bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotypic and Phenotypic Analysis of
Enterobacter sakazakii
Strains from an Outbreak Resulting in Fatalities in a Neonatal Intensive Care Unit in France
Authors: Caubilla-Barron J. , Hurrell E. , Townsend S. , Cheetham P. , Loc-Carrillo C. , Fayet O. , Prère M.-F. , Forsythe S. J. 
Published: October 2007

ABSTRACT

In 1994, an outbreak of
Enterobacter sakazakii
infections occurred in a neonatal intensive care unit in France from 5 May to 11 July. During the outbreak, 13 neonates were infected with
E. sakazakii
, resulting in 3 deaths. In addition, four symptomless neonates were colonized by
E. sakazakii
. The strains were subjected to 16S rRNA gene sequence analysis, genotyped using pulsed-field gel electrophoresis, and phenotyped for a range of enzyme activities.
E. sakazakii
was isolated from various anatomical sites, reconstituted formula, and an unopened can of powdered infant formula. A fourth neonate died from septic shock, attributed to
E. sakazakii
infection, during this period. However, 16S rRNA gene sequence analysis revealed that the organism was
Enterobacter cloacae
. There were three pulsotypes of
E. sakazakii
associated with infected neonates, and three neonates were infected by more than one genotype. One genotype matched isolates from unused prepared formula and unfinished formula. However, no pulsotypes matched the
E. sakazakii
strain recovered from an unopened can of powdered infant formula. One pulsotype was associated with the three fatal cases, and two of these isolates had extended-spectrum β-lactamase activity. It is possible that
E. sakazakii
strains differ in their pathogenicities, as shown by the range of symptoms associated with each pulsotype.
Isolation and Characterization of a Novel Helicobacter Species, “
Helicobacter macacae
,” from Rhesus Monkeys with and without Chronic Idiopathic Colitis
Authors: Fox James G. , Boutin Samuel R. , Handt Laurence K. , Taylor Nancy S. , Xu Shilu , Rickman Barry , Marini Robert P. , Dewhirst Floyd E. , Paster Bruce J. , Motzel Sherri , Klein Hilton J. 
Published: October 2007

ABSTRACT

Chronic idiopathic colitis is a common clinical entity in young captive rhesus monkeys. Eight isolates, cultured from five monkeys in colony 1 with endemic diarrhea and three from colony 2 without diarrhea, were grown under microaerobic conditions on selective agar and were classified by full 16S rRNA sequence, biochemical, and phenotypic analysis as a novel helicobacter, “
Helicobacter macacae
” (proposed name). All eight strains of
H. macacae
had 99.5% identical 16S rRNA sequences.
Comparison of Microsatellite Length Polymorphism and Multilocus Sequence Typing for DNA-Based Typing of
Candida albicans
Authors: Garcia-Hermoso Dea , Cabaret Odile , Lecellier Gael , Desnos-Ollivier Marie , Hoinard Damien , Raoux Dorothée , Costa Jean-Marc , Dromer Françoise , Bretagne Stéphane 
Published: October 2007

ABSTRACT

For genotyping
Candida albicans
isolates, two PCR-based methods have recently emerged: multilocus sequence typing (MLST), based on the sequence of selected genes, and microsatellite length polymorphism (MLP), based on the length of PCR products containing variable numbers of short DNA repeats. To compare the two methods in their abilities to differentiate and group
C. albicans
isolates, we selected 50 independent isolates collected at the National Reference Center for Mycoses and Antifungals. MLST typing was performed using sequencing of seven loci as described at
http://test1.mlst.net
. The MLP method consisted of a single multiplex PCR testing three different loci. Dendrograms were constructed by the unweighted pair group cluster method with Euclidean metric for both methods. The correlation between the distance matrices was performed with a Mantel test tested with 1,000 random permutations. The sensitivity and specificity of the MLP typing system were determined after allocating MLST groups for the greater number of isolates of each distinct MLP group. The discriminatory power index was >0.99, and the distances between the isolates were highly correlated with both systems. The Mantel coefficient and the Pearson product-moment correlation coefficient were 35,699 and 0.32, respectively (
P
≤ 1.2 × 10
−6
). Using MLP, the average specificity and sensitivity of clustering compared to MLST were 83% and 73%, respectively, when the singletons were excluded. The two methods are similarly discriminatory and can be interchangeable depending on the objectives. MLP is less expensive and faster than MLST. However, MLST is currently more accurate and additional standardization is needed for MLP.
Canine Parvovirus Types 2c and 2b Circulating in North American Dogs in 2006 and 2007
Authors: Kapil Sanjay , Cooper Emily , Lamm Cathy , Murray Brandy , Rezabek Grant , Johnston Larry , Campbell Gregory , Johnson Bill 
Published: October 2007

