Unraveling Bacterial Single-Stranded Sequence Specificities: Insights from Molecular Dynamics and MMPBSA Analysis of Oligonucleotide Probes

We utilized molecular dynamics (MD) simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) free energy calculations to investigate the specificity of two oligonucleotide probes, namely probe B and probe D, in detecting single-stranded DNA (ssDNA) within three bacteria families: Enterobacteriaceae, Pasteurellaceae, and Vibrionaceae. Due to the limited understanding of molecular mechanisms in the previous research, we have extended the discussion to focus specifically on investigating the binding process of bacteria-probe DNA duplexes, with an emphasis on analyzing the binding free energy. The role of electrostatic contributions in the specificity between the oligonucleotide probes and the bacterial ssDNAs was investigated and found to be crucial. Our calculations yielded results that were highly consistent with the experimental data. Through our study, we have successfully exhibited the benefits of utilizing in-silico approaches as a powerful virtual-screening tool, particularly in research areas that demand a thorough comprehension of molecular interactions.

Macrolide resistance in Mannheimia haemolytica isolates associated with bovine respiratory disease from the German national resistance monitoring program GERM-Vet 2009 to 2020

Data collected from the German national resistance monitoring program GERM-Vet showed slowly increasing prevalence of macrolide resistance among bovine respiratory disease (BRD)-associated Pasteurellacae from cattle over the last decade. The focus of this study was to analyze the genetic basis of antimicrobial resistance (AMR) and the prevalence of multidrug-resistance (MDR)-mediating integrative and conjugative elements (ICEs) in 13 German BRD-associated Mannheimia haemolytica isolates collected between 2009 and 2020 via whole-genome sequencing. Antimicrobial susceptibility testing (AST) was performed via broth microdilution according to the recommendations of the Clinical and Laboratory Standards Institute for the macrolides erythromycin, tilmicosin, tulathromycin, gamithromycin, tildipirosin, and tylosin as well as 25 other antimicrobial agents. All isolates either had elevated MICs or were resistant to at least one of the macrolides tested. Analysis of whole-genome sequences obtained by hybrid assembly of Illumina MiSeq and Oxford Nanopore MinION reads revealed the presence of seven novel Tn7406-like ICEs, designated Tn7694, and Tn7724- Tn7729. These ICEs harbored the antimicrobial resistance genes erm(T), mef (C), mph(G), floR, catA3, aad(3")(9), aph(3')-Ia, aac(3)-IIa, strA, strB, tet(Y), and sul2 in different combinations. In addition, mutational changes conferring resistance to macrolides, nalidixic acid or streptomycin, respectively, were detected among the M. haemolytica isolates. In addition, four isolates carried a 4,613-bp plasmid with the β-lactamase gene blaROB - 1. The detection of the macrolide resistance genes erm(T), mef (C), and mph(G) together with other resistance genes on MDR-mediating ICEs in bovine M. haemolytica may explain the occurrence of therapeutic failure when treating BRD with regularly used antimicrobial agents, such as phenicols, penicillins, tetracyclines, or macrolides. Finally, pathogen identification and subsequent AST is essential to ensure the efficacy of the antimicrobial agents applied to control BRD in cattle.

Impact of bronchoalveolar lavage from influenza A virus diseased pigs on neutrophil functions and growth of co-infecting pathogenic bacteria

Introduction

Influenza A viruses (IAVs) infect the respiratory tract of mainly humans, poultry, and pigs. Co-infections with pathogenic lung bacteria are a common event and contribute to the severity of disease progression. Neutrophils are a major cell type of the innate immune system and are rapidly recruited to the site of infection. They have several effector functions to fight invading pathogens such as the secretion of reactive oxygen species (ROS) or the release of neutrophil extracellular traps (NETs). NETs are known to promote the growth of Pasteurellaceae bacteria, especially if degraded by nucleases.

Methods

In this study, bronchoalveolar lavage fluid (BALF) from 45 field-infected pigs was analyzed for 1) NET markers, 2) influence on growth of lung bacteria, and 3) impact on neutrophil functions. BALF samples from 21 IAV-positive pigs and 24 lung diseased but IAV-negative pigs were compared.

Results

Here, we show that neutrophils in the lungs of IAV-positive pigs release vesicular NETs. Several NET markers were increased in the BALF of IAV-positive pigs compared with the BALF from IAV-negative pigs. The amount of NET markers positively correlated with the viral load of the IAV infection. Interestingly, the BALF of IAV-positive pigs enhanced the growth of bacteria belonging to the family of Pasteurellaceae as potential coinfecting bacteria. These effects were weaker with the BALF derived from IAV-negative pigs with other lung infections. The intensity of oxidative burst in neutrophils was significantly decreased by BALF from IAVpositive pigs, indicating impaired antimicrobial activity of neutrophils. Finally, the lung milieu reflected by IAV-positive BALF does not enable neutrophils to kill Actinobacillus pleuropneumoniae but rather enhances its growth.

Discussion

In summary, our data show that an IAV infection is affecting neutrophil functions, in particular the release of NETs and ROS. Furthermore, IAV infection seems to provide growth-enhancing factors for especially coinfecting Pasteurellaceae and reduces the killing efficiency of neutrophils.

Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice

Symbiotic microbial communities affect the host immune system and produce molecules contributing to the odor of an individual. In many mammalian species, saliva and vaginal fluids are important sources of chemical signals that originate from bacterial metabolism and may act as honest signals of health and reproductive status. In this study, we aimed to define oral and vaginal microbiomes and their dynamics throughout the estrous cycle in wild house mice. In addition, we analyzed a subset of vaginal proteomes and metabolomes to detect potential interactions with microbiomes. 16S rRNA sequencing revealed that both saliva and vagina are dominated by Firmicutes and Proteobacteria but differ at the genus level. The oral microbiome is more stable during the estrous cycle and most abundant bacteria belong to the genera Gemella and Streptococcus, while the vaginal microbiome shows higher bacterial diversity and dynamics during the reproductive cycle and is characterized by the dominance of Muribacter and Rodentibacter. These two genera cover around 50% of the bacterial community during estrus. Proteomic profiling of vaginal fluids revealed specific protein patterns associated with different estrous phases. Highly expressed proteins in estrus involve the keratinization process thus providing estrus markers (e.g., Hrnr) while some proteins are downregulated such as immune-related proteins that limit bacterial growth (Camp, Clu, Elane, Lyz2, and Ngp). The vaginal metabolome contains volatile compounds potentially involved in chemical communication, for example, ketones, aldehydes, and esters of carboxylic acids. Data integration of all three OMICs data sets revealed high correlations, thus providing evidence that microbiomes, host proteomes, and metabolomes may interact.IMPORTANCEOur data revealed dynamic changes in vaginal, but not salivary, microbiome composition during the reproductive cycle of wild mice. With multiple OMICs platforms, we provide evidence that changes in microbiota in the vaginal environment are accompanied by changes in the proteomic and metabolomics profiles of the host. This study describes the natural microbiota of wild mice and may contribute to a better understanding of microbiome-host immune system interactions during the hormonal and cellular changes in the female reproductive tract. Moreover, analysis of volatiles in the vaginal fluid shows particular substances that can be involved in chemical communication and reproductive behavior.

Rodentibacter caecimuris comb. nov., arising from the heterotypic synonymy between Pasteurella caecimuris Lagkouvardos et al. 2016 and Rodentibacter heylii Adhikary et al. 2017

The misclassification of the species Pasteurella caecimuris Lagkouvardos et al. 2016 along with the heterotypic synonymy between P. caecimuris and Rodentibacter heylii Adhikary et al. 2017 has long been recognized. However, no formal assignment of P. caecimuris to its correct taxonomic position has been made accordingly and therefore the nomenclatural consequences have not been implemented. In the present study, the author first re-evaluates the taxonomic relationships of P. caecimuris using genome-based approaches, confirming the need of reclassification to the genus Rodentibacter and presenting evidence of the synonymy between R. heylii and P. caecimuris. Next, the author proposes a new name Rodentibacter caecimuris comb. nov. and, based on the priority of their specific epithets, treats Rodentibacter heylii as a later heterotypic synonym of Rodentibacter caecimuris.

