Some modifications in the procedure of direct sequencing of PCR amplified 16S rDNA

Uterine microbial profiles in healthy postpartum dairy cows do not vary with sampling techniques or phases of estrous cycle

In this study, we aimed to compare uterine microbial profiles in postpartum dairy cows, determined by bacteriological culture and next-generation sequencing, using three uterine sampling techniques (swab, cytobrush, and lavage) and induced phases of the estrous cycle (estrus and diestrus). Fifteen healthy postpartum dairy cows at 53 ± 5 days postpartum were enrolled in the study. Uterine samples were collected during a fixed-time artificial insemination protocol. Viable bacteria were aerobically cultured from part of each sample, and bacterial isolates were identified through Sanger sequencing of the 16S rRNA gene. Total genomic DNA was extracted from the remainder of undiluted samples to quantify bacterial load using 16S rRNA qPCR and characterize the microbiome by metagenomic sequencing of the V1-V3 region of the 16S rRNA gene. Microbial profiles and composition were analyzed using the Shannon-Weaver diversity index and principal component analysis, respectively. Out of 87 samples, 88 % (77/87) were culture positive. The proportion of culture-positive uterine samples did not differ between sampling techniques (P = 0.39) or estrous cycle phases (P = 0.99). However, swab, cytobrush, and lavage techniques yielded 1.5, 9 and 9 times greater bacterial loads (P < 0.01), respectively, during diestrus than estrus phase. Moreover, during diestrus phase, the cytobrush method yielded 3 and 6 times more bacteria (P < 0.01) than both the lavage and swab methods. The most abundant bacterial genera identified from both bacteriological culture and metagenomic sequencing were Bacillus and Enterococcus, regardless of sampling technique or phases of the estrous cycle. Bacterial genera in moderate to low abundance through metagenomic sequencing included Streptococcus, Oscillospiraceae, and Lachnospiraceae. Notably, the uterine microbial profiles and composition, determined by metagenomic sequencing, did not differ by sampling techniques (P = 0.55 and P = 0.60, respectively) or estrous cycle phases (P = 0.34 and P = 0.17, respectively). In conclusion, our results suggest that any of the sampling techniques can be reliably used to study the uterine microbiome of healthy cows at random phases of the estrous cycle. However, it is important to consider potential differences in bacterial yield as a confounding factor.

Epidemiology and genetic diversity of Streptococcus suis in smallhold swine farms in the Philippines

This study aimed to determine the presence and characteristics of locally circulating strains of Streptococcus suis, the most important streptococcal pathogen in swine. Oral swab samples were collected from pigs from 664 representative smallhold farms across nine provinces in the Philippines. Isolates were identified and characterized using PCR assays. The study revealed an isolation rate of 15.8% (105/664, 95% CI: 13.0-18.6) among the sampled farms. Two hundred sixty-nine (269) S. suis isolates were recovered from 119 unique samples. Serotype 31 was the most prevalent (50/269, 95% CI: 13.9-23.2) among the other serotypes identified: 5, 6, 8, 9, 10, 11, 15, 16, 17, 21, 27, 28, and 29. The detection of the three 'classical' S. suis virulence-associated genes showed that 90.7% (244/269, 95% CI: 87.2-94.2) were mrp-/epf-/sly-. Multilocus sequence typing (MLST) analysis further revealed 70 novel sequence types (STs). Notably, several local isolates belonging to these novel STs formed clonal complexes (CC) with S. suis strains recovered from Spain and USA, which are major pork-exporting countries to the Philippines. This study functionally marks the national baseline knowledge of S. suis in Philippines.

The Hyphosphere of Leaf-Cutting Ant Cultivars Is Enriched with Helper Bacteria

Bacteria can live in a variety of interkingdom communities playing key ecological roles. The microbiome of leaf-cutting attine ant colonies are a remarkable example of such communities, as they support ants' metabolic processes and the maintenance of ant-fungus gardens. Studies on this topic have explored the bacterial community of the whole fungus garden, without discerning bacterial groups associated with the nutrient storage structures (gongylidia) of ant fungal cultivars. Here we studied bacteria isolated from the surface of gongylidia in the cultivars of Atta sexdens and Acromyrmex coronatus, to assess whether the bacterial community influences the biology of the fungus. A total of 10 bacterial strains were isolated from gongylidia (Bacillus sp., Lysinibacillus sp., Niallia sp., Staphylococcus sp., Paenibacillus sp., Pantoea sp., Staphylococcus sp., and one Actinobacteria). Some bacterial isolates increased gongylidia production and fungal biomass while others had inhibitory effects. Eight bacterial strains were confirmed to form biofilm-like structures on the fungal cultivar hyphae. They also showed auxiliary metabolic functions useful for the development of the fungal garden such as phosphate solubilization, siderophore production, cellulose and chitin degradation, and antifungal activity against antagonists of the fungal cultivar. Bacteria-bacteria interaction assays revealed heterogeneous behaviors including synergism and competition, which might contribute to regulate the community structure inside the garden. Our results suggest that bacteria and the ant fungal cultivar interact directly, across a continuum of positive and negative interactions within the community. These complex relationships could ultimately contribute to the stability of the ant-fungus mutualism.

Birth Mode Does Not Determine the Presence of Shared Bacterial Strains between the Maternal Vaginal Microbiome and the Infant Stool Microbiome

Dysbiosis of the neonatal gut microbiome during early life has been suggested as the missing link that may explain higher rates of certain diseases in caesarean section-delivered infants. Many studies report delivery mode-related dysbiosis in infants due to a lack of maternal vaginal microbiome exposure, prompting interventions to correct the neonatal gut microbiome by transferring these missing microbes after caesarean delivery. The maternal vaginal microbiome is among the first microbial exposures that many infants experience, yet little is known about the extent of direct transmission of maternal vaginal microbes. As part of the Maternal Microbiome Legacy Project, we aimed to determine if maternal vaginal bacteria are vertically transmitted to infants. We employed cpn60 microbiome profiling, culture-based screening, molecular strain typing, and whole-genome sequencing to determine whether identical maternal vaginal strains were present in infant stool microbiomes. We identified identical cpn60 sequence variants in both halves of maternal-infant dyads in 204 of 585 Canadian women and their newborn infants (38.9%). The same species of Bifidobacterium and Enterococcus were cultured from maternal and corresponding infant samples in 33 and 13 of these mother-infant dyads, respectively. Pulsed-field gel electrophoresis and whole-genome sequencing determined that near-identical strains were detected in these dyads irrespective of delivery mode, indicating an alternative source in cases of caesarean delivery. Overall, we demonstrated that vertical transmission of maternal vaginal microbiota is likely limited and that transmission from other maternal body sites, such as the gut and breast milk, may compensate for the lack of maternal vaginal microbiome exposure during caesarean delivery. IMPORTANCE The importance of the gut microbiome in human health and disease is widely recognized, and there has been a growing appreciation that alterations in gut microbiome composition during a "critical window" of development may impact health in later life. Attempts to correct gut microbiome dysbiosis related to birth mode are underpinned by the assumption that the lack of exposure to maternal vaginal microbes during caesarean delivery is responsible for dysbiosis. Here, we demonstrate that there is limited transmission of the maternal vaginal microbiome to the neonatal gut, even in cases of vaginal delivery. Furthermore, the presence of identical strains shared between mothers and infants in early life, even in cases of caesarean delivery, highlights compensatory microbial exposures and sources for the neonatal stool microbiome other than the maternal vagina.

Antiscalants Used in Seawater Desalination: Biodegradability and Effects on Microbial Diversity

Antiscalants are organic polymers widely used for scale inhibition in seawater desalination. While they are susceptible to biodegradation, they provide nutrients for bacterial cell growth and energy for the microbes that assimilate and degrade them. This paper shows the biodegradability of three commercial antiscalants (polyacrylate—CA, polyphosphonate—PP, and carboxylated dendrimers—DN) applied in seawater reverse osmosis desalination (SWRO) as well as analyzing the antiscalant’s effects on microbial diversity using microbial cultures grown in seawater, under semi-continuous batch conditions. Nutritional uptake and contribution of the antiscalants to microbial growth were investigated by measuring DOC, TDN, NO₃⁻, NO₂⁻, PO₄⁻, NH₄⁺, and TP of the filtered samples of the incubated batch, twice a month, for twelve months. The microbial community was estimated by 16S rRNA sequencing. The main changes in the microbial communities were determined by the incubation period. However, bacterial orders of the antiscalant treatments differed significantly from the control treatment, namely Planctomycetales, Clostridiales, Sphingobacteriales, Rhodobacterales, and Flavobacteriales, and other unclassified bacterial orders, which were found in various relative abundances dependent on incubation times. The results showed the PP antiscalant to be the least biodegradable and to have the least effect on the bacterial community composition compared to the control. This result emphasizes the need to reassess the suitability criteria of antiscalants, and to further monitor their long-term environmental effects.

