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

Ariff, Amir; Wise, Michael J.; Kahler, Charlene M.; Tay, Chin Yen; Peters, Fanny; Perkins, Timothy T.; Chang, Barbara J.

doi:10.1186/s12864-015-2104-1

Table 1 Strains analysed in this study

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

Strain	Source^a	Clinical/Commensal	MLST^b	Phage presence^c			Phage name^d (%GC)	att site^e	NCBI prophage accession number
Strain	Source^a	Clinical/Commensal	MLST^b	I	Q	C	Phage name^d (%GC)	att site^e	NCBI prophage accession number
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
A16	Frozen stocks, saliva, Australia	Commensal	^h	0	0	0	Mcat28 (42.24 %)	5’-AAAAAACTTAAC-3’	KR093652
ATCC43617^f	Trans-tracheal aspirate from coal miner with bronchitis	Clinical	25	1	1	1	Mcat5 (43.30 %)	N/A	KR093629
ATCC43617a^f	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
12P80B1^g	GCA_000192965.2	Clinical	185	1	0	0
O35E^g	GCA_000193085.2	Clinical	146	0	0	0
46P47B1^g	GCA_000192945.2	Clinical	^h	1	0	1	Mcat21 (42.26 %)	N/A	KR093645
101P10B1^g	GCA_000193065.2	Clinical	218	1	1	0
103P14B1^g	GCA_000192925.2	Clinical	187	1	1	1	Mcat14 (43.39 %)	N/A	KR093638
7169^g	GCA_000192905.2	Clinical	82	3	2	0
BC1^g	GCA_0000192985.2	Clinical	216	2	1	0
BC7^g	GCA_000193005.2	Clinical	217	1	0	0
BC8^g	GCA_0000193025.2	Clinical	162	1	1	1	Mcat1 (43.62 %)	5’-TTTCAAATTTTA-3’	KR093625
CO72^g	GCA_000193045.2	Clinical	199	2	0	1	Mcat27 (42.57 %)	5’-TGTGTACATAATTGTGTACATA-3’	KR093651
RH4^g	GCA_000302495.1	Clinical	^h	0	0	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])
^bMulti locus sequence typing strain types
^cPhage presence as annotated by PHAST, where I = incomplete prophage, Q = questionable prophage, and C = complete prophage
^dComplete prophages were named Mcat1 to Mcat32
^e att sites are putative flanking attachment sites identified in M. catarrhalis genomes by PHAST. Prophages without identified att sites are labelled N/A
^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]
^gStrains not sequenced in this study, but are available on the NCBI database; GenBank accession numbers current at time of manuscript submission [15]
^hdenotes novel strain types

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