Genotyping of methicillin-resistant Staphylococcus aureus isolates obtained in the Northeast region of Brazil

Comparative genomics of MRSA strains from human and canine origins reveals similar virulence gene repertoire

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen associated with a wide variety of infections in humans. The ability of MRSA to infect companion animals has gained increasing attention in the scientific literature. In this study, 334 dogs were screened for MRSA in two cities located in Rio de Janeiro State. The prevalence of MRSA in dogs was 2.7%. Genotyping revealed isolates from sequence types (ST) 1, 5, 30, and 239 either colonizing or infecting dogs. The genome of the canine ST5 MRSA (strain SA112) was compared with ST5 MRSA from humans-the main lineage found in Rio de Janeiro hospitals-to gain insights in the origin of this dog isolate. Phylogenetic analysis situated the canine genome and human strain CR14-035 in the same clade. Comparative genomics revealed similar virulence profiles for SA112 and CR14-035. Both genomes carry S. aureus genomic islands νSAα, νSAβ, and νSAγ. The virulence potential of the canine and human strains was similar in a Caenorhabditis elegans model. Together, these results suggest a potential of canine MRSA to infect humans and vice versa. The circulation in community settings of a MRSA lineage commonly found in hospitals is an additional challenge for public health surveillance authorities.

The History of Methicillin-Resistant Staphylococcus aureus in Brazil

Since the emergence of MRSA in the 1960s, a gradual increase in infections by resistant bacteria has been observed. Clinical manifestations may vary from brand to critical condition due to host risk factors, as well as pathogen virulence and resistance. The high adaptability and pathogenic profile of MRSA clones contributed to its spread in hospital and community settings. In Brazil, the first MRSA isolates were reported in the late 1980s, and since then different genetic profiles, such as the Brazilian epidemic clone (BEC) and other clones considered a pandemic, became endemic in the Brazilian population. Additionally, Brazil's MRSA clones were shown to be able to transfer genes involved in multidrug resistance and enhanced pathogenic properties. These events contributed to the rise of highly resistant and pathogenic MRSA. In this review, we present the main events which compose the history of MRSA in Brazil, including numbers and locations of isolation, as well as types of staphylococcal cassette chromosome mec (SCCmec) found in the Brazilian territory.

Genomic profile of Brazilian methicillin-resistant Staphylococcus aureus resembles clones dispersed worldwide

PURPOSE

Comparative genomic analysis of strains may help us to better understand the wide diversity of their genetic profiles. The aim of this study was to analyse the genomic features of the resistome and virulome of Brazilian first methicillin-resistant Staphylococcus aureus (MRSA) isolates and their relationship to other Brazilian and international MRSA strains.

METHODOLOGY

The whole genomes of three MRSA strains previously isolated in Vitória da Conquista were sequenced, assembled, annotated and compared with other MRSA genomes. A phylogenetic tree was constructed and the pan-genome and accessory and core genomes were constructed. The resistomes and virulomes of all strains were identified.Results/Key findings. Phylogenetic analysis of all 49 strains indicated different clones showing high similarity. The pan-genome of the analysed strains consisted of 4484 genes, with 31 % comprising the gene portion of the core genome, 47 % comprising the accessory genome and 22 % being singletons. Most strains showed at least one gene related to virulence factors associated with immune system evasion, followed by enterotoxins. The strains showed multiresistance, with the most recurrent genes conferring resistance to beta-lactams, fluoroquinolones, aminoglycosides and macrolides.

CONCLUSIONS

Our comparative genomic analysis showed that there is no pattern of virulence gene distribution among the clones analysed in the different regions. The Brazilian strains showed similarity with clones from several continents.

Clonal diversity and epidemiological characteristics of Staphylococcus aureus: high prevalence of oxacillin-susceptible mecA-positive Staphylococcus aureus (OS-MRSA) associated with clinical isolates in Brazil

Background

Staphylococcus aureus is the major cause of global and nosocomial infections with a significant impact in hospitals worldwide. Our objective was to investigate clinical and molecular characteristics of S. aureus isolates causing infections in patients admitted to hospitals from Recife city, Brazil, and investigate the prevalence of oxacillin-susceptible mecA-positive S. aureus (OS-MRSA) in the region, as well as genetically characterize the isolates and compare with epidemic clones.

Results

We characterized 89 isolates in total, 31 clinical methicillin-resistant S. aureus (MRSA) and 58 methicillin-sensitive (MSSA) isolates by PFGE, MLST, spa typing and SCCmec genotyping. Isolates belonging to international MRSA clones were present: Brazilian epidemic clone (BEC) (61 % of MRSA isolates), Paediatric (36 %), New York/Japan (3 %). Some MSSA isolates were related to MRSA clones: USA400-related (10 % of MSSA isolates), Berlin clone (2 %), Paediatric (14 %), New York/Japan (2 %) and Southwest Pacific clone (17 %). MLST revealed new sequence types (ST’s): ST2381, ST2382, and ST2383 and new spa types: 10548 and 10550. Among isolates phenotypically identified as MSSA by antimicrobial susceptibility assays, we verified 30 oxacillin-susceptible isolates, which exhibited the mecA gene, without mec complex amplification and were thus classified as OS-MRSA. We observed clonal spread of MRSA and MSSA, including OS-MRSA, within several areas of the main hospital investigated and closely related isolates between hospitals analyzed.

