Introducing a Dynamic Reconstruction Methodology for Multilayered Structures in Atom Probe Tomography

Atom probe tomography (APT) is a powerful three-dimensional nanoanalyzing microscopy technique considered key in modern materials science. However, progress in the spatial reconstruction of APT data has been rather limited since the first implementation of the protocol proposed by Bas et al. in 1995. This paper proposes a simple semianalytical approach to reconstruct multilayered structures, i.e., two or more different compounds stacked perpendicular to the analysis direction. Using a field evaporation model, the general dynamic evolution of parameters involved in the reconstruction of this type of structure is estimated. Some experimental reconstructions of different structures through the implementation of this method that dynamically accommodates variations in the tomographic reconstruction parameters are presented. It is shown both experimentally and theoretically that the depth accuracy of reconstructed APT images is improved using this method. The method requires few parameters in order to be easily usable and substantially improves atom probe tomographic reconstructions of multilayered structures.

Machine-learning-enhanced time-of-flight mass spectrometry analysis

Mass spectrometry is a widespread approach used to work out what the constituents of a material are. Atoms and molecules are removed from the material and collected, and subsequently, a critical step is to infer their correct identities based on patterns formed in their mass-to-charge ratios and relative isotopic abundances. However, this identification step still mainly relies on individual users' expertise, making its standardization challenging, and hindering efficient data processing. Here, we introduce an approach that leverages modern machine learning technique to identify peak patterns in time-of-flight mass spectra within microseconds, outperforming human users without loss of accuracy. Our approach is cross-validated on mass spectra generated from different time-of-flight mass spectrometry (ToF-MS) techniques, offering the ToF-MS community an open-source, intelligent mass spectra analysis.

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A machine-learning method provides reliable atomic/molecular labels for ToF-MS

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No human labeling or prior information required

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The training dataset is artificially generated based on isotopic abundances

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Method validated on a variety of materials and two ToF-MS-based techniques

Time-of-flight mass spectrometry (ToF-MS) is a mainstream analytical technique widely used in biology, chemistry, and materials science. ToF-MS provides quantitative compositional analysis with high sensitivity across a wide dynamic range of mass-to-charge ratios. A critical step in ToF-MS is to infer the identity of the detected ions. Here, we introduce a machine-learning-enhanced algorithm to provide a user-independent approach to performing this identification using patterns from the natural isotopic abundances of individual atomic and molecular ions, without human labeling or prior knowledge of composition. Results from several materials and techniques are compared with those obtained by field experts. Our open-source, easy-to-implement, reliable analytic method accelerates this identification process. A wide range of ToF-MS-based applications can benefit from our approach, e.g., hunting for patterns of biomarkers or for contamination on solid surfaces in high-throughput data.

Scolopostethus affinis (Schilling) (Hemiptera, Heteroptera, Rhyparochromidae, Drymini): a new alien established in North America

Scolopostethusaffinis, a species native to the Palearctic region, is reported from two localities in Montreal, Quebec. The species appears established and breeding in Quebec and is a new alien species in North America. A description of S.affinis is given, with illustrations, and details of the life cycle and diagnostic characters.

A Study of Parameters Affecting Atom Probe Tomography Specimen Survivability

Specimen survivability is a primary concern to those who utilize atom probe tomography (APT) for materials analysis. The state-of-the-art in understanding survivability might best be described as common-sense application of basic physics principles to describe failure mechanisms. For example, APT samples are placed under near-failure mechanical-stress conditions, so reduction in the force required to initiate field evaporation must provide for higher survivability-a common sense explanation of survivability. However, the interplay of various analytical conditions (or instrumentation) and how they influence survivability (e.g., decreasing the applied evaporation field improves survivability), and which factors have more impact than others has not been studied. In this paper, we report on the systematic analysis of a material composed of a silicon-dioxide layer surrounded on two sides by silicon. In total, 261 specimens were fabricated and analyzed under a variety of conditions to correlate statistically significant survivability trends with analysis conditions and other specimen characteristics. The primary result suggests that, while applied field/force plays an obvious role in survivability for this material, the applied field alone does not predict survivability trends for silicon/silicon-dioxide interfaces. The rate at which ions are extracted from the specimen (both in terms of ions-per-pulse and pulse-frequency) has similar importance.

