Predominant Clone Research Articles

High prevalence of ST5-SCCmec II-t311 clone of methicillin-resistant Staphylococcus aureus isolated from bloodstream infections in East China

ObjectivesMethicillin-resistant Staphylococcus aureus (MRSA) is a challenging global health threat, resulting in significant morbidity and mortality worldwide. This study aims to determine the molecular characteristics and antimicrobial susceptibility of 263 MRSA isolates in Zhejiang Province, east China.MethodsFrom 2014 to 2019, a total of 263 MRSA isolates from bloodstream infections (BSIs) were collected from 6 hospitals in 4 cities in Zhejiang province, east China. Antimicrobial susceptibility tests were conducted according to the guidelines set forth by the Clinical and Laboratory Standards Institute (CLSI). To characterize and analyze these isolates, multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec) typing, staphylococcal protein A (spa) typing and virulence genes gene profiles were performed.ResultsThe most predominant clone was ST5-SCCmec II-t311, which accounted for 41.8% (110/263), followed by ST59 (44/263, 16.7%). Compared with non-ST5-II-t311 isolates, ST5-II-t311 isolates were more resistant to erythromycin, tetracycline, levofloxacin, moxifloxacin, and ciprofloxacin, but more susceptible to clindamycin. Moreover, the rates of multidrug resistance were higher in ST5-II-t311 isolates compared to the non-ST5-II-t311 isolates. In comparison to the non-ST5-II-t311 isolates, ST5-II-t311 isolates showed no significant difference in virulence genes detected.ConclusionsMRSA ST5-II-t311 clone has become the most predominant clone in Zhejiang Province, east China and has higher rates of multidrug resistance than other isolates, that should be kept in mind when treating BSI. Moreover, MRSA ST59 clone shows an upward trend and has begun to spread into hospitals. Our findings highlight the importance of epidemiological studies of S. aureus carriage in the eastern region.

Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization.

The molecular epidemiology of carbapenem-resistant Enterobacterales in Cape Town remains largely unknown. This study aimed to describe the molecular epidemiology, resistome, virulome and mobilome of carbapenem-resistant Klebsiella pneumoniae (CRKP) within Cape Town to guide therapy, antimicrobial stewardship and infection prevention and control practices. Eighty-five CRKP isolates from hospitalized patients underwent WGS as part of a prospective, multicentre, cross-sectional study, conducted between 1 November 2020 and 30 November 2022, across public-sector and private-sector hospitals in Cape Town, South Africa. MLST revealed three novel types, ST6785, ST6786 and ST6787, while the most common were ST219, ST307, ST17, ST13 and ST2497. Different predominant clones were noted in each hospital. The most common carbapenemase gene was blaOXA-48-like, detected in 71% of isolates, with blaNDM detected in 5%. Notably, co-detection of two carbapenemase genes (blaOXA-48-like and blaNDM) occurred in 13% of isolates. The yersiniabactin siderophore was detected in 73% of isolates, and was most commonly associated with the ICEKp5 mobile element. All carbapenemases were located on plasmids. The genes blaOXA-181 and blaOXA-232 colocalized with a ColKP3 replicon type on assembled contigs in 83% and 100% of cases, respectively. CRKP epidemiology in Cape Town reflects institutionally dominant, rather than regional, clones. The most prevalent carbapenemase gene was blaOXA-48-like, in keeping with CRKP epidemiology in South Africa in general. Emerging clones harbouring both blaOXA-48-like and blaNDM, such as ST17, ST2497 and the novel ST6787, are a concern due to the limited availability of appropriate antimicrobial agents in South Africa.

Genomic analysis of extensively drug resistant (XDR) Klebsiella pneumoniae high-risk clone ST14 co-harboring blaNDM and blaOXA-48 recovered from Saudi Arabia

