Community-associated strains of methicillin-resistant Staphylococccus aureus as the cause of healthcare-associated infection

Genome Sequences of Community Carriage Strains of Staphylococcus aureus from Yuma, Arizona

Staphylococcus aureus exists as a pathogen and commensal. Individuals with asymptomatic carriage serve as a reservoir for transmission and are at increased risk of infecting themselves. In order to characterize the genomic diversity of S. aureus circulating in the community, we sequenced 166 genomes collected from individuals in Yuma, AZ.

Genomic Epidemiology and Global Population Structure of Exfoliative Toxin A-Producing Staphylococcus aureus Strains Associated With Staphylococcal Scalded Skin Syndrome

Staphylococci producing exfoliative toxins are the causative agents of staphylococcal scalded skin syndrome (SSSS). Exfoliative toxin A (ETA) is encoded by eta, which is harbored on a temperate bacteriophage ΦETA. A recent increase in the incidence of SSSS in North America has been observed; yet it is largely unknown whether this is the result of host range expansion of ΦETA or migration and emergence of established lineages. Here, we detail an outbreak investigation of SSSS in a neonatal intensive care unit, for which we applied whole-genome sequencing (WGS) and phylogenetic analysis of Staphylococcus aureus isolates collected from cases and screening of healthcare workers. We identified the causative strain as a methicillin-susceptible S. aureus (MSSA) sequence type 582 (ST582) possessing ΦETA. To then elucidate the global distribution of ΦETA among staphylococci, we used a recently developed tool to query extant bacterial WGS data for biosamples containing eta, which yielded 436 genomes collected between 1994 and 2019 from 32 countries. Applying population genomic analysis, we resolved the global distribution of S. aureus with lysogenized ΦETA and assessed antibiotic resistance determinants as well as the diversity of ΦETA. The population is highly structured with eight dominant sequence clusters (SCs) that generally aligned with S. aureus ST clonal complexes. The most prevalent STs included ST109 (24.3%), ST15 (13.1%), ST121 (10.1%), and ST582 (7.1%). Among strains with available data, there was an even distribution of isolates from carriage and disease. Only the SC containing ST121 had significantly more isolates collected from disease (69%, n = 46) than carriage (31%, n = 21). Further, we identified 10.6% (46/436) of strains as methicillin-resistant S. aureus (MRSA) based on the presence of mecA and the SCCmec element. Assessment of ΦETA diversity based on nucleotide identity revealed 27 phylogroups, and prophage gene content further resolved 62 clusters. ΦETA was relatively stable within lineages, yet prophage variation is geographically structured. This suggests that the reported increase in incidence is associated with migration and expansion of existing lineages, not the movement of ΦETA to new genomic backgrounds. This revised global view reveals that ΦETA is diverse and is widely distributed on multiple genomic backgrounds whose distribution varies geographically.

Novel strategies for rapid identification and susceptibility testing of MRSA

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs. Rapid diagnosis of MRSA infections has been associated with positive impact on clinical outcomes.

AREAS COVERED

We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review describes screening and diagnostic test methods for MRSA and their analytical performances with a focus on rapid molecular-based assays including those that are on the horizon. Future novel technologies will allow more rapid detection of phenotypic resistance. In the case of whole-genome sequencing, detection of mutations may predict resistance, transmission, and virulence.

EXPERT OPINION

Currently there are many diagnostic options for the detection of MRSA in surveillance and clinical samples. In general, these are highly accurate and have resulted in improvements in targeted management and reduction in hospital or intensive care unit length of stay for both MSSA and MRSA. Impact on mortality has been variable. Promising novel technologies will not only accurately identify pathogens and detect their resistance markers but will allow discovery of virulence determinants that might further affect patient management.

Prevalence, molecular characteristics and antimicrobial susceptibility patterns of MRSA in hospitalized and nonhospitalized patients in Barbados

The epidemiology and clonality of methicillin-resistant Staphylococcus aureus (MRSA) has not been investigated, as not much research or surveillance has been undertaken to identify and characterize the circulating MRSA strains in Barbados. Prevalence rates, molecular characteristics and antimicrobial susceptibility pattern of MRSA infections in hospitalized and nonhospitalized patients were investigated. A total of 293 isolates were included in the study, with 100 from the hospital and 193 from the public health laboratory. Isolates were collected over a period of 1 (2015–2016) and 3 years (2013–2016) respectively. MRSA was identified using standard microbiologic techniques and was further analysed by multiplex PCR for the presence of the spa, mec gene complex typing and PVL genes (lukS-PV and lukF-PV). A prevalence rate of 19.7% was calculated for those hospitalized. All hospital isolates were sensitive to vancomycin, rifampin, linezolid and cotrimoxazole (trimethoprim/sulfamethoxazole), whilst 82% were sensitive to clindamycin. The PVL gene was detected in 76% of hospital isolates. In the community isolates, resistance was observed in erythromycin (100%), ciprofloxacin (97.4%), clindamycin (13%) and cotrimoxazole (5.7%). There was no resistance to vancomycin. The PVL gene was detected in 97.9% of the isolates, the mecA gene in only 2.1% and the mecC gene in 0%. Most MRSA isolates were community acquired in both settings, and the antimicrobial susceptibility profile was similar, suggesting transmission of community-associated MRSA into the hospital environment. Further harmonization of antimicrobial policy for the treatment of MRSA (and by extension other pathogens) should be implemented to quell ongoing transmission. We found that 93.4% of MRSA in Barbados treated in the primary healthcare system were sensitive to cotrimoxazole. By typing MRSA isolates and drawing interferences on transmission on the basis of genetic relatedness, transmission pathways may be tracked. Further studies must be performed for this high level of comprehensiveness so that with the surveillance of MRSA, effective strategies may be developed to prevent or limit transmission.

Prevalence and characteristics of Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) isolated from chicken meat in the province of Quebec, Canada

This study was conducted to estimate the prevalence of Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) in retail chicken meat and broiler chickens from the Province of Quebec, Canada, and to characterize LA-MRSA isolates. A total of 309 chicken drumsticks and thighs were randomly selected in 2013 from 43 retail stores in the Monteregie. In addition, nasal swabs and caeca samples were collected in 2013-2014 from 200 broiler chickens of 38 different flocks. LA-MRSA was not detected in broiler chickens. Fifteen LA-MRSA isolates were recovered from four (1.3%) of the 309 chicken meat samples. Multi-Locus Sequence Typing (MLST) and SCCmec typing revealed two profiles (ST398-MRSA-V and ST8-MRSA-IVa), which were distinct using pulse-field gel electrophoresis (PFGE) and microarray (antimicrobial resistance and virulence genes) analyses. In addition to beta-lactam resistance, tetracycline and spectinomycin resistance was detected in all isolates from the 3 positive samples of the ST398 profile. Southern blot hybridization revealed that the resistance genes aad(D) and lnu(A), encoding resistances to aminoglycosides and lincosamides respectively, were located on plasmid. All isolates were able to produce biofilms, but biofilm production was not correlated with hld gene expression. Our results show the presence of two separate lineages of MRSA in retail chicken meat in Quebec, one of which is likely of human origin.

Clinical, Epidemiologic, and Laboratory Aspects of Methicillin-Resistant Staphylococcus aureus Infections

Oxacillin-resistant Staphylococcus aureus (abbreviated MRSA for historical reasons) is a major pathogen responsible for both hospital- and community-onset disease. Resistance to oxacillin in most clinical isolates of S. aureus is mediated by PBP2a, a penicillin-binding protein with low affinity to beta-lactams, encoded primarily by the mecA gene. Rapid and accurate methods of susceptibility testing of S. aureus isolates to identify MRSA infections are important tools to limit the spread of this organism. This review focuses on the clinical significance of MRSA infections and new approaches for the laboratory diagnosis and epidemiologic typing of MRSA strains.

Prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carriage and pattern of antibiotic resistance among sheep farmers from Southern Italy

PURPOSE

We conducted a cross-sectional study to measure the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) colonization, with a particular focus on livestock associated (LA)-MRSA in farmers working in contact with livestock (sheep) in one Italian region. Furthermore, we have assessed the antimicrobial resistance pattern of isolates and the association of carriage with specific characteristic of farms and working tasks.

PATIENTS AND METHODS

Demographic data, occupational history, and contact with animals information was collected. Nasal and oropharyngeal swabs were collected and all samples were tested for the isolation and identification of S. aureus. Isolates were examined for antimicrobial susceptibility and all MRSA strains underwent molecular analyses through multiple-locus variable number of tandem repeat analysis (MLVA).

