Carrier state of enterotoxigenic Escherichia coli virulence markers in pigs: Effects on gut microbiota modulation and immune markers transcription

Enterotoxigenic Escherichia coli (ETEC) causes diarrhea in pigs at early age, leading to high mortality rates and significant economic losses in the swine industry. ETEC effect on gut microbiota and immune system is mostly studied in diarrheic model under controlled laboratory conditions, however its impact on asymptomatic carriers remains unknown. Thus, we investigated whether ETEC can modulate gut microbiota or regulate the transcription of immune markers in asymptomatic pigs in farm environment. Stool samples from newborn piglets, nursery and growing pigs, and sows were screened for ETEC markers, then submitted to 16S-rDNA sequencing to explore gut microbiota composition in carriers (ETEC+) and non-carriers (ETEC-) animals. We observed a reduced α-diversity in ETEC+ animals (p < 0.05), while bacterial compositions were mostly driven by ageing (p > 0.05). Prevotella marked ETEC-carrier group, while Rikenellaceae RC9 gut group was a marker for a healthy gut microbiota, suggesting that they might be biomarker candidates for surveillance and supplementation purposes. Furthermore, we observed transcription regulation of il6 and tff2 genes in ETEC+ in newborn and nursery stages, respectively. Our findings indicate that ETEC presence modulate gut microbiota and the immune response in asymptomatic pigs; nevertheless, further studies using a probabilistic design must be performed to assess the effect of ETEC presence on gut imbalance in pigs despite the age bias.

Exploring bacterial diversity and antimicrobial resistance gene on a southern Brazilian swine farm

The bacterial composition of and the circulation of antimicrobial resistance genes (ARGs) in waste from Brazilian swine farms are still poorly understood. Considering that antimicrobial resistance (AMR) is one of the main threats to human, animal, and environmental health, the need to accurately assess the load of ARGs released into the environment is urgent. Therefore, this study aimed to characterize the microbiota in a swine farm in southern Brazil and the resistome in swine farm wastewater treated in a series of waste stabilization ponds (WSPs). Samples were collected from farm facilities and the surrounding environment, representing all levels of swine manure within the treatment system. Total metagenomic sequencing was performed on samples from WSPs, and 16S-rDNA sequencing was performed on all the collected samples. The results showed increased bacterial diversity in WSPs, characterized by the presence of Caldatribacteriota, Cloacimonadota, Desulfobacterota, Spirochaetota, Synergistota, and Verrucomicrobiota. Furthermore, resistance genes to tetracyclines, lincosamides, macrolides, rifamycin, phenicol, and genes conferring multidrug resistance were detected in WSPs samples. Interestingly, the most abundant ARG was linG, which confers resistance to the lincosamides. Notably, genes conferring macrolide (mphG and mefC) and rifamycin (rpoB_RIF) resistance appeared in greater numbers in the late WSPs. These drugs are among the high-priority antibiotic classes for human health. Moreover, certain mobile genetic elements (MGEs) were identified in the samples, notably tnpA, which was found in high abundance. These elements are of particular concern due to their potential to facilitate the dissemination of ARGs among bacteria. In summary, the results indicate that, in the studied farm, the swine manure treatment system could not eliminate ARGs and MGEs. Our results validate concerns about Brazil's swine production system. The misuse and overuse of antimicrobials during animal production must be avoided to mitigate AMR.

Escherichia coli isolated from pyometra and cystitis in the same animal exhibit a wide phenotypic similarity

AIMS

Pyometra and cystitis caused by Escherichia coli are common diseases identified in canine or feline females. The origin of pyometra infection remains uncertain, and effective prevention strategies for this disease are still unknown. This study aimed to provide a phenotypic characterization, including antimicrobial resistance and virulence profiles, of endometrial pathogenic (EnPEC) and uropathogenic (UPEC) E. coli strains isolated simultaneously from the same animal.

METHODS AND RESULTS

Sixteen E. coli strains, from eight different animals, were analyzed in this study. The antimicrobial susceptibility profile of EnPEC and UPEC strains was determined using the disc diffusion method, which showed a similar susceptibility profile among strains (EnPEC and UPEC) from the same animal. The virulence profile of the strains was assessed through biofilm formation, as well as serum resistance abilities. EnPEC and UPEC strains from the same animal exhibited slight variations in their virulence and antimicrobial resistance capabilities. Overall, most of the strain pairs showed a high similarity in their ability to establish biofilms and survive in serum complement activity.

CONCLUSIONS

Overall, strains of E. coli isolated from both pyometra and cystitis in the same animal, despite presenting distinct clinical diseases, exhibit a wide phenotypic similarity, suggesting a common origin for the strains.

Alternative amplicon-PCR protocol for maximizing bacterial and fungal sequencing in low-biomass samples

Determining bacterial and fungal communities from low-biomass samples remains a challenge for high-throughput sequencing. Due to the low microbial load and host contamination, some sites, including the female upper reproductive tract and the lower respiratory tract, were even considered sterile until recent years. Despite efforts to improve sampling and DNA isolation protocols, some samples provide insufficient microbial DNA input for library preparation and sequencing. Herein, we propose an alternative amplicon-PCR protocol to be used in bacterial and fungal sequencing in low-biomass samples, targeting 16S-rDNA and the internal transcribed spacer region (ITS), respectively. Similar to a nested-PCR, we performed two sequential PCR reactions to maximise the target amplicon. We compared metagenomic results from the original Illumina protocol (Protocol 1 - P1) and the alternative one (Protocol 2 - P2), using a mock community and clinical samples with different microbial loads. Our findings showed no significant differences in data generated by P1 and P2, indicating that the second amplification round does not bias the microbiota diversity rates. Thus, the alternative protocol can be applied for low-biomass samples when the original protocol results in spurious output, preventing library preparation and sequencing.

Genome analysis of Pseudomonas strain 4B with broad antagonistic activity against toxigenic fungi

Pseudomonas sp. 4B isolated from the effluent pond of a bovine abattoir was investigated as antifungal against toxigenic fungi. The complete genome of Pseudomonas 4B was sequenced using the Illumina MiSeq platform. Phylogenetic analysis and genome comparisons indicated that the strain belongs to the Pseudomonas aeruginosa group. In silico investigation revealed gene clusters associated with the biosynthesis of several antifungals, including pyocyanin, rhizomide, thanamycin, and pyochelin. This bacterium was investigated through antifungal assays, showing an inhibitory effect against all toxigenic fungi tested. Bacterial cells reduced the diameter of fungal colonies, colony growth rate, and sporulation of each indicator fungi in 10-day simultaneous growing tests. The co-incubation of bacterial suspension and fungal spores in yeast extract-sucrose broth for 48 h resulted in reduced spore germination. During simultaneous growth, decreased production of aflatoxin B1 and ochratoxin A by Aspergillus flavus and Aspergillus carbonarius, respectively, was observed. Genome analysis and in vitro studies showed the ability of P. aeruginosa 4B to reduce fungal growth parameters and mycotoxin levels, indicating the potential of this bacterium to control toxigenic fungi. The broad antifungal activity of this strain may represent a sustainable alternative for the exploration and subsequent use of its possible metabolites in order to control mycotoxin-producing fungi.

