bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candida guilliermondii and Other Species of Candida Misidentified as Candida famata: Assessment by Vitek 2, DNA Sequencing Analysis, and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry in Two Global Antifungal Surveillance Programs
Authors: Castanheira Mariana , Woosley Leah N. , Diekema Daniel J. , Jones Ronald N. , Pfaller Michael A. 
Published: October 2012

ABSTRACT

Candida famata
(teleomorph
Debaryomyces hansenii
) has been described as a medically relevant yeast, and this species has been included in many commercial identification systems that are currently used in clinical laboratories. Among 53 strains collected during the SENTRY and ARTEMIS surveillance programs and previously identified as
C. famata
(includes all submitted strains with this identification) by a variety of commercial methods (Vitek, MicroScan, API, and AuxaColor), DNA sequencing methods demonstrated that 19 strains were
C. guilliermondii
, 14 were
C. parapsilosis
, 5 were
C. lusitaniae
, 4 were
C. albicans
, and 3 were
C. tropicalis
, and five isolates belonged to other
Candida
species (two
C. fermentati
and one each
C. intermedia
,
C. pelliculosa
, and
Pichia fabianni
). Additionally, three misidentified
C. famata
strains were correctly identified as
Kodomaea ohmeri
,
Debaryomyces nepalensis
, and
Debaryomyces fabryi
using intergenic transcribed spacer (ITS) and/or intergenic spacer (IGS) sequencing. The Vitek 2 system identified three isolates with high confidence to be
C. famata
and another 15 with low confidence between
C. famata
and
C. guilliermondii
or
C. parapsilosis
, displaying only 56.6% agreement with DNA sequencing results. Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) results displayed 81.1% agreement with DNA sequencing. One strain each of
C. metapsilosis
,
C. fermentati
, and
C. intermedia
demonstrated a low score for identification (<2.0) in the MALDI Biotyper.
K. ohmeri
,
D. nepalensis
, and
D. fabryi
identified by DNA sequencing in this study were not in the current database for the MALDI Biotyper. These results suggest that the occurrence of
C. famata
in fungal infections is much lower than previously appreciated and that commercial systems do not produce accurate identifications except for the newly introduced MALDI-TOF instruments.
Diagnostic Usefulness of Ribosomal Protein L7/L12 for Pneumococcal Pneumonia in a Mouse Model
Authors: Sawa Tomoka , Kimura Soichiro , Honda Natsue Hosono , Fujita Kazue , Yoshizawa Sadako , Harada Yoshihiro , Sugiyama Yuya , Matsuyama Kenji , Sohka Takayuki , Saji Tsutomu , Yamaguchi Keizo , Tateda Kazuhiro 
Published: October 2012

ABSTRACT

The capsular antigen detection (CAD) kit is widely used in clinics to detect
Streptococcus pneumoniae
infection from urine, because it is rapid, convenient, and effective. However, there are several disadvantages, including false-positive results in children colonized with
S. pneumoniae
and prolonged positive readings even after the bacteria have been cleared. RP-L7/L12 is a component of the 50S ribosome that is abundant in all bacteria and is specific for each bacterial species. We investigated whether RP-L7/L12 could be used to accurately diagnose pneumococcal pneumonia infection in mouse models of pneumonia and colonization generated by infecting CBA/JN or CBA/N mice, respectively, with
S. pneumoniae
strain 741. RP-L7/L12 detection by enzyme-linked immunosorbent assay accurately assessed active lung infection, as RP-L7/L12 levels decreased simultaneously with the bacterial lung burden after imipenem administration in the pneumonia mouse model. Based on the data, antibodies detecting RP-L7/L12 were applied to rapid immunochromatographic strips (ICS) for urine sample testing. When we compared the ICS test with the CAD kit in the pneumonia model, the results correlated well. Interestingly, however, when the lung bacterial burden became undetectable after antibiotic treatment, the ICS test was correspondingly negative, even though the same samples tested by the CAD kit remained positive. Similarly, while the ICS test exhibited negative results in the nasal colonization model, the CAD kit demonstrated positive results. Bacterial RP-L7/L12 may be a promising target for the development of new methods to diagnose infectious disease. Further studies are warranted to determine whether such a test could be useful in children.
Detection, Identification, and Distribution of Fungi in Bronchoalveolar Lavage Specimens by Use of Multilocus PCR Coupled with Electrospray Ionization/Mass Spectrometry
Authors: Shin Jeong Hwan , Ranken Raymond , Sefers Susan E. , Lovari Robert , Quinn Criziel D. , Meng Shufang , Carolan Heather E. , Toleno Donna , Li Haijing , Lee Jeong Nyeo , Stratton Charles W. , Massire Christian , Tang Yi-Wei 
Published: October 2012

