bluuebunny/crossref_metadata_2025 huggingface dataset:
Prospective Cohort Study on the Effectiveness of Influenza and Pneumococcal Vaccines in Preventing Pneumonia Development and Hospitalization
Authors: Song Joon Young , Lee Jin Soo , Wie Seong-Heon , Kim Hyo Youl , Lee Jacob , Seo Yu Bin , Jeong Hye Won , Kim Shin Woo , Lee Sun Hee , Park Kyung-Hwa , Noh Ji Yun , Choi Won Suk , Cheong Hee Jin , Kim Woo Joo
Published: December 2014

Pneumonia and acute exacerbation of chronic illness are leading causes of influenza-related hospitalization. Therefore, influenza and pneumococcal vaccinations are strongly recommended for adults with comorbidities. Using a hospital-based influenza surveillance system, we performed a multicenter, prospective cohort study of patients visiting emergency rooms with influenza-like illness (ILI) during the influenza epidemic period in 2013 to 2014. Patients aged ≥19 years were enrolled, and clinical data were collected. Multivariate analyses were performed to estimate the effectiveness of influenza and pneumococcal vaccination in preventing pneumonia development and hospitalization. During study periods, 2,262 patients with ILI were registered. Among 2,217 patients with available vaccination records, 31.9% (707 patients) and 9.7% (216 patients) had received influenza and pneumococcal vaccines, respectively. Among patients who had been administered a pneumococcal vaccine, 94.4% had received the 23-valent polysaccharide vaccine (PPV23). The adjusted rates of effectiveness of the influenza vaccine for preventing pneumonia development and hospitalization were 64.0% (95% confidence interval [CI] = 29% to 81%) and 35.0% (95% CI = 12% to 52%), respectively. Pneumococcal vaccination did not reduce pneumonia development or hospitalization. In conclusion, influenza rather than PPV23 vaccination may reduce pneumonia development and hospitalization in patients with preceding ILI.
Immunogenicity, Safety, and Antibody Persistence at 3, 5, and 10 Years Postvaccination in Adolescents Randomized to Booster Immunization with a Combined Tetanus, Diphtheria, 5-Component Acellular Pertussis, and Inactivated Poliomyelitis Vaccine Administered with a Hepatitis B Virus Vaccine Concurrently or 1 Month Apart
Authors: Embree Joanne , Law Barbara , Voloshen Tim , Tomovici Antigona
Published: December 2014

An understanding of the antibody persistence elicited by a combined tetanus, diphtheria, 5-component acellular pertussis, and inactivated poliovirus vaccine (Tdap-IPV) after adolescent vaccination is important to optimize booster dosing intervals. Our objectives were to compare the safety and immunogenicity of Tdap-IPV coadministered with hepatitis B vaccine (HepB) and sequential administration and evaluate humoral immunity at 3, 5, and 10 years after Tdap-IPV vaccination in adolescents. This phase II randomized, controlled, and open-label study enrolled 280 11- to 14-year-old adolescents with up to 10 years postvaccination follow-up. Group 1 (
n
= 145) received Tdap-IPV, followed by a HepB dose 1 month later, and group 2 (
n
= 135) received both vaccines simultaneously. No consistent increases in solicited reactions or unsolicited adverse events occurred with coadministration. All vaccinees attained seroprotective antibody levels at ≥0.01 IU/ml for diphtheria and tetanus, at a ≥1:8 dilution for poliovirus (serotypes 1, 2, and 3), and ≥10 mIU/ml for hepatitis B at 1 month postvaccination. Clinically relevant immunologic interactions did not occur with coadministration. For pertussis, all participants achieved seropositivity levels (at or above the lower limit of quantitation), and 72.7% to 95.8% had 4-fold increases in pertussis antibodies at 1 month postvaccination. At 10 years postvaccination, the remaining participants (62.8% of the original cohort) maintained seroprotective levels of ≥0.01 IU/ml for diphtheria and tetanus, a ≥1:8 dilution for all 3 poliovirus serotypes, and 74.1% to 98.2% maintained pertussis seropositivity levels depending on the antigen tested. There were no differences between the groups. These results support the coadministration of Tdap-IPV and HepB to adolescents and suggest that vaccination with Tdap-IPV can offer protection for 10 years after an adolescent booster vaccination.
Chikungunya Virus RNA and Antibody Testing at a National Reference Laboratory since the Emergence of Chikungunya Virus in the Americas
Authors: Prince Harry E. , Seaton Brent L. , Matud Jose L. , Batterman Hollis J.
Published: December 2014

Since first reported in the Americas in December 2013, chikungunya virus (CHIKV) infections have been documented in travelers returning from the Caribbean, with many cases identified by CHIKV antibody and/or RNA testing at our laboratory. We used our large data set to characterize the relationship between antibody titers and RNA detection and to estimate IgM persistence. CHIKV RNA was measured by nucleic acid amplification and CHIKV IgG/IgM by indirect immunofluorescence. Of the 1,306 samples submitted for RNA testing in January through September 2014, 393 (30%) were positive; for 166 RNA-positive samples, CHIKV antibody testing was also ordered, and 84% were antibody negative. Of the 6,971 sera submitted for antibody testing in January through September 2014, 1,811 (26%) were IgM positive; 1,461 IgM positives (81%) were also IgG positive. The relationship between the CHIKV antibody titers and RNA detection was evaluated using 376 IgM-positive samples (138 with RNA testing ordered and 238 deidentified and tested for RNA). RNA detection showed no significant association with the IgM titer but was inversely related to the IgG titer; 63% of the IgG negative sera were RNA positive, compared to 36% of sera with low IgG titers (1:10 to 1:80) and 16% with IgG titers of ≥1:160. Using second-sample results from 62 seroconverters, we estimated that CHIKV IgM persists for 110 days (95% confidence interval, 78 to 150 days) after the initial antibody-negative sample. These findings indicate that (i) RNA detection is more sensitive than antibody detection early in CHIKV infection, (ii) in the absence of RNA results, the IgG titer of the IgM-positive samples may be a useful surrogate for viremia, and (iii) CHIKV IgM persists for approximately 4 months after symptom onset.
Complete Genome Sequence of Porcine Circovirus Type 2 Strain HB-MC1
Authors: Yuan Wanzhe , Li Jiefeng , Zuo Yi , Sun Jiguo , Xie Chunfu , Wei Xiaoyuan , Zhang Qiuliang , Yan Guohua , Yang Yuzeng , Li Qingsuo
Published: December 2014

