ABSTRACT
BACKGROUND: Sublineage BA.5 of the SARS-CoV-2 Omicron variant rapidly spread and replaced BA.2 in July 2022 in Tokyo. A high viral load can be a possible cause of high transmissibility. METHODS AND RESULTS: The copy numbers of SARS-CoV-2 in nasopharyngeal swab samples obtained from all patients visiting the hospital where this research was conducted were measured using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Viral genotypes were determined using PCR-based melting curve analysis. Next, whole-genome sequencing was performed using approximately one fifth of the samples to verify the viral genotypes determined using PCR. Then, the copy numbers of the BA.1, BA.2, and BA.5 cases were compared. Contrary to expectations, the copy numbers of the BA.5 cases (median 4.7 × 104 copies/µL, n = 291) were significantly (p = .001) lower than those of BA.2 cases (median 1.1 × 105 copies/µL, n = 184). There was no significant difference (p = .44) between the BA.5 and BA.1 cases (median, 3.3 × 104 copies/µL; n = 215). CONCLUSION: The results presented here suggest that the increased infectivity of BA.5 is not caused by higher viral loads, but presumably by other factors such as increased affinity to human cell receptors or immune escape due to its L452R mutation.
Subject(s)
COVID-19 , Humans , SARS-CoV-2 , Viral Load , GenotypeABSTRACT
OBJECTIVES: The emergence and spread of carbapenemase-producing Enterobacteriaceae is a worldwide concern. This study reports the whole genome sequence of an NDM-5-, CTX-M-14-, OXA-10- and MCR-1-co-producing Escherichia coli sequence type 167 (ST167) multidrug-resistant clinical strain (EC129) isolated from a sputum sample of a hospitalised patient diagnosed with pneumonia. METHODS: The genome of E. coli EC129 was subjected to next-generation sequencing and reads were assembled. The draft genome was annotated using DDBJ Read Annotation Pipeline DFAST server, followed by subsequent in silico analysis. RESULTS: The genome of E. coli ST167 strain EC129 is 5319159 bp in length and contains 5022 protein-coding sequences. The blaNDM-5, blaCTX-M-14, blaOXA-10 and mcr-1 genes were detected along with other antimicrobial resistance genes conferring resistance to aminoglycosides, fluoroquinolones, sulfonamides, trimethoprim and tetracyclines. Antimicrobial susceptibility testing revealed that the isolate was resistant to all antimicrobial agents except colistin. CONCLUSION: To our knowledge, this study is the first to report anE. coli ST167 strain co-producing NDM-5, CTX-M-14, OXA-10 and MCR-1 isolated from a sputum sample of an individual with pneumonia in Japan, thus elucidating the molecular characteristics and resistance gene diversity of this strain.