Suppurative meningoencephalitis and perineuritis caused by Streptococcus gallolyticus in a Japanese Black calf

A 179-day-old calf, which was weak and stunted, showed neurological signs and was euthanized. Postmortem examination revealed extensive and severe cloudy area in the meninges, and pleural pneumonia. Gram-positive cocci were isolated from systemic organs. Biochemical and 16S rRNA gene sequence analyses identified the isolate as Streptococcus gallolyticus, and its subspecies was suggested to be gallolyticus (SGG). The isolate was classified as a novel sequence type (ST115) by the multilocus sequence typing scheme for SGG and showed susceptibility to penicillin, ampicillin, amoxicillin, florfenicol, sulfamethoxazole-trimethoprim, and chloramphenicol. Histopathologically, suppurative meningoencephalitis and perineuritis were detected. As SGG has been isolated solely from a cow with mastitis in Japan, this is the first SGG infection in a calf with suppurative meningoencephalitis and perineuritis in this country.

Antimicrobial Resistance Genes in Bacteria Isolated From Japanese Honey, and Their Potential for Conferring Macrolide and Lincosamide Resistance in the American Foulbrood Pathogen Paenibacillus larvae

American foulbrood (AFB) is the most serious bacterial disease of honey bee brood. Spores of the causative agent Paenibacillus larvae are ingested by bee larvae via brood foods and germinated cells proliferate in the larval midgut. In Japan, a macrolide antibiotic, tylosin, is used as the approved prophylactic for AFB. Although tylosin-resistant P. larvae has yet to be found in Japan, it may emerge in the future through the acquisition of macrolide resistance genes from other bacteria, and bacteria latent in brood foods, such as honey, may serve as a source of resistance genes. In this study, to investigate macrolide resistance genes in honey, we attempted to isolate tylosin-resistant bacteria from 53 Japanese honey samples and obtained 209 isolates from 48 samples in the presence of 1 μg/ml of tylosin. All isolates were Gram-positive spore-forming bacteria mainly belonging to genera Bacillus and Paenibacillus, and 94.3% exhibited lower susceptibility to tylosin than Japanese P. larvae isolates. Genome analysis of 50 representative isolates revealed the presence of putative macrolide resistance genes in the isolates, and some of them were located on mobile genetic elements (MGEs). Among the genes on MGEs, ermC on the putative mobilizable plasmid pJ18TS1mac of Oceanobacillus strain J18TS1 conferred tylosin and lincomycin resistance to P. larvae after introducing the cloned gene using the expression vector. Moreover, pJ18TS1mac was retained in the P. larvae population for a long period even under non-selective conditions. This suggests that bacteria in honey is a source of genes for conferring tylosin resistance to P. larvae; therefore, monitoring of bacteria in honey may be helpful to predict the emergence of tylosin-resistant P. larvae and prevent the selection of resistant strains.

Characteristics of DNA polymerase I from an extreme thermophile, Thermus scotoductus strain K1

Several native and engineered heat‐stable DNA polymerases from a variety of sources are used as powerful tools in different molecular techniques, including polymerase chain reaction, medical diagnostics, DNA sequencing, biological diversity assessments, and in vitro mutagenesis. The DNA polymerase from the extreme thermophile, Thermus scotoductus strain K1, (TsK1) was expressed in Escherichia coli, purified, and characterized. This enzyme belongs to a distinct phylogenetic clade, different from the commonly used DNA polymerase I enzymes, including those from Thermus aquaticus and Thermus thermophilus. The enzyme demonstrated an optimal temperature and pH value of 72–74°C and 9.0, respectively, and could efficiently amplify 2.5 kb DNA products. TsK1 DNA polymerase did not require additional K⁺ ions but it did need Mg²⁺ at 3–5 mM for optimal activity. It was stable for at least 1 h at 80°C, and its half‐life at 88 and 95°C was 30 and 15 min, respectively. Analysis of the mutation frequency in the amplified products demonstrated that the base insertion fidelity for this enzyme was significantly better than that of Taq DNA polymerase. These results suggest that TsK1 DNA polymerase could be useful in various molecular applications, including high‐temperature DNA polymerization.

Infection With a Novel Rickettsiella Species in Emperor Scorpions (Pandinus imperator)

Rickettsiella infection was diagnosed in 4 adult emperor scorpions (Pandinus imperator) from 2 different collections over a 3-year period. One case had a 2-day history of weakness, failure to lift the tail, or respond to stimulation, with rapid progression to death. The other 3 cases were found dead. There were no gross lesions, but histologically the hemolymphatic vasculature and sinuses, presumed hematopoietic organ, heart, midgut and midgut diverticula, nerves, and skeletal muscle were infiltrated with phagocytic and granular hemocytes with necrosis. Phagocytic hemocytes contained abundant intracellular microorganisms that were Fite's acid-fast-positive, Macchiavello-positive, variably gram-positive or gram-negative, and Grocott's methenamine silver-negative. By transmission electron microscopy, hemocytes contained numerous phagocytic vacuoles with small dense bacterial forms (mean 0.603 × 0.163 μm) interspersed with large bacterial forms (mean 1.265 × 0.505 μm) and few intermediary forms with electron-dense nucleoids and membrane-bound crystalline arrays (average 4.72 μm). Transmission electron microscopy findings were consistent with bacteria of the family Coxiellaceae. Based on sequencing the 16S ribosomal RNA gene, the identity was confirmed as Rickettsiella, and phylogenetic analysis of protein-coding genes gidA, rspA, and sucB genes suggested the emperor scorpion pathogen as a new species. This study identifies a novel Rickettsiella causing infection in emperor scorpions and characterizes the unique pathological findings of this disease. We suggest this organism be provisionally named Rickettsiella scorpionisepticum.

Detection of multidrug-resistant Gram-negative bacteria from imported reptile and amphibian meats

AIMS

The food supply is a potential source of antimicrobial resistance. Current surveillance programmes targeting food are limited to beef, pork and poultry and do not capture niche products. In this study, imported reptile and amphibian products were screened for antimicrobial-resistant bacteria.

METHODS AND RESULTS

In all, 53 items including soft shell turtles, frog legs, geckos, snakes and a turtle carapace were purchased from specialty markets in Vancouver and Saskatoon, Canada. Samples were selectively cultured for Salmonella sp., Escherichia coli, extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae and meropenem-resistant organisms. Salmonella, all pan-susceptible, were grown from six dried geckos. Escherichia coli were isolated from 19 samples, including ESBL producers from six items. One multidrug-resistant E. coli possessed both the bla_CTX-M-55 and mcr-1 genes. An NDM-1-producing Acinetobacter sp. was also isolated from a dried turtle carapace.

CONCLUSIONS

Our results suggest that imported reptile and amphibian meats are an underappreciated source of resistant bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

The international trade of food may play a role in the dissemination of resistant bacteria. The presence of these bacteria in niche market foods represents a risk of unknown magnitude to public health and a gap in current national resistance surveillance programmes.

Identification of antimicrobial resistant bacteria from plant-based food products imported into Canada

The role of plant-based foods in the epidemiology of antimicrobial resistance has been inadequately studied. In this investigation, resistant organisms from vegetables, fruits and spices imported into Canada were identified and characterized. A total of 143 products imported from primarily Asian and African countries were purchased from international markets in Saskatoon, Saskatchewan. Samples were selectively cultured for bacterial species where resistance is known to be emerging. The proportions of samples positive for each organism were as follows: E. coli (n = 13, 9.1%), Salmonella spp. (n = 2, 1.4%), ESBL producing Enterobacter spp. (n = 2, 1.4%) and K. pneumoniae (n = 2, 1.4%), S. aureus (n = 7, 4.9%) and Enterococcus spp. (n = 66, 46.2%). Antimicrobial minimum inhibitory concentrations were determined by broth micro-dilution and agar-dilution. Based on the susceptibility of each organism, isolates were screened for resistance genes (β-lactamases and plasmid mediated quinolones resistance determinants) by PCR. Extended-spectrum β-lactamase producing Enterobacteriaceae and methicillin resistant S. aureus (MRSA) were identified from 6/143 (4.2%) and 2/143 (1.4%) of samples respectively. The qnrB, qnrS and aac(6')-Ib-cr plasmid mediated quinolone resistance determinants were identified in 2/143 (1.4%) of samples tested. None of the Enterobacteriaceae isolates were resistant to meropenem or colistin. Similarly, all Enterococcus isolates remained susceptible to ampicillin, penicillin and vancomycin. Finding multi-drug resistant bacteria which are frequently isolated from human infections is concerning, although the contribution of the global food trade to the dissemination of resistance remains cryptic. These results suggest that imported plant-based foods may be an underappreciated source of clinically relevant resistant organisms. Further study is required to address these gaps in our understanding of the epidemiology of resistance, and the magnitude of the risk posed to human health by these organisms.

Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities

Feeding a global population of 8 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. Members of the genera Butyrivibrio and Pseudobutyrivibrio are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings have highlighted the immense enzymatic machinery of Butyrivibrio and Pseudobutyrivibrio species for the degradation of plant fiber, suggesting that these bacteria occupy similar niches but apply different degradation strategies in order to coexist in the competitive rumen environment.

Plant polysaccharide breakdown by microbes in the rumen is fundamental to digestion in ruminant livestock. Bacterial species belonging to the rumen genera Butyrivibrio and Pseudobutyrivibrio are important degraders and utilizers of lignocellulosic plant material. These bacteria degrade polysaccharides and ferment the released monosaccharides to yield short-chain fatty acids that are used by the ruminant for growth and the production of meat, milk, and fiber products. Although rumen Butyrivibrio and Pseudobutyrivibrio species are regarded as common rumen inhabitants, their polysaccharide-degrading and carbohydrate-utilizing enzymes are not well understood. In this study, we analyzed the genomes of 40 Butyrivibrio and 6 Pseudobutyrivibrio strains isolated from the plant-adherent fraction of New Zealand dairy cows to explore the polysaccharide-degrading potential of these important rumen bacteria. Comparative genome analyses combined with phylogenetic analysis of their 16S rRNA genes and short-chain fatty acid production patterns provide insight into the genomic diversity and physiology of these bacteria and divide Butyrivibrio into 3 species clusters. Rumen Butyrivibrio bacteria were found to encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) and binding proteins. In total, 4,421 glycoside hydrolases (GHs), 1,283 carbohydrate esterases (CEs), 110 polysaccharide lyases (PLs), 3,605 glycosyltransferases (GTs), and 1,706 carbohydrate-binding protein modules (CBM) with predicted activities involved in the depolymerization and transport of the insoluble plant polysaccharides were identified. Butyrivibrio genomes had similar patterns of CAZyme families but varied greatly in the number of genes within each category in the Carbohydrate-Active Enzymes database (CAZy), suggesting some level of functional redundancy. These results suggest that rumen Butyrivibrio species occupy similar niches but apply different degradation strategies to be able to coexist in the rumen.

IMPORTANCE Feeding a global population of 8 billion people and climate change are the primary challenges facing agriculture today. Ruminant livestock are important food-producing animals, and maximizing their productivity requires an understanding of their digestive systems and the roles played by rumen microbes in plant polysaccharide degradation. Members of the genera Butyrivibrio and Pseudobutyrivibrio are a phylogenetically diverse group of bacteria and are commonly found in the rumen, where they are a substantial source of polysaccharide-degrading enzymes for the depolymerization of lignocellulosic material. Our findings have highlighted the immense enzymatic machinery of Butyrivibrio and Pseudobutyrivibrio species for the degradation of plant fiber, suggesting that these bacteria occupy similar niches but apply different degradation strategies in order to coexist in the competitive rumen environment.

Genotypic diversity of Streptococcus suis and the S. suis-like bacterium Streptococcus ruminantium in ruminants

Although Streptococcus suis has attracted public attention as a major swine and human pathogen, this bacterium has also been isolated from other animals, including ruminants. However, recent taxonomic studies revealed the existence of other species that were previously identified as S. suis, and some of these isolates were reclassified as the novel species Streptococcus ruminantium. In Japan, biochemically identified S. suis is frequently isolated from diseased ruminants; however, such isolates have not yet been identified accurately, and their aetiological importance in ruminants is unclear. Therefore, to understand the importance of S. suis and S. suis-like bacteria in ruminants, we reclassified S. suis isolates from ruminants according to the updated classification and investigated their genetic diversity. Although both S. suis and S. ruminantium were isolated from healthy and diseased ruminants, most of the isolates from diseased animals were S. ruminantium, implying that S. ruminantium is more likely to be associated with ruminant disease than S. suis. However, the ruminant S. suis and S. ruminantium isolates from diseased animals were classified into diverse genotypes rather than belonging to certain clonal groups. Genome sequence analysis of 20 S. ruminantium isolates provided information about the antibiotic resistance, potential virulence, and serological diversity of this species. We further developed an S. ruminantium-specific PCR assay to aid in the identification of this bacterium. The information obtained and the method established in this study will contribute to the accurate diagnosis of ruminant streptococcal infections.

Production of lipolytic enzymes by bacteria isolated from biological effluent treatment systems

This work aimed to evaluate the production of lipolytic complexes, produced by microorganisms isolated from a biological treatment system of effluents from a hotel. To select the best lipolytic microorganism for use in biotechnological processes, we tested 45 bacterial isolates recovered from the raw effluent of the hotel's restaurant waste tank. Lipase production was assayed in culture medium supplemented with olive oil and rhodamine B, incubated at 25 °C and 30 °C for 24 h - 48 h. Results showed 22 isolates lipase producers. All isolates were inoculated on medium without yeast extract to select the ones with highest enzyme yields. Out of these, nine isolates showed high lipase activity. The strain with the larger halo was assayed in submerged culture using an orbital shaker and a bioreactor, with three different substrates (olive oil, grape seed oil, and canola oil). Isolate G40 identified as Acinetobacter baylyi was selected to run the production assays because it showed the best result in the solid medium. In the bioreactor, maximum lipase production was obtained after 12 h of culture with the three substrates evaluated: 0,358 U/mL.min-1 in olive oil, 0,352 U/mL.min-1 with grapeseed oil, and 0,348 U/mL.min-1 with canola oil.

Solitalea longa sp. nov., isolated from freshwater and emended description of the genus Solitalea

A Gram-negative, strictly aerobic, oxidase-positive, catalase-negative and yellow-pigmented bacterium, designated strain HR-AV^T, was isolated from a water sample of the Han River. Cells were elongated rods with gliding motility without flagellum. Growth was observed at 5-30 °C (optimum, 20 °C), pH 7-8 and 0-0.5 % NaCl. The major respiratory quinone was menaquinone-7. The major fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and anteiso-C15 : 0. The polar lipids comprised phosphatidylethanolamine, an unidentified amino lipid and five unidentified lipids. The DNA G+C content of strain HR-AV^T was 38.4 mol%. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HR-AV^Tbelonged to the family Sphingobacteriaceae in the phylum Bacteroidetes and formed a phylogenic lineage with Solitalea canadensis DSM 3403^T and Solitalea koreensis R2A36-4^T. Strain HR-AV^T was most closely related to S. canadensis DSM 3403^T and S. koreensis R2A36-4^T with 97.3 and 94.0 % 16S rRNA gene sequence similarities, respectively, and then had low similarities (below 90.9 %) with other bacteria with validly published names. Average nucleotide identity and in silico DNA-DNA hybridization values between strain HR-AV^T and S. canadensis were 74.0 and 19.7 %, respectively. Based on these results, strain HR-AV^T represents a novel species of the genus Solitalea, for which the name Solitalea longa sp. nov. is proposed. The type strain is HR-AV^T (=KACC 19411^T=JCM 32259^T). An emended description of the genus Solitalea is also proposed.

Development of PCR for identifying Streptococcus parasuis, a close relative of Streptococcus suis

Streptococcus parasuis has recently been removed taxonomically from Streptococcus suis, a zoonotic pathogen. S. parasuis has been detected in healthy pigs and in diseased pigs, which suggests that S. parasuis is involved in the normal microbiota of pigs and has potential pathogenicity. However, the pathogenicity of S. parasuis in pigs is unclear because of the lack of appropriate detection methods that discriminate S. parasuis from S. suis. In this study, we developed a PCR method that is specific for S. parasuis. The detection limit of the PCR was 350 CFU per reaction. Bacteria isolated from the saliva of eight pigs were collected and examined by PCR. Sixty-four isolates positive for PCR were obtained from the samples of all pigs. Thirteen of the 64 isolates were genetically confirmed as S. parasuis, and biologically and biochemically had nearly the same features of known S. parasuis strains, which suggested that strains positive for PCR were S. parasuis. Among the 64 isolates, 28 isolates were serotypes 20, 22, or 26 in the S. suis serotyping scheme. The remaining 36 isolates were untypeable, which suggested the presence of novel serotypes or a capsule-negative form. Therefore, the PCR method described in this study is a useful tool for identifying S. parasuis, and can be used in etiological studies on this bacterium.

