Unknown Organisms Research Articles

Surgical Treatment of Infected Thoracic and Abdominal Aortic Aneurysms

Twelve patients with infected aneurysms of the thoracic and abdominal aorta were evaluated. Aneurysmal location, aetiology, bacteriology and treatment modality were analysed to determine the relationship between these factors and outcome. Patients were divided into two groups based on the preoperative states of their infections. Group 1 patients ( n = 7) underwent resection after resolution of their active infection. The causative organisms included Staphylococcus epidermidis (two cases), Salmonella spp. (one), Acinetobacter (one), Mycobacterium tuberculosis (one) and unknown organisms (two). Group 2 patients ( n = 5) required urgent surgery because of uncontrolled sepsis despite intensive treatment with antibiotics. The causative organisms included Staphylococcus aureus (two cases). Pseudomonas aeruginosa (two) and Salmonella spp. (one). In group 1, three patients underwent closed en bloc excision of the aneurysm with in- situgraft replacement, and four underwent partial resection with in-situ graft replacement. In group 2. three patients underwent resection of the aneurysm with ligation of aorta and extra-anatomic bypass, and two underwent in-situ graft replacement after débridement of infected tissue. Overall, patients in group 1 had a mortality rate of 14% compared with 80% in group 2. These results suggest that the operative approach and method chosen to restore arterial continuity have less of an impact on outcome. The primary determinants of outcome are virulence of the infecting organism and the preoperative state of the infection.

Isolation, purification, and analysis of nuclear DNA in yeast taxonomy.

The advent of molecular techniques has greatly influenced yeast taxonomy. Although it has become easier to identify an unknown organism, the use of these methods has caused a general reassessment of those tests previously considered important for the classification of yeasts.

Isolation of a hyperthermophilic archaeum predicted by in situ RNA analysis.

A variety of hyperthermophilic bacteria and archaea have been isolated from high-temperature environments by plating and serial dilutions. However, these techniques allow only the small percentage of organisms able to form colonies, or those that are predominant within environmental samples, to be obtained in pure culture. Recently, in situ 16S ribosomal RNA analyses of samples from the Obsidian hot pool at Yellowstone National Park, Wyoming, revealed a variety of archaeal sequences, which were all different from those of previously isolated species. This suggests substantial diversity of archaea with so far unknown morphological, physiological and biochemical features, which may play an important part within high-temperature ecosystems. Here we describe a procedure to obtain pure cultures of unknown organisms harbouring specific 16S rRNA sequences identified previously within the environment. It combines visual recognition of single cells by phylogenetic staining and cloning by 'optical tweezers'. Our result validates polymerase chain reaction data on the existence of large archael communities.

Isolation ofCoxiella burnetii and of an unknown rickettsial organism fromIxodes ricinus ticks collected in Austria

Two strains of Coxiella burnetii and two strains of an unidentified rickettsial organism were isolated for the first time from Ixodes ricinus ticks collected in the Alpine region of Tirol, Austria. The C. burnetii strains belong to the group of agents causing acute forms of Q fever. The other two strains of isolated rickettsial agent share some antigenic epitopes with C. burnetii and R. prowazekii but they differ from them by their high sensitivity to freezing and refreezing and by poor multiplication in yolk sacs of chick embryos. There is at present no evidence that these organisms cause human illness and no ecological information is available. We suggest they may be some new species of rickettsiae or rickettsia-like organisms.

Characterization of a psychrotrophic Clostridium causing spoilage in vacuum-packed cooked pork: description of Clostridium algidicarnis sp. nov.

A Clostridium species causing spoilage of vacuum-packed refrigerated pork was isolated and characterized. The unknown organism differed phenotypically from other clostridial species usually associated with spoilage. Phylogenetic analyses based on 16S rRNA gene sequencing demonstrated that the psychrotroph represents a distinct line of descent within the genus Clostridium. It is proposed that the organism be classified as a new species of the genus Clostridium, Clostridium algidicarnis.

