Disease-associated Streptococcus suis (DASS) is one of the most impacting bacterial diseases in swine worldwide. A key aspect to the control and prevention of DASS in swine farms hinges upon accurate detection of the disease-causing strains within the herd. This can be challenging due to its commensal nature, variability of on farm sampling methodologies, and lack of feasible diagnostic methods that predict virulence with high sensitivity. Developing improved sampling and testing methodologies allow veterinarians and producers to improve S. suis surveillance programs and make timely adjustments to prevention programs. Recent data indicates that identification of DASS carriers using culture and colony-based testing may result in underestimation of carriage because of co-colonization of the same pigs with multiple strains of S. suis. In addition, although serotyping methods and PCR-based tests are available, these tools are useful only for characterizing isolates obtained by culture and are less useful in surveillance programs at the population level. Therefore, novel diagnostic strategies are needed to understand the infection dynamics of virulent strains and the value of potential interventions. Understanding the infection dynamics of key agents that drive antimicrobial use in swine farms is paramount, and there is limited data on the infection dynamics of DASS strains in swine farms. Although it has been reported that colonization of piglets with S. suis occurs early on and is widespread, the actual colonization rate by DASS strains in sows and pigs remains primarily unknown. In this study, we implemented a novel way of tracking DASS in a prospective cohort study in two pig flows, using an informative virulence-associated marker. A sensitive and specific real time PCR was validated, optimized and used to test antemortem samples from a longitudinal study to track DASS dynamics (e.g., detects only disease associated strains), without the need to pursue bacteriological culture. All samples were also tested by a species-specific PCR (e.g. detects all strains from the species). This longitudinal study on two farms revealed tonsil scrapings and nasal swabs as the samples of choice for detection of DASS in healthy dams compared to vaginal. In fact, in one farm, nasal swabs provided the same or a better level of detection of DASS, compared to tonsil scrapings, suggesting the use of a more convenient sample type for surveillance of DASS. All dams and piglets were recN positive in tonsil swabs, which highlights the high frequency of this species within pig population. In terms of 1130 carriage in dams from farm 1, The odds of 1130 gene positivity was 82% lower in sows compared to gilts (odds ratio 0.17, 95% CI 0.4=35, 0.53, P < 0.05). In contrast, no association between dam group and 1130 positivity (P > 0.05) was observed in Farm 2. At the piglet level, the piglet 1130 positivity followed a similar pattern between the two farms (Figure 6), however, farm 1 had a numerically lower overall piglet prevalence across all points compared to farm 2. In these herds between 20-70% of piglets were positive at birth, with a significant decrease in prevalence observed at day 7 (18-45%), followed by a significant increase in the prevalence of 1130 at day 21. The decrease at day 7 could reflect a transient detection at birth, or the effect of antibodies in colostrum. Furthermore, the 1130 gene positivity was 83% and 63% lower in piglets from sow than
piglets from gilts on farms 1 and 2, respectively (p<0.05). At the litter level, in farm 1 overall average litter prevalence was 32.7% and for farm 2 the overall average litter prevalence was 64.97%. A total of 10 litters on farm 1 remained consistently negative. Furthermore, in farm 1 the dam positivity was a predictor for litter prevalence. That is, litters from positive gilts had a 37% higher prevalence than litters from positive sows (P < 0.05). In contrast, dam positivity was not a predictor for litter prevalence in farm 2. That is, at day 0, litters from negative gilts had a 26% higher prevalence than litters from positive sows (P < 0.05). The latter result could reflect alternate sources of infection for piglets. In fact, DASS was detected in farrowing crate, fecal, and udder samples, suggesting relevant sources of infection for piglets, that should be further explored. Determining the timing and prevalence of colonization with virulent S. suis strains allows for the refinement of control and/or elimination strategies, such as strategic medication and vaccination, early weaning or test and removal of individuals harboring DASS. Ultimately, these strategies allow swine producers and veterinarians to mitigate the impact of S. suis-associated disease and therefore allow for the reduction in antimicrobial use in swine farms. Since piglets are likely colonized the first days of life it may not be feasible to wean piglets very early to secure elimination of DASS strains. However, future work should evaluate the potential of medicated early wean programs for both sows and piglets to eliminate DASS, as well as understanding the specific genotypes colonizing pigs over time.
