Emergence of Brachyspira species and strains: reinforcing the need for surveillance

Antimicrobial susceptibility of U.S. porcine Brachyspira isolates and genetic diversity of B. hyodysenteriae by multilocus sequence typing

Swine dysentery, caused by Brachyspira hyodysenteriae and the newly recognized Brachyspira hampsonii in grower-finisher pigs, is a substantial economic burden in many swine-rearing countries. Antimicrobial therapy is the only commercially available measure to control and prevent Brachyspira-related colitis. However, data on antimicrobial susceptibility trends and genetic diversity of Brachyspira species from North America is limited. We evaluated the antimicrobial susceptibility profiles of U.S. Brachyspira isolates recovered between 2013 and 2022 to tiamulin, tylvalosin, lincomycin, doxycycline, bacitracin, and tylosin. In addition, we performed multilocus sequence typing (MLST) on 64 B. hyodysenteriae isolates. Overall, no distinct alterations in the susceptibility patterns over time were observed among Brachyspira species. However, resistance to the commonly used antimicrobials was seen sporadically with a higher resistance frequency to tylosin compared to other tested drugs. B. hampsonii was more susceptible to the tested drugs than B. hyodysenteriae and B. pilosicoli. MLST revealed 16 different sequence types (STs) among the 64 B. hyodysenteriae isolates tested, of which 5 STs were previously known, whereas 11 were novel. Most isolates belonged to the known STs: ST93 (n = 32) and ST107 (n = 13). Our findings indicate an overall low prevalence of resistance to clinically important antimicrobials other than tylosin and bacitracin, and high genetic diversity among the clinical Brachyspira isolates from pigs in the United States during the past decade. Further molecular, epidemiologic, and surveillance studies are needed to better understand the infection dynamics of Brachyspira on swine farms and to help develop effective control measures.

First molecular detection of Brachyspira suanatina on pig farms in Poland

Introduction

Prior to the 2000s, swine dysentery was considered to be caused only by Brachyspira hyodysenteriae with contributing commensal intestinal anaerobes. Nowadays, it is known that the disease is caused by three strongly beta-haemolytic species of the anaerobic spirochaetal genus Brachyspira, i.e. B. hyodysenteriae and newly emerged B. hampsonii and B. suanatina.

Material and Methods

The present investigation was carried out in November 2022 on nine Polish high-performing finisher pig farms. At every location one fresh pooled faecal sample was collected from 40 randomly selected pigs of between 60 and 110 kg live weight. Nucleic acid extracted from each pooled faecal sample was analysed by an in-house multiplex PCR for Brachyspira spp., which is capable of confirming the Brachyspira genus and detecting and differentiating Brachyspira species.

Results

From a total of nine samples examined, the genetic material of B. suanatina was detected in seven. Non-pathogenic/questionably pathogenic Brachyspira spp. were found in six samples.

Conclusion

To the best of our knowledge, this is the first report on the identification of B. suanatina in pigs outside Scandinavia, Germany and the United Kingdom. Our research not only provides valuable epidemiological data on B. suanatina infection in Europe but also highlights both the importance of modern laboratory diagnostics and the need for thorough investigation across regions, including retrospective studies.

Prevalence and risk factors of Brachyspira spp. in pig herds with a history of diarrhoea in six European countries

Swine dysentery and porcine intestinal spirochaetosis caused by Brachyspira (B.) hyodysenteriae and B. pilosicoli, respectively, are important diseases in swine production worldwide. The aim of this study was to assess the prevalence of both pathogens in farms with a history of diarrhoea within the last 12 months in Denmark, France, Germany, the Netherlands, Spain, and United Kingdom. In addition, risk factors for their prevalence and correlations between presence of different Brachyspira spp. and Lawsonia intracellularis were investigated. Therefore, faecal samples of 6355 nursery to finishing pigs out of 144 herds were sampled in 2017/2018 during a prevalence study on Lawsonia intracellularis, followed by polymerase chain reaction analysis for Brachyspira spp. detection. Herd prevalence differed significantly between countries, from 4.2% to 45.8% for B. hyodysenteriae and 8.3-87.5% for B. pilosicoli, respectively (p < 0.01). For the within-herd prevalence (in positive herds), these values ranged from 2.2% to 27.0% for B. hyodysenteriae and 3.3-50.8% for B. pilosicoli. Mixed infections occurred in 34.1% and 58.7% of B. hyodysenteriae positive samples with Lawsonia intracellularis or B. pilosicoli, respectively. In 43.2% of B. pilosicoli positive samples, Lawsonia intracellularis was detected simultaneously. Overall, nursery pigs were significantly less often positive for one of the pathogens than growing or finishing pigs (p < 0.001). The absence of gastrointestinal problems like diarrhoea, routine use of antimicrobials and well performed biosecurity measures were some of the factors associated with lower detection rate of Brachyspira spp. Surprisingly, deworming of different age categories also showed associations with the detection of Brachyspira spp. which, however, were not always equally directed, and therefore require further investigations. The only risk factor significant for both Brachyspira spp. was the median number of ≥ 30 nursery pigs per pen after weaning, compared to smaller group sizes. Both pathogens were detected with varying frequency between the six European countries. This should be considered in the probability of disease and in case of transnational transport, to prevent spread of pathogens. In addition, the frequent presence of mixed infections in some countries should be taken into account in diagnostics. The most important protective factors against Brachyspira spp. presence on farm are biosecurity measures, while potential new factors such as deworming still require further investigation.