Non-toxigenic Corynebacterium ulcerans sequence types 325 and 339 isolated from two dogs with ulcerative lesions in Italy

Corynebacterium ulcerans, an emerging pathogen related to C. diphtheriae and C. pseudotuberculosis, is able to cause disease in both human and animal hosts. C. ulcerans may harbor acquired virulence factors such as dermonecrotic exotoxin phospholipase D (PLD) and the prophage-encoded diphtheria toxin (DT). Infections typically occur in persons reporting close contact with animals. In pets, C. ulcerans has been isolated from both asymptomatic carriers and clinically affected dogs and cats. We describe the isolation and characterization of C. ulcerans strains from 2 pet dogs with ulcerative lesions in Italy. The 2 isolates tested negative for both DT genes, but were PLD-producers and belonged to sequence types (STs) 325 and 339. These 2 cases highlight that C. ulcerans cutaneous infections might be underestimated in pets, given that many veterinary laboratories do not routinely consider and/or identify Corynebacterium species from cutaneous samples. Early detection and molecular typing of C. ulcerans is essential in order to implement effective treatment and to prevent diffusion and possible zoonotic transmission of certain STs.

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome

Phytoremediation using willows is thought to be a sustainable alternative to traditional remediation techniques involving excavation, transport, and landfilling. However, the complexity of the interaction between the willow and its associated highly diverse microbial communities makes the optimization of phytoremediation very difficult. Here, we have sequenced the rhizosphere metatranscriptome of four willow species and the plant root metatranscriptome for two willow species growing in petroleum hydrocarbon-contaminated and non-contaminated soils on a former petroleum refinery site. Significant differences in the abundance of transcripts related to different bacterial and fungal taxa were observed between willow species, mostly in contaminated soils. When comparing transcript abundance in contaminated vs. non-contaminated soil for each willow species individually, transcripts for many microbial taxa and functions were significantly more abundant in contaminated rhizosphere soil for Salix eriocephala, S. miyabeana and S. purpurea, in contrast to what was observed in the rhizosphere of S. caprea. This agrees with the previously reported sensitivity of S. caprea to contamination, and the superior tolerance of S. miyabeana and S. purpurea to soil contamination at that site. The root metatranscriptomes of two species were compared and revealed that plants transcripts are mainly influenced by willow species, while microbial transcripts mainly responded to contamination. A comparison of the rhizosphere and root metatranscriptomes in the S. purpurea species revealed a complete reorganization of the linkages between root and rhizosphere pathways when comparing willows growing in contaminated and non-contaminated soils, mainly because of large shifts in the rhizosphere metatranscriptome.

Nocardia cyriacigeorgica as the causative agent of mandibular osteomyelitis (lumpy jaw) in a cat

An unusual case of osteomyelitis caused by Nocardia cyriacigeorgica infection and resulting in mandibular osteomyelitis and cellulitis (lumpy jaw) is described in a young cat. A 1-cm hard nodular mass was an incidental finding in the right mandible of a 14-month-old cat during routine physical examination. The lesion was fast growing, reaching up to 6 cm in its largest dimension over a 5-week period. A core biopsy of the affected mandible revealed foci of osteolysis, woven bone formation, and a few large clusters of filamentous bacteria surrounded by fine eosinophilic amorphous material bordered by neutrophils, plasma cells, macrophages, and occasional multinucleated giant cells. Pure cultures of acid-fast variable, Gram-positive filamentous bacteria were recovered on blood and chocolate agar plates at 48-hr postinoculation. On amplification and sequencing of the 16S ribosomal RNA and 65-kDa heat shock protein genes, the microorganisms were identified as N. cyriacigeorgica, within the actinomycetes.

Ocular localization of mycobacterial lesions in tank-reared juvenile cobia, Rachycentron canadum

Severe clinical mycobacteriosis with consistent ocular lesion localization was diagnosed in a population of 800 juvenile tank-reared Cobia (Rachycentron canadum) which experienced a sudden increase in mortality approximately 5 months after arriving into Trinidad and Tobago from Florida, USA. Moderate daily mortality (15-20 animals per day) persisted for just over 1 month. Moribund fish displayed circling behaviour and had an open-mouth gape upon death. Fish consistently presented with bilateral exophthalmia, corneal cloudiness and hyphema. Non-branching acid-fast rods were detected in aqueous humour touch preparations. Histological analysis revealed severe bilateral intra-ocular granulomatous responses in all specimens. Mycobacterium sp. was identified using a real-time PCR assay detecting the RNA polymerase β-subunit (rpoB) gene in different tissue samples. Specimens did not present with characteristic granulomatous responses usually seen in viscera. To the best of our knowledge, this represents only the third documentation of piscine mycobacterial infection presenting with only localized ocular lesions, and the second documented case of mycobacteriosis in cobia. It is, however, the first documentation of an ocular presentation of mycobacteriosis in a marine species and is the first documentation of such a presentation in cobia.

Defining the taxonomic status of Streptococcus suis serotype 33: the proposal for Streptococcus ruminantium sp. nov

To clarify the taxonomic classification of Streptococcus suis serotype 33, we performed biochemical and molecular genetic analyses using isolates (GUT-183, GUT-184, GUT-185, GUT-186, GUT-187T, GUT-188, GUT-189, GUT-190, GUT-191, GUT-192 and GUT-193) from bovine endocarditis. A comparative sequence analysis showed 99.2-100 % sequence similarity among the reference strain of S. suis serotype 33 and our isolates for the 16S rRNA gene. These similarities were higher than those between the isolate GUT-187T and S. suis and other streptococci. Comparison of sodA genes also showed high degrees of similarities among the reference strain of S. suis serotype 33 and our isolates (99.7-100 %), which were higher than those between the GUT-187T and S. suis and other streptococci. DNA-DNA relatedness among three isolates (GUT-186, GUT-187T, the reference strain of S. suis serotype 33) was over 76.7 %. In contrast, the relatedness between GUT-187T and the other streptococcal species (S. suis, Streptococcus parasuis, Streptococcus acidominimus and Streptococcus porci) was 8.4-24.9 %. Phylogenetic analyses showed that the isolates did not affiliate closely to any known species of the genus Streptococcus. Moreover, GUT-187T could be distinguished from S. suis and other closely related species of genus Streptococcus using biochemical tests. On the basis of the phenotypic and molecular genetic data, we propose that the isolates of S. suis serotype 33 should be classified into the genus Streptococcus, Streptococcus ruminantium sp. nov. with the type strain GUT-187T (=DSM 104980T=JCM 31869T).

Co-infection of Acipenserid herpesvirus 2 (AciHV-2) and Streptococcus iniae in cultured white sturgeon Acipenser transmontanus

A mortality event in cultured white sturgeon Acipenser transmontanus (Richardson, 1836) sub-adults was investigated. After transfer between farms, high mortality was observed in fish, associated with back arching, abnormal swimming, and ulcerative skin lesions. Necropsy of moribund individuals revealed hemorrhagic ascites and petechial hemorrhages in the coelomic peritoneum and serosa of internal organs. Acipenserid herpesvirus 2 (AciHV-2) was isolated from external tissue samples, then identified and genotyped by sequencing of the terminase and polymerase genes. In addition, Streptococcus iniae was recovered from internal organs of affected fish. Histologic changes were limited to interstitial hematopoietic areas of the kidney and consisted of small foci of necrosis accompanied by fibrin deposition, minimal inflammatory response, and small numbers of bacterial cocci compatible with streptococci. Identity was confirmed by partial sequencing of the 16S rRNA, rpoB, and gyrB genes. Genetic fingerprinting demonstrated a genetic profile distinct from S. iniae isolates recovered from previous outbreaks in wild and cultured fish in North America, South America, and the Caribbean. Although the isolates were resistant to white sturgeon complement in serum killing assays, in vivo challenges failed to fulfill Koch's postulates. However, the clinical presentation, coupled with consistent recovery of S. iniae and AciHV-2 from moribund fish, suggests viral and bacterial co-infection were the proximate cause of death. To our knowledge, this represents the first report of AciHV-2 and S. iniae co-infection in cultured white sturgeon.

