Dengue fever outbreaks have been repeatedly reported in Cote d’Ivoire. In 2019 outbreak, DENV-1 was predominant and phylogenetic analysis of the DENV-1 strain detected in a present patient who returning to Japan in January 2019 revealed high homology with the 2013-2014 Southeast Asian strains. Previous outbreak in 2017, DENV-1 accounted for 5% of the DENV serotypes. The endemic DENV-1 strain in Abidjan in 2019 could be a strain that was imported from Southeast Asia. Dengue virus spreads intercontinentally and imported dengue fever case could be an alert for the outbreaks in the exporting country.

Pulmonary nocardiosis is a common disease among HIV-infected patients. In most cases, the disease progresses slowly. Here, we present a case whose disease progressed rapidly. A 35-year-old female with AIDS and superior vena cava (SVC) syndrome who was lost to follow-up visited our hospital. She presented with a chronic non-productive cough and her CD4 count was 33 (4%). Her chest x-ray showed opacity in the right upper lobe of her lung and her sputum acid-fast stain was negative. Anti-tuberculosis agents were prescribed. Two weeks later, superficial vein dilatation appeared on her chest wall and her chest x-ray became worse. CT chest showed a mass in her right lung. The size of the mass was 9.6 x 9.8×8.3 cm. The mass was heterogeneous. Necrotic mediastinal nodes nearly obliterated the SVC. Gram-positive beading and branching filamentous organisms were identified in her sputum by modified acid-fast stain. She was diagnosed with pulmonary nocardiosis. This diagnosis was confirmed by culture. She had Nocardia beijingensis with SVC syndrome. She responded to treatment. After two weeks of parenteral agents, we switched her to oral trimethoprim/sulfamethoxazole which was later followed by antiretroviral agents.

Five novel strains of Serratia fonticola that produce FONA, a minor extended spectrum beta-lactamase (ESBL), were isolated during the routine surveillance of ESBLproducing Enterobacteriaceae in imported chicken meat in Japan in 2017 and 2018. These strains exhibited a clear ESBL phenotype in susceptibility tests carried out in the presence of clavulanic acid; however, they were all negative in the multiplex polymerase chain reaction assay used to detect the TEM, SHV and CTX-M β-lactamase genes. After identification of the bacterial species as S. fonticola, full bla_FONA genes were amplified and the DNA sequences were determined. The bla_FONA genes from all five strains were different from those previously reported (bla_FONA-1 to bla_FONA-6); they clustered closely with one another but were distinct from previously reported blaFONA genes in a phylogenic analysis based on amino acid sequences.

Delayed diagnosis of congenital tuberculosis (TB) in a neonatal intensive care unit (NICU) is a serious problem in terms of infection control. Here, we report our preemptive infection control activities implemented after the diagnosis of miliary TB in a mother of preterm twins (index twins, NB1 and NB2) in NICU. Added to this, we reviewed previous case reports of congenital TB exposure in the NICU setting. Immediately after recognizing miliary TB of the mother, the index twins were isolated before their TB diagnosis and received preemptive antiTB medication, and contact investigations were also conducted. Eventually, NB1 was diagnosed with congenital TB at 29 days of age and NB2 showed no definite evidence of TB. Through contact investigation, 11 of 16 exposed infants received isoniazid prophylaxis and no positive TST result was detected after 3 months. One of 31 exposed health care workers showed new interferon-gamma release assay conversion. Moreover, our case showed much shorter contagious period compared to those of the previous reports (8 versus 17–102 days). This suggests that a high index of suspicion and prompt measures can help prevent congenital TB outbreak and reduce the burden of infection control activities in NICU.

We report a hospitalized patient with COVID-19 whose fecal samples turned negative 22 days later than the respiratory samples. It highlights that the duration of virus release from patients is longer than previously expected. Current clinical examinations for treatment and discharge standard are limited to respiratory samples. However, we believe that nucleic acid testing of both respiratory and fecal samples is necessary for discharged patients. Further studies are needed to confirm the potential for fecal-oral transmission or fecal-respiratory transmission via aerosols.

To analyze clinical characteristics and potential predictors of disease severity in patients with COVID-19.Clinical data from 64 patients with COVID-19 were retrospectively analyzed. Of the 64 patients, 37 were male and 27 were female. Their mean age was 47.8 years, 43 (67.2%) cases were non-severe, 21 (32.8%) were severe, and 2 patients (3.1%) died. Age and serum ferritin were significantly associated with COVID-19 severity. Repeated monitoring of ferritin, interleukin-6, C-reactive protein, lactic acid dehydrogenase, and erythrocyte sedimentation rate during COVID-19 treatment may assist the prediction of disease severity and evaluation of treatment effects. There were no significant differences in the duration of severe illness or the number of days on high-level respiratory support between a low-dose methylprednisolone group and a high-dose methylprednisolone group. The mean number of days in hospital in the high dose group was higher than that in the low-dose group. Repeated monitoring of ferritin, interleukin-6, C-reactive protein, lactic acid dehydrogenase, and erythrocyte sedimentation rate during COVID-19 treatment may assist the prediction of disease severity and evaluation of treatment effects.

