Comparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation

Dietzia strains are widely distributed in the environment, presenting an opportunistic role, and some species have undetermined taxonomic characteristics. Here, we propose the existence of errors in the classification of species in this genus using comparative genomics. We performed ANI, dDDH, pangenome and genomic plasticity analyses better to elucidate the phylogenomic relationships between Dietzia strains. For this, we used 55 genomes of Dietzia downloaded from public databases that were combined with a newly sequenced. Sequence analysis of a phylogenetic tree based on genome similarity comparisons and dDDH, ANI analyses supported grouping different Dietzia species into four distinct groups. The pangenome analysis corroborated the classification of these groups, supporting the idea that some species of Dietzia could be reassigned in a possible classification into three distinct species, each containing less variability than that found within the global pangenome of all strains. Additionally, analysis of genomic plasticity based on groups containing Dietzia strains found differences in the presence and absence of symbiotic Islands and pathogenic islands related to their isolation site. We propose that the comparison of pangenome subsets together with phylogenomic approaches can be used as an alternative for the classification and differentiation of new species of the genus Dietzia.

Positive Influence of a Probiotic Mixture on the Intestinal Morphology and Microbiota of Farmed Guinea Fowls (Numida meleagris)

To understand the effectiveness of a probiotic mixture on intestinal morphology, mucus layer composition, and cecal microbiota diversity, 40 10-day-old Guinea fowls (Numida meleagris) were assigned to two groups: the control group (C), receiving drinking water, and the treated group (P), receiving water plus a commercial multi-strain probiotic (Slab51®, 2 × 10¹¹ CFU/L). Birds were slaughtered after 4 months, and the intestines were collected. Samples from the duodenum, ileum, and cecum were processed for morphological and morphometric studies, and conventional glycohistochemistry. Cecal samples were also used to assess the microbiota by 16S metataxonomic approach. Group P showed significant increase in the villus height (p < 0.001 in the duodenum and p < 0.05 in the ileum and cecum), villus width (p < 0.05 in all investigated tracts), depth of crypts (p < 0.001 in the duodenum and cecum; p < 0.05 in the ileum), and goblet cells per villus (p < 0.001 in all investigated tracts) compared with group C. Cecal microbiota of the birds varied considerably and comparing the relative abundance of the main observational taxonomic units (OTUs), a positive enrichment of several beneficial taxa, such as Oscillospira, Eubacterium, Prevotella, and members of the Ruminococcaceae, was observed. The enrichment of those taxa can improve microbiota stability and resilience facing environmental stresses, enhancing its resistance against invading pathogens. Ruminococcaceae, which represent the most important taxon in both groups, and Prevotella have a key role in the gut physiology due to the production of short-chain fatty acids (SCFAs), which are a vital energy source for enterocytes, improve glucose metabolism, and exert an overall anti-inflammatory effect. Probiotic administration enriches the presence of Coprococcus, Oscillospira, and Eubacterium taxa that produce butyrate, which exerts a beneficial effect on growth performance, structure of villi, and pathogen control and has anti-inflammatory properties too. This study indicates that Slab51® supplementation positively affects the morphology and microbiota diversity of the guinea fowl intestine.

Health assessment of wild speckled dwarf tortoises, CHERSOBIUS SIGNATUS

BACKGROUND

In free-ranging reptile populations, bacterial, fungal, viral and parasitic pathogens may affect hosts through impairment in movements, thermoregulation, reproduction, survival, and population dynamics. The speckled dwarf tortoise (Chersobius [Homopus] signatus) is a threatened species that is mostly restricted to the Succulent Karoo biome in South Africa, and little information on pathogens of this species is available yet. We derived baseline parameters for five males and five females that were captured to genetically enhance a conservation breeding program in Europe. Upon collection of the tortoises, ticks were removed and identified. Immediately upon arrival in Europe, ocular, nasal, oral and cloacal swabs were taken for viral, bacteriological and mycological examinations. Fecal samples were collected before and 1 month after fenbendazole treatment, and analyzed for parasites. A panel of PCR, aiming to detect herpesviruses, adenoviruses and iridoviruses, was carried out.