From whole genome sequencing (WGS) data, critical information from each strain can be extracted; serotyping, antimicrobial resistance genes, multi-locus sequence typing profile, virulence markers, and phylogenetic profiles. Also, it provides key data for ongoing efforts to identify novel and globally relevant virulence-associated markers and thus potential vaccine candidates. Whole-genome sequencing revealed ST1 (serotype 1 or 14), ST28 (serotype 2 or 1/2), ST961(serotype 2 or 1/2), ST108 (serotype 23), and ST977 (serotype 4 or 5) as the top 5 genotypes associated with disease that were present in approximately 230/364 (63.2%) of the farms, and thus should be targets for autogenous vaccine development in North America. Serotyping alone can be misleading in that there is variability in some serotypes. For example, some serotype 9, 1, 7 and 2 isolates can be pathogenic while others have features of being opportunistic/commensal. While the data show a wide diversity of S. suis strains present in NA swine herds, usually one or two strains predominate within a farm or flow in disease associated cases, and these same strains tend to persist over time (e.g., the same strain was detected over a 6-year period). Most isolates (~80%) were positive for the ermB and tetO genes which encode for MLS (Streptogramin, Macrolides, Lincosamide) and tetracycline resistance, respectively. The low levels of antimicrobial resistance noted at the genomic level are in alignment with the low levels of phenotypic resistance observed at the ISU VDL. Currently, distribution of AMR genes aids in determining the clinical relevance of strains. Within our database roughly 10% of isolates are untypeable by both serotyping (conventional and WGS) and MLST. Most of these isolates either originated from polymicrobial cases (e.g., viral and bacterial agents) or the isolation of S. suis did not align with lesions present in the tissue, suggesting possible contamination. This indicates that these strains potentially represent opportunistic or commensal strains. Contamination of a systemic sample with commensal strains can misguide diagnosis, treatment, and autogenous vaccine development. Several educational materials were developed on proper sample collection to guide veterinarians and farmers to avoid cross-contamination and improve the likelihood of detecting the clinically relevant strains. These resources are currently available on the AASV and ISU VDL websites. Characterization of isolates using WGS provides critical information in their clinical relevance, which is key for autogenous vaccine development, and understanding the carriage of antimicrobial resistance. Systemic sites isolates are optimal for the detection of DASS compared to tonsil samples in clinical animals. However, sample collection from systemic lesions should be done with care to avoid commensal strains contamination. This project developed surveillance tools and knowledge to enable effective control of DASS. Knowledge and assays developed in this project will improve our surveillance methodologies and therefore, better understand the epidemiology of DASS in endemically infected farms. The RT-PCR assay developed can be used to track DASS in farms which shed light on the epidemiology of DASS and could aid in the design of improved control and elimination strategies. The genomic characterization of a significant set of isolates from 60 top production systems and 361 individual pig sites provided key information that can aid in the refinement of prevention strategies, such as selecting autogenous vaccine candidates, placing strategic medication, and improving pig flow management and gilt acclimation efforts.
- Serotype 1 or 14), ST28 (serotype 2 or 1/2), ST961(serotype 2 or 1/2), ST108 (serotype 23), and ST977 (serotype 4 or 5) were among the top 5 pathogenic S. suis genotypes submitted to the ISU VDL – NGS services.
- Next-generation sequencing provides the best resolution for strain characterization Swine practitioners can utilize this information to identify the most frequent strains found in disease-associated cases, improve vaccine candidate selection or antimicrobial to use on farm, and optimize mixing of pig populations.
- Meningeal swabs, cerebro-spinal fluid, spleen and joints are good samples for DASS detection in diseased pigs.
- The newly developed and validated PCR in this study can be used to track carriage of DASS strains in antemortem samples from pigs.
- Transient detection and varying prevalence of S. suis was observed at the dam, litter and piglet level over time.
- Piglets are positive for DASS in tonsil swabs shortly after birth, however within the first 7 days the prevalence did not reach 100%, and some litters can remain negative throughout the lactation phase.
- Gilts and gilt litters were more likely to carry DASS.
- Nasal swabs seemed to be as good or better than tonsil swabs at identifying dams carrying DASS. DASS could be detected in multiple dam-related samples, including the feces, farrowing crate, vaginal swabs and the udder, suggesting multiple sources of infection for the piglets.