On the feeding and comparative biology of iron in coelenterate-associated gammaridean Amphipoda (Crustacea) from N. Norway

Data are presented on the morphology of the mandible, morphometry of the stomach, composition of stomach contents, fine structure of the ventral caeca, and concentration of trace metals (Fe, Cu, Zn, Cd, Mn) in three species of coelenterophagous amphipod: Andaniexis sp. L (Stegocephalidae), Stenothoe brevicornis G.O. Sars (Stenothoidae) and Onisimus normani G.O. Sars (Lysianassidae) collected from sites off Tromsø, N. Norway. Andaniexis sp.L. has a blade-like incisor and highly distensible stomach compatible with functioning ecologically as a gluttonous batch processor of soft food. Stomachs in animals of this species from one site contained nematocyst-bearing soft tissue of coelenterate origin (identity not established) and sand grains, together with occasional polychaete remains. Andaniexis sp. L. from two sites differed in terms of their gut fullness and contribution of coelenterate material to the diet. Octahedral crystals of ferritin were variably present in cells of the ventral caeca; these crystals being a typical feature of the Fe detoxification system of stegocephalid amphipods. The Fe, Cu and Zn concentrations of Andaniexis sp. L., however, did not differ between sites. Stenothoe brevicomis also has a well developed, cutting incisor. This species, though, has a small stomach, compatible with its continuous association with its host sea anemone [ Actinostola callosa (Verrill)]. Analysis of stomach contents showed that it can consume the tentacular tissue of Actinostola callosa. Onisimus normani, also has a blade-like incisor. It lives within the enteron of sea anemones ( Actinostola callosa, Bolocera tuediae) and consumes mesenterial tissue. Although both Stenothoe brevicomis and Onisimus normani proved to have Fe concentrations which were no different from those in Andaniexis sp. L., only the last-mentioned species exhibited ferritin crystals. The reason for this difference in Fe handling strategy is presently unclear and may require knowledge of the Fe challenge posed by the unknown food organism of Andaniexis sp. L. in explanation. This stegocephalid genus is proving to be a less specific feeder on coelenterates than related genera which have been the subject of previous investigations. Calcium phosphate granules detoxify a range of potentially toxic trace metals including Fe in Andaniexis sp. L., Stenothoe brevicornis and Onisimus normani.

Parasites of Small Mammals in Grand Teton National Park: Babesia and Hepatozoon

In a review of the parasites of Microtus, Timm (1985) lists no protozoan endoparasites whatsoever for this genus. The role of parasitism, whether macro- or microparasites, and whether endo- or ectoparasites, in the demographic machinery of microtines is poorly understood. Timm (1985) astutely observes that one of the most challenging and fruitful directions of future research with Microtus will be the statistical quantification of the cost of parasitism. In addition, since humans in the Grand Teton National Park may encounter protozoon parasites that are potentially pathogenic to humans, it is useful to characterize the occurrence and biology of such organisms in the parko Babesia microti, a parasitic protozoon, is transmitted by a tick vector and reproduces in the erythrocytes of its mammalian host. Initially, Babesia was thought to be restricted to small mammals; however, in 1970 the first human cases were diagnosed in residents of Nantucket Island, Massachusetts (Western et al, 1970). Over 200 cases of human babesiosis have been documented worldwide. In the United States, human babesiosis is caused by B. microti. Most of these cases have occurred in the eastern United States. The earliest report of an organism that fits the description of Babesia in human erythrocytes is that of Wilson et al. (1904), who found an unknown organism in human erythrocytes while investigating the cause of Rocky Mountain Spotted fever. Documented cases of babesiosis in many areas of the United States are increasing (Steketee et al, 1985). As humans insert themselves into places where they have historically been present only occasionally, they often contract new diseases. A second protozoon parasite, Hepatozoon sp., which is widespread in small mammals in Europe, is also found in reptiles throughout the world. The record of Hepatozoon in North American small mammals is not extensive. Fewer than 10 species of mammals have been shown to harbor Hepatozoon parasites. Like Babesia, Hepatozoon is a two-host parasite. Unlike Babesia, for which the intermediate host is always a tick, the intermediate host in the Hepatozoon may be a tick, a mite, a flea, or a mosquito. The method of transmission by the vector also differs in the two parasites. Babesia is transmitted in saliva when the tick bites, whereas Hepatozoon infection requires the vertebrate host to swallow the vector. In our 1994 studies, we sought to extend knowledge of these two parasites. The specific objectives for 1994 were: to sample specific populations of M. molltanus, in which we have previously documented Hepatozoon infections, to determine whether there are differences in the infection rates at different study sites in the park; to search for the vector of Hepatozoon sp. infections in M. montanus by examining ectoparasites; to collect and rear ticks from M. montanus for use in R microti transmission studies; and to complete a comparison of the spleen histology of babesiosis in infected and uninfected laboratory animals, with inclusion of data from wild animals, as available. Our long-term objectives are to document the effects and cost of parasitism on vole populations and to determine the potential of small mammals of Grand Teton National Park to serve as reservoirs of human parasites.

