Molecular characterization of Mycoplasma synoviae isolated from broiler chickens of West Azarbaijan province by PCR of vlhA gene

Document Type: Original Article

Author

Department of Poultry Diseases, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran

Abstract

Mycoplasma synoviae (MS) is a pathogen responsible for respiratory and locomotor disorders and causes major economic losses in poultry industry. Early and accurate diagnosis of MS infection plays a major role in control of the infection. This study was conducted to characterize Iranian field isolates of MS isolated from broiler chickens of West Azarbaijan province (Northwest of Iran), and differentiate them from vaccine strain MS-H. Two encoding genes, 16S rRNA and vlhA were employed. PCR results using primers related to 16s rRNA and vlhA genes were analyzed and compared. Out of 21 field samples, eight samples (38.0%) were positive using both sets of primers. Amplified products of vlhA gene were sequenced for MS strain identification. The results showed that Iranian field isolates of MS had high nucleotide and amino acid similarity. Iranian field isolates were distinct from vaccine strain MS-H. Results presented in this study showed that characterization of field isolates of MS by sequencing of vlhA gene and is beneficial for strain typing and differentiating them from vaccine strain. To our knowledge, this is the first study characterizing vlhA gene of MS isolates from broiler chickens in the West Azarbaijan province.

Keywords

Main Subjects


Introduction

 

Mycoplasma synoviae (MS) is an important poultry pathogen; causing infectious synovitis and respiratory disease. Most frequently, respiratory involvement occurs as subclinical upper respiratory disease in which many birds are infected lifelong and become carriers.1 It may be transmitted laterally via direct contact and vertically via eggs.2 Rapid and accurate identification of MS isolates are of great importance in control of the infection. In this regard, molecular assays such as polymerase chain reaction (PCR) have been applied. Earlier MS specific PCRs were based on the 16S rRNA gene.3,4 Recently, other genes such as variable lipoprotein hemagglutinin (vlhA) are used.

Genome of MS encodes many proteins,5 however, only expression of a few of them have been documented.6 Hem-agglutinins account among the most important surface proteins involved in colonization and virulence of avian mycoplasmas.7 In MS, hemagglutinins are encoded by related sequences of a multigene family referred to as vlhA genes.8 It was found that vlhA antigenic variation was achieved by the vlhA gene conversion in which a pseudo-gene sequence replaced the previously expressed sequence in the vlhA gene.9 Recently, sequence analysis of the single-copy conserved region of the MS vlhA gene has been used for investigations of MSstrains and epidemiological analyses.9-13 The PCR based mutation detection techniques provide useful and cost-effective alternatives for the direct analysis of genetic variation.14

In countries, that poultry flocks are vaccinated with the live MSstrain MS-H, such as Iran, gene sequencing and strain typing of MSisolates are of critical importance, due to differentiation between field and vaccine isolates. The main purpose of the present study was to characterize Iranian field isolates of MS and differentiate them from vaccine isolates.

 

Materials and Methods

 

Samples. A total number of 21 broiler chicken farms of older than three weeks of age in West Azarbaijan province (Northwest of Iran) were sampled from April 2014 to February 2015. All samples were obtained from un-vaccinated flocks. Four out of 21 samples were taken from  apparently healthy flocks and 17 from flocks with respiratory involvement. From each farm, five swab samples obtained from the choanal cleft and trachea and suspended in 1.5 mL of phosphate-buffered saline and considered one sample.

DNA extraction. Each sample (1 mL) was centrifuged for 30 min at 14,000 gat 4 ˚C. The supernatant was removed and the contents were dissolved in 25 µL deionized water. Samples were boiled for 10 min and then placed on ice for 10 min. Afterwards, they were centrifuged at 14,000 gfor 5 min. The supernatant containing DNA was used as template in amplification reaction.15

