Yohei Doi
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View article: Genome sequences of two highly colistin-resistant <i>Pseudomonas aeruginosa</i> clinical isolates from the cystic fibrosis lung
Genome sequences of two highly colistin-resistant <i>Pseudomonas aeruginosa</i> clinical isolates from the cystic fibrosis lung Open
The genomes of two highly colistin-resistant strains of Pseudomonas aeruginosa (MICs ≥ 1,024 mg/mL) isolated from cystic fibrosis lung infections were sequenced and analyzed. Genes associated with colistin resistance ( pmrAB , phoPQ ) show…
View article: Integrated analysis of Tn-Seq and pangenome reveals core and lineage-specific essential genes in <i>Mycobacterium avium</i> subsp. <i>hominissuis</i>
Integrated analysis of Tn-Seq and pangenome reveals core and lineage-specific essential genes in <i>Mycobacterium avium</i> subsp. <i>hominissuis</i> Open
Pulmonary disease caused by nontuberculous mycobacteria (NTM-PD) is an emerging global health concern. Among NTM, Mycobacterium avium subsp. hominissuis (MAH) is the major causative agent of NTM-PD. Similar to Mycobacterium tuberculosis ( …
View article: <i>In vitro</i> evolution of durlobactam resistance in NDM-producing <i>Escherichia coli</i> due to a single mutation in <i>mrdA</i> encoding penicillin-binding protein 2
<i>In vitro</i> evolution of durlobactam resistance in NDM-producing <i>Escherichia coli</i> due to a single mutation in <i>mrdA</i> encoding penicillin-binding protein 2 Open
Durlobactam, a diazabicyclooctane β-lactamase inhibitor, exhibits direct antibacterial activity by binding to penicillin-binding protein 2 (PBP2). We generated a mutant strain of New Delhi metallo-β-lactamase-producing Escherichia coli wit…
View article: Features of Carbapenem-resistant Gram-negative Bacterial Infections in Japan Based on the Setting of Onset
Features of Carbapenem-resistant Gram-negative Bacterial Infections in Japan Based on the Setting of Onset Open
Background Carbapenem-resistant Gram-negative bacilli (CR-GNB) are a major public health threat, traditionally linked to hospital settings. However, infections are increasingly reported in the community, and the clinical distinctions betwe…
View article: Evolutionary loss of an antibiotic efflux pump increases Pseudomonas aeruginosa quorum sensing mediated virulence in vivo
Evolutionary loss of an antibiotic efflux pump increases Pseudomonas aeruginosa quorum sensing mediated virulence in vivo Open
View article: Exploring the complex interplay of polymyxin resistance mechanisms, lipid A variations, and virulence factors in Escherichia coli and Klebsiella pneumoniae
Exploring the complex interplay of polymyxin resistance mechanisms, lipid A variations, and virulence factors in Escherichia coli and Klebsiella pneumoniae Open
The global emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Escherichia coli and Klebsiella pneumoniae poses a serious public health concern due to limited therapeutic options. Polymyxins, often considered last-r…
View article: Dalbavancin for Treatment of <i>Staphylococcus aureus</i> Bacteremia
Dalbavancin for Treatment of <i>Staphylococcus aureus</i> Bacteremia Open
Importance Dalbavancin is a long-acting intravenous lipoglycopeptide that may be effective for treatment of complicated Staphylococcus aureus bacteremia without requiring long-term intravenous access. Objective To evaluate the efficacy and…
View article: A network analysis of carbapenem-resistant Klebsiella pneumoniae among healthcare facilities
A network analysis of carbapenem-resistant Klebsiella pneumoniae among healthcare facilities Open
View article: Genomic epidemiology and antimicrobial resistance of <i>Corynebacterium macclintockiae</i> , the predominant species of human pathogens within the <i>Corynebacterium jeikeium</i> complex
Genomic epidemiology and antimicrobial resistance of <i>Corynebacterium macclintockiae</i> , the predominant species of human pathogens within the <i>Corynebacterium jeikeium</i> complex Open
Genomic characteristics and optimal treatment of Corynebacterium jeikeium remain largely unknown. We collected clinical information and performed whole-genome sequencing analysis of the causative strains of six cases of C. jeikeium infecti…
View article: The global epidemiology of carbapenem-resistant <i>Acinetobacter baumannii</i>
The global epidemiology of carbapenem-resistant <i>Acinetobacter baumannii</i> Open
Carbapenem-resistant Acinetobacter baumannii (CRAb) is a challenging, environmentally hardy organism with a propensity to spread within hospitals and a predilection to infect critically ill, vulnerable patients. With its potential for rapi…
View article: Limitations of MALDI-TOF MS in identifying anaerobic bacteremia: challenges in polymicrobial infections and the role of whole-genome sequencing