Dopant Distribution in Atomic Layer Deposited ZnO:Al Films Visualized by Transmission Electron Microscopy and Atom Probe Tomography

The maximum conductivity achievable in Al-doped ZnO thin films prepared by atomic layer deposition (ALD) is limited by the low doping efficiency of Al. To better understand the limiting factors for the doping efficiency, the three-dimensional distribution of Al atoms in the ZnO host material matrix has been examined on the atomic scale using a combination of high-resolution transmission electron microscopy (TEM) and atom probe tomography (APT). Although the Al distribution in ZnO films prepared by so-called "ALD supercycles" is often presented as atomically flat δ-doped layers, in reality a broadening of the Al-dopant layers is observed with a full-width-half-maximum of ∼2 nm. In addition, an enrichment of the Al at grain boundaries is observed. The low doping efficiency for local Al densities > ∼1 nm^-3 can be ascribed to the Al solubility limit in ZnO and to the suppression of the ionization of Al dopants from adjacent Al donors.

Atomic-scale age resolution of planetary events

Resolving the timing of crustal processes and meteorite impact events is central to understanding the formation, evolution and habitability of planetary bodies. However, identifying multi-stage events from complex planetary materials is highly challenging at the length scales of current isotopic techniques. Here we show that accurate U-Pb isotopic analysis of nanoscale domains of baddeleyite can be achieved by atom probe tomography. Within individual crystals of highly shocked baddeleyite from the Sudbury impact structure, three discrete nanostructural domains have been isolated yielding average ²⁰⁶Pb/²³⁸U ages of 2,436±94 Ma (protolith crystallization) from homogenous-Fe domains, 1,852±45 Ma (impact) from clustered-Fe domains and 1,412±56 Ma (tectonic metamorphism) from planar and subgrain boundary structures. Baddeleyite is a common phase in terrestrial, Martian, Lunar and asteroidal materials, meaning this atomic-scale approach holds great potential in establishing a more accurate chronology of the formation and evolution of planetary crusts.

Constraining the timing of crustal processes and impact events remains challenging. Here, the authors show that atom probe tomography can produce highly accurate U-Pb isotopic age constraints in baddeleyite crystals, which is a common phase in terrestrial, Martian, Lunar and asteroidal materials.

Modern Focused-Ion-Beam-Based Site-Specific Specimen Preparation for Atom Probe Tomography

Approximately 30 years after the first use of focused ion beam (FIB) instruments to prepare atom probe tomography specimens, this technique has grown to be used by hundreds of researchers around the world. This past decade has seen tremendous advances in atom probe applications, enabled by the continued development of FIB-based specimen preparation methodologies. In this work, we provide a short review of the origin of the FIB method and the standard methods used today for lift-out and sharpening, using the annular milling method as applied to atom probe tomography specimens. Key steps for enabling correlative analysis with transmission electron-beam backscatter diffraction, transmission electron microscopy, and atom probe tomography are presented, and strategies for preparing specimens for modern microelectronic device structures are reviewed and discussed in detail. Examples are used for discussion of the steps for each of these methods. We conclude with examples of the challenges presented by complex topologies such as nanowires, nanoparticles, and organic materials.

Twelve new species and fifty-three new provincial distribution records of Aleocharinae rove beetles of Saskatchewan, Canada (Coleoptera, Staphylinidae)

One hundred twenty species of aleocharine beetles (Staphylinidae) are recognized in the province of Saskatchewan. Sixty-five new provincial records, including twelve new species and one new North American record, are presented. Oligotainflata (Mannerheim), a Palearctic species, is newly recorded for North America. The following twelve species are described as new to science: Acrotonapseudopygmaea Klimaszewski & Larson, sp. n., Agaricomorphapulchra Klimaszewski & Larson, sp. n. (new genus record for Canadian fauna), Aleocharaelisabethae Klimaszewski & Larson, sp. n., Atheta (Dimetrota) larsonae Klimaszewski & Larson, sp. n., Atheta (Microdota) pseudopittionii Klimaszewski & Larson, sp. n., Atheta (Microdota) spermathecorum Klimaszewski & Larson, sp. n., Atheta (sensu lato) richardsoni Klimaszewski & Larson, sp. n., Brachyusasaskatchewanae Klimaszewski & Larson, sp. n., Dochmonotalangori Klimaszewski & Larson, sp. n., Dochmonotasimulans Klimaszewski & Larson, sp. n., Dochmonotawebsteri Klimaszewski & Larson, sp. n., and Oxypodadomestica Klimaszewski & Larson, sp. n. Colour images of habitus and black and white images of the median lobe of the aedeagus, spermatheca, and tergite and sternite VIII are presented for all new species, Oligotainflata Mannerheim and Dochmonotarudiventris (Eppelsheim). A new synonymy is established: Tetralinafilitarsus Casey, syn. n. = Tetralinahelenae Casey, now placed in the genus Brachyusa Mulsant & Rey.

