The emerging ST8 methicillin-resistant Staphylococcus aureus clone in the community in Japan: associated infections, genetic diversity, and comparative genomics

Comparison of the effectiveness of core genome multilocus sequence typing and polymerase chain reaction-based open reading frame typing in tracing nosocomial methicillin-resistant Staphylococcus aureus transmission

INTRODUCTION

A clonal shift from staphylococcal cassette chromosome mec (SCCmec) type II/ST5 methicillin-resistant Staphylococcus aureus (MRSA) to SCCmec type IV/clonal complex (CC)1 MRSA has occurred rapidly in Japan. Our previous research in a geriatric hospital found SCCmec type IV/CC1 MRSA prevalence in long-term care wards. Due to intensive personal care requirements, frequent contact with healthcare providers can potentially cause unintentional nosocomial MRSA transmission. We performed polymerase chain reaction-based open reading frame typing (POT) and core genome multilocus sequence typing (cgMLST) to investigate the occurrence of nosocomial transmission and to compare the results of these methods.

METHODS

POT and whole genome sequencing were performed in 83 MRSA isolates. Commercial automated software (Ridom SeqSphere+) was used to perform cgMLST. MRSA isolates with 0-8 allelic differences were considered related, and medical records were consulted in these cases.

RESULTS

SCCmec type IV/CC1 MRSA was the most frequently detected clone (n = 56, 67.5 %), which was divided into 14 POT types, followed by SCCmec type I/ST8 (n = 9) and SCCmec type IV/ST8 (n = 8). Identical POT types were found across 7 of 11 wards. However, cgMLST analysis identified only three cases (six strains) of high genetic similarity, indicating nosocomial transmission; only one involved SCCmec type IV/CC1 (two strains). The mean allelic difference in the core genomes between strains with identical POT types in the same ward was 55.3 ± 22.0.

CONCLUSIONS

The cgMLST method proved more effective for identifying nosocomial transmissions compared to POT, highlighting its utility in tracking MRSA spread in healthcare settings.

Unilateral lymphadenitis caused by community-associated methicillin-resistant Staphylococcus aureus ST834 strain

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a global concern, primarily as a cause of skin and soft tissue infections, particularly in young people. Here, we describe a case of unilateral multiple lymphadenitis caused by the CA-MRSA sequence type (ST) 834 strain. A previously healthy 15-year-old girl was referred to our hospital with fever and swollen lymph nodes in the right axillary, cubital, and groin regions. Imaging examinations revealed enlargement of the lymph nodes in these areas but no swelling in any other lymph nodes. The patient had self-destructive lymph nodes in her groin. MRSA was detected in all swollen lymph node samples. Antimicrobial susceptibility tests showed that MRSA was susceptible to clindamycin and levofloxacin, leading to the suspicion of CA-MRSA. Genetic analysis revealed that all strains were ST834 and carried the staphylococcal cassette chromosome mec IV and the toxic shock syndrome toxin-1 gene but not the Panton-Valentine leukocidin gene. The patient was treated with linezolid followed by oral clindamycin. This was a rare case of unilateral multiple lymphadenitis caused by ST834 CA-MRSA. Although ST834 strains are rarely reported, lymphadenitis has been frequently reported and is considered more likely to cause lymphadenitis than other CA-MRSA strains.

Genomic characterization of Staphylococcus aureus isolated from patients admitted to intensive care units of a tertiary care hospital: epidemiological risk of nasal carriage of virulent clone during admission

We conducted a molecular epidemiological study of Staphylococcus aureus using whole-genome sequence data and clinical data of isolates from nasal swabs of patients admitted to the intensive care unit (ICU) of Hiroshima University hospital. The relationship between isolate genotypes and virulence factors, particularly for isolates that caused infectious diseases during ICU admission was compared with those that did not. The nasal carriage rates of methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) in patients admitted to the ICU were 7.0% and 20.1%, respectively. The carriage rate of community-acquired (CA)-MRSA was 2.3%, accounting for 32.8% of all MRSA isolates. Whole-genome sequencing analysis of the MRSA isolates indicated that most, including CA-MRSA and healthcare-associated (HA)-MRSA, belonged to clonal complex (CC) 8 [sequence type (ST) 8] and SCCmec type IV. Furthermore, results for three disease foci (pneumonia, skin and soft tissue infection, and deep abscess) and the assessment of virulence factor genes associated with disease conditions [bacteremia, acute respiratory distress syndrome (ARDS), disseminated intravascular coagulopathy (DIC), and septic shock] suggested that nasal colonization of S. aureus clones could represent a risk for patients within the ICU. Particularly, MRSA/J and MSSA/J may be more likely to cause deep abscess infection; ST764 may cause ventilation-associated pneumonia, hospital-acquired pneumonia and subsequent bacteremia, and ARDS, and tst-1-positive isolates may cause DIC onset.IMPORTANCENasal colonization of MRSA in patients admitted to the intensive care unit (ICU) may predict the development of MRSA infections. However, no bacteriological data are available to perform risk assessments for Staphylococcus aureus infection onset. In this single-center 2-year genomic surveillance study, we analyzed all S. aureus isolates from nasal swabs of patients admitted to the ICU and those from the blood or lesions of in-patients who developed infectious diseases in the ICU. Furthermore, we identified the virulent clones responsible for causing infectious diseases in the ICU. Herein, we report several virulent clones present in the nares that are predictive of invasive infections. This information may facilitate the design of preemptive strategies to identify and eradicate virulent MRSA strains, reducing nosocomial infections within the ICU.

Prevalence and Genetic Characterization of Methicillin-Resistant Staphylococcus aureus Isolated from Pigs in Japan

We investigated the prevalence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in pig slaughterhouses from 2018 to 2022 in Japan and the isolates were examined for antimicrobial susceptibility and genetic characteristics by whole-genome analysis. Although the positive LA-MRSA rates on farms (29.6%) and samples (9.9%) in 2022 in Japan remained lower than those observed in European countries exhibiting extremely high rates of confirmed human LA-MRSA infections, these rates showed a gradually increasing trend over five years. The ST398/t034 strain was predominant, followed by ST5/t002, and differences were identified between ST398 and ST5 in terms of antimicrobial susceptibility and the resistance genes carried. Notably, LA-MRSA possessed resistance genes toward many antimicrobial classes, with 91.4% of the ST398 strains harboring zinc resistance genes. These findings indicate that the co-selection pressure associated with multidrug and zinc resistance may have contributed markedly to LA-MRSA persistence. SNP analysis revealed that ST398 and ST5 of swine origin were classified into a different cluster of MRSA from humans, showing the same ST in Japan and lacking the immune evasion genes (scn, sak, or chp). Although swine-origin LA-MRSA is currently unlikely to spread to humans and become a problem in current clinical practice, preventing its dissemination requires using antimicrobials prudently, limiting zinc utilization to the minimum required nutrient, and practicing fundamental hygiene measures.

The clinical characteristics and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) among very elderly people in Japan

AIM

Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial infection-causing pathogen. The clonal shift from staphylococcal cassette chromosome mec (SCCmec) type II MRSA to SCCmec type IV MRSA has occurred rapidly in acute-care hospitals. However, the epidemiology and clinical impacts of MRSA in geriatric hospitals are poorly documented. We performed a molecular epidemiological analysis of the clinical isolates and retrospectively investigated the clinical characteristics of SCCmec type IV MRSA in elderly individuals.

