Bayesian reconstruction of a vancomycin-resistant Enterococcus transmission route using epidemiologic data and genomic variants from whole genome sequencing.

BACKGROUND: Outbreaks of vancomycin-resistant enterococcus (VRE) are a serious problem in hospitals. Inferring the transmission route is an important factor to institute appropriate infection control measures; however, the methodology has not been fully established. AIM: To reconstruct and evaluate the transmission model using sequence variants extracted from whole genome sequencing (WGS) data and epidemiological information from patients involved in a VRE outbreak. METHODS: During a VRE outbreak in our hospital, 23 samples were collected from patients and environmental surfaces and analysed using WGS. By combining genome alignment information with patient epidemiological data, the VRE transmission route was reconstructed using a Bayesian approach. With the transmission model, evaluation and further analyses were performed to identify risk factors that contributed to the outbreak. FINDINGS: All VREs were identified as Enterococcus faecium belonging to sequence type 17, which consisted of two VRE genotypes: vanA (N = 8, including one environmental sample) and vanB (N = 15). The reconstruction model using the Bayesian approach showed the transmission direction with posterior probability and revealed transmission through an environmental surface. In addition, some cases acting as VRE spreaders were identified, which can interfere with appropriate infection control. Vancomycin administration was identified as a significant risk factor for spreaders. CONCLUSION: A Bayesian approach for transmission route reconstruction using epidemiologic data and genomic variants from WGS can be applied in actual VRE outbreaks. This may contribute to the design and implementation of effective infection control measures.

Characteristics of paediatric patients with 2009 pandemic influenza A(H1N1) and severe, oxygen-requiring pneumonia in the Tokyo region, 1 September-31 October 2009.

Few reports describe the features of 2009 pandemic influenza A(H1N1) pneumonia in children. We retrospectively reviewed 21 consecutive children admitted to hospital from September to October 2009 in the Tokyo region. The diagnosis of 2009 pandemic influenza A(H1N1) virus infection was based on positive results of real-time RT-PCR or rapid influenza antigen test. All patients were hospitalised for pneumonia with respiratory failure and severe hypoxia. The median interval from onset of influenza symptoms to admission was 14 hours (range: 5-72 hours) and the median interval from the onset of fever (≥38 degrees C) to hospitalisation was 8.5 hours (range: 0-36 hours). All patients required oxygen inhalation. Four patients required mechanical ventilation. Chest radiography revealed patchy infiltration or atelectasis in all patients. Antiviral agents and antibiotics were administrated to all patients. Antiviral agents were administered to 20 patients within 48 hours of influenza symptom onset. No deaths occurred during the study period. Paediatric patients with this pneumonia showed rapid aggravation of dyspnoea and hypoxia after the onset of influenza symptoms.

Nationwide surveillance of bacterial respiratory pathogens conducted by the Japanese Society of Chemotherapy in 2007: general view of the pathogens' antibacterial susceptibility.

For the purpose of a nationwide surveillance of the antimicrobial susceptibility of bacterial respiratory pathogens in patients in Japan, the Japanese Society of Chemotherapy conducted their second year survey, during the period from January to August, 2007. A total of 1178 strains were collected from clinical specimens obtained from adult patients with well-diagnosed respiratory tract infections. Susceptibility testing was evaluable for 1108 strains (226 Staphylococcus aureus, 257 Streptococcus pneumoniae, 6 Streptococcus pyogenes, 206 Haemophilus influenzae, 120 Moraxella catarrhalis, 122 Klebsiella pneumoniae, and 171 Pseudomonas aeruginosa). A total of 44 antibacterial agents, including 26 beta-lactams (four penicillins, three penicillins in combination with beta-lactamase inhibitors, four oral cephems, eight parenteral cephems, one monobactam, five carbapenems, and one penem), three aminoglycosides, four macrolides (including ketolide), one lincosamide, one tetracycline, two glycopeptides, six fluoroquinolones, and one oxazolidinone were used for the study. Analysis was conducted at the central reference laboratory according to the method recommended by the Clinical and Laboratory Standards Institute (CLSI). The incidence of methicillinresistant Staphylococcus aureus (MRSA) was high, at 59.7%, and the incidences of penicillin-intermediateresistant and -resistant Streptococcus pneumoniae (PISP and PRSP) were 30.4% and 5.1%, respectively. Among Haemophilus influenzae strains, 19.9% of them were found to be beta-lactamase-non-producing ampicillin (ABPC)-intermediately-resistant (BLNAI), 29.1% to be beta-lactamasenon-producing ABPC-resistant (BLNAR), and 6.7% to be beta-lactamase-producing ABPC-resistant (BLPAR) strains. Extended-spectrum beta-lactamase-producing Klebsiella pneumoniae was not isolated. Two isolates (1.2%) of Pseudomonas aeruginosa were found to be metallo-beta-lactamase-producing strains, including one (0.6%) suspected multidrug-resistant strain showing resistance to imipenem, amikacin, and ciprofloxacin. These data will be a useful reference for future periodic surveillance studies and for investigations to control resistant infections as well. Continued surveillance is required to prevent the further spread of these antimicrobial resistances.

