Severe fever with thrombocytopenia syndrome (SFTS), a novel infectious disease caused by a novel bunyavirus and with a high case fatality rate (CFR), was reported by Chinese scientists in 2011. The causative virus, Dabie bandavirus also known as the SFTS virus (SFTSV), belongs to the genus Bandavirus (formerly named Phlebovirus) of the family Phenuiviridae (formerly named Bunyaviridae). SFTS was also reported to be endemic in South Korea and Japan in 2013. SFTSV circulates between some species of ticks and animals in nature. Humans are infected with SFTSV through bites from ticks such as Haemaphysalis longicornis and Amblyomma testidinarium. Domesticated animals, such as cats and dogs, are also infected with SFTSV and shown SFTS-like symptoms with a high CFR, likely having been infected through tick bites in the living environment. Furthermore, there have been cases of patients with SFTS who were infected with SFTSV through close contact with sick cats or dogs. The CFR in patients with SFTS is approximately 30% in Japan. There is always a risk of SFTSV infection in human populations living in endemic areas. Therefore, the development of specific therapies and vaccines is urgently needed to reduce the number of fatal SFTS cases.

The prevalence and mortality rates of coronavirus disease 2019 (COVID-19) widely vary among populations. Mucosal immunity is the first barrier to the pathogen’s entry into the body. Immunoglobulin A (IgA) is the primary antibody responsible for mucosal immunity. We explored the relationship between selective IgA deficiency (SIgAD) and COVID-19 severity. We included 424 patients (203 women) with COVID-19. Eleven patients had SIgAD. Laboratory data of patients with SIgAD and normal IgA levels were compared. The relationship between SIgAD and severe COVID-19 infection was explored using logistic regression analysis. In the univariate logistic regression analysis, the risk of severe COVID-19 disease in patients with SIgAD was approximately 7.7-fold higher than that in other patients (odds ratio [OR], 7.789; 95% confidence interval [CI], 1.665–36.690, P = 0.008), while it was 4-fold (OR, 4.053; 95% CI, 1.182–13.903, P = 0.026) higher in the multivariate logistic regression analysis. Serum IgA levels were positively correlated with total lymphocyte counts and negatively correlated with C-reactive protein levels, which was a risk factor for severe COVID-19. In patients with SIgAD, the number of severe acute respiratory coronaviruses 2 that pass through mucosal membranes may be increased, leading to complications such as cytokine storm syndrome and acute respiratory distress syndrome.

Increased gallbladder wall thickening (GBWT) is a manifestation of increased capillary permeability caused by severe dengue. This study was carried out to link the severity of GBWT with bleeding risk and the need for transfusion. This retrospective study included all patients diagnosed with dengue infection either via dengue nonstructural protein-1 antigen or IgM antibody. Pearson's correlation, linear regression, and receiver operating characteristic curves were used for predictive analysis of GBWT with events of bleeding and need for transfusion of platelets during the hospital stay. A total of 177 participants met the inclusion criteria; the mean age was 33.17 ± 13.63 years. Mean GBWT was found to be 0.37 ± 0.15 cm, with 46.3% of patients having a thickness greater than 0.30 cm. A total of 16 patients had bleeding events, of which 7.3% had minor bleeding and 1.7% had a major bleeding event. Linear regression analysis showed that increased GBWT was associated with decreased platelet count on admission (P = 0.002) and lowest platelet counts (P = 0.004). GBWT was found to be predictive of bleeding events and transfusion of platelets at higher sensitivity and specificity than was either platelet count on admission and lowest platelet counts.

