Open Access

Complete genome sequence of Actinobacillus equuli subspecies equuli ATCC 19392T

  • Barbara F Huang1,
  • Andrew M Kropinski1,
  • Adina R Bujold1 and
  • Janet I MacInnes1Email author
Standards in Genomic Sciences201510:32

DOI: 10.1186/s40793-015-0009-x

Received: 7 October 2014

Accepted: 16 April 2015

Published: 7 June 2015

Abstract

Actinobacillus equuli subsp. equuli is a member of the family Pasteurellaceae that is a common resident of the oral cavity and alimentary tract of healthy horses. At the same time, it can also cause a fatal septicemia in foals, commonly known as sleepy foal disease or joint ill disease. In addition, A. equuli subsp. equuli has recently been reported to act as a primary pathogen in breeding sows and piglets. To better understand how A. equuli subsp. equuli can cause disease, the genome of the type strain of A. equuli subsp. equuli, ATCC 19392T, was sequenced using the PacBio RSII sequencing system. Its genome is comprised of 2,431,533 bp and is predicted to encode 2,264 proteins and 82 RNAs.

Keywords

Actinobacillus equuli subsp. equuli Sleepy foal disease Joint ill disease Commensal Equine

Introduction

Actinobacillus equuli subsp. equuli, previously known as ‘Bacillus viscosum-equi’, or ‘Shigella equirulis’, is a common resident of the oral flora of healthy horses, as well as that of the alimentary and genital tracts [1,2]. It has also been reported to be present in other host species such as mice, seemingly without ill effect [3] and on rare occasions, has been transmitted through bite wounds to humans [4]. A. equuli subsp. equuli is the etiological agent of sleepy foal disease, an acute form of fatal septicemia in neonatal foals that may progress to a chronic form, joint ill disease, producing lesions in the kidneys, joints, and lungs [5-8]. Horses with A. equuli infection can present with arthritis, bronchitis, pneumonia, pleuritis, peritonitis, sepsis, endocarditis, pericarditis, nephritis, meningitis, metritis, and abortion [7,9-12]. A. equuli subsp. equuli was previously proposed to act as a secondary pathogen in foals; however, a recent study by Layman and colleagues [13] has revealed that A. equuli subsp. equuli has the potential to act as a primary pathogen given favourable conditions. Recently, it has been reported to also be a primary pathogen in sows and piglets [14,15].

The hemolytic counterpart of this bacterium, A. equuli subsp. haemolyticus , is isolated more frequently from the respiratory tract rather than the oral cavity. It can also cause septicemia and sequelae such as arthritis and meningitis, respiratory tract infections, and mare reproductive loss syndrome [8,10,16].

The similar colonial morphology and biochemical markers and shared 16S rRNA sequences make differentiation of A. equuli from Actinobacillus suis difficult [8]. In addition, little is known about the virulence factors of A. equuli subsp. equuli . To be better able to identify and to improve our understanding of the mechanism of pathogen-host interactions [7], the genome of the type strain A. equuli subsp. equuli strain ATCC 19392 T was sequenced. This strain was isolated from foal blood and deposited in the American Type Culture Collection by the Equine Research Station (New Market, UK) in 1953 [17].

Organism information

Classification and features

As a member of the genus Actinobacillus , A. equuli subsp . equuli belongs to the family Pasteurellaceae, class Gammaproteobacteria [18] (Table 1). Phylogenetic analysis using 16S rRNA sequences suggests that A. equuli subsp . equuli is most closely related to A. suis and A. hominis (Figure 1).
Table 1

Classification and features of A. equuli subsp. equuli ATCC 19392 T

MIGS ID

Property

Term

Evidence code a

 

Classification

Domain Bacteria

TAS [21]

Phylum Proteobacteria

TAS [22]

Class Gammaproteobacteria

TAS [23,24]

Order Pasteurellales

TAS [25]

Family Pasteurellaceae

TAS [26,27]

Genus Actinobacillus

TAS [28,29]

Species Actinobacillus equuli

TAS [28,30,31]

