Predictive Power of Long-Read Whole-Genome Sequencing for Rapid Diagnostics of Multidrug-Resistant Brachyspira hyodysenteriae Strains.

Infections with Brachyspira hyodysenteriae, the etiological agent of swine dysentery, result in major economic losses in the pig industry worldwide. Even though microbial differentiation of various Brachyspira species can be obtained via PCR, no quick diagnostics for antimicrobial susceptibility testing are in place, which is mainly due to the time-consuming (4 to 7 days) anaerobic growth requirements of these organisms. Veterinarians often rely on a clinical diagnosis for initiating antimicrobial treatment. These treatments are not always effective, which may be due to high levels of acquired resistance in B. hyodysenteriae field isolates. By using long-read-only whole-genome sequencing and a custom-trained Bonito base-calling model, 81 complete B. hyodysenteriae genomes with median Q51 scores and 99% completeness were obtained from 86 field strains. This allowed the assessment of the predictive potential of genetic markers in relation to the observed acquired resistance phenotypes obtained via agar dilution susceptibility testing. Multidrug resistance was observed in 77% and 21% of the tested strains based on epidemiological cutoff and clinical breakpoint values, respectively. The predictive power of genetic hallmarks (genes and/or gene mutations) for antimicrobial susceptibility testing was promising. Sensitivity and specificity for tiamulin [tva(A) and 50SL3N148S, 99% and 67%], valnemulin [tva(A), 97% and 92%), lincomycin (23SA2153T/G and lnuC, 94% and 100%), tylvalosin (23SA2153T/G, 99% and 93%), and doxycycline (16SG1026C, 93% and 87%) were determined. The predictive power of these genetic hallmarks is promising for use in sequencing-based workflows to speed up swine dysentery diagnostics in veterinary medicine and determine proper antimicrobial use. IMPORTANCE Diagnostics for swine dysentery rely on the identification of Brachyspira species using molecular techniques. Nevertheless, no quick diagnostic tools are available for antimicrobial susceptibility testing due to extended growth requirements (7 to 14 days). To enable practitioners to tailor antimicrobial treatment to specific strains, long-read sequencing-based methods are expected to lead to rapid methods in the future. Nevertheless, their potential implementation should be validated extensively. This mainly implies assessing sequencing accuracy and the predictive power of genetic hallmarks in relation to their observed (multi)resistance phenotypes.

Comparison of Primary Virus Isolation in Pulmonary Alveolar Macrophages and Four Different Continuous Cell Lines for Type 1 and Type 2 Porcine Reproductive and Respiratory Syndrome Virus.

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) has a highly restricted cellular tropism. In vivo, the virus primarily infects tissue-specific macrophages in the nose, lungs, tonsils, and pharyngeal lymphoid tissues. In vitro however, the MARC-145 cell line is one of the few PRRSV susceptible cell lines that are routinely used for in vitro propagation. Previously, several PRRSV non-permissive cell lines were shown to become susceptible to PRRSV infection upon expression of recombinant entry receptors (e.g., PK15Sn-CD163, PK15S10-CD163). In the present study, we examined the suitability of different cell lines as a possible replacement of primary pulmonary alveolar macrophages (PAM) cells for isolation and growth of PRRSV. The susceptibility of four different cell lines (PK15Sn-CD163, PK15S10-CD163, MARC-145, and MARC-145Sn) for the primary isolation of PRRSV from PCR positive sera (both PRRSV1 and PRRSV2) was compared with that of PAM. To find possible correlations between the cell tropism and the viral genotype, 54 field samples were sequenced, and amino acid residues potentially associated with the cell tropism were identified. Regarding the virus titers obtained with the five different cell types, PAM gave the highest mean virus titers followed by PK15Sn-CD163, PK15S10-CD163, MARC-145Sn, and MARC-145. The titers in PK15Sn-CD163 and PK15S10-CD163 cells were significantly correlated with virus titers in PAM for both PRRSV1 (p < 0.001) and PRRSV2 (p < 0.001) compared with MARC-145Sn (PRRSV1: p = 0.22 and PRRSV2: p = 0.03) and MARC-145 (PRRSV1: p = 0.04 and PRRSV2: p = 0.12). Further, a possible correlation between cell tropism and viral genotype was assessed using PRRSV whole genome sequences in a Genome-Wide-Association Study (GWAS). The structural protein residues GP2:187L and N:28R within PRRSV2 sequences were associated with their growth in MARC-145. The GP5:78I residue for PRRSV2 and the Nsp11:155F residue for PRRSV1 was linked to a higher replication on PAM. In conclusion, PK15Sn-CD163 and PK15S10-CD163 cells are phenotypically closely related to the in vivo target macrophages and are more suitable for virus isolation and titration than MARC-145/MARC-145Sn cells. The residues of PRRSV proteins that are potentially related with cell tropism will be further investigated in the future.

Purchasing policy, quarantine and acclimation practices of breeding gilts in Belgian pig farms.