Experimental natural transmission (seeder pig) models for reproduction of swine dysentery

Swine dysentery is causally associated with Brachyspira hampsonii and B. hyodysenteriae infection. Given the importance of transmission models in understanding re-emergent diseases and developing control strategies such as vaccines, the objective of this experiment was to evaluate two experimental natural transmission (seeder pig) models in grower pigs, each with 24 animals. Seeder pigs were intragastrically inoculated using broth cultures of either B. hampsonii strain 30446 (genomovar II) or B. hyodysenteriae strain G44. In trial 1, three seeder pigs were placed into two pens containing nine susceptible contact pigs creating a 1:3 seeder:contact ratio. This was sufficient to achieve natural B. hampsonii infection of 13/18 (72%) contact pigs, however, the incidence of mucoid or mucohemorrhagic diarrhea (MMHD) in contact pigs differed significantly between pens (4/9 versus 9/9; P = 0.03). In trial 2, eight seeder pigs inoculated intragastrically with B. hampsonii did not develop MMHD but when re-inoculated with B. hyodysenteriae 14 days later, all developed mucohemorrhagic diarrhea within 13 days of re-inoculation. Two seeder pigs were placed into each of 4 contact pens each containing 4 pigs. This 1:2 seeder:contact ratio resulted in natural infection of 14/16 (87%) contact pigs with incubation period ranging from 9–15 days. There were no significant differences among pens in incubation period, duration, clinical period or severity of diarrhea. These trials demonstrated that a 1:2 seeder:contact ratio with groups of six grower pigs per pen sustained natural transmission of B. hyodysenteriae G44 with greater consistency in the incidence of MMHD among pens compared to a B. hampsonii 30446 transmission model using 1:3 seeder:contact ratio in pens of 12. Understanding why B. hampsonii intragastric inoculation failed in one experiment warrants additional research.

Experimental Infection of Pigs with a ST 245 Brachyspira hyodysenteriae Isolated from an Asymptomatic Pig in a Herd with No History of Swine Dysentery

Swine dysentery (SD) is characterized by a severe mucohemorrhagic colitis caused by infection with Brachyspira species. In infected herds the disease causes considerable financial loss due to mortality, slow growth rates, poor feed conversion, and costs of treatment. B. hyodysenteriae is the most common etiological agent of SD and infection is usually associated with disease. However, isolated reports have described low pathogenic strains of B. hyodysenteriae. The aim of this study was to describe an experimental infection trial using a subclinical B. hyodysenteriae isolated from an animal without clinical signs and from a disease-free herd, to evaluate the pathogenicity and clinical pathological characteristics compared to a highly clinical isolate. Forty-eight 5-week-old pigs were divided into three groups: control, clinical and the subclinical isolates. The first detection/isolation of B. hyodysenteriae in samples of the animals challenged with a known clinical B. hyodysenteriae strain (clinical group) occurred 5th day post inoculation. Considering the whole period of the study, 11/16 animals from this group were qPCR positive in fecal samples, and diarrhea was observed in 10/16 pigs. In the subclinical isolate group, one animal had diarrhea. There were SD large intestine lesions in 3 animals at necropsy and positive B. hyodysenteriae isolation in 7/15 samples of the subclinical group. In the control group, no diarrhea, gross/microscopic lesions, or qPCR positivity were observed. Clinical signs, bacterial isolation, macroscopic and histologic lesions were significantly difference among groups, demonstrating low pathogenicity of the subclinical isolate in susceptible pigs.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Brachyspira hyodysenteriae in swine

Brachyspira hyodysenteriae (B. hyodysenteriae) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for swine in a previous scientific opinion. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9, and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR B. hyodysenteriae can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33-66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 3 (Categories A, B and C; 1-10%, 10-33% and 10-33% probability of meeting the criteria, respectively) and the AHAW Panel was uncertain whether it meets the criteria in Sections 4 and 5 (Categories D and E, 50-90% and 33-66% probability of meeting the criteria, respectively). The main animal species to be listed for AMR B. hyodysenteriae according to Article 8 criteria are pigs and some species of birds, such as chickens and ducks.

