Clinical evaluation of cell-direct polymerase chain reaction-based nucleic acid lateral flow immunoassay for rapid detection of bacterial pathogens in clinically suspected sepsis: A multi-center study in Japan.

Blood culture, a method for identifying causative agents of bacterial sepsis, requires several days. The combination of cell-direct polymerase chain reaction and nucleic acid lateral flow immunoassay (cdPCR-NALFIA) is a simple and sensitive detection method for identifying pathogenic bacteria. Furthermore, this assay, when applied directly to blood samples yields results within 4.5 h, without requiring culture. This study was performed at five hospitals in Japan between 2013 and 2016. Blood samples from 73 patients with clinically suspected sepsis yielded 18 positive blood cultures, and the isolated bacterial species were detectable using cdPCR-NALFIA in nine samples. Thirteen samples were positive on cdPCR-NALFIA. In total, 17 samples confirmed to have bacterial species were detectable using cdPCR-NALFIA and/or blood culture with a true positive rate of 76.5% and 64.7%, respectively. The combination of blood culture and cdPCR-NALFIA could improve the rate of detection of bacterial sepsis.

The first assimilation of Akatsuki single-layer winds and its validation with Venusian atmospheric waves excited by solar heating.

The planetary missions including the Venus Climate Orbiter 'Akatsuki' provide new information on various atmospheric phenomena. Nevertheless, it is difficult to elucidate their three-dimensional structures globally and continuously only from observations because satellite observations are considerably limited in time and space. We constructed the first 'objective analysis' of Venus' atmosphere by assimilating cloud-top horizontal winds on the dayside from the equator to mid-latitudes, which is frequently obtained from Akatsuki's Ultraviolet Imager (UVI). The three-dimensional structures of thermal tides, found recently to play a crucial role in maintaining the super rotation, are greatly improved by the data assimilation. This result is confirmed by comparison with Akatsuki's temperature observations. The momentum transport caused by the thermal tides and other disturbances are also modified by the wind assimilation and agrees well with those estimated from the UVI observations. The assimilated dataset is reliable and will be open to the public along with the Akatsuki observations for further investigation of Venus' atmospheric phenomena.

Pulmonary and Disseminated Mycobacterium avium Complex Cases Confirmed by Tissue-Direct Polymerase Chain Reaction-Based Nucleic Acid Lateral Flow Immunoassay of Formalin-Fixed Paraffin-Embedded Tissues.

Background: Detection of Mycobacterium avium complex (MAC) in tissue is essential for the diagnosis of MAC infections when the Mycobacterium is not isolated from sputum. However, detection of MAC in paraffin-embedded sections has not been established. Methods: We encountered two patients with suspected MAC infections after surgery: patient 1 had a pulmonary nodule that was initially suspected to be lung cancer and was excised under video-assisted thoracoscopic surgery (VATS). Patient 2, who was under treatment with steroids and anti-IL-6 inhibitors for rheumatoid arthritis, was suspected to have disseminated ileocecal cancer with metastasis to the lung and skin. In both cases, we postoperatively detected MAC genes in paraffin-embedded tissue sections using the novel mycobacterial nucleic acid identification test, ie tissue-direct polymerase chain reaction (tdPCR)-based nucleic acid lateral flow immunoassay (NALFIA). Both patients showed granulomatous lesions with hematoxylin-eosin staining, and mycobacteria by Ziehl-Neelsen staining in tissue sections from the lung and skin, respectively, although MAC were not isolated from the sections. MAC genes were finally detected by tdPCR-NALFIA in both cases. Conclusion: Although Ziehl-Neelsen staining and culture tests are the gold standard in identifying causative mycobacteria, the rapid results of tdPCR-NALFIA performed simultaneously with sputum and/or tissue culture may make it an important auxiliary diagnostic tool for identifying mycobacterial infection, leading to improvement in the management of MAC patients.

Generation of gravity waves from thermal tides in the Venus atmosphere.

Gravity waves play essential roles in the terrestrial atmosphere because they propagate far from source regions and transport momentum and energy globally. Gravity waves are also observed in the Venus atmosphere, but their characteristics have been poorly understood. Here we demonstrate activities of small-scale gravity waves using a high-resolution Venus general circulation model with less than 20 and 0.25 km in the horizontal and vertical grid intervals, respectively. We find spontaneous gravity wave radiation from nearly balanced flows. In the upper cloud layer (~70 km), the thermal tides in the super-rotation are primary sources of small-scale gravity waves in the low-latitudes. Baroclinic/barotropic waves are also essential sources in the mid- and high-latitudes. The small-scale gravity waves affect the three-dimensional structure of the super-rotation and contribute to material mixing through their breaking processes. They propagate vertically and transport momentum globally, which decelerates the super-rotation in the upper cloud layer (~70 km) and accelerates it above ~80 km.

