Pandemic clone USA300 in a Brazilian hospital: detection of an emergent lineage among methicillin-resistant Staphylococcus aureus from bloodstream infections

doi:10.21203/rs.3.rs-1531882/v1

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Pandemic clone USA300 in a Brazilian hospital: detection of an emergent lineage among methicillin-resistant Staphylococcus aureus from bloodstream infections

https://doi.org/10.21203/rs.3.rs-1531882/v1

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Background

Staphylococcus aureus is one of the leading causes of bloodstream infections (BSI) worldwide. In Brazil, the hospital-acquired methicillin-resistant S. aureus USA100/SCCmecII lineage replaced previously well-established clones. However, the isolation of community-associated (CA) MRSA lineages from hospitalized patients is an increasing issue.

Methods

Consecutive S. aureus isolates recovered from BSI episodes of patients admitted between January 2016 and December 2018 in a Brazilian teaching hospital were tested for antimicrobial resistance, characterized as their genotypic features and the clinical characteristics of the patients were evaluated.

Results

A total of 123 S. aureus isolates were recovered from 113 patients. All isolates were susceptible to linezolid, teicoplanin and vancomycin and 13.8% were non-susceptible for daptomycin. Vancomycin MIC₅₀ and MIC₉₀ = 2 mg/L was found for both MRSA and MSSA isolates. MRSA isolation rate was 30.1% (37/123), and 51.4% of them carried the SCCmecII, followed by SCCmecIV (40.5%). Among the 37 MRSA isolates, the main lineages found were USA100/SCCmecII/ST5 and ST105 (53.7%) and USA800/ST5/SCCmecIV (18.9%). Surprisingly, were detected six (16%) CA MRSA isolates belonged to USA300/ST8/SCCmecIVa and carrying pvl genes and ACME cassette type I. These patients with USA300 BSI had severe comorbidities, including cancer, most had a Charlson score ≥ 5 and attended wards where health professionals were shared. MRSA isolates were associated with hospital acquired infections (p = 0.02) in older patients (p = 0.03) and those diagnosed with hematologic cancer (p = 0.04). A total of 52 (46%) patients died, and 60% of them presented a MRSA BSI.

Conclusions

Pandemic MRSA USA300 was detected for the first time in our hospital, and we hypothesized its cross-transmission between patients with BSI. This lineage can be already circulating among Brazilian hospitals, highlighting the importance of surveillance programs to fight multidrug resistant and hypervirulent isolates.

S. aureus

MRSA

bloodstream infections

USA300 lineage

pvl gene

ACME cassette

USA100/ST5 and ST105 lineages

Staphylococcus aureus is one of the most common causes of bloodstream infections (BSI) worldwide [1, 2]. The presence of an indwelling device or a skin and soft tissue infection (SSTI) associated to hospital (HA) or community (CA) BSI, respectively, are the most common sources of this pathogen [3]. S. aureus BSI, especially those caused by MRSA, imposes higher rates of morbidity and mortality and the costs associated to these infections are troublesome, especially in middle and low-income countries [4]. Moreover, the presence of methicillin-resistant S. aureus (MRSA) as the cause of BSI represents a therapeutic challenge in health care institutions [5]. However, reduced isolation of MRSA isolates from BSI has recently been reported in the world [1, 6]. Diekema and coworkers [1] showed that S. aureus was the main Gram-positive bacteria isolated from BSI in a 20-year surveillance period, between 1997 and 2016, involving 45 nations, including Latin America countries. The authors showed that there was a decline in the number of MRSA isolates over the years and that the daptomycin resistance among S. aureus isolates remained rare (< 0.1%), as well as no trend toward an increase in the vancomycin MIC was detected.