Novel multiplex TaqMan assay for differentiation of the four major pathogenic Brachyspira species in swine

A novel TaqMan 5-plex real-time PCR using a combination of locked nucleic acid-modified (LNA)- and minor groove binding (MGB)-conjugated DNA probes was developed for identification and differentiation between the four main pathogenic Brachyspira species in swine. B. hyodysenteriae, B. pilosicoli, and B. suanatina are identified using three hydrolysis probes targeting cpn60, while B. hampsonii is recognized by another nox specific probe. The assay also includes an exogenous internal control simultaneously verifying the PCR competency of the DNA samples. Validation of the novel assay was performed using DNA samples from 18 Brachyspira reference strains and 477 clinical samples obtained from porcine rectal swabs by comparing them with different PCR-based methods targeting nox, 16S rDNA, and 23S rDNA. The specificity of the assay was 100% without cross-reactivity or detection of different pathogens. Depending on the Brachyspira species, the limit of detection was between 10 and 20 genome equivalents with a cut-off threshold cycle (Ct) value of 37. The developed highly sensitive and specific 5-plex real-time PCR assay is easy to implement in routine veterinary diagnostic laboratories and enables rapid differentiation between the main four pathogenic Brachyspira species recognized in pigs using a single-tube approach.

Exploring the Cause of Diarrhoea and Poor Growth in 8-11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing

Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.

Identification and distribution of Brachyspira species in feces from finishing pigs in Argentina

Background and Aim:

Brachyspira are Gram-negative, aerotolerant spirochetes that colonize the large intestine of various species of domestic animals and humans. The aim of this study was to determine the presence and distribution of different species of Brachyspira presents in feces from finishing pigs in Argentina.

Materials and Methods:

Fecal samples (n=1550) were collected from finishing pigs in 53 farms of the most important swine production areas of Argentina, and Brachyspiras species were identified by bacteriological and molecular methods.

Results:

The regional prevalence of Brachyspira spp. was at the level of 75.5% (confidence interval 95%, 62.9-87.9), and it was lower among those farms with >1001 sows. One hundred and twenty-eight isolates of Brachyspira were properly identified and the species found were: Brachyspira hyodysenteriae, Brachyspira pilosicoli, Brachyspira innocens, and Brachyspira murdochii. B. hyodysenteriae and B. pilosicoli had low prevalence (1.9% and 7.5%, respectively), B. innocens was isolated from 34% of the farms and B. murdochii was found in 39.6%.

Conclusion:

The present study provides epidemiological data about herd prevalence of the different Brachyspira species in Argentina, showing that the prevalence figure seems to be higher than that reported in other countries.

Differential expression of hemolysin genes in weakly and strongly hemolytic Brachyspira hyodysenteriae strains

Background

Swine dysentery (SD) is a diarrheal disease in fattening pigs that is caused by the strongly hemolytic species Brachyspira (B.) hyodysenteriae, B. hampsonii and B. suanatina. As weakly hemolytic Brachyspira spp. are considered less virulent or even non-pathogenic, the hemolysin is regarded as an important factor in the pathogenesis of SD. Four hemolysin genes (tlyA, tlyB, tlyC, and hlyA) and four putative hemolysin genes (hemolysin, hemolysin activation protein, hemolysin III, and hemolysin channel protein) have been reported, but their role in strong hemolysis is not entirely clear. Our study aimed to assess the transcriptional activity of eight (putative) hemolysin genes in a strongly hemolytic (B204) and a weakly hemolytic (G423) B. hyodysenteriae strain during non-hemolytic and hemolytic growth stages.

Results

Strongly and weakly hemolytic B. hyodysenteriae strains caused hemolysis on blood agar at different growth stages, namely during log phase (B204) and stationary/death phase (G423). During the lag, early log, late log (stationary phase in G423) and death phase (time points 1–4) strains differed in their hemolysin gene transcription patterns. At time point 1, transcription of the putative hemolysin gene was higher in B204 than in G423. At time point 2, tlyA and tlyC were upregulated in B204 during hemolysis. TlyB and hlyA were upregulated in both strains at all time points, but higher transcription rates were observed in the weakly hemolytic strain G423. The transcription activity of the hemolysin channel protein gene was quite similar in both strains, whereas the hemolysin activation protein gene was upregulated in the non-hemolytic stage of B204 at time point 4. Sequence analysis revealed deletions, insertions and single nucleotide polymorphisms in the G423 hlyA promoter, although without altering the transcription activity of this gene.

Conclusion

Our data indicate a combined activity of TlyA and TlyC as the most probable underlying mechanism of strong hemolysis in B. hyodysenteriae. Further studies should verify if the expression of tlyA is upregulated by the putative hemolysin gene. Depending on their immunogenic potential TlyA and TlyC may serve as possible vaccine candidates, especially since vaccines for an effective control of swine dysentery are currently not available.

