REVIEW article

Front. Pharmacol., 01 October 2025

Sec. Pharmacogenetics and Pharmacogenomics

Volume 16 - 2025 | https://doi.org/10.3389/fphar.2025.1651909

Pharmacogenomics of antibiotic-induced hypersensitivity reactions: current evidence and implications in clinical practice

  • 1. Department of Pharmacy, Faculty of Science, University of Rajshahi, Rajshahi, Bangladesh

  • 2. Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand

  • 3. Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand

  • 4. Pharmacogenomics and Precision Medicine, The Preventive Genomics and Family Check-Up Services Center, Bumrungrad International Hospital, Bangkok, Thailand

  • 5. Faculty of Pharmaceutical Sciences, Burapha University, Saensuk, Chonburi, Thailand

Abstract

Adverse drug reactions (ADRs) are gradually becoming a concerning health threat worldwide in patients undergoing acute or chronic therapy. Antibiotics are the main drugs that cause immune-mediated ADRs, such as severe cutaneous adverse reactions (SCARs), allergic reactions, and organ-specific diseases, representing a significant threat to patient safety. In this review, we present the current genetic evidence available for antibiotic-related toxicities from a pharmacogenomics (PGx) perspective. We also explore the current state of PGx-based dosing recommendations and the factors limiting their widespread application in routine clinical practice. Through a systematic literature review, this study identified at least 12 antibiotic–gene pairs (amikacin–MT-RNR1, gentamicin–MT-RNR1, kanamycin–MT-RNR1, streptomycin–MT-RNR1, neomycin–MT-RNR1, tobramycin–MT-RNR1, isoniazid–NAT2, dapsone–HLA-B, co-trimoxazole–HLA-B, HLA-C, flucloxacillin–HLA-B, daunorubicin–SLC28A3, and doxorubicin–SLC28A3) with moderate to high Pharmacogenomics Knowledgebase (PharmGKB) evidence levels for toxicity. However, PGx-based dosing guidelines, as recommended by the Clinical Pharmacogenetics Implementation Consortium (CPIC), the Dutch Pharmacogenetics Working Group (DPWG), and the Canadian Pharmacogenomics Network for Drug Safety (CPNDS), are currently available only for the following antibiotic–gene pairs: amikacin, gentamicin, kanamycin, streptomycin, neomycin, and tobramycin–MT-RNR1; flucloxacillin–HLA-B; dapsone–G6PD; nitrofurantoin–G6PD; and daunorubicin and doxorubicin–RARG, SLC28A3, and UGT1A6. Despite the established and growing genetic evidence for toxicity, particularly for Co-trimoxazole-induced SCARs by HLA-B and HLA-C, dapsone-induced SCARs by the HLA-B, and isoniazid-induced liver injury by the NAT2, insufficient approaches are being undertaken to translate these findings into routine clinical practice. The lack of validation of preliminary genetic associations, due to the scarcity of proper follow-up and large-scale replication, remains a key setback for PGx-based implementation of antibiotic therapy in clinical settings. More focused clinical studies, cost-effectiveness analyses, and polygenic risk score development are required to enable the PGx-based clinical use of antibiotics and optimize both safety and effectiveness in achieving precision medicine.

1 Introduction

Adverse drug reactions (ADRs) are gradually becoming a concerning health threat worldwide in patients undergoing acute or chronic therapy (). Rawlins and Thompson grouped ADRs into two types: dose-dependent and predictable reactions (type A) and unpredictable dose-independent reactions (type B) (). Hypersensitivity reaction, a type-B ADR, is produced by cellular mediators released through both immunological and non-immune mechanisms (). Allergic reactions are hypersensitivity reactions involving either an immunoglobulin E (IgE)-mediated or non-IgE (e.g., T cell)-mediated mechanism (). Severe cutaneous adverse reactions (SCARs) are potentially fatal T-cell-mediated delayed allergic reactions (). The most prevalent SCARs, contributing to over 85% of the SCARs occurring in adults, are drug reaction with eosinophilia and systemic symptoms (DRESS), Stevens–Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), and acute generalized exanthematous pustulosis (AGEP) (; ).

A high estimated mortality ranging from 10% to 40% for SJS/TEN, <5% for AGEP and 2%–10% for DRESS was reported (; ; ; ; ; ; ). Globally, the prevalence of SCARs was said to be 0.4–1.2 per million/years (). Nevertheless, a racial discrepancy in the prevalence of SCARs has also been recorded. For example, the incidence was reported to be as high as 1.53–1.89 per million/year in the German population, whereas among the Filipino population, the rate of SCARs was reported to be 6.25/10,000 people from 2011 to 2015 (; ; ). Additionally, the prevalence of TEN and SJS was estimated to be 0.4–1.2 and 1-6 per million/year, respectively, among the European population, while the rate was 0.94–1.45 and 3.96–5.03 per million/year, respectively, for Koreans (Yang et al., 2016; ; ).

Antibiotics are the main drugs that cause immune-mediated ADRs, such as SCARs, allergic reactions, and organ-specific diseases, representing an indisputable threat to patient safety (). Several antibiotics (e.g., beta-lactams, co-trimoxazole, vancomycin, and dapsone) have been associated with drug-induced hypersensitivity reactions (DIHRs) and have been associated with different genetic variants (; ; ; ). Apart from DIHRs, other ADRs are also attributable to antibiotics. For example, anti-tuberculosis drug-induced hepatotoxicity (ATDH) represents an important clinical challenge as it is associated with treatment failure and increased mortality. The risk of developing hepatotoxicity ranges from 2% to 18% (; ). Cardiotoxicity is another important ADR related to anthracycline antibiotics and is deemed the most critical ADR in childhood cancer therapy, contributing to substantial mortality and morbidity (). In addition to nephrotoxicity, cochleotoxicity (sensorineural hearing loss) and vestibulotoxicity are the well-established side effects of aminoglycosides, which are typically dose-dependent and occur in the long-term use of high-dose drugs. However, certain individuals have been reported to be sensitive to aminoglycoside-induced hearing loss, even with single doses, resulting in profound bilateral sensorineural hearing loss (; ).

Recently developed cutting-edge technologies have identified the molecular mechanisms of underlying DIHRs and other ADRs. Therefore, in this article, we present the current genetic evidence from a pharmacogenomics (PGx) perspective. We also explore how these PGx–antibiotic associations can be more effectively translated into clinical practice to optimize antibiotic safety or efficacy, thereby serving as a cornerstone of antibiotic precision medicine.

2 Methods

2.1 Literature searching

Following the PRISMA guidelines, an extensive literature search was undertaken on PubMed on 25/5/2025 with the following keywords: pharmacogenomics, hypersensitivity, antibiotics, beta-lactam, sulfonamide, co-trimoxazole, dapsone, vancomycin, fluoroquinolone, anticancer antibiotics, macrolide, aminoglycoside, cephalosporins, tetracyclines, and anti-tubercular drugs to identify relevant articles (). Articles were included if 1 the study was performed on human subjects, 2 the study assessed the pharmacogenomic association of an antibiotic drug, and 3 the study evaluated the association of any gene or variant with antibiotic-induced hypersensitivity or adverse reactions. Studies were excluded if 1 the genetic assessment was conducted only computationally, 2 the study reported the genetic frequency without associating the findings with any drug, 3 the analysis was in vitro or the studies was conducted in an animal model, and 4 the publication was something other than a research article (e.g., review articles, meta-analysis, book chapter, editorial, case report, letter, and conference paper),

We utilized Rayyan QCRI, a web-based tool for systematic reviews, to select the primary studies (). We obtained the full texts of initially selected studies and reviewed them carefully to determine the final set of studies for inclusion. Two researchers independently performed the study selection using Rayyan QCRI software, and any disagreements during data extraction were resolved through mutual discussion.

2.2 Identification of the PGx-based evidence level, drug label, and therapeutic and testing guidelines for antibiotics

To assess the current state of PGx-based evidence for gene variants involved in the toxicity, metabolism/pharmacokinetics (PK), and efficacy of antibiotics, we utilized clinical annotations provided by the Pharmacogenomics Knowledgebase (PharmGKB), which is a comprehensive PGx resource managed by Stanford University to support, expand, and promote the implementation and education of PGx knowledge. PGx-based drug label information for the antibiotics was sourced from various internationally acknowledged pharmacogenetics working bodies, namely, the Health Canada Santé Canada (HCSC)-approved drug label, the US Food and Drug Administration (FDA)-approved drug label, the Swissmedic (Swiss Agency of Therapeutic Products)-approved drug label, the Pharmaceuticals and Medical Devices Agency (Japan) (PMDA)-approved drug label, and the European Medicines Agency (EMA)-approved drug label. We accessed all the information from the PharmGKB website (). To obtain current information on therapeutic and testing guidelines for antibiotics, we searched different guideline-providing PGx working groups and included recommendations from the Clinical Pharmacogenetics Implementation Consortium (CPIC), the Dutch Pharmacogenetics Working Group (DPWG), and the Canadian Pharmacogenomics Network for Drug Safety (CPNDS) (; ; ).

3 Results

3.1 Literature search results

The strategic search using the aforementioned keywords generated 2,357 records, and after removal of duplicates, 1,405 remained for screening. Through initial screening with title and abstract, we excluded 1,258, and after another round of screening, we identified 147 articles for full-text eligibility assessment. Following the predefined inclusion and exclusion criteria (detailed in the Section 2), we identified 65 articles that examined the PGx associations of genes with the DIHRs and other adverse effects of antibiotics for inclusion in this review. The whole selection process is shown in a PRISMA flowchart in Figure 1.

FIGURE 1

Of the identified 65 articles, PGx assessments are presented for beta-lactams in 8 studies, anti-tuberculosis drugs in 25 studies, anticancer antibiotics in 13 studies, sulfonamides in 6 studies, aminoglycosides in 4 studies, and other antibiotics in the remaining 9 studies. Table 1 summarizes the key PGx associations for antibiotics from the included studies.

