Whole-genome sequencing analysis on drug resistance and virulence genes of carbapenem-resistant Acinetobacter baumannii

doi:10.3877/cma.j.issn.1674-1358.2020.05.003

Abstract

Abstract:

Objective

To definite the distribution and molecular characteristics of drug resistance genes and virulence genes in clonal complex 92 (CC92) which was a major epidemic strain of carbapenem-resistant Acinetobacter baumannii (CRAB).

Methods

Total of 33 strains of CRAB from different clinical samples during January to July, 2019 in Beijing Ditan Hospital, Capital Medical University were analyzed by whole genome sequencing analysis. The quality of the whole genome sequencing data were modified by CLC Genomics Workbench v10.0 software, then the sequence splicing, assembly and annotation were carried out, and the drug resistance genes and virulence genes were studied, and the distribution of the drug resistance genes and virulence genes carried by CRAB of the genome of the clone complex group were analyzed.

Results

The analysis of whole genome sequence of CRAB showed that among 33 strains of CRAB, 30 strains belonged to CC92, including ST195, ST208, ST369 and ST540. Two strains belonged to ST229, and the other one was identified as a new sequence type which had not been reported internationally. The analysis of the drug resistance genes showed the genome of these CRAB strains carried 8-18 drug resistance genes, covering carbapenem, macrolides, tetracycline, streptomycin resistance genes, etc and 12 kinds of virulence genes, which encoded adherence-related protein and invasion-related protein, etc. Meanwhile, the CC92 clone complex carried not only carbapenem resistance genes, but also other drug resistance genes (such as bla_OXA-66 and bla_TEM-1D) and virulence genes (such as bauA and bap) which cannot be found in non-CC92 clone complex. In addition, potential genetic integrations in macrolides [msr(E) and mph (E)], aminoglycoside (armA), streptomycin (strA, strB) and tetracycline [tet(B)] drug-resistance genes in CC92 genome were found.

Conclusions

CC92 carried a large number of drug-resistance genes and virulence genes, exhibited gene integration phenomenon which requires further investigation. An urgent need for clinical CRAB whole genomic surveillance should be carried out in order to provide the necessary basis for the diagnosis and treatment of clinical pathogens.

Key words: Carbapenem-resistant Acinetobacter baumannii, Drug resistence, Virulence

Xinzhe Liu, Mingxi Hua, Huizhu Wang, Pengcheng Du, Xinmin Xu, Haofeng Xiong, Ang Li, Chen Chen. Whole-genome sequencing analysis on drug resistance and virulence genes of carbapenem-resistant Acinetobacter baumannii[J]. Chinese Journal of Experimental and Clinical Infectious Diseases(Electronic Edition), 2020, 14(05): 367-373.

