Comprehensive analysis of extensive drug-resistant Salmonella Typhi in Gujarat region, India: genomic findings and prospective alternative therapy

ABSTRACT Antimicrobial resistance (AMR) in Salmonella Typhi ( S . Typhi) is a serious health issue that can complicate typhoid fever treatment and increase fatality rates. The National Centre for Disease Control, Government of India, established a National Antimicrobial Surveillance Network to detect AMR in high-priority infections, including S . Typhi throughout geographical areas of India, and understand AMR dissemination and possible treatment options. The Gujarat State Biotechnology Mission, Government of Gujarat, India, has funded the “Network Program on Antimicrobial Resistance, Superbugs, and One Health” to track antibiotic resistance patterns in the Gujarat region. Given the enormity of the AMR problem in S . Typhi, in Gujarat, this study evaluated the antibiotic resistance patterns of S . Typhi isolates from the Ahmedabad and Vadodara regions of Gujarat, India, were used to determine the mechanism underlying antibiotic resistance and developed combination treatments to combat the extensive drug-resistant isolates. We collected 122 Salmonella isolates periodically (2022–2023) in the Ahmedabad and Vadodara regions of Gujarat, India. The antibiotic susceptibility for 122 S . Typhi isolates was prepared using the disc diffusion method and VITEK II compact system. Whole-genome sequencing and in-silico analysis were performed to identify potential antibiotic resistance genes (ARGs); in addition, combination antibiotic therapies were investigated, and resistance patterns were predicted for key antibiotics used in the treatment of typhoid fever. The study discovered notable levels of antibiotic resistance, specifically to cefuroxime (97.54%), doxycycline (97.54%), ceftriaxone (95.90%), cotrimoxazole (95.90%), ampicillin/sulbactam (95.90%), cefotaxime (94.26%), and ciprofloxacin (94.26%). Genetic analysis revealed the presence of aph(3'')-Ib (40.16%), aph(6)-Id (95.08%), bla CTX-M (89.39%), dfrA14 (68.85%), plasmid-mediated quinolone resistance (PMQR), and the qnrS1 gene (94.26%). IncFIB(K) and IncFIB(pHCM2) were detected in 96.71% of S . Typhi isolates. Point mutations in the QRDR region of gyrA identified three distinct modifications: Ser83Phen (91.80%), Ser83Leu (1.64%), and Ser83Tyr (0.82%). Three genes exhibited point mutations: gyrB (100%), Ile253Val, and parC (6.56%) multiple mutations, and the efflux gene mdtK (100%) Thr224Lys. By evaluating phenotype and genotype, the tests showed an average concordance of 91.69% and a discordance of 8.31%. The study revealed that 97.54% of isolates belonged to the H58 haplotype lineage II (ST1: 4.3.1.2), which is associated with high resistance to cephalosporins and fluoroquinolones in Southeast Asia. The combination therapy of β -lactam/ β -lactamase inhibitors (BL/BLI) demonstrated good outcomes, with low MICs (<0.5 µg/mL) of ceftazidime/tazobactam, cefixime/tazobactam, and ceftriaxone/tazobactam effective against highly resistant S . Typhi. The emergence of MDR–XDR S . Typhi, attributed to mutations in gyrA , parC, and the H58 lineage, highlights widespread resistance. According to our research, a potential strategy against XDR S . Typhi is a combination treatment with BL/BLI. IMPORTANCE One of the first studies to assess the antimicrobial resistance patterns of S . Typhi isolates from the Ahmedabad and Vadodara regions; this particular investigation provides vital information on the occurrence of key resistance genes and mechanisms. This study has significantly contributed by finding the β-lactam/β-lactamase inhibitor combination therapy as an appropriate treatment choice for XDR, which can potentially use S . Typhi on a larger scale. Additionally, it provides the antibiotic resistance prediction of key antibiotics used for treating typhoidal fever. The outcomes of this investigation highlight the urgent need to address the surge of XDR S . Typhi in high-burden regions of Gujarat. Our study highlights the possibility of rapid dissemination of antibiotic resistance due to chromosomal point mutations and plasmid-mediated gene transfer. The effectiveness of β-lactam/β-lactamase inhibitors in handling XDR S . Typhi suggests a plausible strategy for treatment that may be included among clinical guidelines.