In December 2019, a cluster of cases of acute respiratory illness, novel coronavirus-infected pneumonia, occurred in Wuhan, Hubei Province, China. The false-negative nasopharyngeal swabs for SARS-CoV-2 caused 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 has rarely been addressed previously. This study evaluated two clusters of COVID-19 in six patients, four of whom (66.7%) tested negative for RNA of SARS-CoV-2 on RT-PCR of nasopharyngeal swabs. All epidemiological, clinical, and laboratory data were collected. The first cluster was a nosocomial infection of four health care providers in early January. One case resulted in a sequential familial cluster of infection. All patients either self-quarantined at home or were admitted to hospital for isolated treatment. All recovered and were anti-SARS-CoV-2 IgG- and/or IgM-positive (100%) for serological detection of SARS-CoV-2 at the recovery stage. Our study provides a cautionary warning that negative results for 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 diagnosis of COVID-19.

This study aims to investigate blood and biochemical laboratory findings in patients with severe coronavirus disease 2019 (COVID-19) and to develop a joint predictor for predicting the likelihood of severe COVID-19 and its adverse clinical outcomes and to provide more information for treatment. We collected the data of 88 patients with laboratory-confirmed COVID-19. Further, the 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 ratio, lactate dehydrogenase 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 curve revealed that the combination of IL-6 level, absolute lymphocyte count, and age is superior to a single factor as predictors for severe COVID-19, regardless of whether it is in terms of the area under the curve or the prediction sensitivity and specificity. Early application is beneficial to early identification of critically ill patients and timing individual treatments to reduce mortality.

Dengue virus (DENV), one of the 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 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 this study, conducted in 2018 at the Bamrasnaradura Infectious Diseases Institute, was to study the prevalence of DENV genotype. A total of 100 patients, hospitalized with severe dengue infection, were enrolled with written informed consent. Serum specimens were tested by multiplex real-time reverse transcription–polymerase chain reaction. Among them, 94 were DENV-positive, with 46 DENV-1, 38 DENV-2, 10 DENV-4, and no DENV-3 cases. Nucleotide sequence of DENV gene for envelope-protein was determined in 73 cases. Genotyping of the sequences revealed 40 cases with DENV-1 genotype I, 26 with DENV-2, that included 18 of Cosmopolitan and 8 Asian I genotypes, and 7 with DENV-4 genotype I. DENV-1 was the most prevalent in this study, and the frequency of DENV-2 Cosmopolitan genotype appears to have increased since our previous study, indicating that genotypic diversity of DENV is increasing in Thailand.

Myroides spp. are low-grade opportunistic pathogens. Outbreaks due to Myroides spp. have rarely been described in the literature to date. We report a healthcare-associated outbreak of urinary tract infections (UTIs), caused by Myroides odoratimimus, in a Turkish hospital. As of March 2019 until May 2019, 6 strains of M. odoratimimus were isolated from the urine samples of patients, all of whom were hospitalized in intensive care units. After identification and antibiotic susceptibility testing using the 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 performed in order to investigate the clonal relatedness of the isolates. All the patients were immunocompromised and underwent urinary catheterization. None of the patients had urinary neoplasm, surgery, or calculi. VITEK 2 and MALDI-TOF-MS systems revealed that the isolates belonged to the Myroides genus; however, the aforementioned systems neglected to identify the isolates at the species level. The isolates were all successfully identified as M. odoratimimus through 16S rRNA-based sequencing. The isolates were resistant to every antibiotic tested. All isolates had an indistinguishable PFGE pattern, thus 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 infectious outbreaks.

Rotavirus and norovirus are well-known causes of viral infectious diarrhea. There are few reports on diarrhea caused by other viruses in Korea, although cases of gastroenteritis attributable to other viruses are 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 diarrheal 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 reverse transcription polymerase chain reaction (RT-PCR). At least one diarrheal virus was detected in 223 (27.8%) fecal specimens. Among them, two viruses were detected in 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 detected. We confirmed that various diarrheal viruses can be detected in fecal specimens. We must consider the possibility of viruses other than rotavirus and norovirus being present in cases of diarrhea.

