are verified. We also introduce extended verification from literature surveys, where the high unified scores correspond to even higher verification percentage. The top scored patterns are confirmed to match the known WRKY binding cores with no available 3D structures and agree well with the top binding affinities of in vivo experiments.

Characterization of Erysipelothrix rhusiopathiae strains isolated from recent swine erysipelas outbreaks in Japan.

The objective of the present study was to characterize Erysipelothrix sp. strains from recent erysipelas outbreaks in Japan. Eighty-three (100%) strains were identified as E. rhusiopathiae, based on serotyping and spaA PCR. Fifty (60.3%), 5 (6.0%), and 28 (33.7%) strains were isolated from animals with acute, subacute and chronic outbreaks, respectively, of which 79 (95.2%), 1 (1.2%), and 3 (3.6%) belonged to serotypes 1a, 2a, and untypeable, respectively. Fifteen strains (including 3, 2, and 10 from acute, subacute, and chronic cases, respectively) were sensitive to acriflavine, and showed high levels of virulence in mice; of which strains from acute cases, and from subacute and chronic cases killed 100%, and 80 to 100% mice, respectively at challenge doses of 10(2) CFU per mouse. Based on sequence analysis of a 432-bp hypervariable region in spaA gene, 83 strains could be divided into 3 groups: (i) group 1 (3 strains of serotype 1a) had Ala-195 and Ile-203; (ii) group 2 (76 strains of serotype 1a and 3 of untypeable) had Asp-195 and Met-203; and (iii) group 3 (one strain of serotype 2a) had Asn-195 and Ile-203. The results of the present study suggest that the serotype 1a strains belonging to the group 2 might be widespread in pig populations in Japan.

Single-dose time-resolved contrast enhanced hybrid MR angiography in diagnosis of peripheral arterial disease: compared with digital subtraction angiography.

PURPOSE: To prospectively study the diagnostic performance of hybrid single-dose contrast-enhanced MRA of peripheral arterial disease (PAD), with digital subtraction angiography (DSA) as the reference standard. MATERIALS AND METHODS: Hybrid MRA, combining time resolved imaging of contrast kinetics and two-station bolus-chase sequences, of lower limb was performed in 31 PAD patients (21 men, 10 women; mean age, 72 years) with two separate gadobenate dimeglumine (8 mL) injections in each sequence. Two independent blinded readers analyzed the vascular stenosis (32 segments in each limb). Sensitivity, specificity, and accuracy in all vascular segments and segments below popliteal artery were calculated. Interobserver agreements on MRA and intermodality agreements between MRA and DSA were calculated by using k statistics. RESULTS: Sensitivity, specificity, and accuracy of the hybrid MRA with regard to hemodynamically significant stenosis in all vascular segments were 92%, 97%, and 95% for reader 1, and 90%, 92%, and 92%, for reader 2, respectively. The interobsever agreements on MRA were good (k = 0.77-0.74) for all-grade stenosis, and excellent (k = 0.82-0.81) for hemadynamically significant stenosis. The intermodality agreements are good to excellent (k = 0.73-0.94). CONCLUSION: Single-dose hybrid MRA is a safe and reliable noninvasive alternative to conventional DSA in the assessment of PAD patients.

Immunization with truncated recombinant protein SpaC of Erysipelothrix rhusiopathiae strain 715 serovar 18 confers protective immunity against challenge with various serovars.

Previously, we showed that surface protective antigen (Spa) proteins of Erysipelothrix rhusiopathiae can be classified into three molecular species-SpaA, SpaB, and SpaC-and that SpaC is the most broadly cross-protective antigen among the three Spa proteins. In this study, we examined the ability of the α-helical domain, which comprises the N-terminal half of SpaC, to elicit cross-protective immunity in mice and pigs. Mice actively immunized with the full-length protein (rSpaC664) or the α-helical domain (rSpaC427), but not the C-terminal domain (rSpaC253), were protected against challenge with E. rhusiopathiae serovars 1a, 2, 6, 19, and 18 expressing heterologous (SpaA or SpaB) and homologous (SpaC) Spas. The α-helical domain seemed to provide better protection than rSpaC664, although the differences did not reach statistical significance. Similarly, mice passively immunized with rabbit anti-rSpaC664 or anti-rSpaC427 sera, but not anti-rSpaC253 serum, were protected from challenge with various serovars. Pigs immunized with SpaC427 also developed specific antibodies against Spa proteins and were protected from challenge with the highly virulent heterologous E. rhusiopathiae strain Fujisawa (serovar 1a). Taken together, these results demonstrate for the first time the striking protective efficacy of the α-helical domain-mediated immunization in both mice and pigs, thereby highlighting its utility as the most promising candidate for the development of a safe and effective vaccine against erysipelas.