bluuebunny/crossref_metadata_2025_split huggingface dataset:
First Description of KPC-2-Producing Pseudomonas putida in Brazil
Authors: Almeida Anna C. S. , Vilela Marinalda A. , Cavalcanti Felipe L. S. , Martins Willames M. B. S. , Morais Marcos A. , Morais Marcia M. C. 
Published: January 2012

ABSTRACT

This work reports the identification of the first case of a KΡC-2-producing
Pseudomonas putida
isolate (PP36) in Brazil. The PP36 isolate was resistant to all the antimicrobials tested except polymyxin B. In addition to the discovered
bla
KPC-2
gene, genetic analysis showed the presence of a class 1 integron containing the
dhfr
XVb gene and the new allele
arr-6
, which codes for resistance to rifampin. These elements were found in an IncFI 65-kb plasmid.
Involvement of the AcrAB-TolC Efflux Pump in the Resistance, Fitness, and Virulence of Enterobacter cloacae
Authors: Pérez Astrid , Poza Margarita , Fernández Ana , del Carmen Fernández Maria , Mallo Susana , Merino María , Rumbo-Feal Soraya , Cabral María P. , Bou Germán 
Published: January 2012

ABSTRACT

Multidrug efflux pumps have emerged as important mechanisms of antimicrobial resistance in bacterial pathogens. In order to cause infection, pathogenic bacteria require mechanisms to avoid the effects of host-produced compounds, and express efflux pumps may accomplish this task. In this study, we evaluated the effect of the inactivation of AcrAB-TolC on antimicrobial resistance, fitness, and virulence in
Enterobacter cloacae
, an opportunistic pathogen usually involved in nosocomial infections. Two different clinical isolates of
E. cloacae
were used, EcDC64 (multidrug resistance overexpressing the AcrAB-TolC efflux pump) and Jc194 (basal AcrAB-TolC expression). The
acrA
and
tolC
genes were deleted in strains EcDC64 and Jc194 to produce, respectively, EcΔ
acrA
and EcΔ
tolC
and JcΔ
acrA
and JcΔ
tolC
knockout (KO) derivatives. Antibiotic susceptibility testing was performed with all isolates, and we discovered that these mechanisms are involved in the resistance of
E. cloacae
to several antibiotics. Competition experiments were also performed with wild-type and isogenic KO strains. The competition index (CI), defined as the mutant/wild-type ratio, revealed that the
acrA
and
tolC
genes both affect the fitness of
E. cloacae
, as fitness was clearly reduced in the
acrA
and
tolC
KO strains. The median CI values obtained
in vitro
and
in vivo
were, respectively, 0.42 and 0.3 for EcDC64/EcΔ
acrA
, 0.24 and 0.38 for EcDC64/EcΔ
tol
C, 0.15 and 0.11 for Jc194/JcΔ
acrA
, and 0.38 and 0.39 for Jc194/JcΔ
tolC
. Use of an intraperitoneal mouse model of systemic infection revealed reduced virulence in both
E. cloacae
clinical strains when either the
acrA
or
tolC
gene was inactivated. In conclusion, the structural components of the AcrAB-TolC efflux pump appear to play a role in antibiotic resistance as well as environmental adaptation and host virulence in clinical isolates of
E. cloacae
.
Association of the Emerging Carbapenemase NDM-1 with a Bleomycin Resistance Protein in Enterobacteriaceae and Acinetobacter baumannii
Authors: Dortet Laurent , Nordmann Patrice , Poirel Laurent 
Published: January 2012

