Strong Homology Between Colonizing and Bloodstream Carbapenem-Resistant Acinetobacter Spp.: Implications for Empiric Antibiotic Therapy in Hematological Patients

Figures & data

Table 1 Comparison of Outcomes in Hematological Patients During Acinetobacter Spp. Bloodstream Infection, Stratified by Acinetobacter Spp. Colonization Status

Outcomes	Total n=46	Colonized n=18	Not Colonized n=28	P value
Resistance profiles of BSI
Carbapenem-resistant	18 (39.1)	13 (72.2)	5 (17.9)	<0.001*
Multidrug-resistant	21 (45.7)	14 (77.8)	7 (25.0)	<0.001*
Extensively drug-resistant	5 (10.9)	4 (22.2)	1 (3.6)	0.069
Fluoroquinolones-resistant	13 (28.3)	9 (50.0^)	4 (14.3)	0.009*
Aminoglycosides-resistant	14 (30.4)	9 (50.0)	5 (17.9)	0.021*
Piperacillin-tazobactam-resistant	19 (41.3)	14 (77.8)	5 (17.9)	<0.001*
Inappropriate empirical therapy	16 (34.8)	12 (66.7)	4 (14.3)	<0.001*
Polymicrobial BSI	15 (32.6)	9 (50.0)	6 (21.4)	0.044*
Laboratory results at the onset of BSI
PCT (ug/L)	0.49 (0.12–1.89)	1.46 (0.71–8.32)	0.17 (0.09–0.69)	0.008*
CRP (mg/L)	31.81 (10.43–123.71)	92.29 (16.50–194.00)	12.88 (5.65–51.85)	0.013*
Respiratory failure	10 (21.7)	7 (38.9)	3 (10.7)	0.033*
Sepsis or septic shock	11 (23.9)	8 (44.4)	3 (10.7)	0.014*
30-day clinical recovery	22 (47.8)	4 (22.2)	18 (64.3)	0.005*
30-day death	15 (32.6)	9 (50.0)	6 (21.4)	0.044*

Note: Categorical variables are presented as numbers (percentiles); continuous variables are presented as median (interquartile range, IQR). A P value in italics and bold means <0.1, followed by * means <0.05.

Abbreviations: OR, odds ratio; CI, confidence interval; PCT, procalcitonin; CRP, C-reactive protein; AST, aspartate aminotransferase. BSI, bloodstream infection.

Figure 1 Kaplan-Meier curves of the 30-day probability of survival in hematological patients with Acinetobacter spp. bloodstream infection, comparing patients with and without previous Acinetobacter spp. colonization.

Table 2 The Sequence Types of 21 Carbapenem-Resistant Acinetobacter Spp. Isolates and Four Reference Types Using the Pasteur Multilocus Sequence Typing (MLST) Scheme

			Housekeeping Genes
Sample ID	Case ID	Strain	cpn60	fusA	gltA	pyrG	recA	rplB	rpoB	STs
A-6	Case 1	A. pittii	17	21	23	10	20	18	27	248
A-8	Case 1	A. pittii	17	21	23	10	20	18	27	248
A-32		A. pittii	17	21	23	10	488	13	20	2230
A-37		A. pittii	17	20	23	10	20	13	20	63
A-44	Case 2	A. baumannii	2	2	2	2	2	2	2	2
A-45	Case 2	A. baumannii	2	2	2	2	2	2	2	2
A-69		A. baumannii	3	1	16	1	7	2	3	1627
A-76	Case 3	A. baumannii	2	2	2	2	2	2	2	2
A-77	Case 3	A. baumannii	2	2	2	2	2	2	2	2
A-136	Case 4	A. pittii	17	21	23	10	20	18	27	248
A-140	Case 4	A. pittii	17	21	23	10	20	18	27	248
A-169	Case 5	A. baumannii	2	2	2	2	2	2	2	2
A-172	Case 5	A. baumannii	2	2	2	2	2	2	2	2
A-193		A. nosocomialis	47	47	50	14	26	16	49	224
A-223	Case 6	A. pittii	17	20	23	10	20	131	446	2229
A-225	Case 6	A. pittii	17	20	23	10	20	131	20	1611
A-231	Case 7	A. baumannii	1	2	2	2	5	1	2	105
A-233	Case 7	A. baumannii	1	2	2	2	5	1	2	105
A-337	Case 8	A. oleivorans	491	94	434	38	33	22	447	2231
A-339	Case 8	A. oleivorans	491	94	434	38	33	22	447	2231
A-340		A. pittii	17	20	23	10	20	131	20	1611
ATCC 19606		A. baumannii	3	2	2	7	9	1	5	52
NIPH 2119		A. nosocomialis	20	26	26	18	27	19	23	76
JCM 16667		A. oleivorans	78	94	71	38	82	22	72	560
DSM 25618		A. pittii	17	20	23	10	20	13	20	63

Note: Only case IDs of patients who had respiratory colonization were noted. The new housekeeping genes and STs are marked in bold. STs, sequence types.