METHODS

MRSA isolates were grouped according to the SCCmec type and virulence genes (tst, sea, seb, sec, and lukS/F-PV), and multi-locus sequence typing (MLST) was performed.

RESULTS

Of the 145 MRSA isolates obtained from patients with a median age of 85 years, 100 (69.0%) were obtained from sputum samples, 22 (15.2%) from skin and soft tissues, and seven (4.8%) from blood samples. The most prevalent clone was SCCmec type IV/clonal complex (CC)1/sea+ (59.3%), followed by SCCmec type I/sequence type (ST) 8 (17.3%). Of the 17 (11.7%) strains to which an anti-MRSA drug was administered by a physician, only three were SCCmec type IV/CC1/sea+ (17.6%) and five were SCCmec type I/ST8 (29.4%). SCCmec type IV/CC1/sea+ MRSA was more frequently isolated in long-term care wards than were SCCmec type I/ST8 strains (odds ratio: 2.85, 95% confidence interval: 1.08-7.54) and was less frequently treated as the cause of MRSA infections (odds ratio: 0.15, 95% confidence interval: 0.03-0.73).

CONCLUSIONS

SCCmec type IV/CC1/sea+ MRSA was the predominant clone and could be easily transmissible and be capable of colonization. Geriatr Gerontol Int 2023; 23: 744-749.

Whole-genome sequencing analysis of molecular epidemiology and silent transmissions causing meticillin-resistant Staphylococcus aureus bloodstream infections in a university hospital

BACKGROUND

The emergence of novel genomic-type clones, such as community-associated meticillin-resistant Staphylococcus aureus (MRSA) and livestock-associated MRSA, and their invasion into hospitals have become major concerns worldwide; however, little information is available regarding the prevalence of MRSA in Japan. Whole-genome sequencing (WGS) has been conducted to analyse various pathogens worldwide. Therefore, it is important to establish a genome database of clinical MRSA isolates available in Japan.

AIM

A molecular epidemiological analysis of MRSA strains isolated from bloodstream-infected patients in a Japanese university hospital was conducted using WGS and single-nucleotide polymorphism (SNP) analysis. Additionally, through a review of patients' clinical characteristics, the effectiveness of SNP analysis as a tool for detecting silent nosocomial transmission that may be missed by other methods was evaluated in diverse settings and various time points of detection.

METHODS

Polymerase-chain-reaction-based staphylococcal cassette chromosome mec (SCCmec) typing was performed using 135 isolates obtained between 2014 and 2018, and WGS was performed using 88 isolates obtained between 2015 and 2017.

FINDINGS

SCCmec type II strains, prevalent in 2014, became rare in 2018, whereas the prevalence of SCCmec type IV strains increased from 18.75% to 83.87% of the population, and became the dominant clones. Clonal complex (CC) 5 CC8 and CC1 were detected between 2015 and 2017, with CC1 being dominant. In 88 cases, SNP analyses revealed nosocomial transmissions among 20 patients which involved highly homologous strains.

CONCLUSIONS

Routine monitoring of MRSA by whole-genome analysis is effective not only for gaining knowledge regarding molecular epidemiology, but also for detecting silent nosocomial transmission.

Relationship between mortality and molecular epidemiology of methicillin-resistant Staphylococcus aureus bacteremia

Staphylococcus aureus is the primary cause of bacteremia, and methicillin-resistant S. aureus bacteremia is associated with a high mortality rate. Methicillin-resistant S. aureus clones are widespread worldwide, and molecular epidemiological studies are important. Therefore, this study aimed to determine the characteristics of patients who died due to methicillin-resistant S. aureus bacteremia and microbiological characteristics of methicillin-resistant S. aureus strains in a tertiary teaching hospital. This single-center, retrospective study included patients with methicillin-resistant S. aureus isolated from blood bacterial culture performed at Kyoto Prefectural University of Medicine Hospital, from October 2016 to May 2019. The data analyzed included patient background, clinical strain characteristics, and molecular epidemiology. Of 41 patients with methicillin-resistant S. aureus bacteremia (median age, 60 [28–70] years; 24 (59%) were men), and 7 (17%) died due to methicillin-resistant S. aureus bacteremia. The median age of those who died in the methicillin-resistant S. aureus bacteremia group was predominantly higher than that of those in the alive group (p = 0.03). The most common cause of methicillin-resistant S. aureus bacteremia was endovascular devices, which occurred in 20 (49%), 18 (53%), and 2 (29%) patients in the total, alive, and died groups, respectively. Bacteriological characteristics showed that type IV Staphylococcal Cassette Chromosome mec genotype was most frequently detected in the total (n = 34 [83%]), alive (n = 29 [85%]), and died (n = 5 [71%]) groups. In the molecular cluster analysis, CC8, ST8, staphylococcal Cassette Chromosome mec type IV, and community-acquired-methicillin-resistant S. aureus formed the largest groups. The diversity of methicillin-resistant S. aureus clones is evident, and it is possible that clones with new virulence factors may still emerge. In the future, it will be crucial to monitor the epidemiological trends of methicillin-resistant S. aureus to respond quickly to changes in pathogenic and clonal factors, to clarify the gene expression network by identifying old and new virulence factors.

Changes in the Genotypic Characteristics of Community-Acquired Methicillin-Resistant Staphylococcus aureus Collected in 244 Medical Facilities in Japan between 2010 and 2018: a Nationwide Surveillance

Although community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged worldwide, no nationwide CA-MRSA surveillance has been conducted in Japan to determine the changes in its molecular characteristics over time. We aimed to characterize the molecular epidemiology of Panton-Valentine leucocidin (PVL)-positive CA-MRSA strains collected from across Japan in the past decade. We isolated 1,770 MRSA strains from the skin and pus samples of outpatients of 244 medical facilities in 31 prefectures between 2010 and 2018 (2010, 2012, 2014, 2016, and 2018). Regions, hospitals, and periods in which strains were isolated and patient age group and sex were tabulated. Staphylococcal cassette chromosome mec (SCCmec) typing, detection of virulence factor genes, and antimicrobial susceptibility testing were performed. Whole-genome analysis was performed for the PVL-positive strains isolated in 2018. All strains harbored the mecA gene. Compared to that in 2010, the percentage of SCCmec type IV increased in 2018, with a corresponding increase in the proportion of PVL-positive strains (10% to 26%). Of the isolates obtained in 2018, clonal complex 8 (CC8) was dominant among PVL-positive strains. Core-genome single-nucleotide polymorphism analysis, using whole-genome sequencing, suggested that the CC8 PVL-positive strains spread throughout Japan over the last decade. Furthermore, a unique ST22 clone carrying both the PVL- and toxic shock syndrome toxin-1-encoding genes has emerged. We demonstrated that the molecular epidemiology of CA-MRSA in Japan differs from that in Europe and the United States; thus, it is crucial to monitor the trend of changes in CA-MRSA characteristics in Japan.