ABSTRACT

Parvovirus is the most common viral cause of diarrhea in young puppies. Based on the analysis of a partial VP2 sequence of 54 samples, canine parvovirus type 2c (CPV-2c) (
n
= 26), CPV-2b (
n
= 25), and CPV-2 (
n
= 3) were detected in the United States. The American CPV-2b isolates have unique codons (494 and 572) in VP2.
Population-Based Molecular Epidemiological Study of Tuberculosis in Malatya, Turkey
Authors: Durmaz Riza , Zozio Thierry , Gunal Selami , Allix Caroline , Fauville-Dufaux Maryse , Rastogi Nalin 
Published: October 2007

ABSTRACTThis investigation describes drug resistance patterns and genotyping data on a total of 145Mycobacterium tuberculosisstrains isolated between 2000 and 2004 in Malatya, Turkey. Drug susceptibility results indicated a total of 20% resistant and 4.8% of multidrug-resistant isolates. Spoligotyping resulted in 25 unique patterns and 120 strains in 19 clusters (2 to 33 strains per cluster). When the results were compared to an international spoligotyping database, 19 of 25 unique patterns matched existing shared spoligotype international types (SITs). This led to the description of 38 SITs with 139 strains and 6 orphan patterns (not previously reported). Five of the SITs (SIT759, SIT1936, SIT1937, SIT1938, and SIT2285) were newly created. The most prevalent spoligotype was SIT41 (LAM7-TUR) with 33 (23.9%) isolates. The repartition of strains according to majorM. tuberculosisclades (in decreasing order) was as follows: ill-defined T clade (45.7%) > Latin American and Mediterranean (LAM; 29%) > Haarlem (15.9%). Strains belonging to Central Asian (CAS), East-African Indian (EAI), Beijing, and Africanum clades were absent in this setting. IS6110-restriction fragment length polymorphism (RFLP) resulted in 19 clusters (52 strains), with a final clustering rate of 35.9% and a recent transmission rate of 22.8%. Typing based on mycobacterial interspersed repetitive units (MIRUs) permitted us to identify 65 patterns (23 orphan patterns and 42 patterns that matched existing MIRU international types in an updated database). The combination of the three typing methods allowed us to calculate a final clustering rate of 22% and a significantly lower transmission rate of 13.1%. The discrimination achieved by IS6110-RFLP/MIRUs was not significantly improved by adding spoligotyping results (1.4%). We conclude that our patient population is infected by diverseM. tuberculosispopulations; however, the majority of the ongoing transmission is due to “evolutionary recent” tuberculosis lineages belonging to principal genetic group 2 (PGG2; Haarlem and LAM) and PGG3 (ill-defined T clade), and most of it is attributable to the LAM7-TUR sublineage with an enhanced phylogeographical specificity for Turkey. An absence of lineages belonging to PGG1 clones (EAI, CAS, and Beijing, essentially found in Central, South, and Southeast Asia), is noteworthy.
Norovirus Infections in Symptomatic and Asymptomatic Food Handlers in Japan
Authors: Ozawa Kazuhiro , Oka Tomoichiro , Takeda Naokazu , Hansman Grant S. 
Published: October 2007

