Complete genome sequence of a clinical isolate harboring a novel variant of the carbapenemase gene, .

strain CRE21025 was isolated from a gallbladder abscess of a patient admitted to the hospital in Shimane Prefecture in 2021. Here, we present the complete genome sequence of this isolate, bearing a novel variant of the imipenemase-type gene, , by whole-genome sequencing using Oxford Nanopore and Illumina methods.

Acute Hepatitis E virus Subtype 3e Infection with Prolonged Jaundice Improved with Inchinkoto - A Case Report.

Hepatitis E virus (HEV) is a globally prevalent waterborne and zoonotic infection, with approximately 20 million infections occurring annually in developing and industrialized countries. Reported here are the details of a 73-year-old Japanese man who contracted HEV subtype 3e after consuming self-prepared pork liver from a domestically raised pig and presented with severe liver enzyme elevation. Conservative treatment, including hepatoprotective therapy and Inchinkoto, an herbal medicine, was administered for prolonged jaundice, and recovery was achieved.

Impact of the polymerase acidic protein E199K substitution in influenza A viruses on baloxavir susceptibility.

Baloxavir marboxil, a cap-dependent endonuclease inhibitor, was approved in Japan in 2018 for the treatment and prophylaxis of influenza. Its active form, baloxavir acid, binds to the polymerase acidic (PA) protein endonuclease domain, inhibiting viral RNA cleavage. PA substitutions (e.

Intra-individual polymorphisms in the mitochondrial COI gene of tick-killing Ixodiphagus wasps parasitizing Haemaphysalis flava ticks.

Ixodid ticks are significant vectors of pathogens affecting both humans and animals. Biological control with natural enemies represents a sustainable tool for managing ticks. However, there is a substantial lack of knowledge about the natural enemies of ticks.

Persistent SARS-CoV-2 infection resolved after B-cell recovery in a patient with follicular lymphoma treated with B-cell depletion therapy.

A 68-year-old woman with follicular lymphoma was treated with chemotherapy, including the anti-CD20 monoclonal antibody obinutuzumab, and achieved remission. A month after the administration of obinutuzumab, the patient contracted coronavirus disease 2019 (COVID-19), and various antiviral drugs were administered. However, the infection had not been eliminated.

Transmission Cycle of Shimokoshi-Type Orientia tsutsugamushi in Shimane Prefecture, Japan.

To demonstrate the transmission cycle of Shimokoshi-type Orientia tsutsugamushi in Shimane Prefecture, field rodents were captured from areas where four human infections caused by the pathogen have been reported. The rodents were investigated for the transmission cycle of the pathogen based on the pathogen's genome, antibodies against the pathogen, and the vector of the pathogen (Leptotrombidium palpale). In addition, the vector was captured from the soil in the study area.

Quantitative detection and genetic characterization of thermotolerant spp. in fresh chicken meats at retail in Japan.

and are one of the leading causes of gastrointestinal illnesses, and which are considered to be transmitted to humans mainly from chicken meats. Considering the less availability of quantitative contamination data in the retail chicken meats in Japan, 510 fresh chicken meats retailed at five distinct regions in Japan between June 2019 and March 2021 were examined. The quantitative testing resulted that 45.

Rapid detection and discrimination of potentially toxigenic Corynebacterium ulcerans and Corynebacterium pseudotuberculosis by multiplex real-time PCR and amplicon melting curve analysis.

We developed a multiplex real-time PCR assay with amplicon melting curve analysis to rapidly discriminate Corynebacterium ulcerans from Corynebacterium pseudotuberculosis and detect the bacterial diphtheria toxin gene. This assay should be a valuable tool for identification of potentially toxigenic C. ulcerans.

Bacterial Distribution and Community Structure in Beef Cattle Liver and Bile at Slaughter.

Abstract: In this study, the distribution of hygienic indicator bacteria in cattle livers and bile was examined at slaughterhouses. One hundred twenty-seven cattle livers with gallbladders were carefully eviscerated from carcasses at 10 slaughterhouses. Microbiological examination revealed that nine bile samples (7.

Long-Term Grow-Out Affects Colonization Fitness in Coincidence With Altered Microbiota and Lipid Composition in the Cecum of Laying Hens.

is one of the leading causes of gastrointestinal illness worldwide and is mainly transmitted from chicken through the food chain. Previous studies have provided increasing evidence that this pathogen can colonize and replicate in broiler chicken during its breeding; however, its temporal kinetics in laying hen are poorly understood. Considering the possible interaction between and gut microbiota, the current study was conducted to address the temporal dynamics of in the cecum of laying hen over 40 weeks, with possible alteration of the gut microbiota and fatty acid (FA) components.

Time-resolved characterization of organic compounds in PM collected at Oki Island, Japan, affected by transboundary pollution of biomass and non-biomass burning from Northeast China.

To evaluate the transboundary pollution of organic aerosols from Northeast Asia, a highly time-resolved measurement of organic compounds was performed in March 2019 at Oki Island located in Japan, which is a remote site and less affected by local anthropogenic sources. PM, water-soluble organic carbon (WSOC) concentrations, and WSOC fraction in PM showed high values on March 22-23 (high-WSOC period (HWSOC)) when the air mass passed through the area where many fire spots were detected in Northeast China. Biomass burning tracers showed higher concentration, especially levoglucosan exceeded 1 μg/m during the HWSOC than the low-WSOC period (LWSOC).

