Table 1: Features of Bacteriophage Φ3396 Orfs and Predicted Functions A

Table 1: Features of Bacteriophage Φ3396 Orfs and Predicted Functions A

Supplementary Table 1: Features of bacteriophage Φ3396 ORFs and predicted functionsa.

ORF / Position (bp) / No. AA / DNA Strand / % G/C
content / AA identity / Gene number / Predicted function
Start / Stop
1 / 1302 / 106 / 398 / - / 35.09 / 99% / SpyM3_0681 / Integrase
2 / 2353 / 1613 / 246 / - / 36.71 / 100% / SpyM3_0682 / Hypothetical
3 / 2759 / 2364 / 131 / - / 34.6 / 69% / SpyM3_0683 / Hypothetical
4 / 3147 / 2725 / 140 / - / 31.68 / 49% / SpyM3_0684 / Repressor
5 / 3369 / 3533 / 54 / + / 32.73 / 87% / SAG1880 (GBS) / Hypothetical
6 / 3575 / 3778 / 67 / + / 38.73 / 48% / SAG1878 (GBS) / Hypothetical
7 / 3780 / 3914 / 44 / + / 31.11 / 96% / SpyM18_0343 / Hypothetical
8 / 3911 / 4666 / 251 / + / 37.57 / 79% / SpyM3_0687 / Anti-repressor
9 / 4680 / 4997 / 105 / + / 33.02 / 99% / SpyM3_0688 / Hypothetical
10 / 4885 / 5001 / 38 / + / 32.48 / ND / ND / ND
11 / 4976 / 5116 / 46 / + / 31.91 / ND / ND / ND
12 / 5336 / 5920 / 194 / + / 32.99 / 56% / SAG1872 (GBS) / Hypothetical
13 / 5959 / 6873 / 304 / + / 33.44 / 54% / SAG0559 (GBS) / Replication protein
14 / 6860 / 7051 / 63 / + / 28.65 / ND / ND / ND
15 / 7132 / 7371 / 79 / + / 40.0 / 94% / SpyM3_0699 / Single-strand binding protein 1
16 / 7386 / 7664 / 92 / + / 34.41 / 85% / SpyM3_0700 / Hypothetical
17 / 7679 / 7795 / 38 / + / 35.04 / 86% / SpyM18_0736 / Hypothetical
18 / 7864 / 8238 / 124 / + / 34.13 / 38% / TIGR01671 (GBS) / Hypothetical
19 / 8235 / 8519 / 94 / + / 38.25 / 88% / SpyM3_0696 / Hypothetical
20 / 8516 / 9190 / 224 / + / 38.07 / 47% / Flavobacterium sp. / DNA Methylase
21 / 9203 / 9430 / 75 / + / 40.79 / ND / ND / ND
22 / 9432 / 10031 / 199 / + / 36.5 / 60% / SpyM18_1487 / Hypothetical
23 / 10050 / 10328 / 92 / + / 37.63 / 88% / SpyM3_0700 / Hypothetical
24 / 10325 / 10663 / 112 / + / 34.51 / 92% / SpyM3_0701 / Immunity repressor protein
25 / 10651 / 11493 / 280 / + / 37.49 / 99% / SpyM3_0702 / Prohibitin
26 / 11490 / 11909 / 139 / + / 32.86 / 100% / SpyM3_0703 / Transcriptional Activator
27 / 12069 / 12644 / 191 / + / 36.28 / 99% / SpyM3_0704 / Recombinase xerC-like
28 / 12799 / 12969 / 56 / + / 31.58 / ND / ND / ND
29 / 13160 / 13597 / 145 / + / 36.3 / 93% / SpyM3_0707 / Hypothetical
30 / 13584 / 13895 / 103 / + / 43.59 / 96% / SpyM3_0708 / Endonuclease
