Antimicrobial resistance, virulence genes profiling and molecular relatedness of methicillin-resistant Staphylococcus aureus strains isolated from hospitalized patients in Guangdong Province, China

Figures & data

Table 1 Prevalence and resistance pattern of MRSA isolates

Clinical sample (N=103)	Hospitals			Resistance pattern (%)
Isolates	H1	H2	H3	P	FOX	DA	SXT	RFD	TGC	GEN	VAN	CLI	ERY	CHL	CIP	NIT	MDR
SSTI (58, 56.3%)	11, 18.97%	0	47, 81.03%	58, 100%	5, 100%	5, 8.62%	4, 6.9%	10, 17.24%	1, 1.72%	8, 12.07%a	0	31, 53.45%	34, 58.62%	9, 15.51%	7, 12.07%a	0	30, 51.72%a
Sputum (25, 24.3%)	24, 96%	1, 4%	0	25, 100%	25, 100%	3, 12%	4, 16%	7, 28%	1, 4%	24, 96%b	0	11, 44%	20, 80%	0%	21, 84%b	0	24, 96%b
BSI (15, 14.6%)	2, 13.33%	1, 6.67%	12, 80%	15, 100%	15, 100%	1, 6.67%	3, 20%	1, 6.67%	0%	4, 26.67%a	0	6, 40%	7, 46.67%	2, 13.33%	5, 33.33%a	0	9, 60%a
Others (5, 4.9%)	3, 60%	0	2, 40%	5, 100%	5, 100%	0	0%	1, 20%	0%	2, 40%a	0	2, 40%	5, 100%	1, 20%	2, 40%a,b	0	5, 100%a,b
Total	40, 38.83%	2, 1.94%	61, 59.22%	103, 100%	103, 100%	9, 8.74%	11, 10.68%	19, 18.45%	2, 1.94%	38, 36.89%	0	50, 48.54%	66, 64.07%	12, 11.65%	35, 33.98%	0	68, 66.02%
P-value				–	–	0.927	0.287	0.371	0.685	<0.01	–	0.734	0.039	0.731	<0.01	–	<0.01

Note:

a,b Each subscript letter denotes a subset of group categories whose column proportions do not differ significantly from each other at the 0.01 level.

Abbreviations: BSI, blood stream infection; CHL, chloramphenicol; CIP, ciprofloxacin; CLI, clindamycin; ERY, erythromycin; FOX, cefoxitin; GEN, gentamicin; MDR, mutidrug resistance; MRSA, methicillin-resistant Staphylococcus aureus; NIT, nitrofurantoin; RFD, rifampicin; SSTI, skin and soft tissue infection; SXT, trimethoprim– sulfamethoxazole; TGC, tigecycline; VAN, vancomycin.

Figure 1 Percentages of antibiotic resistance rates of MRSA isolated from various clinical sources.

Abbreviations: BSI, blood stream infection; CHL, chloramphenicol; CIP, ciprofloxacin; CLI, clindamycin; ERY, erythromycin; FOX, cefoxitin; GEN, gentamicin; MRSA, methicillin-resistant Staphylococcus aureus; NIT, nitrofurantoin; P, penicillin; RFD, rifampicin; SSTI, skin and soft tissue infection; SXT, trimethoprim–sulfamethoxazole; TGC, tigecycline; VAN, vancomycin.

Table 2 Resistance pattern and virulence genes of MRSA isolates from different clinical sources

