Japan Nosocomial Infections Surveillance (JANIS) is one of the largest national antimicrobial resistance (AMR) surveillance systems in the world. The JANIS Clinical Laboratory division collects comprehensive specimen-based data from diagnostic microbiology laboratories of participating hospitals to monitor the isolation rate of 11 major bacteria and specific AMR bacteria, and creates antibiograms of approximately 20 bacterial species. Data on the JANIS web database system are also annually tabulated and shared with the WHO Global Antimicrobial Resistance Surveillance System. To create a network of international AMR surveillance systems among Asian countries, Japan is developing an international web database system named ASIan Antimicrobial Resistance Surveillance Network (ASIARS-Net) based on the JANIS system; ASIARS-Net is an open-source database and confidentially available at almost no cost. JANIS continues to evolve in multiple directions; some are discussed at the end of this review.

Delayed diagnosis of congenital tuberculosis (TB) in the 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 the NICU. In addition, we reviewed previous case reports of congenital TB exposure in the NICU setting. Immediately after diagnosing miliary TB in the mother, the index twins were isolated before their TB diagnosis and received preemptive anti-TB medication; 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 the 16 exposed infants received isoniazid prophylaxis and no positive tuberculin skin test results were obtained after 3 months. One of the 31 exposed healthcare workers showed new interferon-gamma release assay conversion. Moreover, our case showed a much shorter contagious period compared to that in previous reports (8 versus 17–102 days). This suggests that a high index of suspicion and prompt measures can help prevent congenital TB outbreaks and reduce the burden of infection control activities in the NICU.

Non-pathogenic Rickettsia species LON strains closely related to an agent of Japanese spotted fever (JSF), R. japonica, were isolated in Japan from Haemaphysalis longicornis ticks in 2001. However, the biological properties of LONs in mammalian host cells are poorly understood. In this study, microscopic analysis showed that LONs in a mouse-derived L929 host cell line were rod shaped with sizes of 0.3–0.5 × 0.5–2.0 μm. Molecular analysis revealed the existence of a LON-specific disrupted open reading frame in R. japonica-related group-specific DNA regions. Growth kinetics of LON-2 and LON-13 strains analyzed by a quantitative real-time PCR showed 100-fold or more increment of LONs cultured in L929 host cells at 30°C and slightly less increment at 33°C, and 25-fold increment in human-derived THP-1 host cells at 35°C on day 7 (168 h) post infection. The generation times of the two LON strains cultured in L929 and THP-1 were estimated to be 9.4–12.9 h and 9.6–10.9 h, respectively. To our knowledge, this is the first report on the biological characteristics of Rickettsia sp. LON strains in mammalian cells, which may provide significant information for the experimental approaches for other rickettsiae.

Leprosy is a socially stigmatized granulomatous skin disease caused by Mycobacterium leprae. Due to improvements in medicine and hygiene in Taiwan, the incidence is very low, up to one dozen per year; however, leprosy has never been eradicated due to the increased numbers of immigrants from Southeast Asia. This study aimed to characterize the clinical and histopathological features of patients with leprosy in the context of near elimination. Fifteen cases of pathologically proven leprosy were identified from 2000 to 2016 in Kaohsiung Chang Gung Memorial Hospital. The clinical presentations, demographic details, treatment responses, and disease outcomes were reviewed. The mean age was 46 years (range: 26–73 years). Eight cases were native Taiwanese, while 6 cases and 1 case involved foreign workers from Indonesia and Thailand, respectively. The diagnosis was made 3–6 months on average after skin lesions appeared. The most common clinical subtype was lepromatous leprosy (n = 7). Ten patients were multibacillus microscopically. Three cases were deported. The remaining 12 patients received dapsone and rifampicin for 12 months without recurrence to date. In the near leprosy-eradicated country, early diagnosis and physician vigilance are critical in disease control. Immigrants from endemic countries require strict and professional dermatological examinations and regular follow-up.

