Correspondence of SARS-CoV-2 genomic sequences obtained from wastewater samples and COVID-19 patient at long-term care facilities.

Wastewater-based epidemiology (WBE) has been in the spotlight because of applicability of early detection of virus outbreak and new variants at the catchment area. However, there has been a notable absence of research directly confirming the association between SARS-CoV-2 in wastewater and patient specimens. In this study, we performed a quantitative and qualitative investigation with a genetic-level comparison of SARS-CoV-2 between COVID-19 patients and SARS-CoV-2 positive wastewater samples at long-term care facilities. Wastewater samples were collected via passive sampling from manholes, and SARS-CoV-2 load in wastewater was determined by qPCR. We performed correlation analysis between SARS-CoV-2 load and COVID-19 case number, which suggested that SARS-CoV-2 was detected from wastewater earlier than ascertainment of COVID-19 case. Six and six RNA samples from COVID-19 positive cases and wastewater, respectively, from two facilities were then applied for amplicon sequencing analysis. Mutation analysis revealed high sequence similarity of SARS-CoV-2 variants between wastewater and patient samples (>99 %). To the best of our knowledge, this is the first study demonstrating that WBE is also effective in predicting predominant SARS-CoV-2 variant at facility-level, which is helpful to develop early-warning system for outbreak occurrence with predominant variant.

Prediction of heading date, culm length, and biomass from canopy-height-related parameters derived from time-series UAV observations of rice.

Unmanned aerial vehicles (UAVs) are powerful tools for monitoring crops for high-throughput phenotyping. Time-series aerial photography of fields can record the whole process of crop growth. Canopy height (CH), which is vertical plant growth, has been used as an indicator for the evaluation of lodging tolerance and the prediction of biomass and yield. However, there have been few attempts to use UAV-derived time-series CH data for field testing of crop lines. Here we provide a novel framework for trait prediction using CH data in rice. We generated UAV-based digital surface models of crops to extract CH data of 30 Japanese rice cultivars in 2019, 2020, and 2021. CH-related parameters were calculated in a non-linear time-series model as an S-shaped plant growth curve. The maximum saturation CH value was the most important predictor for culm length. The time point at the maximum CH contributed to the prediction of days to heading, and was able to predict stem and leaf weight and aboveground weight, possibly reflecting the association of biomass with duration of vegetative growth. These results indicate that the CH-related parameters acquired by UAV can be useful as predictors of traits typically measured by hand.

Comparative analyses of Stvb-allelic genes reveal japonica specificity of rice stripe resistance in Oryza sativa.

Rice stripe, a viral disease, causes widespread damage to japonica rice (Oryza sativa ssp. japonica). A rice stripe virus (RSV) bioassay revealed that many indica and japonica upland varieties exhibit resistance, whereas japonica paddy varieties are susceptible. However, the genetic background for this subspecies-dependent resistance is unclear. Herein, we focused on rice stripe resistance genes located at the Stvb locus. Three resistant alleles, Stvb-i (indica), Stvb (japonica upland), and Stvb-o (Oryza officinalis) were compared with the susceptible allele, stvb-j (japonica paddy). The expression of the resistance genes was higher than that of stvb-j. Sequence comparison revealed that the resistant and susceptible alleles had different 5'-end sequences and 61-bp element(s) in the fourth intron. The insertion of an LTR-retrotransposon modified the exon 1 sequence of stvb-j. We then developed four DNA markers based on gene structure information and genotyped resistant and susceptible varieties. The LTR-retrotransposon insertion was detected only in susceptible varieties. Resistant genotypes were primarily found in indica and upland japonica, whereas paddy japonica carried the susceptible genotype. Our results characterize the genetic differences associated with RSV resistance and susceptibility in O. sativa and provide insights on the application of DNA markers in rice stripe disease management.

A rice gene that confers broad-spectrum resistance to ß-triketone herbicides.