Polymerase chain reaction. In this study, a 530 base pair portion of avian mitochondrial DNA was amplified using 12S rRNA primers to rule out false negative results.16 For detection of MS genome in swab samples, 2 sets of primers were used. The first was 16S rRNA primers. 16S-F: 5´-GAAGCAAAATAGTGATATCA-3´ and 16S-R: 5´-GTCGTCTCCGAAGTTAACAA-3´ previously designed by Lauerman et al., 3 amplifying a 207 bp region of the 16S rRNA gene of MS. The PCR reactions were carried out in 25 µL volume of 2.5 µL of 10X PCR buffer, 0.5 µL of dNTP (10 mM), 1 µL of each primer (10 pmol µL-1), 0.5 µL of Taq DNA polymerase (5U per µL), 0.5 µL of Mgcl2 (50 mM), 17 µL of deionized water and 2 µL of extracted DNA. Thermal condition of amplification included initial denaturation of 95 ˚C for 5 min, followed by 35 cycles of 94 ˚C for 30 sec, 51 ˚C for 30 sec and 72 ˚C for 90 sec. Final extension was done in 72 ˚C for 10 min.

The second specific MS primers, for amplifying vlhA gene, were as the following: vlhA-F: 5'- ATTAGCAGCTA GTGCAGTGGCC -3', vlhA-R2: 5'- AGTAACCGATCCGCTTAA TGC -3'. The 350-400 bp fragments of MS vlhA gene were amplified.12 The vlhA-PCR mix was performed in a total volume of 25 μL per sample, containing 2.5 μL of 10X PCR buffer, 0.5 μL of 50 mM MgCl2, 0.5 μL of 10 mM dNTPs, 1 μL of each primer, 0.25 μL of Taq DNA polymerase (5U per μL). Consequently 17.25 µL of deionized distilled water and 2 μL of extracted DNA as template, were added. The vlhA-PCR reaction was conducted in Eppendorff thermal cycler (Eppendorff, Hamburg, Germany) as follows: 5 min at 94 ˚C, followed by 35 cycles of 60 sec at 94 ˚C, 60 sec at 53 ˚C and 1 min at 72 ˚C, with a final extension cycle of 10 min at 72 ˚C. Amplified products were stained using ethidium bromide (0.5 µg per mL) and subjected to agarose gel electrophoresis.

Sequencing and data analysis. Four PCR products of vlhA gene of MS isolates (MS01, MS06, MS07, and MS16) were submitted for sequencing to the Bioneer Inc. (Daejeon, South Korea) using vlhA primers as the sequencing primers. Nucleotide (nt) and predicted amino acid (aa) sequences data were aligned with clustal W alignment algorithms. The sequence alignments were checked by eye for ambiguities and errors by the examination of chromatograms. Phylogenetic analysis was conducted based on the nt sequences using a distance method and an un-weighted pair group with arithmetic mean and by calculating bootstrap values for 1000 replicates in MEGA software (Version 6.0; Biodesign Institute, Tempe, USA).17

 

Results

 

Eight swab samples out of 21 (38.1%) were positive for MS using PCR of both primers (16S rRNA and vlhA) as diagnostic method for MS. Since live MS vaccine was not used in these broiler flocks, amplified products of field strains were compared to vaccine strain (MS-H). Also, some published vlhA sequence of field strains were included in this comparison (Table 1).

 

Table 1. Published MS sequences of vlhA used for multiple alignment analysis.

Name

Gene bank accession no.

Country of origin

*MS01

KT880075

Iran

*MS06

KT880076

Iran

*MS07

KT880077

Iran

*MS16

KT880078

Iran

MSR836

JX233544.1

Iran

MSR371

JX233546.1

Iran

MSR850

JX233549.1

Iran

MSR-20 1

JX960386

Iran

MSR-25 2

JX960390

Iran

MSR-12 3

JX960384

Iran

MSR-15 4

JX960385

Iran

MSR-30 5

JX960392

Iran

MSR-11 6

JX960383

Iran

MSR-21 7

JX960387

Iran

MSR-7 8

JX960381

Iran

MS-H

AF464936.1

Australia

B1185

FM164346

UK

B9504K261

FM164372

Germany

B9196798

FM164349

UK

J1585

AJ580981

UK

WVU1853

AM998371

USA

* indicates MS field isolates of the current study; Superscript numbers indicate group number based on Bayatzadeh et al.,classification. 24

 

Alignment of four field isolates of this study and other Iranian isolates revealed high nucleotide and amino acid similarity (Fig. 1 and Table 2). Iranian isolates of current study were distinct from vaccine strain MS-H based on sequence alignment similarity and phylogenetic analysis (Fig. 2 and Table 2).