RESULTS

A total of 115 sheep farms and 275 sheep farmers were enrolled. MRSA colonized workers were found in three farms; S. aureus was isolated in 97 workers (35.5%), whereas MRSA was isolated in 3 (1.1%) workers. All MRSA isolates were classified as multidrug resistant. Two of the MRSA isolates were resistant to quinupristin/dalfopristin (QDA), mupirocin, erythromycin, and tetracycline. Among methicillin-susceptible S. aureus (MSSA), 32 (34%) were resistant to tetracycline, 31 (33%) to erythromycin, 26 (27.6%) to QDA, and 22 (23.4%) to linezolid and clindamycin. One MRSA belonged to MLVA complex (MC) 001, found to colonize both humans and animals.

CONCLUSION

The picture of MRSA transmission among sheep farmers does not seem to be critical, although there is the need to improve adequate control measures to prevent and minimize any biological risk in sheep farms for both animal and human health. Specific monitoring/surveillance programs would help in better understanding the epidemiology of resistant strains.

Methicillin-Resistant Staphylococcus aureus: Molecular Characterization, Evolution, and Epidemiology

Staphylococcus aureus, a major human pathogen, has a collection of virulence factors and the ability to acquire resistance to most antibiotics. This ability is further augmented by constant emergence of new clones, making S. aureus a "superbug." Clinical use of methicillin has led to the appearance of methicillin-resistant S. aureus (MRSA). The past few decades have witnessed the existence of new MRSA clones. Unlike traditional MRSA residing in hospitals, the new clones can invade community settings and infect people without predisposing risk factors. This evolution continues with the buildup of the MRSA reservoir in companion and food animals. This review focuses on imparting a better understanding of MRSA evolution and its molecular characterization and epidemiology. We first describe the origin of MRSA, with emphasis on the diverse nature of staphylococcal cassette chromosome mec (SCCmec). mecA and its new homologues (mecB, mecC, and mecD), SCCmec types (13 SCCmec types have been discovered to date), and their classification criteria are discussed. The review then describes various typing methods applied to study the molecular epidemiology and evolutionary nature of MRSA. Starting with the historical methods and continuing to the advanced whole-genome approaches, typing of collections of MRSA has shed light on the origin, spread, and evolutionary pathways of MRSA clones.

A Sporadic Four-Year Hospital Outbreak of a ST97-IVa MRSA With Half of the Patients First Identified in the Community

This study describes a sporadically occurring 4-year outbreak of methicillin-resistant Staphylococcus aureus (MRSA) originating from a surgical ward. Whole-genome sequencing (WGS) identified the outbreak clone as spa type t267, sequence type ST97, and SCCmec IVa. Prompted by the finding of four patients within 6 months in the same ward with this unusual MRSA type, an outbreak was suspected. Subsequent MRSA screening in the ward in February 2017 identified three-additional patients and two health care workers (HCWs) with t267/ST97-IVa. WGS linked these 9 isolates to 16 previous isolates in our WGS database and the outbreak thus included 23 patients and two HCWs. Twenty-one patients had a connection to the surgery ward during the period 2013-2017, but half of them had MRSA diagnosed in the community long after discharge. The community debut of several patients MRSA infections weeks to months after hospital discharge made the identification of a hospital source difficult and it was the SNP relatedness of the isolates that led us to identify the common denominator of hospitalization. An index patient was not identified, but our hypothesis is that HCWs with unrecognized long-term MRSA colonization could have caused sporadic nosocomial transmission due to intermittent breaches in infection prevention and control practice.

Detection and Molecular Characterization of Methicillin-Resistant Staphylococcus aureus from Table Eggs in Haripur, Pakistan

Table eggs are nutritionally important food consumed globally. Despite being protected inside the hard shell and a semipermeable membrane, the egg contents may be contaminated with microbes and thus become a possible carrier of infectious agents to humans. A number of medically significant bacterial species such as Salmonella enterica, Listeria monocytogenes, and Yersinia enterocolitica have already been reported from table eggs. More important is the presence of antimicrobial-resistant bacterial strains in this food source. The present study was aimed at detection and characterization of Staphylococcus aureus from table eggs collected from different retail shops in Haripur city of Pakistan. Staphylococci were isolated from 300 eggs collected from December 2015 to May 2016. S. aureus isolates were tested for antimicrobial susceptibility using broth microdilution and characterized using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec) typing, and spa typing. The presence of Panton-Valentine leukocidin and antimicrobial resistance genes were detected using PCR. Staphylococci were isolated from 21.3% (64/300) of the table eggs tested. Of those, 59% (38/64) were identified as S. aureus, of which 33 (86.8%) were positive for mecA (MRSA, methicillin-resistant S. aureus). All MRSA were multidrug resistant (resistant to two or more antimicrobial classes), contained aac-aph (encoding aminoglycosides), and were pvl⁺. Using MLST, spa typing, and SCCmec typing, three genotypic patterns were assigned: ST8-t8645-MRSA-IV, associated with USA300; and ST772-t657-MRSA-IV and ST772-t8645-MRSA-IV, both characteristic of the Bengal Bay community-associated MRSA clone. Molecular typing by PFGE revealed that the bacterial population was highly homogenous with only two patterns observed. This study is the first report of detection of human-associated pvl⁺ MRSA from table eggs. The genetic similarities of MRSA present in the eggs to that of humans may suggest human to poultry transmission of MRSA via contamination.

Prevention of Recurrent Staphylococcal Skin Infections

Staphylococcus aureus infections pose a significant health burden. The emergence of community-associated methicillin-resistant S aureus has resulted in an epidemic of skin and soft tissue infections (SSTI), and many patients experience recurrent SSTI. As S aureus colonization is associated with subsequent infection, decolonization is recommended for patients with recurrent SSTI or in settings of ongoing transmission. S aureus infections often cluster within households, and asymptomatic carriers serve as reservoirs for transmission; therefore, a household approach to decolonization is more effective than measures performed by individuals alone. Novel strategies for the prevention of recurrent SSTI are needed.

Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic

Staphylococcus aureus USA300 represents the dominant community-associated methicillin-resistant S. aureus lineage in the USA, where it is a major cause of skin and soft tissue infections. Previous comparative genomic studies have described the population structure and evolution of USA300 based on geographically restricted isolate collections. Here, we investigated the USA300 population by sequencing genomes of a geographically distributed panel of 191 clinical S. aureus isolates belonging to clonal complex 8 (CC8), derived from the Tigecycline Evaluation and Surveillance Trial program. Isolates were collected at 12 healthcare centres across nine USA states in 2004, 2009 or 2010. Reconstruction of evolutionary relationships revealed that CC8 was dominated by USA300 isolates (154/191, 81 %), which were heterogeneous and demonstrated limited phylogeographic clustering. Analysis of the USA300 core genomes revealed an increase in median pairwise SNP distance from 62 to 98 between 2004 and 2010, with a stable pattern of above average dN/dS ratios. The phylogeny of the USA300 population indicated that early diversification events led to the formation of nested clades, which arose through cumulative acquisition of predominantly non-synonymous SNPs in various coding sequences. The accessory genome of USA300 was largely homogenous and consisted of elements previously associated with this lineage. We observed an emergence of SCCmec negative and ACME negative USA300 isolates amongst more recent samples, and an increase in the prevalence of ϕSa5 prophage. Together, the analysed S. aureus USA300 collection revealed an evolving pan-genome through increased core genome heterogeneity and temporal variation in the frequency of certain accessory elements.

Molecular characterization of community- & hospital-acquired methicillin-resistant & methicillin-sensitive Staphylococcus aureus isolates in Sikkim

Background & objectives:

The two major genotypic markers that distinguish community acquired (CA) from hospital acquired (HA) methicillin resistant Staphylococcus aureus (MRSA) isolates are the architecture of mobile genetic element (SCCmec type) and presence of panton valentine leukocidin (PVL) toxin. This study was conducted to determine the molecular characteristics of CA- and HA- MRSA and methicillin sensitive S. aureus (MSSA) isolates in Sikkim.

Methods:

A total of 150 clinical isolates of S. aureus isolated from various clinical specimens were subjected to duplex (mec-A and pvl gene) and multiplex (SCCmec typing) PCR.

