Molecular Epidemiological Characterization of Methicillin-Resistant Staphylococcus aureus from Bloodstream Infections in Northern Japan: Increasing Trend of CC1 and Identification of ST8-SCCmec IVa USA300-Like Isolate Lacking Arginine Catabolic Mobile Element

Long-term impact of molecular epidemiology shifts of methicillin-resistant Staphylococcus aureus on severity and mortality of bloodstream infection

A 2019 nationwide study in Japan revealed the predominant methicillin-resistant Staphylococcus aureus (MRSA) types in bloodstream infections (BSIs) to be sequence type (ST)8-carrying SCCmec type IV (ST8-MRSA-IV) and clonal complex 1-carrying SCCmec type IV (CC1-MRSA-IV). However, detailed patient characteristics and how these MRSA types evolve over time remain largely unknown. In this long-term single-center study, MRSA strains isolated from blood cultures at Nagasaki University Hospital from 2012 to 2019 were sequenced and analyzed. Additionally, we compared the SCCmec types and patient characteristics identified in this study with previous data from our hospital spanning 2003-2007 and 2008-2011. Over this 16-year period, SCCmec type II decreased significantly from 79.2% to 15.5%, while type IV increased from 18.2% to 65.5%. This shift in SCCmec types was associated with notable changes in severity and outcomes; the sequential organ failure assessment (SOFA) score decreased from 5.8 to 3.1; in-hospital mortality declined from 39.8% to 15.5%. In contrast, no significant changes in patient demographics, such as age, sex, or underlying diseases, were observed. Between 2012 and 2019, the major combinations of SCCmec type and sequence type were ST8-MRSA-IV, ST8-MRSA-I, CC1-MRSA-IV, and ST5-MRSA-II. Additionally, ST8-MRSA-IV was divided into CA-MRSA/J, t5071-ST8-MRSA-IV, and USA300-like clone based on the results of molecular analysis. These major combinations showed similar drug resistance patterns, molecular characteristics, and phylogenetic features to those identified in nationwide surveillance. This study highlights the evolving nature of MRSA types in bloodstream infections, correlating with improved patient outcomes over time.

Molecular characterization of methicillin-susceptible/resistant Staphylococcus aureus from bloodstream infections in northern Japan: The dominance of CC1-MRSA-IV, the emergence of human-associated ST398 and livestock-associated CC20 and CC97 MSSA

OBJECTIVES

Staphylococcus aureus (S. aureus) is a major cause of bloodstream infections. The recent epidemiological features and antimicrobial resistance trend were analysed for methicillin-resistant and susceptible S. aureus (MRSA/MSSA) isolates from blood samples in people from northern Japan.

METHODS

The S. aureus isolates from blood culture were screened by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and genotyped by the schemes of multilocus sequence typing (MLST), coa, agr, spa, and SCCmec types. Antimicrobial resistance genes and virulence factors were detected by multiplex/uniplex polymerase chain reaction (PCR). Antimicrobial susceptibility was examined using a broth microdilution test.

RESULTS

A total of 301 isolates (163 MRSA and 138 MSSA) were isolated from bloodstream infections in 2023 (from April to December). The MRSA isolates were classified into three groups, that is, clonal complexes (CC)1-SCCmec-IV (CC1-IV) (52%), CC5-II (36%), and CC8-IV (12%). The prevalence of CC1 was significantly higher than those in our previous studies (2017-2021). Four CC8-IVa isolates with PVL genes on ΦSa2usa were considered to be the USA300 clone (sequence type [ST]8/spa-t008/coa IIIa/agr I) or its variants that were genotyped as those closely related to ST8/t008 or lacking arginine catabolic mobile element (ACME). In contrast, MSSA was genetically highly divergent and classified into 22 STs, with CC1 (ST1 and ST188) being the most common (25%). It was notable that 29 MSSA isolates (21%) were classified into livestock-associated (LA) genotypes, ST20, ST97, and CC398 (ST398 and ST291). Genetic characterization of the CC398 isolates suggested that these belong to human-adapted MSSA clones.

