The Brazilian Journal of Infectious Diseases The Brazilian Journal of Infectious Diseases
Braz J Infect Dis 2017;21:185-9 - Vol. 21 Num.2 DOI: 10.1016/j.bjid.2016.09.015
Brief communication
Complete substitution of the Brazilian endemic clone by other methicillin-resistant Staphylococcus aureus lineages in two public hospitals in Rio de Janeiro, Brazil
Raiane Cardoso Chamona,1, Sthefanie da Silva Ribeiroa,1, Thaina Miranda da Costaa, Simone Aranha Nouérb, Katia Regina Netto dos Santosa,,
a Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Departamento de Microbiologia Médica, Rio de Janeiro, RJ, Brazil
b Universidade Federal do Rio de Janeiro, Faculdade de Medicina, Hospital Universitário Clementino Fraga Filho, Rio de Janeiro, RJ, Brazil
Received 21 July 2016, Accepted 28 September 2016
Abstract

Staphylococcus aureus is an important cause of bloodstream infections. Therefore, the main purpose of this work was to characterize a collection of 139 S. aureus isolates from bloodstream infections in two public hospitals in relation to their antimicrobial susceptibility profile, staphylococcal cassette chromosome mec types, and clonal relationship. Methicillin resistance and resistance to other 12 agents were accessed by the disk diffusion test. Minimum inhibitory concentration to mupirocin was also determined. The SCCmec types were accessed by multiplex PCR, and the clonal relationship was determined by pulsed field gel electrophoresis method and restriction modification system characterization. Besides, multilocus sequence typing was performed for representative methicillin-resistant S. aureus isolates. The military hospital showed a dissemination of the New York/Japan (USA100/ST5/CC5/SCCmecII) lineage associated to multidrug resistance, including mupirocin resistance, and the teaching hospital presented polyclonal and non-multidrug resistant MRSA isolates. Complete substitution of the Brazilian endemic clone by other lineages was found in both hospitals. These findings can highlight differences in policy control and prevention of infections used in the hospitals and a change in the epidemiological profile of MRSA in Brazilian hospitals, with the replacement of BEC, a previously well-established clone, by other lineages.

Keywords
Staphylococcus aureus, Bloodstream infections, USA100, Mupirocin resistance

Staphylococcus aureus is considered an important cause of bloodstream infections (BSI), which is associated with high rates of mortality and morbidity.1 Analysis of molecular characteristics of S. aureus isolates have indicated a variety of circulating lineages inside hospitals, according to the geographic area. In United States, the New York/Japan clone (USA100/ST5/CC5/SCCmecII) has been replaced by the community-acquired MRSA (USA300/ST8/CC8/SCCmecIV) lineage.1 In China, two pandemic hospital-acquired MRSA (HA-MRSA) clones are disseminated, the Brazilian endemic clone (BEC/ST239/CC8/SCCmecIII) and the USA100.2 In Brazil, the BEC lineage remained prevalent inside hospitals,3 but an increasing presence of the clones USA400 (ST1/CC1/SCCmecIV) and the Pediatric clone (USA800/ST5/CC5/SCCmecIV) have been reported in the last decade.3,4 More recently, SCCmecII carrying isolates associated to the CC5 were detected replacing, almost completely the BEC lineage among BSI isolates at a hospital located in São Paulo city.5

The implementation of a Health Care Associated Prevention and Control Committee (HAIPCC) is mandatory by law in Brazilian hospitals since 1997.6 These measures apply to the whole health care system, such as the public and the private sector. Public hospitals are responsible for the care of about 75% of the Brazilian population, estimated in 192 millions of habitants (2012 data). However, funding for the Unified Health System (Sistema Único de Saúde – SUS) has not been sufficient to ensure adequate financial resources for the public health system, leading to inappropriate control of dissemination of endemic resistant microorganisms.6 The aim of the present study was to characterize S. aureus isolates from BSI at two public hospitals as their antimicrobial resistance and clonal dissemination associated with clinical aspects.

