Antimicrobial Resistance Gene Detection and Plasmid Typing Among Multidrug Resistant Enterococci Isolated from Freshwater Environment

Abstract

In this study, mechanisms of antimicrobial resistance (AR) as well as the abundance and diversity of plasmids were determined among multidrug resistant (MDR) enterococci from surface water in GA, USA. A total of 51 enterococci isolates were screened for the presence of 27 AR genes conferring resistance to ciprofloxacin, erythromycin, tylosin, kanamycin, streptomycin, lincomycin, Quinupristin/Dalfopristin (Q/D), and tetracycline. A plasmid classification system based on replication genes was used to detect 19 defined Gram-positive plasmid replicon families. Twelve genes were identified as conferring resistance to erythromycin and tylosin (erm(B) and erm(C)), kanamycin (aph(3′)-IIIa), streptomycin (ant(6)-Ia), lincomycin (lnu(B)), Q/D (vat(E)), ciprofloxacin (qnr_{E. faecalis}), and tetracycline (tet(K), tet(L), tet(M), tet(O) and tet(S)). Twelve different rep-families were identified in two-thirds of the isolates. While AR genes commonly found in human and animals were detected in this study among environmental enterococci, resistance genes could not be determined for many of the isolates, which indicates that diverse AR mechanisms exist among enterococci, and the understanding of AR mechanisms for environmental enterococci is limited. Diverse rep-families were identified among the enterococci recovered from the aquatic environment, and these rep-families appear to be quite different from those recovered from other sources. This work expands knowledge of AR gene reservoirs and enterococcal plasmids across a wider range of environments.

1. Introduction

Enterococci are Gram-positive bacteria that are a part of the intestinal microbiota of warm-blooded animals. However, as opportunistic pathogens, they are among the major causes of nosocomial infections. Enterococcus faecalis and E. faecium account for most of the enterococcal infections in humans, but other species, including E. avium, E. casseliflavus, E. durans, E. gallinarum, E. hirae, E. mundtii, and E. raffinosus, have also caused human infections [1]. The treatment of enterococcal infections is often complicated by antimicrobial resistant enterococci, particularly those that are resistant to multiple drugs, and this is a major problem for public health worldwide as it results in limited therapeutic options [2]. Enterococci are intrinsically resistant to a broad range of antimicrobials, such as β-lactams and aminoglycosides, and are also adept at acquiring resistance to antimicrobial drugs and disseminating antimicrobial resistance (AR) determinants via horizontal gene transfer [3].

Antimicrobial resistant enterococci released into surface water through human and agricultural wastes are a public health concern, not only due to human exposure to these bacteria through water-related activities, but also due to potential dissemination of genes encoding AR to other bacteria present in the environment. However, studies reporting enterococci and their AR from the environment are scarce since enterococci are generally not considered important pathogens outside of hospitals and healthcare settings. A limited number of studies on environmental enterococci are mostly focused on water environments polluted by human inputs, such as wastewater, on species that are associated with human infections, such as E. faecalis and E. faecium, and on certain antimicrobial drugs, such as vancomycin [4,5,6,7]. Data concerning the presence of resistant enterococci in the aquatic environment is limited and still fewer data exists on the genetic content of waterborne antimicrobial resistant enterococci. A reservoir of resistant enterococci in the aquatic environment could potentially enhance the dissemination of resistance genes to other bacteria of the same genus and different genera in the environment via mobile genetic elements, such as conjugative plasmids [2]. Furthermore, enterococci are used as a sentinel organism for AR, whose resistance level may indicate the burden of AR in a population [8,9,10]. Monitoring resistant enterococci present in the environment and investigating a potential transfer of AR determinants to other bacteria in the same niche would enhance the understanding of AR from the one health perspective [11].

The significance of enterococci as clinically important pathogens is often associated with acquisition of AR via horizontal gene transfer using mobile genetic elements, especially plasmids in the strains. In our previous study, we demonstrated prevalence of enterococci that are resistant to antimicrobials commonly used in human and veterinary medicine from surface water of the Upper Oconee Watershed in GA, USA [12]. To further characterize AR in enterococci from freshwater environments, mechanisms conferring AR were examined. In addition, antimicrobial resistant enterococci were tested using a PCR-based plasmid typing system to identify and characterize plasmid replicons, and thus determine the plasmid contents of the antimicrobial resistant enterococci in the aquatic environment.

2. Materials and Methods

2.1. Enterococcus Isolates

Enterococci were isolated from surface water of the Upper Oconee Watershed, GA, USA, and their AR patterns were described in our previous study [12]. From the previous study, a total of 637 enterococci were isolated, of which, 93.1% (593/637) were resistant to at least one of the 16 antimicrobial drugs tested [12]. A total of 51 multidrug resistant (MDR; resistance ≥ 3 antimicrobial classes) Enterococcus isolates were used in the present study. They encompassed six different species, namely, E. casseliflavus, E. faecalis, E. faecium, E. gallinarum, E. hirae, and E. mundtii, exhibiting 18 different AR phenotypes with resistance up to six antimicrobial drugs (Table 1).

Table 1.

