bluuebunny/crossref_metadata_2025 huggingface dataset:
The Fate of Haloacetic Acids and Trihalomethanes in an Aquifer Storage and Recovery Program, Las Vegas, Nevada
Authors: Thomas James M. , McKay W. Alan , Cole Erin , Landmeyer James E. , Bradley Paul M.
Published: August 2005

The fate of disinfection byproducts during aquifer storage and recovery (ASR) is evaluated for aquifers in southern Nevada. Rapid declines of haloacetic acid (HAA) concentrations during ASR, with associated little change in Cl concentration, indicate that (HAAs) decline primarily by in situ microbial oxidation. Dilution is only a minor contributor to HAA concentration declines during ASR. Trihalomethane (THM) concentrations generally increased during storage of artificial recharge (AR) water and then declined during recovery. The decline of THM concentrations during recovery was primarily from dilution of current season AR water with residual AR water remaining in the aquifer from previous ASR seasons and native ground water. In more recent ASR seasons, for wells with the longest history of ASR, brominated THMs declined during storage and recovery by processes in addition to dilution. These conclusions about THMs are indicated by THM/Cl values and supported by a comparison of measured and model predicted THM concentrations. Geochemical mixing models were constructed using major‐ion chemistry of the three end‐member waters to calculate predicted THM concentrations. The decline in brominated THM concentrations in addition to that from dilution may result from biotransformation processes.
Fractured‐Aquifer Hydrogeology from Geophysical Logs: Brunswick Group and Lockatong Formation, Pennsylvania
Authors: Morin Roger H. , Senior Lisa A. , Decker Edward R.
Published: August 2005

The Brunswick Group and the underlying Lockatong Formation are composed of lithified Mesozoic sediments that constitute part of the Newark Basin in southeastern Pennsylvania. These fractured rocks form an important regional aquifer that consists of gradational sequences of shale, siltstone, and sandstone, with fluid transport occurring primarily in fractures. An extensive suite of geophysical logs was obtained in seven wells located at the borough of Lansdale, Pennsylvania, in order to better characterize the areal hydrogeologic system and provide guidelines for the refinement of numerical ground water models. Six of the seven wells are approximately 120 m deep and the seventh extends to a depth of 335 m. Temperature, fluid conductivity, and flowmeter logs are used to locate zones of fluid exchange and to quantify transmissivities. Electrical resistivity and natural gamma logs together yield detailed stratigraphic information, and digital acoustic televiewer data provide magnetically oriented images of the borehole wall from which almost 900 fractures are identified.

Analyses of the geophysical data indicate that the aquifer penetrated by the deep well can be separated into two distinct structural domains, which may, in turn, reflect different mechanical responses to basin extension by different sedimentary units:

1. In the shallow zone (above 125 m), the dominant fracture population consists of gently dipping bedding plane partings that strike N46°E and dip to the northwest at about 11 degrees. Fluid flow is concentrated in the upper 80 m along these subhorizontal fractures, with transmissivities rapidly diminishing in magnitude with depth.

2. The zone below 125 m marks the appearance of numerous high‐angle fractures that are orthogonal to the bedding planes, striking parallel but dipping steeply southeast at 77 degrees.

This secondary set of fractures is associated with a fairly thick (approximately 60 m) high‐resistivity, low‐transmissivity sandstone unit that is abruptly terminated by a thin shale bed at a depth of 190 m. This lower contact effectively delineates the aquifer's vertical extent at this location because no detectable evidence of ground water movement is found below it. Thus, fluid flow is controlled by fractures, but fracture type and orientation are related to lithology. Finally, a transient thermal‐conduction model is successfully applied to simulate observed temperature logs, thereby confirming the effects of ground‐surface warming that occurred in the area as a result of urbanization at the turn of the century. The systematic warming of the upper 120 m has increased the transmissivity of this aquifer by almost 10%, simply due to changes in fluid viscosity and density.
Empirical Assessment of the Influence of the Unsaturated Zone on Aquifer Vulnerability, Manawatu Region, New Zealand
Authors: Bekesi Gabor , McConchie Jack
Published: August 2005

Vulnerability assessments provide essential screening tools to focus efforts on prevention of ground water contamination. The unsaturated zone, between the base of the soil and the phreatic surface, has an important role on the fate of contaminants. Yet most vulnerability assessments either do not address the unsaturated zone or overly simplify its effect on ground water contamination.

In the Manawatu region of New Zealand, four factors have been found to predominantly control vulnerability: the soil, the unsaturated zone, rainfall recharge, and the aquifer medium. This paper focuses on assessing the spatial variability of the unsaturated zone. The model is based on an assessment of the total surface area available for sorption, or total sorption capacity of the unsaturated zone at each borehole. This assessment uses well drillers’logs, which provide the only available database covering the entire unsaturated zone of the study area, and published sorption values of various sediments to estimate vulnerability resulting from sorption capacity. These “point estimates” are treated as a spatially distributed parameter that can be contoured as a continuous surface. The entire modeling process was computerized in a geographical information system.