Genotypic characterization of Streptococcus didelphis causative of fatal infection in white-eared opossums

Streptococcus didelphis was once reported as related to severe infections in opossums. Thus, we present the first comprehensive whole-genome characterization of clinical S. didelphis strains isolated from white-eared opossums (Didelphis albiventris). Long-read whole-genome sequencing was performed using the MinION platform, which allowed the prediction of several genomic features. We observed that S. didelphis genomes harbor a cluster for streptolysin biosynthesis and a conserved genomic island with genes involved in transcriptional regulation (arlR) and transmembrane transport (bcrA). Antimicrobial resistance genes for several drug classes were found, including beta-lactam, which is the main antimicrobial class used in Streptococcus spp. infections; however, no phenotypical resistance was observed. In addition, we predicted the presence of 33 virulence factors in the analyzed genomes. High phylogenetic similarity was observed between clinical and reference strains, yet no clonality was suggested. We also proposed dnaN, gki, pros, and xpt as housekeeping candidates to be used in S. didelphis sequence typing. This is the first whole-genome characterization of S. didelphis, whose data provide important insights into its pathogenicity.

A cross-sectional study on Campylobacter fetus subsp. venerealis prevalence and associated factors in Brazilian southern cattle farms

Cattle farming is a major livestock activity with economic relevance in Rio Grande do Sul (RS), Brazil. However, this activity is still considered of intermediate to low technological level, and in this region, there are few epidemiologic reports of Campylobacter fetus subsp. venerealis (Cfv), the causative agent of bovine genital campylobacteriosis (BGC). Thus, we designed a cross-sectional study to assess the prevalence and Cfv-associated factors in cattle farms in RS, Brazil. In total, 99 farms were randomly selected to participate in the survey. Preputial mucus samples from selected bulls were collected twice (within a 15-day interval) and subjected to Cfv molecular detection. A farm was considered positive when at least one sample was positive for Cfv. Our findings indicate that the farm-level Cfv prevalence in RS is 67.67%. On average, the chance of a farm using natural service to be Cfv-positive increased approximately twice compared to farms that do not use natural service. We also determined that Cfv routine tests reduce the chance of a farm being positive by 92%. Therefore, both Cfv detection tests and the reduction of natural services decrease the chance of a farm being positive for Cfv. Finally, we conclude that Cfv is widely spread in Southern Brazil cattle farms and it is urgent the implementation of control measures to reduce Cfv prevalence in the target population.

Streptococcus canis prostatitis and endocarditis with thromboembolism in a dog with sertoli cell tumour in a cryptic testis and prostatic squamous metaplasia

We describe an unusual case of prostatitis caused by Streptococcus canis evolving to endocarditis and splenic, renal, and cerebral thromboembolism in a dog, associated with a Sertoli cell tumour in a cryptic testis and diffuse prostatic squamous metaplasia. A nine-year-old, intact male, mixed-breed dog was presented to a veterinary teaching hospital with abdominal pain and prostration. Physical examination and abdominal ultrasonography revealed an atrophic right testicle located in the subcutaneous tissue. The left testicle was in the abdominal cavity with increased dimensions and irregular contours. Complete blood count analysis showed marked neutrophilic leukocytosis and thrombocytopenia. After clinical worsening, euthanasia was performed, and the dog was submitted to post-mortem examination. The main gross findings included testicular malposition with one cryptic and one ectopic testis, enlarged prostate with purulent content, distension of the urinary bladder with cloudy urine, vegetative valvular endocarditis in the mitral valve, and spleen and renal infarcts. Histological examination showed a Sertoli cell tumour in the abdominal testis, diffuse prostatic squamous metaplasia with marked keratinization associated with bacterial prostatitis, fibrinonecrotic cystitis, bacterial endocarditis with marked myxomatous degeneration in the mitral valve, and splenic, renal, and cerebral thromboembolism. Microbiological analysis identified Streptococcus canis in the prostate and mitral valve. Sertoli cell tumour of cryptic testis increases oestrogen production and leads to squamous metaplasia of the prostate, which should be considered as predisposing factors for ascending S. canis infection from the urogenital tract to the prostate. Then, haematogenous spread of S. canis from the prostate to mitral valve cause endocarditis and subsequent thromboembolism and infarcts, all decisive to poor prognosis in this case.

Virulent potential of methicillin-resistant and methicillin-susceptible Staphylococcus pseudintermedius in dogs

Staphylococcus pseudintermedius is a zoonotic pathogen responsible for several infectious diseases in pet animals, yet its pathogenic potential is not fully understood. Thus, this study aims to unravel the virulence profile of S. pseudintermedius from canine origin. Methicillin-resistant (MRSP) and methicillin-susceptible (MSSP) strains were isolated from different infection sites and their genotypic and phenotypic features were compared to determine the clinical implications of MRSP and MSSP strains. Bacterial identification was performed using MALDI-TOF and 16S-rDNA sequencing. In addition, we used multilocus sequence typing (MLST) for strains' sequence type (ST) determination and phylogenetic relationship. The strains were screened for toxin genes, including cytotoxins (lukS, lukF), exfoliative toxin (siet), enterotoxins (sea, seb, sec, secCanine, sel, sem, and seq) and toxic shock syndrome toxin (tst-1). In vitro phenotypic analyses assessing antimicrobial susceptibility profile, biofilm formation ability, and expression of extracellular matrix components were performed. The investigated S. pseudintermedius strains belong to 17 unique ST, most of which were classified as ST71. MSSP and MRSP strains shared siet, lukS, and lukF virulence markers. Our findings showed that some MSSP strains also harbored sel, seq, and sem enterotoxin genes, suggesting a more diverse virulence profile. All MRSP strains and 77% of MSSP strains were classified as multidrug resistant (MDR). Moreover, all investigated S. pseudintermedius strains showed strong biofilm formation ability. In summary, our findings highlight the wide spread of highly virulent and drug-resistant zoonotic S. pseudintermedius strains, being a potential concern for One Health issues.

Genetic and molecular Omp25 analyses from worldwide Brucella canis strains: Possible mutational influences in protein function

Brucella canis is responsible for canine brucellosis, a neglected zoonotic disease. The omp25 gene has been described as an important marker for Brucella intra-species differentiation, in addition to the ability to interact with the host immune system. Therefore, this study investigated the omp25 sequence from B. canis strains associated to a phylogenetic characterization and the unveiling of the molecular structure. In vitro analyses comprised DNA extraction, PCR, and sequencing of omp25 from 19 B. canis strains. Moreover, in silico analyses were performed at nucleotide level for phylogenetic characterization and evolutionary history of B. canis omp25 gene; and in amino acid level including modeling, dynamics, and epitope prediction of B. canis Omp25 protein. Here, we identified a new mutation, L109P, which diverges the worldwide omp25 sequences in two large branches. Interestingly, this mutation appears to have epidemiology importance, based on a geographical distribution of B. canis strains. Structural and molecular dynamics analyses of Omp25 revealed that Omp25L109P does not sustain its native β-barrel. Likewise, the conformation of B-cell epitope on the mutated region was changed in Omp25L109P protein. Even without an evolutive marker, the new identified mutation appears to affect the basic function of B. canis Omp25 protein, which could indicate virulence adaptation for some B. canis strains in a context of geographical disposition.

