DNA microarray profiling of a diverse collection of nosocomial methicillin-resistant staphylococcus aureus isolates assigns the majority to the correct sequence type and staphylococcal cassette chromosome mec (SCCmec) type and results in the subsequent identification and characterization of novel SCCmec-SCCM1 composite islands

Diversity of clonal complex 22 methicillin-resistant Staphylococcus aureus isolates in Kuwait hospitals

CC22-MRSA is a major MRSA lineage that is widely reported globally. To characterize CC22-MRSA for trends in antibiotic resistance and emergence of variants, a total of 636 CC22 isolates identified by DNA microarray in 2016 (n = 195), 2017 (n = 227) and 2018 (n = 214) were investigated further using staphylococcal protein A (spa) typing and multilocus sequence typing. The isolates belonged to 109 spa types dominated by t223 (n = 160), t032 (n = 60), t852 (n = 59), t005 (n = 56) and t309 (n = 30) and 10 sequence types (STs) dominated by ST22 (85.5%). Genotypes CC22-MRSA-IV [tst1⁺]; CC22-MRSA-IV UK-EMRSA-15/Barnim EMRSA variants, CC22-MRSA-IV [PVL⁺], CC22-MRSA-IV [tst1⁺/PVL⁺] and CC22-MRSA-IV + V constituted >50% of the isolates. An increase from 2016 to 2018 were shown in isolates belonging to spa types t223 (43 to 62), t032 (18 to 27) and t309 (10 to 15) and genotypes CC22-MRSA-IV [tst1⁺] (89 to 102), CC22-MRSA-IV + V (12 to 30) and CC22-MRSA-IV [tst1⁺/PVL⁺] (12 to 22). Ninety-nine CC22-MRSA isolates were multi-resistant to three or more antibiotic classes with 76.7% of them belonging to CC22-MRSA-IV [PVL⁺] and CC22-MRSA-IV [tst1⁺/PVL⁺]. The study revealed an ongoing domination of the CC22-MRSA-[tst1⁺] genotype and the emergence of new clones bearing SCCmec IV + V and multiply resistant variants.

Characterizing a novel SCCmec with a composite structure from a clinical strain of Staphylococcus hominis, C34847

Staphylococcal cassette chromosome mec (SCCmec) has predominantly been described in methicillin-resistant Staphylococcus aureus. However, studies have indicated that coagulase-negative staphylococci (CoNS) carry a larger diversity of SCC elements. We characterized a composite SCCmec element carrying an uncharacterized ccr1 and type A mec gene combination, in conjunction with a secondary element bearing ccr4, from a clinical strain of S. hominis. The element's complex structure points to a high degree of recombination occurring in SCCmec in CoNS.

The global prevalence of fusidic acid resistance in clinical isolates of Staphylococcus aureus: a systematic review and meta-analysis

BACKGROUND AND AIM

Staphylococcus aureus (S. aureus) is one of the most common pathogens causing nosocomial and community-acquired infections with high morbidity and mortality rates. Fusidic acid has been increasingly used for the treatment of infections due to methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). The present study aimed to determine the precise prevalence of fusidic acid resistant MRSA (FRMRSA), fusidic acid resistant MSSA (FRMSSA), and total fusidic acid resistant S. aureus (FRSA) on a global scale.

METHODS

Several international databases including Medline, Embase, and the Web of Sciences were searched (2000-2020) to discern studies addressing the prevalence of FRSA, FRMRSA, and FRMSSA. STATA (version14) software was used to interpret the data.

RESULTS

Of the 1446 records identified from the databases, 215 studies fulfilled the eligibility criteria for the detection of FRSA (208 studies), FRMRSA (143 studies), and FRMSSA (71 studies). The analyses manifested that the global prevalence of FRSA, FRMRSA, and FRMSSA was 0.5%, 2.6% and 6.7%, respectively.

CONCLUSION

This meta-analysis describes an increasing incidence of FRSA, FRMSSA, and FRMRSA. These results indicate the need for prudent prescription of fusidic acid to stop or diminish the incidence of fusidic acid resistance as well as the development of strategies for monitoring the efficacy of fusidic acid use.

Novel staphylococcal cassette chromosome mec (SCCmec) type XIV (5A) and a truncated SCCmec element in SCC composite islands carrying speG in ST5 MRSA in Japan

BACKGROUND

Staphylococcal cassette chromosome mec (SCCmec) elements are highly diverse and have been classified into 13 types. The arginine catabolic mobile element (ACME) is an SCC-like element harbouring an arginine deiminase pathway gene cluster (ACME-arc). ACME type I (ACME I), additionally including a spermidine/spermine-N1-acetyltransferase gene (speG), is considered to have contributed to the rapid spread of the most successful MRSA clone, USA300.

