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Alvarez-Molina A, Cobo-Díaz JF, Alexa EA, Crispie F, Prieto M, López M, Cotter PD, Alvarez-Ordóñez A. Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes. Food Res Int 2023; 173:113442. [PMID: 37803768 DOI: 10.1016/j.foodres.2023.113442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/11/2023] [Accepted: 09/09/2023] [Indexed: 10/08/2023]
Abstract
In the last years, advances in high throughput sequencing technologies have opened the possibility to broaden environmental monitoring activities in facilities processing food, offering expanded opportunities for characterizing in an untargeted manner the microbiome and resistome of foods and food processing environments (FPE) with huge potential benefits in food safety management systems. Here the microbiome and resistome of FPE from slaughterhouses (n = 3), dairy (n = 12) and meat (n = 10) processing plants were assessed through whole metagenome sequencing of 2 composite samples for each facility, comprising 10 FPE swabs taken from food contact surfaces and 10 FPE samples from non-food contact surfaces, respectively. FPE from slaughterhouses had more diverse microbiomes and resistomes, while FPE from dairy processing plants showed the highest β-dispersion, consistent with a more heterogeneous microbiome and resistome composition. The predominant bacterial genera depended on the industry type, with Pseudomonas and Psychrobacter being highly dominant in surfaces from slaughterhouses and meat industries, while different lactic acid bacteria predominated in dairy industries. The most abundant antimicrobial resistance genes (ARG) found were associated with resistance to aminoglycosides, tetracyclines and quaternary ammonium compounds (QAC). ARGs relating to resistance to aminoglycosides and tetracyclines were significantly more prevalent in slaughterhouses than in food processing plants, while QAC resistance genes were particularly abundant in some food contact surfaces from dairy and meat processing plants, suggesting that daily sanitation under suboptimal conditions may be selecting for persistent microbiota tolerant to these biocides in some facilities. The taxonomic mapping of ARG pointed to specific bacterial genera, such as Escherichia, Bacillus, or Staphylococcus, as carriers of the most relevant resistance determinants. About 63% of all ARG reads were assigned to contigs classified as plasmid-associated, indicating that the resistome of FPE may be strongly shaped through the spread of mobile genetic elements. Overall, the relevance of FPE as reservoirs of ARG was confirmed and it was demonstrated that next generation sequencing technologies allowing a deep characterisation of sources and routes of spread of microorganisms and antimicrobial resistance determinants in food industry settings hold promise to be integrated in monitoring and food safety management programmes.
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Affiliation(s)
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Elena A Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain.
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2
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Alioto TS, Gut M, Rodiño-Janeiro BK, Cruz F, Gómez-Garrido J, Vázquez-Ucha JC, Mata C, Antoni R, Briansó F, Dabad M, Casals E, Ingham M, Álvarez-Tejado M, Bou G, Gut IG. Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales. Microb Genom 2023; 9. [PMID: 38010338 DOI: 10.1099/mgen.0.001132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
In response to the threat of increasing antimicrobial resistance, we must increase the amount of available high-quality genomic data gathered on antibiotic-resistant bacteria. To this end, we developed an integrated pipeline for high-throughput long-read sequencing, assembly, annotation and analysis of bacterial isolates and used it to generate a large genomic data set of carbapenemase-producing Enterobacterales (CPE) isolates collected in Spain. The set of 461 isolates were sequenced with a combination of both Illumina and Oxford Nanopore Technologies (ONT) DNA sequencing technologies in order to provide genomic context for chromosomal loci and, most importantly, structural resolution of plasmids, important determinants for transmission of antimicrobial resistance. We developed an informatics pipeline called Assembly and Annotation of Carbapenem-Resistant Enterobacteriaceae (AACRE) for the full assembly and annotation of the bacterial genomes and their complement of plasmids. To explore the resulting genomic data set, we developed a new database called inCREDBle that not only stores the genomic data, but provides unique ways to filter and compare data, enabling comparative genomic analyses at the level of chromosomes, plasmids and individual genes. We identified a new sequence type, ST5000, and discovered a genomic locus unique to ST15 that may be linked to its increased spread in the population. In addition to our major objective of generating a large regional data set, we took the opportunity to compare the effects of sample quality and sequencing methods, including R9 versus R10 nanopore chemistry, on genome assembly and annotation quality. We conclude that converting short-read and hybrid microbial sequencing and assembly workflows to the latest nanopore chemistry will further reduce processing time and cost, truly enabling the routine monitoring of resistance transmission patterns at the resolution of complete chromosomes and plasmids.
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Affiliation(s)
- Tyler S Alioto
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Bruno Kotska Rodiño-Janeiro
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
| | - Fernando Cruz
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Jèssica Gómez-Garrido
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Juan Carlos Vázquez-Ucha
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Caterina Mata
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Regina Antoni
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Ferran Briansó
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona (UB), Barcelona, Spain
- Roche Diagnostics, Sant Cugat del Vallès, Barcelona, Spain
| | - Marc Dabad
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Eloi Casals
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Matthew Ingham
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | | | - Germán Bou
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
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Lee JH, Kim NH, Jang KM, Jin H, Shin K, Jeong BC, Kim DW, Lee SH. Prioritization of Critical Factors for Surveillance of the Dissemination of Antibiotic Resistance in Pseudomonas aeruginosa: A Systematic Review. Int J Mol Sci 2023; 24:15209. [PMID: 37894890 PMCID: PMC10607276 DOI: 10.3390/ijms242015209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Pseudomonas aeruginosa is the primary opportunistic human pathogen responsible for a range of acute and chronic infections; it poses a significant threat to immunocompromised patients and is the leading cause of morbidity and mortality for nosocomial infections. Its high resistance to a diverse array of antimicrobial agents presents an urgent health concern. Among the mechanisms contributing to resistance in P. aeruginosa, the horizontal acquisition of antibiotic resistance genes (ARGs) via mobile genetic elements (MGEs) has gained recognition as a substantial concern in clinical settings, thus indicating that a comprehensive understanding of ARG dissemination within the species is strongly required for surveillance. Here, two approaches, including a systematic literature analysis and a genome database survey, were employed to gain insights into ARG dissemination. The genome database enabled scrutinizing of all the available sequence information and various attributes of P. aeruginosa isolates, thus providing an extensive understanding of ARG dissemination within the species. By integrating both approaches, with a primary focus on the genome database survey, mobile ARGs that were linked or correlated with MGEs, important sequence types (STs) carrying diverse ARGs, and MGEs responsible for ARG dissemination were identified as critical factors requiring strict surveillance. Although human isolates play a primary role in dissemination, the importance of animal and environmental isolates has also been suggested. In this study, 25 critical mobile ARGs, 45 critical STs, and associated MGEs involved in ARG dissemination within the species, are suggested as critical factors. Surveillance and management of these prioritized factors across the One Health sectors are essential to mitigate the emergence of multidrug-resistant (MDR) and extensively resistant (XDR) P. aeruginosa in clinical settings.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Nam-Hoon Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Kyung-Min Jang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Hyeonku Jin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Kyoungmin Shin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Dae-Wi Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
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Huang G, Zhou X, Zhang Z, Lai W, Zhong Q, Wu D, Ye X. Acute Porphyromonas gingivalis Subdural Abscess with Brain Abscess in the Left Temporal Lobe: A Case Report and Review of Literature. Infect Drug Resist 2023; 16:6487-6491. [PMID: 37795204 PMCID: PMC10546930 DOI: 10.2147/idr.s422691] [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: 05/24/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Background Brain abscesses are a rare but serious complication of focal intracerebral infection. Case Description We present a patient of acute subdural abscess with brain abscess in the left temporal lobe. After craniotomy, combined with the Third Next Generation Sequencing and Gene Diagnosis (TNGS & GD) of abscess, we prescribed sensitive antibiotics; the patient recovers well and the abscess did not recur. Conclusion For patients with acute subdural abscess, combined craniotomy and the TNGS & GD of abscess could achieve good results.