Masterfile of multidrug resistant (MDR) enterococci from surface water with their antimicrobial resistance (AR) gene and rep-family profiles.

Isolate ID	Species	AR Phenotype 1	AR Gene	Plasmid
				Rep-Family	Prototype
2 Ent	E. faecium	CipLinTet	tet(M), tet(O)
2 mE	E. faecium	CipLinTet	tet(M), tet(O)
3 mE	E. casseliflavus	CipLinSyn		3, 11	pAW63, pEF1071
7 mE	E. casseliflavus	CipLinSyn		11	pEF1071
23 mE	E. gallinarum	CipLinTet	tet(S)	11	pEF1071
24 Ent	E. faecium	CipDapTet	tet(M)
24 mE	E. faecium	CipDapTet	tet(M)
25 mE	E. faecium	CipEryLinTetTyl	lnu(B), tet(L), tet(M), erm(B), erm(C)	2	pRE25
25 Ent	E. faecium	LinStrTet	ant(6)-Ia
26 mE	E. casseliflavus	CipLinSyn		3, 11, 16	pAW63, pEF1071, pSAS16
27 Ent	E. hirae	DapLinTet	lnu(B), tet(L), tet(M)	5, 13, 15	pSAS, pC194, pUSA03
72 mE	E. casseliflavus	KanLinStrTetTyl	tet(M), erm(B), erm(C), aph(3′)-IIIa	3, 11, 12	pAW63, pEF1071, pBMB67
97 mE	E. casseliflavus	CipLinSyn		3, 11	pAW63, pEF1071
101 mE	E. casseliflavus	CipLinTet	tet(M), qnrE. faecalis	11	pEF1071
118 mE	E. faecalis	ChlDapEryLinTetTyl	tet(M), erm(B), erm(C)
131c- mE	E. hirae	DapLinTet	lnu(B), tet(L), tet(M)	5	pSAS
134a- mE	E. gallinarum	EryLinTetTyl	tet(S), erm(B), erm(C)
134c- CHR	E. gallinarum	EryLinSynTetTyl	tet(S)
137a- Ent	E. faecalis	LinPenTet	tet(M)	9	pCF10
139a- Ent	E. gallinarum	CipLinTet	tet(K), tet(M)	11, 15	pEF1071, pUSA03
139b- Ent	E. gallinarum	CipLinTet	tet(M)
157a- mE	E. hirae	DapLinTet	lnu(B), tet(L), tet(M)	16	pSAS16
160a- Ent	E. faecalis	EryLinTetTyl	tet(M), erm(B), erm(C)
160b- mE	E. faecalis	EryLinTetTyl	tet(M), erm(B), erm(C)	16	pSAS16
163a- mE	E. hirae	DapLinTet	lnu(B), tet(L), tet(M), tet(O)	5	pSAS
164 Ent	E. casseliflavus	CipLinTig		11	pEF1071
168 Ent	E. casseliflavus	LinSynTig		11	pEF1071
169 Ent	E. casseliflavus	CipLinTig	qnrE. faecalis	3, 11	pAW63, pEF1071
170 Ent	E. gallinarum	LinSynTig
173 Ent	E. casseliflavus	CipLinTig		3, 11	pAW63, pEF1071
177 Ent	E. gallinarum	LinSynTig
182 Ent	E. casseliflavus	LinSynTig		11	pEF1071
184 Ent	E. casseliflavus	CipLinTig		3, 11	pAW63, pEF1071
193 Ent	E. casseliflavus	CipLinTig		3, 11	pAW63, pEF1071
206 Ent	E. casseliflavus	LinSynTig	vat(E)	11	pEF1071
222 Ent	E. casseliflavus	CipLinTetTig
251 Ent	E. faecalis	LinStrTet	tet(M)	8, 9	pAM373, pCF10
253 Ent	E. hirae	DapLinTet	lnu(B), tet(L), tet(M)	6, 12	pS86, pBMB67
262 Ent	E. faecium	CipLinTet	lnu(B), tet(M)
314 Ent	E. gallinarum	CipLinTet	tet(S)
317 Ent	E. hirae	DapLinTet	lnu(B), tet(M)	3, 11	pAW63, pEF1071
339 Ent	E. casseliflavus	EryLinTetTyl	tet(L), tet(M), erm(B), erm(C)	2, 5	pRE25, pSAS
379 Ent	E. mundtii	DapLinTig		3, 4, 11	pAW63, pMBB1, pEF1071
384 Ent	E. casseliflavus	CipLinSynTig	qnrE. faecalis	11	pEF1071
394 Ent	E. hirae	DapLinTig	lnu(B)	6	pS86
396 Ent	E. gallinarum	CipLinTetTig	tet(S)	5	pSAS
407 Ent	E. faecalis	KanLinTet	tet(K), tet(L), tet(M), aph(3′)-IIIa	6, 12	pS86, pBMB67
420 Ent	E. hirae	CipLinSyn
421 Ent	E. gallinarum	CipLinTetTig	tet(M)	4	pMBB1
423 Ent	E. faecalis	LinTetTig	tet(M)	9, 15	pCF10, pUSA03
436 Ent	E. faecalis	LinTetTig	tet(K), tet(M)	15	pUSA03

¹ Antimicrobials: Chloramphenicol (Chl), Ciprofloxacin (Cip), Daptomycin (Dap), Erythromycin (Ery), Kanamycin (Kan), Lincomycin (Lin), Penicillin (Pen), Synercid (Q/D) (Syn), Streptomycin (Str), Tetracycline (Tet), Tigecycline (Tig), and Tylosin (Tyl).