Aerossacolitis and Pneumonia in an Indian Peafowl Caused by Lactobacillus agilis

Background: The peafowl is an ornamental bird that has the habit of eating directly from the earthy soil, which makes this bird more susceptible to endoparasites. One important endoparasite is Eucoleus contortus, which leads to inflammatory processes that alter the local microbiota, potentializing disease. By the other way, a member of the bird’s microbiota there is the genus Lactobacillus, but when occurs some imbalance, these bacteria can overgrowth and even cause some infection. This report describes the pathological and microbiological findings of chronic necrotizing pneumonia and aerossacolitis caused by Lactobacillus agilis in a peafowl, associated with parasitism by E. contortus. Case: A peafowl (Pavo cristatus), adult, male, who lived on a farm with contact with other species of animal, was submitted to post-mortem examination due to sudden death. This animal lived in an extensive system on the property and was the only one of its species. During the gross evaluation, the air sacs were filled with solid yellowish crumbly material. The same material was observed forming well-defined nodules that occupied > 50% of the lung parenchyma. Histological analysis showed multiple parabronchi dilated and filled with caseous necrosis, characterized by abundant cellular debris and fibrin deposition. These areas were surrounded by the proliferation of fibrous connective tissue and inflammatory infiltrate of macrophages, giant cells, lymphocytes, and plasma cells. The air sacs parenchyma showed fibrin deposition and mixed inflammatory infiltrate. Multiple gram-positive bacilli were observed within the caseous foci in Gram-stained slides. In the crop and esophageal mucosa, cross-sections of filiform nematodes morphologically compatible with E. contortus were associated with chronic inflammatory infiltrate and epidermal hyperkeratosis. A lung section was submitted to Gram-Brown-Hopps and Ziehl-Neelsen (ZN) stains for bacterial investigation, and Grocott's methenamine silver (GMS) stain for fungal investigation. Short gram-positive bacilli bacteria are observed within the caseous foci in Gram-stained slides. By the other way, no agents were identified on the ZN and GMS stains. Following the analysis, lung fragments were cultivated at aerobic and microaerophilic conditions on sheep blood agar and McConkey agar. All the microbial cultures were incubated at 37°C to 48 h. Pure culture, in microaerophilic condition, of Gram-positive bacilli, was observed. The isolated bacterium was identified by MALDI-TOF MS as L. agilis.Discussion: Although uncommon, L. agilis was the single bacterium identified and therefore, associated as a primary cause of necrotic pneumonia and aerossacolitis in the studied peafowl. The presence of E. contortus could induce the aspiration of regurgitated of little amount of material from the gastrointestinal tract with sufficient bacterial load to initiate an infection, but not enough to smother the animal. The gradual aspiration can induce a chronic inflammatory condition. Infections by bacteria from the host microbiota have been observed in animals and humans with immunodeficiency. In summary, both the parasitosis and the inflammation could be resulted by the parasite and the aspiration of gastric product, which probably interfered in the immune response and allowed the overgrowth of L. agilis. In the current case report, based on macroscopic, microscopic and bacteriological results, we have provided insights to understand how the parasitosis made possible a pneumonia from a bacterium from the host's microbiota. Finally, to the best of our knowledge, this is the first report of L. agilis as causal agent of fatal necrotic pneumonia and aerossacolitis in peafowl.Keywords: respiratory infection, ornamental birds, secondary infection, parasitosis.

Genomic analysis of Enterococcus durans LAB18S, a potential probiotic strain isolated from cheese

Gut microbiota exerts a fundamental role in human health and increased evidence supports the beneficial role of probiotic microorganisms in the maintenance of intestinal health. Enterococcus durans LAB18S was previously isolated from soft cheese and showed some desirable in vitro probiotic properties, for that reason its genome was sequenced and evaluated for genes that can be relevant for probiotic activity and are involved in selenium metabolism. Genome sequencing was performed using the Illumina MiSeq System. A variety of genes potentially associated with probiotic properties, including adhesion capability, viability at low pH, bile salt resistance, antimicrobial activity, and utilization of prebiotic fructooligosaccharides (FOS) were identified. The strain showed tolerance to acid pH and bile salts, exhibited antimicrobial activity and thrived on prebiotic oligosaccharides. Six genes involved in selenium metabolism were predicted. Analysis of the SECIS element showed twelve known selenoprotein candidates. E. durans LAB18S was the only food isolate showing absence of plasmids, virulence and antimicrobial resistance genes, when compared with other 30 E. durans genomes. The results of this study provide evidence supporting the potential of E. durans LAB18S as alternative for probiotic formulations.

Cows' reproductive performances and parity order influences the cervicovaginal fungal community

Fungi have already been described as etiological agents of reproductive diseases such as endometritis and infertility in cows. However, few studies have been developed to elucidate the entire cervicovaginal fungal communities in cows. Therefore, our study aimed to characterize the fungal community present in the cervix of cows with different reproductive performances. Cervicovaginal mucus was collected from 36 Angus breed cows (1.5-12 years old) on a commercial beef cattle ranch. Twenty-one cows had a history of infertility in the year prior to the collection, showing early return to estrus. Ten cows were sampled at 60-70 days postpartum being considered fertile cows. Additionally, five non-sexually active heifers were employed as control group. Ascomycota and Basidiomycota were the predominant fungal phyla in the analyzed animals. Diversity metrics of the cervicovaginal fungal community revealed statistical differences in the composition of the fungal community among infertile cows, fertile cows and non-sexually active heifers. In addition, the cervicovaginal fungal microbiota had significative increased richness and evenness in nulliparous cows and non-sexually active heifers, while in multiparous cows a decreased richness and evenness of the fungal microbiota were identified. These results provide an unprecedented understanding of the cervicovaginal fungal structure associated with infertility and parity order.

The influence of regulatory elements on Mycoplasma hyopneumoniae 7448 transcriptional response during oxidative stress and heat shock

BACKGROUND

The comprehension of genome organization and gene modulation is essential for understanding pathogens' infection mechanisms. Mycoplasma hyopneumoniae 7448 genome is organized in transcriptional units (TUs), which are flanked by regulatory elements such as putative promoters, terminators and repetitive sequences. Yet the relationship between the presence of these elements and bacterial responses during stress conditions remains unclear. Thus, in this study, in silico and RT-qPCR analyses were associated to determine the effect of regulatory elements in gene expression regulation upon heat shock and oxidative stress conditions.

METHODS AND RESULTS

Thirteen TU's organizational profiles were found based on promoters and terminators distribution. Differential expression in genes sharing the same TUs was observed, suggesting the activity of internal regulatory elements. Moreover, 88.8% of tested genes were differentially expressed under oxidative stress in comparison to the control condition, being 81.3% of them surrounded by their own regulatory elements. Similarly, under heat shock, 44.4% of the genes showed regulation when compared to control condition, being 75.0% of them surrounded by their own regulatory elements.

CONCLUSIONS

Altogether, this data suggests the activity of internal regulatory elements in gene modulation of M. hyopneumoniae 7448 transcription.

Pet Pyometra: Correlating Bacteria Pathogenicity to Endometrial Histological Changes

Pyometra is a life-threatening infectious disease that frequently affects bitches and queens. Although histopathological patterns of pyometra have been extensively explored, the microbiological aspects, such as bacteria pathogenicity, have not been correlated to microscopy endometrial lesions so far. In this study, these two pathological aspects of pyometra were analysed and correlated. Uterus fragments and intrauterine content samples were collected from pets diagnosed with pyometra (30) and submitted to histopathology analysis and bacterial culture, respectively. The degree of endometrial histopathological lesions in pyometra cases were classified as mild, moderate and severe. Thirty different bacteria isolates were identified from intrauterine content culture. Escherichia coli (E. coli) was pure isolated in 57.7% and highly related to severe endometrial lesions. Immunohistochemistry assay revealed the adhesion and invasion of this bacteria agent to the injured endometrium. Virulence aspects of these E. coli strains were explored, demonstrating biofilm formation ability and a set of virulence genes in most isolates. These results support the adaptive genetic and phenotypic advantages of E. coli for uterus infection, and justify the high frequency of this agent involved in pyometra cases.