ABSTRACT

As pulmonary fungal infections continue to increase due to an increasing number of immunocompromised patients, rapid detection and accurate identification of these fungal pathogens are critical. A broad fungal assay was developed by incorporating broad-range multilocus PCR amplification and electrospray ionization/mass spectrometry (PCR/ESI-MS) to detect and identify fungal organisms directly from clinical specimens. The aims of this study were to evaluate the performance of PCR/ESI-MS for detection, identification, and determination of the distribution of fungal organisms in bronchoalveolar lavage (BAL) fluid specimens. The BAL fluid specimens submitted for fungal culture at Vanderbilt University Medical Center between May 2005 and October 2011 were included. Cultures and identification were done using standard procedures. In addition, DNA was extracted from BAL fluid specimens, and fungal DNA amplification/identification were performed by PCR/ESI-MS. The results were compared with those of the standard cultures. A total of 691 nonduplicated BAL fluid specimens with sufficient leftover volume for molecular testing were evaluated using PCR/ESI-MS. Among them, 134 specimens (19.4%) were positive for fungi by both culture and PCR/ESI-MS testing. Of the dual-positive specimens, 125 (93.3%) were positive for
Candida
and
Aspergillus
species, with concordances between culture and PCR/ESI-MS results being 84 (67.2%) at the species level and 109 (87.2%) at the genus level. In addition, 243 (35.2%) and 30 (4.3%) specimens were positive only by PCR/ESI-MS or by culture, respectively (odds ratio [OR] = 11.95, 95% confidence interval [CI] = 7.90 to 18.17,
P
= 0.0000). Codetection of fungal organisms was noted in 23 (3.3%) specimens by PCR/ESI-MS, which was significantly higher than the 4 (0.6%) in which they were noted by culture (OR = 5.91, 95% CI = 1.93 to 20.27,
P
= 0.0002). Among 53 specimens in which cultures failed because of bacterial overgrowth, at least one fungus was identified in 26 specimens (47.3%) by PCR/ESI-MS. PCR/ESI-MS provides an advanced tool for rapid and sensitive detection, identification, and determination of the distribution of fungal organisms directly from BAL fluid specimens. Moreover, it detected fungal organisms in specimens in which cultures failed because of bacterial overgrowth. The clinical relevance of the significantly higher detection rate of fungal organisms by PCR/ESI-MS merits further investigation.
A Novel, Sensitive Assay for High-Throughput Molecular Detection of Plasmodia for Active Screening of Malaria for Elimination
Authors: Cheng Zhibin , Sun Xiaodong , Yang Ye , Wang Heng , Zheng Zhi 
Published: October 2012