Although the quality of drillers’logs varies considerably, high and low sorption areas can be distinguished readily, and the final map of unsaturated zone sorption shows clear regional trends. The sorption index generally decreases with distance from the recharge areas. The methods developed here can be applied and modified when necessary at other hydrogeological settings.
Effect of Sorption Assumptions on Aquifer Remediation Designs
Authors: Aksoy Aysegul , Culver Teresa B.
Published: August 2005

Genetic algorithm optimization of pump‐and‐treat ground water remediation is used to explore the extent of bias introduced into remediation designs and costs by sorption assumptions. Remediation problems with equilibrium sorption and two‐site kinetic sorption with different mass transfer rates are addressed. Under the time‐scales and flow conditions of contamination, all of these sorption assumptions created similar initial plumes. Thus, calibration of sorption parameters to the initial plume may be insufficient information to differentiate between sorption rates. Two optimization formulations were considered for each sorption assumption. In one formulation, the final water quality goal is with respect to the aqueous concentration; in the other, the goal is with respect to the total concentration (aqueous and sorbed). While remediation designs could be found with the aqueous concentration formulation, the total mass of contaminant remaining within the aquifer increases with decreasing mass transfer rates, creating the potential for concentration rebound after the pumping period ends. The designs found with the total concentration formulation avoid this difficulty, although it may not always be possible to find feasible remediation schemes within the specified remediation period. If an optimal design based on the assumption of equilibrium sorption is applied to an aquifer with mass transfer limitations, the water quality goals may not be met within the specified remediation period. The length of time required to meet the water quality goals with this suboptimal design may increase exponentially as the mass transfer rate decreases, although aquifer heterogeneity reduces the scale of this effect.
Prediction of the Quality and Quantity of Maramec Spring Water
Authors: Wicks Carol M. , Hoke John A.
Published: August 2005

Our ability to predict the response of large karstic basins to contaminant pulses and recharge events is limited due to an inability to model flow through these highly hetereogeneous and anisotropic basins. The linear systems technique is useful for simulating hydrologic processes occurring in karstic basins because detailed knowledge about the internal structure of the basin is not required. The objectives of this study were to predict changes in the quantity and quality of spring water in a large karstic basin using the linear systems approach. Using a dimensionless unit hydrograph, the change in quantity of spring water was predicted and the correlation coefficient, r, between predicted and observed discharges was 0.94. A nonpoint source kernel was used to predict the change in the specific conductance of the spring water (r = 0.97). A point‐source kernel derived from a quantitative dye trace was used to predict the first arrival and dispersion of a contaminant at the spring (r = 0.11). Even though the correlation coefficient is low, the prediction matched the first and last appearances of the contaminant. Quantitative dye traces can be used to predict the movement of aqueous contaminants through karstic aquifers using the linear systems approach. Given the findings of this research, the linear systems approach is a useful predictive tool that would enable better management of ground water resources in karstic basins.
Impact of Biomass‐Decay Terms on the Simulation of Pulsed Bioremediation
Authors: Cirpka Olaf A. , Kitanidis Peter K.
Published: August 2005

A numerical model is used for simulating the stimulation of biomass growth by injection of alternating pulses of a primary substrate and oxygen. We consider that the substrate sorbs, whereas oxygen does not undergo mass transfer, and mixing of the reacting compounds is dominated by the chromatographic effect. Different mathematical formulations for biomass growth and decay are compared. In models considering biomass decay, a minimal time of joint exposure to both reactants can be determined. This leads to a multimodal distribution of the biomass after multiple injection cycles. In multidimensional heterogeneous domains, the location of the biomass peaks is determined by the advective arrival time. The biomass is much more homogeneously distributed when biomass decay is neglected, because under this condition there is no constraint by a minimal joint exposure time. For the case of oxygen‐dependent biomass decay, an injection scheme using shorter pulses of higher oxygen concentrations is shown to be superior to a scheme with equally long pulses of oxygen and the substrate.
Age of Irrigation Water in Ground Water from the Eastern Snake River Plain Aquifer, South‐Central Idaho
Authors: Plummer L.N. , Rupert M.G. , Busenberg E. , Schlosser P.
Published: August 2005

Stable isotope data (2H and 18O) were used in conjunction with chlorofluorocarbon (CFC) and tritium/helium‐3 (3H/3He) data to determine the fraction and age of irrigation water in ground water mixtures from farmed parts of the Eastern Snake River Plain (ESRP) Aquifer in south‐central Idaho. Two groups of waters were recognized: (1) regional background water, unaffected by irrigation and fertilizer application, and (2) mixtures of irrigation water from the Snake River with regional background water. New data are presented comparing CFC and 3H/3He dating of water recharged through deep fractured basalt, and dating of young fractions in ground water mixtures. The 3H/3He ages of irrigation water in most mixtures ranged from about zero to eight years. The CFC ages of irrigation water in mixtures ranged from values near those based on 3H/3He dating to values biased older than the 3H/3He ages by as much as eight to 10 years. Unsaturated zone air had CFC‐12 and CFC‐113 concentrations that were 60% to 95%, and 50% to 90%, respectively, of modern air concentrations and were consistently contaminated with CFC‐11. Irrigation water diverted from the Snake River was contaminated with CFC‐11 but near solubility equilibrium with CFC‐12 and CFC‐113. The dating indicates ground water velocities of 5 to 8 m/d for water along the top of the ESRP Aquifer near the southwestern boundary of the Idaho National Engineering and Environmental Laboratory (INEEL). Many of the regional background waters contain excess terrigenic helium with a 3He/4He isotope ratio of 7 × 10−6 to 11 × 10−6 (R/Ra= 5 to 8) and could not be dated. Ratios of CFC data indicate that some rangeland water may contain as much as 5% to 30% young water (ages of less than or equal to two to 11.5 years) mixed with old regional background water. The relatively low residence times of ground water in irrigated parts of the ESRP Aquifer and the dilution with low‐NO3 irrigation water from the Snake River lower the potential for NO3 contamination in agricultural areas.
Estimation of Vertical Concentration Profiles from Existing Wells
Authors: Sukop Michael C.
Published: August 2005