Non-lactose-fermenting uropathogenic Escherichia coli from dogs: virulence profile characterization

Non-lactose-fermenting Escherichia coli (NLFEC) has a few descriptive studies restricted to human infections. In the present study, isolates of NLFEC obtained from urine samples of dogs with hyperadrenocorticism were characterized regarding their virulence ability, biofilm formation capacity and antimicrobial susceptibility profile. Escherichia coli lactose-fermenting strains from urinary infection in dogs with the same conditions were analysed to provide comparisons. The non-lactose-fermenting E. coli strains were classified as belonging to clade I E. coli, whereas the lactose-fermenting strains were classified in phylogroup B2. All strains presented virulence markers to adhesion, iron acquisition, toxins, colicin and cytotoxin production, and biofilm regulation. Components of the extracellular matrix in addition to the in vitro biofilm formation ability were observed in the strains. Multidrug resistance (MDR) profiles were observed by in vitro susceptibility tests to all NLFEC strains. In summary, non-lactose-fermenting uropathogenic E. coli from dogs behaves similar to lactose-fermenting E. coli, exhibiting MDR profile, and pathogenic potential of promote animal infections.

Clinical and microbiological characterization of subclinical bacteriuria and sporadic bacterial cystitis in dogs with spontaneous hypercortisolism

Study's aims were to characterize subclinical bacteriuria (SB) and sporadic bacterial cystitis (SBC) in dogs with spontaneous hypercortisolism (HC). Prospective cross-sectional design divided patients as newly diagnosed (n = 27), poorly controlled (n  = 21), well controlled (n  = 34), and controls (n  = 19). Urine culture positive results were identified by MALDI-TOF and submitted to antibiogram. Escherichia coli was the most common microorganism (36%). The majority of positive cultures in HC were SB (12.2%). All 4.1% SBC cases were in well controlled HC cases. Bacteriuria correlated with low urine specific gravity and low lymphocyte count. HC degree of control correlated with leukocyturia. SB/SBC cases were treated based in antimicrobial susceptibility leading to microbiological cure in 75% of HC cases. Persistent infections occurred only in SB cases, all by E. coli which became more resistant. SB/SBC prevalence in canine HC is actually lower. Further evidence for current ISCAID guideline contraindication for SB treatment due to HC were provided.

Functional characterization of the putative FAD synthase from Mycoplasma hyopneumoniae

In bacteria, the biosynthesis of the cofactor flavin adenine dinucleotide (FAD), important in many physiological responses, is catalyzed by the bifunctional enzyme FAD synthase (FADSyn) which converts riboflavin into FAD by both kinase and adenylylation activity. The in silico 3D structure of a putative FADSyn from Mycoplasma hyopneumoniae (MhpFADSyn), the etiological agent of enzootic pneumonia was already reported, nevertheless, the in vitro functional characterization was not yet demonstrated. Our phylogenetic analysis revealed that MhpFADSyn is close related to the bifunctional FADSyn from Corynebacterium ammoniagenes. However, only the domain related to adenylylation was assigned by InterPro database. The activity of MhpFADSyn was evaluated through in vitro enzymatic assays using cell extracts from IPTG-inducible heterologous expression of MhpFADSyn in Escherichia coli. The flavoproteins were analyzed by HPLC and results showed that IPTG-induced cell lysate resulted in the formation of twofold increased amounts of FAD if compared to non IPTG-induced cells. Consumption of riboflavin substrate was also threefold greater in IPTG-induced lysate compared to non IPTG-induced cell extract. Thus, the recombinant MhpFADSyn protein could be associated to FAD biosynthesis. These findings contribute to expand the range of potential drug targets in diseases control and unveil metabolic pathways that could be attribute to mycoplasmas.

Microbial Contamination and Antimicrobial Resistance Profiles Indicate Potential Risks of Infection at the Veterinary Medical Teaching Hospital - UFRGS, Porto Alegre, Brazil

Background: This study aimed to assess the level of bacterial contamination in the Small Animals Sector of the Veterinary Medical Teaching Hospital (HCV) of the Universidade Federal do Rio Grande do Sul (UFRGS). Firstly, a committee was invited to complete a questionnaire and to list critical sample sites for collection. With the identification of the places to be sampled, collections were made with sterile swabs on different surfaces of environments of the Veterinary Hospital. The identification of important bacteria in the veterinary area, in the different sampled environments, raises the concern for hygiene procedures in the veterinary hospital environment.Materials, Methods & Results: Sixteen samples were collected from these different areas, and microbiological analyses were performed. Standard counts of viable and strictly aerobic mesophilic microorganisms were realized. Collections were made to assess ambient air quality. With the microbiological analysis performed, bacteria of clinical importance were identified. To assess the resistance profile of the bacteria, the susceptibility test to antimicrobials was performed. MALDI-TOF/MS measurement identified 29 bacteria at the genus level and 10 bacteria at the species level and the antimicrobial susceptibility test was realized. Most of the isolates identified (60%) were bacteria of the genus Staphylococcus spp. Regarding antimicrobial susceptibility analysis the 10 bacteria identified at the species level were assessed. Test results showed that the isolates S. aureus, S. epidermidis and S. haemolyticus - collected from treatment room 2 - and S. haemolyticus, which had been isolated from samples from treatment room 2 of the cattery, presented multiresistance. Pantoea ananatis isolates from room 5 also showed a multiresistant profile for erythromycin, cephalothin, vancomycin and ampicillin. Micrococcus luteus isolates from the x-ray room and the kennel showed resistance to ceftazidime. Staphylococcus equorum isolates from room 4 were sensitive to all tested antimicrobials. Discussion: In Brazilian legislation there are no official microbiological parameters for surfaces in a veterinary hospital environment. The microorganisms present in the air are transient and variable, and the number and types of airborne agents is determined by the various sources of contamination in the environment. These microorganisms can be found in suspension, particulate matter and water droplets. Veterinary medical care tables are potentially contaminated by the animals handling, including those that sometimes defecate or urinate during their medical visit. Frequent handwashing is also known to be an important means of personal protection and disease prevention, although it is estimated that only 40% of practitioners do so routinely. Based on these results, we recommend a plan of bacterial control and disinfection that should be implemented to ensure more effective sanitary conditions. Microorganism counts were high in some of the veterinary hospital environments tested, indicating that current disinfection and hygiene practices are not sufficient to control the establishment of these microorganisms at the study sites. In view of this, it is reasonable to conclude that permanent monitoring and assessment of the effectiveness of hygiene protocols is needed in different sectors of the hospital. This may be an essential tool in a preventive approach to stop the spread of selectively resistant microorganisms, as well as cases of hospital infections. In addition, continuous staff training and awareness of the importance of personal and environmental hygiene is vital for minimizing the presence of these microorganisms in hospitals and avoid their transmission to patients. Finally, a more systematic hygiene guideline should be implemented in areas that showed higher counts.