Clinical sample (N=103)	Resistance genes and mutation (%)														Virulence genes (%)
	aac6-aph2	dfrG	rpoB	cfr	fexA	gyrA	gyrB	grlA	grlB	ermA	ermB	ermC	lnuA	sea		seb	sec	sed	hla	hlb	hld	hlg	Tsst-1	Pvl
SSTI (58, 56.3%)	4, 6.9%a	4, 6.9%	11, 8.97%	0	1, 1.7%	8, 13.8%a	0, 0a	5, 8.6%a	2, 3.44%a	5, 8.6%a	13, 22.4%a,b	12, 20.7%	12, 20.7%a,b	7, 12.1%		18, 31.03%a	0	1, 1.7%	44, 75.9%	9, 15.5%	26, 44.8%	5, 8.6%	2, 3.44%	25, 43.10%c
Sputum (25, 24.3%)	18, 72%b	5, 20%	9, 36%	0	1, 4%	21, 84%b	1, 4%b	14, 56%b	7, 28%b	14, 56%b	0b	8, 32%	0b	3, 12%		0, 0%b	0	0	25, 100%	4, 16%	23, 92%	6, 24%	1, 4%	0a
BSI (15, 14.6%)	3, 20%a	2, 13.3%	1, 6.7%	0	0	6, 40%a	0, 0%a	2, 13.3%a	2, 13.3%a,b	2, 13.3%a	4, 26.7%a	0	5, 33.3%a	1, 6.7%		4, 26.7%a	0	0	15, 100%	3, 20%	3, 20%	0	0	1, 6.7%a,b
Others (5, 4.9%)	0a	0	1, 20%	0	0	2, 40%a,b	0, 0%a,b	0, 0%a,b	0a,b	1, 20%a,b	2, 40%a	2, 40%	2, 40%a	1, 20%		0, 0%a,b	1, 20%	0	5, 100%	2, 40%	3, 60%	0	1, 4%	2, 40%b,c
Total	25, 24.3%	11, 10.7%	22, 21.4%	0	2, 1.94%	37, 35.92%	1, 0.97%	21, 20.4%	11, 10.68%	22, 21.4%	19, 18.5%	22, 21.4%	19, 18.5%	12, 11.7%		22, 21.4%	1, 0.97%	1, 0.97%	89, 86.4%	18, 17.5%	55, 53.4%	11, 10.7%	4, 3.9%	28, 27.2%
P-value	<0.01	0.275	0.151	–	0.685	<0.01	0.437	<0.01	<0.01	<0.01	0.0102	0.042	<0.01	0.797		<0.01	0.194	1	<0.01	0.51	<0.01	0.095	0.31	<0.01

Note:

a,b,c Each subscript letter denotes a subset of group categories whose column proportions do not differ significantly from each other at the 0.01 level.

Abbreviations: BSI, blood stream infection; MRSA, methicillin-resistant Staphylococcus aureus; SSTI, skin and soft tissue infection.

Figure 2 Phylogenetic tree of 103 MRSA isolates.

Notes: A maximum likelihood phylogeny was used of every MRSA isolate. Strain names are color-coded based on the hospital: blue is hospital 1, black is hospital 2 and red is hospital 3. The main molecular types are shown in various colors as shown in the legend. The inner bar indicates the main SCCmecA and the outer bar indicates the main spa types. Main STs are indicated by the middle bar.

Abbreviations: MRSA, methicillin-resistant Staphylococcus aureus; SCCmec, staphylococcal chromosomal cassette mec; ST, sequence type.

Table 3 General characteristics of the genomes of QY152, L2316 and L2317 in comparison with SO385

Elements and characteristics	SO385a	QY152	L2316	L2317
Chromosome
Size (bp)	2,872,582	2,715,979	2,799,472	2,792,378
G + C content (%)	32.9	32.8	32.7	32.7
tRNA gene	59	57	57	57
rRNA operon	6	8	7	6
Protein-coding genes	2,699	2,502	2,659	2,592
Insertion sequences	12	6	5	5
Bacteriophages	2	1	3	2
Plasmids	3	0	0	0
Resistance genes	copA, tet(M), tet(K), str	blaZ, ermC, norA, mepA, tet(38), sav1866	blaZ, ermC, norA, mepA, tet(38), sav1866, tet(L), ant(4’)-Ib, aac(6’)-aph(2″), fosB, dfrG, fexA	blaZ, ermC, norA, mepA, tet(38), sav1866, tet(L), ant(4’)-Ib, aac(6’)-aph(2″), fosB, dfrG, fexA
Virulence factors	νSaβ, NWMN0280	Hemolysin, adhesin, staphostatin B and others	Hemolysin, adhesin, aur and others	Hemolysin, adhesin, aur and others

Note:

a SO385 livestock-associated MRSA (ST398 isolate) from the Netherlands. GenBank: AM990992.

Abbreviation: MRSA, methicillin-resistant Staphylococcus aureus.