BACKGROUND: The breeding population is very important in pig herds, for productivity, health and profitability. Replacement of breeding animals can be accomplished by own rearing of breeding gilts or by purchasing them. Purchasing breeding gilts is a hazardous event in terms of biosecurity and introduction of pathogens into a farm. However, in literature, little is known about gilt introduction in a herd. The present study investigated the introduction procedures of purchased breeding gilts in Belgian pig herds, and the compliance of these herds to the optimal introduction procedures. A questionnaire consisting of twenty questions related to farm characteristics (n = 2), purchasing policy (n = 6), quarantine period (n = 5), and acclimation practices (n = 7) was designed, and 68 farms completed the questionnaire during an on-farm interview. RESULTS: The median (min. - max.) number of sows on the farms was 300 (85-2500). Fifty-seven per cent of the farms purchased breeding gilts, and there was a lot of variation in the frequency of purchase and the age at which gilts are purchased. On 95 % of those farms, a quarantine unit was used, and on most of these farms the quarantine was located on the farm itself (internal quarantine). The median (min. - max.) duration of the quarantine period was 42 (14-140) days. The most common acclimation practice was vaccination against Porcine parvovirus (96 %) and Erysipelothrix rhusiopathiae (94 %), although in some farms exposure of gilts to farm-specific micro-organisms was done by providing faeces from suckling piglets (18 %) and bringing gilts in contact with sows that will be culled (16 %). Only 10 % of the farms complied with the optimal introduction procedures, i.e. purchasing policy, quarantine building and quarantine management. CONCLUSIONS: This study showed that in many farms, practices related to purchasing, quarantine and acclimation could be improved to maintain optimal biosecurity.

New insights about vaccine effectiveness: Impact of attenuated PRRS-strain vaccination on heterologous strain transmission.

Vaccination is the main tool for controlling infectious diseases in livestock. Yet current vaccines only provide partial protection raising concerns about vaccine effectiveness in the field. Two successive transmission trials were performed involving 52 pigs to evaluate the effectiveness of a Porcine Reproductive and Respiratory Syndrome (PRRS) vaccinal strain candidate against horizontal transmission of a virulent heterologous strain. PRRS virus, above the specified limit of detection, was observed in serum and nasal secretions for all but one pig (the exception only tested positive for serum), indicating that vaccination did not protect pigs from becoming infected and shedding the heterologous strain. However, vaccination delayed the onset of viraemia, reduced the duration of shedding and significantly decreased viral load throughout infection. Serum antibody profiles indicated that 4 out of 13 (31%) vaccinates in one trial had no serological response (NSR). A Bayesian epidemiological model was fitted to the data to assess the impact of vaccination and presence of NSRs on PRRS virus transmission dynamics. Despite little evidence for reduction in the transmission rate, vaccinated animals were on average slower to become infectious, experienced a shorter infectious period and recovered faster. The overall PRRSV transmission potential, represented by the reproductive ratio R0 was lower for the vaccinated animals, although there was substantial overlap in the credibility intervals for both groups. Model selection suggests that transmission parameters of vaccinated pigs with NSR were more similar to those of unvaccinated animals. The presence of NSRs in a population, however, seemed to only marginally affect the transmission dynamics. The results suggest that even when vaccination can't prevent infection, it can still have beneficial impacts on the transmission dynamics and contribute to reducing a herd's R0. However, biosecurity and other measures need to be considered to decrease contact rates and lower R0 below 1.

Immunity raised by recent European subtype 1 PRRSV strains allows better replication of East European subtype 3 PRRSV strain Lena than that raised by an older strain.

Stable spatial distribution of porcine reproductive and respiratory syndrome (PRRSV)-1 subtypes in Europe is accompanied by a strong population immunity induced by local PRRSV strains. In the present study, it was examined if the immunity induced by three West European subtype 1 PRRSV strains (2007 isolate 07V063 and 2013 isolates 13V091 and 13V117) offers protection against the highly virulent East European subtype 3 PRRSV strain Lena. The number of fever days was greater (p < 0.05) in the control group (7.6 ± 1.7 days) compared to the immune groups (07V063-immune: 4.0 ± 1.2 days, 13V091-immune: 4.6 ± 1.1 days, 13V117-immune: 4.0 ± 2.9 days). In all groups, protection was characterized by reduction (p < 0.05) of AUC values of nasal shedding (control: 14.6, 07V063-immune: 3.4, 13V091-immune: 8.9, 13V117-immune: 8.0) and viremia (control: 28.1, 07V063-immune: 5.4, 13V091-immune: 9.0, 13V117-immune: 8.3). Reduction of respiratory disease, nasal shedding (mean AUC and mean peak values) and viremia (mean AUC and mean peak values) was more pronounced in 07V063-immune (p < 0.05) than in 13V091-immune and 13V117-immune animals. Inoculation with subtype 1 PRRSV strains caused priming of the Lena-specific virus neutralization antibody response. Upon challenge with Lena, we observed a very strong serological booster effect for neutralizing antibodies against strains used for the first inoculation. Our results indicate that inoculation with subtype 1 PRRSV strains can partially protect against antigenically divergent subtype 3 strains. The lower protection level elicited by recently isolated subtype 1 PRRSV strains may impair the outcome of the spatial expansion of subtype 3 strains from East Europe to West Europe.