RESULTS

Samples were negative for viruses, while bacteriological examination yielded detectable growth in 82.5% of the swabs with a mean load of 16 × 107 ± 61 × 108 colony forming units (CFU) per swab, representing 34 bacterial species. Cloacal and oral swabs yielded higher detectable growth loads than nasal and ocular swabs, but no differences between sexes were observed. Fungi and yeasts (mean load 5 × 103 ± 13 × 103 CFU/swab) were detected in 25% of the swabs. All pre-treatment fecal samples were positive for oxyurid eggs, ranging from 200 to 2400 eggs per gram of feces, whereas after the treatment a significantly reduced egg count (90-100% reduction) was found in seven out of 10 individuals. One remaining individual showed 29% reduction, and two others had increased egg counts. In five tortoises, Nycthocterus spp. and coccidian oocysts were also identified. Soft ticks were identified as Ornithodoros savignyi.

CONCLUSIONS

Our baseline data from clinically healthy individuals will help future studies to interpret prevalences of microorganisms in speckled dwarf tortoise populations. The study population did not appear immediately threatened by current parasite presence.

Effects of the Probiotic Mixture Slab51® (SivoMixx®) as Food Supplement in Healthy Dogs: Evaluation of Fecal Microbiota, Clinical Parameters and Immune Function

The gut microbiota plays a crucial role in several physiologic functions of the host. In humans and animals, manipulation of the intestinal microbiota by oral administration of probiotic lactic acid bacteria plays a significant role in modulating the immune system. The aim of this study was to evaluate the safety of the probiotic mixture Slab51® and the capacity of this mixture to stimulate immune function in healthy dogs. Twenty dogs were divided in two groups and received a control diet or the same diet supplemented with a dose of 400 billion cfu of lyophilized bacteria for a period of 60 days. Body weight, food intake, body condition score (BCS), fecal score (FSS), fecal immunoglobulin IgA concentration, plasma IgG concentration, and fecal microbiota composition were monitored. Weight, food intake, BCS, FSS, and biochemical parameters remained unchanged during the treatment in both groups of animals. The fecal microbiota showed a significant decrease in the abundance of Clostridium perfringens and a significant increase in the abundance of beneficial Bifidobacterium and Lactobacillus organisms (p < 0.05). Fecal IgA and plasma IgG levels were significantly higher in the group receiving the probiotic compared to healthy controls. These data show that dietary supplementation with the probiotic mixture Slab51® is safe and well-tolerated, modulating the composition of the intestinal microbiota, and enhancing specific immune functions in healthy dogs.

Complete genome analysis of Glutamicibacter creatinolyticus from mare abscess and comparative genomics provide insight of diversity and adaptation for Glutamicibacter

Bacteria of the genusGlutamicibacterare considered ubiquitous because they can be found in soil, water and air. They have already been isolated from different habitats, including different types of soil, clinical samples, cheese and plants. Glutamicibacter creatinolyticus is a Gram-positive bacterium important to various biotechnological processes, however, as a pathogen it is associated to urinary tract infections and bacteremia. Recently,Glutamicibacter creatinolyticusLGCM 259 was isolated from a mare, which displayed several diffuse subcutaneous nodules with heavy vascularization. In this study, sequencing, genomic analysis ofG. creatinolyticusLGCM 259 and comparative analyseswere performedamong 4representatives of different members of genusfromdifferent habitats, available in the NCBI database. The LGCM 259 strain's genome carries important factors of bacterial virulence that are essential in cell viability, virulence, and pathogenicity. Genomic islands were predicted for 4 members of genusGlutamicibacter,showing ahigh number of GEIs,which may reflect a high interspecific diversity and a possible adaptive mechanism responsible for the survival of each species in its specific niche. Furthermore,G. creatinolyticusLGCM 259 sharessyntenicregions, albeit with a considerable loss of genes, in relation to the other species. In addition,G. creatinolyticusLGCM 259 presentsresistancegenes to 6 differentclasses ofantibiotics and heavy metals, such as: copper, arsenic, chromium and cobalt-zinc-cadmium.Comparative genomicsanalysescouldcontribute to the identification of mobile genetic elements particular to the speciesG. creatinolyticuscompared to other members of genus. The presence of specific regions inG. creatinolyticuscould be indicative of their rolesin host adaptation, virulence, and the characterization ofastrain that affects animals.