Porcine circovirus type 2 (PCV2) is the primary causative agent of porcine circovirus-associated disease (PCVAD). Here, we report the complete genome sequence of PCV2 strain HB-MC1, which belongs to PCV2d.
Whole-Genome Sequencing Identifies an Atypical Listeria monocytogenes Strain Isolated from Pet Foods
Authors: Burall Laurel S. , Grim Christopher , Gopinath Gopal , Laksanalamai Pongpan , Datta Atin R.
Published: December 2014

Four
Listeria
isolates, including an atypical strain, were isolated from various pet foods and sequenced. We report here the draft genome sequences of these isolates and a comparative genomic analysis with a closely related human clinical isolate. An analysis of the atypical strain identified a frameshift mutation in the
prfA
gene.
Draft Genome Sequence of Pseudomonas mediterranea Strain CFBP 5447
T
, a Producer of Filmable Medium-Chain-Length Polyhydroxyalkanoates
Authors: Licciardello G. , Bella P. , Devescovi G. , Strano C. P. , Sarris P. F. , Catara A. F. , Venturi V. , Catara V.
Published: December 2014

Pseudomonas mediterranea
strain CFBP 5447
T
is a phytopathogenic bacterium isolated from tomato plants affected by pith necrosis disease. Moreover, its ability to produce medium-chain-length polyhydroxyalkanoates (mcl-PHAs) in culture from different carbon sources and valuable microbial products, such as cyclic lipopeptides, has been well documented. Here, we report the first draft genome sequence of this species.
Genome Sequence of a Pandrug-Resistant Pseudomonas aeruginosa Strain, YN-1
Authors: Tan Hong-Li , Wang Yong , Cheng Xue-Qin , Huang Yan-Mei , Liu Wei , Zhang Li-Juan
Published: December 2014

A highly rampant multidrug-resistant strain of
Pseudomonas aeruginosa
appeared in a hospital in Yunnan Province, China. Here, we report the genome sequence of the pandrug-resistant (PDR)
P. aeruginosa
strain recovered from a patient in 2013.
Complete Genome Sequences of Bordetella pertussis Isolates B1917 and B1920, Representing Two Predominant Global Lineages
Authors: Bart Marieke J. , Zeddeman Anne , van der Heide Han G. J. , Heuvelman Kees , van Gent Marjolein , Mooi Frits R.
Published: December 2014

Bordetella pertussis
is the causative agent of pertussis, a disease which has resurged despite vaccination. We report the complete, annotated genomes of isolates B1917 and B1920, representing two lineages predominating globally in the last 50 years. The B1917 lineage has been associated with the resurgence of pertussis in the 1990s.
Complete Genome Sequencing of Borrelia valaisiana and Borrelia afzelii Isolated from
Ixodes persulcatus
Ticks in Western Siberia
Authors: Kurilshikov Alexander M. , Fomenko Nataliya V. , Stronin Oleg V. , Tikunov Artem Y. , Kabilov Marsel R. , Tupikin Alexei E. , Tikunova Nina V.
Published: December 2014

Lyme disease, caused by bacteria of the
Borrelia burgdorferi
sensu lato
complex, is the most frequent tick-borne infection in Eurasia. Here, we report the complete genome sequence of the
Borrelia valaisiana
Tom 4006 and
Borrelia afzelii
Tom 3107 strains isolated from
Ixodes persulcatus
ticks in western Siberia.
Draft Genome Sequence of Lactobacillus casei Lbs2
Authors: Bhowmick Swati , Malar Mathu , Das Abhishek , Kumar Thakur Bhupesh , Saha Piu , Das Santasabuj , Rashmi H. M. , Batish Virender K. , Grover Sunita , Tripathy Sucheta
Published: December 2014

We report here a 3.2-Mb draft assembled genome of
Lactobacillus casei
Lbs2. The bacterium shows probiotic and immunomodulatory activities. The genome assembly and annotation will help to identify molecules and pathways responsible for interaction between the host immune system and the microbe.
Complete Genome Sequence for
Treponema
sp. OMZ 838 (ATCC 700772, DSM 16789), Isolated from a Necrotizing Ulcerative Gingivitis Lesion
Authors: Chan Yuki , Ma Angel P. Y. , Lacap-Bugler Donnabella C. , Huo Yong-Biao , Keung Leung W. , Leung Frederick C. , Watt Rory M.
Published: December 2014

The oral treponeme bacterium
Treponema
sp. OMZ 838 was originally isolated from a human necrotizing ulcerative gingivitis (NUG) lesion. Its taxonomic status remains uncertain. The complete genome sequence length was determined to be 2,708,067 bp, with a G+C content of 44.58%, and 2,236 predicted coding DNA sequences (CDS).
Genome Sequences of Three Highly Copper-Resistant Salmonella enterica subsp. I Serovar Typhimurium Strains Isolated from Pigs in Denmark
Authors: Qin Yanan , Hasman Henrik , Aarestrup Frank M. , Alwathnani Hend A. , Rensing Christopher
Published: December 2014