Phylogeography and host specificity of Pasteurellaceae pathogenic to sea-farmed fish in the north-east Atlantic

The present study was undertaken to address the recent spate of pasteurellosis outbreaks among sea-farmed Atlantic salmon (Salmo salar) in Norway and Scotland, coinciding with sporadic disease episodes in lumpfish (Cyclopterus lumpus) used for delousing purposes in salmon farms. Genome assemblies from 86 bacterial isolates cultured from diseased salmon or lumpfish confirmed them all as bona fide members of the Pasteurellaceae family, with phylogenetic reconstruction dividing them into two distinct branches sharing <88% average nucleotide identity. These branches therefore constitute two separate species, namely Pasteurella skyensis and the as-yet invalidly named "Pasteurella atlantica". Both species further stratify into multiple discrete genomovars (gv.) and/or lineages, each being nearly or fully exclusive to a particular host, geographic region, and/or time period. Pasteurellosis in lumpfish is, irrespective of spatiotemporal origin, linked almost exclusively to the highly conserved "P. atlantica gv. cyclopteri" (Pac). In contrast, pasteurellosis in Norwegian sea-farmed salmon, dominated since the late-1980s by "P. atlantica gv. salmonicida" (Pas), first saw three specific lineages (Pas-1, -2, and -3) causing separate, geographically restricted, and short-lived outbreaks, before a fourth (Pas-4) emerged recently and became more widely disseminated. A similar situation involving P. skyensis (Ps) has apparently been unfolding in Scottish salmon farming since the mid-1990s, where two historic (Ps-1 and -2) and one contemporary (Ps-3) lineages have been recorded. While the epidemiology underlying all these outbreaks/epizootics remains unclear, repeated detection of 16S rRNA gene amplicons very closely related to P. skyensis and "P. atlantica" from at least five cetacean species worldwide raises the question as to whether marine mammals may play a part, possibly as reservoirs. In fact, the close relationship between the studied isolates and Phocoenobacter uteri associated with harbor porpoise (Phocoena phocoena), and their relatively distant relationship with other members of the genus Pasteurella, suggests that both P. skyensis and "P. atlantica" should be moved to the genus Phocoenobacter.

Characterization of small plasmids carrying florfenicol resistance gene floR in Actinobacillus pleuropneumoniae and Pasteurella multocida isolates from swine in China

Actinobacillus pleuropneumoniae and Pasteurella multocida are two important bacterial pathogens in swine industry. In the present study, resistance profiles of nine commonly used antibiotics of A. pleuropneumoniae and P. multocida isolates of swine origin from different regions of China were investigated by determination of minimum inhibitory concentrations (MICs). In addition, genetic relationship of the florfenicol-resistant A. pleuropneumoniae and P. multocida isolates was determined by pulsed-field gel electrophoresis (PFGE). The genetic basis of florfenicol resistance in these isolates were explored by floR detection and whole genome sequencing. High resistance rates (>25%) of florfenicol, tetracycline and trimethoprim- sulfamethoxazole were observed for both bacteria. No ceftiofur- and tiamulin- resistant isolates were detected. Furthermore, all the 17 florfenicol-resistant isolates (nine for A. pleuropneumoniae and eight for P. multocida) were positive for floR gene. The presence of similar PFGE types in these isolates suggested that clonal expansion of some floR-producing strains occurred in the pig farms from same regions. WGS and PCR screening showed that three plasmids, named pFA11, pMAF5, and pMAF6, were the cargos of the floR genes in the 17 isolates. Plasmid pFA11 exhibited novel structure and carried several resistance genes, including floR, sul2, aacC2d, strA, strB, and bla _{ROB - 1}. Plasmids pMAF5 and pMAF6 were presented in A. pleuropneumoniae and P. multocida isolates from different regions, suggesting horizontal transfer of the two plasmids are important for the floR dissemination in these Pasteurellaceae pathogens. Further studies of florfenicol resistance and its transfer vectors in Pasteurellaceae bacteria of veterinary origin are warranted.

Infective endocarditis due to Haemophilus sputorum

Introduction

Haemophilus species are gram-negative, non-motile, facultative anaerobic coccobacilli in the larger family of Pasteurellaceae . Implicated in a variety of human diseases, Haemophilus species are also included in the 'HACEK' group of organisms, which are fastidious gram-negative bacteria, a well-described but uncommon cause of endocarditis. Among the Haemophilus species responsible for endocarditis, Haemophilus parainfluenzae is the most frequently isolated. However, novel species of Haemophilus have recently been described, and their clinical significance remains uncertain.

Case presentation

A 35-year-old man was admitted to the hospital after presenting with a 3 month history of nightly fevers, night sweats and unintentional weight loss, with a new murmur detected on cardiac auscultation. Blood cultures returned positive for Haemophilus sputorum identified by matrix assisted laser desorption ionization - time of flight MS, and confirmed with whole genome sequencing. Echocardiography revealed the presence of an aortic valve vegetation, with aortic and mitral valve leaflet perforations. He was successfully treated with surgical bioprosthetic valve replacements and pathogen-directed antibiotics without complications.

Conclusion

We describe a case of infective endocarditis due to H. sputorum , a newly identified Haemophilus species, which to the best of our knowledge has yet to be reported, and discuss the available literature regarding this organism.

Identification of small RNAs associated with RNA chaperone Hfq reveals a new stress response regulator in Actinobacillus pleuropneumoniae

The RNA chaperone Hfq promotes the association of small RNAs (sRNAs) with cognate mRNAs, controlling the expression of bacterial phenotype. Actinobacillus pleuropneumoniae hfq mutants strains are attenuated for virulence in pigs, impaired in the ability to form biofilms, and more susceptible to stress, but knowledge of the extent of sRNA involvement is limited. Here, using A. pleuropneumoniae strain MIDG2331 (serovar 8), 14 sRNAs were identified by co-immunoprecipitation with Hfq and the expression of eight, identified as trans-acting sRNAs, were confirmed by Northern blotting. We focused on one of these sRNAs, named Rna01, containing a putative promoter for RpoE (stress regulon) recognition. Knockout mutants of rna01 and a double knockout mutant of rna01 and hfq, both had decreased biofilm formation and hemolytic activity, attenuation for virulence in Galleria mellonella, altered stress susceptibility, and an altered outer membrane protein profile. Rna01 affected extracellular vesicle production, size and toxicity in G. mellonella. qRT-PCR analysis of rna01 and putative cognate mRNA targets indicated that Rna01 is associated with the extracytoplasmic stress response. This work increases our understanding of the multilayered and complex nature of the influence of Hfq-dependent sRNAs on the physiology and virulence of A. pleuropneumoniae.

A Conserved Histophilus somni 23S Intervening Sequence Yields Functional, Fragmented 23S rRNA

Histophilus somni is a Gram-negative bacterial organism that acts as an opportunistic pathogen and is a fastidious member of the Pasteurellaceae family associated with diseases of respiratory, reproductive, cardiac, and other tissues of ruminants. We identified an intervening sequence (IVS) embedded in all five copies of the 23S rRNA gene in the closed genome sequence of the H. somni isolate USDA-ARS-USMARC-63250 that may play an important role in affecting the biology of the organism. Sequencing the RNA from this isolate shows that most of the IVS is cleaved from the transcript, resulting in independent fragments of this structural rRNA that remain functional within the bacterial ribosome. The IVS lies between positions 1170 and 1278 bp of the 3,017-bp gene and exhibits self-complementarity between its 5′ and 3′ ends that predicts a stem-loop structure interrupting helix-45 in the transcribed 23S rRNA. Excision removes a 94-nucleotide (nt) stem-loop structure that displays an unusual 1-nt 3′ end overhang instead of the more typical 2-nt overhang commonly observed at the ends of other excised IVS stem-loops. A comparison with genomes of other H. somni isolates indicates that this IVS is highly conserved, with 31 of 32 complete genomes having similar interruptions of canonical 23S rRNA genes. The potential biological effects of either the released IVS or the fragmentation of the functional 23S rRNA are unknown, but fragmentation may enhance rRNA degradation in ways that contribute to the regulation of gene expression.

IMPORTANCE The genome biology underlying H. somni virulence, pathogenicity, environmental adaptability, and broad tissue tropism is understood poorly. We identified a novel H. somni 109-nt IVS stem-loop structure, of which the central portion is excised from the 23S rRNA transcript, resulting in the fragmentation of this rRNA in the H. somni isolate USDA-ARS-USMARC-63250 and the release of a 94-nt structured RNA of unknown function. We determined that this peculiar rRNA biology is widespread among sequenced H. somni isolates, suggesting it has importance to organism biology. The fragmented 23S rRNA molecules remain functional in the ribosome, given that the isolate grows in culture. The structured excised portion of the IVS, presumably due to the action of the endoribonuclease III, has an unusual 1-nt 3′ end overhang. This newly discovered H. somni 23S rRNA fragmentation may enhance rRNA degradation providing a previously unrecognized avenue for regulating H. somni biological processes.

Comparative Genomics Analyses Support the Reclassification of Bisgaard Taxon 40 as Mergibacter gen. nov., With Mergibacter septicus sp. nov. as Type Species: Novel Insights Into the Phylogeny and Virulence Factors of a Pasteurellaceae Family Member Associated With Mortality Events in Seabirds

The Pasteurellaceae family has been associated with fatal diseases in numerous avian species. Several new taxa within this family, including Bisgaard taxon 40, have been recently described in wild birds, but their genomic characteristics and pathogenicity are not well understood. We isolated Bisgaard taxon 40 from four species of seabirds, including one sampled during a mass, multi-species mortality event in Florida, United States. Here, we present a comprehensive phenotypic and genetic characterization of Bisgaard taxon 40 and comparative genomic analysis with reference strains from the Pasteurellaceae family, aiming at determining its phylogenetic position, antimicrobial susceptibility profile, and identifying putative virulence factors. In silico multilocus sequence-based and whole-genome-based phylogenetic analysis clustered all Bisgaard taxon 40 strains together on a distinct branch separated from the other members of the Pasteurellaceae family, indicating that Bisgaard taxon 40 could represent a new genus. These findings were further supported by protein similarity analyses using the concatenation of 31 conserved proteins and other taxonomic approaches such as the percentage of conserved protein test. Additionally, several putative virulence factors were identified, including those associated with adhesion (capsule, ompA, ompH) and colonization (exbD, fur, galU, galE, lpxA, lpxC, and kdsA) of the host and a cytolethal distending toxin (cdt), which may have played a role in disease development leading to the mortality event. Considerably low minimum inhibitory concentrations (MICs) were found for all the drugs tested, in concordance with the absence of antimicrobial resistance genes in these genomes. The novel findings of this study highlight genomic and phenotypic characteristics of this bacterium, providing insights into genome evolution and pathogenicity. We propose a reclassification of these organisms within the Pasteurellaceae family, designated as Mergibacter gen. nov., with Mergibacter septicus sp. nov. as the type species. The type strain is Mergibacter septicus A25201^T (=DSM 112696).