Management of otitis externa with an led-illuminated gel: a randomized controlled clinical trial in dogs

BACKGROUND

Canine otitis externa is a painful condition which can be challenging to treat due to difficulties in the administration of otic medication. This can be due to lack of owner compliance in the application of ear drops or due to the resentment that some dogs demonstrate when attempts are made to administer topical medication into a sensitive ear canal. The aim of the study was to assess the efficacy of a topical LED-illuminated gel (LIG) in canine otitis externa in comparison to standard of care therapy. Dogs with spontaneous otitis externa were randomly allocated in three groups: groups QW received LIG once weekly; BW received LIG twice weekly; group C received enrofloxacin and silver sulfadiazine twice daily. LIG consists of a topical application of a gel containing chromophores that, when illuminated by a LED lamp, re-emit fluorescent light which can stimulate physiological responses, promoting healing and controlling bacteria. The evaluation protocol (T0 to T5) considered clinical assessment (OTIS-3-index-scoring-system; pruritus-severity-scale; pain-severity-score; aural temperature), cytological scoring system, quali-quantitative bacteriologic assessment.

RESULTS

All groups (QW, n = 21; BW, n = 23; C, n = 20) showed improvement during the study (QW: P < 0.02 for cytological and pain scores, P < 0.003 for bacteriologic assessment, P < 10- 4 for pruritus, total OTIS-3 and temperature assessments; BW: P < 10- 4 for all clinical, cytological and bacteriologic assessments; C: P < 0.02 for all clinical and cytological assessments, P < 10- 4 for bacteriologic assessment). The highest clinical score reduction occurred in Group BW (P < 0.014 in T3; P < 0.001 in T4 and P < 10- 4 in T5). BW reached the clinically relevant effect level at T3 (- 3.26 ± 1.21 levels), QW reached it at T4 (- 3.24 ± 0.99), C did not reach it. No differences between groups were seen in the reduction of CFU/mL (T0-T5).

CONCLUSIONS

All treatment groups showed a positive clinical effect. LIG administered twice-a-week was the most favourable protocol of the study. LIG may be considered beneficial in the management of canine otitis externa; it seems to be effective in controlling the clinical condition, including the signs of inflammation and local pain, the bacterial growth, and it may help increasing treatment compliance.

Evaluation of cranial tibial translation in dogs: Diagnostic accuracy of radiographic method using a simple device

A hand-made, radiolucent, custom-designed device having a mobile and a non-mobile platforms was used to objectively quantify the in vivo cranial tibial translation, in order to assess the functional status of cranial-cruciate-ligament (CrCL) in dogs. The hypothesis was that changes in CrCL integrity would result in detectable changes in tibial translation. To validate the diagnostic method, data from injured (PA, n = 32), contralateral (CO, n = 32) and healthy stifles (HE, n = 32) were compared. Normalized tibial translation (Δ_N) of each stifle was measured in medio-lateral radiographic projection obtained before and during standard thrust force application, in PA (43.59±12.97%), CO (20.32±6.69%) and HE (12.22±3.77%). Comparing PA with HE and CO (Δ_N cut-off value: 29.73%), diagnosis could be issued with very high probability. Comparing HE with CO (Δ_N cut-off value: 14.80%), high performance was obtained. The translator device could be a useful tool to objectively quantify the in vivo tibial translation in dogs with CrCL rupture, before surgery and during post-operatory follow-up.