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References 30

[1]	张银维. 鲍曼不动杆菌血流感染临床特征和死亡危险因素研究[D]. 浙江大学. 2016.
[2]	陈佰义，何礼贤，胡必杰, 等. 中国鲍曼不动杆菌感染诊治与防控专家共识[J]. 中国医药科学,2012,2(8):13-18.
[3]	Peleg AY, Seifert H, Paterson DL. Acinetobacter baumannii: emergence of a successful pathogen[J]. Clin Microbiol Rev,2008,21(3):538-582.
[4]	Vijayakumar S, Mathur P, Kapil A, et al. Molecular characterization & epidemiology of carbapenem-resistant Acinetobacter baumannii collected across India[J]. Indian J Med Res,2019,149(2):240-246.
[5]	王金良. 密切注视鲍曼不动杆菌的耐药发展趋势[J]. 中华检验医学杂志,2005,28(4):355-356.
[6]	Correa A, Del Campo R, Escandón-Vargas K, et al. Distinct genetic diversity of carbapenem-resistant Acinetobacter baumannii from Colombian hospitals[J]. Microb Drug Resist,2017,24(1):48-54.
[7]	杨均均，黄文祥，史芳静, 等. 耐碳青霉烯鲍曼不动杆菌流行特征及耐药基因分析[J]. 中国抗生素杂志,2012,37(5):343-347.
[8]	Wong D, Nielsen TB, Bonomo RA, et al. Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges[J]. Clin Microbiol Rev,2017,30(1):409-447.
[9]	Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing. Twenty-fourth informational supplement[S]. CLSI document, approved standard M100-S24. Wayne (PA): The Institute; 2014.
[10]	Bartual SG, Seifert H, Hippler C, et al. Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii[J]. J Clin Microbiol,2005,43(9):4382-4390.
[11]	凌保东. 鲍曼不动杆菌抗生素多重耐药性:耐药机制与感染治疗对策[J]. 中国抗生素杂志,2010,35(4):241-254.
[12]	Aly MM, Abu Alsoud NM, Elrobh MS, et al. High prevalence of the PER-1 gene among carbapenem-resistant Acinetobacter baumanniiin Riyadh, Saudi Arabia[J]. Eur J Clin Microbiol,2016,35(11):1759-1766.
[13]	Biglari S, Hanafiah A, Mohd Puzi S, et al. Antimicrobial resistance mechanisms and genetic diversity of multidrug-resistant Acinetobacter baumannii isolated from a teaching hospital in Malaysia[J]. Microb Drug Resist,2017,23(5):545-555.
[14]	Lee CR, Lee JH, Park KS, et al. Quantitative proteomic view associated with resistance to clinically important antibiotics in Gram-positive bacteria: a systematic review[J]. Front Microbiol,2015,6:828.
[15]	Liu Y, Liu X. Detection of AmpC β-lactamases in Acinetobacter baumannii in the Xuzhou region and analysis of drug resistance[J]. Exp Ther Med,2015,10(3):933-936.
[16]	Corvec S, Poirel L, Naas T, et al. Genetics and expression of the carbapenem-hydrolyzing oxacillinase gene blaOXA-23 in Acinetobacter baumannii[J]. Antmicrob Agents Ch,2007,51(4):1530-1533.
[17]	Nigro SJ, Hall RM. Structure and context of Acinetobacter transposons carrying the oxa23 carbapenemase gene[J]. J Antimicrob Chemoth,2016,71(5):1135-1147.
[18]	Fournier PE, Vallenet D, Barbe V, et al. Comparative genomics of multidrug resistance in Acinetobacter baumannii[J]. PLoS Genet,2006,2(1):62-72.
[19]	姜旻，孟现民，赵赟. 浅析近十年我国鲍曼不动杆菌检出率和耐药性变化[J]. 世界临床药物,2016,37(4):254-257.
[20]	Smani Y, Fàbrega A, Roca I, et al. Role of OmpA in the multidrug resistance phenotype of Acinetobacter baumannii[J]. Antmicrob Agents Ch,2014,58(3):1806-1808.
[21]	李志涛，张扣兴. 鲍曼不动杆菌的致病力毒力因素[J]. 中国抗生素杂志,2014,39(8):566-570.
[22]	McConnell M J, Actis L, Pachón J. Acinetobacter baumannii: human infections, factors contributing to pathogenesis and animal models[J]. Fems Microbiol Rev,2013,37(2):130-155.
[23]	Vila-Farrés X, Ferrer-Navarro M, Callarisa AE, et al. Loss of LPS is involved in the virulence and resistance to colistin of colistin-resistant Acinetobacter nosocomialis mutants selected in vitro[J]. J Antimicrob Chemoth,2015,70(11):2981-2986.
[24]	Harding CM, Hennon SW, Feldman MF. Uncovering the mechanisms of Acinetobacter baumannii virulence[J]. Nat Rev Microbiol,2018,16(2):91.
[25]	Ali HM, Salem MZM, El-Shikh MS, et al. Investigation of the virulence factors and molecular characterization of the clonal relations of multidrug-resistant Acinetobacter baumannii isolates[J]. J Aoac Int,2017,100(1):152-158.
[26]	Lee CR, Lee JH, Park M, et al. Biology of Acinetobacter baumannii: pathogenesis, antibiotic resistance mechanisms, and prospective treatment options[J]. Front Cell Infect Microbiol,2017,7:55.
[27]	马晓春，代军，徐磊, 等. 鲍曼不动杆菌生物膜形成机制研究进展[J]. 中国感染与化疗杂志,2018,18(1):124-128.
[28]	Gaddy JA, Arivett BA, McConnell MJ, et al. Role of acinetobactin-mediated iron acquisition functions in the interaction of Acinetobacter baumannii strain ATCC 19606T with human lung epithelial cells, Galleria mellonella caterpillars, and mice[J]. Infect Immun,2012,80(3):1015-1024.
[29]	Penwell WF, Arivett BA, Actis LA. The Acinetobacter baumannii entA gene located outside the Acinetobactin cluster is critical for siderophore production, iron acquisition and virulence[J]. PLoS One,2012,7(5):e36493.
[30]	Parsek MR, Fuqua C. Biofilms 2003: Emerging themes and challenges in studies of surface-associated microbial life[J]. J Bacteriol, 2004,186(14):4427-4440.