2.2. PCR

Isolates were tested for the presence of AR genes for the specific AR phenotype exhibited except for resistance to daptomycin and tigecycline, whose resistance mechanisms will be discussed elsewhere. Resistance determinants for chloramphenicol and penicillin were not determined as resistance to these antimicrobial drugs was seen in only one isolate each. Resistant isolates were tested by PCR for the presence of genes encoding resistance to aminoglycosides [aac(6′)-Ii, aac(6′)-Ie-aph(6″)-Ia, aph(6″)-Ib, aph(6″)-Ic, aph(6″)-Id, aph(3′)-IIIa, ant(3″)-Ia, ant(4′)-Ia, ant(6)-Ia, ant(9)-Ia], ciprofloxacin [qnr_{E. faecalis}], macrolides [erm(A), erm(B) and erm(C)], lincosamides [lnu(A) and lnu(B)], Quinupristin/Dalfopristin (Q/D) [vat(A), vat(B), vat(C), vat(D) and vat(E)], and tetracycline [tet(K), tet(L), tet(M), tet(S), tet(O), tet(U)] as previously described (Supplementary Table S1) [13]. PCR assays were performed using whole-cell templates that were prepared by suspending a single bacterial colony in 200 µL of sterile deionized water. Amplified PCR products were separated by electrophoresis on a 1.5% agarose gel and visualized by staining with ethidium bromide.

Replicon families were determined as previously described using a PCR-based plasmid rep-typing system to detect 19 defined Gram-positive plasmid replicon families [14]: rep₁ (prototype pIP501), rep₂ (prototype pRE25), rep₃ (prototype pAW63), rep₄ (prototype pMBB1), rep₅ (prototype pN315), rep₆ (prototype pS86), rep₇ (prototype pUSA02), rep₈ (prototype pAM373), rep₉ (prototype pCF10), rep₁₀ (prototype pIM13), rep₁₁ (prototype pEF1071), rep₁₂ (pBMB67), rep₁₃ (prototype pC194), rep₁₄ (prototype pRI1), rep₁₅ (prototype pUSA03), rep₁₆ (prototype pSAS), rep₁₇ (prototype pRUM), rep₁₈ (prototype pEF418), rep₁₉ (prototype pUB101), and the unique plasmid sequence of pMG1. PCR assays were performed using whole-cell templates, and amplified PCR products were separated by electrophoresis and visualized by staining with ethidium bromide as described above.

2.3. Statistical Methods

Pearson correlation coefficients were performed using Microsoft Excel. p values of ≤ 0.05 were considered significant.

3. Results

3.1. AR Genes

Twelve resistance genes were detected among the Enterococcus isolates (Table 2). Of the lincomycin-resistant isolates, 18.4% (9/49) contained lnu(B), while lnu(A) was not found in any of the isolates. Six enterococcal species were resistant to lincomycin, but lnu(B) was found in only two species, E. faecium and E. hirae. Of the 25 enterococcal isolates that were resistant to ciprofloxacin, three isolates contained qnr_{E. faecalis}, all of which were E. casseliflavus. Only one out of the 12 Q/D-resistant isolates was positive for the presence of vat(E). Other Q/D resistance genes, vat(A), vat(B), vat(C), and vat(D), were not detected. Six of the seven enterococcal isolates that were resistant to macrolides i.e., erythromycin and tylosin, were positive for the presence of both erm(B) and erm(C), while erm(A) was not detected in any of the isolates.

Table 2.

AR genes detected among MDR enterococci from surface water.

AR Phenotype (No. of Isolates)	AR Gene	No. of Gene (%)	Species (No. of Isolates)
Lincomycin (n = 49)	lnu(B)	9 (18.4)	E. faecium (2)
			E. hirae (7)
Tetracycline (n = 33)	tet(K)	3 (9.1)	E. faecalis (2)
			E. gallinarum (1)
	tet(L)	8 (24.2)	E. casseliflavus (1)
			E. faecalis (1)
			E. faecium (1)
			E. hirae (5)
	tet(M)	26 (78.8)	E. casseliflavus (3)
			E. faecalis (8)
			E. faecium (6)
			E. gallinarum (3)
			E. hirae (6)
	tet(O)	3 (9.1)	E. faecium (2)
			E. hirae (1)
	tet(S)	5 (15.2)	E. gallinarum (5)
Ciprofloxacin (n = 25)	qnrE. faecalis	3 (12.0)	E. casseliflavus (3)
Q/D (n = 12)	vat(E)	1 (8.3)	E. casseliflavus (1)
Macrolides (tylosin, erythromycin) (n = 7)	erm(B)	6 (85.7)	E. casseliflavus (1)
			E. faecalis (3)
			E. faecium (1)
			E. gallinarum (1)
	erm(C)	6 (85.7)	E. casseliflavus (1)
			E. faecalis (3)
			E. faecium (1)
			E. gallinarum (1)
Streptomycin (n = 3)	ant(6)-Ia	1 (33.3)	E. faecium (1)
Kanamycin (n = 2)	aph(3′)-IIIa	2 (100.0)	E. casseliflavus (1)
			E. faecalis (1)