Thermal structure of the Venusian atmosphere from the sub-cloud region to the mesosphere as observed by radio occultation.

We present distributions of the zonal-mean temperature and static stability in the Venusian atmosphere obtained from Venus Express and Akatsuki radio occultation profiles penetrating down to an altitude of 40 km. At latitudes equatorward of 75°, static stability derived from the observed temperature profiles is consistent with previous in-situ measurements in that there is a low-stability layer at altitudes of 50-58 km and highly and moderately stratified layers above 58 km and below 50 km, respectively. Meanwhile, at latitudes poleward of 75°, a low-stability layer extends down to 42 km, which has been unreported in analyses of previous measurements. The deep low-stability layer in the polar region cannot be explained by vertical convection in the middle/lower cloud layer, and the present result thus introduces new constraints on the dynamics of the sub-cloud atmosphere. The Venusian atmosphere is in striking contrast to the Earth's troposphere, which generally has a deeper low-stability layer at low latitudes than at mid- and high latitudes.

Planetary-scale streak structure reproduced in high-resolution simulations of the Venus atmosphere with a low-stability layer.

Cloud patterns are important clues for revealing the atmospheric circulation of Venus. Recently, a planetary-scale streak structure has been discovered in middle- and lower-cloud images of Venus' night-side taken by IR2, the 2-µm camera, on board the Akatsuki orbiter. However, its formation mechanism has not been investigated. Here we succeed, for the first time, in reproducing the patterns of the observed streak structure, as regions of strong downward flows that develop in high-resolution global simulations of the Venus atmosphere. The streaks are formed in both hemispheres with equatorial symmetry, which is caused by equatorial Rossby-like and Kelvin-like waves with zonal wavenumber one. The low-stability layer that has been suggested by past observations is essential for reproducing the streak structure. The streaks of downward flow result from the interaction of the meridionally tilted phase lines of the Rossby-like waves and the characteristics of baroclinic instability produced around the low-stability layer.

Development of an ensemble Kalman filter data assimilation system for the Venusian atmosphere.

The size and mass of Venus is similar to those of the Earth; however, its atmospheric dynamics are considerably different and they are poorly understood due to limited observations and computational difficulties. Here, we developed a data assimilation system based on the local ensemble transform Kalman filter (LETKF) for a Venusian Atmospheric GCM for the Earth Simulator (VAFES), to make full use of the observational data. To examine the validity of the system, two datasets were assimilated separately into the VAFES forecasts forced with solar heating that excludes the diurnal component Qz; one was created from a VAFES run forced with solar heating that includes the diurnal component Qt, whereas the other was based on observations made by the Venus Monitoring Camera (VMC) onboard the Venus Express. The VAFES-LETKF system rapidly reduced the errors between the analysis and forecasts. In addition, the VAFES-LETKF system successfully reproduced the thermal tide excited by the diurnal component of solar heating, even though the second datasets only included horizontal winds at a single altitude on the dayside with a long interval of approximately one Earth day. This advanced system could be useful in the analysis of future datasets from the Venus Climate Orbiter 'Akatsuki'.

The puzzling Venusian polar atmospheric structure reproduced by a general circulation model.

Unlike the polar vortices observed in the Earth, Mars and Titan atmospheres, the observed Venus polar vortex is warmer than the midlatitudes at cloud-top levels (∼65 km). This warm polar vortex is zonally surrounded by a cold latitude band located at ∼60° latitude, which is a unique feature called 'cold collar' in the Venus atmosphere. Although these structures have been observed in numerous previous observations, the formation mechanism is still unknown. Here we perform numerical simulations of the Venus atmospheric circulation using a general circulation model, and succeed in reproducing these puzzling features in close agreement with the observations. The cold collar and warm polar region are attributed to the residual mean meridional circulation enhanced by the thermal tide. The present results strongly suggest that the thermal tide is crucial for the structure of the Venus upper polar atmosphere at and above cloud levels.

A new variant of cytolethal distending toxin in a clinical isolate of Campylobacter hyointestinalis.

