High-level antiseptic resistance of Staphylococcus aureus is mediated by multidrug efflux pumps encoded by qacA and qacB genes. We investigated distribution and genomic diversity of these antiseptic resistance genes in a total of 522 clinical strains of S. aureus isolated recently in a Japanese hospital. The qacA/B gene was detected in 32.6% of methicillin-resistant S. aureus (MRSA) and 7.5% of methicillin-susceptible S. aureus (MSSA), whereas the low-level resistance gene smr, which was examined simultaneously, was detected at lower frequencies in both MRSA (3.3%) and MSSA (5.9%). Epidemiologic typing of S. aureus isolates suggested that higher prevalence of qacA/B in MRSA may be due to spread of a single predominant MRSA strain carrying qacA/B in the hospital. Restriction fragment length polymorphism (RFLP) analysis indicated higher prevalence of the qacB-type gene (59.3%) than the qacA-type gene (40.7%) among the qacA/B genes detected. Nucleotide sequencing analysis revealed the presence of two genetic variants in qacA (V1 and V2) and four variants in qacB (V1-V4) that differ from the qacA prototype in pSK1 by 1-5 nucleotides and 7-9 nucleotides, respectively. Although most strains with qacA-V1, qacA-V2, qacB-V3, and qacB-V4 showed high-level resistance to ethidium bromide (EB)(MIC > 100 microg/ml), all of the S. aureus isolates carrying qacB-V1 and qacB-V2 showed lower MICs of EB and some monovalent cationic antiseptic substances. By analysis of the genomic organization of the qacA/B downstream region, divergent forms of this region rearranged with an insertion of IS256 or IS257 were found primarily for qacB. The downstream region of qacA-V1 was suggested to be an evolutionary origin for other divergent forms. These findings indicated that both qacA and qacB are prevalent in recent clinical isolates, especially in MRSA, and these genes consist of variable genetic variants that may be responsible for different resistance levels against antiseptic substances.

This study reports the first complete genome sequence of a caprine group A rotavirus (GAR) strain, GO34. The VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes of strain GO34, detected in Bangladesh, were assigned to the G6-P[1]-I2-R2-C2-M2-A11-N2-T6-E2-H3 genotypes, respectively. Strain GO34 was closely related to the VP4, VP6-7 and NSP4-5 genes of bovine GARs and the NSP1 gene of GO34 to an ovine GAR. Strain GO34 shared low nucleotide sequence identities (,90 %) with VP2-3 genes of other GARs, and was equally related to NSP3 genes of human, ruminant and camelid strains. The VP1, VP6 and NSP2 genes of strain GO34 also exhibited a close genetic relatedness to human G2, G6, G8 and G12 DS-1-like GARs, whereas the NSP1 of GO34 was also closely related to human G6P [14] strains. All these findings point to a common evolutionary origin of GO34 and bovine, ovine, antelope, guanaco and human G6P [14] GARs, although phylogenetically GO34 is not particularly closely related to any other rotavirus strains known to date.Group A rotaviruses (GARs) are a major cause of acute viral gastroenteritis in the young of humans and animals (Estes & Kapikian, 2007). The GAR genome consists of 11 segments of double-stranded RNA, encoding six structural and six non-structural proteins (Estes & Kapikian, 2007). Recently, the 11 GAR gene segments (VP1, VP2, VP3, VP4, VP6, VP7, NSP1, NSP2, NSP3, NSP4 and NSP5 genes) have been classified into at least six R, six C, seven M, 31 P, 13 I, 23 G, 16 A, six N, eight T, 12 E and eight H genotypes, respectively, based on specific nucleotide sequence identity cut-off percentages for each gene segment (Matthijnssens et al., 2008a(Matthijnssens et al., , b, 2009(Matthijnssens et al., , 2010aSchumann et al., 2009;Solberg et al., 2009;Trojnar et al., 2009;Ursu et al., 2009). Applying this classification scheme, the full genomes of GAR strains from antelope, birds, cattle, cats, dogs, guanacos, humans, monkeys, pigs, rabbits and sheep were successfully analysed, providing vital insights into the complex genetic diversity of GARs (Ghosh et al., 2010;Heiman et al., 2008;Matthijnssens et al., 2008a Matthijnssens et al., , b, 2009Matthijnssens et al., , 2010aSchumann et al., 2009;Trojnar et al., 2009;Tsugawa & Hoshino, 2008).GARs have been associated with diarrhoea in goats from different parts of the world (Kaminjolo & Adesiyun, 1994;Lee et al., 2003;Mendes et al., 1994; Muñoz et al., 1996;Pratelli et al., 1999; Takahashi et al., 1979;Scott et al., 1978). Moreover, in rural areas, caprine GARs might pose a threat to humans living in close proximity to livestock. However, to date, few caprine GAR strains have been molecularly characterized. Among them, the VP7, VP4 and NSP4 gene sequences of a Korean caprine strain, GRV, were assigned to G3, P[3] and E3 genotypes, respectively, and this strain was believed to be derived from reassortment events and/or interspecies transmission of canine, feline and/or simian GARs (Lee et al., 2003). The fulllength VP7 and partial VP4 gene sequences (GenBank accessi...