Results:

Of the 150 isolates, 53 (35.33%) and 66 (44%) were positive for mec-A (MRSA) and pvl genes, respectively. Thirty eight (25.33%) met the definition of CA-MRSA and 15 (10%) of HA-MRSA and the remaining 63 (42%) and 34 (22.66%) as CA- and HA-MSSA, respectively. No significant difference was seen in the distribution of PVL toxin in MRSA and MSSA isolates, but it was significantly (P<0.001) high in overall MRSA isolates than in MSSA. The majority of the MRSA isolates showed a double amplification band of SCCmec type III plus V (54.71%), and only a fewer isolates were amplified by single DNA fragments of type I (1.88%), III (3.77%), IVa (1.88%) and V (11.32%). SCCmec types I, III, IVa, were found only in HA-MRSA isolates, whereas type V in both the CA- and HA-MRSA. AST pattern showed that 18.42 per cent (7/38) and 46.66 per cent (7/15) were multidrug resistant (MDR)-CA-MRSA and MDR-HA-MRSA, respectively.

Interpretation & conclusions:

The present results show that SCCmec type V MRSA has been on the rise, and genotypic markers such as pvl gene detection used for the differentiation of these clinically distinct isolates of MRSA may not be reliable.

Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data

BACKGROUND

Identifying and tackling the social determinants of infectious diseases has become a public health priority following the recognition that individuals with lower socioeconomic status are disproportionately affected by infectious diseases. In many parts of the world, epidemiologically and genotypically defined community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) strains have emerged to become frequent causes of hospital infection. The aim of this study was to use spatial models with adjustment for area-level hospital attendance to determine the transmission niche of genotypically defined CA- and health-care-associated (HA)-MRSA strains across a diverse region of South East London and to explore a potential link between MRSA carriage and markers of social and material deprivation.

METHODS AND FINDINGS

This study involved spatial analysis of cross-sectional data linked with all MRSA isolates identified by three National Health Service (NHS) microbiology laboratories between 1 November 2011 and 29 February 2012. The cohort of hospital-based NHS microbiology diagnostic services serves 867,254 usual residents in the Lambeth, Southwark, and Lewisham boroughs in South East London, United Kingdom (UK). Isolates were classified as HA- or CA-MRSA based on whole genome sequencing. All MRSA cases identified over 4 mo within the three-borough catchment area (n = 471) were mapped to small geographies and linked to area-level aggregated socioeconomic and demographic data. Disease mapping and ecological regression models were used to infer the most likely transmission niches for each MRSA genetic classification and to describe the spatial epidemiology of MRSA in relation to social determinants. Specifically, we aimed to identify demographic and socioeconomic population traits that explain cross-area extra variation in HA- and CA-MRSA relative risks following adjustment for hospital attendance data. We explored the potential for associations with the English Indices of Deprivation 2010 (including the Index of Multiple Deprivation and several deprivation domains and subdomains) and the 2011 England and Wales census demographic and socioeconomic indicators (including numbers of households by deprivation dimension) and indicators of population health. Both CA-and HA-MRSA were associated with household deprivation (CA-MRSA relative risk [RR]: 1.72 [1.03-2.94]; HA-MRSA RR: 1.57 [1.06-2.33]), which was correlated with hospital attendance (Pearson correlation coefficient [PCC] = 0.76). HA-MRSA was also associated with poor health (RR: 1.10 [1.01-1.19]) and residence in communal care homes (RR: 1.24 [1.12-1.37]), whereas CA-MRSA was linked with household overcrowding (RR: 1.58 [1.04-2.41]) and wider barriers, which represent a combined score for household overcrowding, low income, and homelessness (RR: 1.76 [1.16-2.70]). CA-MRSA was also associated with recent immigration to the UK (RR: 1.77 [1.19-2.66]). For the area-level variation in RR for CA-MRSA, 28.67% was attributable to the spatial arrangement of target geographies, compared with only 0.09% for HA-MRSA. An advantage to our study is that it provided a representative sample of usual residents receiving care in the catchment areas. A limitation is that relationships apparent in aggregated data analyses cannot be assumed to operate at the individual level.

CONCLUSIONS

There was no evidence of community transmission of HA-MRSA strains, implying that HA-MRSA cases identified in the community originate from the hospital reservoir and are maintained by frequent attendance at health care facilities. In contrast, there was a high risk of CA-MRSA in deprived areas linked with overcrowding, homelessness, low income, and recent immigration to the UK, which was not explainable by health care exposure. Furthermore, areas adjacent to these deprived areas were themselves at greater risk of CA-MRSA, indicating community transmission of CA-MRSA. This ongoing community transmission could lead to CA-MRSA becoming the dominant strain types carried by patients admitted to hospital, particularly if successful hospital-based MRSA infection control programmes are maintained. These results suggest that community infection control programmes targeting transmission of CA-MRSA will be required to control MRSA in both the community and hospital. These epidemiological changes will also have implications for effectiveness of risk-factor-based hospital admission MRSA screening programmes.

Comparative Genomics of Community-Associated Methicillin-Resistant Staphylococcus aureus Shows the Emergence of Clone ST8-USA300 in Geneva, Switzerland

BACKGROUND

Previous investigations of community-associated methicillin-resistant Staphylococcus aureus(CA-MRSA) isolates have revealed a wide diversity of genetic backgrounds, with only sporadic occurrence of ST8-USA300, in Geneva, Switzerland. We conducted a molecular epidemiologic analysis to identify the origin of a sudden increase of ST8 PVL-positive isolates in Geneva during 2013.

METHODS

On the basis of prospective CA-MRSA surveillance, we collected colonizing and infecting ST8-USA300 isolates and compared them to non-ST8 CA-MRSA isolates. Whole-genome sequencing (WGS) was performed for each isolate of this collection, and discriminating molecular features were linked to patient data.

RESULTS

In 2013, 22 isolates with the ST8-USA300 profile were identified among 46 cases of CA-MRSA. WGS revealed 2 groups of strains that differed by the type of the SCCmec IV element encoded and whether they harbored an arginine catabolism mobile element (ACME) locus. ACME-negative strains were mainly isolated from patients traveling in or originating from South America. Single-nucleotide polymorphism positions in isolate groups were used to infer their common ancestor, determine their geographical origin, and trace their relatedness.

CONCLUSIONS

WGS allowed the identification of transmission events and revealed that the increased prevalence of USA300 CA-MRSA isolates resulted from multiple importation events from the Americas but not from local clonal expansion of a successful clone.

Molecular Characteristics of Disease-Causing and Commensal Staphylococcus lugdunensis Isolates from 2003 to 2013 at a Tertiary Hospital in Taiwan

Objectives

Staphylococcus lugdunensis can cause community- and healthcare-associated infections. This study investigated the molecular characteristics of S. lugdunensis isolates collected at our hospital and compared the characteristics of the infectious and commensal isolates.

Methods

We collected the S. lugdunensis isolates between 2003 and 2013. The antimicrobial resistance test, SCCmec typing, accessory gene regulator (agr) typing, pulsed-field gel electrophoresis (PFGE), and δ-like hemolysin activity were performed.

Results

In total, 118 S. lugdunensis isolates were collected, of which 67 (56.8%) were classified into the infection group and 51 (43.2%) into the commensal group. The oxacillin resistance rate was 36.4%. The most common SCCmec types were SCCmec types V (51.4%) and II (32.6%). In total, 34 pulsotypes were identified. The PFGE typing revealed five clones (pulsotypes A, J, M, N, and P) at our hospital. Pulsotypes A and N caused the spread of high oxacillin resistance. In total, 10.2% (12 of 118) of the isolates lacked δ-like hemolysin activity. Compared with the infection group, the commensal group showed a higher percentage of multiple drug resistance and carried a higher percentage of SCCmec type II (11 of 22, 50% and 3 of 21, 14.3%) and a lower percentage of SCCmec type V (8 of 22, 36.4% and 14 of 21, 66.7%). The commensal group (27 PFGE types) showed higher genetic diversity than did the infection group (20 PFGE types). No difference was observed in the distribution of the five main pulsotypes, agr typing, and the presence of δ-like hemolysin activity between the two groups.

Conclusions

Five main clones were identified at our hospital. The commensal group showed higher genetic diversity, had a higher percentage of multidrug resistance, and carried a higher percentage of SCCmec type II and a lower percentage of SCCmec type V than did the infection group.

Whole-genome sequencing targets drug-resistant bacterial infections

During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.

Autophagy mediates tolerance to Staphylococcus aureus alpha-toxin

Resistance and tolerance are two defense strategies employed by the host against microbial threats. Autophagy-mediated degradation of bacteria has been extensively described as a major resistance mechanism. Here we find that the dominant function of autophagy proteins during infections with the epidemic community-associated methicillin-resistant Staphylococcus aureus USA300 is to mediate tolerance rather than resistance. Atg16L1 hypomorphic mice (Atg16L1(HM)), which have reduced autophagy, were highly susceptible to lethality in both sepsis and pneumonia models of USA300 infection. Autophagy confers protection by limiting the damage caused by α-toxin, particularly to endothelial cells. Remarkably, Atg16L1(HM) mice display enhanced survival rather than susceptibility upon infection with α-toxin-deficient S. aureus. These results identify an essential role for autophagy in tolerance to Staphylococcal disease and highlight how a single virulence factor encoded by a pathogen can determine whether a given host factor promotes tolerance or resistance.