JC polyomavirus (JCPyV) causes progressive multifocal leukoencephalopathy (PML), a demyelinating disease of the central nervous system in immunocompromised patients. Study of PML-type JCPyV in vitro has been limited due to difficulty in efficient propagation of the virus in cultured cells. In this study, we carried out long term cultivation of COS-7 cells (designated as COS-IMRb cells) transfected with PML type M1-IMRb, an adapted viral DNA with a rearranged non-coding control region (NCCR). The JCPyV derived from COS-IMRb cells was characterized by analyzing viral replication, amount of virus by hemagglutination (HA), production of viral protein 1 (VP1), and structure of the NCCR. HA assays indicated that a high amount of PML type JCPyV was present in COS-IMRb cells. Immunostaining showed that VP1-positive cells were a small population in COS-IMRb cells that represented a JCPyV carrier cell culture. Sequencing analysis of the NCCR of JCPyV after long-term cultivation showed that the NCCR of M1-IMRb was conserved in COS-IMRb cells without any point mutation. The JCPyV genomic DNA derived from a clone of COS-IMRb-3 cells was detected by Southern blotting as a single band of approximately 5.1 kbp without deletion. These findings support that COS-IMRb-3 cells may offer a useful tool for screening anti-JCPyV drugs.

In the last decade, methicillin-resistant Staphylococcus aureus (MRSA) has been identified in livestock animals, such as swine, poultry, and veal calves, and termed livestock-associated MRSA (LA-MRSA). LA-MRSA sequence type (ST) 398 strains can effectively colonize and infect humans, with subsequent transmission in both community and hospital settings. Unlike other countries, LA-MRSA was not yet reported in Japanese patients until 2019. However, we recently reported a case of intractable arthritis caused by a LA-MRSA CC398 (ST1232) clone, which is a single locus variant of ST398, in a patient in Tokyo, Japan, with no animal contact (Emerg Infect Dis 2020; 26: 795-97). Uniquely, the strain was positive for Panton-Valentine leukocidin. Here, we report the second such case ever found in Japan. To prevent dissemination of LA-MRSA in the Japanese community, the prevalence of the CC398 MRSA clone should be closely monitored in the future.

High-level aminoglycoside resistance (HLAR) limits treatment options for invasive enterococcal infections. We examined the prevalence of HLAR by disk diffusion method, carriage of genes for aminoglycoside-modifying enzymes by PCR, and production of β-lactamase by nitrocefin-based test in Enterococcus faecalis and Enterococcus faecium isolated from patients at a university hospital in Tokyo in 2010. Of the 100 E. faecalis isolates analyzed, 30 isolates had high-level resistance (HLR) to gentamicin and 22 isolates had HLR to streptomycin. Of the 40 E. faecium isolates analyzed, nine isolates had HLR to gentamicin and nine isolates had HLR to streptomycin. Of the 39 gentamicin-HLR enterococcal isolates, 24 isolates were non-HLR to streptomycin. All 39 isolates with HLR to gentamicin as well as 19 of 101 without HLR carried aac(6’)-Ie-aph(2’’)-Ia. Carriage of ant(6')-Ia was confirmed in 25 of 31 streptomycin-HLR isolates. Production of β-lactamase was documented in none of the E. faecalis and E. faecium isolates. Whole-genome sequencing analysis revealed that all but one E. faecalis isolates that carried aac(6’)-Ie-aph(2’’)-Ia and ant(6')-Ia belonged to sequence type (ST) 4 (n=8), ST16 (n=4), or ST179 (n=9). Nevertheless, most of the pairs of isolates had > 10 single-nucleotide polymorphisms even among the isolates of the same ST.

Dengue virus (DENV) infection is still a serious health problem in Indonesia. Community based dengue study to determine circulated DENV in certain place and time is limited due to expensive cost and effort. Many DENV infected patients are not admitted to the hospital, and many patients come to the hospital at later phase of disease. In this study, we developed active DENV cases finding in the community in Jakarta to study circulating dengue serotypes where adult febrile patients with fever less than 48 hours were recruited. Disease severities were defined using the World Health Organization (WHO) 1997 guideline. Rapid NS1 dengue antigen detection were used to screen DENV patients in the community. Viral isolation in C6/36 cell line or increased antibody titer by HI and ELISA or RT–PCR were performed to confirm DENV infection.Viral serotype was investigated through RT-PCR. From 102 patients, 68 (66.7%) patients were confirmed DENV infection with DENV-2 is the most dominant serotype followed by DENV-3, DENV-1 and DENV-4, in concordance with several cases of mixed DENV infection. Interestingly, in terms of disease severity, although DENV-3 infection is not the predominant circulating serotype, but its infection tend to give more severe disease compare to DENV-2 infection.

Low levels of blood vitamin D have been reported in children who have frequent respiratory tract infections. We measured serum concentrations of 25-hydroxy (OH) vitamin D in Japanese infants less than 3-months old infected with respiratory syncytial virus (RSV). Serum levels of 25-OH vitamin D of the 10 infants, excluding those with underlying diseases, were between less than 4 to 29.8 ng/mL. In 8 out of 10 subjects (80.0%), serum 25-OH vitamin D levels were less than 20 ng/mL. There was no statistically significant association between levels of 25-OH vitamin D and age, duration of admission, respiratory severity score, white blood cell count, blood gas levels, and NT-proBNP levels. Levels of serum 25-OH vitamin D in children who required hospitalization owing to RSV infection were low, indicating deficiency. These results suggested that vitamin D deficiency affects the susceptibility to RSV infection, but not the severity of the RSV respiratory infection.