Malaria is parasitic disease cause by Plasmodium infection. In Thailand, coinfections of Plasmodium vivax and Plasmodium falciparum are commonly found. P. vivax infection has been increasing in the past decade. The objective of this study was to investigate the genetic diversity patterns of P. vivax merozoite surface protein 3 (PvMSP-3) genes in a total of 450 isolates collected from Thai-neighboring border areas during two different periods (2009–2014 and 2015–2016) using polymerase chain reaction (PCR)-restriction fragment length polymorphism method. Three major types of PvMSP-3α (A, B, and C) and PvMSP-3β (A, B, and C) were detected based on PCR product size. In total, 45 and 23 alleles of PvMSP-3α and 41 and 30 alleles of PvMSP-3β with different frequencies of samples were distinguished from the first and second period, respectively. Our results strongly indicate genetic diversity patterns of PvMSP-3 in isolates from the second period, especially in samples from the Thai–Myanmar border area. These two polymorphic genes could be used as molecular epidemiologic markers for genotyping P. vivax isolate in Thailand.

A rapid and simple alternative test to real-time reverse transcription-polymerase chain reaction (RT-PCR) is required for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to help curb the spread of coronavirus disease (COVID-19). In the present study, we compared the RT-PCR method with chemiluminescent enzyme immunoassay (CLEIA) and reverse transcription loop-mediated isothermal amplification (RT-LAMP). We observed that the number of SARS-CoV-2 RNA copies and the CLEIA antigen quantification values were highly correlated. The detection limit for antigen quantification was 42.8 RNA copies for saliva samples and 23.4 copies for nasopharyngeal swab samples. For both purified RNA and purification-free crude RNA, the number of RNA copies and RT-LAMP threshold time (Tt) values were inversely correlated. RT-LAMP with purified RNA detected low copy numbers of RNA (5–50 copies), whereas fewer than 250 RNA copies could not be detected using crude RNA. CLEIA antigen quantification is potentially useful for large-scale screening, as it is compatible with high-throughput testing. RT-LAMP with crude RNA samples is applicable for rapid point-of-care testing because it can directly use patient specimens. It is important to select a diagnostic method that is simple and rapid when compared with RT-PCR, depending on the situation.

Data on antifungal utilization trends are important for encouraging antifungal stewardship. This study explored the use of antifungal agents for systemic application and the impact of reimbursement policy changes in Australia. We analyzed national data from the Australian Pharmaceutical Benefits Scheme (PBS) (2005–2016) and determined patterns of use over time and the impact of reimbursement decisions using an interrupted time-series model. From 2005–2016, there was an increase in the use of most antifungals, especially fluconazole, itraconazole, and posaconazole. Ketoconazole was the most commonly dispensed systemic antifungal agent (46.0%) prior to being removed from the PBS list and being replaced by fluconazole (69.8%). The PBS event “Fluconazole and itraconazole restrictions eased” led to the immediate increased use of fluconazole (0.025/1,000 per day), with both the highest rates and numerical increases attributed to obstetricians and gynecologists (1,969%; 1,851 dispensed prescriptions), as well as dermatologists (1,723%; 1,689 dispensed prescriptions) in 2010 and 2016. This is the first Australian national longitudinal estimate of systemic antifungal use. Our findings show an overall increase in the prescription of most antifungals during the investigated period, with reimbursement decisions impacting utilization. These data provide a baseline to inform the development of national antifungal guidelines and policies to encourage more targeted antifungal stewardship.

The global prevalence of inflammatory bowel disease (IBD) is continuously rising; however, little is known about intestinal parasitic infections (IPIs) and IBD. We aimed to evaluate the prevalence of IPIs among IBD patients through a case-control study and to correlate the positive cases to the sociodemographic risk factors of IPIs among the study groups. A one-year case–control study included patients with IBD (n = 125) and healthy controls (n = 125). The fecal samples were examined using classical parasitological methods for intestinal parasites, including, in vitro culture (for Blastocystis sp.) and immunochromatography (for Cryptosporidium/ Giardia/ Entamoeba). IBD patients had a significantly higher positivity rate of IPIs than the healthy controls (adjusted OR = 9.60, 95% CI: 4.51–20.41, P = 0.0001) with Blastocystis sp., Entamoeba dispar/histolytica, and Cryptosporidium sp. being highly significant in IBD patients. In addition to IBD, living in rural areas, low socioeconomic status, raw/contaminated food consumption, and age group >50 years were the significant risk factors for IPIs. In conclusion, our results support a possible association between IPIs and IBD.