Novel rotavirus strains B219 and ADRV-N derived from adult diarrheal cases in Bangladesh and China, respectively, are considered to belong to a novel rotavirus group (species) distinct from groups A, B, and C, by genetic analysis of five viral genes encoding VP6, VP7, NSP1, NSP2, and NSP3. In this study, the nucleotide sequences of the remaining six B219 gene segments encoding VP1, VP2, VP3, VP4, NSP4, and NSP5 were determined. The nucleotide sequences of the group B human rotavirus VP1 and VP3 genes were also determined in order to compare the whole genome of B219 with those of group A, B, and C rotavirus genomes. The nucleotide and deduced amino acid sequences of all B219 gene segments showed considerable identity to the ADRV-N (strain J19) sequences (87.7-94.3% and 88.7-98.7%, respectively). In contrast, sequence identity to groups A-C rotavirus genes was less than 61%. However, functionally important domains and structural characteristics in VP1-VP4, NSP4, and NSP5, which are conserved in group A, B, or C rotaviruses, were also found in the deduced amino acid sequences of the B219 proteins. Hence, the basic structures of all B219 viral proteins are considered to be similar to those of the known rotavirus groups.

An unusual human rotavirus strain B219 was detected in a stool specimen from a 65-year old patient with diarrhea in Bangladesh during April 2002. Cloning and sequence analysis of five genes of the B219 strain indicated that this virus is genetically closely related to the ADRV-N strain, which caused an adult diarrhea outbreak in China, but distinct from groups A, B, and C rotaviruses known to cause diarrheal diseases in humans. Accordingly, rotavirus strains B219 and ADRV-N were considered to belong to a novel group of human rotavirus, and the ADRV-N-like novel human rotaviruses were suggested to be distributed to a geographically wider area.

To clarify the phylogenetic relatedness of rotaviruses causing gastroenteritis in children and adults, an epidemiologic investigation was conducted in Mymensingh, Bangladesh, during the period between July 2004 and June 2006. A total of 2,540 stool specimens from diarrheal patients from three hospitals were analyzed. Overall, rotavirus-positive rates in children and adults were 26.4 and 10.1%, respectively. Among the 155 rotavirus specimens examined genetically from both children and adults, the most frequent G genotype was G2 (detection rate: 54.0 and 47.6%, respectively), followed by G1 (21.2 and 26.2%, respectively), and G9 (15.9 and 9.5%, respectively). G12 was also detected in five specimens (3.2% in total; four children and one adult). Sequence identities of VP7 genes of G2 rotaviruses from children and adults were higher than 97.8%, while these Bangladeshi G2 viruses showed generally lower identities to G2 rotaviruses reported elsewhere in the world, except for some strains reported in African countries. Similarly, extremely high sequence identities between children and adults were observed for VP7 genes of G1, G9 and G12 rotaviruses, and also for the VP4 genes of P[4], P[6], and P[8] viruses. Rotaviruses from children and adults detected in this study were included in a single cluster in phylogenetic dendrograms of VP7 or VP4 genes of individual G/P types. Rotaviruses with two emerging types, G9 and G12, had VP7 genes that were phylogenetically close to those of individual G-types recently reported in Bangladesh and India and were included in the globally spreading lineages of these G-types. These findings suggested that genetically identical rotaviruses, including those with the emerging types G9 and G12, were circulating among children and adults in city and rural areas of Bangladesh.