TABLE 1

DrugGeneOR (95% CI)p-valueAdverse effectPopulation/raceReference
Beta-lactams
Amoxicillin, benzyl penicillin, amoxicillin–clavulanic acid, and cephalosporinsLGALS3 (rs11125)4<0.0001Allergic reactionSpanish
5.1Italian
Penicillin and cephalosporinHLA DQA1*01:052.935.4 × 10−7Immediate hypersensitivity reactionsEuropean
HLA DRB1*10:012.9355.4 × 10−7
TNFA–308AANR0.0046IgE-mediated allergyItalian
CephalosporinsHLA-B*55:021.76 (1.18–2.61)0.005Allergic reactionTaiwanese
HLA-C*01:021.36 (1.05–1.77)0.018
HLA-DQB1*06:092.58 (1.62–4.12)<0.001
PenicillinHLA-B*55:011.41 (1.33–1.49)2.04 × 10−31Allergic reactionEuropean
HLA-DPB1*05:011.360.004Hypersensitivity reactionsTaiwanese
HLA-DQB1*05:011.540.03
FlucloxacillinHLA-A*01:011.86 (1.5–2.31)1.8 × 10−8Drug-induced liver injuryUnited Kingdom, Sweden, Netherlands, and Australia
HLA-B*57:0136.62 (26.14–51.29)2.67 × 10−97
HLA-B*57:0379.21 (3.37–116.1)1.2 × 10−6
HLA-C*06:0210.11 (7.88–12.97)4.3 × 10−74
HLA-DQA1*02:014.02 (3.22–5.01)4.5 × 10−35
HLA-DQB1*03:0310.18 (7.77–13.34)1.1 × 10−63
HLA-DRB1*07:014.02 (3.23–5.02)3.8 × 10−35
CefaclorHLA-DRB1*04:034.61 (1.51–14.09)<0.002Immediate hypersensitivityKorean
HLA-DRB1*14:543.86 (1.09–13.67)<0.002
LIMD1 (rs62242177 and rs62242178)NR5 × 10−8
Anti-tuberculosis drugs
Isoniazid, rifampicin, pyrazinamide, and ethambutolCYP2D6 (rs1135840)2.52 (1.43–4.44)0.009Hepatotoxicity and leukopeniaChinese
CYP3A4*18 heterozygous genotype3.24 (1.06–9.86)0.034HepatotoxicityTaiwanese
CYP2E1 C1/C1 + NAT2 slow acetylators (NAT2*5B/7B, *6A/6A, *6A/19, *6A/7B, *6J/7B, *7A/7B, and *7B/7B)5.33 (1.80–15.80)0.003HepatotoxicityChinese
GSTM1 null2.14 (1.1–4.1)0.02Anti-tuberculosis drug-induced hepatotoxicityWestern Indian
GSTM1 and T1 null7.18 (1.7–32.6)0.007
GSTT1 null2.03 (0.9–4.4)0.08
GSTM1 nullNR0.007Intensity of the anti-tuberculosis drug-induced liver injuryBrazilian
GSTM1 (rs412543)4.44 (1.53–12.89)0.01Treatment-related adverse events including hepatotoxicityBrazilian
HLA-DQB1*05/*055.284 (1.134–24.615)0.034Liver injuryChinese
IL6 (rs1800796G)2.48 (1.40–4.40)0.002HepatotoxicityChinese
NAT2*6A4.75 (1.8–12.55)0.00077Liver injuryIndonesianYuliwulandari et al. (2016)
NAT2*5B, NAT2*5C, NAT2*6A, NAT2*7A, and NAT2*7B3.45 (1.79–6.67)1.7 × 10−4
NAT2*6A/7B9.57 (2.72–33.62)<0.001HepatotoxicityChinese
NAT2*6A/6A5.24 (1.41–19.46)0.013
NAT2 slow acetylator3.64 (2.21–6.00)0.0000002Anti-tuberculosis drug-induced liver injuryIndonesianYuliwulandari et al. (2019)
NAT2 ultra-slow acetylator3.37 (2.00–5.68)0.0000043
Slow acetylators (NAT2 *5/*5, *5/*6, *5/*7, *6/*6, *6/*7, *6/*14, and *7/*7)NR0.03HepatotoxicityEuropean, African, Latin, Asian, and Indian
Slow NAT2 acetylators (patients lacking NAT2*4)8.80 (4.01–19.31)1.53*10−8Liver injuryThai
Slow acetylators [rs1801280 (NAT2*5), rs1799930 (NAT2*6), rs1799931 (NAT2*7), and rs1801279 (NAT2*14)]2.32 (0.79–6.77)Treatment-related adverse events including hepatotoxicityBrazilian
Slow acetylators (NAT2 *5/*5, *5/*6, *5/*7, *6/*6, *6/*7, and *7/*7)3.56 (1.256–10.119)Liver injuryMongolianZhang et al. (2020)
NR1I2 (rs7643645)1.64 (1.03–2.62)0.04Treatment failure/recurrentBrazilian
rs14957416.01 (3.42–10.57)6.86E-11Anti-tuberculosis drug-induced liver injuryThai
NUDT15 (rs116855232)4.97 (2.06–11.97)0.003Hepatotoxicity and leukopeniaChinese
PXR 63396TT4.575 (1.388–15.083)0.007Higher risk of deathUgandan
PXR 63396TT2.944 (1.164–7.443)0.018Worsening peripheral neuropathy
SLCO1B1 (rs11045819)2.89 (1.26–6.62)0.01Treatment-related hepatic adverse effectsBrazilian
TNF-a-308G/A1.94 (1.04–3.63)0.034Anti-tuberculosis drug-induced hepatitisKorean
IsoniazidASTN2 (rs117491755)4.37 (2.25–16.29)1.0 × 10−4Liver injuryEuropean and Indian
CYP2E1 *1A/*1A0.4 (1.1–12)0.02HepatitisCaucasians, Hispanic, African, South Americans, Asians, and Middle Eastern
DraI C/D (CYP2E1) and slow acetylator of NAT2 (NAT2 *5/*5, *5/*6, *5/*7, *6/*6, *6/*7, and *7/*7)8.41 (1.54–45.76)0.01HepatotoxicityTunisian
HLA-B*52:012.67 (1.63–4.37)9.4 × 10−5Liver injuryEuropean and Indian
NAT2*50.69 (0.57–0.83)0.01
Ultra- slow (NAT2*6/*6, *6/*7, and *7/*7)1.89 (0.84–4.22)0.004
NAT2 (rs1041983)13.86 (4.3044.70)4.754 × 10−4Liver injurySingaporean
NAT2(rs1495741)0.10 (0.03–0.33)0.004
NAT2 slow acetylator9.98 (3.32–33.80)8.36 × 10−5
Rapid acetylators (NAT2∗4, ∗12A, and ∗13A)1.26 (0.67–2.37)0.47Fatal treatment outcome incidenceThai
rs1041983 (282c > T) (NAT2)NR0.002Liver injuryIndian
rs1799931 (857G > A) (NAT2)NR0.009
Levofloxacin, bedaquiline, ethionamide, cycloserine, delamanid, pyrazinamide, meropenem, linezolid, and moxifloxacinCYP2E1 C1/C1 + NAT2 slow acetylators (NAT2*5B/7B, *6A/6A, *6A/19, *6A/7B, *6J/7B, *7A/7B, and *7B/7B)5.33 (1.80–15.80)0.003Central nervous system toxicityNigerian
RifampinSLCO1B1*152.04 (1.05–3.96)0.03Liver injuryChinese
Aminoglycosides
GentamicinMT-RNR1 m.1555A>G1.26 (1.07–1.49)0.0058OtotoxicityNR
NOS3 (p Glu298Asp)NR<0.03Vestibular dysfunctionWhite
Anticancer antibiotics
DoxorubicinABCC1 (rs2889517 and rs2074087)0.54 (0.34–0.84)0.006Gastrointestinal toxicityEuropean American, African American, Asian, and othersYao et al. (2014)
ALDH1A1 (rs3764435 and rs168351)1.44 (1.16–1.78)0.0008Hematological toxicity
SLC22A16 T > C (rs714368)0.31 (0.12–0.75)0.01NeutropeniaEgyptian
SLC22A16 T > C (rs714368)0.18 (0.07–0.5)0.001Leukopenia
TACR1 1323C > T: TT2.556 (1.206–5.415)0.0143Nausea and vomitingJapanese
Doxorubicin, daunomycin, epirubicin, and idarubicinCBR3:GG (with low dose, 1–250 mg/m2)5.48 (1.81–16.63)0.003CardiomyopathyHispanic, Non-Hispanic, Black, and others
CBR3:GG (with low to moderate dose, 1–250; 250 mg/m2)3.30 (1.41–7.73)0.006
EpirubicinGSTP1A>G6.4 (1.05–39.0)0.044Hematological toxicitySpanishZárate et al. (2007)
GSTP1A>G6.5 (1.4–31)0.018Overall toxicities
MTHFR 1298A>C24 (2.3–254)0.008Non-hematological toxicities
MTHFR 1298A>C5.7 (1.8–17.6)0.003Overall toxicities
MTHFR + NQO1 (Either variant)0.36 (0.14–0.94)0.038AnemiaIndian
NQO1609TT0.34 (0.12–0.95)0.041
NQO1609TT0.33 (0.12–0.88)0.027Grade 2–4 anemia, leukopenia, or thrombocytopenia
Doxorubicin, daunorubicin, epirubicin, and otherSLC28A3 (rs7853758)0.46 (0.20–1.08)1.6 × 10−5CardiotoxicityNR
SLC28A3 (rs885004)0.42 (0.16–1.10)3.0 × 10−5
UGT1A6 (rs17863783)7.98 (1.85–34.4)2.4 × 10−4
Doxorubicin and daunorubicinABCA1 (rs3887137)2.33 (1.31–4.15)0.0041CardiotoxicityCanadian
ABCB4 (rs1149222)1.87 (1.20–2.92)0.0054
ABCB11 (rs10497346)2.29 (1.16–4.54)0.018
ABCC1 (rs4148350)3.44 (1.65–7.15)0.0012
ABCC9 (rs11046217)4.48 (2.10–9.57)7.1 × 10−5
ABCC10 (rs1214763)0.34 (0.15–0.75)0.0031
COL1A2 (rs42524)1.78 (1.11–2.88)0.018
CYP2J2 (rs2294950)0.41 (0.19–0.90)0.015
FMO2 (rs2020870)0.14 (0.03–0.59)4.2 × 10−4
GPX3 (rs2233302)0.27 (0.11–0.65)7.4 × 10−4
GSTM3 (rs12059276)0.37 (0.14–0.96)0.027
HNMT (rs17583889)1.91 (1.21–3.02)0.0057
SERPINA6 (rs10144771)2.23 (1.39–3.58)9.0 × 10−4
SLC28A3 (rs7853758)0.31 (0.16–0.60)1.0 × 10−4
SLC10A2 (rs9514091)0.43 (0.23–0.78)0.0033
SLC28A3 (rs4877847)0.60 (0.41–0.89)0.0092
SLC22A17 (rs4982753)0.52 (0.31–0.85)0.0078
SLC22A7 (rs4149178)0.41 (0.21–0.77)0.0034
SLCO4C1 (rs2600834)2.01 (1.28–3.16)0.0022
SLCO6A1 (rs12658397)1.83 (1.20–2.80)0.0048
SOD2 (rs7754103)0.30 (0.10–0.94)0.02
SPG7 (rs2019604)0.39 (0.20–0.76)0.0021
SULT2B1 (rs10426628)1.60 (1.03–2.48)0.037
UGT1A6 (rs6759892)1.77 (1.20–2.61)0.0038
XDH (rs4407290)0.26 (0.06–1.16)0.035
BleomycinBLMH (rs1050565GG)16.73 (1.78–157.15)0.014PainChilean
CYP3A41B (rs2740574AG)6.87 (1.02–46.06)0.047Alopecia
ERCC2 (rs1799793AA)27.00 (1.68–434.44)0.02Anemia
ERCC2 (rs238406AA)5.50 (1.26–24.10)0.024Leukopenia
ERCC2 (rs238406CA + AA)4.58 (1.20–17.45)0.026
ERCC2 (rs13181TG)10.86 (1.16–101.35)0.036Alopecia
GSTP1(rs1695GG)12.25 (1.05–143.09)0.046Infections
GSTT1 null17.67 (1.23–252.73)0.034Lymphocytopenia
GSTM1 poor/intermediate genotypeNR0.05Anemia, neutropenia, hemorrhagic cystitis, infections, mucositis, nausea and vomiting, and cardiac, renal, or respiratory toxicitiesSpanish
Sulfonamides
Co-trimoxazoleGCLC (rs761142 TG)2.2 (1.4–3.7)0.0014HypersensitivityUSA
GCLC (rs761142 GG)3.3 (1.6–6.8)0.001
HLA-A*11:016.97 (1.45–33.67)0.0067DRESSThai
HLA-B*13:0115.20 (3.68–62.83)7.2 × 10−5
HLA-B*15:025.16 (1.63–16.33)0.0075SJS/TEN
HLA-B*38:024.05 (1.25–13.18)0.0249
HLA-B*07:02NR0.000001Respiratory failureWhite, Asian, and mixed
HLA-B*13:018.44 (2.66–26.77)2.94 × 10−4SCARs (specifically DRESS)Thai
HLA-C*03:044.67 (1.34–16.24)0.0162DRESSThai
HLA-C*07:2743.57 (1.96–969.96)0.0126DRESSThai
HLA-C*07:2727.73 (1.27–604.11)0.0259SJS/TENThai
HLA-C*08:015.79 (1.79–18.70)0.0049
HLA-C*07:02NR0.000018Respiratory failureWhite, Asian, and mixed
HLA-C*08:018.51 (2.18–33.14)8.60 × 10−4SJS/TEN in AIDS patientsThai
SulfasalazineHLA- B*13:0111.16 (1.98–62.85)0.007DRESSChineseYang et al. (2014)
HLA- B*15:0556.40 (3.07–1034.74)0.041
HLA- B*39:0120.14 (1.77–229.18)0.025
Other antibiotics
LevofloxacinHLA-B*13:014.5 (1.15–17.65)0.043SCARsChinese
HLA-B*13:026.14 (1.73–21.76)7.21 × 10−3
HLA-Serotype B1317.73 (3.61–86.95)4.85 × 10−5
HLA-DQA1*03:013.0 (1.5–6.1)0.005Liver injuryWhite, Black, Asian, and other
HLA-DQA1*03:01 or HLA-B*57:013.2 (1.16–8.85)0.01
CiprofloxacinHLA-B*57:013.1 (1.1–6.9)0.03
MoxifloxacinHLA-DQA1*03:014.2 (1.3–13.4)0.03
HLA-B*57:016.3 (1.4–28.2)0.05
HLA-DQA1*03:01 or HLA-B*57:019.3 (1.5–97.4)0.006
VancomycinHLA-A*32:01NR<0.001DRESS and liver injuryNR
HLA-A*32:01NR1 × 10−8DRESSCaucasian, Hispanic, and African American
ClindamycinHLA-B*15:2755.600 (4.647–665.240)0.0138cADRsChineseYang et al. (2017)
HLA-B*51:019.731 (2.927–32.353)0.0018
HLA-B*51:0124.000 (3.247–177.405)0.0024cADRs (with IV drip)
DapsoneHLA-B*13:0154.00, 95% CI: 7.96–366.160.0001SCARSThai
HLA-B*15:0214.00 (1.45–134.87)0.013
HLA-B*13:0160.75 (7.44–496.18)0.0001DRESS
HLA-B*13:0140.50 (2.78–591.01)0.007SJS/TEN
HLA-B*15:0228.00 (1.71–458.84)0.0326
HLA-B*13:0139.00 (7.67–198.21)5.344 × 10−7SCARsThai and Taiwanese
HLA-B*13:0136.00 (3.19–405.89)2.165 × 10−3SJS/TEN
HLA-B*13:0140.50 (6.38–257.03)1.078 × 10−5DRESS
HLA-C*03:049.00 (2.17–37.38)0.0023SCARs
HLA-C*03:0413.50 (1.71–106.56)0.0212SJS/TEN
HLA-C*03:047.50 (1.56–36.17)0.0155DRESS
HLA-DQB1*06:015.44 (1.39–21.24)0.0258SCARs
HLA-DQB1*06:015.83 (1.29–26.46)0.0274DRESS
HLA-DRB1*15:015.44 (1.39–21.24)0.0258SCARs
HLA-DRB1*15:0110.50 (1.39–79.13)0.0327SJS/TEN
AzithromycinHLA-DQA1*03:013.44 (1.73, 6.47)0.001Liver injuryNon-Hispanic white
MinocyclineHLA-B*35:0229.6 (7.8–89.8)2.5 × 10−8HepatotoxicityCaucasian