There was epidemiological correlation in time and in space between gonorrhea and genital chlamydia and between condyloma and genital herpes. There was, however, no correlation in other combinations, such as, gonorrhea and condyloma, genital herpes and chlamydia, etc. The annual incidence of gonorrhea and that of genital chlamydia were mono-phasic with a peak in 2005-2006. The annual incidence of condyloma and that of genital herpes were biphasic with the first distinct peak in 2004-2006 borne by younger generation and the second broad peak borne by the older generation that experienced the first wave.The epidemiology of syphilis was entirely different from gonorrhea, genital chlamydia, condyloma and genital herpes: the incidence of early, late and asymptomatic syphilis all started increasing around 2010 attaining total 1,576 notifications in 2017. The increase was associated with shift of patients’ peak age to younger generation. Preceding this increase, however, between 2005 and 2006, the annual number of congenital syphilis that had been ≥200 dropped to 12, and asymptomatic syphilis that had been annually <10 jumped up to 195 and increased continuously thereafter.

Zoonotic Cutaneous Leishmaniasis (ZCL) is one of the most prevalent zoonoses in Iran, especially in its central and northeast parts. This research aims to examine if there are spatiotemporal clusters of the ZCL cases, and if so, whether there are disparities in clustering according to age, gender, home situation, and occupation. The spatial analysis, including global and local spatial autocorrelations, inverse distance weighting, and space-time scan statistics were applied to determine potential clusters in Golestan villages during 2011-2016. Several spatially significant (p < 0.05) clusters were observed in the north and the northeastern regions, where most of them persisted for the last years of the study period. Children (0–10 years) living in rural settings were more likely to have the infection than those living in other areas. Despite the focus of the disease in the northern regions, housekeepers, females, and patients aged 21-30 and 41-50 years were found to be the high-risk groups in the southern areas. The seasonal pattern indicates that the outbreak mainly begins in late summer, peaks in October, and diminishes in December. By exploring spatiotemporal variations of ZCL by sociodemographic information, this study can identify priority areas for health decision-makers and resource allocation.

High-risk human papilloma virus (hrHPV) plays an important role in the cause of cervical cancer. The aim of this study is to investigate the distribution of HPV genotypes in the region and to correlate with the liquid-based-cytology (LBC) and colposcopic biopsy results. Furthermore, the potential relationship between HPV infections and bacterial vaginosis (BV) was investigated. HPV genotypes were determined by real-time PCR using a commercial kit at molecular microbiology. LBC, biopsies and BV examinations were performed at Pathology& Cytology. The consecutive cervical specimens of 409 women having both of cytology and HPV-DNA tests were included in the study. A total of 172(42.1%) patients [107(26.2%) with hrHPV] had HPV-DNA positive. The most common HPV genotypes were HPV 59,16,33,52, 51 (16.6%,15.9%,13.4%,13.4%,8.9%) respectively. Epithelial cell abnormality was detected in 11.5% of the LBC tests. The genotypes of HPV 33,56, 66, and 68 were found at a higher rate in patients who had epithelial cell abnormalities than in those with no detected abnormalities. Bacterial vaginosis was found in 24 (5.9%) of the patients. HPVDNA positivity was observed statistically higher in patients with BV than non-BV.

Non-O157 Shiga toxin-producing Escherichia coli (STEC) are a growing concern for public health. The number of sporadic cases and outbreaks due to non-O157 STEC are increasing. Molecular subtyping that discriminates the isolates rapidly with high resolution is essential to identify clusters of cases and/or detect and investigate outbreaks. Multiple-locus variable-number tandem repeat analysis (MLVA) is one of the most useful typing methods for isolates responsible for foodborne diseases. In Japan, serogroups O26, O111, O103, O121, O145, O165, and O91 are frequently isolated or associated with severe cases of non-O157 STEC infections. In this study, we designed an MLVA scheme (MLVA43) by adding 26 loci to an MLVA scheme (MLVA17) previously developed by our group for O157, O26, and O111 using 17 loci; the current scheme focused on serogroups O103, O121, O145, O165, and O91. Discriminatory power of MLVA43 was comparable to that of pulsed-field gel electrophoresis (PFGE) for serogroups O103, O145, O165, and O91, and superior to that of PFGE for O121. MLVA43 identified more profiles than did MLVA17, except for serogroup O111 with 707 isolates. The new MLVA43 scheme would enable rapid identification of clusters and outbreaks, which will help rapid measure against non-O157 STEC infections.

Respiratory tract infections (RTIs) are the most common diseases globally among children. This study aimed to assess the epidemiology of admission-requiring pediatric RTI cases and to evaluate the effect of pathogen type on length of hospital stay (LOS) using the FilmArray^® respiratory panel, a multiplex PCR test. The age-specific distribution and seasonality of viruses were investigated between March 26, 2018 and April 12, 2019. Multivariable linear regression analyses were performed to evaluate the effect of pathogen type and coinfection on LOS. Among 153 hospitalized RTI patients, respiratory syncytial virus (RSV) was the leading cause of hospitalization in infants <12 months old (27.7%). Among 2-3 years olds, human metapneumovirus (hMPV) and parainfluenza were also major causes of hospitalization (22.6% and 22.6%, respectively). In the multivariable linear regression model excluding rhinovirus/enterovirus, there wasa a significant association of viral coinfection with longer LOS infection (p=0.012), while any types of single viral infection was not positively correlated with LOS. This study revealed the epidemiology of admission-requiring pediatric RTIs.