ABSTRACT

The carbapenemase NDM-1 has been identified recently in
Enterobacteriaceae
and
Acinetobacter baumannii
as a source of multidrug resistance, including resistance to carbapenems. By analyzing the immediate genetic environment of the
bla
NDM-1
carbapenemase gene among a series of NDM-1-producing enterobacterial isolates, a novel gene (
ble
MBL
, for
ble
gene associated with the metallo-β-lactamase NDM-1) was identified. The
ble
MBL
gene encodes a novel bleomycin resistance protein (BRP), named BRP
MBL
, that shares weak similarities with known BRPs (less than 60% amino acid identity). The expression of BRP
MBL
conferred resistance to bleomycin and to bleomycin-like molecules in
Enterobacteriaceae
and
A. baumannii
. The
bla
NDM-1
and
ble
MBL
genes were coexpressed under the control of the same promoter, located upstream of the
bla
NDM-1
gene and at the extremity of the insertion sequence IS
Aba125
. Most of the NDM producers possessed the
ble
MBL
gene. Although BRP
MBL
did not modify the growth or death rates of
Escherichia coli
under experimental conditions, it suppressed the mutation rate of hypermutable
E. coli
and therefore may stabilize the plasmid-borne
bla
NDM-1
gene. This study suggests that the emerging carbapenemase NDM-1 is selected by bleomycin-like molecules, and that BRP
MBL
producers (and consequently NDM producers) are better suited to various environments.
Comparison of Four Renal Function Estimation Equations for Pharmacokinetic Modeling of Gentamicin in Geriatric Patients
Authors: Charhon Nicolas , Neely Michael N. , Bourguignon Laurent , Maire Pascal , Jelliffe Roger W. , Goutelle Sylvain 
Published: January 2012

ABSTRACT
Most aminoglycoside pharmacokinetic models include an index of renal function, such as creatinine clearance, to describe drug clearance. However, the best clinical descriptor of renal function for the pharmacokinetic modeling of aminoglycosides has not been established. This analysis was based on 412 gentamicin concentrations from 92 geriatric patients who received intravenous gentamicin for various infectious diseases. Four two-compartment population models were fitted to gentamicin concentrations in a learning set of 64 patients using the nonparametric adaptive grid (NPAG) algorithm. Each model included an index of renal function, namely, the Cockcroft-Gault (CG), Jelliffe (JEL), modification of diet in renal disease (MDRD), or modified MDRD (MDRDm; adjusted to individual body surface area) equation as a covariate influencing gentamicin serum clearance. Goodness of fit and predictive performance of the four models were compared using standard criteria in both the learning set and in a validation set of 28 patients. A final analysis was performed to estimate the population pharmacokinetic parameter values of the entire 92-patient group. In the learning set, the CG-based model best fit the data, followed by JEL-, MDRD-, and MDRDm-based models, with relative reductions of the Akaike information criterion of 29.4, 20.2, 14.2, and 4.2, respectively. Bias and precision of population predictions were significantly different among the four models. In the validation set, individual predictions from the four models showed marginally different biases. The final estimation confirmed the previous results. Specifically, the CG-based model showed predictive performance that was comparable to or better than that of the MDRD-based model at each stage of the analysis. This study shows that methods used to estimate renal function should not be considered interchangeable for the model-based estimation of gentamicin concentrations.
Clinical and Microbiologic Characteristics of Cephalosporin-Resistant Escherichia coli at Three Centers in the United States
Authors: Park Yoon Soo , Adams-Haduch Jennifer M. , Shutt Kathleen A. , Yarabinec Daniel M. , Johnson Laura E. , Hingwe Ameet , Lewis James S. , Jorgensen James H. , Doi Yohei 
Published: January 2012