Salmonella typhimurium
is the causative agent of typhoid fever, which causes nearly 21.7 million illnesses and 217,000 deaths around the world each year. Here, we describe the draft genome sequences of the
Salmonella typhimurium
strains S7, S15, and S23, isolated from copper-fed pigs in Denmark and containing additional putative determinants conferring resistances to copper and other metals and metalloids.
Draft Genome Sequence of Elizabethkingia meningoseptica, Isolated from a Postoperative Endophthalmitis Patient
Authors: Pradeep Bulagonda Eswarappa , Mahalingam Niranjana , Manivannan Bhavani , Padmanabhan Krishnanand , Nilawe Pravin , Gurung Girija , Chhabra Amit , Nagaraja Valakunja
Published: December 2014

We present the draft genome assembly of an
Elizabethkingia meningoseptica
strain isolated from a 67-year-old postoperative endophthalmitis patient who suffered loss of vision in the right eye. The draft genome assembly has 167 contigs with a total size of 4,019,665 bp encoding multiple drug-resistant genes.
Complete Genome Sequence of Klebsiella pneumoniae Sequence Type 17, a Multidrug-Resistant Strain Isolated during Tigecycline Treatment
Authors: Hua Xiaoting , Chen Qiong , Li Xi , Feng Ye , Ruan Zhi , Yu Yunsong
Published: December 2014

Klbesiella pneumoniae
is one of the most important human pathogens and frequently causes many diseases. To facilitate the comparative genome analysis in tigecycline resistance mechanism, we report the complete chromosomal sequence of a multidrug-resistance
K. pneumoniae
strain before tigecycline treatment for reference genome.
Complete Genome Sequence of Streptococcus agalactiae CNCTC 10/84, a Hypervirulent Sequence Type 26 Strain
Authors: Hooven Thomas A. , Randis Tara M. , Daugherty Sean C. , Narechania Apurva , Planet Paul J. , Tettelin Hervé , Ratner Adam J.
Published: December 2014

Streptococcus agalactiae
(group B
Streptococcus
[GBS]) is a human pathogen with a propensity to cause neonatal infections. We report the complete genome sequence of GBS strain CNCTC 10/84, a hypervirulent clinical isolate frequently used to study GBS pathogenesis. Comparative analysis of this sequence may shed light on novel pathogenic mechanisms.
Genome Sequences of Two Copper-Resistant Escherichia coli Strains Isolated from Copper-Fed Pigs
Authors: Lüthje Freja L. , Hasman Henrik , Aarestrup Frank M. , Alwathnani Hend A. , Rensing Christopher
Published: December 2014

The draft genome sequences of two copper-resistant
Escherichia coli
strains were determined. These had been isolated from copper-fed pigs and contained additional putative operons conferring copper and other metal and metalloid resistances.
Draft Genome Sequence of Rice Isolate Pseudomonas chlororaphis EA105
Authors: McCully Lucy M. , Bitzer Adam S. , Spence Carla A. , Bais Harsh P. , Silby Mark W.
Published: December 2014

Pseudomonas chlororaphis
EA105, a strain isolated from rice rhizosphere, has shown antagonistic activities against a rice fungal pathogen, and could be important in defense against rice blast. We report the draft genome sequence of EA105, which is an estimated size of 6.6 Mb.
Draft Genome Sequence of Violacein-Producing Marine Bacterium
Pseudoalteromonas
sp. 520P1
Authors: Dang Hoang Tran , Yotsumoto Kentarou , Enomoto Keiichi
Published: December 2014

Here, we report a draft 5.25-Mb genome sequence of
Pseudoalteromonas
sp. 520P1, a marine violacein-producing bacterium isolated from the Pacific coast of Japan. Genome annotation by BLAST searches revealed the presence of one acylhomoserine lactone (AHL) synthase (
luxI
) and five AHL receptor protein (
luxR
) gene homologs.
Influenza pH1N1 Virus Accumulated H275Y Mutation in Neuraminidase during Propagation in MDCK Cells
Authors: Mishel Polina , Bychkov Dmitrii , Kallio-Kokko Hannimari , Valkonen Miia , Kantele Anu , Mattila Pirkko , Almusa Henrikki , Jalovaara Petri , Kainov Denis
Published: December 2014

Here, we sequenced the genome of the influenza A/Finland/741 M/2014(H1N1) virus and found that the virus accumulated oseltamivir resistance mutation H275Y in its neuraminidase during propagation in cell culture. This indicates that propagation in cell culture modifies virus genomes. The instability of influenza genomes should be taken into consideration during drug-sensitivity studies.
Whole-Genome Sequence of “
Candidatus
Liberibacter solanacearum” Strain R1 from California
Authors: Zheng Z. , Clark N. , Keremane M. , Lee R. , Wallis C. , Deng X. , Chen J.
Published: December 2014

The draft whole-genome sequence of “
Candidatus
Liberibacter solanacearum” strain R1, isolated from and maintained in tomato plants in California, is reported. The R1 strain has the genome size of 1,204,257 bp, G+C content of 35.3%, 1,101 predicted open reading frames, and 57 RNA genes.
Genome Sequence of Afipia felis Strain 76713, Isolated in Hospital Water Using an Amoeba Co-Culture Procedure
Authors: Benamar Samia , La Scola Bernard , Croce Olivier
Published: December 2014

Afipia felis
is a Gram-negative alphaproteobacterium originally described as the agent of cat-scratch disease (CSD). We sequenced the genome from a strain of
A. felis
, which was recovered from a hospital water sample using an amoebal co-culture procedure. It is composed of 3,989,646 bp, with a G+C content of 61.27% and encodes 4,068 protein-coding genes and 53 RNA genes.
A Valuable Antigen Detection Method for Diagnosis of Acute Hepatitis E
Authors: Wen Gui-Ping , Tang Zi-Min , Yang Fan , Zhang Ke , Ji Wen-Fang , Cai Wei , Huang Shou-Jie , Wu Ting , Zhang Jun , Zheng Zi-Zheng , Xia Ning-Shao
Published: December 2014

