Table 1 Common MDR bacterial agents of epidemiological importance causing severe infections in hospitals (H) and communities (C)
From: Whole-genome sequencing targets drug-resistant bacterial infections
Bacterial agent | Diseases | Resistance | Example of main resistance determinants revealed in whole sequenced genomes |
|---|---|---|---|
Escherichia coli (H, C) | UTI, BSI | β-Lactams (cephalosporins) | ampC, 2 copies of bla T [74] |
Quinolones (fluoroquinolones) | gyrA (Ser83Leu,Asp87Asn), parC (Ser80Ile,Glu84Gly) [74, 188] | ||
Klebsiella pneumonia (H, C) | UTI, BSI, pneumonia | β-Lactams (cephalosporins, carbapenems) | bla SHV-75 , bla SHV-60 , bla KPC-2 , bla TEM-1 , bla TEM-12 , bla P1 , bla CTX-M [132, 145] |
Quinolones (fluoroquinolones) | qnrA1, qnrB4, oqxAB, gyrA (Ser 83Phe), parC (Ala339Gly, Asp641Tyr) [209] | ||
Amynoglycosides | armA, aph [209] | ||
Colistin | |||
Staphylococcus aureus (H, C) | WSI, BSI | β-Lactams (methicillin) | mecC [157] |
Aminoglycosides | aadD [258] | ||
Mupirocines | ileS-2 [258] | ||
Mercury resistance | mer operon [258] | ||
Antiseptic resistance | qacA [258] | ||
Streptococcus pneumonia (C) | Pneumonia, meningitis, otitis | β-Lactams | pbp2a, pbp2b, pbp2x, spr1238 [56] |
Tetracycline | rpsJ, patA, patB [153] | ||
Salmonella enterica subsp. enterica, Typhimurium, Choleraesuis (C) | Salmonellosis, foodborne diarrhea, BS | β-Lactams | |
Quinolones (fluoroquinolones) | gyrA (Ser83Leu), parC (Ser80Leu), acrAB-tolC [31] | ||
Aminoglycosides | 2 copies aadA1, 3 copies aadA3, aac3, aph, strA, strB, sat-1 [91, 109] | ||
Shigella spp. (C) | “Bacillary dysenteria” | β-Lactams | bla TEM-1 , bla OXA-1 [257] |
Fluoroquinolones | mutated parC and gyrA [257] | ||
Aminoglycosides | aadA1, aadA2, sat-1 [257] | ||
Neisseria gonorrhoeae (C) | Gonorrhea | β-Lactams (3rd gen. cephalosporins) | mtrR (G45D, A39T), mtrCDE (del1327932), penB (G101K, A102D), penA (mosaic) [54, 83, 240] |
Tetracycline | rpsJ (V57M), tetM including its promoter, penB [54] | ||
Coagulase-negative Staphylococci spp. (CoNS) (H, C) | SSI, endocarditis, and BSI | β-Lactams | |
Enterobacter aerogenes (H) | SSI and BSI | β-Lactams | bla TEM-24 , 2 copies ampC, 3 copies M-bla, 4 copies bla [48] |
Quinolones | |||
Aminoglycosides | |||
Rifampicin | |||
Acinetobacter baumannii (H, C) | BSIs, VAP, HAP, SSI, CA-UTI, ventilator-associated pneumonia | β-Lactams (3rd gen. cephalosporins) | bla class A, ISAba1, bla OXA-23, bla OXA-10 , bla OXA-69 , bla ampC , bla OXA-23 , bla OXA-66 , bla ADC (Nigro et al. 2013 [173]); [2, 76, 83, 173, 195, 240]), ampC, bla OXA-51 -like [74], bla TEM-1 [2], 5 copies M-bla, 2 copies ampC, bla OXA-82 [204] |
Amynoglycosides | Modified armA, aac(3′), aac(3)-la, aac(6ʹ), aac(2ʹ)-Ib, aadA1, aadAB, aphA1, aph(3′), aph6, strAB [2, 71, 204, 254, 265] adeT, aadA2 [204] | ||
Quinolones | |||
BSIs, VAP, HAP, SSI, CA-UTI, ventilator-associated pneumonia | Colistin | pmrB [90] | |
Tetracyclines | |||
Chloramphenicol | |||
Pseudomonas aeruginosa (H, C) | BSIs, VAP, HAP, SSI, CA-UTI, cystic fibrosis (CF) | β-Lactams (3rd gen. cephalosporins) | |
Quinolones | gyrA (Thr83Ile), parC (Ser87Leu) [247] | ||
Aminoglycosides | aac(6′) [163], aph, ant(4′)-IIb, strAB [247], aacA29a/aacA29b [124] | ||
Colistin | pmrAB, phoPQ [247] | ||
Wide range of antibacterial agents | mexAB-oprM, mexXY, mexCD-oprJ, mexEF-oprN, mexHI-opmD, mexR, nfxB, mexT, mexG [124] | ||
Mycobacterium tuberculosis (H, C) | Tuberculosis | Rifampicin | rpoB (S450L) [52] |
Isoniazid | katG (P7 frameshift), ptrBa, fadD15, ppsB, atsH [88] | ||
Fluoroquinolone ethambutol amikacin para-aminosalicylic acid | gyrB (T500N), embB (D1024N), rrs(A514C, A1401G), thyA (P17L) [52] |