Diarrheagenic Escherichia coli (DEC), an important agent of infectious diarrhea, is constantly evolving, making its periodic monitoring necessary. However, the DEC genotypes in Ghana remain uncharacterized. We focused on characterizing the molecular serotypes, virulence factors, multilocus sequence types, and the phylogenetic relatedness among different DEC pathotypes recovered from stool samples of pediatric patients with symptoms of diarrhea from the Western region of Ghana. We detected all five common DEC pathotypes, with the majority of the isolates being enterotoxigenic E. coli (ETEC) harboring the heat-labile enterotoxin gene. The DEC strains exhibited diverse serotypic identity with novel and previously reported outbreak strains. Sequence types (ST) ST38, ST316, and ST1722 were most prevalent, and clonal complex 10 (CC10) was the most common CC. A close evolutionary distance was observed among most of the isolates. Coli surface antigen 6 was the most prevalent (44%, n = 11) ETEC-specific colonization factor. Nearly all the isolates harbored lpfA, and the frequencies of other virulence genes such as pap and cnf1 were 7.9% and 18.4%, respectively. This study provides insights into the important and novel genotypes circulating in the Western region of Ghana that should be monitored for public health.

Companion animals can become infected with tick-borne diseases (TBDs) becoming a reservoir for human transfer, thereby damaging human health. To evaluate whether companion animals are infested with ticks harboring human TBD pathogens, we detected TBD pathogens in ticks collected from dogs and cats brought to animal hospitals in the Yamagata prefecture of Japan. An investigation of 164 adult ticks collected from 88 dogs and 41 cats between March and July 2018 revealed that this region was dominated by three tick species, Ixodes ovatus (n = 95, 57.9%), Ixodes nipponensis (n = 37, 22.6%) and Haemaphysalis flava (n = 10, 6.1%). To evaluate their pathogenic potential, we went on to test each tick for spotted fever group rickettsiae, Lyme disease borreliae, relapsing fever borreliae, tick-borne encephalitis virus, and Huaiyangshan banyangvirus (formerly SFTS virus). Our results identified two I. ovatus ticks infected with Borrelia miyamotoi, which causes emerging relapsing fever; several I. nipponensis ticks infected with Rickettsia monacensis, which cause rickettsiosis; and several Ixodes persulcatus ticks infected with Rickettsia helvetica, which can also cause rickettsiosis. These results suggest that dogs and cats, and veterinary professionals and pet owners, in the Yamagata prefecture have some risk of exposure to several TBDs. This means that there should be continuous monitoring and reporting of TBDs, even those known to be uncommon in Japan, in both companion animals and humans to ensure the health and safety of both humans and animals in Japan.

This study evaluated the cell invasion ability (CIA) of Streptococcus canis isolates, and clarified the relationship between high-frequency CIA and its microbiological features. Of the companion animal-origin isolates (n = 117) that were obtained in 2017, 40 isolates were randomly selected with the host information, with two human blood-origin isolates included. CIA was measured using human colon carcinoma epithelium and the hemolytic activity (HA) using sheep blood, along with S. canis M-like protein (SCM) allele typing, sequence type (ST) determination, and antimicrobial resistance (AMR) phenotyping/genotyping. CIA measurements revealed that 19 and 24 isolates had high- and low-frequencies, respectively. HA assessment revealed that 24 and 19 isolates were categorized as high- and low- level, respectively. No difference was observed in the high-/low-level HA between the high- /low-frequency CIA populations. A significant difference was found in the high-/low-frequency CIA between the SCM group I/II populations. Additionally, a significantly higher CIA was found in the SCM allele type 10/type 11 than in the others. A significant association was observed between high-frequency CIA and the ST21/ST41 populations. No difference was found in the high-/low-frequency CIA between the presence and absence of the AMR phenotype/genotype. These observations suggest a relationship between high-frequency CIA and its microbiological characteristics (SCM allele type 10/type 11 or ST21/ST41).