Overview of the included studies that reported significant PGx associations of different genes/variants for antibiotic drugs.

Here, DRESS, drug reaction with eosinophilia and systemic symptoms; SJS, Stevens-Johnson syndrome; TEN, toxic epidermal necrolysis; SCAR, severe cutaneous adverse reactions; cADR, cutaneous adverse drug reaction; Ig, immunoglobulin; PGx, pharmacogenomics; NR, not reported; OR, odds ratio; CI, confidence interval.

3.2 Current evidence of PGx for antibiotic-induced hypersensitivity and adverse drug reactions

3.2.1 Beta-lactam antibiotics

We identified eight studies assessing the PGx associations of genes with beta-lactam antibiotics for DIHRs and other adverse effects. These studies primarily investigated the genetic associations with the DIHRs, with only one study examining the genetic link to flucloxacillin-induced liver injury (; ; ; ; ; ; ; ). proposed that LGALS3 could be a potential genetic predictor of immediate drug reactions and reported that rs11125 of LGALS3 (odds ratio, OR = 5.1 in the Italian population (p < 0.0001)) was strongly associated with beta-lactam (BL)-induced allergy. Mast cells release tumor necrosis factor-α (TNF-α) via an immunoglobulin E (IgE)-dependent mechanism. TNFA–308G>A is part of the extended haplotype HLA-A1-B8-DR3-DQ2 and influences the expression of the gene. evaluated this variant in relation to IgE-mediated reactions to BLs and reported its association with the BL-induced immediate allergic reactions. They observed that individuals carrying the –308AA genotype exhibited significantly higher specific IgE serum levels compared to those with the –308GA/GG genotype (p = 0.0046) ().

Other studies aimed to evaluate the association between different HLA genes and DIHRs. identified HLA-DRB1*10:01 (OR = 2.93; p = 5.4 × 10−7) as a risk factor for immediate reaction with BLs even without the HLA-DQA1*01:05 allele (OR = 2.93, p = 5.4 × 10−7). identified LIMD1 (rs62242177 and rs62242178) (significance level 5 × 10−8), HLA-DRB1*04:03 (OR = 4.61, 95% confidence interval (CI): 1.51–14.09, p < 0.002), and HLA-DRB1*14:54 (OR = 3.86, 95% CI: 1.09–13.67, p < 0.002) as potential factors influencing susceptibility to cefaclor-induced type I hypersensitivity. provided robust evidence of HLA-B *55:01 (OR = 1.41; 95% CI: 1.33–1.49, p = 2.04 × 10−31) being associated with the occurrence of penicillin allergy through a genome-wide study. reported HLA-DPB1*05:01 (OR = 1.36, p = 0.004) and HLA-DQB1*05:01 (OR = 1.54, p = 0.03) to be significantly linked with penicillin allergy among Taiwanese. For cephalosporin, on the other hand, identified HLA-DQB1*06:09 (OR = 2.58, 95% CI: 1.62–4.12, p < 0.001), HLA-C*01:02 (OR = 1.36, 95% CI: 1.05–1.77, p = 0.018), and HLA-B*55:02 (OR = 1.76, 95% CI: 1.18–2.61, p = 0.005) alleles to be linked with cephalosporin-induced allergy. performed a genome-wide association study and reported the following associations with flucloxacillin-induced liver injury: HLA-B *57:01 (allelic OR = 36.62, 95% CI: 26.14–51.29, p = 2.67 × 10−97), HLA-A *01:01(OR = 1.86, 95% CI: 1.5–2.31, p = 1.8 × 10−8), HLA-C*06:02 (OR = 10.11, 95% CI: 7.88–12.97, p = 4.3 × 10−74), HLA-B *57:03 (OR = 79.21, 95% CI: 3.37–116.1, p = 1.2 × 10−6), HLA-DQB1*03:03 (OR = 10.18, 95% CI: 7.77–13.34, p = 1.1 × 10−63), HLA-DRB1*07:01 (OR = 4.02, 95% CI: 3.23–5.02, p = 3.8 × 10−35), HLA-DQA1*02:01 (OR = 4.02, 95% CI: 3.22–5.01, p = 4.5 × 10−35). They also stated no association of HLA-B*57 with drug-induced liver injury (DILI) for other isoxazolyl penicillin or amoxicillin ().

These studies are population-based and involve varying sample sizes. Consequently, studies with smaller case numbers may either underestimate or overestimate the findings. Therefore, further evaluation with a larger sample size was encouraged for better understanding, rationalization, and integration of that information in clinical practice.

3.2.2 Aminoglycosides

We identified at least four studies that associated aminoglycoside-induced ototoxicity with MT-RNR1 mutations (; ; ; ). , using a multivariable logistic regression, demonstrated treatment with aminoglycosides in m.1555A>G-carriers was associated with the failed hearing screening (OR = 1.26; 95% CI: 1.07–1.49; p = 0.0058). They also observed the m.1555A>G mutation in all the mothers of the children carrying the m.1555A>G mutation, which was absent in the mothers of the non-carrier children of the m.1555A>G mutation. They suggested antenatal screening of the m.1555A>G mutation through maternal genotyping of pregnant women with preterm labor may potentially be a rational approach to identifying infants with an increased risk of permanent hearing loss (). observed 745A>G, 792C>T, 801A>G, 839A>G, 856A>G, 1027A>G, 1192C>T, 1192C>A, 1310C>T, 1331A>G, 1374A>G, and 1452T>C variants to confer increased sensitivity to nonsyndromic deafness or ototoxic drugs. Bilateral and sensorineural hearing loss was exhibited in 65 Chinese individuals who carried the 1555A>G mutation (). explored the irreversible sensorineural hearing loss (SNHL) with the use of aminoglycosides (streptomycin, gentamicin, kanamycin, amikacin, and neomycin) due to m.1555A > G variants in mitochondrial 12S RNA and observed the presence of polymorphism in 17% of the total population having SNHL after aminoglycoside exposure, and among them, more than half had a family history of SNHL with aminoglycosides. Therefore, they recommended clinical screening and appropriate familial evaluation to avoid associated ototoxicity (). stated that carriers of risk alleles of NOS3 (p.Glu298Asp), GSTZ1 (p.Lys32Glu), and GSTP1 (p.Ile105Val) are relevant for the elevated risk of vestibular dysfunction with gentamicin (p < 0.03).

3.2.3 Sulfonamides

We identified at least five studies that correlated co-trimoxazole/sulfamethoxazole/trimethoprim with genetic association (; ; ; ; ). Similarly, one such study explored the genetic association with sulfasalazine-induced ADRs (Yang et al., 2014). reported that the HLA-B*13:01 allele was significantly associated with co-trimoxazole-induced SCARs, particularly DRESS (OR = 8.44, 95% CI: 2.66–26.77, p = 2.94 × 10−4). Additionally, the HLA-C*08:01 allele was observed to have a significant association with SJS/TEN induced by co-trimoxazole in HIV/AIDS patients [OR of 8.51, 95% CI: 2.18–33.14, p = 8.60 × 10−4] (). evaluated respiratory failure with trimethoprim/sulfamethoxazole and HLA and identified HLA-B *07:02 (p = 0.000001) and HLA-C *07:02 (p = 0.000018) to be significantly associated with the increased risk of respiratory failure. However, stated that MHC polymorphisms were not a major predisposing factor for co-trimoxazole hypersensitivity, although a minor contribution cannot be ruled out. For sulfamethoxazole (SMX)-induced hypersensitivity in HIV/AIDS patients, reported that GCLC (rs761142 T>G) was significantly associated with hypersensitivity induced by SMX (adjusted p-value = 0.045). In a replicated cohort with 249 patients, the result was replicated (p = 0.025). For the combined cohort, homozygous and heterozygous carriers of the minor G allele were recorded for an increased risk of hypersensitivity (GT vs TT, OR = 2.2, 95% CI: 1.4–3.7, p = 0.0014; GG vs. TT, OR = 3.3, 95% CI: 1.6–6.8, p = 0.0010). Each minor allele copy increased the risk of developing hypersensitivity 1.9-fold (95% CI: 1.4–2.6, p = 0.00012) (). identified HLA-C*08:01 (OR = 5.79, 95% CI: 1.79–18.70, p = 0.0049) and HLA-B*15:02 (OR = 5.16, 95% CI: 1.63–16.33, p = 0.0075) alleles as significantly associated with SJS/TEN induced by co-trimoxazole, and the HLA-B*13:01 allele was significantly linked to co-trimoxazole-induced DRESS (OR = 15.20, 95% CI: 3.68–62.83, p = 7.2 × 10−5). Additionally, significantly high frequency of HLA-B*13:01-C*03:04 (OR = 14.53, 95% CI: 3.74–56.47, p = 1.8 × 10−4) and HLA-A*11:01-B*15:02 (OR = 6.00, 95% CI: 1.72–20.88, p = 0.0074) haplotypes were observed in the group of co-trimoxazole-induced DRESS and SJS/TEN, respectively ().