IMPORTANCE Community-associated MRSA, which is a multidrug-resistant organism and can cause infections in otherwise-healthy individuals, has become a global problem. This paper describes a nationwide surveillance conducted in Japan to investigate changes in molecular epidemiological characteristics of CA-MRSA over the past decade and provides a detailed review of the characteristics of Panton-Valentine leucocidin (PVL)-positive strains isolated in 2018. Although CA-MRSA is rare in Japan to date, we found that the isolation of PVL-positive strains has been increasing over the past decade. In particular, the PVL-positive strains wherein CC8 was dominant exhibited high interstrain similarity, suggesting that a limited number of clones have spread over the past decade. Furthermore, a unique ST22 clone carrying both PVL-encoding and toxic shock syndrome toxin-1-encoding genes has emerged. This study shows that various changes can be observed when molecular epidemiological analysis, combined with next-generation sequencing, is conducted over a long period.

Characterization of Methicillin-Resistant Staphylococcus aureus Isolates from Periprosthetic Joint Infections

Periprosthetic joint infection (PJI) is a troublesome clinical issue in total joint arthroplasty (TJA). Although methicillin-resistant Staphylococcus aureus (MRSA) is considered to be the most serious pathogen in PJIs, little is known about the genotypic and phenotypic characteristics of MRSA clones isolated from PJI patients. A total of 36 MRSA isolates from PJI patients were collected at the Chang-Gung Memorial Hospital in Taiwan from May 2016 to October 2019. All MRSA isolates were subjected to genome typing. The prevalence of Panton–Valentine leucocidin (PVL), the antibiotic susceptibility profile, and the biofilm formation ability were compared among different MRSA genogroups. Additionally, demographics and clinical manifestations of patients infected with different MRSA genogroups were investigated. Eight sequence types (STs) were identified among 36 isolated from PJIs. According to the incidence of MRSA genotypes in PJIs, in this study, we divided them into four groups, including ST8 (n = 10), ST59 (n = 8), ST239 (n = 11), and other STs (n = 7). For the antibiotic susceptibility testing, we found that all MRSA isolates in the ST239 group were highly resistant to ciprofloxacin, gentamicin trimethoprim-sulfamethoxazole, and levofloxacin. Additionally, ST239 MRSA also had a higher ability to form biofilm than other groups. Importantly, patients with ST239 infection typically had a fever and exhibited higher levels of inflammatory markers, including C-reactive protein (CRP) and white blood cell count (WBC). Epidemiological investigations revealed that knee PJIs were mainly attributed to infection with ST59 MRSA and increasing trends for infection with ST8 and other ST types of MRSAs in PJI patients were observed from 2016 to 2019. The identification of MRSA genotypes in PJIs may be helpful for the management of PJIs.

Pneumonia Caused by Community-Acquired Methicillin-Resistant Staphylococcus aureus Positive for Exfoliative Toxin A and Secondary to Allergic Bronchopulmonary Aspergillosis

Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) causes severe pneumonia. Previous reports found that CA-MRSA producing the Panton-Valentine leukocidin (PVL) or toxic shock syndrome toxin-1 (TSST-1) triggered severe necrotizing pneumonia. However, other toxins and genetic factors responsible for CA-MRSA pneumonia are rarely analyzed in Japan. In this study, we performed whole-genome sequencing (WGS) to analyze the clinical features of CA-MRSA genetically. As a result, we identified a strain with a rare sequence-type of MRSA. Herein, we present a case of CA-MRSA pneumonia in a 64-year-old woman. Her condition improved rapidly with vancomycin therapy. Draft WGS led to identifying the genotype and virulence factors and showed that the strain was a rare sequence-type of MRSA with the following characteristics: staphylococcal cassette chromosome mec (SCCmec) type IV, sequence type 121, exfoliative toxin A-positive, and specific staphylococcal protein A type t5110. To the best of our knowledge, a strain with this profile has not been previously reported. Our findings provide new insights into CA-MRSA pneumonia and its genetic and clinical features. Therefore, we recommend accumulating genetic profiles of CA-MRSA pneumonia to identify genetic features and the clinical characteristics of the patients.

Current Status of Staphylococcal Cassette Chromosome mec (SCCmec)

Staphylococcal cassette chromosome mec (SCCmec) typing was established in the 2000s and has been employed as a tool for the molecular epidemiology of methicillin-resistant Staphylococcus aureus, as well as the evolution investigation of Staphylococcus species. Molecular cloning and the conventional sequencing of SCCmec have been adopted to verify the presence and structure of a novel SCCmec type, while convenient PCR-based SCCmec identification methods have been used in practical settings for many years. In addition, whole-genome sequencing has been widely used, and various SCCmec and similar structures have been recently identified in various species. The current status of the SCCmec types, SCCmec subtypes, rules for nomenclature, and multiple methods for identifying SCCmec types and subtypes were summarized in this review, according to the perspective of the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements.

Antimicrobial Resistance and Molecular Epidemiological Characteristics of Methicillin-Resistant and Susceptible Staphylococcal Isolates from Oral Cavity of Dental Patients and Staff in Northern Japan

The acquisition of drug resistance and virulence by staphylococcal species colonizing humans is a growing public health concern. The present study was conducted to investigate the prevalence, antimicrobial resistance and genetic characteristics of Staphylococcus isolates from the oral cavity and skin (hand) of systemically healthy subjects with dental disease and dental staff in northern Japan. Among a total of 133 subjects (91 patients and 42 staff), 87 coagulase-positive Staphylococcus (83 S. aureus/4 S. argenteus) and 162 coagulase-negative Staphylococcus (CoNS) isolates were recovered from 59 (44.4%) and 95 (71.4%) subjects, respectively. Three oral isolates were methicillin-resistant S. aureus (MRSA) (3.6%, 3/83) that were genotyped as ST8-SCCmec-IVl, ST4775(CC1)-SCCmec-IVa and ST6562(CC8)-SCCmec-IVa. Remarkably, the ST6562 isolate harbored PVL genes on ΦSa2usa and type I ACME (arginine catabolic mobile element). Four methicillin-susceptible isolates were identified as S. argenteus belonging to ST1223 and ST2250, which harbored enterotoxin genes egc-2 and sey, respectively. Among the fourteen CoNS species identified, methicillin-resistant (MR) isolates were detected in five species (11 isolates, 13.3% of CoNS), with S. saprophyticus and S. haemolyticus being the most common. ACME was prevalent in only S. epidermidis and S. capitis. These findings indicated the potential distribution of USA300 clone-like MRSA, toxigenic S. argenteus and MR-CoNS in the oral cavity of dental patients.

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.

Unique surface structures of community-associated methicillin-resistant Staphylococcus aureus ST8/SCCmecIVl

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) threatens human health. A local CA-MRSA with ST8/SCCmecIVl (CA-MRSA/J) has emerged in Japan, being associated with progression from bullous impetigo to potentially fatal invasive infection. We found that CA-MRSA/J has unique bacterial surface structures, spikes, spikes with a cap, and long spikes, reflecting clinical origins.