BackgroundThis study presents a comprehensive genomic analysis of NDM and OXA-48-producing Klebsiella pneumoniae in the Western region of Saudi Arabia, traversed by tens of millions of Muslims from various countries annually. This significant influx of visitors invariably leads to the spread and diversity of MDR bacteria. MethodsGenome sequencing was performed using MiSeq system of 29 CPKP isolates that were NDM and OXA-48-positive isolated from nosocomial infections and demonstrated resistance to most antibiotics, including carbapenems. ResultsWGS analysis showed that 12 (41.3%) isolates co-harbored blaOXA-48,blaCTX-M-15 and blaNDM genes. Notably, 16 (55.1%) isolates were identified as high-risk clone ST14, with 50% of these isolates co-harbored blaOXA-48, blaNDM and blaCTX-M-15 genes. All ST14 isolates were identified as capsular genotype KL2 and O1/O2v1 antigen with yersiniabactin locus ypt 14 carried by ICEKp5. The two isolates were identified as ST2096/KL64 hypervirulent K. pneumoniae (hvKp) clone harboring several virulence factors, including the regulator of the mucoid phenotype rmpA2 and aerobactin (iuc-1). Interestingly, two of the hvKp ST383/KL30 isolates were resistant to all tested antimicrobials except colistin and tigecycline, and simultaneously carried numerous ESBLs and carbapenemase genes. These isolates also harbor several virulence factors such as rmpA1, rmpA2, carried on KpVP-1, and aerobactin (iuc-1). Conclusionthis study provides insights into the spread and prevalence of high-risk clones of CPKP in the Western region of Saudi Arabia. The ST14 high-risk clone appears to be the predominant CPKP clone in this region, posing a significant threat to public health. This study also reports the presence of two globally disseminated hypervirulent K. pneumoniae (hvKp) clones, namely ST2096 and ST383. Therefore, it is essential to improve surveillance and implement strict infection control measures in this region, which receives a substantial number of visitors to effectively monitor and reduce the spread of high-risk clones of antimicrobial-resistant bacteria, including CPKP.

Genomic insights and antimicrobial resistance profiles of CRKP and non-CRKP isolates in a Beijing geriatric medical center: emphasizing the blaKPC-2 carrying high-risk clones and their spread.

The escalating resistance of Klebsiella pneumoniae, a prevalent pathogen in healthcare settings, especially its carbapenem-resistant K. pneumoniae (CRKP), to a wide array of antibiotics, notably β-lactams, constitutes a formidable challenge for healthcare and global public health management. This research compared the resistance phenotypes and genomic profiles of CRKP and Non-CRKP isolates in a Beijing hospital, focusing on high-risk blaKPC-2 gene-bearing CRKP clones and the structure of mobile genetic elements facilitating their spread across hospital departments. Forty K. pneumoniae isolates were collected from various departments of the hospital and subjected to antimicrobial susceptibility testing and whole-genome sequencing to analyze their resistance phenotypes and genomic features. The study revealed that among the 31 CRKP isolates, ST11 is the most common sequence type, with K47 and OL101 being the dominant capsule types, primarily observed in the respiratory department. In terms of antimicrobial susceptibility: 87.5% of the isolates exhibited multidrug resistance (MDR), with a high resistance rate of 30% against tigecycline. All CRKP isolates demonstrated resistance to multiple drug classes (≥5 CLSI classes). Non-CRKP isolates also showed high resistance rates to minocycline and doxycycline (77.8%). the ST11-KL47-OL101 type emerged as the predominant clone among the CRKP isolates carrying the blaKPC-2 gene. This dominance appears to be mediated by the pKpnR03_2 plasmid, which harbors not only blaKPC-2 and rmtb but also gene clusters pertinent to iron transport and arsenic resistance. These isolates, clustering in the C3 clade of the phylogenetic tree, exhibited minor genetic variations and close evolutionary relationships, suggesting a plasmid-driven spread across various hospital departments. In summary, our study highlights the extensive spread of antibiotic-resistant K. pneumoniae across various departments in our hospital, with a particular emphasis on the dominant clonal proliferation of the ST11-KL47-OL101 CRKP strain. This finding underscores the significant role of plasmid-mediated gene transfer in the evolution and dissemination of resistant strains within hospital environments. The study emphasizes the necessity for ongoing surveillance of antibiotic resistance and genomic analysis in hospital settings to effectively monitor and manage these challenges.

Tandem gene duplications contributed to high-level azole resistance in a rapidly expanding Candida tropicalis population

Invasive diseases caused by the globally distributed commensal yeast Candida tropicalis are associated with mortality rates of greater than 50%. Notable increases of azole resistance have been observed in this species, particularly within Asia-Pacific regions. Here, we carried out a genetic population study on 1571 global C. tropicalis isolates using multilocus sequence typing (MLST). In addition, whole-genome sequencing (WGS) analysis was conducted on 629 of these strains, comprising 448 clinical invasive strains obtained in this study and 181 genomes sourced from public databases. We found that MLST clade 4 is the predominant azole-resistant clone. WGS analyses demonstrated that dramatically increasing rates of azole resistance are associated with a rapid expansion of cluster AZR, a sublineage of clade 4. Cluster AZR isolates exhibited a distinct high-level azole resistance, which was induced by tandem duplications of the ERG11A395T gene allele. Ty3/gypsy-like retrotransposons were found to be highly enriched in this population. The alarming expansion of C. tropicalis cluster AZR population underscores the urgent need for strategies against growing threats of antifungal resistance.

Clonal Flux and Spread of Staphylococcus aureus Isolated from Meat and Its Genetic Relatedness to Staphylococcus aureus Isolated from Patients in Saudi Arabia.

