Table 2 List of the putative genetic markers obtained by WGS for diagnostics of the bacterial agents of epidemiological importance

mecA/mecC

Chr

Adapter protein/Penicillin-binding protein 2a

MRSA/S. aereus

[184]

tetM

Chr

Tetracycline resistance protein

Livestock-associated S. aereus CC398

[157]

ϕ3/ϕ7

Chr

Bacteriophages

Human-specific S. aereus CC398

[157]

Chp

Chemotaxis inhibitory protein

Scn

Staphylococcal complement inhibitor

Sak

Staphylokinase

gp20

Chr

Putative prophage DNA transfer protein

Verocytotoxin-producing E. coli O104:H4

[102, 193]

impB

Pl

DNA polymerase type Y

usid000007 (contig 69, 14714:14853)

Chr

Sequence positions 47–69 similar to Ricinus communis putative receptor serine-threonine kinase mRNA (XM_002525007.1)

usid000002 (contig 43, 1486:1633)

Chr

Positions 4–34 similar to Pseudomonas putida BIRD-1 major facilitator transporter protein coding sequence (ADR60257.1)

ISAba1

Chr

Transposase of ISAba1, IS4 family

MDR A. baumannii

[166, 254]

csuE

Chr

Chaperone-usher pili assembly system

MDR A. baumannii,

[254]

bla _OXA-51

Bla_OXA-51-like beta-lactamase

GC2 (SG1)

Coding SNP:

Chr

Colistin-resistant K. pneumonia KPNIH1

[216]

ind(GA) 321 in KPNIH1_08595 CTG→ATG

Microcin B17 transporter

(L→M) at 130 in KPNIH1_18808 ACC→ATC

Putative membrane protein

(T→I) at 1106 in KPNIH1_07189 GGC→TGC

l-Ala-D/l-Glu epimerase and methyl viologen resistance protein SmvA

(G → C) at 811 in KPNIH1_05438

Putative transport protein

ampC

Pl/

β-Lactamase

β-Lactam resistant Enterobacteriaceae and P. aeruginosa

[110, 162, 247]

ampD

Chr

N-acetylmuramyl-l-alanine amidase, negative regulator of AmpC,AmpD

ampR

HTH-type transcriptional activator AmpR

ampG

Putative transporter

gyrA (Thr83Ile)

Chr

DNA gyrase subunit A

P. aeruginosa resistant to fluoroquinolones

[247]

parC (Ser87Leu)

DNA topoisomerase 4 subunit A

bla _VIM-2

Pl

Beta-lactamase class B VIM-2

P. aeruginosa resistant to β-lactams except monobactams

[247]

aacA29a/aacA29b putative aph ant(4′)-IIb

Chr^a

6′-N-aminoglycoside acetyltransferase type I, phosphotransferases

Aminoglycoside resistant P. aeruginosa

[247]

mexAB-oprM

Chr

Efflux pumps and multidrug resistance operon repressors

MDR P. aeruginosa

[247]

mexCD-oprJ

mexEF-oprN

mexHI-opmD

mexR

Operons respective regulator Genes

nfxB

mexT

mexG

mexMN

mexVW

mexXY

muxABC-opmB

emrAB-opmG

SMR

Small multidrug resistance family of proteins

triABC

Chr

Presence triclosan efflux pump operon

Triclosan resistant P. aeruginosa

[247]

mexJKL

Resistance nodulation cell division efflux pump

czcCBA

Chr

Cobalt-zinc-cadmium efflux resistance operon

Heavy metal resistant P. aeruginosa

[247]

pmrAB

Chr

Membrane bound sensor

Colistin and polymyxin resistant P. aeruginosa, S. enterica subsp. Typhimurium, and A. baumannii

[139, 247]

phoPQ

Chr

Kinases and cytosolic response regulator

60 SNPs

Intergenic regions, enzymes, regulatory and membrane proteins

S. enterica subsp. Enteritidis

[87, 176]

iniBAC

Drug efflux operon

M.tuberculosis resistant to rifampicin, isoniazid, fluoroquinolone ethambutol, amikacin, para-aminosalicylic acid

[52]

rpoB (S450L)

katG (P7 frameshift) gyrB (T500N)

embB (D1024N)

rrs (A514C, A1401G) thyA (P17L)