Genomic portrait of community-associated methicillin-resistant Staphylococcus aureus ST772-SCCmec V lineage from India
Introduction
Methicillin-resistant Staphylococcus aureus (MRSA) is of significant clinical concern in causing both community-associated (CA) and healthcare-associated (HA) infections. MRSA was first reported in 1961 (Barber, 1961). Methicillin resistance is conferred by the acqusition of staphylococcal cassette chromosome mec (SCC mec) carrying methicillin resistance determinant mecA (Robinson and Enright, 2003). The HA-MRSA strains carry the SCCmec types I, II or III are often multi-drug resistant. Typically, the CA-MRSA strains carry the SCCmec types IV or V and a Panton-Valentine leukocidin (PVL) toxin are frequently susceptible to non-beta-lactam antibiotics (Boyle-Vavra and Daum, 2007). Most of the HA-MRSA clones belong to the clonal complex (CC), CC5, CC8, CC22, CC30 and CC45 (Donker et al., 2009). In contrast, CA-MRSA clones are geographically more diverse. In the Asia-pacific region, five distinct sequence types (STs); ST59, ST30, ST72, ST8, and ST772 are the predominant and often spread to hospitals (Huh and Chung, 2016). In India, MRSA accounts for 37% of S. aureus infections (Rajkumar et al., 2017, Veeraraghavan and Walia, 2019). However, very few studies have reported the molecular epidemiology of S. aureus.
In early 2000, in India, most of the MRSA isolates belongs to the lineage ST239-SCCmec III and were restricted only to hospitals (Arakere et al., 2005; Arakere et al., 2009; Gadepalli et al., 2009). In 2004, a novel CA-methicillin susceptible S. aureus (MSSA) clone, ST772 was reported from a hospital in Bangladesh (Afroz et al., 2008) and a ST772-SCCmec V (Bengal bay clone) isolated from the community and hospitals in India have been described (Goering et al., 2008). During the same year, a variant of epidemic MRSA (EMRSA-15, ST22) carries SCCmec IV and a PVL have also been reported from India (Goering et al., 2008). Later, ST772 and ST22 were predominant from all infection sites have been reported in India (Kulkarni et al., 2009; Bouchiat et al., 2015; Dhawan et al., 2015; D'souza et al., 2010; Shambat et al., 2012; Bakthavatchalam et al., 2019).
Studies have emphasized the contribution of mobile genetic elements (MGEs) in the emergence of ST772-SCCmec V as a multi-drug resistant and highly virulent lineage (Monecke et al., 2013; Steinig et al., 2015). The notable feature of ST772-SCCmec V lineage including the presence of SCCmec V, PVL carrying ΦIND772 prophage, three distinct pathogenicity islands (vSa-alpha, beta, and gamma) and an integrated resistance plasmid (IRP) encoding a cluster of resistant genes such as blaZ (beta-lactam resistance), mphC and msrA (macrolide resistance) aphA III and a partial aadE (aminoglycoside resistance) as well as sat4 (streptothricin resistance). A recent phylogenetic analysis predicted that Indian subcontinent was an early hub for ST772-SCCmec V, from which it was disseminated across the globe (Steinig et al., 2019). However, only a limited number of isolates from India have been included in this previous study. Consequently, understanding the expansion of this lineage and the phylogenetic relationship of ST772 S. aureus isolates within India is crucial.
Studies focusing on S. aureus genomics remain largely unexplored in India. Further, the use of a phylogenomic approach to focus on the origin and spread of ST772 S. aureus is India has been hindered by the lack of whole genome data and sparse geographic sampling. Therefore, the on-going public health significance of this Bengal bay clone in India remains unknown. Here, we investigated the molecular epidemiology of MRSA causing bloodstream infection in the hospital setting between 2013 and 2019. Further, the genomes of ST772 S. aureus isolates from India were compared to understand the introduction and expansion of this multi-drug resistant (MDR) lineages. Bayesian phylogenetic analysis was performed for STT72 S. aureus isolates from India, to demonstrate the evolution of this lineage. In addition, virulence and resistance profile were analysed and correlated with the previously defined ST772 S. aureus subgroups.
Section snippets
Bacterial isolates
Non-repetitive MRSA (n = 233, one isolate per patient) isolated from the blood cultures between 2013 and 2019 at the Department of Clinical Microbiology, Christian Medical College and hospital, Vellore, India were included in this study. MRSA isolates were identified using standard bacteriological methods including gram staining, culture and tube coagulase test. The study was approved by the Institutional Review Board of Christian Medical College, Vellore.
Molecular characterisation of MRSA
SCCmec types were determined using
Molecular epidemiology of MRSA isolates
The distribution of SCCmec types and spa types among various STs of MRSA isolates is shown in Table 1. SCCmec V (42%) was the predominant gene followed by SCCmec III (27%), SCCmec IV (13%), SCCmec I (7%) and SCCmec II (3%). Notably, eighteen isolates had multiple SCCmec types and the most common combination was SCCmec III with SCCmec V. MLST analysis revealed ten different CC and three singletons (ST616, ST1598, ST1947) (Table 1). Three major CCs were CC1 (ST1, ST772), CC22 (ST22, ST217, ST636,
Discussion
In India, PVL positive ST772-SCCmec V and ST22-SCCmec IV are reported as the dominant lineages in causing MRSA infections in community and hospitals (Dhawan et al., 2015; D'souza et al., 2010; Shambat et al., 2012). This was confirmed in the present study. Remarkably, in this study, a high degree of variability was seen among PVL positive ST22 MRSA, which affects not only the SCCmec marker but also the core genome. The presence of unusual SCCmec types in ST22 MRSA indicates an evolutionary
Conclusion
In this study, ST772, ST22 and ST239 were observed as the predominant MRSA STs in causing bloodstream infections. Phylogenetic analysis of ST772 S. aureus lineage revealed that nearly three-fourth of the Indian STT72-SCCmec V isolates belongs to dominant (ST772-A2) and emerging subgroups (ST772-A3). Multi-drug resistance is mainly contributed by the presence of IRP carrying resistance clusters for beta-lactam (blaZ), macrolides (mphC, msrA), and aminoglycoside resistance (aphA-III, sat-4, aad
CRediT authorship contribution statement
YDB - Conceptualization, methodology, formal analysis, data curation, writing Original Draft, writing- review and editing, Visualization. KV- Bioinformatic analysis, data curation. SVR, SV and PR – Investigation and critical review.MG, MZ and JVP- Investigation, data curation and critical review. BV – Conceptualization, critical review and supervision.
Declaration of competing interest
All of the authors declare that there are no commercial, personal, political, and any other potential conflicting interests related to the submitted manuscript.
Acknowledgements
None.
Funding
None.
Availability of data and materials
The genome shotgun sequencing data are deposited at NCBI/GenBank under the following bioprojects PRJNA498584, PRJNA348458, PRJNA326798, PRJNA318841, PRJNA348465, PRJNA520811 and PRJNA348412.
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