The genetic variation of rice cultivars provides a resource for further varietal improvement through breeding. Some rice varieties are sensitive to benzobicyclon (BBC), a ß-triketone herbicide that inhibits 4-hydroxyphenylpyruvate dioxygenase (HPPD). Here we identify a rice gene, HIS1 (HPPD INHIBITOR SENSITIVE 1), that confers resistance to BBC and other ß-triketone herbicides. We show that HIS1 encodes an Fe(II)/2-oxoglutarate-dependent oxygenase that detoxifies ß-triketone herbicides by catalyzing their hydroxylation. Genealogy analysis revealed that BBC-sensitive rice variants inherited a dysfunctional his1 allele from an indica rice variety. Forced expression of HIS1 in Arabidopsis conferred resistance not only to BBC but also to four additional ß-triketone herbicides. HIS1 may prove useful for breeding herbicide-resistant crops.

Comparison of textural properties and structure of gels prepared from cooked rice grain under different conditions.

The objective of this study was to investigate the effects of rice variety, water content, and preparation temperature on the textural properties of gels processed from cooked rice grains via high-speed shear homogenization. Rice gels were prepared from seven high-amylose rice varieties. The results demonstrated the significant differences in rice gel hardness and hardening rates during storage based on the rice variety used. The proportion of short chains of amylopectin was negatively correlated with the hardness of the rice gel. The sample temperature before shear treatment also influenced the rice gel hardness. Rice gels prepared from cooked rice maintained at 75°C prior to homogenization showed a higher breaking force than those from cooked rice at 25°C. Observation using scanning electron microscopy demonstrated the tendency of the cooked rice sample maintained at 75°C to form a finer gel network after homogenization than those at 25°C from the same rice variety.

One Pot Cooking of Rice Grains for Preparation of Rice-Gel Samples Using a Small-Scale Viscosity Analyzer: Small-scale Rice-gel Preparation from Grains.

Rice-gel prepared by the following three steps: rice grain cooking, shearing of the cooked rice, and cooling for gel formation, is expected as a novel food ingredient for modification of various food products such as bread and noodles. To meet the demand for high-throughput systems for research and developments on the new rice gels, herein we established a mini-cooking system for preparation of rice gel samples from grains using a small-scale viscosity analyzer (Rapid Visco Analyzer; RVA). Polished rice grains (4 g) were cooked with 22 mL of water in a canister, and the paddle equipped in the canister was rotated at 2,000 rpm for 30 min (80 °C was used as a representative) to shear the cooked rice. The sheared paste was cooled to 10 °C at 160 rpm, and the initial gelation property was evaluated by viscosity analysis within the RVA. Alternatively, the sheared paste was transferred to an acrylic mold and kept at 4 °C for 0, 1, 3, and 5 days for determination of the hardness with a compression test. Compressive forces required to penetrate 20 % thickness for three tested rice cultivars were measured, and the trend of the value shifts during preservation is similar to the corresponding trend obtained in 300-g grain scale laboratory tests, whereas the individual values were halved in the former. This small cooking method could offer a useful assay system for a rapid evaluation in the breeding programs and in the high-throughput screening of additives for the modification of properties.

Quantitative trait loci analysis of grain appearance in Oryza sativa L. 'Emi-no-kizuna'.

A quantitative trait locus (QTL) analysis was conducted on grain appearance in Emi-no-kizuna, a rice cultivar that has superior and stable appearance of the brown rice grain and high tolerance to high temperature stress, by using F3 lines derived from Emi-no-kizuna and Tomohonami. The investigation was performed 2013 and 2015. In summer 2013 the air temperature was higher and the larger differences in grain appearance were observed. In the QTL analysis, a highly contributing locus, qGA8, was detected at the end of the short arm of chromosome 8. Because trends of reduced the occurrence of white immature kernel and increased the percentage of perfect grain were observed in Emi-no-kizuna genotype in both years, qGA8 is likely to be an important QTL that is dominant in the superior grain appearance of Emi-no-kizuna. Also, qGA8 was linked to a QTL associated with days to heading. Another QTL, qGA7, associated with grain appearance was detected on chromosome 7 in 2013. Because no negative correlation was found between the genotype of qGA8 and thousand grain weight, it should be possible to breed cultivars that possess Emi-no-kizuna genotype qGA8 without a decrease in thousand grain weight.

