601
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Sekizuka T, Matsui M, Takahashi T, Hayashi M, Suzuki S, Tokaji A, Kuroda M. Complete Genome Sequence of bla IMP-6-Positive Metakosakonia sp. MRY16-398 Isolate From the Ascites of a Diverticulitis Patient. Front Microbiol 2018; 9:2853. [PMID: 30524415 PMCID: PMC6262049 DOI: 10.3389/fmicb.2018.02853] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/06/2018] [Indexed: 01/09/2023] Open
Abstract
A novel species of carbapenemase-producing Enterobacteriaceae (CPE) was isolated from a patient diagnosed with sigmoid colon diverticulitis. At first, laboratory testing suggested it was Klebsiella oxytoca or Pantoea sp.; however, a complete genome sequence of the isolate, MRY16-398, revealed that it could be novel species, most similar to [Kluyvera] intestini, of which taxonomic nomenclature is still under discussion. Orthologous conserved gene analysis among 42 related bacterial strains indicated that MRY16-398 was classified as the newly proposed genus Metakosakonia. Further, MRY16-398 was found to harbor the blaIMP-6 gene-positive class 1 integron (In722) in plasmid pMRY16-398_2 (IncN replicon, 47.4 kb in size). This finding implies that rare and opportunistic bacteria could be potential infectious agents. In conclusion, our results highlight the need for continuous monitoring for CPE even in nonpathogenic bacteria in the nosocomial environment.
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Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mari Matsui
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Tomiyo Takahashi
- The Public Health Institute of Kochi Prefecture, Kōchi City, Japan
| | - Michiko Hayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Satowa Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Japan
| | - Akihiko Tokaji
- The Public Health Institute of Kochi Prefecture, Kōchi City, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
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602
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Ríhová J, Nováková E, Husník F, Hypša V. Legionella Becoming a Mutualist: Adaptive Processes Shaping the Genome of Symbiont in the Louse Polyplax serrata. Genome Biol Evol 2018; 9:2946-2957. [PMID: 29069349 PMCID: PMC5714129 DOI: 10.1093/gbe/evx217] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2017] [Indexed: 12/14/2022] Open
Abstract
Legionellaceae are intracellular bacteria known as important human pathogens. In the environment, they are mainly found in biofilms associated with amoebas. In contrast to the gammaproteobacterial family Enterobacteriaceae, which established a broad spectrum of symbioses with many insect taxa, the only instance of legionella-like symbiont has been reported from lice of the genus Polyplax. Here, we sequenced the complete genome of this symbiont and compared its main characteristics to other Legionella species and insect symbionts. Based on rigorous multigene phylogenetic analyses, we confirm this bacterium as a member of the genus Legionella and propose the name Candidatus Legionella polyplacis, sp.n. We show that the genome of Ca. Legionella polyplacis underwent massive degeneration, including considerable size reduction (529.746 bp, 484 protein coding genes) and a severe decrease in GC content (23%). We identify several possible constraints underlying the evolution of this bacterium. On one hand, Ca. Legionella polyplacis and the louse symbionts Riesia and Puchtella experienced convergent evolution, perhaps due to adaptation to similar hosts. On the other hand, some metabolic differences are likely to reflect different phylogenetic positions of the symbionts and hence availability of particular metabolic function in the ancestor. This is exemplified by different arrangements of thiamine metabolism in Ca. Legionella polyplacis and Riesia. Finally, horizontal gene transfer is shown to play a significant role in the adaptive and diversification process. Particularly, we show that Ca. L. polyplacis horizontally acquired a complete biotin operon (bioADCHFB) that likely assisted this bacterium when becoming an obligate mutualist.
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Affiliation(s)
- Jana Ríhová
- Department of Parasitology, University of South Bohemia, Ceské Budejovice, Czech Republic
| | - Eva Nováková
- Department of Parasitology, University of South Bohemia, České Budějovice, Czech Republic.,Biology Centre, Institute of Parasitology, CAS, v.v.i., České Budějovice, Czech Republic
| | - Filip Husník
- Department of Parasitology, University of South Bohemia, Ceské Budejovice, Czech Republic
| | - Václav Hypša
- Department of Parasitology, University of South Bohemia, České Budějovice, Czech Republic.,Biology Centre, Institute of Parasitology, CAS, v.v.i., České Budějovice, Czech Republic
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603
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Kayansamruaj P, Soontara C, Unajak S, Dong HT, Rodkhum C, Kondo H, Hirono I, Areechon N. Comparative genomics inferred two distinct populations of piscine pathogenic Streptococcus agalactiae, serotype Ia ST7 and serotype III ST283, in Thailand and Vietnam. Genomics 2018; 111:1657-1667. [PMID: 30453061 DOI: 10.1016/j.ygeno.2018.11.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/06/2018] [Accepted: 11/13/2018] [Indexed: 11/16/2022]
Abstract
The genomes of Streptococcus agalactiae (group B streptococcus; GBS) collected from diseased fish in Thailand and Vietnam over a nine-year period (2008-2016) were sequenced and compared (n = 21). Based on capsular serotype and multilocus sequence typing (MLST), GBS isolates are divided into 2 groups comprised of i) serotype Ia; sequence type (ST)7 and ii) serotype III; ST283. Population structure inferred by core genome (cg)MLST and Bayesian clustering analysis also strongly indicated distribution of two GBS populations in both Thailand and Vietnam. Deep phylogenetic analysis implied by CRISPR array's spacer diversity was able to cluster GBS isolates according to their temporal and geographic origins, though ST7 has varying CRISPR1-spacer profiles when compared to ST283 strains. Based on overall genotypic features, Thai ST283 strains were closely related to the Singaporean ST283 strain causing foodborne illness in humans in 2015, thus, signifying zoonotic potential of this GBS population in the country.
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Affiliation(s)
| | - Chayanit Soontara
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Ha Thanh Dong
- Department of Science, Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok, Thailand
| | - Channarong Rodkhum
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand; Research Unit of Fish Infectious Diseases (RU-FIDs), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Nontawith Areechon
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
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604
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Genome Sequences of
Vibrio maerlii
sp. nov. and
Vibrio rhodolitus
sp. nov., Isolated from Rhodoliths. Microbiol Resour Announc 2018; 7:MRA01039-18. [PMID: 30533792 PMCID: PMC6256479 DOI: 10.1128/mra.01039-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/17/2018] [Indexed: 11/20/2022] Open
Abstract
We report here the genome sequences of the novel isolates G62
T
and G98
T
from rhodoliths. The nearly complete genomes consisted of 4.7 Mbp (4,233 coding sequences [CDS]) for G62
T
and 4.5 Mbp (4,085 CDS) for G98
T
.
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605
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Li L, Wang J, Zhou YJ, Lin HW, Lu YH. Streptomyces reniochalinae sp. nov. and Streptomyces diacarni sp. nov., from marine sponges. Int J Syst Evol Microbiol 2018; 69:99-104. [PMID: 30427301 DOI: 10.1099/ijsem.0.003109] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two marine actinomycete strains, LHW50302T and LHW51701T, were isolated from marine sponges collected in Sansha, Hainan Province, China. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with their classification in the genus Streptomyces. The strains formed hooked and looped chains of arthrospores with smooth surfaces. The cell-wall hydrolysates of the strains contained ll-diaminopimelic acid as the diagnostic diamino acid. MK-9(H8) was the predominant menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Major fatty acids of the strains were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The 16S rRNA gene sequences indicated that the strains clustered together with Streptomyces albus CGMCC 4.1640T and Streptomyces qinglanensis CGMCC 4.6825T. Multilocus sequence analysis (MLSA) confirmed their relationship. Genome relatedness in forms of average nucleotide identity, digital DNA-DNA hybridization value and MLSA evolutionary distance between each of the strains and its closest relatives showed that they belonged to distinct species. On the basis of these results, strains LHW50302T and LHW51701T belong to two novel species in the genus Streptomyces, for which the names Streptomyces reniochalinae sp. nov. (type strain LHW50302T=CCTCC AA 2018013T=DSM 106194T) and Streptomyces diacarni sp. nov. (type strain LHW51701T=CCTCC AA 2018017T=DSM 106126T) are proposed, respectively.
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Affiliation(s)
- Lei Li
- 1State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China.,2Marine Drugs Research Center, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Jie Wang
- 2Marine Drugs Research Center, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Yong-Jun Zhou
- 2Marine Drugs Research Center, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Hou-Wen Lin
- 2Marine Drugs Research Center, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PR China
| | - Yan-Hua Lu
- 1State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, PR China
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606
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Nagano N, Koide S, Hayashi W, Taniguchi Y, Tanaka H, Maeyama Y, Suzuki M, Kimura K, Arakawa Y, Nagano Y. Population-level transition of capsular polysaccharide types among sequence type 1 group B Streptococcus isolates with reduced penicillin susceptibility during a long-term hospital epidemic. Int J Antimicrob Agents 2018; 53:203-210. [PMID: 30414439 DOI: 10.1016/j.ijantimicag.2018.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/30/2018] [Accepted: 11/04/2018] [Indexed: 10/27/2022]
Abstract
Over a 35-month period, group B Streptococcus isolates with reduced penicillin susceptibility (PRGBS) were detected from elderly patients at a regional hospital in Japan, accompanying population-level transition of PRGBS serotypes. The genetic relatedness of 77 non-duplicate PRGBS from 73 patients was analysed. Serotype III PRGBS predominated (16 serotype III/1 serotype Ib) in the first 9 months (period I), then 3 serotype Ib isolates appeared transiently for the next 3 months (period II), which was replaced predominantly by serotype Ia (20 serotype Ia/1 serotype III/1 non-typeable) for 9 months (period III). In the last 14 months (period IV), besides 25 serotype Ia isolates, 10 serotype III were also identified. Serotypes III and Ia isolates, belonging to ST1, shared G329V, G398A, V405A and G429D substitutions in penicillin-binding protein 2X. Of three strains subjected to whole-genome sequencing, serotype III strain SU12 (period I) had a higher degree of genomic similarity with serotype Ia strain SU97 (period III) than serotype Ib strain SU67 (period II) based on average nucleotide identity and single nucleotide polymorphisms. Analysis of the cps gene clusters and the upstream and downstream flanking sequences revealed that disruption of the hyaluronidase gene located upstream of cpsY by insertion of IS1548 was found in strain SU12, whereas ΔISSag8 was inserted between tRNA-Arg and rpsA genes located downstream of cpsL in strain SU97. Interestingly, most serotype III PRGBS re-emerging in period IV had this tRNA-Arg-ΔISSag8-rpsA region. Capsular switching and nosocomial transmission may possibly contribute to population-level serotype replacement among ST1 PRGBS isolates.