A method of computing the vertical distributions of solute concentrations in aquifer strata penetrated by an existing well or borehole can be developed from a simple solute mass/water balance approach. This approach allows refinement of site characterization without the cost of drilling additional wells or using other site characterization methods. This method also allows pre‐diction of the water quality impacts of different well construction and screening options when the vertical distribution of flows from an aquifer and the aquifer water concentrations are known or can be estimated. Data requirements and methods of data collection for use of the technique are reviewed. Flowmeter or spinner logging surveys indicate the flow contribution of each portion of the well. When depth‐specific samples are collected under the same pumping conditions as the spinner logging, a solute mass/water balance approach allows vertical concentration distributions in the aquifer to be estimated. Application to a well containing arsenic concentrations that approach the maximum contaminant level (MCL) of 50 μ/L indicates that water with arsenic concentrations of nearly 100 μ/L enters the well from a particular stratum.
Transient Flow to a Horizontal Water Well
Authors: Kawecki M.W.
Published: August 2005

Equations that approximately relate the transient head in a horizontal well to a constant well discharge are selected from the petroleum literature and converted from the notation and eclectic system of units used in the oil industry to ground water notation with consistent units. A homogeneous but not necessarily isotropic aquifer is assumed. Depending on the time since the start of discharge, the equations are basically the same in form as for flow to either a fully penetrating channel or to a vertical well, but they contain an additional term accounting for vertical flow. A modification is introduced to make the equations, which were derived for confined flow, approximately applicable to unconfined ground water conditions. The simple form of the equations makes their use practical.
Chlorine‐36 in Ground Water Containing Low Chloride Concentrations
Authors: Davis Stanley N. , Fabryka‐Martin June , Wolfsberg Laura , Moysey Stephen , Shaver Robert , Alexander E. Calvin , Krothe Noel
Published: August 2005

Analyses of ground water from wells and springs in the United States indicate a broad regional trend in preanthropogenic (36Cl/total Cl) ×1015 ratios in potable water. Coastal areas influenced by marine chloride have ratios less than 100. These ratios increase inland and reach a maximum of about 1400 in the central and northern Rocky Mountains. However, the magnitude of these regional variations is greatly exceeded at a local level if water samples are considered regardless of age or origin. Most local departures from regional trends can be attributed to mixing of ground water recharge with either 36Cl from nuclear fusion tests to produce higher ratios or mixing with sources of old chloride such as from evaporite minerals to produce lower ratios. A useful interpretation of 36Cl data is difficult unless the origin of the chloride is understood. The interpretation is an unusually difficult problem for water having low chloride concentrations. The assumption that low concentrations originate primarily from wet and dry atmospheric deposition can be questioned even for some dilute waters with less than 2.0 mg/L chloride. Chloride/bromide ratios in ground water can help decipher the origin of the chloride. The presence of nonatmospheric chloride can be identified in part by its association with chloride/bromide mass ratios greater than about 200 in coastal areas and 100 in inland areas. Accurate chloride and bromide analyses are recommended for virtually all studies of 36Cl in natural waters, and particularly those with low concentrations of chloride.
Ineffective Natural Attenuation of Degradable Organic Compounds in a Phenol‐Contaminated Aquifer
Authors: Lerner David N. , Thornton Steven F. , Spence Michael J. , Banwart Steven A. , Bottrell Simon H. , Higgo Jenny J. , Mallinson Helen E. H. , Pickup Roger W. , Williams Geoffrey M.
Published: August 2005

Two detailed vertical profiles through a complex plume of phenolic contaminants in a Triassic sandstone aquifer show that natural attenuation by biodegradation and dispersion is active but very slow. The plume has a microbially active aerobic and NO3 reducing fringe that is less than 2 m thick at both 150 and 350 m downstream of the source. The anaerobic core has evidence of active bacterial populations and degradation at total organic carbon (TOC) concentrations up to at least 1400 mg/L (1800 mg/L total phenolics), although gross half‐lives are more than 50 years. There is evidence from the same locations of Mn, Fe, and SO4 reduction, with the latter inhibited by the pollutant matrix and not significant at concentrations more than 1000 mg/L TOC. Degradation of these contaminants in this aquifer is influenced by a range of environmental factors, including the chemical toxicity and pH of the contaminant matrix, and inputs of electron acceptors into the plume by dispersion. The results show that the plume is likely to grow under the present conditions, despite the biodegradable nature of the organic pollutants and availability of suitable electron acceptors. Vertical profiles have proved a cost‐effective method of understanding the evolution of the plume.
Evaluation of Ground‐Penetrating Radar to Detect Free‐Phase Hydrocarbons in Fractured Rocks—Results of Numerical Modeling and Physical Experiments
Authors: Lane J.W. , Buursink M.L. , Haeni F.P. , Versteeg R.J.
Published: August 2005

The suitability of common‐offset ground‐penetrating radar (GPR) to detect free‐phase hydrocarbons in bedrock fractures was evaluated using numerical modeling and physical experiments. The results of one‐ and two‐dimensional numerical modeling at 100 megahertz indicate that GPR reflection amplitudes are relatively insensitive to fracture apertures ranging from 1 to 4 mm. The numerical modeling and physical experiments indicate that differences in the fluids that fill fractures significantly affect the amplitude and the polarity of electromagnetic waves reflected by subhorizontal fractures. Air‐filled and hydrocarbon‐filled fractures generate low‐amplitude reflections that are in‐phase with the transmitted pulse. Water‐filled fractures create reflections with greater amplitude and opposite polarity than those reflections created by air‐filled or hydrocarbon‐filled fractures.