Molecular and clinical characteristics of hospital and community onset methicillin-resistant Staphylococcus aureus strains associated with bloodstream infections

Methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSI) are classified epidemiologically as health care-associated hospital onset (HAHO)-, health care-associated community onset (HACO)-, or community-associated (CA)-MRSA. Clinical and molecular differences between HAHO- and HACO-MRSA BSI are not well known. Thus, we evaluated clinical and molecular characteristics of MRSA BSI to determine if distinct features are associated with HAHO- or HACO-MRSA strains. Molecular genotyping and medical record reviews were conducted on 282 MRSA BSI isolates from January 2007 to December 2009. MRSA classifications were 38% HAHO-, 54% HACO-, and 8% CA-MRSA. Comparing patients with HAHO-MRSA to those with HACO-MRSA, HAHO-MRSA patients had significantly higher rates of malignancy, surgery, recent invasive devices, and mortality and longer hospital stays. Patients with HACO-MRSA were more likely to have a history of renal failure, hemodialysis, residence in a long-term-care facility, long-term invasive devices, and higher rate of MRSA relapse. Distinct MRSA molecular strain differences also were seen between HAHO-MRSA (60% staphylococcal cassette chromosome mec type II [SCCmec II], 30% SCCmec III, and 9% SCCmec IV) and HACO-MRSA (47% SCCmec II, 35% SCCmec III, and 16% SCCmec IV) (P < 0.001). In summary, our study reveals significant clinical and molecular differences between patients with HAHO- and HACO-MRSA BSI. In order to decrease rates of MRSA infection, preventive efforts need to be directed toward patients in the community with health care-associated risk factors in addition to inpatient infection control.

Emergence of Staphylococcal Cassette ChromosomemecType IV Methicillin-ResistantStaphylococcus aureusas a Cause of Ventilator-Associated Pneumonia

Staphylococcal cassette chromosomemec(SCCmec) type IV methicillin-resistantStaphylococcus aureus(MRSA) strains were identified in 8 (19.5%) of 41 consecutive patients with MRSA ventilator-associated pneumonia (VAP) in this retrospective, observational study. There were no significant differences in VAP severity and crude mortality rates between patients with SCCmectype II strains and patients with SCCmectype IV strains.

Prevalence of Colonization With Community-Associated Methicillin-ResistantStaphylococcus aureusAmong End-Stage Renal Disease Patients and Healthcare Workers

Objective.

To evaluate the prevalence, epidemiologic features, and molecular characteristics of colonization with community-associated methicillin-resistantStaphylococcus aureus(CA-MRSA) among hospitalized dialysis patients and their healthcare workers (HCWs).

Design.

Prospective observational clinical and laboratory study of nasal colonization.

Setting.

A 600-bed urban academic medical center.

Subjects.

One hundred twenty hospitalized dialysis inpatients and 100 HCWs.

Results.

Of 120 patients, 40 (33%) were colonized withS. aureus; 26 (65%) of these 40 were colonized with MRSA. Among the 26 MRSA isolates, 10 (38.5%) carried staphylococcal cassette chromosome (SCC)mectype IV (ie, CA-MRSA), and 7 of these 10 carried the genes for the Panton-Valentine leukocidin (PVL) toxin. Patients colonized with healthcare-associated MRSA strains and those colonized with CA-MRSA strains were similar, except for a higher frequency of a history of congestive heart failure among those with healthcare-associated MRSA strains (P= .014). Among 10 patients who presented with or developed anS. aureusinfection while hospitalized, 8 were colonized withS. aureus, 7 with MRSA, and 3 with SCCmectype IV strains. Among 100 HCWs, 31 were colonized withS. aureus, including 6 with MRSA; 2 of the MRSA isolates belonged to CA-MRSA strains, and soft-tissue infections were reported in one of the HCWs and in the family member of the other HCW colonized with these strains.

Conclusions.

There is a high rate of colonization with MRSA and CA-MRSA among hospitalized dialysis patients and their HCWs. As other studies have found, it appears that individuals are being colonized with both CA-MRSA strains and healthcare-associated MRSA strains.

Epidemiology of Healthcare-Associated Bloodstream Infection Caused by USA300 Strains of Methicillin-ResistantStaphylococcus aureusin 3 Affiliated Hospitals

Objective.

To describe the epidemiology of bloodstream infection caused by USA300 strains of methicillin-resistantStaphylococcus aureus(MRSA), which are traditionally associated with cases of community-acquired infection, in the healthcare setting.

Design.

Retrospective cohort study.

Setting.

Three academically affiliated hospitals in Denver, Colorado.

Methods.

Review of cases of S.aureusbloodstream infection during the period from 2003 through 2007. Polymerase chain reaction was used to identify MRSA USA300 isolates.

Results.

A total of 330 cases of MRSA bloodstream infection occurred during the study period, of which 286 (87%) were healthcare-associated. The rates of methicillin resistance among theS. aureusisolates recovered did not vary during the study period and were similar among the 3 hospitals. However, the percentages of cases of healthcare-associated MRSA bloodstream infection due to USA300 strains varied substantially among the 3 hospitals: 62%, 19%, and 36% (P< .001) for community-onset cases and 33%, 3%, and 33% (P= .005) for hospital-onset cases, in hospitals A, B, and C, respectively. In addition, the number of cases of healthcare-associated MRSA bloodstream infection caused by USA300 strains increased during the study period at 2 of the 3 hospitals. At each hospital, USA300 strains were most common among cases of community-associated infection and were least common among cases of hospital-onset infection. Admission to hospital A (a safety-net hospital), injection drug use, and human immunodeficiency virus infection were independent risk factors for healthcare-associated MRSA bloodstream infection due to USA300 strains.

Conclusions.

The prevalence of USA300 strains among cases of healthcare-associated MRSA bloodstream infection varied dramatically among geographically clustered hospitals. USA300 strains are replacing traditional healthcare-related strains of MRSA in some healthcare settings. Our data suggest that the prevalence of USA300 strains in the community is the dominant factor affecting the prevalence of this strain type in the healthcare setting.

Emergence of Community-Associated Methicillin-ResistantStaphylococcus aureusStrains as a Cause of Healthcare-Associated Bloodstream Infections in Korea

Background.

The prevalence of community-associated methicillin-resistantStaphylococcus aureus(CA-MRSA) strains causing bloodstream infection (BSI) has not been studied in Korea.

Objective.

We sought to determine the prevalence of CA-MRSA strains among isolates recovered from patients with MRSA BSIs and to explore epidemiological changes in Korea. We also sought to evaluate clinical characteristics relevant to the development of healthcare-associated BSIs.

Methods.

We prospectively collected consecutive MRSA isolates from patients with BSI at 4 hospitals from July 1 through November 30, 2007, and we also included MRSA isolates recovered from culture of blood samples collected during a previous year (October 1, 2004 through September 30, 2005) at a different hospital. Molecular typing studies were performed, including pulsed-field gel electrophoresis (PFGE), multilocus sequence typing,Staphylococcusprotein A (spa) typing, and staphylococcal cassette chromosomemec(SCCmec) typing. We compared the clinical characteristics and outcomes of patients with healthcare-associated BSI due to CA-MRSA strains with those of patients with healthcare-associated BSI due to healthcare-associated MRSA (HA-MRSA) strains.

Results.

There were 76 cases of MRSA BSI, of which 4 (5.3%) were community-associated and 72 (94.7%) were healthcare-associated. Among the 72 HA-MRSA BSIs, 18 (25%) were community onset, and 54 (75%) were hospital onset. PFGE type D-ST72–spaB-SCCmectype IVA MRSA, the predominant genotype of CA-MRSA in Korea, accounted for 19 (25%) of all 76 MRSA BSIs, including 17 (23.6%) of 72 HA-MRSA BSIs and 11 (20.8%) of 53 hospital-onset HA-MRSA BSIs. Patients with healthcare-associated BSIs due to CA-MRSA strains carrying SCCmectype IVA tended to have fewer healthcare-associated risk factors, compared with patients with healthcare-associated BSIs due to HA-MRSA strains carrying other SCCmectypes. The presence of a central venous catheter or other invasive device was the only independent factor differentiating patients infected with hospital-associated genotype strains from patients infected with other strains. Clinical outcomes were similar between both groups.

Conclusions.