In the Chinese Han population, Yang et al. (2014) explored sulfasalazine-induced DRESS and identified HLA-B*13:01 as a potential biomarker for increasing the risk of DRESS since the distribution of the HLA-B*13:01 allele was significantly higher in sulfasalazine-induced DRESS patients than in sulfasalazine-tolerant patients (OR = 13.00, 95% CI: 1.76–95.80, p = 0.004) (Yang et al., 2014).

3.2.4 Anti-tuberculous drugs

We identified at least 25 studies evaluating the PGx associations of different genes with anti-tuberculous drug (ATD)-induced adverse effects (; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; Yamada et al., 2010; Yuliwulandari et al., 2019; Yuliwulandari et al., 2016; Zhang et al., 2020). Of these, the study by Li et al. evaluated the association of ATDs in pediatric patients and reported a striking difference in the allele distribution of rs1800796 in the IL6 gene between the control and case groups, and the G allele of rs1800796 was linked with an elevated risk for anti-tuberculosis drug-induced hepatotoxicity (OR = 2.48, 95% CI: 1.40–4.40, p = 0.002). After Bonferroni correction, no significant difference was observed in the allele and genotype distributions of the other SNPs in the IL6, XO, and NOS2 genes between the control and case groups (). Three studies evaluated the association of GSTM1 and GSTT1 with ATDs. They reported that the homozygous null mutation of the GSTM1 gene, either alone or in combination with T1, was significantly associated with anti-tuberculosis drug-induced hepatotoxicity (p < 0.02 and p < 0.007, respectively); one study further reported that the GSTM1 polymorphism (rs412543) (p = 0.01) was linked to an elevated risk of treatment-related adverse events, including hepatotoxicity. Conversely, another study found no significant role of the GSTM1 and GSTT1 null genotypes in anti-tuberculosis drug-induced liver injury, although there was evidence that GSTM1 polymorphisms may be related to the intensity of toxicity (p = 0.007) (; ; ).

Yuliwulandari et al. (2019) found that the NAT2 slow-acetylator phenotype was significantly associated with the risk of AT-DILI (p = 2.7 × 10−7, OR = 3.64, 95% CI: 2.21–6.00). The NAT2 ultra-slow acetylator showed an even stronger association with AT-DILI risk in the subgroup analysis (p = 4.3 × 10−6, OR = 3.37, 95% CI: 2.00–5.68). In the Thai population, reported that the A allele of rs1495741, the top SNP in the intergenic region of NAT2 and PSD3, was significantly associated with anti-tuberculosis drug-induced liver injury (ATDILI) (OR = 6.01, 95% CI: 3.42–10.57, p = 6.86E-11), identifying that NAT2 ultra-slow acetylator as the most important risk factor for ATDILI. In the Indian population, observed that allele T (rs1041983) (p = 0.002) and allele A (rs1799931) (p = 0.009) were associated with an elevated risk of drug-induced liver injury in patients receiving anti-tubercular drugs, compared to allele C and allele G, respectively. reported that NAT2*5/*5, *5/*6, *5/*7, *6/*6, *6/*7, *6/*14, and *7/*7 (grouped as the slow-acetylator phenotype) were linked to an increased likelihood of toxic liver disease during treatment with ethambutol and isoniazid/pyrazinamide/rifampin in individuals with tuberculosis (p = 0.03), compared to NAT2*1/*5, *1/*6, and *1/*7 (grouped as intermediate acetylator and rapid acetylator phenotypes). Three additional studies confirmed that slow NAT2 acetylators are a risk factor for ATDILI. Specifically, NAT2*6 was associated with an increased risk (OR = 4.75, 95% CI: 1.80–12.55, p = 0.00077), while no significant association was observed for NAT2*5 or *7. On the contrary, NAT2*4 was associated with a decreased risk of drug-induced liver injury (p = 1.8 × 10−6, OR = 0.2, 95% CI: 0.1–0.39); compared to intermediate or rapid acetylators (NAT2*4, NAT2*12A, and NAT2*13), slow acetylators due to NAT2 genotypes (NAT2*5B, NAT2*5C, NAT2*6A, NAT2*7A, and NAT2*7B) exhibited a higher risk of liver injury (p = 1.7 × 10−4, OR = 3.45, 95% CI: 1.79–6.67). Overall, the slow-acetylator type due to the polymorphism of NAT2 was considered a risk factor for ATDILI (OR = 3.56, 95% CI: 1.256–10.119), and slow NAT2 acetylators (patients lacking NAT2*4) showed a significant association with ATDILI risk (OR = 8.80; 95% CI = 4.01–19.31, p = 1.53 × 10−8) (; Yuliwulandari et al., 2016; Zhang et al., 2020). In patients with tuberculosis, observed that rapid acetylators due to NAT2 polymorphism had a 1.26-fold higher incidence of fatal treatment outcomes (95% CI: 0.67–2.37) compared to intermediate acetylators.

reported an increased risk of leukopenia and hepatotoxicity associated with CYP2D6 rs1135840 and NUDT15 rs116855232, with ORs of 2.52 (95% CI: 1.43–4.44, p = 0.009) and 4.97 (95% CI: 2.06–11.97, p = 0.003), respectively. For multidrug-resistant tuberculosis treatment, reported a significant association between CNS toxicity and the dominant model of inheritance for the crude model (p = 0.024; OR = 3.57; 95% CI: 1.18–10.76) and the adjusted model (p = 0.031, OR = 3.92, 95% CI: 1.13–13.58). They reported that the AT + TT genotype of IL8 (rs4073) is associated with a 3.92-fold increased risk of CNS toxicity compared to the AA genotype ().

Apart from the GSTM1 association as mentioned earlier, also explored other genetic associations and stated that NAT2 slow acetylator status was linked with an increased risk of treatment-related adverse events, including hepatotoxicity, compared with rapid acetylator (OR = 2.32, 95% CI: 0.79–6.77). Treatment failure or recurrence was more likely among NAT2 rapid acetylators. Similarly, SLCO1B1 (p = 0.01) was linked with an elevated risk of treatment-related adverse events, including hepatotoxicity. Polymorphisms in NR1I2 were associated with decreased risk of adverse effects but increased risk of failure/recurrence (p = 0.04). Although in whole exome sequencing, hepatotoxicity was associated with a polymorphism in VTI1A, and the genes METTL17 and PRSS57, but none achieved genome-wide significance (). reported that NAT2 (rs1799930), SLCO1B1 (rs4149032), and PXR (rs2472677) variants affected isoniazid exposure. Genotype TT (rs2472677) was linked with an elevated peripheral nervous system disease (p = 0.018) and elevated death risk (p = 0.007) with treatment with ethambutol, isoniazid, efavirenz, and rifampin in people with HIV and tuberculosis compared with genotypes CC and CT.

Although univariate analyses by and found no statistically significant association between ATDILI and the frequency of HLA-DQB1 genotypes, multivariate analysis revealed that individuals carrying two DQB1*05 alleles had a higher risk of ATDILI compared to the control group (OR = 5.28 adjusted for use of liver-protective drugs and weight 10/88 VS 2/88, 95% CI: 1.134–24.615, p = 0.034). Regardless of the presence of pre-existing liver disease, the heterozygous CYP3A4*18 genotype was associated with anti-tuberculosis drug-induced hepatotoxicity (ATDH) in a study by (OR: 3.24, 95% CI: 1.06–9.86). Although among the subjects without having liver disease, CYP3A4*18 heterozygotes were observed to have a significantly higher risk of ATDH (OR: 9.10, 95% CI: 1.56–53.16), in subjects with previous liver disease, CYP3A4*18 heterozygotes had a lower risk of ATDH (OR: 0.21, 95% CI: 0.05–0.98) (). The frequency of -308AG/AA carriers was found to be significantly higher in ATD-induced hepatitis patients than the ATD-tolerant patients (p = 0.034, OR = 1.94; 95% CI = 1.04–3.64) and the frequency of the A allele significantly differed between the two groups (p = 0.018, OR 1.95, 95% CI = 1.11–3.44). These results indicated that the TNFA-308G/A polymorphism was significantly associated with ATDH (). deemed slow acetylators due to NAT2 genotypes (particularly, NAT2*6A/7B and NAT2*6A/6A) risk factors for drug-induced hepatotoxicity (DIH) (OR = 9.57; p < 0.001) for NAT2*6A/7B; OR 5.24 (p = 0.02) for NAT2*6A/6A). Although the CYP2E1 genotype was not significantly linked with the development of anti-tuberculosis DIH, the combination of the CYP2E1 C1/C1 genotype and the NAT2 genotype of slow acetylator was observed to increase the risk of anti-tuberculosis (OR = 5.33; p = 0.003) compared to the combination of the NAT2 rapid acetylator genotype paired with either a C1/C2 or C2/C2 genotype ().

Six of the studies evaluated PGx’s association with the adverse effects of isoniazid alone. , on the Singaporean population, performed a study and identified a significant association of two SNPs of NAT2 (rs1041983 and rs1495741) and NAT2 slow acetylators with isoniazid-induced liver injury (OR = 13.86, 95% CI: 4.30–44.70; OR = 0.10, 95% CI = 0.03–0.33 and OR = 9.98, 95% CI = 3.32–33.80, respectively). They also stated a model based on clinical and NAT2 acetylator status resulted in much better prediction for isoniazid-induced liver injury compared to a clinical model alone (area under the receiver operating characteristic curve = 0.863 vs. 0.766, respectively, p = 0.027) (). A genome-wide association study by Nicoletti et al. identified rs117491755 in ASTN2 as being significantly associated with DILI in European patients only. HLA-B*52:01 was also found to be significant (OR = 2.67, 95% CI = 1.63–4.37, p = 9.4 × 10−5). The frequency of NAT2*5 was lower for cases (OR = 0.69, 95% CI = 0.57–0.83, p = 0.01). NAT2*6 and NAT2*7 were relatively common, homozygotes for NAT2*6 and/or NAT2*7 being enriched in cases (OR = 1.89, 95% CI = 0.84–4.22, p = 0.004). They reported that HLA genotypes made a minimal contribution to ATDILI and that the contribution of NAT2 was complex. However, their findings were consistent with previous studies when considering differences in metabolic effects between NAT2*5, NAT2*6, and NAT2*7 alleles (). Two separate studies reported that NAT2 and CYP2E1 variants were not associated an increased risk of isoniazid-induced hepatotoxicity when analyzed independently; however, Vuilleumier et al. found that compared with other CYP2E1 genotypes, a significant association between the CYP2E1 *1A/*1A genotype and isoniazid-induced elevated liver enzymes, including hepatitis (OR: 3.4; 95% CI:1.1–12; p = 0.02), and a non-significant trend for isoniazid induced hepatotoxicity was also recorded (OR: 5.9; 95% CI: 0.69–270; p = 0.13). Similarly, Ben Fredj et al. stated that a combined analysis of the polymorphism in the NAT2/CYP2E1 gene revealed that individuals with both DraI C/D (CYP2E1) and slow acetylator (NAT2) genotypes have an elevated risk of isoniazid-induced hepatotoxicity as compared to other combined NAT2/CYP2E1 genotype profiles (OR: 8.41, p = 0.01, 95% CI: 1.54–45.76) (; ). Yamada et al. (2010) found no association between isoniazid-induced hepatotoxicity SNPs and haplotypes at CES2 and CES1/CES4.

evaluated the PGx association of rifampin and identified an association between SLCO1B1*15 and the increased risk of drug-induced liver injury (p = 0.03, OR = 2.04, 95% CI: 1.05–3.96). No such association was found for SLCO1B1*5 and *1.