Current status of Panton-Valentine leukocidin-positive methicillin-resistant Staphylococcus aureus isolated from patients with skin and soft tissue infections in Japan

The USA300 clone, which produces Panton-Valentine leukocidin (PVL), is a major pathogenic community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) clone that causes intractable skin infections. Recently, PVL-positive CA-MRSA, including USA300 clones, have emerged in both communities and hospitals in Japan. To prevent an outbreak of PVL-positive MRSA, infected patients should be treated with effective antimicrobial agents at community clinics. Herein, we investigate molecular epidemiological characteristics of PVL-positive MRSA isolated from outpatients with skin and soft tissue infections (SSTI), which are common community-onset infectious diseases. The detection rate of MRSA was 24.9% (362 strains) out of 1455 S. aureus strains isolated between 2013 and 2017. Among the MRSA strains, 15.5% (56 strains) were PVL-positive strains and associated with deep-seated skin infections. Molecular epidemiological analyses of PVL-positive MRSA showed that USA300 was the predominant clone (53.6%, 30 strains) and was identified in Kanto (18 strains), Kagawa (nine strains), Tohoku (two strains) and Hokkaido (one strain). Notably, minocycline and fusidic acid were effective against all PVL-positive MRSA strains. Hence, our data reveals the current status of PVL-positive MRSA isolated from patients with SSTI in Japan. Continuous surveillance of CA-MRSA is necessary to monitor latest prevalence rates and identify effective antimicrobial agents for PVL-positive MRSA strains.

Monomicrobial Fournier's Gangrene Caused by Panton-Valentine Leukocidin-negative Methicillin-susceptible Staphylococcus aureus ST8 in Japan

Methicillin-resistant Staphylococcus aureus USA300, belonging to sequence type (ST) 8, is a rare cause of necrotizing fasciitis in the USA. We herein report a case of monomicrobial Fournier's gangrene caused by an ST8, methicillin-susceptible Staphylococcus aureus (designated ksw1). Whole-genome sequencing and analyses for virulence determinants revealed that, unlike USA300, ksw1 lacked virulence genes, such as Panton-Valentine leukocidin and SCCmec, while harboring the toxic shock syndrome toxin-1 gene. These genomic features correlate with ST8 CA-MRSA/J, which is the major genotype of ST8 in Japan.

Methicillin-Resistant Staphylococcus Aureus in Community Settings: Spread of Drug Resistance and Uncontrollable Infections

Methicillin-resistant Staphylococcus aureus (MRSA) is a major multidrug-resistant bacterial pathogen. The evolution of MRSA is dynamic posing an ongoing threat to humans. The evolution of MRSA includes horizontal gene transfer, which is mediated by mobile genetic elements, plasmids, and bacteriophages, and also mutations. In this review, we clarify the recent trends in MRSA from the perspectives of drug-resistance transfer and uncontrollable infections, particularly those occurring in community settings. We first address the role of MRSA as a disseminator of multidrug resistance. We have studied the cell-to-cell transfer of drug resistance, in which transfer frequencies range from 10-3 to 10-8. The mechanisms of drug-resistance transfers include the self-transmission of large plasmids, the mobilization of small nonconjugative plasmids, the generalized transduction of phages, and the transfer of transposons with circular intermediates. We then discuss uncontrollable infections. Although several anti-MRSA agents have been developed, uncontrollable cases of MRSA infections are still reported. Examples include a case of uncontrollable sepsis arising from a community-associated MRSA (CA-MRSA) with the ST8/SCCmecIVl genotype, and a relapsing severe invasive infection of ST30/SCCmecIVc CA-MRSA in a student athlete. Some of these cases may be attributable to unique adhesins, superantigens, or cytolytic activities. The delayed diagnosis of highly adhesive and toxic infections in community settings may result in CA-MRSA diseases that are difficult to treat. Repeated relapse, persistent bacteremia, and infections of small-colony variants may occur. To treat MRSA infections in community settings, these unique features of MRSA must be considered to ensure that diagnostic delay is avoided.

Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm

Food waste diversion and composting, either mandated or voluntary, are growing alternatives to traditional waste disposal. An acceptable source of agricultural feed and composting material, methane-emitting food residuals, including post-consumer food scraps, are diverted from landfills allowing recapture of nutrients that would otherwise be lost. However, risk associated with the transfer of antimicrobial resistant bacteria (ARB), antibiotic resistance genes (ARGs), or pathogens from food waste is not well characterized. Using shotgun metagenomic sequencing, ARGs, microbial content, and associated virulence factors were successfully identified across samples from an integrated poultry farm that feeds post-consumer food waste. A total of 495 distinct bacterial species or sub-species, 50 ARGs, and 54 virulence gene sequences were found. ARG sequences related to aminoglycoside, tetracycline, and macrolide resistance were most prominent, while most virulence gene sequences were related to transposon or integron activity. Microbiome content was distinct between on-farm samples and off-farm food waste collection sites, with a reduction in pathogens throughout the composting process. While most samples contained some level of resistance, only 3 resistance gene sequences occurred in both on- and off-farm samples and no multidrug resistance (MDR) gene sequences persisted once on the farm. The risk of incorporating novel or multi-drug resistance from human sources appears to be minimal and the practice of utilizing post-consumer food scraps as feed for poultry and composting material may not present a significant risk for human or animal health. Pearson correlation and co-inertia analysis identified a significant interaction between resistance and virulence genes (P = 0.05, RV = 0.67), indicating that ability to undergo gene transfer may be a better marker for ARG risk than presence of specific bacterial species. This work expands the knowledge of ARG fate during food scrap animal feeding and composting and provides a methodology for reproducible analysis.

Association between cell growth and vancomycin resistance in clinical community-associated methicillin-resistant Staphylococcus aureus

OBJECTIVES

We investigated the association between the rate of cell growth and vancomycin (VAN) resistance by comparing the genomic and phenotypic characteristics of different sized colonies isolated from a single origin.

METHODS

Vancomycin-intermediate Staphylococcus aureus (VISA) strain TMUS2136 was isolated from the pus of a patient with a brain abscess and a chronic subdural abscess. This strain grew slowly and formed colonies poorly on agar plates within 24 h of incubation. However, variously sized colonies were observed after 48 h of incubation. We isolated five strains from different sized colonies and compared their VAN susceptibility and genomic sequences using next-generation sequencing.

RESULTS

The five strains showed different rates of growth and susceptibilities to VAN (range of MIC after 48 h of incubation; 3-5 mg/L), and slower growing strains tended to be more VAN resistant. Deletion of the spdC gene and SNPs in the sarA gene was confirmed in all five strains and six SNPs in other genes (including mreC, hssS, prs, SA2339, sun, and SA1132) were confirmed when comparing the five strains.

CONCLUSIONS

Deletion of the spdC gene, a novel virulence factor of S. aureus, and SNPs in the sarA gene may be associated with VAN resistance. It was hypothesized that any of the six genes in which SNPs were detected could affect cell growth rate and VAN resistance in slow-VISA strains.

The good side of inflammation: Staphylococcus aureus proteins SpA and Sbi contribute to proper abscess formation and wound healing during skin and soft tissue infections

Staphylococcus aureus is the most prominent cause of skin and soft tissue infections (SSTI) worldwide. Mortality associated with invasive SSTI is a major threat to public health considering the incidence of antibiotic resistant isolates in particular methicillin resistant S. aureus both in the hospital (HA-MRSA) and in the community (CA-MRSA). To overcome the increasing difficulties in the clinical management of SSTI due to MRSA, new prophylactic and therapeutic approaches are urgently needed and a preventive vaccine would be welcome. The rational design of an anti-S. aureus vaccine requires a deep knowledge of the role that the different bacterial virulence factors play according to the type of infection. In the present study, using a set of isogenic deficient mutants and their complemented strains we determined that the staphylococcal surface proteins SpA and Sbi play an important role in the induction of inflammatory cytokines and chemokines in the skin during SSTI. SpA and Sbi initiate signaling cascades that lead to the early recruitment of neutrophils, modulate their lifespan in the skin milieu and contribute to proper abscess formation and bacterial eradication. Moreover, the expression of SpA and Sbi appear critical for skin repair and wound healing. Thus, these results indicate that SpA and Sbi can promote immune responses in the skin that are beneficial for the host and therefore, should not be neutralized with vaccine formulations designed to prevent SSTI.