 

Fig. 1. Nucleotide sequence alignment of vlhA genes of MS field isolates (MS01, MS06, MS07, and MS16 are isolates of this study; MS371 is from a study by Pourbakhsh et al.,23; MS12, MS15, MS7, MS11, MS20, MS21, MS25, and MS30 are representatives of eight groups based on Bayatzadeh et al.,24) and vaccine strain MS-H. Note the 12 additional same nucleotides of MS isolates of the current study, MS371, and MS12, MS15 at the positions 100 to 111, which were not present in vaccine strain MS-H.

 

Table 2. Percentage of nucleotide and amino acid identities for the vlhA genes of 19 strains of Mycoplasma synoviaea. MS01, MS06, MS07, and MS16 are sequences that identified in current study; MSR371 is representative of Iranian field isolates from Pourbakhsh et al. study. 23

Strains

Similarity

 

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

MS01

1

 

98

99

100

82

86

78

91

79

99

69

69

98

89

87

66

68

72

73

MS06

2

99

 

98

98

83

87

79

92

78

98

69

69

98

88

88

66

68

72

73

MS07

3

99

99

 

100

77

86

75

87

76

98

64

64

98

86

84

61

63

67

71

MS16

4

100

99

100

 

83

81

84

82

88

100

59

59

100

100

85

63

64

100

84

B1185

5

97

97

96

88

 

82

92

88

93

83

86

85

82

91

82

79

82

74

85

B9504K261

6

92

93

91

87

94

 

88

91

88

86

75

75

85

77

95

71

73

87

79

B9196798

7

94

94

92

89

97

98

 

82

97

76

83

84

77

84

85

78

81

76

90

J1585

8

95

95

93

88

98

96

94

 

82

90

75

75

90

81

94

72

72

85

77

MS-H

9

88

88

86

90

96

98

99

95

 

76

84

83

77

86

84

81

85

75

90

MSR371

10

100

99

99

100

97

92

94

95

100

 

69

72

100

90

88

67

68

79

76

MSR20 1

11

95

96

94

87

96

97

96

96

97

95

 

99

69

77

73

90

93

67

80

MSR25 2

12

96

96

95

87

96

97

96

96

97

96

100

 

72

77

74

89

92

68

80

MSR12 3

13

100

99

99

100

97

92

93

94

87

100

95

96

 

90

88

67

68

79

75

MSR15 4

14

97

96

95

100

95

92

92

96

92

97

93

93

97

 

79

76

73

67

80

MSR30 5

15

92

92

91

89

94

97

94

97

95

92

96

95

92

93

 

73

74

90

79

MSR11 6

16

96

96

95

89

91

98

90

98

91

96

94

93

96

84

99

 

98

70

77

MSR21 7

17

96

96

94

89

90

99

91

96

92

96

95

94

96

84

98

98

 

67

80

MSR7 8

18

96

95

95

100

97

97

97

97

97

96

98

97

96

95

91

99

98

 

70

WVU1853

19

95

94

94

88

92

97

93

95

95

95

91

92

94

87

95

88

88

97

 

a Percentage of amino acid identity is in upper triangle; percentage of nucleotide identity is in lower triangle; Superscript numbers indicate group number based on Bayatzadeh et al. classification. 24

 

Fig. 2. Phylogenetic tree of MS isolates based on the nucleotide sequence of vlhA gene. Branched distances correspond to a sequence divergence.

 

Discussion

 

Most infections of MS occur as subclinical upper respiratory infection. Combination of MS infection with Newcastle disease and infectious bronchitis may lead to air sac disease.1 In this study, amplification of 16S rRNA and vlhA genes of MS attempted to demonstrate presence of MS in swab samples taken from broiler flocks with respiratory signs. Two sets of MS specific primers (16S rRNA and vlhA) were used for comparison and confirmation of the results. Results of the present study showed no difference between PCRs. Ghafouri et al. also used two PCRs (16S rRNA and vlhA) for detection of MS isolates. However, their results showed that results of two sets of primers were not the same.18 The MS primers selected from 16S rRNA gene, published by Lauerman et al.3 These primers were used by other researchers.19,20 Newer approach to differentiate between MS strains is based on vlhA gene. The vlhA gene product is an abundant immuno-dominant surface lipoprotein with a conserved and variable region.9