Rationally designed mariner vectors for functional genomic analysis of Actinobacillus pleuropneumoniae and other Pasteurellaceae species by transposon-directed insertion-site sequencing (TraDIS)

Comprehensive identification of conditionally essential genes requires efficient tools for generating high-density transposon libraries that, ideally, can be analysed using next-generation sequencing methods such as Transposon Directed Insertion-site Sequencing (TraDIS). The Himar1 (mariner) transposon is ideal for generating near-saturating mutant libraries, especially in AT-rich chromosomes, as the requirement for integration is a TA dinucleotide, and this transposon has been used for mutagenesis of a wide variety of bacteria. However, plasmids for mariner delivery do not necessarily work well in all bacteria. In particular, there are limited tools for functional genomic analysis of Pasteurellaceae species of major veterinary importance, such as swine and cattle pathogens, Actinobacillus pleuropneumoniae and Pasteurella multocida, respectively. Here, we developed plasmids, pTsodCPC9 and pTlacPC9 (differing only in the promoter driving expression of the transposase gene), that allow delivery of mariner into both these pathogens, but which should also be applicable to a wider range of bacteria. Using the pTlacPC9 vector, we have generated, for the first time, saturating mariner mutant libraries in both A. pleuropneumoniae and P. multocida that showed a near random distribution of insertions around the respective chromosomes as detected by TraDIS. A preliminary screen of 5000 mutants each identified 8 and 14 genes, respectively, that are required for growth under anaerobic conditions. Future high-throughput screening of the generated libraries will facilitate identification of mutants required for growth under different conditions, including in vivo, highlighting key virulence factors and pathways that can be exploited for development of novel therapeutics and vaccines.

Polar bear-adapted Ursidibacter maritimus are remarkably conserved after generations in captivity

Most species in the bacterial family of Pasteurellaceae colonize one specific host species. Vertebrates of very different evolutionary descent including fish, turtles, marsupials, eutherians and birds are colonized by different members of Pasteurellaceae. This one-to-one microbial-host species partnership makes Pasteurellaceae species valuable candidates to study biodiversity, bacterial-host co-evolution and host adaptation, and their widespread distribution across vertebrates provide the possibility to collect a wide array of data, where wildlife species are essential. However, obtaining samples from wild animals comes with logistic, technical and ethical challenges, and previous microbiota studies have led to the presumption that captive animals are poor models for microbial studies in wildlife. Here, we show that colonization of polar bears by Ursidibacter maritimus is unaffected by factors related to captivity, reflecting a deep symbiotic bond to the host. We argue that the study of ecological and evolutionary principles in captive wildlife is possible for host-adapted taxa such as those in the Pasteurellaceae family. Moreover, studying captive, often trained animals protects wild populations from the stress associated with obtaining samples.

Antimicrobial Resistance in Pasteurellaceae Isolates from Pyrenean Chamois (Rupicapra pyrenaica) and Domestic Sheep in an Alpine Ecosystem

Antimicrobial resistance (AMR) has spread worldwide due to the inappropriate use of antimicrobial drugs in human and veterinary medicine, becoming a public health problem. However, little is known about its occurrence and maintenance in wild animals, and very few studies have been carried out in ecosystems subjected to low human pressure. In our study, nasal and lung swabs were collected from hunted Pyrenean chamois (Rupicapra pyrenaica), and nasal swabs from sympatric domestic sheep were also collected. The swabs were cultured in agar plates to obtain bacterial isolates from the Pasteurellaceae family. The presence of AMR was assessed in a total of 28 Pasteurellaceae isolates from 45 Pyrenean chamois, and 9 isolates from sympatric domestic sheep found in the National Hunting Reserve of Freser-Setcases (Northeastern Pyrenees, Spain). The isolates belonged to one of the following three species: Pasteurella multocida, Mannheimia haemolytica and Bibersteinia trehalosi. Some P. multocida and M. haemolytica isolates tested positive for AMR. The statistical analysis revealed no differences between the AMR levels from chamois and domestic sheep isolates. However, one P. multocida of chamois origin presented resistance to cephalosporins and fluoroquinolones, which are antibiotics of critical importance for human health. Further studies are required to elucidate potential routes of dissemination of AMR genes in natural environments and assess any significant persistence in wildlife to design risk mitigation actions.

Occurrence of major and minor pathogens in calves diagnosed with bovine respiratory disease

Bovine respiratory disease (BRD) is caused by a mixture of viruses and opportunistic bacteria belonging to Pasteurellaceae and Mycoplasma bovis. However, these organisms are also commonly isolated from healthy calves. This study aimed to determine whether the organisms are present in higher numbers in calves sick with acute BRD than in clinically healthy calves, and further to genetically characterize bacteria of the family Pasteurellaceae to understand whether particular types are associated with disease. Forty-six clinically healthy and 46 calves with BRD were sampled by broncheoalveolar lavage (BAL) method in 11 herds geographically spread over Denmark to determine presence and quantity of microorganisms by culture and quantitative real time qPCR. Isolates of Pasteurellaceae were tested for antibiotic resistance and were whole genome sequenced to determine genotypes. Histophilus somni was in particular positively associated with BRD, suggesting particular importance of this organism as likely aetiology of BRD. In addition, quantification of bacteria revealed that higher counts of H. somni as well as of M. haemolytica was also a good indicator of the disease. Pasteurellaceae isolates were susceptible to the commonly used antibiotics in treatment of BRD, and genotypes were shared between isolates from clinically healthy and sick calves.

Nicoletella semolina in the airways of healthy horses and horses with severe asthma

Background

Nicoletella semolina was identified in the airways of horses and its low prevalence could be because of its difficult differentiation from other Pasteurellaceae.

Objectives

To develop a molecular method for the identification of N. semolina and to evaluate its prevalence in the mouth and the airways of healthy and severe asthmatic horses.

Animals

Six healthy and 6 severely asthmatic horses in phase I, 10 severely asthmatic horses in phase II, and 10 healthy horses in phase III.

Methods

Cohort (phases I and II) and cross‐sectional (phase III) studies. Quantitative polymerase chain reaction primers targeting the sodA gene were optimized. N. semolina was quantified in oral and nasal washes and in bronchoalveolar lavage fluid (BALF; phase I, sampled twice), in nasal washes and BALF (phase II, sampled twice), and in nasal washes (phase III).

Results

N. semolina was found in the nose of 5, 10, and 9 horses in phases I, II, and III, respectively (first sampling for phases I and II). Six BALF from 5 different horses were positive for N. semolina in phase II. In phase I, there was no significant difference in the nasal loads of healthy horses (median (range): 2.04 × 10⁴ copies/mL (0‐2.44 × 10⁵)) and asthmatic horses in exacerbation (3.75 × 10² (0‐4.84 × 10⁶); Wilcoxon's rank sum test, P = .57).

Conclusions and Clinical Importance

N. semolina is commonly found in the airways of horses. The potential pathogenicity of N. semolina remains to be elucidated, but the molecular technique we developed will facilitate future studies.

Classification of Bisgaard's taxa 14 and 32 and a taxon from kestrels demonstrating satellitic growth and proposal of Spirabiliibacterium gen. nov., including the description of three species: Spirabiliibacterium mucosae sp. nov., Spirabiliibacterium pneumoniae sp. nov. and Spirabiliibacterium falconis sp. nov

Avian Pasteurella-like organisms tentatively named taxon 14 of Bisgaard have been obtained from different lesions in birds including ducks, turkeys, pigeons, geese and peafowl. Taxon 32 of Bisgaard was first reported from lesions in pigeon hawks (Accipiter gentiles). The taxon isolated from kestrels (Falco tinnunculus) was V-factor dependent and originally reported as Haemophilus-like. The results of 16S rRNA gene sequence based phylogenetic analysis recently indicated that the taxa 14 and 32 and the kestrel taxon were located in a monophyletic group distantly related to [Pasteurella] testudinis with 92-93 % 16S rRNA gene sequence similarity. Comparison of 41 conserved protein sequences confirmed the monophyletic nature of the three taxa. Partial rpoB gene sequencing of 43 strains of taxon 14, taxon 32 and the kestrel taxon showed a relationship between taxon 14 and 32 of 88.2-90.0 % similarity. Within taxon 14, 93.3-100 % similarity was found, whereas the two strains of taxon 32 showed 99.8 % rpoB similarity. Sequencing of 16S rRNA genes of strains representing the rpoB diversity outlined showed more than 98 % similarity within taxon 14 and 99.4 % within taxon 32, while the kestrel strains showed 100 % 16S rRNA gene sequence similarity. A new genus, Spirabiliibacterium gen. nov., is proposed to include taxon 14, taxon 32 and the kestrel taxon. Phenotypically, members of the genus Spirabiliibacterium can be separated from members of the genera Aggregatibacter, Avibacterium and Volucribacter by maltose, oxidase and methyl red, respectively. Two or more phenotypic characters separate members of the genus Spirabiliibacterium from members of the remaining 27 genera of the family Pasteurellaceae.The G+C content of DNA ranged from 42.9 to 51.2 % (genome sequence) for members of the genus Spirabiliibacterium. The type strain of Spirabiliibacterium mucosae (taxon 14 of Bisgaard) is 20609/3^T (=CCUG 16499^T=DSM 111429^T=HIM 913-3^T). The type strain of Spirabiliibacterium pneumoniae is HPA106^T (=CCUG 74731^T=DSM 111430^T). The type strain of Spirabiliibacterium falconis (kestrel taxon) is IPDH 2176^T (=NCTC 11878^T=CCUG 28587^T).