Using bacterial pan-genomes obtained through whole genome sequencing (WGS), coding DNA sequences (CDSs) can be clustered into pan-genome orthologous groups (POGs). We aimed to investigate comparative genomic features of Streptococcus canis based on POG analysis and to determine CDSs specific to prevalent sequence type (ST) 9. Twenty WGS datasets from S. canis strains, including invasive and non-invasive specimens, were retrieved from the National Center for Biotechnology Information Assembly database. Based on the WGS data, we performed comparative genome hybridization (CGH), pan- and core-genome prediction, Venn diagram testing with five ST9 strains, and phylogenetic analysis with ST determination. We compared the CDSs of seven ST9 and 13 non-ST9 strains. We observed genomic diversity based on CGH and Venn diagram analyses. The predicted pan- and core-genomes contained 4,772 and 1,403 genes, respectively. We found five clades consisting of different STs (ST1, ST44/2, ST13/14, ST21/15/41, and ST9) based on the phylogenetic tree. There were differences in four pathways (DNA restriction-modification system, DNA-mediated transposition, extracellular region, and response to oxidative stress) regulated by CDSs specific to ST9. Our findings describe genomic diversity in CGH and Venn diagram testing, pan- and core-genomes, five clades of genomes consisting of different STs, and unique CDS features associated with ST9.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China, in December 2019. Despite the recent introduction of vaccines against SARS-CoV-2, more effective vaccines and antiviral drugs must be developed. Here, we isolated five SARS-CoV-2 strains from four patients with coronavirus disease (COVID-19) and an asymptomatic individual using pharyngeal swabs, nasopharyngeal swabs, and sputum samples. Cytopathic effects in inoculated Vero cells were observed between days 3 and 7. SARS-CoV-2 infection was confirmed by quantitative reverse-transcription polymerase chain reaction (RT-qPCR) and next-generation sequencing. Phylogenetic analyses of the whole genome sequences showed that the virus isolates from the clinical samples belonged to the Wuhan and European lineages. These findings and the isolated viruses may contribute to the development of diagnostic tools, vaccines, and antiviral drugs for COVID-19.

The characteristics of coronavirus disease 2019 (COVID-19) clusters in medical and social welfare facilities and the factors associated with cluster size are still not yet fully understood. We reviewed COVID-19 cases in Japan identified from January 15 to April 30, 2020 and analyzed the factors associated with cluster size in medical and social welfare facilities. In this study, COVID-19 clusters were identified in 56 medical and 34 social welfare facilities. The number of cases in those facilities peaked after the peak of the general population. The duration of occurrence of new cases in clusters was positively correlated with the number of cases in both types of facilities (rho = 0.44, P < 0.001; and rho = 0.69, P < 0.001, respectively). However, the number of days between the first case in a prefecture and the onset of clusters was negatively correlated with the number of cases only in clusters in social welfare facilities (rho = − 0.4, P = 0.004). Our results suggest that COVID-19 cases in those facilities were prevalent in the latter phase of the disease’s community transmission, although the underlying mechanisms for such a trend could differ between medical and social welfare facilities.

