Convenient PCR method for variable-number tandem-repeat typing of Mycobacterium tuberculosis clinical isolates

Variable-number tandem-repeat typing for Mycobacterium tuberculosis clinical isolates contributes to evidence-based tuberculosis control. However, cumbersome PCR procedures for the typing have disturbed routine analyses. We proposed a convenient PCR method for the typing using a PCR master mix that provides rapidity and long-term stability of the frozen PCR cocktail.

Seroepidemiology of human parechovirus types 1, 3, and 6 in Yamagata, Japan, in 2014

To clarify the seroepidemiology of human parechovirus type 1 (HPeV1), 3 and 6, neutralizing antibodies (NT Abs) were measured in 214 serum specimens collected in 2014 in Yamagata, Japan. The seroprevalence against HPeV1 was 100% in all age groups, while that against HPeV3 and HPeV6 was 79.4% and 66.8%, respectively, overall. The geometric mean titers of NT Abs against HPeV1, 3 and 6 were 755.2, 255.0 and 55.9, respectively, overall. Our findings indicate that HPeV1 is the most prevalent HPeV circulating in Yamagata, followed by HPeV3 and HPeV6.

Relationship Between Graft Liver Function and the Change of Graft Liver and Spleen Volumes After Technical Variant Liver Transplantation

BACKGROUND

Although there have been a few reports describing the changes of graft liver and spleen volumes after liver transplantation (LT), little is known about the relationship between graft liver function and the changes of these volumes after technical variant liver transplantation (TVLT). We therefore performed a retrospective study to investigate the relationship between graft liver function and these volumes after TVLT.

METHODS

We retrospectively investigated the cases of 140 TVLT procedures that were performed in our department between July 1987 and October 2012 and in which follow-up was conducted at our department. We calculated the graft liver volume to standard liver volume (GV/SLV) ratio, the spleen volume to standard spleen volume (SV/SSV) ratio, and the spleen volume to graft liver volume (S/L) ratio by CT volumetry. We clarified the relationship between graft liver function (according to the pathological findings) and the graft liver and spleen volumes at 2, 5, and 10 years after TVLT.

RESULTS

In the normal liver function group, the GV/SLV, SV/SSV, and S/L ratios decreased until 6 months after TVLT and then converged at 10 years after TVLT to 0.95, 1.27, and 0.27, respectively. In the graft liver failure group, the GV/SLV, SV/SSV, and S/L ratios at 10 years after TVLT were 0.67, 5.01, and 1.55, respectively. A significant correlation was observed between the GV/SLV ratio and the presence of mild liver fibrosis at 2 and 5 years after TVLT (P = .03 and P = .04, respectively).

CONCLUSIONS

Post-transplant CT-volumetry is a noninvasive and effective means of evaluating graft liver status.

Complementary Indicators for Diagnosis of Hepatic Vein Stenosis After Pediatric Living-donor Liver Transplantation

INTRODUCTION

Although hepatic vein stenosis after liver transplantation is a rare complication, the complication rate of 1% to 6% is higher in pediatric living-donor liver transplantation than that in other liver transplantation cases. Diagnosis is very important because this complication can cause hepatic congestion that develops to liver cirrhosis, graft loss, and patient loss. However, this is unlikely in cases where there are no ascites or hypoalbuminemia.

OBJECTIVES

Eleven of 167 patients who had undergone pediatric living-donor liver transplantation were identified in the outpatient clinic at Jichi Medical University as having suffered from hepatic vein stenosis, and were enrolled in the study.

METHODS

We conducted a retrospective study in which we reviewed historical patient records to investigate the parameters for diagnosis and examine treatment methods and outcomes.

RESULTS

The 11 patients were treated with 16 episodes of balloon dilatation. Three among these received retransplantation and another 2 cases required the placement of a metallic stent at the stenosis. Histological examination revealed severe fibrosis in four of nine patients who had a liver biopsy, with mild fibrosis revealed in the other five grafts. Furthermore, hepatomegaly and splenomegaly diagnosed by computed tomography, elevated levels of hyarulonic acid, and/or a decrease in calcineurin inhibitor clearance were found to be pathognomonic at diagnosis, and tended to improve after treatment.