Recently, sequence analysis of the single-copy conserved region of the MS vlhA gene has been used for investigations of MS strains and epidemiological studies.9,12,13 In countries like Iran that poultry flocks are vaccinated with live MS-H vaccine, differentiating of field and vaccine strains has critical importance. Ghafouri et al.,18 Ansari et al.,21 Jamshidi et al.,22 and Pourbakhsh et al.,23 used vlhA based PCR for differentiation of Iranian field isolates of MS. In order to differentiate field and vaccine strains of MS, Bayatzadeh et al. analyzed and sequenced vlhA gene of 21 Iranian field isolates. They also used PCR-restriction fragment length polymorphism (RFLP) for characterization of isolates. They stated that DNA sequence analysis and PCR-RFLP were suitable tools for distinction between wild type and vaccine strains of MS.24 Amplification of haemagglutinin-encoding vlhA gene, sequencing and phylogenetic studies have been reported earlier by researchers to apperceive the relationships between the MS field and MS-H strain.2,14,23

Broiler flocks of older than 3 weeks old with respiratory involvement were investigated to elucidate role of MS in respiratory complexes. Eight samples (38.1%) out of 21 were positive using both MS specific primers. Four apparently healthy flocks were also included in this survey. Two of them were positive, that emphasize role of MS as subclinical respiratory pathogen. Bayatzadeh et al., analyzed 43 broiler flocks for MS contamination. They noted 55.9% of swab samples were positive by PCR of 16S rRNA.25 In another study, 24 (55.0%) out of 43 samples of suspected flocks of three provinces of Iran were positive by PCR of vlhA.26 Results of above mentioned studies indicated relatively high prevalence of MS in poultry flocks of Iran.

Bayatzadeh et al., classified Iranian field isolates of MS to eight groups based on sequence similarity and phylogeny.24 Three out of four Iranian strains of current study including MS01, MS06, and MS07 had high sequence similarity with strains of group 3 (MSR12 is representative of group 3). MS16 had high sequence similarity with strains of group 3 and 4 (MSR15 is representative of group 4), (Table 2). Phylogenetic analyses based on nucleotide sequences also showed that Iranian field isolates of the current study clustered together with strains of group 3 and 4 (Fig. 2). It must be noted that nucleotide and amino acid sequence alignments of MS16 and MSR7 (representative of group 8 in Bayatzadeh et al.24 scheme) were the same (Table 2). However, phylogenetic analysis showed that they were distinct from each other.

Alignment of Iranian field isolates and MS-H showed that these isolates had 12 additional nucleotides, which were absent in MS-H (Fig. 1). Bayatzadeh et al. stated that Iranian isolates in groups 3 and 4 had 12 additional identical nucleotides, which were not present in MS-H vaccine strain.24 This was consistent with our findings. Based on sequence similarity and phylogeny, isolates of this study belonged to groups 3 and 4. Ogino et al., also noted 12 additional nucleotide in Japanese field isolates, which were not present in MS-H.27 They suggested this difference as a method for rapid identification of field and vaccines strains.

Iranian field isolates in the present study had high nucleotide and amino acid similarity (>98.0%). MS01, MS06, MS07, and MS16 had 88.0%, 88.0%, 86.0%, and 90.0% nt identity with MS-H, respectively. At amino acid level, these numbers were somewhat different. Amino acid identity of MS01, MS06, MS07, and MS16 with MS-H were 79.0%, 78.0%, 76.0%, and 88.0%, respectively. Four Iranian MS isolates of this study had G at nucleotide position 106 (Fig. 1). Isolates that were representatives of groups 3 and 4 (i.e. MSR12 and MSR15) according to Bayatzadeh et al., 24 scheme, also had G at this position.

Phylogenetic analysis of the vlhA gene of MS strains revealed that Iranian field isolates of current study clustered independently from the isolates of other countries and vaccine strain MS-H. Bayatzadeh et al. also cited that MS isolates of Iran are local strains.24

This study certified the potential value of strain typing for epidemiological reasons and suggested that phylo-genetic study of vlhA genes was essential to understand the true relationships between strains. Such investigations provide researchers with a better knowledge on the distribution, variability, and phylogenetic relationships of different MS isolated in Iran and other parts of the world.

 

Acknowledgments

 

This study was fully supported by grants (No. 92-D-002) from Vice Chancellor for Research and Technology of Urmia University that is acknowledged by the author.

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