Hiroshi Yoshikura

Outbreaks of Multidrug-Resistant Pseudomonas aeruginosa in Community Hospitals in Japan

ABSTRACT We previously reported an outbreak in a neurosurgery ward of catheter-associated urinary tract infection with multidrug-resistant (MDR) Pseudomonas aeruginosa strain IMCJ2.S1, carrying the 6′-N-aminoglycoside acetyltransferase gene [aac(6′)-Iae]. For further epidemiologic studies, 214 clinical isolates of MDR P. aeruginosa showing resistance to imipenem (MIC ≥ 16 μg/ml), amikacin (MIC ≥ 64 μg/ml), and ciprofloxacin (MIC ≥ 4 μg/ml) were collected from 13 hospitals in the same prefecture in Japan. We also collected 70 clinical isolates of P. aeruginosa that were sensitive to one or more of these antibiotics and compared their characteristics with those of the MDR P. aeruginosa isolates. Of the 214 MDR P. aeruginosa isolates, 212 (99%) were serotype O11. We developed a loop-mediated isothermal amplification (LAMP) assay and a slide agglutination test for detection of the aac(6′)-Iae gene and the AAC(6′)-Iae protein, respectively. Of the 212 MDR P. aeruginosa isolates, 212 (100%) and 207 (98%) were positive in the LAMP assay and in the agglutination test, respectively. Mutations of gyrA and parC genes resulting in amino acid substitutions were detected in 213 of the 214 MDR P. aeruginosa isolates (99%). Of the 214 MDR P. aeruginosa isolates, 212 showed pulsed-field gel electrophoresis patterns with ≥70% similarity to that of IMCJ2.S1 and 83 showed a pattern identical to that of IMCJ2.S1, indicating that clonal expansion of MDR P. aeruginosa occurred in community hospitals in this area. The methods developed in this study to detect aac(6′)-Iae were rapid and effective in diagnosing infections caused by various MDR P. aeruginosa clones.

A subcutaneously injected UV-inactivated SARS coronavirus vaccine elicits systemic humoral immunity in mice

Abstract The recent emergence of severe acute respiratory syndrome (SARS) was caused by a novel coronavirus, SARS-CoV. It spread rapidly to many countries and developing a SARS vaccine is now urgently required. In order to study the immunogenicity of UV-inactivated purified SARS-CoV virion as a vaccine candidate, we subcutaneously immunized mice with UV-inactivated SARS-CoV with or without an adjuvant. We chose aluminum hydroxide gel (alum) as an adjuvant, because of its long safety history for human use. We observed that the UV-inactivated SARS-CoV virion elicited a high level of humoral immunity, resulting in the generation of long-term antibody secreting and memory B cells. With the addition of alum to the vaccine formula, serum IgG production was augmented and reached a level similar to that found in hyper-immunized mice, though it was still insufficient to elicit serum IgA antibodies. Notably, the SARS-CoV virion itself was able to induce long-term antibody production even without an adjuvant. Anti-SARS-CoV antibodies elicited in mice recognized both the spike and nucleocapsid proteins of the virus and were able to neutralize the virus. Furthermore, the UV-inactivated virion induced regional lymph node T-cell proliferation and significant levels of cytokine production (IL-2, IL-4, IL-5, IFN-γ and TNF-α) upon restimulation with inactivated SARS-CoV virion in vitro. Thus, a whole killed virion could serve as a candidate antigen for a SARS vaccine to elicit both humoral and cellular immunity.

Report of an international survey of molecular genetic testing laboratories

Objective: To collect data on the practices of molecular genetic testing (MGT) laboratories for the development of national and international policies for quality assurance (QA). Methods: A web-based survey of MGT laboratory directors (n = 827; response rate 63%) in 18 countries on 3 continents. QA and reporting indices were developed and calculated for each responding laboratory. Results: Laboratory setting varied among and within countries, as did qualifications of the directors. Respondents in every country indicated that their laboratory receives specimens from outside their national borders (64%, n = 529). Pair-wise comparisons of the QA index revealed a significant association with the director having formal training in molecular genetics (p < 0.005), affiliation with a genetics unit (p = 0.003), accreditation of the laboratory (p < 0.005) and participation in proficiency testing (p < 0.005). Research labs had a lower mean report score compared to all other settings (p < 0.05) as did laboratories accessioning <150 samples per year. Conclusion: MGT is provided under widely varying conditions and regulatory frameworks. The data provided here may be a useful guide for policy action at both governmental and professional levels.

Genotyping of Hepatitis E Virus from Vietnam

To identify the genotype of Vietnamese isolates of human hepatitis E virus (HEV), phylogenetic analysis was performed for the open reading frame (ORF) 1 and ORF2 nucleotide sequences of the viral genome. HEV was detected by RT-PCR in 9 out of 141 sera collected from patients with a diagnosis of acute sporadic hepatitis in Hanoi, Vietnam. All of them had sequences related most closely to genotype 4. In addition, the Vietnamese isolate had a single nucleotide insertion in the ORF 3 region, a characteristic reported for genotype 4 with the possible change of initiation of ORF 3 and ORF 2.

Statistics of trinucleotides in coding sequences and evolution

The aim of this paper is to give measurements indicative of evolutional stages of the species. Two types of statistics of trinucleotides in coding regions are analysed for 27 species. The first one is the codon space, the nucleotide ratio for each of the three codon positions. We apply principal component analysis on this space and extract two principal components faithfully describing the original distribution of the codon space. The first principal component corresponds to the GC content. The second principal component classifies the species into three evolutional groups, Archaea, Bacteria and Eukaryota. The second statistics is the real and theoretical frequency of amino acids. The real frequency of an amino acid in a coding sequence is its frequency in the translated protein. The theoretical frequency is the expected frequency calculated from the ratio of nucleotides. We introduce the discrepancy between these two frequencies as an index of non-randomness of nucleotides in the sequence. This index of non-randomness divides the species into two groups: eukaryotes having smaller non-randomness (i.e. being more random) and prokaryotes having higher non-randomness.