In this study, we investigated both meat-derived and methicillin-resistant Staphylococcus aureus (MRSA), exploring their genetic relatedness to patient-derived MRSA isolates in Saudi Arabia. We collected 250 meat samples and identified 53 S. aureus isolates, with 79% being methicillin-sensitive Staphylococcus aureus (MSSA) and 21% being MRSA. Moreover, we included 80 clinically confirmed patient-derived MRSA isolates. We identified the most common S. aureus clone in both patients and retail meat. In meat, ST6 and ST97 were the most common clones in 55% of the MRSA isolates, and ST1153 and ST672 were the most common in 21% and 17% of the MSSA isolates. In patients, ST5 and ST6 were the predominant clones in 46% of the S. aureus isolates. CC5/ST5-SCCmecVc-t311 and CC361/ST672-SCCmecV-t3841 were common MRSA clones in both meat and patients. CC97 and CC361 clones were the second most prevalent S. aureus clones in meat and were relatively common in patients. Furthermore, we sequenced and characterized novel S. aureus strains ST8109, ST8110, and ST8111. The genomic similarities between meat- and patient-derived S. aureus isolates suggest that retail meat might be a reservoir for S.aureus and MRSA transmission. Therefore, a structured One Health approach is recommended for S. aureus dissemination, genetic characterization, antibiotic resistance, and impact on human health.

A 10-year retrospective study of methicillin-resistant Staphylococcus aureus from burn wound infection in southeast China from 2013 to 2022.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most commonly encountered pathogens among burn patients incurring substantial morbidity and mortality. To investigate the epidemiology and features of MRSA in burn wound infections, we conducted a 10-year retrospective study on MRSA isolated from burn patients with burn wound infections from southeast China from 2013 to 2022. One hundred MRSA isolates (10 isolates each year) from burn wound infection among burn patients from 2013 to 2022 were randomly selected and enrolled. In addition to the clinical data of the 100 burn patients, MRSA isolates were characterized by antimicrobial susceptibility testing, detection of toxin genes, and molecular typing. The median time from the onset of burns and admission to MRSA detected was 13 and 5 days, respectively. No MRSA isolate was found resistant to quinupristin/dalfopristin, linezolid, and vancomycin. Toxin gene seg was found most frequently (90%) followed by sea (70%) and eta (64%). CC8 (74%), ST239 (70%), and SCCmec III (72%) were the most common CC, ST, and SCCmec types, respectively. ST239-III (70%) was the predominant clone found in MRSA from burn wound infection among burn patients in southeast China. ST239-III was less found from 2018 to 2022. A higher diversity of MRSA clones was observed in these recent 5 years than that from 2013 to 2017.

A High-Risk Subgroup Multiple Myeloma Classification Based on the Detection of PR Minor Subclones

In the last two decades several classifications of Multiple Myeloma (MM) have been proposed based on gene expression signatures. These include the supervised translocation and cyclin D (TC) molecular subgroup approach or unsupervised methods to elucidate the molecular heterogeneity of MM and identify high risk subgroups. In particular, two RNA based gene expression studies have identified 8 to 10 unique subtypes, including the MS, MAF, CD1, CD2, and PR subtypes. The PR subgroup represents a highly proliferative gene signature that is associated with very poor survival outcomes. However, assigning this PR subgroup based on bulk transcriptome signatures can be challenging giving the mixture of genetic backgrounds that can be observed within this subtype. Furthermore, the presence of a minor PR subclone can often be missed with bulk genomic studies leading to the misclassification of a patient as standard risk. We here postulated that minor PR subclones expand under selective therapeutic pressures to become the predominant clones at subsequent relapses and the presence of PR subclones can impact any of the molecular subgroups pertaining poor survival outcomes. Bulk RNA or single cell RNA (scRNAseq) analysis were performed in bone marrow sorted primary MM cells obtained from 718 patients from the CoMMpass trialand 32 relapse/refractory MM patients, respectively. For scRNAseq, serial samples with paired baseline and relapse samples were available in 18 cases. Bone marrow plasma cells samples were separated from bone marrow aspirates using positive sorting selection of CD138 + cells. For bulk RNA-seq we used the mRNA HyperPrep kit (Kapa Biosystems) with RNA from 50,000 cells.For scRNA studiesunbiased mRNA profiling was conducted using the GemCode system (10x Genomics). Cell Ranger and Seurat were used for sample de-multiplexing, barcode processing, single-cell 3' gene and data analysis. Sequencing was performed on Illumina. By performing GSEA at the single cell level using the Zhan gene data set we have classified patients in the appropriate TC groups. FISH data was used to insure accurate calls. For the survival analysis OS was analyzed by the Kaplan-Meier method. In the CoMMpass dataset, with bulk RNA sequencing, the PR subtype contained 7.1% of patients with an admixture of classic genetic subtypes and very poor clinical outcome, with a median OS of 21.3 months. High proliferation index scores were concentrated in this subtype. There was also a strong tendency for patients to transition to the PR subtype at progression, with 25.5% of patients in a non-PR subtype at diagnosis transitioning to PR. Regardless of original subtype, patients that transitioned to the PR subtype rapidly succumbed to their disease with a median OS after the detected progression of 88 days. Using subtype prediction weight we could identify non-PR patients with PR subtype weights above 5% and these patients have a significantly shorter OS of 50 months compared to patients with <5% PR. At the single cell level, investigating the relapsed patients cohort, we have analyzed 92,139 cells and identified 59 clusters. A PR signature (defined as present in ≥15% of cells) was identified in 38% of cases despite baseline favorable prognostic group by FISH cytogenetics (7% HP, 28% t(11;14), and 57% normal FISH). A good concordance with FISH data was observed. In serially relapsed paired samples, all the PR patients maintain their signature overtime and 44% of patients transitioned to PR at subsequent relapse (Fig1A). Survival analyses were performed to evaluate how the presence of minor PR clones at the single cell level relate to clinical outcomes. Notably, the overall survival of patients classified as PR was dramatically reduced with a median OS of 6 months compared to 34 months for non-PR patients (Fig1B). In conclusion, we here show that minor PR clones defined by transcriptional signature through bulk or scRNA may be detectable in patients with variable MM molecular subgroups, including those classified as standard risk by the currently adopted classifications. We also show that the presence of these PR minor clones pertains adverse outcomes with very poor survivals. At relapse, most acquired PR cases originated from standard-risk presentations consistent with a Darwinian clonal evolution. Future classifications should account for the presence of these PR subclones for a better disease prognostication and developments of novel therapeutics.