OBJECTIVES

To characterize the SCC composite islands (SCC-CIs) in ST5 MRSA positive for both ACME-arc and speG.

METHODS

Three ST5 MRSA strains (SC640, SC792 and SC955) collected in Hokkaido, Japan were subjected to WGS and the SCC-CIs were determined.

RESULTS

The SCC-CIs consisted of four (SC640 and SC792) or three (SC955) SCC/SCC-like elements and commonly harboured both an ACME type II' and an SCC encoding speG. These SCC-CIs appear to mimic ACME I in USA300, in that they are equipped with ACME-arc and speG. The SCC-CIs of SC640 and SC792 contained novel SCCmec/SCCmec-like elements at the 3' end, whereas SC955 contained SCCmec type V. The SCCmec of SC792 carried mec complex A and ccrC1, which was determined to be novel and designated as SCCmec type XIV (5A). SC640 harboured an SCCmec-like element derived from SCCmec type XIV. It lacked most of the downstream region of the mec complex, including the left chromosomal attachment site (SCCmec XIV Δkdp/DR-L), and lost its capability for chromosomal excision, suggesting that the mecA gene is immobilized on the chromosome.

CONCLUSIONS

These findings provide evidence for increasing complexity of SCC-CIs.

Epidemiological typing of methicillin resistant Staphylococcus aureus recovered from patients attending a maternity hospital in Ireland 2014-2019

It has previously been reported that maternity hospitals have lower levels of MRSA compared to other healthcare facilities, due to the patient population - mostly healthy patients with limited healthcare contact. In this epidemiological study, all MRSA isolates recovered from patients attending a maternity hospital from 2014 – 2019 were investigated. 171 isolates from adults (n=120) and babies (n=51) from diagnostic and screening investigations were submitted to the National MRSA Reference Laboratory (NMRSARL). Investigations included: spa typing, antimicrobial susceptibility testing, detection of the mecA/mecC genes and lukS-PV and lukF-PV. All were susceptible to glycopeptides, linezolid, rifampicin and mupirocin, while 29 of 171 (17%) were resistant to β-lactam agents only. Thirteen isolates (8%) were resistant to two classes of antibiotic; one resistant to three. All isolates harboured mecA and 33 of 171 (19%) harboured PV-lukF/S. Among the collection, 21 multilocus sequence types (ST) were inferred from 63 spa types. EARS-NET data shows that ST22-MRSA-IV accounts for approximately 75% of MRSA recovered in Irish hospitals. Here, it accounted for only 25.7%. MLST types associated with community acquired MRSA accounted for the remaining 74.3%. These included ST8, ST30, ST1, ST5 and ST88, suggesting a diverse population, harbouring multiple resistance and virulence genes, some of which have been previously associated with outbreaks in Ireland. This study exposes a reservoir of MRSA in the community which may be imported into hospitals, leading to outbreaks. The diversity of MRSA lineages with enhanced virulence factors highlights the need for regular surveillance to ensure appropriate infection prevention and control interventions are implemented promptly.

Clonal diversity of methicillin-resistant Staphylococcus aureus (MRSA) from bloodstream infections in northern Japan: Identification of spermidine N-acetyltransferase gene (speG) in staphylococcal cassette chromosomes (SCCs) associated with type II and IV SCCmec

OBJECTIVES

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the leading causes of bloodstream infections (BSIs). We aimed to study molecular epidemiological characteristics of MRSA isolates from BSIs in northern Japan to elucidate the recent trend of their clonal diversity.

METHODS

MRSA isolates (n = 277) were collected from blood samples of patients who attended healthcare facilities in Hokkaido, the northern main island of Japan, for a two-year period from August 2017. Genotypes, virulence factors/drug-resistance determinants, and structure of SCCmec complex were analysed by PCR and sequencing analysis.

RESULTS

SCCmec-IIa (n = 171, 61.7%) with coagulase genotype (coa-) II, ST5/ST764/ST2389 was the most common genetic trait, followed by SCCmec-IVa (n = 78, 28.2%), and IVl (n = 10, 3.6%). Among the MRSA-IVa, 14 isolates (5.1% of all the isolates) had genetic features identical to USA300 clone (ST8/coa-IIIa/spa-t008 having ΦSa2USA and ACME-I), while PVL/ACME-negative MRSA-IVa isolates (n = 64) were classified into coa-IIa/IIIa/VIIa/VIIb, with coa-VIIa/spa-t1784/ST1 being dominant. Other minor clones included ST8-SCCmec-I, and ST30/ST45/ST81/ST121/ST1232-SCCmec-V, among which the ST1232 isolate harboured PVL genes. Spermidine N-acetyltransferase gene (speG), which is typically present in ACME-I of USA300 clone, was also identified in two isolates, ACME-II'-positive ST764-MRSA-IIa and ACME-negative ST1-MRSA-IVa, showing resistance to spermine. speG of these isolates was located in additional SCCs adjacent to SCCmec.