ABSTRACT

We investigated the clinical and microbiologic features of 300 cases of cephalosporin-resistant
Escherichia coli
producing extended-spectrum β-lactamase (ESBL) or plasmid-mediated AmpC β-lactamase (pAmpC) at three medical centers in the United States. Solid-organ malignancy, connective tissue disease, and a recent history of surgery were more common among pAmpC-producing cases (
n
= 49), whereas urinary catheter at enrollment, diabetes, and hospitalization in the past year were more common among ESBL-producing cases (
n
= 233). The factors independently associated with clinical outcome were the following: the presence of cardiovascular disease (odds ratio [OR], 2.88; 95% confidence interval [CI], 1.29 to 6.43), intra-abdominal infection (OR, 6.35; 95% CI, 1.51 to 26.7), other or multiples sources of infection (OR, 8.12; 95% CI, 2.3 to 28.6), age of 65 years or greater (OR, 0.43; 95% CI, 0.2 to 0.95), favorable baseline health status (OR, 0.39; 95% CI, 0.16 to 0.95), and appropriate empirical antimicrobial therapy given in the first 72 h (OR, 0.42; 95% CI, 0.20 to 0.88). β-Lactamase genes responsible for cephalosporin resistance were identified in 291 cases. CTX-M-type ESBLs accounted for 72.0%. Of those, 88.0% were CTX-M-15. The next most common type was CMY-type pAmpC (16.7%), followed by SHV- and TEM-type ESBLs (6.3 and 1.3%, respectively). Seven cases (2.3%) had KPC-type β-lactamase. Ertapenem, imipenem, meropenem, doripenem, piperacillin-tazobactam, amikacin, nitrofurantoin, and tigecycline were highly active, with greater than 90% of the isolates being susceptible. Cefepime was less active, with only 74.2% being susceptible due to the predominance of CTX-M-15. These findings have implications in the selection of appropriate empirical therapy when infection due to cephalosporin-resistant
E. coli
is suspected.
Novel Variants of AbaR Resistance Islands with a Common Backbone in Acinetobacter baumannii Isolates of European Clone II
Authors: Šeputienė Vaida , Povilonis Justas , Sužiedėlienė Edita 
Published: January 2012

ABSTRACT

In this study, the genetic organization of three novel genomic antibiotic resistance islands (AbaRs) in
Acinetobacter baumannii
isolates belonging to group of European clone II (EC II)
comM
integrated sequences of 18-, 21-, and 23-kb resistance islands were determined. These resistance islands carry the backbone of AbaR-type transposon structures, which are composed of the transposition module coding for potential transposition proteins and other genes coding for the intact universal stress protein (
uspA
), sulfate permease (
sul
), and proteins of unknown function. The antibiotic resistance genes
strA
,
strB
,
tetB
, and
tetR
and insertion sequence CR2 element were found to be inserted into the AbaR transposons. GenBank homology searches indicated that they are closely related to the AbaR sequences found integrated in
comM
in strains of EC II (
A. baumannii
strains 1656-2 and TCDC-AB0715) and AbaR4 integrated in another location of
A. baumannii
AB0057 (EC I). All of the AbaRs showed structural similarity to the previously described AbaR4 island and share a 12,008-bp backbone. AbaRs contain Tn
1213
, Tn
2006
, and the multiple fragments which could be derived from transposons Tn
3
, Tn
10
, Tn
21
, Tn
1000
, Tn
5393
, and Tn
6020
, the insertion sequences IS
26
, IS
Aba1
, IS
Aba14
, and IS
CR2
, and the class 1 integron. Moreover, chromosomal DNA was inserted into distinct regions of the AbaR backbone. Sequence analysis suggested that the AbaR-type transposons have evolved through insertions, deletions, and homologous recombination. AbaR islands, sharing the core structure similar to AbaR4, appeared to be distributed in isolates of EC I and EC II via integration into distinct genomic sites, i.e.,
pho
and
comM
, respectively.
Carbapenem Resistance in Elizabethkingia meningoseptica Is Mediated by Metallo-β-Lactamase BlaB
Authors: González Lisandro J. , Vila Alejandro J. 
Published: January 2012

