Genome Sequences of Four Clinical Staphylococcus aureus Strains with

Diverse Drug Resistance Profiles Isolated from Diabetic Foot Ulcers

Department of Biotechnology, School of Life Sciences, Manipal University, Manipal, Indiaa; Invitrogen Bioservices Pvt., Ltd., Gurgaon, Indiab

Staphylococcus aureus is a major pathogen associated with diabetic foot ulcer infections. To gain insight into their pathogenicity
and virulence potential, we report draft genome sequences of four strains of Staphylococcus aureus, isolated from diabetic foot
ulcers, showing profiles with various degrees of resistance to common antibiotics.
Received 21 February 2014 Accepted 27 February 2014 Published 20 March 2014
Citation Murali TS, Paul B, Parikh H, Singh RP, Kavitha S, Bhat MK, Satyamoorthy K. 2014. Genome sequences of four clinical Staphylococcus aureus strains with diverse drug
resistance profiles isolated from diabetic foot ulcers. Genome Announc. 2(2):e00204-14. doi:10.1128/genomeA.00204-14.
Copyright 2014 Murali et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Kapaettu Satyamoorthy, ksatyamoorthy@manipal.edu.

nfections in diabetic foot ulcers are among the major comorbid

conditions leading to mortality in diabetic individuals (1, 2). To
elucidate the pathogenic potential of bacterial communities associated with infected diabetic foot ulcers, we carried out culturedependent isolation of bacteria from infected wound beds. Samples were obtained from patients visiting a tertiary hospital,
Kasturba Medical College, Manipal, India, and a total of 357 diabetic ulcer samples were collected. From these samples, we isolated 940 bacterial strains, and these were further analyzed using
traditional and molecular techniques to assess the diversity.
Though an abundance of Gram-negative bacilli and Grampositive cocci were obtained, Staphylococcus aureus was frequently
isolated from the wound samples. Staphylococcus aureus is considered the major pathogen associated with diabetic foot ulcers and is
also one of the most adaptable human pathogens, known to cause
a wide range of diseases (3). Though worldwide methicillinresistant Staphylococcus aureus (MRSA) strains are a major cause
of hospital-acquired infections, there are also reports of emergence of MRSA and methicillin-susceptible S. aureus (MSSA)
from other environmental settings (4). Extensive structural features, including specific surface components that aid in adhesion
to host tissues and an array of secreted proteins/toxins expressed
by S. aureus strains, play major roles in enhancing the virulence
potential of these organisms (5, 6). The strains obtained were
tested for their sensitivity to amikacin, ampicillin, amoxyclav, ciprofloxacin, chloramphenicol, erythromycin, gentamicin, linezolid, vancomycin, and cefoxitin. We selected four strains with
profiles showing various degrees of resistance (resistance to one to

nine antibiotics tested) to the above-listed antibiotics for wholegenome sequencing, and the draft genome sequences are reported
here. Genomic DNAs from the S. aureus strains were isolated using the phenol-chloroform method, and whole-genome sequencing was performed with the Ion Torrent Personal Genome Machine (Life Technologies, CA) per the manufacturers guidelines.
A total of 1,624,573 to 2,469,063 reads were obtained, with coverages of 59.3 to 83.97 (Table 1). De novo assembly was performed using the MIRA-4 assembler (7), which yielded 59, 58,
125, and 74 contigs for Staphylococcus aureus strain MUF168, S.
aureus strain MUF256, S. aureus strain MUF270, and S. aureus
strain MUF475, respectively. The GC contents for the four strains
ranged from 32.66 to 32.78%. The functional annotation of the
assembled genomes was performed by the Prokaryotic Genome
Annotation Pipeline v2.0 (NCBI) for deposition with the Genome database. A total of 2,433 to 2,728 coding sequences
(CDS) were predicted for these four strains (Table 1). All four
of the genomes harbored genes coding for beta-lactamase,
acyl carrier protein, chloramphenicol resistance, teicoplanin
resistance-associated membrane protein TcaB, fibronectin
binding proteins A and B, polysaccharide intracellular adhesin
biosynthesis proteins, siderophore staphylobactin biosynthesis
proteins, staphostatin A, staphylocoagulase, and staphylokinase.
Nucleotide sequence accession numbers. The draft genome
sequences have been deposited at GenBank under the accession
numbers AZQR00000000, AZSE00000000, AZSF00000000, and
AZSG00000000.

TABLE 1 Staphylococcus aureus genome assembly and annotation statistics

Strain

No. of contigs

Fold coverage

N50 (bp)

Consensus length (bp)

GC content (%)

No. of CDS

Accession no.

MUF168
MUF256
MUM270
MUM475

59
58
125
74

67.67
69.54
83.97
59.3

96,843
87,410
52,369
128,108

2,752,244
2,783,966
2,834,436
2,852,107

32.78
32.66
32.76
32.67

2,433
2,433
2,728
2,620

AZQR00000000
AZSE00000000
AZSF00000000
AZSG00000000

March/April 2014 Volume 2 Issue 2 e00204-14

Genome Announcements

genomea.asm.org 1

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Thokur Sreepathy Murali,a Bobby Paul,a Hersh Parikh,b Rana Pratap Singh,b Shettigar Kavitha,a Manoj K. Bhat,a
Kapaettu Satyamoorthya

Murali et al.

ACKNOWLEDGMENTS
The study was supported by the TIFAC-CORE in Pharmacogenomics,
Indo-Australia Biotechnology Fund, Department of Biotechnology, Government of India, and Manipal University, Manipal, India.
We thank Ganesh Kumar and Divya for help rendered in sample processing.

1. Dowd SE, Sun Y, Secor PR, Rhoads DD, Wolcott BM, James GA,
Wolcott RD. 2008. Survey of bacterial diversity in chronic wounds using
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2. Dowd SE, Wolcott RD, Sun Y, McKeehan T, Smith E, Rhoads D. 2008.
Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP).
PLoS One 3:e3326. http://dx.doi.org/10.1371/journal.pone.0003326.
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