A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii

Chan, Agnes P.; Sutton, Granger; DePew, Jessica; Krishnakumar, Radha; Choi, Yongwook; Huang, Xiao-Zhe; Beck, Erin; Harkins, Derek M.; Kim, Maria; Lesho, Emil P.; Nikolich, Mikeljon P.; Fouts, Derrick E.

doi:10.1186/s13059-015-0701-6

Table 3 Diversity of virulence gene content across A. baumannii isolates

From: A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii

							Gene clusters
Isolates	Genome category	Source	Year	ST	Allele summary	Country	1	2	3	4
Type I pili
AYE	Global	Urinary	2001	1	1-1-1-1-5-1-1	France	+	+	+
ACICU	Global	Internal	2005	2	2-2-2-2-2-2-2	Italy	+	+	-
SDF	Global	Miscellaneous	2000	17	3-29-30-1-9-1-4	France	-	-	-
NIPH 335	Global	Respiratory	1994	10	1-3-2-1-4-4-4	Czech Republic	-	+	+
OIFC098*	WRAIR	Miscellaneous	2003	10	1-3-2-1-4-4-4	Germany	-	+	+
MDR-ZJ06	Global	Blood	2006	2	2-2-2-2-2-2-2	China	-¹	+	-
UH clade B²	US hospital	Respiratory³	2007	2	2-2-2-2-2-2-2	USA	-¹	+	-
NIPH 60	Global	Respiratory	1992	34	8-1-14-3-12-1-13	Czech Republic	+	-	+
NIPH 528	Global	Unknown	1982	2	2-2-2-2-2-2-2	Netherlands	+	+	-⁴
MDR-TJ	Global	Miscellaneous	Before 2011	2	2-2-2-2-2-2-2	China	+	+	-⁴
OIFC143*	WRAIR	Wound	2003	25	3-3-2-4-7-2-4	USA	+	+	-⁴
Siderophores
AYE	Global	Urinary	2001	1	1-1-1-1-5-1-1	France	+	-	+	-
ACICU	Global	Internal	2005	2	2-2-2-2-2-2-2	Italy	+	-	+	-
SDF	Global	Miscellaneous	2000	17	3-29-30-1-9-1-4	France	-	-	-	-
NIPH 190	Global	Unknown	1993	9	3-1-5-3-6-1-3	Czech Republic	-	-	+	-
NIPH 410 ⁵	Global	Blood	1996	39	10-4-3-2-13-1-2	Czech Republic	-	-	+	-
OIFC0162*	WRAIR	Respiratory	2003	412	1-52-2-2-67-4-5	USA	-	-	+	-
OIFC047* ⁵	WRAIR	Miscellaneous	2003	Novel	1-75-2-2-67-1-2	USA	-	-	+	-
Naval-82*	WRAIR	Blood	2006	410	3-1-2-3-6-1-16	USA	-	-	+	-
WC-348*	WRAIR	Skin	2008	412	1-52-2-2-67-4-5	Iraq	-	-	+	-
ATCC 17978	Global	Miscellaneous	1951	437	3-2-2-2-30-4-28	NA	+	+⁶	+	-
6013113	Global	Skin	2007	81	1-1-1-1-5-1-2	England	+	+	+	-
6013150	Global	Skin	2007	81	1-1-1-1-5-1-2	England	+	+	+	-
MRSN 3527*	MRSN	Wound	2011	81	1-1-1-1-5-1-2	USA	+	+	+	-
MRSN 3405*	MRSN	Wound	2011	94	1-2-2-1-5-1-1	USA	+	+	+	-
MRSN 3942*	MRSN	Wound	2011	94	1-2-2-1-5-1-1	USA	+	+	+	-
MRSN 4106*	MRSN	Wound	2011	94	1-2-2-1-5-1-1	USA	+	+	+	-
WC-487* ⁷	WRAIR	Skin	2008	410	20-26-26-14-26-16-23	Iraq	-	-	-	+⁸
Efflux pumps
AYE	Global	Urinary	2001	1	1-1-1-1-5-1-1	France	+	+	+
ACICU	Global	Internal	2005	2	2-2-2-2-2-2-2	Italy	+	+	+
SDF	Global	Miscellaneous	2000	17	3-29-30-1-9-1-4	France	-	+	+
NIPH 60	Global	Respiratory	1992	34	8-1-14-3-12-1-13	Czech Republic	-	+	+
NIPH 80	Global	Blood	1993	37	3-2-2-2-7-1-2	Czech Republic	-	+	+
NIPH 615	Global	Respiratory	1994	12	3-5-7-1-7-2-6	Czech Republic	-	+	+
NIPH 410 ⁵	Global	Blood	1996	39	10-4-3-2-13-1-2	Czech Republic	-	+	+
OIFC047* ⁵	WRAIR	Miscellaneous	2003	Novel	1-75-2-2-67-1-2	USA	-	+	+
OIFC111*	WRAIR	Miscellaneous	2003	49	3-3-6-2-3-1-5	USA	-	+	+
AB900	WRAIR	Skin	2003	49	3-3-6-2-3-1-5	USA	-	+	+
AB_TG27343	Global	Wound	2005	422	26-72-2-2-29-4-5	USA	-	+	+
AB_1536-8	Global	Unknown	2006	413	1-3-2-2-5-8-12	USA	-	+	+
AB_1583-8	Global	Unknown	2006	422	26-72-2-2-29-4-5	USA	-	+	+
Naval-72*	WRAIR	Wound	2006	405	5-3-16-4-29-1-60	USA	-	+	+
ZWS1122	Global	Blood	2011	2	2-2-2-2-2-2-2	China	-	+	+
ZWS1219	Global	Blood	2011	2	2-2-2-2-2-2-2	China	-	+	+
BJAB0715	Global	Miscellaneous	5/2007–4/2008	23	1-3-10-1-4-4-4	China	-	+	+

Isolate name: finished genomes (bold), pre-2000 isolates (underline), sequenced in this study (italics with asterisk)
Specific gain or loss of gene clusters with respect to majority of isolates analyzed and reference genomes AYE, ACICU, SDF shown as “+” and “-” signs, respectively
(1) A 42 kb deletion was detected in ST2 strain MDR-ZJ06 and the UH clade B isolates, in contrast to the 17 kb deletion observed in ST10 strains NIPH 335 and OIFC098
(2) Nine UH clade B isolates carry a deletion of the type I pili csu gene cluster [40]
(3) Six out of nine UH clade B isolates which showed a loss of the type I pili csu gene cluster are of respiratory origin
(4) Loss of type I pili cluster 3 was detected in 133 isolates, including ST2, ST25, ST79, ST113, and ST215. Only three isolates are shown. Similar gene loss was not detected in ST1 or ST3 isolates
(5) Two isolates (NIPH 410, OIFC047) had a dual loss of siderophore cluster 1 and efflux cluster 1 (AdeABC)
(6) Insertion of siderophore cluster 2 was detected at 3 Mb in ATCC 17978, which differed from the location identified in ST81 and ST94 isolates at 3.8 Mb (coordinates based on ACICU genome)
(7) WC-487 is a non-baumannii Acinetobacter sp. isolate
(8) Siderophore cluster 4 was also detected in A. baumannii 8399 [78, 80]
ATCC American Type Culture Collection, NA not available, WRAIR Walter Reed Army Institute of Research

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