2846. Microbiological Characteristics of the Patients with Acute Pyelonephritis who experienced Urinary Tract Infections within prior to 1 year

Abstract Background Approximately 15% of patients with acute pyelonephritis (APN) experience another urinary tract infection (UTI) within 1 year in South Korea. The purpose of this study is to examine the microbiological characteristics of patients with APN who experienced UTIs within prior to 1 year. Methods A retrospective cohort study was performed in a tertiary-care hospital in South Korea from July 2019 to December 2021. All female patients who were diagnosed with community acquired APN at admission were recruited. Patients who had prolonged hospitalization period due to medical problems that were not associated with APN treatment were excluded. We regarded recurrent group as the cases which have history of UTI within 1 year. Types of causative organism, major antibiotic resistance of E.coli isolated from patients' urine or blood, and the genetic characteristics of E.coli were compared between recurrent group and non-recurrent group. Results A total of 285 APN patients were finally included in this study, of which 41 (14.4%) were belong to recurrent group. E.coli was the most common causative pathogens in both groups, but the proportions of some pathogens, such as Klebsiella pneumonia (17.1 vs. 4.7%, P=0.007) and Pseudomonas aeruginosa (5.7 vs. 0.5%, P=0.014) were higher in the recurrent group than the non-recurrent group. There were no significant differences between the two groups in the proportions of antibiotic resistances to E.coli, such as amikacin (0 vs. 1.2%, P=0.597), cefotaxime (25.0 vs. 22.5%, P=0.788), and fluoroquinolone (20.8 vs. 28.9%, P=0.409), etc. The most prevalent β-lactamase and PMQR determinant were CTX-M-1G (44.4 vs 60.0%, P=0.308) and aac(6’)-lb-cr (50.0 vs 36.2%, P=0.303), respectively, and the predominant clone was ST131 (22.2 vs 17.8%, P=0.744) in both groups. However, there were no significant differences in the proportions of phylogenic groups, resistance genes, and virulence factors between the two groups. Conclusion E.coli was the most common causative pathogens in both groups, but the proportion of pathogens except E.coli was higher in the recurrent group than the non-recurrent group. There were no significant differences between the two groups in the proportions of antibiotic resistances to E.coli, phylogenic groups, resistance genes, and virulence factors. Disclosures All Authors: No reported disclosures

Molecular epidemiology and change trend of methicillin-resistant Staphylococcus aureus from invasive infections of a hospital in Hangzhou from 2012 to 2018.