Structures of a highly variable cell-wall anchored protein-encoding the spj gene from ST8/SCCmecIVl community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA/J) isolated from 2003 onwards: An indicator of a strongly invasive pathotype

The cell wall‐anchored protein‐encoding spj gene on staphylococcal cassette chromosome mec IVl (SCCmecIVl) was found to vary in size because of its 22‐ and 86‐aa repeat domains. The 22‐aa repeats are the more flexible of the two repeats, comprising three 11‐aa units, and were classified into three groups with eleven types. The 11/22‐aa repeats are longer in individuals with bullous impetigo, shorter in those with invasive disease and were absent in a fatal case, this last one having been rapidly diagnosed by PCR. IS431‐flanking pUB110 (bleO, aadD) is present on SCCmecIVl at 90%. The bacterial surface has the spj product and a unique surface layer.

Investigation of the susceptibility trends in Japan to fluoroquinolones and other antimicrobial agents in a nationwide collection of clinical isolates: A longitudinal analysis from 1994 to 2016

The susceptibilities of clinical isolates to fluoroquinolones and other antimicrobial agents were surveyed to obtain an accurate understanding of trends in incidence and antimicrobial resistance. The samples were collected from across Japan, biennially or triennially, between 1994 and 2016 and a defined level of resistance to fluoroquinolone was determined. Streptococcus pneumoniae, Streptococcus pyogenes and Haemophilus influenzae exhibited stable and high rates of susceptibility to fluoroquinolones over the period examined. For methicillin-resistant Staphylococcus aureus the rate of resistance to levofloxacin and ciprofloxacin was 81.3-93.5% and 83.2-94.2%, respectively, which was markedly higher than that of methicillin-susceptible S. aureus, while sitafloxacin-resistant methicillin-susceptible and methicillin-resistant S. aureus were isolated at 0.3-0.7% and 16.9-36.5%, respectively. The rate of levofloxacin or ciprofloxacin-resistant Escherichia coli increased from around 2-3% between 1994 and 1998 to around 35% in 2016, but the rate of fluoroquinolone-susceptible Klebsiella pneumoniae stayed high at over 94.6% during the study period. Although no fluoroquinolone-resistance in clinical isolates of Salmonella spp. was detected from 1994 to 2002, the resistance rate increased slightly after 2004 and reached to 1.9%-4.7% in 2016. The rate of fluoroquinolone-susceptible Pseudomonas aeruginosa isolated from urinary tract and respiratory tract infections improved during the period examined from 41.8-67.0% to 91.2-94.2%, and from 78.9-88.5% to 90.1-94.6%, respectively. Against Acinetobacter spp., the susceptibility rate of fluoroquinolones was almost constant at around 90%, but one multidrug-resistant isolate was detected in 2013. Overall, the susceptibility to fluoroquinolones was maintained over 20 years against tested bacteria except for MRSA and E. coli.

Prosthetic Valve Endocarditis Caused by ST8 SCCmecIVl Type Community-associated Methicillin-resistant Staphylococcus aureus

The emergence of a Japan-intrinsic community associated methicillin-resistant Staphylococcus aureus strain (CA-MRSA/J) has been reported. A 70-year-old man with recurrent colon cancer and a history of mitral valve replacement was admitted to the hospital in a state of shock. He was diagnosed with prosthetic valve endocarditis (PVE) caused by MRSA and underwent cardiac surgery. The MRSA isolates belonged to multilocus sequence type 8 and carried staphylococcal cassette chromosome mec IVl and the genes of toxic shock syndrome toxin-1, enterotoxin C, and enterotoxin L. These characteristics indicated a CA-MRSA/J clone. This is the first reported case of PVE caused by CA-MRSA/J.

Clonal change of methicillin-resistant Staphylococcus aureus isolated from patients with impetigo in Kagawa, Japan

Recently, the USA300 clone, which is a Panton-Valentine leukocidin (PVL)-positive clonal complex 8-staphylococcal cassette chromosome mec type IV (CC8-IV) community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) strain, emerged in community and hospital settings in Japan. Hence, clonal types of CA-MRSA strains are predicted to be changing. Nonetheless, long-term surveillance of CA-MRSA has not been conducted in Japan. Here, we investigated the transition and current status of CA-MRSA strains isolated from outpatients with impetigo; the samples were collected between 2007 and 2016 in Kagawa, Japan. The detection rate (22.8%, 488/2139 strains) of MRSA slightly decreased in these 10 years. Molecular epidemiological analyses showed that the prevalence of the CC89-II clone, which is a typical CA-MRSA genotype of causative agents of impetigo, significantly decreased from 48.0% (48/100 strains) in 2007-2009 to 21.9% (16/73 strains) in 2013-2016. By contrast, a non-USA300 CC8-IV clone, which is a highly pathogenic CA-MRSA/J clone, significantly increased in prevalence from 9.0% (9/100 strains) to 32.9% (24/73 strains). The prevalence of PVL-positive CA-MRSA strains increased annually from 2012 (0%) to 2015 (6.7%), whereas only one of these strains turned out to be the USA300 clone. Antibiotic susceptibility data revealed that the rates of resistance to gentamicin and clindamycin among CA-MRSA strains decreased along with the decreased prevalence of the CC89-II clone and increased prevalence of the CA-MRSA/J clone. Our data strongly suggest that the clonal types and antibiotic susceptibility of CA-MRSA isolated from patients with impetigo dramatically changed during the last 10 years in Japan.

Prevalence and Genetic Characteristics of Methicillin-Resistant Staphylococcus aureus and Coagulase-Negative Staphylococci Isolated from Oral Cavity of Healthy Children in Japan

Prevalence and genetic characteristics of methicillin-resistant Staphylococcus aureus (MRSA) and coagulase-negative staphylococci in oral cavity of healthy children were studied in Hokkaido, northern main island of Japan. From saliva of 526 children, a total of 248 staphylococcal isolates comprising S. aureus (n = 143), S. epidermidis (n = 84), S. warneri (n = 13), S. haemolyticus (n = 5), S. hominis (n = 2), and S. intermedius (n = 1) were recovered. Presence of mecA was confirmed in 6.3% of S. aureus, 50% of S. epidermidis, and 7.7% in S. warneri. SCCmec was mostly classified into type IV, and ACME (arginine catabolic mobile element)-arcA was detected in S. epidermidis (23.8%) and S. intermedius. Nine MRSA isolates belonged to staphylocoagulase gene (coa) type Ia, IIa, IIIa, VIIb/sequence type 1 (ST1), ST5, ST8, ST89, ST120, and were negative for PVL (Panton-Valentine leukocidin) genes. These isolates included two clones of emerging community-acquired MRSA (CA-MRSA) that had been described recently in Japan: ST5/SCCmec IVc, which resembles the "Pediatric clone," and ST8/SCCmec IVl belonging to coa-IIIa/agr-I with sasL gene, designated "CA-MRSA/J" clone. Various enterotoxin genes were found in all the MRSA and some methicillin-susceptible S. aureus (MSSA) isolates examined, while tst-1 was detected in four MRSA isolates. Notably, a variant of elastin-binding protein gene (ebpS-v) was identified in ST120 MRSA and ST45 MSSA isolates, and exfoliative toxin D gene (etd) was detected in an MSSA isolate. The present study revealed the presence of MRSA, including the novel CA-MRSA clones, and high prevalence of methicillin-resistant S. epidermidis in oral cavity of healthy children in Japan.