Increasing numbers of Campylobacter hyointestinalis have been isolated from humans and animals with gastroenteritis, although the virulence mechanism of this species remains largely unknown. Here, we show that C. hyointestinalis isolated from a patient with diarrhoea in Thailand produced a novel variant of cytolethal distending toxin (CDT). Sequencing of a 13 965 bp genomic region of C. hyointestinalis carrying the genes coding for Ch-CDT revealed three ORFs of 798, 804 and 537 bp, which code for the Ch-CdtA, Ch-CdtB and Ch-CdtC subunits, respectively. The deduced amino acid sequence of Ch-CdtA showed ∼38.9 % homology with the CdtA of Campylobacter coli, but sequences of Ch-CdtB and Ch-CdtC were homologous to CdtB (65.7 %) and CdtC (33.1 %) of Campylobacter upsaliensis, respectively. Filter-sterilized sonic lysate of C. hyointestinalis demonstrated distension and death of HeLa cells by arresting the cell cycle at the G(2)/M phase and phosphorylation of host histone H2AX, a sensitive marker of DNA double-strand breaks. Rabbit antiserum raised against recombinant Ch-CdtB was not reactive against the recombinant CdtB protein of Campylobacter jejuni. A reconstituted Ch-CDT holotoxin prepared using each of the recombinant subunit proteins demonstrated distension and death of HeLa cells, suggesting that the C. hyointestinalis isolate indeed produced functionally active Ch-CDT. Furthermore, the immunological distinctiveness of the Ch-CDT produced by C. hyointestinalis and the increasing prevalence of the species in patients and animals with gastroenteritis suggest that this species may be an important emerging zoonotic pathogen.

Molecular characterizations of cytolethal distending toxin produced by Providencia alcalifaciens strains isolated from patients with diarrhea.

Cytolethal distending toxins (CDTs), which block eukaryotic cell proliferation by acting as inhibitory cyclomodulins, are produced by diverse groups of Gram-negative bacteria. Active CDT is composed of three polypeptides--CdtA, CdtB, and CdtC--encoded by the genes cdtA, cdtB, and cdtC, respectively. We developed a PCR-restriction fragment length polymorphism assay for the detection and differentiation of five alleles of cdtB (Cdt-I through Cdt-V) in Escherichia coli and used the assay to investigate the prevalence and characteristic of CDT-producing E. coli in children with diarrhea (A. Hinenoya et al., Microbiol. Immunol. 53:206-215, 2009). In these assays, two untypable cdtB genes were detected and the organisms harboring the cdtB gene were identified as Providencia alcalifaciens (strains AH-31 and AS-1). Nucleotide sequence analysis of the cdt gene cluster revealed that the cdtA, cdtB, and cdtC genes of P. alcalifaciens are of 750, 810, and 549 bp, respectively. To understand the possible horizontal transfer of the cdt genes among closely related species, the presence of cdt genes was screened in various Providencia spp. by colony hybridization assay, and the cdt gene cluster was found in only limited strains of P. alcalifaciens. Genome walking revealed that the cdt gene cluster of P. alcalifaciens is located adjacent to a putative transposase gene, suggesting the locus might be horizontally transferable. Interestingly, the CDT of P. alcalifaciens (PaCDT) showed some homology with the CDT of Shigella boydii. Whereas filter-sterilized lysates of strains AH-31 and AS-1 showed distention of CHO but not of HeLa cells, E. coli CDT-I exhibited distention of both cells. This activity of PaCDT was confirmed by generating recombinant PaCDT protein, which could also be neutralized by rabbit anti-PaCdtB antibody. Furthermore, recombinant PaCDT was found to induce G(2)/M cell cycle arrest and phosphorylation of host histone H2AX, a sensitive marker of DNA double-strand breaks. To our knowledge, this is the first report showing that certain clinical P. alcalifaciens strains could produce variants of the CDTs compared.

Evaluation of a PCR-restriction fragment length polymorphism (PCR-RFLP) assay for molecular epidemiological study of Shiga toxin-producing Escherichia coli.

In this study, we have evaluated our recently developed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay for the molecular subtyping of Shiga toxin-producing Escherichia coli (STEC). A total of 200 STEC strains including O157 (n=100), O26 (n=50), O111 (n=10), and non-O26/O111/O157 (n=40) serogroups isolated during 2005-2006 in Japan, which were identified to be clonally different by pulsed-field gel electrophoresis (PFGE) were further analyzed by the PCR-RFLP assay in comparison to PFGE. Ninety-five of O157, 48 of O26, five of O111 and 19 of non-O26/O111/O157 STEC strains yielded one to three amplicons ranging from 6.0 to 15.5 kb in size by the specific primer set targeting region V which is located in the upstream of stx genes. These strains were classified into 41 (O157), 8 (O26), 4 (O111) and 17 (non-O26/O111/O157) groups based on the RFLP patterns obtained by subsequent restriction digestion, respectively. Although the discriminatory power of PCR-RFLP assay was somewhat less than that of PFGE, it is more convenient for molecular subtyping of STEC strains especially for O157, the most important serogroup implicated in human diseases, as well as to identify the outbreak-associated isolates because of its simplicity, rapidity, ease and good reproducibility.

