Elsevier

Gene Reports

Volume 24, September 2021, 101235
Gene Reports

Genomic portrait of community-associated methicillin-resistant Staphylococcus aureus ST772-SCCmec V lineage from India

https://doi.org/10.1016/j.genrep.2021.101235Get rights and content

Highlights

  • ST772, ST22 and ST239 are the predominant MRSA clones in causing bloodstream infection

  • Indian isolates were distributed across all previously defined subgroups (Basal strains, ST772-A1, ST772-A2 and ST772-A3)

  • The mean substitution rate of ST772 S. aureus lineage was estimated to be 1.22 X10-6 substitution per site per year

  • The most recent common ancestor (MRCA) of ST772 S. aureus was estimated as 1964 (95% HPD, 1956-1970)

  • Acquisition of IRP and a variant of SCCmec V (5C2) are likely attributes for the success of this lineage

Abstract

Background

Significant changes in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) were recognised with the emergence of community-associated methicillin-resistant Staphylococcus aureus. However, studies on the molecular epidemiology and the genomic investigation of MRSA are limited in India.

Aim

The study was aims to understand the molecular epidemiology of MRSA causing bloodstream infection and also to investigate the origin and evolution of ST772 S. aureus isolated from India.

Methods

A total of 233 non-repetitive MRSA isolates were screened for the presence staphylococcal cassette chromosome (SCCmec) types, multi-locus sequence types (MLST) and staphylococcal protein A (spa) types. Whole genome sequence data of ST772-SCCmec V (n = 32) isolates were generated and comparative analysis was performed.

Results

MLST analysis revealed ten different clonal complexes and three singletons. ST772 (27%), ST22 (19%) and ST239 (16%) were the predominant MRSA genotypes in causing bloodstream infection. The spa types were highly diverse. Phylogenetic analysis revealed that nearly three-fourth of the Indian STT72-SCCmec V isolates belongs to dominant (ST772-A2) and emerging subgroups (ST772-A3). A pattern of increasing antimicrobial resistance was noticed in the dominant and emerging subgroups. An integrated resistance plasmid encoding resistance clusters for beta-lactam (blaZ), macrolides (mphC, msrA), and aminoglycoside resistance (aphA-III, sat-4, aadE) was identified in all isolates, except four basal strains. ST772-SCCmec V was emerged on the Indian subcontinent in 1964 and diverged into a dominant subgroup in 1991. Furthermore, the expansion is likely to be associated with the acqusition of mobile genetic elements such as integrated resistance plasmid and SCCmec V (5C2) as well as the fixation of double serine mutation (S84L, S80Y) in the quinolone resistance determining region.

Conclusions

ST772 S. aureus have consistent virulence and resistance determinants which may results in successful survival in both community and hospital settings.

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.

References (48)

  • Y.D. Bakthavatchalam et al.

    Genomic insights on heterogeneous resistance to vancomycin and teicoplanin in methicillin-resistant Staphylococcus aureus: a first report from South India

    PLoS One

    (2019)
  • J. Balakuntla et al.

    Novel rearrangements in the staphylococcal cassette chromosome mec type V elements of Indian ST772 and ST672 methicillin resistant Staphylococcus aureus strains

    PLoS One

    (2014)
  • A. Bankevich et al.

    SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing

    J. Comput. Biol.

    (2012)
  • M. Barber

    Methicillin-resistant staphylococci

    J. Clin. Pathol.

    (1961)
  • C. Bertelli et al.

    IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

    Nucleic Acids Res.

    (2017)
  • K.O. Bhutia et al.

    Molecular characterization of community- & hospital-acquired methicillin-resistant & methicillin-sensitive Staphylococcus aureus isolates in Sikkim

    Indian J. Med. Res.

    (2015)
  • G.I. Brennan et al.

    Emergence of hospital- and community-associated panton-valentine leukocidin-positive methicillin-resistant Staphylococcus aureus genotype ST772-MRSA-V in Ireland and detailed investigation of an ST772-MRSA-V cluster in a neonatal intensive care unit

    J. Clin. Microbiol.

    (2012)
  • L. Chen et al.

    VFDB: a reference database for bacterial virulence factors

    Nucleic Acids Res.

    (2005)
  • N.J. Croucher et al.

    Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

    Nucleic Acids Res.

    (2015)
  • B. Dhawan et al.

    Dissemination of methicillin-resistant Staphylococcus aureus SCCmec type IV and SCCmec type V epidemic clones in a tertiary hospital: challenge to infection control

    Epidemiol. Infect.

    (2015)
  • A.J. Drummond et al.

    BEAST: Bayesian evolutionary analysis by sampling trees

    BMC Evol. Biol.

    (2007)
  • N. D’souza et al.

    Molecular characterization of methicillinresistant Staphylococcus aureus with emergence of epidemic clones of sequence type (ST) 22 and ST 772 in Mumbai, India

    J. Clin. Microbiol.

    (2010)
  • M.C. Enright et al.

    Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus

    J. Clin. Microbiol.

    (2000)
  • E. Garrison et al.

    Haplotype-based variant detection from short-read sequencing

    arXiv

    (2012)
  • Cited by (5)

    • The prevalence and characterization of the epidemic ST239-MRSA clone

      2024, Reviews and Research in Medical Microbiology
    • Phylodynamic signatures in the emergence of community-associated MRSA

      2022, Proceedings of the National Academy of Sciences of the United States of America
    View full text