Table 1.

Currently available genomes of Phytobacter strains (December 2021) as extracted from NCBI GenBank. The whole-genome-based core phylogeny of these strains is shown in Fig. 1. The name under which the strain was originally or intermediary described is given between double quotation marks in the second column

Strain	Former/Misidentified name	Source	Source type1	Origin	Year	MDR genes2	Reference
Phytobacter diazotrophicus
DSM 17806 T		Wild rice (Oryza rufipogon)	E	People’s Republic of China, Lingshui	2004	None	[17]
5110RM		Total parenteral nutrition	H	Brazil, Curitiba	2013	None	[24]
5020RM		Human, blood	H	Brazil, Curitiba	2013	None	[24]
10289RM		Human, rectal swab	H	Brazil, Curitiba	2015	bla KPC	[24]
Bisph2	“Enterobacter” sp.	Sandy soil	E	Algeria, Biskra	2012	ND2	[41]
ENNIH2	“Enterobacteriaceae” bacterium	Hospital wastewater	H	USA, MD	2012–2016	bla KPC	[42]
ENNIH3	“Enterobacteriaceae” bacterium	Hospital wastewater	H	USA, MD	2012–2016	bla KPC	[42]
GT-16	“Kluyvera intestini”	Human, stomach	H	USA	2015	bla	[21, 43]
SCO41	Phytobacter sp.	Gut of C. elegans	E	People’s Republic of China	2013	ND	[44]
MRY16-398	“Metakosakonia” sp.	Human, sigmoid colon diverticulitis	H	Japan	2015	bla IMP—6	[23]
AG753	“Grimontella” sp.	Rice bacterial endophyte	E	Italy	2011	ND	Unpublished
Nf5 (SCK5)	“Kluyvera” sp.	Plant growth promoting bacterium from sugarcane	E	Colombia, Valle del Cauca	2014	ND	[45]
NFR05	“Enterobacter” sp.	Bacterial root endophyte of switchgrass	E	USA	NI2	ND	Unpublished
AF18		Bile sample, coinfection with K. pneumoniae	H	People’s Republic of China, Peking	2020	bla CTX-M3	[46]
UAEU22		Rhizosphere of date palm	E	Ras Al Khaimah, United Arab Emirates	2019	ND	[47]
BDA59-3	“Citrobacter” sp.	Rice leaves	E	Italy	2019	ND	[48]
CCUG 74074		Blood	H	Sweden	2019	ND	Unpublished
UBA869	“Enterobacteriaceae” bacterium	MAG2, terrestrial metagenome	E	USA, New York City	NI	ND	[38]
UBA2606	“Enterobacteriaceae” bacterium	MAG, terrestrial metagenome	E	USA, New York City	NI	ND	[38]
UBA4747	“Enterobacteriaceae” bacterium	MAG, terrestrial metagenome	E	USA, New York City	NI	ND	[38]
L1-008-030G1	“Enterobacteriaceae” bacterium	MAG, infant faeces, human gut metagenome	H	USA, Pittsburgh	2016/2019	ND	Unpublished
CP_BM_RX_33	“Metakosakonia” sp.	MAG, rhizosphere of Barbacenia macrantha	E	Brazil, Minas Gerais	2017	ND	Unpublished
Phytobacter ursingii
ATCC 27989 T	“Enterobacter agglomerans” “Pantoea agglomerans”	Human, sputum	H	USA, SC	1974	None	[24, 30]
CAV1151	“Kluyvera intermedia”	Human, perirectal	H	USA, VA	2009	bla KPC	[39]
ENNIH1	“Enterobacteriaceae” bacterium	Hospital wastewater	H	USA, MD	2012–2016	bla KPC	[42]
FOSA7093	“Kluyvera intermedia”	Intraabdominal pancreas cyst	H	Denmark, Copenhagen	2016	bla CTX-M-type	[22]
1-RC-17–04352	“Escherichia coli”	Sink	H	USA, Milwaukee	2017	ND	Unpublished
UBA3136	“Enterobacteriaceae” bacterium “Stenotrophomonas maltophilia”	MAG, terrestrial metagenome	E	USA, New York City	NI	ND	[38]
UHGG_MGYG-HGUT-02521	“Kluyvera intermedia”	Human gut	H	NI	NI	bla KPC	[49]
Phytobacter palmae
S29T	“Kosakonia” sp.	Oil palm	E	Malaysia	2012	ND	[34]
Phytobacter massiliensis
JC163T	“Enterobacter massiliensis””Metakosakonia massiliensis”	Human, stool sample	H	Senegal	2011	ND	[2, 18, 35]
MGYG-HGUT-01426	“Metakosakonia massiliensis”	Human gut	H	NI	NI	ND	[49]
Novel MAG species
UBA3516	“Enterobacteriaceae” bacterium	MAG, terrestrial metagenome	E	USA, New York City	NI	ND	[38]

¹E: environmental isolate; H: hospital-associated isolate

²Abbreviations: MDR, multidrug resistance; ND, not determined; NI, no indications; MAG, metagenome-assembled genome