In the past years, the substitution of well-established MRSA lineages has been described in the hospital environment [7, 8]. In Brazilian hospitals, the previously predominant MRSA lineage, known as Brazilian Endemic Clone (BEC/ST239), had been fully replaced by the New York/Japan lineage among BSI isolates (USA100/ST5 or ST105) [9–11]. Lately, our group has also detected the emergence of USA1100/ST30, a CA-MRSA lineage, into Brazilian hospital settings [8, 10]. Curiously, in Brazil, the pandemic clone USA300/ST8/SCCmecIVa and the USA300-Latin American Variant (LV)/SCCmecIVc-e lineages remain rare [11]. These related lineages present different SCCmec subtypes and the USA300-LV lacks the operon ACME [12]. However, they could carry the Panton-Valentine leukocidin (PVL) and are considered as hypervirulent. Thus, once present in the environment, they can spread, leading to infections with high mortality rates [13].

Molecular studies have helped the epidemiological surveillance of S. aureus BSI, highlighting the constant clonal change that has been taking place in health institutions and the dissemination of MRSA clones that can lead to higher rates of morbidity and mortality [14]. Besides, the constantly monitoring of S. aureus BSI could help surveillance programs in containing the spread of their resistance and virulence. Over the last years, our group has conducted the surveillance of S. aureus BSI in a University Hospital of Rio de Janeiro, Brazil, to identify the emergence of new clones or new resistance traits that may alter the epidemiology and treatment of these infections. Therefore, this study aimed to continue this surveillance through characterization of S. aureus isolates from BSI over a period of three years in relation to antimicrobials resistance and virulence associated with different clones and relate these results with clinical data of the patients.

1. Clinical isolates and setting

This prospective cohort study evaluated phenotypic and molecular profiles of S. aureus isolates recovered from consecutive episodes of BSI occurring in adults (> 18 years old), between January 2016 and December 2018. Patients were admitted at the Hospital Universitário Clementino Fraga Filho (HUCFF), a tertiary public teaching hospital in Rio de Janeiro, Brazil, which currently has 300 active beds.

The first isolate of an episode of S. aureus BSI were analyzed, being an episode defined as the isolation of S. aureus in blood culture, with subsequent documentation of negative blood cultures, clinical improvement, and anti-staphylococcal therapy. Patient demographics, classification of the BSI episode [15] treatment, length of stay and discharge were collected for each patient.

All blood cultures were processed using BacT/ALERT₁ (BioMerieux, Durham, NC, USA). Bacterial identification was performed by the automated VITEK2® system (BioMerieux) and confirmed by MALDI-TOF MS (Matriz Assisted Laser Desorption Ionization/ Time of Flight) (Bruker Daltonics, Billerica, MA, USA) [16].

2. Antimicrobial susceptibility tests and SCC mec typing

Susceptibility to methicillin and trimethoprim-sulfamethoxazole (TMP/STX) was determined using the disk-diffusion test (Oxoid, Cambrigde, UK) according to CLSI guidelines [17]. Minimal inhibitory concentrations (MICs) for daptomycin, linezolid, oxacillin, teicoplanin and vancomycin (Sigma-Aldrich Chemical Company, St Louis, MO, USA) were determined by broth microdilution (BMD), using fresh cation-adjusted Muller-Hinton broth (CAMHB), supplemented with calcium (50 µg/mL) for daptomycin [17]. Ceftaroline MICs determination was performed by Etest® (BioMérieux) for all MRSA isolates. S. aureus ATCC 25923 and ATCC 29213 were used as controls for the disk-diffusion and BMD, respectively.

For isolates resistant to oxacillin by the disk-diffusion method, the SCCmec typing [18], and subtyping [19] were accessed by multiplex polymerase chain reaction, using bacterial DNA obtained by the QIAamp DNA Mini Kit (QIAGEN, Hilden, Germany). Staphylococcus strains used as positive controls are described in Salgueiro et al. [20].