Since the beginning of the SARS-CoV-2/COVID-19 epidemic in China, elderly and multimorbid subjects showed a higher mortality rate. However, other factors could influence the mortality and the spread of contagion such as the population density. An archival research based on the Italian data stratified by region was performed in order to quantify the association between the population density, ageing index, number of positive cases, number of deaths, case-fatality rate, and medical equipment (gloves, masks, and ventilators). Results showed a significant positive linear relationship between the population density and cases, deaths, and case-fatality rate. No correlation with the ageing index was shown. Furthermore, we found a significant positive correlation between the number of medical supplies and population density, cases, and deaths. However, the medical supplies did not show any correlation with the case-fatality rate. Taken together, these findings suggest that the population density and the lack of medical equipment are key factors explaining morbidity and mortality of COVID-19 in Italy.

A pandemic named coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbroke in China since December 2019. This disease has caused more than 70000 deaths worldwide. We intend to analyze the risk factors of death and establish a prognosis nomogram for critical patients with COVID-19. We analyzed the clinical data of COVID-19 patients in Zhongnan Hospital of Wuhan University who were critical cases with COVID-19 before March 20, 2020. Data were collected at admission and compared between survivors and non-survivors and analyzed by univariable and multivariable logistic regression analysis. Finally, 104 patients were included, and 50 of whom died. Age [ OR 5.73 (95% CI, 1.14-28.81)], chest tightness [OR 5.50 (95%CI, 1.02-29.64)], AST [OR 6.57 (95%CI, 1.33-32.48)]and BUN [5.59 (95%CI, 1.05-29.74)] at admission were considered to predict the risk of death in critical patients and were selected to construct the nomogram. Subsequently, we established a nomogram model and validated it. The sensitivity and specificity of the nomogram were 96.0% and 74.1%, respectively. The AUC was 0.893 (95% CI, 0.807-0.980).

Eleven asymptomatic carriers who received nasal or throat swab test for SARS-CoV-2 after close contacts with patients who developed symptomatic 2019 coronavirus disease (COVID-19) were enrolled in this study. The chest CT images of enrolled patients were analyzed qualitatively and quantitatively. There were 3 (27.3%) patients had normal first chest CT, two of which were under age of 15 years. Lesions in 2 (18.2%) patients involved one lobe with unifocal presence. Subpleural lesions were seen in 7 (63.6%) patients. Ground glass opacity (GGO) was the most common sign observed in 7 (63.6%) patients. Crazy-paving pattern and consolidation were detected in 2 (18.2%) and 4 (36.4%) cases, respectively. Based on deep learning quantitative analysis, volume of intrapulmonary lesions on first CT scans was 85.73±84.46 cm³. In patients with positive findings on CT images, average interval days between positive real-time reverse transcriptase polymerase chain reaction assay and peak volume on CT images were 5.1±3.1 days. In conclusion, typical CT findings can be detected in over 70% of asymptomatic SARS-CoV-2 carriers. It mainly starts as GGO along subpleural regions and bronchi, and absorbs in nearly 5 days.

The morphological changes in structure of HSV-1 viral thymidine kinase (vTK) polypeptide usually leads to conferring acyclovir (ACV)-resistance. HSV-1 I4-2, in which an amber UAG stop codon is present at the 8th position between the 1st initiation AUG codon (1st position) and the 2nd initiation AUG codon (46th position) of HSV-1 vTK gene, showed sensitivity to acyclovir (ACV), whereas HSV-1 KG111, in which an amber codon was artificially inserted at the 44th position, showed resistance to ACV at 39˚C. The mechanism for the difference in the sensitivity profiles was elucidated. The virus recombinants HSV-1-TK(8UAG) and HSV-1-TK(44UAG) containing an amber codon at the 8th and 44th positions counted from the 1st initiation codon, respectively, were generated and tested for susceptibility to antiviral compounds. HSV-1-TK(8UAG) and HSV-1-TK(44UAG) were sensitive and resistant to ACV and BVdU at 37˚C, respectively. The expression level of the truncated viral thymidine kinase translated from the 2nd initiation codon in Vero cells infected with HSV-1-TK(44UAG) was clearly less than that with HSV-1-TK(8UAG) in a temperature-dependent manner. The differences in the antiviral sensitivity profiles were due to the position of the amber UAG codon between the 1st and the 2nd initiation codons.

The disease caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) in Wuhan, China, in December 2019 is currently spreading rapidly worldwide. SARS-CoV-2 is usually detected via real-time RT-PCR. However, as institutions/hospitals deal with increasing numbers of specimens, a simpler detection system is required. Here, we present an ultra-rapid, real-time RT-PCR assay for SARS-CoV-2 using the PCR1100 device. Although this tests only one specimen at any one time, the amplification period is <20 min, with maintenance of the sensitivity and specificity of conventional real-time RT-PCR performed using large instruments. The method will be very helpful if SARS-CoV-2 testing is required a few times daily, for example to confirm virus-free status prior to discharge.

We analyzed the trends in the coronavirus disease 2019 (COVID-19) outbreak in Tokyo and Osaka from January 25 to May 06, 2020. To analyze the trends and to identify significant changes in trends we performed a joinpoint regression analysis. Since the last of March, COVID-19 cases soared up in Tokyo (β = 103.51) and Osaka (β = 28.07). During the 2^nd and 3^rd weeks of April, both Tokyo (β = 157.53) and Osaka (β = 60.96) experienced the peak growth in COVID-19 cases. Since then, with some hope, almost after 14 days of the state of emergency declaration, the cases showed a containment trend but still increasing at a concerning rate in Tokyo (β = 90.66).