The results from the numerical modeling and physical experiments demonstrate it is possible to distinguish water‐filled fracture reflections from air‐ or hydrocarbon‐filled fracture reflections, nevertheless subsurface heterogeneity, antenna coupling changes, and other sources of noise will likely make it difficult to observe these changes in GPR field data. This indicates that the routine application of common‐offset GPR reflection methods for detection of hydrocarbon‐filled fractures will be problematic. Ideal cases will require appropriately processed, high‐quality GPR data, ground‐truth information, and detailed knowledge of subsurface physical properties.

Conversely, the sensitivity of GPR methods to changes in subsurface physical properties as demonstrated by the numerical and experimental results suggests the potential of using GPR methods as a monitoring tool. GPR methods may be suited for monitoring pumping and tracer tests, changes in site hydrologic conditions, and remediation activities.
Coupling Between Neuronal Firing, Field Potentials, and fMRI in Human Auditory Cortex
Authors: Mukamel Roy , Gelbard Hagar , Arieli Amos , Hasson Uri , Fried Itzhak , Malach Rafael
Published: August 2005

Functional magnetic resonance imaging (fMRI) is an important tool for investigating human brain function, but the relationship between the hemodynamically based fMRI signals in the human brain and the underlying neuronal activity is unclear. We recorded single unit activity and local field potentials in auditory cortex of two neurosurgical patients and compared them with the fMRI signals of 11 healthy subjects during presentation of an identical movie segment. The predicted fMRI signals derived from single units and the measured fMRI signals from auditory cortex showed a highly significant correlation (
r
= 0.75,
P
< 10
–47
). Thus, fMRI signals can provide a reliable measure of the firing rate of human cortical neurons.
Probing the Ultrafast Charge Translocation of Photoexcited Retinal in Bacteriorhodopsin
Authors: Schenkl S. , van Mourik F. , van der Zwan G. , Haacke S. , Chergui M.
Published: August 2005

The ultrafast evolution of the electric field within bacteriorhodopsin was measured by monitoring the absorption changes of a tryptophan residue after excitation of retinal. The Trp absorption decreases within the first 200 femtoseconds and then recovers on time scales typical for retinal isomerization and vibrational relaxation. A model of excitonic coupling between retinal and tryptophans shows that the signal reflects a gradual rise of the retinal difference dipole moment, which precedes and probably drives isomerization. The results suggest an intimate connection between the progressive dipole moment change and the retinal skeletal changes reported over the same time scale.
A Crossover in the Mechanical Response of Nanocrystalline Ceramics
Authors: Szlufarska Izabela , Nakano Aiichiro , Vashishta Priya
Published: August 2005

Multimillion-atom molecular dynamics simulation of indentation of nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, resulting from the coexistence of brittle grains and soft amorphous grain boundary phases. Simulations predict a crossover from intergranular continuous deformation to intragrain discrete deformation at a critical indentation depth. The crossover arises from the interplay between cooperative grain sliding, grain rotations, and intergranular dislocation formation similar to stick-slip behavior. The crossover is also manifested in switching from deformation dominated by indentation-induced crystallization to deformation dominated by disordering, leading to amorphization. This interplay between deformation mechanisms is critical for the design of ceramics with superior mechanical properties.
Containing Pandemic Influenza at the Source
Authors: Longini Ira M. , Nizam Azhar , Xu Shufu , Ungchusak Kumnuan , Hanshaoworakul Wanna , Cummings Derek A. T. , Halloran M. Elizabeth
Published: August 2005

Highly pathogenic avian influenza A (subtype H5N1) is threatening to cause a human pandemic of potentially devastating proportions. We used a stochastic influenza simulation model for rural Southeast Asia to investigate the effectiveness of targeted antiviral prophylaxis, quarantine, and pre-vaccination in containing an emerging influenza strain at the source. If the basic reproductive number (
R
0
) was below 1.60, our simulations showed that a prepared response with targeted antivirals would have a high probability of containing the disease. In that case, an antiviral agent stockpile on the order of 100,000 to 1 million courses for treatment and prophylaxis would be sufficient. If pre-vaccination occurred, then targeted antiviral prophylaxis could be effective for containing strains with an
R
0
as high as 2.1. Combinations of targeted antiviral prophylaxis, pre-vaccination, and quarantine could contain strains with an
R
0
as high as 2.4.
Characterization of Excess Electrons in Water-Cluster Anions by Quantum Simulations
Authors: Turi László , Sheu Wen-Shyan , Rossky Peter J.
Published: August 2005

Water-cluster anions can serve as a bridge to understand the transition from gaseous species to the bulk hydrated electron. However, debate continues regarding how the excess electron is bound in

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, as an interior, bulklike, or surface electronic state. To address the uncertainty, the properties of