The aim of this study was to evaluate the prevalence and characteristics of carbapenemase-producing Enterobacteriaceae (CPE) from 3 tertiary-care Korean university hospitals between 2017 and 2018. Non-duplicated clinical isolates of Enterobacteriaceae showing resistance to any carbapenem agents were collected prospectively from 3 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 was performed. Among the 690 potential carbapenem-resistant Enterobacteriaceae (CRE) isolates, 66.8% (N = 461) were CPE. The species distribution of CPE was as follows: Klebsiella pneumoniae was most common (75.9%), followed by Escherichia coli (15.0%), Citrobacter freundii (4.6%), Enterobacter cloacae (2.6%), Klebsiella. aerogenes (0.7%), and Klebsiella. oxytoca (0.4%). All 11 CPE genes were detected, particularly K. pneumoniae carbapenemase (KPC)-2 (87.6%), New Delhi metallo-β-lactamase (NDM)-1 (7.4%), NDM-5 (1.7%), KPC-3 (1.3%), oxacillinase (OXA)-232 (1.1%), and OXA-181 (1.1%). Six isolates produced 2 or 3 carbapenemases. The majority of the carbapenemase-producing C. freundii tested positive for NDM-1. We confirmed a high proportion of CPE among the CRE isolates with a high prevalence of KCP-2-producing K. pneumoniae and E. coli. Therefore, there is a need for undertaking continuous surveillance to monitor the prevalence of CPE.

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 the tumor regions and 279 from the non-tumor regions. clb⁺ bacteria were found in tumor regions of 11 patients (11/34, 32.4%) and they were also detected in the non-tumor regions of 7 out of these 11 patients (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 by-product 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 and, consequently, might play a role in carcinogenesis. The presence of hlyA⁺ clb⁺ bacteria in healthy individuals is a potential risk marker of colorectal cancer.

Low blood levels of 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 under 3 months of age who had respiratory syncytial virus (RSV) infection. Serum levels of 25-OH vitamin D in the 10 infants, excluding those with underlying diseases, were between < 4 and 29.8 ng/mL. In 8 out of 10 subjects (80.0%), serum 25-OH vitamin D levels were lower than 20 ng/mL. There was no statistically significant association between the levels of 25-OH vitamin D and age, duration of admission, respiratory severity score, white blood cell count, blood gas levels, and N-terminal pro-natriuretic peptide levels. Levels of serum 25-OH vitamin D in children who required hospitalization owing to RSV infection were low, indicating deficiency. These results suggest that vitamin D deficiency affects the susceptibility to RSV infection, but not the severity of the infection.

Morphological changes in the structure of the herpes simplex virus 1 (HSV-1) viral thymidine kinase (vTK) polypeptide usually lead to conferring acyclovir (ACV) resistance. HSV-1 I4-2, in which a 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 the HSV-1 vTK gene, showed sensitivity to ACV. In contrast, HSV-1 KG111, in which a UAG stop codon was artificially inserted at the 44th position, showed resistance to ACV at 39˚C. The mechanism underlying the difference in the sensitivity profiles was elucidated. The virus recombinants HSV-1-TK(8UAG) and HSV-1-TK(44UAG) containing a UAG stop 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 vTK 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 UAG stop codon between the 1st and the 2nd initiation codons.

The outbreak of the coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, occurred in China in December 2019. This disease has caused more than 70,000 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 in the critical state before March 20, 2020. Data were collected on admission and compared between survivors and non-survivors and analyzed by univariable and multivariable logistic regression analyses. Finally, 104 patients were included, 50 of whom died. Age (odds ratio, OR 5.73 [95% confidence interval, CI, 1.14–28.81]), chest tightness (OR 5.50 [95% CI, 1.02–9.64]), AST (OR 6.57 [95% CI, 1.33–32.48]), and blood urea nitrogen (5.59 [95% CI, 1.05–29.74]) at admission were considered predictors of 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 area under the curve was 0.893 (95% CI, 0.807–0.980).