Current studies have indicated association of gut microbiome composition with varieties of disorders including infectious diseases. The microbiome composition is different among races and countries, possibly resulting in diversified interaction between host immune and gut microbiome. Characterization of the baseline microbiota in healthy people is an essential step to understand this biological interaction in individual populations. However, data on gut/fecal microbiome has not been accumulated in West Africa. In the present study, we examined fecal microbiome composition in healthy adults in Ghana. The 16S rRNA gene libraries were prepared using bacteria fractions derived from 55 Ghanaian adults and subjected to next generation sequencing. Fecal microbiome of Ghanaian adults was dominated by Firmicutes (Faecalibacterium, Subdoligranulum, and Ruminococcaceae UCG-014), Proteobacteria (Escherichia-Shigella and Klebsiella), and Bacteroidetes (Prevotella 9 and Bacteroides), consistent with previous observations in African cohorts. Analysis found difference in composition and lower diversity of fecal microbiome in our cohort compared to non-African countries. This is the first study that describes substantial fecal microbiome data obtained by using high throughput metagenomic tools in Ghana. These data would be valuable as a basis for determination of the association between fecal microbiome and progression of varieties of diseases in West African populations.

We report the case of a 76-year-old woman whose infection was rapidly diagnosed as human granulocytic anaplasmosis (HGA) through a peripheral blood smear that showed characteristic intragranulocytic morulae. The smear was prepared on the day of hospitalization, which was 1–2 weeks before results were available from serology or the polymerase chain reaction (PCR). On the basis of the blood smear test, we started timely and appropriate antimicrobial treatment. The peripheral blood smear is known to have the lowest sensitivity when compared with serological or PCR tests for the diagnosis of HGA, but we suggest that the sensitivity of peripheral blood smear tests could be increased by employing experienced staff. The patient was confirmed as having HGA by PCR 7 days after the positive peripheral blood smear test, and 14 days later by serology. Morulae in neutrophils are an important diagnostic indicator of HGA, especially in febrile patients with a history of tick-bites or outdoor activities in rural areas.

The aim of this study was to evaluate the prevalence and characteristics of carbapenemase-producing Enterobacteriaceae (CPE) from three tertiary-care Korean university hospitals between 2017 and 2018. Non-duplicated clinical isolates of Enterobacteriaceae revealing resistance to any carbapenem agents were collected prospectively from three tertiary university hospitals between 2017 and 2018. The presence of carbapenemase genes was detected by multiplex PCR and sequencing for bla_KPC, bla_VIM, bla_NDM, bla_IMP, bla_OXA, and bla_GES. Among the 690 carbapenem-resistant Enterobacteriaceae (CRE) isolates, 66.8% (N=461) were CPE. The species distribution of CPE was as follows: K. pneumoniae was most common (75.9%), followed by E. coli (15.0%), C. freundii (4.6%), E. cloacae (2.6%), K. aerogenes (0.7%), and K. oxytoca (0.4%). All 11 CPE genes were detected, particularly KPC-2 (87.6%), NDM-1 (7.4%), NDM-5 (1.7%), KPC-3 (1.3%), OXA-232 (1.1%), and OXA-181 (1.1%). Six isolates produced two or three carbapenemases. Most of the carbapenemase-producing C. freundii were positive for NDM-1. We confirmed a high proportion of CPE among CRE with a high prevalence of KCP-2-producing K. pneumoniae and E. coli. We need to institute continuous surveillance to monitor the prevalence of CPE

Dengue virus (DENV), one of the most rapidly spreading mosquito-borne pathogens, causes acute febrile illness with various clinical symptoms. Four DENV serotypes are known, designated DENV-1 to -4. We previously determined whole-genome sequences of 21 DENV isolates obtained during 2016-2017 and reported the emergence of the Cosmopolitan genotype of DENV-2 and genotype III of DENV-3 in Thailand. The objective of the present study, conducted in 2018 at the Bamrasnaradura Infectious Diseases Institute, was to characterize the DENV genotype distribution among severe dengue patients. A total of 100 hospitalized severe dengue patients were enrolled with written informed consent. Serum specimens were tested by multiplex real-time reverse transcription–polymerase chain reaction. A total of 94 cases were DENV detected, with 46 DENV-1, 38 DENV-2, 10 DENV-4, and no DENV-3 cases. Sequence determination of the DENV envelope-protein gene was successful in 73 cases. Genotyping of the resultant sequences revealed 40 DENV-1 genotype I, 26 DENV-2 including 18 genotype Cosmopolitan and 8 genotype Asian I, and 7 DENV-4 genotype I cases. DENV-1 was the most prevalent in the current study, and the ratio of DENV-2 genotype Cosmopolitan apparently increased since our previous study. These results suggest that genotypic diversity might be increasing in Thailand. (200 words)

We investigated the relationship between colibactin-producing (clb⁺) Escherichia coli and colorectal adenocarcinoma. In total, 729 E. coli colonies were isolated from tumor and surrounding non-tumor regions in resected specimens from 34 Japanese patients; 450 colonies were from tumor regions and 279 from non-tumor regions. clb⁺ bacteria were found in tumor regions of 11 patients (11/34, 32.4%) and in non-tumor regions of seven of the 11 (7/34, 20.6%). The prevalence of clb⁺ isolates was 72.7% (327/450) and 44.1% (123/279) in tumor and non-tumor regions, respectively. All the recovered clb⁺ isolates belonged to the phylogenetic group B2 and were the most predominant type in tumor regions. Hemolytic (α-hemolysin-positive, hlyA⁺) and non-hemolytic (α-hemolysin-negative, hlyA^-) clb⁺ isolates were obtained from patient #19; however, the prevalence of hlyA⁺ clb⁺ isolates was significantly higher in tumor regions (35/43, 81.4%) than in non-tumor regions (3/19, 15.8%). Moreover, a significantly higher production of N-myristoyl-D-asparagine, a byproduct of colibactin biosynthesis, was observed in hlyA⁺ clb⁺ isolates than in hlyA^- clb⁺ isolates. Our results suggest that hlyA⁺ clb⁺ E. coli may have a selective advantage in colorectal colonization, consequently playing a role in carcinogenesis. The presence of hlyA⁺ clb⁺ bacteria in healthy individuals is a risk marker of colorectal cancer.