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Affiliation(s)
- Noriyuki Nagano
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.
| | - Shota Koide
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Wataru Hayashi
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Yui Taniguchi
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Hayato Tanaka
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Yoshihiko Maeyama
- Department of Health and Medical Sciences, Shinshu University Graduate School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Kouji Kimura
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Yukiko Nagano
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
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607
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Genomes of Escherichia coli bacteraemia isolates originating from urinary tract foci contain more virulence-associated genes than those from non-urinary foci and neutropaenic hosts. J Infect 2018; 77:534-543. [PMID: 30391630 PMCID: PMC6293314 DOI: 10.1016/j.jinf.2018.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/18/2018] [Accepted: 10/27/2018] [Indexed: 01/01/2023]
Abstract
Objectives Escherichia coli is the leading cause of bacteraemia. In an era of emerging multi-drug-resistant strains, development of effective preventative strategies will be informed by knowledge of strain diversity associated with specific infective syndromes/patient groups. We hypothesised that the number of virulence factor (VF) genes amongst bacteraemia isolates from neutropaenic patients would be lower than isolates from immunocompetent patients. Methods Immunocompetent and neutropaenic adults with E. coli bacteraemia were recruited prospectively and the source of bacteraemia determined. VF gene profiles were established in silico following whole genome sequencing. Results Isolates from individual patients were monoclonal. Strains from immunocompetent patients with urinary tract infective foci (UTIF) harboured more VF genes (median number of VF genes 16, range 8–24) than isolates from both immunocompetent patients with non-UTIF (10, 2–22, p = 0.0058) and neutropaenic patients with unknown focus of infection (NPUFI) (8, 3–13, p < 0.0001). Number of VF genes (OR 1.21, 95% CIs 1.01–1.46, p = 0.039) and urinary catheter/recurrent urinary tract infection (OR 12.82, 95% CIs 1.24–132.65, p = 0.032) were independent predictors of bacteraemia secondary to UTIF vs. non-UTIF in immunocompetent patients. papA, papC, papE/F, papG, agn43, tia, iut, fyuA, kpsM and sat were significantly more prevalent amongst UTIF- vs non-UTIF-originating isolates amongst immunocompetent patients, while papC, papE/F, papG, agn43, tia, fyuA, hlyA, usp and clb were significantly more prevalent amongst UTIF- vs NPUFI-associated isolates. Conclusions Bacteraemia-associated E. coli strains originating from UTIF have distinct VF gene profiles from strains associated with non-UTIF- and NPUFI. This diversity must be addressed in the design of future vaccines to ensure adequate coverage of strains responsible for site-specific disease.
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608
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Brashear WA, Raudsepp T, Murphy WJ. Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation. Genome Res 2018; 28:1841-1851. [PMID: 30381290 PMCID: PMC6280758 DOI: 10.1101/gr.237586.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/27/2018] [Indexed: 12/20/2022]
Abstract
Despite claims that the mammalian Y Chromosome is on a path to extinction, comparative sequence analysis of primate Y Chromosomes has shown the decay of the ancestral single-copy genes has all but ceased in this eutherian lineage. The suite of single-copy Y-linked genes is highly conserved among the majority of eutherian Y Chromosomes due to strong purifying selection to retain dosage-sensitive genes. In contrast, the ampliconic regions of the Y Chromosome, which contain testis-specific genes that encode the majority of the transcripts on eutherian Y Chromosomes, are rapidly evolving and are thought to undergo species-specific turnover. However, ampliconic genes are known from only a handful of species, limiting insights into their long-term evolutionary dynamics. We used a clone-based sequencing approach employing both long- and short-read sequencing technologies to assemble ∼2.4 Mb of representative ampliconic sequence dispersed across the domestic cat Y Chromosome, and identified the major ampliconic gene families and repeat units. We analyzed fluorescence in situ hybridization, qPCR, and whole-genome sequence data from 20 cat species and revealed that ampliconic gene families are conserved across the cat family Felidae but show high transcript diversity, copy number variation, and structural rearrangement. Our analysis of ampliconic gene evolution unveils a complex pattern of long-term gene content stability despite extensive structural variation on a nonrecombining background.
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Affiliation(s)
- Wesley A Brashear
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
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609
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Wan J, Li Y, Wang H, Tang L, Li Z, Zhou C, Tan Q, Bao D, Yang R. Three complete mitochondrial genomes of straw-rotting edible fungus Volvariella volvacea using next generation sequencing. Mitochondrial DNA B Resour 2018; 3:1054-1056. [PMID: 33474412 PMCID: PMC7799644 DOI: 10.1080/23802359.2018.1511849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/10/2018] [Indexed: 11/01/2022] Open
Abstract
The straw-rotting edible fungus Volvariella volvacea is a widely cultivated edible fungus across China and Southeast Asian countries. Three complete mitochondrial genomes of V. volvacea from China, Thailand, and India were determined using the next-generation sequencing technology. The genome sizes of the three strains (China, Thailand, and India) were 62,541 bp, 64,531 bp, and 65,668 bp with GC contents of 38.46%, 38.56%, and 38.52%, respectively. All the genomes encoded 14 conserved protein-coding genes, the small ribosomal RNA subunits (rns), large ribosomal RNA subunits (rnl), and 23 tRNAs were located on the same strand. In the putative protein-coding genes, four introns were distributed in cox1 in the genomes of V23-1 and V8. 5 introns (four introns invaded into cox1and one intron invaded into cob) were detected in Tai8. The phylogenetic analysis confirmed that V. volvacea was a number of Agaricales. This mitochondrial genome may open new avenues for understanding the phylogeny and evolution of Pluteaceae and Agaricales.
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Affiliation(s)
- Jianing Wan
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Li
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hong Wang
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Lihua Tang
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhengpeng Li
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chenli Zhou
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qi Tan
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ruiheng Yang
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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610
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Typing and Species Identification of Clinical Klebsiella Isolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2018; 56:JCM.00843-18. [PMID: 30135233 DOI: 10.1128/jcm.00843-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/19/2018] [Indexed: 12/18/2022] Open
Abstract
Klebsiella pneumoniae and related species are frequent causes of nosocomial infections and outbreaks. Therefore, quick and reliable strain typing is crucial for the detection of transmission routes in the hospital. The aim of this study was to evaluate Fourier transform infrared spectroscopy (FTIR) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as rapid methods for typing clinical Klebsiella isolates in comparison to whole-genome sequencing (WGS), which was considered the gold standard for typing and identification. Here, 68 clinical Klebsiella strains were analyzed by WGS, FTIR, and MALDI-TOF MS. FTIR showed high discriminatory power in comparison to the WGS reference, whereas MALDI-TOF MS exhibited a low ability to type the isolates. MALDI-TOF mass spectra were further analyzed for peaks that showed high specificity for different Klebsiella species. Phylogenetic analysis revealed that the Klebsiella isolates comprised three different species: K. pneumoniae, K. variicola, and K. quasipneumoniae Genome analysis showed that MALDI-TOF MS can be used to distinguish K. pneumoniae from K. variicola due to shifts of certain mass peaks. The peaks were tentatively identified as three ribosomal proteins (S15p, L28p, L31p) and one stress response protein (YjbJ), which exhibit amino acid differences between the two species. Overall, FTIR has high discriminatory power to recognize the clonal relationship of isolates, thus representing a valuable tool for rapid outbreak analysis and for the detection of transmission events due to fast turnaround times and low costs per sample. Furthermore, specific amino acid substitutions allow the discrimination of K. pneumoniae and K. variicola by MALDI-TOF MS.
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611
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Versluis D, Nijsse B, Naim MA, Koehorst JJ, Wiese J, Imhoff JF, Schaap PJ, van Passel MWJ, Smidt H, Sipkema D. Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio. Genome Biol Evol 2018; 10:125-142. [PMID: 29319806 PMCID: PMC5765558 DOI: 10.1093/gbe/evx271] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2017] [Indexed: 12/19/2022] Open
Abstract
Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesized that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways, albeit with substantial differences in overall gene content. Based on gene composition, Pseudovibrio spp. clustered by geographic region, indicating geographic speciation. Furthermore, the fact that isolates from the Mediterranean Sea clustered by sponge species suggested host-specific adaptation or colonization. Genome analyses suggest that Pseudovibrio hongkongensis UST20140214-015BT is only distantly related to other Pseudovibrio spp., thereby challenging its status as typical Pseudovibrio member. All Pseudovibrio genomes were found to encode numerous proteins with SEL1 and tetratricopeptide repeats, which have been suggested to play a role in host colonization. For evasion of the host immune system, Pseudovibrio spp. may depend on type III, IV, and VI secretion systems that can inject effector molecules into eukaryotic cells. Furthermore, Pseudovibrio genomes carry on average seven secondary metabolite biosynthesis clusters, reinforcing the role of Pseudovibrio spp. as potential producers of novel bioactive compounds. Tropodithietic acid, bacteriocin, and terpene biosynthesis clusters were highly conserved within the genus, suggesting an essential role in survival, for example through growth inhibition of bacterial competitors. Taken together, these results support the hypothesis that Pseudovibrio spp. have mutualistic relations with sponges.
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Affiliation(s)
- Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
| | - Bart Nijsse
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University & Research, The Netherlands
| | - Mohd Azrul Naim
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, The Netherlands
| | - Jutta Wiese
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Johannes F Imhoff
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, The Netherlands
| | - Mark W J van Passel
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands.,National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
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612
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Vickers C, Liu F, Abe K, Salama-Alber O, Jenkins M, Springate CMK, Burke JE, Withers SG, Boraston AB. Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-l-fucosidases from GH29. J Biol Chem 2018; 293:18296-18308. [PMID: 30282808 DOI: 10.1074/jbc.ra118.005134] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Indexed: 11/06/2022] Open
Abstract
Fucoidans are chemically complex and highly heterogeneous sulfated marine fucans from brown macro algae. Possessing a variety of physicochemical and biological activities, fucoidans are used as gelling and thickening agents in the food industry and have anticoagulant, antiviral, antitumor, antibacterial, and immune activities. Although fucoidan-depolymerizing enzymes have been identified, the molecular basis of their activity on these chemically complex polysaccharides remains largely uninvestigated. In this study, we focused on three glycoside hydrolase family 107 (GH107) enzymes: MfFcnA and two newly identified members, P5AFcnA and P19DFcnA, from a bacterial species of the genus Psychromonas Using carbohydrate-PAGE, we show that P5AFcnA and P19DFcnA are active on fucoidans that differ from those depolymerized by MfFcnA, revealing differential substrate specificity within the GH107 family. Using a combination of X-ray crystallography and NMR analyses, we further show that GH107 family enzymes share features of their structures and catalytic mechanisms with GH29 α-l-fucosidases. However, we found that GH107 enzymes have the distinction of utilizing a histidine side chain as the proposed acid/base catalyst in its retaining mechanism. Further interpretation of the structural data indicated that the active-site architectures within this family are highly variable, likely reflecting the specificity of GH107 enzymes for different fucoidan substructures. Together, these findings begin to illuminate the molecular details underpinning the biological processing of fucoidans.
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Affiliation(s)
- Chelsea Vickers
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Feng Liu
- the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada, and
| | - Kento Abe
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Orly Salama-Alber
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Meredith Jenkins
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | | | - John E Burke
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada
| | - Stephen G Withers
- the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada, and
| | - Alisdair B Boraston
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia 8W 3P6, Canada,.
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613
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Laothanachareon T, Tamayo-Ramos JA, Nijsse B, Schaap PJ. Forward Genetics by Genome Sequencing Uncovers the Central Role of the Aspergillus niger goxB Locus in Hydrogen Peroxide Induced Glucose Oxidase Expression. Front Microbiol 2018; 9:2269. [PMID: 30319579 PMCID: PMC6165874 DOI: 10.3389/fmicb.2018.02269] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 09/05/2018] [Indexed: 01/09/2023] Open
Abstract
Aspergillus niger is an industrially important source for gluconic acid and glucose oxidase (GOx), a secreted commercially important flavoprotein which catalyses the oxidation of β-D-glucose by molecular oxygen to D-glucolactone and hydrogen peroxide. Expression of goxC, the GOx encoding gene and the concomitant two step conversion of glucose to gluconic acid requires oxygen and the presence of significant amounts of glucose in the medium and is optimally induced at pH 5.5. The molecular mechanisms underlying regulation of goxC expression are, however, still enigmatic. Genetic studies aimed at understanding GOx induction have indicated the involvement of at least seven complementation groups, for none of which the molecular basis has been resolved. In this study, a mapping-by-sequencing forward genetics approach was used to uncover the molecular role of the goxB locus in goxC expression. Using the Illumina and PacBio sequencing platforms a hybrid high quality draft genome assembly of laboratory strain N402 was obtained and used as a reference for mapping of genomic reads obtained from the derivative NW103:goxB mutant strain. The goxB locus encodes a thioredoxin reductase. A deletion of the encoding gene in the N402 parent strain led to a high constitutive expression level of the GOx and the lactonase encoding genes required for the two-step conversion of glucose in gluconic acid and of the catR gene encoding catalase R. This high constitutive level of expression was observed to be irrespective of the carbon source and oxidative stress applied. A model clarifying the role of GoxB in the regulation of the expression of goxC involving hydrogen peroxide as second messenger is presented.