Cytological Findings in Bronchoalveolar Lavage Fluid of Foals With Pneumonia Caused by Rhodococcus equi and Other Bacteria

The distinction between lower respiratory tract infections caused by Rhodococcus equi and those caused by other pathogens is difficult. The aim of this retrospective study was to describe cytological findings in bronchoalveolar lavage fluid (BALF) of foals with pneumonia caused by R. equi or other bacteria. Nineteen foals aged from 3 weeks to 6 months with evidence of respiratory disease between 2015 and 2016 were selected from the database of the Veterinary Teaching Hospital "Mario Modenato" of the University of Pisa. Eight foals of 19 (42.1%) had R. equi pneumonia, whereas 11 of 19 (57.9%) had another bacterial pneumonia. R. equi-positive foals had statistically significant higher total nucleated cell count (P = .02) and neutrophils percentage (P = .002) than R. equi-negative ones. Macrophages proportion (P = .01) was lower in R. equi-positive than in R. equi-negative foals. Bronchoalveolar lavage is a quite easy procedure that can be performed in the field with minimal equipment required. Here we reported significant differences in the cellular composition of BALF that can be used to differentiate foals with R. equi bronchopneumonia from those with other bacterial pneumonias, whereas waiting for culture results.

Platelet-rich Plasma and Other Hemocomponents in Veterinary Regenerative Medicine

Platelet-rich plasma, platelet-rich fibrin, fibrin glue, and platelet lysate are the most widely used nontransfusional hemocomponents that, as biological and therapeutic aids, enhance the physiological reactions after an injury to facilitate the repair and regeneration processes. Recently, this type of therapy also has significantly expanded in veterinary medicine. Due to many similarities, the animal patient could be a good reference as a study model for humans, especially for chronic and difficult-to-heal injuries. This review discusses the current state of hemocomponent use for topical application in veterinary medicine, with a comparison with human medicine.

Platelet-rich plasma to treat experimentally-induced skin wounds in animals: A systematic review and meta-analysis

The objective of the study was to review current literature to determine whether the topical application of platelet-rich plasma (PRP) promotes healing in experimentally-induced full-thickness skin wounds in animals. The hypothesis was that the adjunct of PRP has a positive effect on wound healing. An electronic search was carried out on the following databases: Web of Science, Cochrane Library, PubMed, Research Gate, Cochrane Wounds Group, Veterinary Information Network. No publication date nor language restrictions were applied. Randomised and not randomised controlled clinical trials comparing PRP with placebo or with other treatments were included. The reduction of open wound area in PRP-treated (test) wounds compared to control wounds was the primary outcome. Secondary outcomes were healing time and number of healed cases in test group compared to control. The following effect sizes were calculated: the Hedges' g for continuous variables; the odds ratio for binary data. Eighteen controlled clinical trials were included in the qualitative and quantitative synthesis, with a total of 661 wounds. All studies were published in the period 2007-2016. Eight studies were carried out on rodent/lagomorph mammals and 10 on non-rodent/lagomorph mammals. In all included studies, control wounds underwent placebo or were left untreated. The PRP group showed a better healing performance than the control group in each outcome. The effect size was statistically significant considering the primary outcome and the overall aggregation of the three outcomes. The effect size, although in favour of the treatment with PRP, was not significant considering the healing time and the number of healings. The overall heterogeneity was mild or moderate. Five studies reported a high risk of selection bias. The publication bias was always mild or absent. The results support the hypothesis of the positive effects of the PRP when compared to control groups in the treatment of experimentally-induced full-thickness skin wounds in animals. PRP can therefore be considered an effective adjunctive therapy in stimulating second intention healing of acute wounds in healthy animals.

