Skip to main content

Table 2 Context analysis of selected latent core-resistome ARGs

From: Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes

Cluster ID\(^1\)

Closest ARG\(^2\)

Host

Host\(^3\)

Associated

Co-localized

Environments\(^4\)

ARG class

[% identity]

phyla

species

MGE/integron

ARGs

 

Tetracyclines

C8 RPG

Tet(W/N/W)

Act,

Collinsella sp.,

MPF\(_{\textrm{FATA}}\), MOB\(_{\textrm{Q}}\)

erm(B)

Birds, Bovine,

[12]

[80%]

Firmicutes

LActinobacteriaobacillus sp.

  

Humans, Mice,

      

Pigs, Wastewater

C7 RPG

Tet(44)

Pro,

Campylobacter fetus [P]

MPF\(_{\textrm{FATA}}\),

 

Birds, Bovine,

[2]

[86%]

Firmicutes

 

MOB\(_{\textrm{Q}}\), MOB\(_{\textrm{P1}}\)

 

Humans, Mice, Pigs

C10 RPG

Tet(32)

Firmicutes

Clostridium clostridioforme,

MPF\(_{\textrm{FA}}\), MOB\(_{\textrm{P}1}\)

 

Birds, Bovine,

[7]

[76%]

 

Dorea formicigenerans,

  

Mice, Pigs

C14 RPG

Tet(32)

Firmicutes

Acetatifactor muris,

MPF\(_{\textrm{FATA}}\), MOB\(_{\textrm{Q}}\),

 

Birds, Bovine,

[3]

[88%]

 

Blautia coccoides

MOB\(_{\textrm{P1}}\)

 

Humans, Mice, Pigs

\(\beta\)-lactams

C34 A

CepA-44

Bacteroidetes

Bacteroides vulgatus [P],

  

Humans

[31]

[54%]

 

Bacteroides massiliensis [P]

   

C46 A

cepA

Bacteroidetes

Bacteroides caecimuris,

MPF\(_{\textrm{FA}}\),

 

Mice

[11]

[41%]

 

Parabacteroides distasonis

MPF\(_{\textrm{FATA}}\)

  

C35 A

CfxA3

Bacteroidetes

Bacteroides fragilis [P],

MPF\(_{\textrm{B}}\)

 

Humans, Pigs,

[8]

[84%]

 

Bacteroides eggerthii

  

Respiratory system

C37 A

CfxA6

Bacteroidetes

Bacteroides vulgatus [P],

MOB\(_{\textrm{B}}\)

 

Pigs

[3]

[81%]

 

Bacteroides ovatus

   

C30 C

ACC-7

Proteobacteria

Thauera humireducens,

Class 1 integrase,

tet(G)

Activated

[3]

[47%]

 

Thauera sp.

IS91-family transposase

 

sludge, Wastewater

C22 C

ADC-221

Proteobacteria

Acinetobacter baumannii [P],

MOB\(_{\textrm{Q}}\)

bla\(_{\mathrm {OXA-58}}\)

Wastewater

[6]

[61%]

 

Acinetobacter bereziniae

   

C89 D

OXA-209

Bacteroidetes

Myroides odoratimimus [P]

MPF\(_{\textrm{B}}\)

bla\(_{\mathrm {OXA-347}}\),

Wastewater

[1]

[89%]

   

tet(X)

 

C94 D

OXA-209

Bacteroidetes

Vaginella massiliensis

 

tet(X4)

Wastewater

[1]

[73%]

     

Macrolides

C50 erm

Erm(42)

Firmicutes,

Anaerofustis stercorihominis,

MPF\(_{\textrm{FA}}\)

 

Birds, Bovine,

[6]

[48%]

Proteobacteria

Dechloromonas aromatica,

  

Pigs, Wastewater

C41 erm

Erm(42)

Firmicutes,

Salmonella enterica [P],

MPF\(_{\textrm{FATA}}\),

 

Birds

[4]

[42%]

Proteobacteria

Eubacterium rectale

MOB\(_{\textrm{Q}}\), MOB\(_{\textrm{P1}}\)

  

C105 erm

Erm(F)

Bacteroidetes

Bacteroides fragilis [P],

MPF\(_{\textrm{B}}\), MOB\(_{\textrm{P1}}\)

tet(Q)

Wastewater

[3]

[63%]

 

Alistipes onderdonkii

   

C38 erm

Erm(42)

Firmicutes

Solobacterium sp.

MPF\(_{\textrm{FA}}\), MPF\(_{\textrm{FATA}}\),

 

Pigs

[5]

[49%]

  

MOB\(_{\textrm{V}}\)

  

C109 erm

Erm(X)

Actinobacteria

Corynebacterium dentalis,

MOB\(_{\textrm{F}}\)

 

Birds

[2]

[57%]

 

Trueperella pyogenes

   

C67 mph

Mph(E)

Bacteroidetes

Myroides odoratimimus [P]

MOB\(_{\textrm{P1}}\)

 

Wastewater

[1]

[83%]

     

Aminoglycosides

C87 aac(3)

AAC(3’)-IXa

Firmicutes

Lactobacillus amylovorus,

MOB\(_{\textrm{T}}\)

 

Birds, Pigs

[13]

[30%]

 

Lactobacillus gallinarum

   

C132 aac(6’)

AAC(6’)-Iad

Firmicutes

Clostridioides difficile [P]

MPF\(_{\textrm{FATA}}\),

 

Pigs

[2]

[56%]

  

MOB\(_{\textrm{Q}}\)

  

C130 aac(6’)

AAC(6’)-Im

Firmicutes

Ruminococcus flavefaciens,

MPF\(_{\textrm{FATA}}\)

 

Bovine

[14]

[55%]

 

Butyrivibrio sp.

   

C128 aac(6’)

AAC(6’)-Ib7

Proteobacteria

Pseudomonas aeruginosa [P]

Class 1 integron

aac(6’)-31, aadA6,

Birds,

[1]

[74%]

   

sul1, bla\(_{\mathrm {OXA-2}}\)

Wastewater

C84 aph(3’)

APH(\(3^{\prime \prime }\))-Ib

Proteobacteria

Vibrio cholerae [P]

 

aph(6)-Id

Birds, Activated

[1]

[89%]

    

sludge, Wastewater

  1. Gene sequences of the 1429 variants (clustered into 133 ARGs) of all latent core-resistome ARGs are found in Additional File 3: Table S5. The corresponding information for all latent core-resistome ARGs is found in Additional File 3: Table S6.\(^{1}\)Cluster ID and ARG class with the number of gene sequences in the cluster given in brackets.\(^{2}\)The closest established ARG identified by protein alignment against CARD with the identity level given in brackets. \(^{3}\)Pathogenic species are indicated with [P].\(^{4}\)Environments where the ARG was considered part of the core-resistome.