ABSTRACT

Although malaria remains one of the leading infectious diseases in the world, the decline in malaria transmission in some area makes it possible to consider elimination of the disease. As countries approach elimination, malaria diagnosis needs to change from diagnosing ill patients to actively detecting infections in all carriers, including asymptomatic and low-parasite-load patients. However, few of the current diagnostic methods have both the throughput and the sensitivity required. We adopted a sandwich RNA hybridization assay to detect genus
Plasmodium
18S rRNA directly from whole-blood samples from
Plasmodium falciparum
and
Plasmodium vivax
patients without RNA isolation. We tested the assay with 202 febrile patients from areas where malaria is endemic, using 20 μl of each blood sample in a 96-well plate format with a 2-day enzyme-linked immunosorbent assay (ELISA)-like work flow. The results were compared with diagnoses obtained using microscopy, a rapid diagnostic test (RDT), and genus-specific real-time PCR. Our assay identified all 66 positive samples diagnosed by microscopy, including 49 poorly stored samples that underwent multiple freeze-thaw cycles due to resource limitation. The assay uncovered three false-negative samples by microscopy and four false-negative samples by RDT and agreed completely with real-time PCR diagnosis. There was no negative sample by our assay that would show a positive result when tested with other methods. The detection limit of our assay for
P. falciparum
was 0.04 parasite/μl. The assay's simple work flow, high throughput, and sensitivity make it suitable for active malaria screening.
Development and Application of Real-Time PCR for Detection of Subgroup J Avian Leukosis Virus
Authors: Qin Liting , Gao Yulong , Ni Wei , Sun Meiyu , Wang Yongqiang , Yin Chunhong , Qi Xiaole , Gao Honglei , Wang Xiaomei 
Published: October 2012

ABSTRACT

Subgroup J avian leukosis virus (ALV-J) is an avian retrovirus that causes severe economic losses in the poultry industry. The early identification and removal of virus-shedding birds are important to reduce the spread of congenital and contact infections. In this study, a TaqMan-based real-time PCR method for the rapid detection and quantification of ALV-J with proviral DNA was developed. This method exhibited a high specificity for ALV-J. Moreover, the detection limit was as low as 10 viral DNA copies. The coefficients of variation (CVs) of both interassay and intra-assay reproducibility were less than 1%. The growth curves of ALV-J in DF-1 cells were measured by real-time PCR, yielding a trend line similar to those determined by 50% tissue culture infective dose (TCID
50
) and p27 antigen detection. Tissue samples suspected of ALV infection were evaluated using real-time PCR, virus isolation, and routine PCR, and the positivity rates were 60.1%, 41.6% and 44.5%, respectively. Our data indicated that the real-time PCR method provides a sensitive, specific, and reproducible diagnostic tool for the identification and quantification of ALV-J for clinical diagnosis and in laboratory research.
Comparison of the Staphylococcus QuickFISH BC Test with the Tube Coagulase Test Performed on Positive Blood Cultures for Evaluation and Application in a Clinical Routine Setting
Authors: Carretto E. , Bardaro M. , Russello G. , Mirra M. , Zuelli C. , Barbarini D. 
Published: October 2012

ABSTRACT

Many studies demonstrate that delayed proper therapy in bloodstream infections caused by
Staphylococcus aureus
increases the mortality rate, emphasizing the need to shorten the turnaround time for positive blood cultures. Different techniques are currently available, from phenotypic methods to more complex tests such as matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF), real-time PCR (RT-PCR), and fluorescence in situ hybridization using peptide nucleic acid probes (PNA FISH). This study evaluated the performance of the
Staphylococcus
QuickFISH BC test (QFT), a novel FISH methodology, compared with the direct tube coagulase test (DTCT) on blood cultures exhibiting Gram-positive cocci in clusters. A total of 173 blood cultures collected from 128 different patients were analyzed using the DTCT, evaluated after both 4 and 24 h, and the QFT. A total of 179 isolates were identified using the Vitek2 system. Thirty-five out of 35
Staphylococcus aureus
were correctly identified by the QFT (sensitivity = 100%), with a specificity of 100% (no green fluorescence was detected for strains different from
S. aureus
). The DTCT was positive after 4 h for 28 out of the 35 samples (sensitivity = 80%) and after 24 h for 31 out of the 35 samples (sensitivity = 88.57%). Among the remaining 144 isolates, one was then identified as
Corynebacterium striatum
and two as
Micrococcus luteus
. QFT identified 139 out of the 141 coagulase-negative staphylococci (CoNS) (sensitivity = 98.58%), showing again a specificity of 100% (no fluorescent red signals were detected for strains different from CoNS). We also discuss also the implementation process of this methodology in our setting, with particular emphasis on the workflow and the cost-effectiveness.
Evaluation of the Abbott HBV RUO Sequencing Assay Combined with Laboratory-Modified Interpretive Software
Authors: Germer Jeffrey J. , Abraham Priya , Mandrekar Jayawant N. , Yao Joseph D. C. 
Published: October 2012

