71 research outputs found
Redescriptions of two species of microcotylid monogeneans from three arripid hosts in southern Australian waters
No full textMicrocotyle arripis Sandars, 1945 is redescribed from Arripis georgianus from four localities: Spencer Gulf, Gulf St. Vincent, off Kangaroo Island and Coffin Bay, South Australia, Australia. Kahawaia truttae (Dillon & Hargis, 1965) Lebedev, 1969 is reported from A. trutta off Bermagui, New South Wales and is redescribed from a new host, A. truttaceus, from four localities in South Australian waters: Spencer Gulf, Gulf St. Vincent, off Kangaroo Island and Coffin Bay. Phylogenetic analysis of the partial 28S ribosomal RNA gene (28S rRNA) nucleotide sequences for both microcotylid species and comparison with other available sequence data for microcotylid species across four genera contributes to our understanding of relationships in this monogenean family.Sarah R. Catalano, Kate S. Hutson, Rodney M. Ratcliff and Ian D. Whittingto
The value of host and parasite identification for arripid fish
No full textAccurate identification of fishes and their parasites is fundamental to the development, management and sustainability of fisheries and aquaculture worldwide. We examined three commercially and recreationally exploited Australian arripid species (Pisces: Arripidae), namely Australian herring (Arripis georgianus), eastern Australian salmon (A. trutta) and western Australian salmon (A. truttaceus), to determine their metazoan parasite assemblages and infection parameters. We identified 49 parasite species including 35 new parasite–host records and recognised seven ambiguous parasite–host records in the literature, largely a consequence of unsubstantiated host identifications in previous studies. Morphological and molecular methods confirmed a new western extension for the range of A. trutta, ~1000 km west of the previous record. Confusion about host identification and the range extension documented here has implications for the management of these economically important arripid species in southern Australian waters. Our examination of an endemic Australian fish family emphasises that accurate identification of fishes and their parasites is a fundamental pre-requisite for efficient and sustainable resource management.Sarah R. Catalano, Kate S. Hutson, Rodney M. Ratcliff and Ian D. Whittingto
Legionella steelei sp. nov., isolated from human respiratory specimens in California, USA, and South Australia
No full textThe GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, mip, proA, rnpB and rpoB gene sequences of strain IMVS-3376T are HQ398202–HQ398206, respectively.Legionella-like bacteria were isolated from the respiratory tract of two patients in California, USA, and South Australia, but were not thought to cause disease. These bacteria, strains F2632 and IMVS-3376T, were found to have identical Legionella macrophage infectivity potentiator (mip) gene sequences and were therefore further characterized to determine their genetic and phenotypic relatedness and properties. Both of these Gram-negative-staining bacterial strains grew on buffered charcoal yeast extract medium, were cysteine auxotrophs and made a characteristic diffusible bright yellow fluorescent pigment, with one strain making a late appearing colony-bound blue–white fluorescent pigment. The optimal in vitro growth temperature was 35 °C, with very poor growth at 37 °C in broth or on solid media. There was no growth in human A549 cells at either 35 or 37 °C, but excellent growth in Acanthamoeba castellani at 30 °C and poorer growth at 35 °C. Phylogenetic analysis of these bacteria was performed by sequence analysis of 16S rRNA, mip, ribonuclease P, ribosomal polymerase B and zinc metalloprotease genes. These studies confirmed that the new strains represented a single novel species of the genus Legionella for which the name Legionella steelei sp. nov. is proposed. The type strain is IMVS-3376T ( = IMVS 3113T = ATCC BAA-2169T).Paul H. Edelstein, Martha A. Edelstein, Lisa J. Shephard, Kevin W. Ward and Rodney M. Ratcliff
A Novel Bocavirus Associated with Acute Gastroenteritis in Australian Children