Phylogeny, Prevalence, and Shiga Toxin (Stx) Production of Clinical Escherichia coli O157 Clade 2 Strains Isolated in Shimane Prefecture, Japan.

This study investigated the genetic and pathogenic variation of the subgroups of clade 2 strains of Shiga toxin (Stx)-producing Escherichia coli (STEC) O157. A total of 111 strains of STEC O157 isolated in Shimane prefecture, Japan, were classified in clade 2 (n = 39), clade 3 (n = 16), clade 4/5 (n = 3), clade 7 (n = 14), clade 8 (n = 17), and clade 12 (n = 22) by single-nucleotide polymorphism analysis and lineage-specific polymorphism assay-6. These results showed a distinct difference from our previous study in which clade 3 strains were the most prevalent strains in three other prefectures in Japan, indicating that the clade distribution of O157 strains was different in different geographic areas in Japan.

Sensitive Gas Chromatography Detection of Nanomolar Hydroxylamine in Environmental Water by Fe(III) Oxidation.

Nanomolar concentrations of NHOH in natural water sources were determined using an Fe oxidation method. A pH of 2.35 - 2.

Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses.

Sapoviruses are increasingly being recognized as pathogens associated with gastroenteritis in humans. Human sapoviruses are currently assigned to 18 genotypes (GI.1-7, GII.

Influenza A(H1N1)pdm09 virus exhibiting reduced susceptibility to baloxavir due to a PA E23K substitution detected from a child without baloxavir treatment.

Human-to-human transmission of PA I38 mutant influenza A(H3N2) viruses with reduced baloxavir susceptibility has been reported in Japan. In December 2019, we detected a PA E23K mutant A(H1N1)pdm09 virus from a child without baloxavir treatment. The PA E23K mutant virus exhibited reduced baloxavir susceptibility but remained susceptible to neuraminidase inhibitors.

Severe fever with thrombocytopenia syndrome complicated with subdural hematoma: A rare case and literature review.

A 79-year-old woman presented with fever and general malaise. Examination revealed hepatic injury, thrombocytopenia, skin lesions, and regional lymphadenopathy; severe fever with thrombocytopenia syndrome (SFTS) was diagnosed using polymerase chain reaction. The patient developed impaired consciousness that worsened after 4 days.

T serotyping of group a streptococcus isolated from patients with pharyngitis or streptococcal toxic shock syndrome in Japan between 2005 and 2017.

Streptococcus pyogenes (group A streptococcus; GAS) is an important gram-positive human pathogen capable of causing diseases ranging from mild superficial skin and pharyngeal infections to more severe invasive diseases, including streptococcal toxic shock syndrome (STSS). GAS produces a T protein, and T serotyping has considerable discriminatory power for epidemiological characterization of GAS. To clarify the relationship between STSS and pharyngitis in Japan, we examined the T serotypes of GAS strains isolated from clinical specimens of streptococcal infections (STSS, 951 isolates; pharyngitis, 16268 isolates) from 2005 to 2017.

Neonicotinoids disrupt aquatic food webs and decrease fishery yields.

Invertebrate declines are widespread in terrestrial ecosystems, and pesticide use is often cited as a causal factor. Here, we report that aquatic systems are threatened by the high toxicity and persistence of neonicotinoid insecticides. These effects cascade to higher trophic levels by altering food web structure and dynamics, affecting higher-level consumers.

Increased community-acquired upper urinary tract infections caused by extended-spectrum beta-lactamase-producing Escherichia coli in children and the efficacy of flomoxef and cefmetazole.

Background: Urinary tract infections caused by extended-spectrum beta-lactamase-producing bacteria are increasing worldwide. At our hospital, the number of pediatric patients hospitalized because of an upper urinary tract infection has dramatically increased since 2016. In total, 60.

Identification of geosmin biosynthetic gene in geosmin-producing colonial cyanobacteria Coelosphaerium sp. and isolation of geosmin non-producing Coelosphaerium sp. from brackish Lake Shinji in Japan.

Geosmin is an earthy-muddy smelling compound produced in aquatic ecosystems by microorganisms including cyanobacteria. An increase in geosmin levels affecting the local fishery occurred in May 2007 in Lake Shinji, Japan, and geosmin-producing colonial cyanobacterium, Coelosphaerium sp. G2, was isolated from a water sample from the lake and identified.

Broadly reactive real-time reverse transcription-polymerase chain reaction assay for the detection of human sapovirus genotypes.

Sapoviruses are associated with acute gastroenteritis. Human sapoviruses are classified into four distinct genogroups (GI, GII, GIV, and GV) based on their capsid gene sequences. A TaqMan probe-based real-time reverse transcription-polymerase chain reaction (RT-PCR) assay that detects the representative strains of these four genogroups is widely used for screening fecal specimens, shellfish, and environmental water samples.

Comparison of Neutralizing Antibody Titers against Japanese Encephalitis Virus Genotype V Strain with Those against Genotype I and III Strains in the Sera of Japanese Encephalitis Patients in Japan in 2016.

Japanese encephalitis (JE) is an acute viral disease caused by the Japanese encephalitis virus (JEV). JEV strains are classified into 5 genotypes (I-V). JEV genotype V strains have never been detected in Japan to date, but they were recently detected in South Korea.