3. Phenotypic tests for screening of hVISA isolates

All isolates presenting a MIC ≥ 2 mg/L for vancomycin were screened for hVISA phenotype [21, 22]. Plates with BHI agar (Becton Dickson, Franklin Lakes, NJ, USA), containing 3 and 4 mg/L of vancomycin were swabbed with 0.5 McFarland standard suspension (10⁸ CFU/mL) of S. aureus and incubated at 35 to 37°C for 24h. Reduced susceptibility to vancomycin was defined as growth of one or more colonies forming units (CFU) at any of the two concentrations. BHI agar plates with 4 mg/L of vancomycin, supplemented with 16 g/L of pancreatic casein digestion (Merck), were inoculated using four 10µL spots from a 0.5 McFarland inoculum [22]. An isolate was considered to have reduced susceptibility to vancomycin if at least one spot had two or more CFUs. S. aureus ATCC 29213 (MSSA) and Mu3 (hVISA) were used as controls [23].

4. Genotypic profile of MRSA isolates

All MRSA isolates were typed by pulsed-field gel electrophoresis (PFGE) after digestion of whole cell DNA with SmaI in a CHEF-DRIII system (Bio-Rad, Richmond, CA, USA), as previously described [24]. The PFGE fingerprints were compared by the unweighted pair-group method arithmetic mean clustering analysis, applying the Dice correlation coefficient. Isolates with four or fewer bands of difference or minimum of 80% similarity were classified as belonging to the same genotype [25]. The clonal lineages were defined by comparison with national [10] and international clones [26]. Multilocus Sequence Typing (MLST) was performed for one isolate from each genotype identified in PFGE [27].

5. Detection of virulence genes

PCR for detection of pvl were carried out in all MRSA isolates [28]. The ACME typing was additionally performed in isolates belonging to USA300/ST8/SCCmecIV lineage [29]. Staphylococcus strains used as positive controls are described in Schuenck et al [28].

6. Statistical analysis

Categorical variables were compared using chi-square or Fisher exact tests, and continuous variables were compared using the Wilcoxon test. A p value < 0.05 was considered to be statistically significant. All analyses were performed using SPSS 21.0 for Windows (SPSS, Inc).

1. Baseline characteristics of patients presenting S. aureus BSI

During the period of study, 113 patients developed S. aureus BSI. Ten of them presented two BSI episodes. Thus, a total of 123 S. aureus isolates were recovered. Most of patients (53.1%; 60/113) were men, presented at least one comorbidity (89.4%) and developed central line-associated BSI (55.8%) or secondary bacteremia due to SSTI (24.8%). MRSA was associated to older age (p = 0.03), hematologic cancer (p = 0.04) and hospital-acquired BSI (p = 0.02). A total of 52 (46%) patients died, and 60% of them presented a MRSA BSI (Table 1).

