Infectious diarrheal diseases remain a leading cause of morbidity and mortality in developing and underdeveloped countries. The present study documented the etiology of bacterial enteropathogens in three tribal districts of Odisha from July 2010 to September 2013. A total of 1427 rectal swabs were collected and bacteriologically analyzed by following standard procedure. Among the 930 (65.2%) culture positive samples, Escherichia coli (E. coli) constituted 636 (44.6%); Vibrio cholerae (V. cholerae) O1, 146 (10.2%); Salmonella species (spp.), 10 (0.7%); Shigella spp., 79 (5.5%); and Aeromonas spp., 59 (4.1%). Of the 729 environmental water samples taken from river, open well, Nala (a small stream), and Chua (a shallow pit on a river bed), 14 (1.9%) contained non-O1/non-O139 V. cholerae and 13 (1.8%) had V. cholerae O1 strains. An analysis of the demographics showed that people in the 14 to 40-year age group were highly susceptible to diarrhea caused by V. cholerae which occurred mainly during the rainy and post-rainy seasons. All enteropathogens were multidrug-resistant and found throughout the study period. The V. cholerae strains isolated were El Tor variants carrying the classical, El Tor, and Haitian cholera toxin subunit B (ctxB) genes. The classical ctxB was the dominant allele, and the prevalence of the Haitian ctxB allele increased during the test period. These findings indicate that active surveillance is needed to monitor the changing antibiotic resistance patterns of V. cholerae serogroups and biotypes present in this region.

Station staff may be at high risk for influenza due to high frequency contact with other people. We examined the risk of influenza by occupational group in a railway company. A retrospective observational study was conducted among employees at a branch office of a railway company in eastern Japan, located in a metropolitan area, for 2012/13, 2013/14, and 2014/15 influenza seasons. The study population included employees who had received influenza vaccination for the season in question and the previous season. Outcome was defined as self-reported influenza illness during the respective season, identified through the vaccine screening questionnaire in the following season. Study participants included employees whose outcome information could be obtained. Standardized morbidity ratios (SMRs) by occupational group (station staff, engineers, train crew) for each season were calculated. For 2012/13, 2013/14, and 2014/15 seasons, attack rates were 4.7% (19/403), 5.2% (21/407), and 7.8% (31/397), respectively. Among the participants, SMRs of station staff were lower in the 2012/13 (SMR = 57; 95% confidence intervals [CI] = 18–133) and 2014/15 (SMR = 75; 95%CI = 36–138) seasons and similar to other groups in the 2013/14 season. Enhanced countermeasures, regardless of occupational group, may be effective in preventing the spread of influenza infection.

The diagnosis of tuberculosis (TB) in endemic countries is challenging due to high caseloads and limited resources. A simple and cost-effective diagnostic test for the rapid detection of Mycobacterium tuberculosis (M. tuberculosis) in clinical specimens is crucially needed. We evaluated the performance of an in-house assay based on loop-mediated isothermal amplification (LAMP) targeting the M. tuberculosis 16S ribosomal RNA (rRNA) gene for the diagnosis of TB in Thailand. A total of 252 sputum samples from suspected cases of pulmonary TB were analyzed. The sensitivity of LAMP was 99.04% (103/104; 95% confidence interval [CI]: 94.76–9.98%) and 72.73% (16/22; 95% CI: 49.78–89.27%) for smear-positive and smear-negative samples with TB-culture positivity, respectively. LAMP detected 20.69% (24/116) of TB culture negative samples but all those were positive by conventional polymerase chain reaction (PCR). The sensitivity of LAMP was higher than that of sputum microscopy while the performance of LAMP was similar to PCR. None of the samples positive for non-tuberculous mycobacteria by culture and PCR were positive by LAMP. Compared to TB culture, the positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient of LAMP were 83.22%, 88.33%, and 0.75 respectively. Based on the diagnostic performance, we propose that LAMP would be suitable as a potential diagnostic test for rapid TB diagnosis in resource-limited laboratory settings.