A survey of the antimicrobial susceptibility of Escherichia coli isolated from Sable Island horses

The feral horses of Sable Island are a geographically isolated population located ∼160 km off the east coast of Nova Scotia, Canada. Because these horses have no contact with domestic animals, have minimal contact with people, and have never received antimicrobials, they offer a unique opportunity to study the dissemination of antimicrobial resistance in unmanaged populations. As part of an ongoing multidisciplinary and individual-based monitoring program, we collected feces from 508 geolocalized horses (92% of the total population) between July and September 2014. We selectively cultured Escherichia coli on MacConkey and CHROMagar ESBL media. Antimicrobial susceptibilities were determined, and organisms resistant to β-lactam antimicrobials were screened for β-lactamase genes by PCR. Escherichia coli was recovered from 146 (28.7%) individuals, and the majority of isolates (97%) were susceptible to all drugs tested. Resistance to tetracycline was most common, including organisms isolated from 4 (2.7%) of the colonized horses. A single isolate resistant to ampicillin, ceftriaxone, and ceftiofur was identified, which possessed the CTX-M-1 gene. Our findings demonstrate that although antimicrobial resistance is not common in this remote population, clinically relevant resistance genes are present.

Cyanotoxin degradation activity and mlr gene expression profiles of a Sphingopyxis sp. isolated from Lake Champlain, Canada

A bacterium capable of degrading five microcystin (MC) variants, microcystin-LR, YR, LY, LW and LF at an initial total concentration of 50 μg l^-1 in less than 16 hours was isolated from Missisquoi Bay, in the south of Quebec, Canada. Phylogenetic analysis of the 16S rRNA gene sequence identified the bacterium as Sphingopyxis sp., designated strain MB-E. It was shown that microcystin biodegradation activity was reduced at acidic and basic pH values. Even though no biodegradation occurred at pH values of 5.05 and 10.23, strain MB-E was able to degrade MCLR and MCYR at pH 9.12 and all five MCs variants tested at pH 6.1. Genomic sequencing revealed that strain MB-E contained the microcystin degrading gene cluster, including the mlrA, mlrB, mlrC and mlrD genes, and transcriptomic analysis demonstrated that all of these genes were induced during the degradation of MCLR alone or in the mixture of all five MCs. This novel transcriptomic analysis showed that the expression of the mlr gene cluster was similar for MCLR alone, or the mixture of MCs, and appeared to be related to the total concentration of substrate. The results suggested that the bacterium used the same pathway for the degradation of all MC variants.

Riemerella anatipestifer infection in domestic ducks in Japan, 2014

The outbreak of Riemerella anatipestifer (RA) infection has been confirmed in meat-type domestic ducks (Anas platyrhynchos) for the first time in 27 years in Japan. In January 2014, increased mortality in a 14- to 21-day-old duck flock was reported to veterinary officials by the owner. The affected ducks exhibited reduced movement, ataxia and dorsal recumbency with leg paddling. Pathological findings were typical for an RA infection. Fibrinous and heterophilic pericarditis, airsacculitis, perihepatitis, ventriculitis and meningitis were observed. The bacterial isolate from duck organs was identified as RA by PCR-based 16S ribosomal RNA sequencing.

Bovine mastitis outbreak in Japan caused by methicillin-resistant Staphylococcus aureus New York/Japan clone

Many methicillin-resistant Staphylococcus aureus (MRSA) strains are multidrug-resistant; consequently, infectious diseases involving MRSA are recognized as troublesome diseases not only in human health care but also in animal health care. A bovine mastitis case caused by MRSA isolates of the New York/Japan clone (NJC), which occurred in Japan in 2005, was monitored in the current study. Isolates of the NJC are typical of hospital-acquired MRSA in Japan. The genetic backgrounds of these strains differ from those of bovine-associated S. aureus, which are typically of clonal complex (CC)97, CC705, and CC133. Moreover, the NJC isolates in this bovine outbreak possessed a β-hemolysin-converting bacteriophage and an immune evasion cluster, as found in the NJC isolates from humans, so it is possible that this clone was introduced into the dairy herd by a human carrier. Most bovine intramammary infections (IMIs) caused by the NJC isolates in our study were asymptomatic, and obvious clinical signs were recognized in only the first 3 infected cows. Of a total of 78 cows, 31 cows were MRSA carriers, and these carrier cows were detected by testing the milk of all lactating cows at 1-month intervals. These S. aureus carrier cows were culled or the infected quarter was dried off and no longer milked. Both IMI and mastitis caused by MRSA were completely eradicated after 5 months. Genotyping data suggested that exchanging of the staphylococcal cassette chromosome mec (the determining factor in methicillin resistance) occurred easily between MRSA and methicillin-sensitive S. aureus in the udders of carrier cows. This case study demonstrates an effective procedure against the spread of MRSA in a dairy herd, and highlights the risk of emergence of new MRSA strains in a dairy herd.

Existence of Paenibacillus larvae genotypes ERIC I-ST2, ERIC I-ST15 and ERIC II-ST10 in the western region of Aichi prefecture, Japan

American foulbrood is the most destructive honeybee bacterial disease. The etiological agent, Paenibacillus larvae, has been classified into four genotypes by a repetitive-element PCR (ERIC I-IV) and 21 sequence types by multilocus sequence typing (ST1-21). In this study, we genotyped Japanese P. larvae isolates for the first time and revealed the presence of three genotypes (ERIC I-ST2, ERIC I-ST15 and ERIC II-ST10) in the western region of Aichi prefecture. ERIC I-ST15 and ERIC II-ST10 are globally distributed types, whereas the ERIC I-ST2 isolate was the first isolate of this genotype identified outside the native range of the European honeybee. The ERIC I and II isolates differed in phenotypes including cell morphology, and these may be useful for predicting ERIC types.

The Metabolically Active Bacterial Microbiome of Tonsils and Mandibular Lymph Nodes of Slaughter Pigs

The exploration of microbiomes in lymphatic organs is relevant for basic and applied research into explaining microbial translocation processes and understanding cross-contamination during slaughter. This study aimed to investigate whether metabolically active bacteria (MAB) could be detected within tonsils and mandibular lymph nodes (MLNs) of pigs. The hypervariable V1-V2 region of the bacterial 16S rRNA genes was amplified from cDNA from tonsils and MLNs of eight clinically healthy slaughter pigs. Pyrosequencing yielded 82,857 quality-controlled sequences, clustering into 576 operational taxonomic units (OTUs), which were assigned to 230 genera and 16 phyla. The actual number of detected OTUs per sample varied highly (23–171 OTUs). Prevotella zoogleoformans and Serratia proteamaculans (best type strain hits) were most abundant (10.6 and 41.8%, respectively) in tonsils and MLNs, respectively. To explore bacterial correlation patterns between samples of each tissue, pairwise Spearman correlations (r_s) were calculated. In total, 194 strong positive and negative correlations |r_s| ≥ 0.6 were found. We conclude that (i) lymphatic organs harbor a high diversity of MAB, (ii) the occurrence of viable bacteria in lymph nodes is not restricted to pathological processes and (iii) lymphatic tissues may serve as a contamination source in pig slaughterhouses. This study confirms the necessity of the EFSA regulation with regard to a meat inspection based on visual examinations to foster a minimization of microbial contamination.

Carbapenemase producing bacteria in the food supply escaping detection

Carbapenem antimicrobials are critically important to human health and they are often the only remaining effective antibiotics for treating serious infections. Resistance to these drugs mediated by acquired carbapenemase enzymes is increasingly encountered in gram-negative bacteria and is considered a public health emergency. Animal origin food products are recognized as a potential source of resistant organisms, although carbapenem resistance has only recently been reported. In western countries there are active resistance surveillance programs targeting food animals and retail meat products. These programs primarily target beef, pork and poultry and focus exclusively on E. coli, Salmonella, Campylobacter spp. and Enterococcus spp. This global surveillance strategy does not capture the diversity of foods available nor does it address the presence of resistance gene-bearing mobile genetic elements in non-pathogenic bacterial taxa. To address this gap, a total of 121 seafood products originating in Asia purchased from retail groceries in Canada were tested. Samples were processed using a taxa-independent method for the selective isolation of carbapenem resistant organisms. Isolates were characterized by phenotypic antimicrobial susceptibility testing, PCR and DNA sequencing. Carbapenemase producing bacteria, all bla_OXA-48, were isolated from 4 (3.3%) of the samples tested. Positive samples originated from China (n=2) and Korea (n=2) and included squid, sea squirt, clams and seafood medley. Carbapenemase producing organisms found include Pseudomonas, Stenotrophomonas and Myroides species. These findings suggest that non-pathogenic bacteria, excluded from resistance surveillance programs, in niche market meats may serve as a reservoir of carbapenemase genes in the food supply.