Cholera posed a significant threat causing outbreaks/epidemics with high morbidity and mortality in Odisha. This study envisages the characterisation of isolated pathogen from two cholera outbreaks reported in 2018 and 2019 from Bargarh and Rayagada districts of Odisha respectively. Vibrio cholerae O1 were isolated following standard techniques. The different virulent and drug resistant genes were detected by multiplex PCR assays; whereas the ctxB genotypes were characterised through double mismatch amplification mutation (DMAMA) PCR assay. The ctxB genes were further sequenced and pulse-field gel electrophoresis (PFGE) was done on some selected strains. The clinical and water isolates of Haitian variant (HCT) V. cholerae O1 Ogawa biotype El Tor with multi drug resistant strains were isolated from both the places. All the V. cholerae O1 strains were positive for virulence genes. The antibiotic resistant genes like dfrA1 (100%), strB (76.9%), intSXT (61.5%) were detected. The PFGE results on V. cholerae O1 strains exhibited two different pulsotypes. These cholera outbreaks were due to multidrug resistant HCT variant V. cholerae O1 strains which were circulating and caused the cholera outbreaks in Odisha. So continuous surveillance on diarrheal disorders is highly essential to prevent the future diarrheal outbreaks in this region.

To investigate the clinical use of multiplex polymerase chain reaction (mPCR) in Japan, epidemiological and clinical data for central nervous infections are needed. Here, we report on the epidemiology and economic burden of central nervous system infections and a simulation of the cost-benefit analysis of the Filmarray® Meningitis/Encephalitis (FAME) test for possible clinical use in Japan. We performed FAME tests on samples from 27 patients with pleocytosis aged between 0 and 20 years seen in six community hospitals in Nara and Osaka prefectures. All clinical management procedures were performed without knowledge of the mPCR test results. We analyzed the clinical data and calculated the required reduction in average length of stay for the FAME test to be cost-beneficial. Among the 27 cases, the FAME test revealed causal pathogens in 13 cases (48.1%). The average medical and social costs per case were ¥299,118 ($2,719.2) and ¥171,768 ($1,561.5), respectively. The minimal needed reduction in average length of stay for the FAME test to be cost-beneficial was 0.32– 0.86 days per meningitis case. The result can be informative for evaluating the cost-effectiveness of the clinical use of the FAME test in Japan.

Dengue fever outbreaks have been repeatedly reported in Côte d’Ivoire. During the 2019 outbreak, DENV-1 was the predominant strain and phylogenetic analysis of the DENV-1 genome obtained from the present patient who returned to Japan in January 2019 revealed a high homology with the 2013–2014 Southeast Asian strains. In a 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 can spread globally, and imported dengue fever cases could serve as an alert for outbreaks in the exporting country.

Pulmonary nocardiosis is a common disease in human immunodeficiency virus (HIV)infected patients. In most cases, the disease progresses slowly. Here, we have presented a case of pulmonary nocardiosis that rapidly progressed. A 35-year-old woman with acquired immune deficiency syndrome and superior vena cava (SVC) syndrome, who was previously lost to follow-up, presented to our hospital chronic non-productive cough. Her CD4 count was 33 cells/µL (4%). Chest X-ray revealed opacity in the right upper lobe of the lung, and the results of sputum acid-fast staining were negative. Anti-tuberculosis agents were prescribed. Two weeks later, superficial vein dilatation was noted on her chest wall and the chest X-ray revealed worse findings. Chest CT showed a heterogeneous mass measuring 9.6 × 9.8 × 8.3 cm in the right lung. Further, necrotic mediastinal nodes nearly obliterated the SVC. Gram-positive beaded branching filamentous organisms were identified in the sputum by modified acid-fast staining. Hence, she was diagnosed with pulmonary nocardiosis. Culture results confirmed the presence of Nocardia beijingensis with SVC syndrome. She responded to treatment. After 2 weeks of parenteral administration, we switched her to oral trimethoprim/sulfamethoxazole, which was later followed by antiretroviral agents.