ABSTRACT

Elizabethkingia meningoseptica
, a Gram-negative rod widely distributed in the environment, is resistant to most β-lactam antibiotics. Three
bla
genes have been identified in
E. meningoseptica
, coding for the extended-spectrum serine-β-lactamase CME (class D) and two unrelated wide-spectrum metallo-β-lactamases, BlaB (subclass B1) and GOB (subclass B3).
E. meningoseptica
is singular in being the only reported microorganism possessing two chromosomally encoded MBL genes. Real-time PCR and biochemical analysis demonstrate that the three
bla
genes are actively expressed
in vivo
as functional β-lactamases. However, while CME elicits cephalosporin resistance, BlaB is the only β-lactamase responsible for
E. meningoseptica
resistance to imipenem, as GOB activity is masked by higher cellular levels of BlaB. On the other hand, we demonstrate that
bla
BlaB
expression is higher in the stationary phase or under conditions that mimic the nutrient-limiting cerebrospinal fluid colonized by
E. meningoseptica
in human meningitis.
IMP-29, a Novel IMP-Type Metallo-β-Lactamase in Pseudomonas aeruginosa
Authors: Jeannot Katy , Poirel Laurent , Robert-Nicoud Marjorie , Cholley Pascal , Nordmann Patrice , Plésiat Patrick 
Published: January 2012

ABSTRACT

Analysis of two clonally related multiresistant
Pseudomonas aeruginosa
isolates led to the identification of a novel IMP-type metallo-β-lactamase. IMP-29 was significantly different from the other IMP variants (the closest variant being IMP-5 with 93% amino acid identity). The
bla
IMP-29
gene cassette was carried by a class 1 integron in strain 10.298, while in strain 10.266 it was located in a rearranged DNA region on a 30-kb conjugative plasmid. Biochemical analysis confirmed that IMP-29 efficiently hydrolyzed carbapenems.
Comparative
In Vitro
Activities of LFF571 against Clostridium difficile and 630 Other Intestinal Strains of Aerobic and Anaerobic Bacteria
Authors: Citron Diane M. , Tyrrell Kerin L. , Merriam C. Vreni , Goldstein Ellie J. C. 
Published: January 2012

ABSTRACT

The
in vitro
activities of LFF571, a novel analog of GE2270A that inhibits bacterial growth by binding with high affinity for protein synthesis elongation factor Tu, fidaxomicin, and 10 other antimicrobial agents were determined against 50 strains of
Clostridium difficile
and 630 other anaerobic and aerobic organisms of intestinal origin. LFF571 possesses potent activity against
C. difficile
and most other Gram-positive anaerobes (MIC
90
, ≤0.25 μg/ml), with the exception of bifidobacteria and lactobacilli. The MIC
90
s for aerobes, including enterococci,
Staphylococcus aureus
(as well as methicillin-resistant
S. aureus
[MRSA] isolates),
Streptococcus pyogenes
, and other streptococci were 0.06, 0.125, 2, and 8 μg/ml, respectively. Comparatively, fidaxomicin showed variable activity against Gram-positive organisms: MIC
90
s against
C. difficile
,
Clostridium perfringens
, and
Bifidobacterium
spp. were 0.5, ≤0.015, and 0.125 μg/ml, respectively, but >32 μg/ml against
Clostridium ramosum
and
Clostridium innocuum
. MIC
90
for
S. pyogenes
and other streptococci was 16 and >32 μg/ml, respectively. LFF571 and fidaxomicin were generally less active against Gram-negative anaerobes.
Small-Angle X-Ray Scattering Analysis of the Bifunctional Antibiotic Resistance Enzyme Aminoglycoside (6′) Acetyltransferase-Ie/Aminoglycoside (2″) Phosphotransferase-Ia Reveals a Rigid Solution Structure
Authors: Caldwell Shane J. , Berghuis Albert M. 
Published: January 2012