Taxonomic studies on some leuconostoc‐like organisms from fermented sausages: description of a new genus Weissella for the Leuconostoc paramesenteroides group of species

Taxonomic studies were performed on some unknown Leuconostoc-like organisms from fermented Greek sausage. Comparative 16S rRNA sequence analysis showed the unidentified organisms represent a new line within the Leuconostoc paramesenteroides group of species. On the basis of the results of this and earlier phylogenetic investigations, it is proposed that Leuconostoc paramesenteroides and related species be reclassified in a new genus Weissella. In addition a new species, Weissella hellenica, is proposed for the isolates from fermented sausage.

Rapid identification of streptomycetes by artificial neural network analysis of pyrolysis mass spectra.

An artificial neural network was trained to distinguish between three putatively novel species of Streptomyces using normalised, scaled prolysis mass spectra from three representative strains of each of the taxa, each sampled in triplicate. Once trained, the artificial neural network was challenged with spectral data from the original organisms, the 'training set', from additional members of the putative novel taxa and from over a hundred strains representing six other actinomycete genera. All of the streptomycetes were correctly identified but many of the other actinomycetes were mis-identified. A modified network topology was developed to recognise the mass spectral patterns of the non-streptomycete strains. The resultant neural network correctly identified the streptomycetes, whereas all of the remaining actinomycetes were recognised as unknown organisms. The improved artificial neural network provides a rapid, reliable and cost-effective method of identifying members of the three target streptomycete taxa.

Therapeutic percutaneous aspiration of hepatic abscesses: effectiveness in 25 patients.

The objective of this study was to evaluate the effectiveness of sonographically guided needle aspiration and systemic antibiotic therapy for the treatment of hepatic abscesses. From June 1989 to September 1991, sonographically guided needle aspiration and systemic antibiotics were used to treat 25 consecutive patients with 25 hepatic abscesses. Among 36 patients with hepatic abscesses who were admitted to the hospital during that time, six had antibiotic therapy only; of these, three had microabscesses, two had abscesses less than 3.0 cm in diameter, and one refused needle aspiration. Four patients had surgical external drainage (three had cholelithiasis in addition to hepatic abscesses, and one did not respond to needle aspiration). Two patients treated in 1989 had drainage via an indwelling catheter, which was the preferred method at that time. The remaining 24 patients and one patient who had needle aspiration followed by surgical drainage made up the study group. Seventeen of the hepatic abscesses were caused by pyogenic organisms, six by amoeba, and two by unknown organisms. Eighteen abscesses (72%) were aspirated once, four (16%) were aspirated twice in 8 days, two (8%) were aspirated three times in 14 days, and one (4%) was aspirated four times in 10 days. Persistent fever, pain and tenderness in the right upper quadrant, and leukocytosis were the indications for multiple aspirations. Follow-up sonography was performed to evaluate the outcome of treatment. In 16 cases (64%), the abscesses disappeared within a mean of 84 days. In eight cases (32%) with only partial follow-up, the patients were asymptomatic at the time of discharge and the abscesses were markedly smaller on the last follow-up sonograms (mean, 43 days). One patient (4%) did not respond to aspiration and had surgical drainage. The length of hospitalization varied from 5 to 42 days (mean, 22 days). In patients who became afebrile during the treatment, the fever had lasted from 0 to 10 days (mean, 3 days). Only one patient had a complication of the procedure, a pleural effusion that was treated conservatively. Our results show that sonographically guided needle aspiration combined with antibiotic therapy is effective as the initial treatment for hepatic abscesses.