31 / 14038 / 14355 / 105 / + / 31.76 / 99% / SpyM3_0709 / Terminase small subunit
32 / 14368 / 16098 / 576 / + / 35.12 / 97% / SpyM3_0710 / Terminase large subunit
33 / 16089 / 16313 / 74 / + / 28.89 / ND / ND / ND
34 / 16489 / 17676 / 395 / + / 36.03 / 96% / SpyM3_0711 / Portal protein
35 / 17657 / 18463 / 268 / + / 39.65 / 98% / SpyM3_0712 / Head maturation protease
36 / 18480 / 19613 / 377 / + / 38.10 / 97% / SpyM3_0713 / Major coat protein
37 / 19627 / 19800 / 57 / + / 38.51 / 95% / SpyM3_0714 / Hypothetical
38 / 19800 / 20108 / 102 / + / 37.54 / 98% / SpyM3_0715 / Hypothetical
39 / 20101 / 20463 / 120 / + / 36.91 / 97% / SpyM3_0716 / Hypothetical
40 / 20447 / 20863 / 138 / + / 41.25 / 100% / SpyM3_0717 / Hypothetical
41 / 20856 / 21236 / 126 / + / 35.43 / 99% / SpyM3_0718 / Hypothetical
42 / 21233 / 21823 / 196 / + / 39.42 / 90% / SpyM3_0719 / Major tail protein
43 / 21916 / 22218 / 100 / + / 39.6 / 96% / SpyM3_0720 / Hypothetical
44 / 22284 / 22400 / 38 / + / 35.04 / 97% / SPs1131 (M3) / Hypothetical Protein
45 / 22410 / 26537 / 1375 / + / 39.68 / 72% / SpyM3_0722 / Phage Tail Protein
46 / 26547 / 27320 / 257 / + / 36.18 / 87% / SpyM3_0723 / Hypothetical
47 / 27317 / 29374 / 685 / + / 41.64 / 87% / SpyM3_0724 / Endopeptidase
48 / 29371 / 30426 / 351 / + / 40.44 / 92% / M3_Spy0593 / Hyaluronoglucosaminidase
49 / 30426 / 31058 / 210 / + / 38.7 / 58% / SpyM3_1302 / Hypothetical
50 / 31069 / 33111 / 680 / + / 43.76 / 70% / M3_Spy0595 / Phage Infection protein
51 / 33125 / 33550 / 141 / + / 38.03 / 91% / SpyM3_1099 / Hypothetical
52 / 33543 / 33070 / 157 / - / 37.55 / 63% / SpyM18_0773 / Hypothetical
53 / 33556 / 34173 / 205 / + / 43.2 / 88% / M3_Spy0597 / Hypothetical
54 / 34184 / 34504 / 106 / + / 41.74 / ND / ND / ND
55 / 34506 / 34838 / 110 / + / 35.14 / 97% / SpyM3_1307 / Holin
56 / 34816 / 35592 / 258 / + / 43.76 / 99% / M6_Spy1544 / Cell Wall Hydrolase
57 / 36024 / 35743 / 93 / - / 30.14 / 96% / SpyM3_0734 / Hypothetical
58 / 36290 / 36135 / 51 / - / 39.74 / 96% / SpyM3_0735 / Hypothetical
59 / 36383 / 36643 / 86 / + / 33.33 / 100% / SpyM3_0736 / Hypothetical
60 / 37116 / 36826 / 96 / - / 37.80 / ND / ND / ND
61 / 37317 / 37132 / 61 / - / 35.48 / 36% / EF0599 (S. Faecalis) / Hypothetical
62 / 37805 / 37314 / 163 / - / 33.94 / ND / ND / ND
63 / 38135 / 37827 / 102 / - / 36.25 / ND / ND / ND
64 / 38259 / 38441 / 60 / + / 39.89 / 72% / SpyM3_1408 / Hypothetical Paratox