The first nationwide surveillance of bacterial respiratory pathogens conducted by the Japanese Society of Chemotherapy. Part 1: a general view of antibacterial susceptibility.

The Japanese Society of Chemotherapy (JSC) conducted the first nationwide surveillance of bacterial respiratory pathogens during the period from January to August 2006. With the cooperation of 32 medical institutions throughout Japan, a total of 924 strains belonging to seven clinically relevant bacterial species were collected from adult patients with well-diagnosed respiratory tract infections (RTIs). Antimicrobial susceptibility testing of the 887 evaluable strains (205 Staphylococcus aureus, 200 Streptococcus pneumoniae, 9 Streptococcus pyogenes, 165 Haemophilus influenzae, 91 Moraxella catarrhalis, 74 Klebsiella pneumoniae, and 143 Pseudomonas aeruginosa) to 42 antibacterial agents was conducted at the Central Laboratory of the Research Center for Anti-infective Drugs of the Kitasato Institute, according to recommendations issued by the Clinical and Laboratory Standards Institute (CLSI). The antibacterial agents employed were 25 beta-lactams, three aminoglycosides, four macrolides (including one azalide and one ketolide), one lincosamide, one tetracycline, two glycopeptides, five fluoroquinolones, and one oxazolidinone. The incidence of methicillin-resistant S. aureus (MRSA) was 63.4%, and the incidences of penicillin-intermediately resistant S. pneumoniae (PISP) and penicillin-resistant S. pneumoniae (PRSP) were 35.0% and 4.0%, respectively. Among H. influenzae, 21.2% of the strains were found to be beta-lactamase-nonproducing ampicillin (ABPC)-intermediately resistant (BLNAI), 29.1% to be beta-lactamase-nonproducing ABPC-resistant (BLNAR), and 4.8% to be beta-lactamaseproducing ABPC-resistant (BLPAR) strains. The incidence of extended-spectrum beta-lactamase-producing K. pneumoniae was 2.7% (2 of 74 strains). Three (2.1%) of the 143 P. aeruginosa strains were found to be metallo-beta-lactamaseproducing, including 1 (0.7%) multidrug-resistant strain. Through the nationwide surveillance, we obtained fundamental antimicrobial susceptibility data of clinically relevant bacterial pathogens in adult RTI to various antibacterial agents. These data will be a useful reference for future periodic surveillance studies, as well as for investigations to control antimicrobial-resistant pathogens.

Quantitative and qualitative abnormalities in HIV-1-specific T cells.

OBJECTIVE: To assess the characteristics of CD4 and CD8 T cells specific for HIV-1 and cytomegalovirus (CMV) antigens in untreated and treated HIV-1-infected patients. METHODS: Antigen-specific T cell frequencies were determined by flow cytometric detection of antigen-induced intracellular cytokines. RESULTS: In untreated patients, HIV-1-specific CD4 T cell counts in peripheral blood were less than one tenth of CMV-specific CD4 T cell counts, while the number of specific CD8 T cells was approximately the same for both HIV-1 and CMV. In patients treated with highly active antiretroviral therapy (HAART) for less than 1.5 years, HIV-1-specific CD4 and CD8T cell counts were significantly lower than those in untreated patients. Perforin expression in HIV-1-specific CD8 T cells was significantly lower than that in CMV-specific CD8 T cells. CONCLUSION: These data indicate that HIV-1-specific T cells in HIV-1-infected patients have quantitative and qualitative abnormalities.

[Comparison of five guidelines of community-acquired pneumonia].

The aim of this retrospective study was to elucidate the characteristics of five guidelines of community-acquired pneumonia: ATS (1993), ATS (2001), IDSA (1998), IDSA (2000) and the guidelines of the Japan Respiratory Society (2000). One hundred community-acquired pneumonia patients admitted to the International Medical Center of Japan were investigated in accordance with each set of guidelines based on the physical, laboratory, and chest radiography findings on the first day of treatment. According to the ATS (1993) guidelines, 33% of the cases were classified as "severe" pneumonia. On the other hand, according to the ATS (2001) guidelines, only 8% of the cases were classified as "severe" pneumonia. According to the IDSA guidelines, 35% of the patients were classified as "outpatients". Fluoroquinolone appears to be a very important antibiotic drug in the new guidelines of both ATS and IDSA. The scoring system of IDSA suggested a correlation between the patient's score and the pathogenic bacteria. According to the guidelines of the Japan Respiratory Society, 42% of the cases were classified as "severe" pneumonia. There are evident differences between these guidelines, and clinicians need to have a full understanding of their respective characteristics.

The dynamics of a neuronal culture of dissociated cortical neurons of neonatal rats.