The disease caused by methicillin-resistant Staphylococcus aureus (MRSA) is a global public health challenge that threatens society and patients seriously. Therefore, the molecular epidemiology and change trend of MRSA is essential for the control and treatment of diseases caused by the pathogen in their regions. To explore molecular epidemiology of MRSA in Hangzhou, we collected 162 MRSA isolates from 2012 to 2018, conducted the antimicrobial susceptibility and used polymerase chain reaction(PCR) to test the molecular typing including multilocus sequence typing (MLST), staphylococcal chromosome cassette mec (SCCmec), staphylococcal protein A (spa A) and Panton-Valentine leucocidin (PVL). All the strains was divided into community-associated MRSA (CA-MRSA) or hospital-associated MRSA (HA-MRSA). 162 MRSA isolates were divided into 16 STs and 30 spa types. The major ST type was ST5 (96/162, 59.3%) and the predominant spa type was t311 (83/162, 51.2%). Five SCCmec types were found and the most common SCCmec type was type II (101/162, 61.7%). ST5-II-t311 was the predominant MRSA clone. And the prevalence of ST5 MRSA gradually declined from 2014 to 2018 but the prevalence of ST59 MRSA significantly increased. At the same time, livestock-associated methicillin-resistant Staphylococcus aureus(LA-MRSA) ST398 and ST9 were detected. Twenty-eight isolates were PVL gene positive (28/162, 17.3%). The most prevalent PVL-positive clone was ST59-IVa-t437. Comparing with HA-MRSA, CA-MRSA had a lower probability of ST5 (9.1% vs 67.1%, P=0.000) but a higher probability of ST59 (63.6% vs 11.4%, P=0.000), not only that, it was more likely to carrying PVL-positive gene (36.4% vs 14.3%, P=0.028). In summary, the molecular types of MRSA were getting complex over time. ST5-II-t311 was the predominant clone of MRSA isolate with a downward incidence from 2014 to 2018. ST59 MRSA strains, which is thought community related strain are spreading into hospitals and has an upward incidence from 2014 to 2018.

Australian Group on Antimicrobial Resistance (AGAR) Australian Staphylococcus aureus Surveillance Outcome Program (ASSOP) Bloodstream Infection Annual Report 2022.

From 1 January to 31 December 2022, fifty-five institutions across Australia participated in the Australian Staphylococcus aureus Surveillance Outcome Program (ASSOP). The aim of ASSOP 2022 was to determine the proportion of Staphylococcus aureus bacteraemia (SAB) isolates in Australia that were antimicrobial resistant, with particular emphasis on susceptibility to methicillin and on characterisation of the molecular epidemiology of the methicillin-resistant isolates. A total of 3,214 SAB episodes were reported, of which 77.5% were community-onset. Overall, 15.0% of S. aureus were methicillin resistant. The 30-day all-cause mortality associated with methicillin-resistant SAB was 21.4%, which was significantly different to the 16.8% all-cause mortality associated with methicillin-susceptible SAB (p = 0.02). With the exception of the β-lactams and erythromycin, antimicrobial resistance in methicillin-susceptible S. aureus was rare. However, in addition to the β-lactams, approximately 31% of methicillin-resistant S. aureus (MRSA) were resistant to ciprofloxacin; 30% to erythromycin; 13% to tetracycline; 11% to gentamicin; and 2% to co-trimoxazole. One MRSA isolate, with a daptomycin MIC of 1.5 mg/L, harboured the A302V mprF and A23V cls2 mutations. When applying the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints, teicoplanin resistance was detected in one MRSA isolate. Resistance to vancomycin or linezolid was not detected. Resistance to non-β-lactam antimicrobials was largely attributable to the healthcare-associated MRSA (HA-MRSA) clone ST22-IV [2B] (EMRSA-15), and to the community-associated MRSA (CA-MRSA) clone ST45-V [5C2&5] which has acquired resistance to multiple antimicrobials including ciprofloxacin, clindamycin, erythromycin, gentamicin, and tetracycline. The ST22-IV [2B] (EMRSA-15) clone is the predominant HA-MRSA clone in Australia. Nonetheless, 86% of methicillin-resistant SAB episodes were due to CA-MRSA clones. Although polyclonal, approximately 72% of CA-MRSA clones were characterised as ST93-IV [2B] (Queensland clone); ST5-IV [2B]; ST45-V [5C2&5]; ST1-IV [2B]; ST30-IV [2B]; ST97-IV [2B]; ST953-IV [2B]; and ST8-IV [2B]. As CA-MRSA is well established in the Australian community, it is important to monitor antimicrobial resistance patterns in community- and healthcare-associated SAB as this information will guide therapeutic practices in treating S. aureus bacteraemia.

Distribution of Extended-Spectrum-β-Lactamase-Producing Diarrheagenic Escherichia coli Clonal Complex 10 Isolates from Patients with Diarrhea in the Republic of Korea.