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Affiliation(s)
- Guanlin Huang
- Department of Neurosurgery, Ganzhou People’s Hospital, Ganzhou, Jiangxi, People’s Republic of China
| | - Xiaoping Zhou
- Department of Neurosurgery, Ganzhou People’s Hospital, Ganzhou, Jiangxi, People’s Republic of China
| | - Zhenyu Zhang
- Department of Neurosurgery, Ganzhou People’s Hospital, Ganzhou, Jiangxi, People’s Republic of China
| | - Wentao Lai
- Department of Neurosurgery, Ganzhou People’s Hospital, Ganzhou, Jiangxi, People’s Republic of China
| | - Qi Zhong
- Department of Neurosurgery, Ganzhou People’s Hospital, Ganzhou, Jiangxi, People’s Republic of China
| | - Daxing Wu
- Department of Neurosurgery, Ganzhou People’s Hospital, Ganzhou, Jiangxi, People’s Republic of China
| | - Xinyun Ye
- Department of Neurosurgery, Ganzhou People’s Hospital, Ganzhou, Jiangxi, People’s Republic of China
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5
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Balarezo-Cisneros LN, Timouma S, Hanak A, Currin A, Valle F, Delneri D. High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries. Commun Biol 2023; 6:918. [PMID: 37679437 PMCID: PMC10484914 DOI: 10.1038/s42003-023-05285-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Kazachstania bulderi is a non-conventional yeast species able to grow efficiently on glucose and δ-gluconolactone at low pH. These unique traits make K. bulderi an ideal candidate for use in sustainable biotechnology processes including low pH fermentations and the production of green chemicals including organic acids. To accelerate strain development with this species, detailed information of its genetics is needed. Here, by employing long read sequencing we report a high-quality phased genome assembly for three strains of K. bulderi species, including the type strain. The sequences were assembled into 12 chromosomes with a total length of 14 Mb, and the genome was fully annotated at structural and functional levels, including allelic and structural variants, ribosomal array and mating type locus. This high-quality reference genome provides a resource to advance our fundamental knowledge of biotechnologically relevant non-conventional yeasts and to support the development of genetic tools for manipulating such strains towards their use as production hosts in biotechnological processes.
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Affiliation(s)
| | - Soukaina Timouma
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Alistair Hanak
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew Currin
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | - Daniela Delneri
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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6
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Rose R, Nolan DJ, Ashcraft D, Feehan AK, Velez-Climent L, Huston C, Lain B, Rosenthal S, Miele L, Fogel GB, Pankey G, Garcia-Diaz J, Lamers SL. Comparing antimicrobial resistant genes and phenotypes across multiple sequencing platforms and assays for Enterobacterales clinical isolates. BMC Microbiol 2023; 23:225. [PMID: 37596530 PMCID: PMC10436404 DOI: 10.1186/s12866-023-02975-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
INTRODUCTION Whole genome sequencing (WGS) of bacterial isolates can be used to identify antimicrobial resistance (AMR) genes. Previous studies have shown that genotype-based AMR has variable accuracy for predicting carbapenem resistance in carbapenem-resistant Enterobacterales (CRE); however, the majority of these studies used short-read platforms (e.g. Illumina) to generate sequence data. In this study, our objective was to determine whether Oxford Nanopore Technologies (ONT) long-read WGS would improve detection of carbapenem AMR genes with respect to short-read only WGS for nine clinical CRE samples. We measured the minimum inhibitory breakpoint (MIC) using two phenotype assays (MicroScan and ETEST) for six antibiotics, including two carbapenems (meropenem and ertapenem) and four non-carbapenems (gentamicin, ciprofloxacin, cefepime, and trimethoprim/sulfamethoxazole). We generated short-read data using the Illumina NextSeq and long-read data using the ONT MinION. Four assembly methods were compared: ONT-only assembly; ONT-only assembly plus short-read polish; ONT + short-read hybrid assembly plus short-read polish; short-read only assembly. RESULTS Consistent with previous studies, our results suggest that the hybrid assembly produced the highest quality results as measured by gene completeness and contig circularization. However, ONT-only methods had minimal impact on the detection of AMR genes and plasmids compared to short-read methods, although, notably, differences in gene copy number differed between methods. All four assembly methods showed identical presence/absence of the blaKPC-2 carbapenemase gene for all samples. The two phenotype assays showed 100% concordant results for the non-carbapenems, but only 65% concordance for the two carbapenems. The presence/absence of AMR genes was 100% concordant with AMR phenotypes for all four non-carbapenem drugs, although only 22%-50% sensitivity for the carbapenems. CONCLUSIONS Overall, these findings suggest that the lack of complete correspondence between CRE AMR genotype and phenotype for carbapenems, while concerning, is independent of sequencing platform/assembly method.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA.