CONCLUSIONS

Our present study revealed clonal diversity of MRSA from BSIs in Japan, with increased prevalence of ST8-USA300. Distinct types of speG-carrying SCCs associated with SCCmec-II or IV were identified.

Mobile genetic elements responsible for discordant Staphylococcus aureus phenotypes and genotypes in the same blood culture bottle

Approximately 15-20% of the S. aureus genome contains mobile genetic elements that can cause discrepancies between phenotypic and genotypic identification methods. Three blood culture bottles (each from a different patient) that showed discordant results, were shown to contain 2 S. aureus isolates after additional subcultures. One bottle had MRSA and MSSA that by DNA sequence analysis differed only by 31 kb; however, the deletions encompassed parts of SCCmec including mecA and SCC_M1. The second bottle contained MRSA and MSSA that differed by 124 kb; the MSSA was missing the entire SCCmec and spa regions. The last bottle contained 2 MRSA, one with ACME II disrupting SCCmec and a 24 bp spa deletion. The deletions in SCCmec and the other elements gave rise to the discrepancies between molecular and the original culture results. Such discrepancies should prompt a search for additional strains in the blood culture bottle.

Updating Molecular Diagnostics for Detecting Methicillin-Susceptible and Methicillin-Resistant Staphylococcus aureus Isolates in Blood Culture Bottles

Molecular diagnostic tests can be used to provide rapid identification of staphylococcal species in blood culture bottles to help improve antimicrobial stewardship. However, alterations in the target nucleic acid sequences of the microorganisms or their antimicrobial resistance genes can lead to false-negative results.

Molecular diagnostic tests can be used to provide rapid identification of staphylococcal species in blood culture bottles to help improve antimicrobial stewardship. However, alterations in the target nucleic acid sequences of the microorganisms or their antimicrobial resistance genes can lead to false-negative results. We determined the whole-genome sequences of 4 blood culture isolates of Staphylococcus aureus and 2 control organisms to understand the genetic basis of genotype-phenotype discrepancies when using the Xpert MRSA/SA BC test (in vitro diagnostic medical device [IVD]). Three methicillin-resistant S. aureus (MRSA) isolates each had a different insertion of a genetic element in the staphylococcal cassette chromosome (SCCmec)-orfX junction region that led to a misclassification as methicillin-susceptible S. aureus (MSSA). One strain contained a deletion in spa, which produced a false S. aureus-negative result. A control strain of S. aureus that harbored an SCCmec element but no mecA (an empty cassette) was correctly called MSSA by the Xpert test. The second control contained an SCC_M1 insertion. The updated Xpert MRSA/SA BC test successfully detected both spa and SCCmec variants of MRSA and correctly identified empty-cassette strains of S. aureus as MSSA. Among a sample of 252 MSSA isolates from the United States and Europe, 3.9% contained empty SCCmec cassettes, 1.6% carried SCC_M1, <1% had spa deletions, and <1% contained SCCmec variants other than those with SCC_M1. These data suggest that genetic variations that may interfere with Xpert MRSA/SA BC test results remain rare. Results for all the isolates were correct when tested with the updated assay.

Livestock-Associated Methicillin-Resistant Staphylococcus aureus From Animals and Animal Products in the UK

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an emerging problem in many parts of the world. Although animal-adapted LA-MRSA has been known for many years, recent reports suggest a possible increasing trend in the zoonotic transmission of LA-MRSA in Europe. Since its emergence in the early 2000's, several investigations have indicated that persons in prolonged, repeated contact with affected livestock are at a higher risk of becoming colonized with LA-MRSA. LA-MRSA monitoring in livestock is voluntary under current EU legislation, and not all member states, including the UK, participate. UK LA-MRSA isolates have been detected through scanning surveillance, where samples are submitted from clinically diseased livestock for diagnostic investigation, and research studies. Surveys conducted on retail beef, pig and poultry meat on sale in the UK have also detected LA-MRSA. Taken together these results suggest that LA-MRSA is present in the UK, possibly at low prevalence level, as suggested by available evidence. In this review, we examine the data available from UK livestock and animal products, and make recommendations for future. We also review the findings from whole genome sequencing (WGS) of the possible lineage of some UK livestock isolates.

Emerging variants of methicillin-resistant Staphylococcus aureus genotypes in Kuwait hospitals

Background

Frequent changes in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) occurring worldwide demand regular surveillance to study their composition and distribution in healthcare facilities. We investigated the genotypic characteristics of MRSA obtained in Kuwait hospitals to better understand their clonal distribution.

