bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Epidemiology of the Pertussis Epidemic in Washington State in 2012
Authors: Bowden Katherine E. , Williams Margaret M. , Cassiday Pamela K. , Milton Andrea , Pawloski Lucia , Harrison Marsenia , Martin Stacey W. , Meyer Sarah , Qin Xuan , DeBolt Chas , Tasslimi Azadeh , Syed Nusrat , Sorrell Ronald , Tran Mike , Hiatt Brian , Tondella Maria Lucia 
Published: July 2014

ABSTRACT

Although pertussis disease is vaccine preventable, Washington State experienced a substantial rise in pertussis incidence beginning in 2011. By June 2012, the reported cases reached 2,520 (37.5 cases per 100,000 residents), a 1,300% increase compared with the same period in 2011. We assessed the molecular epidemiology of this statewide epidemic using 240 isolates collected from case patients reported from 19 of 39 Washington counties during 2012 to 2013. The typing methods included pulsed-field gel electrophoresis (PFGE), multilocus variable number tandem repeat analysis (MLVA), multilocus sequence typing (MLST), and pertactin gene (
prn
) mutational analysis. Using the scheme PFGE-MLVA-MLST-
prn
mutations-Prn deficiency, the 240 isolates comprised 65 distinct typing profiles. Thirty-one PFGE types were found, with the most common types, CDC013 (
n
= 51), CDC237 (
n
= 44), and CDC002 (
n
= 42), accounting for 57% of them. Eleven MLVA types were observed, mainly comprising type 27 (
n
= 183, 76%). Seven MLST types were identified, with the majority of the isolates typing as
prn2-ptxP3-ptxA1-fim3-1
(
n
= 157, 65%). Four different
prn
mutations accounted for the 76% of isolates exhibiting pertactin deficiency. PFGE provided the highest discriminatory power (
D
= 0.87) and was found to be a more powerful typing method than MLVA and MLST combined (
D
= 0.67). This study provides evidence for the continued predominance of MLVA 27 and
prn2-ptxP3-ptxA1
alleles, along with the reemergence of the
fim3-1
allele. Our results indicate that the
Bordetella pertussis
population causing this epidemic was diverse, with a few molecular types predominating. The PFGE, MLVA, and MLST profiles were consistent with the predominate types circulating in the United States and other countries. For
prn
, several mutations were present in multiple molecular types.
The Bristol Stool Scale and Its Relationship to Clostridium difficile Infection
Authors: Caroff Daniel A. , Edelstein Paul H. , Hamilton Keith , Pegues David A. 
Published: July 2014

ABSTRACT

The Bristol stool form scale classifies the relative density of stool samples. In a prospective cohort study, we investigated the associations between stool density,
C. difficile
assay positivity, hospital-onset
C. difficile
infection, complications, and severity of
C. difficile
. We describe associations between the Bristol score, assay positivity, and clinical
C. difficile
infection.
Genetic and Molecular Predictors of High Vancomycin MIC in Staphylococcus aureus Bacteremia Isolates
Authors: Holmes Natasha E. , Turnidge John D. , Munckhof Wendy J. , Robinson J. Owen , Korman Tony M. , O'Sullivan Matthew V. N. , Anderson Tara L. , Roberts Sally A. , Warren Sanchia J. C. , Coombs Geoffrey W. , Tan Hui-Leen , Gao Wei , Johnson Paul D. R. , Howden Benjamin P. 
Published: July 2014

ABSTRACT

An elevated vancomycin MIC is associated with poor outcomes in
Staphylococcus aureus
bacteremia (SAB) and is reported in patients with methicillin-susceptible
S. aureus
(MSSA) bacteremia in the absence of vancomycin treatment. Here, using DNA microarray and phenotype analysis, we investigated the genetic predictors and accessory gene regulator (
agr
) function and their relationship with elevated vancomycin MIC using blood culture isolates from a multicenter binational cohort of patients with SAB. Specific clonal complexes were associated with elevated (clonal complex 8 [CC8] [
P
< 0.001]) or low (CC22 [
P
< 0.001], CC88 [
P
< 0.001], and CC188 [
P
= 0.002]) vancomycin MIC.
agr
dysfunction (
P
= 0.014) or
agr
genotype II (
P
= 0.043) were also associated with an elevated vancomycin MIC. Specific resistance and virulence genes were also linked to an elevated vancomycin MIC, including
blaZ
(
P
= 0.002),
sea
(
P
< 0.001),
clfA
(
P
< 0.001),
splA
(
P
= 0.001), and the arginine catabolic mobile element (ACME) locus (
P
= 0.02). These data suggest that inherent organism characteristics may explain the link between elevated vancomycin MICs and poor outcomes in patients with SAB, regardless of the antibiotic treatment received. A consideration of clonal specificity should be included in future research when attempting to ascertain treatment effects or clinical outcomes.
Fast and Accurate Identification of Dermatophytes by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: Validation in the Clinical Laboratory
Authors: Packeu A. , De Bel A. , l'Ollivier C. , Ranque S. , Detandt M. , Hendrickx M. 
Published: July 2014