Footnotes: ORF, open reading frame; AA, amino acid; ND, no database homology

aPredicted function, assigned gene number and amino acid identity were determined through BlastP analysis of the non-redundant GenBank database at the National Centre for Biotechnology Information. The gene with strongest homology is represented. Genes with less than 35% identity to the GenBank database are defined as ND.

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Supplementary 2. PCR screening of Φ3396 phage modules within group A and G streptococcal isolates from GAS endemic and GAS non-endemic regions.

Isolate / emm typea / Source / Φ3396Region onec / Φ3396.1 Region twoc / Φ3396.1 Region threec
Φ3396_0682F
Φ3396_0682R / Φ3396_0713F
Φ3396_0721R / Φ3396_0734F
Φ3396_0734R
GGS isolates from a GAS-endemic region b
NS3396 / STG480 / RDH, NT / + / + / +
GGS10 / STG6 / NT / - / - / -
GGS24 / STG6 / NT / + / + / -
GGS48 / STG4831 / NT / + / - / -
G120 / STG4831 / RDH, NT / + / + / -
G121 / STC74A / NT / - / - / -
G122 / STC74A / NT / - / - / -
NS383 / New type / RDH, NT / - / + / -
NS542 / STG652 / RDH, NT / - / - / -
NS752 / STG6 / RDH, NT / - / - / -
NS1121 / STG4831 / NT / - / + / -
GGS isolates from a GAS non-endemic regionb
MD01 / STG11 / RBH / - / - / -
MD02 / STG10 / RBH / - / - / -
MD03 / STG2078 / RBH / - / - / -
MD04 / STG6.1 / RBH / - / - / -
MD05 / STG6 / RBH / - / - / -
MD06 / STC74A / RBH / - / - / -
MD07 / STG6.1 / RBH / - / - / -
MD08 / STG2078 / RBH / - / - / -
MD09 / STG10 / RBH / - / - / -
MD10 / STG6 / RBH / - / - / -
GAS isolates from a GAS-endemic regionb
NS1 / Emm100 / RDH, NT / - / - / -
NS6 / Emm123 / RDH, NT / - / - / -
NS8 / Emm98.1 / RDH, NT / - / - / -
NS14 / Emm102 / RDH, NT / + / + / +
NS20 / Emm6.5 / RDH, NT / - / - / +
NS32 / Emm101 / RDH, NT / + / + / +
NS43 / Emm98.1 / RDH, NT / - / - / -
NS50 / ST854.1 / RDH, NT / - / - / +
NS50.1 / Emm108 / RDH, NT / + / + / +
NS53 / Emm71 / RDH, NT / - / - / -
NS66 / Emm14.4 / RDH, NT / + / + / -
NS80 / Emm70 / RDH, NT / + / + / +
NS83 / Emm98.1 / RDH, NT / - / - / -
NS88.2 / Emm98.1 / RDH, NT / - / - / -
NS90 / STNS90 / RDH, NT / + / + / -
NS125 / Emm95 / RDH, NT / +/- / - / -
NS178 / Emm54 / RDH, NT / - / - / -
NS179 / Emm98.1 / RDH, NT / +/- / - / -
NS180 / Emm74 / RDH, NT / - / - / -
NS195 / Emm19.7 / RDH, NT / + / - / +
GAS isolates from a GAS non-endemic regionb
ES69 / Emm91 / Sydney / - / - / -
ES71 / Emm4 / Sydney / - / - / -
ES100 / Emm1 / Sydney / - / - / -
ES73 / Emm77 / Sydney / - / - / -
ES101 / Emm82 / Sydney / - / - / -
ES76 / Emm101 / Sydney / - / - / -
ES79 / ND / Sydney / - / - / -
ES78 / ND / Sydney / - / - / -
ES89 / ND / Sydney / - / - / -
ES92 / Emm92 / Sydney / - / - / -
ES94 / Emm58.2 / Sydney / - / - / -
ES95 / Emm49 / Sydney / - / - / -

FOOTNOTES: ‘+’ refers to the presence of a PCR product of expected size; ‘-’ no PCR product detected; ‘+/-’ ambiguous; RBH, Royal Brisbane Hospital; RDH, Royal Darwin Hospital; NT, Northern Territory of Australia.

aemm type was determined from Blast analysis of the emm sequence database (

bGAS and GGS endemic isolates are from the Northern Territory of Australia with high endemicity for GAS infection. GGS non-endemic isolates are from BrisbaneAustralia, while GAS non-endemic isolates are from Sydney Australia.

c‘Region one’ amplifies ORF2 within the lysogeny module of Φ3396. ‘Region two’ amplifies ORF36 to ORF44 encompassing the DNA packaging, Head-joining-tail and tail modules of Φ3396. ‘Region three’ amplifies ORF57 within the lysogenic conversion module of Φ3396. PCR primers were designed from the genome sequence of the group A streptococcal phage Φ315.1 (NC_004584).

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