Five tetracycline resistance genes (tet(K), tet(L), tet(M), tet(O) and tet(S)) were found in 93.9% (31/33) of the tetracycline-resistant isolates; tet(U) was not detected. tet(M) was most often detected (26/33; 78.8%) and was found across all five enterococcal species. Alternatively, tet(S) was only detected in E. gallinarum. tet(L) was found among four different enterococcal species, but the majority (5/8) was detected in E. hirae. Combinations of tetracycline resistance genes were not uncommon, with 12 tetracycline-resistant isolates carrying more than one resistance gene. Five different tetracycline gene combinations were exhibited: tet(K), tet(M); tet(L), tet(M); tet(M), tet(O); tet(K), tet(L), tet(M); tet(L), tet(M), tet(O) (Table 3). tet(L), tet(M) was the most common combination.

Table 3.

Profiles of AR genes detected among enterococci isolated from surface water.

AR Gene Profile	No. of Isolates	Species (No. of Isolates)
none	15	E. casseliflavus (11), E. gallinarum (2), E. hirae (1), E. mundtii (1)
ant(6)-Ia	1	E. faecium (1)
lnu(B)	1	E. hirae (1)
qnrE. faecalis	2	E. casseliflavus (2)
tet(M)	7	E. faecium (2), E. faecalis (3), E. gallinarum (2)
tet(S)	4	E. gallinarum (4)
vat(E)	1	E. casseliflavus (1)
lnu(B), tet(M)	2	E. faecium (1), E. hirae (1)
tet(K), tet(M)	2	E. gallinarum (1), E. faecalis (1)
tet(M), qnrE. faecalis	1	E. casseliflavus (1)
tet(M), tet(O)	2	E. faecium (2)
lnu(B), tet(L), tet(M)	4	E. hirae (4)
tet(M), erm(B), erm(C)	3	E. faecalis (3)
tet(S), erm(B), erm(C)	1	E. gallinarum (1)
lnu(B), tet(L), tet(M), tet(O)	1	E. hirae (1)
tet(K), tet(L), tet(M), aph(3′)-IIIa	1	E. faecalis (1)
tet(L), tet(M), erm(B), erm(C)	1	E. casseliflavus (1)
tet(M), erm(B), erm(C), aph(3′)-IIIa	1	E. casseliflavus (1)
lnu(B), tet(L), tet(M), erm(B), erm(C)	1	E. faecium (1)

Of the four enterococcal isolates that were resistant to aminoglycosides, one isolate was resistant to kanamycin, two isolates were resistant to streptomycin, and one isolate was resistant to both kanamycin and streptomycin. ant(6)-Ia was observed in one out of the three streptomycin-resistant isolates, while aph(3′)-IIIa was observed in both isolates that were resistant to kanamycin. The isolate that was resistant to both kanamycin and streptomycin only carried one gene, aph(3′)-IIIa.

Profiles of AR genes among the Enterococcus isolates are shown in Table 3. Not all the isolates with resistance phenotypes carried AR genes. Of the 51 MDR Enterococcus isolates that were tested for the presence of resistance genes, 15 of the isolates did not harbor any of the tested genes, most of which were E. casseliflavus (11/15; 73.3%). Of the 17 E. casseliflavus tested, only six isolates were positive for AR genes. However, all of the E. faecalis (n = 8) and E. faecium (n = 7) isolates were positive for at least one of the AR genes tested. AR gene patterns ranged from one resistance gene to five genes, with 44.4% (16/36) of isolates consisting of one resistance gene. The most common AR gene pattern was tet(M) (n = 7), followed by tet(S) (n = 4) and lnu(B), tet(L), tet(M) (n = 4).

3.2. Replicon Families

The presence of 19 rep-families was investigated among the 51 MDR Enterococcus isolates from surface water. Not all the Enterococcus isolates with AR phenotypes yielded amplicons for the rep-families, and the isolate with resistance to six antimicrobial classes was negative for all the rep genes tested. Two-thirds (35/51; 68.6%) of the enterococci were positive for at least one rep-family with up to 3 rep-families detected in four of the isolates (Table 4). Of the 19 rep-families tested, the MDR Enterococcus isolates represented 12 different rep-families. The rep-families detected and the number of Enterococcus isolates of different species that carried the rep-families are shown in Table 5. The most common rep-family among all the isolates was rep_{11 (pEF1071)} (n = 19), followed by rep_{3 (pAW63)} (n = 10). The majority of the rep_{11 (pEF1071)}- and rep_{3 (pAW63)}- positive isolates were E. casseliflavus, 78.9% (15/19) and 80.0% (8/10), respectively. The rep_{9 (pCF10)} family was only found in E. faecalis.

Table 4.