- FoxSeq, LLC, Thibodaux, LA, USA.
| | - David J Nolan
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Deborah Ashcraft
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Amy K Feehan
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | | | - Benjamin Lain
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Simon Rosenthal
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Lucio Miele
- Translational Science and Genetics at Louisiana State University Health Science Center, New Orleans, LA, USA
| | | | - George Pankey
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Julia Garcia-Diaz
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Susanna L Lamers
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
- FoxSeq, LLC, Thibodaux, LA, USA
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Liu Y, Chen X, Yin Y, Li X, He K, Zhao X, Li X, Luo X, Mei Y, Wang Z, Shu R, Cheng Z, Gebretsadik KG, Luo C, Wang R, Lv Y, Chen A, Li F. A chromosome-level genome assembly of tomato pinworm, Tuta absoluta. Sci Data 2023; 10:390. [PMID: 37330594 PMCID: PMC10276875 DOI: 10.1038/s41597-023-02299-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 06/09/2023] [Indexed: 06/19/2023] Open
Abstract
The tomato pinworm, Tuta absoluta, or Phthorimaea absouta, is native to South America, but quickly spread to other regions of world, including Europe, Africa, and Asia, devastating to global tomato production. However, a lack of high-quality genome resources makes it difficult to understand its high invasiveness and ecological adaptation. Here, we sequenced the genome of the tomato pinworm using Nanopore platforms, yielding a genome assembly of 564.5 Mb with contig N50 of 3.33 Mb. BUSCO analysis demonstrated that this genome assembly has a high-level completeness of 98.0% gene coverage. In total, 310 Mb are repeating sequences accounting for 54.8% of genome assembly, and 21,979 protein-coding genes are annotated. Next, we used the Hi-C technique to anchor 295 contigs to 29 chromosomes, yielding a chromosome-level genome assembly with a scaffold N50 of 20.7 Mb. In sum, the high-quality genome assembly of the tomato pinworm is a useful gene resource that contributes to a better understanding of the biological characteristics of its invasiveness and will help in developing an efficient control policy.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China.
| | - Xi Chen
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanqiong Yin
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Xiaowei Li
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xueqing Zhao
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Xiangyong Li
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Xiyan Luo
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Runguo Shu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ziqi Cheng
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kifle Gebreegziabiher Gebretsadik
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
- Tigray Agricultural Research Institute (TARI), Mek'ele, Tigray, +492, Ethiopia
| | - Chen Luo
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Ran Wang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yaobin Lv
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Aidong Chen
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China.
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
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8
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Concha-Toloza M, Lopez-Cantillo M, Molina-Mora JA, Collado L. Genomic Characterization of Antibiotic-Resistant Campylobacterales Isolated from Chilean Poultry Meat. Antibiotics (Basel) 2023; 12:antibiotics12050917. [PMID: 37237819 DOI: 10.3390/antibiotics12050917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
Due to the lack of knowledge about Campylobacterales in the Chilean poultry industry, the objective of this research was to know the prevalence, resistance, and genotypes of Campylobacter, Arcobacter and Helicobacter in 382 samples of chicken meat purchased in Valdivia, Chile. The samples were analyzed using three isolation protocols. Resistance to four antibiotics was evaluated by phenotypic methods. Genomic analyses were performed on selected resistant strains to detect resistance determinants and their genotypes. A total of 59.2% of the samples were positive. Arcobacter butzleri (37.4%) was the most prevalent species, followed by Campylobacter jejuni (19.6%), C. coli (11.3%), A. cryaerophilus (3.7%) and A. skirrowii (1.3%). Helicobacter pullorum (14%) was detected by PCR in a subset of samples. Campylobacter jejuni was resistant to ciprofloxacin (37.3%) and tetracycline (20%), while C. coli and A. butzleri were resistant to ciprofloxacin (55.8% and 2.8%), erythromycin (16.3% and 0.7%) and tetracycline (4.7% and 2.8%), respectively. Molecular determinants were consistent with phenotypic resistance. The genotypes of C. jejuni (CC-21, CC-48, CC-49, CC-257, CC-353, CC-443, CC-446 and CC-658) and C. coli (CC-828) coincided with genotypes of Chilean clinical strains. These findings suggest that besides C. jejuni and C. coli, chicken meat could play a role in the transmission of other pathogenic and antibiotic-resistant Campylobacterales.
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Affiliation(s)
- Macarena Concha-Toloza
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Mónica Lopez-Cantillo
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Luis Collado
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5110566, Chile
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Mierke F, Brink DP, Norbeck J, Siewers V, Andlid T. Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates. Fungal Genet Biol 2023; 166:103783. [PMID: 36870442 DOI: 10.1016/j.fgb.2023.103783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 02/10/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of the recently isolated P. hubeiensis BOT-O strain was sequenced using MinION long-read sequencing and resulted in the most contiguous P. hubeiensis assembly to date with 18.95 Mb in 31 contigs. Using transcriptome data as experimental support, we generated the first mRNA-supported P. hubeiensis genome annotation and identified 6540 genes. 80% of the predicted genes were assigned functional annotations based on protein homology to other yeasts. Based on the annotation, key metabolic pathways in BOT-O were reconstructed, including pathways for storage lipids, mannosylerythritol lipids and xylose assimilation. BOT-O was confirmed to consume glucose and xylose at equal rates, but during mixed glucose-xylose cultivation glucose was found to be taken up faster. Differential expression analysis revealed that only a total of 122 genes were significantly differentially expressed at a cut-off of |log2 fold change| ≥ 2 when comparing cultivation on xylose with glucose, during exponential growth and during nitrogen-starvation. Of these 122 genes, a core-set of 24 genes was identified that were differentially expressed at all time points. Nitrogen-starvation resulted in a larger transcriptional effect, with a total of 1179 genes with significant expression changes at the designated fold change cut-off compared with exponential growth on either glucose or xylose.