Hepatitis E virus (HEV) is a serious public health problem. The commonly used tests that are specific for current HEV infection diagnosis include the detection of anti-HEV IgM and HEV RNA. Here, we report an improved enzyme-linked immunosorbent assay (ELISA) method for HEV antigen detection with a linear range equivalent to 6.3 × 10
3
to 9.2 × 10
5
RNA copies per ml. The monoclonal antibody (MAb) 12F12, a high-ability MAb that binds HEV virus, was selected as the capture antibody from a panel of 95 MAbs. The positive period of HEV antigenemia in infected monkeys using this test was, on average, 3 weeks longer than previously reported and covered the majority of the acute phase. The positive detection rates of IgM, RNA, and new antigen from the first serum samples collected from 16 confirmed acute hepatitis E patients were 81% (13/16), 81% (13/16), and 100% (16/16), respectively. In three patients, the initial serum specimens that tested negative for IgM, despite the presence of symptoms of acute hepatitis and elevated alanine aminotransferase (ALT) levels, were positive for HEV antigen and HEV RNA. In contrast, the serum samples of the three RNA-negative patients were antigen positive (and IgM positive), possibly due to the degradation of HEV nucleic acids. Our results suggest that this new antigen detection method has acceptable concordance with RNA detection and could serve as an important tool for diagnosing acute hepatitis E.
Global Multilocus Sequence Typing Analysis of Mycoplasma bovis Isolates Reveals Two Main Population Clusters
Authors: Rosales R. S. , Churchward C. P. , Schnee C. , Sachse K. , Lysnyansky I. , Catania S. , Iob L. , Ayling R. D. , Nicholas R. A. J.
Published: December 2014

Mycoplasma bovis
is a major bovine pathogen associated with bovine respiratory disease complex and is responsible for substantial economic losses worldwide.
M. bovis
is also associated with other clinical presentations in cattle, including mastitis, otitis, arthritis, and reproductive disorders. To gain a better understanding of the genetic diversity of this pathogen, a multilocus sequence typing (MLST) scheme was developed and applied to the characterization of 137
M. bovis
isolates from diverse geographical origins, obtained from healthy or clinically infected cattle. After
in silico
analysis, a final set of 7 housekeeping genes was selected (
dnaA
,
metS
,
recA
,
tufA
,
atpA
,
rpoD
, and
tkt
). MLST analysis demonstrated the presence of 35 different sequence types (STs) distributed in two main clonal complexes (CCs), defined at the double-locus variant level, namely, CC1, which included most of the British and German isolates, and CC2, which was a more heterogeneous and geographically distant group of isolates, including European, Asian, and Australian samples. Index of association analysis confirmed the clonal nature of the investigated
M. bovis
population, based on MLST data. This scheme has demonstrated high discriminatory power, with the analysis showing the presence of genetically distant and divergent clusters of isolates predominantly associated with geographical origins.
Pyogranulomatous Pneumonia in Goats Caused by an Undescribed Porphyromonas Species, “Porphyromonas katsikii”
Authors: Filioussis George , Petridou Evanthia , Karavanis Emmanouel , Frey Joachim
Published: December 2014

A yet-undescribed bacterial species, tentatively named “
Porphyromonas
katsikii
,” was isolated from individuals of a small goat herd with pyogranulomatous pneumonia during an outbreak of acute respiratory disease. The isolated bacteria grew in the form of black-pigmented colonies after 14 days of incubation under anaerobic conditions at 37°C on a tryptic soy blood agar medium. The bacteria were identified as a yet-undescribed
Porphyromonas
species by determination of the nucleotide sequence of the
rrs
16S rRNA gene, and this species was tentatively named
Porphyromonas
katsikii
. PCR amplification with specific primers for this yet-undescribed species revealed the presence of
P. katsikii
in the lung tissue of all affected animals, while no PCR signals were evidenced from the lungs of healthy goats or from goats with pasteurellosis caused by
Mannheimia haemolytica
. These data indicate
P. katsikii
as the causative agent of acute respiratory distress.
P. katsikii
is phylogenetically related to
Porphyromonas
somerae
and
Porphyromonas levii
, which cause pathologies in humans and animals, respectively.
P. katsikii
was not detected by PCR from samples of the gingival pockets or of the faces of healthy goats.
Performance of Vitek 2 for Antimicrobial Susceptibility Testing of Enterobacteriaceae with Vitek 2 (2009 FDA) and 2014 CLSI Breakpoints
Authors: Bobenchik April M. , Deak Eszter , Hindler Janet A. , Charlton Carmen L. , Humphries Romney M.
Published: December 2014

Vitek 2 (bioMérieux Inc., Durham, NC) is a widely used commercial antimicrobial susceptibility test system. We compared the MIC results obtained using the Vitek 2 AST-GN69 and AST-XN06 cards to those obtained by CLSI broth microdilution (BMD) for 255 isolates of
Enterobacteriaceae
, including 25 isolates of carbapenem-resistant
Enterobacteriaceae
. In total, 25 antimicrobial agents were examined. For 10 agents, the MIC data were evaluated using two sets of breakpoints: (i) the Vitek 2 breakpoints, which utilized the 2009 FDA breakpoints at the time of the study and are equivalent to the 2009 CLSI M100-S19 breakpoints, and (ii) the 2014 CLSI M100-S24 breakpoints. There was an overall 98.7% essential agreement (EA). The categorical agreement was 95.5% (CA) using the Vitek 2 breakpoints and 95.7% using the CLSI breakpoints. There was 1 very major error (VME) (0.05%) observed using the Vitek 2 breakpoints (cefazolin) and 8 VMEs (0.5%) using the CLSI breakpoints (2 each for aztreonam, cefepime, and ceftriaxone, and 1 for cefazolin and ceftazidime). Fifteen major errors (MEs) (0.4%) were noted using the Vitek 2 breakpoints and 8 (0.5%) using the CLSI breakpoints. Overall, the Vitek 2 performance was comparable to that of BMD for testing a limited number of
Enterobacteriaceae
commonly isolated by clinical laboratories. Ongoing studies are warranted to assess performance in isolates with emerging resistance.
Septic Arthritis and Osteomyelitis Due to Bordetella petrii
Authors: Nogi Masayuki , Bankowski Matthew J. , Pien Francis D.
Published: December 2014

