Yukio Morita

Prevalence of Arcobacter species in retail meats and antimicrobial susceptibility of the isolates in Japan

A survey was conducted to examine the prevalence of Arcobacter species among meat samples and to investigate the antimicrobial susceptibility of the isolates in Japan. In 1998 and 1999, samples of beef (n=90), pork (n=100) and chicken meat (n=100) were purchased from seven retail shops. Arcobacter species were isolated from 2.2%, 7.0% and 23.0% of beef, pork and chicken meat samples, respectively. The rate of isolations in chicken meats was shown to be significantly higher than those of beef and pork. Species-specific polymerase chain reaction (PCR) demonstrated that the most dominant Arcobacter species was Arcobacter butzleri among the isolates examined. Multiple contaminations with different Arcobacter species were observed in 5% of the chicken samples. Almost all the strains tested showed resistance to vancomycin (100%) and methicillin (97.5%). Strains resistant to cephalothin, sulfamethoxazole-trimethoprim, nalidixic acid and chloramphenicol were detected at the rate of 81.1%, 67.2%, 53.5% and 24.6%, respectively. All Arcobacter strains examined were susceptible to ampicillin, tetracycline, streptomycin and kanamycin.

Distribution of Arcobacter species among livestock in Japan

A survey was conducted to examine the distribution of Arcobacter species among livestock in Japan. During May 1999 and May 2000, fecal samples from cattle (n=332) and swine (n=250), chicken cloacal swabs (n=234), and vaginal swabs of cattle (n=61) and swine (n=15) were submitted for the isolation of Arcobacter species. Arcobacter species were isolated from 3.6 and 10.0% of the cattle and swine fecal samples, respectively, along with 14.5% of chicken cloacal swabs. No significant seasonal differences were observed. Species-specific polymerase chain reaction assay showed that A. butzleri was the most prevalent species (83.3, 60.0 and 47.1% of the cattle, swine and chicken isolates, respectively), followed by A. cryaerophilus 1B (16.7, 36.0 and 55.9% of the cattle, swine and chicken isolates, respectively). Of the samples from vaginal swabs, 8.1 and 13.3% were positive for Arcobacter in cattle and swine, respectively. This is the first report demonstrating the distribution of Arcobacter species among livestock in Japan.

Isolation and phylogenetic analysis of Arcobacter spp. in ground chicken meat and environmental water in Japan and Thailand

Prevalence of Arcobacter spp. in chicken meat samples and environmental water samples in Japan and Thailand was investigated. Arcobacter was isolated from 48% of chicken meat samples (20/41) and 23% of river water samples (4/17) from Japan, and 100% of chicken meat samples (10/10) and 100% of canal water samples (7/7) from Thailand. A. butzleri was among the species isolated from all positive samples. About 10% genetic diversity was seen in the rpoB‐rpoC in Arcobacters, and phylogenetic trees were divided into two clusters. In both countries, the results suggested that chicken and environmental water were highly contaminated with a genetically diverse population of Arcobacter.

Rotavirus associated acute encephalitis/encephalopathy and concurrent cerebellitis : report of two cases

It is known that rotavirus gastroenteritis can accompany some neurological manifestations, including encephalitis/encephalopathy or seizures. However, the detailed pathogenesis involved has not been fully understood. To date, acute cerebellitis associated rotavirus gastroenteritis has not been previously reported, except for one case. Herein, we describe two cases of acute encephalitis/encephalopathy and concurrent cerebellitis, associated rotavirus gastroenteritis. Following vomiting and diarrhea, case 1 experienced convulsions and consciousness disturbance and case 2, transient loss of consciousness with eye deviation. After these symptoms subsided, cerebellar signs became evident and a brain MRI showed cerebellar involvement in both cases. Both cases showed speech disturbances, such as mutism, slow speech and dysarthria. In this report, we will discuss the possible pathogenesis of rotavirus associated acute encephalitis/encephalopathy and concurrent cerebellitis.

Genetic analysis of attachment glycoprotein (G) gene in new genotype ON1 of human respiratory syncytial virus detected in Japan

We studied the evolution of the G gene in the new genotype ON1 of RSV detected from patients with acute respiratory infection in Japan. Phylogenetic analyses and the evolutionary timescale were obtained by the Bayesian MCMC method. We also analyzed p‐distance and positive selection sites. A new genotype ON1 emerged around 2001. The evolution rate was rapid (3.57 × 10−3 substitutions/site per year). The p‐distance was short and no positive selection site was found in the present strains. These results suggested that a new genotype ON1 of RSV‐A emerged approximately10 years ago and spread to some countries with a high evolution rate.