Improvement of seed shattering and dormancy in Oryza sativa L. 'Hokuriku 193' based on genetic information.

In this study, we investigated the genetic basis of seed shattering and dormancy in Hokuriku 193 and bred an NIL improved these traits. Analysis of an F3 population from Hokuriku 193 × Koshihikari revealed a general correspondence between seed shattering and genotypes at the qSH1 locus, suggesting a strong influence of this locus on the seed shattering in Hokuriku 193. An F2 population from [ms-bo] Nekken 2 × Hokuriku 193 was also analyzed to identify quantitative trait loci (QTLs) for seed dormancy as measured by germination rate in the first December and March after seed harvest. The results revealed a concurrence QTLs of on chromosomes 1, 3, and 6 (qSDo1, qSDo3, qSDo6). In particular, qSDo1 and qSDo6 were considered regions worthy of active modification because they were QTL regions that promoted seed dormancy when carrying Hokuriku 193 genome regions around. SSDo_NIL, a near isogenic line (NIL) derived from Hokuriku 193 by introgressing Nekken 2 alleles only at the qSH1 locus and qSDo1, did not shatter, and its germination rate was significantly higher than that of Hokuriku 193. Yield performance was similar between SSDo_NIL and Hokuriku 193, suggesting that improvement of seed shattering and dormancy does not affect yield.

Quantitative trait loci analysis of blast resistance in Oryza sativa L. 'Hokuriku 193'.

To investigate the genetic background responsible for blast resistance in Oryza sativa L. 'Hokuriku 193', QTL analysis was conducted using the F3 lines from the cross [ms-bo] Nekken 2 × Hokuriku 193 that were artificially infected with rice blast fungus (Magnaporthe grisea). QTLs were detected on chromosomes 1, 4, 6 and 12 that correlated with greater blast resistance in the Hokuriku 193-type lines. Notably, the QTL on chromosome 12 had a major effect and localized to the same region where Pi20(t), a broad-spectrum blast resistance gene, is positioned, suggesting strongly that the blast resistance of Hokuriku 193 was controlled by Pi20(t). Also, QTL analysis of the lines found to have no Pi20(t) detected two QTLs on chromosome 4 (qBR4-1 and qBR4-2) and one QTL on chromosome 6 (qBR6), of which qBR4-2 and qBR6 correlated with higher percentages of resistant plants in the Hokuriku 193-type lines. The blast susceptibility of BR_NIL (a NIL of Hokuriku 193 from which Pi20(t) was eliminated) was greater than that of Hokuriku 193, suggesting that elimination of Pi20(t) may markedly increase blast susceptibility. The disease severity of BR_NIL was mild, which might be the effect of qBR4-2 and/or qBR6.

[An autochthonous outbreak of dengue type 1 in Tokyo, Japan 2014].