A case of
Bordetella petrii
septic arthritis and osteomyelitis in an elbow resulted from a dirt bike accident in Hawaii. Two months of intravenous antibiotics and repeated surgeries were required to cure this infection. Our case, and literature review, suggests that extended-spectrum penicillins, tetracycline, and trimethoprim-sulfamethoxazole are good treatment options.
Bartonella, a Common Cause of Endocarditis: a Report on 106 Cases and Review
Authors: Edouard Sophie , Nabet Cecile , Lepidi Hubert , Fournier Pierre-Edouard , Raoult Didier
Published: December 2014

Bartonella
spp. are fastidious bacteria that cause blood culture-negative endocarditis and have been increasingly reported. In this study, we included all patients retrospectively and prospectively diagnosed with
Bartonella
endocarditis in our French reference center between 2005 and 2013. Our diagnosis was based on the modified Duke criteria and microbiological findings, including serological and PCR results. To review the published literature, we searched all human
Bartonella
endocarditis cases published in the PubMed database between January 2005 and October 2013. We report here a large series of 106 cases, which include 59 cases that had not previously been reported or mentioned. Indirect immunofluorescence assays, Western blotting, and real-time PCR from total blood, serum, and valve tissue exhibited sensitivities of 58%, 100%, 33%, 36%, and 91%, respectively. The number of cases reported in the literature between 2005 and 2013 increased to reach a cumulative number of 196 cases. The number of cases reported in the literature by other centers is increasing more rapidly than that reported by our French reference center (
P
< 10
−2
). Currently, there is a lack of criteria for the diagnosis of
Bartonella
endocarditis. We suggest that a positive PCR result from a cardiac valve or blood specimen, an IgG titer of ≥800 using an immunofluorescence assay, or a positive Western blot assay be considered major Duke criteria for
Bartonella
endocarditis. There is no real increase in the incidence of these infections but rather a better understanding and interest in the disease resulting from the improvement of diagnostic tools.
(1,3)-β-
d
-Glucan in Cerebrospinal Fluid for Diagnosis of Fungal Meningitis Associated with Contaminated Methylprednisolone Injections
Authors: Malani Anurag N. , Singal Bonita , Wheat L. Joseph , Al Sous Ola , Summons Theresa A. , Durkin Michelle M. , Pettit April C.
Published: December 2014

Prompt diagnosis and treatment of fungal meningitis are critical, but culture is insensitive. (1,3)-β-
d
-Glucan (BDG) testing is FDA approved for serological diagnosis of invasive fungal disease; however, BDG testing is not approved for cerebrospinal fluid (CSF), and the appropriate cutoff value is unknown. We aimed to validate the diagnostic accuracy of CSF BDG measurements for fungal meningitis among patients exposed to contaminated methylprednisolone acetate (MPA). A retrospective observational study was conducted at St. Joseph Mercy Hospital and Vanderbilt University from November 2013 to February 2014. Patients were included if they had received a contaminated MPA injection. Cases were classified as probable or proven meningitis according to Centers for Disease Control and Prevention guidelines. CSF BDG testing was performed according to the package insert instructions for serum samples, and results were validated using Clinical and Laboratory Standards Institute procedures (MiraVista Diagnostics). Of 233 patients, 45 had meningitis (28 proven cases), 53 had spinal/paraspinal infections (19 proven cases), and 135 did not develop disease. Using the manufacturer's cutoff value (≥80 pg/ml), the sensitivity and specificity were 96% and 95%, respectively, for proven meningitis and 84% and 95% for probable or proven meningitis. Receiver operating characteristic analysis identified the optimal cutoff value for proven meningitis to be 66 pg/ml (sensitivity, 100%; specificity, 94%) and that for probable or proven meningitis to be 66 pg/ml (sensitivity, 91%; specificity, 92%). Our results suggest that CSF BDG measurements are highly sensitive and specific for the diagnosis of fungal meningitis associated with contaminated MPA injections. Further study on the utility of CSF BDG testing for other types of fungal meningitis is needed.
gyrB
Analysis as a Tool for Identifying Nocardia Species and Exploring Their Phylogeny
Authors: Carrasco Gema , Valdezate Sylvia , Garrido Noelia , Medina-Pascual María J. , Villalón Pilar , Sáez-Nieto Juan A.
Published: December 2014

gyrB
is used to improve the identification of the
Nocardia
species
N. brasiliensis
,
N. higoensis
,
N. ignorata
,
N. otitidiscaviarum
,
N. paucivorans
,
N. pneumoniae
,
N. puris
,
N. takedensis
,
N. veterana
, and
N. vinacea
, but it does not improve the identification of another 12
Nocardia
studied species.
gyrB
provides typing and phylogenetic markers for
N. carnea
,
N. transvalensis
,
N. brasiliensis
, and
N. otitidiscaviarum
.
High Staphylococcus aureus Colonization Prevalence among Patients with Skin and Soft Tissue Infections and Controls in an Urban Emergency Department
Authors: Kumar Neha , David Michael Z. , Boyle-Vavra Susan , Sieth Julia , Daum Robert S.
Published: December 2014