Risk factors for the infection with Brachyspira hyodysenteriae in pig herds

Swine dysentery (SD), caused by infection with Brachyspira hyodysenteriae, is a serious disease in pig production worldwide. Quantitative risk factors triggering the occurrence of infection are unknown. The present case-control study aimed at identifying major risk factors related to presence of B. hyodysenteriae in pig herds. Twenty case herds and 60 randomly selected control herds with a minimum herd size of '10 sows/ 80 fattening pigs' were examined by means of a questionnaire-based interview and a herd examination. Herds with previous eradication of SD were excluded. Logistic regression models revealed that the 'positive/suspicious SD status of source herds', the regular application of treatment, purchasing more than 4 batches/ year, contact to foxes, diagnostics performed during last 12 months, liquid feeding systems, rats on farm, and >250 fatting places were associated with higher chances of a herd to be infected. On the contrary, having different sources of grower pigs within one batch, the presence of raptor birds and the presence of martens in the region were associated with fewer chances of being infected. The final multivariable logistic regression model identified purchasing more than 4 batches/ year (OR = 7.5, 95 % CI 1.8-54.3) and contact to foxes (OR = 5.9; 97.5 % CI 1.2-34.6) as the two main risk factors in our study. 'More than 4 batches/ year' implies continuous herd management supporting persistence of B. hyodysenteriae in an infected herd, but also increased number of purchases each increasing the risk of B. hyodysenteriae introduction by carrier pigs or transport vehicles. Foxes might be infected with B. hyodysenteriae by feeding on positive piglets and rodents. Besides, 'contact to foxes' might represent a lack in biosecurity. In conclusion, the risk factors detected underline the importance of biosecurity in SD prevention and control.

A survey on the occurrence of Brachyspira pilosicoli and Brachyspira hyodysenteriae in growing-finishing pigs

Background: The major pathogenic intestinal spirochetes affecting pigs during the growing- finishing stage of production include Brachyspira hyodysenteriae and Brachyspira pilosicoli. Infections by these pathogens, which affect the economics of pig production, can result in mortality, growth rate losses and substantial antibiotic costs. The aim of this study was to assess the current occurrence of B. hyodysenteriae and B. pilosicoli in Polish pig herds. Moreover, associations between the presence of diarrhea or other intestinal pathogens and occurrence of B. hyodysenteriae and B. pilosicoli in pigs were investigated. Methods: Between January 2017 and August 2019, a total of 401 samples of pig feces from 95 different herds were submitted to the National Veterinary Research Institute of Poland. These samples were obtained from pigs older than 7 weeks. All the received fecal samples were examined for the presence of B. hyodysenteriae, B. pilosicoli and Lawsonia intracellularis by real-time PCR. Results: For B. pilosicoli, 4.5% (95% CI, 2.5-7.0%) of samples and 13.7% (95% CI, 7.5-22.3%) of herds were positive. Out of 12 samples, B. pilosicoli was detected simultaneously with L. intracellularis, B. hyodysenteriae and B. pilosicoli were detected alone in two samples each. In terms of B. hyodysenteriae, 7.0% of samples (95% CI, 4.7-9.9%) from 18.9% of herds (95% CI, 11.6-28.3%) were positive in real time PCR. The presence of B. hyodysenteriae in fecal samples was associated with the presence of diarrhea in pigs. Conclusions: This study confirmed that B. pilosicoli infections occur in Polish pig herds, but the prevalence is at a low level and the presence of B. pilosicoli is not associated with the development of diarrhea in pigs. B. hyodysenteriae is still a common cause of diarrhea among pigs from Polish herds.

A survey on the occurrence of Brachyspira pilosicoli and Brachyspira hyodysenteriae in growing-finishing pigs

Background: The major pathogenic intestinal spirochetes affecting pigs during the growing- finishing stage of production include Brachyspira hyodysenteriae and Brachyspira pilosicoli. The aim of this study was to assess the current occurrence of B. hyodysenteriae and B. pilosicoli in Polish pig herds. Moreover, associations between the presence of diarrhea or other intestinal pathogens and occurrence of B. hyodysenteriae and B. pilosicoli in pigs were investigated. Methods: Between January 2017 and August 2019, a total of 401 samples of pig feces from 95 different herds were submitted to the National Veterinary Research Institute of Poland. These samples were obtained from pigs older than 7 weeks. All the received fecal samples were examined for the presence of B. hyodysenteriae, B. pilosicoli and Lawsonia intracellularis by real-time PCR. Results: B. pilosicoli was detected in 4.5% (95% CI, 2.5-7.0%) (18/401) of pig fecal samples. At the herd level 13.7% (95% CI, 7.5-22.3%) (13/95) of herds were positive for B. pilosicoli. B. hyodysenteriae was detected in 7.0% (95% CI, 4.7-9.9%) (28/401) of pig fecal samples and 18.9% (95% CI, 11.6-28.3%) (18/95) of pig herds were positive. Out of 18 B. pilosicoli positive samples, this pathogen was detected alone in 5 samples; simultaneously with L. intracellularis in 9 samples; simultaneously with B. hyodysenteriae in 1 sample and in 3 samples was detected simultaneously with both of these bacteria. The presence of B. hyodysenteriae in fecal samples was associated with the presence of diarrhea in pigs. Conclusions: This study confirmed that B. pilosicoli infections occur in Polish pig herds, but the prevalence is at a low level and the presence of B. pilosicoli is not associated with the development of diarrhea in pigs. B. hyodysenteriae is still a common cause of diarrhea among pigs from Polish herds.