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Affiliation(s)
- Thanaporn Laothanachareon
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands.,Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand
| | | | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
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614
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Mohr KI, Wolf C, Nübel U, Szafrańska AK, Steglich M, Hennessen F, Gemperlein K, Kämpfer P, Martin K, Müller R, Wink J. A polyphasic approach leads to seven new species of the cellulose-decomposing genus Sorangium, Sorangium ambruticinum sp. nov., Sorangium arenae sp. nov., Sorangium bulgaricum sp. nov., Sorangium dawidii sp. nov., Sorangium kenyense sp. nov., Sorangium orientale sp. nov. and Sorangium reichenbachii sp. nov. Int J Syst Evol Microbiol 2018; 68:3576-3586. [PMID: 30234476 DOI: 10.1099/ijsem.0.003034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seventy-three strains of Sorangium have been isolated from soil samples collected from all over the world. The strains were characterized using a polyphasic approach and phenotypic, genotypic and chemotype analyses clarified their taxonomic relationships. 16S rRNA, xynB1, groEL1, matrix-assisted laser desorption/ioniziation time-of-flight mass spectrometry and API-ZYM analyses were conducted. In addition, from selected representative strains, fatty acids, quinones and phospholipids were analysed. In silico DNA-DNA hybridization and DNA-DNA hybridization against the current type species of Sorangiumcellulosum strain Soce 1871T (DSM 14627T) completed the analyses. Finally, our study revealed seven new species of Sorangium: Sorangium ambruticinum (Soce 176T; DSM 53252T, NCCB 100639T, sequence accession number ERS2488998), Sorangium arenae (Soce 1078T; DSM 105768T, NCCB 100643T, ERS2489002), Sorangium bulgaricum (Soce 321T; DSM 53339T, NCCB 100640T, ERS2488999), Sorangium dawidii (Soce 362T; DSM 105767T, NCCB 100641T, ERS2489000), Sorangium kenyense (Soce 375T; DSM 105741T, NCCB 100642T, ERS2489001), Sorangium orientale (Soce GT47T; DSM 105742T, NCCB 100638T, ERS2501484) and Sorangium reichenbachii (Soce 1828T; DSM 105769T, NCCB 100644T, ERS2489003).
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Affiliation(s)
- Kathrin I Mohr
- 1Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Corinna Wolf
- 2Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Ulrich Nübel
- 3Leibniz Institute DSMZ, Braunschweig, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany.,4German Centre of Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Anna K Szafrańska
- 3Leibniz Institute DSMZ, Braunschweig, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany.,4German Centre of Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Matthias Steglich
- 3Leibniz Institute DSMZ, Braunschweig, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany.,4German Centre of Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Fabienne Hennessen
- 5Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, D-66041 Saarbrücken, Germany
| | - Katja Gemperlein
- 5Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, D-66041 Saarbrücken, Germany
| | - Peter Kämpfer
- 6Department of Applied Microbiology, Justus Liebig University Gießen, 35392 Gießen, Germany
| | - Karin Martin
- 7Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institut, 07745 Jena, Germany
| | - Rolf Müller
- 4German Centre of Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.,5Department of Pharmaceutical Biotechnology, Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Saarland University, D-66041 Saarbrücken, Germany
| | - Joachim Wink
- 2Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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615
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Bender JK, Fleige C, Lange D, Klare I, Werner G. Rapid emergence of highly variable and transferable oxazolidinone and phenicol resistance gene optrA in German Enterococcus spp. clinical isolates. Int J Antimicrob Agents 2018; 52:819-827. [PMID: 30236952 DOI: 10.1016/j.ijantimicag.2018.09.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/07/2018] [Accepted: 09/09/2018] [Indexed: 01/12/2023]
Abstract
The number of linezolid-resistant Enterococcus spp. isolates received by the National Reference Centre for Staphylococci and Enterococci in Germany has been increasing since 2011. Although the majority are E. faecium, clinical linezolid-resistant E. faecalis have also been isolated. With respect to the newly discovered linezolid resistance protein OptrA, the authors conducted a retrospective polymerase chain reaction screening of 698 linezolid-resistant enterococcus clinical isolates. That yielded 43 optrA-positive strains, of which a subset was analysed by whole-genome sequencing in order to infer linezolid resistance-associated mechanisms and phylogenetic relatedness, and to disclose optrA genetic environments. Multiple optrA variants were detected. The originally described variant from China (optrAWT) was the only variant shared between the two Enterococcus spp.; however, distinct optrAWT loci were detected for E. faecium and E. faecalis. Generally, optrA localized to a plethora of genetic backgrounds that differed even for identical optrA variants. This suggests transmission of a mobile genetic element harbouring the resistance locus. Additionally, identical optrA variants detected on presumably identical plasmids, that were present in unrelated strains, indicates dissemination of the entire optrA-containing plasmid. In accordance, in vitro conjugation experiments verified transfer of optrA plasmids between enterococci of the same and of different species. In conclusion, multiple optrA variants located on distinct plasmids and mobile genetic elements with the potential for conjugative transfer are supposedly causative for the emergence of optrA-positive enterococci. Hence, rapid dissemination of the resistance determinant under selective pressure imposed by extensive use of last-resort antibiotics in clinical settings could be expected.
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Affiliation(s)
- Jennifer K Bender
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Saxony-Anhalt, Germany.
| | - Carola Fleige
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Saxony-Anhalt, Germany
| | - Dominik Lange
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Saxony-Anhalt, Germany
| | - Ingo Klare
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Saxony-Anhalt, Germany
| | - Guido Werner
- National Reference Centre for Staphylococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode, Saxony-Anhalt, Germany
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616
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Genome Sequence of the Probiotic Strain Bacillus velezensis Variant polyfermenticus GF423. Microbiol Resour Announc 2018; 7:MRA01000-18. [PMID: 30533616 PMCID: PMC6256592 DOI: 10.1128/mra.01000-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 08/14/2018] [Indexed: 11/20/2022] Open
Abstract
The genome sequence of the commercial probiotic strain “Bacillus polyfermenticus” GF423 was determined. Comparison of the 4.1-Mb genome sequence revealed Bacillus velezensis FZB42 as its closest relative. The genome sequence of the commercial probiotic strain “Bacillus polyfermenticus” GF423 was determined. Comparison of the 4.1-Mb genome sequence revealed Bacillus velezensis FZB42 as its closest relative. Based on the genome sequence, we propose that this probiotic strain be renamed Bacillus velezensis variant polyfermenticus.
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617
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Colistin Heteroresistance and Involvement of the PmrAB Regulatory System in Acinetobacter baumannii. Antimicrob Agents Chemother 2018; 62:AAC.00788-18. [PMID: 29914966 DOI: 10.1128/aac.00788-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/14/2018] [Indexed: 02/08/2023] Open
Abstract
Multidrug-resistant Acinetobacter baumannii infection has recently emerged as a worldwide clinical problem, and colistin is increasingly being used as a last-resort therapy. Despite its favorable bacterial killing, resistance and heteroresistance (HR) to colistin have been described. The purpose of the present study was to investigate the role of the PmrAB regulatory pathway in laboratory-selected mutants representative of global epidemic strains. From three unrelated A. baumannii clinical strains (sequence types 2, 3, and 20), eight colistin-resistant mutants were selected. Half of the mutants showed HR to colistin according to the reference method (population analysis profiling), whereas the other half exhibited stable resistance. M12I mutation within pmrA and M308R, S144KLAGS, and P170L mutations for pmrB were associated with HR to colistin, while T235I, A226T, and P233S mutations within pmrB were associated with stable resistance. The transcript levels of the pmrCAB operon were upregulated in all the mutants. Compensatory mutations were explored for some mutants. A single mutant (T235I mutant) displayed a compensatory mutation through ISAba1 mobilization within the pmrB gene that was associated with the loss of colistin resistance. The mutant resistance phenotype associated with T235I was partially restored in a trans-complementation assay turning to HR. The level of colistin resistance was correlated with the level of expression of pmrC in the trans-complemented strains. This report shows the role of different mutations in the PmrAB regulatory pathway and warns of the development of colistin HR that could be present but not easily detected through routine testing.
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618
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Snitkin ES, Won S, Pirani A, Lapp Z, Weinstein RA, Lolans K, Hayden MK. Integrated genomic and interfacility patient-transfer data reveal the transmission pathways of multidrug-resistant Klebsiella pneumoniae in a regional outbreak. Sci Transl Med 2018; 9:9/417/eaan0093. [PMID: 29167391 DOI: 10.1126/scitranslmed.aan0093] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/16/2017] [Accepted: 08/18/2017] [Indexed: 12/15/2022]
Abstract
Development of effective strategies to limit the proliferation of multidrug-resistant organisms requires a thorough understanding of how such organisms spread among health care facilities. We sought to uncover the chains of transmission underlying a 2008 U.S. regional outbreak of carbapenem-resistant Klebsiella pneumoniae by performing an integrated analysis of genomic and interfacility patient-transfer data. Genomic analysis yielded a high-resolution transmission network that assigned directionality to regional transmission events and discriminated between intra- and interfacility transmission when epidemiologic data were ambiguous or misleading. Examining the genomic transmission network in the context of interfacility patient transfers (patient-sharing networks) supported the role of patient transfers in driving the outbreak, with genomic analysis revealing that a small subset of patient-transfer events was sufficient to explain regional spread. Further integration of the genomic and patient-sharing networks identified one nursing home as an important bridge facility early in the outbreak-a role that was not apparent from analysis of genomic or patient-transfer data alone. Last, we found that when simulating a real-time regional outbreak, our methodology was able to accurately infer the facility at which patients acquired their infections. This approach has the potential to identify facilities with high rates of intra- or interfacility transmission, data that will be useful for triggering targeted interventions to prevent further spread of multidrug-resistant organisms.
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Affiliation(s)
- Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA. .,Division of Infectious Diseases, Department of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Won
- Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - Ali Pirani
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.,Division of Infectious Diseases, Department of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zena Lapp
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert A Weinstein
- Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA.,Division of Infectious Diseases, Department of Medicine, Cook County Health and Hospitals System, Chicago, IL 60612, USA
| | - Karen Lolans
- Division of Clinical Microbiology, Department of Pathology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA. .,Division of Clinical Microbiology, Department of Pathology, Rush University Medical Center, Chicago, IL 60612, USA
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619
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Nakanishi N, Nomoto R, Sato K, Koike C, Kusuki M, Nakamura T, Shigemura K, Shirakawa T, Fujisawa M, Tokimatsu I, Osawa K. Acquisition of antimicrobial-resistant variants in repeated infections caused by Pseudomonas aeruginosa revealed by whole genome sequencing. J Infect Chemother 2018; 25:154-156. [PMID: 30126693 DOI: 10.1016/j.jiac.2018.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 11/24/2022]
Abstract
Pseudomonas aeruginosa, responsible for serious nosocomial-acquired infections, possesses intrinsic antibiotic resistance mechanisms and commonly exhibits multidrug resistance. Here, we report the evolving resistance profiles of strains isolated from the sputum of a patient being treated for repeated P. aeruginosa infections following cancer resection. Whole genome sequencing of six isolates obtained over a 2-month period revealed two key single nucleotide polymorphisms in the mexR and gyrB genes that affected efflux pump expression and antimicrobial resistance.