ABSTRACT

Noroviruses are the leading cause of outbreaks of gastroenteritis in the world. At present, norovirus genogroup II, genotype 4 (GII/4), strains are the most prevalent in many countries. In this study we investigated 55 outbreaks and 35 sporadic cases of norovirus-associated gastroenteritis in food handlers in food-catering settings between 10 November 2005 and 9 December 2006 in Japan. Stool specimens were collected from both symptomatic and asymptomatic individuals and were examined for norovirus by real-time reverse transcription-PCR; the results were then confirmed by sequence analysis. Norovirus was detected in 449 of 2,376 (19%) specimens. Four genogroup I (GI) genotypes and 12 GII genotypes, including one new GII genotype, were detected. The GII/4 sequences were predominant, accounting for 19 of 55 (35%) outbreaks and 16 of 35 (46%) sporadic cases. Our results also showed that a large number of asymptomatic food handlers were infected with norovirus GII/4 strains. Norovirus GII had a slightly higher mean viral load (1 log unit higher) than norovirus GI, i.e., 3.81 × 10
8
versus 2.79 × 10
7
copies/g of stool. Among norovirus GI strains, GI/4 had the highest mean viral load, whereas among GII strains, GII/4 had the highest mean viral load (2.02 × 10
8
and 7.96 × 10
9
copies/g of stool, respectively). Importantly, we found that asymptomatic individuals had mean viral loads similar to those of symptomatic individuals, which may account for the increased number of infections and the predominance of an asymptomatic transmission route.
Cavitary Disease and Quantitative Sputum Bacillary Load in Cases of Pulmonary Tuberculosis
Authors: Palaci Moises , Dietze Reynaldo , Hadad David Jamil , Ribeiro Fabiola Karla Corrêa , Peres Renata Lyrio , Vinhas Solange Alves , Maciel Ethel Leonor Noia , do Valle Dettoni Valdério , Horter Libby , Boom W. Henry , Johnson John L. , Eisenach Kathleen D. 
Published: October 2007

ABSTRACT
We examined sputum bacterial loads in adults with newly diagnosed tuberculosis using quantitative culture and time-until-positive (DTP) culture in BACTEC 460. Patients with cavitary disease had higher CFU levels than those without cavities and shorter DTPs. Within radiographic strata of moderately and far advanced tuberculosis, higher CFU counts were associated with cavitary disease.
The Zinc Finger Antiviral Protein Acts Synergistically with an Interferon-Induced Factor for Maximal Activity against Alphaviruses
Authors: MacDonald Margaret R. , Machlin Erica S. , Albin Owen R. , Levy David E. 
Published: October 2007

ABSTRACTType I interferons (IFNs) signal through specific receptors to mediate expression of genes, which together confer a cellular antiviral state. Overexpression of the zinc finger antiviral protein (ZAP) imparts a cellular antiviral state againstRetroviridae,Togaviridae, andFiloviridaevirus family members. Since ZAP expression is induced by IFN, we utilized Sindbis virus (SINV) to investigate the role of other IFN-induced factors in ZAP's inhibitory potential. Overexpressed ZAP did not inhibit virion production or SINV-induced cell death in BHK cells deficient in IFN production (and thus IFN signaling), suggesting a role for an IFN-induced factor in ZAP's activity. IFN pretreatment in the presence of ZAP resulted in greater inhibition than IFN alone. Using mouse embryo fibroblast (MEF) cells deficient in Stat1, we showed that signaling through the IFN receptor is necessary for IFN′s enhancement of ZAP activity. Unlike in BHK cells, however, overexpressed ZAP exhibited antiviral activity in the absence of IFN. In wild-type MEFs with an intact Stat1 gene, IFN pretreatment synergized with ZAP to generate a potent antiviral response. Despite failing to inhibit SINV virion production and virus-induced cell death in BHK cells, ZAP inhibited translation of the incoming viral RNA. IFN pretreatment synergized with ZAP to further block protein expression from the incoming viral genome. We further show that silencing of IFN-induced ZAP reduces IFN efficacy. Our findings demonstrate that ZAP can synergize with another IFN-induced factor(s) for maximal antiviral activity and that ZAP's intrinsic antiviral activity on virion production and cell survival can have cell-type-specific outcomes.
Identification of Novel Antipoxviral Agents: Mitoxantrone Inhibits Vaccinia Virus Replication by Blocking Virion Assembly
Authors: Deng Liang , Dai Peihong , Ciro Anthony , Smee Donald F. , Djaballah Hakim , Shuman Stewart 
Published: October 2007