CA-MRSA strains are emerging as a major cause of BSI in healthcare settings in Korea. This changing epidemiology of MRSA poses a challenge to public health and infection control in hospital settings.

Screening agars for MRSA: evaluation of a stepwise diagnostic approach with two different selective agars for the screening for methicillin-resistant Staphylococcus aureus (MRSA)

BACKGROUND

Colonization with methicillin-resistant Staphylococcus aureus (MRSA) poses a hygiene risk that does not spare field hospitals or military medical field camps during military deployments. Diagnostic options for unambiguously identifying MRSA isolates are usually scarce in military environments. In this study, we assessed the stepwise application of two different selective agars for the specific identification of MRSA in screening analyses.

METHODS

Nasal swabs from 1541 volunteers were subjected to thioglycollate broth enrichment and subsequently screened on CHROMagar MRSA selective agar for the identification of MRSA. The MRSA identity of suspicious-looking colonies was confirmed afterwards or excluded by another selective agar, chromID MRSA. All isolates from the selective agars with MRSA-specific colony morphology were identified by biochemical methods and mass spectrometry.

RESULTS

The initial CHROMagar MRSA screening identified suspicious colonies in 36 out of 1541 samples. A total of 25 of these 36 isolates showed MRSA-like growth on chromID agar. Out of these 25 isolates, 24 were confirmed as MRSA, while one isolate was identified as Staphylococcus kloosii. From the 11 strains that did not show suspicious growth on chromID agar, 3 were methicillin-sensitive Staphylococcus aureus (MSSA, with one instance of co-colonization with Corynebacterium spp.), 2 were confirmed as MRSA (with 1 instance of co-colonization with MSSA), 2 were lost during passaging and could not be re-cultured, one could not be identified by the applied approaches, and the remaining 3 strains were identified as Staphylococcus saprophyticus, Staphylococcus hominis (co-colonized with Macrococcus caseolyticus) and Staphylococcus cohnii, respectively.

CONCLUSIONS

The application of the selective agar CHROMagar MRSA alone proved to be too non-specific to allow for a reliable diagnosis of the presence of MRSA. The combined use of two selective agars in a stepwise approach reduced this non-specificity with an acceptably low loss of sensitivity. Accordingly, such a stepwise screening approach might be an option for resource-restricted military medical field camps.

Hospitalist perspective on the treatment of skin and soft tissue infections

The prevalence of skin and soft tissue infections (SSTIs) has been increasing in the United States. These infections are associated with an increase in hospital admissions. Hospitalists play an increasingly important role in the management of these infections and need to use hospital resources efficiently and effectively. When available, observation units are useful for treating low-risk patients who do not require hospital admission. Imaging tools may help to exclude abscesses and necrotizing soft tissue infections; however, surgical exploration remains the principal means of diagnosing necrotizing soft tissue infections. The most common pathogens that cause SSTIs are streptococci and Staphylococcus aureus. Methicillin-resistant S aureus (MRSA) is a prevalent pathogen, and concerns are increasing regarding the unclear distinctions between community-acquired and hospital-acquired MRSA. Other less frequent pathogens that cause SSTIs include Enterococcus species, Escherichia coli, Klebsiella species, Enterobacter species, and Pseudomonas aeruginosa. Cephalexin and clindamycin are suitable options for infections caused by streptococcal species and methicillin-susceptible S aureus. The increasing resistance of S aureus and Streptococcus pyogenes to erythromycin limits its use in these infections, and better alternatives are available. Parenteral cefazolin, nafcillin, or oxacillin can be used in hospitalized patients with nonpurulent cellulitis caused by streptococci and methicillin-susceptible S aureus. When oral MRSA therapy is indicated, clindamycin, doxycycline, trimethoprim-sulfamethoxazole, or linezolid is appropriate. Vancomycin, linezolid, daptomycin, tigecycline, telavancin, and ceftaroline fosamil are intravenous options that should be used in MRSA infections that require patient hospitalization. In the treatment of patients with SSTIs, hospitalists are at the forefront of providing proper patient care that reduces hospital costs, duration of therapy, and therapeutic failures. This review updates guidelines on the management of SSTIs with a focus on infections caused by S aureus, particularly MRSA, and outlines the role of the hospitalist in the effective management of SSTIs.

Predictors of skin and soft tissue infections in HIV-infected outpatients in the community-associated methicillin-resistant Staphylococcus aureus era

Skin and soft tissue infections (SSTIs) are common in the era of community-associated methicillin-resistant Staphylococcus aureus (MRSA) among human immunodeficiency virus (HIV)-infected patients, but the risk factors are not well defined. We sought to elucidate the risk factors for SSTI occurrence in an HIV cohort. This investigation was a retrospective, single-center cohort study, carried out during the period 2005-2009. In this cohort of 511 HIV-infected individuals, 133 SSTIs occurred in 87 individuals over 1,228.6 person-years of follow-up, for an incidence of 108 SSTIs/1,000 person-years [95 % confidence interval (CI) 87-135]. The incidence declined significantly over time (p < 0.01). In a multivariable Cox regression, diabetes [hazard ratio (HR) 2.01; 95 % CI 1.04-3.89], psoriasis (HR 5.77; 95 % CI 1.86-17.9), lymphedema (HR 6.84; 95 % CI 2.59-18.1), intravenous catheter presence (HR 3.38; 95 % CI 1.00-11.5), and HIV viral load greater than 1,000 copies/mL (HR 2.13; 95 % CI 1.33-3.41) were most strongly associated with development of the first SSTI. Trends toward an association between SSTI risk and Medicaid insurance (HR 1.67; 95 % CI 0.98-2.83) and sexually transmitted disease during follow-up (HR 1.66; 0.99-2.78) were present. CD4+ count and trimethoprim-sulfamethoxazole use were not associated with SSTI risk. HIV-infected individuals are at high risk for SSTIs. In a primarily urban, African-American cohort, we found that a number of immunologic and demographic factors were associated with SSTI risk.

Molecular epidemiology of methicillin-resistant Staphylococcus aureus isolated in serial cultures from the respiratory tract of children with cystic fibrosis

BACKGROUND

Little is known about strain relatedness of methicillin-resistant Staphyloccocus aureus (MRSA) isolated at serial time points from the respiratory tract of patients with cystic fibrosis (CF). The objectives are to interrogate the genetic diversity of MRSA recovered in serial cultures from children with CF and to correlate strain relatedness with clinical characteristics.

METHODS

We performed a retrospective analysis of children with CF from whom MRSA was isolated from serial respiratory cultures from 2005 to 2011. Within individual patients, relatedness of isolated strains was determined by repetitive-sequence polymerase chain reaction, and the staphylococcal cassette chromosome mec type of each isolate was characterized. Medical records corresponding to the MRSA cultures were reviewed.

RESULTS

We identified 54 CF patients with serial MRSA cultures (145 distinct cultures). Over time, 45 (83%) patients maintained the same strain type and 9 (17%) possessed at least 2 distinct strain types. A total of 91 pairs of isolates were analyzed for strain relatedness. Of these, 81 (89%) were identical and 10 (11%) were distinct strain types. About 117 (83%) isolates were staphylococcal cassette chromosome mec type II, 24 (17%) were staphylococcal cassette chromosome mec type IV and 4 were other types not resolvable with our assay. Clinical factors, including time interval and prescription of antibiotics effective against MRSA between positive cultures, did not correlate with acquisition of a distinct MRSA strain by individual patients.

CONCLUSIONS

Our data suggest that sustained presence of MRSA in CF patients is most commonly attributable to identical strain types. Acquisition of distinct MRSA strains in the airway is infrequent.

SCCmec types and pvl gene in methicillin-resistant Staphylococcus aureus strains from children hospitalized in a tertiary care hospital in Mexico

BACKGROUND

The aim of this study was to determine the prevalence, SCCmec types, presence of the Panton-Valentine leukocidin (PVL) gene, and susceptibility to antibiotics of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from hospitalized children.

METHODS

From August 2009 to September 2011, 291 S. aureus strains were isolated from normally sterile body sites, of which 190 (65%) were MRSA. One hundred and two of the MRSA strains were genetically evaluated. SCCmec genotypes were identified by M-PCR and the PVL gene (pvl) by end-point PCR. Resistance to erythromycin, rifampicin, clindamycin, and trimethoprim-sulfamethoxazole (SXT) was assessed by Kirby-Bauer disk diffusion method in accordance with the Clinical and Laboratory Standards Institute guidelines of 2012.

RESULTS

Of the 102 strains evaluated, 97 (95%) were SCCmec type II, 5 (5%) were SCCmec type IVa, and all (100%) were pvl-negative. Resistance to erythromycin, clindamycin, rifampicin, and SXT was 97%, 95%, 0%, and 0%, respectively.

