tet(X4)

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Accession	ARO:3004720
Synonym(s)	tetX4
CARD Short Name	tet(X4)
Definition	A tetracyline resistance gene located on an approximately 180-kb plasmid, designated p47EC. It inactivates all tetracyclines, including tigecycline, eravacycline, and omadacycline.Adjacent to insertion sequence ISVsa3 on the conjugative plasmid.
AMR Gene Family	tetracycline inactivation enzyme
Drug Class	tetracycline antibiotic, glycylcycline
Resistance Mechanism	antibiotic inactivation
Resistomes with Perfect Matches	Acinetobacter indicus^g+wgs, Acinetobacter towneri^g, Aeromonas caviae^g, Aeromonas hydrophila^g, Citrobacter freundii^p+wgs, Citrobacter portucalensis^wgs, Citrobacter werkmanii^p, Enterobacter cloacae^p, Enterobacter hormaechei^p+wgs, Escherichia coli^p+wgs, Escherichia fergusonii^p+wgs, Klebsiella aerogenes^p, Klebsiella michiganensis^p+wgs, Klebsiella pneumoniae^p+wgs, Klebsiella quasipneumoniae^p+wgs, Morganella morganii^wgs, Proteus mirabilis^wgs, Proteus vulgaris^wgs, Salmonella enterica^p+wgs, Shigella flexneri^wgs
Resistomes with Sequence Variants	Acinetobacter indicus^g+wgs, Acinetobacter towneri^g, Aeromonas caviae^g, Aeromonas hydrophila^g, Bacteroides ovatus^wgs, Bacteroides thetaiotaomicron^wgs, Citrobacter freundii^p+wgs, Citrobacter portucalensis^wgs, Citrobacter werkmanii^p, Enterobacter cloacae^p, Enterobacter hormaechei^p+wgs, Escherichia coli^p+wgs, Escherichia fergusonii^p+wgs, Klebsiella aerogenes^p+wgs, Klebsiella michiganensis^p+wgs, Klebsiella pneumoniae^p+wgs, Klebsiella quasipneumoniae^p+wgs, Morganella morganii^wgs, Myroides phaeus^g, Proteus mirabilis^p+wgs, Proteus vulgaris^wgs, Riemerella anatipestifer^g+p+wgs, Salmonella enterica^p+wgs, Shigella flexneri^wgs
Classification	9 ontology terms \| Show + process or component of antibiotic biology or chemistry + antibiotic molecule + mechanism of antibiotic resistance + tetracycline antibiotic [Drug Class] + determinant of antibiotic resistance + antibiotic inactivation [Resistance Mechanism] + antibiotic inactivation enzyme + hydroxylation of antibiotic conferring resistance + glycylcycline [Drug Class]
Parent Term(s)	3 ontology terms \| Show + confers_resistance_to_antibiotic tigecycline [Antibiotic] + confers_resistance_to_antibiotic tetracycline [Antibiotic] + tetracycline inactivation enzyme [AMR Gene Family]
Publications	He T, et al. 2019. Nat Microbiol : Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans. (PMID 31133751)

Resistomes

Prevalence of tet(X4) among the sequenced genomes, plasmids, and whole-genome shotgun assemblies available at NCBI or IslandViewer for 414 important pathogens (see methodological details and complete list of analyzed pathogens). Values reflect percentage of genomes, plasmids, genome islands, or whole-genome shotgun assemblies that have at least one hit to the AMR detection model. Default view includes percentages calculated based on Perfect plus Strict RGI hits. Select the checkbox to view percentages based on only Perfect matches to AMR reference sequences curated in CARD (note: this excludes resistance via mutation as references in protein variant models are often wild-type, sensitive sequences).