ABSTRACT
The bioterror threat of a smallpox outbreak in an unvaccinated population has mobilized efforts to develop new antipoxviral agents. By screening a library of known drugs, we identified 13 compounds that inhibited vaccinia virus replication at noncytotoxic doses. The anticancer drug mitoxantrone is unique among the inhibitors identified in that it has no apparent impact on viral gene expression. Rather, it blocks processing of viral structural proteins and assembly of mature progeny virions. The isolation of mitoxantrone-resistant vaccinia strains underscores that a viral protein is the likely target of the drug. Whole-genome sequencing of mitoxantrone-resistant viruses pinpointed missense mutations in the N-terminal domain of vaccinia DNA ligase. Despite its favorable activity in cell culture, mitoxantrone administered intraperitoneally at the maximum tolerated dose failed to protect mice against a lethal intranasal infection with vaccinia virus.
Nef-Mediated Enhancement of Virion Infectivity and Stimulation of Viral Replication Are Fundamental Properties of Primate Lentiviruses
Authors: Münch Jan , Rajan Devi , Schindler Michael , Specht Anke , Rücker Elke , Novembre Francis J. , Nerrienet Eric , Müller-Trutwin Michaela C. , Peeters Martine , Hahn Beatrice H. , Kirchhoff Frank 
Published: October 2007

ABSTRACTNef is a multifunctional accessory protein of primate lentiviruses. Recently, it has been shown that the ability of Nef to downmodulate CD4, CD28, and class I major histocompatibility complex is highly conserved between most or all primate lentiviruses, whereas Nef-mediated downregulation of T-cell receptor-CD3 was lost in the lineage that gave rise to human immunodeficiency virus type 1 (HIV-1). Whether or not other Nef activities are preserved between different groups of primate lentiviruses remained to be determined. Here, we show thatnefgenes from a large variety of HIVs and simian immunodeficiency viruses (SIVs) enhance virion infectivity and stimulate viral replication in human cells and/or in ex vivo infected human lymphoid tissue (HLT). Notably,nefalleles from unpassaged SIVcpz and SIVsmm enhanced viral infectivity, replication, and cytopathicity in cell culture and in ex vivo infected HLT as efficiently as those from HIV-1 and HIV-2, their human counterparts. Furthermore,nefgenes from several highly divergent SIVs that have not been found in humans were also highly active in human cells and/or tissues. Thus, most primate lentiviral Nefs enhance virion infectivity and stimulate viral replication. Moreover, our data show that SIVcpz and SIVsmm Nefs do not require adaptive changes to perform these functions in human cells or tissues and support the idea thatnefalleles from other primate lentiviruses would also be capable of promoting efficient virus spread in humans.
A Protective and Broadly Cross-Neutralizing Epitope of Human Papillomavirus L2
Authors: Gambhira Ratish , Karanam Balasubramanyam , Jagu Subhashini , Roberts Jeffrey N. , Buck Christopher B. , Bossis Ioannis , Alphs Hannah , Culp Timothy , Christensen Neil D. , Roden Richard B. S. 
Published: October 2007