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Affiliation(s)
- Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Ryohei Nomoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Kanako Sato
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Chihiro Koike
- Department of Infection Prevention and Control, Kobe University Hospital, Kobe, Japan; Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Mari Kusuki
- Department of Infection Prevention and Control, Kobe University Hospital, Kobe, Japan; Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Tatsuya Nakamura
- Department of Infection Prevention and Control, Kobe University Hospital, Kobe, Japan; Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Katsumi Shigemura
- Department of Infection Prevention and Control, Kobe University Hospital, Kobe, Japan; Division of Urology, Department of Organ Therapeutics, Faculty of Medicine, Kobe University Graduate School of Medicine, Kobe Japan
| | - Toshiro Shirakawa
- Division of Urology, Department of Organ Therapeutics, Faculty of Medicine, Kobe University Graduate School of Medicine, Kobe Japan; Division of Translational Research for Biologics, Department of Internal Medicine Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masato Fujisawa
- Division of Urology, Department of Organ Therapeutics, Faculty of Medicine, Kobe University Graduate School of Medicine, Kobe Japan
| | - Issei Tokimatsu
- Department of Infection Prevention and Control, Kobe University Hospital, Kobe, Japan
| | - Kayo Osawa
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan; Department of Infection Prevention and Control, Kobe University Hospital, Kobe, Japan.
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620
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Hayashi T, Tsukagoshi H, Sekizuka T, Ishikawa D, Imai M, Fujita M, Kuroda M, Saruki N. Next-generation DNA sequencing analysis of two Streptococcus suis ST28 isolates associated with human infective endocarditis and meningitis in Gunma, Japan: a case report. Infect Dis (Lond) 2018; 51:62-66. [PMID: 30111218 DOI: 10.1080/23744235.2018.1490813] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Streptococcus suis (S. suis) is an important emerging zoonotic agent. Here, we report two cases of S. suis infection in pig farmers in Gunma Prefecture, Japan. We conducted a high-resolution molecular epidemiologic analysis on the basis of whole-genome sequencing data of each isolate using next-generation sequencing (NGS). NGS analysis revealed that the two S. suis clinical isolates were belonged to serotype 2 ST28. Phylogenetic analysis showed that two isolates were closely related to S. suis strains isolated from pigs in Japan at least until 1995. Since 41 nucleotide substitutions were found between the two strains, these strains might be derived from the same genetic lineage but distinct sporadic cases. NGS analysis is a powerful diagnostic tool for analysing bacterial infections. The database is more fulfilling, and more detailed analysis will become possible in the near future. Attention should be paid to S. suis infections, especially if the patient works on a livestock farm.
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Affiliation(s)
| | - Hiroyuki Tsukagoshi
- b Gunma Prefectural Institute of Public Health and Environmental Sciences , Maebashi-shi , Japan
| | - Tsuyoshi Sekizuka
- c Pathogen Genomics Center National Institute of Infectious Diseases , Tokyo , Japan
| | | | - Michiko Imai
- a Maebashi Red Cross Hospital , Maebashi-shi , Japan
| | - Masahiro Fujita
- b Gunma Prefectural Institute of Public Health and Environmental Sciences , Maebashi-shi , Japan
| | - Makoto Kuroda
- c Pathogen Genomics Center National Institute of Infectious Diseases , Tokyo , Japan
| | - Nobuhiro Saruki
- b Gunma Prefectural Institute of Public Health and Environmental Sciences , Maebashi-shi , Japan
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621
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Pietsch M, Irrgang A, Roschanski N, Brenner Michael G, Hamprecht A, Rieber H, Käsbohrer A, Schwarz S, Rösler U, Kreienbrock L, Pfeifer Y, Fuchs S, Werner G. Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany. BMC Genomics 2018; 19:601. [PMID: 30092762 PMCID: PMC6085623 DOI: 10.1186/s12864-018-4976-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/31/2018] [Indexed: 01/09/2023] Open
Abstract
Background Resistance to 3rd-generation cephalosporins in Escherichia coli is mostly mediated by extended-spectrum beta-lactamases (ESBLs) or AmpC beta-lactamases. Besides overexpression of the species-specific chromosomal ampC gene, acquisition of plasmid-encoded ampC genes, e.g. blaCMY-2, has been described worldwide in E. coli from humans and animals. To investigate a possible transmission of blaCMY-2 along the food production chain, we conducted a next-generation sequencing (NGS)-based analysis of 164 CMY-2-producing E. coli isolates from humans, livestock animals and foodstuff from Germany. Results The data of the 164 sequenced isolates revealed 59 different sequence types (STs); the most prevalent ones were ST38 (n = 19), ST131 (n = 16) and ST117 (n = 13). Two STs were present in all reservoirs: ST131 (human n = 8; food n = 2; animal n = 6) and ST38 (human n = 3; animal n = 9; food n = 7). All but one CMY-2-producing ST131 isolates belonged to the clade B (fimH22) that differed substantially from the worldwide dominant CTX-M-15-producing clonal lineage ST131-O25b clade C (fimH30). Plasmid replicon types IncI1 (n = 61) and IncK (n = 72) were identified for the majority of blaCMY-2-carrying plasmids. Plasmid sequence comparisons showed a remarkable sequence identity, especially for IncK plasmids. Associations of replicon types and distinct STs were shown for IncK and ST57, ST429 and ST38 as well as for IncI1 and ST58. Additional β-lactamase genes (blaTEM, blaCTX-M, blaOXA, blaSHV) were detected in 50% of the isolates, and twelve E. coli from chicken and retail chicken meat carried the colistin resistance gene mcr-1. Conclusion We found isolates of distinct E. coli clonal lineages (ST131 and ST38) in all three reservoirs. However, a direct clonal relationship of isolates from food animals and humans was only noticeable for a few cases. The CMY-2-producing E. coli-ST131 represents a clonal lineage different from the CTX-M-15-producing ST131-O25b cluster. Apart from the ST-driven spread, plasmid-mediated spread, especially via IncI1 and IncK plasmids, likely plays an important role for emergence and transmission of blaCMY-2 between animals and humans. Electronic supplementary material The online version of this article (10.1186/s12864-018-4976-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Pietsch
- Robert Koch-Institute, FG 13 Nosocomial Pathogens and Antibiotic Resistance, Burgstr, 37 38855, Wernigerode, Germany
| | - Alexandra Irrgang
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Nicole Roschanski
- Freie Universität Berlin, Institute for Animal Hygiene and Environmental Health, Berlin, Germany
| | - Geovana Brenner Michael
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany.,Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Heime Rieber
- Medizinisches Versorgungszentrum Dr. Stein, Division of Microbiology, Mönchengladbach, Germany
| | - Annemarie Käsbohrer
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany.,Veterinary University Vienna, Vienna, Austria
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany.,Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Uwe Rösler
- Freie Universität Berlin, Institute for Animal Hygiene and Environmental Health, Berlin, Germany
| | - Lothar Kreienbrock
- Institute for Biometrics, Epidemiology and Data Processing, University of Veterinary Medicine, Hanover, Germany
| | - Yvonne Pfeifer
- Robert Koch-Institute, FG 13 Nosocomial Pathogens and Antibiotic Resistance, Burgstr, 37 38855, Wernigerode, Germany
| | - Stephan Fuchs
- Robert Koch-Institute, FG 13 Nosocomial Pathogens and Antibiotic Resistance, Burgstr, 37 38855, Wernigerode, Germany
| | - Guido Werner
- Robert Koch-Institute, FG 13 Nosocomial Pathogens and Antibiotic Resistance, Burgstr, 37 38855, Wernigerode, Germany.
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622
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Yahara K, Nakayama SI, Shimuta K, Lee KI, Morita M, Kawahata T, Kuroki T, Watanabe Y, Ohya H, Yasuda M, Deguchi T, Didelot X, Ohnishi M. Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages. Microb Genom 2018; 4:e000205. [PMID: 30063202 PMCID: PMC6159555 DOI: 10.1099/mgen.0.000205] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/09/2018] [Indexed: 12/24/2022] Open
Abstract
The first extensively drug resistant (XDR) Neisseria gonorrhoeae strain with high resistance to the extended-spectrum cephalosporin ceftriaxone was identified in 2009 in Japan, but no other strain with this antimicrobial-resistance profile has been reported since. However, surveillance to date has been based on phenotypic methods and sequence typing, not genome sequencing. Therefore, little is known about the local population structure at the genomic level, and how resistance determinants and lineages are distributed and evolve. We analysed the whole-genome sequence data and the antimicrobial-susceptibility testing results of 204 strains sampled in a region where the first XDR ceftriaxone-resistant N. gonorrhoeae was isolated, complemented with 67 additional genomes from other time frames and locations within Japan. Strains resistant to ceftriaxone were not found, but we discovered a sequence type (ST)7363 sub-lineage susceptible to ceftriaxone and cefixime in which the mosaic penA allele responsible for reduced susceptibility had reverted to a susceptible allele by recombination. Approximately 85 % of isolates showed resistance to fluoroquinolones (ciprofloxacin) explained by linked amino acid substitutions at positions 91 and 95 of GyrA with 99 % sensitivity and 100 % specificity. Approximately 10 % showed resistance to macrolides (azithromycin), for which genetic determinants are less clear. Furthermore, we revealed different evolutionary paths of the two major lineages: single acquisition of penA X in the ST7363-associated lineage, followed by multiple independent acquisitions of the penA X and XXXIV in the ST1901-associated lineage. Our study provides a detailed picture of the distribution of resistance determinants and disentangles the evolution of the two major lineages spreading worldwide.
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Affiliation(s)
- Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shu-ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken-ichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takuya Kawahata
- Virology Section, Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Toshiro Kuroki
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Kanagawa, Japan
- Present address: Faculty of Veterinary Medicine, Okayama University of Science, 1-3, Ikoinooka, Imabari, Ehime 794-8555, Japan
| | - Yuko Watanabe
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Kanagawa, Japan
| | - Hitomi Ohya
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Kanagawa, Japan
| | - Mitsuru Yasuda
- Department of Urology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Takashi Deguchi
- Department of Urology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - Makoto Ohnishi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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Phenotypic Divergence along Geographic Gradients Reveals Potential for Rapid Adaptation of the White-Nose Syndrome Pathogen, Pseudogymnoascus destructans, in North America. Appl Environ Microbiol 2018; 84:AEM.00863-18. [PMID: 29915107 DOI: 10.1128/aem.00863-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/05/2018] [Indexed: 01/01/2023] Open
Abstract
White-nose syndrome (WNS) is an ongoing epizootic affecting multiple species of North American bats, caused by epidermal infections of the psychrophilic filamentous fungus Pseudogymnoascus destructans Since its introduction from Europe, WNS has spread rapidly across eastern North America and resulted in high mortality rates in bats. At present, the mechanisms behind its spread and the extent of its adaptation to different geographic and ecological niches remain unknown. The objective of this study was to examine the geographic patterns of phenotypic variation and the potential evidence for adaptation among strains representing broad geographic locations in eastern North America. The morphological features of these strains were evaluated on artificial medium, and the viability of asexual arthroconidia of representative strains was investigated after storage at high (23°C), moderate (14°C), and low (4°C) temperatures at different lengths of time. Our analyses identified evidence for a geographic pattern of colony morphology changes among the clonal descendants of the fungus, with trait values correlated with increased distance from the epicenter of WNS. Our genomic comparisons of three representative isolates revealed novel genetic polymorphisms and suggested potential candidate mutations that might be related to some of the phenotypic changes. These results show that even though this pathogen arrived in North America only recently and reproduces asexually, there has been substantial evolution and phenotypic diversification during its rapid clonal expansion.IMPORTANCE The causal agent of white-nose syndrome in bats is Pseudogymnoascus destructans, a filamentous fungus recently introduced from its native range in Europe. Infections caused by P. destructans have progressed across the eastern parts of Canada and the United States over the last 10 years. It is not clear how the disease is spread, as the pathogen is unable to grow above 23°C and ambient temperature can act as a barrier when hosts disperse. Here, we explore the patterns of phenotypic diversity and the germination of the fungal asexual spores, arthroconidia, from strains across a sizeable area of the epizootic range. Our analyses revealed evidence of adaptation along geographic gradients during its expansion. The results have implications for understanding the diversification of P. destructans and the limits of WNS spread in North America. Given the rapidly expanding distribution of WNS, a detailed understanding of the genetic bases for phenotypic variations in growth, reproduction, and dispersal of P. destructans is urgently needed to help control this disease.