A survey on the occurrence of Brachyspira pilosicoli and Brachyspira hyodysenteriae in growing-finishing pigs

Background: The major pathogenic intestinal spirochetes affecting pigs during the growing- finishing stage of production include Brachyspira hyodysenteriae and Brachyspira pilosicoli. The aim of this study was to assess the current occurrence of B. hyodysenteriae and B. pilosicoli in Polish pig herds. Moreover, associations between the presence of diarrhea or other intestinal pathogens and occurrence of B. hyodysenteriae and B. pilosicoli in pigs were investigated. Methods: Between January 2017 and August 2019, a total of 401 samples of pig feces from 95 different herds were submitted to the National Veterinary Research Institute of Poland. These samples were obtained from pigs older than 7 weeks. All the received fecal samples were examined for the presence of B. hyodysenteriae, B. pilosicoli and Lawsonia intracellularis by real-time PCR. Results: B. pilosicoli was detected in 4.5% (95% CI, 2.5-7.0%) (18/401) of pig fecal samples. At the herd level 13.7% (95% CI, 7.5-22.3%) (13/95) of herds were positive for B. pilosicoli. B. hyodysenteriae was detected in 7.0% (95% CI, 4.7-9.9%) (28/401) of pig fecal samples and 18.9% (95% CI, 11.6-28.3%) (18/95) of pig herds were positive. Out of 18 B. pilosicoli positive samples, this pathogen was detected alone in 5 samples; simultaneously with L. intracellularis in 9 samples; simultaneously with B. hyodysenteriae in 1 sample and in 3 samples was detected simultaneously with both of these bacteria. The presence of B. hyodysenteriae in fecal samples was associated with the presence of diarrhea in pigs. Conclusions: This study confirmed that B. pilosicoli infections occur in Polish pig herds, but the prevalence is at a low level and the presence of B. pilosicoli is not associated with the development of diarrhea in pigs. B. hyodysenteriae is still a common cause of diarrhea among pigs from Polish herds.

An atypical weakly haemolytic strain of Brachyspira hyodysenteriae is avirulent and can be used to protect pigs from developing swine dysentery

The anaerobic intestinal spirochaete Brachyspira hyodysenteriae colonises the large intestine of pigs and causes swine dysentery (SD), a severe mucohaemorrhagic colitis. SD occurs worldwide, and control is hampered by a lack of vaccines and increasing antimicrobial resistance. B. hyodysenteriae strains typically produce strong beta-haemolysis on blood agar, and the haemolytic activity is thought to contribute to the pathogenesis of SD. Recently, weakly haemolytic variants of B. hyodysenteriae have been identified in Europe and Australia, and weakly haemolytic strain D28 from Belgium failed to cause disease when used experimentally to infect pigs. Moreover, pigs colonised with D28 and then challenged with virulent strongly haemolytic strain B204 showed a delay of 2–4 days in developing SD compared to pigs not exposed to D28. The current study aimed to determine whether Australian weakly haemolytic B. hyodysenteriae strain MU1, which is genetically distinct from D28, could cause disease and whether exposure to it protected pigs from subsequent challenge with strongly haemolytic virulent strains. Three experimental infection studies were undertaken in which no diseases occurred in 34 pigs inoculated with MU1, although mild superficial lesions were found in the colon in 2 pigs in one experiment. In two experiments, significantly fewer pigs exposed to MU1 and then challenged with strongly haemolytic virulent strains of B. hyodysenteriae developed SD compared to control pigs not previously exposed to MU1 (p = 0.009 and p = 0.0006). These data indicate that MU1 lacks virulence and has potential to be used to help protect pigs from SD.

Polymerase chain reaction assay targeting nox gene for rapid identification of Brachyspira canis in dogs

Genus Brachyspira, as Gram negative anaerobic bacteria, colonize in dogs intestine. The aim of the current study was to determine the prevalence of Brachyspira spp. for the first time in Iran and rapid identification of Brachyspira spp. in dogs by a new designment of a species-specific primer set for B. canis. One hundred fifty-one fecal samples were obtained from dogs by rectal swab. Twenty dogs suffered from diarrhea and 131 of them were healthy. In 9.27% (14/151) of samples, spirochaetes were detected on primary cultures by weak hemolysis and positive Gram staining and then Brachyspira genus was confirmed by NADH oxidase (nox) gene via polymerase chain reaction. Among 14 isolates, twelve isolates were B. canis, one isolate was B. intermedia and another one was non-typeable. From 12 B. canis, only eight isolates were detected by designed specific primers. Ten Brachyspira spp. were isolated from dogs ≤ 1 year old (10/67, 14.92%) and 4 isolates were from > 1 year old dogs (4/84, 4.76%). The isolation rates from healthy and diarrheic dogs were (12/131, 9.16%) and (2/20, 10.00%), respectively. A statistically significant association was observed between the presence of Brachyspira spp. and the age under one year. Based on our findings, the nox gene in B. canis might have more sequence variability compared to other Brachyspira spp.