ABSTRACT

We generated a monoclonal antibody, RG-1, that binds to highly conserved L2 residues 17 to 36 and neutralizes human papillomavirus 16 (HPV16) and HPV18. Passive immunotherapy with RG-1 was protective in mice. Antiserum to the HPV16 L2 peptide comprising residues 17 to 36 (peptide 17-36) neutralized pseudoviruses HPV5, HPV6, HPV16, HPV 18, HPV31, HPV 45, HPV 52, HPV 58, bovine papillomavirus 1, and HPV11 native virions. Depletion of HPV16 L2 peptide 17-36-reactive antibodies from cross-neutralizing rabbit and human L2-specific sera abolished cross-neutralization and drastically reduced neutralization of the cognate type. This cross-neutralization of diverse HPVs associated with cervical cancer, genital warts, and
epidermodysplasia verruciformis
suggests the possibility of a broadly protective, peptide-based vaccine.
Proteolysis of the Ebola Virus Glycoproteins Enhances Virus Binding and Infectivity
Authors: Kaletsky Rachel L. , Simmons Graham , Bates Paul 
Published: October 2007

ABSTRACT
Cellular cathepsins are required for Ebola virus infection and are believed to proteolytically process the Ebola virus glycoprotein (GP) during entry. However, the significance of cathepsin cleavage during infection remains unclear. Here we demonstrate a role for cathepsin L (CatL) cleavage of Ebola virus GP in the generation of a stable 18-kDa GP1 viral intermediate that exhibits increased binding to and infectivity for susceptible cell targets. Cell binding to a lymphocyte line was increased when CatL-proteolysed pseudovirions were used, but lymphocytes remained resistant to Ebola virus GP-mediated infection. Genetic removal of the highly glycosylated mucin domain in Ebola virus GP resulted in cell binding similar to that observed with CatL-treated full-length GP, and no overall enhancement of binding or infectivity was observed when mucin-deleted virions were treated with CatL. These results suggest that cathepsin cleavage of Ebola virus GP facilitates an interaction with a cellular receptor(s) and that removal of the mucin domain may facilitate receptor binding. The influence of CatL in Ebola virus GP receptor binding should be useful in future studies characterizing the mechanism of Ebola virus entry.
Double-Labeled Rabies Virus: Live Tracking of Enveloped Virus Transport
Authors: Klingen Yvonne , Conzelmann Karl-Klaus , Finke Stefan 
Published: October 2007

ABSTRACT

Here we describe a strategy to fluorescently label the envelope of rabies virus (RV), of the
Rhabdoviridae
family, in order to track the transport of single enveloped viruses in living cells. Red fluorescent proteins (tm-RFP) were engineered to comprise the N-terminal signal sequence and C-terminal transmembrane spanning and cytoplasmic domain sequences of the RV glycoprotein (G). Two variants of tm-RFP were transported to and anchored in the cell surface membrane, independent of glycosylation. As shown by confocal microscopy, tm-RFP colocalized at the cell surface with the RV matrix and G protein and was incorporated into G gene-deficient virus particles. Recombinant RV expressing the membrane-anchored tm-RFP in addition to G yielded infectious viruses with mosaic envelopes containing both tm-RFP and G. Viable double-labeled virus particles comprising a red fluorescent envelope and a green fluorescent ribonucleoprotein were generated by expressing in addition an enhanced green fluorescent protein-phosphoprotein fusion construct (S. Finke, K. Brzozka, and K. K. Conzelmann, J. Virol. 78:12333-12343, 2004). Individual enveloped virus particles were observed under live cell conditions as extracellular particles and inside endosomal vesicles. Importantly, double-labeled RVs were transported in the retrograde direction over long distances in neurites of in vitro-differentiated NS20Y neuroblastoma cells. This indicates that the typical retrograde axonal transport of RV to the central nervous system involves neuronal transport vesicles in which complete enveloped RV particles are carried as a cargo.
Preserved Central Memory and Activated Effector Memory CD4+T-Cell Subsets in Human Immunodeficiency Virus Controllers: an ANRS EP36 Study
Authors: Potter Simon J. , Lacabaratz Christine , Lambotte Olivier , Perez-Patrigeon Santiago , Vingert Benoît , Sinet Martine , Colle Jean-Hervé , Urrutia Alejandra , Scott-Algara Daniel , Boufassa Faroudy , Delfraissy Jean-François , Thèze Jacques , Venet Alain , Chakrabarti Lisa A. 
Published: October 2007