Profiles of rep-families detected among MDR enterococci from surface water.

No. of Rep-Families	Plasmid		No. of Isolates	Species (No. of Isolates)
	Rep-Family	Prototype
0			16	E. casseliflavus (1), E. faecalis (2), E. faecium (6), E. gallinarum (6), E. hirae (1)
1	2	pRE25	1	E. faecium (1)
	5	pSAS	3	E. gallinarum (1), E. hirae (2)
	4	pMBB1	1	E. gallinarum (1)
	6	pS86	1	E. hirae (1)
	9	pCF10	1	E. faecalis (1)
	11	pEF1071	8	E. casseliflavus (7), E. gallinarum (1)
	15	USA03	1	E. faecalis (1)
	16	pSAS16	2	E. faecalis (1), E. hirae (1)
2	3, 11	pAW63, pEF1071	7	E. casseliflavus (6), E. hirae (1)
	2, 5	pRE25, pSAS	1	E. casseliflavus (1)
	8, 9	pAM373, pCF10	1	E. faecalis (1)
	9, 15	pCF10, pUSA03	1	E. faecalis (1)
	6, 12	pS86, pBMB67	2	E. faecalis (1), E. hirae (1)
	11, 15	pEF1071, pUSA03	1	E. gallinarum (1)
3	3, 4, 11	pAW63, pMBB1, pEF1071	1	E. mundtii (1)
	3, 11, 16	pAW63, pEF1071, pSAS16	1	E. casseliflavus (1)
	3, 11, 12	pAW63, pEF1071, pBMB67	1	E. casseliflavus (1)
	5, 13, 15	pSAS, pC194, pUSA03	1	E. hirae (1)

Table 5.

Frequency of rep-families detected among MDR enterococci from surface water.

Plasmid		No. of Isolates	Species (No. of Isolates)
Rep-Family	Prototype
2	pRE25	2	E. casseliflavus (1), E. faecium (1)
3	pAW63	10	E. casseliflavus (8), E. hirae (1), E. mundtii (1)
4	pMBB1	2	E. gallinarum (1), E. mundtii (1)
5	pSAS	5	E. casseliflavus (1), E. gallinarum (1), E. hirae (3)
6	pS86	3	E. faecalis (1), E. hirae (2)
8	pAM373	1	E. faecalis (1)
9	pCF10	3	E. faecalis (3)
11	pEF1071	19	E. casseliflavus (15), E. gallinarum (2), E. hirae (1), E. mundtii (1)
12	pBMB67	3	E. casseliflavus (1), E. faecalis (1), E. hirae (1)
13	pC194	1	E. hirae (1)
15	pUSA03	4	E. faecalis (2), E. gallinarum (1), E. hirae (1)
16	pSAS16	3	E. casseliflavus (1), E. faecalis (1), E. hirae (1)

The number of different rep-families detected varied among Enterococcus isolates, with the greatest number of rep-families detected among E. hirae and the least number of rep-families among E. faecium (Table 5). Eight different rep-families were found among E. hirae (rep_{3 (pAW63)}, rep_{5 (pN315)}, rep_{6 (pS86)}, rep_{11 (pEF1071)}, rep_{12 (pBMB67)}, rep_{13 (pC194)}, rep_{15 (pUSA03)}, rep_{16 (pSAS)}), while only one rep-family was found among E. faecium (rep_{2 (pRE25)}). Both E. casseliflavus (rep_{2 (pRE25)}, rep_{3 (pAW63)}, rep_{5 (pN315)}, rep_{11 (pEF1071)}, rep_{12 (pBMB67)}, rep_{16 (pSAS)}) and E. faecalis (rep_{6 (pS86)}, rep_{8 (pAM373)}, rep_{9 (pCF10)}, rep_{12 (pBMB67)}, rep_{15 (pUSA03)}, rep_{16 (pSAS)}) were positive for six rep amplicons, while four rep amplicons were detected in E. gallinarum (rep_{4 (pMBB1)}, rep_{5 (pN315)}, rep_{11 (pEF1071)}, rep_{15 (pUSA03)}). E. mundtii, for which there was only one isolate, was positive for three different rep-families, rep_{3 (pAW63)}, rep_{4 (pMBB1)}, and rep_{11 (pEF1071)}.

Many of the Enterococcus isolates that belonged to the same species and had the same AR profiles had different rep-family profiles. For example, six E. hirae isolates with the same phenotypic resistance profile i.e., resistance to daptomycin, lincomycin, and tetracycline, had five different rep-family profiles i.e., rep_{5 (pN315)}; rep_{16 (pSAS)}; rep_{6 (pS86)}, rep_{12 (pBMB67)}; rep_{3 (pAW63)}, rep_{11 (pEF1071)}; rep_{5 (pN315)}, rep_{13 (pC194)}, rep_{15 (pUSA03)} (Table 1) suggesting that different plasmids can carry the same resistance genes to confer resistance to the same set of antimicrobial drugs. On the other hand, isolates with the same rep-family profiles exhibited different AR profiles in different species. For example, the same rep_{3 (pAW63)}, rep_{11 (pEF1071)} profile was detected in six E. casseliflavus isolates that were resistant to either ciprofloxacin, lincomycin, and Q/D, or ciprofloxacin, lincomycin, and tigecycline, as well as in one E. hirae isolate that was resistant to daptomycin, lincomycin, and tetracycline (Table 1). This indicates that the same plasmids can acquire different sets of AR genes to exhibit different resistance profiles.