Antimicrobial resistance in Brachyspira - An increasing problem for disease control

Across all bacterial species the continuing reduction in susceptibility to antimicrobial agents is a critical and increasing threat for disease control. This mini-review outlines the extent of this problem amongst anaerobic intestinal spirochaetes of the genus Brachyspira, of which there are currently nine officially recognised species. These include some important pathogens that may cause colitis with diarrhoea and/or dysentery in various mammalian and avian species, but most notably in pigs and in adult chickens. The most economically significant pathogen is Brachyspira hyodysenteriae, the spirochaete which causes swine dysentery in countries throughout the world. Control of infections with Brachyspira species has long relied on the prophylactic or therapeutic use of antimicrobials, but increasingly strains with reduced susceptibility and sometimes multidrug resistance to previously effective antimicrobial agents are being encountered. In this mini-review we outline these problems and explain the extent and molecular basis of the emerging resistance. Future control will rely on developing and applying standardised methods for measuring antimicrobial susceptibility; improving surveillance of resistance using traditional phenotypic as well as genomic analysis of known resistance determinants; improving understanding of the molecular basis of resistance to different drug classes; improving farmer and veterinarian education about prudent antimicrobial use so as to reduce selective pressure on the emergence of resistance; and developing alternatives to antimicrobials as a means to control these infections.

Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications

The PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera.  Although the PubMLST website was conceived as part of the development of the first multi-locus sequence typing (MLST) scheme in 1998 the software it uses, the Bacterial Isolate Genome Sequence database (BIGSdb, published in 2010), enables PubMLST to include all levels of sequence data, from single gene sequences up to and including complete, finished genomes.  Here we describe developments in the BIGSdb software made from publication to June 2018 and show how the platform realises microbial population genomics for a wide range of applications.  The system is based on the gene-by-gene analysis of microbial genomes, with each deposited sequence annotated and curated to identify the genes present and systematically catalogue their variation.  Originally intended as a means of characterising isolates with typing schemes, the synthesis of sequences and records of genetic variation with provenance and phenotype data permits highly scalable (whole genome sequence data for tens of thousands of isolates) means of addressing a wide range of functional questions, including: the prediction of antimicrobial resistance; likely cross-reactivity with vaccine antigens; and the functional activities of different variants that lead to key phenotypes.  There are no limitations to the number of sequences, genetic loci, allelic variants or schemes (combinations of loci) that can be included, enabling each database to represent an expanding catalogue of the genetic variation of the population in question.  In addition to providing web-accessible analyses and links to third-party analysis and visualisation tools, the BIGSdb software includes a RESTful application programming interface (API) that enables access to all the underlying data for third-party applications and data analysis pipelines.

Microbiota and metabolic diseases

The microbiota is a complex ecosystem of microorganisms consisting of bacteria, viruses, protozoa, and fungi, living in different districts of the human body, such as the gastro-enteric tube, skin, mouth, respiratory system, and the vagina. Over 70% of the microbiota lives in the gastrointestinal tract in a mutually beneficial relationship with its host. The microbiota plays a major role in many metabolic functions, including modulation of glucose and lipid homeostasis, regulation of satiety, production of energy and vitamins. It exerts a role in the regulation of several biochemical and physiological mechanisms through the production of metabolites and substances. In addition, the microbiota has important anti-carcinogenetic and anti-inflammatory actions. There is growing evidence that any modification in the microbiota composition can lead to several diseases, including metabolic diseases, such as obesity and diabetes, and cardiovascular diseases. This is because alterations in the microbiota composition can cause insulin resistance, inflammation, vascular, and metabolic disorders. The causes of the microbiota alterations and the mechanisms by which microbiota modifications can act on the development of metabolic and cardiovascular diseases have been reported. Current and future preventive and therapeutic strategies to prevent these diseases by an adequate modulation of the microbiota have been also discussed.

The Efficacy of Two Phytogenic Feed Additives in the Control of Swine Dysentery

Control of swine dysentery with antibiotics is often ineffective due to the resistance of Brachyspira hyodysenteriae. The potential of some herbal-based components against B. hyodysenteriae was previously studied in vitro. This study aims at the evaluation of in vivo efficacy of phytogenic feed additives in the control of swine dysentery

The study involved 64 seven-week old weaned pigs allotted to 4 groups: two were fed on feed supplemented with either Patente Herba® or Patente Herba® Plus, the third received tiamulin (positive control), while the negative control was not given antibiotics or additives. Fecal consistency was recorded daily. The presence of B. hyodysenteriae in the feces was investigated weekly using microbiological assays and the PCR test. Weight gain and feed conversion ratio were calculated for each week, and for the whole experiment.

B. hyodysenteriae was detected in all samples by both methods. The additives showed efficacy in the prevention and control of swine dysentery as only normal and soft stool was observed in the treated groups. By contrast, in the negative control all feces categories were detected. Frequencies of feces categories significantly differed (p<0.001) between feed-supplemented groups and the negative control. Efficacy of both additives in the prevention of SD is comparable to tiamulin, based on insignificant differences in the frequency of the various feces categories.

Beneficial effects of both additives resulted in significantly (p≤0.05) higher weight gain and lower feed conversion ratio in comparison to the negative control. The average weight gains between additive-fed groups and tiamulin-treated group did not differ significantly.