ABSTRACTThe Abbott HBV RUO Sequencing assay (Abbott Molecular Inc., Des Plaines, IL), which combines automated sample processing, real-time PCR, and bidirectional DNA sequencing, was evaluated for detection of nucleos(t)ide analogue (NA) resistance-associated mutations located in the hepatitis B virus (HBV) polymerase (Pol) gene. Interpretive software from the assay manufacturer was modified to allow interrogation of the overlapping HBV surface (S) gene sequence for HBV genotype determination and detection of immune escape mutations. Analytical sensitivity (detection and sequencing) of the assay was determined to be 103.9 IU/ml (95% confidence interval [CI], 80.0 to 173.3) for HBV genotype A. Testing of commercially available HBV genotype panels consisting of 23 individual members yielded complete agreement between expected results and results obtained from the laboratory-developed HBV genotype library. Excellent specificity was observed among clinical specimens with serologic or molecular markers for various unrelated blood-borne viruses (n= 6) and sera obtained from healthy, HBV-negative blood donors (n= 20). Retrospectively selected clinical specimens tested by a commercial reference laboratory HBV sequencing assay (n= 54) or the TrugeneHBVGenotyping kit (n= 7) and the Abbott HBV RUO Sequencing assay showed minor differences in detection and reporting of NA resistance-associated mutations in 7 of 61 (11.5%) specimens but complete agreement of genotype results. The Abbott HBV RUO Sequencing assay provided a convenient and efficient assay workflow suitable for routine clinical laboratory use, with the flexibility to be modified for customized detection of NA resistance-associated mutations, HBV genotype determination, and detection of immune escape mutations from a single contiguous HBV sequence.
Ring Infiltrate in Staphylococcal Keratitis
Authors: Wallang Batriti S. , Das Sujata , Sharma Savitri , Sahu Srikant K. , Mittal Ruchi 
Published: October 2012

ABSTRACT

Smear and culture tests of corneal scrapings from a patient with a ring infiltrate confirmed significant growth of a
Staphylococcus
species resistant to fluoroquinolones. Because of nonresponse to medical management, the patient underwent therapeutic penetrating keratoplasty. Staphylococcal infection of the cornea may appear as a ring-like infiltrate that is recalcitrant to medical management.
Human Cryptosporidiosis Caused by
Cryptosporidium tyzzeri
and
C. parvum
Isolates Presumably Transmitted from Wild Mice
Authors: Rašková Veronika , Květoňová Dana , Sak Bohumil , McEvoy John , Edwinson Adam , Stenger Brianna , Kváč Martin 
Published: October 2012

ABSTRACT

We report a case of severe human cryptosporidiosis caused by
Cryptosporidium tyzzeri
and
C. parvum
with an unusually high frequency of liquid stools. Wild mice were the most likely source of infection, demonstrating the potential for wild-mouse-borne
Cryptosporidium
to infect humans and highlighting the health risks associated with synantropic rodents.
APOBEC3G Restricts HIV-1 to a Greater Extent than APOBEC3F and APOBEC3DE in Human Primary CD4
+
T Cells and Macrophages
Authors: Chaipan Chawaree , Smith Jessica L. , Hu Wei-Shau , Pathak Vinay K. 
Published: October 2012