4. Discussion

In our previous study, most of the Enterococcus isolates from surface water were resistant to at least one antimicrobial drug with multiple resistant phenotypes identified in a total of 51 isolates [12]. For the current study, those isolates that were resistant to three or more antimicrobial classes were further tested to investigate the molecular mechanism of AR and the abundance and diversity of plasmids among enterococci from surface water. The study was undertaken to improve the understanding of AR in the environment from the perspective of the One Health approach.

Resistance to macrolides (erythromycin and tylosin) was attributed to erm(B) and erm(C), which is consistent with Mlynarczyk et al. who described erm(B) as the most prevalent gene conferring erythromycin resistance in enterococci [15]. Interestingly, erm(B) and erm(C) were detected together in all the isolates positive for macrolides resistance genes, an observation that was not commonly observed but previously reported in E. faecalis from cattle [16]. For lincomycin resistance, lnu(B) was the only gene detected, and this is consistent with the previous findings that while lnu(A) was originally described in Staphylococcus, lnu(B) has been described only in Enterococcus [17,18]. Only a small portion of the lincomycin-resistant isolates (18.4%) were positive for the gene, which was also reported in a previous study [13], suggesting that there may be mechanisms for lincomycin resistance among enterococci other than lnu(A) and lnu(B). Similarly, only one isolate out of the 12 Q/D-resistant isolates was positive for a Q/D resistance gene, vat(E), which encodes a streptogramin A acetyltransferase. Of all the Q/D resistance gene, vat(E) is the most frequent gene found in enterococci of different sources, including human, animals, and the environment [19,20,21].

A number of genes encoding tetracycline resistance were detected in several species, including E. casseliflavus, E. faecalis, E. faecium, E. gallinarum, and E. hirae. tet(M), which encodes for ribosomal protection protein, was the most frequently detected gene, followed by tet(L), which encodes for a tetracycline efflux, similar to the findings previously reported [4,13,22]. Tetracycline resistance is most often mediated by tet(M) in enterococci from humans, animals, food, and the environment [4,13,23,24,25]. tet(S) is a less commonly detected tetracycline gene in enterococci, but most of the studies that reported the presence of tet(S) were conducted on E. faecalis and E. faecium only [4,23,24]. This study detected five isolates with tet(S), and they were all E. gallinarum. Similarly, Cauwerts et al. detected tet(S) in six isolates from their study, all of which belonged to non-faecalis, non-faecium species, including E. avium, E. casseliflavus, and E. gallinarum, with three of the isolates identified as E. gallinarum [25]. This data, along with our finding, suggests that tet(S) is found more commonly in non-faecalis and non-faecium enterococcal species. Overall, most of the tetracycline-resistant enterococcal isolates (93.9%) carried tet(K), tet(L), tet(M), tet(O) and tet(S) alone or in combination, while tet(U) was not detected in any of the isolates. The resistance mechanism of tet(U), which is known to confer low-level resistance to tetracycline, is unknown, although a report by Caryl et al. questioned the role of tet(U) as a resistance determinant [26,27].

Kanamycin-resistant isolates were tested for eight different resistance genes, including aac(6′)-Ie-aph(6″)-Ia, which encodes a bifunctional enzyme that confers high-level resistance to all clinically important aminoglycosides except streptomycin, that is often detected in human and animal isolates [18,28]. However, both kanamycin-resistant isolates were positive for another frequently detected gene aph(3′)-IIIa, which confers high-level kanamycin resistance in enterococci [13,29,30,31]. Three streptomycin-resistant isolates were tested for the presence of the two commonly detected streptomycin resistance genes, but only one isolate carried ant(6)-Ia. The high prevalence of ant(6)-Ia was also observed in other studies, not only for human and animals but also for environmental water [4,13,30,32,33].

Three isolates, out of the 25 ciprofloxacin-resistant enterococcal isolates, were positive for qnr_{E. faecalis}. This qnr-like gene, which was originally identified on the chromosome of E. faecalis, unlike the plasmid-borne fluoroquinolone resistance gene, qnr, found in Enterobacteriaceae, is known to contribute to fluoroquinolone resistance in E. faecalis [34]. However, none of the 25 ciprofloxacin-resistant isolates in this study were E. faecalis, and the three isolates carrying the qnr_{E. faecalis} gene were identified as E. casseliflavus, suggesting that an investigation of qnr-like genes in enterococcal species other than E. faecalis is needed.