Mannheimia pernigra sp. nov., isolated from bovine respiratory tract

Over a period of 1 year, 270 isolates identified as Taxon 39 of Bisgaard were obtained from the nasopharynx of veal calves at 11 epidemiologically independent Swiss fattening farms. Two isolates from each farm and the Australian Taxon 39 reference strain BNO311 were further characterized by genetic and phenotypic methods. Phylogenetic analysis of 16S rRNA and recN gene sequences placed the isolates in a single, distinct cluster within the genus Mannheimia. As to the rpoB gene, most isolates clustered together, but four strains formed a separate cluster close to Mannheimia varigena. Genome sequence analysis of isolates from both rpoB clusters confirmed their species status, with an average nucleotide identity (ANI) >98.9 % between isolates and <84 % to the closest species, M. varigena. Based upon whole genome sequences, the G+C content was determined as 39.1 mol%. Similarly, analysis of MALDI-TOF MS reference spectra clustered the isolates clearly separated from the other Mannheimia species, making this the method of choice for identification. In addition, numerous biochemical markers based on classical as well as commercial identification schemes were determined, allowing separation from other Mannheimia species and identification of the new taxon. Major fatty acids for strain 17CN0883^T are C_14 : 0, C_16 : 0, C_16 : 1ω7c and C_18 : 1ω7c. Major respiratory quinones are ubiquinone-7 and ubiquinone-8. We propose the name Mannheimia pernigra sp. nov. for former Taxon 39 of Bisgaard. The type strain is 17CN0883^T (=CCUG 74657^T=DSM 111153^T) isolated from a veal calf in Switzerland.

Mortality in Common (Sterna hirundo) and Sandwich (Thalasseus sandvicensis) Terns Associated with Bisgaard Taxon 40 Infection on Marco Island, Florida, USA

Widely distributed aquatic species such as terns are highly dependent on, and can serve as indicators of, the global health of marine and other aquatic environments. Documented mass mortality events in terns have been associated with anthropogenic, weather-related and, less commonly, infectious causes. This study describes a multispecies mortality event associated with brevetoxicosis and Bisgaard taxon 40-induced sepsis involving common (Sterna hirundo) and sandwich (Thalasseus sandvicensis) terns off the southwest coast of Florida, USA, in November and December 2018. During an approximately 6-8-week period, a large number of birds were found dead or displayed weakness, ataxia or other neurological signs. Many were admitted to a wildlife hospital for evaluation, but most died or were euthanized due to poor prognosis. Necropsy of 12 birds revealed minimal or non-specific gross lesions. Initial toxicology screening of tissues for brevetoxins revealed levels that could be consistent with brevetoxicosis. However, histology revealed multiorgan inflammation and necrosis associated with a gram-negative bacillus. A bacterium isolated on aerobic culture of liver and heart tissues was unidentifiable in the MALDI-TOF database. Subsequently, 16 S rRNA gene sequencing revealed that the isolate shared 99.33% homology with Bisgaard taxon 40 from the Pasteurellaceae family. While the source of the bacterium and potential association with brevetoxin exposure are unclear, histopathology suggests that the bacterium was the proximate cause of clinical signs and mortality in all birds examined as well as the scale of the mortality event. This report highlights the need to conduct detailed investigations into wildlife mortality events and expands on the current, limited knowledge of the effects of novel Pasteurellaceae bacteria on avian health.

Identification of mcr-1 and a novel chloramphenicol resistance gene catT on an integrative and conjugative element in an Actinobacillus strain of swine origin

The aim of this study was to characterize a mcr-1-carrying integrative and conjugative element (ICE) in a novel Pasteurellaceae-like bacteria of swine origin. The mcr-1-positive GY-402 strain, recovered from a pig fecal sample, was subjected to whole genome sequencing with the combination of Illumina Hiseq and MinION platforms. Genome-based taxonomy revealed that strain GY-402 exhibited highest ANI value (84.89 %) to Actinobacillus succinogenes, which suggested that it represented a novel Actinobacillus species. Sequence analysis revealed that mcr-1 was clustered with eight other resistance genes in the MDR region of a novel ICE element, named ICEAsp1. Inverse PCR and mating assays showed that ICEAsp1 is active and transferrable. In addition, six circular forms mediated by four ISApl1 elements were detected with different inverse PCR sets, indicating that flexible composite transposons could be formed by pairwise combinations of multiple IS copies. Cloning experiment and phylogenetic analysis revealed that the novel Cat protein, designated CatT, belongs to type-A family and confers resistance to chloramphenicol. In conclusion, this is, to the best of our knowledge, the first report of mcr-1 gene on ICE structure and also in Pasteurellaceae bacteria. The diverse composite transposons mediated by multicopy IS elements may facilitate the dissemination of different resistance genes.

Multidrug Resistance in Pasteurellaceae Associated With Bovine Respiratory Disease Mortalities in North America From 2011 to 2016

Multidrug-resistant (MDR; resistance to ≥3 antimicrobial classes) members of the Pasteurellaceae family may compromise the efficacy of therapies used to prevent and treat bovine respiratory disease (BRD) in feedlot cattle. This study examined the prevalence of multidrug resistance in strains of Mannheimia haemolytica and Pasteurella multocida collected from BRD cattle mortalities in North America. Isolates of M. haemolytica (n = 147) and P. multocida (n = 70) spanning 69 Alberta feedlots from 2011 to 2016 and two United States feedlots from 2011 to 2012 were examined for antimicrobial resistance (AMR) in association with integrative and conjugative elements (ICEs). Overall, resistance was high in both bacterial species with an increase in the prevalence of MDR isolates between 2011 and 2016. Resistance to >7 antimicrobial drugs occurred in 31% of M. haemolytica and 83% of P. multocida isolates. Resistance to sulfadimethoxine, trimethoprim/sulfamethoxazole, neomycin, clindamycin oxytetracycline, spectinomycin, tylosin, tilmicosin, and tulathromycin was most common. Although >80% of strains harbored three or more ICE-associated genes, only 12% of M. haemolytica and 77% of P. multocida contained all six, reflecting the diversity of ICEs. There was evidence of clonal spread as P. multocida and M. haemolytica isolates with the same pulsed-field gel electrophoresis profile from the United States in 2011 were isolated in Alberta in 2015–2016. This work highlights that MDR strains of Pasteurellaceae containing ICEs are widespread and may be contributing to BRD therapy failure in feedlot cattle. Given the antimicrobial resistance gene profiles identified, these MDR isolates may be selected for by the use of macrolides, tetracyclines, and/or in-feed supplements containing heavy metals.

Occurrence of Pasteurellaceae and Neisseriaceae bacteria in the pharyngeal and respiratory tract of dogs and cats - Short communication

The occurrence of members of the Pasteurellaceae and Neisseriaceae families was studied in dogs and cats. A total of 110 nasal and pharyngeal swab samples from 47 dogs and 8 cats were collected. Most of the strains were identified by 16S rDNA sequencing, except Frederiksenia canicola and Pasteurella multocida where species-specific polymerase chain reactions were applied. The most frequently isolated species was F. canicola, which occurred only in dogs, mainly in the pharyngeal cavity. The second commonest bacterium, P. multocida was found in both types of samples and in both hosts. Other species from the family Pasteurellaceae, such as Haemophilus haemoglobinophilus, Pasteurella canis and P. dagmatis, were detected only in dogs. All isolated species belonging to the family Neisseriaceae, mainly representing Neisseria weaveri, were found only in the pharyngeal cavity. Neisseria weaveri and N. zoodegmatis could be detected in both hosts. Neisseria dumasiana and N. canis were isolated from dogs, while N. shayeganii only from a cat. For phylogenetic analysis, rpoB gene sequencing was performed, where the strains were on monophyletic branches and clearly separated from each other. In this study, recently described species such as F. canicola, N. shayeganii and N. dumasiana were detected that had never been isolated in Hungary before.