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clusters with 20 to 200 water molecules have been evaluated by mixed quantum-classical simulations. The theory reproduces every observed energetic, spectral, and structural trend with cluster size that is seen in experimental photoelectron and optical absorption spectra. More important, surface states and interior states each manifest a characteristic signature in the simulation data. The results strongly support assignment of surface-bound electronic states to the water-cluster anions in published experimental studies thus far.
Real-Time Quantitative PCR for Determining the Burden ofPlasmodium falciparumParasites during Pregnancy and Infancy
Authors: Malhotra Indu , Dent Arlene , Mungai Peter , Muchiri Eric , King Christopher L.
Published: August 2005

Real-time quantitative PCR (RTQ-PCR) provides a quick, accurate, and reproducible quantification of parasites. However, the value of RTQ-PCR for predicting clinical outcomes of malaria is unknown. Here, we compared RTQ-PCR to microscopy of blood smears, nested PCR (nPCR), and parasite circulating-antigen (CAg) assays for detection ofPlasmodium falciparumin pregnant Kenyan women and their infants and related these findings to parity and birth weights in their newborns (n= 554). nPCR was the most sensitive assay for detection of malaria in pregnancy, followed in decreasing order of sensitivity by RTQ-PCR, CAg assays, and blood smears. RTQ-PCR detected a higher frequency of malaria infection (46%) in maternal peripheral blood in primiparous than in multiparous women (35%;P< 0.001), with a >12-fold difference in parasite burden (geometric mean = 25,870 versus 2,143 amplicons/μl blood;P< 0.0001). Similarly, the presence of placental malaria determined by RTQ-PCR was approximately twofold higher in primiparous versus multiparous women (21% versus 13%;P< 0.01). The presence and intensity of malaria infection in pregnant women estimated by RTQ-PCR strongly correlated with low-birth-weight babies, especially in those with high amplicon numbers. RTQ-PCR identified malaria-infected women, missed by blood smear, who were at risk for having underweight offspring. By contrast, malaria detected by nPCR and CAg assay showed a much weaker association with parity or low birth weight. Thus, RTQ-PCR provides an estimate of parasite burden that is more sensitive than blood smear and is predictive of clinical outcomes of malaria infection in pregnant women and newborns.
Molecular Model for Studying the Uncultivated Fungal Pathogen
Lacazia loboi
Authors: Vilela Raquel , Mendoza Leonel , Rosa Patricia S. , Belone Andréa Faria Fernandes , Madeira Suzana , Opromolla Diltor Vladimir Araújo , de Resende Maria Aparecida
Published: August 2005

Lacazia loboi
is an uncultivated fungal pathogen of humans and dolphins that causes cutaneous and subcutaneous infections only in the tropical areas of the Americas. It was recently found by phylogenetic analysis that this unusual pathogen is closely related to
Paracoccidioides brasiliensis
and to the other fungal dimorphic members of the order
Onygenales
. That original phylogenetic study used universal primers to amplify well-known genes. However, this approach cannot be applied to the study of other proteins. We have developed a strategy for studying the gene encoding the gp43 homologous protein of
P. brasiliensis
in
L. loboi
. The gp43 protein was selected because it has been found that this
P. brasiliensis
antigen strongly reacts when it is used to test sera from patients with lacaziosis. The principle behind this idea was to obtain the gp43 amino acid sequence of
P. brasiliensis
and other homologous fungal sequences from GenBank and design primers from their aligned conserved regions. These sets of primers were used to amplify the selected regions with genomic DNA extracted from the yeast-like cells of
L. loboi
from experimentally infected mice. Using this approach, we amplified 483 bp of the
L. loboi
gp43-like gene. These sequences had 85% identity at the nucleotide level and 75% identity with the deduced amino acid sequences of the
P. brasiliensis
gp43 protein. The identity of the 483-bp DNA fragment was confirmed by phylogenetic analysis. This analysis revealed that the
L. loboi
gp43-like deduced amino acid sequence formed a strongly supported (100%) sister group with several
P. brasiliensis
gp43 sequences and that this taxon in turn was linked to the other fungal sequences used in this analysis. This study shows that the use of a molecular model for investigation of the genes encoding important proteins in
L. loboi
is feasible.
Strain Variation among
Bordetella pertussis
Isolates in Finland, Where the Whole-Cell Pertussis Vaccine Has Been Used for 50 Years
Authors: Elomaa Annika , Advani Abdolreza , Donnelly Declan , Antila Mia , Mertsola Jussi , Hallander Hans , He Qiushui
Published: August 2005