3.2.5 Anticancer antibiotics

We identified at least 11 studies assessing the association of genes with the adverse effects of anthracyclines (; Yao et al., 2014; ; ; ; ; ; ; Zárate et al., 2007; ; ). Five of them were on pediatric patients. Among those, reported that G6PD deficiency did not have any effect on the hemolytic toxicities with daunorubicin during the induction treatment for acute lymphoblastic leukemia (p = 0.73). observed the exposure of low-to-moderate doses of anthracyclines in individuals carrying the variant A allele (CBR1:GA/AA and/or CBR3:GA/AA) did not raise the risk of cardiomyopathy, but with similar doses, an increased risk of cardiomyopathy was observed in individuals with the CBR3 V244M homozygous G genotypes (CBR3:GG) compared to the individuals with the CBR3:GA/AA genotypes unexposed to anthracyclines (OR = 5.48; p = 0.003) and exposed to low-to-moderate doses of anthracyclines (OR = 3.30; p = 0.006). High doses of anthracyclines, irrespective of CBR genotype status, were associated with increased cardiomyopathy risk (). Visscher et al. identified a highly significant association with a synonymous coding variant, rs7853758 (L461L), in the SLC28A3 gene with anthracycline-induced cardiotoxicity in children (OR = 0.35; p = 1.8 × 10−5, single marker test). Additionally, other significant associations with protective and risk variants in other genes, including SLC28A1, ABCB1, ABCB4, and ABCC1, were present. For safer treatment options, combining genetic risk profiles may be considered (). In this replication cohort, Visscher et al. confirmed the association of rs17863783 (UGT1A6) and anthracycline-induced cardiotoxicity (p = 0.0062, OR = 7.98). Additionally, evidence for the association of rs885004 (p = 0.058, OR 0.42) and rs7853758 (p = 0.058, OR 0.46) in SLC28A3 was reported (combined p = 3.0 × 10−5 and p = 1.6 × 10−5, respectively). Unlike a previously constructed model for prediction, the improved prediction model constructed utilizing the replicated genetic variants alongside the clinical factors discriminated significantly better among cases and controls against only clinical factors, both in the original (AUC 0.77 vs. 0.68, p = 0.0031) and replication cohort (AUC 0.77 vs. 0.69, p = 0.060) (). In this study, Visscher et al. identified significant associations of SLC22A7 (rs4149178, p = 0.0034) and SLC22A17 (rs4982753, p = 0.0078) with anthracycline-induced cardiotoxicity in both discovery and replication cohort. Additionally, evidence was found for SULT2B1 and several other genes related to oxidative stress ().

Yao et al. (2014) observed in breast cancer patients that rs3764435 and rs168351 (ALDH1A1) were significantly associated with hematological toxicity (OR = 1.44, 95% CI: 1.16–1.78, p = 0.0008), and rs2889517 and rs2074087 (ABCC1) were significantly associated with gastrointestinal toxicity (OR = 0.54, 95% CI: 0.34–0.84, p = 0.006). , in a study on Zimbabwean breast cancer patients, found no significant association between doxorubicin-induced cardiotoxicity and SLC28A3 (rs7853758, p = 0.408), UGT1A6*4 (rs17863783, p = 0.354), or RARG (rs2229774, p = 0.471). , in Egyptian breast cancer patients, reported that carriers of CBR1 C>T (rs20572) had significantly higher doxorubicin concentrations, but no significant association with hematological toxicity was observed. On the contrary, although no significant effect of SLC22A16 T>C (rs714368) on the plasma concentration was observed, it was significantly correlated with a lower risk of neutropenia (OR 0.31, 95% CI = 0.12–0.75, p = 0.01) and leucopenia (OR 0.18, 95% CI = 0.07–0.5, p = 0.001). Doxorubicin-related cardiotoxicity was associated with the cumulative doxorubicin dose (OR = 0.238, p = 0.017), but not with any of the two SNPs examined (). reported that in breast cancer patients receiving triplet antiemetic combination regimens, ABCB1 2677G>T/A was not predictive of the antiemetic response. However, an association was observed between the TACR1 1323C>T polymorphism and complete response in the acute phase.

Among Indian breast cancer patients treated with 5-fluorouracil, epirubicin/methotrexate/adriamycin, and cyclophosphamide regimens, observed that grade 2–4 toxicity (anemia, leucopenia, or thrombocytopenia) was significantly associated with NQO1609TT (OR = 0.33, 95% CI: 0.12–0.88, p = 0.027). Further analysis for anemia found a significant association with NQO1609TT (OR = 0.34; 95% CI: 0.12–0.95; p = 0.041) and the combination of MTHFR + NQO1 (either variant) (OR = 0.36; 95% CI = 0.14–0.94; p = 0.038) (). For breast cancer adjuvant therapy with anthracycline (epirubicin), Zárate et al. (2007) found that hematological GIII-IV toxicity was associated with GSTP1 polymorphism (p = 0.044, hazard ratio, HR = 6.4, 95% CI: 1.05–39). Evaluation of non-hematological toxicities revealed increased and significant HR for GIII-IV toxicities in the MTHFR-1298 AC + CC group (HR = 24, 95% CI = 2.3 to 254, p = 0.008). They identified GSTP1 and MTHFR-1298A>C polymorphisms as independent risk factors regarding overall toxicities (Zárate et al., 2007). Two studies establishing a genetic association with bleomycin-induced ADRs were selected for the study. The first one, by , explored the use of bleomycin in Hodgkin lymphoma and found that the carrier of GSTM1 extensive or ultrahigh activity was linked to a decreased risk of grade III/IV toxicity development (p = 0.05), but with efficacy analysis, they concluded that compared to PGx determinants, clinical determinants could be more relevant for the Hodgkin lymphoma treatment. The other study explored the genetic association of toxicities with the bleomycin-containing regimen in Chilean testicular cancer patients and emphasized the need of PGx implementations for severe ADR prediction based on some robust genetic associations, including ERCC2 (rs1799793AA) and anemia (OR = 27.00, 95% CI = 1.68–434.44, p = 0.020), ERCC2 (rs238406AA) and leukopenia (OR = 5.50, 95% CI = 1.26–24.10, p = 0.024), GSTT1 null and lymphocytopenia (OR = 17.67, 95% CI = 1.23–252.73, p = 0.034), CYP3A41B (rs2740574GG) and alopecia (OR = 6.87, 95% CI = 1.02–46.06, p = 0.047), BLMH (rs1050565) and pain (OR = 16.73, 95% CI = 1.78–157.15, p = 0.014) and GSTP1 (rs1695GG) and infections (OR = 12.25, 95% CI = 1.05–143.09, p = 0.046) ().

3.2.6 Other antibiotics

A study of genetic association of levofloxacin-induced SCARs in the Chinese population by Jiang et al. revealed that compared to levofloxacin-tolerant patients, significantly higher frequencies of HLA-B*13:01 (OR: 4.50, 95% CI: 1.15–17.65, p = 0.043), HLA-B*13:02 (OR: 6.14, 95% CI: 1.73–21.76, p = 0.0072), and serotype B13 (OR: 17.73, 95% CI: 3.61–86.95, p = 4.85 × 10−5) were observed in patients with levofloxacin-induced SCARs. They proposed prospective screening or alternative therapy that may benefit the patient in concern (). found a significant association with HLA-DQA1*03:01 and HLA -B*57:01 for DILI induced by fluoroquinolones (ciprofloxacin, levofloxacin, and moxifloxacin). Details of the specific ORs are presented in Table 1.

Of the included studies, we identified two studies that evaluated the association of HLA with vancomycin-induced adverse effects, such as liver injury and DRESS. reported that HLA-A*32:01 was associated with vancomycin-induced liver injury and DRESS (p < 0.001). noted that the carriage of the HLA-A*32:01 allele is significantly associated (p = 1 × 10−8) with the development of DRESS induced by vancomycin.

Yang et al. (2017) evaluated the genetic association with clindamycin-induced cADRs in the Chinese population and observed that compared to the control and clindamycin-tolerant groups, the frequency of HLA-B*51:01 was significantly higher in the case group. They identified HLA-B*51:01 as a risk allele for clindamycin-related cADRs in the Han Chinese population, particularly with clindamycin administration via an intravenous drip (OR = 24.00, 95% CI: 3.25–177.41, p = 0.0024). HLA-B*15:27 was also found to have a link with clindamycin-induced cADRs (OR = 55.60, 95% CI: 4.647–665.24, p = 0.0046, pc = 0.0184) (Yang et al., 2017).

explored the genetic link with minocycline hepatotoxicity and noted HLA-B*35:02 to have a significant association with the risk for minocycline-induced liver injury (OR: 29.6, 95% CI: 7.8–89.8, p = 2.5 × 10−8). Sequence-based HLA typing verified this association ().

Two of the included studies explored the PGx association of dapsone-induced SCARs. reported that the HLA-B*13:01 allele had a significant association with SCARs induced by dapsone compared to the dapsone-tolerant controls (OR: 54.00, 95% CI: 7.96–366.16, p = 0.0001) and the general population (OR: 26.11, 95% CI: 7.27–93.75, p = 0.0001). Additionally, HLA-B*13:01 was found to be associated with dapsone-induced DRESS (OR: 60.75, 95% CI: 7.44–496.18, p = 0.0001) and SJS-TEN (OR: 40.50, 95% CI: 2.78–591.01, p = 0.0070) in non-leprosy Thai patients (). Of all HLA alleles, reported that only the HLA-B*13:01 allele was significantly associated with dapsone-induced SCARs (OR = 39.00, 95% CI: 7.67–198.21, p = 5.3447 × 10−7), DRESS (OR = 40.50, 95% CI: 6.38–257.03, p = 1.0784 × 10−5), and SJS-TEN (OR = 36.00, 95% CI: 3.19–405.89, p = 2.1657 × 10−3) compared with dapsone-tolerant controls. The HLA-B*13:01 allele was also strongly associated with dapsone-induced SCARs among the Taiwanese population (OR = 31.50, 95% CI: 4.80–206.56, p = 2.5519 × 10−3) and Asians (OR = 36.00, 95% CI = 8.67–149.52, p = 2.8068 × 10−7) (). Compared to the control population, observed a significant association with HLA-DQA1*03:01 for azithromycin-induced liver injury (OR = 3.44, 95% CI: 1.73, 6.47, p = 0.001) and recommend further exploration for a comprehensive understanding of the mechanism involved and clinical role ().

3.3 Current state of PGx-based clinical annotations and drug labels for antibiotics

We used the PharmGKB clinical annotations to determine the current PGx evidence level for the variants and genes involved in the safety and effectiveness of the antibiotics. Based on variant annotations and incorporating available variant-specific prescribing guidelines and FDA-approved drug labels, these annotations provide information on the drug–variant pairs. Following a scoring system, these annotations are then assigned a level of evidence ranging from level-4 (unsupported) to level-1A (high) (; ). Our search across PharmGKB revealed clinical annotations for at least 36 antibiotic drugs, each with various variants of at least 85 genes. These annotations are presented in Tables 2, 3.

