Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing

Sanderson, Haley; McCarthy, Madeline C.; Nnajide, Chinenye R.; Sparrow, Jessica; Rubin, Joseph E.; Dillon, Jo-Anne R.; White, Aaron P.

doi:10.1186/s12864-023-09784-6

BMC Genomics

Table 2 Characteristics of different plasmid clusters identified in avian-associated E. coli by MOB-suite software

From: Identification of plasmids in avian-associated Escherichia coli using nanopore and illumina sequencing

Plasmid Cluster ID^a	% G + C	E. coli Pathotype / Potential Source^b	E. coli Isolates^c	Nearest Neighbour^d	Average Size (bp)	# ORFs^e
AA176	50.2	APEC, UPEC	4957-C3, 6245-C4, 4957-3S1, 9226-2S1, 9226-3H1, 2402-1H1, 3862-S2, 0205-3S1	CP033091, CP012113, CP001122, CP031107, KU578032, CP012636, CU928146, CP018994	155,753	941–2165 (1157)
AA474	49.7	UPEC, APEC, Salmonella enterica	9413-C4, 23,315-C5, 6245-1H1, 6245-2L1, 9226-2S1, 9226-3H1, 9619-3S1	HE654725, NC_019131, CP024093, KT779550, CP039714, CP032264, CP044183, CP016522, CP019996	104,545	513–2359 (893)
AA175	49.2	APEC	6245-1H1, 6245-2L1, 4957-3S1, 9226-2S1, 9226-3H1, 0012-2L1	CP022732, LC484363	123,558	260–1505 (1240)
AC509	48.5	UPEC, Salmonella enterica	23,315-C5, 4957-3S1, 9226-2S1, 2402-1H1, 0205-3S1	CP010175, CP019025, CP032941, CP016519, LT985237	7,917	41–105 (55)
AA378	47.9	UPEC	0205-C9, 4957-C3, 2402-1H1, 0205-3S1	CP012494, CP020522, MH844525, CP022733	95,605	698–827 (751)
AB241	55.6	Salmonella enterica	6245-1H1, 6245-2L1, 4957-3S1, 4957-C3	CP038600	2,189	13–46 (17)
AB685	51.7	UPEC, Klebsiella pneumoniae	23,315-C5, 9226-2S1, 9226-3H1, 9619-3S1	CP023858, CP026493, CP006785, CP024465	1,914	13–35 (20)
AA281	52.6	APEC	4957-3S1, 9226-2S1, 9226-3H1	CP033633, KR905386, CP018772, KR905389, KR905384	136,115	317–1507 (1245)
AA329	52.1	EHEC	0012-C5, 0205-C9, 9226-C5	NC_013362, CP024284	79,383	398–878 (720)
AB233	41.5	Salmonella enterica	23,315-C5, 2402-1H1, 0205-3S1	CP024290, EU219533	40,792	185–516 (253)
AB690	42.3	APEC	4957-C3, 2402-1H1, 0205-3S1	CP005932	6,259	15–92 (53)
AA162	50.4	APEC, Salmonella enterica	9226-2S1, 9226-3H1	CP039570, CP011433, CP010318, CP030004, CP012684	7,126	36–115 (52)
AA179	49.4	Unknown Pathotype	9619-2L1, 7578-1L2	CP021198, CP019018	155,108	878–1677 (900)
AA313	50.7	Unknown Pathotype	2402-1H1, 3862-S2	CP024287	53,144	388–529 (444)
AA738	45.6	Salmonella enterica	4957-3S1, 9619-3S1	MK169211, CP045449	251,326	1660–2080 (1877)
AB443	46.8	UPEC	0012-C5, 0205-C9	CP035351	7,633	35–132 (44)
AB714	49.0	Salmonella enterica	2402-1H1, 3862-S2	CP022453	21,326	157–205 (181)
AC748	47.2	NMEC	0012-C5, 0205-C9	CP030115, CP034961	2,235	10–22 (15)
AA178	49.6	APEC	23,315-C5	CP043952	189,407	1481–1601 (1493)
AA315	48.2	UPEC	9226-C5	KU254579	89,815	711–789 (731)
AA372	42.2	Salmonella enterica	9226-2S1	CP028155	60,009	247–508 (450)
AA374	47.4	Unknown Pathotype	6245-C4	CP042894, CP029181	152,238	1125–1228 (1152)
AA476	57.0	STEC	9619-3S1	CP031897	11,442	113 (113)
AA551	51.8	Unknown Pathotype	9226-C5	HE613857	46,517	307–402 (327)
AA664	53.7	Arthrobacter	3862-S2	CP011006	4,354	42–43 (42)
AA736	54.6	Unknown Pathotype	9226-3H1	CP018771	17,590	160 (160)
AB229	42.5	Unknown Pathotype	23,315-C5	CP023379	38,502	271–288 (280)
AB238	57.3	Salmonella enterica	9619-2L1	AY178821	3,389	12–32 (21)
AC026	52.2	Unknown Pathotype	6245-2L1	CP040923	22,046	221–228 (224)
AC028	46.3	UPEC	9226-2S1	KU043116	14,509	134–137 (136)
AC662	49.1	Shigella sonnei	6245-1H1	CP019691	43,325	429 (429)
AD482	48.8	Unknown Pathotype	0205-C9	CP033763	3,343	21–26 (24)
AD669	53.7	ETEC	9619-3S1	CP002733	45,498	363–423 (400)
AF267	47.3	Salmonella enterica	9226-3H1	CP022065	21,883	190 (190)

^aThe plasmid cluster ID names were generated by MOB-suite software; each represents a group of related plasmids
^bThe E. coli pathotypes: APEC, avian-pathogenic; UPEC, urinary-pathogenic; EHEC, enterohemorrhagic; NMEC, neonatal meningitis-causing; STEC, shiga toxin-producing; ETEC, enterotoxigenic, and Unknown, and other bacterial species listed were associated with “Nearest Neighbour” plasmids and could represent a potential source of the plasmid
^cNames of the E. coli strains in this study where this plasmid cluster ID was detected
^dPlasmids that were genetically similar to the plasmid cluster IDs are listed by accession numbers to the NCBI nucleotide database
^eThe range in the number of open reading frames (ORFs) in each plasmid cluster (taking into account 8-12 different DNA sequence assemblies for each isolate) is shown with the average number of ORFs in parentheses

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ISSN: 1471-2164

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