Pertussis is an infectious disease of the respiratory tract caused by
Bordetella pertussis
. Despite the introduction of mass vaccination against pertussis in Finland in 1952, pertussis has remained an endemic disease with regular epidemics. To monitor changes in the Finnish
B. pertussis
population, 101 isolates selected from 1991 to 2003 and 21 isolates selected from 1953 to 1982 were studied together with two Finnish vaccine strains. The analyses included serotyping of fimbriae (Fim), genotyping of the pertussis toxin S1 subunit (
ptxA
) and pertactin (
prn
), and pulsed-field gel electrophoresis (PFGE) after digestion of
B. pertussis
genomic DNA with XbaI restriction enzyme. Strains isolated before 1977 were found to harbor the same
ptxA
as the strains used in the Finnish whole-cell pertussis vaccine, and strains isolated before 1982 harbored the same
prn
as the strains used in the Finnish whole-cell pertussis vaccine. All recent isolates, however, represented genotypes distinct from those of the two vaccine strains. A marked shift of predominant serotype from Fim serotype 2 (Fim2) to Fim3 has been observed since the late 1990s. Temporal changes were seen in the genome of
B. pertussis
by PFGE analysis. Three PFGE profiles (BpSR1, BpSR11, and BpSR147) were distinguished by their prevalence between 1991 and 2003. The yearly emergence of the three profiles was distributed periodically. Our study stresses the importance of the continuous monitoring of emerging strains of
B. pertussis
and the need to obtain a better understanding of the relationship of the evolution of
B. pertussis
in vaccinated populations.
DNA Sequence-Based Subtyping and Evolutionary Analysis of Selected
Salmonella enterica
Serotypes
Authors: Sukhnanand Sharinne , Alcaine Sam , Warnick Lorin D. , Su Wan-Lin , Hof Jessica , Craver Mary Pat J. , McDonough Patrick , Boor Kathryn J. , Wiedmann Martin
Published: August 2005

While serotyping and phage typing have been used widely to characterize
Salmonella
isolates, sensitive subtyping methods that allow for evolutionary analyses are essential for examining
Salmonella
transmission, ecology, and evolution. A set of 25
Salmonella enterica
isolates, representing five clinically relevant serotypes (serotypes Agona, Heidelberg, Schwarzengrund, Typhimurium, and Typhimurium var. Copenhagen) was initially used to develop a multilocus sequence typing (MLST) scheme for
Salmonella
targeting seven housekeeping and virulence genes (
panB
,
fimA
,
aceK
,
mdh
,
icdA
,
manB
, and
spaN
). A total of eight MLST types were found among the 25 isolates sequenced. A good correlation between MLST types and
Salmonella
serotypes was observed; only one serotype Typhimurium var. Copenhagen isolate displayed an MLST type otherwise typical for serotype Typhimurium isolates. Since
manB
,
fimA
, and
mdh
allowed for the highest subtype discrimination among the initial 25 isolates, we chose these three genes to perform DNA sequencing of an additional 41
Salmonella
isolates representing a larger diversity of serotypes. This “three-gene sequence typing scheme” allowed discrimination of 25 sequence types (STs) among a total of 66 isolates; STs correlated well with serotypes and allowed within-serotype differentiation for 9 of the 12 serotypes characterized. Phylogenetic analyses showed that serotypes Kentucky and Newport could each be separated into two distinct, statistically well supported evolutionary lineages. Our results show that a three-gene sequence typing scheme allows for accurate serotype prediction and for limited subtype discrimination among clinically relevant serotypes of
Salmonella
. Three-gene sequence typing also supports the notion that
Salmonella
serotypes represent both monophyletic and polyphyletic lineages.
Use of the Genotype MTBDR Assay for Rapid Detection of Rifampin and Isoniazid Resistance in
Mycobacterium tuberculosis
Complex Isolates
Authors: Hillemann Doris , Weizenegger Michael , Kubica Tanja , Richter Elvira , Niemann Stefan
Published: August 2005

A commercially available DNA strip assay (Genotype MTBDR; Hain Lifescience, Nehren, Germany) was evaluated for its ability to detect mutations conferring resistance to rifampin (RMP) and isoniazid (INH) in clinical
Mycobacterium tuberculosis
complex isolates. A total of 103 multidrug-resistant (MDR; i.e., at least resistant to RMP and INH) and 40 fully susceptible strains isolated in Germany in 2001 in which resistance mutations have been previously defined by DNA sequencing and real-time PCR analysis were investigated. The Genotype MTBDR assay identified 102 of the 103 MDR strains with mutations in the
rpoB
gene (99%) and 91 strains (88.4%) with mutations in codon 315 of
katG
. All 40 susceptible strains showed a wild-type MTBDR hybridization pattern. The concordance between the MTBDR assay and the DNA sequencing results was 100%. Compared to conventional drug susceptibility testing, the sensitivity and specificity were 99 and 100% for RMP resistance and 88.4 and 100% for INH resistance, respectively. In conclusion, the MTBDR assay is a rapid and easy-to-perform test for the detection of the most common mutations found in MDR
M. tuberculosis
strains that can readily be included in a routine laboratory work flow.
Genomic Polymorphisms forMycobacterium aviumsubsp.paratuberculosisDiagnostics
Authors: Semret Makeda , Alexander David C. , Turenne Christine Y. , de Haas Petra , Overduin Pieter , van Soolingen Dick , Cousins Debby , Behr Marcel A.
Published: August 2005

