Molecular typing of methicillin-resistant Staphylococcus aureus: Comparison of PCR-based open reading frame typing, multilocus sequence typing, and Staphylococcus protein A gene typing

Assessing the discriminability of PCR-based open reading frame typing versus single-nucleotide polymorphism analysis via draft whole-genome sequencing of methicillin-resistant Staphylococcus aureus in nosocomial transmission analysis

Phylogenetic analysis based on single-nucleotide polymorphism (SNP)-based through whole-genome sequencing is recognized as the standard method for probing nosocomial transmission. However, the application of WGS is constrained by the high cost of equipment and the need for diverse analysis tools, which limits its widespread use in clinical laboratory settings. In Japan, the prevalent use of PCR-based open reading frame typing (POT) for tracing methicillin-resistant Staphylococcus aureus (MRSA) transmission routes is attributed to its simplicity and ease of use. Although POT's discriminatory power is considered insufficient for nosocomial transmission analysis, conclusive data supporting this notion is lacking. This study assessed the discriminatory capabilities of SNP analysis and POT across 64 clinical MRSA strains. All 21 MRSA strains of ST5/SCCmec IIa, having more than 16 SNPs, demonstrated distinct clones. Conversely, two strains shared the same POT number and were identified as group A. Among the 12 MRSA strains of ST8/SCCmec IVl with over nine SNPs, five fell into POT group B, and five into POT group C. All four MRSA strains of ST8/SCCmec IVa were classified into POT group D, although they included strains with more than 30 SNPs. Among the 27 MRSA strains of ST1/SCCmec IVa, 14 were classified into POT group E. However, except for two clusters (each comprising two or three strains), all had SNP counts >10 (Fig.1-D). SNP analysis of MRSA in CC1/SCCmec IV showed that several strains had the same number of SNPs in POT number (106-183-37), even among bacteria with >100 SNPs, indicating POT's limited use in detailed nosocomial transmission analysis.

Importance of Toxin Genes and Polymerase Chain Reaction-Based Open Reading Frame Type Analyses for Severe Staphylococcus aureus Infection in Children

This study analyzed 26 Staphylococcus aureus strains, including 16 methicillin-resistant S. aureus (MRSA) and 10 methicillin-susceptible S. aureus (MSSA), collected from eight medical institutions in the Chiba Prefecture that requested a toxin gene analysis between 2015 and 2021. A total of 14 Panton-Valentine leukocidin (PVL) positive strains were identified, including MSSA. PVL-positive strains were classified into seven types according to polymerase chain reaction-based open reading frame typing (POT); of these types, three POT MRSA strains have not been previously reported, and one has been previously reported as PVL-negative. Some strains tested positive for both PVL and toxic shock syndrome toxin 1. One POT type was identified in both PVL-positive and PVL-negative strains. To the best of our knowledge, this is the first report on the regional spread of highly pathogenic S. aureus strains based on the POT method in children from multiple medical institutions. This method is useful for estimating the spread of toxin gene-carrying strains in the community owing to its association with toxin genes. As the number of PVL-positive strains in Japan increases, it is important to analyze the isolates of severe S. aureus infections in children by combining toxin gene analyses with the POT method.

Estimated medical costs of methicillin-resistant Staphylococcus aureus infection classified by polymerase chain reaction-based open reading frame typing in Japan

This retrospective, observational cohort study investigated the economic impact of genotype by classifying methicillin-resistant Staphylococcus aureus (MRSA) by using the polymerase chain reaction-based open reading frame typing (POT) method. Using administrative claims and bacteriological data for April 2016 to March 2021 from the University of Yamanashi Hospital, we ascertained the POT1 numbers and classified MRSA as either "hospital-derived" or "community-derived". We defined MRSA-associated medical practices and estimated the associated medical costs. After applying inverse probability of treatment weighting (IPTW)-based adjustment for patient characteristics between the two groups, we estimated the differences in medical costs during the "total therapy period" (defined as the interval from specimen submission to Day 42 after the susceptibility report) and the "definitive therapy period" (defined as the interval from susceptibility reporting to Day 42). Among the 135 MRSA-infected patients, 54 and 81 were classified as having hospital-derived and community-derived MRSA infections, respectively. Significant differences in patient characteristics were observed with regard to age (p = 0.0478), sex (p = 0.0422), surgery (p = 0.0349), chemotherapy (p = 0.0457) and immunosuppressive drug use (p = 0.0222). The median duration of the definitive therapy was 29 and 27 days, and the mortality rate during this period was 11% and 5% for the hospital-derived and community-derived types, respectively. After IPTW-based adjustment, the medical costs for the total therapy period were 324,480 and 296,462 Japanese yen (JPY) per patient for the hospital-derived and community-derived types, respectively, whereas the medical costs for the definitive therapy period were 279,635 and 256,542 JPY per patient for the hospital-derived and community-derived types, respectively. No statistically significant difference was detected (p = 0.5813 and p = 0.6355, respectively). In this study, MRSA healthcare costs were compared according to the POT scores, and no statistically significant differences were observed between hospital-derived and community-derived MRSA infections.

Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches

Whole genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) provides high-resolution typing, facilitating surveillance and outbreak investigations. The aim of this study was to evaluate the genomic variation rate in MRSA, by comparing commonly used core genome multilocus sequencing (cgMLST) against single nucleotide polymorphism (SNP) analyses. WGS was performed on 95 MRSA isolates, collected from 20 carriers during years 2003–2019. To assess variation and methodological-related differences, two different cgMLST schemes were obtained using Ridom SeqSphere+ and the cloud-based 1928 platform. In addition, two SNP methods, 1928 platform and Northern Arizona SNP Pipeline (NASP) were used. The cgMLST using Ridom SeqSphere+ and 1928 showed a median of 5.0 and 2.0 allele variants/year, respectively. In the SNP analysis, performed with two reference genomes COL and Newman, 1928 showed a median of 13 and 24 SNPs (including presumed recombination) and 3.8 respectively 4.0 SNPs (without recombination) per individual/year. Accordantly, NASP showed a median of 5.5 and 5.8 SNPs per individual/year. In conclusion, an estimated genomic variation rate of 2.0–5.8 genetic events per year (without recombination), is suggested as a general guideline to be used at clinical laboratories for surveillance and outbreak investigations independently of analysis approach used.

Evaluation of polymerase chain reaction-based open reading frame typing method for the clonality investigation of Clostridioides difficile isolates

Here, we assessed the utility of a polymerase chain reaction-based open reading frame typing assay for investigating the clonality of Clostridioides difficile isolates. This assay has a higher discriminatory power than multi-locus sequence typing for molecular epidemiological analysis of C. difficile isolates and can provide additional information about toxin genotypes.