Table S1 Mutation of gyrA, gyrB, grlA and grlB among MRSA isolates from different sources

No.	gyrA	gyrB	grlA	grlB
QY3	C251T (Ser84Leu)	/	/	/
QY35	C251T (Ser84Leu)	/	/	/
QY56	G317A (Phe106Tyr)	/	/	/
QY110	C251T (Ser84Leu)	/	/	/
L2301	C251T (Ser84Leu)	/	/	/
L2303	C251T (Ser84Leu), T290A (Met90Lys)	/	/	/
L2307	C251T (Ser84Leu)	/	/	/
L2308	C251T (Ser84Leu)	/	/	/
L2309	C251T (Ser84Leu)	/	G253A (Arg85Gln)	/
L2311	C251T (Ser84Leu)	/	C242T (Ser81Phe)	/
L2312	C251T (Ser84Leu)	/	T138G (Ile46Met)	A1266T (Glu422Asp)
L2313	C251T (Ser84Leu)	/	C242T (Ser81Phe), G253A (Arg85Gln)	/
L2314	C251T (Ser84Leu)	/	/	/
L2315	C251T (Ser84Leu)	/	/	/
L2316	T250G (Ser84Ala)	/	C242T (Ser81Phe)	/
L2317	T250G (Ser84Ala)	/	C242T (Ser81Phe)	/
L2318	C251T (Ser84Leu)	/	G253A (Arg85Gln)	/
L2319	C251T (Ser84Leu)	/	/	G1294A (Asp432Asn)
L2320	C251T (Ser84Leu)	/	/	C1351T (Pro451Leu)
L2321	C251T (Ser84Leu)	/	C242T (Ser81Phe)	/
L2322	C251T (Ser84Leu), G317A (Phe106Tyr)	/	C242T (Ser81Phe)	G1294A (Asp432Asn)
L2323	C251T (Ser84Leu)	/	C242T (Ser81Phe)	/
L2325	C251T (Ser84Leu)	/	G253A (Arg85Gln)	/
L2326	C251T (Ser84Leu)	/	C242T (Ser81Phe)	C1351T (Pro451Leu)
L2327	C251T (Ser84Leu), G317A (Phe106Tyr)	/	G253A (Arg85Gln)	/
L2328	C251T (Ser84Leu)	/	G253A (Arg85Gln)	/
L2330	C251T (Ser84Leu)	/	/	/
L2331	C251T (Ser84Leu), T253C (Ser85Pro)	/	/	/
L2332	C251T (Ser84Leu)	/	G253A (Arg85Gln)	/
L2335	C251T (Ser84Leu)	/	/	/
L2336	C251T (Ser84Leu)	/	C242T (Ser81Phe)	A1266T (Glu422Asp), C1387A, T1389A (Gly463Arg)
L2337	C251T (Ser84Leu)	/	C242T (Ser81Phe)	C1351T (Pro451Leu)
L2338	C251T (Ser84Leu)	/	C242T (Ser81Phe)	G1294A (Asp432Asn)
L2343	C251T (Ser84Leu), G317A (Phe106Tyr)	/	C242T (Ser81Phe)	G1294A (Asp432Asn)
L2344	C251T (Ser84Leu)	/	G253A (Arg85Gln)	/
L2503	C251T (Ser84Leu), A263T (Glu88Asp), G286A, A287C, T288A (Asp96Thy)	/	/	C1282T (Ser428Phe), C1330A, C1332A (Leu444Ile), A1346T (Tyr449Phe), T1358A (Val453Asp), C1387A, T1389A (Gly463Arg)
L2508	C251T (Ser84Leu)	G1390A (Val464Ile)	C242T (Ser81Phe)	G1294A (Asp432Asn)

Note: Reference: GenBank: AASB02000026.1 (gyrA/gyrB), GenBank: AKYW15.1 (grlA/grlB).

Abbreviation: MRSA, methicillin-resistant Staphylococcus aureus.

Table S2 MLST, SCCmec types and spa types of MRSA isolates from different sources