Campylobacter fetus in Abomasal Fluid from Spontaneously Aborted Bovine and Ovine Fetuses

Background: Pregnancy losses are a major concern in livestock industry due to their economic impact on producers. Campylobacter fetus subspecies fetus (Cff) and C. fetus subspecies venerealis (Cfv) are directly related to reproductive failures in ruminants. Cff colonizes the gastrointestinal tract of a wide range of hosts leading to abortion, while Cfv is restricted to genital tract being generally associated to infertility in bovine. Considering the great economic losses related to campylobacteriosis in cattle and ovine herds, this study aims to investigate the occurrence of C. fetus, considering Cff and Cfv subspecies, in bovine and ovine spontaneously aborted fetuses in state of Rio Grande do Sul, Brazil.Materials, Methods & Results: In this study, samples of abomasal fluid collected from 30 spontaneously aborted bovine (n = 18) and ovine (n = 12) fetuses were investigated for the detection of Campylobacter fetus throughout conventional PCR. Positive fetuses for C. fetus presence were further analyzed by molecular assays for Cff and Cfv detection, in order to determine subspecies identification. When available, samples of the main organs of the thoracic and abdominal cavities, as well as the brain, skeletal muscle, eyelid, skin, and placenta were collected for further histopathological analyses and bacterial culture, aiming to assess the presence of infection lesions and pathogens in those sites, respectively. Additionally, RT-qPCR assays were also performed for the detection of ruminant pestivirus, in order to detect bovine viral diarrhea cases. Throughout the present methodology, C. fetus was detected in the abomasal fluid samples of 2 bovine fetuses, being both identified as Cfv subspecies by PCR. Histopathological analyses demonstrated that macroscopic and microscopic changes found in the Cfv-positive animals were not either specific or directly related to Campylobacter infections. Moreover, no significant bacterial growth was observed in microbiological culture from the collected tissues, and both fetuses were negative for ruminant pestivirus. Differently, there was no detection of C. fetus in any of the analyzed ovine fetuses.Discussion: Considering that abortion diagnosis rates reported in cattle and sheep industry are highly variable among the published studies, and that abortion diagnoses are commonly inconclusive due to difficulties in sampling methodology and inadequate identification of the pathogen involved, it is important to investigate the etiological causes of abortion the herds for better understanding the causes of pregnancy issues and monitoring their occurrence. In addition, the absence of pathognomonic lesions in the tissues investigated in the histopathological analyses observed in this study strongly suggests that well-known etiological agents commonly associated to abortion, such as Leptospira spp., Toxoplasma spp., Chlamydia spp. and Neospora caninum, are unlikely to be the cause of infection of the analyzed fetuses. Taking this into account, the presence of C. fetus in the abomasal fluid samples from two bovine fetuses demonstrated in the present study suggests the possible association of Cfv not only with infertility, but also with cases of bovine abortion, highlighting the importance of investigating unusual causal agents of abortions in sheep and cattle. Overall, an adequate diagnosis is essential for establishing better prevention strategies to avoid the circulation of abortion-related infectious agents in the herds.Keywords: campylobacteriosis, molecular diagnosis, venereal disease, abortion, reproductive disease.

Frozen bovine preputial mucus as a suitable sample for the direct molecular diagnosis of Campylobacter fetus subsp. venerealis

Long transportation times remain a challenge to the satisfactory diagnosis of Campylobacter fetus subsp. venerealis (Cfv). Here we demonstrated that samples of frozen bovine preputial mucus maintained at -20 °C for 10 days can be used as an alternative source for molecular diagnosis of Cfv. This approach will improve the analysis of this bacterium.

Mycobacterium tuberculosis var. tuberculosis infection in two captive black capuchins (Sapajus nigritus) in Southern Brazil

Tuberculosis is a common zooanthroponosis in humans with a high incidence in Brazil, but it may also affect non-human primates (NHPs), of which Old World primates are most commonly involved. Nonetheless, its occurrence in New World primates is unknown, and therefore, this study aimed to describe the infection by Mycobacterium tuberculosis variant tuberculosis in two captive black capuchin monkeys (Sapajus nigritus) in Southern Brazil. The primates were housed in the same enclosure, wherein close contact with humans frequently occurred, and presented apathy, anorexia, and death in a clinical course of 15 days to 2 months. At the necropsy, the tracheobronchial lymph nodes were markedly enlarged and firm to hard and on the cut surface had a caseous aspect. The lungs exhibited two injury patterns: multifocal and disseminated. Microscopically, the lungs exhibited multifocal to coalescing necrotic granulomas and non-necrotic granulomas, with multiple acid-fast bacilli within the cytoplasm of epithelioid macrophages and multinucleated giant cells. Bacilli were also labeled upon immunohistochemistry (IHC) for Mycobacterium tuberculosis. Microbiological culture of lung samples from both cases yielded colonies compatible with M. tuberculosis. The isolates were identified as M. tuberculosis var. tuberculosis through polymerase chain reaction (PCR). Although tuberculosis is poorly described in New World primates, M. tuberculosis var. tuberculosis may cause a highly contagious and progressive disease with high mortality in black capuchin monkeys (S. nigritus).

Caution at choosing a particular colony-forming unit from faecal Escherichia coli: it may not represent the sample profile

Data about phylogenetic classification of Escherichia coli colonizing calves, lambs and foals are routinely neglected and restricted to outdated methodologies, even in the context of antimicrobial susceptibility (AS) testing. Thus, the aim of this study was to determine the phylogenetic diversity and the AS profile of E. coli colony-forming units (CFUs) from faecal samples of healthy animals. Five CFUs of E. coli were randomly selected from each faecal culture of calves (n = 13), foals (n = 13) and lambs (n = 13), totalizing 195 CFUs phylo-typed by quadruplex PCR. The AS profile of five CFUs from 15 samples (five from each animal species; n = 75 isolates) against nine drugs was determined by agar diffusion test. We found E. coli belonging to all phylo-groups already described, except D group, with the predominance of B1 (65% CFUs; 126/195) in the three-animal species sampled. Most faecal samples of calves (77%; 10/13) and foals (69%; 9/13) harboured both pathogenic and nonpathogenic E. coli. All faecal samples showed CFUs with diverse AS profile, highlighting the ineffectiveness of tetracycline, sulphonamide and ampicillin. As a key point, our data reinforce the importance to select at least four E. coli CFUs for AS testing. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides relevant data about the high phylogenetic and antimicrobial susceptibility diversity observed in Escherichia coli colony-forming units (CFUs) from a bacteriological culture of faeces from healthy calves, foals and lambs. The selection pressure exerted by the herd treatment may directly impact the intestinal microflora of animals that have never been treated. Finally, we emphasize the importance of Clinical Laboratory Standards Institute guidelines and we recommended to analyse at least four E. coli CFUs to determine, in particular, the antimicrobial susceptibility profile of faecal isolates, independent of the animal's health status.

Clonality of Mycoplasma hyopneumoniae in swine farms from Brazil

Mycoplasma hyopneumoniae causes enzootic pneumonia (EP) in swine, a disease related to high economic losses in production systems. Epidemiological spread of M. hyopneumoniae clones was studied by multi-locus sequence typing (MLST) in several swine production regions but so far not in South America. Using MLST, we have therefore investigated M. hyopneumoniae clones circulating in farms from three main swine production regions in Brazil. Porcine lungs samples were collected between 2015 and 2016 in farms with EP outbreaks. Three geographically distant regions were selected, and 67 M. hyopneumoniae positive samples, each one from a different farm, were included in the study. The occurrence of five sequence types (ST) was demonstrated and the majority of the samples were identified as ST-69 (n = 60; 89.5%), followed by ST-70 (n = 3; 4.5%), ST-123 (n = 2; 3%), ST-124 (n = 1; 1.5%) and ST-127 (n = 1; 1.5%). There was no association of any specific ST with region or production system. The five STs were all new ones, probably representing unique Brazilian clones. ST-69 and ST-70 on one side and ST-123 and ST-124 on the other side are phylogenetically close, while ST-127 is singleton. In conclusion, our results showed a low variability and high clonality of M. hyopneumoniae genotypes from Brazilian farms affected by EP.