Subspecies Actinobacillus equuli subsp. equuli

TAS [20]

Type strain ATCC 19392T

 
 

Gram stain

Negative

TAS [32]

 

Cell shape

Rods (pleomorphic)

TAS [33]

 

Motility

Non-motile

TAS [33]

 

Sporulation

Non-sporulating

TAS [33]

 

Temperature range

Mesophile (20 - 44°C)

TAS [33]

 

Optimum temperature

37°C

TAS [20]

 

pH range

6.0 – 8.4

TAS [1]

 

Carbon source

Saccharolytic

TAS [19]

MIGS-6

Habitat

Host, equine or swine upper respiratory tract, alimentary tract, and genital tract

TAS [4,5,19]

MIGS-6.3

Salinity

0.5% NaCl

NAS

MIGS-22

Oxygen requirement

Facultative anaerobe

TAS [19,33]

MIGS-15

Biotic relationship

Commensal or opportunistic

TAS [14,15]

MIGS-14

Pathogenicity

Variable

TAS [13]

MIGS-4

Geographic location

New Market, UK

TAS [17]

MIGS-5

Sample collection

1953

TAS [17]

MIGS-4.1 MIGS-4.2

Latitude

Not reported

 

Longitude

Not reported

MIGS-4.4

Altitude

Not reported

 

aEvidence codes - TAS: Traceable Author Statement; NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [34].

Figure 1

Phylogenetic tree based on 16S rRNA sequences of Actinobacillus sensu stricto species plus A. capsulatus and H. parasuis as outgroups. A. equuli subsp. equuli is indicated in bold. The RDP aligner, which applies the Jukes-Cantor corrected distance model to align sequences, and the RDP Tree Builder, which implements the Weighbor algorithm [36] for tree construction were used. Tree building also involved a bootstrapping process in which the values to the left of the branches illustrate the frequency of occurrence of a branch in 100 replicates [37].

A. equuli subsp. equuli is a small, Gram-negative, nonmotile, pleomorphic bacterium [15,16,19] (Figure 2). It is NAD-independent, nonhemolytic, and CAMP negative [15,20]. A. equuli subsp. equuli produces large amounts of extracellular slime that imparts sticky properties in solid and liquid media cultures [19,31]. On nutrient or blood agar, smooth, grayish-white, circular colonies are produced with an average diameter of 1-2 mm after growth for 24 h [35] (Figure 3). On initial culture from clinical material, colonies are viscous and usually rough but become smooth in successive subcultures [1,19]. Growth using liquid culturing methods has been reported to increase viability in comparison to solid media cultures, and viscosity is retained upon repeated subculturing [1,19]. The usual temperature range for growth of this bacterium is 20-39°C, with an optimum at 37°C, though some A. equuli subsp. equuli strains have been shown to grow at temperatures as high as 44°C [33]. Acid but not gas is produced from sucrose, mannitol, galactose, lactose, maltose, mannose, melibiose, trehalose, raffinose, and glycerol fermentation [19,20,33]. A. equuli subsp. equuli is capable of reducing nitrate and produces α-galactosidase, α-glucosidase, β-xylosidase, urease, and oxidase [19,20,33].
Figure 2

Gram stain of A. equuli subsp. equuli ATCC 19392T at 1000 X magnification.

Figure 3

A. equuli subsp. equuli ATCC 19392T colonies on sheep blood agar.

Genome sequencing information

Genome project history

A. equuli subsp. equuli was selected for sequencing because of its importance to the horse industry as the etiologic agent of sleepy foal disease and joint ill disease [7]. Sequencing was done at the McGill University and Génome Québec Innovation Centre (Montréal, QC, Canada) using the PacBio RS II DNA Sequencing System, and assembled using PacBio RS II software and Celera Assembler. A. equuli subsp. equuli was annotated using the NCBI Prokaryotic Genome Annotation Pipeline. A summary of the project information and the Minimum Information about a Genomic Sequence is shown in Table 2 [38].
Table 2