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Affiliation(s)
- Friederike Mierke
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden; Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Daniel P Brink
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Joakim Norbeck
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
| | - Thomas Andlid
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
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Li J, Wang H, Zhu J, Yang Q, Luan Y, Shi L, Molina-Mora JA, Zheng Y. De novo assembly of a chromosome-level reference genome of the ornamental butterfly Sericinus montelus based on nanopore sequencing and Hi-C analysis. Front Genet 2023; 14:1107353. [PMID: 36968580 PMCID: PMC10030965 DOI: 10.3389/fgene.2023.1107353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Sericinus montelus (Lepidoptera, Papilionidae, Parnassiinae) is a high-value ornamental swallowtail butterfly species widely distributed in Northern and Central China, Japan, Korea, and Russia. The larval stage of this species feeds exclusively on Aristolochia plants. The Aristolochia species is well known for its high levels of aristolochic acids (AAs), which have been found to be carcinogenic for numerous animals. The swallowtail butterfly is among the few that can feed on these toxic host plants. However, the genetic adaptation of S. montelus to confer new abilities for AA tolerance has not yet been well explored, largely due to the limited genomic resources of this species. This study aimed to present a chromosome-level reference genome for S. montelus using the Oxford Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C technology. The final assembly was composed of 581.44 Mb with an expected genome size of 619.27 Mb. Further, 99.98% of the bases could be anchored onto 30 chromosomes. The N50 of contigs and scaffolds was 5.74 and 19.12 Mb, respectively. Approximately 48.86% of the assembled genome was suggested to be repeat elements, and 13,720 protein-coding genes were predicted in the current assembly. The phylogenetic analysis indicated that S. montelus diverged from the common ancestor of swallowtails about 58.57-80.46 million years ago. Compared with related species, S. montelus showed a significant expansion of P450 gene family members, and positive selections on eloa, heatr1, and aph1a resulted in the AA tolerance for S. montelus larva. The de novo assembly of a high-quality reference genome for S. montelus provided a fundamental genomic tool for future research on evolution, genome genetics, and toxicology of the swallowtail butterflies.
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Affiliation(s)
- Jingjing Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Grandomics Biosciences Institute, Wuhan, China
| | - Haiyan Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | | | - Qi Yang
- Grandomics Biosciences Institute, Wuhan, China
| | - Yang Luan
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- Cancer Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - José Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- *Correspondence: José Arturo Molina-Mora, ; Yuanting Zheng,
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
- *Correspondence: José Arturo Molina-Mora, ; Yuanting Zheng,
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11
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Shen L, Wu H, Chen H, Jiang Y. A case report: Intermittent catheterization combined with rehabilitation in the treatment of carbapenem-resistant Klebsiella pneumoniae catheter-associated urinary tract infection. Front Cell Infect Microbiol 2022; 12:1027576. [PMID: 36439230 PMCID: PMC9682002 DOI: 10.3389/fcimb.2022.1027576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
Catheter-related urinary tract infections, especially those caused by multidrug-resistant (MDR) bacteria, are extremely difficult to treat due to limited therapeutic choices. Therefore, removing catheters as soon as possible is pivotal to successful treatment. Herein, we report a case of catheter-related urinary tract infection caused by carbapenem-resistant Klebsiella pneumoniae (CRKP). Intermittent catheterization was used to reduce biofilm occurrence and exercise bladder function on the basis of an active and adequate anti-infection strategy. Simultaneously, combined with acupuncture treatment and strengthening the patient’s pelvic floor muscle training to improve urinary retention, the catheter was eventually removed to obtain autonomous urination in this patient, and this led to the successful treatment for a CRKP catheter-related urinary tract infection.
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Affiliation(s)
- Lihua Shen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huiying Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Yan Jiang,
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12
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Molina-Mora JA, Cordero-Laurent E, Calderón-Osorno M, Chacón-Ramírez E, Duarte-Martínez F. Metagenomic pipeline for identifying co-infections among distinct SARS-CoV-2 variants of concern: study cases from Alpha to Omicron. Sci Rep 2022; 12:9377. [PMID: 35672431 PMCID: PMC9172093 DOI: 10.1038/s41598-022-13113-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/03/2022] [Indexed: 01/04/2023] Open
Abstract
Concomitant infection or co-infection with distinct SARS-CoV-2 genotypes has been reported as part of the epidemiological surveillance of the COVID-19 pandemic. In the context of the spread of more transmissible variants during 2021, co-infections are not only important due to the possible changes in the clinical outcome, but also the chance to generate new genotypes by recombination. However, a few approaches have developed bioinformatic pipelines to identify co-infections. Here we present a metagenomic pipeline based on the inference of multiple fragments similar to amplicon sequence variant (ASV-like) from sequencing data and a custom SARS-CoV-2 database to identify the concomitant presence of divergent SARS-CoV-2 genomes, i.e., variants of concern (VOCs). This approach was compared to another strategy based on whole-genome (metagenome) assembly. Using single or pairs of sequencing data of COVID-19 cases with distinct SARS-CoV-2 VOCs, each approach was used to predict the VOC classes (Alpha, Beta, Gamma, Delta, Omicron or non-VOC and their combinations). The performance of each pipeline was assessed using the ground-truth or expected VOC classes. Subsequently, the ASV-like pipeline was used to analyze 1021 cases of COVID-19 from Costa Rica to investigate the possible occurrence of co-infections. After the implementation of the two approaches, an accuracy of 96.2% was revealed for the ASV-like inference approach, which contrasts with the misclassification found (accuracy 46.2%) for the whole-genome assembly strategy. The custom SARS-CoV-2 database used for the ASV-like analysis can be updated according to the appearance of new VOCs to track co-infections with eventual new genotypes. In addition, the application of the ASV-like approach to all the 1021 sequenced samples from Costa Rica in the period October 12th-December 21th 2021 found that none corresponded to co-infections with VOCs. In conclusion, we developed a metagenomic pipeline based on ASV-like inference for the identification of co-infection with distinct SARS-CoV-2 VOCs, in which an outstanding accuracy was achieved. Due to the epidemiological, clinical, and molecular relevance of the concomitant infection with distinct genotypes, this work represents another piece in the process of the surveillance of the COVID-19 pandemic in Costa Rica and worldwide.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica.
