Genome Sequence of a Highly Virulent pvl-positive Vancomycin-intermediate-resistant Staphylococcus aureus Sequence Type 30.

BACKGROUND: Staphylococcus aureus isolates expressing the Panton-Valentine Leukocidin (PVL) have been related to a wide range of diseases. Recently, pvl-positive community-associated methicillin-resistant S. aureus belonging to USA1100 (ST30/CC30/SCCmec IV) lineage has emerged in Brazilian hospitals. OBJECTIVE: The aim of this work was to sequence the genome of a pvl-positive USA1100 Vancomycin-Intermediate-Resistant S. aureus (VISA) isolate from Rio de Janeiro, Brazil. METHODS: The 13420 genome was sequenced using the HiSeq 2500 platform. The draft genome, plasmids annotation, and genome analysis were performed using RAST. Comparison of the relative pvl gene expression of six S. aureus isolates was performed by qRT-PCR. RESULTS: The isolate presented the ϕPVL phage codifying for the H2b PVL protein isoform, and another prophage carrying a PVL variant named lukF and lukS-PV.2. The 13420 genome presented a high number of virulence determinants, such as genes codifying for serine-protease proteins, enterotoxins (egc), the immune evasion cluster (IEC), adhesion proteins, spermine/spermidine acetyltransferase gene (blt), superantigen-like proteins, as well as the ica operon. Point mutations at vraS, tcaA, and tcaB genes were detected. Moreover, the PVL mRNA relative expression of the 13420 isolate was five times higher than mRNA PVL levels of the USA300/ST8 reference strain. CONCLUSION: We described for the first time the genome sequence of a VISA isolate harboring two pvl-associated genes and other virulence factors that may improve the USA1100/ST30 lineage fitness and impact its pathogenicity and spreading at Brazilian hospitals.

High virulence of methicillin resistant Staphylococcus aureus ST30-SCCmecIVc-spat019, the dominant community-associated clone in Argentina.

Community-acquired methicillin resistant Staphylococcus aureus emerged as a worldwide health problem in the last few years. In Argentina, it is found in 70% of skin and skin structure infections in previously healthy adult patients and causes severe invasive diseases. The ST30-SCCmecIVc-spat019 clone is predominant in adult infections and has displaced the previously prevalent ST5-SCCmecIVa-spat311 clone in community settings. In the present work we compared the virulence of both clones in order to explain the displacement, and found that ST30-IVc is associated with invasive infections in adult patients from Argentina and possesses a different virulence-associated genes profile compared to ST5-IVa. A representative strain of ST30 lineage has a more aggressive behavior in animal models of infection and expresses higher level of Fibronectin binding protein A coding gene, which could enhance the bacterial invasion capacity.

A unique SaeS allele overrides cell-density dependent expression of saeR and lukSF-PV in the ST30-SCCmecIV lineage of CA-MRSA.

ST30 (CC30)-SCCmec IV (USA1100) is one of the most common community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) lineages. ST30 isolates typically carry lukSF-PV genes encoding the Panton-Valentine leukocidin (PVL) and are responsible for outbreaks of invasive infections worldwide. In this study, twenty CC30 isolates were analyzed. All were very susceptible to non-ß-lactam antimicrobials, 18/20 harbored the lukSF-PV genes, only 1/20 exhibited agr-rnaIII dysfunction, and the majority was not able to form biofilm on inert surfaces. Analysis of lukSF-PV temporal regulation revealed that opposite to other CA-MRSA isolates, these genes were more highly expressed in early log phase than in stationary phase. This inverted lukSF-PV temporal expression was associated with a similar pattern of saeRS expression in the ST30 isolates, namely high level expression in log phase and reduced expression in stationary phase. Reduced saeRS expression in stationary phase was associated with low expression levels of the sae regulators, agr and agr-upregulator sarA, which activate the stationary phase sae-P1 promoter and overexpression of agr-RNAIII restored the levels of saeR and lukSF-PV trancripts in stationary phase. Altered SaeRS activity in the ST30 isolates was attributed to amino acid substitutions (N227S, E268K and S351T) in the HTPase_c domain of SaeS (termed SaeS(SKT)). Complementation of a USA300 saeS mutant with the saeS(SKT) and saeS alleles under the direction of the log phase sae-P3 promoter revealed that saeR and lukSF-PV transcription levels were more significantly activated by saeS(SKT) than saeS. In summary our data identify a unique saeS allele (saeS(SKT)) which appears to override cell-density dependent SaeR and PVL expression in ST30 CA-MRSA isolates. Further studies to determine the contribution of saeS(SKT) allele to the pathogenesis of infections caused by ST30 isolates are merited.