OBJECTIVES: An outbreak of autochthonous dengue fever was reported in August 2014, with cases suspected mainly from Yoyogi Park in Tokyo. This is the first epidemic of dengue fever in Japan since 1945. METHODS: From August to October 2014, the following measures were taken to control the outbreak: 1) risk communication and information sharing; 2) active case finding; 3) vector surveillance in affected sites; and 4) laboratory testing. We also reviewed the surveillance data as reported to the National Epidemiological Surveillance of Infectious Diseases during the 44 epidemiological weeks. results: An official dengue fever call center was set up temporarily for the general public and 3,005 calls were received. The Tokyo Metropolitan Government issued 39 press releases regarding patients and nine related to dengue virus (DENV) detection and vector control activities for the media. Confirmed autochthonous dengue fever cases were reported between the 35th and 44th epidemiological weeks. Out of 160 cases of outbreak, 108 (67.5%) confirmed cases were reported in Tokyo. The estimated illness onset dates were between August 9 and October 7, and estimated dates of infections were between August 3 and October 3, 2014. The data suggest that the infective mosquitoes had already been present in Yoyogi Park at the end of July 2014. During the weekly vector surveillance at Yoyogi Park, a total of 1,152 adult mosquitoes, of which 856 (73.3%) were Aedes mosquitoes, were collected over 11 weeks by a light trap with dry ice. DENV was detected from adult Aedes mosquito samples collected on the 2nd, 9th, and 16th of September, 2014. Serum samples from 240 suspected cases were examined at the Tokyo Metropolitan Institute of Public Health, and 78 were positive for the DENV NS1 antigen, DENV-specific IgM antibody, or DENV nucleic acid with reverse transcriptase polymerase chain reaction (RT-PCR) (NS1: 66 cases; IgM: 50 cases; PCR: 57 cases). Genetic analysis of DENV-positive serum and mosquito samples found all to be categorized as DENV-serotype 1 (gene type I). Phylogenetic analysis of the envelope protein genome sequence from patients and mosquitoes in Tokyo revealed more than 99% similarity with each other and with the strain from the first outbreak-associated patient in Saitama. CONCLUSION: Measures important for control of infectious disease epidemic were learned during this recent indigenous dengue outbreak in Tokyo. It also highlighted the importance of preparedness for epidemics of indigenous or imported infectious diseases, especially in light of the fact that Tokyo is in preparation for the Olympic and Paralympic Games in 2020.

Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars.

BACKGROUND: High-yielding cultivars of rice (Oryza sativa L.) have been developed in Japan from crosses between overseas indica and domestic japonica cultivars. Recently, next-generation sequencing technology and high-throughput genotyping systems have shown many single-nucleotide polymorphisms (SNPs) that are proving useful for detailed analysis of genome composition. These SNPs can be used in genome-wide association studies to detect candidate genome regions associated with economically important traits. In this study, we used a custom SNP set to identify introgressed chromosomal regions in a set of high-yielding Japanese rice cultivars, and we performed an association study to identify genome regions associated with yield. RESULTS: An informative set of 1152 SNPs was established by screening 14 high-yielding or primary ancestral cultivars for 5760 validated SNPs. Analysis of the population structure of high-yielding cultivars showed three genome types: japonica-type, indica-type and a mixture of the two. SNP allele frequencies showed several regions derived predominantly from one of the two parental genome types. Distinct regions skewed for the presence of parental alleles were observed on chromosomes 1, 2, 7, 8, 11 and 12 (indica) and on chromosomes 1, 2 and 6 (japonica). A possible relationship between these introgressed regions and six yield traits (blast susceptibility, heading date, length of unhusked seeds, number of panicles, surface area of unhusked seeds and 1000-grain weight) was detected in eight genome regions dominated by alleles of one parental origin. Two of these regions were near Ghd7, a heading date locus, and Pi-ta, a blast resistance locus. The allele types (i.e., japonica or indica) of significant SNPs coincided with those previously reported for candidate genes Ghd7 and Pi-ta. CONCLUSIONS: Introgression breeding is an established strategy for the accumulation of QTLs and genes controlling high yield. Our custom SNP set is an effective tool for the identification of introgressed genome regions from a particular genetic background. This study demonstrates that changes in genome structure occurred during artificial selection for high yield, and provides information on several genomic regions associated with yield performance.

[Health examination in future at the era of low tuberculosis incidence--from contacts examination toward active epidemiological studies].