Table 1

Baseline characteristics of 113 patients presenting Staphylococcus aureus bloodstream infection according to methicillin resistance
Clinical characteristics	MSSA (N = 78)	MRSA (N = 35)	TOTAL (N = 113)	p-value
Gender, n (%) = male	41 (52.6)	19 (54.3)	60 (53.1)	1.00
Age (years), mean (range)	58.4 (18–98)	64.5 (39–87)	62 (18–98)	0.03
Underlaying comorbidities, n (%)
Diabetes	22 (28.2)	11 (31.4)	33 (29.2)	0.83
Previous neutropenia	2 (2.6)	3 (8.6)	5 (4.4)	0.33
Acute renal insufficiency	3 (3.8)	3 (8.6)	6 (5.3)	0.38
End stage renal disease	35 (44.9)	8 (22.9)	43 (38.0)	0.16
Cardiopathy	56 (71.8)	21 (60.0)	77 (68.1)	0,62
Pneumopathy	5 (6.4)	7 (20.0)	12 (10.6)	0.10
Neurologic disease	7 (8.9)	2 (5.7)	9 (8.0)	0.72
Hepatopathy	6 (7.7)	6 (17.1)	12 (10.6)	0.20
Renal replacement therapy	30 (38.5)	8 (22.9)	38 (33.6)	0.30
Solid cancer	12 (15.4)	7 (20.0)	19 (16.8)	0.60
Hematologic cancer	1 (1.3)	4 (11.4)	5 (4.4)	0.04
Autoimmune disease	1 (1.3)	3 (8.6)	4 (3.5)	0.09
Solid organ transplant	11 (14.1)	3 (8.6)	14 (12.4)	0.55
Previous BSI	11 (14.1)	7 (20.0)	18 (15.9)	0.59
Acquisition, n (%)
HA-BSI	35 (44.9)	26 (74.6)	61 (53.9)	0.02
CA-BSI	22 (28.2)	5 (14.3)	27 (23.9)
HCA-BSI	21(26.9)	4 (11.4)	25 (22.1)
Infection source, n (%)
Central line vascular catheter	42 (53.8)	21 (60.0)	63 (55.8)	0.5
Pulmonary	5 (6.4)	1 (2.9)	6 (5.3)
SSTI	18 (23.1)	10 (28.6)	28 (24.8)
Primary bacteremia	13 (16.7)	3 (8.6)	16 (14.2)
Outcome, n (%)
Death	31 (39.7)	21 (60.0)	52 (46.0)	0.29
MSSA- Methicillin-susceptible Staphylococcus aureus; MRSA- Methicillin-resistant Staphylococcus aureus; BSI- Bloodstream infection; HA- Hospital-acquired; CA- Community-acquired; HCA- Healthcare-associated; SSTI- Skin and soft tissue infection, ND- Not determined; A value of p ≤ 0.05 was considered statistically significant. For patients that presented two BSI episodes, the first episode was considered.

2. Antimicrobial susceptibility, hVISA screening and SCC mec typing

According to the disk-diffusion method, 30.1% (37/123) of S. aureus isolates were resistant to cefoxitin disk, being characterized as MRSA. Overall, 51.4% (19/37) of these isolates carried the SCCmecII, followed by SCCmecIV (15/37; 40.5%), SCCmecIII (2/37; 5.4%) and SCCmecV (1/37; 2.7%). Among SCCmecIV isolates those were subtyped as SCCmecIVa belonged to USA300 lineage. Only the SCCmecIII isolates were resistant to TMP-SXT disk.

The MIC results are showed in Table 2. For vancomycin, both MRSA and MSSA isolates presented MIC₅₀ and MIC₉₀ = 2 mg/L. This MIC value was found in 90% of SCCmecII isolates and in 53.3% of those that carried the SCCmecIV. Ceftaroline MIC was accessed in MRSA isolates and ranged from 0.25 to 0.75 mg/L. Regarding to oxacillin, MIC₅₀ and MIC₉₀ were, respectively, 256 and ≥ 256 mg/L, in MRSA isolates, and 1 and 2 mg/L among MSSA ones. All isolates were susceptible to linezolid, teicoplanin and vancomycin. Seventeen (13.8%) S. aureus isolates were non-susceptible to daptomycin, and among them, five (29.4%) were MRSA isolates.

Table 2

– Minimal inhibitory concentration of different antimicrobials against 123 Staphylococcus aureus isolates from bloodstream infections
Antimicrobial*	MSSA (N = 86)				MRSA (N = 37)
Antimicrobial*	MIC range	MIC₅₀	MIC₉₀	Non-susceptible^a isolates (%)	MIC range	MIC₅₀	MIC₉₀	Non-susceptible^a isolates (%)
Oxacillin	0.25–2	1	2	0	16 – ≥256	256	≥ 256	100^b
Vancomycin	0.5–2	2	2	0	0.5–2	2	2	0
Teicoplanin	0.25–2	0.5	1	0	0.25–1	0.5	0.5	0
Linezolid	0.25–1	1	1	0	0.25–2	0.5	1	0
Daptomycin	0.5–2	1	2	13.9	0.5–2	1	2	13.5
Ceftaroline	NA	NA	NA	NA	0.25–0.75	0.5	0.75	0
The Minimal inhibitory concentration (MIC) values for oxacillin, vancomycin, teicoplanin, linezolid and daptomycin were determined by the broth microdilution method and for ceftaroline by E-test® and presented in mg/L. MSSA - Methicillin-susceptible Staphylococcus aureus; MRSA - Methicillin-resistant Staphylococcus aureus*; NA – Not applicable; ^a % of non-susceptible isolates was determined according to CLSI and EUCAST interpretation criteria. ^b Resistant isolates for oxacillin were also considered as non-susceptible isolates.

