Recent emergence of cephalosporin-resistant Salmonella Typhi in India due to the endemic clone acquiring IncFIB(K) plasmid encoding blaCTX-M-15 gene

Abstract

The emergence and spread of Salmonella Typhi (S. Typhi) resistant to third-generation cephalosporins is a serious global health concern. In this study, we genomically characterized 142 cephalosporin-resistant S. Typhi strains isolated from India. Comparative genome analysis revealed the emergence of a new clone of ceftriaxone-resistant S. Typhi harboring three plasmids of the incompatibility groups IncFIB(K), IncX1, and IncFIB(pHCM2). Among these, the IncFIB(K) plasmid confers resistance to third-generation cephalosporins through the bla_CTX-M-15 gene, along with other resistance determinants such as aph(3"), aph(6'), sul2, dfrA14, qnrS, and tet(A). Phylogenetic analysis showed that the isolates from Gujarat (n = 140/142) belong to a distinct subclade (genotype 4.3.1.2.2) within genotype 4.3.1.2 (H58 lineage II). Single nucleotide polymorphism-based phylogenetic analysis of the core genes in IncFIB(K) suggested a close relatedness of the plasmid backbone to that of IncFIB(K) from other Enterobacteriales, indicating that H58 lineage II possesses the capability to acquire MDR plasmids from these organisms. This could indicate the potential onset of a new wave of ceftriaxone-resistant S. Typhi in India. The implementation of control measures-such as vaccination and improved water, sanitation, and hygiene systems-is crucial in areas where MDR or extensively drug-resistant S. Typhi strains are prevalent to curb the spread and impact of these resistant strains.

Importance: Typhoid fever remains a global health concern, especially in areas lacking sanitation and clean water. The rise of drug-resistant strains complicates treatment, increasing illness, death, and healthcare expenses. Travel facilitates the spread of these strains worldwide. Multidrug-resistant and extensively drug-resistant (XDR) strains, including those resistant to first-line antibiotics and fluoroquinolones, pose significant challenges. Azithromycin and third-generation cephalosporins are now preferred treatments. Recently, XDR typhoid emerged in Pakistan, resistant even to third-generation cephalosporins. India also faces challenges, with sporadic cases initially declining but now re-emerging. New strains in India show resistance to third-generation cephalosporins due to plasmid acquisition from other bacteria, particularly bla_CTX-M-carrying IncFIB(K). Due to the ongoing nature of this outbreak, the data from this study deserve further consideration in order to control its spread in India.

Keywords: India; Salmonella Typhi; antimicrobial resistance; cephalosporin resistant; genome analysis; plasmid.

Fig 1

Population structure of H58 S. Typhi isolates. Maximum likelihood phylogenetic tree based on core genome sequence SNPs of 247 global H58 S. Typhi mapped to S. Typhi CT18 and rooted to outgroup isolates (Genotype 4.3.1). Major H58 sublineages such as 4.3.1.1EA1, 4.3.1.1P1, 4.3.1.3, and 4.3.1.2.1 are shaded in different colors. Red-colored dots at the tip of the branches indicate the position of this study isolates. Metadata are labeled as color strips, and the key for each variable was mentioned. Strips 1, 2, and 3 indicate the genotype, region of isolation, and location in South Asia for each genomes. The heatmap represents the plasmid-mediated resistance genes, QRDR mutations that confer resistance to fluoroquinolone, and the presence of plasmids. The scale bar indicates substitutions per site. Color keys for all the variables are given in the inset legend. The tree was visualized and labeled using iTOL (https://itol.embl.de/).

Fig 2

Comparison of IncFIB(K) plasmid. IncFIB(K) plasmid from ceftriaxone-resistant S. Typhi isolates from Ahmedabad (accession number CP168964) is compared to the plasmid of the same incompatibility group from other Enterobacteriales (accession number CP116920[2023], CP097833[2022], CP123602[2023], and LT904889[2017]) using Proksee (https://proksee.ca/). GC-content and GC-skew of the reference are depicted in the two innermost circles.

Fig 3

(a) An unrooted maximum likelihood phylogenetic tree of global IncFIB(K) plasmids based on alignment of core genes. Phylogenetic clustering of different lineages is represented by RhierBAPS population clustering (level 1). Clusters are shaded in different colors. (b) A higher-resolution diagram of cluster 1 where IncFIB(K) plasmids from Gujarat were located. Metadata are labeled as color strips, and the key for each variable was mentioned. Strips 1 and 2 indicate the MOB type and host organism. The heatmap represents the plasmid-mediated resistance genes. Red-colored dots at the tip of the branches indicate the position of plasmids identified in this study.