Staphylococcus aureus
is a commensal species that can also be a formidable pathogen. In the United States, an epidemic of community-acquired methicillin-resistant
Staphylococcus aureus
(MRSA) infections has been occurring for the last 15 years. In the context of a study in which we identified patients with skin and soft tissue infections (SSTIs) and randomized them to receive one of two antimicrobial treatment regimens, we assessed
S. aureus
colonization in the nares, throat, and perianal skin on the day of enrollment and 40 days after therapy. We compared the prevalence of colonization between the SSTI patients and an uninfected control population. A total of 144 subjects and 130 controls, predominantly African American, participated in this study, and 116 returned for a 40-day follow-up visit. Of the SSTI patients, 76% were colonized with
S. aureus
at enrollment, as were 65% of the controls. Patients were more likely than the controls to be colonized with USA300 MRSA (62/144 [43.1%] versus 11/130 [8.5%], respectively;
P
< 0.001). The nares were not the most common site of colonization. The colonization prevalence diminished somewhat after antibiotic treatment but remained high. The isolates that colonized the controls were more likely than those in the patients to be methicillin-susceptible
S. aureus
(MSSA) (74/84 [88.1%] versus 56/106 [52.8%], respectively;
P
< 0.001). In conclusion, the prevalence of
S. aureus
colonization among SSTI patients was high and often involved USA300 MRSA. The prevalence diminished somewhat with antimicrobial therapy but remained high at the 40-day follow-up visit. Control subjects were also colonized at a high prevalence but most often with a genetic background not associated with a clinical infection in this study.
S. aureus
is a commensal species and a pathogen. Plans for decolonization or eradication should take this distinction into account.
Molecular Profiling of Escherichia coli O157:H7 and Non-O157 Strains Isolated from Humans and Cattle in Alberta, Canada
Authors: Chui Linda , Li Vincent , Fach Patrick , Delannoy Sabine , Malejczyk Katarzyna , Patterson-Fortin Laura , Poon Alan , King Robin , Simmonds Kimberley , Scott Allison N. , Lee Mao-Cheng
Published: December 2014

Virulence markers in Shiga toxin-producing
Escherichia coli
(STEC) and their association with diseases remain largely unknown. This study determines the importance of 44 genetic markers for STEC (O157 and non-O157) from human clinical cases and their correlation to disease outcome. STEC isolated from a cattle surveillance program were also included. The virulence genes tested were present in almost all O157:H7 isolates but highly variable in non-O157 STEC isolates. Patient age was a significant determinant of clinical outcome.
Upon Intranasal Vesicular Stomatitis Virus Infection, Astrocytes in the Olfactory Bulb Are Important Interferon Beta Producers That Protect from Lethal Encephalitis
Authors: Detje Claudia N. , Lienenklaus Stefan , Chhatbar Chintan , Spanier Julia , Prajeeth Chittappen K. , Soldner Claudia , Tovey Michael G. , Schlüter Dirk , Weiss Siegfried , Stangel Martin , Kalinke Ulrich
Published: December 2014

Previously we found that following intranasal (i.n.) infection with neurotropic vesicular stomatitis virus (VSV) type I interferon receptor (IFNAR) triggering of neuroectodermal cells was critically required to constrain intracerebral virus spread. To address whether locally active IFN-β was induced proximally, we studied spatiotemporal conditions of VSV-mediated IFN-β induction. To this end, we performed infection studies with IFN-β reporter mice. One day after intravenous (i.v.) VSV infection, luciferase induction was detected in lymph nodes. Upon i.n. infection, luciferase induction was discovered at similar sites with delayed kinetics, whereas on days 3 and 4 postinfection enhanced luciferase expression additionally was detected in the foreheads of reporter mice. A detailed analysis of cell type-specific IFN-β reporter mice revealed that within the olfactory bulb IFN-β was expressed by neuroectodermal cells, primarily by astrocytes and to a lesser extent by neurons. Importantly, locally induced type I IFN triggered distal parts of the brain as indicated by the analysis of ISRE-eGFP mice which after i.n. VSV infection showed enhanced green fluorescent protein (eGFP) expression throughout the brain. Compared to wild-type mice, IFN-β−/−mice showed increased mortality to i.n. VSV infection, whereas upon i.v. infection no such differences were detected highlighting the biological significance of intracerebrally expressed IFN-β. In conclusion, upon i.n. VSV instillation, IFN-β responses mounted by astrocytes within the olfactory bulb critically contribute to the antiviral defense by stimulating distal IFN-β-negative brain areas and thus arresting virus spread.

IMPORTANCEThe central nervous system has long been considered an immune privileged site. More recently, it became evident that specialized immune mechanisms are active within the brain to control pathogens. Previously, we showed that virus, which entered the brain via the olfactory route, was arrested within the olfactory bulb by a type I IFN-dependent mechanism. Since peripheral type I IFN would not readily cross the blood-brain barrier and within the brain thus far no abundant type I IFN responses have been detected, here we addressed from where locally active IFN originated from. We found that upon intranasal VSV instillation, primarily astrocytes, and to a lesser extent neurons, were stimulated within the olfactory bulb to mount IFN-β responses that also activated and protected distal brain areas. Our results are surprising because in other infection models astrocytes have not yet been identified as major type I IFN producers.
Intracellular Expression of Camelid Single-Domain Antibodies Specific for Influenza Virus Nucleoprotein Uncovers Distinct Features of Its Nuclear Localization
Authors: Ashour Joseph , Schmidt Florian I. , Hanke Leo , Cragnolini Juanjo , Cavallari Marco , Altenburg Arwen , Brewer Rebeccah , Ingram Jessica , Shoemaker Charles , Ploegh Hidde L.
Published: December 2014

Perturbation of protein-protein interactions relies mostly on genetic approaches or on chemical inhibition. Small RNA viruses, such as influenza A virus, do not easily lend themselves to the former approach, while chemical inhibition requires that the target protein be druggable. A lack of tools thus constrains the functional analysis of influenza virus-encoded proteins. We generated a panel of camelid-derived single-domain antibody fragments (VHHs) against influenza virus nucleoprotein (NP), a viral protein essential for nuclear trafficking and packaging of the influenza virus genome. We show that these VHHs can target NP in living cells and perturb NP's function during infection. Cytosolic expression of NP-specific VHHs (αNP-VHHs) disrupts virus replication at an early stage of the life cycle. Based on their specificity, these VHHs fall into two distinct groups. Both prevent nuclear import of the viral ribonucleoprotein (vRNP) complex without disrupting nuclear import of NP alone. Different stages of the virus life cycle thus rely on distinct nuclear localization motifs of NP. Their molecular characterization may afford new means of intervention in the virus life cycle.