Prevalence: protein homolog model (view sequences)

Species	NCBI Chromosome	NCBI Plasmid	NCBI WGS	NCBI GI	GRDI-AMR2
Acinetobacter indicus	14.29%	0%	7.79%	0%	0%
Acinetobacter indicus	14.29%	0%	3.9%	0%	0%
Acinetobacter towneri	12.5%	0%	0%	0%	0%
Acinetobacter towneri	12.5%	0%	0%	0%	0%
Aeromonas caviae	2.27%	0%	0%	0%	0%
Aeromonas caviae	2.27%	0%	0%	0%	0%
Aeromonas hydrophila	1.54%	0%	0%	0%	0%
Aeromonas hydrophila	1.54%	0%	0%	0%	0%
Bacteroides ovatus	0%	0%	3.04%	0%	0%
Bacteroides ovatus	0%	0%	0%	0%	0%
Bacteroides thetaiotaomicron	0%	0%	0.35%	0%	0%
Bacteroides thetaiotaomicron	0%	0%	0%	0%	0%
Citrobacter freundii	0%	0.31%	0.97%	0%	0%
Citrobacter freundii	0%	0.31%	0.97%	0%	0%
Citrobacter portucalensis	0%	0%	2.7%	0%	0%
Citrobacter portucalensis	0%	0%	2.7%	0%	0%
Citrobacter werkmanii	0%	10%	0%	0%	0%
Citrobacter werkmanii	0%	10%	0%	0%	0%
Enterobacter cloacae	0%	0.56%	0%	0%	0%
Enterobacter cloacae	0%	0.56%	0%	0%	0%
Enterobacter hormaechei	0%	0.06%	0.26%	0%	0%
Enterobacter hormaechei	0%	0.06%	0.26%	0%	0%
Escherichia coli	0%	0.47%	1.95%	0%	0%
Escherichia coli	0%	0.46%	1.93%	0%	0%
Escherichia fergusonii	0%	0.71%	3.26%	0%	0%
Escherichia fergusonii	0%	0.71%	3.26%	0%	0%
Klebsiella aerogenes	0%	2.17%	0.28%	0%	0%
Klebsiella aerogenes	0%	1.09%	0%	0%	0%
Klebsiella michiganensis	0%	0.57%	0.53%	0%	0%
Klebsiella michiganensis	0%	0.57%	0.53%	0%	0%
Klebsiella pneumoniae	0%	0.07%	0.08%	0%	0%
Klebsiella pneumoniae	0%	0.07%	0.08%	0%	0%
Klebsiella quasipneumoniae	0%	0.21%	1.05%	0%	0%
Klebsiella quasipneumoniae	0%	0.21%	1.05%	0%	0%
Morganella morganii	0%	0%	1.23%	0%	0%
Morganella morganii	0%	0%	1.23%	0%	0%
Myroides phaeus	0%	0%	0%	0%	0%
Myroides phaeus	100%	0%	0%	0%	0%
Proteus mirabilis	0%	1.25%	0.17%	0%	0%
Proteus mirabilis	0%	0%	0.17%	0%	0%
Proteus vulgaris	0%	0%	5.56%	0%	0%
Proteus vulgaris	0%	0%	5.56%	0%	0%
Riemerella anatipestifer	0%	0%	0%	0%	0%
Riemerella anatipestifer	86.11%	15.38%	68.06%	0%	0%
Salmonella enterica	0%	0.05%	0.03%	0%	0%
Salmonella enterica	0%	0.05%	0.03%	0%	0%
Shigella flexneri	0%	0%	0.16%	0%	0%
Shigella flexneri	0%	0%	0.16%	0%	0%

Show Perfect Only

Detection Models

protein homolog model

Model Type: protein homolog model

Model Definition: Protein Homolog Models (PHM) detect protein sequences based on their similarity to a curated reference sequence, using curated BLASTP bitscore cut-offs. Protein Homolog Models apply to all genes that confer resistance through their presence in an organism, such as the presence of a beta-lactamase gene on a plasmid. PHMs include a reference sequence and a bitscore cut-off for detection using BLASTP. A Perfect RGI match is 100% identical to the reference protein sequence along its entire length, a Strict RGI match is not identical but the bit-score of the matched sequence is greater than the curated BLASTP bit-score cutoff, Loose RGI matches have a bit-score less than the curated BLASTP bit-score cut-off.