CONCLUSIONS

Diagnosis of hepatic vein stenosis after liver transplantation can be difficult, so careful observation is crucial to avoid the risk of acute liver dysfunction. Comprehensive assessment using volumetry of the liver and spleen and monitoring of hyarulonic acid levels and/or calcineurin inhibitor clearance, in addition to some form of imaging examination, is important for diagnosis and evaluation of the effectiveness of therapy.

Genetic Lineage and Reassortment of Influenza C Viruses Circulating between 1947 and 2014

Since influenza C virus was first isolated in 1947, the virus has been only occasionally isolated by cell culture; there are only four strains for which complete genome sequences are registered. Here, we analyzed a total of 106 complete genomes, ranging from the first isolate from 1947 to recent isolates from 2014, to determine the genetic lineages of influenza C virus, the reassortment events, and the rates of nucleotide substitution. The results showed that there are six lineages, named C/Taylor, C/Mississippi, C/Aichi, C/Yamagata, C/Kanagawa, and C/Sao Paulo. They contain both antigenic and genetic lineages of the hemagglutinin-esterase (HE) gene, and the internal genes PB2, PB1, P3, NP, M, and NS are divided into two major lineages, a C/Mississippi/80-related lineage and a C/Yamagata/81-related lineage. Reassortment events were found over the entire period of 68 years. Several outbreaks of influenza C virus between 1990 and 2014 in Japan consisted of reassortant viruses, suggesting that the genomic constellation is related to influenza C virus epidemics. The nucleotide sequences were highly homologous to each other. The minimum percent identity between viruses ranged from 91.1% for the HE gene to 96.1% for the M gene, and the rate of nucleotide substitution for the HE gene was the highest, at 5.20 × 10(-4) substitutions/site/year. These results indicate that reassortment is an important factor that increases the genetic diversity of influenza C virus, resulting in its ability to prevail in humans. IMPORTANCE Influenza C virus is a pathogen that causes acute respiratory illness in children and results in hospitalization of infants. We previously demonstrated (Y. Matsuzaki et al., J Clin Virol 61:87-93, 2014, http://dx.doi.org/10.1016/j.jcv.2014.06.017) that periodic epidemics of this virus occurred in Japan between 1996 and 2014 and that replacement of the dominant antigenic group occurred every several years as a result of selection by herd immunity. However, the antigenicity of the HE glycoprotein is highly stable, and antigenic drift has not occurred for at least 30 years. Here, we analyzed a total of 106 complete genomes spanning 68 years for the first time, and we found that influenza C viruses are circulating worldwide while undergoing reassortment as well as selection by herd immunity, resulting in an increased ability to prevail in humans. The results presented in this study contribute to the understanding of the evolution, including reassortment events, underlying influenza C virus epidemics.

Chronological changes of mumps virus genotypes in Japan between 1999-2013

BACKGROUND

The molecular epidemiology of mumps virus (MuV) has been carried out worldwide based on genotyping proposed by the World Health Organisation. However, longitudinal molecular epidemiological studies of MuV are still limited.

METHODS

This study carried out genotyping of MuVs isolated in Yamagata prefecture, which is located in northern Japan, between 1999-2013, using standard nomenclature based on the sequence analysis of the entire 316 nucleotides of the small hydrophobic (SH) gene.

RESULTS

During this 15-year period, 249 MuVs were isolated, with the majority of them belonging to genotype G. Phylogenetic analysis revealed that genotype G strains were divided into two distinct clusters 1 and 2, consisting of 178 and 47 strains, respectively. The cluster 1 strains were isolated every year since 2001, except for 2012. The cluster 2 strains first appeared in 2011 and were dominant in 2011 and 2012. The epidemic pattern of genotype G strains observed in Yamagata was similar to those in Kanagawa and Hyogo prefectures located in eastern and western Japan, respectively. Only one L, three H and one F genotype strains were isolated in 2001, 2004 and 2010, respectively. Almost every year several genotype B strains related to Japanese vaccine strains were isolated.