Subacute sclerosing panencephalitis (SSPE) is a late-onset, intractable, and fatal viral disease caused by persistent infection of the central nervous system with a measles virus mutant (SSPE virus). In Japan, interferon-α and ribavirin are administered intracerebroventricularly to patients with SSPE. However, as the therapeutic effect is insufficient, more effective drugs are needed. Favipiravir, which is clinically used as an anti-influenza drug, demonstrates anti-viral effects against RNA viruses. In this study, the antiviral effect of favipiravir against measles virus (Edmonston strain) and SSPE virus (Yamagata-1 strain) was examined in vitro. The 50% effective concentration (EC₅₀) of favipiravir (inhibiting viral plaque formation by 50%) against Edmonston and Yamagata-1 strains were 108.7 ± 2.0 μM (17.1 ± 0.3 μg/mL) and 38.6 ± 6.0 μM (6.1 ± 0.9 μg/mL), respectively, which were similar to those of ribavirin. The antiviral activity of favipiravir against the SSPE virus was demonstrated for the first time in this study.

Since the coronavirus disease 2019 (COVID-19) emerged in Wuhan, China, in December 2019, it has rapidly spread worldwide, and the number of cases is also increasing in Japan. The number of COVID-19 cases in Japan in the early stages was not uniform, and cases were largely concentrated in several prefectures. There was a strong, positive correlation between the distribution of COVID-19 cases and the number of foreign travelers as well as Chinese travelers, at prefectural level, with coefficients of 0.68 (P < 0.0001) and 0.60 (P < 0.0001), respectively. Moreover, phylogenetic tree analysis revealed that all the registered SARS-CoV-2 detected from January 23 to February 29, 2020, belonged to Chinese lineage, while those detected in March 2020 belonged to American and European lineages. Only 14 (20.3%) were infected outside Japan; however, the majority of the cases (79.7%) were infected domestically. In conclusion, a higher number of COVID-19 cases were identified in prefectures with more Chinese travelers, supporting the importance of enforcing policies that restrict the entry of overseas travelers to control COVID-19 spread. These findings highlight the risk of secondary transmission in the community caused by apparent or silently imported cases.

Real-time reverse transcription polymerase chain reaction (RT-PCR) tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are occasionally repeated when clinicians suspect false-negative results, but the conditions under which repeated RT-PCR testing is warranted remain unclear. We evaluated the practice of repeat RT-PCR testing for SARS-CoV-2 in 45 patients who were retested after an initial negative PCR test. Of these, the diagnosis of coronavirus disease (COVID-19) was confirmed in four patients with typical chest computed tomography (CT) findings and in one patient without typical CT findings in whom the test result was strongly suspected to be false-positive. We recommend repeat RT-PCR testing only for patients with typical CT findings of COVID-19.

Splenic abscess is an uncommon extra-intestinal complication of Salmonella Typhi infection in the post-antibiotic era. The condition is associated with high morbidity and mortality if not diagnosed in a timely manner. We report the case of a 20-year-old man who presented with left upper abdominal pain, high-grade fever, and a lump in the abdomen. Ultrasound and computed tomography scan of the abdomen revealed a large solitary splenic abscess. The abscess was drained percutaneously and Salmonella Typhi was isolated on a culture board, which was an unexpected finding. The patient was prescribed the appropriate antibiotics based on an antimicrobial susceptibility report and periodic follow-up was planned. The clinical condition of the patient improved along with complete resolution of the abscess. This report reiterates the importance of clinical diagnosis and radiological imaging even for common diseases presenting in an unusual fashion. Percutaneous drainage and microbial culture, with antibiotics prescribed based on susceptibility are key to the treatment of such abscesses.

The Vibrio species undergo cryptic changes in their genetic material for better adaptability, which accounts for antibiotic resistance. In the present study, we investigated the emergence and spread of sensitivity to polymyxin B (PB) by El Tor V. cholerae O1 strains from 1995 to 2019 in Odisha, India. The results showed that out of 1200 V. cholerae O1 strains, 89.4% were resistant and the remaining 10.6% strains were sensitive to PB. The sensitivity to PB of V. cholerae O1 strains emerged from 2005 to 2019, except in 2015, clearly signifying the presence of classical biotype characteristics in the El Tor variant of V. cholerae O1 strains. The Etest assay revealed some interesting traits of PB susceptibility in the ctxB1 and ctxB7 genotypes of V. cholerae O1 strains. The minimum inhibitory concentration (MIC) of ctxB7 genotypes showed reduced MIC values of ≤ 4 µg/mL, whereas ctxB1 genotypes exhibited higher MIC values of 24 and 32 µg/mL.