Abbreviation/Code	Definition
aac(6′)-Ib′	aminoglycoside N-acetyltransferase AAC(6′)-Ib′
aadA1	ANT(3″)-Ia family aminoglycoside nucleotidyltransferase AadA1
abaF	fosfomycin efflux MFS transporter AbaF
adeC	multidrug efflux RND transporter AdeABC outer membrane channel subunit AdeC
AMR	antimicrobial resistance
amvA	multidrug efflux MFS transporter AmvA
ANI	average nucleotide identity
ant(3″)-IIa	aminoglycoside nucleotidyltransferase ANT(3″)-IIa
aph(3″)-Ib	aminoglycoside O-phosphotransferase APH(3″)-Ib
aph(3′)-Ia	aminoglycoside O-phosphotransferase APH(3′)-Ia
aph(6)-Id	aminoglycoside O-phosphotransferase APH(6)-Id
armA	16S rRNA (guanine(1405)-N(7))-methyltransferase ArmA
BAL	broncho-alveolar lavage
BfmRS	biofilm-controlling two-component regulatory system
blaADC-186	extended-spectrum class C beta-lactamase ADC-186
blaADC-30	extended-spectrum class C beta-lactamase ADC-30
blaADC-33	cefepime-hydrolyzing class C beta-lactamase ADC-33
blaADC-73	extended-spectrum class C beta-lactamase ADC-73
blaOXA-23	OXA-23 family carbapenem-hydrolyzing class D beta-lactamase OXA-23
blaOXA-66	OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-66
blaOXA-69	OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-69
blaOXA-82	OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-82
catB8	type B-3 chloramphenicol O-acetyltransferase CatB8
CheckM	tool for assessing genome quality (completeness/contamination)
ClusterPicker	software for automatic cluster identification in phylogenetic trees
Csu fimbriae	adhesion factor involved in biofilm formation and immune evasion
cxpE	chloramphenicol efflux transporter CxpE
Element symbol	element name
ftsI_A515V	Acinetobacter baumannii carbapenem/sulbactam-durlobactam resistant FtsI
GTDB-Tk	genome taxonomy database toolkit for taxonomic classification
gyrA_S81L	Acinetobacter baumannii quinolone resistant GyrA
ICU	intensive care unit
kSNP	tool for SNP-based phylogenetic analysis without a reference genome
MALDI-TOF	matrix-assisted laser desorption/ionization–time of flight mass spectrometry
MDR	multi-drug resistant
MEGAHIT	assembler for large and complex metagenomic datasets
MetaVF	tool using VFDB for virulence factor detection
MLST	multilocus sequence typing
mph(E)	Mph(E) family macrolide 2′-phosphotransferase
msr(E)	ABC-F type ribosomal protection protein Msr(E)
qacEdelta1	gene that confers resistance to disinfectants, specifically quaternary ammonium compounds.
ST	sequence type: identifier assigned to a specific allelic profile in the MLST scheme.
tetA	gene codifying for metal-tetracycline/H(+) antiporter conferring resistance to tetracycline by an active tetracycline efflux.
tetB	Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline, doxycycline, and minocycline, but not tigecycline.