Group B rotavirus (GBR) is a rare enteric pathogen that causes severe diarrhoea, primarily in adults. Nearly full-length sequences of all 11 RNA segments were determined for human GBRs detected recently in India (IDH-084 in 2007, IC-008 in 2008, Bangladesh (Bang117 in 2003) and Myanmar (MMR-B1 in 2007), and analysed phylogenetically with the sequence data of GBRs reported previously. All RNA segments of GBR strains from India, Bangladesh and Myanmar showed .95 % nucleotide sequence identities. Among the 11 RNA segments, the VP6 and NSP2 genes showed the highest identities (.98 %), whilst the lowest identities were observed in the NSP4 gene (96.1 %), NSP5 gene (95.6 %) and VP8*-encoding region of the VP4 gene (95.9 %). Divergent or conserved regions in the deduced amino acid sequences of GBR VP1-VP4 and NSP1-NSP5 were similar to those in group A rotaviruses (GARs), and the functionally important motifs and structural characteristics in viral proteins known for GAR were conserved in all of the human GBRs. These findings suggest that, whilst the degree of genetic evolution may be dependent on each RNA segment, human GBR may have been evolving in a similar manner to GAR, associated with the similar functional roles of individual viral proteins. INTRODUCTIONRotavirus, a member of the family Reoviridae, is the most important viral pathogen causing gastroenteritis in humans. Rotavirus has 11 segments of double-stranded RNA (dsRNA) as a genome, and the virus particle is composed of three concentric layers, i.e. the outer capsid, inner capsid and core (Estes & Kapikian, 2007). The outer capsid consists of two structural proteins, VP4 and VP7, which are neutralization antigens. The inner capsid consists of structural protein VP6. Rotavirus is classified into five groups (A-E) and two putative groups (F and G), based on the antigenicity of the inner capsid protein VP6 and genomic characteristics (Kapikian et al., 2001). In humans, groups A, B and C have so far been detected. Group A rotavirus (GAR) is the most prevalent throughout the world and is recognized as the leading viral pathogen of acute gastroenteritis in children.Group B rotavirus (GBR) is genetically and antigenically distinct from GAR and has been detected in humans, mice, calves, pigs and sheep. In humans, GBR has been noted because it causes severe, cholera-like diarrhoea, mostly in adults (Mackow, 1995). GBR was first identified as adult diarrhoea rotavirus (ADRV) in nationwide outbreaks in China in 1982-1983 (Hung et al., 1983, 1984Wang et al., 1985), and the detection of this virus has been limited to China (Dai et al., 1987; Fang et al., 1989). They were subsequently detected in sporadic cases in India in 1997 and in Bangladesh in 2000, demonstrating the distribution of GBRs in Asian countries outside China (Krishnan et al., 1999;Sanekata et al., 2003). Thereafter, GBRs have again been detected in these countries in sporadic cases of diarrhoea (Barman et al., 2006;Rahman et al., 2007). The GenBank/EMBL/DDBJ accession numbers for the nucleotide sequen...

A human group B rotavirus strain WH-1 was detected in an adult sporadic case of diarrhea in Wuhan, China in 2002. In this study, the gene sequences of WH-1 were determined in order to examine the phylogenetic relatedness to other human group B rotaviruses found previously in China (ADRV, in 1982), India (CAL-1, in 1998), and Bangladesh (Bang373, in 2000), as well as animal viruses, and to estimate the mutation rate of group B rotavirus. VP7 (major outer capsid protein) gene of WH-1 showed extremely high sequence identity (98.6%) to ADRV and showed relatively high sequence identities to CAL-1 (92.5%) and Bang373 (92.4%). In contrast, identities to animal (bovine and murine) group B rotaviruses were considerably lower (61-64%). Other gene segments of WH-1 encoding VP2, VP4, VP6, NSP1-NSP3, and NSP5 also showed high sequence identities to ADRV genes (98-99%), which were generally higher than those to CAL-1 genes and Bang373 genes (90-95%). However, amino acid sequence identities between WH-1 and ADRV were almost the same (VP2, VP6, and NSP3), or lower (NSP2) than those between WH-1 and CAL-1 (or Bang373). Since rates of synonymous substitution and transition between WH-1 and ADRV were similar for all the segments analyzed, genetic evolution was considered to have occurred neutrally and at a similar speed in most of the RNA segments. Based on the sequence divergence between WH-1 and ADRV, the mutation rate in natural condition of human group B rotavirus was estimated as 7.9 x 10(-4) substitution/site per year. The frequency of synonymous substitution between ADRV and Bang373 was 5.7 times higher than that between ADRV and WH-1, suggesting that the group B rotaviruses of Indian-Bangladeshi lineage diverged from that of Chinese lineage several decades ago.

The G1 and G9 rotavirus strains MMC71 and MMC38 (subgroup II, NSP4 genogroup B), respectively, isolated from children in Bangladesh, were analyzed genetically. Full-length VP4 genes of these strains had 98.9% identity to each other and showed 83.9-89.4% identity to those of the P[4] and P[8] rotaviruses. Phylogenetic analysis of VP4 nucleotide sequences revealed that strains MMC38 and MMC71 were located in a lineage of P[8] strains. However, the cluster was highly divergent from the previously established P[8] strains. The VP8* portions of strains MMC38 and MMC71 showed more than 93.9% nucleotide sequence identity to OP354-like P[8] strains, and these strains were clustered into the same lineage. These findings indicate that the VP4 of these strains should be classified into a subtype of the P[8] genotype (P[8]b) that is distinct from that of common P[8] rotaviruses (P[8]a).