| | - Estela Cordero-Laurent
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica
| | - Melany Calderón-Osorno
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica
| | - Edgar Chacón-Ramírez
- Centro de Investigación en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Francisco Duarte-Martínez
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica
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Bonardi S, Cabassi CS, Manfreda G, Parisi A, Fiaccadori E, Sabatino A, Cavirani S, Bacci C, Rega M, Spadini C, Iannarelli M, Crippa C, Ruocco F, Pasquali F. Survey on Carbapenem-Resistant Bacteria in Pigs at Slaughter and Comparison with Human Clinical Isolates in Italy. Antibiotics (Basel) 2022; 11:777. [PMID: 35740183 PMCID: PMC9219774 DOI: 10.3390/antibiotics11060777] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022] Open
Abstract
This study is focused on resistance to carbapenems and third-generation cephalosporins in Gram-negative microorganisms isolated from swine, whose transmission to humans via pork consumption cannot be excluded. In addition, the common carriage of carbapenem-resistant (CR) bacteria between humans and pigs was evaluated. Sampling involved 300 faecal samples collected from slaughtered pigs and 300 urine samples collected from 187 hospitalised patients in Parma Province (Italy). In swine, MIC testing confirmed resistance to meropenem for isolates of Pseudomonas aeruginosa and Pseudomonas oryzihabitans and resistance to cefotaxime and ceftazidime for Escherichia coli, Ewingella americana, Enterobacter agglomerans, and Citrobacter freundii. For Acinetobacter lwoffii, Aeromonas hydrofila, Burkolderia cepacia, Corynebacterium indologenes, Flavobacterium odoratum, and Stenotrophomonas maltophilia, no EUCAST MIC breakpoints were available. However, ESBL genes (blaCTXM-1, blaCTX-M-2, blaTEM-1, and blaSHV) and AmpC genes (blaCIT, blaACC, and blaEBC) were found in 38 and 16 isolates, respectively. P. aeruginosa was the only CR species shared by pigs (4/300 pigs; 1.3%) and patients (2/187; 1.1%). P. aeruginosa ST938 carrying blaPAO and blaOXA396 was detected in one pig as well as an 83-year-old patient. Although no direct epidemiological link was demonstrable, SNP calling and cgMLST showed a genetic relationship of the isolates (86 SNPs and 661 allele difference), thus suggesting possible circulation of CR bacteria between swine and humans.
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Affiliation(s)
- Silvia Bonardi
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Clotilde Silvia Cabassi
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Gerardo Manfreda
- Food Safety Unit, Department of Agricultural and Food Sciences Alma Mater Studiorum, University of Bologna, 40064 Ozzano dell’Emilia, Italy; (G.M.); (C.C.); (F.P.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 70017 Putignano, Italy;
| | - Enrico Fiaccadori
- Nephrology Unit, Parma University-Hospital, Department of Medicine and Surgery, Parma University, 43126 Parma, Italy; (E.F.); (A.S.)
| | - Alice Sabatino
- Nephrology Unit, Parma University-Hospital, Department of Medicine and Surgery, Parma University, 43126 Parma, Italy; (E.F.); (A.S.)
| | - Sandro Cavirani
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Cristina Bacci
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Martina Rega
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Costanza Spadini
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Mattia Iannarelli
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (C.S.C.); (S.C.); (C.B.); (M.R.); (C.S.); (M.I.)
| | - Cecilia Crippa
- Food Safety Unit, Department of Agricultural and Food Sciences Alma Mater Studiorum, University of Bologna, 40064 Ozzano dell’Emilia, Italy; (G.M.); (C.C.); (F.P.)
| | | | - Frédérique Pasquali
- Food Safety Unit, Department of Agricultural and Food Sciences Alma Mater Studiorum, University of Bologna, 40064 Ozzano dell’Emilia, Italy; (G.M.); (C.C.); (F.P.)
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14
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Hai DM, Yen DT, Liem PT, Tam BM, Huong DTT, Hang BTB, Hieu DQ, Garigliany MM, Coppieters W, Kestemont P, Phuong NT, Farnir F. A High-Quality Genome Assembly of Striped Catfish ( Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data. Genes (Basel) 2022; 13:923. [PMID: 35627308 PMCID: PMC9141817 DOI: 10.3390/genes13050923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/26/2022] Open
Abstract
The HiFi sequencing technology yields highly accurate long-read data with accuracies greater than 99.9% that can be used to improve results for complex applications such as genome assembly. Our study presents a high-quality chromosome-scale genome assembly of striped catfish (Pangasianodon hypophthalmus), a commercially important species cultured mainly in Vietnam, integrating HiFi reads and Hi-C data. A 788.4 Mb genome containing 381 scaffolds with an N50 length of 21.8 Mb has been obtained from HiFi reads. These scaffolds have been further ordered and clustered into 30 chromosome groups, ranging from 1.4 to 57.6 Mb, based on Hi-C data. The present updated assembly has a contig N50 of 14.7 Mb, representing a 245-fold and 4.2-fold improvement over the previous Illumina and Illumina-Nanopore-Hi-C based version, respectively. In addition, the proportion of repeat elements and BUSCO genes identified in our genome is remarkably higher than in the two previously released striped catfish genomes. These results highlight the power of using HiFi reads to assemble the highly repetitive regions and to improve the quality of genome assembly. The updated, high-quality genome assembled in this work will provide a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of striped catfish.
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Affiliation(s)
- Dao Minh Hai
- FARAH/Sustainable Animal Production, Faculty of Veterinary Medicine, University of Liege (B43), 4000 Liege, Belgium;
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Duong Thuy Yen
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Pham Thanh Liem
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Bui Minh Tam
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Do Thi Thanh Huong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Bui Thi Bich Hang
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Dang Quang Hieu
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Mutien-Marie Garigliany
- FARAH/Veterinary Public Health, Faculty of Veterinary Medicine, University of Liege (B43), 4000 Liege, Belgium;
| | | | - Patrick Kestemont
- Research Unit in Environmental and Evolutionary Biology, Institute of Life, Earth & Environnment, University of Namur, rue de Bruxelles 61, 5000 Namur, Belgium;
| | - Nguyen Thanh Phuong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho 900000, Vietnam; (D.T.Y.); (P.T.L.); (B.M.T.); (D.T.T.H.); (B.T.B.H.); (D.Q.H.); (N.T.P.)
| | - Frédéric Farnir
- FARAH/Sustainable Animal Production, Faculty of Veterinary Medicine, University of Liege (B43), 4000 Liege, Belgium;
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Characterization of a Conjugative Multidrug Resistance IncP-2 Megaplasmid, pPAG5, from a Clinical Pseudomonas aeruginosa Isolate. Microbiol Spectr 2022; 10:e0199221. [PMID: 35171033 PMCID: PMC8849076 DOI: 10.1128/spectrum.01992-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The spread of resistance genes via horizontal plasmid transfer plays a significant role in the formation of multidrug-resistant (MDR) Pseudomonas aeruginosa strains. Here, we identified a megaplasmid (ca. 513 kb), designated pPAG5, which was recovered from a clinical multidrug-resistant P. aeruginosa PAG5 strain. The pPAG5 plasmid belonged to the IncP-2 incompatibility group. Two large multidrug resistance regions (MDR-1 and MDR-2) and two heavy metal resistance operons (merEDACPTR and terZABCDE) were identified in the pPAG5 plasmid. Genetic analysis demonstrated that the formation of MDR regions was mediated by several homologous recombination events. Further conjugation assays identified that pPAG5 could be transferred to P. aeruginosa but not Escherichia coli. Antimicrobial susceptibility testing on transconjugants demonstrated that pPAG5 was capable of transferring resistance genes to transconjugants and producing a multidrug-resistant phenotype. Comparative analysis revealed that pPAG5 and related plasmids shared an overall similar backbone, including genes essential for replication (repA), partition (par), and conjugal transfer (tra). Further phylogenetic analysis showed that pPAG5 was closely related to plasmids pOZ176 and pJB37, both of which are members of the IncP-2-type plasmid group. IMPORTANCE The emergence and spread of plasmid-associated multidrug resistance in bacterial pathogens is a key global threat to public health. It is important to understand the mechanisms of the formation and evolution of these plasmids in patients, hospitals, and the environment. In this study, we detailed the genetic characteristics of a multidrug resistance IncP-2 megaplasmid, pPAG5, and investigated the formation of its MDR regions and evolution. To the best of our knowledge, plasmid pPAG5 is the largest multidrug resistance plasmid ever sequenced in the Pseudomonas genus. Our results may provide further insight into the formation of multidrug resistance plasmids in bacteria and the molecular evolution of plasmids.