Detection of Frederiksenia sp. isolated from a cat with nephritis - Short communication

In this paper we report the phenotypic and partial genetic characterisation of a novel bacterium strain isolated from a cat with severe nephritis. Multilocus sequence analysis was performed on the 16S rRNA and three housekeeping (recN, rpoB, infB) gene sequences obtained by PCR. In accordance with the results of phenotypic tests, the phylogenetic analyses confirmed the relatedness of the new strain (6036) to the family Pasteurellaceae. On the phylogenetic trees, strain 6036 appeared in a separate branch, closest to that of the type species (Frederiksenia canicola) of the genus Frederiksenia. These two bacteria shared 95.14 and 76.88% identity in their partial 16S rRNA and recN gene sequences, respectively. The rpoB- and infB-based phylogenetic analyses indicated that strain 6036 is most closely related to Bibersteinia trehalosi (with 90.58% identity) and [Haemophilus] felis ATCC 49733 (89.50% identity), respectively. The predicted genome identity values, based on the recN gene sequences, suggested that strain 6036 can be classified into the genus Frederiksenia as a novel species. A PCR method, specific to strain 6036, was developed to allow its rapid and accurate identification and differentiation from F. canicola and other species of Pasteurellaceae. The minimal inhibitory concentrations of 18 antimicrobial agents for strain 6036 were also determined.

Storage time and temperature affect the isolation rate of Mannheimia haemolytica and Pasteurella multocida from bovine bronchoalveolar lavage samples

Background

A microbiological diagnosis is essential to better target antimicrobial treatment, control and prevention of respiratory tract infections in cattle. Under field conditions, non-endoscopic broncho-alveolar lavage (nBAL) samples are increasingly collected. To what extent the highly variable turnaround time and storage temperatures between sampling and cultivation affect the isolation rate of bacterial pathogens is unknown. Therefore, the objective of this experimental study was to determine the effect of different storage temperatures (0 °C, 8 °C, 23 °C and 36 °C) and times (0,2,4,6,8,24,48 h) on the isolation rate and concentration of Pasteurellaceae in nBAL samples from clinically affected animals.

Results

At a storage temperature temperature of 36 °C isolation rates of Mannheimia haemolytica and Pasteurella multocida were significantly reduced 6 h and 48 h after sampling, respectively. At room temperature (23 °C), a decrease in M. haemolytica and P. multocida isolation rate was noticed, starting at 24 and 48 h after sampling, respectively, but only significant for P. multocida at 48 h. The presence of microbial contamination negatively affected the isolation of P. multocida in clinical nBAL samples, but not of M. haemolytica.

Conclusion

Optimal M. haemolytica and P. multocida isolation rates from clinical nBAL samples are obtained after storage at 0 °C or 8 °C, provided that the sample is cultivated within 24 h after sampling. The maximum period a sample can be stored without an effect on the M. haemolytica and P. multocida isolation success varies and is dependent on the storage temperature and the degree of microbial contamination.

Glaesserella australis sp. nov., isolated from the lungs of pigs

Twenty-nine isolates of an unknown haemophilic organism were isolated from the lungs of pigs from 14 farms in Australia. Phylogenetic analyses based on the 16S rRNA gene, recN and rpoA showed a monophyletic group that was most closely related to Glaesserella parasuis and [Actinobacillus] indolicus. Whole genome sequence analysis indicated that the Glaesserella parasuis and this group, using the type strain HS4635^T for comparison, showed a similarity of 30.9 % DNA-DNA renaturation. The isolates were Gram-stain-negative, NAD-dependent, CAMP-negative and were oxidase-positive, catalase-negative and produced indole but not urease. The isolates could be separated from all currently recognized haemophilic and non-haemophilic members of the family Pastuerellaceae. Key phenotypic properties were the production of indole, the lack of urease activity, production of β-galactosidase but not α-fucosidase, acid formation from (-)-d-arabinose, (+)-d-galactose, maltose and trehalose and a failure to produce acid from (-)-d-mannitol. Taken together, these data indicate that the isolates belong to a novel species for which the name Glaesserella australis sp. nov. is proposed. The type strain is HS4635^T (=CCUG 71931^T and LMG 30645^T).

Ocular findings and selected ophthalmic diagnostic tests in a group of young commercially available Guinea and Skinny pigs (Cavia porcellus)

OBJECTIVE

The purpose of this study is to evaluate a group of young commercially available Skinny pigs, to gain information regarding ocular findings in this breed of guinea pig. Comparisons of ocular findings are to be made between Skinny pigs and haired guinea pigs.

ANIMAL STUDIED

Ten haired guinea pigs and ten Skinny pigs were examined.

PROCEDURE

A complete ophthalmic examination including Schirmer tear test-II (STT-II), phenol red thread test (PRTT), rebound tonometry with TonoVet PLUS, Fluorescein and Rose Bengal stain was performed. Microbiology swabs for aerobic bacterial growth were collected from conjunctiva of both eyes prior to the ophthalmic examination.

RESULTS

The ophthalmic examination revealed seven abnormal ocular findings: trichiasis, mucopurulent discharge, hyperemia/chemosis of the conjunctiva, corneal fibrosis, corneal vascularization, and foreign body on the cornea or conjunctiva. Skinny pigs had a significantly higher amount of mucopurulent discharge (P = .0133) and a significantly higher STT-II (P < .001) than haired guinea pigs. Although not significant, trichiasis, keratitis with corneal vascularization, and foreign body presence were more common in Skinny pigs. Significantly more Skinny pigs had Pasteurellaceae isolated from their conjunctiva than haired guinea pigs (P = .0112). Antimicrobial susceptibility for the five Pasteurellaceae organisms isolated revealed susceptibility toward oxytetracycline, tobramycin, ciprofloxacin, and ofloxacin, whereas resistance was found toward erythromycin, trimethoprim-sulfamethoxazole, and moxifloxacin.

CONCLUSION

Young Skinny pigs have a higher risk of Pasteurellaceae-associated conjunctivitis. Oxytetracycline, tobramycin, ciprofloxacin, and ofloxacin were identified as topical antibiotics that may be useful for Pasteurellaceae-associated conjunctivitis in Skinny pigs.

Identification of Lonepinella sp. in Koala Bite Wound Infections, Queensland, Australia

We report 3 cases of koala bite wound infection with Lonepinella koalarum–like bacteria requiring antimicrobial and surgical management. The pathogens could not be identified by standard tests. Phylogenetic analysis of 16S rRNA and housekeeping genes identified the genus. Clinicians should isolate bacteria and determine antimicrobial susceptibilities when managing these infections.

Evidence of Illegitimate Recombination Between Two Pasteurellaceae Plasmids Resulting in a Novel Multi-Resistance Replicon, pM3362MDR, in Actinobacillus pleuropneumoniae

Evidence of plasmids carrying the tetracycline resistance gene, tet(B), was found in the previously reported whole genome sequences of 14 United Kingdom, and 4 Brazilian, isolates of Actinobacillus pleuropneumoniae. Isolation and sequencing of selected plasmids, combined with comparative sequence analysis, indicated that the four Brazilian isolates all harbor plasmids that are nearly identical to pB1001, a plasmid previously found in Pasteurella multocida isolates from Spain. Of the United Kingdom isolates, 13/14 harbor plasmids that are (almost) identical to pTetHS016 from Haemophilus parasuis. The remaining United Kingdom isolate, MIDG3362, harbors a 12666 bp plasmid that shares extensive regions of similarity with pOV from P. multocida (which carries bla_ROB-1 , sul2, and strAB genes), as well as with pTetHS016. The newly identified multi-resistance plasmid, pM3362MDR, appears to have arisen through illegitimate recombination of pTetHS016 into the stop codon of the truncated strB gene in a pOV-like plasmid. All of the tet(B)-carrying plasmids studied were capable of replicating in Escherichia coli, and predicted origins of replication were identified. A putative origin of transfer (oriT) sequence with similar secondary structure and a nic-site almost identical to that of RP4 was also identified in these plasmids, however, attempts to mobilize them from an RP4-encoding E. coli donor strain were not successful, indicating that specific conjugation machinery may be required.

A Survey of Bacterial Respiratory Pathogens in Native and Introduced Mountain Goats ( Oreamnos americanus)

In contrast to broad range expansion through translocations, many mountain goat ( Oreamnos americanus) populations have shown signs of decline. Recent documentation of pneumonia in mountain goats highlights their susceptibility to bacterial pathogens typically associated with bighorn sheep ( Ovis canadensis) epizootics. Respiratory pathogen communities of mountain goats are poorly characterized yet have important implications for management and conservation of both species. We characterized resident pathogen communities across a range of mountain goat populations as an initial step to inform management efforts. Between 2010 and 2017, we sampled 98 individuals within three regions of the Greater Yellowstone Area (GYA), with a smaller sampling effort in southeast Alaska, US. Within the GYA, we detected Mycoplasma ovipneumoniae in two regions and we found at least two Pasteurellaceae species in animals from all regions. Mannheimia haemolytica was the only pathogen that we detected in southeast Alaska. Given the difficult sampling conditions, limited sample size, and imperfect detection, our failure to detect specific pathogens should be interpreted with caution. Nonetheless, respiratory pathogens within the GYA may be an important, yet underappreciated, cause of mountain goat mortality. Moreover, because of the strong niche overlap of bighorn sheep and mountain goats, interspecific transmission is an important concern for managers restoring or introducing mountain ungulates within sympatric ranges.