All the 72 (58.5%) isolates that presented vancomycin MIC = 2 mg/L were screening for the detection of hVISA phenotype. However, no hVISA isolate was found.

3. Genotypic profiles and virulence genes in MRSA isolates

The PFGE patterns and general characteristics of 37 MRSA isolates recovered from BSI are presented in Fig. 1. The isolates were clustered among specific lineages: USA100/SCCmecII of ST5 (3 isolates; 8.1%) and ST105 (16; 43.2%), USA800/ST5/SCCmecIV (7; 18.9%), USA300/ST8/SCCmecIVa (6; 16.2%), USA1100/ST30/SCCmecIV (2; 5.4%) and BEC/ST239/SCCmecIII (2; 5.4%). One isolate carrying the SCCmec type V and related to ST1 was also found.

The pvl gene was found in all isolates of the USA300/ST8 and USA1100/ST30 lineages.

4. Characteristics of USA300 isolates

All USA300/ST8/SCCmeIVa isolates (1963, 1967, 1982, 1988, 2013, 2020) carried the pvl and fnbB virulence genes as well as the ACME cassette type I (Table 3). These isolates were recovered from different patients, which developed hospital or healthcare associated BSIs. All these individuals had severe comorbidities and all, but one patient (isolate number 2020), presented central line at the moment of BSI diagnosis. Four patients presented Charlson score ≥ 5. Most of these patients were undergoing cancer treatment, although not at the same unit. Timeline distribution of the six patients with BSI caused by USA300 isolates according to hospital ward are represented in Fig. 2. Although some patients were admitted to the hospital in close periods, and the ≥ 90% similarity between the isolates (Fig. 1), a direct nosocomial transmission could not be clearly established. However, the wards occupied by these patients are physically close to each other (same corridor), and the healthcare workers and staff (cleaning service) were shared by these sectors.

Table 3

Clinical and microbiological characteristics related to six patients that presented bloodstream infections caused by the pandemic MRSA USA300/ST8/SCCmecIVa lineage
Isolate No.	Admission (MM/DD/YY)	Gender/ Age (Y)	Cormobidities	Charlson score	Ward	Acquisition	Antimicrobial treatment	Isolation date (MM/DD/YY)	MIC (mg/L)			Virulence genes	PFGE Pulsotype
Isolate No.	Admission (MM/DD/YY)	Gender/ Age (Y)	Cormobidities	Charlson score	Ward	Acquisition	Antimicrobial treatment	Isolation date (MM/DD/YY)	OXA	VAN	DAP	Virulence genes	PFGE Pulsotype
1963†	07/11/17	Male/79	SC	5	Gen Surg	HA	VAN	08/05/17	128	1	1	pvl, ACME-I	A2
1967	07/21/17	Male/43	SC	2	Int Med	HA	VAN	08/19/17	128	1	1	pvl, ACME-I	A2
1982†	10/26/17	Male/68	D, C, SC	10	Int Med	HA	VAN	10/27/17	128	1	1	pvl, ACME-I	A3
1988†	09/11/17	Male/61	HC	6	Hem	HA	PIP + TAZ	12/05/17	128	2	2	pvl, ACME-I	A1
2013†	06/11/18	Female/40	L, ESRD, C, P	3	Emer	HCA	VAN	06/11/18	64	2	1	pvl, ACME-I	A1
2020	07/20/18	Male/67	D, C, HC	5	Int Med	HCA	VAN + CEFP	07/22/18	256	0.5	1	pvl, ACME-I	A4
ST- Sequence Type; SCCmec – Staphylococcal cassette chromosome mec; MRSA – Methicillin-resistant S. aureus; M – Month; D – Day; Y- Year; SC – Solid cancer; D – Diabetes; C – Cardiopathy; HC - Hematological cancer; L – Lupus; ESRD – End stage renal disease; P – Pneumopathy; NA – Not applicable; Gen Surg- General Surgery; Int Med -Internal medicine; Hem – Hematology; Emer – Emergence Room; VAN- Vancomycin; PIP-Piperacillin; TAZ - Tazobactan; CEFP – Cefepime; HA – Hospital acquired; HCA – healthcare associated; OXA – Oxacillin; DAP – Daptomycin; MIC - Minimal inhibitory concentration; pvl – Panton-Valentine leucocidin gene; ACME- Arginine catabolic mobile element; PFGE – Pulsed field gel electrophoresis; † – death as outcome