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624
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Rajwani R, Shehzad S, Siu GKH. MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis. PeerJ 2018; 6:e5090. [PMID: 30018852 PMCID: PMC6045920 DOI: 10.7717/peerj.5090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/05/2018] [Indexed: 11/20/2022] Open
Abstract
Background Tuberculosis (TB) resulted in an estimated 1.7 million deaths in the year 2016. The disease is caused by the members of Mycobacterium tuberculosis complex, which includes Mycobacterium tuberculosis, Mycobacterium bovis and other closely related TB causing organisms. In order to understand the epidemiological dynamics of TB, national TB control programs often conduct standardized genotyping at 24 Mycobacterial-Interspersed-Repetitive-Units (MIRU)-Variable-Number-of-Tandem-Repeats (VNTR) loci. With the advent of next generation sequencing technology, whole-genome sequencing (WGS) has been widely used for studying TB transmission. However, an open-source software that can connect WGS and MIRU-VNTR typing is currently unavailable, which hinders interlaboratory communication. In this manuscript, we introduce the MIRU-profiler program which could be used for prediction of MIRU-VNTR profile from WGS of M. tuberculosis. Implementation The MIRU-profiler is implemented in shell scripting language and depends on EMBOSS software. The in-silico workflow of MIRU-profiler is similar to those described in the laboratory manuals for genotyping M. tuberculosis. Given an input genome sequence, the MIRU-profiler computes alleles at the standard 24-loci based on in-silico PCR amplicon lengths. The final output is a tab-delimited text file detailing the 24-loci MIRU-VNTR pattern of the input sequence. Validation The MIRU-profiler was validated on four datasets: complete genomes from NCBI-GenBank (n = 11), complete genomes for locally isolated strains sequenced using PacBio (n = 4), complete genomes for BCG vaccine strains (n = 2) and draft genomes based on 250 bp paired-end Illumina reads (n = 106). Results The digital MIRU-VNTR results were identical to the experimental genotyping results for complete genomes of locally isolated strains, BCG vaccine strains and five out of 11 genomes from the NCBI-GenBank. For draft genomes based on short Illumina reads, 21 out of 24 loci were inferred with a high accuracy, while a number of inaccuracies were recorded for three specific loci (ETRA, QUB11b and QUB26). One of the unique features of the MIRU-profiler was its ability to process multiple genomes in a batch. This feature was tested on all complete M. tuberculosis genome (n = 157), for which results were successfully obtained in approximately 14 min. Conclusion The MIRU-profiler is a rapid tool for inference of digital MIRU-VNTR profile from the assembled genome sequences. The tool can accurately infer repeat numbers at the standard 24 or 21/24 MIRU-VNTR loci from the complete or draft genomes respectively. Thus, the tool is expected to bridge the communication gap between the laboratories using WGS and those using the conventional MIRU-VNTR typing.
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Affiliation(s)
- Rahim Rajwani
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, China
| | - Sheeba Shehzad
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, China
| | - Gilman Kit Hang Siu
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, China
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625
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Soto-Rodriguez SA, Lozano-Olvera R, Garcia-Gasca MT, Abad-Rosales SM, Gomez-Gil B, Ayala-Arellano J. Virulence of the fish pathogen Aeromonas dhakensis: genes involved, characterization and histopathology of experimentally infected hybrid tilapia. DISEASES OF AQUATIC ORGANISMS 2018; 129:107-116. [PMID: 29972371 DOI: 10.3354/dao03247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aeromonas dhakensis (Ad) CAIM 1873 growth was evaluated at different conditions and antibiotic susceptibility. Mortality and histopathological damages in hybrid tilapia Oreochromis niloticus × O. mossambicus, and virulence factors caused by Ad bacterial cells and extracellular products (ECPs) were evaluated, and the whole genome was obtained. Ad grew between 0.0 and 5.5% NaCl at a pH of between 4 and 10 and from 4 to 37°C. The lowest minimum inhibitory concentration was found for enrofloxacin (<5 µg ml-1), and bacteria were resistant to erythromycin, amoxicillin and ampicillin. Ad bacterial cells (1.86 × 105 cells g-1) and ECPs (0.462 µg protein fish-1) were highly virulent to challenged hybrid tilapia and caused over 80% mortality at 24 h. The primary clinical sign caused was haemorrhage, and damage was most marked in the spleen, liver, kidney and brain of fish challenged with bacterial cells. To our knowledge, this is the first report that Ad causes pyknotic and karyorrhectic nuclei of erythrocytes in the internal organs of hybrid tilapia, which was the most striking histopathological observation. The virulence of Ad to hybrid tilapia may be primarily related to the activity of haemolysins (hlyA genes) and cytotoxins (aerolysin aerA), along with the production of siderophores and proteases. We also found β-lactamase, tetracycline and multiple antibiotic resistance genes, as well as adherence, iron acquisition, toxins (aerolysin family, haemolysins) and diverse protease genes.
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Affiliation(s)
- S A Soto-Rodriguez
- CIAD, AC Mazatlan Unit for Aquaculture and Environmental Management, 82112 Mazatlan, Sinaloa, Mexico
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626
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Croxen MA, Lee TD, Azana R, Hoang LM. Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae. Microb Genom 2018; 4:e000175. [PMID: 29629856 PMCID: PMC6113875 DOI: 10.1099/mgen.0.000175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
Distinuishing the species of mitis group streptococci is challenging due to ambiguous phenotypic characteristics and high degree of genetic similarity. This has been particularly true for resolving atypical Streptococcus pneumoniae and Streptococcus pseudopneumoniae. We used phylogenetic clustering to demonstrate specific and separate clades for both S. pneumoniae and S. pseudopneumoniae genomes. The genomes that clustered within these defined clades were used to extract species-specific genes from the pan-genome. The S. pneumoniae marker was detected in 8027 out of 8051 (>99.7 %) S. pneumoniae genomes. The S. pseudopneumoniae marker was specific for all genomes that clustered in the S. pseudopneumoniae clade, including unresolved species of the genus Streptococcus sequenced by the BC Centre for Disease Control Public Health Laboratory that previously could not be distinguished by other methods. Other than the presence of the S. pseudopneumoniae marker in six of 8051 (<0.08 %) S. pneumoniae genomes, both the S. pneumoniae and S. pseudopneumoniae markers showed little to no detectable cross-reactivity to the genomes of any other species of the genus Streptococcus or to a panel of over 46 000 genomes from viral, fungal, bacterial pathogens and microbiota commonly found in the respiratory tract. A real-time PCR assay was designed targeting these two markers. Genomics provides a useful technique for PCR assay design and development.
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Affiliation(s)
- Matthew A. Croxen
- BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Provincial Laboratory for Public Health (ProvLab), University of Alberta Hospital, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
- Present address: Provincial Laboratory for Public Health, Edmonton, Canada
- Present address: Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Canada
| | - Tracy D. Lee
- BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Robert Azana
- BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
| | - Linda M. Hoang
- BC Centre for Disease Control Public Health Laboratory, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, Canada
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627
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Collins A, Wakeland EK, Raj P, Kim MS, Kim J, Tareen NG, Copley LAB. The impact of Staphylococcus aureus genomic variation on clinical phenotype of children with acute hematogenous osteomyelitis. Heliyon 2018; 4:e00674. [PMID: 30003165 PMCID: PMC6039886 DOI: 10.1016/j.heliyon.2018.e00674] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/18/2018] [Accepted: 06/26/2018] [Indexed: 11/27/2022] Open
Abstract
Background Children with acute hematogenous osteomyelitis (AHO) have a broad spectrum of illness ranging from mild to severe. The purpose of this study is to evaluate the impact of genomic variation of Staphylococcus aureus on clinical phenotype of affected children and determine which virulence genes correlate with severity of illness. Methods De novo whole genome sequencing was conducted for a strain of Community Acquired Methicillin Resistant Staphylococcus aureus (CA-MRSA), using PacBio Hierarchical Genome Assembly Process (HGAP) from 6 Single Molecule Real Time (SMRT) Cells, as a reference for DNA library assembly of 71 Staphylococcus aureus isolates from children with AHO. Virulence gene annotation was based on exhaustive literature review and genomic data in NCBI for Staphylococcus aureus. Clinical phenotype was assessed using a validated severity score. Kruskal-Wallis rank sum test determined association between clinical severity and virulence gene presence using False Discovery Rate (FDR), significance <0.01. Results PacBio produced an assembled genome of 2,898,306 bp and 2054 Open Reading Frames (ORFs). Annotation confirmed 201 virulence genes. Statistical analysis of gene presence by clinical severity found 40 genes significantly associated with severity of illness (FDR ≤0.009). MRSA isolates encoded a significantly greater number of virulence genes than did MSSA (p < 0.0001). Phylogenetic analysis by maximum likelihood (PAML) demonstrated the relatedness of genomic distance to clinical phenotype. Conclusions The Staphylococcus aureus genome contains virulence genes which are significantly associated with severity of illness in children with osteomyelitis. This study introduces a novel reference strain and detailed annotation of Staphylococcus aureus virulence genes. While this study does not address bacterial gene expression, a platform is created for future transcriptome investigations to elucidate the complex mechanisms involved in childhood osteomyelitis.
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Affiliation(s)
- Angela Collins
- McLaren Medical Center, Department of Orthopaedic Surgery, Flint, Michigan, USA
| | - Edward K Wakeland
- University of Texas Southwestern, Department of Immunology, Dallas, Texas, USA
| | - Prithvi Raj
- University of Texas Southwestern, Department of Immunology, Dallas, Texas, USA
| | - Min S Kim
- University of Texas Southwestern, Department of Clinical Science, Dallas, Texas, USA
| | - Jiwoong Kim
- University of Texas Southwestern, Department of Clinical Science, Dallas, Texas, USA
| | - Naureen G Tareen
- Children's Health System of Texas, Department of Orthopaedic Surgery, Dallas, Texas, USA
| | - Lawson A B Copley
- University of Texas Southwestern, Department of Orthopaedic Surgery, Dallas, Texas, USA
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628
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Basharat Z, Tanveer F, Yasmin A, Shinwari ZK, He T, Tong Y. Genome of Serratia nematodiphila MB307 offers unique insights into its diverse traits. Genome 2018; 61:469-476. [PMID: 29957088 DOI: 10.1139/gen-2017-0250] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A pigment-producing species of Serratia was isolated from the rhizosphere of a heavy metal resistant Cannabis sativa plant growing in effluent-affected soil of Hattar Industrial Estate, Haripur, Pakistan. Here, we report the genome sequence of this bacterium, which has been identified as Serratia nematodiphila on the basis of whole genome comparison using the OrthoANI classification scheme. The bacterium exhibited diverse traits, including plant growth promotion, antimicrobial, bioremediation, and pollutant tolerance capabilities including metal tolerance, azo dye degradation, ibuprofen degradation, etc. Plant growth-promoting exoenzyme production as well as phosphate solubilisation properties were observed. Genes for phosphate solubilisation, siderophore production, and chitin destruction were identified in addition to other industrially important enzymes like nitrilase and lipase. Secondary metabolite producing apparatus for high value chemicals in the whole genome was also analysed. The number of antibiotic resistance genes was then profiled in silico, through a match with Antibiotic Resistant Gene and CAR database. This is the first report of a S. nematodiphila genome from a polluted environment. This could significantly contribute to the understanding of pollution tolerance, antibiotic resistance, association with nematodes, production of bio-pesticide, and their role in plant growth promotion.