Regional outbreak of community-associated methicillin-resistant Staphylococcus aureus ST834 in Japanese children

Background

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infection has recently become a challenging problem worldwide and in Japan. We experienced 10 pediatric patients infected with CA-MRSA and hospitalized from 2011 to 2014 in a tertiary care hospital in Saitama, Japan, and assessed the characteristic of the strains using a whole genome sequencing (WGS)-based approach.

Methods

CA-MRSA strains isolated from infected patients who required hospitalization for treatment were evaluated in this study. Antimicrobial susceptibility tests, molecular typing by PCR and pulse-field gel electrophoresis (PFGE) were performed to characterize MRSA strains. WGS was performed for detailed genetic analysis.

Results

A total of 582 MRSA strains (35.2%) were identified among 1625 S. aureus strains collected during the study period. Ten MRSA strains (1.7%) were defined as CA-MRSA clinically, and all were isolated from pediatric patients. All strains mainly caused purulent lymphadenitis, were susceptible to fluoroquinolone and tetracycline, exhibited sequence type (ST) 834 or its single-locus variants and contained staphylococcal cassette chromosome mec (SCCmec) type IVc. Phylogenic analysis by PFGE and WGS revealed close relatedness of all strains, with the number of single nucleotide polymorphisms ranging from 35 to 119 by WGS. Out of the ten strains, nine possessed the genomic island SaPISaitama2 containing tst, sec and sel genes. SaPISaitama2 comprises a mosaic of genomic islands SaPIm4 and SaPIm1 harbored by a hospital-associated MRSA strain Mu50.

Conclusions

This study describes a regional outbreak of ST834-related CA-MRSA in children with a unique pathogenicity island in Japan. Pediatric patient tropism of this clone could be enhanced by susceptibility to fluoroquinolones and tetracyclines, which cannot be prescribed to children.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3646-z) contains supplementary material, which is available to authorized users.

Clinical and Molecular Characterization of Panton-Valentine Leukocidin-Positive Invasive Staphylococcus aureus Infections in Korea

AIM

Panton-Valentine leukocidin (PVL) is a virulent cytotoxin and an indicator of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infection. In this study, we evaluated the prevalence and clinical and molecular characteristics of PVL-positive invasive S. aureus (ISA) infections in Korea.

RESULTS

A collection of 1,962 nonduplicate clinical isolates were screened for multilocus sequence typing, staphylococcal cassette chromosome mec (SCCmec), accessory gene regulator typing, major toxins, and antimicrobial susceptibility. Twenty-eight (1.4%) PVL-positive S. aureus samples were found; of them 19 (67.9%) were MRSA (8 CA and 11 healthcare-associated infections). Seventeen patients (60.7%) were men (median age: 63 years; range: 13-93 years) and 12 patients (42.9%) had no underlying comorbidities. The most common infections were skin and skin structure infection (SSSI) and pneumonia. The 30-day mortality rate was 37.0%. The most common PVL-positive MRSA clones were ST8-SCCmec IVa and ST30-SCCmec IVc along with their single-locus variants. Antimicrobial susceptibility and toxin-gene profile differed according to the clone.

CONCLUSIONS

ISA infections caused by PVL-positive strains are rare in Korea, with the two most common infections being SSSI and pneumonia. Our findings indicated that several PVL-positive MRSA clones, predominantly ST8-SCCmecIVa and ST30-SCCmecIVc, were circulating and causing sporadic cases of ISA infections in the community and hospital settings.

Mobile Genetic Elements Associated with Antimicrobial Resistance

Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.

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.

Methicillin-resistant Staphylococcus aureus nasal carriage in international medical conference attendees

BACKGROUND

Carriage of methicillin-resistant Staphylococcus aureus (MRSA) is associated with its transmission. International travels and massive gatherings may accelerate such transmission. MRSA carriage was surveyed among the attendees of two international medical conferences held in Taipei in 2010.

METHODS

A total of 209 attendees from 23 countries were recruited. Nasal specimens were collected from each volunteer and subjected to polymerase chain reaction (PCR) detection for MRSA. Molecular analysis, including pulsed-field gel electrophoresis, multilocus sequence typing (MLST), typing of staphylococcal cassette chromosome mec (SCCmec) and staphylococcal protein A (spa) genes, and detection of Panton-Valentine leukocidin (PVL) and sasX genes, was performed.

RESULTS

MRSA carriage was detected in 10 (4.8%) attendees from Vietnam (3/8, 37.5%), Korea (2/6, 33.3%), Japan (2/41, 4.9%), Philippines (2/52, 3.8%), and Bangladesh (1/4, 25.0%). The proportion of MRSA colonizers was significantly higher in the local hospital group compared to those from the other groups (3/17 vs. 7/192, p < 0.05). Six MRSA isolates were available for molecular analysis. They all carried a type IV SCCmec gene. Five pulsotypes were identified; four genotypes, respectively, were identified by MLST and spa typing. None of the isolates carried either PVL or sasX genes. None of common molecular characteristics was shared by isolates from different countries. Most of these isolates were local endemic community clone in each country.

CONCLUSIONS

As healthcare workers, a certain proportion of international medical conference attendees harbored MRSA in their nares, mostly local endemic community clones in each country, which has the potential of spread among attendees.

Fatal case of ST8/SCCmecIVl community-associated methicillin-resistant Staphylococcus aureus infection in Japan

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) with ST8/SCCmecIV threatens human health. However, its pathogenesis remains unclear. ST8 CA-MRSA (CA-MRSA/J) with SCCmecIVl, which carries the large LPXTG-motif-containing putative adhesin gene, spj, has emerged in Japan. We present the first reported case of death from CA-MRSA/J. The patient was a 64-year-old woman with iliopsoas abscesses complicated by septic pulmonary embolism and multiorgan abscesses. Vancomycin, arbekacin, daptomycin and rifampicin were ineffective. CA-MRSA/J was resistant to erythromycin, clindamycin and antiseptics and was invasive in a HEp-2 cell assay, in contrast to skin-derived villous-adherent CA-MRSA/J. This suggests the strongly invasive pathotype of CA-MRSA/J.