A quality control algorithm for DNA sequencing projects.

Heterologous DNA sequences from rearrangements with the genomes of host cells, genomic fragments from hybrid cells, or impure tissue sources can threaten the purity of libraries that are derived from RNA or DNA. Hybridization methods can only detect contaminants from known or suspected heterologous sources, and whole library screening is technically very difficult. Detection of contaminating heterologous clones by sequence alignment is only possible when related sequences are present in a known database. We have developed a statistical test to identify heterologous sequences that is based on the differences in hexamer composition of DNA from different organisms. This test does not require that sequences similar to potential heterologous contaminants are present in the database, and can in principle detect contamination by previously unknown organisms. We have applied this test to the major public expressed sequence tag (EST) data sets to evaluate its utility as a quality control measure and a peer evaluation tool. There is detectable heterogeneity in most human and C.elegans EST data sets but it is not apparently associated with cross-species contamination. However, there is direct evidence for both yeast and bacterial sequence contamination in some public database sequences annotated as human. Results obtained with the hexamer test have been confirmed with similarity searches using sequences from the relevant data sets.

Rapid recovery from cytopenia in hairy cell leukemia after treatment with 2-chloro-2'-deoxyadenosine (CdA): relation to opportunistic infections

Sixteen patients with symptomatic hairy cell leukemia were treated with a single course of 2-chloro-2′-deoxyadenosine (CdA), 0.7 mg/kg total dose. Twelve patients achieved complete remission (CR). One patient with a CD19+/CD5+/CD25- phenotype and one with a pentostatin-treated CD19+/CD25- variant form had minor responses. Two patients with advanced disease and poor performance status died early from invasive mycosis. Three patients recovered from infections caused by cytomegalovirus and by candida. No patient had infections caused by bacteria or by unknown organisms. The median time to full recovery from anemia and thrombocytopenia was 6 and 2 weeks from start of therapy, respectively. Patients with infections, however, recovered at 13 and 5 weeks, respectively. Neutrophil, monocyte, and lymphocyte counts returned to normal at a median of 5, 5, and 10 weeks, respectively. Infections developed more frequently in pancytopenic patients than in those with one or more blood cell count within the normal range (P less than .01). All patients with one or no previous therapy had a CR, whereas those with more than one previous regimen had a lower CR rate (P less than .01). Thus, 1 week of CdA therapy frequently induced CR also in patients resistant to interferon. Toxicity was limited, and recovery from cytopenia was faster than what is reported during interferon therapy.

Rapid Recovery From Cytopenia in Hairy Cell Leukemia After Treatment With 2-Chloro-2' x2018;-Deoxyadenosine (CdA): Relation to Opportunistic Infections

Sixteen patients with symptomatic hairy cell leukemia were treated with a single course of 2-chloro-2'-deoxyadenosine (CdA), 0.7 mg/kg total dose. Twelve patients achieved complete remission (CR). One patient with a CD19+/CD5+/CD25- phenotype and one with a pentostatin-treated CD19+/CD25- variant form had minor responses. Two patients with advanced disease and poor performance status died early from invasive mycosis. Three patients recovered from infections caused by cytomegalovirus and by candida. No patient had infections caused by bacteria or by unknown organisms. The median time to full recovery from anemia and thrombocytopenia was 6 and 2 weeks from start of therapy, respectively. Patients with infections, however, recovered at 13 and 5 weeks, respectively. Neutrophil, monocyte, and lymphocyte counts returned to normal at a median of 5, 5, and 10 weeks, respectively. Infections developed more frequently in pancytopenic patients than in those with one or more blood cell count within the normal range (P less than .01). All patients with one or no previous therapy had a CR, whereas those with more than one previous regimen had a lower CR rate (P less than .01). Thus, 1 week of CdA therapy frequently induced CR also in patients resistant to interferon. Toxicity was limited, and recovery from cytopenia was faster than what is reported during interferon therapy.