Materials and methods

A total of 1,327 MRSA isolates obtained from clinical samples in 13 Kuwait hospitals from 1 January to 31 December 2016 were investigated using antibiogram, SCCmec typing, spa typing and DNA microarray.

Results

The isolates belonged to six SCCmec types with the majority belonging to type IV (658; 49.5%) and type V (355; 26.7%). Two hundred and sixty-one spa types were identified with spa types t688, t304, t860, t127, t044, t311, t002, t223, t267, t019, t3841, t005, t084, t852, and t657 constituting 51.0% (n = 677) of the isolates. Among the 1,327 MRSA isolates, 102 (7.68%) isolates were identified as novel variants of internationally recognized MRSA clones. These 102 isolates were investigated further and belonged to 14 clonal complexes (CCs) with CC361 (32; 32.3%), CC30 (15; 14.7%), CC22 (13; 12.7%) and CC1 (11, 10.7%) as the dominant CCs. Eighty-one (79.4%) of the novel isolates harbored SCCmec IV or V+fusC composite genetic elements. Four isolates (3.9%) harbored unusual combinations of ccr and mec complexes comprising of CC6-MRSA [IV+fusC+ccrC], CC97-MRSA [V/V_T+fusC+ccrAB2], CC121-MRSA [V/V_T+fusC+ccrB4] and CC1-MRSA-pseudoSCCmec [class B mec+fusc+ccrAB1]. Forty-six (45.1%) of these isolates were positive for PVL and 89 (87.2%) were resistant to fusidic acid mediated by fusC.

Conclusions

The study showed the emergence of novel variants of previously recognized MRSA genotypes with unusual genetic characteristics including high prevalence of PVL and fusidic acid resistance in Kuwait hospitals. This has added to the dynamic lists of known variations in MRSA genomes which can impose serious challenges for infection control and treatment of MRSA infections.

Distribution of the Most Prevalent Spa Types among Clinical Isolates of Methicillin-Resistant and -Susceptible Staphylococcus aureus around the World: A Review

Background:Staphylococcus aureus, a leading cause of community-acquired and nosocomial infections, remains a major health problem worldwide. Molecular typing methods, such as spa typing, are vital for the control and, when typing can be made more timely, prevention of S. aureus spread around healthcare settings. The current study aims to review the literature to report the most common clinical spa types around the world, which is important for epidemiological surveys and nosocomial infection control policies.

Methods: A search via PubMed, Google Scholar, Web of Science, Embase, the Cochrane library, and Scopus was conducted for original articles reporting the most prevalent spa types among S. aureus isolates. The search terms were “Staphylococcus aureus, spa typing.”

Results: The most prevalent spa types were t032, t008 and t002 in Europe; t037 and t002 in Asia; t008, t002, and t242 in America; t037, t084, and t064 in Africa; and t020 in Australia. In Europe, all the isolates related to spa type t032 were MRSA. In addition, spa type t037 in Africa and t037and t437 in Australia also consisted exclusively of MRSA isolates. Given the fact that more than 95% of the papers we studied originated in the past decade there was no option to study the dynamics of regional clone emergence.

Conclusion: This review documents the presence of the most prevalent spa types in countries, continents and worldwide and shows big local differences in clonal distribution.

Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools

The magnitude of interest in the epidemiology of transmissible human diseases is reflected in the vast number of tools and methods developed recently with the expressed purpose to characterize and track evolutionary changes that occur in agents of these diseases over time. Within the past decade a new suite of such tools has become available with the emergence of the so-called "omics" technologies. Among these, two are exponents of the ongoing genomic revolution. Firstly, high-density nucleic acid probe arrays have been proposed and developed using various chemical and physical approaches. Via hybridization-mediated detection of entire genes or genetic polymorphisms in such genes and intergenic regions these so called "DNA chips" have been successfully applied for distinguishing very closely related microbial species and strains. Second and even more phenomenal, next generation sequencing (NGS) has facilitated the assessment of the complete nucleotide sequence of entire microbial genomes. This technology currently provides the most detailed level of bacterial genotyping and hence allows for the resolution of microbial spread and short-term evolution in minute detail. We will here review the very recent history of these two technologies, sketch their usefulness in the elucidation of the spread and epidemiology of mostly hospital-acquired infections and discuss future developments.