In this study, we characterized consecutive S. aureus isolates from BSI in a teaching hospital at Rio de Janeiro for three years and we detected for the first time in our hospital the emergence of the pandemic CA-MRSA USA300/ST8/SCCmecIVa lineage. These patients attended wards where health professionals were shared and, therefore, we hypothesized a cross-transmission of these isolates in the hospital. Although we know that other hospitals may not have the same epidemiological situation seen here, our results may reflect a picture of the circulating strains of S. aureus that cause BSI in the region.

Although CA-MRSA lineages were classically related to SSTI, they have also been widely implicated in HA-BSI [30, 31]. According to Kourtis et al. [32] CA-MRSA infections provide a reservoir that contributes to the incidence of healthcare-associated diseases and fuels transmission both outside and within healthcare settings. Our group has been carrying out a surveillance in S. aureus BSI in the study hospital for years and, despite we have described the presence of community S. aureus lineages in hospital settings since 2009 [8, 10, 33–35] we had not yet seen the spread of USA300/ST8/SCCmecIVa. Some Brazilian studies have shown the presence of CA-MRSA isolates in hospitals recovered from different clinical sources, including occasionally USA300/ST8/SCCmecIV isolates [36–39]. However, these studies did not provide accurate characterization of isolates of this lineage. Furthermore, different from what has been described in Latin America countries about the occurrence of the USA300-LV lineage [11], here, the isolates belonged to USA300/ST8 carried the pvl genes, the SCCmec type IVa, as well as the ACME-I cassette, being characterized as the USA300/ST8 North American lineage. Patients with USA300 BSI presented severe comorbidities and most had a Charlson score ≥ 5 and cancer. Curiously, among the patients with MRSA BSI this pathology was most frequently associated to those presenting USA300 (p < 0.05) (data not shown). Despite we were not able to demonstrate a time-space relationship to almost all of them, a close genetic similarity of the isolates leads us to suggest a possible horizontal transmission associated with this clonal lineage. Furthermore, even if all the patients involved did not occupy the same ward at the same time, there would be a possible sharing of unscreened patients, which may be the focus of the outbreak, pointing out to the need of constantly surveillance of this pandemic clonal lineage into the present hospital.

In the present study, we demonstrate a great diversify of MRSA clonal lineages causing BSI in our teaching hospital, also observed in previous studies of our group [8, 9]. Here, the USA100 lineage remains as the main MRSA clone (51.4%). These data confirm the replacement of the prior prevalent BEC clone, which now represents only 5.4% of MRSA isolates found. Bride et al. [38], in a study conducted in a southeast Brazilian hospital characterized S. aureus isolates from various clinical sources and USA100/ST5 lineage was prevalent among HA-infections. Of note, in our study, most of USA100 isolates belonged to ST105 (84.2%). Despite this is the first report of this lineage in our hospital, it was already detected in S. aureus isolated from BSI in other Brazilian hospitals [8, 9]. Viana and coworkers recently evaluated MRSA isolates from different hospitals in Rio de Janeiro, between 2014 and 2017, and observed the emergence of this SCCmecII/ST105 lineage, which has presented multidrug resistance characteristics and seems to be associated with increased evasion when exposure to monocytic cells [40].