CONCLUSIONS

The prevalence of hospital-acquired MRSA was high. SCCmec type II was predominant and the pvl gene appeared not to play any role in the virulence of the MRSA strains from hospitalized children.

Staphylococcus aureus - antimicrobial resistance and the immunocompromised child

Children with immunocompromising conditions represent a unique group for the acquisition of antimicrobial resistant infections due to their frequent encounters with the health care system, need for empiric antimicrobials, and immune dysfunction. These infections are further complicated in that there is a relative paucity of literature on the clinical features and management of Staphylococcus aureus infections in immunocompromised children. The available literature on the clinical features, antimicrobial susceptibility, and management of S. aureus infections in immunocompromised children is reviewed. S. aureus infections in children with human immunodeficiency virus (HIV) are associated with higher HIV viral loads and a greater degree of CD4 T-cell suppression. In addition, staphylococcal infections in children with HIV often exhibit a multidrug resistant phenotype. Children with cancer have a high rate of S. aureus bacteremia and associated complications. Increased tolerance to antiseptics among staphylococcal isolates from pediatric oncology patients is an emerging area of research. The incidence of S. aureus infections among pediatric solid organ transplant recipients varies considerably by the organ transplanted; in general however, staphylococci figure prominently among infections in the early posttransplant period. Staphylococcal infections are also prominent pathogens among children with a number of immunodeficiencies, notably chronic granulomatous disease. Significant gaps in knowledge exist regarding the epidemiology and management of S. aureus infection in these vulnerable children.

Carriage of methicillin-resistant staphylococci by healthy companion animals in the US

Antimicrobial-resistant staphylococci have been associated with wounded or ill companion animals, but little is known about the prevalence of resistant staphylococci among healthy animals. In this study, 276 healthy dogs and cats from veterinary clinics were tested for the presence of antimicrobial-resistant Staphylococcus spp. Isolates were tested for antimicrobial susceptibility and the presence of select resistance genes, and typed using Pulsed-Field Gel Electrophoresis (PFGE). Staphylococcus aureus and Staphylococcus pseudintermedius were also characterized using multilocus sequence typing (MLST), spa typing and SCCmec typing. Approximately 5% (14/276) of the animals were positive by enrichment for five species of staphylococci [Staph. aureus (n = 11), Staph. pseudintermedius (n = 4), Staphylococcus sciuri (n = 6), Staphylococcus simulans (n = 1) and Staphylococcus warneri (n = 1)]. Seventy-eight per cent (18/23) of staphylococci were resistant to oxacillin and also multidrug resistant (resistance to ≥ 2 antimicrobials). All Staph. aureus isolates were mecA+ and blaZ+, SCCmec type II, spa type t002, ST5 and clonal using PFGE. Staphylococcus pseudintermedius were SCCmec type IV or V, spa type t06 and ST170; two of the isolates were pvl(+) . These results suggest that healthy companion animals may be a reservoir of multidrug-resistant staphylococci, which may be transferred to owners and others who handle companion animals.

SIGNIFICANCE AND IMPACT OF THE STUDY

In this study, antimicrobial-resistant coagulase-negative and coagulase-positive staphylococci were isolated from various body sites on healthy dogs and cats. Resistance to 14 antimicrobials was observed including resistance to oxacillin; the majority of staphylococci were also multidrug resistant. Results from this study suggest that healthy dogs and cats may act as reservoirs of antimicrobial-resistant bacteria that may be transferred to people by simple interaction with the animals. Such carriage poses an underlying risk of infection, which should be considered during handling of healthy dogs and cats by pet owners and veterinary personnel.

Dissemination of methicillin-resistant Staphylococcus aureus SCCmec type IV and SCCmec type V epidemic clones in a tertiary hospital: challenge to infection control

Two-hundred MRSA strains from inpatients with healthcare-associated (HA) and 100 MRSA strains from outpatients with community-associated (CA) skin and soft tissue infections (SSTIs) were tested for antimicrobial susceptibility, staphylococcal cassette chromosome mec (SCCmec) typing, Panton-Valentine leucocidin (PVL) toxin, seh and arcA genes. Based on SCCmec typing, HA-MRSA isolates were further divided into HA-SCCmec I/II/III MRSA and HA-SCCmec IV/V MRSA, and CA-MRSA isolates into CA-SCCmec I/II/III MRSA and CA-SCCmec IV/V MRSA. SCCmec types were further characterized by pulsed-field gel electrophoresis, spa typing and multi-locus sequence typing. Seventy-five (37·5%) HA-MRSA isolates and 83/100 CA-MRSA isolates were SCCmec IV/V genotype. HA-SCCmec IV/V MRSA was associated with malignancy (P = 0·03) and bone fractures (P = 0·02) compared to CA-SCCmec IV/V MRSA. HA-SCCmec IV/V MRSA was associated with PVL gene carriage compared to HA-SCCmec I/II/III MRSA (P < 0·001). ST22-MRSA-IV (EMRSA-15), ST772-MRSA-V, and ST36-MRSA-IV and ST239:EMRSA-I:III were the major clones identified. Our study documents the emergence of SCCmec IV and SCCmec V MRSA clones in an Indian hospital.

Clinical, epidemiologic, and laboratory aspects of methicillin-resistant Staphylococcus aureus infections

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen responsible for both hospital and community onset disease. Resistance to methicillin in S. aureus is mediated by PBP2a, a penicillin-binding protein with low affinity to beta-lactams, encoded by the mecA gene. Accurate susceptibility testing of S. aureus isolates and screening of patients for colonization with MRSA are important tools to limit the spread of this organism. This review focuses on the clinical significance of MRSA infections and new approaches for the laboratory diagnosis and epidemiologic typing of MRSA strains.

Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: a cross-sectional study

Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of healthcare-associated infections and significant contributor to healthcare cost. Community-associated-MRSA (CA-MRSA) strains have now invaded healthcare settings. A convenience sample of 97 clinical MRSA isolates was obtained from seven hospitals during a one-week period in 2010. We employed a framework integrating Staphylococcus protein A typing and full-genome next-generation sequencing. Single nucleotide polymorphisms were analyzed using phylodynamics. Twenty-six t002, 48 t008, and 23 other strains were identified. Phylodynamic analysis of 30 t008 strains showed ongoing exponential growth of the effective population size the basic reproductive number (R0) ranging from 1.24 to 1.34. No evidence of hospital clusters was identified. The lack of phylogeographic clustering suggests that community introduction is a major contributor to emergence of CA-MRSA strains within hospitals. Phylodynamic analysis provides a powerful framework to investigate MRSA transmission between the community and hospitals, an understanding of which is essential for control.

Community-acquired, healthcare-associated and hospital-acquired bloodstream infection definitions in children: a systematic review demonstrating inconsistent criteria

BACKGROUND

Historically, bacterial infections were categorized as either community-acquired (CA) or hospital-acquired (HA). However, the CA/HA dichotomy no longer adequately reflects patterns of emerging healthcare-associated (HCA) infections in complex patients managed between hospital and the community. Studies trying to define this evolving epidemiology often excluded children.

AIM

To identify what criteria have been used to distinguish between CA, HCA and HA bloodstream infections (BSIs) in children, and the proportional distribution of CA, HCA and HA among total BSIs and by organism.

METHODS

We systematically reviewed published literature from PubMed, UK Department of Health and US Centers for Disease Control and Prevention websites.

FINDINGS

Results from 23 studies and the websites highlighted the use of inconsistent criteria. There were 13 and 15 criteria variations for CA and HA BSI respectively, although a 48h cut-off for cultures sampled post admission was most commonly reported. Five studies used variable clinical criteria to define HCA. The mean proportion of paediatric CA BSI in nine studies was 50%. Only four BSI organisms from five studies were predominantly CA (Streptococcus pneumoniae, Salmonella spp.) or HA (coagulase-negative staphylococci, Enterococcus spp.), whereas Pseudomonas spp., Klebsiella spp. and Enterobacter spp. did not clearly fit into either category.

CONCLUSIONS

Our study reveals inconsistent use of criteria, and a lack of evidence upon which to base them, to distinguish between CA, HCA and HA BSI in children. Criteria for CA, HCA and HA BSI need to be developed using population-based studies that consider patients' clinical characteristics, recent healthcare exposure as well as isolated organism species.