Characterization of mucosa-associated bacterial communities in abomasal ulcers by pyrosequencing

Abomasal ulcers are important pathological alterations of the gastrointestinal tract in cattle and are exceptionally hard to diagnose in vivo. The microbiome of the abomasum in cattle with or without ulcers has hardly been studied to date, and if so, the studies used culture-dependent methods. In the present study, the bacterial communities associated with abomasal ulcers of slaughter cows, bulls, and calves in Austria were described using 16S rRNA gene pyrosequencing. Sequences were clustered into 10,459 operational taxonomic units (OTUs), affiliating to 28 phyla with Proteobacteria, Firmicutes, Bacteroidetes and Tenericutes dominating (96.4% of all reads). The most abundant genera belonged to Helicobacter, Acetobacter, Lactobacillus, and novel Mycoplasma-like phylotypes. Significant differences between the microbial communities of healthy and ulcerated calves compared to cows and bulls could be observed. However, only few statistically significant differences in the abundances of certain OTUs between healthy and ulcerated abomasal mucosa were found. Additionally, near full-length 16S rRNA gene sequences of the most abundant phylotypes were obtained by cloning and Sanger sequencing (n=88). In conclusion, our results allow the first deep insights into the composition of abomasal mucosal bacterial communities in cattle and describe a hitherto unknown high diversity and species richness of abomasal bacteria in cattle. Our results suggest that bacteria may have only limited involvement in the etiology of abomasal ulcers. However, future research will be needed to verify the contribution of bacteria to abomasal ulcer formation as presence or absence of bacteria does not necessarily correlate with etiology of disease.

Efficacy of Florfenicol for Control of Mortality Associated with Edwardsiella ictaluri in Three Species of Catfish

The efficacy of florfenicol for control of mortality associated with Edwardsiella icatluri was studied in fingerlings of Channel Catfish Ictalurus puntatus (Delta strain), Blue Catfish I. furcatus (D&B strain), and a hybrid catfish (Delta strain Channel Catfish × D&B strain Blue Catfish). On day 0, fish were immersion challenged in 65-L aquaria. For each of the three species of catfish, 10 aquaria were randomly assigned to two treatment groups, either treated with florfenicol at 0 mg/kg of body weight (unmedicated feed) or at 10 mg/kg (medicated feed). Fish were treated for 10 consecutive days, monitored for mortality during this treatment period, and observed for 14 d afterwards. Post observation, all survivors were humanely euthanized in tricaine methanesulfonate, cultured for E. ictaluri, and examined for gross pathology. The mean cumulative percent mortality from enteric septicemia of catfish (ESC) challenge among the three genotypes of catfish did not differ between Blue Catfish, hybrid, and Channel Catfish in treated or control groups. However, the florfenicol-treated fish had a significantly lower mean cumulative mortality (6%) than the controls (78%). All genotypes of catfish tested were responsive to treatment with florfenicol-medicated feed for control of mortality associated with ESC. There were no significant differences in mortality associated with hybrid catfish, blue catfish, and Channel Catfish (Delta strain).

Strain-specific bioaccumulation and intracellular distribution of Cd²⁺ in bacteria isolated from the rhizosphere, ectomycorrhizae, and fruitbodies of ectomycorrhizal fungi

Bioaccumulation of Cd(2+) in soil bacteria might represent an important route of metal transfer to associated mycorrhizal fungi and plants and may have potential as a tool to accelerate Cd(2+) extraction in the bioremediation of contaminated soils. The present study examined the bioaccumulation of Cd(2+) in 15 bacterial strains representing three phyla (Firmicutes, Proteobacteria, and Bacteroidetes) that were isolated from the rhizosphere, ectomycorrhizae, and fruitbody of ectomycorrhizal fungi. The strains Pseudomonas sp. IV-111-14, Variovorax sp. ML3-12, and Luteibacter sp. II-116-7 displayed the highest biomass productivity at the highest tested Cd(2+) concentration (2 mM). Microscopic analysis of the cellular Cd distribution revealed intracellular accumulation by strains Massilia sp. III-116-18, Pseudomonas sp. IV-111-14, and Bacillus sp. ML1-2. The quantities of Cd measured in the interior of the cells ranged from 0.87 to 1.31 weight % Cd. Strains originating from the rhizosphere exhibited higher Cd(2+) accumulation efficiencies than strains from ectomycorrhizal roots or fruitbodies. The high Cd tolerances of Pseudomonas sp. IV-111-16 and Bacillus sp. ML1-2 were attributed to the binding of Cd(2+) as cadmium phosphate. Furthermore, silicate binding of Cd(2+) by Bacillus sp. ML1-2 was observed. The tolerance of Massilia sp. III-116-18 to Cd stress was attributed to a simultaneous increase in K(+) uptake in the presence of Cd(2+) ions. We conclude that highly Cd-tolerant and Cd-accumulating bacterial strains from the genera Massilia sp., Pseudomonas sp., and Bacillus sp. might offer a suitable tool to improve the bioremediation efficiency of contaminated soils.

Molecular diagnostic tools for detection and differentiation of phytoplasmas based on chaperonin-60 reveal differences in host plant infection patterns

Phytoplasmas (‘Candidatus Phytoplasma’ spp.) are insect-vectored bacteria that infect a wide variety of plants, including many agriculturally important species. The infections can cause devastating yield losses by inducing morphological changes that dramatically alter inflorescence development. Detection of phytoplasma infection typically utilizes sequences located within the 16S–23S rRNA-encoding locus, and these sequences are necessary for strain identification by currently accepted standards for phytoplasma classification. However, these methods can generate PCR products >1400 bp that are less divergent in sequence than protein-encoding genes, limiting strain resolution in certain cases. We describe a method for accessing the chaperonin-60 (cpn60) gene sequence from a diverse array of ‘Ca.Phytoplasma’ spp. Two degenerate primer sets were designed based on the known sequence diversity of cpn60 from ‘Ca.Phytoplasma’ spp. and used to amplify cpn60 gene fragments from various reference samples and infected plant tissues. Forty three cpn60 sequences were thereby determined. The cpn60 PCR-gel electrophoresis method was highly sensitive compared to 16S-23S-targeted PCR-gel electrophoresis. The topology of a phylogenetic tree generated using cpn60 sequences was congruent with that reported for 16S rRNA-encoding genes. The cpn60 sequences were used to design a hybridization array using oligonucleotide-coupled fluorescent microspheres, providing rapid diagnosis and typing of phytoplasma infections. The oligonucleotide-coupled fluorescent microsphere assay revealed samples that were infected simultaneously with two subtypes of phytoplasma. These tools were applied to show that two host plants, Brassica napus and Camelina sativa, displayed different phytoplasma infection patterns.

Phenotypic and genotypic heterogeneity among Streptococcus iniae isolates recovered from cultured and wild fish in North America, Central America and the Caribbean islands

Streptococcus iniae, the etiological agent of streptococcosis in fish, is an important pathogen of cultured and wild fish worldwide. During the last decade outbreaks of streptococcosis have occurred in a wide range of cultured and wild fish in the Americas and Caribbean islands. To gain a better understanding of the epizootiology of S. iniae in the western hemisphere, over 30 S. iniae isolates recovered from different fish species and geographic locations were characterized phenotypically and genetically. Species identities were determined biochemically and confirmed by amplification and sequencing of the 16S rRNA gene. Repetitive-element palindromic PCR fingerprinting as well as biochemical and antimicrobial susceptibility profiles suggest that a single strain of S. iniae was responsible for two different disease outbreaks among reef fishes in the Caribbean, one in 1999 and another in 2008. Interestingly, a majority of the isolates recovered from cultured fish in the Americas were genetically distinct from the Caribbean isolates and exhibited a trend toward higher minimal inhibitory concentration with respect to several antibiotics as well as greater genetic variability. The biological significance of this genetic variability is unclear, but it could have implications for future vaccine development and treatment.