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National surveillance pilot study unveils a multicenter, clonal outbreak of VIM-2-producing Pseudomonas aeruginosa ST111 in the Netherlands between 2015 and 2017. Sci Rep 2021; 11:21015. [PMID: 34697344 PMCID: PMC8545960 DOI: 10.1038/s41598-021-00205-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/29/2021] [Indexed: 02/01/2023] Open
Abstract
Verona Integron-encoded Metallo-beta-lactamase (VIM) is the most frequently-encountered carbapenemase in the healthcare-related pathogen Pseudomonas aeruginosa. In the Netherlands, a low-endemic country for antibiotic-resistant bacteria, no national surveillance data on the prevalence of carbapenemase-producing P. aeruginosa (CPPA) was available. Therefore, in 2016, a national surveillance pilot study was initiated to investigate the occurrence, molecular epidemiology, genetic characterization, and resistomes of CPPA among P. aeruginosa isolates submitted by medical microbiology laboratories (MMLs) throughout the country. From 1221 isolates included in the study, 124 (10%) produced carbapenemase (CIM-positive); of these, the majority (95, 77%) were positive for the blaVIM gene using PCR. Sequencing was performed on 112 CIM-positive and 56 CIM-negative isolates (n = 168), and genetic clustering revealed that 75/168 (45%) isolates were highly similar. This genetic cluster, designated Group 1, comprised isolates that belonged to high-risk sequence type ST111/serotype O12, had similar resistomes, and all but two carried the blaVIM-2 allele on an identical class 1 integron. Additionally, Group 1 isolates originated from around the country (i.e. seven provinces) and from multiple MMLs. In conclusion, the Netherlands had experienced a nationwide, inter-institutional, clonal outbreak of VIM-2-producing P. aeruginosa for at least three years, which this pilot study was crucial in identifying. A structured, national surveillance program is strongly advised to monitor the spread of Group 1 CPPA, to identify emerging clones/carbapenemase genes, and to detect transmission in and especially between hospitals in order to control current and future outbreaks.
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Genome Analyses of the Less Aggressive Rhizoctonia solani AG1-IB Isolates 1/2/21 and O8/2 Compared to the Reference AG1-IB Isolate 7/3/14. J Fungi (Basel) 2021; 7:jof7100832. [PMID: 34682252 PMCID: PMC8537455 DOI: 10.3390/jof7100832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 01/26/2023] Open
Abstract
Rhizoctonia solani AG1-IB of the phylum Basidiomycota is known as phytopathogenic fungus affecting various economically important crops, such as bean, rice, soybean, figs, cabbage and lettuce. The isolates 1/2/21 and O8/2 of the anastomosis group AG1-IB originating from lettuce plants with bottom rot symptoms represent two less aggressive R. solani isolates, as confirmed in a pathogenicity test on lettuce. They were deeply sequenced on the Illumina MiSeq system applying the mate-pair and paired-end mode to establish their genome sequences. Assemblies of obtained sequences resulted in 2092 and 1492 scaffolds, respectively, for isolate 1/2/21 and O8/2, amounting to a size of approximately 43 Mb for each isolate. Gene prediction by applying AUGUSTUS (v. 3.2.1.) yielded 12,827 and 12,973 identified genes, respectively. Based on automatic functional annotation, genes potentially encoding cellulases and enzymes involved in secondary metabolite synthesis were identified in the AG1-IB genomes. The annotated genome sequences of the less aggressive AG1-IB isolates were compared with the isolate 7/3/14, which is highly aggressive on lettuce and other vegetable crops such as bean, cabbage and carrot. This analysis revealed the first insights into core genes of AG1-IB isolates and unique determinants of each genome that may explain the different aggressiveness levels of the strains.
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Liu YY, Chen BH, Chen CC, Chiou CS. Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type. PeerJ 2021; 9:e11842. [PMID: 34466283 PMCID: PMC8380430 DOI: 10.7717/peerj.11842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/01/2021] [Indexed: 12/16/2022] Open
Abstract
With the reduction in the cost of next-generation sequencing, whole-genome sequencing (WGS)–based methods such as core-genome multilocus sequence type (cgMLST) have been widely used. However, gene-based methods are required to assemble raw reads to contigs, thus possibly introducing errors into assemblies. Because the robustness of cgMLST depends on the quality of assemblies, the results of WGS should be assessed (from sequencing to assembly). In this study, we investigated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. Different combinations of read lengths and read depths were simulated from the complete genomes of three common food-borne pathogens: Escherichia coli, Listeria monocytogenes, and Salmonella enterica. We found that the quality of assemblies was mainly affected by read depth, irrespective of the assembler used. In addition, we suggest several cutoff values for future cgMLST experiments. Furthermore, we recommend the combinations of read lengths, read depths, and assemblers that can result in a higher cost/performance ratio for cgMLST.