ABSTRACT
The performance of a matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) workflow using an extensive reference database for dermatophyte identification was evaluated on 176 clinical strains. Using a direct-deposit procedure after 3 incubation days yielded 40% correct identification. Both increasing incubation time and using an extraction procedure resulted in 100% correct identification.
Up to Four Distinct Polypeptides Are Produced from the γ34.5 Open Reading Frame of Herpes Simplex Virus 2
Authors: Korom Maria , Davis Katie L. , Morrison Lynda A. 
Published: July 2014

ABSTRACT
The herpes simplex virus 1 (HSV-1) ICP34.5 protein strongly influences neurovirulence and regulates several cellular antiviral responses. Despite the clinical importance of HSV-2, relatively little is known about its ICP34.5 ortholog. We found that HSV-2 produces up to four distinct forms of ICP34.5 in infected cells: a full-length protein, one shorter form sharing the N terminus, and two shorter forms sharing the C terminus. These forms appeared with similar kinetics and accumulated in cells over much of the replication cycle. We confirmed that the N-terminal form is translated from the primary unspliced transcript to a stop codon within the intron unique to HSV-2 γ34.5. We found that the N-terminal form was produced in a variety of cell types and by 9 of 10 clinical isolates. ICP27 influenced but was not required for expression of the N-terminal form. Western blotting and reverse transcription-PCR indicated the C-terminal forms did not contain the N terminus and were not products of alternative splicing or internal transcript initiation. Expression plasmids encoding methionine at amino acids 56 and 70 generated products that comigrated in SDS-PAGE with the C1 and C2 forms, respectively, and mutation of these sites abolished C1 and C2. Using a recombinant HSV-2 encoding hemagglutinin (HA)-tagged ICP34.5, we demonstrated that the C-terminal forms were also produced during infection of many human and mouse cell types but were not detectable in mouse primary neurons. The protein diversity generated from the HSV-2 γ34.5 open reading frame implies additional layers of cellular regulation through potential independent activities associated with the various forms of ICP34.5.

IMPORTANCE
The herpes simplex virus 1 (HSV-1) protein ICP34.5, encoded by the γ34.5 gene, interferes with several host defense mechanisms by binding cellular proteins that would otherwise stimulate the cell's autophagic, translational-arrest, and type I interferon responses to virus infection. ICP34.5 also plays a crucial role in determining the severity of nervous system infections with HSV-1 and HSV-2. The HSV-2 γ34.5 gene contains an intron not present in HSV-1 γ34.5. A shorter N-terminal form of HSV-2 ICP34.5 can be translated from the unspliced γ34.5 mRNA. Here, we show that two additional forms consisting of the C-terminal portion of ICP34.5 are generated in infected cells. Production of these N- and C-terminal forms is highly conserved among HSV-2 strains, including many clinical isolates, and they are broadly expressed in several cell types, but not mouse primary neurons. Multiple ICP34.5 polypeptides add additional complexity to potential functional interactions influencing HSV-2 neurovirulence.
High-Risk Human Papillomavirus E6 Protein Promotes Reprogramming of Fanconi Anemia Patient Cells through Repression of p53 but Does Not Allow for Sustained Growth of Induced Pluripotent Stem Cells
Authors: Chlon Timothy M. , Hoskins Elizabeth E. , Mayhew Christopher N. , Wikenheiser-Brokamp Kathryn A. , Davies Stella M. , Mehta Parinda , Myers Kasiani C. , Wells James M. , Wells Susanne I. 
Published: July 2014