In December 2019, there was an outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China. The number of patients in China has risen to 31,000. We collected patient data from four Chinese cities (Hefei, Hangzhou, Wenzhou, Shenzhen) and described epidemiologic characteristics. As of 6 February 2020, we extracted data from 950 patients from the four cities. There were 477 (50.21%) males and 473 (49.79%) females of age (mean ± SD) 45.64 ± 15.59 years. Before contracting COVID-19, 299 patients had contact with Wuhan residents or contact with patients diagnosed with COVID-19 (31.47%). Also, 138 patients had SARS-CoV-2 infection of unknown source (14.53%). COVID-19 patients in the four cities were mainly from Wuhan originally, and had spread infection locally. Therefore, the initial stage of SARS-CoV-2 transmission in cities outside Wuhan were mainly input. Cutting off input and controlling community communication would reduce local incidence.

Rotavirus and norovirus are well-known causes of viral infectious diarrhea. There are few reports about diarrhea caused by other viruses in Korea, although gastroenteritis attributable to other viruses is increasing worldwide. The aims of this study were to detect various causes of viral diarrhea and to investigate their prevalence. A total of 801 fecal specimens submitted to a clinical microbiology laboratory for the detection of diarrhea viruses were included. We sought to detect rotavirus A/B/C, adenovirus, astrovirus, norovirus GI/GII, sapovirus, Aichi virus, human parechovirus, enterovirus, human cosavirus, human bocavirus, and Saffold virus using multiplex RT-PCR. At least one diarrhea virus was detected in 223 (27.8%) fecal specimens. Among them, two viruses were detected in each of 11 specimens. Rotavirus A was most common (17.1%; N=137), followed by norovirus GII (5.0%; N=40), enterovirus (4.2%; N=34), adenovirus (1.0%; N=8), astrovirus (1.0%; N=8), human parechovirus (0.6%; N=5), and human bocavirus (0.2%; N=2). Rotaviruses B and C, norovirus GI, sapovirus, Aichi virus, human cosavirus, and Saffold virus were not found. We confirmed that various diarrheal viruses can be detected in fecal specimens. We need to consider the possibility of viruses other than rotavirus and norovirus being present in cases of diarrhea.

The number of reported cases of the new coronavirus disease named “severe acute respiratory syndrome-coronavirus 2” (SARS-CoV-2) has increased since December 2019. The initial high-resolution computed tomography (HRCT) images of seven patients with diagnosed COVID-19 in the Affiliated Hospital of Hangzhou Normal University, China, were collected and analyzed. The study showed that all patients had close contact with COVID-19 patient and presented with fever. The initial white blood cell counts of all patients were normal. The percentage of lymphocytes decreased in three patients. In all seven patients with COVID-19, ground glass opacity (GGO) was found in the HRCT images, mainly distributed in the subpleural region of the lungs. The HRCT scans of six patients showed bilateral lobar lesions, mainly peripheral subpleural distribution; one patients showed unilateral lobar involvement. The right lung was more extensively involved than the left lung in six patients, and the lower lobe was more extensively involved than the upper lobe in five patients. The initial chest HRCT images of the lungs of COVID-19 patients had specific characteristics; the typical manifestations of the bilateral lungs showed extensive GGO-type infiltrate, with thickened vascular bundles and focal center consolidation. Pleural effusion, bilateral hilar, and mediastinal lymphadenopathy were rare.

In December 2019, a cluster of cases of acute respiratory illness, novel coronavirusinfected pneumonia, occurred in Wuhan, Hubei Province, China. The false-negative nasopharyngeal swabs of SARS-CoV-2 caused the delayed diagnosis of COVID-19 which hindered the prevention and control of the pandemic. The transmission risk of SARS-CoV-2 in negative nasopharyngeal swabs cases were little addressed previously. This study evaluated two clusters of COVID-19 in six patients. Four of six (66.7%) showed negative RNA of SARS-CoV-2 by nasopharyngeal swabs. All epidemiological, clinical and laboratory information was collected. The first cluster was a nosocomial infection of four health care providers at early January. One of them made sequential familial cluster of infection. All patients received either selfquarantined at home or were admitted to hospital for isolated treatment. All recovered and had anti-SARS-CoV-2 IgG and/or IgM positive (100%) for serological detection of SARS-CoV-2 at recovery stage. Our study provides a cautionary warning that negative results of nasopharyngeal swabs of suspected SARS-CoV-2 infection can increase the risk of nosocomial infection among health care providers. Serologic detection for anti-SARS-CoV-2 IgG and/or IgM is an important test in the assistant diagnosis of COVID-19.

