Molecular Epidemiology and Characterization of Multidrug-Resistant MRSA ST398 and ST239 in Himachal Pradesh, India

Aim

Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of severe and difficult-to-treat infections in humans and animals. We aimed to identify the predominant lineages of methicillin-resistant S. aureus in Himachal Pradesh, India, to understand the genomic epidemiology along with the genotypic and phenotypic characteristics.

Methods

We isolated 250 S. aureus from two district hospitals in Himachal Pradesh, India. Methicillin-Resistant S. aureus (MRSA) isolates were subjected to MLST, SCCmec typing, and resistance as well as virulence determinants were determined by PCR and sequencing. Bio-typing was also performed for source tracking.

Results

A 17.6% (44/250) of isolates were classified as MRSA by both the MRSA detection kit and disc diffusion methods. Antimicrobial Susceptibility Testing of MRSA isolates (n = 44) showed high resistance to oxacillin (77.27%), erythromycin (77.27%), tetracycline (75%), cefoxitin (65.9%), and gentamicin (61.36%), while low resistance was observed for teicoplanin (36.36%), vancomycin and levofloxacin (31.81%) and fusidic acid (18.18%). All isolates were sensitive to linezolid, quinupristin-dulfopristin, dalbavancin, and cefazoline. The SCCmec-II was observed in 20.45% of isolates, SCCmec-I in 11.36%, SCCmec-III in 9%, SCCmec-IV in 40.9% and SCCmec-V in 18.18%. The mecA gene was present in all isolates (n = 44) and 50% also had the vanA gene. 35% of isolates had the lukS-PV/lukf-PV toxin gene and 11.36% had the co-existence of mecA, vanA, and lukS-PV/lukf-PV. The major strain was ST398 (39%) followed by ST239 (27%), ST217 (16%), ST121 (11%), and ST338 (7%). The MRSA isolates produced staphylokinase and β-hemolysis but were negative for bovine plasma coagulation tests.

In Conclusion

The predominant MRSA clones in Himachal Pradesh, India, were hospital-associated multi-drug resistant-MRSA ST239 with PVL and community-associated MRSA ST398.

Genetic Characterization of Colistin-Resistant Salmonella enterica ST34 Co-Harbouring Plasmid-Borne mcr-1, blaCTX-M-15 and blaKPC-2 Recovered from a Paediatric Patient in Shenzhen, China

Background

Since 2015, plasmid-borne mcr-1 has been reported in various bacterial strains in the clinical setting globally. However, the transmission mechanisms of this gene in Salmonella are not well defined. This study aimed to characterize the genomic features of a Salmonella enterica ST34 isolate, which carried a mcr-1, mapped to a carbapenemase and extended spectrum β-lactamase encoding gene located on the IncX4 plasmid.

Methods

Salmonella enterica was recovered from a diarrheal paediatric patient in Shenzhen, China. Antimicrobial susceptibility testing was performed by using the VITEK 2 system. Drug resistance genes were identified using targeted primers and Sanger sequencing. The transferability and genome location of mcr-1 was determined by performing conjugation, S1-PFGE and Southern blot hybridization analysis. WGS was performed by Illumina MiSeq sequencing and was assembled using the A5-Miseq pipeline, and gene annotation was performed using RAST 2.0. The database Centre for Genomic Epidemiology’s website was used to identify resistance genes and sequence types (STs).

Results

We found that the isolate was extensively drug resistant and belonging to ST34, carrying an IncX4 plasmid with mcr-1, bla_KPC-2 and bla_CTX-M-15. We also noticed that genes bla_PAO, fosA, catB, the mutation in oprD and mexT (MexEF-OprN efflux regulator), and exotoxin-encoding genes (exoS, exoY and exoT) were associated with resistance and virulence in the genome. In addition, heavy metal resistance genes as silP and silE were determined.

Conclusion

This study highlights the potential risk of ST34 of Salmonella enterica serotype Typhimurium carrying multiple drug resistance encoding genes in a single IncX4 plasmid.