Implementing Transmission Electron Backscatter Diffraction for Atom Probe Tomography

There are advantages to performing transmission electron backscattering diffraction (tEBSD) in conjunction with focused ion beam-based specimen preparation for atom probe tomography (APT). Although tEBSD allows users to identify the position and character of grain boundaries, which can then be combined with APT to provide full chemical and orientation characterization of grain boundaries, tEBSD can also provide imaging information that improves the APT specimen preparation process by insuring proper placement of the targeted grain boundary within an APT specimen. In this report we discuss sample tilt angles, ion beam milling energies, and other considerations to optimize Kikuchi diffraction pattern quality for the APT specimen geometry. Coordinated specimen preparation and analysis of a grain boundary in a Ni-based Inconel 600 alloy is used to illustrate the approach revealing a 50° misorientation and trace element segregation to the grain boundary.

On the roles of graphene oxide doping for enhanced supercurrent in MgB2 based superconductors

Due to their graphene-like properties after oxygen reduction, incorporation of graphene oxide (GO) sheets into correlated-electron materials offers a new pathway for tailoring their properties. Fabricating GO nanocomposites with polycrystalline MgB2 superconductors leads to an order of magnitude enhancement of the supercurrent at 5 K/8 T and 20 K/4 T. Herein, we introduce a novel experimental approach to overcome the formidable challenge of performing quantitative microscopy and microanalysis of such composites, so as to unveil how GO doping influences the structure and hence the material properties. Atom probe microscopy and electron microscopy were used to directly image the GO within the MgB2, and we combined these data with computational simulations to derive the property-enhancing mechanisms. Our results reveal synergetic effects of GO, namely, via localized atomic (carbon and oxygen) doping as well as texturing of the crystals, which provide both inter- and intra-granular flux pinning. This study opens up new insights into how low-dimensional nanostructures can be integrated into composites to modify the overall properties, using a methodology amenable to a wide range of applications.

Focused ion beam fabrication of solidified ferritin into nanoscale volumes for compositional analysis using atom probe tomography

The purpose of this investigation was to conduct atom probe tomography (APT) analyses on ferritin specimens prepared with focused ion beam (FIB) to assess whether this approach can be used to effectively characterize biomaterials. Soft matter is particularly sensitive to ion beam exposure which can induce physical and chemical changes. We employ protective metal films and low-energy ion fluence to mitigate potential problems that may be introduced by FIB. This study had two major objectives: (1) to qualitatively assess the viability of the specimens when subjected to the unique physical conditions of APT analysis, namely ultrahigh vacuum, high electric field, and thermal pulsing using a laser and (2) to quantitatively assess the data from such specimens under various experimental parameters and compare the results with appropriate control specimens. For the first objective, a range of experimental parameters were determined that met the basic criteria necessary to validate that ferritin-based specimens prepared with FIB can retain structural integrity during APT analysis. Initial field evaporation time-of-flight mass spectrometry (TOF-MS) data show that the specimens fabricated with FIB are capable of emitting ions under various laser pulsing conditions with a high electric field applied. For the second objective, the experimental parameter space was narrowed to a range that yielded data quality sufficient to produce meaningful comparison between the ferritin-based specimens and the salt-only controls.