Ichnology of a reworked strandplain complex: Mississippian Hartselle Sandstone of Alabama

The Hartselle Sandstone of northern Alabama represents a mesotidal strandplain complex of Hombergian (middle Chesterian) age that was reworked by a transgressing sea. Transgressive reworking resulted in complex facies patterns that can best be deciphered by ichnology. Thickly bedded, unbioturbated beach to shoreface sandstone is widespread at the base of the formation. Wavy-bedded back-barrier to shelf sandstone and shale predominate in the middle and upper parts of the formation and contain distinctive assemblages of trace fossils, invertebrates, and plants.Barriers with a broad, gently sloping beach face and muddy coastal swamps typified the Hartselle strandplain which extended across northern Alabama. Barrier and coastal-swamp deposits lack trace fossils but locally contain an indigenous lycopod flora including stumps and Stigmaria root systems.Back-barrier tidal flats and lagoon deposits have trace-fossil assemblages dominated by bivalve traces that probably represent brackish environments. Marginal-marine sandstone contains chiefly monospecific assemblages and is reworked by bivalves and unknown organisms; Lockeia, Uchirites, and Rosselia are dominant at different sites. The Lockeia assemblage includes bedding surfaces with crowded bivalve resting traces. The abundance, density, and small size of monospecific burrows suggests estuarine conditions with high food supply and rapid larval colonization. The Uchirites assemblage is characterized by bivalve trails, representing probably brackish substrates with a high sedimentation rate.Shelf sandstone and shale include bivalve resting traces and trails (Lockeia ispp., Uchirites isp. aff. U. triangularis, Walcottia rugosa, and W. imbricata), asteroid and ophiuroid resting traces (Asteriacites stelliforme and Pentichnus pratti), trilobite resting traces and trackways (Rusophycus ispp. and Petalichnus isp.), and dwelling burrows, feeding burrows, trails, and trackways of unknown organisms (Chondrites-like burrows, Phycodes isp., Haplotichnus isp., Rosselia isp., Planolites montanus, Nereites missouriensis, Tasmanadia twelvetreesi, imbricate burrows, and wavelike burrows). Some shelf areas even supported diverse calcified faunas containing crinoids, fenestrate bryozoans, and articulate brachiopods.The Hartselle Sandstone is a facies mosaic that records indundation of an extensive strandplain complex and a distinctive stratigraphic succession of lithofacies and biofacies. Hartselle ichnofacies have unique aspects, but are similar to those of other marginal-marine Carboniferous strata in eastern North America. The paleoecologic complexity of the Hartselle Sandstone helps to establish the dynamic range of Carboniferous ecosystems, which have yet to be fully explored.

Clinical studies on the treatment of Campylobacter enteritis--emergence of quinolone-resistant Campylobacter jejuni after treatment with new quinolones

In recent years, new quinolones such as ofloxacin (OFLX) and tosufloxacin (TFLX) have been frequently used in the treatment of bacterial enteritis caused by unknown organisms. The agent of first choice for the treatment of Campylobacter enteritis is one of the macrolides, but new quinolones are often administered accidentally to adult patients with Campylobacter enteritis. We have detected quinolone-resistant strains of Campylobacter jejuni (C. jejuni) after the treatment of some patients with new quinolones, and accordingly we reviewed the treatment of Campylobacter enteritis. We experienced 178 adult patients with Campylobacter enteritis from January 1989 to November 1991 at our hospital. From them, we selected 52 patients (32 males and 20 females) in whom stool culture were performed both before and after treatment. The initially administered antimicrobial agent was a macrolide (rokitamycin, RKM) in 6 cases, a new quinolone in 22 cases, and kanamycin (KM) in 24 cases. The new quinolone used was OFLX in 17 cases, TFLX in 3 cases, and norfloxacin (NFLX) in 2 cases. Fifty-one of the 52 C. jejuni strains isolated before treatment were susceptible to OFLX and erythromycin (EM) according to antimicrobial disc susceptibility tests. C. jejuni was eradicated in all patients treated with RKM or KM. However, treatment failed to achieve bacteriological cure in 8/22 (36.4%) patients given new quinolones. In these patients, the strains of C. jejuni isolated before treatment were susceptible to OFLX, but the strains isolated after treatment were all resistant to OFLX according to disc susceptibility tests.(ABSTRACT TRUNCATED AT 250 WORDS)

A phylogenetic analysis of an atypical leuconostoc: description of Leuconostoc fallax sp. nov.