A Novel Glaesserella sp. Isolated from Pigs with Severe Respiratory Infections Has a Mosaic Genome with Virulence Factors Putatively Acquired by Horizontal Transfer

An unknown member of the family Pasteurellaceae was repeatedly isolated from 20- to 24-week-old pigs with severe pulmonary lesions reared on the same farm in Victoria, Australia. The etiological diagnosis of the disease was inconclusive. The complete genome sequence analysis of one strain, 15-184, revealed some phylogenic proximity to Glaesserella (Haemophilus) parasuis, the cause of Glasser's disease. However, the sequences of the 16S rRNA and housekeeping genes, as well as the average nucleotide identity scores, differed from those of all other known species in the family Pasteurellaceae The protein content of 15-184 was composite, with 60% of coding sequences matching known G. parasuis products, while more than 20% had a closer relative in the genera Actinobacillus, Mannheimia, Pasteurella, and Bibersteinia Several putative virulence genes absent from G. parasuis but present in other Pasteurellaceae were also found, including the apxIII RTX toxin gene from Actinobacillus pleuropneumoniae, ABC transporters from Actinobacillus minor, and iron transporters from various species. Three prophages and one integrative conjugative element were present in the isolate. Horizontal gene transfers might explain the mosaic genomic structure and atypical metabolic and virulence characteristics of 15-184. This organism has not been assigned a taxonomic position in the family, but this study underlines the need for a large-scale epidemiological and clinical characterization of this novel pathogen in swine populations, as a genomic analysis suggests it could have a severe impact on pig health.IMPORTANCE Several species of Pasteurellaceae cause a range of significant diseases in pigs. A novel member of this family was recently isolated from Australian pigs suffering from severe respiratory infections. Comparative whole-genome analyses suggest that this bacterium represents a new species, which possesses a number of virulence genes horizontally acquired from a diverse range of other Pasteurellaceae While the possible contribution of other coinfecting noncultivable agents to the disease has not been ruled out in this study, the repertoire of virulence genes found in this organism may nevertheless explain some aspects of the associated pathology observed on the farm. The prevalence of this novel pathogen within pig populations is currently unknown. This finding is of particular importance for the pig industry, as this organism can have a serious impact on the health of these animals.

Revised taxonomy and nomenclature of rodent Pasteurellaceae: Implications for monitoring

Pasteurellosis is a well-recognized disease with similar pathology in all laboratory rodent species. Pasteurella pneumotropica is the most frequently mentioned member of the Pasteurellaceae isolated from mice and rats. Numerous other Pasteurellaceae taxa have been obtained from mice, rats, and other rodent species. Recently, rodent Pasteurellaceae have been submitted to comprehensive genetic and phenotypic (polyphasic) taxonomic studies. As a result they are now classed within six validly published new genera, namely Cricetibacter, Mesocricetibacter, Mannheimia, Muribacter, Necropsobacter, and Rodentibacter. All previously used names such as P. pneumotropica have become obsolete. The new classification forms a firm basis for the correct phenotypic identification of Pasteurellaceae from laboratory animals and for the selection of strains for pathogenicity studies. Consequences of taxonomic changes notably involve molecular methods used for the detection of Pasteurellaceae infection in laboratory animal colonies. Testing may be done using primer sets that detect all Pasteurellaceae taxa or sets developed to detect host-specific members of the family.

Reclassification of Bisgaard taxon 5 as Caviibacterium pharyngocola gen. nov., sp. nov. and Bisgaard taxon 7 as Conservatibacter flavescens gen. nov., sp. nov

A total of 29 strains mainly from guinea pigs were investigated by a polyphasic approach that included previously published data. The strains were classified as Bisgaard taxa 5 and 7 by comparison of phenotypic characteristics and the strains showed typical cultural characteristics for members of family Pasteurellaceae and the strains formed two monophyletic groups based on 16S rRNA gene sequence comparison. Partial rpoB sequence analysis as well as published data on DNA-DNA hybridization showed high genotypic relationships within both groups. A new genus with one species, Caviibacterium pharyngocola gen. nov., sp. nov., is proposed to accommodate members of taxon 5 of Bisgaard, whereas members of taxon 7 are proposed as Conservatibacter flavescens gen. nov., sp. nov. The two genera are clearly separated by phenotype from each other and from existing genera of the family Pasteurellaceae. The type strain of Caviibacterium pharyngocola is 7.3^T (=CCUG 16493^T=DSM 105478^T) and the type strain of Conservatibacter flavescens is 7.4^T (=CCUG 24852^T=DSM 105479^T=HIM 794-7^T), both were isolated from the pharynx of guinea pigs.

Molecular study on Pasteurella multocida and Mannheimia granulomatis from Kenyan Camels (Camelus dromedarius)

BACKGROUND

Outbreaks of a Haemorrhagic Septicaemia (HS) like disease causing large mortalities in camels (Camelus dromedarius) in Asia and in Africa have been reported since 1890. Yet the aetiology of this condition remains elusive. This study is the first to apply state of the art molecular methods to shed light on the nasopharyngeal carrier state of Pasteurellaceae in camels. The study focused on HS causing Pasteurella multocida capsular types B and E. Other Pasteurellaceae, implicated in common respiratory infections of animals, were also investigated.

METHODS

In 2007 and 2008, 388 nasopharyngeal swabs were collected at 12 locations in North Kenya from 246 clinically healthy camels in 81 herds that had been affected by HS-like disease. Swabs were used to cultivate bacteria on blood agar and to extract DNA for subsequent PCR analysis targeting P. multocida and Mannheimia-specific gene sequences.

RESULTS

Forty-five samples were positive for P. multocida genes kmt and psl and for the P. multocida Haemorrhagic Septicaemia (HS) specific sequences KTSP61/KTT72 but lacked HS-associated capsular type B and E genes capB and capE. This indicates circulation of HS strains in camels that lack established capsular types. Sequence analysis of the partial 16S rRNA gene identified 17 nasal swab isolates as 99% identical with Mannheimia granulomatis, demonstrating a hitherto unrecognised active carrier state for M. granulomatis or a closely related Mannheimia sp. in camels.

CONCLUSIONS

The findings of this study provide evidence for the presence of acapsular P. multocida or of hitherto unknown capsular types of P. multocida in camels, closely related to P. multocida strains causing HS in bovines. Further isolations and molecular studies of camelid P. multocida from healthy carriers and from HS-like disease in camels are necessary to provide conclusive answers. This paper is the first report on the isolation of M. granulomatis or a closely related new Mannheimia species from camelids.

Prevalence and antimicrobial susceptibility of Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni isolated from the lower respiratory tract of healthy feedlot cattle and those diagnosed with bovine respiratory disease

Current information on prevalence and antimicrobial resistance (AMR) of bacterial respiratory pathogens is crucial to guide antimicrobial choice for control and treatment of bovine respiratory disease (BRD). The objectives were to describe the prevalence of three BRD-associated bacteria (Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni) in the lower airways of feedlot cattle, and to analyze AMR in these bacteria. Cattle with (n=210) and without (n=107) BRD were sampled by trans-tracheal aspiration at four feedlots (Nov. 15-Jan. 16). These cattle had received 2.5mg/kg of tulathromycin on arrival at the feedlot for BRD control and two in-feed pulses of chlortetracycline (5g/animal/day for 5days) within the first 21days on feed to prevent histophilosis. Bacteria were detected by culture and AMR was tested by microdilution. Pasteurella multocida was the most frequent bacterium isolated in cattle with BRD (54.8%), followed by M. haemolytica (30.5%) and H. somni (22.9%). Compared to those with BRD, healthy cattle were less likely to be positive for P. multocida (OR=0.27), M. haemolytica (OR=0.32), or H. somni (OR=0.25). There were high levels of resistance (>70%) against tulathromycin and oxytetracycline in M. haemolytica and P. multocida isolates and high levels of resistance against oxytetracycline (67%) and penicillin (52%) in H. somni isolates. None or few isolates were resistant to florfenicol, enrofloxacin and ceftiofur. The high prevalence of resistance against tulathromycin and oxytetracycline suggests that these antimicrobials should not be repeatedly used for both control and treatment of BRD and/or histophilosis.

p518, a small floR plasmid from a South American isolate of Actinobacillus pleuropneumoniae

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Smallest floR plasmid in the Pasteurellaceae.

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Unique arrangement with complete strA, but partial strB and sul2 sequences.

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Loss of mobilisation genes indicated by partial mobC; no other mob genes.

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Not transferrable by conjugation or natural transformation.

A small (3.9 kb) plasmid (p518), conferring resistance to florfenicol (MIC >8 μg/mL) and chloramphenicol (MIC >8 μg/mL) was isolated from an Actinobacillus pleuropneumoniae clinical isolate from Southeastern Brazil. To date, this is the smallest florfenicol resistance plasmid isolated from a member of the Pasteurellaceae. The complete nucleotide of this plasmid revealed a unique gene arrangement compared to previously reported florfenicol resistance plasmids found in other members of the Pasteurellaceae. In addition to the floR gene and a lysR gene, common to various florfenicol resistance plasmids, p518 also encodes strA and a partial strB sequence. An origin of replication (oriV) similar to that in the broad host range plasmid, pLS88, was identified in p518, and transformation into Escherichia coli MFDpir confirmed the ability to replicate in other species. Mobilisation genes appear to have been lost, with only a partial mobC sequence remaining, and attempts to transfer p518 from a conjugal donor strain (E. coli MFDpir) were not successful, suggesting this plasmid is not mobilisable. Similarly, attempts to transfer p518 into a competent A. pleuropneumoniae strain, MIDG2331, by natural transformation were also not successful. These results suggest that p518 may be only transferred by vertical descent.