We evaluated 139 S. aureus consecutive isolates from BSI recovered in a 532-bed military hospital (Hospital 1) and in a 490-bed university teaching hospital (Hospital 2), both located in Rio de Janeiro city, between January 2008 and June 2009. This study was approved by the Research Ethics Committee under No. 159/07. Clinical data from patients with S. aureus BSI were retrospectively abstracted from the hospital records. S. aureus isolates were identified by standard methods. BSIs were classified as hospital-acquired (HA) or community-acquired (CA) according to the Centers for Disease Control (CDC) criteria.

In order to characterize methicillin resistance, cefoxitin disk diffusion test was used according to CLSI.7 Isolates identified as MRSA were also submitted to antimicrobial susceptibility test for 12 agents by the disk diffusion method.7 Minimum inhibitory concentration (MIC) to mupirocin was determined by Etest® (AB-Biodisk, Solna, Sweden). The SCCmec types were assessed by multiplex-PCR for MRSA isolates.8 Clonal relationship was determined by pulsed-field gel electrophoresis (PFGE).9 Restriction modification system characterization (RM test)10 was used to identify the clonal complexes (CC) of methicillin susceptible S. aureus (MSSA) isolates. Besides, multilocus sequence typing (MLST) was performed for representative MRSA isolates.11 The Fisher's exact test and chi-square test were used to compare categorical data. Significance level was established at 5% (p<0.05).

The distribution of the 139 S. aureus isolates and their SCCmec types and clonal complexes in each hospital is shown in Table 1. Out of 75 isolates of Hospital 1 (H1), 32 (43%) were characterized as MRSA, whereas in Hospital 2 (H2) from 64 isolates 13 (20%) were MRSA isolates (p=0.006). While at H1 the majority of MRSA isolates carried the SCCmec type II (69%), at H2 the SCCmec type IV (69%) was the most prevalent. Overall, only one isolate from H2 carried the SCCmec type III and was assigned as ST889/CC5. In relation to the CC assignment, the majority of MRSA and MSSA isolates (83%; 62/75) at H1 were related to CC1 and CC5. However, there was a polyclonal distribution of S. aureus isolates causing BSI (CCs 1, 5, 8, 30, 45, 221) at H2 regardless of their methicillin resistance.

Table 1.

Distribution of 139 methicillin-susceptible and -resistant Staphylococcus aureus isolates, SCCmec types and clonal complexes from bloodstream infections.

Hospital/methicillin-resistance (number of isolates)  N (%) of isolates
  SCCmec typeClonal complexes
  II  III  IV  30  45  221  ND 
Hospital 1
MRSA (32)  22 (69)  10 (31)  9 (28)  23 (72) 
MSSA (43)  –  –  –  14 (32)  16 (37)  1 (3)  2 (5)  4 (9)  6 (14) 
Total (75)        23 (31)  39 (52)  1 (1)  2 (3)  4 (5)  6 (8) 
Hospital 2
MRSA (13)  2 (23)  1a (8)  9 (69)  3 (23)  7 (53)  1 (8)  1 (8)  1 (8) 
MSSA (51)  –  –  –  17 (33)  6 (12)  7 (14)  7 (14)  4 (8)  10 (19) 
Total (64)        20 (31)  13 (20)  7(11)  8 (12.5)  5 (8)  1 (2)  10 (15.5) 

MRSA, methicillin-resistant S. aureus; MSSA, methicillin-susceptible S. aureus; SCCmec, Staphylococcal cassette chromosome mec; ND, not determined; N, number.

a

ST889/CC5.