On the use of simulated field-evaporated specimen apex shapes in atom probe tomography data reconstruction

The ability to accurately reconstruct original spatial positions of field-evaporated ions emitted from a surface is fundamental to the success of atom probe tomography. As such, a clear understanding of the evolution of specimen shape and the resultant ions' trajectories during field evaporation plays an important role in improving reconstruction accuracy. To further this understanding, field-evaporation simulations of a bilayer specimen composed of two materials having an evaporation field difference of 20% were performed. The simulated field-evaporation patterns qualitatively compare favorably with experimental data, which provides confidence in the accuracy of specimen shapes predicted by the simulation. Correlations of known original atom positions with detector hit positions as a function of lateral detector position and evaporated depth were derived from the simulation. These correlations are contrasted with the current state-of-the-art reconstruction method thus outlining limitations of the current methodology. A pair of transformations are defined that take into account field-evaporated specimen shapes, and the resulting radial magnifications, to relate recorded ion positions in detector space to reconstructed atomic positions in specimen space. This novel process, when applied to simulated data, results in approximately a factor of 2 improvement in accuracy for reconstructions of interfaces with unequal fields (most general interfaces). This method is not constrained by the fundamental assumption of a hemispherical specimen shape.

AQUATIC COLEOPTERA OF PEATLANDS AND MARSHES IN CANADA

A rich fauna of water beetles, comprising 11 families and 485 species, occurs in Canadian peatlands and marshes. These beetles are diverse with respect to morphology, feeding habits, life-history patterns, and even in the degree to which they occur in water. Major adaptations to peatland and marsh habitats are described. Based on species composition, the following regional communities of marsh-inhabiting beetles are recognized: arctic, boreal, Cordilleran, grasslands, and eastern temperate. Peatlands possess a community of beetles similar to that of boreal marshes but contain enough unique elements to warrant separate recognition. However, based on water beetle distribution, it is not possible to subdivide peatlands into bog and fen communities because these habitats have many species in common. Future needs for research on wetland water beetles are identified.

Hot electron temperature and coupling efficiency scaling with prepulse for cone-guided fast ignition

The effect of increasing prepulse energy levels on the energy spectrum and coupling into forward-going electrons is evaluated in a cone-guided fast-ignition relevant geometry using cone-wire targets irradiated with a high intensity (10(20) W/cm(2)) laser pulse. Hot electron temperature and flux are inferred from Kα images and yields using hybrid particle-in-cell simulations. A two-temperature distribution of hot electrons was required to fit the full profile, with the ratio of energy in a higher energy (MeV) component increasing with a larger prepulse. As prepulse energies were increased from 8 mJ to 1 J, overall coupling from laser to all hot electrons entering the wire was found to fall from 8.4% to 2.5% while coupling into only the 1-3 MeV electrons dropped from 0.57% to 0.03%.

Atomic-scale phase composition through multivariate statistical analysis of atom probe tomography data

We demonstrate for the first time that multivariate statistical analysis techniques can be applied to atom probe tomography data to estimate the chemical composition of a sample at the full spatial resolution of the atom probe in three dimensions. Whereas the raw atom probe data provide the specific identity of an atom at a precise location, the multivariate results can be interpreted in terms of the probabilities that an atom representing a particular chemical phase is situated there. When aggregated to the size scale of a single atom (∼0.2 nm), atom probe spectral-image datasets are huge and extremely sparse. In fact, the average spectrum will have somewhat less than one total count per spectrum due to imperfect detection efficiency. These conditions, under which the variance in the data is completely dominated by counting noise, test the limits of multivariate analysis, and an extensive discussion of how to extract the chemical information is presented. Efficient numerical approaches to performing principal component analysis (PCA) on these datasets, which may number hundreds of millions of individual spectra, are put forward, and it is shown that PCA can be computed in a few seconds on a typical laptop computer.

Spatial distribution maps for atom probe tomography

A real-space technique for finding structural information in atom probe tomographs, spatial distribution maps (SDM), is described. The mechanics of the technique are explained, and it is then applied to some test cases. Many applications of SDM in atom probe tomography are illustrated with examples including finding crystal lattices, correcting lattice strains in reconstructed images, quantifying trajectory aberrations, quantifying spatial resolution, quantifying chemical ordering, dark-field imaging, determining orientation relationships, extracting radial distribution functions, and measuring ion detection efficiency.

Review of atom probe FIB-based specimen preparation methods

Several FIB-based methods that have been developed to fabricate needle-shaped atom probe specimens from a variety of specimen geometries, and site-specific regions are reviewed. These methods have enabled electronic device structures to be characterized. The atom probe may be used to quantify the level and range of gallium implantation and has demonstrated that the use of low accelerating voltages during the final stages of milling can dramatically reduce the extent of gallium implantation.