Hemorrhagic Stroke in a Dog with Anaplastic Carcinoma of the Mammary Gland

Background: anaplastic carcinoma of the mammary gland is considered a highly invasive and malignant neoplasia, which usually leads to neoplastic thrombosis and epidermal ulceration due to invasiveness of lymphatic vessels by tumor emboli. Loss of epidermal barrier predisposes to secondary bacterial infection, mainly by commensal bacteria of the skin, and septicemia can be observed in cases of systemic dissemination. Neoplastic emboli and septic thrombi can lead to vascular obstruction, which can predispose to infarction in multiple organs. The aim of this case report is to describe a case of hemorrhagic stroke in a dog with anaplastic carcinoma of the mammary gland.Case: a 12-year-old, mixed breed, female spayed canine presented with mammary tumor with plaque formation, associated with skin ulceration which extended to the medial region of pelvic limbs. The animal also displayed neurologic clinical signs characterized by stupor, opisthotonos and apathy. Due to poor prognosis, the canine was euthanized and submitted to necropsy. During external examination, the animal was in a good body condition, had moderately pale mucosae, and it was noted a nodular plaque in the abdominal ventral area extending from thoracic to inguinal mammary gland. The mass was firm and white, extensively ulcerated, and extending from the thoracic to inguinal mammary gland. There was a well circumscribed area of infarction in the spleen and kidney. In the cerebral cortex it was observed an extensive area of hemorrhage with adhered blood clot from frontal to temporal lobe. There were multiple well circumscribed, firm, and white areas in the myocardium. Histologically, the neoplastic proliferation was composed by epithelial cells with high pleomorphism, features of malignancy, and no delimitations, leading to the diagnosis of anaplastic carcinoma of the mammary gland. Admixed with tumor cells there were multiple areas of hemorrhage, necrosis and thrombosis. In the cerebral cortex there was a focally extensive area of hemorrhage, multifocal thrombosis, abundant amount of gitter cells, and moderate perivascular inflammatory infiltrate of lymphocytes. There was neoplastic infiltrate in the bladder, adrenal glands, and lungs. There were multiple areas of necrosis and thrombosis in spleen and heart. Bacterial examination was performed in fragments of cerebral cortex and kidney, and Staphylococcus pseudintermedius was isolated.Discussion: anaplastic carcinoma of the mammary gland has an epithelial origin and is considered the most malignant neoplasm with worst prognosis due to its characteristic of high cellular pleomorphism and the ability of invasiveness of vessels and adjacent tissues. Therapeutic options are scarce and palliative, and surgical removal is not indicated. Dermal ulceration usually is infected by opportunistic bacteria that can lead to inflammation and pain, and treatment in these cases is focused on pain management with analgesics. The bacterial infection can evolve to septicemia with decrease of endogenous anticoagulants and consequent blood hypercoagulability. Moreover, studies demonstrate the higher risk of clotting abnormalities when associated to progression of mammary carcinomas, which includes anaplastic carcinoma of the mammary gland. In this study, two causes which may have led to thromboembolism and cerebral hemorrhage are discussed: septicemia after invasion of lymphatic vessels by the anaplastic carcinoma or hypercoagulability caused by the systemic neoplasia, which could have reduce the blood flow to vessels of the cerebral cortex.

Global analysis of sRNA target genes in Mycoplasma hyopneumoniae

BACKGROUND

Small RNAs (sRNAs) are noncoding molecules that regulate different cellular activities in several bacteria. The role of sRNAs in gene expression regulation is poorly characterized in the etiological agent of porcine enzootic pneumonia Mycoplasma hyopneumoniae. We performed a global analysis of the sRNAs, sRNA target genes and regulatory elements previously identified in their genome and analyzed the expression of some sRNAs and their target genes by quantitative RT-PCR (qPCR) in three different culture conditions.

RESULTS

Seven of the 145 sRNA target genes are organized as monocistronic genes (mCs) while the other 138 sRNA target genes are organized into transcriptional units (TU). The identification of transcriptional regulatory elements (promoter motif, DNA repeat sequence or intrinsic terminator) was verified in 116 of the 145 sRNA target genes. Moreover, the 29 sRNA target genes without regulatory elements revealed the presence of at least one regulatory element in the boundaries of the TU or in other internal genes of the TU. We verified that 16 sRNAs showed differential expression, seven in heat shock condition and 14 in oxidative stress condition. Analysis of the differential expression of the sRNA target genes showed that the tested sRNAs possibly regulate gene expression. The sRNA target genes were up- or down-regulated possibly in response to sRNA only under oxidative stress condition. Moreover, the sRNA target genes are involved in diverse processes of the cell, some of which could be linked to transcription processes and cell homeostasis.

CONCLUSION

Our results indicate that bacterial sRNAs could regulate a number of targets with various outcomes, and different correlations between the levels of sRNA transcripts and their target gene mRNAs were found, which suggest that the regulation of gene expression via sRNAs may play an important role in mycoplasma.

Histomorphometric study of the anterior latissimus dorsi muscle and evaluation of enzymatic markers of broilers affected with dorsal cranial myopathy

Dorsal cranial myopathy (DCM), which affects the anterior latissimus dorsi (ALD) muscles of commercial broilers, is of unknown etiology, and it represents up to 6% of the partial condemnations in Brazilian slaughterhouses. This study was performed to achieve histomorphometric characterizations of the ALD muscles from male Cobb 500 broilers slaughtered at either 35 d or 42 d and to evaluate the effects of DCM on the enzymatic markers aspartate aminotransferase (AST), alanine aminotransferase (ALT), creatine kinase (CK), and lactate dehydrogenase (LDH) and on uric acid and creatinine metabolites. Blood samples (1.5 to 3 mL) and ALD muscle fragments were collected from each carcass, all of which were processed in a commercial inline processing system. For each age, twelve macroscopically normal animals and twelve animals found to exhibit DCM were randomly selected for histomorphometric evaluation and analysis of serologic profiles. Microscopic evaluations demonstrated that the muscle fibers of those with DCM exhibited a strong presence of multifocal regenerative myodegeneration as well as a substitution of muscle tissue with connective tissue (P < 0.001) through fibrosis, thus characterizing the chronicity and hardness of the affected muscle. It is suggested that DCM is a localized muscle lesion because the detected serum levels of CK (P < 0.001), AST (P < 0.001), ALT (P = 0.01), and LDH (P < 0.001) enzymes were strongly associated with the group affected by DCM. Additional studies are needed to gain an understanding of this myopathy because it is an emerging problem in the poultry industry. In addition, it is related to DCM lesions in fast-growing broilers with the greatest slaughter weights.

Genome sequencing of two Bacillus anthracis strains: a virulent strain and a vaccinal strain

Bacillus anthracis strain SPV842_15 was isolated from bovine fetus, while B. anthracis strain Brazilian vaccinal was recovered from a commercial vaccine. We report here the genome sequences of both strains. The SPV842_15 genome is composed of a single circular chromosome with a length of 5,228,664 base pairs, and comprises 5911 coding sequences. In turn, the Brazilian vaccinal genome remains in 201 contigs with 5733 coding sequences. Both genomes have an overall C + G content of 35.4%, and 11 genes encoding the ribosomal RNAs (rRNAs) 5S, 16S and 23S. Only the plasmid pX01 sequence, which carries genes for toxins synthesis, was detected and completely assembled for both strains. These plasmids have a length of 181,684 base pairs and a C + G content of 32.5%. These genomic data generate insights about vaccinal B. anthracis virulence.