Characterization of SCCmec type IV methicillin-resistant Staphylococcus aureus clones increased in Japanese hospitals

Recently, the prevalence of staphylococcal cassette chromosome mec (SCCmec) type IV isolates, which are the major community-acquired methicillin-resistant Staphylococcus aureus (MRSA), have increased in Japanese hospitals. The aim of this study was to elucidate the detailed molecular epidemiological features of the SCCmec type IV clones in Japanese hospitals. When 2589 MRSA isolated from four hospitals in Tokyo, Japan between 2010 and 2014 were analysed, the proportion of SCCmec type IV overtook that of type II, which was the major type of hospital-acquired MRSA in 2014. Multilocus sequence typing showed that CC1 was the most predominant clone in the SCCmec type IV isolates. The clinical departments that the patients belonged to, pulsed-field gel electrophoresis analysis and antimicrobial susceptibility profiles suggested that the origin of the CC1-SCCmec type IV (CC1-IV) clone was a community setting. Our data show that the CC1-IV clone is becoming a predominant MRSA clone in Japanese hospitals.

Molecular Characterization of Methicillin-Resistant Staphylococcus aureus Isolates, Isolated from a Burn Hospital in Southwest Iran in 2006 and 2014

OBJECTIVES

Incidence of methicillin-resistant Staphylococcus aureus (MRSA) is increasing every year, especially in burn patients with a high rate of morbidity and mortality. Molecular and epidemiologic studies are useful practices for understanding the relatedness of isolates in a single patient or a hospital. This study aimed at determining molecular characterizations of isolates collected in 2006 and 2014 using S. aureus-specific staphylococcal protein A (Spa) typing and Multilocus Sequence Typing (MLST) methods.

MATERIALS AND METHODS

Totally, 71 MRSA isolates were collected during the last two studies (2006 and 2014) from burn patients at Taleghani Burn Centre. After confirmation, all isolates were analysed using MLST and Spa typing methods.

RESULTS

We reported the emergence of Spa type t021, ST-30-IV MRSA isolates, which were PVL-positive in 14.6% of the cases and t12366, ST-8-IV isolates, which were PVL-negative in 9.8% of the cases. In 2014 study, Spa typing of MRSA isolates revealed five different spa types. Overall, in two studies, t037, ST-239, SCCmec III, and CC8 were predominant clones and they were reported in 63% of the cases.

CONCLUSION

The predominance of ST-239 in this region during the last eight years is a major concern. It also has a disturbing impact on the management of staphylococcal infections. Moreover, the SCCmec type IV strain is able to disseminate rapidly in hospital environments, demanding an improvement in infection-control policy.

Origin, evolution, and global transmission of community-acquired Staphylococcus aureus ST8

USA300 is a hypervirulent, community-acquired, multidrug-resistant Staphylococcus aureus clone that started to spread in the United States around 17 years ago. Many studies detected it also in South America, Europe, and the Asia-Pacific region. In this study, we show that USA300 is also circulating in sub-Saharan Africa. Locating the temporal and spatial origin of clonal lineages is important with respect to epidemiology and molecular evolution of pathogens. We show that USA300 evolved from a less virulent and less resistant ancestor circulating in Central Europe around 160 years ago. Constant surveillance of pathogen transmission routes is vital to prevent and control potential outbreaks. Whole genome sequencing proved to be a useful tool for epidemiological surveillance.

USA300 is a pandemic clonal lineage of hypervirulent, community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) with specific molecular characteristics. Despite its high clinical relevance, the evolutionary origin of USA300 remained unclear. We used comparative genomics of 224 temporal and spatial diverse S. aureus isolates of multilocus sequence type (ST) 8 to reconstruct the molecular evolution and global dissemination of ST8, including USA300. Analyses of core SNP diversity and accessory genome variations showed that the ancestor of all ST8 S. aureus most likely emerged in Central Europe in the mid-19th century. From here, ST8 was exported to North America in the early 20th century and progressively acquired the USA300 characteristics Panton–Valentine leukocidin (PVL), SCCmec IVa, the arginine catabolic mobile element (ACME), and a specific mutation in capsular polysaccharide gene cap5E. Although the PVL-encoding phage ϕSa2USA was introduced into the ST8 background only once, various SCCmec types were introduced to ST8 at different times and places. Starting from North America, USA300 spread globally, including Africa. African USA300 isolates have aberrant spa-types (t112, t121) and form a monophyletic group within the clade of North American USA300. Large parts of ST8 methicillin-susceptible S. aureus (MSSA) isolated in Africa represent a symplesiomorphic group of ST8 (i.e., a group representing the characteristics of the ancestor), which are rarely found in other world regions. Isolates previously discussed as USA300 ancestors, including USA500 and a “historic” CA-MRSA from Western Australia, were shown to be only distantly related to recent USA300 clones.

Complete Genome Sequence of Systemically Disseminated Sequence Type 8 Staphylococcal Cassette Chromosome mec Type IVl Community-Acquired Methicillin-Resistant Staphylococcus aureus

Staphylococcus aureus JH4899, a community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) isolate collected from a patient with systematically disseminated infection, is classified as sequence type 8 and carries the staphylococcal cassette chromosome mec type IVl (SCCmecIVl). It produces TSST-1, SEC, a newly discovered enterotoxin (SE1), and epidermal cell differentiation inhibitor A (EDIN-A). Here, we present the complete genome sequence of the chromosome and a plasmid harboring the se1 and ednA genes.

Genetic diversity of pvl-positive community-onset methicillin-resistant Staphylococcus aureus isolated at a university hospital in Japan

Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is pathogenic to healthy individuals and a significant issue throughout the world. Panton-Valentine leukocidin gene (pvl)-positive sequence type (ST) 8-staphylococcal cassette chromosome (SCC) mec type IV (ST8-IV) as represented by the USA300 clone, is the most prevalent CA-MRSA in many countries. However, the prevalence of pvl-positive CA-MRSA was limited in Japan. Here, we report the incidence of pvl-positive community-onset MRSA (CO-MRSA) isolated from 10 patients seen between 2009 and 2014 at a Japanese university hospital. All patients were Japanese and eight cases involved severe skin infections. Antimicrobial susceptibility patterns of the pvl-positive isolates were consistent with those of a typical CA-MRSA clone. Detailed molecular epidemiological analyses showed that three isolates were ST8-IV USA300 clones, whereas the other seven were ST30-IV (three isolates), ST30-I (one isolate), ST59-V (two isolates), and ST1-V (one isolate) clones. No clear difference of infection severity was found between the patients associated with the USA300 clone and those with the other clones. Our findings show that, not only the USA300 clone, but also diverse pvl-positive CO-MRSA clones exist in the community and cause severe skin infections in Japan.

Transfer of Antibiotic Resistance in Staphylococcus aureus

Staphylococcus aureus is a serious human pathogen with remarkable adaptive powers. Antibiotic-resistant clones rapidly emerge mainly by acquisition of antibiotic-resistance genes from other S. aureus strains or even from other genera. Transfer is mediated by a diverse complement of mobile genetic elements and occurs primarily by conjugation or bacteriophage transduction, with the latter traditionally being perceived as the primary route. Recent work on conjugation and transduction suggests that transfer by these mechanisms may be more extensive than previously thought, in terms of the range of plasmids that can be transferred by conjugation and the efficiency with which transduction occurs. Here, we review the main routes of antibiotic resistance gene transfer in S. aureus in the context of its biology as a human commensal and a life-threatening pathogen.