ABSTRACT

APOBEC3 proteins inhibit HIV-1 replication in experimental systems and induce hypermutation in infected patients; however, the relative contributions of several APOBEC3 proteins to restriction of HIV-1 replication in the absence of the viral Vif protein in human primary CD4
+
T cells and macrophages are unknown. We observed significant inhibition of HIV-1Δ
vif
produced in 293T cells in the presence of APOBEC3DE (A3DE), APOBEC3F (A3F), APOBEC3G (A3G), and APOBEC3H haplotype II (A3H HapII) but not APOBEC3B (A3B), APOBEC3C (A3C), or APOBEC3H haplotype I (A3H HapI). Our previous studies showed that Vif amino acids Y
40
RHHY
44
are important for inducing proteasomal degradation of A3G, whereas amino acids
14
DRMR
17
are important for degradation of A3F and A3DE. Here, we introduced substitution mutations of
40
YRHHY
44
and
14
DRMR
17
in replication-competent HIV-1 to generate
vif
mutants NL4-3 YRHHY>A5 and NL4-3 DRMR>A4 to compare the antiviral activity of A3G to the combined antiviral activity of A3F and A3DE in activated CD4
+
T cells and macrophages. During the first 15 days (round 1), in which multiple cycles of viral replication occurred, both the NL4-3 YRHHY>A5 and NL4-3 DRMR>A4 mutants replicated in activated CD4
+
T cells and macrophages, and only the NL4-3 YRHHY>A5 mutant showed a 2- to 4-day delay in replication compared to the wild type. During the subsequent 27 days (round 2) of cultures initiated with peak virus obtained from round 1, the NL4-3 YRHHY>A5 mutant exhibited a longer, 8- to 10-day delay and the NL4-3 DRMR>A4 mutant exhibited a 2- to 6-day delay in replication compared to the wild type. The NL4-3 YRHHY>A5 and NL4-3 DRMR>A4 mutant proviruses displayed G-to-A hypermutations primarily in GG and GA dinucleotides as expected of A3G- and A3F- or A3DE-mediated deamination, respectively. We conclude that A3G exerts a greater restriction effect on HIV-1 than A3F and A3DE.
Influenza A Viruses Grow in Human Pancreatic Cells and Cause Pancreatitis and Diabetes in an Animal Model
Authors: Capua Ilaria , Mercalli Alessia , Pizzuto Matteo S. , Romero-Tejeda Aurora , Kasloff Samantha , De Battisti Cristian , Bonfante Francesco , Patrono Livia V. , Vicenzi Elisa , Zappulli Valentina , Lampasona Vito , Stefani Annalisa , Doglioni Claudio , Terregino Calogero , Cattoli Giovanni , Piemonti Lorenzo 
Published: October 2012

ABSTRACT

Influenza A viruses commonly cause pancreatitis in naturally and experimentally infected animals. In this study, we report the results of
in vivo
investigations carried out to establish whether influenza virus infection could cause metabolic disorders linked to pancreatic infection. In addition,
in vitro
tests in human pancreatic islets and in human pancreatic cell lines were performed to evaluate viral growth and cell damage. Infection of an avian model with two low-pathogenicity avian influenza isolates caused pancreatic damage resulting in hyperlipasemia in over 50% of subjects, which evolved into hyperglycemia and subsequently diabetes. Histopathology of the pancreas showed signs of an acute infection resulting in severe fibrosis and disruption of the structure of the organ. Influenza virus nucleoprotein was detected by immunohistochemistry (IHC) in the acinar tissue. Human seasonal H1N1 and H3N2 viruses and avian H7N1 and H7N3 influenza virus isolates were able to infect a selection of human pancreatic cell lines. Human viruses were also shown to be able to infect human pancreatic islets.
In situ
hybridization assays indicated that viral nucleoprotein could be detected in beta cells. The cytokine activation profile indicated a significant increase of MIG/CXCL9, IP-10/CXCL10, RANTES/CCL5, MIP1b/CCL4, Groa/CXCL1, interleukin 8 (IL-8)/CXCL8, tumor necrosis factor alpha (TNF-α), and IL-6. Our findings indicate that influenza virus infection may play a role as a causative agent of pancreatitis and diabetes in humans and other mammals.
Naturally Acquired Picornavirus Infections in Primates at the Dhaka Zoo
Authors: Oberste M. Steven , Feeroz Mohammed M. , Maher Kaija , Nix W. Allan , Engel Gregory A. , Begum Sajeda , Hasan Kamrul M. , Oh Gunwha , Pallansch Mark A. , Jones-Engel Lisa 
Published: October 2012