The success in the spread of S. aureus isolates is commonly attributed to their antimicrobial resistance profile, but virulence may play a crucial role in colonization and infection [41]. In the present study, the presence of pvl genes was evaluated in all MRSA isolates and only CA-MRSA lineages related to USA300/ST8 and USA1100/ST30 were positive. Besides, USA300 presented the two virulence determinants investigated, pvl and ACME I. Some authors have reported association between virulence and mortality among patients with S. aureus BSI, indicating that the transmission of a virulent pathogen to an already debilitated patient can worsen his clinical condition [7] However, more studies are needed to better understand the relevance of virulence determinants in S. aureus bloodstream infections.

Among Latin America countries, MRSA isolates accounted for almost half of S. aureus BSI in the past few years [1, 11]. In Brazil, the MRSA isolation rate vary according to specific regions. For example, a study conducted at a tertiary oncology care center in Rio de Janeiro detected 26.3% of methicillin resistance among S. aureus isolates recovered from BSI episodes [42]. On the other hand, Primo and coworkers [4] showed a MRSA isolation rate of 58.3% among S. aureus BSI in a central western Brazilian teaching hospital. The MRSA isolation rate in our hospital in Rio de Janeiro has remained around 30% in BSI caused by S. aureus, since 2011, as previously described by our group [10], similarly to the findings of the present study, reinforcing the need for constant surveillance directed towards this pathogen.

It is well established that a structured management in diagnostic and treatment of S. aureus BSI, which differs accordingly to methicillin-resistance, is crucial for an optimal outcome [43]. Vancomycin is the first line to treat MRSA BSI worldwide [5], despite non-susceptible isolates have been already reported [21, 4]. In the present study, no hVISA/VISA or VRSA (Vancomycin-resistant S. aureus) isolates were detected. However, 58.5% of isolates presented high vancomycin MIC, being 76% (28/37) of them MRSA isolates. It is known that the clinical performance for this antimicrobial can be critically affected by the MIC = 2 mg/L [21]. Thus, daptomycin has become an important alternative to treat MRSA BSI [45]. However, it was noteworthy that 13.5% of MRSA isolates in the present study were characterized as non-susceptible for daptomycin. Although daptomycin resistance among S. aureus remains rare worldwide (< 0.1%) [1], Silva et al. [4] just like we found isolates non-susceptible to daptomycin (4.7%) in a Brazilian study involving 128 clinical S. aureus isolates. We have already described BSI caused by daptomycin non-susceptible S. aureus isolates (MIC of 2 and 4 mg/L) among MRSA-VISA isolates in the same hospital of the present study [2], data of great concern because of is impact on the patient’s outcome.

In a previously Brazilian study, Silva et al suggested that comorbidities can contribute to a greater susceptibility of elderly for acquiring bacterial infections, such as MRSA BSI [4]. We also verified that MRSA BSI was associated with older age (p = 0.03). In fact, in our study most patients (101/113; 89.4%) presented at least one comorbidity, which may indicate a close relationship with age decline. Although the global prevalence of MRSA BSI in patients with malignancy is relatively low [4], in this study this pathogen was detected in 46% of them. Despite our study demonstrated that elderly and cancer patients were the most affected, we concluded that higher mortality rates found may not be due to MRSA infection, but to the severe health condition of the patients evaluated.