Project information and its association with MIGS version 2.0 compliance [38]

MIGS ID

Property

Term

MIGS-31

Finishing quality

Complete

MIGS-28

Libraries used

SMRTbell library

MIGS-29

Sequencing platforms

PacBio RS II

MIGS-31.2

Fold coverage

196x

MIGS-30

Assemblers

PacBio RS II, Celera

MIGS-32

Gene calling method

GeneMarkS+

 

Locus Tag

ACEE

 

Genbank ID

CP007715

 

GenBank Date of Release

December 15, 2014

 

GOLD ID

Gp0095186

 

BIOPROJECT

PRJNA247050

MIGS-13

Source Material Identifier

ATCC 19392T

 

Project relevance

Equine and swine pathogenesis

Growth conditions and genomic DNA preparation

A. equuli subsp. equuli was grown from a frozen (-70°C) seed stock on sheep blood agar plates overnight in an atmosphere of 5% CO2 at 37°C. After subculture, well-isolated colonies were used for genomic DNA isolation. Cells were lysed using modified B1 (150 mM Tris · Cl, 50 mM EDTA, 0.5% Tween®-20, 0.5% Triton X-100, pH 8.0) and B2 (750 mM NaCl, 50 mM MOPS, 15% isopropanol, 0.15% Triton X-100, pH 7.0) buffers. DNA was then column purified using a QIAGEN Plasmid Midi Kit (Qiagen, Germany) following manufacturer's protocol for binding and elution. The resultant DNA preparation was characterized using a NanoDrop model ND1000 Spectrophotometer and was diluted to a concentration of ~0.47 mg/μl.

Genome sequencing and assembly

Single Molecule, Real-Time DNA sequencing (Pacific Biosciences) [39] was done to obtain the genome sequence of the A. equuli subsp. equuli ATCC 19392 T. A total of 133,616 raw subreads were generated with an average length of 4,348 bp using two SMRT Cells in a PacBio RSII sequencer. The resultant subread length cutoff value, 29.42, was used in the Basic Local Alignment with Successive Refinement step [40] where short reads were used to correct for errors on long reads [39]. The corrected reads were assembled into contigs according to the Hierarchical Genome Assembly Process (HGAP) workflow using the Celera Assembler and refined using BLASR to align raw reads on contigs [39]. Final processing was conducted using Quiver, a variant calling algorithm, to generate high quality consensus sequences [39]. There were a total of 4,777 corrected reads with an average length of 7,804 bp and a final product of one contig.

Genome annotation

Genes were identified using the NCBI Prokaryotic Genome Annotation Pipeline. The prediction software, GeneMark, is integrated into the pipeline and performs unsupervised gene finding using heuristic Markov Models [41]. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes (IMG) platform [42] developed by the Joint Genome Institute [43] (Table 3).
Table 3

Genome statistics

Attribute

Value

% of total a

Genome size (bp)

2,431,533

100.00

DNA coding (bp)

2,169,474

89.22

DNA G + C (bp)

979,048

40.26

DNA scaffolds

1

100.00

Total genesb

2,264

100.00

Protein coding genes

2,182

96.38

RNA genes

82

3.62

Pseudo genesc

11

0.49

Genes in internal clusters

1,466

64.75

Genes with function prediction

1,993

88.03

Genes assigned to COGs

1,752

77.39

Genes with Pfam domains

1,964

86.75

Genes with signal peptides

235

10.38

Genes with transmembrane helices

508

22.44

CRISPR repeats

2

0.08

aThe total is based on either the size of the genome in base pairs or the total number of protein coding genes in the annotated genome.

bAlso includes 11 pseudogenes and one other RNA gene that does not belong to rRNA or tRNA categories.

cPseudogenes are not additive under total genes and may be counted as either protein coding or RNA genes.