CONCLUSIONS

The present study revealed the increasing trend of CC1 MRSA surpassing CC5, and the emergence of MSSA representing human-adapted CC398, and LA types ST97 and ST20 from bloodstream infections in people in Japan. © 2024 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.

Genotypic Shift and Diversification of MRSA Blood Stream Isolates in a University Hospital Setting: Evidence from a 12-Year Observational Study

There have been few reports regarding the long-term trends in the genotypes of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream isolates. Therefore, this study was performed to investigate the longitudinal trends in the genotypes of MRSA bloodstream isolates obtained from hospitalized patients during a 12-year study period from 2010 to 2021 at a tertiary care university hospital. Over the 12-year period from 2010 to 2021, we conducted a genetic investigation focusing on 245 MRSA strains isolated from the blood of hospitalized patients. The genotypes of the MRSA bloodstream isolates were determined by Staphylococcal Cassette Chromosome mec (SCCmec) typing, accessory gene regulator (agr) typing, PCR-based ORF typing (POT), and multilocus sequence typing (MLST). Strains with the same POT type detected in two or more isolates were designated as epidemic clones, while strains without a common POT type were classified as sporadic clones. Until 2015, isolates with SCCmec II/agr II were prevalent, but isolates with SCCmec IV/agr III increased from 2016. A total of 128 strains (52%) were identified as epidemic clones, while 117 strains (48%) were classified as sporadic clones. The detection rate of sporadic clones increased significantly since 2016 (p < 0.05). The epidemic clones were classified into three clusters, with MRSA of clonal complex (CC) 1 being prominent after 2016. This study showed that the genotypes of MRSA bloodstream isolates underwent a shift from SCCmec II/agr II type to SCCmec IV/agr III type, with a notable increase in MRSA of CC1, after 2016. There was a significant increase in the proportion of sporadic strains among the isolates, suggesting the diversification of genotypes.

Demographic fluctuations in bloodstream Staphylococcus aureus lineages configure the mobile gene pool and antimicrobial resistance

Staphylococcus aureus in the bloodstream causes high morbidity and mortality, exacerbated by the spread of multidrug-resistant and methicillin-resistant S. aureus (MRSA). We aimed to characterize the circulating lineages of S. aureus from bloodstream infections and the contribution of individual lineages to resistance over time. Here, we generated 852 high-quality short-read draft genome sequences of S. aureus isolates from patient blood cultures in a single hospital from 2010 to 2022. A total of 80 previously recognized sequence types (ST) and five major clonal complexes are present in the population. Two frequently detected lineages, ST5 and ST8 exhibited fluctuating demographic structures throughout their histories. The rise and fall in their population growth coincided with the acquisition of antimicrobial resistance, mobile genetic elements, and superantigen genes, thus shaping the accessory genome structure across the entire population. These results reflect undetected selective events and changing ecology of multidrug-resistant S. aureus in the bloodstream.

Whole Genome Sequencing and Comparative Genomics of Six Staphylococcus schleiferi and Staphylococcus coagulans Isolates

Staphylococcus schleiferi and Staphylococcus coagulans, closely related bacterial species within the Staphylococcus genus, present a challenge in classification and diagnosis due to their close genetic proximity and overlapping phenotypic features. Moreover, our understanding of the virulence mechanisms in staphylococcal species, beyond the extensively studied Staphylococcus aureus, remains limited, underscoring the importance of using comparative data to enhance our insights into virulence within these bacterial species. This study employed a comprehensive approach, utilizing comparative genomics, to identify genomic distinctions between S. schleiferi and S. coagulans, aiming to address the challenges in the accurate classification and diagnosis of these organisms and identify unique features. Whole genome sequencing was performed on six clinical isolates, and their genomes were compared to identify variations in gene content and virulence factors. De novo assembly and annotation revealed two samples as S. coagulans and four samples as S. schleiferi. Analysis of the core genomes revealed conserved regions crucial for defining species identity, while accessory genomic elements contained unique genes, possibly impacting the pathogenicity of the species.