ABSTRACTThe conditions in densely populated Bangladesh favor picornavirus transmission, resulting in a high rate of infection in the human population. Data suggest that nonhuman primates (NHP) may play a role in the maintenance and transmission of diverse picornaviruses in Bangladesh. At the Dhaka Zoo, multiple NHP species are caged in close proximity. Their proximity to other species and to humans, both zoo workers and visitors, provides the potential for cross-species transmission. To investigate possible interspecies and intraspecies transmission of picornaviruses among NHP, we collected fecal specimens from nine NHP taxa at the Dhaka Zoo at three time points, August 2007, January 2008, and June 2008. Specimens were screened using real-time PCR for the generaEnterovirus,Parechovirus,and Sapelovirus, and positive samples were typed by VP1 sequencing. Fifty-two picornaviruses comprising 10 distinct serotypes were detected in 83 fecal samples. Four of these serotypes, simian virus 19 (SV19), baboon enterovirus (BaEV), enterovirus 112 (EV112), and EV115, have been solely associated with infection in NHP. EV112, EV115, and SV19 accounted for 88% of all picornaviruses detected. Over 80% of samples from cages housing rhesus macaques, olive baboons, or hamadryas baboons were positive for a picornavirus, while no picornaviruses were detected in samples from capped langurs or vervet monkeys. In contrast to our findings among synanthropic NHP in Bangladesh where 100% of the picornaviruses detected were of human serotypes, in the zoo population, only 15% of picornaviruses detected in NHP were of human origin. Specific serotypes tended to persist over time, suggesting either persistent infection of individuals or cycles of reinfection.
Differential Effects of Human Immunodeficiency Virus Type 1 Capsid and Cellular Factors Nucleoporin 153 and LEDGF/p75 on the Efficiency and Specificity of Viral DNA Integration
Authors: Koh Yasuhiro , Wu Xiaolin , Ferris Andrea L. , Matreyek Kenneth A. , Smith Steven J. , Lee KyeongEun , KewalRamani Vineet N. , Hughes Stephen H. , Engelman Alan 
Published: October 2012

ABSTRACT
Retroviruses integrate into cellular DNA nonrandomly. Lentiviruses such as human immunodeficiency virus type 1 (HIV-1) favor the bodies of active genes and gene-enriched transcriptionally active regions of chromosomes. The interaction between lentiviral integrase and the cellular protein lens epithelium-derived growth factor (LEDGF)/p75 underlies the targeting of gene bodies, whereas recent research has highlighted roles for the HIV-1 capsid (CA) protein and cellular factors implicated in viral nuclear import, including transportin 3 (TNPO3) and nucleoporin 358 (NUP358), in the targeting of gene-dense regions of chromosomes. Here, we show that CA mutations, which include the substitution of Asp for Asn74 (N74D), significantly reduce the dependency of HIV-1 on LEDGF/p75 during infection and that this difference correlates with the efficiency of viral DNA integration. The distribution of integration sites mapped by Illumina sequencing confirms that the N74D mutation reduces integration into gene-rich regions of chromosomes and gene bodies and reveals previously unrecognized roles for NUP153 (another HIV-1 cofactor implicated in viral nuclear import) and LEDGF/p75 in the targeting of the viral preintegration complex to gene-dense regions of chromatin. A role for the CA protein in determining the dependency of HIV-1 on LEDGF/p75 during infection highlights a connection between the viral capsid and chromosomal DNA integration.