Whole Genome Sequencing for Surveillance of Antimicrobial Resistance in Actinobacillus pleuropneumoniae

The aim of this study was to evaluate the correlation between antimicrobial resistance (AMR) profiles of 96 clinical isolates of Actinobacillus pleuropneumoniae, an important porcine respiratory pathogen, and the identification of AMR genes in whole genome sequence (wgs) data. Susceptibility of the isolates to nine antimicrobial agents (ampicillin, enrofloxacin, erythromycin, florfenicol, sulfisoxazole, tetracycline, tilmicosin, trimethoprim, and tylosin) was determined by agar dilution susceptibility test. Except for the macrolides tested, elevated MICs were highly correlated to the presence of AMR genes identified in wgs data using ResFinder or BLASTn. Of the isolates tested, 57% were resistant to tetracycline [MIC ≥ 4 mg/L; 94.8% with either tet(B) or tet(H)]; 48% to sulfisoxazole (MIC ≥ 256 mg/L or DD = 6; 100% with sul2), 20% to ampicillin (MIC ≥ 4 mg/L; 100% with bla_ROB-1), 17% to trimethoprim (MIC ≥ 32 mg/L; 100% with dfrA14), and 6% to enrofloxacin (MIC ≥ 0.25 mg/L; 100% with GyrAS83F). Only 33% of the isolates did not have detectable AMR genes, and were sensitive by MICs for the antimicrobial agents tested. Although 23 isolates had MIC ≥ 32 mg/L for tylosin, all isolates had MIC ≤ 16 mg/L for both erythromycin and tilmicosin, and no macrolide resistance genes or known point mutations were detected. Other than the GyrAS83F mutation, the AMR genes detected were mapped to potential plasmids. In addition to presence on plasmid(s), the tet(B) gene was also found chromosomally either as part of a 56 kb integrative conjugative element (ICEApl1) in 21, or as part of a Tn7 insertion in 15 isolates. Our results indicate that, with the exception of macrolides, wgs data can be used to accurately predict resistance of A. pleuropneumoniae to the tested antimicrobial agents and provides added value for routine surveillance.

Assessing Timing and Causes of Neonatal Lamb Losses in a Bighorn Sheep ( Ovis canadensis canadensis ) Herd via Use of Vaginal Implant Transmitters

We evaluated the use of vaginal implant transmitters (VITs) as a means of detecting, capturing, and radio collaring Rocky Mountain bighorn sheep ( Ovis canadensis canadensis) lambs to estimate survival and to facilitate carcass recovery to assess causes of mortality. We focused on one of several bighorn herds in Colorado, US, suffering from depressed recruitment that was not preceded by a classic all-age die-off. We captured, radio-collared, diagnosed pregnancy by ultrasound examination, and inserted VITs into 15 pregnant ewes from a herd residing near Granite, Colorado. We were subsequently able to collar a lamb from each of 13 VITs, and two additional lambs opportunistically from ewes without transmitters. As lambs died, we recovered and submitted carcasses for necropsy and laboratory assessment. All lambs captured and one additional lamb (carcass found opportunistically) were dead by about 130 d of age: 11 died of apparent pneumonia (all within 8-10 wk of age), one died from trauma after being kicked or trampled, one was killed by a mountain lion ( Puma concolor ), and three died of starvation likely caused by abandonment after capture. Pneumonic lambs had involvement of Mycoplasma ovipneumoniae and leukotoxigenic Bibersteinia trehalosi . The use of VITs and lamb collars enabled us to efficiently identify pneumonia as the predominant cause of depressed lamb recruitment in this herd; however, we urge care in neonatal lamb handling to minimize abandonment.

[Bacterial resistance in bacteria isolated from the nasal cavity of Swiss dairy calves]

INTRODUCTION

Fifty-six E. coli, 37 P. multocida und 8 M. haemolytica were isolated from 157 nasal swabs taken from calves in 52 dairy herds. The antibiotic susceptibility of the organisms was determined by measurement of the minimal inhibitory concentrations. Of the 56 E. coli isolates, 55.3% exhibited resistance to tetracyclines, 55.3% to sulfonamides, 39.3% to beta-lactams, 30.3% to aminoglycosides, 8.9% to fluorochinolones and 3.5% to 3rd generation cephalosporins. The 3rd generation cephalosporin- resistant isolates contained the extended spectrum-beta-lactamase gene blaCTX-M-14 and came from 2 farms where the milk of cows under antimicrobial treatment was fed to the calves and mastitis was treated with cefquinome as first line therapy. Of the 37 P. multocida isolates, 48.6% exhibited resistance to tetracyclines, 16.2% to beta-lactams, and 5.4% each to macrolides, aminoglycosides and sulfonamides. The 8 M. haemolytica isolates showed no resistances against the tested antibiotics.

Pasteurellaceae bacteria from the oral cavity of Tasmanian devils (Sarcophilus Harrisii) show high minimum inhibitory concentration values towards aminoglycosides and clindamycin

Threatened by Devil Facial Tumor Disease, the Tasmanian devil populations are vulnerable and decreasing. Additionally, the devils' biting behaviour elevates their risk of acquiring bite wound infections caused by members of the bacterial Pasteurellaceae family that are natural inhabitants of the oral microbiota. In medical management of such bite wounds, antimicrobial susceptibility profiles are crucial. Prior to this investigation, no available data on minimal inhibitory concentration (MIC) values existed. A total of 26 isolates obtained from the oral cavity of 26 healthy Tasmanian devils were tested for their antimicrobial susceptibility by broth micro dilution. Most prominently, high MIC values for clindamycin (≥4 μg ml(-1) ), gentamicin (≥8 μg ml(-1) ) and amikacin (≥32 μg ml(-1) ), were observed for 92, 77 and 73% of the strains tested respectively. This study may be used as a guideline for antimicrobial therapy against bite wound infections caused by Pasteurellaceae originating from the oral cavity of Tasmanian devils.

SIGNIFICANCE AND IMPACT OF THE STUDY

Tasmanian devils' aggressive behaviour makes bite wounds in fellow devils and human caretakers a common entity. Pasteurellaceae bacteria are common inhabitants of the oral microbiota of Tasmanian devils and a likely cause of bite wound infections. Here, for the first time, we report antimicrobial sensitivity profiles from a broad collection of Pasteurellaceae isolates obtained from the oral cavity of Tasmanian devils. Low MIC values were observed for the majority of the 22 antimicrobial agents included, yet nearly all strains were tolerant to clindamycin and the aminoglycosides. The work can serve as a guide for clinicians involved in treatment of bite wounds inflicted by devils in animals and humans.

Differential expression of putative adhesin genes of Actinobacillus suis grown in in vivo-like conditions

Actinobacillus suis is an opportunistic pathogen that resides in the tonsils of the soft palate of swine. Unknown stimuli can cause this organism to invade the host, resulting in septicaemia and sequelae including death. To better understand its pathogenesis, the expression of several adhesin genes was evaluated by semi-quantitative real-time PCR in A. suis grown in conditions that mimic the host environment, including different nutrient and oxygen levels, exponential and stationary phases of growth, and in the presence of the stress hormone epinephrine. Fifty micromolar epinephrine did not affect the growth rate or expression of A. suis adhesin genes, but there was a significant growth phase effect for many genes. Most adhesin genes were also differentially expressed during anoxic static growth or aerobic growth, and in this study, all genes were differentially expressed in either exponential or stationary phase. Based on the time*treatment interactions observed in the anoxic study, a model of persistence of A. suis in the host environment in biofilm and planktonic states is proposed. Biofilm dynamics were further studied using wild type and isogenic mutants of the type IVb pilin (Δ flp1), the OmpA outer membrane protein (ΔompA), and the fibronectin-binding (ΔcomE1) genes. Disruption of these adhesin genes affected the early stages of biofilm formation, but in most cases, biofilm formation of the mutant strains was similar to that of the wild type by 24h of incubation. We postulate that other adhesins may have overlapping functions that can compensate for those of the missing adhesins.

A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies.