ABSTRACT

Aminoglycoside (6′) acetyltransferase-Ie/aminoglycoside (2″) phosphotransferase-Ia [AAC(6′)-Ie/APH(2″)-Ia] is one of the most problematic aminoglycoside resistance factors in clinical pathogens, conferring resistance to almost every aminoglycoside antibiotic available to modern medicine. Despite 3 decades of research, our understanding of the structure of this bifunctional enzyme remains limited. We used small-angle X-ray scattering (SAXS) to model the structure of this bifunctional enzyme in solution and to study the impact of substrate binding on the enzyme. It was observed that the enzyme adopts a rigid conformation in solution, where the N-terminal AAC domain is fixed to the C-terminal APH domain and not loosely tethered. The addition of acetyl-coenzyme A, coenzyme A, GDP, guanosine 5′-[β,γ-imido]triphosphate (GMPPNP), and combinations thereof to the protein resulted in only modest changes to the radius of gyration (
R
G
) of the enzyme, which were not consistent with any large changes in enzyme structure upon binding. These results imply some selective advantage to the bifunctional enzyme beyond coexpression as a single polypeptide, likely linked to an improvement in enzymatic properties. We propose that the rigid structure contributes to improved electrostatic steering of aminoglycoside substrates toward the two active sites, which may provide such an advantage.
Surface Water Vapor Pressure and Temperature Trends in North America during 1948–2010
Authors: Isaac V. , van Wijngaarden W. A. 
Published: January 2012

Abstract
Over one-quarter billion hourly values of temperature and relative humidity observed at 309 stations located across North America during 1948–2010 were studied. The water vapor pressure was determined and seasonal averages were computed. Data were first examined for inhomogeneities using a statistical test to determine whether the data were fit better to a straight line or a straight line plus an abrupt step, which may arise from changes in instruments and/or procedure. Trends were then found for data not having discontinuities. Statistically significant warming trends affecting the Midwestern United States, Canadian prairies, and the western Arctic are evident in winter and to a lesser extent in spring while statistically significant increases in water vapor pressure occur primarily in summer for some stations in the eastern half of the United States. The temperature (water vapor pressure) trends averaged over all stations were 0.30 (0.07), 0.24 (0.06), 0.13 (0.11), 0.11 (0.07) °C decade−1 (hPa decade−1) in the winter, spring, summer, and autumn seasons, respectively. The averages of these seasonal trends are 0.20°C decade−1 and 0.07 hPa decade−1, which correspond to a specific humidity increase of 0.04 g kg−1 decade−1 and a relative humidity reduction of 0.5% decade−1.
Interactive Crop Management in the Community Earth System Model (CESM1): Seasonal Influences on Land–Atmosphere Fluxes
Authors: Levis Samuel , Bonan Gordon B. , Kluzek Erik , Thornton Peter E. , Jones Andrew , Sacks William J. , Kucharik Christopher J. 
Published: January 2012

AbstractThe Community Earth System Model, version 1 (CESM1) is evaluated with two coupled atmosphere–land simulations. The CTRL (control) simulation represents crops as unmanaged grasses, while CROP represents a crop managed simulation that includes special algorithms for midlatitude corn, soybean, and cereal phenology and carbon allocation. CROP has a more realistic leaf area index (LAI) for crops than CTRL. CROP reduces winter LAI and represents the spring planting and fall harvest explicitly. At the peak of the growing season, CROP simulates higher crop LAI. These changes generally reduce the latent heat flux but not around peak LAI (late spring/early summer). In midwestern North America, where corn, soybean, and cereal abundance is high, simulated peak summer precipitation declines and agrees better with observations, particularly when crops emerge late as is found from a late planting sensitivity simulation (LateP). Differences between the CROP and LateP simulations underscore the importance of simulating crop planting and harvest dates correctly. On the biogeochemistry side, the annual cycle of net ecosystem exchange (NEE) also improves in CROP relative to Ameriflux site observations. For a global perspective, the authors diagnose annual cycles of CO2 from the simulated NEE (CO2 is not prognostic in these simulations) and compare against representative GLOBALVIEW monitoring stations. The authors find an increased (thus also improved) amplitude of the annual cycle in CROP. These regional and global-scale refinements from improvements in the simulated plant phenology have promising implications for the development of the CESM and particularly for simulations with prognostic atmospheric CO2.
A Minimum Threshold for Wind Profiler Signal-to-Noise Ratios
Authors: Riddle Anthony C. , Hartten Leslie M. , Carter David A. , Johnston Paul E. , Williams Christopher R. 
Published: January 2012