Coronavirus disease 2019 (COVID-19) is a severe infectious disease of the respiratory tract caused by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2, and has a high mortality rate. The disease emerged from Wuhan, China, in late 2019, and spread to Japan, including Hokkaido, in January 2020. In February 2020, three children were diagnosed with COVID-19 in Furano, Hokkaido, Japan. During this period, influenza and human metapneumovirus infections were prevalent among children in the Furano region. Two of the three cases experienced co-infection with other respiratory viruses, including influenza virus A or human metapneumovirus. To the authors’ knowledge, the cases described in the present report were the first pediatric patients with COVID-19 in Japan. In children with COVID-19, the possibility of co-infection with other respiratory pathogens should be considered.

Human orthopneumovirus, also known as the respiratory syncytial virus (RSV), is a leading cause of respiratory tract infections in children worldwide. The World Health Organization has taken steps toward establishing a global surveillance system for RSV, based on the global influenza surveillance and response system initiated in 2015. The US Center for Disease Control and Prevention (CDC) has developed a genetic detection method based on real-time RT-PCR, which is used in global RSV surveillance. In Japan, immunoassay-based rapid antigen detection kits are widely used for the detection of RSV. In this study, an ultra-rapid real-time RT-PCR method for the rapid detection of RSV was developed using the PCR1100 device based on the US CDC assay in order to detect RSV in comparable time to rapid test kits. The ultra-rapid real-time RT-PCR could detect RSV viral RNA in less than 20 min while maintaining sensitivity and specificity comparable to conventional real-time RT-PCR using large installed instruments. Furthermore, combining ultra-rapid real-time RT-PCR with the M1 Sample Prep kit reduced the total working time for the detection of RSV from clinical specimen to less than 25 min, suggesting this method could be used for point-of-care RSV testing.

This study aims to investigate blood and biochemical laboratory findings in patients with severe Corona Virus Disease 2019 (COVID-19) and to develop a joint predictor for predicting the likelihood of severe COVID-19 and its adverse clinical outcomes, to provide more information for treatment. We collected the data of 88 patients with laboratory-confirmed COVID-19. Then patients were divided into a non-severe group and a critical group (including critically ill cases). Univariate analysis showed that the absolute lymphocyte count, albumin level, albumin/globulin (A/G) ratio, lactate dehydrogenase (LDH) level, interleukin-6 (IL-6) level, erythrocyte count, globulin level, blood glucose level, and age were significantly correlated with the severity of COVID-19. The multivariate binary logistic regression model revealed that Age, absolute lymphocyte count, and IL-6 level were independent risk factors in patients with COVID-19. The receiver operating characteristic (ROC) curve revealed that the combination of IL-6 level, absolute lymphocyte count and age is superior to a single factor as predictors for predicting severe COVID-19, regardless of whether it is the area under curve (AUC) or the prediction sensitivity and specificity. Early application is beneficial to early identification of critically ill patients and timing individual treatments to reduce mortality.

We report a case of patient in Japan with Coronavirus disease 2019 (COVID-19) with false-negative of reverse transcription polymerase chain reaction for Severe Acute Respiratory Syndrome Coronavirus 2 of pharyngeal swab, from a Chinese traveller returning from Wuhan, Hubei Province, China. If a patient is clinically or epidemiologically suspected of COVID-19, appropriate infection and prevention control measures such as standard, contact, and droplet precaution are needed until the patient is proven to be true-negative.

Myroides spp. are low-grade opportunistic pathogens. There were only a few outbreaks due to Myroides spp. described in the literature to date. We report a healthcare–associated outbreak of urinary tract infections caused by Myroides odoratimimus in a Turkish hospital. From March to May 2019, six strains of M. odoratimimus were isolated from the urine samples of patients hospitalized in the intensive care units (ICUs). After identification and antibiotic susceptibility testing with VITEK 2 system, MALDI‐TOF-MS and 16S rRNA based sequencing methods were performed for confirmation and species level identification. Pulsed-field gel electrophoresis (PFGE) was used to investigate clonal relatedness of the isolates. All the patients were immunocompromised and underwent urinary catheterization. None of them had urinary neoplasm, surgery or calculi. VITEK 2 and MALDI-TOF-MS systems revealed that the isolates belong to the Myroides genus but lacked to identify the isolates at the species level. 16S rRNA based sequencing successfully identified all the isolates as M. odoratimimus. The isolates were resistant to all antibiotics tested. All isolates had indistinguishable PFGE pattern indicating cross-transmission between cases. Although M. odoratimimus is rarely isolated from human specimens, clinicians should be aware of its ability to cause UTIs and outbreaks.

Marine bacterium Vibrio cholerae, belonging to serogroups O1 and O139 are responsible to cause cholera in human. Pentose sugar arabinose is nonmetabolizable by the pathogen and is present in environmental niches as well as in the human intestine. In this study, arabinose mediated V. cholerae growth interference has been assessed in M9 minimal medium containing gluconate as sole carbon source in the light of Entner-Doudoroff (ED) pathway, an obligatory metabolic route for gluconate utilization. V. cholerae O1 and O139 strains failed to grow in presence of ≥0.3% arabinose in M9 with 0.2% gluconate but no growth inhibition in presence of arabinose in M9 with 0.2% glucose. Transcriptional analysis of edd and eda, the genes constituting the ED pathway, showed ~100 and ~17 folds increase, respectively, in M9-gluconate. Minor increase of ~4 and ~2 folds for the edd and eda, respectively, was noted in 0.5% arabinose supplemented AKI. Observed arabinose mediated growth inhibition also contributes to understanding of altered phenotypes, if any, during complementation/expression studies in V. cholerae with PBAD vectors and arabinose as an inducer.