The aim of this study was to evaluate the clinical performance of AdvanSure GenoBlot assay using nontuberculous mycobacteria (NTM) isolates and clinical specimens. A total of 136 NTM isolates and 176 clinical specimens were used in this study. AdvanSure Mycobacteria GenoBlot assay was performed according to the manufacturer’s instructions. We compared the results with those of 16S rRNA and rpoB genes sequencing. Out of the 136 NTM isolates, 111 (81.6%) were correctly identified to the species level using the GenoBlot assay. The final concordance rate was 89.7% (122/136), including 11 Mycobacterium genus positive control (GPC) results for uncommon NTM. The most common NTM, M. avium, M. fortuitum, M. gordonae, M. intracellulare, M. chelonae, M. abscessus, and M. kansasii, were correctly identified using the GenoBlot assay. For 176 organisms in clinical specimens, 117 were identified to the species level, including single species for 111 specimens and two species for 6 specimens. The final detection and identification rates for clinical specimens were 94.9% and 66.5%, respectively. The AdvanSure GenoBlot assay performs well in identifying the most common NTM, and would be useful in a clinical laboratory.

Nontuberculous mycobacteria (NTM) disease is of increasing public health concern; however, data regarding pleural effusion in NTM disease patients are limited. The purpose of this study was to investigate the clinical relevance and characteristics of NTM pleuritis. Patients with pleural effusion and NTM disease diagnosed between April 2012 and November 2017 were enrolled and their medical records were retrospectively reviewed. Clinical characteristics and treatment outcomes were analyzed. A total of seven among 100 patients with NTM disease had NTM pleuritis (7%). Flow cytometry of T and B lymphocytes revealed varying degrees of cellular immunodeficiency in five cases (71.4%). NTM pleuritis with pneumothorax occurred in five patients (71.4%) and bronchopleural fistula (BPF) was also found in four of them. All seven patients had delayed diagnosis and the mean time of diagnosis was 7 months (1–24 months). Four patients successfully completed treatment, while three patients (42.8%) succumbed to progressing NTM disease. Low CD4-positive T-cell counts were common in NTM pleuritis patients. Delayed diagnosis and treatment resulted in increased incidence of NTM pleurisy and poor prognosis. Moreover, BPF is perhaps a characteristic feature of Mycobacterium avium complex-associated pleuritis.

A 5-year multicenter retrospective cohort study was conducted across six hospitals in Niigata, Japan. Patients (n = 179) with bacteremia due to extended-spectrum β-lactamase (ESBL)producing organisms were included in the study. The rates of appropriate carbapenem prescription were 61% (n = 41) in patients aged 65–84 years and 89% (n = 31) in those aged ≥ 85 years. Patients aged ≥ 85 years were significantly more likely to receive carbapenem than their younger counterparts. After propensity score matching, 65 patients were assigned to two groups based on age (65–84 years or ≥ 85 years). Multivariate regression analysis showed that other sites of infection had a positive association with 30-day mortality (odds ratio [OR], 27.50; 95% confidence interval [CI], 2.90–260.00) and biliary tract infection tended to have a positive association with 30-day mortality (OR, 8.90; 95% CI, 0.88– 89.90) compared with urinary tract infection. However, an age ≥ 85 years was not associated with 30-day mortality. Elderly patients aged ≥ 85 years were more likely to be treated with carbapenem; however, old age was not associated with 30-day mortality when bacteremia was caused by ESBLproducing organisms. These results may help clinicians justify withholding carbapenem in patients aged ≥ 85 years.

Antimicrobial resistance is an emerging problem in both acute care hospitals and nursing homes. From January to December 2016, we conducted a pilot, descriptive epidemiological study to examine antimicrobial use (AMU) among 6 nursing homes in Tokyo, Japan. AMU was extracted from prescription data of a pharmacy that received all prescriptions from the 6 nursing homes. To standardize the comparison of drug usage, AMU was measured using the defined daily dose (DDD) and estimated as DDDs/1,000 resident-days. The overall AMU was 15.3/1,000 resident-days, including oral antimicrobials (15.2/1,000 resident-days [99.3%]). The most frequently prescribed oral-antimicrobials was macrolides (5.8/1,000 resident-days [38.2%]) and quinolones (4.2/1,000 resident-days [27.6%]). Oral macrolides and quinolones were thought to be a convenience in prescription among nursing homes with resource limiting due to smaller defined the number of daily doses compared to penicillins and cephalosporins. In addition, multicenter studies that include resident-specific data (demographics and diagnosis) and focus on the purpose of antimicrobials (treatment or prevention) are needed to evaluate the appropriateness of antimicrobials.