Abstract
One limiting factor in atmospheric radar observations is the inability to distinguish the often weak atmospheric signals from fluctuations of the noise. This study presents a minimum threshold of usability, SNRmin, for signal-to-noise ratios obtained from wind profiling radars. The basic form arises from theoretical considerations of radar noise; the final form includes empirical modifications based on radar observations. While SNRmin was originally developed using data from the 50-MHz profiler at Poker Flat, Alaska, it works well with data collected from a wide range of locations, frequencies, and parameter settings. It provides an objective criterion to accept or reject individual spectra, can be quickly applied to a large quantity of data, and has a false-alarm rate of approximately 0.1%. While this threshold’s form depends on the methods used to calculate SNR and spectral moments, variations of the threshold could be developed for use with data processed by other methods.
Rank Histograms of Stratified Monte Carlo Ensembles
Authors: Siegert Stefan , Bröcker Jochen , Kantz Holger 
Published: January 2012

AbstractThe application of forecast ensembles to probabilistic weather prediction has spurred considerable interest in their evaluation. Such ensembles are commonly interpreted as Monte Carlo ensembles meaning that the ensemble members are perceived as random draws from a distribution. Under this interpretation, a reasonable property to ask for is statistical consistency, which demands that the ensemble members and the verification behave like draws from the same distribution. A widely used technique to assess statistical consistency of a historical dataset is the rank histogram, which uses as a criterion the number of times that the verification falls between pairs of members of the ordered ensemble. Ensemble evaluation is rendered more specific by stratification, which means that ensembles that satisfy a certain condition (e.g., a certain meteorological regime) are evaluated separately. Fundamental relationships between Monte Carlo ensembles, their rank histograms, and random sampling from the probability simplex according to the Dirichlet distribution are pointed out. Furthermore, the possible benefits and complications of ensemble stratification are discussed. The main conclusion is that a stratified Monte Carlo ensemble might appear inconsistent with the verification even though the original (unstratified) ensemble is consistent. The apparent inconsistency is merely a result of stratification. Stratified rank histograms are thus not necessarily flat. This result is demonstrated by perfect ensemble simulations and supplemented by mathematical arguments. Possible methods to avoid or remove artifacts that stratification induces in the rank histogram are suggested.
The Making of Chile: With Poems and Guns
Authors: Bray Marjorie Woodford 
Published: January 2012

After the overthrow of Chilean President Salvador Allende in 1973, several professors, graduate students, and filmmakers, with help from the Los Angeles Group for Latin American Solidarity, joined to create a film “pamphlet” documenting the social and cultural accomplishments of Allende’s Unidad Popular administration and exposing the machinations of the U.S. government and the Chilean upper class that provoked the coup. Using footage generously lent by the producer that been made in Chile for another film, as well as Chilean archival footage and segments produced locally, Chile: With Poems and Guns, first shown in January 1974 in Los Angeles, became widely distributed nationally and internationally. Some of the participants in making the film remained together to continue making films as a collective known as Lucha. Después del golpe de estado en contra del presidente chileno Salvador Allende en 1973, varios profesores, estudiantes de posgrado y cineastas se unieron con el Los Angeles Group for Latin American Solidarity para crear un “panfleto” cinematográfico que documentase los logros del gobierno de Unidad Popular de Allende y las maquinaciones del gobierno estadounidense y la clase alta chilena para provocar el golpe. Haciendo uso de material de archivos chilenos, segmentos producidos localmente y película rodada en Chile para otro filme y generosamente suministrada por el productor, Chile: With Poems and Guns (“Chile: con poemas y armas”) se estrenó en enero de 1974 en Los Angeles y se distribuyó ampliamente a nivel nacional e internacional. Algunos de los participantes en el rodaje se mantuvieron juntos y continuaron produciendo películas bajo el nombre de Lucha.