Genome properties

The genome of A. equuli subsp. equuli is a single circular chromosome that is 2,431,533 bp in length with a G + C content of approximately 40.3%. It is predicted to contain 2,264 genes, of which 2,182 code for proteins and 82 for RNA; 11 pseudogenes are also present (Table 3 and Figure 3). Approximately 3/4 of the predicted genes can be assigned to one of 25 functional COG categories (Table 4). Of particular note with regard to virulence are several lipopolysaccharide genes predicted to encode biosynthetic enzymes for the O-antigen and lipid A components. Adhesins of different types were observed including several autotransporters; a tight adherence locus; prepilins, and fimbriae; a filamentous hemagglutinin homolog was also detected. In addition, several putative iron acquisition systems are present including those for siderophores, hemoglobin and transferrin. A number of toxin and hemolysin genes were also identified including an aqxCABD operon, although compared to the aqxCABD of A. equuli subsp. haemolyticus there are many point mutations and sizable deletions at both ends of the aqxA gene. Other regions of particular interest include an integron and Mu-like phage, identified using PHAST [44].
Table 4

Number of genes associated with general COG functional categories

Code

Value

% age

Description

J

159

8.49

Translation

A

1

0.05

RNA processing and modification

K

94

5.02

Transcription

L

105

5.61

Replication, recombination and repair

B

-

-

Chromatin structure and dynamics

D

24

1.28

Cell cycle control, mitosis and meiosis

Y

-

-

Nuclear structure

V

18

0.96

Defense mechanisms

T

35

1.87

Signal transduction mechanisms

M

136

7.26

Cell wall/membrane biogenesis

N

4

0.21

Cell motility

Z

-

-

Cytoskeleton

W

2

0.11

Extracellular structures

U

44

2.35

Intracellular trafficking and secretion

O

92

4.91

Posttranslational modification, protein turnover, chaperones

C

117

6.25

Energy production and conversion

G

126

6.73

Carbohydrate transport and metabolism

E

176

9.40

Amino acid transport and metabolism

F

63

3.36

Nucleotide transport and metabolism

H

108

5.77

Coenzyme transport and metabolism

I

45

2.40

Lipid transport and metabolism

P

133

7.10

Inorganic ion transport and metabolism

Q

14

0.75

Secondary metabolites biosynthesis, transport and catabolism

R

194

10.36

General function prediction only

S

183

9.77

Function unknown

-

512

22.61

Not in COGs

Insights from the genome sequence

Given the marked similarities of A. equuli and A. suis there has been some debate as to whether these organisms should be a single species. In the current study we determined that the A. equuli subsp. equuli 16S genes are 99% identical to those of both A. suis H91-0380 and the A. suis type strain, ATCC 33415, consistent with membership in the same species. Further, as can be seen in the circular maps below, the genome of A. equuli subsp. equuli is very similar to that of A. suis again suggesting that A. equuli subsp . equuli and A. suis might be the same species (Figure 4). On the other hand, when genomes of A. suis H91-0380 and A. suis ATCC 33415 were compared with that of A. equuli subsp. equuli using the ANI calculator [45], the ANI value of both comparisons was 93.82%, which is lower than 95%, the recommended cutoff value for delineating species [46].
Figure 4

Circular map of the A. equuli subsp. equuli ATCC 19392T genome generated using the CGView Server [49]. From the outside to the center: coding sequences (CDSs) in positive strand, reverse strand CDSs, BLASTN versus A. suis strain H91-0380 (CP003875), BLASTN versus A. suis ATCC 33415 (CP009159), GC content, and GC skew.

In-silico DNA-DNA hybridization, done using a Genome Blast Distance Phylogeny approach to generate genome based distance measures for phylogenetic inferences, also demonstrated differences between A. equuli and A. suis. The Genome-to-Genome Distance Calculator [47] revealed a distance of 0.0685 between A. suis H91-0380 and A. equuli subsp. equuli , with a DDH estimate of 51.40% +/- 2.66. A DDH similarity below 70% is interpreted as two species being distinct; 79% is used to discriminate between subspecies [48]. The DDH estimate exceeding the 70% species threshold was determined from logistic regression to be 23.14%. In terms of subspecies relatedness, the probability of exceeding the 79% threshold was 4.82% between A. equuli subsp. equuli and A. suis H91-0380. The distance calculated between A. suis ATCC 33415 and A. equuli subsp. equuli and their DDH estimate was 0.0681 and 51.60% +/- 2.66, respectively. The probability that DDH exceeded 70% and 79% for A. suis ATCC 33415 and A. equuli subsp. equuli were 23.66% and 4.94%, respectively.