ESBL-producing E. coli is a public health concern in healthcare settings and the community. Between 2009 and 2018, a total of 187 ESBL-producing pathogenic E. coli isolates were identified, and clonal complex (CC) 10 was the predominant clone (n = 57). This study aimed to characterize the ESBL-producing pathogenic E. coli CC10 strains obtained from patients with diarrhea to improve our understanding of CC10 distribution in the Republic of Korea. A total of 57 CC10 strains were selected for comprehensive molecular characterization, including serotype identification, the analysis of antibiotic resistance genes, the investigation of genetic environments, the determination of plasmid profiles, and the assessment of genetic correlations among CC10 strains. Among the CC10 isolates, the most prevalent serotype was O25:H16 (n = 21, 38.9%), followed by O6:H16 (10, 19.6%). The most dominant ESBL genes were blaCTX-M-15 (n = 31, 55%) and blaCTX-M-14 (n = 15, 27%). Most blaCTXM genes (n = 45, 82.5%) were located on plasmids, and these incompatibility groups were confirmed as IncB/O/K/Z, IncF, IncI1, and IncX1. The mobile elements located upstream and downstream mainly included ISEcp1 (complete or incomplete) and IS903 or orf477. Phylogenetic analysis showed that the CC10 strains were genetically diverse and spread among several distinct lineages. The results of this study show that ESBL-producing pathogenic E. coli CC10 has been consistently isolated, with CTX-M-15-producing E. coli O25:H16 isolates being the major type associated with the distribution of CC10 clones over the past decade. The identification of ESBL-producing pathogenic E. coli CC10 isolates underscores the possible emergence of resistant isolates with epidemic potential within this CC. As a result, continuous monitoring is essential to prevent the further dissemination of resistant ESBL-producing E. coli CC10 strains.

Significant increase in the prevalence of Panton–Valentine leukocidin-positive methicillin-resistant Staphylococcus aureus , particularly the USA300 variant ΨUSA300, in the Japanese community

ABSTRACT USA300, a major Panton–Valentine leukocidin (PVL)-producing methicillin-resistant Staphylococcus aureus (MRSA) clone associated with skin and soft tissue infections (SSTIs), carries a type IV staphylococcal cassette chromosome mec (SCC mec ) element. Recently, a USA300 variant, ΨUSA300, with a 12-bp deletion of ccrB2 in the SCC mec element, was identified in Japan by Takadama et al. (15). To understand the current status of PVL-positive MRSA in the community, a nationwide surveillance of MRSA isolated from outpatients at dermatology departments was conducted. This study included 1,619 outpatients who visited dermatology departments at 22 healthcare facilities in 11 prefectures in Japan between 2018 and 2021; S. aureus were isolated from these outpatients. Molecular epidemiological analysis was performed using PCR, SCC mec and spa typing, pulsed-field gel electrophoresis, multilocus sequence typing, and antimicrobial susceptibility testing. A total of 980 S . aureus were isolated, 293 of which were identified as MRSA. Among MRSA isolates, PVL genes were detected in 18 of 63 (28.6%) in 2018, 34 of 85 (40.0%) in 2019, 29 of 65 (44.6%) in 2020, and 40 in 80 (50.0%) in 2021. Among the PVL-positive MRSA, 16 of 121 (13.2%) and 94 of 121 (77.7%) isolates were identified as USA300 and ΨUSA300, respectively. ΨUSA300 strains were collected from six prefectures in Japan: Kagawa, Osaka, Tokyo, Kanagawa, Fukushima, and Saitama. ΨUSA300 was isolated more frequently than USA300 from patients with deep-seated SSTIs ( P < 0.05). Our findings showed that PVL-positive MRSA isolates were significantly increased in the Japanese community. Furthermore, the USA300 variant ΨUSA300 has emerged as the predominant PVL-positive MRSA clone across the Kanto, Kinki, and Shikoku regions of Japan, and this variant may possess a greater propensity to cause deep-seated SSTIs than in USA300. IMPORTANCE USA300 is an MRSA clone producing PVL, a toxin associated with SSTIs. ΨUSA300 is a USA300 variant recently identified in Japan by Takadama et al. (15). Here, we found that the prevalence rate of PVL-positive MRSA in S. aureus was elevated in the Japanese community, and ΨUSA300 accounted for most of them. ΨUSA300 strains have been isolated from several areas in Japan and were associated with deep-seated SSTIs. This study highlighted the emerging threat posed by ΨUSA300 in Japan.

An integrated nationwide genomics study reveals transmission modes of typhoid fever in China.

Typhoid fever is a life-threatening disease caused by Salmonella enterica serovar Typhi, resulting in a significant disease burden across developing countries. Historically, China was very much close to the global epicenter of typhoid, but the role of typhoid transmission within China and among epicenter remains overlooked in previous investigations. By using newly produced genomics on a national scale, we clarify the complex local and global transmission history of such a notorious disease agent in China spanning the most recent five decades, which largely undermines the global public health network.

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

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. 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. 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). 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.

Comprehensive Genomic Characterization of Staphylococcus aureus Isolated from Atopic Dermatitis Patients in Japan: Correlations with Disease Severity, Eruption Type, and Anatomical Site.