Imaging of Arsenic Cottrell Atmospheres Around Silicon Defects by Three-Dimensional Atom Probe Tomography

Discrete control of individual dopant or impurity atoms is critical to the electrical characteristics and fabrication of silicon nanodevices. The unavoidable introduction of defects into silicon during the implantation process may prevent the uniform distribution of dopant atoms. Cottrell atmospheres are one such nonuniformity and occur when interstitial atoms interact with dislocations, pinning the dislocation and trapping the interstitial. Atom probe tomography has been used to quantify the location and elemental identity of the atoms proximate to defects in silicon. We found that Cottrell atmospheres of arsenic atoms form around defects after ion implantation and annealing. Furthermore, these atmospheres persist in surrounding dislocation loops even after considerable thermal treatment. If not properly accommodated, these atmospheres create dopant fluctuations that ultimately limit the scalability of silicon devices.

In situ site-specific specimen preparation for atom probe tomography

Techniques for the rapid preparation of atom-probe samples extracted directly from a Si wafer are presented and discussed. A systematic mounting process to a standardized microtip array allows approximately 12 samples to be extracted from a near-surface region and mounted for subsequent focused-ion-beam sharpening in a short period of time, about 2h. In addition, site-specific annular mill extraction techniques are demonstrated that allow specific devices or structures to be removed from a Si wafer and analyzed in the atom-probe. The challenges presented by Ga-induced implantation and damage, particularly at a standard ion-beam accelerating voltage of 30 keV, are shown and discussed. A significant reduction in the extent of the damaged regions through the application of a low-energy "clean-up" ion beam is confirmed by atom-probe analysis of the damaged regions. The Ga+ penetration depth into {100} Si at 30 keV is approximately 40 nm. Clean-up with either a 5 or 2 keV beam reduces the depth of damaged Si to approximately 5 nm and <1 nm, respectively. Finally, a NiSi sample was extracted from a Si wafer, mounted to a microtip array, sharpened, cleaned up with a 5 keV beam and analyzed in the atom probe. The current results demonstrate that specific regions of interest can be accessed and preserved throughout the sample-preparation process and that this preparation method leads to high-quality atom probe analysis of such nano-structures.

Introduction: a special issue on nanoscale characterization using atom probe field ion microscopy

While searching the internet for “nanotechnology,” I was not surprised to find many definitions. Two of these are as follows: (1) nanotechnology is the development and use of devices that have a size of only a few nanometers; and (2) nanotechnology can best be considered as a “catch-all” description of activities at the level of atoms and molecules that have applications in the real world. While nanotechnology is usually focused on the building of structures at the atomic scale, the characterization of such structures should also be considered as nanotechnology. At the Microscopy and Microanalysis 2002 Meeting in Quebec City, together with Tom Kelly and Mike Thompson, I organized a symposium entitled “Advances in Nanoscale Technology.” The response to this symposium was impressive, with 32 contributed and 7 invited presentations. Some of these presentations concentrated on atom probe field ion microscopy and form the basis for the invited contributions in this special issue of Microscopy and Microanalysis.

Modeling image distortions in 3DAP

A numerical model has been developed to simulate images obtained from the three-dimensional atom probe. This model was used to simulate the artefacts commonly observed in two-phase materials. This model takes into account the dynamic evolution of the atomic-scale shape of the specimen during field evaporation. This article reviews the model and its applications to some specific cases. Local magnification effects were studied as a function of the size, the shape, and the orientation of precipitated phases embedded in the matrix. Small precipitates produce large aberrations in good agreement with experiments. The magnification from such precipitates, as measured from the simulation, is only found to match the theoretical value for mesoscopic scale precipitates (size similar to the specimen size). Orientation effects are also observed in excellent agreement with experiments. The measured thickness of a grain-boundary-segregated film in the simulation is found to decrease with the angle between the normal to the grain boundary and the tip axis. Depth scaling artefacts caused by variation in the evaporation field of atoms in multilayer structures were successfully simulated and again showed good agreement with effects observed experimentally.

