Advances in the Discovery of Novel Antibiotic-resistant Genes Based on Functional Metagenomics

doi:10.13560/j.cnki.biotech.bull.1985.2022-0537

Abstract

Abstract:

The widespread use of various antibiotics in the treatment of bacterial infections and the widespread clinical use of antibiotics drives the continuous evolution of various antibiotic resistance genes（ARGs）, leading to the increasing problem of drug resistance. The global spread of antibiotic-resistant genes and bacteria severely threatens the public health and results in tremendous economic losses in recent decades. Of note, the excessive usage of antibiotics not only led to the occurrence of antibiotics-resistant bacteria, but also constitutively elevated the selection pressure of environmental microbiome, indirectly accelerated the development and evolution of antibiotics-resistant genes, making environmental microbiome as the storage reservoir of antibiotics-resistant genes. Therefore, the extensive monitoring of antibiotics-resistant bacteria and the early exploration of new antibiotics-resistant genes are of great clinical significance and research value. However, traditional methodologies for ARGs identification and profiling largely depend on the molecular characterization of cultivable bacteria, hardly providing a comprehensive landscape of the resistome in a given ecological niche. To cope with the increasing necessity to uncover the ARGs in uncultivable bacteria, the functional metagenomics emerged as a promising toolkit that combines the phenotypic profiling with next high-throughput sequencing, it does not depend on the culture of specific bacteria with target genes, and thus it is deemed as a powerful alternative to reveal all novel functional genes. In the present review, we systematically summarized the latest advances in the field of functional metagenomics and dated their recent applications in unveiling the unknown ARGs from environments. This review offers a solid theoretical foundation for in-depth understanding the resistant mechanism of antibiotics.

Key words: functional metagenomics, environmental microbiome, novel resistance genes, antibiotic

LU Zhao-xiang, WANG Xi-ran, LIAN Xin-lei, LIAO Xiao-ping, LIU Ya-hong, SUN Jian. Advances in the Discovery of Novel Antibiotic-resistant Genes Based on Functional Metagenomics[J]. Biotechnology Bulletin, 2022, 38(9): 17-27.

Figures/Tables 3

References 76

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抗生素类别 Class of antibiotic	药物 Drug	耐药率 Resistance rate/%	参考文献 Reference
β-内酰胺类 β-lactam antibiotics	头孢曲松 Ceftriaxone	81	[10]
	头孢他啶 Ceftazidime	87.5
	美罗培南 Meropenem	99.7
	氨苄西林 Ampicillin	97.5	[11]
	头孢哌酮-舒巴坦Cefperazone-sulbactam	98.9
	哌拉西林-他唑巴坦Piperacillin-tazobactam	98.9
	头孢吡肟 Cefepime	100	[21]
四环素类 Tetracyclines	四环素 Tetracycline	85.0	[16]
	替加环素 Tigecycline	98.9	[11]
大环内酯类 Macrolides	红霉素 Erythrocin	74.1	[22]
	螺旋霉素I Spiramycin I	48.1
	阿奇霉素 Azithromycin	74.1
	克拉霉素 Clarithromycin	74.1
林可酰胺类Lincoamide antibiotics	林可霉素 Lincomycin	77.8
酮内酯类 Ketolide antibiotics	泰立霉素 Telithromycin	77.8
氨基糖苷类 Aminoglycosides	阿米卡星 Amikacin	100	[21]
	庆大霉素 Gentamicin	31.4	[11]
多磷类 Polyphosphorous	磷霉素 Fosfomycin	66.7
多黏菌素类 Polymyxins	黏菌素 Colistin	73.3
磺胺类药物 Sulfonamides	复方磺胺甲恶唑 Sulfadimidine	53.3
喹诺酮类 Quinolones	环丙沙星 Ciprofloxacin	93.3
	左氧氟沙星 Levofloxacin	100	[21]