Community-acquired necrotizing pneumonia caused by methicillin-resistant Staphylococcus aureus ST30-SCCmecIVc-spat019-PVL positive in San Antonio de Areco, Argentina.

Community-acquired methicillin-resistant Staphylococcus aureus is the first cause of skin and soft tissue infections, but can also produce severe diseases such as bacteremia, osteomyelitis and necrotizing pneumonia. Some S. aureus lineages have been described in cases of necrotizing pneumonia worldwide, usually in young, previously healthy patients. In this work, we describe a fatal case of necrotizing pneumonia due to community-acquired methicillin-resistant S. aureus clone ST30-SCCmecIVc-spat019-PVL positive in an immunocompetent adult patient.

New patterns of methicillin-resistant Staphylococcus aureus (MRSA) clones, community-associated MRSA genotypes behave like healthcare-associated MRSA genotypes within hospitals, Argentina.

Methicillin-resistant Staphylococcus aureus (MRSA) burden is increasing worldwide in hospitals [healthcare-associated (HA)-MRSA] and in communities [community-associated (CA)-MRSA]. However, the impact of CA-MRSA within hospitals remains limited, particularly in Latin America. A countrywide representative survey of S. aureus infections was performed in Argentina by analyzing 591 clinical isolates from 66 hospitals in a prospective cross-sectional, multicenter study (Nov-2009). This work involved healthcare-onset infections-(HAHO, >48 hospitalization hours) and community-onset (CO) infections [including both, infections (HACO) in patients with healthcare-associated risk-factors (HRFs) and infections (CACO) in those without HRFs]. MRSA strains were genetically typed as CA-MRSA and HA-MRSA genotypes (CA-MRSAG and HA-MRSAG) by SCCmec- and spa-typing, PFGE, MLST and virulence genes profile by PCR. Considering all isolates, 63% were from CO-infections and 55% were MRSA [39% CA-MRSAG and 16% HA-MRSAG]. A significantly higher MRSA proportion among CO- than HAHO-S. aureus infections was detected (58% vs 49%); mainly in children (62% vs 43%). The CA-MRSAG/HA-MRSAG have accounted for 16%/33% of HAHO-, 39%/13% of HACO- and 60.5%/0% of CACO-infections. Regarding the epidemiological associations identified in multivariate models for patients with healthcare-onset CA-MRSAG infections, CA-MRSAG behave like HA-MRSAG within hospitals but children were the highest risk group for healthcare-onset CA-MRSAG infections. Most CA-MRSAG belonged to two major clones: PFGE-type N-ST30-SCCmecIVc-t019-PVL(+) and PFGE-type I-ST5-IV-SCCmecIVa-t311-PVL(+) (45% each). The ST5-IV-PVL(+)/ST30-IV-PVL(+) clones have caused 31%/33% of all infections, 20%/4% of HAHO-, 43%/23% of HACO- and 35%/60% of CACO- infections, with significant differences by age groups (children/adults) and geographical regions. Importantly, an isolate belonging to USA300-0114-(ST8-SCCmecIVa-spat008-PVL(+)-ACME(+)) was detected for the first time in Argentina. Most of HA-MRSAG (66%) were related to the Cordobes/Chilean clone-(PFGE-type A-ST5-SCCmecI-t149) causing 18% of all infections (47% of HAHO- and 13% of HACO-infections). Results strongly suggest that the CA-MRSA clone ST5-IV-PVL(+) has begun to spread within hospitals, replacing the traditional Cordobes/Chilean-HA-MRSA clone ST5-I-PVL(-), mainly in children. Importantly, a growing MRSA reservoir in the community was associated with spreading of two CA-MRSA clones: ST5-IV-PVL(+), mainly in children with HRFs, and ST30-IV-PVL(+) in adults without HRFs. This is the first nationwide study in Argentina providing information about the molecular and clinical epidemiology of CA-MRSA, particularly within hospitals, which is essential for designing effective control measures in this country and worldwide.

