Enhanced automated detection of outbreaks of a rare antimicrobial-resistant bacterial species.

Surveillance of antimicrobial resistance (AMR) is a crucial strategy to combat AMR. Using routine surveillance data, we could detect and control hospital outbreaks of AMR bacteria as early as possible. Previously, we developed a framework for automatic detection of clusters of AMR bacteria using SaTScan, a free cluster detection tool integrated into WHONET.

Development of selective isolation media for detecting the genera Actinomyces and Schaalia from oral specimens containing indigenous bacteria.

To isolate specific bacteria from samples constituting the microbiota, it is essential to employ selective media that suppress the growth of resident bacteria other than specific target bacteria. Selective media for clinically important (including , which was previously taxonomically classified as part of the genus ) have been limited because they have been designed for a limited range of species within the genus and require ingredients which are difficult to prepare and handle. This study aimed to develop a selective medium [referred to as and Selective Medium (ASSM)] for the isolation of a broad range of and species from samples mixed with resident bacteria.

In vitro activity of cefiderocol against carbapenemase-producing and meropenem-non-susceptible Gram-negative bacteria collected in the Japan Antimicrobial Resistant Bacterial Surveillance.

Objectives: The treatment options available for infections caused by multidrug-resistant Gram-negative pathogens are often limited. Cefiderocol (CFDC) is a novel siderophore cephalosporin that exhibits activity against these pathogens. Several studies have reported the in vitro activity of CFDC against isolates from Europe, the United States, and China, but the activity against carbapenem-resistant bacteria with IMP-type carbapenemase has not been extensively studied.

Emergence of an IncX3 plasmid co-harbouring the carbapenemase genes and .

Background: The spread of transmissible plasmids with carbapenemase genes has contributed to a global increase in carbapenemase-producing Enterobacterales over the past two decades, with and among the most prevalent carbapenemase genes.

Objectives: To characterize an isolate co-carrying and (JBEHAAB-19-0176) that was isolated in the Japan Antimicrobial Resistant Bacterial Surveillance in 2019-20, and to evaluate the functional advantage of carrying both genes as opposed to only one.

Methods: The whole-genome sequence of the isolate was determined using long- and short-read sequencing.

Epistasis, core-genome disharmony, and adaptation in recombining bacteria.

Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome and are frequently observed as tightly linked cassettes with major effects. By contrast, interspecific recombination in the core genome is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis.

Nationwide genome surveillance of carbapenem-resistant in Japan.

Japan is a country with an approximate 10% prevalence rate of carbapenem-resistant (CRPA). Currently, a comprehensive overview of the genotype and phenotype patterns of CRPA in Japan is lacking. Herein, we conducted genome sequencing and quantitative antimicrobial susceptibility testing for 382 meropenem-resistant CRPA isolates that were collected from 78 hospitals across Japan from 2019 to 2020.

Antimicrobial use and combination of resistance phenotypes in bacteraemic Escherichia coli in primary care: a study based on Japanese national data in 2018.

Background: Antimicrobial use (AMU) in primary care is a contributing factor to the emergence of antimicrobial-resistant bacteria. We assessed the potential effects of AMU on the prevalence of a combination of resistance phenotypes in bacteraemic Escherichia coli in outpatient care settings between primary care facilities ('clinics') and hospitals.

Methods: Population-weighted total AMU calculated from the national database was expressed as DDDs per 1000 inhabitants per day (DID).

Genetic and phenotypic characterizations of IncX3 plasmids harboring and in Japan.

IncX3 plasmids harboring play a major role in the spread of carbapenem resistance in Asia, particularly in China, in clinical and environmental settings. In this study, we present that Enterobacterales isolates carrying IncX3 plasmids harboring have been disseminated in Japan, where their identification was previously rare. In addition, , a single-nucleotide variant of , was found to be carried by an identical IncX3 plasmid.

Contrasting genes conferring short- and long-term biofilm adaptation in .

is an opportunistic food-borne bacterium that is capable of infecting humans with high rates of hospitalization and mortality. Natural populations are genotypically and phenotypically variable, with some lineages being responsible for most human infections. The success of is linked to its capacity to persist on food and in the environment.

Association between the proportion of laparoscopic approaches for digestive surgeries and the incidence of consequent surgical site infections, 2009-2019: A retrospective observational study based on national surveillance data in Japan.

Background: Surgical site infections (SSIs) are among the most common healthcare-associated infections. Laparoscopy is increasingly being used in various surgical procedures. However, no study has examined the association between the proportion of laparoscopic procedures and the incidence of SSIs in digestive surgery using nationwide surveillance data.

Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing.

Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and mycobacteria (Mycobacterium tuberculosis and nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages.

Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations.

Helicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them.