Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent

Abstract

The evolution and global transmission of antimicrobial resistance have been well documented for Gram-negative bacteria and health care-associated epidemic pathogens, often emerging from regions with heavy antimicrobial use. However, the degree to which similar processes occur with Gram-positive bacteria in the community setting is less well understood. In this study, we traced the recent origins and global spread of a multidrug-resistant, community-associated Staphylococcus aureus lineage from the Indian subcontinent, the Bengal Bay clone (ST772). We generated whole-genome sequence data of 340 isolates from 14 countries, including the first isolates from Bangladesh and India, to reconstruct the evolutionary history and genomic epidemiology of the lineage. Our data show that the clone emerged on the Indian subcontinent in the early 1960s and disseminated rapidly in the 1990s. Short-term outbreaks in community and health care settings occurred following intercontinental transmission, typically associated with travel and family contacts on the subcontinent, but ongoing endemic transmission was uncommon. Acquisition of a multidrug resistance integrated plasmid was instrumental in the emergence of a single dominant and globally disseminated clade in the early 1990s. Phenotypic data on biofilm, growth, and toxicity point to antimicrobial resistance as the driving force in the evolution of ST772. The Bengal Bay clone therefore combines the multidrug resistance of traditional health care-associated clones with the epidemiological transmission of community-associated methicillin-resistant S. aureus (MRSA). Our study demonstrates the importance of whole-genome sequencing for tracking the evolution of emerging and resistant pathogens. It provides a critical framework for ongoing surveillance of the clone on the Indian subcontinent and elsewhere.IMPORTANCE The Bengal Bay clone (ST772) is a community-associated and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh and India in 2004. In this study, we showed that the Bengal Bay clone emerged from a virulent progenitor circulating on the Indian subcontinent. Its subsequent global transmission was associated with travel or family contact in the region. ST772 progressively acquired specific resistance elements at limited cost to its fitness and continues to be exported globally, resulting in small-scale community and health care outbreaks. The Bengal Bay clone therefore combines the virulence potential and epidemiology of community-associated clones with the multidrug resistance of health care-associated S. aureus lineages. This study demonstrates the importance of whole-genome sequencing for the surveillance of highly antibiotic-resistant pathogens, which may emerge in the community setting of regions with poor antibiotic stewardship and rapidly spread into hospitals and communities across the world.

Keywords: Bengal Bay; CA-MRSA; India; ST772; South Asia; Staphylococcus aureus; WGS; antimicrobial resistance; genomic epidemiology; global transmission; phenotyping; phylodynamics.

FIG 1

Evolutionary history and population structure of ST772. (a) Maximum likelihood phylogeny of ST772 (n = 340) based on 7,063 core genome SNPs. Branch colors indicate country of isolation, the inner ring delineates presence and type of SCCmec, the middle ring shows presence of the integrated resistance plasmid, and the outer ring indicates community membership of the population graph shown in panel c. Communities match the tree topology, with several basal isolates (n = 11) and a single derived clade, ST772-A (n = 329), composed of three population subgroups (A1 to A3). Isolates from two outbreaks in neonatal intensive care units in Ireland are indicated in gray (NICU-1 and NICU-2). Only one representative isolate from longitudinal sampling of a single health care worker (VET, n = 39) is shown (red circle). (b) Basal strains of ST772 showing positions of isolates from India and Bangladesh at the root of the phylogeny (RG28, DAR4066, and NKD122). (c) Population graph based on pairwise SNP distances, showing SCCmec type (node color as for panel a) and population subgroups (polygons, A1 to A3). Dashed circles indicate hospital-associated outbreaks in Ireland (NICU-1 and NICU-2).

FIG 2

Molecular epidemiology of ST772. (a) Patient family or travel background in South Asia (India, Pakistan, Nepal, and Bangladesh) (59.5%, purple), or other countries (21.2%, green) or unknown status (19.3%, gray) is widely distributed across the phylogenetic topology of ST772 (n = 340). Only one representative isolate from longitudinal sampling of a single health care worker (n = 39) is included (circle). Clusters of isolates that are within 4 SNPs of each other and thus likely instances of transmission are shaded gray. (b) Average pairwise nucleotide diversity per site (π), measured by region (Australasia: orange, n = 36; Europe: blue, n = 244; South Asia: purple, n = 52). Error bars indicate 95% confidence intervals using nonparametric bootstrapping. Isolates from the Arabian Peninsula (n = 2) and Hong Kong (n = 6) were excluded from the diversity analysis due to the small number of samples from these regions.

FIG 3

Molecular-clock estimates in the emergence of ST772. Shown is a phylogenetic time tree with the timescale estimated in Least Squares Dating (LSD). The annotations for nodes represent the time of origin (in years) of basal strains and subgroups A1, A2, A3, including 95% confidence intervals (CIs) and the most recent common ancestor (MRCA) of ST772. Tips are colored according to the subgroup, and the position of the root was optimized during the analysis. Arrows indicate acquisition of three critical mobile genetic elements: the PVL/sea-prophage φ-IND772, an integrated multidrug resistance plasmid, and the short staphylococcal cassette chromosome SCCmec-V (5C2).

FIG 4

Resistome and predicted resistance phenotypes across ST772. (a) Resistome mapped to maximum likelihood phylogeny of ST772. The predicted resistant phenotype is depicted in red, while the susceptible phenotype is depicted in blue. The presence of acquired resistance genes and mutations responsible for phenotype predictions is shown in red, while the absence of these determinants is shown in gray. (b) Percentages of isolates predicted resistant (gray) or susceptible (white) for all antimicrobials included in Mykrobe Predictor.

FIG 5

Integrated resistance plasmid in ST772. (a) Proportion of isolates predicted resistant to common antibiotics for basal isolates (n = 11) and isolates from ST772-A (n = 291). Values above bars are statistically significant differences between groups using Fisher’s exact test where P < 0.01. (b) BLAST comparison of the multidrug resistance plasmid in DAR4145 (middle) with the extrachromosomal plasmid 11809-p03 (top) and the SCCmec-IV integrated plasmid in ST80 (bottom), showing alignments of >1,000 bp and >95% nucleotide identity. The comparison highlights three regions harboring resistance genes (dark blue) and their regulators (light blue), which are flanked by transposition elements (green) and appear to have integrated with reversions and rearrangements into ST80 and ST772. Resistance genes include the β-lactam blaZ complex, aminoglycoside cluster aphA3-sat4-aadE and bacitracin resistance loci bcrA/B, as well as macrolide efflux genes msrA and mphC. Hypothetical proteins and genes of other annotated function are shown in white and dark gray, respectively.