Limitations of MALDI-TOF MS in identifying anaerobic bacteremia: challenges in polymicrobial infections and the role of whole-genome sequencing Open
With the widespread use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), the number of identifiable bacterial species has increased. However, anaerobic bacteremia remains challenging to accura…
View article: Comparative <i>in vitro</i> activity of sulbactam with avibactam or durlobactam against carbapenem-resistant <i>Acinetobacter baumannii</i>
Comparative <i>in vitro</i> activity of sulbactam with avibactam or durlobactam against carbapenem-resistant <i>Acinetobacter baumannii</i> Open
Objective To determine the in vitro activity of sulbactam in combination with avibactam or durlobactam with and without meropenem or imipenem against carbapenem-resistant Acinetobacter baumannii clinical isolates. Methods Standardized susc…
View article: Multiplex PCR assay to identify clinically important <i>Aeromonas</i> species
Multiplex PCR assay to identify clinically important <i>Aeromonas</i> species Open
The genus Aeromonas is increasingly implicated in human infections. However, accurate species-level identification remains challenging, particularly in clinical microbiology laboratories. This study aimed to develop a multiplex polymerase …
View article: Restoring the 2-set blood culture practice after the resolution of supply shortage
Restoring the 2-set blood culture practice after the resolution of supply shortage Open
Supply shortage of blood culture bottles occurred between July and September 2024, which substantially impacted infectious diseases practice globally. However, blood culture practice in the post shortage period is not well documented. We d…
View article: Clinical and molecular landscape of prolonged SARS-CoV-2 infection with resistance to remdesivir in immunocompromised patients
Clinical and molecular landscape of prolonged SARS-CoV-2 infection with resistance to remdesivir in immunocompromised patients Open
Patients with hematologic diseases have experienced coronavirus disease 2019 (COVID-19) with a prolonged, progressive course. Here, we present clinical, pathological, and virological analyses of three cases of prolonged COVID-19 among pati…
View article: Safety and Efficacy of Ephedrine Alkaloids-Free Ephedra Herb Extract (EFE) for Mild COVID-19: A Double-Blind, Placebo-Controlled, Randomized Comparative Trial
Safety and Efficacy of Ephedrine Alkaloids-Free Ephedra Herb Extract (EFE) for Mild COVID-19: A Double-Blind, Placebo-Controlled, Randomized Comparative Trial Open
Several Ephedra Herb-containing Kampo medicines are common initial treatments for various infections; however, the ephedrine alkaloids in Ephedra Herb can cause side effects by stimulating adrenergic receptors. Accordingly, an ephedrine al…
View article: A Systematic Review and Meta-analysis of the Effectiveness of Remdesivir to Treat SARS-CoV-2 in Hospitalized Patients: Have the Guidelines Evolved With the Evidence?
A Systematic Review and Meta-analysis of the Effectiveness of Remdesivir to Treat SARS-CoV-2 in Hospitalized Patients: Have the Guidelines Evolved With the Evidence? Open
Background With progressive accumulation of knowledge on SARS-CoV-2 infection clinical management, treatment guidelines recommended several options including remdesivir, a broad-spectrum antiviral. Given the evolving nature of coronavirus …
View article: Molecular epidemiology and patient outcome of carbapenem-resistant <i>Enterobacterales, Pseudomonas aeruginosa</i> and <i>Acinetobacter baumannii</i> in Japan: a multicenter study from MultiDrug-Resistant organisms clinical research network
Molecular epidemiology and patient outcome of carbapenem-resistant <i>Enterobacterales, Pseudomonas aeruginosa</i> and <i>Acinetobacter baumannii</i> in Japan: a multicenter study from MultiDrug-Resistant organisms clinical research network Open
Background and objectives Carbapenem-resistant Gram-negative bacilli (CRGNB), especially Enterobacterales, Pseudomonas aeruginosa and Acinetobacter baumannii, are critical pathogens associated with excess morbidity and mortality. To elucid…
View article: Ensitrelvir as a novel treatment option for mild-to-moderate COVID-19: a narrative literature review
Ensitrelvir as a novel treatment option for mild-to-moderate COVID-19: a narrative literature review Open
To address the coronavirus disease 2019 (COVID-19) pandemic, several antiviral agents targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed for clinical use. However, antivirals that can be administered…
View article: Global emergence of Carbapenem-resistant Hypervirulent Klebsiella pneumoniae driven by an IncFIIK34 KPC-2 plasmid
Global emergence of Carbapenem-resistant Hypervirulent Klebsiella pneumoniae driven by an IncFIIK34 KPC-2 plasmid Open
National Natural Science Foundation of China and National Institutes of Health.