Conclusions

The results of this study suggest a possible spread of the strains in hospital environment that could be responsible for nosocomial infections. We documented the presence of several MRSA clones, as well as new MLST and spa types, that were responsible for severe infections in hospitalized patients. The finding of OS-MRSA isolates could have implications for therapy, because testing for mecA and PBP2a is not a routine procedure performed by clinical microbiology laboratories in Brazil and, as consequence, these isolates could be misclassified as MSSA. Our data alert to the necessity to develop more effective strategies for epidemiological control of S. aureus in order to avoid an increase of hospital infections provoked by this pathogen. We reinforce the use of genetic methods, in addition to phenotypic tests, for a precise identification of MRSA.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0733-4) contains supplementary material, which is available to authorized users.

Complete genome sequence of an agr-dysfunctional variant of the ST239 lineage of the methicillin-resistant Staphylococcus aureus strain GV69 from Brazil

Staphylococcus aureus is a versatile Gram-positive coccus frequently found colonizing the skin and nasal membranes of humans. The acquisition of the staphylococcal cassette chromosome mec was a major milestone in the evolutionary path of methicillin-resistant S. aureus. This genetic element carries the mecA gene, the main determinant of methicillin resistance. MRSA is involved in a plethora of opportunistic infectious diseases. The accessory gene regulator is the major S. aureus quorum sensing system, playing an important role in staphylococcal virulence, including the development of biofilms. We report the complete genome sequence (NCBI BioProject ID: PRJNA264181) of the methicillin-resistant S. aureus strain GV69 (= CMVRS P4521), a variant of the ST239 lineage that presents with a natural attenuation of agr-RNAIII transcription and a moderate accumulation of biofilm.

Mupirocin resistance in nasal carriage of Staphylococcus aureus among healthcare workers of a tertiary care rural hospital

Introduction:

Mupirocin (pseudomonic acid A) is a topical antimicrobial agent with excellent antistaphylococcal and antistreptococcal activity. A nasal formulation is approved by the United States Food and Drug Administration for eradicating nasal carriage in adult patients as well as in health care personnel. Resistance to mupirocin has already been reported worldwide. The increasing prevalence of mupirocin resistance among Staphylococcus aureus and coagulase-negative Staphylococcus (CoNS) species could be an important threat to the future use of mupirocin against methicillin-resistant S. aureus (MRSA). Thus, this study was carried out to find the prevalence of mupirocin resistance in S. aureus and CoNS by disc diffusion and to determine the rates of high-level and low-level mupirocin resistance in S. aureus and CoNS by disc diffusion.

Materials and Methods:

A total of 140 healthcare workers (HCWs) (doctor, nursing staff, housekeeping staff) were randomly selected. S. aureus and CoNS isolates were tested for mupirocin resistance by the disk diffusion method using 5 μg and 200 μg mupirocin discs. MRSA isolates were tested for antibiotics by Kirby-Bauer disc-diffusion method as per Clinical and Laboratory Standards Institute guidelines.

Results:

Out of 140 nasal swabs collected from HCWs, S. aureus was isolated in 38 (27.14%), and CoNS was isolated in 73 (52.14%). MRSA was isolated in 20 (14.28%) and methicillin-resistant coagulase-negative Staphylococci (MRCoNS) in 34 (24.29%. Methicillin-sensitive S. aureus (MSSA) and MSCoNS isolates were 100% sensitive to mupirocin, but two isolates from MRSA (1.43%) and five from MRCoNS (3.57%) were mupirocin resistant.

Conclusion:

The presence of mupirocin resistance in MRSA and MRCoNS is a cause for concern. It could be limited by regular surveillance and effective infection control initiatives so to inform health care facilities to guide therapeutic and prophylactic use of mupirocin.

Molecular characterization of methicillin-resistant Staphylococcus aureus isolated from a Brazilian university hospital

The aim of this study was to perform SCCmec typing in Staphylococcus aureus isolates and to characterize the clonal profile of these isolates. Forty-six mecA gene-positive strains isolated between 2002 and 2006 were submitted to antimicrobial resistance testing by the E-test, SCCmec typing by multiplex PCR, and clonal profile analysis by pulsed-field gel electrophoresis. Forty-one (89.1%) isolates were typed as SCCmec III and five (10.9%) as SCCmec IV. Four circulating clones were detected, one of them comprising isolates related to the Brazilian epidemic clone. This clone was detected throughout the study period. The SCCmec III isolates were associated with a high rate of multidrug resistance and clonal dissemination of methicillin-resistant S. aureus in the wards of the University Hospital of the Botucatu School of Medicine, Universidade Estadual Paulista.