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Affiliation(s)
- Yen-Yi Liu
- Department of Public Health, China Medical University, Taichung, Taiwan
| | - Bo-Han Chen
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taichung, Taiwan
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chien-Shun Chiou
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taichung, Taiwan
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Molina-Mora JA, Cordero-Laurent E, Godínez A, Calderón-Osorno M, Brenes H, Soto-Garita C, Pérez-Corrales C, Drexler JF, Moreira-Soto A, Corrales-Aguilar E, Duarte-Martínez F. SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 92:104872. [PMID: 33905892 PMCID: PMC8065237 DOI: 10.1016/j.meegid.2021.104872] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 02/07/2023]
Abstract
Genome sequencing is a key strategy in the surveillance of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Latin America is the hardest-hit region of the world, accumulating almost 20% of COVID-19 cases worldwide. In Costa Rica, from the first detected case on March 6th to December 31st almost 170,000 cases have been reported. We analyzed the genomic variability during the SARS-CoV-2 pandemic in Costa Rica using 185 sequences, 52 from the first months of the pandemic, and 133 from the current wave. Three GISAID clades (G, GH, and GR) and three PANGOLIN lineages (B.1, B.1.1, and B.1.291) were predominant, suggesting multiple re-introductions from other regions. The whole-genome variant calling analysis identified a total of 283 distinct nucleotide variants, following a power-law distribution with 190 single nucleotide mutations in a single sequence, and only 16 mutations were found in >5% sequences. These mutations were distributed through the whole genome. The prevalence of worldwide-found variant D614G in the Spike (98.9% in Costa Rica), ORF8 L84S (1.1%) is similar to what is found elsewhere. Interestingly, the frequency of mutation T1117I in the Spike has increased during the current pandemic wave beginning in May 2020 in Costa Rica, reaching 29.2% detection in the full genome analyses in November 2020. This variant has been observed in less than 1% of the GISAID reported sequences worldwide in 2020. Structural modeling of the Spike protein with the T1117I mutation suggests a potential effect on the viral oligomerization needed for cell infection, but no differences with other genomes on transmissibility, severity nor vaccine effectiveness are predicted. In conclusion, genome analyses of the SARS-CoV-2 sequences over the course of the COVID-19 pandemic in Costa Rica suggest the introduction of lineages from other countries and the detection of mutations in line with other studies, but pointing out the local increase in the detection of Spike-T1117I variant. The genomic features of this virus need to be monitored and studied in further analyses as part of the surveillance program during the pandemic.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, Costa Rica.
| | - Estela Cordero-Laurent
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
| | - Adriana Godínez
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
| | - Melany Calderón-Osorno
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
| | - Hebleen Brenes
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
| | - Claudio Soto-Garita
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
| | - Cristian Pérez-Corrales
- Hospital Nacional De Niños Dr. Carlos Sáenz Herrera, Caja Costarricense de Seguro Social (CCSS), Costa Rica
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany.
| | - Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany.
| | - Eugenia Corrales-Aguilar
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, Costa Rica.
| | - Francisco Duarte-Martínez
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica.
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20
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Strateva T, Setchanova L, Peykov S. Characterization of a Bulgarian VIM-2 metallo-β-lactamase-producing Pseudomonas aeruginosa clinical isolate belonging to the high-risk sequence type 111. Infect Dis (Lond) 2021; 53:883-887. [PMID: 34060977 DOI: 10.1080/23744235.2021.1934531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Tanya Strateva
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Lena Setchanova
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Slavil Peykov
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria.,BioInfoTech Laboratory, Sofia, Bulgaria
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21
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Murphy TR, Xiao R, Hamilton-Brehm SD. Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13 T. BMC Genomics 2021; 22:209. [PMID: 33757423 PMCID: PMC7988955 DOI: 10.1186/s12864-021-07535-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface. Coupled with even fewer cultured isolates, study and understanding of how life endures in the extreme oligotrophic subsurface environments is greatly hindered. Using a de novo hybrid assembly of Illumina and Oxford Nanopore sequences we produced a circular genome with corresponding methylome profile of the recently characterized thermophilic, anaerobic, and fumarate-respiring subsurface bacterium, Thermanaerosceptrum fracticalcis, strain DRI-13T to understand how this microorganism survives the deep subsurface. RESULTS The hybrid assembly produced a single circular genome of 3.8 Mb in length with an overall GC content of 45%. Out of the total 4022 annotated genes, 3884 are protein coding, 87 are RNA encoding genes, and the remaining 51 genes were associated with regulatory features of the genome including riboswitches and T-box leader sequences. Approximately 24% of the protein coding genes were hypothetical. Analysis of strain DRI-13T genome revealed: 1) energy conservation by bifurcation hydrogenase when growing on fumarate, 2) four novel bacterial prophages, 3) methylation profile including 76.4% N6-methyladenine and 3.81% 5-methylcytosine corresponding to novel DNA methyltransferase motifs. As well a cluster of 45 genes of unknown protein families that have enriched DNA mCpG proximal to the transcription start sites, and 4) discovery of a putative core of bacteriophage exclusion (BREX) genes surrounded by hypothetical proteins, with predicted functions as helicases, nucleases, and exonucleases. CONCLUSIONS The de novo hybrid assembly of strain DRI-13T genome has provided a more contiguous and accurate view of the subsurface bacterium T. fracticalcis, strain DRI-13T. This genome analysis reveals a physiological focus supporting syntrophy, non-homologous double stranded DNA repair, mobility/adherence/chemotaxis, unique methylome profile/recognized motifs, and a BREX defense system. The key to microbial subsurface survival may not rest on genetic diversity, but rather through specific syntrophy niches and novel methylation strategies.
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Affiliation(s)
- Trevor R Murphy
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Rui Xiao
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Scott D Hamilton-Brehm
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA.
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22
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Molina Mora JA, Montero-Manso P, García-Batán R, Campos-Sánchez R, Vilar-Fernández J, García F. A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach. Biosystems 2021; 205:104411. [PMID: 33757842 DOI: 10.1016/j.biosystems.2021.104411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/27/2023]
Abstract
Tolerance to stress conditions is vital for organismal survival, including bacteria under specific environmental conditions, antibiotics, and other perturbations. Some studies have described common modulation and shared genes during stress response to different types of disturbances (termed as perturbome), leading to the idea of central control at the molecular level. We implemented a robust machine learning approach to identify and describe genes associated with multiple perturbations or perturbome in a Pseudomonas aeruginosa PAO1 model. Using microarray datasets from the Gene Expression Omnibus (GEO), we evaluated six approaches to rank and select genes: using two methodologies, data single partition (SP method) or multiple partitions (MP method) for training and testing datasets, we evaluated three classification algorithms (SVM Support Vector Machine, KNN K-Nearest neighbor and RF Random Forest). Gene expression patterns and topological features at the systems level were included to describe the perturbome elements. We were able to select and describe 46 core response genes associated with multiple perturbations in P. aeruginosa PAO1 and it can be considered a first report of the P. aeruginosa perturbome. Molecular annotations, patterns in expression levels, and topological features in molecular networks revealed biological functions of biosynthesis, binding, and metabolism, many of them related to DNA damage repair and aerobic respiration in the context of tolerance to stress. We also discuss different issues related to implemented and assessed algorithms, including data partitioning, classification approaches, and metrics. Altogether, this work offers a different and robust framework to select genes using a machine learning approach.