Isolation of community-associated methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 30 from house rats (Rattus tanezumi) in Hong Kong.

Methicillin-resistant Staphylococcus aureus (MRSA) is of major public health concern due to its resistance to multiple antibiotics. This resistance has been observed in various settings, including hospitals and communities, and has been detected in both animals and humans. Although peridomestic rat species (Rattus spp.) are well described reservoirs of several human pathogens and antimicrobial resistant bacteria, little is known about their role in MRSA epidemiology. In order to investigate whether Rattus spp. in Hong Kong are potential carriers of MRSA, 221 rats were caught from various ecological areas and nasopharyngeal samples were cultured on MRSA selective media. Genotypic characteristics of MRSA were confirmed by whole genome sequencing. Two clonal sequence type (ST) 30 MRSA isolates, harbouring mecA on staphylococcal chromosome cassette (SCC) mec type IVc, were cultured from two house rats (Rattus tanezumi) caught in two densely populated urban areas. To the best of the authors' knowledge, this is the first detection of community-associated (CA)-MRSA strain ST30 SCCmec IVc in peridomestic rodents in Hong Kong and globally. Our finding indicates that house rats can be carriers of MRSA strains that are widely distributed in the community.

Different evolution of S. aureus methicillin-resistant and methicillin-susceptible infections, Argentina.

Staphylococcus aureus-(SA) is widespread among healthcare-associated-(HA) and the community-associated-(CA) infections. However, the contributions of MRSA and MSSA to the SA overall burden remain unclear. In a nationally-representative-survey conducted in Argentina, 668 SA clinical isolates from 61 hospitals were examined in a prospective, cross-sectional, multicenter study in April 2015. The study aimed to analyze MRSA molecular epidemiology, estimate overall SA infection incidence (MSSA, MRSA, and genotypes) in community-onset (CO: HACO, Healthcare-Associated-CO and CACO, Community-Associated-CO) and healthcare-onset (HO: HAHO, Healthcare-associated-HO) infections, stratified by age groups. Additionally temporal evolution was estimated by comparing this study's (2015) incidence values with a previous study (2009) in the same region. Erythromycin-resistant-MSSA and all MRSA strains were genetically typed. The SA total-infections (TI) overall-incidence was 49.1/100,000 monthly-visits, 25.1 and 24.0 for MRSA and MSSA respectively (P = 0.5889), in April 2015. In adults with invasive-infections (INVI), MSSA was 15.7 and MRSA was 11.8 (P = 0.0288), 1.3-fold higher. HA SA infections, both MSSA and MRSA, surpassed CA infections by over threefold. During 2009-2015, there was a significant 23.4 % increase in the SA infections overall-incidence, mainly driven by MSSA, notably a 54.2 % increase in INVI among adults, while MRSA infection rates remained stable. The MSSA rise was accompanied by increased antimicrobial resistance, particularly to erythromycin, linked to MSSA-CC398-t1451-ermT + -IEC+-pvl- emergence. The SA-infections rise was primarily attributed to community-onset-infections (37.3 % and 62.4 % increase for TI and INVI, respectively), particularly HACO-MSSA and HACO-MRSA in adults, as well as CACO-MSSA. The main CA-MRSA-PFGE-typeN-ST30-SCCmecIVc-PVL+/- clone along with other clones (USA300-ST8-IV-LV-PVL+/-, PFGE-typeDD-ST97-IV- PVL-) added to rather than replaced CA-MRSA-PFGE-typeI-ST5-SCCmecIVa-PVL+/- clone in HA invasive-infections. They also displaced clone HA-MRSA-PFGE-typeA-ST5-SCCmecI, mainly in HAHO infections. The overall-burden of SA infections is rising in Argentina, driven primarily by community-onset MSSA, particularly in adults, linked to increased erythromycin-resistance and MSSA-CC398-t1451-ermT + -IEC+-pvl- emergence. Novel knowledge and transmission-control strategies are required for MSSA.