CONCLUSIONS

These data demonstrated that the genotype G strains have been endemically perpetuating as the major type over a wide area of Japan since 2001, although the genotype G strains that emerged after 2011 differed from the earlier strains.

Influenza C Virus and Human Metapneumovirus Infections in Hospitalized Children With Lower Respiratory Tract Illness

A 6-month prospective study in a hospital setting detected influenza C virus and human metapneumovirus in 10.0% (29/289) and 16.6% (48/289), respectively, of children hospitalized with lower respiratory tract illness. Influenza C virus infection had a similar rate of pneumonia (53.3% vs. 57.1%), significantly lower frequency of wheezing (13.3% vs. 68.6%) and higher values of white blood cell and C-reactive protein than human metapneumovirus infection.

Characteristics of Mycoplasma pneumoniae infection identified on culture in a pediatric clinic

BACKGROUND

The appropriate choice of antibiotics against Mycoplasma pneumoniae infection has become difficult, as the prevalence of macrolide-resistant M. pneumoniae has increased.

METHODS

Throat swab specimens were collected from children with clinically suspected M. pneumoniae infection while visiting an outpatient clinic. Cultures for M. pneumoniae were done, and all isolates were sequenced for the presence of a mutation in 23S rRNA.

RESULTS

Of the 80 specimens collected between February 2012 and March 2013, 27 (34%) were positive for M. pneumoniae on culture. Macrolide-resistant mutation was detected in 24 isolates (89%): 23 isolates had an A2063G transition, and one had a C2617G mutation. Both the median age and the prevalence of pneumonia were significantly higher in M. pneumoniae-positive than in M. pneumoniae-negative children (median, 7 years vs 4 years; 88.9% vs 60.4%, respectively). The percentage of serum samples with particle agglutination titer ≥ 1:160 was 69.6% in M. pneumoniae-positive cases and 17.6% in M. pneumoniae-negative cases when the serum was collected ≥ 4 days after the onset of fever. Defervescence within 72 h after the initiation of macrolides never occurred in M. pneumoniae-positive children and also did not occur in 54% of M. pneumoniae-negative children. Switching to either minocycline or tosufloxacin resulted in fever resolution within 48 h in M. pneumoniae-positive children.

CONCLUSIONS

The described clinical and laboratory characteristics of M. pneumoniae infection may be useful in guiding appropriate treatment in an outpatient clinic.

Molecular epidemiology of human metapneumovirus from 2005 to 2011 in Fukui, Japan

To investigate the molecular epidemiology of human metapneumovirus (HMPV) infections in acute respiratory infections (ARI), we performed genetic analysis of the F gene in HMPV from patients with ARI in Fukui Prefecture from August 2005 to July 2011. HMPV was detected in 53 of 741 nasopharyngeal swabs (7.2%). Phylogenetic analysis helped us assign 31 strains to subgroup A2, 1 strain to subgroup B1, and 21 strains to subgroup B2. The prevalence of HMPV was peaked between January and June. A high degree of nucleotide identity was seen among subgroup A2 strains (95.6-100%) and subgroup B2 strains (97.5-100%). In addition, no positively selected sites (substitutions) were found in the F gene in these HMPV strains. The results suggest that the prevalent HMPV strains in Fukui were associated with various ARI in Japan during the investigation period.