View article: Cefotaxime-Resistant <i>Neisseria meningitidis</i> Sequence Type 4821 Causing Fulminant Meningitis
Cefotaxime-Resistant <i>Neisseria meningitidis</i> Sequence Type 4821 Causing Fulminant Meningitis Open
We explored the role of commensal Neisseria in the emergence of third-generation cephalosporin-resistant N. meningitidis. Cefotaxime resistance-conferring penA795 was prevalent among commensal Neisseria isolates in Shanghai, China, and was…
View article: Phenotypic and in silico characterization of carbapenem-resistant Serratia marcescens clinical strains
Phenotypic and in silico characterization of carbapenem-resistant Serratia marcescens clinical strains Open
S. marcescens has shown increased adaptive, resistance, and pathogenic potential, being responsible for different nosocomial infections.
View article: In vitro activity of aztreonam in combination with relebactam against gram-negative pathogens producing various serine and metallo-β-lactamases
In vitro activity of aztreonam in combination with relebactam against gram-negative pathogens producing various serine and metallo-β-lactamases Open
The addition of relebactam has a potential to restore the activity of aztreonam against strains that produce metallo-β-lactamase and serine‑β-lactamase. The combination may have a role in the treatment of infections due to these strains in…
View article: The impact of infectious diseases department on the incidence of hospital-onset bacteremia and fungemia at a tertiary care center: a retrospective cohort study
The impact of infectious diseases department on the incidence of hospital-onset bacteremia and fungemia at a tertiary care center: a retrospective cohort study Open
Introduction: Cases of hospital-onset bacteremia and fungemia (HOBF) are on the rise in Japanese hospitals, but little is known about their incidence in hospitals and how it relates to the availability of services provided by infectious di…
View article: Ensitrelvir treatment–emergent amino acid substitutions in SARS-CoV-2 3CLpro detected in the SCORPIO-SR phase 3 trial
Ensitrelvir treatment–emergent amino acid substitutions in SARS-CoV-2 3CLpro detected in the SCORPIO-SR phase 3 trial Open
The impact of treatment-emergent amino acid substitutions (TEAASs) in severe acute respiratory syndome coronavirus 2 (SARS-CoV-2) 3C-like protease (3CLpro) on clinical and virologic outcomes was evaluated in patients with mild-t…
View article: P-2163. Inconsistent identification of <i>Corynebacterium</i> species by MALDI-TOF MS and molecular characteristics of <i>Corynebacterium jeikeium</i> complex isolates causing invasive infections in Japan
P-2163. Inconsistent identification of <i>Corynebacterium</i> species by MALDI-TOF MS and molecular characteristics of <i>Corynebacterium jeikeium</i> complex isolates causing invasive infections in Japan Open
Background Corynebacterium spp. is increasingly identified due to widespread use of MALDI-TOF MS in clinical laboratories. However, accuracy of identification of Corynebacterium spp. and genetic characteristics of clinical isolates are unc…
View article: P-285. Effects of Comorbidities and Charlson Comorbidity Index Application on Patient Outcomes in Blood and Respiratory Carbapenem-Resistant Gram-Negative Bacterial Infections
P-285. Effects of Comorbidities and Charlson Comorbidity Index Application on Patient Outcomes in Blood and Respiratory Carbapenem-Resistant Gram-Negative Bacterial Infections Open
Background Infections with carbapenem-resistant (CR) organisms are more likely in patients with comorbidities and are associated with worse prognosis. The effect of specific and multiple comorbidities on the outcomes of patients with CR in…
View article: P-2021. How Have COVID-19 Treatment Guidelines and the Scientific Evidence Evolved throughout the Pandemic and Endemic Eras?
P-2021. How Have COVID-19 Treatment Guidelines and the Scientific Evidence Evolved throughout the Pandemic and Endemic Eras? Open
Background With progressive understanding of the natural history of COVID-19 and accumulation of knowledge on clinical management, treatment guidelines recommended several options including remdesivir (RDV), a broad-spectrum antiviral. Giv…
View article: P-1826. Genomic Epidemiology and Clinical Characteristics of <i>Stenotrophomonas maltophilia</i> at an academic medical center
P-1826. Genomic Epidemiology and Clinical Characteristics of <i>Stenotrophomonas maltophilia</i> at an academic medical center Open
Background S. maltophilia is an opportunistic pathogen in critically-ill and immunocompromised patients. Distinguishing between colonization and infection is challenging and genomic surveillance data are scarce. This study seeks to define …
View article: P-833. The trends of hospital-onset bacteremia at a tertiary care center and the impact of the establishment of infectious diseases department on its incidence: a 10-year longitudinal study
P-833. The trends of hospital-onset bacteremia at a tertiary care center and the impact of the establishment of infectious diseases department on its incidence: a 10-year longitudinal study Open
Background Hospital-onset bacteremia (HOB) is defined as the onset of bacteremia occurring three or more days after hospitalization. The incidence density of HOB has recently been used to assess the quality of overall hospital infection co…