Amphixenosic Aspects of Staphylococcus aureus Infection in Man and Animals

According to the mode of transmission, Staphylococcus aureus infection between hosts is classified as "direct zoonoses," or infection that is transmitted from an infected vertebrate host to a susceptible host (man) by direct contact, by contact with a fomite or by a mechanical vector. The agent itself undergoes little or no propagative or developmental changes during transmission. According to the reservoir host, staphylococcosis is most precisely defined as "zooanthroponoses" or infections transmitted from man to lower vertebrate animals (e.g., streptococci, diphtheria, Enterobacteriaceae, human tuberculosis in cattle and parrots), but also "anthropozoonoses" or infections transmitted to man from lower vertebrate animals. In particular, actually, the correct definition of S. aureus infections between humans and animals is "amphixenoses" or infections maintained in both man and lower vertebrate animals and transmitted in either direction. S. aureus exhibits tropisms to many distinct animal hosts. While spillover events can occur wherever there is an interface between host species, changes in host tropism only occur with the establishment of sustained transmission in the new host species, leading to clonal expansion. Although the genomic variation underpinning adaptation in S. aureus genotypes infecting bovids and poultry has been well characterized, the frequency of switches from one host to another remains obscure. In this review, we sought to identify the sustained switches in host tropism in the S. aureus population, both anthroponotic and zoonotic, and their distribution over the species phylogeny. S. aureus is an organism with the capacity to switch into and adapt to novel hosts, even after long periods of isolation in a single host species. Based on this evidence, animal-adapted S. aureus lineages exhibiting resistance to antibiotics must be considered a major threat to public health, as they can adapt to the human population.

Conjunctival bacterial and fungal flora in clinically normal sheep

Objectives

The aim was to identify conjunctival bacterial and fungal flora in clinically normal sheep.

Design

Prospective study.

Setting

Tuscany.

Participants

100 eyes from 50 adult Massese female sheep were examined. The sheep included in the study were considered free of anterior ophthalmic abnormalities.

Primary and secondary outcome measures

Bacteria were identified by morphological assessment, Gram staining, biochemical tests. Identification of filamentous fungi was achieved at the genus level, and Aspergillus species were identified based on keys provided by other authors. Yeast colonies were highlighted, but not identified.

Results

Positive cultures were obtained from 100/100 eyes for bacteria, and from 86/100 eyes for fungi. A total of 14 types of bacteria and 5 types of fungi were isolated. Yeasts were isolated from 13/100 eyes. The most frequent fungal isolates were saprophytic fungi.

Conclusions

Conjunctival bacterial and fungal flora of clinically normal eyes were reported in sheep. The positivity obtained for conjunctival bacteria was higher compared to findings in the literature by other authors in the same species (100 per cent v 40 per cent), while our results were in line with a recent work performed on mouflons (Ovis Musimon) with a 100 per cent positivity for bacterial conjunctival fornix. In our survey, Gram-positive species were prevalent, as reported by other authors in different species. Few data are available in the literature regarding conjunctival fungal flora in healthy small ruminants. The prevalence of conjunctival fungal flora in this study was higher than findings reported in mouflons (86 per cent v 45 per cent). Differences in fungal prevalence may be due to different methods of managing herds, though further studies are required to verify this hypothesis. The similarities in bacterial and fungal isolates between sheep and mouflons suggest a genera pattern of conjunctival colonisation by bacteria and fungi.

Autologous platelet gel to treat chronic decubital ulcers: a randomized, blind controlled clinical trial in dogs

OBJECTIVE

To determine the efficacy of topical application of the autologous platelet gel (PG) in canine chronic protracted decubital ulcers.

STUDY DESIGN

Prospective, randomized, blind controlled clinical trial.

ANIMALS

Dogs (n = 18) with bilateral chronic wounds caused by protracted decubitus ulcers.

METHODS

For each dog, wound side was randomized to receive either platelet gel (group PG) every 5 days for 5 dressing changes, or paraffin gauzes dressings (group C), as negative control. Wound healing and wound surfaces were compared at admission and then evaluated every 5th day, until day 25. Outcome variables were: open wound area, reduction of open wound surface compared to admission and to each preceding dressing change, time to complete epithelialization.

RESULTS

Significant differences in healing process were observed at day 5 and continued throughout the entire study period (P < .00001). At 25 days, mean percent reduction in wound area was 93.5% in group PG and 13.2% in group C (P < .00001).

CONCLUSIONS

Appropriately prepared autologous PG, an inexpensive, readily available blood derivative, applied topically results in more rapid healing of chronic non-healing decubital ulcers in dogs than those treated by use of paraffin-impregnated gauzes.