The number of reported cases of the new coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), has increased since December 2019. The initial high-resolution computed tomography (HRCT) images of 7 patients diagnosed with COVID-19 in the Affiliated Hospital of Hangzhou Normal University, China, were collected and analyzed. The study showed that all patients had had close contact with other COVID-19 patients and presented with fever. The initial white blood cell counts of all patients were normal. Subsequently, the percentage of lymphocytes decreased in 3 patients. In all 7 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 6 patients showed bilateral lobar lesions, with mainly peripheral subpleural distribution; 1 patient, instead, showed unilateral lobar involvement. The right lung was more extensively involved than the left lung in 6 patients, and the lower lobe was more extensively involved than the upper lobe in 5 patients. The initial chest HRCT images of the lungs of the analyzed COVID-19 patients had specific characteristics. The typical manifestation at both lungs was an extensive GGO-type infiltrate, with thickened vascular bundles and focal center consolidation. Pleural effusion, bilateral hilar, and mediastinal lymphadenopathy were rare.

We report a case of coronavirus disease (COVID-19) in a Japanese patient with a false-negative result in the reverse-transcription polymerase chain reaction for severe acute respiratory syndrome coronavirus 2 detection in the pharyngeal swab. The patient had acquired the infection from a Chinese traveler returning from Wuhan, Hubei Province, China. If a patient is clinically or epidemiologically suspected with COVID-19, appropriate infection and prevention control measures such as standard, contact, and droplet precaution are necessary until the patient is proven to have a true-negative result.

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 Centers for Disease Control and Prevention (CDC) has developed a genetic detection method based on real-time reverse transcription polymerase chain reaction (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.

We report a case of human granulocytic anaplasmosis (HGA) in a 76-year-old woman, diagnosed rapidly based on the characteristic peripheral blood smear finding of intragranulocytic morulae. The smear was prepared on the day of hospitalization, which was 1–2 weeks before results of the serology test or polymerase chain reaction (PCR) became available. Owing to the blood smear test, we could start timely and appropriate antimicrobial treatment. The sensitivity of peripheral blood smear is lower compared to that of serology or PCR for the diagnosis of HGA but may increase with the examiner's experience. In our case, the diagnosis of HGA was confirmed based on PCR and serology 7 and 14 days after the positive peripheral blood smear test, respectively. Morulae in neutrophils are a diagnostic indicator of HGA, particularly for febrile patients with a history of tick bites or outdoor activities in rural areas.

In December 2019, there was an outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China. To date, the number of patients in China has risen to 31,000. We collected patient data from 4 Chinese cities (Hefei, Hangzhou, Wenzhou, and Shenzhen) and described epidemiologic characteristics. As of February 6, 2020, we have extracted data from 950 patients from the 4 cities, including 477 (50.21%) men and 473 (49.79%) women. The age (mean ± standard deviation) was 45.64 ±15.59 years. Before contracting COVID-19, 299 (31.47%) patients had come in contact with Wuhan residents or patients diagnosed with COVID-19, while 138 (14.53%) patients had severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from an unknown source. Most COVID-19 patients in the 4 cities were from Wuhan originally and had spread the infection locally. Therefore, the initial stage of SARS-CoV-2 transmission in cities outside of Wuhan were mainly input. Cutting off the input and controlling the community communication could reduce local incidence.

High-level aminoglycoside resistance (HLAR) limits treatment options for invasive enterococcal infections. We examined the prevalence of HLAR, carriage of genes encoding aminoglycoside-modifying enzymes, and production of β-lactamase using the disk diffusion method, polymerase chain reaction, and a nitrocefin-based test, respectively, 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, 9 isolates had HLR to gentamicin, and 9 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 isolate 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.

Non-O157 Shiga toxin-producing Escherichia coli (STEC) infections are a growing concern for public health. The number of sporadic cases and outbreaks of non-O157 STEC infections have increased in recent years. Molecular subtyping is an essential tool that allows high-resolution and rapid differentiation of isolates, identification of case clusters, and detection of outbreak clusters. Multiple-locus variable-number tandem repeat analysis (MLVA) is one of the most useful typing methods for differentiating isolates that cause foodborne diseases. In Japan, serogroups O26, O111, O103, O121, O145, O165, and O91 have been frequently isolated or associated with severe cases of non-O157 STEC infections. In this study, we designed an MLVA scheme (MLVA43) for serogroups O103, O121, O145, O165, and O91 by adding 26 new loci to an MLVA scheme (MLVA17) previously developed by our group for serogroups O157, O26, and O111 using 17 loci. We found that the 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 MLVA43 scheme will enable rapid detection of outbreak clusters, which will aid in implementing rapid control measures against non-O157 STEC infections.