The role of atomic scale investigation in the development of nanoscale materials for information storage applications

It is well established that the response of devices based on the giant magnetoresistance (GMR) effect depends critically on film microstructure, with parameters such as interfacial abruptness, the roughness and waviness of the layers, and grain size being crucial. Such devices have applications in information storage systems, and are therefore of great technological interest as well as being of fundamental scientific interest. The layers must be studied at high spatial resolution if the microstructural parameters are to be characterized with sufficient detail to enable the effects of fabrication conditions on properties to be understood, and the techniques of high resolution electron microscopy, transmission electron microscopy chemical mapping, and atom probe microanalysis are ideally suited. This article describes the application of these techniques to a range of materials including spin valves, spin tunnel junctions, and GMR multilayers.

Porcine circovirus type 2 (PCV-2) coinfections in US field cases of postweaning multisystemic wasting syndrome (PMWS)

The prevalence of different pathogens detected in combination with porcine circovirus type 2 (PCV-2) was studied retrospectively in field cases of postweaning multisystemic wasting syndrome (PMWS) diagnosed at the Iowa State University Veterinary Diagnostic Laboratory, Ames, Iowa, between January 2000, and September 2001. The presence of PCV-2 antigen in lymphoid tissues and/or lung, demonstrated by immunohistochemistry, together with moderate to severe lymphoid depletion and/or granulomatous lymphadenitis, was used as the criteria for the diagnosis of PMWS. A total of 484 cases fulfilled these criteria. Most of the cases (294/369) of PMWS occurred in pigs between the ages of 8 and 18 weeks, with a peak at 10 weeks of age. Porcine reproductive and respiratory syndrome virus was detected in 51.9% of the cases, Mycoplasma hyopneumoniae in 35.5%, bacterial septicemia in 14.0%, bacterial pneumonia in 7.6%, swine influenza virus in 5.4%, and PCV-2 alone in 1.9%. In cases with bacterial septicemia the most frequently isolated pathogen was Streptococcus suis. In cases with bacterial pneumonia, Pasteurella multocida was the most prevalent.

A case report of sporadic ovine listerial menigoencephalitis in Iowa with an overview of livestock and human cases

A case of ovine listeriosis was examined in a flock of sheep. The index case was a male lamb, which was part of a flock of 85 sheep located in central Iowa. Because the sheep were raised on a premise where soybean sprouts were also cultivated for the organic foods market, the potential of a public health concern was addressed. To identify the source of contaminations, clinical and environmental samples were cultured for Listeria monocytogenes. Isolates were serotyped and analyzed using pulsed-field gel electrophoresis (PFGE). Listeria monocytogenes (serotype 1) was recovered from the brain of a male lamb with clinical signs of listerial encephalitis. Isolates of serotypes 1 and 4 were also cultured from feces of clinically healthy lambs, compost piles, and soybean cleanings. By PFGE, the clinical isolate was distinctly different from the other isolates. Environmental isolates were identified as L. monocytogenes serotypes 1 and 4. However, by PFGE, none matched the profile of the single clinical isolate. Thus, the ultimate source of contamination is unknown.

Detection of Arcobacter species in gastric samples from swine

Swine stomachs were surveyed for evidence of Arcobacter spp. and Helicobacter spp. infections associated with gastric ulceration. A nested PCR test targeted to the 16S rRNA was developed to detect many Arcobacter spp. and Helicobacter spp. An internal oligonucleotide probe was used for differentiation and confirmation of the PCR product. Tissue samples were obtained from the nonglandular and glandular regions of 86 swine stomachs. Evidence of infection with these microbes was detected in 51%, with 77% of the positive samples being identified as A. butzleri using a highly specific probe. Nonglandular stomach samples (44%) were more likely to be positive by PCR than samples from the glandular (23%) region. Gross lesions of any stage of gastric ulceration, ranging from parakeratosis, erosions and ulceration, were observed in 24% of stomachs examined. Of 21 samples with lesions, 52% were positive by the broadly reactive PCR assay for Arcobacter spp. and Helicobacter spp. The majority of PCR-positive samples (75%) had no gross lesions. When a single step PCR assay that was more specific for Arcobacter spp. was used on the nonglandular stomach samples, 10.4% of the 86 samples were positive. Arcobacter spp. were cultured from four of the sample stomachs. Partial sequencing of the 16S rRNA gene identified the isolates as A. butzleri (n = 2), A. cryaerophilus, (n = 1), and a mixed culture of A. butzleri and another Arcobacter spp. (n = 1). A single step PCR assay targeted to the urease gene and culturing methods were used to screen for H. pylori or other closely related urease positive bacteria, but none were found.