Phylogenetic diversity, antimicrobial susceptibility and virulence gene profiles of Brachyspira hyodysenteriae isolates from pigs in Germany

Swine dysentery (SD) is an economically important diarrheal disease in pigs caused by different strongly hemolytic Brachyspira (B.) species, such as B. hyodysenteriae, B. suanatina and B. hampsonii. Possible associations of epidemiologic data, such as multilocus sequence types (STs) to virulence gene profiles and antimicrobial susceptibility are rather scarce, particularly for B. hyodysenteriae isolates from Germany. In this study, B. hyodysenteriae (n = 116) isolated from diarrheic pigs between 1990 and 2016 in Germany were investigated for their STs, susceptibility to the major drugs used for treatment of SD (tiamulin and valnemulin) and genes that were previously linked with virulence and encode for hemolysins (tlyA, tlyB, tlyC, hlyA, BHWA1_RS02885, BHWA1_RS09085, BHWA1_RS04705, and BHWA1_RS02195), outer membrane proteins (OMPs) (bhlp16, bhlp17.6, bhlp29.7, bhmp39f, and bhmp39h) as well as iron acquisition factors (ftnA and bitC). Multilocus sequence typing (MLST) revealed that 79.4% of the isolates belonged to only three STs, namely ST52 (41.4%), ST8 (12.1%), and ST112 (25.9%) which have been observed in other European countries before. Another 24 isolates belonged to twelve new STs (ST113-118, ST120-123, ST131, and ST193). The temporal distribution of STs revealed the presence of new STs as well as the regular presence of ST52 over three decades (1990s-2000s). The proportion of strains that showed resistance to both tiamulin und valnemulin (39.1%) varied considerably among the most frequent STs ranging from 0% (0/14 isolates resistant) in ST8 isolates to 46.7% (14/30), 52.1% (25/48), and 85.7% (6/7) in isolates belonging to ST112, ST52, and ST114, respectively. All hemolysin genes as well as the iron-related gene ftnA and the OMP gene bhlp29.7 were regularly present in the isolates, while the OMP genes bhlp17.6 and bhmp39h could not be detected. Sequence analysis of hemolysin genes of selected isolates revealed co-evolution of tlyB, BHWA1_RS02885, BHWA1_RS09085, and BHWA1_RS02195 with the core genome and suggested independent evolution of tlyA, tlyC, and hlyA. Our data indicate that in Germany, swine dysentery might be caused by a limited number of B. hyodysenteriae clonal groups. Major STs (ST8, ST52, and ST112) are shared with other countries in Europe suggesting a possible role of the European intra-Community trade of pigs in the dissemination of certain clones. The identification of several novel STs, some of which are single or double locus variants of ST52, may on the other hand hint towards an ongoing diversification of the pathogen in the studied area. The linkage of pleuromutilin susceptibility and sequence type of an isolate might reflect a clonal expansion of the underlying resistance mechanism, namely mutations in the ribosomal RNA genes. A linkage between single virulence-associated genes (VAGs) or even VAG patterns and the phylogenetic background of the isolates could not be established, since almost all VAGs were regularly present in the isolates.

Brachyspira hyodysenteriae detection in the large intestine of slaughtered pigs

Detection of subclinical Brachyspira hyodysenteriae infection in pig herds using feces is challenging. However, the ability to detect the pathogen in intestinal samples of slaughtered pigs has not been investigated, to our knowledge. Therefore, we determined the detection of B. hyodysenteriae in the colon, cecum, and rectum from slaughtered pigs. We analyzed the correlation between detection rates and intestinal lesions, ingesta or fecal consistency, and time from sample collection until processing. A total of 400 ingesta-mucosal (colon, cecum) and 200 fecal (rectum) samples from 200 pigs originating from 20 different herds were bacteriologically examined using selective culture followed by Brachyspira spp. identification by PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Ingesta or fecal consistency and intestinal lesions were scored. Brachyspira hyodysenteriae was detected in 23 samples from 16 intestines originating from 7 herds. Brachyspira spp. were detected in 96 samples. More intestinal (16) than fecal (7) samples tested positive for B. hyodysenteriae. For Brachyspira spp., this difference was significant (69 vs. 27; p < 0.01). In particular, colon samples tested positive ( n = 42, p = 0.06). Most (91%) of the intestines showed no lesions typical for clinical B. hyodysenteriae infection, and median ingesta or fecal consistency was "soft and formed," indicating subclinical infection, colonization, or absence of infection. Ingesta from slaughtered pigs, in particular from the colon and sites with lesions, is useful material for detection of B. hyodysenteriae.