Role of carriers in the transmission of pneumonia in bighorn sheep (Ovis canadensis)

In the absence of livestock contact, recurring lamb mortality in bighorn sheep (Ovis canadensis) populations previously exposed to pneumonia indicates the likely presence of carriers of pneumonia-causing pathogens, and possibly inadequate maternally derived immunity. To investigate this problem we commingled naïve, pregnant ewes (n=3) with previously exposed rams (n=2). Post-commingling, all ewes and lambs born to them acquired pneumonia-causing pathogens (leukotoxin-producing Pasteurellaceae and Mycoplasma ovipneumoniae), with subsequent lamb mortality between 4-9 weeks of age. Infected ewes became carriers for two subsequent years and lambs born to them succumbed to pneumonia. In another experiment, we attempted to suppress the carriage of leukotoxin-producing Pasteurellaceae by administering an antibiotic to carrier ewes, and evaluated lamb survival. Lambs born to both treatment and control ewes (n=4 each) acquired pneumonia and died. Antibody titers against leukotoxin-producing Pasteurellaceae in all eight ewes were ‘protective’ (>1:800 and no apparent respiratory disease); however their lambs were either born with comparatively low titers, or with high (but non-protective) titers that declined rapidly within 2-8 weeks of age, rendering them susceptible to fatal disease. Thus, exposure to pneumonia-causing pathogens from carrier ewes, and inadequate titers of maternally derived protective antibodies, are likely to render bighorn lambs susceptible to fatal pneumonia.

Summary: Previously exposed bighorn sheep can become carriers and transmit respiratory pathogens to naïve animals. Successive crops of lambs acquire pathogens and inadequate passive immunity and subsequently succumb to pneumonia.

ICEApl1, an Integrative Conjugative Element Related to ICEHin1056, Identified in the Pig Pathogen Actinobacillus pleuropneumoniae

ICEApl1 was identified in the whole genome sequence of MIDG2331, a tetracycline-resistant (MIC = 8 mg/L) serovar 8 clinical isolate of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia. PCR amplification of virB4, one of the core genes involved in conjugation, was used to identify other A. pleuropneumoniae isolates potentially carrying ICEApl1. MICs for tetracycline were determined for virB4 positive isolates, and shotgun whole genome sequence analysis was used to confirm presence of the complete ICEApl1. The sequence of ICEApl1 is 56083 bp long and contains 67 genes including a Tn10 element encoding tetracycline resistance. Comparative sequence analysis was performed with similar integrative conjugative elements (ICEs) found in other members of the Pasteurellaceae. ICEApl1 is most similar to the 59393 bp ICEHin1056, from Haemophilus influenzae strain 1056. Although initially identified only in serovar 8 isolates of A. pleuropneumoniae (31 from the UK and 1 from Cyprus), conjugal transfer of ICEApl1 to representative isolates of other serovars was confirmed. All isolates carrying ICEApl1 had a MIC for tetracycline of 8 mg/L. This is, to our knowledge, the first description of an ICE in A. pleuropneumoniae, and the first report of a member of the ICEHin1056 subfamily in a non-human pathogen. ICEApl1 confers resistance to tetracycline, currently one of the more commonly used antibiotics for treatment and control of porcine pleuropneumonia.

Impact of Timing and Dosage of a Fluoroquinolone Treatment on the Microbiological, Pathological, and Clinical Outcomes of Calves Challenged with Mannheimia haemolytica

The efficacy of an early and low inoculum-adjusted marbofloxacin treatment was evaluated on microbiological and clinical outcomes in calves infected with 4.10⁷ CFU of Mannheimia haemolytica A1. Twenty-two calves were included based on their rectal temperature rise in the 10 h after challenge and allocated in four groups, receiving a single intramuscular injection of saline (CON), 2 mg/kg marbofloxacin 2–4 h after inclusion (early treatment, E2), 2 or 10 mg/kg marbofloxacin 35–39 h after inclusion (late treatments, L2, L10). In CON calves, M. haemolytica DNA loads in bronchoalveolar lavages continuously increased from inclusion to day 4, and were associated with persistent respiratory clinical signs and lung lesions. At times of early and late treatments, M. haemolytica loads ranged within 3.5–4 and 5.5–6 log₁₀ DNA copies/mL, respectively. Early 2 mg/kg marbofloxacin treatment led to rapid and total elimination of bacteria in all calves. The late treatments induced a reduction of bacterial loads, but 3 of 6 L2 and 1 of 6 L10 calves were still positive for M. haemolytica at day 4. Except for CON calves, all animals exhibited clinical improvement within 24 h after treatment. However, early 2 mg/kg treatment was more efficacious to prevent pulmonary lesions, as indicated by the reduction of the extension and severity of gross lesions and by the histopathological scores. These results demonstrated for the first time that a reduced antibiotic regimen given at an early stage of the disease and targeting a low bacterial load could be efficacious in a natural bovine model of pneumonia.

Bighorn sheep (Ovis canadensis) sinus tumors are associated with coinfections by potentially pathogenic bacteria in the upper respiratory tract

Bighorn sheep (Ovis canadensis) sinus tumors are hyperplastic to neoplastic, predominantly stromal masses of the paranasal sinuses that expand the sinus lining and obstruct the sinus cavities. Obstruction of the sinus cavities and disruption of normal sinus lining anatomy may interfere with clearance of bacterial pathogens from the upper respiratory tract. To examine this possibility, we explored whether the presence of sinus tumor features (tumor score) affected the likelihood of detecting potentially pathogenic bacteria from upper respiratory sinus lining tissues in bighorn sheep. We developed or used existing PCR assays for the detection of leukotoxigenic Pasteurellaceae and Mycoplasma ovipneumoniae in sinus lining tissues collected from 97 bighorn sheep in Colorado, US from 2009 to 2012. With the use of logistic regression analyses we found that tumor score was a good predictor of the probability of detecting potentially pathogenic bacteria in sinus lining tissues; we were more likely to detect potentially pathogenic bacteria from samples with high tumor scores. These findings add to our understanding of possible mechanisms for the maintenance and shedding of bacterial agents from the upper respiratory tracts of bighorn sheep.

Macrolide resistance conferred by rRNA mutations in field isolates of Mannheimia haemolytica and Pasteurella multocida

OBJECTIVES

To determine how resistance to macrolides is conferred in field isolates of Pasteurella multocida and Mannheimia haemolytica that lack previously identified resistance determinants for rRNA methylation, efflux and macrolide-modifying enzymes.

METHODS

Isolates of P. multocida and M. haemolytica identified as being highly resistant (MICs >64 mg/L) to the macrolides erythromycin, gamithromycin, tilmicosin, tildipirosin and tulathromycin were screened by multiplex PCR for the previously identified resistance genes erm(42), msr(E) and mph(E). Strains lacking these determinants were analysed by genome sequencing and primer extension on the rRNAs.

RESULTS

Macrolide resistance in one M. haemolytica isolate was conferred by the 23S rRNA mutation A2058G; resistance in three P. multocida isolates were caused by mutations at the neighbouring nucleotide A2059G. In each strain, all six copies of the rrn operons encoded the respective mutations. There were no mutations in the ribosomal protein genes rplD or rplV, and no other macrolide resistance mechanism was evident.

CONCLUSIONS

High-level macrolide resistance can arise from 23S rRNA mutations in P. multocida and M. haemolytica despite their multiple copies of rrn. Selective pressures from exposure to different macrolide or lincosamide drugs presumably resulted in consolidation of either the A2058G or the A2059G mutation.

Integration host factor is required for replication of pYGK-derived plasmids in Aggregatibacter actinomycetemcomitans

In this study, we show that integration host factor protein (IHF) is required for replication of pYGK plasmids in Aggregatibacter actinomycetemcomitans. YGK plasmids were not replicated in A. actinomycetemcomitans strains lacking either the α- or β- subunit of IHF. However, the deletion mutants were complemented, and plasmid replication was restored when the promoter region and gene for either ihfA or ihfB was cloned into pYGK. We also identified two motifs that resemble the consensus IHF-binding site in a 813-bp fragment containing the pYGK origin of replication. Using electrophoretic mobility shift assays, purified IHFα-IHFβ protein complex was shown to bind to probes containing either of these motifs. To our knowledge, this is the first report showing that plasmid replication is IHF-dependent in the family Pasteurellaceae. In addition, using site-direct mutagenesis, the XbaI and KpnI restriction sites in the suicide vector pJT1 were modified to generate plasmid pJT10. The introduction of these new unique sites in pJT10 facilitates the transfer of transcriptional or translational lacZ fusion constructs for the generation of single-copy chromosomal insertion of the reporter construct. Plasmid pJT10 and its derivatives will be useful for genetic studies in Aggregatibacter (Actinobacillus) and probably other genera of Pasteurellaceae, including Haemophilus, Pasteurella, and Mannheimia.

Acute die-off of chamois (Rupicapra rupicapra) in the Eastern Austrian Alps due to bacterial bronchopneumonia with Pasteurellaceae

Monitoring circulating pathogens in wildlife populations is important in evaluating causes and sources of disease as well as understanding transmission between wild and domestic animals. In spring 2010, a sudden die-off in a chamois (Rupicapra rupicapra) population sharing habitat with livestock occurred in northeastern Austria. Nineteen animals were submitted for examination. Necropsy and pathohistologic and bacteriologic results yielded lesions associated with Pasteurellaceae species. Additional testing included enterobacterial repetitive intergenic consensus and random amplification of polymorphic DNA PCR analysis to evaluate the circulating strains. The isolated strains were most closely related to Mannheimia glucosida and Bibersteinia trehalosi. Reports of mass mortalities in chamois due to pneumonia have been reported previously in the northern Alpine area of Italy. To the authors' knowledge, this is the first report of acute mortality due to strains of Mannheimia and Bibersteinia in Austrian chamois.