Application of multiplex polymerase chain reaction for rapid identification of Campylobacter jejuni and C coli associated with reproductive failure

OBJECTIVE

To evaluate a multiplex polymerase chain reaction (PCR) to distinguish Campylobacter jejuni from C coli as causes of reproductive failure.

PROCEDURE

Review of clinical cases of reproductive failure attributed to C jejuni or C coli.

RESULTS

A case of swine abortion was attributable to infection with C coli. The porcine abortion isolates were verified as C coli by restriction fragment length polymorphism and multiplex PCR. Cases of endometritis in a fox and in mink caused by C jejuni were reviewed, and isolates were confirmed as C jejuni by results of the multiplex PCR.

CONCLUSION

Multiplex PCR was useful in identifying C coli and C jejuni recovered from atypical cases of reproductive failure. Multiplex PCR in conjunction with conventional assays may be useful for verifying other unusual instances of campylobacteriosis.

Infection of cesarean-derived colostrum-deprived 1-day-old piglets with Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii

Neonatal piglets have been used as models to study human campylobacteriosis and helicobacteriosis. The purpose of this study was to determine the relative pathogenicities, on the basis of the duration of fecal shedding and colonization of tissues, of three Arcobacter species in 1-day-old cesarean-derived colostrum-deprived piglets. Two experiments were conducted. In experiment 1, two piglets each were infected per os with either Arcobacter butzleri ATCC 49616, Arcobacter cryaerophilus 1B ATCC 43159, Arcobacter skirrowii CCUG 10374, or the three field strains of A. butzleri (approximately 5 X 10(9) CFU per piglet). Rectal swab samples were taken prior to infection and daily thereafter for up to 7 days. Arcobacter spp. were detected at least once in rectal swab samples of all but one of the experimentally infected piglets but not in the control. At necropsy, A. butzleri was recovered from the lung, kidney, ileum, or brain tissues of the four infected piglets which had received either the field strain or the ATCC type strain of A. butzleri. A. cryaerophilus 1B was detected in rectal swab samples for up to 7 days postinfection but was not cultured from tissues at necropsy. Arcobacters were detected in the rectal swab sample of the A. skirrowii-infected piglet only on day 3 postinfection; no isolates were obtained from tissues at necropsy. No gross pathological lesions were consistently noted in the experimentally infected piglets. In experiment 2, two piglets each were infected per os with A. butzleri ATCC 49616, A. cryaerophilus 1A ATCC 43158, A. skirrowii CCUG 10374, or the single A. butzleri field strain Yard J/c (approximately 5 X 10(9) CFU per piglet). Arcobacter spp. were cultured from rectal swab samples of all but one of the experimentally infected piglets at least once. At necropsy Arcobacter spp. were cultured from the liver, kidney, ileum, or brain tissues of two of the four A. butzleri-infected piglets. However, no severe gross pathology was noted. These data suggest that Arcobacter spp., especially A. butzleri, can colonize neonatal pigs.

Phenotypic and ribosomal RNA characterization of Arcobacter species isolated from porcine aborted fetuses

Aerotolerant organisms resembling Campylobacter, now designated as Arcobacter, have been described from aborted farm animals and from cases of human enteritis worldwide. The goals of this study were 1) to attempt to recover Arcobacter spp. from cases of porcine abortion, 2) to characterize these isolates by phenotype and ribotype, and 3) to compare the usefulness of ribotype and phenotype patterns for identifying Arcobacter butzleri and the DNA hybridization groups 1A and 1B of A. cryaerophilus. Isolates of Arcobacter spp. from North Carolina and Iowa were recovered from porcine tissues. In Iowa, Arcobacter spp. were recovered from 43% (13/30) of porcine abortion cases evaluated. Isolations were made from placenta (44%), kidney (44%), and stomach contents (12%), which were the only tissues examined. The most reliable biochemical tests for A. butzleri included growth in 1% glycine and in 1.5% NaCl, weak catalase activity, and resistance to cadmium chloride. Arcobacter cryaerophilus strains were characterized by strong catalase activity and sensitivity to cadmium chloride. The DNA hybridization groups 1A and 1B of A. cryaerophilus could not be distinguished by biochemical tests. This represents the first description of A. cryaerophilus DNA group 1A in animals within the United States.