TABLE 2

DrugGeneVariantClinical annotationLevel of evidence
AmoxicillinHLA-BHLA-B*18:01Toxicity3
HLA-DQB1rs9274407Toxicity3
CeftriaxoneABCC2rs2273697Metabolism/PK3
ABCG2rs13120400Metabolism/PK3
CefotaximeSLC22A8rs11568482Metabolism/PK3
ErythromycinABCC2rs717620other3
CYP3A4rs35599367other3
AmikacinMT-RNR1rs267606617Toxicity1A
NeomycinMT-RNR1rs267606617Toxicity1A
GentamicinMT-ND1, MT-RNR1rs267606617, rs267606618, rs267606619, and rs28358569Toxicity1A
KanamycinMT-RNR1rs267606617, rs267606618, and rs267606619Toxicity1A
StreptomycinMT-RNR1rs267606617, rs267606618, and rs267606619Toxicity1A
MT-RNR1rs28358569 and rs1556422499Toxicity3
GSTM1GSTM1 non-null and GSTM1 nullToxicity4
GSTT1GSTT1 non-null and GSTT1 nullToxicity4
TobramycinMT-RNR1rs267606617, rs267606619Toxicity1A
CiprofloxacinG6PDG6PD B (reference), G6PD Mediterranean, Dallas, Panama, Sassari, Cagliari, and BirminghamToxicity3
DaptomycinABCB1rs1045642Metabolism/PK3
MinocyclineHLA-BHLA-B*35:02Toxicity3
MetronidazoleCYP2A6CYP2A6*1, CYP2A6*2, CYP2A6*9, and CYP2A6*17Metabolism/PK3
ChloramphenicolG6PDG6PD A- 202A_376G, G6PD B (reference)Toxicity3
MT-RNR1rs28358569 and rs1556422499Toxicity3
GSTT1GSTT1 non-null and GSTT1 nullToxicity4
Penicillin GHLA-BHLA-B*55:01Toxicity3
Penicillin VHLA-BHLA-B*55:02Toxicity3
FlucloxacillinHLA-BHLA-B*57:01Toxicity1A
NR1I2rs3814055Toxicity3
DicloxacillinABCB1rs2032582 and rs1045642Metabolism/PK and others3
ClindamycinHLA-BHLA-B*51:01, HLA-B*15:27Toxicity3
VancomycinHLA-AHLA-A*32:01Toxicity3
GeldanamycinEGFRrs712829Efficacy3

Current PGx-based clinical annotations of various antibiotic–gene pairs with the PharmGKB level of evidence.

Here, evidence level 1A-(High), Level 3-(low) and level 4-(Unsupported); PK-Pharmacokinetics.

TABLE 3

DrugGeneVariantsClinical annotationLevel of evidence
RifampicinGSTT1GSTT1 non-null and GSTT1 nullToxicity4
TNFrs1800629Toxicity3
SLCO1B1rs11045819, rs2306283, rs4149032, rs4149056, SLCO1B1*1, and SLCO1B1*15Metabolism/PK and toxicity3
RIPOR2rs10946737 and rs10946739Toxicity3
NR1I2rs2472677Other3
NOS2rs11080344Toxicity3
NAT2rs4646244, rs1041983, and rs1041983Metabolism/PK and toxicity3
GSTP1rs1695Toxicity3
CYP2C9rs9332096Toxicity3
CYP2C19rs4986893Toxicity3
CYP2B6CYP2B6*1 and CYP2B6*6Toxicity3
CUX2rs7958375Toxicity3
AGBL4rs320003, rs393994, and rs319952Toxicity3
AADACrs1803155Metabolism/PK3
PyrazinamideCYP2B6CYP2B6*1 and CYP2B6*6Toxicity3
CYP2C19rs4986893Toxicity3
CYP2C9rs9332096Toxicity3
NAT2rs4646244, rs1041983, and rs1041983Metabolism/PK and toxicity3
TNFrs1800629Toxicity3
GSTT1GSTT1 non-null and GSTT1 nullToxicity4
IsoniazidNAT2NAT2*4, NAT2*5, NAT2*6, NAT2*7, NAT2*14, and NAT2*16Toxicity1B
NAT2NAT2*4, NAT2*5, NAT2*6, NAT2*7, NAT2*14, NAT2*16, and NAT2*39Metabolism/PK2A
ABCB1rs1045642Toxicity3
BACH1rs2070401Toxicity3
CYP2B6CYP2B6*1 and CYP2B6*6Toxicity3
CYP2C19rs4986893Toxicity3
CYP2C9rs9332096Toxicity3
GSTP1rs1695Toxicity3
MAFKrs4720833Toxicity3
NAT2rs1041983, rs4646244, rs1799930, rs1208, rs1801280, rs1799931, and rs1799929Metabolism/PK and toxicity3
NOS2rs11080344Toxicity3
TNFrs1800629Toxicity3
XPO1rs11125883Toxicity3
GSTT1GSTT1 non-null and GSTT1 nullToxicity4
EthambutolCYP2B6CYP2B6*1 and CYP2B6*6Toxicity3
CYP2C19rs4986893Toxicity3
CYP2C9rs9332096Toxicity3
NAT2rs4646244 and rs1041983Metabolism/PK and toxicity3
TNFrs1800629Toxicity3
GSTT1GSTT1 non-null and GSTT1 nullToxicity4
DapsoneHLA-BHLA-B*13:01Toxicity2A
HLA-AHLA-A*24:02Toxicity3
HLA-BHLA-B*15:02Toxicity3
HLA-DRB1rs17211071, rs701829, rs201929247, HLA-DRB1*15:01, and HLA-DRB1*16:02Toxicity3
G6PDrs1050828Toxicity4
Co-trimoxazoleHLA-BHLA-B*13:01, HLA-B*15:02, and HLA-B*38:02Toxicity2A
HLA-CHLA-C*06:02, HLA-C*07:27, and HLA-C*08:01Toxicity2B
GSTM1GSTM1 non-null and GSTM1 nullToxicity3
HLA-BHLA-B*07:02Toxicity4
HLA-CHLA-C*07:02Toxicity3
NAT2NAT2*4, NAT2*5, NAT2*6, NAT2*7, NAT2*14, NAT2*16, rs1799930, and rs1799931Toxicity3
G6PDG6PD B (reference), G6PD Canton, Taiwan-Hakka, Gifu-like, and Agrigento-likeToxicity4
SulfasalazineABCG2rs2231142 and rs72552713Metabolism/PK and efficacy3
G6PDG6PD A- 202A_376G and G6PD B (reference)Toxicity3
HLA-BHLA-B*39:01, HLA-B*13:01, and HLA-B*15:05Toxicity3
MTRrs1805087Efficacy3
DaunorubicinSLC28A3rs7853758Toxicity2B
ABCB1rs2032582Efficacy3
BMP7rs79085477Toxicity3
DOK5rs117532069Toxicity3
DROSHArs639174Toxicity3
GATA3rs3824662Toxicity3
LINC00251rs141059755Toxicity3
RARGrs2229774Toxicity3
SLCO1B1rs2291075Efficacy3
NOS3rs1799983Efficacy3
NRP2rs10932125Other3
DoxorubicinSLC28A3rs7853758Toxicity2B
ABCB1rs2229109, rs1045642, rs2032582, rs1128503, rs4148737, and rs45511401Efficacy and toxicity3
ABCC2rs8187710, rs3740066, rs17222723, rs2273697, and rs717620Toxicity and efficacy3
ABCC3rs4148416Efficacy3
ABCC4rs9561778Toxicity3
ABCG2rs2231142Toxicity3
AKR1C3rs1937840Efficacy3
ALDH1A1rs6151031Efficacy3
ALDH3A1rs2228100Toxicity3
ATMrs1801516Toxicity3
BMP7rs79085477Toxicity3
CBR1rs9024 and rs20572Dosage, toxicity, and metabolism/PK3
CBR3rs8133052Toxicity and efficacy3
CCND1rs9344Efficacy3
CLCN6 and MTHFRrs1801133Toxicity3
CYBArs4673Toxicity and efficacy3
CYP1B1rs1056836Toxicity3
CYP2B6rs3745274, rs12721655, and rs3211371Dosage, efficacy, and toxicity3
CYP2C19rs4244285 and rs12248560Toxicity and Efficacy3
DOK5rs117532069Toxicity3
ERCC1rs11615 and rs3212986Toxicity3
ERCC2rs13181Toxicity3
GATA3rs3824662Efficacy3
GSTA1rs3957357Efficacy3
GSTM1GSTM1 non-null and GSTM1 nullToxicity and efficacy3
GSTP1rs1695Toxicity and efficacy3
GSTT1GSTT1 non-null and GSTT1 nullEfficacy3
LINC00251rs141059755Toxicity3
MTHFD1rs2236225Efficacy3
NCF4rs1883112Toxicity3
NOS3rs1799983 and rs2070744Efficacy3
NQO2rs1143684Efficacy3
RAC2rs13058338Toxicity3
RARGrs2229774Toxicity3
SLC22A16rs714368, rs6907567, rs12210538, and rs723685Toxicity, dosage, and efficacy3
SLCO1B1rs4149056Toxicity3
TMEM43 and XPCrs2228001Toxicity3
XRCC1rs25487Toxicity3
EpirubicinCBR3rs112783657 and rs74743371Toxicity3
CCNKrs77769901Toxicity3
CYP1B1rs1056836Toxicity and efficacy3
CYP2C8rs117458836Toxicity3
FOXO1rs144991623Toxicity3
GNL3rs112242273Toxicity3
GSTP1rs1695Toxicity and efficacy3
HMMRrs299313, rs299314, and rs299293Toxicity3
INSRrs142244113 and rs41412545Toxicity3
IRS1rs115457081Toxicity3
MDM4rs1563828Efficacy3
NOS1rs149212925Toxicity3
NOS3rs1799983Efficacy3
NQO1rs1800566Efficacy3
PERPrs78428806, rs117101815, rs9402944, and rs9389568Toxicity3
PIGBrs12050587Toxicity3
PIK3R2rs117951771, rs148235907, rs138602176, rs150688309, rs79430272, rs55633228, rs118129530, rs56022120, rs117341846, rs148013902, rs145623321, rs58695150, and rs8110364Toxicity3
PON1rs662Efficacy3
PPP2R5Drs3805945Toxicity3
RBX1rs141084494Toxicity3
SLCO1B1rs4149056Toxicity3
TOP2Ars181501757Toxicity3
TP53rs4968187Toxicity3
MitoxantroneTP53AIP1rs118088833Toxicity3
GALNT14rs9679162 and rs12613732Efficacy3
SLCO1B1rs2291075Efficacy3
BleomycinABCB1rs1045642 and rs2229109Toxicity3
BLMHrs1050565Toxicity3
CYP3A4rs2740574Toxicity3
ERCC1rs3212986 and rs11615Toxicity3
ERCC2rs1799793, rs238406, and rs13181Toxicity3
GSTM1GSTM1 non-null and GSTM1 nullToxicity and efficacy3
GSTP1rs1695Toxicity3

Current PGx-based clinical annotations of various antibiotic–gene pairs with the PharmGKB level of evidence.

PGx, pharmacogenomics; PK, pharmacokinetics.

Although most of the annotations were assigned evidence level-3 (low), for a few antibiotics, we also identified some moderate (2A and 2B) and high (1A and 1B) levels of evidence. Aminoglycosides (amikacin, neomycin, gentamicin, kanamycin, streptomycin, and tobramycin) had a level-1A association for toxicity (ototoxicity) with different variants of MT-RNR1rs267606617 being the variant common to all of them. Other variants are outlined in Tables 2, 3. For flucloxacillin, we observed another level-1A association with HLA-B*57:01 for drug-induced liver injury. For isoniazid induced toxicity, level-1B evidence was assigned with the NAT2 for the variants NAT2*1, NAT2*4, NAT2*5, NAT2*6, NAT2*7, NAT2*14, and NAT2*16.