Molecular and phylogenetic analyses of Salmonella Gallinarum trace the origin and diversification of recent outbreaks of fowl typhoid in poultry farms

Fowl typhoid (FT) and pullorum disease (PD) are two important poultry infections caused by Salmonella enterica subsp. enterica serotype Gallinarum (S. Gallinarum). S. Gallinarum strains are adapted to birds and classified into biovars Gallinarum (bvGA) and Pullorum (bvPU) as they are the causative agent of FT and PD, respectively. In Brazil, FT/PD outbreaks have been reported along the last 50 years, but there was a recent increase of FT field reports with the suspicion it could be due to virulence reversion of the attenuated live vaccine SG9R. In this study, we applied molecular biology assays and phylogenetic methods to detect and investigate S. Gallinarum isolates from commercial poultry flocks in order to understand the evolutionary history and origin of the recent FT outbreaks in Brazil. S. Gallinarum isolates were obtained from thirteen different poultry flocks with clinical signs of FT/PD from 2013 to 2015. These isolates were serotyped, tested with three specific PCR (for the detection of bvGA, bvPU and live vaccine strain SG9R) and submitted to sequencing of a variable genome region (ISR analysis). The complete genome of one bvGA strain (BR_RS12) was also compared to other S. Gallinarum complete genomes (including other two Brazilian ones: bvGA 287/91 and bvPU FCVA198). PCR detected all thirteen isolates as S. Gallinarum (eight bvGA and five bvPU), none positive for SG9R strain. ISR analysis revealed that all eight bvGA isolates showed exactly the same nucleotide sequences with 100% similarity to reference strains, while two patterns were observed for bvPU. Genome phylogeny demonstrated distinct clades for bvGA and bvPU, with the bvGA clade showing a clear subdivision including three genomes: SG9R vaccine, the respective SG9 parent strain and one SG9R revertant field isolate (MB4523). The evolutionary rate of the total S. Gallinarum genome was calculated at 6.15×10^-7 substitutions/site/year, with 2.8 observed substitutions per year per genome (1 SNP per 4292 bases). Phylodynamics analysis estimated that at least two introductions of S. Gallinarum bvGA happened in Brazil, the first in 1885 and the second in 1950. The Brazilian bvGA genomes 287/91 and BR_RS12 analyzed here were related to the early and the late introductions, respectively. In conclusion, these results indicate the occurrence of S. Gallinarum strains associated with FT outbreaks that have been circulating for more than 50 years in Brazil and are not originated from virulence reversion of the SG9R vaccine.

Microbiome overview in swine lungs

Mycoplasma hyopneumoniae is the etiologic agent of swine enzootic pneumonia. However other mycoplasma species and secondary bacteria are found as inhabitants of the swine respiratory tract, which can be also related to disease. In the present study we have performed a total DNA metagenomic analysis from the lungs of pigs kept in a field condition, with suggestive signals of enzootic pneumonia and without any infection signals to evaluate the bacteria variability of the lungs microbiota. Libraries from metagenomic DNA were prepared and sequenced using total DNA shotgun metagenomic pyrosequencing. The metagenomic distribution showed a great abundance of bacteria. The most common microbial families identified from pneumonic swine's lungs were Mycoplasmataceae, Flavobacteriaceae and Pasteurellaceae, whereas in the carrier swine's lungs the most common families were Mycoplasmataceae, Bradyrhizobiaceae and Flavobacteriaceae. Analysis of community composition in both samples confirmed the high prevalence of M. hyopneumoniae. Moreover, the carrier lungs had more diverse family population, which should be related to the lungs normal flora. In summary, we provide a wide view of the bacterial population from lungs with signals of enzootic pneumonia and lungs without signals of enzootic pneumonia in a field situation. These bacteria patterns provide information that may be important for the establishment of disease control measures and to give insights for further studies.

Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation

Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.

Mycoplasma non-coding RNA: identification of small RNAs and targets

Background

Bacterial non-coding RNAs act by base-pairing as regulatory elements in crucial biological processes. We performed the identification of trans-encoded small RNAs (sRNA) from the genomes of Mycoplama hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis, which are Mycoplasma species that have been identified in the porcine respiratory system.

Results

A total of 47, 15 and 11 putative sRNAs were predicted in M. hyopneumoniae, M. flocculare and M. hyorhinis, respectively. A comparative genomic analysis revealed the presence of species or lineage specific sRNA candidates. Furthermore, the expression profile of some M. hyopneumoniae sRNAs was determined by a reverse transcription amplification approach, in three different culture conditions. All tested sRNAs were transcribed in at least one condition. A detailed investigation revealed a differential expression profile for two M. hyopneumoniae sRNAs in response to oxidative and heat shock stress conditions, suggesting that their expression is influenced by environmental signals. Moreover, we analyzed sRNA-mRNA hybrids and accessed putative target genes for the novel sRNA candidates. The majority of the sRNAs showed interaction with multiple target genes, some of which could be linked to pathogenesis and cell homeostasis activity.

Conclusion

This study contributes to our knowledge of Mycoplasma sRNAs and their response to environmental changes. Furthermore, the mRNA target prediction provides a perspective for the characterization and comprehension of the function of the sRNA regulatory mechanisms.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3061-z) contains supplementary material, which is available to authorized users.

Influence of vaccine strains on the evolution of canine distemper virus

Canine distemper virus (CDV) is a major dog pathogen belonging to the genus Morbillivirus of the family Paramyxoviridae. CDV causes disease and high mortality in dogs and wild carnivores. Although homologous recombination has been demonstrated in many members of Paramyxoviridae, these events have rarely been reported for CDV. To detect potential recombination events, the complete CDV genomes available in GenBank up to June 2015 were screened using distinct algorithms to detect genetic conversions and incongruent phylogenies. Eight putative recombinant viruses derived from different CDV genotypes and different hosts were detected. The breakpoints of the recombinant strains were primarily located on fusion and hemagglutinin glycoproteins. These results suggest that homologous recombination is a frequent phenomenon in morbillivirus populations under natural replication, and CDV vaccine strains might play an important role in shaping the evolution of this virus.