Characterization of the virulence potential of Staphylococcus condimenti isolated from a patient with severe soft tissue infection

The coagulase-negative bacterium Staphylococcus condimenti and closely related species are commonly isolated from or found in starter cultures of fermented sausage as well as fish and soy sauces, and have traditionally been considered nonpathogenic. Recently, however, a case of catheter-related bacteraemia caused by S. condimenti was reported. In the present study we identified and characterized a strain of S. condimenti isolated from a patient with a severe soft tissue infection, comparing it to S. condimenti and S. carnosus type strains in order to elucidate the virulence potential of the clinical strain. Genome comparison showed high degree of conservation between the clinical strain and the type strain used in food industry, as well as with S. carnosus. The genome of the clinical S. condimenti strain contains few horizontally transferred regions and 37 putative virulence genes, including genes with similarity to leucocidin and genes involved in immune evasion, proinflammatory and cytolytic activity. However, it remains to be tested whether these putative virulence genes are expressed and functional. Although uncommon, S. condimenti may cause severe infection in previously healthy persons.

Evaluation of HiaureusTM Coagulase Confirmation Kit in Identification of Staphylococcus aureus

INTRODUCTION

Staphylococcus aureus is a facultative anaerobic Gram positive coccal bacterium whose incidence ranges to different infections. It is a cause of various uncomplicated skin infections, abscesses, septicaemia/bacteraemia, gastroenteritis, endocarditis, toxic shock syndrome and food intoxications. Various methods with varied time, sensitivities, specificities and costs are available, but may not be used as a reliable test for the identification and differentiation of S. aureus. Therefore, there is a need to evaluate newer tests.

AIM

To compare the conventional tests with a commercial available kit for reliable, cost effective identification and confirmation of S. aureus.

MATERIALS AND METHODS

The current prospective study was conducted in the Department of Clinical Pathology, Haffkine Institute for a period of six months. A total of 341 clinical isolates of staphylococci isolated from pus, urine, blood culture and sterile body fluids were subjected to conventional tests like Tube Coagulase Test (TCT) using Rabbit Plasma (RP) and Human Plasma (HP), culture media such as Mannitol Salt Agar (MSA) and Deoxyribonuclease (DNase) media in parallel to Hiaureus^TM Coagulase Confirmation Kit (HACCK), a commercially available kit for identification of S. aureus. Amplification of the femA gene was used as a comparative reference point test to calculate the sensitivity, specificity and concordance values of the conventional tests.

RESULTS

Amongst the coagulase based tests, HACCK was 100% sensitive and specific. The TCT using RP was 98.58% sensitive while TCT using HP was less sensitive (95.37%). A total of 100% specificity was observed for TCT using RP while TCT using HP was 96.68% specific. The MSA and DNase media were 97.86% vs 96.44% and 96.67% vs 91.67% sensitive and specific respectively. The combination tests had varying sensitivity and specificity ranges. The HACCK demonstrated 100% concordance with femA amplification and was labelled as an ideal perfect test (κ=1) with MSA as an alternative test for S. aureus identification.

CONCLUSION

The HACCK can be used as an exclusive, reliable and cost effective test for identification of S. aureus. Alternatively, in view of the cost factor MSA either as a single test or in combination with TCT using HP could be used as screening tests and confirm discordant results with HACCK.

Characterization of Methicillin-Resistant Staphylococcus aureus Isolated from Healthy Turkeys and Broilers Using DNA Microarrays

Methicillin-resistant Staphylococcus aureus (MRSA) is a major human health problem and recently, domestic animals are described as carriers and possible reservoirs. Twenty seven S. aureus isolates from five turkey farms (n = 18) and two broiler farms (n = 9) were obtained by culturing of choana and skin swabs from apparently healthy birds, identified by Taqman-based real-time duplex nuc-mecA-PCR and characterized by spa typing as well as by a DNA microarray based assay which covered, amongst others, a considerable number of antibiotic resistance genes, species controls, and virulence markers. The antimicrobial susceptibility profiles were tested by agar diffusion assays and genotypically confirmed by the microarray. Five different spa types (3 in turkeys and 2 in broilers) were detected. The majority of MRSA isolates (24/27) belonged to clonal complex 398-MRSA-V. The most frequently occurring spa types were accordingly t011, t034, and t899. A single CC5-MRSA-III isolated from turkey and CC398-MRSA with an unidentified/truncated SCCmec element in turkey and broiler were additionally detected. The phenotypic antimicrobial resistance profiles of S. aureus isolated from both turkeys and broilers against 14 different antimicrobials showed that all isolates were resistant to ampicillin, cefoxitin, oxacillin, doxycycline, and tetracycline. Moreover, all S. aureus isolated from broilers were resistant to erythromycin and azithromycin. All isolates were susceptible to gentamicin, chloramphenicol, sulphonamides, and fusidic acid. The resistance rate against ciprofloxacin was 55.6% in broiler isolates and 42.1% in turkey isolates. All tetracycline resistant isolates possessed genes tetK/M. All erythromycin-resistant broiler isolates carried ermA. Only one broiler isolate (11.1%) carried genes ermA, ermB, and ermC, while 55.6% of turkey isolates possessed ermA and ermB genes. Neither PVL genes (lukF/S-PV), animal-associated leukocidin (lukM and luk-P83) nor the gene encoding the toxic shock syndrome toxin (tst1) were found in turkey and broiler isolates. In conclusion, the detection of MRSA in healthy turkeys and broilers with even additional antibiotic resistance markers is of major public health concern. The difference in antibiotic resistance and virulence markers between MRSA isolates from turkeys and broilers was addressed.