Staphylococcus aureus: a pathogen with still unresolved issues

Staphylococcus aureus is a major human pathogen, and considerable research efforts have been put forward to improve our understanding of its complex pathogenesis. In spite of these efforts, the burden of staphylococcal infections is still on the rise. This review focuses on a selected set of crucial unresolved questions regarding this pathogen, namely: (i) the nature of the driving forces behind the rise and decline of methicillin-resistant S.aureus (MRSA) clones; (ii) the mechanisms by which a commensal becomes a pathogen; (iii) the molecular underpinnings of toxin overexpression in hypervirulent MRSA clones such as USA300; and (iv) the repeated failures of anti-S.aureus vaccine approaches.

Recurrent furunculosis: a review of the literature

BACKGROUND

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is increasing in incidence and manifests as skin and soft tissue infections including furuncles. The majority of studies have focused on the epidemiology of single furuncles and not recurrent disease. There is a lack of data concerning the incidence of furunculosis outside the U.S.A.

OBJECTIVES

This report reviews the literature of recurrent furunculosis and the impact of CA-MRSA on the disease.

METHODS

Article citations were searched within PubMed. Search terms used were 'furunculosis', 'recurrent furunculosis', 'skin abscess' and 'recurrent boils'. Articles were discarded if they did not refer to furunculosis secondary to S. aureus.

RESULTS

A total of 1515 articles were initially retrieved with the term 'furunculosis', 77 with the term 'recurrent furunculosis', 2778 with the term 'skin abscess', and 1526 with the term 'recurrent boils'. After excluding articles not referring to S. aureus furunculosis, 86 articles were included for this review.

CONCLUSIONS

Furunculosis is increasing within the U.S.A. secondary to the CA-MRSA epidemic and the resistant organism's close association with the Panton-Valentine leucocidin (PVL) virulence factor. PVL is associated with follicular infections in general, having its strongest association with furunculosis and its recurrence. The majority of furuncles in the U.S.A. are caused by CA-MRSA, while elsewhere in the world they are caused by methicillin-sensitive S. aureus. Nasal carriage of S. aureus is the primary risk factor for recurrent furunculosis and occurs in 60% of individuals.

Emergence of methicillin-resistant Staphylococcus aureus USA300 genotype as a major cause of late-onset nosocomial pneumonia in intensive care patients in the USA

OBJECTIVE

To compare demographic and clinical characteristics, and methicillin-resistant Staphylococcus aureus (MRSA) strain characteristics, in patients with early-onset (EO) and late-onset (LO) MRSA nosocomial pneumonia.

METHODS

This was a retrospective analysis of data from a multicenter observational study of nosocomial pneumonia patients admitted between November 2008 and July 2010. Laboratory analyses performed on MRSA isolates included confirmation of antimicrobial susceptibility and heteroresistance to vancomycin, USA typing, staphylococcal cassette chromosome (SCC) mec typing, and detection of Panton-Valentine leukocidin (PVL) genes.

RESULTS

We identified 134 patients; 42 (31%) had EO MRSA pneumonia and 92 (69%) had LO MRSA pneumonia. The patients in the LO group were more likely to have risk factors for multidrug-resistant pathogens (98% vs. 76%, p<0.001). The MRSA USA300 strain was found with equal frequency in the EO and LO groups. Likewise, both groups had similar frequencies of isolates exhibiting PVL and SCCmec type IV.

CONCLUSIONS

Our findings provide further evidence of the continued migration of community-associated MRSA into the healthcare setting in the USA. MRSA USA300 genotype has emerged as a significant cause of LO nosocomial pneumonia in intensive care units. Appropriate anti-MRSA antimicrobial therapy should be considered for both EO and LO hospital-acquired pneumonia and ventilator-associated pneumonia.

Prevalence and characterization of methicillin-resistant Staphylococcus aureus isolates from retail meat and humans in Georgia

There is increasing interest in the presence of Staphylococcus aureus, specifically methicillin-resistant S. aureus (MRSA), on retail meat products. In this study, staphylococci were isolated from retail pork and retail beef in Georgia, and MRSA from the products was compared to human MRSA from the same geographic area using broth microdilution antimicrobial susceptibility testing, multilocus sequence typing (MLST), spa typing, SCCmec typing, and pulsed-field gel electrophoresis (PFGE). S. aureus was isolated from 45% (45/100) of pork products and 63% (63/100) of beef products; mecA was detected in S. aureus from both pork (3/100; 3%) and beef (4/100; 4%). Fifty percent (50/100) of human S. aureus also contained mecA. Multidrug resistance was detected among MRSA from all sources. All MRSA (n = 57) was SCCmec type IV, and nine different spa types were present among the isolates (t002, t008, t012, t024, t179, t337, t548, t681, and t1062). Four sequence types (ST5, ST8, ST9, and ST30) were detected using MLST; the majority of MRSA isolates belonged to ST8, followed by ST5. One retail beef MRSA isolate belonged to ST8, while the remaining three were ST5. In retail pork MRSA, ST5, ST9, and ST30 were observed. The majority of human MRSA isolates belonged to ST8. Thirty-seven MRSA isolates, one of which was a retail beef MRSA isolate, were pvl(+). Using PFGE, MLST, and spa typing, three retail beef MRSA isolates were found to be identical in PFGE pattern, ST, and spa type to two human clonal MRSA isolates (USA100 and USA300). One additional retail beef MRSA isolate had a PFGE pattern similar to that of a human MRSA isolate, whereas none of the retail pork MRSA isolates had PFGE patterns similar to those of human MRSA isolates. These data suggest that the retail beef samples were contaminated by a human source, possibly during processing of the meat, and may present a source of MRSA for consumers and others who handle raw meat.

Multiplex real-time PCR assay for the detection of meticillin-resistant Staphylococcus aureus and Panton-Valentine leukocidin from clinical samples

The control and prevention of meticillin-resistant Staphylococcus aureus (MRSA) is a major challenge for healthcare establishments, especially as this pathogen continues to evolve. The emergence and spread of community associated MRSA producing Panton-Valentine leukocidin (PVL) causing severe, sometimes fatal, infections in otherwise healthy people is a significant cause of concern. Patient screening to detect MRSA is now widely used as part of an effective control program to limit the spread of this pathogen. Real-time PCR targeting specific MRSA markers offers a rapid alternative to conventional methods enabling earlier intervention, such as patient isolation and decolonization treatment. Herein we describe a multiplex real-time assay that combines primers and probes to detect MRSA and the genes for PVL to provide a rapid and informative assay.

A comparison of clinical outcomes between healthcare-associated infections due to community-associated methicillin-resistant Staphylococcus aureus strains and healthcare-associated methicillin-resistant S. aureus strains

There are limited data examining whether outcomes of methicillin-resistant Staphylococcus aureus (MRSA) healthcare-associated infections (HAIs) are worse when caused by community-associated (CA) strains compared to HA strains. We reviewed all patients' charts at our institution from 1999 to 2009 that had MRSA first isolated only after 72 h of hospitalization (n=724). Of these, 384 patients had a MRSA-HAI according to CDC criteria. Treatment failure was similar in those infected with a phenotypically CA-MRSA strain compared to a phenotypically HA-MRSA strain (23% vs. 15%, P=0.10) as was 30-day mortality (16% vs. 19%, P=0.57). Independent risk factors associated with (P<0.05) treatment failure were higher Charlson Comorbidity Index, higher APACHE II score, and no anti-MRSA treatment. These factors were also associated with 30-day mortality, as were female gender, older age, MRSA bloodstream infection, MRSA pneumonia, and HIV. Our findings suggest that clinical and host factors, not MRSA strain type, predict treatment failure and death in hospitalized patients with MRSA-HAIs.

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

Background

The emergence of meticillin-resistant Staphylococcus aureus (MRSA) that can persist in the community and replace existing hospital-adapted lineages of MRSA means that it is necessary to understand transmission dynamics in terms of hospitals and the community as one entity. We assessed the use of whole-genome sequencing to enhance detection of MRSA transmission between these settings.

Methods

We studied a putative MRSA outbreak on a special care baby unit (SCBU) at a National Health Service Foundation Trust in Cambridge, UK. We used whole-genome sequencing to validate and expand findings from an infection-control team who assessed the outbreak through conventional analysis of epidemiological data and antibiogram profiles. We sequenced isolates from all colonised patients in the SCBU, and sequenced MRSA isolates from patients in the hospital or community with the same antibiotic susceptibility profile as the outbreak strain.

Findings

The hospital infection-control team identified 12 infants colonised with MRSA in a 6 month period in 2011, who were suspected of being linked, but a persistent outbreak could not be confirmed with conventional methods. With whole-genome sequencing, we identified 26 related cases of MRSA carriage, and showed transmission occurred within the SCBU, between mothers on a postnatal ward, and in the community. The outbreak MRSA type was a new sequence type (ST) 2371, which is closely related to ST22, but contains genes encoding Panton-Valentine leucocidin. Whole-genome sequencing data were used to propose and confirm that MRSA carriage by a staff member had allowed the outbreak to persist during periods without known infection on the SCBU and after a deep clean.