Identification of Mycobacterium smegmatis in Bovine Mastitis

Background: Rapidly growing mycobacteria (RGM) are ubiquitous in the environment, can be isolated from soil and wa­ter, and demonstrate visible growth on culture media within seven days. Mycobacterium smegmatis is an acid-alcohol fast bacterium, which belong to RGM group. The diagnosis of M. smegmatis infections may be quite difficult by conventional methods; therefore, biochemistry associated to nucleic acid-based approaches provided fast and accurate identification. Although this specie may be associated to animals and humans infections, there is few cases description. Nontuberculous mycobacterial bovine mastitis is uncommon, and bovine mastitis by M. smegmatis has been reported but non-confirmed case once in the past. This paper reports M. smegmatis recovered from a cattle with relapsing pyogranulomatous mastitis.Case: Milk samples from an adult Holstein cow showing relapsing pyogranulomatous mastitis history and by pronounced glandular hardening were cultivated and analyzed accordingly to standard milk cultivation protocols. The animal had been subject to several intramammary and parenteral antibiotic therapies protocols without adequate response. After 48 h incubation, a slow and sparse growth of slightly pigmented, shiny and smooth colonies was observed on the blood agar plate. The bacterium isolated was named as strain 55/08. The morphological and biochemical profile were tested, and the ability of the isolate to grow at Lowenstein-Jensen slants was confirmed. The isolated have showed positive reaction to catalase, glucose, sucrose, mannitol and nitrate. The pigment formation was observed for 14 days incubation, and the colonies produce pigment after prolonged time. Gram and Ziehl-Neelsen staining revealed poorly pigmented, irregular, slender Gram-positive and acid fast rods. The staining and biochemical profile showed closed isolated relationship to M. smegmatis. A discriminatory identification based in the 16S rRNA gene sequence analysis was performed. The total DNA from the strain 55/08 was extracted and the partial 16S rRNA sequence was amplified, using prokaryotic universal primer pairs and the extract DNA as template, by PCR assay following the purification and sequencing of the amplicons. A total of 1,443 nucleotides form consensus sequence were alignment to M. smegmatis and other mycobacteria 16S rRNA avail­able sequences. The sequence analysis confirmed the M. smegmatis identification as etiological agent of bovine relapsing pyogranulomatous mastitis. M. smegmatis strain 55/08 partial 16S rRNA gene sequence was submitted to GenBank. The phylogenetic relationship of the strain 55/08 with other mycobacteria was performed in order to confirm the identification of the isolate as M. smegmatis. Discussion: Nontuberculous mycobacteria are uncommon causes of bovine mastitis. Some old reports have described M. smegmatis as etiological agent of mastitis, but without definitive diagnostic. M. smegmatis mammary quarter introduction may be related to the repeated intramammary treatment protocols, because this mycobacteria is related to environmental infections. The relapsing pyogranulomatous mastitis infection could be associated to other bacteria species. However, the phenotypic and molecular characterization which was performed demonstrated the accurate identification of the isolated as M. smegmatis. Milk contaminated by M. smegmatis may be a potential infection source for human and other animal species. This report reinforces the need to optimize quality programs and laboratorial diagnosis to further the accurate microorganism identification in milk samples.Keywords: RGM mycobacteria, relapsing mastitis, M. smegmatis, molecular identification.

Intrinsic terminators in Mycoplasma hyopneumoniae transcription

Background

Mycoplasma hyopneumoniae, an important pathogen of swine, exhibits a low guanine and cytosine (GC) content genome. M. hyopneumoniae genome is organised in long transcriptional units and promoter sequences have been mapped upstream of all transcription units. These analysis provided insights into the gene organisation and transcription initiation at the genome scale. However, the presence of transcriptional terminator sequences in the M. hyopneumoniae genome is poorly understood.

Results

In silico analyses demonstrated the presence of putative terminators in 82% of the 33 monocistronic units (mCs) and in 74% of the 116 polycistronic units (pCs) considering different classes of terminators. The functional activity of 23 intrinsic terminators was confirmed by RT-PCR and qPCR. Analysis of all terminators found by three software algorithms, combined with experimental results, allowed us to propose a pattern of RNA hairpin formation during the termination process and to predict the location of terminators in the M. hyopneumoniae genome sequence.

Conclusions

The stem-loop structures of intrinsic terminators of mycoplasma diverge from the pattern of terminators found in other bacteria due the low content of guanine and cytosine. In M. hyopneumoniae, transcription can end after a transcriptional unit and before its terminator sequence and can also continue past the terminator sequence with RNA polymerases gradually releasing the RNA.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1468-6) contains supplementary material, which is available to authorized users.

Unravelling the transcriptome profile of the Swine respiratory tract mycoplasmas

The swine respiratory ciliary epithelium is mainly colonized by Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis. While colonization by M. flocculare is virtually asymptomatic, M. hyopneumoniae and M. hyorhinis infections may cause respiratory disease. Information regarding transcript structure and gene abundance provides valuable insight into gene function and regulation, which has not yet been analyzed on a genome-wide scale in these Mycoplasma species. In this study, we report the construction of transcriptome maps for M. hyopneumoniae, M. flocculare and M. hyorhinis, which represent data for conducting comparative studies on the transcriptional repertory. For each species, three cDNA libraries were generated, yielding averages of 415,265, 695,313 and 93,578 reads for M. hyopneumoniae, M. flocculare and M. hyorhinis, respectively, with an average read length of 274 bp. The reads mapping showed that 92%, 98% and 96% of the predicted genes were transcribed in the M. hyopneumoniae, M. flocculare and M. hyorhinis genomes, respectively. Moreover, we showed that the majority of the genes are co-expressed, confirming the previously predicted transcription units. Finally, our data defined the RNA populations in detail, with the map transcript boundaries and transcription unit structures on a genome-wide scale.

New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis

BACKGROUND

Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis live in swine respiratory tracts. M. flocculare, a commensal bacterium, is genetically closely related to M. hyopneumoniae, the causative agent of enzootic porcine pneumonia. M. hyorhinis is also pathogenic, causing polyserositis and arthritis. In this work, we present the genome sequences of M. flocculare and M. hyopneumoniae strain 7422, and we compare these genomes with the genomes of other M. hyoponeumoniae strain and to the a M. hyorhinis genome. These analyses were performed to identify possible characteristics that may help to explain the different behaviors of these species in swine respiratory tracts.

RESULTS

The overall genome organization of three species was analyzed, revealing that the ORF clusters (OCs) differ considerably and that inversions and rearrangements are common. Although M. flocculare and M. hyopneumoniae display a high degree of similarity with respect to the gene content, only some genomic regions display considerable synteny. Genes encoding proteins that may be involved in host-cell adhesion in M. hyopneumoniae and M. flocculare display differences in genomic structure and organization. Some genes encoding adhesins of the P97 family are absent in M. flocculare and some contain sequence differences or lack of domains that are considered to be important for adhesion to host cells. The phylogenetic relationship of the three species was confirmed by a phylogenomic approach. The set of genes involved in metabolism, especially in the uptake of precursors for nucleic acids synthesis and nucleotide metabolism, display some differences in copy number and the presence/absence in the three species.

CONCLUSIONS

The comparative analyses of three mycoplasma species that inhabit the swine respiratory tract facilitated the identification of some characteristics that may be related to their different behaviors. M. hyopneumoniae and M. flocculare display many differences that may help to explain why one species is pathogenic and the other is considered to be commensal. However, it was not possible to identify specific virulence determinant factors that could explain the differences in the pathogenicity of the analyzed species. The M. hyorhinis genome contains differences in some components involved in metabolism and evasion of the host's immune system that may contribute to its growth aggressiveness. Several horizontal gene transfer events were identified. The phylogenomic analysis places M. hyopneumoniae, M. flocculare and M. hyorhinis in the hyopneumoniae clade.

Mycoplasma hyopneumoniae transcription unit organization: genome survey and prediction

Mycoplasma hyopneumoniae is associated with swine respiratory diseases. Although gene organization and regulation are well known in many prokaryotic organisms, knowledge on mycoplasma is limited. This study performed a comparative analysis of three strains of M. hyopneumoniae (7448, J and 232), with a focus on genome organization and gene comparison for open read frame (ORF) cluster (OC) identification. An in silico analysis of gene organization demonstrated 117 OCs and 34 single ORFs in M. hyopneumoniae 7448 and J, while 116 OCs and 36 single ORFs were identified in M. hyopneumoniae 232. Genomic comparison revealed high synteny and conservation of gene order between the OCs defined for 7448 and J strains as well as for 7448 and 232 strains. Twenty-one OCs were chosen and experimentally confirmed by reverse transcription–PCR from M. hyopneumoniae 7448 genome, validating our prediction. A subset of the ORFs within an OC could be independently transcribed due to the presence of internal promoters. Our results suggest that transcription occurs in ‘run-on’ from an upstream promoter in M. hyopneumoniae, thus forming large ORF clusters (from 2 to 29 ORFs in the same orientation) and indicating a complex transcriptional organization.