Eosinophilic granuloma with Splendore-Hoeppli material caused by toxigenic Corynebacterium ulcerans in a heifer

Raised lesions were present on the left nasal vestibule of a 20-month-old Japanese Brown heifer. The largest mass which caused partial nasal obstruction was removed surgically. Corynebacterium ulcerans was identified in the mass. 16S ribosomal RNA and RNA polymerase beta subunit genes were 100% and 98% identical to other C. ulcerans strains. Histologically, multiple foci of eosinophilic granuloma with Splendore-Hoeppli material were seen. Rod-shaped Gram-positive organisms were detected with metachromatic granules, producing diphtheria toxin with 5, 30 and 48 amino acid differences to another C. ulcerans strain, C. diphtheriae or C. pseudotuberculosis, respectively. The toxin is highly cytotoxic and may be responsible for the formation of abundant Splendore-Hoeppli material. The lesion was therefore judged to be an allergic reaction to bacterial antigens or diphtheria toxin.

Development of a two-step multiplex PCR assay for typing of capsular polysaccharide synthesis gene clusters of Streptococcus suis

We developed a practical and easy two-step multiplex PCR assay to aid in serotyping of Streptococcus suis. The assay accurately typed almost all of the serotype reference strains and field isolates of various serotypes and also identified the genotypes of capsular polysaccharide synthesis gene clusters of some serologically nontypeable strains.

Mucosa-associated bacterial microbiome of the gastrointestinal tract of weaned pigs and dynamics linked to dietary calcium-phosphorus

Dietary composition largely influences pig's gastrointestinal microbiota and represents a useful prophylactic tool against enteric disturbances in young pigs. Despite the importance for host-microbe interactions and bacterial colonization, dietary responses of the mucosa-associated bacterial communities are less well investigated. In the present study, we characterized the mucosa-associated bacterial communities at the Pars non-glandularis of the stomach, ileum and colon, and identified shifts in these communities in response to different dietary calcium-phosphorus (Ca-P) contents (100% versus 190% of the Ca and P requirements) in combination with two basal diets (wheat-barley- or corn-based) in weaned pigs. Pyrosequencing of 16S rRNA genes from 93 mucosal samples yielded 447,849 sequences, clustering into 997 operational taxonomic units (OTUs) at 97% similarity level. OTUs were assigned to 198 genera belonging to 14 different phyla. Correlation-based networks revealed strong interactions among OTUs at the various gastrointestinal sites. Our data describe a previously not reported high diversity and species richness at the Pars non-glandularis of the stomach in weaned pigs. Moreover, high versus adequate Ca-P content significantly promoted Lactobacillus by 14.9% units (1.4 fold change) at the gastric Pars non-glandularis (P = 0.035). Discriminant analysis revealed dynamic changes in OTU composition in response to dietary cereals and Ca-P contents at all gastrointestinal sites which were less distinguishable at higher taxonomic levels. Overall, this study revealed a distinct mucosa-associated bacterial community at the different gut sites, and a strong effect of high Ca-P diets on the gastric community, thereby markedly expanding our comprehension on mucosa-associated microbiota and their diet-related dynamics in weaned pigs.

Microbiomes of unreactive and pathologically altered ileocecal lymph nodes of slaughter pigs

Microbe-laden dendritic cells are shifted to ileocecal lymph nodes (ICLNs), where microbes are concentrated and an adequate immune response is triggered. Hence, ICLNs are at a crucial position in immune anatomy and control processes of the local immune system. Pathological alterations in ICLNs, such as reactive hyperplasia, lymphadenitis purulenta, or granulomatosa, can harbor a multitude of pathogens and commensals, posing a potential zoonotic risk in animal production. The aim of this study was to characterize the microbial diversity of unreactive ICLNs of slaughter pigs and to investigate community shifts in reactive ICLNs altered by enlargement, purulence, or granulomatous formations. Pyrosequencing of 16S rRNA gene amplicons from 32 ICLNs yielded 175,313 sequences, clustering into 650 operational taxonomic units (OTUs). OTUs were assigned to 239 genera and 11 phyla. Besides a highly diverse bacterial community in ICLNs, we observed significant shifts in pathologically altered ICLNs. The relative abundances of Cloacibacterium- and Novosphingobium-associated OTUs and the genus Faecalibacterium were significantly higher in unreactive ICLNs than in pathologically altered ICLNs. Enlarged ICLNs harbored significantly more Lactobacillus- and Clostridium-associated sequences. Relative abundances of Mycoplasma, Bacteroides, Veillonella, and Variovorax OTUs were significantly increased in granulomatous ICLNs, whereas abundances of Pseudomonas, Escherichia, and Acinetobacter OTUs were significantly increased in purulent ICLNs (P < 0.05). Correlation-based networks revealed interactions among OTUs in all ICLN groups, and discriminant analyses depicted discrimination in response to pathological alterations. This study is the first community-based survey in ICLNs of livestock animals and will provide a basis to broaden the knowledge of microbe-host interactions in pigs.

Fatal septicemia caused by the zoonotic bacterium Streptococcus iniae during an outbreak in Caribbean reef fish

An outbreak of Streptococcus iniae occurred in the early months of 2008 among wild reef fish in the waters of the Federation of St Kitts and Nevis, lasting almost 2 months. Moribund and dead fish were collected for gross, histological, bacteriological, and molecular analysis. Necropsy findings included diffuse fibrinous pericarditis, pale friable livers, and serosal petechiation. Cytological and histological analysis revealed granulocytic and granulomatous inflammation with abundant coccoid bacterial organisms forming long chains. Necrosis, inflammation, and vasculitis were most severe in the pericardium, meninges, liver, kidneys, and gills. Bacterial isolates revealed β-hemolytic, Gram-positive coccoid bacteria identified as S. iniae by amplification and 16S ribosomal RNA gene sequencing. Results from biochemical and antimicrobial susceptibility analysis, together with repetitive element palindromic polymerase chain reaction fingerprinting, suggest that a single strain was responsible for the outbreak. The inciting cause for this S. iniae-associated cluster of mortalities is unknown.

Characterization and genus identification of rhizobial symbionts from Caragana arborescens in western Canada

Naturally occurring nitrogen-fixing symbionts from root nodules of caragana (Caragana arborescens) growing in central Saskatchewan were isolated following surface sterilization of caragana root nodules and squashing and spreading of the contents on yeast extract – mannitol medium. The symbiotic nature of the strains was confirmed following inoculation onto surface-sterilized C. arborescens seed in a gnotobiotic Leonard jar system. The Rhizobium isolates from C. arborescens root nodules were intermediate in generation time (g) (mean g of 5 isolates was 6.41 h) compared with the fast growers, Rhizobium leguminosarum NRG457 (g: 4.44 h), Rhizobium tropici 899 (g: 3.19 h), and Sinorhizobium meliloti BALSAC (g: 3.45 h), but they were faster than the slow-growing Bradyrhizobium japonicum USDA 110 (g: 13.86 h) and similar to Mesorhizobium amorphae (g: 7.76 h). Nitrogen derived from fixation by measuring changes in δ15N natural abundance in plant tissue confirmed the effectiveness of the strains; approximately 80% N2 from fixation. Strain identification was carried out by determining the sequences of 3 genes: 16S rRNA-encoding genes, cpn60, and recA. This analysis determined that the symbiotic partner of Canadian C. arborescens belongs to the genus Mesorhizobium and seems more related to M. loti than to previously described caragana symbionts like M. caraganae. This is the first report of Mesorhizobium sp. nodulating C. arborescens in western Canada.

Fecal source tracking in water using a mitochondrial DNA microarray

A mitochondrial-based microarray (mitoArray) was developed for rapid identification of the presence of 28 animals and one family (cervidae) potentially implicated in fecal pollution in mixed activity watersheds. Oligonucleotide probes for genus or subfamily-level identification were targeted within the 12S rRNA - Val tRNA - 16S rRNA region in the mitochondrial genome. This region, called MI-50, was selected based on three criteria: 1) the ability to be amplified by universal primers 2) these universal primer sequences are present in most commercial and domestic animals of interest in source tracking, and 3) that sufficient sequence variation exists within this region to meet the minimal requirements for microarray probe discrimination. To quantify the overall level of mitochondrial DNA (mtDNA) in samples, a quantitative-PCR (Q-PCR) universal primer pair was also developed. Probe validation was performed using DNA extracted from animal tissues and, for many cases, animal-specific fecal samples. To reduce the amplification of potentially interfering fish mtDNA sequences during the MI-50 enrichment step, a clamping PCR method was designed using a fish-specific peptide nucleic acid. DNA extracted from 19 water samples were subjected to both array and independent PCR analyses. Our results confirm that the mitochondrial microarray approach method could accurately detect the dominant animals present in water samples emphasizing the potential for this methodology in the parallel scanning of a large variety of animals normally monitored in fecal source tracking.