Molecular typing	Total n (%)	SSTI n (%)	Sputum n (%)	BSI n (%)	Others n (%)
SCCmec
I	0	0	0	0	0
II	2 (1.94)	0	1 (4)	0	1 (20)
III	39 (37.86)	17 (29.31)	16 (64)	4 (26.67)	2 (40)
IV	17 (16.5)	14 (24.14)	1 (4)	2 (13.33)	0
a	15 (88.24)	13 (22.41)		2 (13.33)	0
b	2 (11.76)	1 (1.72)	1 (4)	0	0
c	0	0	0	0	0
d	0	0	0	0	0
V	1 (0.97)	0	1 (4)	0	0
No type	44 (42.72)	27 (26.21)	6 (24)	9 (60)	2 (40)
MLST
239	24 (23.30)	7 (12.07)	14 (56)	2 (13.33)	1 (20)
338	18 (17.48)	16 (27.59)	0	1 (6.67)	1 (20)
59	8 (7.77)	5 (8.62)	0	3 (20)	0
1061	8 (7.77)	2 (3.44)	6 (24)	0	0
88	3 (2.91)	2 (3.44)	0	1 (6.67)	0
45	2 (1.94)	2 (3.44)	0	0	0
398	2 (1.94)	2 (3.44)	0	0	0
965	2 (1.94)	1 (1.72)	0	1 (6.67)	0
1	1 (0.97)	1 (1.72)	0	0	0
5	1 (0.97)	1 (1.72)	0	0	0
6	1 (0.97)	1 (1.72)	0	0	0
9	2 (1.94)	1 (1.72)	1 (4)	0	0
10	1 (0.97)	1 (1.72)	0	0	0
30	1 (0.97)	1 (1.72)	0	0	0
72	1 (0.97)	1 (1.72)	0	0	0
188	1 (0.97)	0	0	1 (6.67)	0
630	1 (0.97)	1 (1.72)	0	0	0
641	1 (0.97)	0	0	0	1 (20)
863	1 (0.97)	0	1 (4)	0	0
889	1 (0.97)	0	1 (4)	0	0
2148	1 (0.97)	0	0	1 (6.67)	0
3188	1 (0.97)	1 (1.72)	0	0	0
4860	1 (0.97)	1 (1.72)	0	0	0
4940	1 (0.97)	0	0	0	1 (20)
4942	1 (0.97)	1 (1.72)	0	0	0
4943	1 (0.97)	0	1 (4)	0	0
4944	1 (0.97)	0	1 (4)	0	0
4945	1 (0.97)	0	0	1 (6.67)	0
4946	1 (0.97)	0	0	1 (6.67)	0
4947	1 (0.97)	0	0	1 (6.67)	0
4948	2 (1.94)	1 (1.72)	0	0	0
4949	1 (0.97)	1 (1.72)	0	0	0
4957	1 (0.97)	0	0	1 (6.67)	0
4958	1 (0.97)	2 (3.44)	0	0	0
4959	1 (0.97)	1 (1.72)	0	0	0
4960	2 (1.94)	2 (1.72)	0	0	0
4961	1 (0.97)	0	0	0	1 (20)
4962	1 (0.97)	1 (1.72)	0	0	0
4963	1 (0.97)	1 (1.72)	0	0	0
4964	1 (0.97)	1 (1.72)	0	0	0
4965	1 (0.97)	0	0	1 (6.67)	0
spa
t437	22 (21.36)	19 (32.76)	1 (4)	2 (13.33)	0
t37	18 (17.48)	6 (10.34)	9 (36)	2 (13.33)	1 (20)
t30	6 (5.83)	1 (1.72)	4 (16)	1 (6.67)	0
t1081	6 (5.83)	0	6 (24)	0	0
t189	4 (3.88)	2 (3.44)	0	2 (13.33)	0
t441	4 (3.88)	2 (3.44)	0	1 (6.67)	1 (20)
t62	3 (2.91)	1 (1.72)	0	1 (6.67)	1 (20)
t116	3 (2.91)	3 (5.17)	0	0	0
t34	2 (1.94)	2 (3.44)	0	0	0
t899	2 (1.94)	1 (1.72)	1 (4)	0	0
t14034	2 (1.94)	1 (1.72)	0	1 (6.67)	0
t2	1 (0.97)	0	0	0	1 (20)
t19	1 (0.97)	1 (1.72)	0	0	0
t114	1 (0.97)	1 (1.72)	0	0	0
t421	1 (0.97)	0	1 (4)	0	0
t701	1 (0.97)	1 (1.72)	0	0	0
t1212	1 (0.97)	1 (1.72)	0	0	0
t1244	1 (0.97)	1 (1.72)	0	0	0
t2358	1 (0.97)	1 (1.72)	0	0	0
t3523	1 (0.97)	1 (1.72)	0	0	0
t5554	1 (0.97)	1 (1.72)	0	0	0
t6497	1 (0.97)	1 (1.72)	0	0	0
t7707	1 (0.97)	0	0	1 (6.67)	0
t12011	1 (0.97)	0	0	0	0
t17403	1 (0.97)	0	1 (4)	0	0
Not available	17 (16.5)	10 (17.24)	2 (8)	4 (26.67)	1 (20)

Abbreviations: BSI, blood stream infection; MLST, multilocus sequence typing; MRSA, methicillin-resistant Staphylococcus aureus; SCCmec, staphylococcal chromosomal cassette mec; SSTI, skin and soft tissue infection.