Mycobacterium aviumsubsp.paratuberculosisis an emerging pathogen of mammals and is being actively investigated as a possible zoonotic agent. The lack of reliable diagnostic assays has hampered rational assessment of the prevalence of this organism in humans and animals. We have used a comparative genomic approach to reveal genomic differences betweenM. aviumsubsp.paratuberculosisand its close relativeM. aviumsubsp.avium, a highly prevalent environmental organism. From computational and DNA microarray-based study of two prototype strains,M. aviumsubsp.aviumstrain 104 andM. aviumsubsp.paratuberculosisstrain K10, we have uncovered two types of large sequence polymorphisms (LSPs): those present in the former but missing in the latter (LSPAs) and those only present in the latter (LSPPs). We examined the distribution of 3 LSPAs and 17 LSPPs across a panel of 383M. aviumcomplex isolates in order to determine their potential utility for the development of accurate diagnostic tests. Our results show that the absence of LSPA8 is 100% specific for the identification ofM. aviumsubsp.paratuberculosis. Of the 17 LSPPs, 10 regions were not specific forM. aviumsubsp.paratuberculosiswhile 7 were shown to be highly specific (>98%) and, in some cases, highly sensitive as well (up to 95%). These data highlight the need to evaluate these regions across a diverse panel of clinical and environmental isolates and indicate the LSPs best suited forM. aviumsubsp.paratuberculosisdiagnostics.
Mannitol Salt Agar-Cefoxitin Combination as a Screening Medium for Methicillin-Resistant
Staphylococcus aureus
Authors: Smyth R. W. , Kahlmeter Gunnar
Published: August 2005

In disk diffusion tests, cefoxitin is now considered a better indicator than oxacillin for the presence of the
mecA
gene in
Staphylococcus aureus
. A logical extension of this work is the incorporation of cefoxitin into media selective for methicillin-resistant
Staphylococcus aureus
(MRSA). This paper describes the development and subsequent testing of mannitol salt agar containing 4 mg/liter cefoxitin with a unique collection of well-characterized MRSA strains, including low-level methicillin-resistant strains and an equal number of known
mecA
-negative
S. aureus
strains. The agar supported the growth of 96.6% of the
mecA
-positive strains in the collection and inhibited the growth of 100% of the
mecA
-negative strains. These results suggest that selective media based on cefoxitin are superior to those based on oxacillin for the detection of MRSA.
Diagnosis of Cat Scratch Disease with Detection of
Bartonella henselae
by PCR: a Study of Patients with Lymph Node Enlargement
Authors: Hansmann Yves , DeMartino Sylvie , Piémont Yves , Meyer Nicolas , Mariet Philippe , Heller Rémy , Christmann Daniel , Jaulhac Benoît
Published: August 2005

Cat scratch disease (CSD) is mostly due to
Bartonella henselae
after inoculation of the organism through a skin injury. Since the causative bacteria cannot be easily cultured from human lymph node samples, the diagnosis usually relies on epidemiological, clinical, histological, and serological criteria (classical criteria). A study was performed to determine the diagnostic value of PCR analysis for the detection of
B. henselae
for the diagnosis of CSD and its place in the diagnostic strategy alongside the classical criteria. Over a 7-year period, lymph node biopsy specimens or cytopunctures from 70 patients were systematically tested by PCR for the presence of
B. henselae
DNA (
htrA
gene) in the Bacteriology Laboratory of the Hôpitaux Universitaires de Strasbourg. Serological testing by an immunofluorescence assay for
B. henselae
antibodies was also performed for each patient, and clinical, epidemiological, and histological data were collected. The patients were then divided into two groups according to the number of positive diagnostic criteria for CSD: 29 patients with definite CSD (two or more classical criteria) and 15 patients with possible CSD (less than two classical criteria). The remaining 26 patients for whom another diagnosis was retained were used as a control group. Among all criteria, PCR analysis had the best specificity (100%). The PCR assay for
B. henselae
was positive for 22 (76%; 95% confidence interval [CI
95
], 56.5 to 89.7%) of the 29 definite CSD patients and 3 (20%; CI
95
, 4.3 to 48.1%) of the 15 possible CSD patients. We then studied combinations of diagnostic criteria, including
B. henselae
PCR analysis. The best diagnostic performance was observed if at least two criteria were present among serologic, epidemiologic, histological, and molecular criteria.
Computational Approach Involving Use of the Internal Transcribed Spacer 1 Region for Identification of
Mycobacterium
Species
Authors: Mohamed Amr M. , Kuyper Dan J. , Iwen Peter C. , Ali Hesham H. , Bastola Dhundy R. , Hinrichs Steven H.
Published: August 2005

The rapid and reliable identification of clinically significant
Mycobacterium
species is a challenge for diagnostic laboratories. This study evaluates a unique sequence-dependent identification algorithm called
MycoAlign
for the differential identification of
Mycobacterium
species. The
MycoAlign
system uses pan-
Mycobacterium
-specific primer amplification in combination with a customized database and algorithm. The results of testing were compared with conventional phenotypic assays and GenBank sequence comparisons using the 16S rRNA target. Discrepant results were retested and evaluated using a third independent database. The custom database was generated using the hypervariable sequences of the internal transcribed spacer 1 (ITS-1) region of the rRNA gene complex from characterized
Mycobacterium
species. An automated sequence-validation process was used to control quality and specificity of evaluated sequence. A total of 181
Mycobacterium
strains (22 reference strains and 159 phenotypically identified clinical isolates) and seven nonmycobacterial clinical isolates were evaluated in a comparative study to validate the accuracy of the
MycoAlign
algorithm.
MycoAlign
correctly identified all referenced strains and matched species in 94% of the phenotypically identified
Mycobacterium
clinical isolates. The ITS-1 sequence target showed a higher degree of specificity in terms of
Mycobacterium
identification than the 16S rRNA sequence by use of GenBank BLAST. This study showed the
MycoAlign
algorithm to be a reliable and rapid approach for the identification of
Mycobacterium
species and confirmed the superiority of the ITS-1 region sequence over the 16S rRNA gene sequence as a target for sequence-based species identification.
Results of Disk Diffusion Testing with Cefoxitin Correlate with Presence of
mecA
in
Staphylococcus
spp
Authors: Swenson Jana M. , Tenover Fred C. ,   the Cefoxitin Disk Study Group
Published: August 2005