Figure 2 The phylogenetic tree of 21 carbapenem-resistant Acinetobacter spp. strains and 4 type strains inferred from a concatenate of the seven alleles used in the Pasteur multilocus sequence typing (MLST) scheme. RT, respiratory tract.

Figure 3 The minimum spanning tree of 21 carbapenem-resistant Acinetobacter spp. (CRA) strains and 4 type strains inferred from a concatenate of the seven alleles used in the Pasteur multilocus sequence typing (MLST) scheme. The sequence types (STs) are indicated by the numbers beside each circle, with the size of each circle proportional to the number of isolates belonging to the same ST type. Branch values indicate the number of loci that differ between adjacent nodes. Grey shading is used to represent the same cluster. Each of the eight pairs of respiratory-bloodstream CRA strains had an identical MLST pattern or was grouped into a clonal complex.

Figure 4 The phylogenetic tree of 21 carbapenem-resistant Acinetobacter spp. strains based on single nucleotide polymorphisms between each strain and strain A-169 by maximum likelihood method. RT, respiratory tract.

Figure 5 (A) The genic and intergenic single nucleotide polymorphisms (SNPs) identified during within-host evolution. (B) Function class of genes with all SNPs based on the Clusters of Orthologous Groups of proteins (COG).

Table 3 Non-Synonymous Genic Single Nucleotide Polymorphisms (SNPs) Found from Respiratory Tract Carriage to Bloodstream Infection in Eight Patients with Carbapenem-Resistant Acinetobacter Spp.

Case ID	Reference Gene	Base chanGe	Amino Acid Change	Mutation Type	Gene or Function	Function Class
Case 1	A-6001176	C—T	Gln—X	Nonsense	rnd	J
	A-6003774	T—C	Asn—Asp	Missense	ahpF	C
	A-6003782	C—A	Pro—Gln	Missense	Hypothetical protein J604-3711	NA
Case 2	A-45003484	T—A	Glu—Asp	Missense	3-oxoadipate CoA-transferase subunit A	I
	A-45001662	T—A	Glu—Asp	Missense	3-oxoadipate CoA-transferase subunit A	I
Case 3	A-76003056	T—A	Tyr—Asn	Missense	Hypothetical protein	NA
	A-76003660	T—G	Lys—Gln	Missense	TMP	D
	A-76003686	A—T	Leu—Phe	Missense	ahpF	C
Case 4	A-140003692	C—T	Arg—Lys	Missense	Integrase	L
	A-140003805	T—C	Ile—Val	Missense	Hypothetical protein ABAYE1233	NA
	A-140003815	C—G	Ser—Thr	Missense	ahpF	C
Case 5	A-172003570	A—G	Leu—Ser	Missense	TMP	NA
Case 6	A-225002091	C—T	Ser—Leu	Missense	rpoB (RNA polymerase subunit B)	K
	A-225001841	A—G	Val—Ala	Missense	Histidine kinase	T
Case 7	A-231000349	T—C	X—Trp	Stop codon mutation	pdaA	G
	A-231003655	T—C	Ser—Pro	Missense	Transposase and inactivated derivatives	L
	A-231003655	C—G	Ser—Cys	Missense	Transposase and inactivated derivatives	L
	A-231003655	A—T	Leu—Phe	Missense	Transposase and inactivated derivatives	L
	A-231003655	A—C	Ile—Leu	Missense	Transposase and inactivated derivatives	L
	A-231001249	T—G	Lys—Asn	Missense	Ata	UW
Case 8	A-339001866	G—A	Arg—Cys	Missense	DUF932 domain-containing protein	NA
	A-339001875	G—A	Arg—Cys	Missense	DUF932 domain-containing protein	NA

Notes: SNPs of the genomes were identified by mapping sequence reads for each bloodstream isolate against the corresponding respiratory isolate in each patient.

Abbreviations: X, unknown amino acid; nonsyn, non-synonymous; C—T, the base of the respiratory sample changed from C into T in bacteremia. Functional classification: NA, unknown function; C, energy production and conversion; D, cell cycle control, cell division, chromosome partitioning; G, carbohydrate transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; W, extracellular structures.