Detection of the human coronavirus 229E, HKU1, NL63, and OC43 between 2010 and 2013 in Yamagata, Japan

The available literature on human coronaviruses (HCoVs) in Japan is limited to epidemiological studies conducted over a maximum of 1 year. We conducted a 4-year study of HCoVs by analyzing 4,342 respiratory specimens obtained in Yamagata, Japan, between January 2010 and December 2013. A pan-coronavirus reverse transcription-PCR screening assay was performed, and all HCoV-positive specimens were subsequently confirmed by sequencing of the PCR products. We detected in 332 (7.6%) HCoV strains during the study period, comprising 133 (3.1%) HCoV-NL63, 83 (1.9%) HCoV-HKU1, 78 (1.8%) HCoV-OC43, and 38 (0.9%) HCoV-229E strains. HCoV detection per year ranged from 3.5% to 9.7%. HCoVs were detected mainly in winter, with January (28.5%) and February (25.3%) 2011 and December 2012 (14.6%) being the only months in which HCoV-NL63 detection per month exceeded 10.0%. HCoV-HKU1 displayed clear biennial peaks in January (18.3%) and February (10.7%) 2010 and in February (18.8%) and March (14.7%) 2012. The peak detection of HCoV-OC43 was 13.6% in November 2010, while that of HCoV-229E was 10.8% in March 2013. Our results indicated that there may be annual variations in the circulation of individual HCoV strains. Further long-term surveillance is necessary to clarify HCoV prevalence and circulation patterns in Japan.

Epitope mapping of the hemagglutinin molecule of A/(H1N1)pdm09 influenza virus by using monoclonal antibody escape mutants

We determined the antigenic structure of pandemic influenza A(H1N1)pdm09 virus hemagglutinin (HA) using 599 escape mutants that were selected using 16 anti-HA monoclonal antibodies (MAbs) against A/Narita/1/2009. The sequencing of mutant HA genes revealed 43 amino acid substitutions at 24 positions in three antigenic sites, Sa, Sb, and Ca2, which were previously mapped onto A/Puerto Rico/8/34 (A/PR/8/34) HA (A. J. Caton, G. G. Brownlee, J. W. Yewdell, and W. Gerhard, Cell 31:417-427, 1982), and an undesignated site, i.e., amino acid residues 141, 142, 143, 171, 172, 174, 177, and 180 in the Sa site, residues 170, 173, 202, 206, 210, 211, and 212 in the Sb site, residues 151, 154, 156, 157, 158, 159, 200, and 238 in the Ca2 site, and residue 147 in the undesignated site (numbering begins at the first methionine). Sixteen MAbs were classified into four groups based on their cross-reactivity with the panel of escape mutants in the hemagglutination inhibition test. Among them, six MAbs targeting the Sa and Sb sites recognized both residues at positions 172 and 173. MAb n2 lost reactivity when mutations were introduced at positions 147, 159 (site Ca2), 170 (site Sb), and 172 (site Sa). We designated the site consisting of these residues as site Pa. From 2009 to 2013, no antigenic drift was detected for the A(H1N1)pdm09 viruses. However, if a novel variant carrying a mutation at a position involved in the epitopes of several MAbs, such as 172, appeared, such a virus would have the advantage of becoming a drift strain.

IMPORTANCE

The first influenza pandemic of the 21st century occurred in 2009 with the emergence of a novel virus originating with swine influenza, A(H1N1)pdm09. Although HA of A(H1N1)pdm09 has a common origin (1918 H1N1) with seasonal H1N1, the antigenic divergence of HA between the seasonal H1N1 and A(H1N1)pdm09 viruses gave rise to the influenza pandemic in 2009. To take precautions against the antigenic drift of the A(H1N1)pdm09 virus in the near future, it is important to identify its precise antigenic structure. To obtain various mutants that are not neutralized by MAbs, it is important to neutralize several plaque-cloned parent viruses rather than only a single parent virus. We characterized 599 escape mutants that were obtained by neutralizing four parent viruses of A(H1N1)pdm09 in the presence of 16 MAbs. Consequently, we were able to determine the details of the antigenic structure of HA, including a novel epitope.