The use of a metofluthrin-impregnated spatial repellent device (MSRD) is a new and effective method for preventing mosquito blood feeding. Indoor environmental factors such as room temperature and ventilation rate are thought to be important for MSRD activity. Measurements of room temperature and vaporization of metofluthrin from MSRD in typical rural metal-roof and thatched-roof houses in southeastern Malawi were conducted. The relationship between house structure and the number of collected Anopheline mosquitoes with and without MSRD treatment was also investigated. The difference between daytime and nighttime room temperature was significantly higher in metal-roof houses than in thatched-roof houses. The vaporization of metofluthrin from the MSRD was not accelerated by the high room temperature, but by the high indoor air flow by ventilation. The number of mosquito collections was significantly higher in thatched-roof houses than in metal-roof houses. MSRD-treated thatched-roof houses have a higher probability of mosquito infestation, but the vaporization of metofluthrin is also higher because of indoor air flow, resulting in a reduction in mosquito numbers. Metal-roof houses with closed eaves reduce the probability of mosquito invasion, and a longer predicted effectiveness occurs with MSRD because of the controlled release of metofluthrin through lower indoor air flow.

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is spreading worldwide and poses a public health issue. Assessing their presence in the environment and food chain products would elucidate the pathway of their foodborne transmission. Here, we investigated the prevalence of ESBL-producing E. coli in fresh vegetables purchased from fresh markets in Chiang Rai, Thailand. Overall, 8.8% of the samples collected contained ESBL-producing E. coli, of which 81.3% were multidrug-resistant. All isolates carried bla_CTX-M-55, and 10 isolates contained ISEcp1. One E. coli strain harbored bla_CTX-M-55 co-occurring with bla_TEM-1. Furthermore, 13 different sequence types (ST48, ST101, ST155, ST165, ST398, ST414, ST457, ST515, ST542, ST1081, ST3045, ST7538, and ST10651) were identified. One E. coli strain belonged to ST101, which is prevalent among human isolates. Thus, our study demonstrated the spread of CTX-M-55 on non-ST131 vegetable isolates that are not global pandemic strains and suggests that they may be a source of antibiotic resistance gene transfer from agricultural foods to humans. Further studies are needed to investigate whether the ESBL-producing E. coli transfer resistance genes to commensal E. coli and cause severe disease.

Based on previous studies, we found that Bacillus Calmette–Guérin (BCG) vaccination may play a role in preventing SARS-CoV-2 infection. Therefore, we conducted a meta-analysis to investigate this protective effect. We searched the Embase, PubMed, Web of Science, Cochrane Library, BioRxiv, and MedRxiv databases for studies that evaluated the relationship between BCG vaccination and SARS-CoV-2 infection or COVID-19 disease. The quality of all included studies was assessed using the Risk of Bias in Non-randomized Studies of Interventions and the Agency for Healthcare Research and Quality data tools. Review Manager (Version 5.3) was used to conduct all the data analyses. A total of eight studies were ultimately included in our meta-analysis. Our primary analysis found a significantly lower SARS-CoV-2 infection rate in the BCG vaccination group compared to the control group, with an odds ratio of 0.61, (95% confidence interval 0.39 to 0.95, P = 0.03; I² = 31%, and P = 0.21, respectively). Our study indicates that BCG vaccination can protect against SARS-CoV-2 infection. However, there is insufficient evidence that BCG vaccination can reduce the severity of COVID-19.

Several commercial nucleic acid amplification tests (NAATs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed. We used 6 kits available in Japan in 13 NAAT-positive specimens with crossing point values >36 and 7 NAAT-negative specimens from patients with coronavirus disease 2019 (COVID-19), and their results were compared. Specimens positive in ≥2 assays were considered true-positive and examined for concordance with the specimen results. The SARS-CoV-2 Detection Kit -Multi- (Toyobo M; Toyobo, Osaka, Japan) using extracted RNA had the highest concordance (κ = 1.00). This was followed by Cobas^® SARS-CoV-2 (Roche, Basel, Switzerland) (κ = 0.79). There was a weak correlation between the number of negative results for each kit and the number of days between onset and testing (Spearman rank correlation: ρ = 0.44; P < 0.05). We believe that the variations in results among kits for specimens with low viral loads should not be problematic when these kits are used for screening infectious patients because these variations are more likely to be observed in specimens tested many days after onset (i.e., those that have lost their infectivity). However, it may be better to use a test for suspected late-stage COVID-19 with a low viral load, such as Toyobo M or Cobas.