ABSTRACTHuman immunodeficiency virus (HIV) controllers are rare individuals who spontaneously control HIV type 1 replication for 10 years or more in the absence of antiretroviral treatment. In the present study, HIV controllers (n= 11) maintained potent HIV-specific CD4 responses in spite of very low antigenic loads. Their CD4+central memory T (TCM) cells were characterized by near-normal numbers and preserved interleukin-2 (IL-2) secretion in response to HIV antigens and uniformly high expression of the survival receptor IL-7 receptor α (IL-7Rα). Controllers expressed CCR7 at higher levels than uninfected controls, suggesting differences in TCM-cell homing patterns. CD4+effector memory T (TEM)-cell responses were polyfunctional in HIV controllers, while IL-2 secretion was lost in viremic patients. Cytokine production was three times higher in controllers than in treated patients with undetectable viral loads, suggesting an intrinsically more efficient response in the former group. The total CD4+TEM-cell pool underwent immune activation in controllers, as indicated by increased HLA-DR expression, decreased IL-7Rα expression, a bias towards gamma interferon production upon polyclonal stimulation, and increased macrophage inflammatory protein 1β secretion associated with chronic CCR5 down-regulation. Thus, HIV controllers showed a preserved CD4+TCM-cell compartment and signs of potent functional activation in the CD4+TEM-cell compartment. While controllers did not show the generalized immune activation pattern associated with disease progression, they had signs of immune activation restricted to the effector compartment. These findings suggest the induction of an efficient, nondetrimental type of immune activation in patients who spontaneously control HIV.
Herpes Simplex Virus Type 2 Glycoprotein G Is Targeted by the Sulfated Oligo- and Polysaccharide Inhibitors of Virus Attachment to Cells
Authors: Adamiak Beata , Ekblad Maria , Bergström Tomas , Ferro Vito , Trybala Edward 
Published: October 2007

ABSTRACT
Variants of herpes simplex virus type 2 (HSV-2) generated by virus passage in GMK-AH1 cells in the presence of the sulfated oligosaccharide PI-88 were analyzed. Many of these variants were substantially resistant to PI-88 in their initial infection of cells and/or their cell-to-cell spread. The major alteration detected in all variants resistant to PI-88 in the initial infection of cells was a frameshift mutation(s) in the glycoprotein G (gG) gene that resulted in the lack of protein expression. Molecular transfer of the altered gG gene into the wild-type background confirmed that the gG-deficient recombinants were resistant to PI-88. In addition to PI-88, all gG-deficient variants of HSV-2 were resistant to the sulfated polysaccharide heparin. The gG-deficient virions were capable of attaching to cells, and this activity was relatively resistant to PI-88. In addition to having a drug-resistant phenotype, the gG-deficient variants were inefficiently released from infected cells. Purified gG bound to heparin and showed the cell-binding activity which was inhibited by PI-88. Many PI-88 variants produced syncytia in cultured cells and contained alterations in gB, including the syncytium-inducing L792P amino acid substitution. Although this phenotype can enhance the lateral spread of HSV in cells, it conferred no virus resistance to PI-88. Some PI-88 variants also contained occasional alterations in gC, gD, gE, gK, and UL24. In conclusion, we found that glycoprotein gG, a mucin-like component of the HSV-2 envelope, was targeted by sulfated oligo- and polysaccharides. This is a novel finding that suggests the involvement of HSV-2 gG in interactions with sulfated polysaccharides, including cell surface glycosaminoglycans.