ABSTRACT
DNA repair plays a crucial role in embryonic and somatic stem cell biology and cell reprogramming. The Fanconi anemia (FA) pathway, which promotes error-free repair of DNA double-strand breaks, is required for somatic cell reprogramming to induced pluripotent stem cells (iPSC). Thus, cells from Fanconi anemia patients, which lack this critical pathway, fail to be reprogrammed to iPSC under standard conditions unless the defective FA gene is complemented. In this study, we utilized the oncogenes of high-risk human papillomavirus 16 (HPV16) to overcome the resistance of FA patient cells to reprogramming. We found that E6, but not E7, recovers FA iPSC colony formation and, furthermore, that p53 inhibition is necessary and sufficient for this activity. The iPSC colonies resulting from each of these approaches stained positive for alkaline phosphatase, NANOG, and Tra-1-60, indicating that they were fully reprogrammed into pluripotent cells. However, FA iPSC were incapable of outgrowth into stable iPSC lines regardless of p53 suppression, whereas their FA-complemented counterparts grew efficiently. Thus, we conclude that the FA pathway is required for the growth of iPSC beyond reprogramming and that p53-independent mechanisms are involved.

IMPORTANCE
A novel approach is described whereby HPV oncogenes are used as tools to uncover DNA repair-related molecular mechanisms affecting somatic cell reprogramming. The findings indicate that p53-dependent mechanisms block FA cells from reprogramming but also uncover a previously unrecognized defect in FA iPSC proliferation independent of p53.
Interferon Regulatory Factor 5-Dependent Immune Responses in the Draining Lymph Node Protect against West Nile Virus Infection
Authors: Thackray Larissa B. , Shrestha Bimmi , Richner Justin M. , Miner Jonathan J. , Pinto Amelia K. , Lazear Helen M. , Gale Michael , Diamond Michael S. 
Published: July 2014

ABSTRACTUpon activation of Toll-like and RIG-I-like receptor signaling pathways, the transcription factor IRF5 translocates to the nucleus and induces antiviral immune programs. The recent discovery of a homozygous mutation in the immunoregulatory gene guanine exchange factor dedicator of cytokinesis 2 (Dock2mu/mu) in severalIrf5−/−mouse colonies has complicated interpretation of immune functions previously ascribed to IRF5. To define the antiviral functions of IRF5in vivo, we infected backcrossedIrf5−/−×Dock2wt/wtmice (here calledIrf5−/−mice) and independently generated CMV-CreIrf5fl/flmice with West Nile virus (WNV), a pathogenic neurotropic flavivirus. Compared to congenic wild-type animals,Irf5−/−and CMV-CreIrf5fl/flmice were more vulnerable to WNV infection, and this phenotype was associated with increased infection in peripheral organs, which resulted in higher virus titers in the central nervous system. The loss of IRF5, however, was associated with only small differences in the type I interferon response systemically and in the draining lymph node during WNV infection. Instead, lower levels of several other proinflammatory cytokines and chemokines, as well as fewer and less activated immune cells, were detected in the draining lymph node 2 days after WNV infection. WNV-specific antibody responses inIrf5−/−mice also were blunted in the context of live or inactivated virus infection and this was associated with fewer antigen-specific memory B cells and long-lived plasma cells. Our results withIrf5−/−mice establish a key role for IRF5 in shaping the early innate immune response in the draining lymph node, which impacts the spread of virus infection, optimal B cell immunity, and disease pathogenesis.IMPORTANCEAlthough the roles of IRF3 and IRF7 in orchestrating innate and adaptive immunity after viral infection are established, the function of the related transcription factor IRF5 remains less certain. Prior studies inIrf5−/−mice reported conflicting results as to the contribution of IRF5 in regulating type I interferon and adaptive immune responses. The lack of clarity may stem from a recently discovered homozygous loss-of-function mutation of the immunoregulatory geneDock2in several colonies ofIrf5−/−mice. Here, using a mouse model with a deficiency in IRF5 and wild-type Dock2 alleles, we investigated how IRF5 modulates West Nile virus (WNV) pathogenesis and host immune responses. Ourin vivostudies indicate that IRF5 has a key role in shaping the early proinflammatory cytokine response in the draining lymph node, which impacts immunity and control of WNV infection.
In Vivo
Reactivation of Latent Herpes Simplex Virus 1 in Mice Can Occur in the Brain before Occurring in the Trigeminal Ganglion
Authors: Yao Hui-Wen , Ling Pin , Tung Yuk-Ying , Hsu Sheng-Min , Chen Shun-Hua 
Published: July 2014