Taken together, these analyses are consistent with the notion that A. suis and A. equuli subsp. equuli are related but distinct species, and care is needed to correctly identify them.

Conclusions

A. equuli subsp. equuli can induce fatal septicemia in foals resulting in significant economic losses in the equine industry; as well, A. equuli subsp. equuli has recently been reported to cause septicemia in swine of all ages. Our analysis of the A. equuli subsp. equuli genome indicates that A. suis and A. equuli subsp. equuli are closely related yet distinct species. At the present time little is known about how A. equuli subsp. equuli causes disease or the factors that control species and tissue tropism. More research including biological experiments is required to better understand the pathogenesis of A. equuli and it is hoped this reported genome sequence of A. equuli subsp. equuli ATCC 19392 T will provide vital information for such studies. In addition, pathway analysis and genome studies may help improve our understanding of host-pathogen interactions of A. equuli subsp. equuli and other Actinobacillus species and aid in the design of diagnostic tools and antimicrobial agents.

Declarations

Acknowledgements

The authors thank Glenn Soltes for expert technical support. This work was supported by a Natural Sciences and Engineering Research Council to JM; ARB was supported by the Ontario Veterinary College and the Ontario Graduate Scholarship programs.

Authors’ Affiliations

(1)
Department of Pathobiology, University of Guelph, Ontario Veterinary College

References

  1. Edwards PR. Studies on Shigella equirulis. Kentucky Agric Exp Stn Bull. 1931;320:289–330.Google Scholar
  2. Sternberg S, Brändström B. Biochemical fingerprinting and ribotyping of isolates of Actinobacillus equuli from healthy and diseased horses. Vet Microbiol. 1999;66:53–65. PubMed.PubMedView ArticleGoogle Scholar
  3. Lentsch RH, Wagner JE. Isolation of Actinobacillus lignieresii and Actinobacillus equuli from laboratory rodents. J Clin Microbiol. 1980;12:351–4. PubMed.PubMed CentralPubMedGoogle Scholar
  4. Ashhurst-Smith C, Norton R, Thoreau W, Peel MM. Actinobacillus equuli Septicemia: an Unusual Zoonotic Infection. J Clin Microbiol. 1998;36:2789–91. PubMed.PubMed CentralPubMedGoogle Scholar
  5. Blackall PJ, Christensen JP, Bisgaard M. Diversity among isolates of Actinobacillus equuli and related organisms as revealed by ribotyping. Aust Vet J. 1998;76:423–5. PubMed.PubMedView ArticleGoogle Scholar
  6. Aalbaek B, Ostergaard S, Buhl R, Jensen HE, Christensen H, Bisgaard M. Actinobacillus equuli subsp. equuli associated with equine valvular endocarditis. APMIS. 2007;115:1437–42. PubMed.PubMedView ArticleGoogle Scholar
  7. Berthoud H, Frey J, Kuhnert P. Characterization of Aqx and its operon: the hemolytic RTX determinant of Actinobacillus equuli. Vet Microbiol. 2002;87:159–74. PubMed.PubMedView ArticleGoogle Scholar
  8. Kuhnert P, Berthoud H, Straub R, Frey J. Host cell specific activity of RTX toxins from haemolytic Actinobacillus equuli and Actinobacillus suis. Vet Microbiol. 2003;92:161–7. PubMed.PubMedView ArticleGoogle Scholar
  9. Sternberg S. Isolation of Actinobacillus equuli from the oral cavity of healthy horses and comparison of isolates by restriction enzyme digestion and Pulsed-Field Gel Electrophoresis. Vet Microbiol. 1998;59:147–56. PubMed.PubMedView ArticleGoogle Scholar