Japan is still "intermediate burden" country as medium-incidence of tuberculosis (TB). But the incidence of TB varies by public health units. The priority for TB control would be lowering in the areas where the incidence of TB is relatively low. In addition, younger age groups get low prevalence of TB infection than elderly persons. As a result, fewer experiences for TB diagnosis and treatment in the hospital and the medical facility would cause the delay in the detection of TB patients which eventually cause outbreaks. Although there are differences in population density and population mobility between urban and rural areas, the socially economic vulnerable patients and foreign patients are the common risks. Any public health units' policies of TB should correspond to the individual situation. At the era of low tuberculosis incidence, the infection risk is to be "From ubiquitous to the uneven distribution". This makes TB detection much more difficult. At this symposium, each speaker presented the case for actually experienced with QFT test and/or VNTR analysis. They mainly focused on the paradigm shift in TB control which is indispensable for resolving the gaps in regional differences and the differences in diagnostic capability. Although the cases in this symposium were not for the low incidence situation, the pioneering approaches presented here would boost the future application of QFT and VNTR analysis nationwide. The discussions also partially covered the technical infrastructure for molecular epidemiology which covers the whole country. By making full use of QFT test and VNTR analysis as a contact screening tool, we can appropriately understand the risk of TB infection in the region from a buildup of bacteria and patient information. Now is the time to prepare for. Active surveillance of TB by this way would clarify the risk of the disease and lead to the advocacy essential for the resolution. 1. Current situation and challenge of contact survey by using QFT test in Tokyo: Hideo MAEDA (Bureau of Social Welfare and Public Health, Tokyo Metropolitan Government). 2. Contact investigation of a tuberculosis outbreak: Kenichi MIYAMOTO (Takaido Community Health Center). We have experienced a TB outbreak in integrated junior and senior high school in Tokyo. Index patient was a student with persistent respiratory symptoms for six months before diagnosis of sputum smear-positive TB. Public health center started contact investigation immediately. QFT-positive rates were high in close contacts, especially in classmates. Additionally, a student outside of contact investigation was diagnosed as TB and considered to be infected from the first patient by VNTR analysis. Therefore, public health center expanded QFT-tests to all students and teachers in this school. Finally, 9 students and 2 teachers in this school were diagnosed as sputum smear-negative TB by contact investigation. 3. Utilization of molecular epidemiological procedure in contact investigation in Kyoto City: Masahiro ITO (Public Health Center of Kyoto City) Molecular epidemiological procedure using VNTR analysis has been used for contact investigation of tuberculosis since January 2011 in Kyoto City. One hundred forty four strains of Mycobacterium tuberculosis from patients with tuberculosis were investigated and 130 strains were fully analyzed. Fourteen clusters were found and the number of strains included in the cluster was ranged from two to 11. Epidemiological relationship between patients in one cluster was found, however, significant relationship in another clusters was not demonstrated. It was suggested that VNTR analysis is useful for molecular epidemiological analysis of tuberculosis. 4. The population based molecular epidemiological studies and QFT test in a contact examination: Riyo FUJIYAMA, Keisuke MATSUBAYASHI, Setsuko MIZUSHIRI, Junko HIGUCHIL Chika SHIRAI, Yuko KATAGAMI, Mieko CHIHARA, Akihiro IJICHI (Kobe City Public Health Center), Kentaro ARIKAWA, Noriko NAKANISHI, Tomotada IWAMOTO (Kobe Institute of Health). The population based molecular epidemiological studies should be made good use of contacts examination. In future, we expect the tuberculosis molecular epdimiological study improve search for the process of tuberculosis infection. The QFT positive rates correlated well with closeness of contact. QFT test is considered useful for diagnosing tuberculosis infection. However, in the judgment of tuberculosis infection, we should consider the total result of contact investigation not only QFT test but also the contact situation. 5. Insights into the TB epidemiology through population based molecular epidemiological studies: Tomotada IWAMOTO (Kobe Institute of Health) The population based molecular epidemiological studies unveiled the transmission dynamics of tuberculosis at bacterial clone level. This provides scientific evidences for achieving better TB control programs. In the advanced stage of the tuberculosis molecular epidemiological study, we expect to change the current geno-typing based molecular epidemiology to whole genome-typing based molecular epidemiology on the basis of the rapid innovation of next-generation sequencing technology.