Characteristics of 45 MRSA isolates from BSI of patients from the two hospitals evaluated are presented in Table 2. Overall, 93% (42 isolates), 75% (34), and 35% (16) of the MRSA isolates were resistant to ciprofloxacin, clindamycin, and mupirocin, respectively. Among the MRSA isolates from H1, resistance to three or more drug classes (multidrug resistance – MDR) was verified in 59.3% (19/32), while among the MRSA isolates from H2, MDR was found in only 23% (3/13) (p=0.05). Moreover, 97% of the MRSA isolates from H1 were related to only two disseminated lineages, USA100/ST5/CC5/SCCmecII (69%) and USA400/ST1/CC1/SCCmecIV (28%), all of them causing hospital-acquired BSI. Furthermore, 94% (15/16) of mupirocin-resistant isolates were found at H1 and it was associated to the USA100 lineage. Two USA100 isolates (1238a and 1240a) showed high levels of mupirocin resistance (MIC>1024μg/mL) (data not shown). In this hospital, the prevalent USA100/ST5/SCCmecII lineage was found widely disseminated. At H2, 62% of MRSA isolates carried the SCCmec IV and were related to USA800 (38%) or USA400 (23%) lineages. Besides, the polyclonal presence of sporadic lineages (STs 484, 889, 3050, and 221) was identified in this hospital, the ST3050 being described for the first time in this study.

Table 2.

General characteristics of 45 methicillin-resistant Staphylococcus aureus isolates from bloodstream infections.

Hospital/genotype (no of isolates)  Isolate number  Isolation date (mm/dd/yy)  Unit or floor  Acquisition mode  SCCmec type  PFGE subtype  Clonality  ST/CC  Antimicrobial resistance profile 
Hospital 1 (32)
A (22)1223a  01/10/2008  11  HA  II  A1  USA100  5/5  cip cli ery mup tec 
1224a  01/12/2008  ICU  HA  II  A1  USA100  5/5  cip cli ery mup 
1255a  09/02/2008  ICU  HA  II  A1  USA100  5/5  cip cli ery mup 
1258a  09/16/2008  ICU  HA  II  A1  USA100  5/5  cip cli ery mup 
1265a  09/23/2008  HA  II  A1  USA100  5/5  cip cli ery mup 
1266a  09/24/2008  HA  II  A1  USA100  5/5  cip cli ery mup 
1276a  02/12/2008  HA  II  A1  USA100  5/5  cip cli ery mup 
1288a  03/12/2009  ICU  HA  II  A1  USA100  5/5  cip cli ery mup 
1289a  03/13/2009  11  HA  II  A1  USA100  5/5  cip cli ery mup 
1309a  03/14/2009  ND  HA  II  A1  USA100  5/5  cip cli ery mup clo rif 
1290a  03/19/2009  11  HA  II  A1  USA100  5/5  cip cli clo ery 
1291a  03/31/2009  HA  II  A1  USA100  5/5  cip cli ery mup 
1305a  06/04/2009  11  HA  II  A1  USA100  5/5  cip cli ery mup clo rif 
1308a  06/15/2009  10  HA  II  A1  USA100  5/5  cip cli ery mup clo rif 
1260a  09/17/2008  10  HA  II  A2  USA100  5/5  cip cli ery 
1263a  09/22/2008  11  HA  II  A2  USA100  5/5  cip cli ery 
1275a  12/02/2008  ICU  HA  II  A2  USA100  5/5  cip cli ery 
1238a  05/26/2008  HA  II  A3  USA100  5/5  cip cli ery mup 
1240a  05/27/2008  Em  HA  II  A3  USA100  5/5  cip cli ery mup 
1284a  02/02/2009  Em  HA  II  A4  USA100  5/5  cip cli ery 
1285a  02/16/2009  11  HA  II  A4  USA100  5/5  cip cli ery 
1301a  05/27/2009  IU  HA  II  A5  USA100  5/5  cip cli clo ery 
B (9)1229a  02/09/2008  11  HA  IV  B1  USA400  1/1  cip cli ery 
1237a  05/20/2008  11  HA  IV  B1  USA400  1/1  cip cli ery 
1307a  06/12/2009  ICU  HA  IV  B1  USA400  1/1  cip clo 
1231a  02/13/2008  11  HA  IV  B2  USA400  1/1  cip 
1282a  01/22/2009  ICU  HA  IV  B2  USA400  1/1  cip clo 
1268a  09/26/2008  10  HA  IV  B3  USA400  1/1  cip cli ery gen 
1283a  01/22/2009  ICU  HA  IV  B3  USA400  1/1  cip clo 
1295a  05/25/2009  HA  IV  B4  USA400  1/1  – 
1302a  05/21/2009  ICU  HA  IV  B5  USA400  1/1  cip clo 
F (1)  1306a  06/04/2009  10  HA  II  ND  105/5  cip cli clo ery 
Hospital 2 (13)
A (1)  1087a  01/20/2008  11  HA  II  A1  USA100  5/5  cip cli ery mup 
B (3)1094a  01/16/2008  CA  IV  B1  USA400  1/1  cip cli ery 
1187a  06/12/2008  HA  IV  B1  USA400  1/1  cip cli clo ery 
1100a  01/27/2008  Em  CA  IV  B2  USA400  1/1  cip cli ery 
C (5)1214a  06/26/2009  HA  IV  C1  USA800  5/5  – 
1318a  08/16/2008  Em  HA  IV  C2  USA800  5/5  cip 
1324a  08/08/2008  Em  HA  IV  C3  USA800  5/5  cip 
1328a  12/23/2008  Em  HA  IV  C4  USA800  5/5  cip cli ery 
1326a  12/25/2008  HA  IV  C4  USA800  5/5  – 
D (1)  1314a  11/08/2008  HA  IV  ND  484/30  cip cli ery 
E (1)  1092a  02/22/2008  HA  III  ND  889/5  cip clo ery gen sut tec 
G (1)  1212a  06/02/2009  ICU  HA  II  ND  3050/45  cip cli ery 
H (1)  1219a  06/06/2009  HA  II  ND  221/221  cip cli ery 