抗生素类别 Class of antibiotic	药物 Drug	耐药率 Resistance rate/%	参考文献 Reference
β-内酰胺类 β-lactam antibiotics	头孢曲松 Ceftriaxone	81	[10]
	头孢他啶 Ceftazidime	87.5
	美罗培南 Meropenem	99.7
	氨苄西林 Ampicillin	97.5	[11]
	头孢哌酮-舒巴坦Cefperazone-sulbactam	98.9
	哌拉西林-他唑巴坦Piperacillin-tazobactam	98.9
	头孢吡肟 Cefepime	100	[21]
四环素类 Tetracyclines	四环素 Tetracycline	85.0	[16]
	替加环素 Tigecycline	98.9	[11]
大环内酯类 Macrolides	红霉素 Erythrocin	74.1	[22]
	螺旋霉素I Spiramycin I	48.1
	阿奇霉素 Azithromycin	74.1
	克拉霉素 Clarithromycin	74.1
林可酰胺类Lincoamide antibiotics	林可霉素 Lincomycin	77.8
酮内酯类 Ketolide antibiotics	泰立霉素 Telithromycin	77.8
氨基糖苷类 Aminoglycosides	阿米卡星 Amikacin	100	[21]
	庆大霉素 Gentamicin	31.4	[11]
多磷类 Polyphosphorous	磷霉素 Fosfomycin	66.7
多黏菌素类 Polymyxins	黏菌素 Colistin	73.3
磺胺类药物 Sulfonamides	复方磺胺甲恶唑 Sulfadimidine	53.3
喹诺酮类 Quinolones	环丙沙星 Ciprofloxacin	93.3
	左氧氟沙星 Levofloxacin	100	[21]

样品来源 Source	抗生素种类及其耐药基因ARGs and associated antibiotics						参考文献Reference
样品来源 Source	酰胺醇类 Phenicols	氨基糖苷类 Aminoglycosides	β-内酰胺类 β-lactam antibiotics	四环素类 Tetracyclines	多药耐药 Multidrug resistance	其他 Others	参考文献Reference
土壤 Soil	AAT、aadA、A3PH、aphD、ARPA、KNT、FAT、HARK、APT、ARPB、aac6、aadB、 GAT、GRP、aac、strA	CAT、catB2、catB3、ceoB、CFE、CFRP、cmlA、cmx、CRD、CT、floR	ACT-1、ampc、CARB、L1、mecA、OXA、PSE-1、Sed1、TEM-21、VIM-18	tet32、tetA、tetA（31）、tetA（33）、tetA（39）、tetA（41）、tetA（B）、tetA（D）、tetA（G）、tetA（M）、tetA（P）、tetB、tetG、tetH、etL、tetM、tetO、tetQ、tetS、tetT、tetV、tetW、tetX、tetX2、tetY	acrA、acrB、adeA、adeB、AmrB、bpeF、ermFS、ermG、ermGM、ermT、ermX、mdfA、mdtF、mdtH、mdtL、mdtO、mef、mexA、mexB、mexD、mexE、mexF、mexG、MLSRP、msrA、oprN、Rpos、sdeY	AcRPB、AFRPB、AEP、AcRPA、AFRPA、fosB、FRP、rosA	[56]
			1,2-GDO				[57]
	3-NAT、6-NAT					ARTs	[52]
	AAT		Class A、B、C、D、Metallo beta-lactamase				[58]
			Bifunctional beta-lactamase				[52]
	2-NAT、2-OXO-DH、3-NAT、6-NAT、AAdT、ATIII、EEL、FAA、GBD、HAD、ICMT、ML、PM、NSDH、TL、tRNAs			AL、STK、otrC、tet（34）、tet（37）、tetV、tetX	ABC、RND		[59]
水 Water	aacA4、aadA、aadB、ereA、strA、strB	ceoB、cmlA	blaA	tet33、tet34、tetC、tetL、tetM、tetX	acrB、mexB、mexF	smeE、ermF、macB、bacA、sul1、sul2	[60]
	strA、strB			tetL		qnrA、mfeE mphB	[61]
	K⁺ transport ptn、3-NAT、PDH、GNAT、AAdt、A3PH、6-NAT、GT、MetRS		TEM beta-lactamase			RecX、RA	[62]
污泥 Sludge	aa6iia、aac6ib、aadD、ant2ia、ant3ia、ant6ia、aph33ib、aph6id、ereA	catB3、ceoB、cml_e3、cmle_8	bl2D_pse3、bl2D_oxa5、bl2_veb、bl2D_oxa10	tet32、tet33、tetA、tetC、tetG、tetO、tetPa、tetPb、tetV、tetW、tetX	acrB、ermB、ermC、ermQ、ermT、mdtF、mexB、mexD、mexF、mexW、mexY	smeB、smeE、lnuA、macB、mefA、rosA、rosB、bacA、arnA、sul1、sul2	[63]
	aac、aadA、AGRPA、aph		Class A BL、NPS-1、 OXA-1、OXA-10、OXA-2、VEB-5	tet39、tetA、tetC、tetG、tetM、tetO、tetP、tetS、tetW、tetX			[64]
	aadA、aadB、aphA-2、strA、strB	catB、cmlA、floR	blaCFX-a、laOXA-10、 blaVEB-5、blaVEB-3	tet33、tet36、tet39、tet40、tetA（P）、tetB（P）、tetG、tetM、tetO、tetW	acrB、adeA、ermB、mdtF、mexB、mexF、mexW	smeB、smeE、macB、bacA、sul1、sul2	[53]
			blaDWA、blaDWA2、blaDWA3、blaDWA4、blaDWB1				[65]