  10. Pusterla N, Jones MEB, Mohr RF, Higgins JK, Mapes S, Jang S, et al. Fatal Pulmonary Hemorrhage Associated with RTX Toxin-Producing Actinobacillus equuli subspecies haemolyticus Infection in an Adult Horse. J Vet Diagnostic Investig. 2008;20:118–21. PubMed http://dx.doi.org/10.1177/104063870802000127.View ArticleGoogle Scholar
  11. Matthews S, Dart AJ, Dowling BA, Hodgson JL. Peritonitis associated with Actinobacillus equuli in horses : 51 cases. Aust Vet J. 2001;79:536–9. PubMed.PubMedView ArticleGoogle Scholar
  12. Patterson-Kane JC, Donahue JM, Harrison LR. Septicemia and Peritonitis Due to Actinobacillus equuli Infection in an Adult Horse. Vet Pathol. 2001;38:230–2. PubMed http://dx.doi.org/10.1354/vp.38-2-230.PubMedView ArticleGoogle Scholar
  13. Layman QD, Rezabek GB, Ramachandran A, Love BC, Confer AW. A retrospective study of equine actinobacillosis cases: 1999-2011. J Vet Diagn Invest. 2014;26:365–75. PubMed http://dx.doi.org/10.1177/1040638714531766.PubMedView ArticleGoogle Scholar
  14. Thompson AB, Postey RC, Snider T, Pasma T. Actinobacillus equuli as a primary pathogen in breeding sows and piglets. Can Vet J. 2010;51:1223–5. PubMed.PubMed CentralPubMedGoogle Scholar
  15. Benavente CE, Fuentealba IC. Actinobacillus suis and Actinobacillus equuli, emergent pathogens of septic embolic nephritis, a new challenge for the swine industry. Arch Med Vet. 2012;44:99–107. http://dx.doi.org/10.4067/S0301-732X2012000200002.View ArticleGoogle Scholar
  16. Castagnetti C, Rossi M, Parmeggiani F, Zanoni RG, Pirrone A, Mariella J. Facial cellulitis due to Actinobacillus equuli infection in a neonatal foal. Vet Rec. 2008;162:347–9. PubMed http://dx.doi.org/10.1136/vr.162.11.347.PubMedView ArticleGoogle Scholar
  17. Public Health England Culture Collections Database. [http://www.phe-culturecollections.org.uk/]
  18. Dewhirst FE, Paster BJ, Olsen I, Fraser GJ. Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences. J Bacteriol. 1992;174:2002–13. PubMed.PubMed CentralPubMedGoogle Scholar
  19. Olsen I, Moller K. Genus II. Actinobacillus. In: Garrity G, Brenner D, Krieg N, Staley J, editors. Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume Two, The Proteobacteria, Part B. Second. New York: Springer; 2005. p. 866–83.Google Scholar
  20. Christensen H, Bisgaard M, Olsen JE. Reclassification of equine isolates previously reported as Actinobacillus equuli, variants of A. equuli, Actinobacillus suis or Bisgaard taxon 11 and proposal of A. equuli subsp. equuli subsp. nov. and A. equuli subsp. haemolyticus subsp. nov. Int J Syst Evol Microbiol. 2002;52:1569–76. PubMed http://dx.doi.org/10.1099/ijs.0.01637-0.PubMedView ArticleGoogle Scholar
  21. Woese CR, Kandlert O, Wheelis ML. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9. PubMed.PubMed CentralPubMedView ArticleGoogle Scholar
  22. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.Google Scholar
  23. List Editor. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int. J. Syst. Evol. Microbiol. 2005;55:2235–2238. http://dx.doi.org/10.1099/ijs.0.64108-0
  24. Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.Google Scholar
  25. Garrity GM, Bell JA, Lilburn T. Pasteurellales ord. nov. In: Garrity GM, Bell JA, Lilburn T. Order XIV. Pasteurellales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 850Google Scholar
  26. List Editor. Validation List no. 7. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1981; 55:382–383. http://dx.doi.org/10.1099/00207713-31-3-382
  27. Pohl SPD. Dissertation, Phillips-Universität Marburg. 1979.Google Scholar
  28. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol. 1980;30:225–420. http://dx.doi.org/10.1099/00207713-30-1-225.View ArticleGoogle Scholar