IMPORTANCE
Many proteins encoded by RNA viruses are refractory to manipulation due to their essential role in replication. Thus, studying their function and determining how to disrupt said function through pharmaceutical intervention are difficult. We present a novel method based on single-domain-antibody technology that permits specific targeting and disruption of an essential influenza virus protein in the absence of genetic manipulation of influenza virus itself. Characterization of such interactions may help identify new targets for pharmaceutical intervention. This approach can be extended to study proteins encoded by other viral pathogens.
Structural and Functional Analysis of Surface Proteins from an A(H3N8) Influenza Virus Isolated from New England Harbor Seals
Authors: Yang Hua , Nguyen Ha T. , Carney Paul J. , Guo Zhu , Chang Jessie C. , Jones Joyce , Davis Charles T. , Villanueva Julie M. , Gubareva Larisa V. , Stevens James
Published: December 2014

In late 2011, an A(H3N8) influenza virus infection resulted in the deaths of 162 New England harbor seals. Virus sequence analysis and virus receptor binding studies highlighted potential markers responsible for mammalian adaptation and a mixed receptor binding preference (S. J. Anthony, J. A. St Leger, K. Pugliares, H. S. Ip, J. M. Chan, Z. W. Carpenter, I. Navarrete-Macias, M. Sanchez-Leon, J. T. Saliki, J. Pedersen, W. Karesh, P. Daszak, R. Rabadan, T. Rowles, W. I. Lipkin, MBio 3:e00166-00112, 2012,
http://dx.doi.org/10.1128/mBio.00166-12
). Here, we present a detailed structural and biochemical analysis of the surface antigens of the virus. Results obtained with recombinant proteins for both the hemagglutinin and neuraminidase indicate a true avian receptor binding preference. Although the detection of this virus in new species highlights an increased potential for cross-species transmission, our results indicate that the A(H3N8) virus currently poses a low risk to humans.

IMPORTANCE
Cross-species transmission of zoonotic influenza viruses increases public health concerns. Here, we report a molecular and structural study of the major surface proteins from an A(H3N8) influenza virus isolated from New England harbor seals. The results improve our understanding of these viruses as they evolve and provide important information to aid ongoing risk assessment analyses as these zoonotic influenza viruses continue to circulate and adapt to new hosts.
Hepatitis B Virus Regulates Apoptosis and Tumorigenesis through the MicroRNA-15a-Smad7-Transforming Growth Factor Beta Pathway
Authors: Liu Ningning , Jiao Tong , Huang Yan , Liu Wenjun , Li Zhiwei , Ye Xin
Published: December 2014

Hepatitis B virus (HBV) infection causes chronic hepatitis in hundreds of millions of people worldwide, which can eventually lead to hepatocellular carcinoma (HCC). Previously, we found that HBV mRNAs can absorb microRNA-15a (miR-15a) to affect apoptosis through the Bcl-2 pathway. We asked whether HBV could inhibit apoptosis and promote tumorigenesis through different pathways. In this study, we found that the transforming growth factor β (TGF-β) pathway-inhibitory factor Smad7 is a novel target of miR-15a. We demonstrated that HBV can upregulate the level of Smad7 by downregulating miR-15a. Furthermore, we examined the level of Smad7 in liver samples from HBV-infected HCC patients and found that HBV mRNAs are positively correlated with the level of Smad7. By taking the approach of using immunoblotting and luciferase reporter assays, we revealed that HBV can abrogate TGF-β signaling via upregulating Smad7. By using annexin V staining and caspase 3/7 activity assays, we found that HBV can inhibit TGF-β-induced apoptosis of HepG2 cells. We also showed that HBV can promote tumor growth in BALB/c nude mice through upregulating the expression of Smad7. In conclusion, we demonstrated that HBV can upregulate Smad7 expression and inhibit TGF-β signaling, which makes the cells resistant to TGF-β-induced apoptosis and promotes tumorigenesis.

IMPORTANCE
Hepatitis B virus (HBV) infection causes chronic hepatitis, which can eventually lead to hepatocellular carcinoma (HCC). TGF-β signaling is closely linked to liver fibrosis, cirrhosis, and subsequent HCC progression and plays a unique role in the pathogenesis of HCC. At the early stage of tumor formation, TGF-β functions as a tumor suppressor that inhibits cell proliferation and induces apoptosis. Previously, we found that HBV mRNAs can sponge off miR-15a to affect apoptosis through the Bcl-2 pathway. In this study, we identified that the TGF-β-inhibitory factor Smad7 is a novel target of miR-15a. We reveal that HBV can abrogate TGF-β signaling via upregulating Smad7, inhibit TGF-β-induced apoptosis, as well as promote tumor development. Our study provides evidence to support the idea that viral RNAs can exert their functions as competing endogenous RNAs (ceRNAs) toward microRNA and participate in important cellular processes.
Alpha-Defensin HD5 Inhibits Furin Cleavage of Human Papillomavirus 16 L2 To Block Infection
Authors: Wiens Mayim E. , Smith Jason G.
Published: December 2014

Human papillomavirus (HPV) is a significant oncogenic virus, but the innate immune response to HPV is poorly understood. Human α-defensin 5 (HD5) is an innate immune effector peptide secreted by epithelial cells in the genitourinary tract. HD5 is broadly antimicrobial, exhibiting potent antiviral activity against HPV at physiologic concentrations; however, the specific mechanism of HD5-mediated inhibition against HPV is unknown. During infection, the HPV capsid undergoes several critical cell-mediated viral protein processing steps, including unfolding and cleavage of the minor capsid protein L2 by host cyclophilin B and furin. Using HPV16 pseudovirus, we show that HD5 interacts directly with the virus and inhibits the furin-mediated cleavage of L2 at the cell surface during infection at a step downstream of the cyclophilin B-mediated unfolding of L2. Importantly, HD5 does not affect the enzymatic activity of furin directly. Thus, our data support a model in which HD5 prevents furin from accessing L2 by occluding the furin cleavage site via direct binding to the viral capsid.