The 16S rRNA sequence of an unknown leuconostoc originally isolated from sauerkraut was investigated by reverse transcription. A comparison of the sequence with those from other lactic acid bacteria revealed the unknown organism represents a new albeit peripheral line within the genus Leuconostoc sensu stricto. A new species, Leuconostoc fallax, is proposed for this organism. The type strain is DSM 20189.

A phylogenetic analysis of an atypical leuconostoc: description ofLeuconostoc fallaxsp. nov.

The 16S rRNA sequence of an unknown leuconostoc originally isolated from sauerkraut was investigated by reverse transcription. A comparison of the sequence with those from other lactic acid bacteria revealed the unknown organism represents a new albeit peripheral line within the genus Leuconostoc sensu stricto. A new species, Leuconostoc fallax, is proposed for this organism. The type strain is DSM 20189.

Deep burrowing in the early Palaeozoic deep sea: examples from the Cambrian(?)–Early Ordovician Meguma Group of Nova Scotia

Enigmatic and heterogeneously deformed burrows are described from the Cambrian?–Early Ordovician Meguma Group of Nova Scotia. Because of their morphological variability and the absence of previously defined morphotypes, the burrows are unnamed yet do provide a cautionary note to the naming of trace fossils, even at the ichnogeneric level, by ichnologists. The traces record the activity of unknown and mobile deposit-feeding organisms that inhabited interchannel or levee areas immediately adjacent to and up to 5 m laterally from a 2 m deep channel developed on a deep-sea, mid–outer submarine-fan complex. Many of the vertically to subvertically oriented systems penetrate up to 40 cm, suggesting that existing models on the depth of early Palaeozoic benthic boundary layers obtained from shelf environments must be utilized with caution.

Sublethal and lethal injuries of Pennsylvanian conulariids from Oklahoma

Many specimens of the conulariid Paraconularia magna (Ries) from the Tackett Formation (Upper Pennsylvanian, Missourian) of Oklahoma exhibit repaired or unrepaired injured exoskeletons. Scalloped, cleft, and embayed patterns are interpreted to be repaired sublethal damages produced by unknown events or organisms. Punctures, which are the first reported in conulariids, were not followed by exoskeletal repair and were probably lethal. Cladodont sharks are implicated as possible predators of P. magna because of a close correspondence in size and pattern between the dentition of some sharks and the punctures preserved in conulariid exoskeletons.

Simple genetic method to identify viridans group streptococci by colorimetric dot hybridization and fluorometric hybridization in microdilution wells.

Simple dot hybridization and fluorometric hybridization methods in microdilution wells were designed and established for rapid and routine genetic identification of viridans group streptococci. Reference DNA extracted from each strain of 24 reference Streptococcus species was fixed both on a nitrocellulose filter and in a microdilution well. A 1-ml portion of the bacterial suspension which matched the turbidity of McFarland no. 2 standard was prepared when a streptococcal strain was isolated. It was lysed with achromopeptidase, and the DNA was quickly labeled with photobiotin under a sunlamp for 15 min. Dot hybridization and fluorometric hybridization were then carried out between the labeled DNA of the unknown organism and 24 unlabeled reference DNAs. Hybridized fragments on a nitrocellulose filter were detected by using alkaline-phosphatase-conjugated streptavidin and analyzed with a color graphic analyzer. Hybridized fragments in microdilution wells were quantitatively detected by using an enzyme, streptavidin-conjugated beta-D-galactosidase, and a fluorogenic substrate, 4-methylumbelliferyl-beta-D-galactoside. Strains belonging to each genetically distinct species could be identified by this dot blot hybridization test. However, some clinical strains cross-hybridized with two or more reference species, and then they were difficult to differentiate by dot blot hybridization. In such a case, fluorometric identification provided reliable results because the fluorometric method was more quantitative than dot blot identification. By these methods, it was possible to determine species assignment within the viridans group.