抗菌药物	R	I	S
氨苄西林	100.00	0.00	0.00
阿莫西林	93.94	0.00	6.06
哌拉西林	100.00	0.00	0.00
阿米卡星	90.91	6.06	3.03
氨曲南	100.00	0.00	0.00
头孢他定	100.00	0.00	0.00
头孢噻肟	100.00	0.00	0.00
头孢唑林	100.00	0.00	0.00
头孢吡肟	100.00	0.00	0.00
美洛配能	100.00	0.00	0.00
亚胺培南	100.00	0.00	0.00
环丙沙星	100.00	0.00	0.00
左旋氧氟沙星	96.97	3.03	0.00
氨苄西林	100.00	0.00	0.00
哌拉西林	100.00	0.00	0.00
复方磺胺	93.94	3.03	3.03
四环素	96.97	0.00	3.03

抗菌药物	R	I	S
氨苄西林	100.00	0.00	0.00
阿莫西林	93.94	0.00	6.06
哌拉西林	100.00	0.00	0.00
阿米卡星	90.91	6.06	3.03
氨曲南	100.00	0.00	0.00
头孢他定	100.00	0.00	0.00
头孢噻肟	100.00	0.00	0.00
头孢唑林	100.00	0.00	0.00
头孢吡肟	100.00	0.00	0.00
美洛配能	100.00	0.00	0.00
亚胺培南	100.00	0.00	0.00
环丙沙星	100.00	0.00	0.00
左旋氧氟沙星	96.97	3.03	0.00
氨苄西林	100.00	0.00	0.00
哌拉西林	100.00	0.00	0.00
复方磺胺	93.94	3.03	3.03
四环素	96.97	0.00	3.03

抗菌药物	耐药基因
碳青霉烯类/β-内酰胺类	bla_OXA-23
	bla_ADC25
	bla_OXA-64
	bla_OXA-66
	bla_PER-7
	blaT_MP-1D
氨基糖苷类	aph3
	aac3-Ia
	aac3-IIa
	ant3/aac-6
	aadA1
	AAR2
	armA
链霉素类	strA
链霉素类	strB
四环素类	tet（B）
磺胺类	sul1
磺胺类	sul2
大环内酯类	msr（E）
大环内酯类	mph（E）
氯霉素	cml（A1）
	catB

抗菌药物	耐药基因
碳青霉烯类/β-内酰胺类	bla_OXA-23
	bla_ADC25
	bla_OXA-64
	bla_OXA-66
	bla_PER-7
	blaT_MP-1D
氨基糖苷类	aph3
	aac3-Ia
	aac3-IIa
	ant3/aac-6
	aadA1
	AAR2
	armA
链霉素类	strA
链霉素类	strB
四环素类	tet（B）
磺胺类	sul1
磺胺类	sul2
大环内酯类	msr（E）
大环内酯类	mph（E）
氯霉素	cml（A1）
	catB

毒力基因	基因名称
Acinetobactin	Acinetobactin（entE）
	Acinetobactin（bauF）
	Acinetobactin（bauD）
	Acinetobactin（bauE）
	Acinetobactin（bauC）
	Acinetobactin（bauB）
	Acinetobactin（bauA）
	Acinetobactin（basJ）
	Acinetobactin（basI）
	Acinetobactin（basH）
	Acinetobactin（basG）
	Acinetobactin（basF）
	Acinetobactin（basD）
	Acinetobactin（basC）
	Acinetobactin（basB）
	Acinetobactin（basA）
	Acinetobactin（barB）
	Acinetobactin（barA）
Capsule	ACICU-00071
	ACICU-00072
	ACICU-00073
	ACICU-00074
	ACICU-00075
	ACICU-00076
	ACICU-00077
	ACICU-00078
	ACICU-00079
	ACICU-00080
	ACICU-00081
	ACICU-00082
	ACICU-00083
	ACICU-00084
	ACICU-00085
	ACICU-00086
	ACICU-00087
	ACICU-00088
	ACICU-00089
	ACICU-00090
	ACICU-00091
Csu-filbriae	csuA
	csuB
	csuA/B
	csuC
	csuD
	csuE
LPS	lpxM
	lpxL
	lpxD
	lpxC
	lpxB
	lpxA
	lspD
PNAG	pgaD
	pgaC
	pgaB
	pgaA
Phospholipases	plcD
	plcD
Quorum-sensing system	Quorum-sensing system
BAP	bap
OmpA	ompA
pbpG	pbpG
Adefgh efflux pumps	adhH
	adhG
	adhF
BfmRS	bfmS
	bfmR

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