ICU, intensive care unit; Em, emergency; ND, not determined; HA, hospital acquired; CA, community acquired; SCCmec, Staphylococcal cassette chromosome mec; PFGE, pulsed field gel electrophoresis; ST, sequence type; CC, clonal complex; cip, ciprofloxacin; cli, clindamycin; ery, erythromycin; mup, mupirocin; tec, teicoplanin; clo, chloramphenicol; rif, rifampin; gen, gentamicin; sut, sulfamethoxazole/trimethoprim.

In our study, 139 S. aureus isolates from BSI obtained at two different public hospitals in Rio de Janeiro city were characterized regarding their antimicrobial resistance and clonal profile. We verified that almost 70% of the BSI isolates from the military public hospital (H1) carried the SCCmecII and were related to the USA100 lineage. All but one isolate were assigned as USA400 lineage. This lineage appears to have survival and growth advantage since it has remained for years as a major hospital-associated lineage in USA and Japan1,12 showing the good adaptability of such clone, even in different geographic areas.

At H2, a reference teaching public hospital, a polyclonal profile was observed for the MRSA isolates. Interestingly, we previously found a similar higher clonal diversity among MRSA isolates at a private hospital.3 These findings may be a reflection of the occurrence of fewer outbreaks due to adequate infection control measures at this particular institution, as found in this teaching public hospital. Padoveze et al.6 conducted a cross-sectional study evaluating a collection of 153 hospitals from five different Brazilian regions. The authors showed that a minimal structure is necessary for an effective prevention of hospital infections, specially the presence of an active HAIPCC, as well as sterilization services, hand hygiene resources, and a microbiology laboratory.

Caboclo et al.3 compared S. aureus isolates from two health institutions in Rio de Janeiro between 2004 and 2007. One of these institutions was the same military hospital (H1) of the current study. The authors showed a dissemination of the USA100, USA400, USA800 and BEC lineages at this military institution. Moreover, around 60% of the isolates were from the BEC lineage, showing that at the time this lineage was still highly present. Simultaneously, similar results were found in a study conducted at a private tertiary care hospital in São Paulo where 40% (13/33) of MRSA isolates belonged to BEC and 21% were related to the USA100 lineage.13 At H2, Cavalcante et al.14 showed that the BEC lineage was responsible for around 30% of all MRSA isolates, between 2005 and 2006. In the present study, carried out between 2008 and 2009, complete absence of the BEC lineage was verified in both public institutions evaluated, showing that certain global MRSA lineages are replacing BEC. Caiaffa-Filho et al.5 recently evaluated a collection of 50 consecutive MRSA BSI isolates in a São Paulo tertiary care teaching hospital, between October and December 2010, and found that a single PFGE clone related to the USA100 lineage was disseminated, almost replacing the BEC in that institution during the study period. This finding highlights a possible change in the epidemiological profile of MRSA in Brazilian hospitals.