Neuronal networks of dissociated cortical neurons from neonatal rats were cultured over a multielectrode dish with 64 active sites, which were used both for recording the electrical activity and for stimulation. After about 4 weeks of culture, a dense network of neurons had developed and their electrical activity was studied. When a brief voltage pulse was applied to one extracellular electrode, a clear electrical response was evoked over almost the entire network. When a strong voltage pulse was used, the response was composed of an early phase, terminating within 25 ms, and a late phase which could last several hundreds of milliseconds. Action potentials evoked during the early phase occurred with a precise timing with a small jitter and the electrical activity initiated by a localized stimulation diffused significantly over the network. In contrast, the late phase was characterized by the occurrence of clusters of electrical activity with significant spatio-temporal fluctuations. The late phase was suppressed by adding small amounts of D(-)-2-amino-5-phosphonovaleric acid to the extracellular medium, or by increasing the amount of extracellular Mg2+. The electrical activity of the network was substantially increased by the addition of bicuculline to the extracellular medium. The results presented here show that the neuronal network may exist in two different dynamical states: one state in which the neuronal network behaves as a non-chaotic deterministic system and another state where the system exhibits large spatio-temporal fluctuations, characteristic of stochastic or chaotic systems.

Wortmannin, a radiation sensitizer, enhances the radiosensitivity of WKAH rat cells but not that of LEC rat cells.

No significant cytotoxic effect was observed in WKAH rat cells by the treatment of wortmannin, a radiation sensitizer, at concentrations lower than 30 microM for 24 hr. The relative surviving fractions of LEC rat cells were slightly, but significantly, lower than those of WKAH rat cells at each concentration of wortmannin. When the wortmannin-treated WKAH rat cells were X-irradiated, the relative surviving fractions decreased in a wortmannin concentration-dependent manner. On the contrary, no significant difference was observed between the survival curves of untreated and wortmannin-treated LEC rat cells after X-irradiation.

Short- and long-range synchronous activities in dimming detectors of the frog retina.

In the visual system, nearby neurons of similar functional type have a tendency to fire synchronously. Cross-correlation analysis of spike discharges recorded from pairs of neurons has revealed that the synchronized activity is frequently associated with oscillatory firing patterns. However, the underlying neural mechanisms and functions of synchronization and oscillations are not well understood. In the present study, we simultaneously recorded spike discharges from multiple OFF-sustained type ganglion cells with no antagonistic surround (the dimming detectors) of the frog retina using a planar multi-electrode array and analyzed the temporal properties of light-evoked spike discharges. With full-field, temporally modulated diffuse illumination, cross-correlation analysis revealed the presence of the synchronous oscillatory pattern. The strength of the synchronized activity decreased slightly with increased intercellular distance. Synchronized spike discharges were detected even in cell pairs more than 2 mm apart. The frequency of oscillations peaked at approximately 30 Hz. The shuffled cross-correlogram was nearly flat, indicating that the synchronous oscillatory activities are most probably of neural origin. When GABA(A) antagonists were applied to the retina, oscillations were suppressed almost completely and the strength of the synchronized activity decreased with increased intercellular distance more sharply than control. When small spot illumination was applied to the overlapping receptive fields of an adjacent cell pair, a weak synchronized activity was evoked without accompanying oscillations. The same cell pair generated a strong synchronized activity accompanied with oscillations with full-field illumination. Our results suggest that local synchronous activities are generated via short-range neural interactions, and that the oscillatory activities are induced by long-range neural interactions and may contribute to the establishment of synchrony between widely separated neuronal populations.

[Body surface ultrasonography-guided bronchofiberscopy].

Transbronchial lung biopsies and cytologic studies under ultrasonographic guidance from the body surface were conducted in 39 patients whose lesions were adjacent to the thoracic wall. In 26 patients, biopsy, curettage, or brushing forceps were visualized in the mass or infiltrative lesion by thoracic echogram. Positive findings were obtained in 23 patients, for a conclusive diagnostic rate of 88.5%. Of the 13 patients in whom forceps could not be visualized by echogram, 10 had positive findings, for a diagnostic rate of 76.9%. For visualization by thoracic echogram, abnormal lung lesions must be in direct contact with the thoracic wall. Occasionally, diagnostic procedures may be impeded by anatomical structures such as shoulder joints or scapula. Despite these disadvantages, the ultrasonography-guided bronchofiberscope is quite useful because it facilitates real-time confirmation of the positioning of the forceps relative to the lesions. It is also useful in cases when the peripheral lesions are too small or vague to be demonstrated by fluoroscopy alone, because the echo probe can be the target of the forceps instead of the missing shadows. The diagnostic rate should be higher when the forceps are visualized in the lesions ultrasonographically.

Properties of the evoked spatio-temporal electrical activity in neuronal assemblies.

Properties of neural computation were studied in two types of neuronal networks: isolated leech ganglia and neuronal cultures of dissociated cortical neurons from neonatal rats. With appropriate experimental set-ups it was possible to obtain a precise description of the spread of excitation induced by specific inputs. The evoked spatio-temporal electrical activity was characterized by large variability and the electrical activity of neurons activated by the same stimulation was found to be statistically independent to a high degree. The variability presumably originates from basic properties of synaptic transmission, which is stochastic in nature. As a consequence, the large variability of the evoked spatio-temporal electrical activity appears to be a general property of neural computation and a typical feature of neuronal assemblies. It is shown, however, that the observed statistical independence of co-activated neurons may be used to reduce the effects of variability by appropriately averaging or pooling the electrical activity.