  29. Brumpt E. Précis de Parasitologie. 1st ed. Paris: Masson et Cie; 1910.Google Scholar
  30. van Straaten H. Bacteriologische bevindingen bij eenigo gevallen van pyo-septicaemie (Lähme) der veuluens. Verslag van den Werksaamheden der Rijksseruminrichting voor 1916-1917, Rotterdam, 1918; 71-76.Google Scholar
  31. Haupt H. Archiv fur wissenschaftliche und praktische Tierheilkunde. 1934; 67:513-524.Google Scholar
  32. Ward CL, Wood JL, Houghton SB, Mumford JA, Chanter N. Actinobacillus and Pasteurella species isolated from horses with lower airway disease. Vet Rec. 1998;143:277–9. PubMed.PubMedView ArticleGoogle Scholar
  33. MacInnes JI, Lally ET. The Genus Actinobacillus. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K, Stackebrandt E, editors. The Prokaryotes, A Handbook on the Biology of Bacteria: Proteobacteria: Gamma Subclass, vol. 6. 3rd ed. New York: Springer; 2006. p. 1094–118.Google Scholar
  34. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene Ontology : tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9. PubMed http://dx.doi.org/10.1038/75556.PubMed CentralPubMedView ArticleGoogle Scholar
  35. Christensen H, Bisgaard M. Revised definition of Actinobacillus sensu stricto isolated from animals. A review with special emphasis on diagnosis. Vet Microbiol. 2004;99:13–30. PubMed http://dx.doi.org/10.1016/j.vetmic.2003.12.002.PubMedView ArticleGoogle Scholar
  36. Bruno WJ, Socci ND, Halpern AL. Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol. 2000;17:189–97. PubMed.PubMedView ArticleGoogle Scholar
  37. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, et al. The Ribosomal Database Project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 2007;35:D169–72. PubMed http://dx.doi.org/10.1093/nar/gkl889.PubMed CentralPubMedView ArticleGoogle Scholar
  38. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7. PubMed http://dx.doi.org/10.1038/nbt1360.PubMed CentralPubMedView ArticleGoogle Scholar
  39. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013;10:563–9. PubMed http://dx.doi.org/10.1038/nmeth.2474.PubMedView ArticleGoogle Scholar
  40. Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics. 2012;13:238. PubMed http://dx.doi.org/10.1186/1471-2105-13-238.PubMed CentralPubMedView ArticleGoogle Scholar
  41. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001;29:2607–8. PubMed.PubMed CentralPubMedView ArticleGoogle Scholar
  42. Integrated Microbial Genome Database. [http://img.jgi.doe.gov/]
  43. Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Pillay M, et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 2014;42:D560–7. PubMed http://dx.doi.org/10.1093/nar/gkt963.PubMed CentralPubMedView ArticleGoogle Scholar
  44. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res. 2011;39:W347–52. PubMed http://dx.doi.org/10.1093/nar/gkr485.PubMed CentralPubMedView ArticleGoogle Scholar
  45. Average Nucleotide Identity Database. [http://enve-omics.ce.gatech.edu/ani/]
  46. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007;57:81–91. PubMed http://dx.doi.org/10.1099/ijs.0.64483-0.PubMedView ArticleGoogle Scholar
  47. Genome-to-Genome Distance Calculator. [http://ggdc.dsmz.de/distcalc2.php]
  48. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics. 2013;14:1–14. PubMed http://dx.doi.org/10.1186/1471-2105-14-60.View ArticleGoogle Scholar
  49. Grant JR, Stothard P. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 2008;36:W181–4. PubMed http://dx.doi.org/10.1093/nar/gkn179.PubMed CentralPubMedView ArticleGoogle Scholar

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