While AR genes found in human and animal isolates were observed in this study among environmental enterococci, indicating the presence of similar mechanisms conferring resistance among enterococci from different sources, many isolates were still negative for the AR genes tested. This indicates the lack of information on the resistance genes present in Enterococcus. Indeed, many E. casseliflavus isolates were negative for AR genes, with only six out of the 17 E. casseliflavus positive for any resistance genes tested, while all of the E. faecalis (n = 8) and E. faecium (n = 7) isolates were positive for at least one of the AR genes tested. This could indicate that the studies on the AR genes present in Enterococcus are mostly biased towards E. faecium and E. faecalis, and the understanding of the genetic mechanisms of AR in enterococcal species other than E. faecium and E. faecalis is still lacking. However, all of the E. faecalis and E. faecium isolates were resistant to tetracycline, and all but one isolate carried at least one of the tetracycline resistance genes. In contrast, half of the non-faecalis, non-faecium enterococcal isolates were susceptible to tetracycline. Most of the non-faecalis, non-faecium enterococcal isolates that were tetracycline-resistant were positive for at least one tetracycline resistance gene, while among those that were not resistant to tetracycline, only four isolates were positive for AR genes. This could indicate that the genetic mechanism for tetracycline resistance is well understood, but not for other drug resistances. A similar finding could be seen among enterococcal isolates from animal and food sources [13,35,36]. Although resistance mechanisms for tetracycline and erythromycin were well understood and present among most of the enterococcal isolates across all species, AR genes could not be identified for many other antimicrobial drugs [13,35,36]. The genetic mechanisms of AR in non-faecalis and non-faecium enterococcal species seem to be quite different from those of E. faecalis and E. faecium, and the understanding of AR mechanisms needs to be improved for different species.

A third of the MDR Enterococcus isolates did not carry any plasmids of 19 replicon families. This is similar to the previous result by Jensen et al., in which 32% of E. faecalis and 33% of E. faecium from their set of human and animal isolates did not harbor any plasmids of 19 rep-families [14]. However, most of the isolates without rep genes were from pigs, and only three isolates, out of the 26 isolates without rep genes, were human clinical isolates [14]. This is similar to other studies that conducted plasmid replicon typing PCR on human isolates. Rosvoll et al. and Wardal et al. detected only 4% (4/99) of E. faecium and 1.3% (2/152) of E. faecalis, respectively, without any rep genes [37,38]. This indicates the presence of plasmids of novel rep-families that are yet to be defined or unique sequences that were not tested, or the presence of other mobile genetic elements that may contain AR genes in non-human enterococcal isolates.

Twelve rep-families were detected in this study, indicating the presence of 12 different plasmids among the 51 MDR Enterococcus isolates from surface water, suggesting the diversity of plasmids among enterococci with the indication of different mechanisms for AR gene transfer. This is a greater variety of rep-families compared to other studies that detected between five and nine rep-families using the same PCR-based rep-typing method [4,14,31,37,38,39,40]. Some of the rep-families that were previously not detected among the enterococci were detected in the current study, including rep_{3 (pAW63)}, rep_{5 (pN315)}, rep_{12 (pBMB67)}, rep_{15 (pUSA03)}, and rep_{16 (pSAS)}. The species in which rep_{3 (pAW63)} and rep_{5 (pN315)} plasmids were detected were non-faecalis, non-faecium enterococcal species, i.e., E. casseliflavus, E. gallinarum, E. hirae, and E. mundtii. This result demonstrates diverse plasmid contents among different species of Enterococcus. The rep-families that were commonly found in E. faecalis and E. faecium isolates from previously conducted studies were not detected in this study among the same species, including rep_{1 (pIP501)}, rep_{7 (pUSA02)}, rep_{14 (pRI)}, rep_{17 (pRUM)}, and rep_{18 (pEF418)} [4,14,31,37,38,39,40]. This may suggest a loss of plasmids, or a change in plasmid content, in E. faecalis and E. faecium in the environment with less selective pressure of antimicrobials. Moreover, the results of this study revealed the presence of multiple rep genes in half of the isolates with positive rep genes, indicating a high abundance of plasmids among enterococci of environmental origin. However, the average number of rep genes present per isolate was lower than the number of rep genes detected in isolates of clinical origin [37,38,40], underscoring the loss of plasmids in the environment with lower antimicrobial levels.

The most common rep-families identified among E. faecalis in the previous studies from their sets of human and animal isolates were rep_{9 (pCF10)} [14,38,39]. Similarly, the current study consisting of environmental isolates found that rep_{9 (pCF10)} was the most frequently detected rep-family among E. faecalis. The rep-families that were detected among E. faecalis in the current study were commonly detected in other studies as well i.e., rep_{2 (pRE25)}, rep_{6 (pS86)}, rep_{8 (pAM373)}, and rep_{9 (pCF10)}, while rep_{12 (pBMB67)}, rep_{15 (pUSA03)}, and rep_{16 (pSAS)} had not been identified in other studies [14,38,39]. This suggests a variability in plasmid content among the isolates of the same species from different sources. Three isolates were positive for rep_{8 (pAM373)} and/or rep_{9 (pCF10)}, and they were all E. faecalis. This was not surprising as pAM373 of rep_{8 (pAM373)} as well as pAD1 and pCF10 of rep_{9 (pCF10)} are pheromone-responsive plasmids, which are known to exist primarily in E. faecalis as most of the pheromone-responsive plasmids have been described in this species [41]. In contrast to the notion that pheromone-responsive plasmids enhance the acquisition of resistance, the isolates that harbored rep_{8 (pAM373)} and rep_{9 (pCF10)} plasmids in this study did not carry multiple AR genes and only harbored tet(M).