Atopic dermatitis (AD) shows frequent recurrence. Staphylococcus aureus is the primary microbial component in AD and is associated with disease activity. However, traditional typing methods have failed to characterize virulent AD isolates at the clone level. We conducted a comprehensive genomic characterization of S. aureus strains isolated from the skin of AD patients and healthy donors, comparing the whole-genome sequences of the 261 isolates with anatomical and lesional (AD-A)/nonlesional (AD-NL)/healthy sites, eruption types, clinical scores, virulence, and antimicrobial resistance gene repertoires in Japan. Sequence type (ST) diversity was lost with worsening disease activity; ST188 was the most frequently detected ST in AD-A and had the strongest correlation with AD according to the culture rate and proportion with worsening disease activity. ST188 and ST20 isolates inhabited all skin conditions, with significantly higher proportions in AD skin than in healthy skin. ST8, ST15, and ST5 proportions were equivalent for all skin conditions; ST30 was detected only in healthy skin; and ST12 was detected only in AD skin. ST97 detected in AD-A and healthy skin was clearly branched into two subclades, designated ST97A and ST97H. A comparison of two genomes led to the discovery that only ST97A possessed the complete trp operon, enabling bacterial survival without exogenous tryptophan (Trp) on AD skin, where the Trp level was significantly reduced. Primary STs showing an AD skin inhabitation trend (ST188, ST97A, ST20, and ST12) were all trp operon positive. The predominant clones (ST188 and ST97) possessed almost no enterotoxin genes, no mecA gene, and few other antimicrobial resistance genes, different from the trend observed in Europe/North America. IMPORTANCE While Staphylococcus aureus is a member of the normal human skin flora, its strong association with the onset of atopic dermatitis (AD) has been suggested. However, previous studies failed to assign specific clones relevant to disease activities. Enterotoxins produced by S. aureus have been suggested to aggravate and exacerbate the inflammation of AD skin, but their role remains ambiguous. We conducted a nuanced comprehensive characterization of isolates from AD patients and healthy donors, comparing the whole-genome sequences of the isolates with anatomical and lesional/nonlesional/healthy sites, eruption types, clinical scores, virulence, and antimicrobial resistance gene repertoires in Japan. We demonstrate that specific clones are associated with disease severity and clinical manifestations, and the dominant clones are devoid of enterotoxin genes and antimicrobial resistance genes. These findings undermine the established notion of the pathophysiological function of S. aureus associated with AD and introduce a new concept of S. aureus colonization in AD.

A Decade-Long Evaluation of Neonatal Septicaemic Escherichia coli: Clonal Lineages, Genomes, and New Delhi Metallo-Beta-Lactamase Variants.

Longitudinal studies of extraintestinal pathogenic Escherichia coli (ExPEC) and epidemic clones of E. coli in association with New Delhi metallo-β-lactamase (blaNDM) in septicaemic neonates are rare. This study captured the diversity of 80 E. coli isolates collected from septicaemic neonates in terms of antibiotic susceptibility, resistome, phylogroups, sequence types (ST), virulome, plasmids, and integron types over a decade (2009 to 2019). Most of the isolates were multidrug-resistant and, 44% of them were carbapenem-resistant, primarily due to blaNDM. NDM-1 was the sole NDM-variant present in conjugative IncFIA/FIB/FII replicons until 2013, and it was subsequently replaced by other variants, such as NDM-5/-7 found in IncX3/FII. A core genome analysis for blaNDM+ve isolates showed the heterogeneity of the isolates. Fifty percent of the infections were caused by isolates of phylogroups B2 (34%), D (11.25%), and F (4%), whereas the other half were caused by phylogroups A (25%), B1 (11.25%), and C (14%). The isolates were further distributed in approximately 20 clonal complexes (STC), including five epidemic clones (ST131, ST167, ST410, ST648, and ST405). ST167 and ST131 (subclade H30Rx) were dominant, with most of the ST167 being blaNDM+ve and blaCTX-M-15+ve. In contrast, the majority of ST131 isolates were blaNDM-ve but blaCTX-M-15+ve, and they possessed more virulence determinants than did ST167. A single nucleotide polymorphism (SNP)-based comparative genome analysis of epidemic clones ST167 and ST131 in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of antibiotic-resistant epidemic clones causing sepsis calls for a modification of the recommended antibiotics with which to treat neonatal sepsis. IMPORTANCE Multidrug-resistant and virulent ExPEC causing sepsis in neonates is a challenge to neonatal health. The presence of enzymes, such as carbapenemases (blaNDM) that hydrolyze most β-lactam antibiotic compounds, result in difficulties when treating neonates. The characterization of ExPECs collected over 10 years showed that 44% of ExPECs were carbapenem-resistant, possessing transmissible blaNDM genes. The isolates belonged to different phylogroups that are considered to be either commensals or virulent. The isolates were distributed in around 20 clonal complexes (STC), including two predominant epidemic clones (ST131 and ST167). ST167 possessed few virulence determinants but was blaNDM+ve. In contrast, ST131 harbored several virulence determinants but was blaNDM-ve. A comparison of the genomes of these epidemic clones in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of epidemic clones in a vulnerable population with contrasting characteristics and the presence of resistance genes call for strict vigilance.