Edwardsiella ictaluri as the causative agent of mortality in cultured Nile tilapia

Edwardsiella ictaluri was consistently isolated from the spleens, livers, and head kidneys of diseased Nile tilapia Oreochromis niloticus from a farm experiencing mortality events in several culture ponds. We describe the first published outbreak of E. ictaluri-induced edwardsiellosis in Nile tilapia. Pure cultures of the isolated bacteria were characterized both biochemically and molecularly. Biochemical analysis was performed using the API-20E and RapID One systems, and antimicrobial susceptibility was determined by the broth microdilution method. Molecular analysis involved sequencing of the 16S rRNA gene, species-specific real-time polymerase chain reaction (PCR), and PCR-mediated genomic fingerprinting (rep-PCR). Pairwise sequence analysis of the 16S rRNA gene identified the case isolates to be a 100% match to E. ictaluri cultured from channel catfish in the southeastern United States. However, rep-PCR analysis identified the case isolates to be genetically different from representative strains isolated from disease outbreaks in cultured channel catfish in Mississippi. Infectivity challenges (intraperitoneal injection and immersion) demonstrated that a representative E. ictaluri strain isolated from tilapia was pathogenic to naive tilapia, reproducing clinical signs and mortality, thereby establishing Koch's postulates.

Characterization of the bacterial archaeal diversity in hydrocarbon-contaminated soil

A polyphasic approach combining culture-based methods with molecular methods is useful to expand knowledge on microbial diversity in contaminated soil. Microbial diversity was examined in soil samples from a former industrial site in the European Alps (mainly used for aluminum production and heavily contaminated with petroleum hydrocarbons) by culture-dependent and culture-independent methods. The physiologically active eubacterial community, as revealed by fluorescence-in-situ-hybridization (FISH), accounted for 6.7% of the total (DAPI-stained) bacterial community. 4.4% and 2.0% of the DAPI-stained cells could be attributed to culturable, heterotrophic bacteria able to grow at 20°C and 10°C, respectively. The majority of culturable bacterial isolates (34/48) belonged to the Proteobacteria (with a predominance of Alphaproteobacteria and Gammaproteobacteria), while the remaining isolates were affiliated with the Actinobacteria, Cytophaga-Flavobacterium-Bacteroides and Firmicutes. A high fraction of the culturable, heterotrophic bacterial population was able to utilize hydrocarbons. Actinobacteria were the most versatile and efficient degraders of diesel oil, n-alkanes, phenol and PAHs. The bacterial 16S rRNA gene clone library contained 390 clones that grouped into 68 phylotypes related to the Proteobacteria, Bacteroidetes, Actinobacteria and Spirochaetes. The archaeal 16S rRNA gene library contained 202 clones and 15 phylotypes belonging to the phylum Euryarchaeota; sequences were closely related to those of methanogenic archaea of the orders Methanomicrobiales, Methanosarcinales, Methanobacteriales and Thermoplasmatales. A number of bacterial and archaeal phylotypes in the clone libraries shared high similarities with strains previously described to be involved in hydrocarbon biodegradation. Knowledge of the bacterial and archaeal diversity in the studied soil is important in order to get a better insight into the microbial structure of contaminated environments and to better exploit the bioremediation potential by identifying potential hydrocarbon degraders and consequently developing appropriate bioremediation strategies.

Diversity of Melissococcus plutonius from honeybee larvae in Japan and experimental reproduction of European foulbrood with cultured atypical isolates

European foulbrood (EFB) is an important infectious disease of honeybee larvae, but its pathogenic mechanisms are still poorly understood. The causative agent, Melissococcus plutonius, is a fastidious organism, and microaerophilic to anaerobic conditions and the addition of potassium phosphate to culture media are required for growth. Although M. plutonius is believed to be remarkably homologous, in addition to M. plutonius isolates with typical cultural characteristics, M. plutonius-like organisms, with characteristics seemingly different from those of typical M. plutonius, have often been isolated from diseased larvae with clinical signs of EFB in Japan. Cultural and biochemical characterization of 14 M. plutonius and 19 M. plutonius-like strain/isolates revealed that, unlike typical M. plutonius strain/isolates, M. plutonius-like isolates were not fastidious, and the addition of potassium phosphate was not required for normal growth. Moreover, only M. plutonius-like isolates, but not typical M. plutonius strain/isolates, grew anaerobically on sodium phosphate-supplemented medium and aerobically on some potassium salt-supplemented media, were positive for β-glucosidase activity, hydrolyzed esculin, and produced acid from L-arabinose, D-cellobiose, and salicin. Despite the phenotypic differences, 16S rRNA gene sequence analysis and DNA-DNA hybridization demonstrated that M. plutonius-like organisms were taxonomically identical to M. plutonius. However, by pulsed-field gel electrophoresis analysis, these typical and atypical (M. plutonius-like) isolates were separately grouped into two genetically distinct clusters. Although M. plutonius is known to lose virulence quickly when cultured artificially, experimental infection of representative isolates showed that atypical M. plutonius maintained the ability to cause EFB in honeybee larvae even after cultured in vitro in laboratory media. Because the rapid decrease of virulence in cultured M. plutonius was a major impediment to elucidation of the pathogenesis of EFB, atypical M. plutonius discovered in this study will be a breakthrough in EFB research.

Interactive and Single Effects of Ectomycorrhiza Formation and Bacillus cereus on Metallothionein MT1 Expression and Phytoextraction of Cd and Zn by Willows

Single and joint ectomycorrhizal (+ Hebeloma mesophaeum) and bacterial (+ Bacillus cereus) inoculations of willows (Salix viminalis) were investigated for their potential and mode of action in the promotion of cadmium (Cd) and zinc (Zn) phytoextraction. Dual fungal and bacterial inoculations promoted the biomass production of willows in contaminated soil. Single inoculations either had no effect on the plant growth or inhibited it. All inoculated willows showed increased concentrations of nutritional elements (N, P, K and Zn) and decreased concentrations of Cd in the shoots. The lowest biomass production and concentration of Cd in the willows (+ B. cereus) were combined with the strongest expression of metallothioneins. It seems that biotic stress from bacterial invasion increased the synthesis of these stress proteins, which responded in decreased Cd concentrations. Contents of Cd and Zn in the stems of willows were combination-specific, but were always increased in dual inoculated plants. In conclusion, single inoculations with former mycorrhiza-associated B. cereus strains decreased the phytoextraction efficiency of willows by causing biotic stress. However, their joint inoculation with an ectomycorrhizal fungus is a very promising method for promoting the phytoextraction of Cd and Zn through combined physiological effects on the plant.

Diets supplemented with chickpea or its main oligosaccharide component raffinose modify faecal microbial composition in healthy adults

The effects of diets supplemented with either chickpea or its main oligosaccharide raffinose on the composition of the faecal microbial community were examined in 12 healthy adults (18-65 years) in a randomised crossover intervention study. Subjects consumed their usual diet supplemented with soups and desserts that were unfortified, or fortified with either 200 g/d of canned chickpeas or 5 g/d of raffinose for 3 week periods. Changes in faecal bacterial populations of subjects were examined using 16S rRNA-based terminal restriction fragment length polymorphisms (T-RFLP) and clone libraries generated from the diet pools. Classification of the clone libraries and T-RFLP analysis revealed that Faecalibacterium prausnitzii, reported to be an efficient butyrate producer and a highly metabolically active bacterium in the human intestinal microbiota, was more abundant in the raffinose diet and the chickpea diet compared to the control diet. However, no significant difference was observed in the faecal total short chain fatty acid concentration or in the levels of the components (butyrate, acetate and propionate) with the chickpea diet or the raffinose diet compared to the control diet. Bifidobacterium species were detected by T-RFLP in all three diet groups and quantitative real-time PCR (qPCR) analysis showed a marginal increase in 16S rRNA gene copies of Bifidobacterium with the raffinose diet compared to control (P>0.05). The number of individuals showing TRFs for the Clostridium histolyticum - Clostridum lituseburense groups, which include pathogenic bacteria species and putrefactive bacteria, were lower in the chickpea diet compared to the other two treatments. Diet appeared to affect colonisation by a high ammonia-producing bacterial isolate which was detected in 83%, 92% and 42% of individuals in the control, raffinose and chickpea groups, respectively. Our results indicate that chickpea and raffinose have the potential to modulate the intestinal microbial composition to promote intestinal health in humans.