The aim of this study was to analyze the prevention and control practices against Zika virus (ZIKV) infection among pregnant women in Malaysia. A cross-sectional study was conducted among pregnant women who received antenatal care. Only 7.8% reported that they abstained from sex or used barrier methods during sexual intercourse to prevent ZIKV transmission. The odds of abstaining from sex or using barrier methods were significantly higher among the Chinese ethnic group than the Malay ethnic group (odds ratio [OR] = 4.569; 95% confidence interval [CI]: 2.696–7.743). A total ZIKV knowledge score of 12–24 was also significantly associated with higher odds of abstaining from sex or using barrier methods than a score of 0–11 (OR = 2.819; 95% CI: 1.682–4.725). In total, 38.6% of women had a higher mean total score for all the current mosquito control practices than they did before hearing of ZIKV. Participants living in bungalows or village houses (OR = 2.006; 95% CI: 1.023–3.936) and low-rise houses (OR = 1.566; 95% CI: 1.109–2.212) were more likely to have a higher mean total score of current mosquito control practices than the practices before hearing of ZIKV compared to those in high-rise houses. The lack of ZIKV knowledge and control practices provides insight for the pre-emptive and prompt development of health education systems for pregnant women during antenatal care visits.

Human parechoviruses (HPeVs) are being increasingly recognized as pathogens that cause mild-to-life-threatening diseases in children and adults. Recently, nucleic acid detection has become the mainstream method for pathogen detection. However, virus isolation is important for virus detection and further virologic characterization studies, and securing human pathogenic virus bioresources. We recently explored conventional cell lines suitable for human sapovirus isolation and accidentally identified a human duodenal cell line, HuTu80, that supported efficient growth of human parechovirus type 3 (HPeV-3) with clear cytopathic effects (CPE). Subsequently, we confirmed that all representative prototype HPeV type 1–6 strains were propagated efficiently in HuTu80 cells with clear CPE within 4 days. Another human ileocecal cell line, HCT-8 (HRT-18), also supports HPeV propagation except for HPeV-3. Titer values in HuTu80 and HCT-8 reached approximately 6.83–8.83 and 6.50–8.17 log₁₀ 50% tissue culture infectious dose/50 μL, respectively, when inoculated with multiplicity of infection of 0.0025. Previously reported cell lines likely support HPeV types 1–6 with different efficiency, especially for HPeV-3. In summary, HuTu80 can be used as an additional cell line for HPeV isolation, propagation with a clear CPE to produce a high titer value and for the virus neutralization assays.

We report a case of Campylobacter lari vertebral osteomyelitis with iliopsoas abscess. This is the first case report of vertebral osteomyelitis due to C. lari, which was identified from a vertebral biopsy sample collected using CT-guided percutaneous needle biopsy in a patient without obvious episodes of immunodeficiency. Cultureing using the HK semisolid medium aided in pathogen ideutification. It is important to make every possible effort to identify the causative pathogen in vertebral osteomyelitis.

Ferrets are animals that are known to be susceptible to influenza A virus (IAV) infection. To evaluate the risk of IAV transmission from diseased ferrets to humans, a survey was performed to detect specific antibodies against the H1, H3, H5, and H7 subtypes of IAV. Using enzyme-linked immunosorbent assay for hemagglutinin proteins, we found a high positive rate for the H1 (24.1%) and H3 (5.2%) subtypes. The results were confirmed by a virus neutralization test for representative antibody-positive serum samples. We also detected hemagglutinin and neuraminidase genes in two ferrets showing acute respiratory disease and whose owner was diagnosed with IAV infection; a human H1N1pdm virus was isolated from one of these ferrets. Our findings suggest that attention should be paid to IAV infection from humans to ferrets and vice versa.