Similarly, level-2A evidence was assigned with isoniazid for metabolism/PK for various variants of the NAT2 gene (i.e., NAT2*1, NAT2*4, NAT2*5, NAT2*6, NAT2*7, NAT2*14, NAT2*16, and NAT2*39). For drug-induced toxicity, an evidence level of 2A was assigned with various variants of HLA-B for co-trimoxazole (HLA-B*13:01, HLA-B*15:02, and HLA-B*38:02) and dapsone (HLA-B*13:01). Co-trimoxazole also had a level-2B association for toxicity with HLA-C*06:02, HLA-C*07:27, and HLA-C*08:01. Anthracycline antibiotics (doxorubicin and daunorubicin) had a level-2A association for drug-induced toxicity with SLC28A3 (rs7853758).

Considering the overall clinical annotations for antibiotics, we identified HLA-B (one level-1A, two level-2A, and eight level-3 associations), MT-RNR1 (six level-1A and two level-3 associations), and NAT2 (one level-1B, one level-2B, and five level-3 associations) as concerning genes for the safety and effectiveness of the antibiotic drug. The clinical annotations of level-1 and level-2 for antibiotics are outlined in Figure 2.

FIGURE 2

The PharmGKB curates and presents the PGx-based drug labels on its site. These labels are sourced from the FDA, EMA, PMDA, HCSC, and Swissmedic and are presented as testing required, testing recommended, actionable PGx, informative PGx, no clinical PGx, and criteria not met (). Our search across the PharmGKB website revealed PGx label information for at least 27 antibiotic drugs, considering the polymorphisms of at least 6 genes (MT-RNR1, G6PD, NAT2, CYB5R3, CYP3A4, and HLA-B) involved. These labels are presented in Table 4. Although the majority of the drugs were labeled as actionable PGx, none were labeled as no clinical PGx, testing required, or testing recommended. Actionable PGx entails contraindication, dose alteration, alternative therapy, or other management for individuals with a specific metabolizer phenotype or genotype (if known). This label, however, does not recommend phenotype or genotype testing prior to the use of the drug. The informative PGx label provides information on a particular variant/gene/phenotype/protein that can potentially affect the metabolism, concentration, and frequency of side effects or impose a general risk for the patients. However, this label provides no further guidance for the actions to be undertaken in such situations (PharmGKB). The overall statistics of the PGx label of antibiotics are shown in Figure 3. The majority of these labels are sourced from the FDA-approved drug label with at least 11 actionable PGx and 12 informative PGx for antibiotic drugs. Swissmedic, with at least 11 actionable PGx, is another important source for PGx-based drug labels for antibiotics.

TABLE 4

DrugGenePGx label informationRecommending body
AmikacinMT-RNR1Actionable PGxFDA
CiprofloxacinG6PDActionable PGxSwissmedic
Co-trimoxazoleG6PDActionable PGxPMDA and Swissmedic
Informative PGxFDA and HCSC
NAT2Informative PGxFDA
DapsoneCYB5R3Actionable PGxFDA and HCSC
G6PDActionable PGxFDA, PMDA, and HCSC
ErythromycinG6PDInformative PGxFDA
FlucloxacillinHLA-BActionable PGxSwissmedic
GentamicinMT-RNR1Actionable PGxFDA
IsoniazidNAT2Informative PGxFDA and PMDA
LevofloxacinG6PDActionable PGxSwissmedic
MafenideG6PDInformative PGxFDA
MoxifloxacinG6PDActionable PGxSwissmedic
Nalidixic acidG6PDActionable PGxFDA and PMDA
NeomycinMT-RNR1Actionable PGxFDA
NitrofurantoinG6PDActionable PGxFDA, HCSC, and Swissmedic
NorfloxacinG6PDActionable PGxSwissmedic
Informative PGxFDA and HCSC
OfloxacinG6PDActionable PGxSwissmedic
PlazomicinMT-RNR1Actionable PGxFDA
PyrazinamideNAT2Informative PGxFDA
RifampicinNAT2Informative PGxFDA
StreptomycinMT-RNR1Actionable PGxFDA
SulfadiazineG6PDActionable PGxHCSC, PMDA, and Swissmedic
Informative PGxFDA
SulfasalazineG6PDActionable PGxFDA, PMDA, HCSC, and Swissmedic
NAT2Informative PGxFDA and HCSC
SulfisoxazoleG6PDInformative PGxFDA
TobramycinMT-RNR1Actionable PGxFDA and HCSC
TrimethoprimG6PDActionable PGxPMDA and Swissmedic
Informative PGxHCSC
G6PD and NAT2Informative PGxFDA
CeftriaxoneCYB5R3 and G6PDCriteria not metFDA
TelithromycinCYP3A4Criteria not metEMA

PGx drug label information for antibiotics.

HCSC, Health Canada Santé Canada; FDA, US Food and Drug Administration; Swissmedic, Swiss Agency of Therapeutic Products; PMDA, Pharmaceuticals and Medical Devices Agency, Japan; EMA, European Medicines Agency; PGx, Pharmacogenomics.

FIGURE 3

3.4 Current state of PGx-based therapeutic and testing guidelines for antibiotics

The search for PGx-based guidelines across CPIC, DPWG, and CPNDS revealed at least six genes i.e., HLA-B, MT-RNR1, G6PD, RARG, SLC28A3, and UGT1A6. These PGx working bodies recommend therapy or testing for optimizing the effectiveness of several antibiotics based on the genetic variants of these six genes (; ; , ). For flucloxacillin-induced liver injury, DPWG deemed genotyping for HLA-B*57:01 to be beneficial and recommended alternative medicine for HLA-B*57:01-positive patients when bilirubin and/or liver enzyme levels are found elevated (). For aminoglycoside-induced hearing loss, CPIC provided a guideline considering the genotype of MT-RNR1, where they classified people into the categories normal, increased, and uncertain risk of aminoglycoside-induced hearing loss based on their genotype. In patients at increased risk, aminoglycoside use is strongly discouraged unless both the lack of safer alternatives and the severity of the infection outweigh the risk of ototoxicity ().

Based on the polymorphism in G6PD, the CPIC provided therapeutic guidelines for dapsone and nitrofurantoin. They classified individuals into normal, deficient, and deficient in chronic non-spherocytic hemolytic anemia (CNSHA) groups and variable and indeterminate groups based on the genotypes of G6PD. Avoidance of dapsone use is strongly recommended in deficient and deficient in CNSHA groups. On the contrary, for those deficient in the CNSHA group, avoidance of nitrofurantoin use is moderately recommended. They also suggested that in the deficient group, nitrofurantoin can be used in a standard dose, optionally with close monitoring for anemia ().

CPNDS, on the other hand, provided a guideline for anthracycline (doxorubicin, daunorubicin, and others)-induced cardiotoxicity based on the polymorphism of RARG, SLC28A3, and UGT1A6. They classified individuals according to their genotype into low, moderate, and high-risk groups. For the high-risk group, comprising individuals carrying RARG rs2229774A or UGT1A6*4, the CPNDS strongly recommended increased monitoring frequency and appropriate management of associated cardiovascular risk factors. They moderately encouraged the use of dexrazoxane and liposome-enclosed anthracycline preparations. As optional recommendations, they suggest slower infusion rates or continuous infusion, use of cardioprotective agents, or choosing alternative therapy with comparable efficacy (if available). For children receiving doxorubicin or daunorubicin therapy, CPNDS moderately recommended genetic testing for RARG rs2229774A, SLC28A3 rs7853758, and UGT1A6*4 rs17863783 variants. They, however, did not recommend genetic testing for children and adults receiving other types of anthracyclines ().

More details on these guidelines provided by DPWG, CPIC, and CPNDS are presented in Table 5.

TABLE 5

DrugGeneLikely phenotypeGenotypeRecommending bodyTherapeutic and dosing recommendationClassification of recommendationsTesting recommendationReference
FlucloxacillinHLA-BPositive/negativeHLA-B*5701DPWGHLA-B*5701-positive patients have an 80-fold higher risk of flucloxacillin-induced liver injury
It is recommended to monitor patient’s liver function regularly and opt for an alternative if the liver enzymes and/or bilirubin levels are increased
-It is recommended to consider genotyping these patients before (or directly after) drug therapy has been initiated to guide drug selectionhttps://www.pharmgkb.org/guidelineAnnotation/PA166182810
Amikacin, dibekacin, gentamicin, kanamycin, neomycin, netilmicin, paromomycin, plazomicin, ribostamycin, streptomycin, and tobramycinMT-RNR1Increased risk of aminoglycoside-induced hearing lossm.1095T>C m.1494C>T m.1555A>GCPICAvoid using aminoglycoside antibiotics except where the severity of infection and unavailability of effective or safe alternative therapies outride the significant risk of permanent hearing lossStrong-2022 McDmmm
Normal risk of aminoglycoside-induced hearing lossm.827A>GIt is advised to use aminoglycoside antibiotics at standard doses for the shortest possible course with careful therapeutic dose monitoring. Hearing loss should be regularly evaluated following the local guidanceStrong
DapsoneG6PDNormalAn individual having one X chromosome carrying a non-deficient allele; an individual having two non-deficient allelesCPICBased on the G6PD status, dapsone needs not to be avoidedStrong-2022 Gammal
DeficientAn individual having one X chromosome carrying a deficient allele. An individual inheriting two deficient alleles or one class I allele and one class II or III alleleAvoidance of dapsone is recommendedStrong
Deficient with CNSHAAn individual having one X chromosome carrying a deficient allele; an individual inheriting two deficient allelesAvoidance of dapsone is recommendedStrong
VariableAn individual inheriting one non-deficient allele and one deficient alleleMeasuring the enzyme activity is necessary for ascertaining the G6PD status, and the use of drug should be according to the recommendations on the basis of the activity-based phenotypeModerate
IndeterminateAn individual having at least one uncertain function alleleMeasuring the enzyme activity is necessary for ascertaining the G6PD status, and the use of drug should be according to the recommendations on the basis of the activity-based phenotypeModerate
NitrofurantoinG6PDNormalAn individual having one X chromosome carrying a non-deficient allele. An individual having two non-deficient allelesCPICBased on the G6PD status, nitrofurantoin need not to be avoidedStrong-2022 Gammal
DeficientAn individual having one X chromosome carrying a deficient allele; an individual inheriting two deficient alleles or one class I allele and one class II or III alleleNitrofurantoin is recommended at standard doses, with close monitoring for anemiaOptional
Deficient with CNSHAAn individual having one X chromosome carrying a deficient allele; an individual inheriting two deficient allelesAvoidance of nitrofurantoin is advisedModerate
VariableAn individual inheriting one non-deficient (class IV) allele and one deficient (class I– III) allele (B/Bangkok, B/Mediterranean, B/A, IV/I, IV/II, and IV/III)Measuring the enzyme activity is necessary for ascertaining the G6PD status, and the use of drug should be according to the recommendations on the basis of the activity-based phenotypeModerate
IndeterminateAn individual having at least one uncertain function alleleMeasuring the enzyme activity is necessary for ascertaining the G6PD status, and the use of drug should be according to the recommendations on the basis of the activity-based phenotypeModerate
Anthracycline (doxorubicin, daunorubicin, and others)RARG, SLC28A3, and UGT1A6High riskRARG rs2229774A and UGT1A6*4CPNDSIncreasing the monitoring frequency is advised. Vigorous monitoring and proper management of the cardiovascular risk factors (e.g., diabetes, obesity, arterial hypertension, lipid disorders, coronary artery disease, and peripheral vascular disease) are recommendedLevel A (strong)Genetic testing for RARG rs2229774, SLC28A3 rs7853758, and UGT1A6*4 rs17863783 variants is recommended in children being treated with doxorubicin or daunorubicin (level B, moderate). In children and adults receiving other types of anthracyclines, genotyping is not currently recommended (level C, optional)2016 - Aminkeng
Dexrazoxane should be prescribed. Use of anthracycline preparations encapsulated in liposome can be consideredLevel B (moderate)
Continuous infusions or slower rates of infusion must be included. The use of cardiotoxic types of anthracyclines should be reduced. Use of other cardioprotective agents can be considered. Alternative chemotherapy regimens can be prescribed for particular type of tumors, where these alternative regimes exhibited comparable efficacyLevel C (optional)
Low riskSLC28A3 rs7853758AA normal follow-up is advisedLevel A (strong)
Moderate riskAll other patientsIncrease the frequency of monitoringLevel A (strong)

Current PGx-based therapeutic and testing guidelines for antibiotics provided by the CPIC, CPNDS, and DPWG.