Japanese encephalitis (JE) is an inflammation of the central nervous system resulting in clinical disease, with symptoms ranging broadly in severity from mild febrile illness to acute meningomyeloencephalitis. JE has been associated with a variety of neurological abnormalities such as altered sensorium, seizures, focal neurological deficit, and acute flaccid paralysis (AFP). However, AFP has never been reported as the initial manifestation of JE. Here we present a case of AFP as the initial manifestation of JE in a Chinese patient. A 30-year-old Chinese man was admitted to West China Hospital of Sichuan University after experiencing AFP in the right upper limb followed by hyperpyrexia and unconsciousness. Assay of cerebrospinal fluid from lumbar puncture revealed high levels of proteins and anti- Japanese encephalitis virus IgM antibodies. Acyclovir (used by intravenous drip) was administered. However, the weakness persisted and more extensive muscle wasting from the proximal to distal right upper limb occurred during seven months. This case reports highlights that JE needs to be added to the differential diagnosis of AFP initiating in an adult in JE endemic seasons and areas.

Scrub typhus is a mite-borne rickettsiosis caused by the intracellular bacterium Orientia tsutsugamushi (OTS), which is classified as a biosafety level-3 (BSL-3) pathogen. For serological tests of scrub typhus, mouse fibroblast cells infected with the five prevalent serotypes of OTS in Japan are generally used as antigens for indirect immunofluorescent assay (IFA). In this study, sf-9 insect cells infected with the recombinant type-specific antigens (rTSA)-expressing baculovirus were applied for IFA. The paired sera samples of 15 scrub typhus-patients, 10 rickettsiosis-patients, and 10 control individuals were used. Both IgM and IgG IFA titers determined by the rTSA based IFA were correlated with those determined with the OTS-infected cell-based IFA (R ² = 0.7319 to 0.7956). Based on the criteria for serological diagnosis, such as the suitable cutoff for single serum (IgM ≥ 1:160) and/or significant increase in IgG titer between paired sera (≥ 4 times), all of the 15 scrub typhus patients diagnosed as positive with OTS-infected cell-based IFA were also diagnosed as positive by the rTSA-based IFA, whereas all 10 rickettsiosis patients and 10 control individuals were not. The rTSAs, which can be prepared in BSL-2 laboratories, are efficacious in the serological diagnosis of scrub typhus.

We report the second case of deceased donor liver transplantation in a patient co-infected with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) in Japan. A 48- year-old patient with hemophilia A was infected with HIV and HCV through a contaminated factor VIII concentrate in his childhood and developed cirrhosis and hepatocellular carcinoma. The patient was on the transplant list for a deceased donor liver. The patient had broad spectrum anti-HLA class I and II antibodies, which may have been due to repeated whole blood transfusions in the past. Catastrophic coagulopathy during the surgery was predicted because of the underlying hemophilic status and severe thrombocytopenia requiring HLA-matched platelet products, which are difficult to obtain quickly. To maintain adequate platelet counts(>5x10⁴/ μl) while waiting liver transplantation, a thrombopoietin receptor agonist and rituximab were administered. During surgery, factor VIII concentrate was administered according to the previously planned protocol. Adequate hemostasis was obtained, and the operation was completed without uncontrollable coagulopathy. The postoperative course was uneventful, and the patient was discharged on postoperative day 41. Detailed planning is required for surgical patients with hemophilia and HIV/HCV cirrhosis, especially for those with a diverse spectrum of anti-HLA antibodies.

Emergence and spread of multidrug-resistant organisms (MDRO) is an urgent social problem. We carried out an epidemiological survey to clarify the geographic characteristics and factors influencing the prevalence of MDRO. Data regarding the prevalence of MDRO in 47 prefectures in Japan was extracted from the Japanese Nosocomial Infection Surveillance, a nationwide database for infection control. Potential factors influencing MDRO were selected from pharmacological, medical service-, infection control-, food-related, environmental and social categories considering the characteristics of each organism, and correlations between them and MDRO prevalence were analyzed. Statistics for potential factors were data from public domains. The use of antibiotics correlated with the prevalence of PRSP, 3 ^rd- generation cephalosporin- and fluoroquinolone-resistant E. coli and MRSA. Negative correlations between the consumption of foods that facilitate the growth of lactic acid bacteria such as kelp and fermented soy beans and the prevalence of 3 ^rd-generation cephalosporin- and fluoroquinolone-resistant E. coli suggested an association between intestinal microflora and MDRO colonization. In addition to the use of antibiotics, lifestyle, food culture and social factors such as tobacco smoking, average temperature, prevalence of three-generation households, ratio of elderlies, average length of tourist stay, chicken consumption, fermented bean consumption, and medical service conditions could modify MDRO prevalence.

We describe herein 4 clinical cases of microbial contamination of in-use intravenous infusion, in which we detected microbial contamination in the infusion fluid by measuring “Adenosine triphosphate (ATP) + adenosine monophosphate (AMP)” values. High “ATP+AMP” values correlate with microbial contamination, and by utilizing these values as indicator for microbial contamination possibility, we were able to rapidly detect the contamination and recommend replacement of catheters and administration sets. In three cases, changing out the infusion fluid led to improvement in patient outcome. The assay used to measure “ATP+AMP” values is fast (several minutes) and convenient, and therefore we recommend measuring the values as one method to ascertain microbial contamination of in-use intravenous infusion fluids.