Impact of Population Size on Incidence of Rubella and Measles in Comparison with That of Other Infectious Diseases

Fig. 1. Measles and rubella cases reported from 47 prefectures and demography of these prefectures; cumulative frequency distribution of patients, population size, and population density. Panels A and B: measles (panel A) and rubella (panel B) in 2008–2012. In Excel file, prefectures are lined in the ascending order of number of cases, and ranked from 1 to 47 (ranking number 1 is the prefecture reporting the least number of cases and ranking number 47 is the prefecture reporting the largest number of cases). Number of cases per prefecture was plotted on the horizontal axis and ranking number of the prefectures on the vertical axis. Thus, the plots give a cumulative frequency distribution of patient number per prefecture (closed squares, 2008; closed diamonds, 2009; closed triangles, 2010; closed circles, 2011, and open circles 2012). Plots in crosses approximated with a dotted line represent percentage of number of prefectures within the log2 range of number of patients (i.e., <2/prefecture, 2–4/prefecture, 4–8/prefecture, etc.). The detailed procedures for obtaining the cumulative frequency distribution is found in the previous publication (6). Panels C and D: cumulative frequency distributions of prefectures according to the population size (×1,000) (closed circles in panel C) and density (closed circles: per sq. km of prefectures total land; closed triangles: per sq. km of prefectures habitable land in panel D). Large open circles in panel C and large squares in panel D indicate number of prefectures at log2-intervals. An insert in panel C indicates classification of population size (transparent: <1,600; moderately shaded (in bold letters in Fig. 6): 1,600–3,200; heavily shaded: >1,600), which is used for Fig. 6. Panel E: Relation between population size (plotted in the x-axis) and population density per land (plotted in the y-axis). Each plot represents a prefecture. Data source for habitable land is http://www.japan-now.com/article/343318758.html. Japanese. Jpn. J. Infect. Dis., 68, 80, 2015

Detection of a 5′ end subgenome of hepatitis C virus terminating at nucleotide 384 in patients’ plasma and liver tissues

Summary.  Quadri and Negro [Dig Liver Dis 2001; 33: 480] reported greater distribution of 5′ end genomic RNA of hepatitis C virus (HCV) over its 3′ end in the liver of patients with recurrent hepatitis C after liver transplantation. We not only confirmed their results by quantifying the 5′ end subgenomes in various specimens by using dilution and real‐time polymerase chain reaction methods, but also discovered that such subgenomes terminated at nucleotide (nt) 384 of the viral genome or in its immediate upstream. The subgenomes in the plasma uniformly, with a few exceptions, ended at this position, while those in the liver more heterogeneously at various points upstream of nt 384. Subgenome populations ending some points in the downstream of nt 384 were not detected. The amount of the 5′ end subgenome, while fluctuating during the clinical course of the patients, exceeded that of the longer sized HCV genomes which included the intact genome, and, when the relative ratio of the 5′ end subgenome increased, the amount of longer sized HCV RNA tended to decrease, suggesting a suppressive effect of the 5′ end subgenome on viral replication.

Geo-Demography of HIV/AIDS in Japan from 1985 to 2011: Incidence and Transmission Mode under Influence of Population Size/Density.

Volume 69, no. 2, p. 97-108, 2016. Page 107, Figure 11 should appear as shown below.

Scale-Free Distribution of Local Infection Cluster Sizes of Measles, Rubella, Syphilis and HIV/AIDS: Correlation with Size Distribution of Municipality Population That Was Also Scale-Free

The size distribution of a local infection cluster (LIC), a group of infections reported from the same prefecture without interruption in successive weeks, was scale-free for infections that are transmitted from person-to-person (e.g., measles, rubella, syphilis, and HIV/AIDS). For infections that do not spread from person-to-person, the distribution was entirely random. The size distribution for measles, rubella, syphilis, and HIV/AIDS could be simulated successfully by random coin tossing with probabilities that were higher for highly populated prefectures. The size distribution of the population in large municipalities (>120,000), as well as that of LICs, was found to be scale free. As the number of patients per prefecture was correlated with the equation P = kNm, where m was 1.38 for syphilis, 1.63 for HIV/AIDS, and 2 for measles or rubella, the frequency distribution of N1.38, N1.63, and N2, where N was population of municipalities, was compared with the frequency distributions of LIC sizes of syphilis, HIV/AIDS, measles, and rubella. The frequency distribution of LICs, particularly those of measles and rubella during the years when the epidemic was more severe, was close to the frequency distribution of Nm. The analysis suggested that LICs were products of stochastic events under the influence of municipality population size.

Population Dependency of Measles, Syphilis and Amebiasis in Japan and Community Evolution

The population dependency of measles, syphilis, and amebiasis was expressed as P = kNm, where P, N, and m were number of patients, population size, and a constant (～2 for measles, and 1.3～1.4 for syphilis and amebiasis), respectively. The population size dependency emerged only when conditions other than population size, such as infant mortality, hygienic condition, vaccination practices, and others, improved to the same level in all the prefectures in Japan. The formation of prefectures and municipalities was well simulated by the random coin toss assuming that people are attracted to a community with a probability proportional to the number of the residents to the 1.3rd power. When the number of inflow population was plotted against the number of the resident population in a prefecture, or when the number of coins that were added in a round was plotted against the number of coins that were present before the coin toss, the plots fell on a straight line with the slope ～1.3, which was almost the same as the slope obtained when the number of cases of syphilis or amebiasis was plotted against the population size.