MRSA isolates were more frequently found at H1 than in the teaching hospital (H2) being associated to a MDR profile and mupirocin resistance. In Brazil, despite the legislation mandating the implementation of HAIPCC in the health system, the lack of qualified professionals, the growing health costs, and limited availability of financial resources are of great impact in the infection control.6 Therefore, the differences regarding resistance rates observed between MRSA isolates from the H1 and H2, as well as the prevalence of specific SCCmec types, may be a reflection of the policy for control and prevention of infections and use of antimicrobials in the hospitals evaluated. Interestingly, the prevalent USA100 clone presenting MDR profile isolated from H1 had already been described as a MRSA-daptomycin-resistant isolate with vancomycin MIC of 4μg/mL, also causing BSI,15 confirming the ability of this lineage to acquire resistance determinants. Moreover, this lineage was also associated with mupirocin resistance, a drug used for decolonizing MRSA nasal carriage.2 Although only two isolates have showed high levels of mupirocin resistance (MIC>1024μg/mL), both high- and low-level resistance have been associated with S. aureus decolonization failure.2 As showed in a study conducted in China,2 USA100/ST5 isolates associated with mupirocin resistance lead to possible outbreaks. The dissemination of mupirocin-resistant MRSA isolates among H1 patients in our study also highlights the importance of the judicious use of mupirocin among the hospitalized patients.

MRSA, as well as MSSA isolates, have been reported as important causes of nosocomial infections, such as BSI.1 The present study showed that S. aureus isolates from the CCs 1 and 5, regardless their methicillin-resistance status, had similar clonality at both hospitals. According to Diep and Otto,16 the emergence of the MRSA lineages around the world may be related to the successful conversion of certain MSSA isolates into MRSA isolates by the acquisition of SCCmec. The presence of MSSA and MRSA isolates presenting the same CCs and/or STs have already been observed in Rio de Janeiro hospitals,4 indicating the ability of certain lineages to acquire the mec cassette thus providing an advantage to their spreading in health institutions.

In conclusion, although both institutions evaluated in the present study are public hospitals, the military hospital showed dissemination of the USA100/ST5/CC5/SCCmecII lineage associated to multidrug resistance, including to mupirocin. On the other hand, the teaching hospital presented polyclonal and non-multidrug resistant MRSA isolates. These differences may reflect the policy of control and prevention of infections and/or use of antimicrobials employed in each hospital evaluated. Moreover, complete substitution of the BEC/ST239/SCCmecIII by other lineages was found in both hospitals, highlighting a change in the epidemiological profile of MRSA in Brazilian hospitals.

Ethics statement

The present study was approved by the Research Ethics Committee under No. 159/07.

Conflicts of interest

The authors declare no conflicts of interest.

Acknowledgments

This study was supported by grants from: Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento Pessoal de Nível Superior (CAPES), Fundação Universitária José Bonifácio (FUJB) and Programa de Núcleos de Excelência (PRONEX).

We acknowledge the contribution of PhD Rosana Barreto Rocha Ferreira (Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro) for providing language help and of the student Juliana Curityba de Mello Campos for the help in some experiments.