Toxic shock syndrome due to community-acquired methicillin-resistant Staphylococcus aureus infection: Two case reports and a literature review in Japan

Community-acquired methicillin-resistant Staphylococcus aureus has been spreading worldwide, including in Japan. However, few cases of toxic shock syndrome caused by Community-acquired methicillin-resistant Staphylococcus aureus have been reported in Japan. We report 2 cases, in middle-aged women, of toxic shock syndrome due to Community-acquired methicillin-resistant Staphylococcus aureus via a vaginal portal of entry. The first patient had used a tampon and the second patient had vaginitis due to a cleft narrowing associated with vulvar lichen sclerosus. Both patients were admitted to our hospital with septic shock and severe acute kidney injury and subsequently recovered with appropriate antibiotic treatment. In our review of the literature, 8 cases of toxic shock syndrome caused by Community-acquired methicillin-resistant Staphylococcus aureus were reported in Japan. In these 8 cases, the main portals of entry were the skin and respiratory tract; however, the portal of entry of Community-acquired methicillin-resistant Staphylococcus aureus from a vaginal lesion has not been reported in Japan previously.

Complete Circular Genome Sequence of Successful ST8/SCCmecIV Community-Associated Methicillin-Resistant Staphylococcus aureus (OC8) in Russia: One-Megabase Genomic Inversion, IS256's Spread, and Evolution of Russia ST8-IV

ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaβ split. The behavior of IS256 was flexible: its insertion site (att) sequences on the genome and junction sequences of extrachromosomal circular DNA were all divergent, albeit with fixed sizes. A similar multi-IS256 system was detected, even in prevalent ST239 healthcare-associated MRSA in Russia, suggesting IS256’s strong transmission potential and advantage in evolution. Regarding epidemiology, all ST8/SCCmecIVc strains from European, Siberian, and Far Eastern Russia, examined had MbIN, and geographical expansion accompanied divergent spa types and resistance to fluoroquinolones, chloramphenicol, and often rifampicin. Russia ST8/SCCmecIVc has been associated with life-threatening infections such as pneumonia and sepsis in both community and hospital settings. Regarding virulence, the OC8 genome carried a series of toxin and immune evasion genes, a truncated giant surface protein gene, and IS256 insertion adjacent to a pan-regulatory gene. These results suggest that unique single ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia ST8-IVc) emerged in Russia, and this was followed by large geographical expansion, with MbIN as an epidemiological marker, and fluoroquinolone resistance, multiple virulence factors, and possibly a multi-IS256 system as selective advantages.

Changing epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the Asia-Pacific region

INTRODUCTION

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has become an important threat to public health in the Asia-Pacific region, which is characterized by a large population and relatively insufficient resources. Better understanding on the current status of CA-MRSA in the region is of paramount importance. Areas covered: This article reviews the published literatures on the prevalence, molecular epidemiology, colonization, and hospital spread of CA-MRSA. Expert commentary: The burden of CA-MRSA has been increasing in the past two decades. The molecular epidemiology of CA-MRSA in the Asia-Pacific region shows a marked diversity in each country. Still, some strains - multilocus sequence type (MLST) ST59, ST30, ST72, ST8, and ST772 - are unique clones that have successfully established themselves as predominant, often spreading into nosocomial settings. More coordinated and comprehensive surveillance to understand the true epidemiology of CA-MRSA in the Asia-Pacific region is urgently needed.

First report of Panton-Valentine leukocidin-positive methicillin-susceptible Staphylococcus aureus ST88 harbouring ΦSa2usa isolated from refractory breast abscesses in Japan

A methicillin-susceptible Staphylococcus aureus with Panton–Valentine leukocidin (PVL) genes was isolated from refractory breast abscesses of 12-year-old girl in Japan, and classified into ST88, spa-t1245 and coa-IIIa. This strain harboured PVL phage ΦSa2usa, which is usually found in ST8 community-acquired methicillin-resistant S. aureus clone USA300.

Invasive Community-Acquired Methicillin-Resistant Staphylococcus aureus in a Japanese Girl with Disseminating Multiple Organ Infection: A Case Report and Review of Japanese Pediatric Cases

Pediatric invasive community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) infection is very serious and occasionally fatal. This infectious disease is still a relatively rare and unfamiliar infectious disease in Japan. We report a positive outcome in a 23-month-old Japanese girl with meningitis, osteomyelitis, fasciitis, necrotizing pneumonia, urinary tract infection, and bacteremia due to CA-MRSA treated with linezolid. PCR testing of the CA-MRSA strain was positive for PVL and staphylococcal enterotoxin b and negative for ACME. SCC mec was type IVa. This case underscores the selection of effective combinations of antimicrobial agents for its treatment. We need to be aware of invasive CA-MRSA infection, which rapidly progresses with a serious clinical course, because the incidence of the disease may be increasing in Japan.

Healthcare- and Community-Associated Methicillin-Resistant Staphylococcus aureus (MRSA) and Fatal Pneumonia with Pediatric Deaths in Krasnoyarsk, Siberian Russia: Unique MRSA's Multiple Virulence Factors, Genome, and Stepwise Evolution

Methicillin-resistant Staphylococcus aureus (MRSA) is a common multidrug-resistant (MDR) pathogen. We herein discussed MRSA and its infections in Krasnoyarsk, Siberian Russia between 2007 and 2011. The incidence of MRSA in 3,662 subjects was 22.0% and 2.9% for healthcare- and community-associated MRSA (HA- and CA-MRSA), respectively. The 15-day mortality rates for MRSA hospital- and community-acquired pneumonia (HAP and CAP) were 6.5% and 50%, respectively. MRSA CAP cases included pediatric deaths; of the MRSA pneumonia episodes available, ≥27.3% were associated with bacteremia. Most cases of HA-MRSA examined exhibited ST239/spa3(t037)/SCCmecIII.1.1.2 (designated as ST239_Kras), while all CA-MRSA cases examined were ST8/spa1(t008)/SCCmecIV.3.1.1(IVc) (designated as ST8_Kras). ST239_Kras and ST8_Kras strongly expressed cytolytic peptide (phenol-soluble modulin α, PSMα; and δ-hemolysin, Hld) genes, similar to CA-MRSA. ST239_Kras pneumonia may have been attributed to a unique set of multiple virulence factors (MVFs): toxic shock syndrome toxin-1 (TSST-1), elevated PSMα/Hld expression, α-hemolysin, the staphylococcal enterotoxin SEK/SEQ, the immune evasion factor SCIN/SAK, and collagen adhesin. Regarding ST8_Kras, SEA was included in MVFs, some of which were common to ST239_Kras. The ST239_Kras (strain OC3) genome contained: a completely unique phage, φSa7-like (W), with no att repetition; S. aureus pathogenicity island SaPI2R, the first TSST-1 gene-positive (tst⁺) SaPI in the ST239 lineage; and a super copy of IS256 (≥22 copies/genome). ST239_Kras carried the Brazilian SCCmecIII.1.1.2 and United Kingdom-type tst. ST239_Kras and ST8_Kras were MDR, with the same levofloxacin resistance mutations; small, but transmissible chloramphenicol resistance plasmids spread widely enough to not be ignored. These results suggest that novel MDR and MVF⁺ HA- and CA-MRSA (ST239_Kras and ST8_Kras) emerged in Siberian Russia (Krasnoyarsk) associated with fatal pneumonia, and also with ST239_Kras, a new (Siberian Russian) clade of the ST239 lineage, which was created through stepwise evolution during its potential transmission route of Brazil-Europe-Russia/Krasnoyarsk, thereby selective advantages from unique MVFs and the MDR.