An Investigation into the Etiological Agents of Swine Dysentery in Australian Pig Herds

Swine dysentery (SD) is a mucohemorrhagic colitis, classically seen in grower/finisher pigs and caused by infection with the anaerobic intestinal spirochete Brachyspira hyodysenteriae. More recently, however, the newly described species Brachyspira hampsonii and Brachyspira suanatina have been identified as causing SD in North America and/or Europe. Furthermore, there have been occasions where strains of B. hyodysenteriae have been recovered from healthy pigs, including in multiplier herds with high health status. This study investigated whether cases of SD in Australia may be caused by the newly described species; how isolates of B. hyodysenteriae recovered from healthy herds compared to isolates from herds with disease; and how contemporary isolates compare to those recovered in previous decades, including in their plasmid gene content and antimicrobial resistance profiles. In total 1103 fecal and colon samples from pigs in 97 Australian herds were collected and tested. Of the agents of SD only B. hyodysenteriae was found, being present in 34 (35.1%) of the herds, including in 14 of 24 (58%) herds that had been considered to be free of SD. Multilocus sequence typing applied to 96 isolates from 30 herds and to 53 Australian isolates dating from the 1980s through the early 2000s showed that they were diverse, distinct from those reported in other countries, and that the 2014/16 isolates generally were different from those from earlier decades. These findings provided evidence for ongoing evolution of B. hyodysenteriae strains in Australia. In seven of the 20 herds where multiple isolates were available, two to four different sequence types (STs) were identified. Isolates with the same STs also were found in some herds with epidemiological links. Analysis of a block of six plasmid virulence-associated genes showed a lack of consistency between their presence or absence and their origin from herds currently with or without disease; however, significantly fewer isolates from the 2000s and from 2014/16 had this block of genes compared to isolates from the 1980s and 1990s. It is speculated that loss of these genes may have been responsible for the occurrence of milder disease occurring in recent years. In addition, fewer isolates from 2014/16 were susceptible to the antimicrobials lincomycin, and to a lesser extent tiamulin, than those from earlier Australian studies. Four distinct multi-drug resistant strains were identified in five herds, posing a threat to disease control.

Comparison of Brachyspira hyodysenteriae Isolates Recovered from Pigs in Apparently Healthy Multiplier Herds with Isolates from Herds with Swine Dysentery

Swine dysentery (SD) is a mucohaemorrhagic colitis of grower/finisher pigs classically resulting from infection by the anaerobic intestinal spirochaete Brachyspira hyodysenteriae. This study aimed to determine whether B. hyodysenteriae isolates from pigs in three healthy German multiplier herds supplying gilts to other farms differed from isolates from nine German production herds with SD. Isolates were subjected to whole genomic sequencing, and in silico multilocus sequence typing showed that those from the three multiplier herds were of previously undescribed sequence types (ST132, ST133 and ST134), with all isolates from the same herd having the same ST. All isolates were examined for the presence of 332 genes encoding predicted virulence or virulence lifestyle associated factors, and these were well conserved. Isolates from one multiplier herd were atypical in being weakly haemolytic: they had 10 amino acid substitutions in the haemolysin III protein and five in the haemolysin activation protein compared to reference strain WA1, and had a disruption in the promoter site of the hlyA gene. These changes likely contribute to the weakly haemolytic phenotype and putative lack of virulence. These same isolates also had nine base pair insertions in the iron metabolism genes bitB and bitC and lacked five of six plasmid genes that previously have been associated with colonisation. Other overall differences between isolates from the different herds were in genes from three of five outer membrane proteins, which were not found in all the isolates, and in members of a block of six plasmid genes. Isolates from three herds with SD had all six plasmid genes, while isolates lacking some of these genes were found in the three healthy herds-but also in isolates from six herds with SD. Other differences in genes of unknown function or in gene expression may contribute to variation in virulence; alternatively, superior husbandry and better general health may have made pigs in the two multiplier herds colonised by "typical" strongly haemolytic isolates less susceptible to disease expression.

Variation in hemolytic activity of Brachyspira hyodysenteriae strains from pigs

Brachyspira hyodysenteriae is the primary cause of swine dysentery, which is responsible for major economic losses to the pig industry worldwide. The hemolytic activity of 10 B. hyodysenteriae strains isolated from stools of pigs with mild to mucohemorrhagic diarrhea was compared and seven hemolysis associated genes were sequenced. Hemolysis induced by these strains varied from strong to near absent. One weakly hemolytic B. hyodysenteriae strain showed sequence changes in five hemolysis associated genes (tlyA, tlyB, hemolysin III, hemolysin activation protein and hemolysin III channel protein) resulting in amino acid substitutions. The occurrence of weakly hemolytic strains identifiable as B. hyodysenteriae should be taken into account in swine dysentery diagnostics. The presence of these strains may affect herd dysentery status, with great impact on a farms trading opportunities.

Brachyspira pilosicoli-induced avian intestinal spirochaetosis

Avian intestinal spirochaetosis (AIS) is a common disease occurring in poultry that can be caused by Brachyspira pilosicoli, a Gram-negative bacterium of the order Spirochaetes. During AIS, this opportunistic pathogen colonises the lower gastrointestinal (GI) tract of poultry (principally, the ileum, caeca, and colon), which can cause symptoms such as diarrhoea, reduced growth rate, and reduced egg production and quality. Due to the large increase of bacterial resistance to antibiotic treatment, the European Union banned in 2006 the prophylactic use of antibiotics as growth promoters in livestock. Consequently, the number of outbreaks of AIS has dramatically increased in the UK resulting in significant economic losses. This review summarises the current knowledge about AIS infection caused by B. pilosicoli and discusses various treatments and prevention strategies to control AIS.