Molecular epidemiological study of human rhinovirus species A, B and C from patients with acute respiratory illnesses in Japan

Recent studies suggest that human rhinovirus species A, B and C (HRV-ABCs) may be associated with both the common cold and severe acute respiratory illnesses (ARIs) such as bronchiolitis, wheezy bronchiolitis and pneumonia. However, the state and molecular epidemiology of these viruses in Japan is not fully understood. This study detected the genomes of HRV-ABCs from Japanese patients (92 cases, 0-36 years old, mean±sd 3.5±5.0 years) with various ARIs including upper respiratory infection, bronchiolitis, wheezy bronchiolitis, croup and pneumonia between January and December 2010. HRV-ABCs were provisionally type assigned from the pairwise distances among the strains. On phylogenetic trees based on the nucleotide sequences of the VP4/VP2 coding region, HRV-A, -B and -C were provisionally assigned to 14, 2 and 12 types, respectively. The present HRV-A and -C strains had a wide genetic diversity (>30 % divergence). The interspecies distances were 0.230±0.063 (mean±sd, HRV-A), 0.218±0.048 (HRV-B) and 0.281±0.105 (HRV-C), based on nucleotide sequences, and 0.075±0.036 (HRV-A), 0.049±0.022 (HRV-B) and 0.141±0.064 (HRV-C) at the deduced amino acid level. Furthermore, HRV-A and -C were the predominant species and were detected throughout the seasons. The results suggested that HRV-A and -C strains have a wide genetic divergence and are associated with various ARIs in Japan.

Serotypes, Antimicrobial Susceptibility, and gyr A Gene Mutation of Campylobacter jejuni Isolates from Humans and Chickens in Thailand

In Thailand, 51% (36/70) Campylobacter jejuni isolates from humans and 68% (47/69) isolates from poultry were classified into 10 Penner serotypes (serotype B, C, R, E, G, A, K, D, I, and L) and 9 serotypes (serotype A, C, I, K, B, E, S, D, and L), respectively. The rate of antimicrobial drug resistance to nalidixic acid, ciprofloxacin, ampicillin, tetracycline, and erythromycin shown by human isolates were 96%, 96%, 29%, 57%, and 14%, while that shown by poultry isolates were 77%, 77%, 22%, 26%, and 17%, respectively. All quinolone‐resistant strains contained a mutation in the gyrA gene (T86→I86), suggesting that the strains were already widespread in Thailand.

Molecular evolution of attachment glycoprotein (G) gene in human respiratory syncytial virus detected in Japan 2008–2011

We investigated the evolution of the C-terminal 3rd hypervariable region of G gene in the prevalent human respiratory syncytial virus (RSV) subgroups A (RSV-A) and B (RSV-B) in Japan in 2008-2011. Phylogenetic analysis and the evolutionary timescale was obtained by the Bayesian Markov Chain Monte Carlo method. All 38 RSV-A strains detected were classified into genotype NA1 and the 17 RSV-B strains detected belonged to genotypes BA and GB2. NA1 subdivided around 1998 in the present phylogenetic tree. Genotype BA subdivided around 1994. The evolutionary rates for RSV-A and RSV-B were estimated at 3.63×10⁻³ and 4.56×10⁻³ substitutions/site/year, respectively. The mean evolutionary rate of RSV-B was significantly faster than that of RSV-A during all seasons. The pairwise distance was relatively short (less than 0.06). In addition, some unique sites under positive selection were found. The results suggested that this region of the RSV strains rapidly evolved with some unique amino acid substitutions due to positive pressure.

Phylogenetic and cluster analysis of human rhinovirus species A (HRV-A) isolated from children with acute respiratory infections in Yamagata, Japan

We performed phylogenetic and cluster analysis of human rhinovirus species A (HRV-A) isolated from 76 children with acute respiratory infection in Yamagata prefecture, Japan during the period 2003-2007. Phylogenetic trees based on the nucleotide and amino acid sequences of the VP4/VP2 coding region showed that the present strains could be classified into 11 and 8 clusters, respectively. The homology among the present strains ranged from 66.6% to 100% at the nucleotide level and 84.7% to 100% at the amino acid level. The interspecies distance (mean+/-standard deviation) was calculated to be 0.235+/-0.048 at the nucleotide level and 0.076+/-0.033 at the amino acid level. In addition, the phylogenetic trees created based on the nucleotide and amino acid sequences showed that HRV-A strains belonging to some clusters were associated with both upper respiratory infection and wheezy bronchiolitis, while other strains were associated with upper respiratory infection alone. These results suggest that the present HRV-A isolates had a wide nucleotide divergence and were associated with acute respiratory infection, including upper respiratory infection and wheezy bronchiolitis, in Yamagata prefecture, Japan during the investigation period.

Molecular evolution of the capsid gene in human norovirus genogroup II.

We studied the molecular evolution of the capsid gene in all genotypes (genotypes 1–9) of human norovirus (NoV) genogroup I. The evolutionary time scale and rate were estimated by the Bayesian Markov chain Monte Carlo (MCMC) method. We also performed selective pressure analysis and B-cell linear epitope prediction in the deduced NoV GI capsid protein. Furthermore, we analysed the effective population size of the virus using Bayesian skyline plot (BSP) analysis. A phylogenetic tree by MCMC showed that NoV GI diverged from the common ancestor of NoV GII, GIII, and GIV approximately 2,800 years ago with rapid evolution (about 10−3 substitutions/site/year). Some positive selection sites and over 400 negative selection sites were estimated in the deduced capsid protein. Many epitopes were estimated in the deduced virus capsid proteins. An epitope of GI.1 may be associated with histo-blood group antigen binding sites (Ser377, Pro378, and Ser380). Moreover, BSP suggested that the adaptation of NoV GI strains to humans was affected by natural selection. The results suggested that NoV GI strains evolved rapidly and date back to many years ago. Additionally, the virus may have undergone locally affected natural selection in the host resulting in its adaptation to humans.