No full textAcute gastroenteritis (AGE) is a common illness affecting all age groups worldwide, causing an estimated three million deaths annually. Viruses such as rotavirus, adenovirus, and caliciviruses are a major cause of AGE, but in many patients a causal agent cannot be found despite extensive diagnostic testing. Proposing that novel viruses are the reason for this diagnostic gap, we used molecular screening to investigate a cluster of undiagnosed cases that were part of a larger case control study into the etiology of pediatric AGE. Degenerate oligonucleotide primed (DOP) PCR was used to non-specifically amplify viral DNA from fecal specimens. The amplified DNA was then cloned and sequenced for analysis. A novel virus was detected. Elucidation and analysis of the genome indicates it is a member of the Bocavirus genus of the Parvovirinae, 23% variant at the nucleotide level from its closest formally recognized relative, the Human Bocavirus (HBoV), and similar to the very recently proposed second species of Bocavirus (HBoV2). Fecal samples collected from case control pairs during 2001 for the AGE study were tested with a bocavirus-specific PCR, and HBoV2 (sequence confirmed) was detected in 32 of 186 cases with AGE (prevalence 17.2%) compared with only 15 controls (8.1%). In this same group of children, HBoV2 prevalence was exceeded only by rotavirus (39.2%) and astrovirus (21.5%) and was more prevalent than norovirus genogroup 2 (13.4%) and adenovirus (4.8%). In a univariate analysis of the matched pairs (McNemar's Test), the odds ratio for the association of AGE with HBoV2 infection was 2.6 (95% confidence interval 1.2–5.7); P = 0.007. During the course of this screening, a second novel bocavirus was detected which we have designated HBoV species 3 (HBoV3). The prevalence of HBoV3 was low (2.7%), and it was not associated with AGE. HBoV2 and HBoV3 are newly discovered bocaviruses, of which HBoV2 is the thirdmost-prevalent virus, after rotavirus and astrovirus, associated with pediatric AGE in this study.Jane L. Arthur, Geoffrey D. Higgins, Geoffrey P. Davidson, Rodney C. Givney and Rodney M. Ratclif
Application of an allele-specific PCR to clinical HIV genotyping samples detects additional K103N mutations in both therapy naive and experienced patients
No full textCopyright © 2009 Wiley-Liss, Inc., A Wiley CompanyLow-level drug resistance is not detected by routine consensus sequence genotype analysis (CSA) but low levels of specific mutations, such as the non-nucleoside reverse transcriptase inhibitor (NNRTI)-resistant mutation K103N, can be quantitated by allele-specific PCR (ASP). This study has applied an ASP to quantitate low-level K103N in patients presenting for clinical HIV genotyping and assess the correlation with antiretroviral treatment history and outcomes. HIV RNA was extracted from patient plasma and subjected to PCR amplification of the reverse transcriptase (RT) region followed by genotyping by CSA and real-time ASP for K103N. When applied to samples from patients presenting for genotyping, the ASP detects K103N, not K103 nor K103R, but cross-reacts with K103S. ASP identified all samples that were K103N by CSA (10.5%) and an additional 14% by ASP only, representing patients who were therapy naïve and with NNRTI treatment history. ASP detected therapy-acquired K103N at low levels up to 6 years after cessation of NNRTI therapy. In three patients with new HIV diagnosis and K103N detected by ASP only, K103N virus declined rapidly from the circulation but persisted in PBMC DNA at >12 months post-diagnosis. Efavirenz (EFV) combination therapy in three patients with low-level K103N suppressed successfully viral load, although one patient developed failure and CSA-detectable K103N after 15 months of therapy. Thus, analysis of K103N by ASP in conjunction with CSA genotyping provides additional information that reflects K103N transmission and persistence but detection of low-level K103N does not preclude successful EFV-containing combination therapy.Jillian M. Carr, Tara Green, David Shaw, Lyndal Daly, Wendy Hart, Rodney Ratcliff, Geoffrey Higgins, Christopher J. Burrell, Peng Li, and Ming Qia
Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics
No full textThe central questions of bacterial ecology and evolution require a method to consistently demarcate, from the vast and diverse set of bacterial cells within a natural community, the groups playing ecologically distinct roles (ecotypes). Because of a lack of theory-based guidelines, current methods in bacterial systematics fail to divide the bacterial domain of life into meaningful units of ecology and evolution. We introduce a sequence-based approach (“ecotype simulation”) to model the evolutionary dynamics of bacterial populations and to identify ecotypes within a natural community, focusing here on two Bacillus clades surveyed from the “Evolution Canyons” of Israel. This approach has identified multiple ecotypes within traditional species, with each predicted to be an ecologically distinct lineage; many such ecotypes were confirmed to be ecologically distinct, with specialization to different canyon slopes with different solar exposures. Ecotype simulation provides a long-needed natural foundation for microbial ecology and systematics.Alexander Koeppel, Elizabeth B. Perry, Johannes Sikorski, Danny Krizanc, Andrew Warner, David M. Ward, Alejandro P. Rooney, Evelyne Brambilla, Nora Connor, Rodney M. Ratcliff, Eviatar Nevo and Frederick M. Coha
Legionella nagasakiensis sp nov., isolated from water samples and from a patient with pneumonia
No full textA novel Legionella species was identified based on analysis of 16S rRNA and mip (macrophage infectivity potentiator) gene sequences, cellular fatty acids, isoprenoid quinones, biochemical reactions, antigens and quantitative DNA–DNA hybridization. Strain CDC-1796-JAP-ET was isolated from well water at the Nagasaki Municipal Medical Center, Japan. Two strains, CDC-3041-AUS-E and CDC-3558-AUS-E, were isolated from water samples during an outbreak of legionellosis in South Australia. Strain CDC-5427-OH-H was isolated from a 66-year-old female patient diagnosed with Legionnaires’ disease in the US. Cells from these four strains were Gram-negative, non-fluorescent, rod-shaped, and positive for alkaline phosphatase, esterase, leucine arylamidase, catalase, gelatinase, β-lactamase and tyrosine browning assay. Phylogenetic analysis of 16S rRNA and mip genes revealed that the four strains formed a distinct cluster within the genus Legionella. The bacteria contained branched-chain fatty acids and quinones that are typical of members of the genus Legionella. Slide agglutination tests demonstrated no cross-reaction with 52 previously described members of the Legionellaceae. DNA–DNA hybridization studies indicated that DNAs from the four strains were highly related (78–84 %) but they showed 29 % relatedness to Legionella oakridgensis ATCC 33761T and less than 10 % to strains of other Legionella species tested. These characterizations suggest that the isolates represent a novel species, for which the name Legionella nagasakiensis sp. nov. is proposed; the type strain is CDC-1796-JAP-ET ( = ATCC BAA-1557T = JCM 15315T).Genyan Yang, Robert F. Benson, Rodney M. Ratcliff, Ellen W. Brown, Arnold G. Steigerwalt, W. Lanier Thacker, Maryam I. Daneshvar, Roger E. Morey, Atsushi Saito, and Barry S. Field
Molecular Diagnosis of Medical Viruses
No full textThe diagnosis of infectious diseases has been revolutionized by the development of molecular techniques, foremost with the applications of the polymerase chain reaction (PCR). The achievable high sensitivity and ease with which the method can be used to detect any known genetic sequence have led to its wide application in the life sciences. More recently, real-time PCR assays have provided additional major contributions, with the inclusion of an additional fluorescent probe detection system resulting in an increase in sensitivity over conventional PCR, the ability to confirm the amplification product and to quantitate the target concentration. Further, nucleotide sequence analysis of the amplification products has facilitated epidemiological studies of infectious disease outbreaks, and the monitoring of treatment outcomes for infections, in particular with viruses which mutate at high frequency. This review discusses the applications of qualitative and quantitative real-time PCR, nested PCR, multiplex PCR, nucleotide sequence analysis of amplified products and quality assurance with nucleic acid testing (NAT) in diagnostic laboratories
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