Table 1.
Variable genomic regions significantly associated with netB-positive C. perfringens poultry isolates
| Variable | Strain associationa | Predicted functionb | Size (bp) | No. of genes | No. of significant genes | Average prevalence (%) |
Predicted locationc | |
|---|---|---|---|---|---|---|---|---|
| netB positive | netB negative | |||||||
| VR-02 | Both | Hypothetical protein(s) | 1,080 | 3 | 3 | 100 | 70 | Chromosome |
| VR-03 | Both | Alternative sigma factor | 1,794 | 2 | 2 | 100 | 72 | Chromosome |
| VR-05 | Both | Carbohydrate ABC transporter system | 6,393 | 5 | 5 | 100 | 70 | Chromosome |
| VR-06 | Both | NELoc-2 | 11,720 | 11 | 11 | 100 | 44 | Chromosome |
| VR-08 | Both | Phage/insertion sequence related | 3,445 | 2 | 1 | 67 | 24 | Chromosome |
| VR-10A | JGS4143 | Two-component system, vWF domain protein | 5,877 | 7 | 5 | 23 | 70 | Chromosome |
| VR-10B | CP4 | Alternative to VR-10A; two-component system, collagen adhesin | 5,743 | 4 | 3 | 87 | 42 | Chromosome |
| VR-16 | CP4 | Oxidoreductase, FAD/FMN-binding | 1,106 | 1 | 1 | 86 | 53 | Chromosome |
| VR-22 | Both | Fe3+-siderophore ABC transporter | 3,882 | 4 | 4 | 100 | 69 | Chromosome |
| VR-27 | Both | Phage/insertion sequence-related, toxin-antitoxin | 2,443 | 2 | 2 | 95 | 63 | Chromosome |
| VR-33 | Both | Phage/insertion sequence-related, toxin-antitoxin | 5,379 | 5 | 1 | 100 | 77 | Chromosome |
| VR-34 | Both | Hypothetical protein(s) | 14,946 | 8 | 3 | 98 | 71 | Chromosome |
| VR-37 | Both | Hydroxylamine reductase | 1,655 | 1 | 1 | 100 | 53 | Chromosome |
| VR-38 | Both | ABC transporter | 6,062 | 4 | 1 | 90 | 61 | Chromosome |
| VR-44 | CP4 | Hypothetical protein(s) | 770 | 1 | 1 | 95 | 55 | Chromosome |
| VR-48 | CP4 | Phage/insertion sequence-related | 152 | 1 | 1 | 90 | 58 | Chromosome |
| VR-52 | CP4 | Hypothetical protein(s) | 503 | 1 | 1 | 95 | 67 | Chromosome |
| VR-59 | CP4 | Phage/insertion sequence-related | 128 | 1 | 1 | 60 | 24 | Chromosome |
| VR-64 | CP4 | Plasmid partitioning, restriction modification system | 755 | 1 | 1 | 81 | 45 | Chromosome |
| VR-65 | Both | Hypothetical protein(s) | 6,351 | 3 | 3 | 100 | 65 | Chromosome |
| VR-68 | Both | AraC family transcriptional regulator | 4,994 | 3 | 1 | 95 | 61 | pTet |
| VR-70 | Both | Hypothetical protein(s) | 1,289 | 3 | 3 | 98 | 64 | Unknown plasmid |
| VR-71 | Both | LexA repressor | 559 | 1 | 1 | 100 | 56 | pTet |
| VR-72 | CP4 | Putative plasmid partitioning protein | 1,135 | 2 | 1 | 95 | 65 | pTet |
| VR-74 | Both | Putative ATPase of HSP70 class | 1,099 | 2 | 1 | 95 | 29 | pNetB |
| VR-83 | CP4 | Collagen adhesin (partial) | 4,754 | 2 | 1 | 81 | 29 | Multiple plasmids |
| VR-84 | CP4 | Collagen adhesin (partial) | 665 | 1 | 1 | 62 | 30 | Multiple plasmids |
| VR-86 | CP4 | FtsK/SpoI | 1,316 | 1 | 1 | 86 | 31 | Multiple plasmids |
| VR-88 | Both | LexA repressor | 404 | 1 | 1 | 100 | 24 | pBeta2 |
| VR-89 | CP4 | Radical SAM domain proteins | 3,737 | 4 | 4 | 69 | 19 | Unknown plasmid |
| VR-90 | Both | Putative ATPase | 1,561 | 3 | 3 | 93 | 41 | pBeta2 |
| VR-91 | CP4 | cpb2 | 1,776 | 2 | 1 | 100 | 79 | pBeta2 |
| VR-92 | Both | NELoc-1 | 42,019 | 34 | 34 | 96 | 28 | pNetB |
| VR-94 | Both | Hypothetical protein(s) | 1,114 | 2 | 1 | 53 | 4 | Multiple plasmids |
| VR-95 | Both | Putative ATPase | 1,503 | 3 | 2 | 92 | 40 | Multiple plasmids |
| VR-96 | CP4 | Hypothetical protein(s) | 2,466 | 2 | 1 | 76 | 29 | pBeta2 |
| VR-97 | CP4 | NELoc-3 | 6,487 | 5 | 5 | 88 | 41 | pBeta2 |
| VR-103 | Both | Hypothetical protein(s) | 371 | 1 | 1 | 100 | 58 | Chromosome |
| VR-105 | Both | Phage/insertion sequence-related | 8,069 | 8 | 3 | 91 | 53 | Chromosome |
| VR-109 | JGS4143 | Capsular polysaccharide | 16,185 | 12 | 1 | 19 | 48 | Chromosome |
| VR-119 | JGS4143 | Hypothetical protein(s) | 323 | 1 | 1 | 43 | 79 | Chromosome |
| VR-126 | Both | RNA polymerase sigma-70 factor | 1,875 | 2 | 1 | 63 | 93 | Chromosome |
| VR-127 | Both | Phage/insertion sequence-related | 8,901 | 15 | 1 | 95 | 71 | Chromosome |
| VR-130 | Both | Endo-alpha-N-acetylgalactosaminidase | 152 | 1 | 1 | 81 | 100 | Chromosome |
| VR-131 | Both | NELoc-1 fragment | 206 | 1 | 1 | 100 | 45 | pNetB |
| VR-133 | JGS4143 | Phage/insertion sequence-related, restriction system | 12,137 | 9 | 1 | 86 | 52 | Chromosome |
| VR-136 | JGS4143 | C4-dicarboxylate transport system | 2,699 | 2 | 1 | 19 | 48 | Chromosome |
| VR-137 | JGS4143 | C4-dicarboxylate transport system | 2,875 | 2 | 1 | 33 | 67 | Chromosome |
| VR-142 | Both | Conjugation | NAd | 6 | 2 | 93 | 60 | Multiple plasmids |
a
The locus is present in CP4, JGS4143, or both strains.
b
vWF, von Willebrand factor; FAD, flavin adenine dinucleotide; FMN, flavin mononucleotide.
c
Predicted location of variable regions based on sequence comparisons with Str13, ATCC 13124, SM101, and 13 plasmid sequences (see Materials and Methods). If an identical alignment to only one plasmid was found, the plasmid name is indicated. “Multiple plasmids” indicates that identical alignments to multiple different plasmids were found. “Unknown plasmid” indicates that only part of the variable region has alignments to a known plasmid.
d
NA, not available.