Dynamics of the MRSA Population in a Chilean Hospital: a Phylogenomic Analysis (2000-2016).

The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCCmecI) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in recent years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary health care center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000 and 2016. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r = 0.8748, P < 0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016, and an effective diversity (Hill number; q = 2) increasing from 1.12 to 2.71. The temporal trend analysis revealed that in the period 2000 to 2003 most of the isolates (94.2%; n = 98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013 to 2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCCmecII and ST72-SCCmecVI. In conclusion, the ChC clone remains the most frequent MRSA lineage, but this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCCmecII. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or more limited typing techniques that lack the resolution to represent an accurate description of the genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000 and 2016 in Chile providing the largest and most detailed study of clonal dynamics of MRSA in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing in frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.

Insight into the Clonal Lineage and Antimicrobial Resistance of Staphylococcus aureus from Vascular Access Infections before and during the COVID-19 Pandemic.

Patients receiving hemodialysis are at risk of vascular access infections (VAIs) and are particularly vulnerable to the opportunistic pathogen Staphylococcus aureus. Hemodialysis patients were also at increased risk of infection during the COVID-19 pandemic. Therefore, this study determined the change in the molecular and antibiotic resistance profiles of S. aureus isolates from VAIs during the pandemic compared with before. A total of 102 S. aureus isolates were collected from VAIs between November 2013 and December 2021. Before the pandemic, 69 isolates were collected, 58%, 39.1%, and 2.9% from arteriovenous grafts (AVGs), tunneled cuffed catheters (TCCs), and arteriovenous fistulas (AVFs), respectively. The prevalence of AVG and TCC isolates changed to 39.4% and 60.6%, respectively, of the 33 isolates during the pandemic. Sequence type (ST)59 was the predominant clone in TCC methicillin-resistant S. aureus (MRSA) and AVG-MRSA before the pandemic, whereas the predominant clone was ST8 in AVG-MRSA during the pandemic. ST59 carrying the ermB gene was resistant to clindamycin and erythromycin. By contrast, ST8 carrying the msrA gene was exclusively resistant to erythromycin. The ST distribution for different VAIs changed from before to during the pandemic. The change in antibiotic resistance rate for different VAIs was closely related to the distribution of specific STs.

Population structure of food-borne Staphylococcus aureus in China

Objective: To understand the population structure of food-borne Staphylococcus (S.) aureus in China. Methods: Whole genome sequencing was used to analyze 763 food-borne S. aureus strains from 16 provinces in China from 2006 to 2020. Multilocus sequence typing (MLST), staphylococcal protein A gene (spa) typing, and staphylococcal chromosome cassettemec (SCCmec) typing were conducted, and minimum spanning tree based on ST types (STs) was constructed by BioNumerics 7.5 software. Thirty-one S. aureus strains isolated from imported food products were also included in constructing the genome phylogenetic tree. Results: A total of 90 STs (20 novel types) and 160 spa types were detected in the 763 S. aureus isolates. The 72 STs (72/90, 80.0%) were related to 22 clone complexes. The predominant clone complexes were CC7, CC1, CC5, CC398, CC188, CC59, CC6, CC88, CC15, and CC25, accounting for 82.44% (629/763) of the total. The STs and spa types in the predominant clone complexes changed over the years. The methicillin-resistant S. aureus (MRSA) detection rate was 7.60%, and 7 SCCmec types were identified. The ST59-t437-Ⅳa (17.24%, 10/58), ST239-t030-Ⅲ (12.07%, 7/58), ST59-t437-Ⅴb (8.62%, 5/58), ST338-t437-Ⅴb (6.90%, 4/58) and ST338-t441-Ⅴb (6.90%, 4/58) were the main types in MRSA strains. The genome phylogenetic tree had two clades, and the strains with the same CC, ST, and spa types clustered together. All CC7 methicillin sensitive S. aureus strains were included in Clade1, while 21 clone complexes and all MRSA strains were in Clade2. The MRSA strains clustered according to the SCCmec and STs. The strains from imported food products in CC398, CC7, CC30, CC12, and CC188 had far distances from Chinese strains in the tree. Conclusions: In this study, the predominant clone complexes of food-borne strains were CC7, CC1, CC5, CC398, CC188, CC59, CC6, CC88, CC15, and CC25, which overlapped with the previously reported clone complexes of hospital and community-associated strains in China, suggesting that close attention needs to be paid to food, a vehicle of pathogen transmission in community and food poisoning.