Methicillin-resistant Staphylococcus aureus nasal carriage in neonates and children attending a pediatric outpatient clinics in Brazil

Background

In Latin America, few studies have been carried out on methicillin-resistant Staphylococcus aureus carriage in the pediatric population. We conducted a survey of nasal S. aureus carriage in neonates and in children attending the pediatric outpatient clinics in a large Brazilian city with high antimicrobial consumption.

Methods

Pernasal swabs of neonates were collected upon admission and at discharge in four neonatal intensive care units and of children less than five years of age during outpatient visits. Methicillin-resistant S. aureus isolates were characterized for antibiotic susceptibility, mec gene presence, pulsed-field gel electrophoresis, spa type, SCCmec-type, multilocus sequence type, and presence of Panton-Valentine leukocidin genes.

Results

S. aureus was carried by 9.1% and 20.1% of the 701 neonates and of 2034 children attending the outpatient clinics, respectively; methicillin-resistant S. aureus carriage was detected in 0.6% and 0.2%, of the these populations, respectively. Healthcare-associated methicillin-resistant S. aureus strains found in neonates from neonatal intensive care units and outpatients were genetically related to the Brazilian (SCCmec-III, ST239) and to the Pediatric (SCCmec-IV, ST5) clones. Community-associated methicillin-resistant S. aureus was only detected in outpatients. None of the methicillin-resistant S. aureus strains contained the Panton-Valentine leukocidin gene. Methicillin-resistant S. aureus strains related to the Brazilian clone showed multidrug resistance pattern.

Conclusions

Despite the high antibiotic pressure in our area, and the cross transmission of the healthcare-associated methicillin-resistant S. aureus clones between neonatal intensive care units and outpatients, the prevalence of methicillin-resistant S. aureus carriage is still low in our setting.

Impact of biocides on biofilm formation by methicillin-resistant Staphylococcus aureus (ST239-SCCmecIII) isolates

Procedures of sterilization and disinfection are essential to ensure that medical and surgical instruments will not transmit infectious pathogens to patients. In the present paper, we tested the residual effect of these compounds on biofilm formation and its efficiency in disrupting preformed biofilms using methicillin-resistant Staphylococcus aureus (MRSA) isolates of the lineage ST239-SCCmecIII. All compounds examined, except 70% alcohol, caused a significant impairment in biofilm formation with concomitant inhibition of cell growth. Among the compounds examined, 10% povidone-iodine (PVP-I) was the only antiseptic that exhibited more than 90% reduction of both biofilm formation and dispersion. In the group of sterilants and disinfectants, a formulation containing 7% hydrogen peroxide and 0.2% peracetic acid (HP-PA), and sodium hypochlorite with 1% active chlorine (NaOCl) were equally effective.

Restriction modification (RM) tests associated to additional molecular markers for screening prevalent MRSA clones in Brazil

In this study, we associated the restriction modification (RM) tests to the polymerase chain reaction (PCR) detection of molecular markers (SCCmec III, seh, agr II-SCCmec IV, and lukSF) for revealing the main methicillin-resistant Staphylococcus aureus (MRSA) clones circulating in Brazil. This simple and rapid approach allowed a precise classification of the MRSA analyzed when compared with pulsed-field gel electrophoresis (PFGE) data.

First report of methicillin-resistant Staphylococcus aureus Cordobes/Chilean clone involved in nosocomial infections in Brazil

SUMMARY Methicillin-resistant Staphylococcus aureus (MRSA) commonly causes infection in hospitalized patients. Resistance is due to the acquisition of mecA gene located on the chromosomal element SCCmec and to date 12 types have been identified. Specific epidemic clones of MRSA have emerged with enhanced ability to spread within and among hospitals and to cross national boundaries. We studied 30 isolates from patients with MRSA infections at two hospitals in Porto Alegre city from April to December, 2008 and determined their SCCmec type by PCR. Representative strains were typed by PFGE. Eighteen (60%) isolates carried SCCmec type III and had PFGE profiles clonally related to the previously characterized Brazilian epidemic clone, and 11 (36·7%) isolates with pulsotypes closely related to the Cordobes/Chilean clone harboured SCCmec type I. To the best of our knowledge, this is the first report of the appearance of Cordobes/Chilean clone involved in nosocomial infection in Brazil.

Evaluation of different methods for detecting methicillin resistance in Staphylococcus aureus isolates in a university hospital located in the Northeast of Brazil

Many methods have been described for the detection of methicillin-resistant Staphylococcus aureus (MRSA), but the heterogeneous expression of methicillin resistance affects the reliability of these methods. The aim of the present study was to evaluate some methods for detecting methicillin resistance in Staphylococcus aureus isolates in a university hospital located in the Northeast of Brazil. Among the isolates, 15 were methicillin-susceptible and 45 were methicillin-resistant, including low-level heterogeneous resistance strains. Both the 30 ηg-cefoxitin disk and PBP2a test had 100% sensibility/specificity and appear to be good options for the detection of MRSA in the clinical laboratory.