ABSTRACT

Herpes simplex virus 1 (HSV-1) establishes latency in neurons of the brains and sensory ganglia of humans and experimentally infected mice. The latent virus can reactivate to cause recurrent infection. Both primary and recurrent infections can induce diseases, such as encephalitis. In humans, the majority of encephalitis cases occur as a recurrent infection. However, in the past, numerous mouse studies documented that viral reactivation occurs efficiently in the ganglion, but extremely rarely in the brain, when assessed
ex vivo
by cultivating minced tissue explants. Here, we compare the brains and the trigeminal ganglia of mice latently infected with HSV-1 (strain 294.1 or McKrae) for levels of viral genomes and
in vivo
reactivation. The numbers of copies of 294.1 and McKrae genomes in the brain stem were significantly greater than those in the trigeminal ganglion. Most importantly, 294.1 and McKrae reactivation was detected in the brain stems earlier than in the trigeminal ganglia of mice treated with hyperthermia to reactivate latent virus
in vivo
. In addition, the brain stem yielded reactivated virus at a high frequency compared with the trigeminal ganglion, especially in mice latently infected with 294.1 after hyperthermia treatment. These results provide evidence that recurrent brain infection can be induced by the reactivation of latent virus in the brain
in situ
.

IMPORTANCE
Herpes simplex virus 1 (HSV-1) establishes latency in neurons of the brains and sensory ganglia of humans and experimentally infected mice. The latent virus can reactivate to cause recurrent infection. In the past, studies of viral reactivation focused on the ganglion, because efficient viral reactivation was detected in the ganglion but not in the brain when assessed
ex vivo
by cultivating mouse tissue explants. In this study, we report that the brain contains more viral genomes than the trigeminal ganglion in latently infected mice. Notably, the brain yields reactivated virus early and efficiently compared with the trigeminal ganglion after mice are stimulated to reactivate latent virus. Our findings raise the potential importance of HSV-1 latent infection and reactivation in the brain.
Shielding of a Lipooligosaccharide IgM Epitope Allows Evasion of Neutrophil-Mediated Killing of an Invasive Strain of Nontypeable Haemophilus influenzae
Authors: Langereis Jeroen D. , Weiser Jeffrey N. 
Published: July 2014

ABSTRACT

Nontypeable
Haemophilus influenzae
is a frequent cause of noninvasive mucosal inflammatory diseases but may also cause invasive diseases, such as sepsis and meningitis, especially in children and the elderly. Infection by nontypeable
Haemophilus influenzae
is characterized by recruitment of neutrophilic granulocytes. Despite the presence of a large number of neutrophils, infections with nontypeable
Haemophilus influenzae
are often not cleared effectively by the antimicrobial activity of these immune cells. Herein, we examined how nontypeable
Haemophilus influenzae
evades neutrophil-mediated killing. Transposon sequencing (Tn-seq) was used on an isolate resistant to neutrophil-mediated killing to identify genes required for its survival in the presence of human neutrophils and serum, which provided a source of complement and antibodies. Results show that nontypeable
Haemophilus influenzae
prevents complement-dependent neutrophil-mediated killing by expression of surface galactose-containing oligosaccharide structures. These outer-core structures block recognition of an inner-core lipooligosaccharide epitope containing glucose attached to heptose HepIII-β1,2-Glc by replacement with galactose attached to HepIII or through shielding HepIII-β1,2-Glc by phase-variable attachment of oligosaccharide chain extensions. When the HepIII-β1,2-Glc-containing epitope is expressed and exposed, nontypeable
Haemophilus influenzae
is opsonized by naturally acquired IgM generally present in human serum and subsequently phagocytosed and killed by human neutrophils. Clinical nontypeable
Haemophilus influenzae
isolates containing galactose attached to HepIII that are not recognized by this IgM are more often found to cause invasive infections.

IMPORTANCE
Neutrophils are white blood cells that specialize in killing pathogens and are recruited to sites of inflammation. However, despite the presence of large numbers of neutrophils in the middle ear cavity and lungs of patients with otitis media or chronic obstructive pulmonary disease, respectively, the bacterium nontypeable
Haemophilus influenzae
is often not effectively cleared from these locations by these immune cells. In order to understand how nontypeable
Haemophilus influenzae
is able to cause inflammatory diseases in the presence of neutrophils, we determined the mechanism that underlies resistance to neutrophil-mediated killing. We have shown that nontypeable
Haemophilus influenzae
prevents binding of antibodies of the IgM subtype through changes in their surface lipooligosaccharide structure, thereby preventing complement activation and clearance by human neutrophils.
Parallel Evolution of Streptococcus pneumoniae and Streptococcus mitis to Pathogenic and Mutualistic Lifestyles
Authors: Kilian Mogens , Riley David R. , Jensen Anders , Brüggemann Holger , Tettelin Hervé 
Published: July 2014