IMPORTANCE
Our study elucidates a new antiviral action for α-defensins against nonenveloped viruses in which HD5 directly interferes with a critical host-mediated viral processing step, furin cleavage of L2, at the cell surface. Blocking this key event has deleterious effects on the intracellular steps of virus infection. Thus, in addition to informing the antiviral mechanisms of α-defensins, our studies highlight the critical role of furin cleavage in HPV entry. Innate immune control, mediated in part by α-defensins expressed in the genital mucosa, may influence susceptibility to HPV infections that lead to cervical cancer. Moreover, understanding the mechanism of these natural antivirals may inform the design of therapeutics to limit HPV infection.
RNase L Targets Distinct Sites in Influenza A Virus RNAs
Authors: Cooper Daphne A. , Banerjee Shuvojit , Chakrabarti Arindam , García-Sastre Adolfo , Hesselberth Jay R. , Silverman Robert H. , Barton David J.
Published: December 2014

Influenza A virus (IAV) infections are influenced by type 1 interferon-mediated antiviral defenses and by viral countermeasures to these defenses. When IAV NS1 protein is disabled, RNase L restricts virus replication; however, the RNAs targeted for cleavage by RNase L under these conditions have not been defined. In this study, we used deep-sequencing methods to identify RNase L cleavage sites within host and viral RNAs from IAV PR8ΔNS1-infected A549 cells. Short hairpin RNA knockdown of RNase L allowed us to distinguish between RNase L-dependent and RNase L-independent cleavage sites. RNase L-dependent cleavage sites were evident at discrete locations in IAV RNA segments (both positive and negative strands). Cleavage in PB2, PB1, and PA genomic RNAs suggests that viral RNPs are susceptible to cleavage by RNase L. Prominent amounts of cleavage mapped to specific regions within IAV RNAs, including some areas of increased synonymous-site conservation. Among cellular RNAs, RNase L-dependent cleavage was most frequent at precise locations in rRNAs. Our data show that RNase L targets specific sites in both host and viral RNAs to restrict influenza virus replication when NS1 protein is disabled.

IMPORTANCE
RNase L is a critical component of interferon-regulated and double-stranded-RNA-activated antiviral host responses. We sought to determine how RNase L exerts its antiviral activity during influenza virus infection. We enhanced the antiviral activity of RNase L by disabling a viral protein, NS1, that inhibits the activation of RNase L. Then, using deep-sequencing methods, we identified the host and viral RNAs targeted by RNase L. We found that RNase L cleaved viral RNAs and rRNAs at very precise locations. The direct cleavage of IAV RNAs by RNase L highlights an intimate battle between viral RNAs and an antiviral endonuclease.
Regulation of Multiple Stages of Hepadnavirus Replication by the Carboxyl-Terminal Domain of Viral Core Protein in trans
Authors: Liu Kuancheng , Ludgate Laurie , Yuan Zhenghong , Hu Jianming
Published: December 2014

Mutational analyses have indicated that the carboxyl-terminal domain (CTD) of hepadnavirus core protein and its state of phosphorylation are critical for multiple steps in viral replication. Also, CTD interacts with host proteins in a phosphorylation state-dependent manner. To ascertain the role of CTD in viral replication without perturbing its sequence and the role of CTD-host interactions, CTD of the human hepatitis B virus (HBV) or duck hepatitis B virus (DHBV) core protein, either the wild type (WT) or with alanine or glutamic acid/aspartic acid substitutions at the phosphorylation sites, was expressed in cells replicating DHBV with the WT core protein. A dramatic decrease in phosphorylation of the DHBV core protein (DHBc) was observed when the WT and most HBV core protein CTD (HCTD) variants were coexpressed in
trans
, which was accompanied by a profound reduction of viral core DNA and, in particular, the double-stranded DNA. One HCTD variant that failed to change DHBc phosphorylation also had no effect on DHBV core DNA. All WT and variant HCTDs and DHBc CTDs (DCTDs) decreased the DHBV covalently closed circular (CCC) DNA. Identification of CTD-host interactions indicated that CDK2 binding by CTD may mediate its inhibitory effect on DHBc phosphorylation and reverse transcription via competition with DHBc for the host kinase, whereas importin α binding by CTD may contribute to inhibition of CCC DNA production by competitively blocking the nuclear import of viral nucleocapsids. These results suggest the possibility of blocking multiple steps of viral replication, especially CCC DNA formation, via inhibition of CTD functions.

IMPORTANCE
Mutational analyses have suggested that the carboxyl-terminal domain (CTD) of hepadnavirus core protein is critical for viral replication. However, results from mutational analyses are open to alternative interpretations. Also, how CTD affects virus replication remains unclear. In this study, we took an alternative approach to mutagenesis by overexpressing CTD alone in cells replicating the virus with the wild-type core protein to determine the roles of CTD in viral replication. Our results revealed that CTD can inhibit multiple stages of viral replication, and its effects may be mediated at least in part through specific host interactions. They suggest that CTD, or its mimics, may have therapeutic potential. Furthermore, our experimental approach should be broadly applicable as a complement to mutagenesis for studying protein functions and interactions while at the same time providing a means to identify the relevant interacting factors.