References
1
Y. Rhee,A. Aroutcheva,B. Hota
Evolving epidemiology of Staphylococcus aureus bacteremia
Infect Control Hosp Epidemiol, 36 (2015), pp. 1417-1422 http://dx.doi.org/10.1017/ice.2015.213
2
Q. Liu,L. Han,B. Li
Virulence characteristic and MLST-agr genetic background of high-level mupirocin-resistant, MRSA isolates from Shanghai and Wenzhou, China
3
R.M. Caboclo,F.S. Cavalcante,N.L. Iorio
Methicillin-resistant Staphylococcus aureus in Rio de Janeiro hospitals: dissemination of the USA400/ST1 and USA800/ST5 SCCmec type IV and USA100/ST5 SCCmec type II lineages in a public institution and polyclonal presence in a private one
Am J Infect Control, 41 (2013), pp. e21-e26 http://dx.doi.org/10.1016/j.ajic.2012.08.008
4
R.P. Schuenck,F.S. Cavalcante,E. Emery
Staphylococcus aureus isolates belonging to different multilocus sequence types present specific virulence gene profiles
FEMS Immunol Med Microbiol, 65 (2012), pp. 501-504 http://dx.doi.org/10.1111/j.1574-695X.2012.00958.x
5
H.H. Caiaffa-Filho,P.A. Trindade,G.P. da Cunha
Methicillin-resistant Staphylococcus aureus carrying SCCmec type II was more frequent than the Brazilian endemic clone as a cause of nosocomial bacteremia
Diagn Microbiol Infect Dis, 76 (2013), pp. 518-520 http://dx.doi.org/10.1016/j.diagmicrobio.2013.04.024
6
M.C. Padoveze,C.M. Fortaleza,C. Kiffer
Structure for prevention of health care-associated infections in Brazilian hospitals: a countrywide study
Am J Infect Control, 44 (2016), pp. 74-79 http://dx.doi.org/10.1016/j.ajic.2015.08.004
7
Clinical and Laboratory Standards Institute – CLSI
Performance standards for antimicrobial disk susceptibility testing. Approved standards: M100-S16. Wayne, Pennsylvania, USA
(2015)
8
C. Milheiriço,D.C. Oliveira,H. De Lencastre
Update to the multiplex PCR strategy for assignment for mec element in Staphylococcus aureus
Antimicrob Agents Chemother, 51 (2007), pp. 3374-3377 http://dx.doi.org/10.1128/AAC.00275-07
9
A.M. Vivoni,B.A. Diep,A.C. De-Gouveia-Magalhães
Clonal composition of Staphylococccus aureus isolates at a Brazilian university hospital: identification of international circulating lineages
J Clin Microbiol, 44 (2006), pp. 1686-1691 http://dx.doi.org/10.1128/JCM.44.5.1686-1691.2006
10
J.D. Cockfield,S. Pathak,J.D. Edgeworth
Rapid determination of hospital-acquired methicillin-resistant Staphylococcus aureus lineages
J Med Microbiol, 56 (2007), pp. 614-619 http://dx.doi.org/10.1099/jmm.0.47074-0
11
M.C. Enright,N.P.J. Day,C.E. Davies
Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus
J Clin Microbiol, 38 (2000), pp. 1008-1015
12
H. Nakaminami,N. Noguchi,A. Ito
Characterization of methicillin-resistant Staphylococcus aureus isolated from tertiary care hospitals in Tokyo, Japan
J Infect Chemother, 20 (2014), pp. 512-515 http://dx.doi.org/10.1016/j.jiac.2014.03.006
13
M.D.V. Martino,L. Correa,A.C.C. Pignatari
Isolates of methicillin-resistant Staphylococcus aureus (MRSA) not belonging to the Brazilian epidemic clone
Saf Health, 1 (2015), pp. 9
14
F.S. Cavalcante,R.P. Schuenck,D.C. Ferreira
Methicillin-resistant Staphylococcus aureus: spread of specific lineages among patients in different wards at a Brazilian teaching hospital
J Hosp Infect, 86 (2014), pp. 151-154 http://dx.doi.org/10.1016/j.jhin.2013.12.004
15
F.S. Cavalcante,D.C. Ferreira,R.C. Chamon
Daptomycin and methicillin-resistant Staphylococcus aureus isolated from a catheter-related bloodstream infection: a case report
BMC Res Notes, 25 (2014), pp. 759
16
B.A. Diep,M. Otto
The role of virulence determinants in community-associated MRSA pathogenesis
Trends Microbiol, 16 (2008), pp. 361-369 http://dx.doi.org/10.1016/j.tim.2008.05.002

The authors contributed equally to this work.

Corresponding author.
Copyright © 2016. Sociedade Brasileira de Infectologia
Braz J Infect Dis 2017;21:185-9 - Vol. 21 Num.2 DOI: 10.1016/j.bjid.2016.09.015