CPIC, Clinical Pharmacogenetics Implementation Consortium; DPWG, Dutch Pharmacogenetics Working Group; CPNDS, Canadian Pharmacogenomics Network for Drug Safety.

4 Discussion

This study identified a total of 65 clinical studies evaluating the genetic impact in producing different drug-induced adverse effects associated with antibiotic drugs. These studies provide a wide range of evidence reinforcing the need for PGx-based antibiotic therapy in clinical practice to achieve precision medicine. This evidence base explored a variety of gene variants associated with the ADRs—for example, beta-lactam-induced hypersensitivity reaction (with a varying OR of 1.36–5.1), flucloxacillin-induced DILI (associated with several HLA genes with ORs ranging from 1.86 to 79.21), anti-tuberculosis drug-induced hepatotoxicity (OR range 0.10–9.57), anthracycline-induced cardiotoxicity (reporting a varied ORs from 0.14 to 7.98), co-trimoxazole-induced SCARs (for a limited number of HLA genes with an OR range of 4.05–43.57), etc. A few of the protective biomarkers were identified during the literature search, such as NAT2*5 and NAT2 (rs1495741) (for isoniazid-induced liver injury, OR = 0.69 and 0.10, respectively), SLC22A16 T>C (rs714368) for doxorubicin-induced neutropenic and leukopenia (OR = 0.31 and 0.18, respectively), NQO1609TT (for epirubicin-induced anemia OR = 0.34 and grade 2–4 toxicity OR = 0.33), SLC28A3 (rs7853758), SLC28A3 (rs885004), ABCC10 (rs1214763), CYP2J2 (rs2294950), FMO2 (rs2020870), GPX3 (rs2233302), GSTM3 (rs12059276), SLC28A3 (rs7853758), SLC10A2 (rs9514091), SLC28A3 (rs4877847), SLC22A17 (rs4982753), SLC22A7 (rs4149178), SOD2 (rs7754103), SPG7 (rs2019604), and XDH (rs4407290) (for anthracycline-induced cardiotoxicity, OR = 0.46, 0.42, 0.34, 0.41, 0.14, 0.27, 0.37, 0.31, 0.43, 0.60, 0.52, 0.41, 0.30, 0.39, and 0.26, respectively) (; ; ; ; ; ). We also explored the PharmGKB evidence level and PGx label information, which provided similar information on the genetic associations for the antibiotic drug-induced ADRs. However, to date, the clinical and dosing guidelines have been suggested for only a limited number of antibiotic drugs, with the aim of optimizing safety and effectiveness while reducing the incidence of ADRs through prediction. The findings of the current study, therefore, encourage policymakers to consider the growing evidence and take the necessary measures for its clinical adoption.

Although some robust literature-based associations were identified in the included studies, most of them provided preliminary associations of the genetic variants and adverse effects and recommended further exploration with a large number of subjects across the population for a comprehensive understanding, validation, and translation into implementable clinical guidelines (; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; Yang et al., 2017; Yuliwulandari et al., 2016). However, such proper large-scale follow-up studies were scarce, keeping these reported preliminary associations largely unexplored, which may contribute to the limited number of clinical guidelines available. Nevertheless, there are several antibiotic candidates with various genetic associations replicated in multiple studies and have moderate to high (level-1 and level-2) PharmGKB evidence level and PGx drug label information. For example, the association between isoniazid and the NAT2 genetic polymorphism has been well studied for toxicity, carries a high PharmGKB evidence level-1B, and has been labeled with informative PGx by the FDA and PMDA (; ; ; ; ). Similarly, the association between co-trimoxazole and HLA genes for SCARs has been reported in multiple clinical studies and has a moderate PharmGKB evidence level of 2A (for HLA-B) and 2B (for HLA-C) for drug-induced toxicity. However, this genetic association with HLA has no PGx label information (; ). It is evident that even after having some considerable and growing evidence for certain genetic associations for antibiotics and toxicity, sufficient measures are not being undertaken to translate them into clinical use. It is about time for the international PGx working bodies to develop PGx-dosing guidelines so that clinicians can easily incorporate recommendations into routine clinical practice.

As of now, no antibiotic drug has a testing-required or recommended label by the FDA, EMA, PMDA, HCSC, or Swissmedic. Nevertheless, several studies reported the importance of genetic testing in the prediction and management of adverse effects associated with antibiotics. For example, informed that the early detection of GSTM1 and T1 null may help lower ATD-induced hepatotoxicity. To reduce the risk of AT-DILI, Yuliwulandari et al. (2016) recommended the NAT2 genotype and corresponding phenotype determination. For customizing the anthracycline therapy in cancer, emphasized the importance of genetic testing for SLC22A16 and CBR1. A prediction model based on both genetic and clinical risk factors was deemed beneficial by in anthracycline therapy for identifying risk profiles for cardiotoxicity. For vancomycin-induced DRESS, stated that HLA-A*32:01 testing may improve safety and efficacy. For levofloxacin-induced SCARs, informed prospective screening of serotype B13, and prescribing alternative drug therapy for the carriers significantly reduces the incidence of adverse effects. supported the genotyping of the HLA-B*13:01 allele to avoid SCARs with dapsone therapy in the Asian population. recommended considering the screening of HLA-A*32:01 for risk stratification in long-term therapy with vancomycin (; ; ; ; ; ; ; ; ; ; ; Yuliwulandari et al., 2016).

Another limiting factor for the adoption of PGx in clinical practice for antibiotic therapy is the paucity of cost-effectiveness studies. Health economics plays a vital role in supporting policymakers in allocating limited resources, and therefore, cost-effectiveness studies are essential for evidence-based decision-making (; ). One such cost-effectiveness analysis conducted by , for preventing SCARs with co-trimoxazole therapy in HIV-infected Thai patients, revealed that the screening of HLA-B*13:01 before initiating the therapy was not likely to be cost-effective. Similar cost-effectiveness studies for the important antibiotic-genetic variant pairs in diverse populations are warranted to provide a comprehensive overview of the effects of PGx in antibiotic therapy and subsequent adoption in clinical practice.

Several complex traits, such as the sensitivity to adverse reactions and efficacy of the drug, are sometimes attributable to several different genetic variants. Owing to the remarkable progress in genome sequencing and genome-wide association studies, several polygenic risk scores, including some related to PGx, have been developed (; ). For antibiotics, such multigene effects have also been recorded. For example, GSTM1 and T1 null genotypes had a significant association with ATD-induced hepatotoxicity (OR = 7.18, 95% CI: 1.7–32.6, p = 0.007), and for isoniazid-induced hepatotoxicity, individuals with both NAT2 slow acetylator and CYP2E1 DraI C/D had an elevated risk (; ). Exploring these and other genetic associations for different antibiotic drugs and further developing polygenic risk scores for them can be a rational approach for adopting PGx-based antibiotic use in clinical practice.

To the best of our knowledge, this is the first comprehensive review showing the current evidence of antibiotic-induced hypersensitivity reactions involving PGx. Furthermore, this review summarized the current state of PGx-based therapeutic and testing guidelines for antibiotics in clinical practice, taking into account PGx-based clinical annotations and drug label information.

Although this comprehensive review has insightful information regarding PGx associations of antibiotic-induced hypersensitivity reactions, there is a limitation of this review. The search for relevant literature was carried out in PubMed only, which may limit the possibility of obtaining all potential evidence.

5 Conclusion

In conclusion, this study identified at least 12 antibiotic–gene pairs (amikacin–MT-RNR1, gentamicin–MT-RNR1, kanamycin–MT-RNR1, streptomycin–MT-RNR1, neomycin–MT-RNR1, tobramycin–MT-RNR1, isoniazid–NAT2, dapsone–HLA-B, co-trimoxazole–HLA-B and HLA-C, flucloxacillin–HLA-B, daunorubicin–SLC28A3, and doxorubicin–SLC28A3) with moderate-to-high PharmGKB evidence level for toxicity. However, PGx-based dosing guidelines, as recommended by the CPIC, DPWG and CPNDS, are available for the following antibiotic–gene pairs: amikacin, gentamicin, kanamycin, streptomycin, neomycin, and tobramycin–MT-RNR1; flucloxacillin–HLA-B; dapsone–G6PD; nitrofurantoin–G6PD; and daunorubicin and doxorubicin–RARG, SLC28A3, and UGT1A6. Despite the established and growing genetic evidence for the toxicity, particularly co-trimoxazole-induced SCARs associated with HLA-B and HLA-C, dapsone-induced SCARs associated with HLA-B, and isoniazid-induced liver injury associated with NAT2, sufficient efforts have not been undertaken to translate findings into routine clinical practice. The lack of validation of preliminary genetic associations, due to the scarcity of proper follow-up and large-scale replication, represents a key setback for the PGx-based implementation of antibiotic therapy in clinical practice. More focused clinical studies, cost-effectiveness analyses, and polygenic risk score development are required for the PGx-based clinical use of antibiotics to optimize the safety and effectiveness.

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Author contributions

MB: Conceptualization, Data curation, Investigation, Methodology, Supervision, Validation, Visualization, Writing – original draft, Writing – review and editing. MM: Data curation, Formal analysis, Writing – original draft. MA: Data curation, Formal analysis, Writing – review and editing. ME: Data curation, Visualization, Writing – review and editing. CS: Conceptualization, Supervision, Validation, Visualization, Writing – review and editing.

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Summary

Keywords

antibiotics, hypersensitivity, severe cutaneous adverse drug reactions, liver injury, pharmacogenomics, precision medicine

Citation

Biswas M, Murad MA, Ashik MIH, Ershadian M and Sukasem C (2025) Pharmacogenomics of antibiotic-induced hypersensitivity reactions: current evidence and implications in clinical practice. Front. Pharmacol. 16:1651909. doi: 10.3389/fphar.2025.1651909

Received

22 June 2025

Accepted

08 September 2025

Published

01 October 2025

Volume

16 - 2025

Edited by

Yaya Kassogue, Université des Sciences, des Techniques et des Technologies de Bamako, Mali

Reviewed by

Nancy Hakooz, The University of Jordan, Jordan

Mara Morelo Rocha Felix, Rio de Janeiro State Federal University, Brazil

Santenna Chenchula, All India Institute of Medical Sciences, Bhopal, India

Updates

Copyright

*Correspondence: Chonlaphat Sukasem,

‡ These authors have contributed equally to this work

ORCID: Chonlaphat Sukasem, orcid.org/0000-0003-0033-5321; Mohitosh Biswas, orcid.org/0000-0003-1432-7701; Murshadul Alam Murad, orcid.org/0009-0006-6113-0687

Disclaimer

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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