Modified-live PRRSV subtype 1 vaccine UNISTRAIN® PRRS provides a partial clinical and virological protection upon challenge with East European subtype 3 PRRSV strain Lena.

BACKGROUND: Western European porcine reproductive and respiratory syndrome virus (PRRSV) strains cause limited and mild clinical signs whereas more virulent strains are circulating in Eastern Europe. The emergence of such highly virulent strains in Western Europe might result in severe clinical problems and a financial disaster. In this context, the efficacy of the commercial modified-live PRRSV subtype 1 vaccine UNISTRAIN® PRRS was tested upon challenge with the East European subtype 3 PRRSV strain Lena. RESULTS: The mean duration of fever was shortened and the number of fever days was significantly lower in vaccinated pigs than in control pigs. Moreover, a lower number of vaccinated animals showed fever, respiratory disorders and conjunctivitis. The mean virus titers in the nasal secretions post challenge (AUC) were significantly lower in the vaccinated group than in the control group. The duration of viremia was slightly shorter (not significantly different) in the vaccinated group as compared to the control group. CONCLUSIONS: Vaccination of pigs with the modified-live vaccine UNISTRAIN® PRRS provides a partial clinical and virological protection against the PRRSV subtype 3 strain Lena.

Different clinical, virological, serological and tissue tropism outcomes of two new and one old Belgian type 1 subtype 1 porcine reproductive and respiratory virus (PRRSV) isolates.

In this study, the pathogenic behavior of PRRSV 13V091 and 13V117, isolated in 2013 from two different Belgian farms with enzootic respiratory problems shortly after weaning in the nursery, were compared with the Belgian strain 07V063 isolated in 2007. Full-length genome sequencing was performed to identify their origin. Twelve weeks-old pigs were inoculated intranasally (IN) with 13V091, 13V117 or 07V063 (9 pigs/group). At 10 days post inoculation (dpi), 4 animals from each group were euthanized and tissues were collected for pathology, virological and serological analysis. 13V091 infection resulted in the highest respiratory disease scores and longest period of fever. Gross lung lesions were more pronounced for 13V091 (13%), than for 13V117 (7%) and 07V063 (11%). The nasal shedding and viremia was also most extensive with 13V091. The 13V091 group showed the highest virus replication in conchae, tonsils and retropharyngeal lymph nodes. 13V117 infection resulted in the lowest virus replication in lymphoid tissues. 13V091 showed higher numbers of sialoadhesin(-) infected cells/mm(2) in conchae, tonsils and spleen than 13V117 and 07V063. Neutralizing antibody response with 07V063 was stronger than with 13V091 and 13V117. It can be concluded that (i) 13V091 is a highly pathogenic type 1 subtype 1 PRRSV strain that replicates better than 07V063 and 13V117 and has a strong tropism for sialoadhesin(-) cells and (ii) despite the close genetic relationship between 13V117 and 07V063, 13V117 has an increased nasal replication and shedding, but a decreased replication in lymphoid tissues compared to 07V063.

Efficacy of an attenuated European subtype 1 porcine reproductive and respiratory syndrome virus (PRRSV) vaccine in pigs upon challenge with the East European subtype 3 PRRSV strain Lena.

The efficacy of a commercial attenuated European subtype 1 PRRSV vaccine was evaluated upon challenge with the East European subtype 3 PRRSV strain Lena (83.3% nucleotide identity). Two vaccination experiments were carried out. Four- and seven-week-old pigs were vaccinated with the modified-live vaccine. Upon vaccination, virus specific IPMA antibodies were detected in all vaccinated animals with titers ranging from 10(2.8) to 10(4.6). No virus neutralizing (VN) antibodies were detected after vaccination. Eight (exp. 1) or six (exp. 2) weeks after vaccination, pigs were challenged with 10(6) (exp. 1) resp. 10(5) (exp. 2) TCID50 of the European subtype 3 PRRSV Lena. Upon challenge, non-vaccinated animals showed fever during 5.1 (exp. 1) or 7.7 (exp. 2) days. In vaccinated pigs, the duration of fever was reduced by 1.8 (exp. 1) or 3.5 (exp. 2) days. The modified-live virus vaccine reduced the mean duration of nasal shedding and viremia. In non-vaccinated pigs, virus shedding lasted 5.8 days (exp. 1), resp. 8.3 days (exp. 2). This period was reduced to 3.6 (exp. 1), resp. 3.0 (exp. 2) days in vaccinated animals. Viremia was observed during a shorter period in vaccinated (exp. 1: 7.4 days, exp. 2: 4.8 days) than in non-vaccinated groups (exp. 1: 11.8 days, exp. 2: 12.3 days). Starting from 5 days post challenge, virus titers in nasal secretions and sera were significantly lower in vaccinated animals (P<0.05). Virus-neutralizing antibodies were detected at low titers (≤ 16) after 7 days post challenge in vaccinated animals and 28 days post challenge in control animals. In conclusion, it can be stated that vaccination of pigs with an attenuated European subtype 1 vaccine provides a partial protection against a subsequent exposure to the highly pathogenic East European subtype 3 PRRSV strain Lena.