Identification of Vibrio campbellii isolated from diseased farm-shrimps from south India and establishment of its pathogenic potential in an Artemia model.

Shrimp diseases are frequently reported to be caused by closely related vibrios, and in many cases they are tentatively but inaccurately identified as Vibrio harveyi and related vibrios. In the present study, 28 biochemically identified V. harveyi-related strains isolated from diseased shrimps were randomly selected for further characterization by molecular tools. Twenty-six strains were identified as Vibrio campbellii and two as V. harveyi by sequence analysis of 16S rRNA and uridylate kinase genes. Haemolysin-gene-based species-specific multiplex PCR also confirmed these results. Experimental challenge studies using Artemia as a model showed that eight isolates were highly pathogenic, three were moderately pathogenic and the remaining 17 were non-pathogenic. Ribotyping with BglI clearly distinguished V. campbellii from V. harveyi, but it failed to separate pathogenic and non-pathogenic clusters. Artemia nauplii challenged with a fluorescently labelled highly pathogenic strain (IPEY54) showed patches in the digestive tract. However, no patches were observed for a non-pathogenic strain (IPEY41). Direct bacterial counts also supported colonization potential for the highly pathogenic strain. To our knowledge, this is the first report on the isolation and accurate identification of large numbers of V. campbellii associated with shrimp disease in aquacultural farms. V. campbellii has long been considered to be non-pathogenic and classified with V. harveyi-related bacteria. However, we show that this species may be an emerging aquaculture pathogen. This study will help to formulate suitable strategies to combat this newly identified pathogen.

Capsaicin, a potential inhibitor of cholera toxin production in Vibrio cholerae.

The use of natural compounds as inhibitory agents for virulence factor production is a new approach to overcome increased antimicrobial resistance in pathogenic bacteria. In this study, we examined whether red chilli (Capsicum annuum) contains any such compound(s) that can repress the cholera toxin (CT) production in Vibrio cholerae. We found that the methanol extract of red chilli could inhibit CT production in recently emerged V. cholerae O1 El Tor variant strains without affecting their viability. Interestingly, capsaicin, a well-studied active component of red chilli, also drastically inhibited CT production in V. cholerae strains belonging to various serogroups including variants. Real-time quantitative reverse transcription-PCR assay revealed that capsaicin effectively repressed the transcription of ctxA, tcpA and toxT genes, but not of toxR and toxS genes. On the contrary, capsaicin significantly enhanced the transcription of the hns gene, the product of which is known to regulate negatively the transcription of ctxAB, tcpA and toxT genes. These results suggest that capsaicin might act as a potent repressor for CT production possibly by enhancing the transcription of hns.

Distribution of virulence genes related to adhesins and toxins in shiga toxin-producing Escherichia coli strains isolated from healthy cattle and diarrheal patients in Japan.

Shiga toxin-producing Escherichia coli (STEC) isolated from Japan were investigated for the distribution of virulence genes. A total of 232 STEC strains including 171 from cattle and 61 from human were examined for the occurrence of genes responsible for bacterial adhesions to intestine, e.g., eae (intimin, E. coli attaching and effacing), saa (STEC autoagglutinating adhesin), iha (irgA homologue adhesin), efa1 (E. coli factor for adherence), lpfA(O113) (long polar fimbriae), and ehaA (EHEC autotransporter) by colony hybridization assay. Similarly, the presence of toxigenic cdt (cytolethal distending toxin), and subAB (subtilase cytotoxin) genes were also checked. Among cattle isolates, 170, 163, 161, 155, 112 and 84 were positive for lpfA(O113) (99%), ehaA (95%), iha (94%), saa (91%), subAB (65%), and cdt-V (49%), respectively, while 2 were positive for eae (1.2%) and efa1 (1.2%) each. In case of human isolates, 60, 59, 58 and 58 were positive for ehaA (98%), iha (97%), efa1 (95%), and eae (95%), respectively, while 11, 2, 2, and 1 were positive for lpfA(O113) (18%), saa (3.3%), cdt-V (3.3%), and subAB (1.6%), respectively. Therefore, in human STEC isolates efa1 and eae whereas in cattle isolates saa, lpfA(O113), cdt-V and subAB were prevalent. These data indicate differential occurrence of some pathogenic genes in human and cattle originated STEC strains in Japan.