Impact of the botanical insecticide Neem Azal on survival and reproduction of the biting louse Damalinia limbata on angora goats

Secondary metabolites present in the neem tree (Azadirachta indica A. Juss, Meliaceae), exhibit a wide range of biological activities in insects. However, few studies have been undertaken to assess the potential of neem products as insecticides for the control of ectoparasites of domestic animals. This study was undertaken to estimate the efficacy of Neem Azal, an azadirachtin-rich extract of neem seeds, in controlling Damalinia limbata (Phthiraptera) louse infestation of angora goats. The study was conducted on a fibre animal farm situated in Central Italy. Groups of 11-12 goats were treated with Neem Azal at an azadirachtin concentration of 650ppm or 125ppm, with Neguvon or were left untreated. Their louse burden was assessed fortnightly to monthly for 22 weeks. A reduction in louse densities of 76-96% was observed from week 2 to week 18 after treatment with the neem solution containing azadirachtin at a concentration of 650ppm. At the lower test concentration (125ppm) a reduction of 60-92% could be recorded from week 2 to week 14. Neem Azal was found to reduce the survival of both adult and nymph stages of D. limbata and to interfere with oviposition and oogenesis of female lice. A decrease in oviposition was observed in neem exposed female lice and the examination of their ovaries revealed morphological alterations in both vitellogenic and previtellogenic ovarioles at the follicular and germinal level. Since neem compounds target different life stages and physiological processes of D. limbata, the development of insecticide resistance by biting lice exposed to neem-based insecticides appears unlikely. For this reason and for its prolonged activity, which in principle allows angora goats to be protected for a large part of the mohair production cycle, neem-based insecticides may have a potential interest for mohair producing breeders.

Seroepidemiological survey of Rhodoccocus equi infection in asymptomatic horses from Bursa, Izmir and Istanbul provinces, Turkey

In order to assess the Rhodococcus equi infection in three provinces of Turkey (Bursa, Izmir and Istanbul), 696 sera from healthy foals and adult horses were tested by indirect ELISA using a R. equi reference strain (ATCC 6939) as antigen. 103 sera (14.80%) with titres >0.646 resulted positive. Seroprevalence was significantly higher (P=0.0053) in male than in female horses of Istanbul province, although higher antibody titres (mean value) were observed in the female group of Bursa and Izmir provinces with differences estimated between provinces (P=0.0002). Seroprevalence was correlated with age: foals aged less than 1 year (P<10(-4)) and horses from 5 to 10 years old (P=0.018) resulted more infected in Bursa and Izmir provinces. Our findings indicate that R. equi infection actually occurs in all investigated provinces, suggesting the importance of serological survey to diagnose the infection and to prevent the zoonotic risk.

An estimation of Toxocara canis prevalence in dogs, environmental egg contamination and risk of human infection in the Marche region of Italy

The human risk of infection with larvae of Toxocara canis was estimated in people from the Marche region of Italy. This region includes both urban and rural areas and its inhabitants frequently keep dogs for company, hunting, as guardians or shepherds. T. canis infection was diagnosed in 33.6% out of 295 dogs examined. Nearly half of the dogs (48.4%) living in rural areas were found T. canis positive, compared to about one-quarter of the dogs (26.2%) from urban areas. Analysis by provenance and role revealed the highest infection rate in rural hunting dogs (64.7%) and the lowest in urban companion dogs (22.1%). According to questionnaire data, the peridomestic environment, i.e. gardens and dog pens, is the most important defecation site in both rural and urban areas. Since over 40% of the dogs who defecate in dog pens are infected and 24% of urban and 47% of rural dogs who leave their droppings in the house surroundings harbour the parasite, it is clear that these environments may constitute sites of zoonotic risk. Our analysis of soil samples from 60 farms confirmed the high contamination level, revealing positive soil samples in more than half of the farms. Substantial egg contamination was also found in urban areas, as 3/6 parks examined were Toxocara spp. positive. Finally, our serological findings indicate that human infection actually occurs in the area: 7 out of 428 adults examined (1.6%) had very high levels of antibodies to T. canis antigen, suggesting a previous contact with the Larva migrans of the nematode.