Table 2 14 gene alleles predicted to be associated with resistance against specific drug classes for individual species

From: Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species

Species

Drug Class

Accession ID (Gene)

Predicted Gene Product

Muts.a

Resistant/ Susceptible

LORs

Acinetobacter baumannii

quinolone

WP_000586912.1 (lptF)

Lipopolysaccharide export system permease protein

–

CIP = 795/166 LVX = 731/143

CIP = 3.0 LVX = 2.5

Acinetobacter baumannii

tetracycline

ADX03353.1 (bccA)

Biotin carboxylase

–

TET = 107/0 MIN = 86/20

TET = 7.4 MIN = 4.0

Campylobacter coli

quinolone

AHK72934.1 (rny)b

Ribonuclease Y

d1-86, V87M

NAL = 41/16 CIP = 39/18

NAL = 2.9 CIP = 2.6

Escherichia coli

beta-lactam

WP_000811566.1 (yjfN)

Putative uncharacterized protein, DUF1471

–

FOX = 46/0 CTT = 4/15 CXM = 246/136

FOX = 9.4 CTT = 4.5 CXM = 3.2

Escherichia coli

beta-lactam

WP_000118520.1 (sugE)

Small multidrug resistance (SMR) efflux transporter

T37A, M85A, A88L, A91G, L95A, +13

FOX = 40/0 CAZ = 101/1 CRO = 85/0

FOX = 9.0 CAZ = 7.7 CRO = 7.5

Escherichia coli

beta-lactam

WP_001588947.1 (frdD)c

Fumarate reductase subunit D

V111D

AMC = 19/1 AMP = 14/0 CXM = 12/1

AMC = 4.7 AMP = 4.5 CXM = 4.4

Escherichia coli

quinolone

WP_000228346.1 (cycA)c

D-serine, D-alanine, glycine transporter

–

LVX = 251/35 CIP = 573/468 NAL = 41/17

LVX = 4.0 CIP = 3.0 NAL = 0.7

Klebsiella pneumoniae

beta-lactam

WP_004183775.1

Cold shock protein of CSP family

V54A, H55L, A57T, Q62P, +2

TIM = 16/2 AMP = 107/0 CEF = 13/0

TIM = 7.0 AMP = 6.8 CEF = 4.1

Salmonella enterica

beta-lactam

WP_001221666.1 (blc)

Lipocalin Blc

L49F, S98D, S175P, +10

CRO = 302/0 AMC = 301/0 CTF = 297/3

CRO = 13.6 AMC = 12.1 CTF = 10.9

Salmonella enterica

beta-lactam

WP_000118520.1 (sugE)

Small multidrug resistance (SMR) efflux transporter

T37A, A104T, +9

CRO = 304/0 AMC = 303/0 CTF = 299/3

CRO = 13.7 AMC = 12.1 CTF = 11.0

Staphylococcus aureus

beta-lactam

WP_000872606.1 (maoC)

MaoC domain protein

–

OXA = 29/3 MET = 201/4 FOX = 713/0

OXA = 15.3 MET = 14.5 FOX = 13.1

Staphylococcus aureus

beta-lactam

WP_000958858.1

Glycerophos

-phoryldiester phosphodiesterase

–

OXA = 29/3 FOX = 775/0 MET = 201/3

OXA = 15.3 FOX = 15.2 MET = 14.8

Streptococcus pneumoniae

beta-lactam

WP_000248982.1

Cell wall surface anchor family protein

V66I, D111E, S160G, E172K

AMX = 13/2 MEM = 15/0 CXM = 15/0

AMX = 13.1 MEM = 10.1 CXM = 9.7

Streptococcus pneumoniae

beta-lactam

WP_000203066.1 (gpo)

Glutathione peroxidase

A80T, S132G

AMX = 13/3 MEM = 16/0 CXM = 16/0

AMX = 12.7 MEM = 10.6 CXM = 10.3

  1. Accession IDs are provided for the exact sequence of each allele (RefSeq when possible, GenBank otherwise), along with gene names when available, gene products, and mutations with respect to the most commonly observed allele. The number of resistant/susceptible genomes and log2 odds ratios (LORs) for resistance are shown for the top three drugs by LOR when data for more than three related drugs was available. Abbreviations are available in Supplementary Data 7.
  2. aWhen more than four mutations are detected, only mutations with BLOSUM62 score ≤0 are shown and the number of additional mutations is listed at the end. Full mutation sets are available in Supplementary Data 7. If no mutations are shown, the allele of interest is the most commonly observed allele.
  3. bNo exact variant was found on GenBank. AHK72934.1 refers to the most common allele of the gene, while the allele of interest contains the 86-amino acid N-terminal truncation d1-86.
  4. cSelected for experimental validation.
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