Candida albicans, Cryptococcus neoformans or Aspergillus fumigatus induces an antifungal activity in mouse serum, which is different from transferrin.

It has been reported that administration of Candida albicans into mouse induces an antifungal activity in serum, which has been identified as transferrin. In the present study, we show that not only C. albicans, but also other fungus such as Cryptococcus neoformans or Aspergillus fumigatus similarly can induce an antifungal activity in mouse serum. This antifungal activity was inhibited by the addition of ferrous ion, indicating that the growth inhibition of C. albicans was due to deficiency of ferrous ion, which may be caused by transferrin. Indeed, addition of transferrin in an in vitro assay system using RPMI1640 culture medium inhibited the growth of C. albicans, C. neoformans or A. fumigatus. However, when C. albicans was grown in RPMI1640 medium with 10% fetal bovine serum (FBS), transferrin was unable to inhibit the growth of C. albicans, in sharp contrast, when C. albicans treated mouse serum was added instead of FBS, the growth of the organism was inhibited. Similar results were obtained when C. neoformans or A. fumigatus was used. Taken together, the results suggest that antifungal activity induced by C. albicans, C. neoformans or A. fumigatus was not due to transferrin but likely due to other unknown serum proteins, which may cut off the source of iron for the growth of these fungi.

Rapid culture-free identification and molecular typing of Shiga toxin-producing Escherichia coli by PCR-RFLP.

Using culture-independent technology, PCR-RFLP were used to identify and type STEC in the stool of a patient with HUS. Fecal PCR-RFLP patterns were identical to those of the STEC O157:H7 isolated from the patient.

An inducible lambdoid prophage encoding cytolethal distending toxin (Cdt-I) and a type III effector protein in enteropathogenic Escherichia coli.

Cytolethal distending toxins (CDTs) are inhibitory cyclomodulins, which block eukaryotic cell proliferation and are produced by a diverse group of Gram-negative bacteria, including Escherichia coli strains associated with intestinal and extraintestinal infections. However, the mode of transmission of the toxin gene clusters among diverse bacterial pathogens is unclear. We found that Cdt-I produced by enteropathogenic E. coli strains associated with diarrhea is encoded by a lambdoid prophage, which is inducible and infectious. The genome of Cdt-I converting phage (CDT-1Phi) comprises 47,021 nucleotides with 60 predicted ORFs organized into six genomic regions encoding the head and tail, virulence, integrase, unknown functions, regulation, and lysis. The genomic organization of CDT-1Phi is similar to those of SfV, a serotype-converting phage of Shigella flexneri, and UTI89, a prophage identified in uropathogenic E. coli. Besides the cdtI gene cluster, the virulence region of CDT-1Phi genome contains sequences homologous to a truncated cycle inhibiting factor and a type 3 effector protein. Mutation analysis of susceptible E. coli strain C600 suggested that the outer membrane protein OmpC is a putative receptor for CDT-1Phi. CDT-1Phi genome was also found to integrate into the host bacterial chromosome forming lysogens, which produced biologically active Cdt-I. Furthermore, phage induction appeared to cause enhanced toxigenicity of the E. coli strains carrying lysogenic CDT-1Phi. Our results suggest that CDT-1Phi is the latest member of a growing family of lambdoid phages encoding bacterial cyclomodulins and that the phage may have a role in horizontal transfer of these virulence genes.

Comparison of a PCR-restriction fragment length polymorphism (PCR-RFLP) assay to pulsed-field gel electrophoresis to determine the effect of repeated subculture and prolonged storage on RFLP patterns of Shiga toxin-producing Escherichia coli O157:H7.

In this study, we compared a recently developed PCR-restriction fragment length polymorphism (PCR-RFLP) assay with pulsed-field gel electrophoresis (PFGE) using three different Shiga toxin-producing Escherichia coli (STEC) strains to understand whether repeated subculture in vitro and prolonged storage at room temperature affect the RFLP patterns of STEC. The PFGE profiles of the STEC strains changed by 1 to 8 fragments after repeated subculture and prolonged storage; one strain was no longer clonal after repeated subculture compared to the original isolate according to the Tenover criteria. In contrast, RFLP patterns obtained by PCR-RFLP were identical after repeated subculture and prolonged storage. These data clearly indicate that the PCR-RFLP assay which is based on the diversity of region V, a regulatory region of Stx-phage, was not affected by repeated subculture and prolonged storage and is a more practical and reliable method for molecular typing of STEC strains.