High incidence of lipid deposition in the liver of rats fed a diet supplemented with branched-chain amino acids under vitamin B6 deficiency.

Male Wistar rats were fed four diets composed of purified 20% vitamin-free casein diet with (+) or without (-) vitamin B(6) (7.0 mg of pyridoxine HCl/kg of diet) and with (+) or without (-) branched-chain amino acids (BCAAs) of valine, leucine, and isoleucine (4.75%): B(6)(+)BCAA(-); B(6)(+)BCAA(+); B(6)(-)BCAA(-); and B(6)(-)BCAA(+) for 21 d. Among rats fed the B(6)(-)BCAA(+) diet, about a half showed lipid deposition in the liver. On the other hand, serum triacylglycerol levels in the B(6)(-)BCAA(+) group tended to be decreased. Hepatic triacylglycerol and cholesterol levels tended to increase in the B(6)(-)BCAA(+) group compared with the other three groups. Serum apolipoprotein B and apolipoprotein E (apo E) levels in the B(6)(-)BCAA(+) group were the lowest among the three groups. In contrast, hepatic apo E levels in the B(6)(-)BCAA(+) group were the highest among the three groups. High-performance liquid chromatography of pooled serum of rats with lipid deposits revealed that triacylglycerol and cholesterol levels in very low-density lipoprotein (VLDL) were decreased compared with other diet groups. These results strongly suggest that one of the mechanisms of lipid deposition in rats fed a B(6)(-)BCAA(+) diet is due to impaired secretion of VLDL.

MACROCALYX and JOINTLESS interact in the transcriptional regulation of tomato fruit abscission zone development.

Abscission in plants is a crucial process used to shed organs such as leaves, flowers, and fruits when they are senescent, damaged, or mature. Abscission occurs at predetermined positions called abscission zones (AZs). Although the regulation of fruit abscission is essential for agriculture, the developmental mechanisms remain unclear. Here, we describe a novel transcription factor regulating the development of tomato (Solanum lycopersicum) pedicel AZs. We found that the development of tomato pedicel AZs requires the gene MACROCALYX (MC), which was previously identified as a sepal size regulator and encodes a MADS-box transcription factor. MC has significant sequence similarity to Arabidopsis (Arabidopsis thaliana) FRUITFULL, which is involved in the regulation of fruit dehiscent zone development. The MC protein interacted physically with another MADS-box protein, JOINTLESS, which is known as a regulator of fruit abscission; the resulting heterodimer acquired a specific DNA-binding activity. Transcriptome analyses of pedicels at the preabscission stage revealed that the expression of the genes involved in phytohormone-related functions, cell wall modifications, fatty acid metabolism, and transcription factors is regulated by MC and JOINTLESS. The regulated genes include homologs of Arabidopsis WUSCHEL, REGULATOR OF AXILLARY MERISTEMS, CUP-SHAPED COTYLEDON, and LATERAL SUPPRESSOR. These Arabidopsis genes encode well-characterized transcription factors regulating meristem maintenance, axillary meristem development, and boundary formation in plant tissues. The tomato homologs were specifically expressed in AZs but not in other pedicel tissues, suggesting that these transcription factors may play key roles in pedicel AZ development.

Genotypic variations in non-structural carbohydrate and cell-wall components of the stem in rice, sorghum, and sugar vane.