The cefoxitin disk diffusion (DD) test for predicting
mecA-
mediated oxacillin resistance in staphylococci was assessed during a three-phase study. In phase 1, one laboratory tested 62 and 53 strains of
Staphylococcus aureus
and coagulase-negative staphylococci (CoNS), respectively. These data were used to choose the provisional cefoxitin DD breakpoints (resistant/susceptible) of ≤19 mm/≥20 mm for
S. aureus
and ≤24 mm/≥25 mm for CoNS for the next phase of testing. In phase 2, 10 laboratories each tested approximately 40 in-house strains of staphylococci (half of which were
S. aureus
) using Mueller-Hinton agar from different manufacturers. In this phase, the sensitivity and specificity, respectively, of the cefoxitin disk test were 98 and 100% for
S. aureus
and 99 and 96% for CoNS. The cefoxitin DD test performed equivalently to oxacillin broth microdilution (BMD) and to oxacillin DD tests among
S. aureus
and
mecA
-positive CoNS strains but gave better results than oxacillin BMD or oxacillin DD for
mecA
-negative strains of CoNS. The cefoxitin DD test also was much easier to read and did not require the use of transmitted light for detection of resistance. Based on data from the first two phases, the Clinical and Laboratory Standards Institute (CLSI; formerly NCCLS) adopted the use of the cefoxitin DD test for predicting
mecA-
mediated oxacillin resistance in staphylococci and revised Table 2C in CLSI document M100-S14 to reflect the change. In the third phase, an additional 61 challenge strains of CoNS for which the oxacillin MICs were 0.5 to 2 μg/ml were tested in a single laboratory to determine the effectiveness of the cefoxitin DD test for this group of borderline-resistant isolates. These data were used to refine the description of the test in CLSI document M100-S15. The cefoxitin DD test is preferred over the oxacillin DD test for predicting
mecA
-mediated oxacillin resistance in
S. aureus
and CoNS.
Nosocomial Outbreak Caused by Multidrug-Resistant
Pseudomonas aeruginosa
Producing IMP-13 Metallo-β-Lactamase
Authors: Pagani Laura , Colinon Céline , Migliavacca Roberta , Labonia Maria , Docquier Jean-Denis , Nucleo Elisabetta , Spalla Melissa , Li Bergoli Michele , Rossolini Gian Maria
Published: August 2005

An outbreak of
Pseudomonas aeruginosa
showing a multidrug-resistant (MDR) phenotype (including carbapenems, ceftazidime, cefepime, gentamicin, tobramycin, and fluoroquinolones) was observed, during a 5-month period, in a general intensive care unit of a large tertiary care and clinical research hospital in southern Italy. The outbreak involved 15 patients, with a total of 87 isolates, mostly from lower respiratory tract specimens. Analysis of isolates involved in the outbreak revealed production of metallo-β-lactamase (MBL) activity, and genotyping by pulsed-field gel electrophoresis of genomic DNA digested by SpeI revealed clonal relatedness among isolates. Molecular analysis of the MBL determinant showed the presence of a
bla
IMP-13
gene carried on a gene cassette inserted in a class 1 integron which also contained an
aacA4
aminoglycoside resistance cassette encoding an AAC(6′)-Ib enzyme. The
bla
IMP-13
-containing integron and its genetic environment appeared to be similar to those found in
P. aeruginosa
isolates producing IMP-13 from a hospital in Rome. The
bla
IMP-13
gene was not transferable by conjugation and was apparently carried on the chromosome. The outbreak was coincidental with a shortage of nursing personnel, and resolution was apparently associated with reinstatement of nursing personnel and reinforcement of general infection control practices within the intensive care unit. To our best knowledge this is the first description of a nosocomial outbreak of relatively large size caused by an IMP-producing gram-negative pathogen in Europe.
Genetic Characteristics of Human Enterovirus 71 and Coxsackievirus A16 Circulating from 1999 to 2004 in Shenzhen, People's Republic of China
Authors: Li Linlin , He Yaqing , Yang Hong , Zhu Junping , Xu Xingye , Dong Jie , Zhu Yafang , Jin Qi
Published: August 2005

The genetic and phylogenetic characteristics of human enterovirus 71 (EV71) and coxsackievirus A16 (CA16) sampled from children with hand, foot, and mouth disease in Shenzhen, People's Republic of China, over a 6-year period (1999 to 2004) were examined with reverse transcription-PCR and DNA sequencing. Out of 147 stool specimens, 60 showed positive signals when screened with EV71- and CA16-specific primers. EV71 was identified in 19 specimens, and CA16 was identified in 41 specimens; coinfection by EV71 and CA16 was not observed. Phylogenetic analysis of all EV71 strains isolated from the mainland Chinese samples established C4 as the predominant genotype. Only one other known strain (3254-TAI-98; AF286531), isolated in Taiwan in 1998, was identified as belonging to genotype C4. Phylogenetic analysis of CA16 strains allowed us to identify three new genetic lineages (A, B, and C), with lineage C recently predominating in Asian countries, such as the People's Republic of China, Malaysia, and Japan. These new observations indicate that CA16 circulating in the People's Republic of China is genetically diverse, and additional surveillance is warranted.