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Table 1 Strains analysed in this study

From: Novel Moraxella catarrhalis prophages display hyperconserved non-structural genes despite their genomic diversity

Strain Sourcea Clinical/Commensal MLSTb Phage presencec Phage named (%GC) att sitee NCBI prophage accession number
I Q C
2019228G PathWest Clinical h 1 0 0    
1020848 M PathWest Clinical 11 2 0 1 Mcat7 (43.62 %) 5’-ATCAAAAAATGG-3’ 5’-AATCAAAAATCT-3’ 5’-TTTTTTATTGGG-3’ KR093631
1028680 K PathWest Clinical 41 1 0 0    
1034084Q PathWest Clinical 224 1 0 0    
2023641 W PathWest Clinical 4 2 1 0    
3331584D PathWest Clinical h 0 1 0    
3476642E PathWest Clinical 46 1 1 0    
3481088Y PathWest Clinical h 2 3 0    
3753746B PathWest Clinical h 0 0 1 Mcat9 (43.94 %) 5’-TGTGTACATAATTGTGTACATA-3’ KR093633
4789849 F PathWest Clinical 67 1 1 0    
5550565E PathWest Clinical h 3 1 1 Mcat32 (42.68 %) N/A KR093656
20236154 PathWest Clinical 236 1 0 0    
20370737 PathWest Clinical 105 1 0 1 Mcat4 (43.21 %) 5’-TTATCAATCAGT-3’ KR093628
2040048B PathWest Clinical 230 0 1 0    
3503282R PathWest Clinical 184 2 0 1 Mcat16 (42.96 %) 5’-TTTTTTTAGGGG-3’ KR093640
5004663G PathWest Clinical 224 1 0 0    
1093063Y PathWest Clinical 230 0 1 0    
4640032P PathWest Clinical 246 1 0 1 Mcat15 (42.71 %) 5’-ATACAAAAAATC-3’ KR093639
2046210Y PathWest Clinical h 2 0 0    
4737718Q PathWest Clinical h 2 0 0    
5012204D PathWest Clinical 250 4 2 1 Mcat24 (42.74 %) N/A KR093648
4840991 N PathWest Clinical 73 1 0 0    
2042044P PathWest Clinical h 0 0 0    
2041717D PathWest Clinical h 0 0 0    
5008863 L PathWest Clinical h 1 1 1 Mcat19 (42.39 %) 5’-ATTTTTTATATT-3’ KR093643
1583718S PathWest Clinical 234 2 1 0    
5267783B PathWest Clinical 234 3 1 0    
4431503 J PathWest Clinical 118 3 2 0    
1111988H PathWest Clinical h 1 2 0    
5021467Y PathWest Clinical 224 1 0 0    
5560626Q PathWest Clinical h 1 0 0    
2047127 K PathWest Clinical 240 1 0 0    
5021466 N PathWest Clinical 224 1 0 0    
2041417P PathWest Clinical h 3 1 1 Mcat3 (43.79 %) 5'-AAAAAAATCAAAG-3’ KR093627
1098655R PathWest Clinical 230 1 1 0    
5157102Y PathWest Clinical 251 1 0 0    
4849094R PathWest Clinical 248 1 0 0    
2050675Y PathWest Clinical h 1 0 0    
5553245S PathWest Clinical h 1 0 0 Mcat13 (42.77 %) 5’-TTTTTCAGCTTC-3’ KR093637
5/131/1 KOMRP Commensal 217 1 0 0    
23/41/1 KOMRP Commensal 235 2 0 0    
39/355/1 KOMRP Commensal 62 1 1 1 Mcat2 (43.64 %) 5’-TTTCAAATTTTA-3’ KR093626
41/539/1 KOMRP Commensal h 1 0 1 Mcat22 (42.48 %) 5’-AAAAATTTGGTT-3’ KR093646
3/7/1 KOMRP Commensal 242 1 1 0    
102/402/3 KOMRP Commensal h 1 3 0    
91/291/2 KOMRP Commensal h 2 0 1 Mcat20 (42.71 %) N/A KR093644
78/191/1 KOMRP Commensal h 4 0 1 Mcat31 (42.68 %) N/A KR093655
96/281/2 KOMRP Commensal 259 1 0 0    
26/133/1 KOMRP Commensal 70 2 0 1 Mcat23 (42.65 %) N/A KR093647
129/414/4 KOMRP Commensal 209 1 0 0    
130/563/4 KOMRP Commensal 74 2 0 0    
60/120/1 KOMRP Commensal 64 1 0 1 Mcat11 (43.92 %) 5’-TAAAAAAAATAAA-3’ KR093635
105/305/2 KOMRP Commensal h 0 1 0    
113/391/3 KOMRP Commensal 232 1 0 0    
20/122/1 KOMRP Commensal 235 2 0 0    
79/220/2 KOMRP Commensal h 1 2 0    
29/50/1 KOMRP Commensal 241 0 1 0    
23/95/1 KOMRP Commensal 233 1 0 0    
107/374/3 KOMRP Commensal 229 2 0 0    
76/204/3 KOMRP Commensal h 1 0 0    