Interpretation

Whole-genome sequencing holds great promise for rapid, accurate, and comprehensive identification of bacterial transmission pathways in hospital and community settings, with concomitant reductions in infections, morbidity, and costs.

Funding

UK Clinical Research Collaboration Translational Infection Research Initiative, Wellcome Trust, Health Protection Agency, and the National Institute for Health Research Cambridge Biomedical Research Centre.

Mupirocin and chlorhexidine resistance in Staphylococcus aureus in patients with community-onset skin and soft tissue infections

Decolonization measures, including mupirocin and chlorhexidine, are often prescribed to prevent Staphylococcus aureus skin and soft tissue infections (SSTI). The objective of this study was to determine the prevalence of high-level mupirocin and chlorhexidine resistance in S. aureus strains recovered from patients with SSTI before and after mupirocin and chlorhexidine administration and to determine whether carriage of a mupirocin- or chlorhexidine-resistant strain at baseline precluded S. aureus eradication. We recruited 1,089 patients with community-onset SSTI with or without S. aureus colonization. In addition to routine care, 483 patients were enrolled in a decolonization trial: 408 received intranasal mupirocin (with or without antimicrobial baths), and 258 performed chlorhexidine body washes. Patients were followed for up to 12 months with repeat colonization cultures. All S. aureus isolates were tested for high-level mupirocin and chlorhexidine resistance. At baseline, 23/1,089 (2.1%) patients carried a mupirocin-resistant S. aureus strain and 10/1,089 (0.9%) patients carried chlorhexidine-resistant S. aureus. Of 4 patients prescribed mupirocin, who carried a mupirocin-resistant S. aureus strain at baseline, 100% remained colonized at 1 month compared to 44% of the 324 patients without mupirocin resistance at baseline (P = 0.041). Of 2 patients prescribed chlorhexidine, who carried a chlorhexidine-resistant S. aureus strain at baseline, 50% remained colonized at 1 month compared to 48% of the 209 patients without chlorhexidine resistance at baseline (P = 1.0). The overall prevalence of mupirocin and chlorhexidine resistance is low in S. aureus isolates recovered from outpatients, but eradication efforts were less successful in patients carrying a mupirocin-resistant S. aureus strain at baseline.

Comparative genomics of community-acquired ST59 methicillin-resistant Staphylococcus aureus in Taiwan: novel mobile resistance structures with IS1216V

Methicillin-resistant Staphylococcus aureus (MRSA) with ST59/SCCmecV and Panton-Valentine leukocidin gene is a major community-acquired MRSA (CA-MRSA) lineage in Taiwan and has been multidrug-resistant since its initial isolation. In this study, we studied the acquisition mechanism of multidrug resistance in an ST59 CA-MRSA strain (PM1) by comparative genomics. PM1’s non-β-lactam resistance was encoded by two unique genetic traits. One was a 21,832-bp composite mobile element structure (MES_PM1), which was flanked by direct repeats of enterococcal IS1216V and was inserted into the chromosomal sasK gene; the target sequence (att) was 8 bp long and was duplicated at both ends of MES_PM1. MES_PM1 consisted of two regions: the 5′-end side 12.4-kb region carrying Tn551 (with ermB) and Tn5405-like (with aph[3′]-IIIa and aadE), similar to an Enterococcus faecalis plasmid, and the 3′-end side 6,587-bp region (MES_cat) that carries cat and is flanked by inverted repeats of IS1216V. MES_cat possessed att duplication at both ends and additional two copies of IS1216V inside. MES_PM1 represents the first enterococcal IS1216V-mediated composite transposon emerged in MRSA. IS1216V-mediated deletion likely occurred in IS1216V-rich MES_PM1, resulting in distinct resistance patterns in PM1-derivative strains. Another structure was a 6,025-bp tet-carrying element (MES_tet) on a 25,961-bp novel mosaic penicillinase plasmid (pPM1); MES_tet was flanked by direct repeats of IS431, but with no target sequence repeats. Moreover, the PM1 genome was deficient in a copy of the restriction and modification genes (hsdM and hsdS), which might have contributed to the acquisition of enterococcal multidrug resistance.

TD-1792 versus vancomycin for treatment of complicated skin and skin structure infections

TD-1792 is a first-in-class glycopeptide-cephalosporin heterodimer that exhibits bactericidal activity against Gram-positive pathogens. We conducted a randomized, double-blind, active-control, phase II trial in patients with complicated skin and skin structure infections caused by suspected or confirmed Gram-positive organisms. Patients 18 to 65 years old were randomized to receive 7 to 14 days of either TD-1792 (2 mg/kg of body weight intravenously [i.v.] every 24 h [q24h]) or vancomycin (1 g i.v. q12h, with dosage regimens adjusted per site-specific procedures). A total of 197 patients were randomized and received at least one dose of study medication. Rates of clinical success at the test-of-cure evaluation were similar in all analysis populations. Among 170 clinically evaluable patients, cure rates were 91.7% and 90.7% in the TD-1792 and vancomycin groups, respectively (95% confidence interval [CI] of -7.9 to 9.7 for the difference). In microbiologically evaluable patients with methicillin-resistant Staphylococcus aureus at baseline (n = 75), cure rates were 94.7% in the TD-1792 group and 91.9% in the vancomycin group. Microbiological eradication of Gram-positive pathogens (n = 126) was achieved in 93.7% and 92.1% of patients in the TD-1792 and vancomycin groups, respectively. Seven patients were discontinued from study medication due to an adverse event (AE): 2 and 5 in the TD-1792 and vancomycin groups, respectively. AEs were of similar types and severities between the two groups, other than pruritus, which was more common in patients who received vancomycin. No patients in the TD-1792 group experienced a serious AE. This study supports further clinical development of TD-1792 in patients with Gram-positive infection.

Rates of killing of methicillin-resistant Staphylococcus aureus by ceftaroline, daptomycin, and telavancin compared to that of vancomycin

Treatment failure of methicillin-resistant Staphylococcus aureus (MRSA) remains an important concern. In order to investigate new MRSA treatment modalities, we used standard time-kill assays to determine the in vitro killing rate of 22 strains of MRSA by vancomycin, telavancin, daptomycin, and ceftaroline. Studies were carried out with 7-10-times the minimum bactericidal concentrations of each antibiotic in broth culture for 24 h, with subculture at 4, 8, and 24 h. We found that killing by ceftaroline closely paralleled that of vancomycin. Telavancin killed bacteria significantly more slowly, whereas daptomycin killed significantly more rapidly.

Impact of USA300 methicillin-resistant Staphylococcus aureus on clinical outcomes of patients with pneumonia or central line-associated bloodstream infections

BACKGROUND

The USA300 methicillin-resistant Staphylococcus aureus (MRSA) strain, which initially emerged as a cause of community-associated infections, has recently become an important pathogen in healthcare-associated infections (HAIs). However, its impact on patient outcomes has not been well studied. We evaluated patients with invasive MRSA infections to assess differences in outcomes between infections caused by USA100 and those caused by USA300.

METHODS

Population-based data for invasive MRSA infections were used to identify 2 cohorts: (1) nondialysis patients with central line-associated bloodstream infections (CLABSIs) and (2) patients with community-onset pneumonia (PNEUMO) during 2005-2007 from 6 US metropolitan areas. Medical records of patients with confirmed MRSA USA100 or USA300 infection were reviewed. Logistic regression and, when appropriate, survival analysis was performed to evaluate mortality, early and late complications, and length of stay.

RESULTS

A total of 236 and 100 patients were included in the CLABSI and PNEUMO cohorts, respectively. USA300 was the only independent predictor of early complications for PNEUMO patients (odds ratio [OR], 2.6; P = .02). Independent predictors of CLABSI late complications included intensive care unit (ICU) admission before MRSA culture (adjusted OR [AOR], 2.1; P= .01) and Charlson comorbidity index (AOR, 2.6; P = .003), but not strain type. PNEUMO patients were significantly more likely to die if they were older (P = .02), black (P < .001), or infected with USA100 strain (P = .02), whereas those with CLABSI were more likely to die if they were older (P < .001), had comorbidities (P < .001), or had an ICU admission before MRSA culture (P = .001).

CONCLUSIONS

USA300 was associated with early complications in PNEUMO patients. However, it was not associated with mortality for either PNEUMO or CLABSI patients. Concerns regarding higher mortality from HAIs caused by USA300 may not be warranted.