Omics Approaches for the Study of Adaptive Immunity to Staphylococcus aureus and the Selection of Vaccine Candidates

Staphylococcus aureus is a dangerous pathogen both in hospitals and in the community. Due to the crisis of antibiotic resistance, there is an urgent need for new strategies to combat S. aureus infections, such as vaccination. Increasing our knowledge about the mechanisms of protection will be key for the successful prevention or treatment of S. aureus invasion. Omics technologies generate a comprehensive picture of the physiological and pathophysiological processes within cells, tissues, organs, organisms and even populations. This review provides an overview of the contribution of genomics, transcriptomics, proteomics, metabolomics and immunoproteomics to the current understanding of S. aureus‑host interaction, with a focus on the adaptive immune response to the microorganism. While antibody responses during colonization and infection have been analyzed in detail using immunoproteomics, the full potential of omics technologies has not been tapped yet in terms of T-cells. Omics technologies promise to speed up vaccine development by enabling reverse vaccinology approaches. In consequence, omics technologies are powerful tools for deepening our understanding of the “superbug” S. aureus and for improving its control.

Coagulase-negative staphylococci

The definition of the heterogeneous group of coagulase-negative staphylococci (CoNS) is still based on diagnostic procedures that fulfill the clinical need to differentiate between Staphylococcus aureus and those staphylococci classified historically as being less or nonpathogenic. Due to patient- and procedure-related changes, CoNS now represent one of the major nosocomial pathogens, with S. epidermidis and S. haemolyticus being the most significant species. They account substantially for foreign body-related infections and infections in preterm newborns. While S. saprophyticus has been associated with acute urethritis, S. lugdunensis has a unique status, in some aspects resembling S. aureus in causing infectious endocarditis. In addition to CoNS found as food-associated saprophytes, many other CoNS species colonize the skin and mucous membranes of humans and animals and are less frequently involved in clinically manifested infections. This blurred gradation in terms of pathogenicity is reflected by species- and strain-specific virulence factors and the development of different host-defending strategies. Clearly, CoNS possess fewer virulence properties than S. aureus, with a respectively different disease spectrum. In this regard, host susceptibility is much more important. Therapeutically, CoNS are challenging due to the large proportion of methicillin-resistant strains and increasing numbers of isolates with less susceptibility to glycopeptides.

Methicillin-resistant Staphylococcus aureus colonization: a three-year prospective study in a neonatal intensive care unit in Italy

BACKGROUND

Methicillin resistant Staphylococcus aureus (MRSA) is a major etiological agent of infection in neonatal intensive care units (NICUs). Routes of entry of this organism can be different and the transmission pathway complex. Colonized neonates are the main endogenous reservoir.

METHODS AND RESULTS

We conducted a prospective three-year study on MRSA colonization recruiting 722 neonates admitted between 2009 and 2012. Nasal swabs were cultured weekly and MRSA isolates were submitted to molecular typing. The annual incidence density of acquisition of MRSA ranged from a maximum of 20.2 cases for 1000 patient-days during the first year to a minimum of 8.8 cases in the second one to raise again up to 13.1 cases during the third year. The mean weekly colonization pressure fluctuated from 19.1% in the first year to 13.4% in the second year and 16.8% in the third year. It significantly correlated with the number of MRSA acquisitions in the following week. Overall, 187 (25.9%) subjects tested positive for MRSA. A non multiresistant, tst positive, ST22-MRSA-IVa spa t223 strain proved to be endemic in the NICU, being identified in 166 (88.8%) out of 187 colonized neonates. Sporadic or epidemic occurrence of other strains was detected.

CONCLUSIONS

An MRSA strain belonging to the tst1 positive, UK-EMRSA-15/ "Middle Eastern Variant" appeared to be endemic in the NICU under investigation. During the three-year period, substantial changes occurred in case-mix of patients moving towards a higher susceptibility to MRSA colonization. The infection control procedures were able to decrease the colonization rate from more than 40% to approximately 10%, except for an outbreak due to a CA-MRSA strain, ST1-MRSA-IVa, and a transient increase in the colonization prevalence rate coincident with a period of substantial overcrowding of the ward. Active surveillance and molecular typing contributed to obtain a reliable picture of the MRSA dissemination in NICU.