MePIC, metagenomic pathogen identification for clinical specimens

Next-generation DNA sequencing technologies have led to a new method of identifying the causative agents of infectious diseases. The analysis comprises three steps. First, DNA/RNA is extracted and extensively sequenced from a specimen that includes the pathogen, human tissue and commensal microorganisms. Second, the sequenced reads are matched with a database of known sequences, and the organisms from which the individual reads were derived are inferred. Last, the percentages of the organisms' genomic sequences in the specimen (i.e., the metagenome) are estimated, and the pathogen is identified. The first and last steps have become easy due to the development of benchtop sequencers and metagenomic software. To facilitate the middle step, which requires computational resources and skill, we developed a cloud-computing pipeline, MePIC: "Metagenomic Pathogen Identification for Clinical specimens." In the pipeline, unnecessary bases are trimmed off the reads, and human reads are removed. For the remaining reads, similar sequences are searched in the database of known nucleotide sequences. The search is drastically sped up by using a cloud-computing system. The webpage interface can be used easily by clinicians and epidemiologists. We believe that the use of the MePIC pipeline will promote metagenomic pathogen identification and improve the understanding of infectious diseases.

Epidemiological information regarding the periodic epidemics of influenza C virus in Japan (1996-2013) and the seroprevalence of antibodies to different antigenic groups

BACKGROUND

Although influenza C virus is widely distributed throughout the world, epidemiological information, based on long-term surveillance, has not yet been acquired.

OBJECTIVES

To clarify the epidemiological features of influenza C virus infection, and to examine whether the prevalence of the antibodies against the influenza C virus is associated with the epidemics.

STUDY DESIGN

Between 1996 and 2013, 36,973 respiratory specimens were collected from two pediatric outpatient clinics in Yamagata, Japan. The specimens were examined for the presence of influenza C virus using cell culture methods. Isolated viruses were antigenically analyzed. The differences in seropositivity, with respect to the different antigenic groups, were examined using serum samples collected in 2001 and 2011 by a hemagglutination inhibition assay.

RESULTS

Influenza C viruses were isolated from 190 specimens during an 18-year period. Most influenza C viruses were isolated from winter to early summer in even-numbered years, and the frequency of virus isolation per year ranged from 0.43% to 1.73%. An antigenic analysis revealed that the dominant antigenic groups were the C/Yamagata/26/81 from 1996 to 2000, the C/Kanagawa/1/76 in 2002 and 2004, and the C/Sao Paulo/378/82 from 2006 to 2012. When compared to the other antigenic groups, the seroprevalence of the C/Sao Paulo/378/82 group was lower in 2001 for individuals older than 5 years and was higher in 2011 in individuals younger than 40 years.

CONCLUSIONS

The results from our study suggest that epidemics of influenza C virus infection periodically occur and the replacement of the dominant antigenic group may be caused by immune selection within older children and/or adults in the community.

Molecular epidemiology of enterovirus 71 strains isolated from children in Yamagata, Japan, between 1990 and 2013

Enterovirus 71 infections have become a major public issue in the Asia-Pacific region due to the large number of fatal cases. To clarify the longitudinal molecular epidemiology of enterovirus 71 (EV71) in a community, we isolated 240 strains from children, mainly with hand-foot-and-mouth diseases, between 1990 and 2013 in Yamagata, Japan. We carried out a sequence analysis of the VP1 region (891 bp) using 223 isolates and identified six subgenogroups (B2, B4, B5, C1, C2 and C4) during the study period. Subgenogroups C1 and B2 were found only between 1990 and 1993 and have not reappeared since. In contrast, strains in subgenogroups C2, C4 and B5 appeared repeatedly with genomic variations. Recent reports from several local communities in Japan have suggested that identical predominant subgenogroup strains, which have also been found in the Asia-Pacific region, have been circulating in a wide area in Japan. However, it is likely that there is a discrepancy between the major subgenogroups circulating in the Asia-Pacific region and those in Europe. It is necessary to continue the analysis of the longitudinal epidemiology of EV71 in local communities, as well as on regional and global levels, to develop strategies against severe EV71 infections.