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Affiliation(s)
- Zarrin Basharat
- a Microbiology & Biotechnology Research Lab, Department of Environmental Sciences, Fatima Jinnah Women University, Rawalpindi 46000, Pakistan
| | - Faouzia Tanveer
- b Department of Biotechnology, Quaid-i-Azam University, Islamabad 44000, Pakistan
| | - Azra Yasmin
- a Microbiology & Biotechnology Research Lab, Department of Environmental Sciences, Fatima Jinnah Women University, Rawalpindi 46000, Pakistan
| | - Zabta Khan Shinwari
- b Department of Biotechnology, Quaid-i-Azam University, Islamabad 44000, Pakistan
| | - Tongtong He
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yigang Tong
- c State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
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629
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Jiang X, Guo Q, Xu J, Liu P, Long C, Dai X. Complete mitochondrial genome of a leaf-mining beetle, Podagricomela nigricollis (Coleoptera: Chrysomelidae). Mitochondrial DNA B Resour 2018; 3:721-722. [PMID: 33474297 PMCID: PMC7800716 DOI: 10.1080/23802359.2018.1483773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 10/31/2022] Open
Abstract
Podagricomela nigricollis is a citrus pest that distributes in South China. Currently, there was no complete mitochondrial genome of Podagricomela species available in GenBank. Here, we reported the complete circular mitogenome of P. nigricollis. It had a total length of 16,756 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one A + T-rich region. Among the 13 PCGs, only four (NAD5, NAD4, NAD4l, NAD1) located on the L-strand, whereas the other nine (NAD2, COX1, COX2, ATP8, ATP6, COX3, NAD3, NAD6, COB) located on the H-strand. Phylogenetic analysis using nucleotide sequences of the 13 PCGs indicated that P. nigricollis were clustered with six Galerucinae species, which was consistent with previous morphological classification.
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Affiliation(s)
- Xilin Jiang
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, China
| | - Qingyun Guo
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, China
| | - Jiasheng Xu
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, China
| | - Peng Liu
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, China
| | - Chengpeng Long
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, China
| | - Xiaohua Dai
- Leafminer Group, School of Life and Environmental Sciences, Gannan Normal University, Ganzhou, Jiangxi Province, China
- National Navel-Orange Engineering Research Center, Ganzhou, Jiangxi Province, China
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630
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Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential. Emerg Microbes Infect 2018; 7:116. [PMID: 29946138 PMCID: PMC6018663 DOI: 10.1038/s41426-018-0118-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/20/2018] [Accepted: 05/24/2018] [Indexed: 01/10/2023]
Abstract
In recent years, an increasing number of Campylobacter species have been associated with human gastrointestinal (GI) diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. Campylobacter concisus, an oral commensal historically linked to gingivitis and periodontitis, has been increasingly detected in the lower GI tract. In the present study, we generated robust genome sequence data from C. concisus strains and undertook a comprehensive pangenome assessment to identify C. concisus virulence properties and to explain potential adaptations acquired while residing in specific ecological niche(s) of the GI tract. Genomes of 53 new C. concisus strains were sequenced, assembled, and annotated including 36 strains from gastroenteritis patients, 13 strains from Crohn’s disease patients and four strains from colitis patients (three collagenous colitis and one lymphocytic colitis). When compared with previous published sequences, strains clustered into two main groups/genomospecies (GS) with phylogenetic clustering explained neither by disease phenotype nor sample location. Paired oral/faecal isolates, from the same patient, indicated that there are few genetic differences between oral and gut isolates which suggests that gut isolates most likely reflect oral strain relocation. Type IV and VI secretion systems genes, genes known to be important for pathogenicity in the Campylobacter genus, were present in the genomes assemblies, with 82% containing Type VI secretion system genes. Our findings indicate that C. concisus strains are genetically diverse, and the variability in bacterial secretion system content may play an important role in their virulence potential.
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631
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Woolums AR, Karisch BB, Frye JG, Epperson W, Smith DR, Blanton J, Austin F, Kaplan R, Hiott L, Woodley T, Gupta SK, Jackson CR, McClelland M. Multidrug resistant Mannheimia haemolytica isolated from high-risk beef stocker cattle after antimicrobial metaphylaxis and treatment for bovine respiratory disease. Vet Microbiol 2018; 221:143-152. [PMID: 29981701 DOI: 10.1016/j.vetmic.2018.06.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 05/16/2018] [Accepted: 06/07/2018] [Indexed: 10/14/2022]
Abstract
Antimicrobial resistance (AMR) in bacterial respiratory pathogens in high-risk stocker cattle has been poorly characterized. The objective of this study was to describe the prevalence of multidrug resistant (MDR; resistance to > 3 antimicrobial classes) respiratory pathogens in 50 conventionally managed stocker cattle over 21 days after arrival. Cattle received tildipirosin metaphylaxis on day 0 and were eligible to receive up to 3 additional antimicrobials for bovine respiratory disease (BRD): florfenicol, ceftiofur and enrofloxacin. Nasopharyngeal swabs were collected on days 0, 7, 14, and 21 for bacterial culture and antimicrobial susceptibility testing using disc diffusion and broth microdilution. Mannheimia haemolytica was isolated from 5 of 48, 27 of 50, 44 of 50, and 40 of 50 cattle on days 0, 7, 14, and 21, respectively. One of 5, 27 of 27, 43 of 44, and 40 of 40 M. haemolytica were MDR on days 0, 7, 14, and 21, respectively. Pasteurella multocida was isolated from 6 of 48 cattle on day 0 and none were MDR; no other pathogens were isolated. Twenty-four cattle required at least one BRD treatment; M. haemolytica was isolated before treatment from 13 of 24 cattle; all were MDR. One hundred-eighteen M. haemolytica isolates were subjected to pulsed-field gel electrophoresis (PFGE); multiple genotypes were identified. Whole genome sequencing of 33 isolates revealed 14 known AMR genes. Multidrug resistant M. haemolytica can be highly prevalent and genetically diverse in stocker cattle; additional research is necessary to determine factors that influence prevalence and the impact on cattle health.
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Affiliation(s)
- Amelia R Woolums
- Department of Veterinary Pathobiology and Population Medicine, Mississippi State University, Mississippi State, MS, USA.
| | - Brandi B Karisch
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, USA
| | - William Epperson
- Department of Veterinary Pathobiology and Population Medicine, Mississippi State University, Mississippi State, MS, USA
| | - David R Smith
- Department of Veterinary Pathobiology and Population Medicine, Mississippi State University, Mississippi State, MS, USA
| | - John Blanton
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Frank Austin
- Department of Veterinary Pathobiology and Population Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Ray Kaplan
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Lari Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, USA
| | - Tiffanie Woodley
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, USA
| | - Sushim K Gupta
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, USA
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, and Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
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632
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Draft Genome Sequence of the Lichen-Forming Fungus Ramalina intermedia Strain YAF0013. GENOME ANNOUNCEMENTS 2018; 6:6/23/e00478-18. [PMID: 29880593 PMCID: PMC5992360 DOI: 10.1128/genomea.00478-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here, we report a draft genome sequence of Ramalina intermedia strain YAF0013. The functional annotation of R. intermedia provides important information related to its ability to produce secondary metabolites. The genome sequence reported here builds the basis for further genome mining.
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633
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Complete Genome Sequence of Actinosynnema pretiosum X47, An Industrial Strain that Produces the Antibiotic Ansamitocin AP-3. Curr Microbiol 2018; 76:954-958. [PMID: 29858620 DOI: 10.1007/s00284-018-1521-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/30/2018] [Indexed: 10/14/2022]
Abstract
Ansamitocins are extraordinarily potent antitumor agents. Ansamitocin P-3 (AP-3), which is produced by Actinosynnema pretiosum, has been developed as a cytotoxic drug for breast cancer. Despite its importance, AP-3 is of limited applicability because of the low production yield. A. pretiosum strain X47 was developed from A. pretiosum ATCC 31565 by mutation breeding and shows a relatively high AP-3 yield. Here, we analyzed the A. pretiosum X47 genome, which is ~8.13 Mb in length with 6693 coding sequences, 58 tRNA genes, and 15 rRNA genes. The DNA sequence of the ansamitocin biosynthetic gene cluster is highly similar to that of the corresponding cluster in A. pretiosum ATCC 31565, with 99.9% identity. However, RT-qPCR analysis showed that the expression levels of ansamitocin biosynthetic genes were significantly increased in X47 compared with the levels in the wild-type strain, consistent with the higher yield of AP-3 in X47. The annotated complete genome sequence of this strain will facilitate understanding the molecular mechanisms of ansamitocin biosynthesis and regulation in A. pretiosum and help further genetic engineering studies to enhance the production of AP-3.
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634
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McFrederick QS, Vuong HQ, Rothman JA. Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov. and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers. Int J Syst Evol Microbiol 2018; 68:1879-1884. [DOI: 10.1099/ijsem.0.002758] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Quinn S. McFrederick
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
- Graduate Program in Microbiology, University of California, Riverside, Riverside, CA 92521, USA
| | - Hoang Q. Vuong
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
- Graduate Program in Microbiology, University of California, Riverside, Riverside, CA 92521, USA
| | - Jason A. Rothman
- Department of Entomology, University of California, Riverside, Riverside, CA 92521, USA
- Graduate Program in Microbiology, University of California, Riverside, Riverside, CA 92521, USA
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635
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Peter S, Bezdan D, Oberhettinger P, Vogel W, Dörfel D, Dick J, Marschal M, Liese J, Weidenmaier C, Autenrieth I, Ossowski S, Willmann M. Whole-genome sequencing enabling the detection of a colistin-resistant hypermutating Citrobacter werkmanii strain harbouring a novel metallo-β-lactamase VIM-48. Int J Antimicrob Agents 2018; 51:867-874. [DOI: 10.1016/j.ijantimicag.2018.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/19/2018] [Accepted: 01/20/2018] [Indexed: 11/27/2022]
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636
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Complete Genome Sequences of Two Escherichia Phages Isolated from Wastewater in Finland. GENOME ANNOUNCEMENTS 2018; 6:6/22/e00401-18. [PMID: 29853497 PMCID: PMC5981032 DOI: 10.1128/genomea.00401-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Escherichia phages vB_EcoM-fFiEco06 and vB_EcoM-fHoEco02 were found to have 167,076-bp and 167,064-bp genomes, respectively. They are members of genus T4virus, and they are 99.96% identical to each other. The host ranges of the phages are different, probably due to a few differences in their tail protein amino acid sequences.
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637
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Mylius M, Dreesman J, Pulz M, Pallasch G, Beyrer K, Claußen K, Allerberger F, Fruth A, Lang C, Prager R, Flieger A, Schlager S, Kalhöfer D, Mertens E. Shiga toxin-producing Escherichia coli O103:H2 outbreak in Germany after school trip to Austria due to raw cow milk, 2017 - The important role of international collaboration for outbreak investigations. Int J Med Microbiol 2018; 308:539-544. [PMID: 29884330 DOI: 10.1016/j.ijmm.2018.05.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/18/2018] [Accepted: 05/28/2018] [Indexed: 11/17/2022] Open
Abstract
Following a school ski-trip to Austria from 10 to 18/02/2017, nine of 25 participants of the group from Lower Saxony (Germany) developed gastroenteritis. The students and teachers (17-41 years) shared meals in a hotel. Active case finding revealed further cases among German school groups from North Rhine-Westphalia and Schleswig-Holstein, staying at the same hotel in February 2017. We conducted two retrospective cohort studies using self-administered questionnaires on clinical symptoms and food consumption. We defined a case as a trip participant in February 2017, staying at the aforementioned hotel and developing diarrhoea, vomiting or abdominal pain during or within ten days after the trip and/or who had a stool sample tested positive for STEC within four weeks after the trip. During the outbreak investigation, Austrian authorities detected that unlabeled raw cow milk delivered by a dairy farm had been offered at the hotel for breakfast during January and February 2017. Stool samples of participants, samples of milk served in the hotel and fecal samples of various animals kept at the milk-delivering farm were examined by culture and polymerase chain reaction. STEC isolates were typed using Pulsed-field Gel Electrophoresis (PFGE) and Whole-Genome Sequencing (WGS). All 25 participants from Lower Saxony completed the questionnaire on symptoms and milk consumption; 14 were cases (56%). Thirteen of 20 participants who had consumed cold milk fell ill (risk ratio (RR): 3.25; 95%-confidence interval (CI): 0.55-19.32). Of 159 trip participants from North Rhine-Westphalia, 81 completed the questionnaire (51%), 25 were cases (31%); RR for cold milk was 2.11 (CI: 0.89-5.03). The combined RR for cold milk in both groups was 2.49 (CI: 1.16-5.35). Shiga toxin 1a-gene and eaeA-gene positive STEC O103:H2 were detected in nine of 32 patients' stool samples and in two of 18 dairy farm cattle. Nine isolates from human stool samples and two isolates from cattle fecal samples yielded the same strain with an almost identical PFGE-pattern and WGS-profile. Microbiological and epidemiological evidence identified raw cow milk as the vehicle. Results may have been compromised by misclassification of cases due to a recall bias and mild symptoms. As a result of this outbreak investigation, the Austrian authorities enforced Austrian law in the hotel, to provide milk only when pasteurized. We recommend re-emphasizing the risk of raw milk consumption to providers.