样品来源 Source	抗生素种类及其耐药基因ARGs and associated antibiotics						参考文献Reference
样品来源 Source	酰胺醇类 Phenicols	氨基糖苷类 Aminoglycosides	β-内酰胺类 β-lactam antibiotics	四环素类 Tetracyclines	多药耐药 Multidrug resistance	其他 Others	参考文献Reference
土壤 Soil	AAT、aadA、A3PH、aphD、ARPA、KNT、FAT、HARK、APT、ARPB、aac6、aadB、 GAT、GRP、aac、strA	CAT、catB2、catB3、ceoB、CFE、CFRP、cmlA、cmx、CRD、CT、floR	ACT-1、ampc、CARB、L1、mecA、OXA、PSE-1、Sed1、TEM-21、VIM-18	tet32、tetA、tetA（31）、tetA（33）、tetA（39）、tetA（41）、tetA（B）、tetA（D）、tetA（G）、tetA（M）、tetA（P）、tetB、tetG、tetH、etL、tetM、tetO、tetQ、tetS、tetT、tetV、tetW、tetX、tetX2、tetY	acrA、acrB、adeA、adeB、AmrB、bpeF、ermFS、ermG、ermGM、ermT、ermX、mdfA、mdtF、mdtH、mdtL、mdtO、mef、mexA、mexB、mexD、mexE、mexF、mexG、MLSRP、msrA、oprN、Rpos、sdeY	AcRPB、AFRPB、AEP、AcRPA、AFRPA、fosB、FRP、rosA	[56]
			1,2-GDO				[57]
	3-NAT、6-NAT					ARTs	[52]
	AAT		Class A、B、C、D、Metallo beta-lactamase				[58]
			Bifunctional beta-lactamase				[52]
	2-NAT、2-OXO-DH、3-NAT、6-NAT、AAdT、ATIII、EEL、FAA、GBD、HAD、ICMT、ML、PM、NSDH、TL、tRNAs			AL、STK、otrC、tet（34）、tet（37）、tetV、tetX	ABC、RND		[59]
水 Water	aacA4、aadA、aadB、ereA、strA、strB	ceoB、cmlA	blaA	tet33、tet34、tetC、tetL、tetM、tetX	acrB、mexB、mexF	smeE、ermF、macB、bacA、sul1、sul2	[60]
	strA、strB			tetL		qnrA、mfeE mphB	[61]
	K⁺ transport ptn、3-NAT、PDH、GNAT、AAdt、A3PH、6-NAT、GT、MetRS		TEM beta-lactamase			RecX、RA	[62]
污泥 Sludge	aa6iia、aac6ib、aadD、ant2ia、ant3ia、ant6ia、aph33ib、aph6id、ereA	catB3、ceoB、cml_e3、cmle_8	bl2D_pse3、bl2D_oxa5、bl2_veb、bl2D_oxa10	tet32、tet33、tetA、tetC、tetG、tetO、tetPa、tetPb、tetV、tetW、tetX	acrB、ermB、ermC、ermQ、ermT、mdtF、mexB、mexD、mexF、mexW、mexY	smeB、smeE、lnuA、macB、mefA、rosA、rosB、bacA、arnA、sul1、sul2	[63]
	aac、aadA、AGRPA、aph		Class A BL、NPS-1、 OXA-1、OXA-10、OXA-2、VEB-5	tet39、tetA、tetC、tetG、tetM、tetO、tetP、tetS、tetW、tetX			[64]
	aadA、aadB、aphA-2、strA、strB	catB、cmlA、floR	blaCFX-a、laOXA-10、 blaVEB-5、blaVEB-3	tet33、tet36、tet39、tet40、tetA（P）、tetB（P）、tetG、tetM、tetO、tetW	acrB、adeA、ermB、mdtF、mexB、mexF、mexW	smeB、smeE、macB、bacA、sul1、sul2	[53]
			blaDWA、blaDWA2、blaDWA3、blaDWA4、blaDWB1				[65]