We evaluated genetic variations in the non-structural carbohydrate (NSC) and the cell-wall components of stem in rice, sorghum, and sugar cane to assess the potential suitability of these gramineous crops for bioethanol production. For NSC, the maximum soluble sugar concentration was highest in sugar cane, followed by sorghum with sucrose. The major NSC in rice was starch, but there were wide variations in the starch to soluble sugar ratios among the cultivars. The total concentration of cell-wall components was negatively correlated with the NSC concentration, indicating competition for carbon sources. Among the cell-wall components, lignin was relatively stable within each group. The major sugar species composing hemicellulose was xylose in all crop groups, but there were differences in composition, with a higher fraction of arabinose and glucose in rice as compared to the other crops. In rice, there was less lignin than in sorghum or sugar cane; this might be advantageous for the efficient saccharification of cellulose.

Transmission of specific genotype streptomycin resistant strains of Mycobacterium tuberculosis in the Tokyo Metropolitan Area in Japan.

BACKGROUND: From 2003 through to 2004, an outbreak of tuberculosis was identified at a university campus in Yokohama City, located in the southern part of the Tokyo Metropolitan Area (TMA). All Mycobacterium tuberculosis (M. tuberculosis) strains detected with regards to this outbreak turned out to be Streptomycin resistant with matched patterns of 14 IS6110 bands of Restriction Fragment Length Polymorphism (RFLP). The M. tuberculosis bacilli, which had the matched IS6110 band patterns with resistance to Streptomycin to those of bacilli isolated in the outbreak, were also concurrently detected through either the population-based or the hospital-based DNA fingerprinting surveillance of M. tuberculosis either in Shinjuku City or in Kawasaki City respectively. The aim of the present study is to describe the spread of the specific genotype strains of M. tuberculosis in the TMA as observed in the above incident, and to identify the possible transmission routes of the strains among people living in urban settings in Japan. METHODS: We applied Variable Numbers of Tandem Repeats (VNTR) analysis to all M. tuberculosis isolates which were resistant to Streptomycin with a matched IS6110-RFLP band pattern (M-strains). They were isolated either from cases related to the tuberculosis outbreak that happened at a university, or through DNA fingerprinting surveillance of M. tuberculosis both in Shinjuku City and in Kawasaki City. For VNTR analysis, 12MIRU loci, 4ETR loci, seven loci by Supply, four loci by Murase (QUB15, Mtub24, VNTR2372, VNTR3336) were selected. RESULTS: Out of a total of 664 isolates collected during the study period, 46 isolates (6.9%) were identified as M-strains. There was a tendency that there was a higher proportion of those patients whose isolates belonged to M4-substrains, with four copies of tandem repeat at the ETR-C locus, to have visited some of the internet-cafés in the TMA than those whose isolates belonged to M5-substrains, with five copies at the ETR-C locus, although statistically not significant (38.1% vs. 10.0%, Exact p = 0.150). CONCLUSION: Although firm conclusions could not be reached through the present study, it suggested that we have to take into consideration that tuberculosis can be transmitted in congregated facilities like internet cafés where tuberculosis high-risk people and general people share common spaces.

[Tuberculosis control in Shinjuku Ward, Tokyo--promoting the DOTS program and its outcome].