Bit-score Cut-off (blastP): 700

Protein
DNA

>gb|QBQ69719.1|-|tet(X4) [Escherichia coli]
MSNKEKQMNLLSDKNVAIIGGGPVGLTMAKLLQQNGIDVSVYERDNDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLALPMGVNIAD
EKGNILSTKNVKPENRFDNPEINRNDLRAILLNSLENDTVIWDRKLVMLEPGKKKWTLTFENKPSETADLVIIANGGMSKVRKFVTDTEV
EETGTFNIQADIHHPEVNCPGFFQLCNGNRLMAAHQGNLLFANPNNNGALHFGISFKTPDEWKNQTQVDFQNRNSVVDFLLKEFSDWDER
YKELIRVTSSFVGLATRIFPLGKSWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLMDALILSDNLTNGKFNSIEEAIENYEQQMFIYGKE
AQEESTQNEIEMFKPDFTFQQLLNV

>gb|MK134376.1|-|325-1482|tet(X4) [Escherichia coli]
ATGAGCAATAAAGAAAAACAAATGAATTTACTTAGTGATAAGAACGTTGCAATAATTGGTGGTGGACCCGTTGGACTGACTATGGCAAAA
TTATTACAGCAAAACGGCATAGACGTTTCAGTTTACGAAAGAGACAACGACCGAGAGGCAAGAATTTTTGGTGGAACCCTTGACCTACAC
AAAGGTTCAGGTCAGGAAGCAATGAAAAAAGCGGGATTGTTACAAACTTATTATGACTTAGCCTTACCAATGGGTGTAAATATTGCTGAT
GAAAAAGGCAATATTTTATCCACAAAAAATGTAAAGCCCGAAAATCGATTTGACAATCCTGAAATAAACAGAAATGACTTAAGGGCTATC
TTGTTGAATAGTTTAGAAAACGACACGGTTATTTGGGATAGAAAACTTGTTATGCTTGAACCTGGTAAGAAGAAGTGGACACTAACTTTT
GAGAATAAACCGAGTGAAACAGCAGATCTGGTTATTATTGCCAATGGTGGAATGTCTAAAGTAAGAAAATTTGTTACCGACACGGAAGTT
GAAGAAACAGGTACTTTCAATATACAAGCCGATATTCATCATCCAGAGGTGAACTGTCCTGGATTTTTTCAGCTATGCAATGGAAACCGG
CTAATGGCTGCTCATCAAGGTAATTTATTATTTGCGAATCCTAATAATAATGGTGCATTGCATTTTGGAATAAGTTTTAAAACACCTGAT
GAATGGAAAAACCAAACGCAGGTAGATTTTCAAAACAGAAATAGTGTCGTTGATTTTCTTCTGAAAGAATTTTCCGATTGGGACGAACGC
TACAAAGAACTGATTCGTGTGACATCATCTTTTGTAGGGTTAGCGACACGAATATTTCCCTTAGGTAAGTCTTGGAAAAGTAAGCGTCCA
TTACCCATAACGATGATTGGAGATGCTGCTCATTTGATGCCTCCTTTTGCAGGACAAGGCGTAAACAGCGGGTTGATGGATGCCTTGATA
TTGTCGGATAATCTGACCAATGGGAAATTTAACAGCATTGAAGAGGCTATTGAAAATTATGAACAGCAAATGTTTATCTATGGCAAAGAA
GCACAAGAAGAATCAACTCAAAACGAAATTGAAATGTTTAAACCCGACTTTACGTTTCAGCAATTGTTAAATGTATAA

Curator Acknowledgements

Curator	Description	Most Recent Edit

tet(X4)

Prevalence: protein homolog model (view sequences)

Graph