Comparative genomics of ST5 and ST30 methicillin-resistant Staphylococcus aureus sequential isolates recovered from paediatric patients with cystic fibrosis.

Staphylococcus aureus chronic airway infection in patients with cystic fibrosis (CF) allows this pathogen to adapt over time in response to different selection pressures. We have previously shown that the main sequence types related to community-acquired methicillin-resistant S. aureus (MRSA) infections in Argentina - ST5 and ST30 - are also frequently isolated from the sputum of patients with CF, but in these patients they usually display multi-drug antimicrobial resistance. In this study, we sequenced the genomes of MRSA from four paediatric CF patients with the goal of identifying mutations among sequential isolates, especially those possibly related to antimicrobial resistance and virulence, which might contribute to the adaptation of the pathogen in the airways of patients with CF. Our results revealed genetic differences in sequential MRSA strains isolated from patients with CF in both their core and accessory genomes. Although the genetic adaptation of S. aureus was distinct in different hosts, we detected independent mutations in thyA, htrA, rpsJ and gyrA - which are known to have crucial roles in S. aureus virulence and antimicrobial resistance - in isolates recovered from multiple patients. Moreover, we identified allelic variants that were detected in all of the isolates recovered after a certain time point; these non-synonymous mutations were in genes associated with antimicrobial resistance, virulence, iron scavenging and oxidative stress resistance. In conclusion, our results provide evidence of genetic variability among sequential MRSA isolates that could be implicated in the adaptation of these strains during chronic CF airway infection.

MRSA dynamic circulation between the community and the hospital setting: New insights from a cohort study.

Dissemination of methicillin-resistant-Staphylococcus aureus/(MRSA) is a worldwide concern both in hospitals [healthcare-associated-(HA)-MRSA] and communities [community-associated-(CA)-MRSA]. Knowledge on when and where MRSA colonization is acquired and what clones are involved is necessary, to focus efforts for prevention of hospital-acquired MRSA-infections. METHODS: A prospective/longitudinal cohort study was performed in eight Argentina hospitals (Cordoba/ October-December/2014). Surveillance cultures for MRSA (nose-throat-inguinal) were obtained on admission and at discharge. MRSA strains were genetically typed as CA-MRSAG and HA-MRSAG genotypes. RESULTS: Overall, 1419 patients were screened and 534 stayed at hospital for ≥3 days. S. aureus admission prevalence was 30.9% and 4.2% for MRSA. Overall MRSA acquisition rate was 2.3/1000 patient-days-at-risk with a MRSA acquisition prevalence of 1.96% (95%CI: 1.0%-3.4%); 3.2% of patients were discharged back to community with MRSA. CA-MRSAG accounted for 84.6% of imported, 100.0% of hospital-acquired and 94% of discharged MRSA strains. Most imported and acquired MRSA strains belonged to two major epidemic CA-MRSA clones spread in Argentina: PFGEtypeI-ST5-IVa-t311-PVL+ and PFGEtypeN/ST30-IVc-t019-PVL+. CONCLUSIONS: CA-MRSA clones, particularly ST5-IV-PVL+ and ST30-IV-PVL+, with main reservoir in the community, not only enter but also are truly acquired within hospital, causing healthcare-associated-hospital-onset infections, having a transmission capacity greater or similar than HA-MRSAG. This information is essential to develop appropriate MRSA infection prevention-control programs, considering hospital and community.

Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus in Cystic Fibrosis Patients from Argentina.

Methicillin-resistant Staphylococcus aureus (MRSA) colonization in cystic fibrosis (CF) patients is an increasing problem in many countries. In our Respiratory Center at the Hospital de Niños "Dr. Ricardo Gutiérrez", Buenos Aires, Argentina, the prevalence has climbed from 23% in 1995 up to 32% in 2011. Our objective was to analyze the diversity of MRSA isolates recovered from respiratory samples of CF patients attending our center, characterizing their phenotypes and clonal distribution. Therefore, a prospective study was conducted on all CF patients attending the pediatric Respiratory Center between June 2012 and May 2013 to collect MRSA isolates. Antibiotic susceptibility testing, multilocus sequence typing, pulsed-field gel electrophoresis, spa typing, and agr genotyping were performed on collected isolates. The prevalence of MRSA during this period was 34.2%, and 71.9% of the patients were infected with isolates that carried SCCmec IV. High resistance rates were detected for gentamicin, erythromycin, clindamycin, ciprofloxacin, and rifampicin. Strains related to the community-associated MRSA clones, ST5-IV and ST30-IV, were the most frequently recovered. Remarkably, even though most of the isolates were related to these clones, the rate of multi-resistance shown in CF patients was higher than that reported for the same lineages recovered from other infections in our country.

Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.

We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755 protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus isolate cluster but is genetically distinct. About 79 % of the protein encoding genes are part of the CC30 core genome (genes common to all CC30 S. aureus isolates), ~18 % were within the variable genome (shared among multiple but not all isolates) and ~ 3 % were found only in the genome of the camel isolate. Among the 85 isolate-specific genes, 79 were located within putative phages and pathogenicity islands. Protein encoding genes associated with bacterial adhesion, and secretory proteins that are essential components of the type VII secretion system were also identified. The complete genome sequence of S. aureus strain ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the accession no LN626917.1.

Molecular characterization of Staphylococcus aureus isolates carrying the Panton-Valentine leukocidin genes from Rio de Janeiro hospitals.

In a collection of 50 pvl-positive Staphylococcus aureus isolates from 10 Rio de Janeiro hospitals, 18 (36%) were from bloodstream infections, and 31 (62%) carried the SCCmec IV. Among 25 (50%) isolates of the USA1100/ST30/CC30 lineage present in 8 hospitals, 1 isolate was characterized as vancomycin-intermediate S. aureus.

Neumonía necrosante adquirida en la comunidad causada por Staphylococcus aureus resistente a meticilina ST30-SCCmecIVc-Spat019-PVL positivo en San Antonio de Areco, Argentina / Community-acquired necrotizing pneumonia caused by methicillin-resistant Staphylococcus aureus ST30-SCCmecIVc-spat019-PVL positive in San Antonio de Areco, Argentina

Community-acquired methicillin-resistant Staphylococcus aureus is the first cause of skin and soft tissue infections, but can also produce severe diseases such as bacteremia, osteomyelitis and necrotizing pneumonia. Some S. aureus lineages have been described in cases of necrotizing pneumonia worldwide, usually in young, previously healthy patients. In this work, we describe a fatal case of necrotizing pneumonia due to community-acquired methicillin-resistant S. aureus clone ST30-SCCmecIVc-spat019-PVL positive in an immunocompetent adult patient.

Staphylococcus aureus resistente a meticilina adquirido en la comunidad es la primera causa de infecciones de piel y partes blandas, aunque también puede producir infecciones graves, como bacteriemia, osteomielitis y neumonía necrotizante. Algunos linajes de S. aureus se han asociado a casos de neumonía necrotizante en el mundo, generalmente en pacientes jóvenes previamente sanos. En este trabajo comunicamos un caso fatal de neumonía necrotizante causado por el clon de S. aureus resistente a meticilina adquirido en la comunidad ST30-SCCmecIVc-spat019-LPV positivo, en un paciente adulto inmunocompetente