We could point out some limitations about our study. First, a lack of national epidemiological data on S. aureus BSI, which can make comparative analyzes in relation to clinical and microbiological aspects related to this type of infection difficult. Besides, we only characterized BSI S. aureus isolates, and we did not assess the colonized patients to confirm the hospital spread of the USA300/ST8. Although we found S aureus isolates from other lineages disseminated in the hospital evaluated that seemed to be endemic, such as the USA100 lineage, the unusual presence of the pandemic and hypervirulent USA300/ST8 clone need to be highlighted, as its ability to establish into hospital settings is well described in North American studies, highlighting the fact that this lineage can also become endemic in a Brazilian hospital.

We showed, for the first time in our hospital, the presence of the pvl gene and ACME-I positive USA300/ST8/SCCmecIVa MRSA lineage associated to a possible hospital spread among patients with BSI. Therefore, we conclude that this pandemic and hypervirulent lineage can be already circulating among Brazilian hospitals and could be associated to future hospital outbreaks.

BSI: bloodstream infections; SSTI: skin and soft tissue infection; HA and CA: hospital and community-associated; MRSA: methicillin-resistant S. aureus; BEC: Brazilian endemic clone; CA-MRSA: community-associated MRSA; BMD: broth microdilution; MIC: minimal inhibitory concentration; CAMHB: cation-adjusted Muller-Hinton broth; PVL: Panton-Valentine leucocidin; ACME: Arginine Catabolic Mobile Element; SCCmec: Staphylococcal Cassette Chromosome mec; PFGE: Pulsed-Field Gel Electrophoresis; MLST: Multilocus Sequence Type; HUCFF: Hospital Universitário Clementino Fraga Filho; ATCC: American Type Culture Collection; LV: Latin American Variant

Ethics approval and consent to participate

The Human Research Ethics Committee of Hospital Universitário Clementino Fraga Filho approved the present study under number CAAE40652714.0.0000.5257.

Consent for publication

Written informed consent was waived for the present study by the Human Research Ethics Committee of Hospital Universitário Clementino Fraga Filho.

Availability of data and materials

The data sets generated and analyzed during the current study, such as the PFGE and MLST are not public available as there is no public database to deposit PFGE results and no new ST was found in the present study. However, those data are available from the corresponding author on reasonable request.

Competing interests

The authors declare that they have no competing interests

Funding

This study was supported by Brazilian grants from Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ, grants #E-26/202.592/2019, #E-26/010.000172/2016, #E-26/010.001463/2019, #E-26/211.554/2019; #E-26/010.002497/2019; #E-26/010.002435/2019), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, grants 301846/2017-0 and 11423381/2018-0), Coordenação de Aperfeiçoamento Pessoal de Nível Superior – Brasil (CAPES)– Finance Code 001.

Authors' contributions

ALPF received the blood cultures and processed them while DCSF were responsible for collect and storage the S. aureus identified. MFA, TLRO and DCFS analyzed the S. aureus isolates, conducing the experiments proposed in the “Methods” section. SAN was responsible for the clinical evaluation of the patients, and for gathering their clinical characteristics, as well as for the final statistical analysis. MFA and TLRO gathered the data and drafted the manuscript. FSC critically reviewed the manuscript. KRNS and RCC supervised and critically reviewed the manuscript. All authors approved the final version.

Acknowledgements

None.

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Pandemic clone USA300 in a Brazilian hospital: detection of an emergent lineage among methicillin-resistant Staphylococcus aureus from bloodstream infections

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Abstract

Background

Methods

Results

Conclusions

Figures

Background

Methods

1. Clinical isolates and setting

3. Phenotypic tests for screening of hVISA isolates

4. Genotypic profile of MRSA isolates

5. Detection of virulence genes

6. Statistical analysis

Results

3. Genotypic profiles and virulence genes in MRSA isolates

4. Characteristics of USA300 isolates

Discussion

Conclusions

List Of Abbreviations

Declarations

References

Additional Declarations

Status:

Version 1