Characterization of the staphylococcal cassette chromosome composite island of Staphylococcus haemolyticus SH32, a methicillin-resistant clinical isolate from China

Staphylococcal cassette chromosome (SCC) elements contribute considerably to virulence and resistance to antibiotic agents in staphylococci. SCC elements in coagulase-negative staphylococci (CoNS) are highly diverse and there is evidence suggesting that they serve as a reservoir for antibiotic resistance genes in methicillin-resistant Staphylococcus aureus (MRSA). However, only a small number of SCC elements have been characterized in CoNS and their exact roles in the emergence and evolution of MRSA remain to be demonstrated. Here, we determined the structure of an SCC composite island (CI_SH32) found in the clinical Staphylococcus haemolyticus isolate SH32 by whole-genome DNA sequencing. CI_SH32 was 48 kb in length and mainly composed of two imperfect SCC elements, namely (i) a ΨSCCmec(SH32) part containing a class C1 mec gene complex but lacking ccr genes and (ii) a SCC_SH32 part with a ccrA5B3 gene complex but lacking mec genes. In addition, CI_SH32 contained a type III restriction-modification system and several resistance loci, for example genes conferring resistance to cadmium and arsenic. ΨSCCmec(SH32) is almost entirely identical to a pseudo SCCmec element found in S. haemolyticus WCH1 and shares pronounced sequence similarity to a ΨSCCmec element of S. haemolyticus JCSC1435. However, staphylococci other than S. haemolyticus, including S. aureus and S. epidermidis, contain homologs of SCC_SH32 that are more similar to SCC_SH32 than those elements found in S. haemolyticus, suggesting that CI_SH32 of S. haemolyticus SH32 was assembled in recent evolutionary events. Moreover, the composite structure of CI_SH32 indicates that the detection of class C1 mec and ccrA5B3 gene complexes in S. haemolyticus does not always indicate the existence of a UT9-type SCCmec element, which has remained questionable.

Extensive genetic diversity identified among sporadic methicillin-resistant Staphylococcus aureus isolates recovered in Irish hospitals between 2000 and 2012

Clonal replacement of predominant nosocomial methicillin-resistant Staphylococcus aureus (MRSA) strains has occurred several times in Ireland during the last 4 decades. However, little is known about sporadically occurring MRSA in Irish hospitals or in other countries. Eighty-eight representative pvl-negative sporadic MRSA isolates recovered in Irish hospitals between 2000 and 2012 were investigated. These yielded unusual pulsed-field gel electrophoresis and antibiogram-resistogram typing patterns distinct from those of the predominant nosocomial MRSA clone, ST22-MRSA-IV, during the study period. Isolates were characterized by spa typing and DNA microarray profiling for multilocus sequence type (MLST) clonal complex (CC) and/or sequence type (ST) and SCCmec type assignment, as well as for detection of virulence and antimicrobial resistance genes. Conventional PCR-based SCCmec subtyping was undertaken when necessary. Extensive diversity was detected, including 38 spa types, 13 MLST-CCs (including 18 STs among 62 isolates assigned to STs), and 25 SCCmec types (including 2 possible novel SCCmec elements and 7 possible novel SCCmec subtypes). Fifty-four MLST-spa-SCCmec type combinations were identified. Overall, 68.5% of isolates were assigned to nosocomial lineages, with ST8-t190-MRSA-IID/IIE±SCCM1 predominating (17.4%), followed by CC779/ST779-t878-MRSA-ψSCCmec-SCC-SCCCRISPR (7.6%) and CC22/ST22-t032-MRSA-IVh (5.4%). Community-associated clones, including CC1-t127/t386/t2279-MRSA-IV, CC59-t216-MRSA-V, CC8-t008-MRSA-IVa, and CC5-t002/t242-MRSA-IV/V, and putative animal-associated clones, including CC130-t12399-MRSA-XI, ST8-t064-MRSA-IVa, ST398-t011-MRSA-IVa, and CC6-t701-MRSA-V, were also identified. In total, 53.3% and 47.8% of isolates harbored genes for resistance to two or more classes of antimicrobial agents and two or more mobile genetic element-encoded virulence-associated factors, respectively. Effective ongoing surveillance of sporadic nosocomial MRSA is warranted for early detection of emerging clones and reservoirs of virulence, resistance, and SCCmec genes.