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Affiliation(s)
- Maren Mylius
- Governmental Institute of Public Health of Lower Saxony (Niedersächsisches Landesgesundheitsamt, NLGA), Hanover, Germany; Postgraduate Training for Applied Epidemiology (PAE), Robert Koch Institute, Berlin, Germany; affiliated with the European Programme for Intervention Epidemiology Training, ECDC, Sweden.
| | - Johannes Dreesman
- Governmental Institute of Public Health of Lower Saxony (Niedersächsisches Landesgesundheitsamt, NLGA), Hanover, Germany.
| | - Matthias Pulz
- Governmental Institute of Public Health of Lower Saxony (Niedersächsisches Landesgesundheitsamt, NLGA), Hanover, Germany.
| | | | - Konrad Beyrer
- Governmental Institute of Public Health of Lower Saxony (Niedersächsisches Landesgesundheitsamt, NLGA), Hanover, Germany.
| | - Katja Claußen
- Governmental Institute of Public Health of Lower Saxony (Niedersächsisches Landesgesundheitsamt, NLGA), Hanover, Germany.
| | | | - Angelika Fruth
- National Reference Centre for Salmonella and other Bacterial Enteritic Pathogens, Division of Enteropathogenic Bacteria and Legionella (FG11), Robert Koch Institute, Wernigerode, Germany.
| | - Christina Lang
- National Reference Centre for Salmonella and other Bacterial Enteritic Pathogens, Division of Enteropathogenic Bacteria and Legionella (FG11), Robert Koch Institute, Wernigerode, Germany
| | - Rita Prager
- National Reference Centre for Salmonella and other Bacterial Enteritic Pathogens, Division of Enteropathogenic Bacteria and Legionella (FG11), Robert Koch Institute, Wernigerode, Germany
| | - Antje Flieger
- National Reference Centre for Salmonella and other Bacterial Enteritic Pathogens, Division of Enteropathogenic Bacteria and Legionella (FG11), Robert Koch Institute, Wernigerode, Germany
| | - Sabine Schlager
- Austrian Agency for Health and Food Safety (AGES), Graz, Austria.
| | | | - Elke Mertens
- Governmental Institute of Public Health of Lower Saxony (Niedersächsisches Landesgesundheitsamt, NLGA), Hanover, Germany.
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638
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Mottawea W, Duceppe MO, Dupras AA, Usongo V, Jeukens J, Freschi L, Emond-Rheault JG, Hamel J, Kukavica-Ibrulj I, Boyle B, Gill A, Burnett E, Franz E, Arya G, Weadge JT, Gruenheid S, Wiedmann M, Huang H, Daigle F, Moineau S, Bekal S, Levesque RC, Goodridge LD, Ogunremi D. Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping. Front Microbiol 2018; 9:836. [PMID: 29780368 PMCID: PMC5945981 DOI: 10.3389/fmicb.2018.00836] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/12/2018] [Indexed: 12/30/2022] Open
Abstract
Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR) of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.
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Affiliation(s)
- Walid Mottawea
- Department of Food Science and Agricultural Chemistry, McGill University, Ste Anne de Bellevue, QC, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.,Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Marc-Olivier Duceppe
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Andrée A Dupras
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Valentine Usongo
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique due Québec, Ste Anne de Bellevue, QC, Canada
| | - Julie Jeukens
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Luca Freschi
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | | | - Jeremie Hamel
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Irena Kukavica-Ibrulj
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Alexander Gill
- Health Canada, Bureau of Microbial Hazards, Ottawa, ON, Canada
| | - Elton Burnett
- Institute of Parasitology, McGill University, Montreal, QC, Canada
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Gitanjali Arya
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Joel T Weadge
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Samantha Gruenheid
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Hongsheng Huang
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - France Daigle
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bioinformatique, Université Laval, Québec City, QC, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique due Québec, Ste Anne de Bellevue, QC, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada
| | - Lawrence D Goodridge
- Department of Food Science and Agricultural Chemistry, McGill University, Ste Anne de Bellevue, QC, Canada
| | - Dele Ogunremi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
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639
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Genome Sequence of Pseudomonas chlororaphis Lzh-T5, a Plant Growth-Promoting Rhizobacterium with Antimicrobial Activity. GENOME ANNOUNCEMENTS 2018; 6:6/18/e00328-18. [PMID: 29724833 PMCID: PMC5940960 DOI: 10.1128/genomea.00328-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas chlororaphis Lzh-T5 is a plant growth-promoting rhizobacterium (PGPR) with antimicrobial activity isolated from tomato rhizosphere in the city of Dezhou, Shandong Province, China. Here, the draft genome sequence of P. chlororaphis Lzh-T5 is reported, and several functional genes related to antifungal antibiotics and siderophore biosynthesis have been found in the genome.
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640
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Becker L, Kaase M, Pfeifer Y, Fuchs S, Reuss A, von Laer A, Sin MA, Korte-Berwanger M, Gatermann S, Werner G. Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014. Antimicrob Resist Infect Control 2018; 7:62. [PMID: 29744043 PMCID: PMC5930415 DOI: 10.1186/s13756-018-0352-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/19/2018] [Indexed: 12/13/2022] Open
Abstract
Background By using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing K. pneumoniae isolated from hospitalized patients in Germany between 2008 and 2014. Methods We selected a representative subset of 107 carbapenemase-producing K. pneumoniae clinical isolates possessing the four most prevalent carbapenemase types in Germany (KPC-2, KPC-3, OXA-48, NDM-1). Isolates were processed via illumina NGS. Data were analysed using different SNP-based mapping and de-novo assembly approaches. Relevant information was extracted from NGS data (antibiotic resistance determinants, wzi gene/cps type, virulence genes). NGS data from the present study were also compared with 238 genome data from two previous international studies on K. pneumoniae. Results NGS-based analyses revealed a preferred prevalence of KPC-2-producing ST258 and KPC-3-producing ST512 isolates. OXA-48, being the most prevalent carbapenemase type in Germany, was associated with various K. pneumoniae strain types; most of them possessing IncL/M plasmid replicons suggesting a preferred dissemination of blaOXA-48 via this well-known plasmid type. Clusters ST15, ST147, ST258, and ST512 demonstrated an intermingled subset structure consisting of German and other European K. pneumoniae isolates. ST23 being the most frequent MLST type in Asia was found only once in Germany. This latter isolate contained an almost complete set of virulence genes and a K1 capsule suggesting occurrence of a hypervirulent ST23 strain producing OXA-48 in Germany. Conclusions Our study results suggest prevalence of "classical" K. pneumonaie strain types associated with widely distributed carbapenemase genes such as ST258/KPC-2 or ST512/KPC-3 also in Germany. The finding of a supposed hypervirulent and OXA-48-producing ST23 K. pneumoniae isolates outside Asia is highly worrisome and requires intense molecular surveillance.
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Affiliation(s)
| | - Martin Kaase
- National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
- Present address: Department of Infection Control and Infectious Diseases, University Medical Centre Goettingen, Goettingen, Germany
| | | | | | | | | | | | - Miriam Korte-Berwanger
- National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
- Fachgruppe Infektiologie und Hygiene, Landeszentrum Gesundheit North-Rhine Westphalia, Gesundheitscampus 10, Bochum, Germany
| | - Sören Gatermann
- National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
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641
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Uyaguari-Díaz MI, Croxen MA, Luo Z, Cronin KI, Chan M, Baticados WN, Nesbitt MJ, Li S, Miller KM, Dooley D, Hsiao W, Isaac-Renton JL, Tang P, Prystajecky N. Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia. Front Microbiol 2018; 9:852. [PMID: 29765365 PMCID: PMC5938356 DOI: 10.3389/fmicb.2018.00852] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/13/2018] [Indexed: 01/08/2023] Open
Abstract
The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes (intI) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds. A metagenomics approach and high-throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and intI. Metagenomic sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a 1-year period. There was a low prevalence of ARGs relative to the microbial population (<1%). Analysis of the metagenomic sequences detected a total of 60 elements of resistance including 46 ARGs, intI1, and groEL/intI1 genes and 12 quaternary ammonium compounds (qac) resistance genes across all watershed locations. The relative abundance and richness of ARGs was found to be highest in agriculture impacted watersheds compared to urban and protected watersheds. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Similar to other reports, this study found a strong association between intI1 and ARGs (e.g., sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was below the detection limit. However, the high richness and gene copy numbers (GCNs) of ARGs in impacted sites suggest that the effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column. Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors such as land-use and water quality parameters accounted for 45% of the variability observed in watershed locations.
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Affiliation(s)
- Miguel I Uyaguari-Díaz
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Matthew A Croxen
- Provincial Laboratory for Public Health, Edmonton, AB, Canada.,Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Zhiyao Luo
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Kirby I Cronin
- Laboratory Services, Public Health Ontario, Toronto, ON, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Michael Chan
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Waren N Baticados
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | | | - Shaorong Li
- Pacific Biological Station, Nanaimo, BC, Canada
| | | | - Damion Dooley
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - William Hsiao
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Judith L Isaac-Renton
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - Natalie Prystajecky
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
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642
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Serratia proteamaculans Strain AGR96X Encodes an Antifeeding Prophage (Tailocin) with Activity against Grass Grub (Costelytra giveni) and Manuka Beetle (Pyronota Species) Larvae. Appl Environ Microbiol 2018; 84:AEM.02739-17. [PMID: 29549100 DOI: 10.1128/aem.02739-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/08/2018] [Indexed: 11/20/2022] Open
Abstract
A highly virulent Serratia proteamaculans strain, AGR96X, exhibiting specific pathogenicity against larvae of the New Zealand grass grub (Costelytra giveni; Coleoptera: Scarabaeidae) and the New Zealand manuka beetle (Pyronota festiva and P. setosa; Coleoptera: Scarabaeidae), was isolated from a diseased grass grub larva. A 12-day median lethal dose of 4.89 × 103 ± 0.92 × 103 cells per grass grub larva was defined for AGR96X, and death occurred within 5 to 12 days following the ingestion of a high bacterial dose. During the infection period, the bacterium rapidly multiplied within the insect host and invaded the hemocoel, leading to a mean bacterial load of 8.2 × 109 cells per larva at 6 days postingestion. Genome sequencing of strain AGR96X revealed the presence of a variant of the Serratia entomophila antifeeding prophage (Afp), a tailocin designated AfpX. Unlike Afp, AfpX contains two Afp16 tail-length termination protein orthologs and two putative toxin components. A 37-kb DNA fragment encoding the AfpX-associated region was cloned, transformed into Escherichia coli, and fed to C. giveni and Pyronota larvae, causing mortality. In addition, the deletion of the afpX15 putative chaperone component abolished the virulence of AGR96X. Unlike S. entomophila Afp, the AfpX tailocin could be induced by mitomycin C. Transmission electron microscopy analysis revealed the presence of Afp-like particles of various lengths, and when the purified AfpX tailocin was fed to grass grub or manuka beetle larvae, they underwent phenotypic changes similar to those of larvae fed AGR96X.IMPORTANCESerratia proteamaculans strain AGR96X shows dual activity against larvae of endemic New Zealand pasture pests, the grass grub (Costelytra giveni) and the manuka beetle (Pyronota spp.). Unlike Serratia entomophila, the causal agent of amber disease, which takes 3 to 4 months to kill grass grub larvae, AGR96X causes mortality within 5 to 12 days of ingestion and invades the insect hemocoel. AGR96X produces a unique variant of the S. entomophila antifeeding prophage (Afp), a cell-free phage-like entity that is proposed to deliver protein toxins to the grass grub target site, causing a cessation of feeding activity. Unlike other Afp variants, AGR96X Afp, named AfpX, contains two tail-length termination proteins, resulting in greater variability in the AfpX length. AfpX shows dual activity against both grass grub and manuka beetle larvae. AGR96X is a viable alternative to S. entomophila for pest control in New Zealand pasture systems.