ABSTRACT

The bacterium
Streptococcus pneumoniae
is one of the leading causes of fatal infections affecting humans. Intriguingly, phylogenetic analysis shows that the species constitutes one evolutionary lineage in a cluster of the otherwise commensal
Streptococcus mitis
strains, with which humans live in harmony. In a comparative analysis of 35 genomes, including phylogenetic analyses of all predicted genes, we have shown that the pathogenic pneumococcus has evolved into a master of genomic flexibility while lineages that evolved into the nonpathogenic
S. mitis
secured harmonious coexistence with their host by stabilizing an approximately 15%-reduced genome devoid of many virulence genes. Our data further provide evidence that interspecies gene transfer between
S. pneumoniae
and
S. mitis
occurs in a unidirectional manner, i.e., from
S. mitis
to
S. pneumoniae
. Import of genes from
S. mitis
and other mitis, anginosus, and salivarius group streptococci ensured allelic replacements and antigenic diversification and has been driving the evolution of the remarkable structural diversity of capsular polysaccharides of
S. pneumoniae
. Our study explains how the unique structural diversity of the pneumococcal capsule emerged and conceivably will continue to increase and reveals a striking example of the fragile border between the commensal and pathogenic lifestyles. While genomic plasticity enabling quick adaptation to environmental stress is a necessity for the pathogenic streptococci, the commensal lifestyle benefits from stability.

IMPORTANCE
One of the leading causes of fatal infections affecting humans,
Streptococcus pneumoniae
, and the commensal
Streptococcus mitis
are closely related obligate symbionts associated with hominids. Faced with a shortage of accessible hosts, the two opposing lifestyles evolved in parallel. We have shown that the nonpathogenic
S. mitis
secured harmonious coexistence with its host by stabilizing a reduced genome devoid of many virulence genes. Meanwhile, the pathogenic pneumococcus evolved into a master of genomic flexibility and imports genes from
S. mitis
and other related streptococci. This process ensured antigenic diversification and has been driving the evolution of the remarkable structural diversity of capsular polysaccharides of
S. pneumoniae
, which conceivably will continue to increase and present a challenge to disease prevention.
Association of socioeconomic status measured by education, and cardiovascular health: a population-based cross-sectional study
Authors: Janković Slavenka , Stojisavljević Dragana , Janković Janko , Erić Miloš , Marinković Jelena 
Published: July 2014

ObjectiveCardiovascular health (CVH) is a relatively new concept defined by the American Heart Association (AHA). The aim of the present study was to assess whether the indices of CVH were discriminators of socioeconomic status (SES) in the adult population of the Republic of Srpska (RS).DesignPopulation-based cross-sectional study.SettingRS, Bosnia and Herzegovina.ParticipantsThe study involved 4165 adults aged ≥18 years (mean age 50.2; 54% women) who participated in the National Health Survey performed from September to November 2010 in the RS.Study variablesParticipant's education was a proxy for SES. Potential discriminators of SES were indices of CVH presented according to AHA as: ideal health behaviours index (non-smoking, body mass index <25 kg/m2, physical activity at goal level and healthy diet); ideal health factors index (untreated total cholesterol <200 mg/dL, untreated blood pressure <120/<80 mm Hg, untreated fasting glucose <100 mg/dL and non-smoking); and ideal CVH status (defined as all seven ideal health metrics present) versus intermediate and poor CVH status.ResultsParticipants with high educational levels had a significantly greater number of ideal CVH metrics, and ideal health factor metrics compared with those with low or medium educational level (OR 0.88 95% CI 0.77 to 0.99 and OR 0.88 95% CI 0.80 to 0.96; OR 0.81 95% CI 0.69 to 0.96 and OR 0.77 95% CI 0.68 to 0.87; respectively). The number of ideal behaviour metrics was not a discriminator of educational groups. Concerning the categories of CVH status the poor CVH was a discriminator for low and medium education compared with those with high education (OR 1.93 95% CI 1.24 to 3.01 and OR 1.54 95% CI 1.08 to 2.19, respectively).ConclusionsOur findings emphasise the large potential for preventing cardiovascular disease, showing a low proportion with a favourable CVH profile, especially among low-educated people. It is necessary to consider prevention strategies aimed at improving CVH in RS, targeting primarily low educational groups.