Only one isolate out of the seven E. faecium isolates tested, was positive for a rep gene, which is a much lower frequency compared to those of the previous studies with detection rates of rep genes between 67% and 100% of the total E. faecium isolates [4,14,31,37,40]. In contrast to the previous studies that indicate E. faecium of the clinical origin as the reservoir of plasmids of various rep-types, the current study only detected one rep gene in one isolate among MDR E. faecium isolates, and this might suggest the variation of plasmid content in enterococci of various source type and a loss of AR plasmids in less-selective environments. Enterococci may lose their AR plasmids in the environment where antimicrobials are less intensively used as they may be a burden for the host [2]. The only rep-family detected among E. faecium in this study was rep_{2 (pRE25)}, which was the most prevalent rep-family in E. faecium previously identified [4,14,31,37,40]. pRE25, which is a member of rep₂ family, is a conjugative multi-resistance plasmid; therefore, the presence of rep_{2 (pRE25)} plasmid in the MDR E. faecium recovered from the aquatic environment was not surprising [42]. The only other species that was positive for rep_{2 (pRE25)} was E. casseliflavus, which is the first instance that this plasmid has been reported in E. casseliflavus. An environmental E. hirae isolated from marine sediment was reported to carry pRE25, and the isolate was resistant to erythromycin, similar to the rep_{2 (pRE25)}-positive E. casseliflavus isolate from this study [43]. The same group also reported an E. faecium isolate positive for pRE25 in marine sediment [44]. These results suggest the frequent presence of this conjugative multi-resistance plasmid in the environment capable of transfer, along with AR genes, to other bacteria [43,44].

The most dominant rep-family among all the isolates in this study was rep_{11 (pEF1071)} (n = 19), followed by rep_{3 (pAW63)} (n = 10). Most of the rep_{11 (pEF1071)} and rep_{3 (pAW63)} were detected in E. casseliflavus, 78.9% and 80% respectively, with a significant positive association (p < 0.05) between the plasmids belonging to rep_{11 (pEF1071)} and rep_{3 (pAW63)} with E. casseliflavus. Even though rep_{11 (pEF1071)} had been detected in E. faecium isolates in several studies, this was the first time rep_{11 (pEF1071)} was reported in E. casseliflavus [31,37,40]. pEF1071 is a member of rep₁₁ family, and enterocins 1071A and 1071B are known to be encoded on pEF1071 [45]. Since enterocins exhibit antimicrobial activity and the producer bearing the plasmid would have a survival advantage over other closely related species present in the same ecological niche [45], it is possible that the presence of pEF1071 enabled E. casseliflavus to be the most frequently identified species and also the most common species with MDR phenotypes found in the surface water [12].

To date, most of studies on the occurrence and distribution of AR genes and plasmids in Enterococcus have focused on human or animal isolates, while data on the distribution of AR genes in Enterococcus recovered from the environment are relatively limited. Moreover, no study has attempted to classify plasmids present in environmental enterococci, especially those including non-faecalis, non-faecium enterococcal species. To the best of our knowledge, this is one of the first investigations, if not the first, of molecular characterization of MDR Enterococcus from surface water that encompasses a significant number of enterococcal species.

5. Conclusions

The mechanisms conferring resistance were determined among the MDR enterococci, but the observation that AR mechanisms could not be determined for many of the resistant isolates indicates that diverse AR mechanisms exist among environmental enterococci, and the understanding of AR mechanisms for enterococci is limited. Furthermore, the plasmid contents of the enterococci in the aquatic environment appears to be quite different from those in hospital settings and livestock. Diverse plasmids were identified among enterococci isolated from surface water, which indicates that environmental enterococci may carry multiple plasmids of different rep-families through which AR genes can be transferred. Moreover, pheromone-responsive plasmids, which could be an effective vector for AR dissemination, were present in surface water. This study indicates that surface water may be a suitable environment for the transfer of AR genes via horizontal gene transfer through plasmids harbored by enterococcal isolates present in the aquatic environment. This may result in the transfer of AR determinants to human strains and contribute to human infections through exposure to contaminated water.

Supplementary Materials

The following table is available online at https://www.mdpi.com/2076-2607/8/9/1338/s1, Table S1: Primers used for the identification of AR genes in MDR enterococci from surface water.

Author Contributions

Conceptualization, S.C., J.G.F., and C.R.J.; methodology, J.B.B.; formal analysis, S.C.; investigation, S.C. and J.B.B.; resources, J.B.B. and C.R.J.; writing—original draft preparation, S.C.; writing—review and editing, J.G.F. and C.R.J.; supervision, J.G.F. and C.R.J.; funding acquisition, J.G.F. and C.R.J. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the U.S. Department of Agriculture, sub-project number 6040-32000-009-00-D, and the Centers for Disease Control and Prevention, sub-project number: 6040-32000-009-08-R.

Conflicts of Interest

The authors declare no conflict of interest. The mention of trade names or commercial products in this manuscript is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.