Panton-Valentine leukocidin-positive Staphylococcus aureus in Ireland from 2002 to 2011: 21 clones, frequent importation of clones, temporal shifts of predominant methicillin-resistant S. aureus clones, and increasing multiresistance

There has been a worldwide increase in community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) infections. CA-MRSA isolates commonly produce the Panton-Valentine leukocidin toxin encoded by the pvl genes lukF-PV and lukS-PV. This study investigated the clinical and molecular epidemiologies of pvl-positive MRSA and methicillin-susceptible S. aureus (MSSA) isolates identified by the Irish National MRSA Reference Laboratory (NMRSARL) between 2002 and 2011. All pvl-positive MRSA (n=190) and MSSA (n=39) isolates underwent antibiogram-resistogram typing, spa typing, and DNA microarray profiling for multilocus sequence type, clonal complex (CC) and/or sequence type (ST), staphylococcal cassette chromosome mec type assignment, and virulence and resistance gene detection. Where available, patient demographics and clinical data were analyzed. The prevalence of pvl-positive MRSA increased from 0.2% to 8.8%, and that of pvl-positive MSSA decreased from 20% to 2.5% during the study period. The pvl-positive MRSA and MSSA isolates belonged to 16 and 5 genotypes, respectively, with CC/ST8-MRSA-IV, CC/ST30-MRSA-IV, CC/ST80-MRSA-IV, CC1/ST772-MRSA-V, CC30-MSSA, CC22-MSSA, and CC121-MSSA predominating. Temporal shifts in the predominant pvl-positive MRSA genotypes and a 6-fold increase in multiresistant pvl-positive MRSA genotypes occurred during the study period. An analysis of patient data indicated that pvl-positive S. aureus strains, especially MRSA strains, had been imported into Ireland several times. Two hospital and six family clusters of pvl-positive MRSA were identified, and 70% of the patient isolates for which information was available were from patients in the community. This study highlights the increased burden and changing molecular epidemiology of pvl-positive S. aureus in Ireland over the last decade and the contribution of international travel to the influx of genetically diverse pvl-positive S. aureus isolates into Ireland.

Prevalence and genetic diversity of arginine catabolic mobile element (ACME) in clinical isolates of coagulase-negative staphylococci: identification of ACME type I variants in Staphylococcus epidermidis

Arginine catabolic mobile element (ACME), a genomic island consisting of the arc and/or opp3 gene clusters found in staphylococcal species, is related to increased bacterial adaptability to hosts. Staphylococcus epidermidis is considered a major ACME reservoir; however, prevalence and genetic diversity of ACME in coagulase-negative staphylococci (CNS) have not yet been well characterized for clinical isolates in Japan. A total of 271 clinical isolates of CNS in a Japanese hospital were investigated for the presence and genotype of ACME and SCCmec. The prevalence of ACME-arcA was significantly higher (p<0.001) in S. epidermidis (45.8%) than in other CNS species (3.7%). ACME in S. epidermidis isolates (n=87) were differentiated into type I (n=33), variant forms of type I (ΔI, n=26) newly identified in this study, type II (n=6), and type ΔII (n=19). ACME-type ΔI, which were further classified into three subtypes, lacked some genetic components between the arc and opp3 clusters in archetypal type I, whereas the arc and opp3 clusters were intact. The arc cluster exhibited high sequence identity (95.8-100%) to that of type I ACME; in contrast, the opp3 cluster was highly diverse, and showed relatively lower identities (94.8-98.7%) to the identical regions in type I ACME. Twenty-one isolates of ΔI ACME-carrying S. epidermidis possessed SCCmec IVa and belonged to ST5 (clonal complex 2). Phylogenetic analysis revealed that isolates harboring ACME ΔI in this study clustered with previously reported S. epidermidis strains with other lineges, suggesting that S. epidermidis originally had some genetic variations in the opp3 cluster. In summary, ACME type ΔI, a truncated variant of ACME-I, was first identified in S. epidermidis, and revealed to be prevalent in ST5 MRSE clinical isolates with SCCmec IVa.

Staphylococcus aureus toxins--their functions and genetics

The outcome of encounters between Staphylococcus (S.) aureus and its human host ranges from life-threatening infection through allergic reactions to symptom-free colonization. The pan-genome of this bacterial species encodes numerous toxins, known or strongly suspected to cause specific diseases or symptoms. Three toxin families are in the focus of this review, namely (i) pore-forming toxins, (ii) exfoliative toxins and (iii) superantigens. The majority of toxin-encoding genes are located on mobile genetic elements (MGEs), resulting in a pronounced heterogeneity in the endowment with toxin genes of individual S. aureus strains. Recent population genomic analysis have provided a framework for an improved understanding of the temporal and spatial scales of the motility of MGEs and their associated toxin genes. The distribution of toxin genes among clonal lineages within the species S. aureus is not random, and phylogenetic (sub-)lineages within clonal complexes feature characteristic toxin signatures. When studying pathogenesis, this lineage association, which is caused by the clonal nature of S. aureus makes it difficult to discriminate effects of specific toxins from contributions of the genetic background and/or other associated genetic factors.