Linezolid resistance has increasingly been described in coagulase negative staphylococci (CoNS) in recent years. Here, we describe the molecular mechanism of linezolid resistance in Staphylococcus haemolyticus using whole genome sequencing. Three S. haemolyticus isolates (VB5326, VB19458, and VB840) carried G2576T mutation at the domain V of the 23S rRNA. In addition, VB5326 and VB19458 carried the cfr gene in the chromosome. The presence of cfr gene, in combination with G2576T mutation in 23S rRNA, resulted in a high linezolid Minimum inhibitory concentration (MIC) of > 256 µg/ml. Three mutations, including D471E, I527M, and S532N, in rpoB contributed to an increased rifampicin MIC of 32 µg/ml. Subsequent development of linezolid and rifampicin resistance in S. haemolyticus is worrisome and greatly limits clinical management.

Dengue viruses (DENVs) affect tropical and subtropical regions, including the Guangdong province of China. Dengue cases are reported almost every year in Shantou city in the Guangdong province. To understand the molecular characteristics of DENVs isolated in Shantou, we performed a molecular epidemiological study based on the envelope protein (E) gene of the DENVs isolated from the cases. Total 174 serum samples were collected from 174 dengue-suspected patients during 2015–2017. A total of 33.9% (59/174) were diagnosed with dengue. Serotypes of DENVs were identified in 27 samples; 37% (10/27), 55.6% (15/27), 3.7% (1/27), 3.7% (1/27) were serotype 1 DENV (DENV-1), serotype 2 DENV (DENV-2), serotype 3 DENV (DENV-3), and serotype 4 DENV (DENV4), respectively. Genotypes Ⅰ and Ⅳ were detected in DENV-1, while only the Cosmopolitan genotype was detected in DENV-2. The replacement of the predominant serotype (genotype), which takes place every year, implied that the dengue endemic in Shantou might be caused by an imported infection rather than by local populations. Our results suggested that DENVs in Shantou are closely related to the strains circulating in Southeast Asian countries, which were possibly transmitted to Shantou through some relay point cities.

During the emergence of novel coronavirus 2019 (nCoV) outbreak in Wuhan city, China at the end of 2019, there was movement of many airline travelers between Wuhan and Japan, suggesting that the Japanese population was at high risk of infection by the virus. Hence, we urgently developed diagnostic systems for detection of 2019 nCoV. Two nested RT-PCR and two real-time RT-PCR assays were adapted for use in Japan. As of February 8, 2020, these assays have successfully detected 25 positive cases of infection in Japan.

This study assessed whether Streptococcus agalactiae isolates from companion animals differed from those of human origin. Beta-hemolytic S. agalactiae was collected from a veterinary laboratory center and a university hospital. Strains were identified using 16S rRNA amplicon sequencing and amplification of the species-specific dltS gene. We conducted virulence gene profiling, capsular genotyping, determination of clonal complex (CC), and antimicrobial resistance (AMR) phenotyping or genotyping. The 20 non-invasive isolates obtained from animals and 15 non-invasive isolates from adult humans were comparatively analyzed in this study. We found significant differences in the virulence gene profiles of bca-rib-lmb-cylE (40.0% vs. 93.3%) and the possession of bac (30.0% vs. 0%) between animal-origin and human-origin non-invasive strains. We observed a significant difference in the distribution of CC1 between the two non-invasive populations. There were significant differences in the prevalence of tetracycline resistance genotypes (60.0% vs. 20.0%) and absence of AMR genotypes (30.0% vs. 80.0%), and AMR rates of tetracycline (35.0% vs. 0%) and fluoroquinolone (20.0% vs. 66.7%) between the two non-invasive populations. These observations suggest that there were different features, in terms of virulence gene profile, CC, and AMR genotype/phenotype in the non-invasive isolates of animal origin compared to those of human origin.