73/187/1 KOMRP Commensal 254 0 1 1 Mcat10 (44.14 %) 5’-TAAAAAAAATAAA-3’ KR093634
24/92/1 KOMRP Commensal 64 0 0 1 Mcat12 (43.56 %) 5’-TTATTTTTAAAA-3’ KR093636
78/325/3 KOMRP Commensal 256 2 0 0    
78/205/2 KOMRP Commensal h 5 0 1 Mcat30 (42.68 %) N/A KR093654
105/417/3 KOMRP Commensal h 1 1 0    
25/44/1 KOMRP Commensal h 1 1 0    
77/338/2 KOMRP Commensal 50 0 2 0    
16/38/1 KOMRP Commensal 157 1 0 1 Mcat26 (42.22 %) N/A KR093650
64/108/1 KOMRP Commensal 140 0 2 1 Mcat17 (42.46 %) 5’-ACCATTTTTTAA-3’ 5’-TTTTTTTCATTTT-3’ KR093641
3/22/1 KOMRP Commensal 242 1 0 0    
80/196/2 KOMRP Commensal h 2 1 0    
15/36/1 KOMRP Commensal 233 1 0 0    
BBH18 Sputum sample, patient with COPD, Holland GCA_000092265.1 Clinical 128 1 0 0    
A16 Frozen stocks, saliva, Australia Commensal h 0 0 0 Mcat28 (42.24 %) 5’-TGTGTACATAATTGTGTACATA-3’ KR093652
5’-AAAAAACTTAAC-3’
ATCC43617f Trans-tracheal aspirate from coal miner with bronchitis Clinical 25 1 1 1 Mcat5 (43.30 %) N/A KR093629
ATCC43617af Trans-tracheal aspirate from coal miner with bronchitis Clinical 25 1 1 1 Mcat6 (43.08 %) N/A KR093630
BE4L PathWest Clinical h 2 0 1 Mcat25 (42.61 %)   
MC4S Alexander project Clinical 188 1 2 1 Mcat8 (41.40 %) 5’-CTTAAAAAAATA-3’ KR093632
MC24 Alexander project Clinical h 1 0 0    
MC1 Alexander project Clinical 131 1 0 0    
BE5 PathWest Clinical h 1 1 1 Mcat18 (42.26 %) 5’-CATTAATCAAAT-3’ KR093642
A6 Frozen stocks, saliva, Australia Commensal 3 6 0 1 Mcat29 (42.23 %) N/A KR093653
T6 Sputum, children 3 – 6 years, Taiwan Commensal h 1 1 0    
T12 Sputum, children 3 – 6 years, Taiwan Commensal h 2 1 0    
T4 Sputum, children 3 – 6 years, Taiwan Commensal 191 1 0 0    
K117 Hospital isolate, Perth, Australia Clinical 40 1 0 0    
12P80B1g GCA_000192965.2 Clinical 185 1 0 0    
O35Eg GCA_000193085.2 Clinical 146 0 0 0    
46P47B1g GCA_000192945.2 Clinical h 1 0 1 Mcat21 (42.26 %) N/A KR093645
101P10B1g GCA_000193065.2 Clinical 218 1 1 0    
103P14B1g GCA_000192925.2 Clinical 187 1 1 1 Mcat14 (43.39 %) N/A KR093638
7169g GCA_000192905.2 Clinical 82 3 2 0    
BC1g GCA_0000192985.2 Clinical 216 2 1 0    
BC7g GCA_000193005.2 Clinical 217 1 0 0    
BC8g GCA_0000193025.2 Clinical 162 1 1 1 Mcat1 (43.62 %) 5’-TTTCAAATTTTA-3’ KR093625
CO72g GCA_000193045.2 Clinical 199 2 0 1 Mcat27 (42.57 %) 5’-TGTGTACATAATTGTGTACATA-3’ KR093651
RH4g GCA_000302495.1 Clinical h 0 0 1    
  1. aSource of collected strain (PathWest: strains obtained from PathWest Laboratory Medicine WA, Australia; KOMRP: strains obtained from the Kalgoorlie Otitis Media Research Project [49])
  2. bMulti locus sequence typing strain types
  3. cPhage presence as annotated by PHAST, where I = incomplete prophage, Q = questionable prophage, and C = complete prophage
  4. dComplete prophages were named Mcat1 to Mcat32
  5. e att sites are putative flanking attachment sites identified in M. catarrhalis genomes by PHAST. Prophages without identified att sites are labelled N/A
  6. fThe strain ATCC43617a is a passaged derivative of ATCC43617 that was obtained from The University of Queensland and sequenced in this study. Additionally, the sequenced genome of ATCC43617 available on the NCBI database was also analysed [15]
  7. gStrains not sequenced in this study, but are available on the NCBI database; GenBank accession numbers current at time of manuscript submission [15]
  8. hdenotes novel strain types