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643
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Chang R, Bird L, Barr C, Osburn M, Wilbanks E, Nealson K, Rowe A. Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments. Int J Syst Evol Microbiol 2018; 68:1652-1658. [DOI: 10.1099/ijsem.0.002723] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rachel Chang
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Lina Bird
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Casey Barr
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Magdalena Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, IL 60208, USA
| | - Elizabeth Wilbanks
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Kenneth Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Annette Rowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
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644
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Arai N, Sekizuka T, Tamamura Y, Tanaka K, Barco L, Izumiya H, Kusumoto M, Hinenoya A, Yamasaki S, Iwata T, Watanabe A, Kuroda M, Uchida I, Akiba M. Phylogenetic Characterization of Salmonella enterica Serovar Typhimurium and Its Monophasic Variant Isolated from Food Animals in Japan Revealed Replacement of Major Epidemic Clones in the Last 4 Decades. J Clin Microbiol 2018; 56:JCM.01758-17. [PMID: 29491013 DOI: 10.1128/jcm.01758-17/suppl_file/zjm999095924sd2.xlsx] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/17/2018] [Indexed: 05/27/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) and its monophasic variant (Salmonella 4,[5],12:i:-) are the major causes of gastroenteritis in both humans and animals. Pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis have been used widely as subtyping methods for these pathogens in molecular epidemiological analyses, but the results do not precisely reflect phylogenetic information. In this study, we performed a phylogenetic analysis of these serovars using whole-genome sequencing data and identified nine distinct genotypic clades. Then, we established an allele-specific PCR-based genotyping method detecting a clade-specific single nucleotide polymorphism to rapidly identify the clade of each isolate. Among a total of 815 isolates obtained from cattle in Japan between 1977 and 2017, clades 1, 7, and 9 contained 77% of isolates. Obvious replacement of the dominant clone was observed five times in this period, and clade 9, which mostly contains Salmonella 4,[5],12:i:-, is currently dominant. Among 140 isolates obtained from swine in Japan between 1976 and 2017, clades 3 and 9 contained 64% of isolates. Clade 9 is the latest clone as is the case in cattle isolates. Clade 9 is similar to an epidemic clone from Europe, which is characterized by sequence type 34 (ST34), chromosomal Salmonella genomic island 3, and a composite transposon containing antimicrobial resistance genes. The increased prevalence of clade 9 among food animals in Japan might be a part of the pandemic of the European Salmonella 4,[5],12:i:- clone.
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Affiliation(s)
- Nobuo Arai
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukino Tamamura
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Kiyoshi Tanaka
- Hokkaido Research Station, National Institute of Animal Health, Sapporo, Hokkaido, Japan
| | - Lisa Barco
- Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Hidemasa Izumiya
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masahiro Kusumoto
- Kyushu Research Station, National Institute of Animal Health, Kagoshima, Japan
| | - Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Taketoshi Iwata
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Ayako Watanabe
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ikuo Uchida
- Unit of Veterinary Bacteriology, Department of Pathology, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Masato Akiba
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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645
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Bogema DR, Micallef ML, Liu M, Padula MP, Djordjevic SP, Darling AE, Jenkins C. Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes. BMC Genomics 2018; 19:298. [PMID: 29703152 PMCID: PMC5921998 DOI: 10.1186/s12864-018-4701-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Theileria orientalis (Apicomplexa: Piroplasmida) has caused clinical disease in cattle of Eastern Asia for many years and its recent rapid spread throughout Australian and New Zealand herds has caused substantial economic losses to production through cattle deaths, late term abortion and morbidity. Disease outbreaks have been linked to the detection of a pathogenic genotype of T. orientalis, genotype Ikeda, which is also responsible for disease outbreaks in Asia. Here, we sequenced and compared the draft genomes of one pathogenic (Ikeda) and two apathogenic (Chitose, Buffeli) isolates of T. orientalis sourced from Australian herds. RESULTS Using de novo assembled sequences and a single nucleotide variant (SNV) analysis pipeline, we found extensive genetic divergence between the T. orientalis genotypes. A genome-wide phylogeny reconstructed to address continued confusion over nomenclature of this species displayed concordance with prior phylogenetic studies based on the major piroplasm surface protein (MPSP) gene. However, average nucleotide identity (ANI) values revealed that the divergence between isolates is comparable to that observed between other theilerias which represent distinct species. Analysis of SNVs revealed putative recombination between the Chitose and Buffeli genotypes and also between Australian and Japanese Ikeda isolates. Finally, to inform future vaccine studies, dN/dS ratios and surface location predictions were analysed. Six predicted surface protein targets were confirmed to be expressed during the piroplasm phase of the parasite by mass spectrometry. CONCLUSIONS We used whole genome sequencing to demonstrate that the T. orientalis Ikeda, Chitose and Buffeli variants show substantial genetic divergence. Our data indicates that future researchers could potentially consider disease-associated Ikeda and closely related genotypes as a separate species from non-pathogenic Chitose and Buffeli.
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Affiliation(s)
- Daniel R Bogema
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Melinda L Micallef
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Michael Liu
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Matthew P Padula
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Steven P Djordjevic
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Aaron E Darling
- The ithree institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Cheryl Jenkins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia.
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646
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Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan. GENOME ANNOUNCEMENTS 2018; 6:6/17/e00362-18. [PMID: 29700164 PMCID: PMC5920169 DOI: 10.1128/genomea.00362-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mycobacterium virginiense, a newly described species of the Mycobacterium terrae complex, is a cause of tenosynovitis and osteomyelitis in the United States. Here, we report the 4,849,424-bp draft genome sequence of M. virginiense strain GF75, isolated from a mud sample taken from a Japanese swine farm.
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647
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Phylogenetic Characterization of Salmonella enterica Serovar Typhimurium and Its Monophasic Variant Isolated from Food Animals in Japan Revealed Replacement of Major Epidemic Clones in the Last 4 Decades. J Clin Microbiol 2018; 56:JCM.01758-17. [PMID: 29491013 DOI: 10.1128/jcm.01758-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/17/2018] [Indexed: 01/28/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) and its monophasic variant (Salmonella 4,[5],12:i:-) are the major causes of gastroenteritis in both humans and animals. Pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis have been used widely as subtyping methods for these pathogens in molecular epidemiological analyses, but the results do not precisely reflect phylogenetic information. In this study, we performed a phylogenetic analysis of these serovars using whole-genome sequencing data and identified nine distinct genotypic clades. Then, we established an allele-specific PCR-based genotyping method detecting a clade-specific single nucleotide polymorphism to rapidly identify the clade of each isolate. Among a total of 815 isolates obtained from cattle in Japan between 1977 and 2017, clades 1, 7, and 9 contained 77% of isolates. Obvious replacement of the dominant clone was observed five times in this period, and clade 9, which mostly contains Salmonella 4,[5],12:i:-, is currently dominant. Among 140 isolates obtained from swine in Japan between 1976 and 2017, clades 3 and 9 contained 64% of isolates. Clade 9 is the latest clone as is the case in cattle isolates. Clade 9 is similar to an epidemic clone from Europe, which is characterized by sequence type 34 (ST34), chromosomal Salmonella genomic island 3, and a composite transposon containing antimicrobial resistance genes. The increased prevalence of clade 9 among food animals in Japan might be a part of the pandemic of the European Salmonella 4,[5],12:i:- clone.
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648
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Liu W, Kong H, Zhou J, Fritsch PW, Hao G, Gong W. Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae. Int J Mol Sci 2018; 19:E1286. [PMID: 29693617 PMCID: PMC5983592 DOI: 10.3390/ijms19051286] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/16/2018] [Accepted: 04/19/2018] [Indexed: 11/17/2022] Open
Abstract
The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.
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Affiliation(s)
- Wanzhen Liu
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Juan Zhou
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107, USA.
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
| | - Wei Gong
- College of Life Sciences, South China Agricultural University, Guangzhou 510614, China.
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649
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Mansonella ozzardi mitogenome and pseudogene characterisation provides new perspectives on filarial parasite systematics and CO-1 barcoding. Sci Rep 2018; 8:6158. [PMID: 29670192 PMCID: PMC5906601 DOI: 10.1038/s41598-018-24382-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/15/2018] [Indexed: 11/26/2022] Open
Abstract
Despite the broad distribution of M. ozzardi in Latin America and the Caribbean, there is still very little DNA sequence data available to study this neglected parasite’s epidemiology. Mitochondrial DNA (mtDNA) sequences, especially the cytochrome oxidase (CO1) gene’s barcoding region, have been targeted successfully for filarial diagnostics and for epidemiological, ecological and evolutionary studies. MtDNA-based studies can, however, be compromised by unrecognised mitochondrial pseudogenes, such as Numts. Here, we have used shot-gun Illumina-HiSeq sequencing to recover the first complete Mansonella genus mitogenome and to identify several mitochondrial-origin pseudogenes. Mitogenome phylogenetic analysis placed M. ozzardi in the Onchocercidae “ONC5” clade and suggested that Mansonella parasites are more closely related to Wuchereria and Brugia genera parasites than they are to Loa genus parasites. DNA sequence alignments, BLAST searches and conceptual translations have been used to compliment phylogenetic analysis showing that M. ozzardi from the Amazon and Caribbean regions are near-identical and that previously reported Peruvian M. ozzardi CO1 reference sequences are probably of pseudogene origin. In addition to adding a much-needed resource to the Mansonella genus’s molecular tool-kit and providing evidence that some M. ozzardi CO1 sequence deposits are pseudogenes, our results suggest that all Neotropical M. ozzardi parasites are closely related.
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650
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Weber N, Liou D, Dommer J, MacMenamin P, Quiñones M, Misner I, Oler AJ, Wan J, Kim L, Coakley McCarthy M, Ezeji S, Noble K, Hurt DE. Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis. Bioinformatics 2018; 34:1411-1413. [PMID: 29028892 PMCID: PMC5905584 DOI: 10.1093/bioinformatics/btx617] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 02/05/2023] Open
Abstract
Motivation Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. Results The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights. Nephele integrates common microbiome analysis tools as well as valuable reference datasets like the healthy human subjects cohort of the Human Microbiome Project (HMP). Nephele is built on the Amazon Web Services cloud, which provides centralized and automated storage and compute capacity, thereby reducing the burden on researchers and their institutions. Availability and implementation https://nephele.niaid.nih.gov and https://github.com/niaid/Nephele. Contact darrell.hurt@nih.gov.
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Affiliation(s)
- Nick Weber
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Liou
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Dommer
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Philip MacMenamin
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mariam Quiñones
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ian Misner
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joe Wan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lewis Kim
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Meghan Coakley McCarthy
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Ezeji
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karlynn Noble
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Darrell E Hurt
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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