OBJECTIVES: The objectives were to report how to promote tuberculosis (TB) control including DOTS (Directly Observed Treatment, Short-course) programs, and to evaluate the results of TB control programs in Shinjuku Ward (Shinjuku-ku). SETTING AND CHARACTERISTICS: Inhabitants and TB patients in Shinjuku Ward. Shinjuku Ward is located in the center of metropolitan Tokyo and has typical urban TB problems, such as high incidence rate and TB among foreigners and the homeless. The TB incidence rates in Shinjuku Ward decreased from 83.9 per 100,000 population in 1999 to 42.5 per 100,000 population in 2006, however, the rates were still two times higher than the national average. Therefore, one of the important TB programs in Shinjuku has been to actively detect cases among high-risk groups such as foreigners and the homeless. METHODS: We observed the trend of case detection rates by health examination with chest X-ray among different high-risk groups, and compared the treatment outcomes before and after DOTS program execution. We also reviewed the changes of re-treatment rates and drug resistance rates. RESULTS: The case detection rates of TB by health examinations of foreign students at Japanese language schools decreased from 0.49% in 1996 to 0.13% in 2006 (p = 0.021). Although the case detection rates decreased, they were still about 26 times higher than those of Japanese students. While, the case detection rates among the homeless remained high with 4.7%, 3.3%, 4.5% and 3.6% in 1999-2002, respectively, since 2003, however, they had decreased and no TB cases were detected in 2005-2006. The DOTS program for homeless TB patients has been carried out since 2000 and that for the foreigners since 2003. The rates of defaulting during treatment before DOTS were very high among both homeless patients (21.4%) and foreigners (29.8%) in 1998-1999. However, after the introduction of DOTS program, those rates declined to 10.4% (p = 0.014) among the homeless and 7.8% (p = 0.002) among foreigners in 2002-2004. The proportion of newly notified patients with previous TB treatment and those with multi-drug resistant TB (MDR-TB) have also decreased after the introduction of DOTS programs. From 2000-2002 to 2003-2006, the re-treatment rates decreased from 19.4% to 10.0% (p < 0.001) and MDR-TB rates decreased from 1.6% to 0.2% (p = 0.042), respectively. DISCUSSION: The key points of TB control in Shinjuku Ward are to detect TB cases early especially among the high-risk groups, and to assist all TB patients to complete their treatment. In order to expand this strategy, besides promoting active case findings among high-risk groups, we have developed many types of DOTS programs, considering each patient's lifestyle and cooperating with school teachers at schools, pharmacists at pharmacies, home-care specialists at homes or facilities for the elderly, and so on. Among others, a major premise for the homeless and some other socially disadvantaged patients was to guarantee the provision of medicine and living by introducing social welfare services, before starting DOTS programs. This approach might have helped to reduce the defaulting rate, relapse rate and MDR-TB rate.

[Implementation and evaluation by a population-based RFLP analysis in an urban area, Shinjuku city, Tokyo--the possibility of application for contact investigations].

OBJECTIVES: The objectives were to examine Mycobacterium tuberculosis transmission patterns by RFLP analysis in Shinjuku city, and to elucidate more effective methods of contact investigations. METHODS: We applied RFLP analysis to 389 M. tuberculosis isolates from 402 TB patients registered in Shinjuku city from September 2002 though August 2006. RESULTS: Forty-six clusters consisting of 155 TB patients (average 3.4 people per cluster) were identified (proportion of clustering: 39.8%). The clustering rates were 34.5% among general patients, and 57.8% among homeless patients, and the latter was higher than that of non-homeless patients (odds ratio: 2.6, 95% CI; 1.6-4.1, p < 0.001). On the other hand, the clustering rates were only 19.4% among foreigners (odds ratio: 0.5, 95% CI; 0.2-1.2, p = 0.090). Twenty-eight of 46 clusters (60.9%) were consisted of mixture of general patients, homeless patients and foreigner patients. Thus, RFLP analysis can detect the transmission route which can not be identified by the routine contact examination, thus enabling contact investigations extended to the appropriate persons. DISCUSSION: The homeless clustering rate was significantly high. This suggests that the proportion of transmission among the homeless patients might be high. However, many clusters were composed of a mixture of homeless patients and non-homeless patients, so transmission patterns are not easy to identify. It is not always true that transmission of tuberculosis to non-homeless patients took place from homeless patients. Clustering rates among homeless patients are high, therefore taking countermeasures for the homeless patients is an effective way to prevent the spread of tuberculosis. Introduction of RFLP analysis is a practical epidemiological methodology to investigate the source of infection and transmission route of infection, and can be applied to contact investigations. If RFLP analysis can be applied in a larger area, yearly changes of notification rates and molecular epidemiological clustering rates will provide indices for preventive measures against tuberculosis.