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Affiliation(s)
- Jose Arturo Molina Mora
- Centro de Investigacion en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.
| | | | - Raquel García-Batán
- Centro de Investigacion en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.
| | - Rebeca Campos-Sánchez
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San José, Costa Rica.
| | | | - Fernando García
- Centro de Investigacion en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San Jose, Costa Rica.
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23
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Molina-Mora JA, Chinchilla-Montero D, García-Batán R, García F. Genomic context of the two integrons of ST-111 Pseudomonas aeruginosa AG1: A VIM-2-carrying old-acquaintance and a novel IMP-18-carrying integron. INFECTION GENETICS AND EVOLUTION 2021; 89:104740. [PMID: 33516973 DOI: 10.1016/j.meegid.2021.104740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/28/2020] [Accepted: 01/23/2021] [Indexed: 12/24/2022]
Abstract
Pseudomonas aeruginosa is an opportunist and versatile organism responsible for infections mainly in immunocompromised hosts. This pathogen has high intrinsic resistance to most antimicrobials. P. aeruginosa AG1 (PaeAG1) is a Costa Rican high-risk ST-111 strain with resistance to multiple antibiotics, including carbapenems, due to the activity of VIM-2 and IMP-18 metallo-β-lactamases (MBLs). These genes are harbored in two class 1 integrons located inone out of the 57 PaeAG1 genomic islands. However, the genomic context associated to these determinants in PaeAG1 and other P. aeruginosa strains is unclear. Thus, we first assessed the transcriptional activity of VIM-2 and IMP-18 genes when exposed to imipenem (a carbapenem) by RT-qPCR. To select related genomes to PaeAG1, we implemented a pan-genome analysis to define and up-date the phylogenetic relationship among complete P. aeruginosa genomes. We also studied the PaeAG1 genomic islands content in the related strains and finally we described the architecture and possible evolutionary steps of the genomic regions around the VIM-2- and IMP-18-carrying integrons. Expression of VIM-2 and IMP-18 genes was demonstrated to be induced after imipenem exposure. In a subsequent comparative genomics analysis with 211 strains, the P. aeruginosa pan-genome revealed that complete genome sequences are able to separate clones by MLST profile, including a clear ST-111 cluster with PaeAG1. The PaeAG1 genomic islands were found to define a diverse presence/absence pattern among related genomes. Finally, landscape reconstruction of genomic regions showed that VIM-2-carrying integron (In59-like) is an old-acquaintance element harbored in the same known region found in other two ST-111 strains. Also, PaeAG1 has an exclusive genomic region containing a novel IMP-18-carrying integron (registered as In1666), with an arrangement never reported before. Altogether, we provide new insights about the genomic determinants associated with the resistance to carbapenems in this high-risk P. aeruginosa using comparative genomics.
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Affiliation(s)
| | | | - Raquel García-Batán
- Research Center in Tropical Diseases (CIET), University of Costa Rica, Costa Rica.
| | - Fernando García
- Research Center in Tropical Diseases (CIET), University of Costa Rica, Costa Rica.
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24
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Berger C, Rückert C, Blom J, Rabaey K, Kalinowski J, Rosenbaum MA. Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics. Sci Rep 2021; 11:1370. [PMID: 33446769 PMCID: PMC7809047 DOI: 10.1038/s41598-020-80592-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/21/2020] [Indexed: 12/31/2022] Open
Abstract
The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.
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Affiliation(s)
- Carola Berger
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Rückert
- Center for Biotechnology - CeBiTec, University of Bielefeld, Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Giessen, Germany
| | - Korneel Rabaey
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Ghent, Belgium
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, University of Bielefeld, Bielefeld, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
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25
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Molina-Mora JA, García F. Molecular Determinants of Antibiotic Resistance in the Costa Rican Pseudomonas aeruginosa AG1 by a Multi-omics Approach: A Review of 10 Years of Study. PHENOMICS 2021; 1:129-142. [PMID: 35233560 PMCID: PMC8210740 DOI: 10.1007/s43657-021-00016-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 01/13/2023]
Abstract
Pseudomonas aeruginosa AG1 (PaeAG1) is a Costa Rican strain that was isolated in 2010 in a major Hospital. This strain has resistance to multiple antibiotics such as β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones. PaeAG1 is considered critical (Priority 1) due to its resistance to carbapenems, and it was the first report of a P. aeruginosa isolate carrying both VIM-2 and IMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes (both with carbapenemase activity). Owing to these traits, we have studied this model for 10 years using diverse approaches including multi-omics. In this review, we summarize the main points of the different steps that we have studied in PaeAG1: preliminary analyses of this strain at the genomic and phenomic levels revealed that this microorganism has particular features of antibiotic resistance. In the multi-omics approach, the genome assembly was the initial step to identify the genomic determinants of this strain, including virulence factors, antibiotic resistance genes, as well as a complex accessory genome. Second, a comparative genomic approach was implemented to define and update the phylogenetic relationship among complete P. aeruginosa genomes, the genomic island content in other strains, and the architecture of the two MBL-carrying integrons. Third, the proteomic profile of PaeAG1 was studied after exposure to antibiotics using 2-dimensional gel electrophoresis (2D-GE). Fourth, to study the central response to multiple perturbations in P. aeruginosa, i.e., the core perturbome, a machine learning approach was used. The analysis revealed biological functions and determinants that are shared by different disturbances. Finally, to evaluate the effects of ciprofloxacin (CIP) on PaeAG1, a growth curve comparison, differential expression analysis (RNA-Seq), and network analysis were performed. Using the results of the core perturbome (pathways that also were found in this perturbation with CIP), it was possible to identify the “exclusive” response and determinants of PaeAG1 after exposure to CIP. Altogether, after a decade of study using a multi-omics approach (at genomics, comparative genomics, perturbomics, transcriptomics, proteomics, and phenomics levels), we have provided new insights about the genomic and transcriptomic determinants associated with antibiotic resistance in PaeAG1. These results not only partially explain the high-risk condition of this strain that enables it to conquer nosocomial environments and its multi-resistance profile, but also this information may eventually be used as part of the strategies to fight this pathogen.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Fernando García
- Centro de Investigación en Enfermedades Tropicales (CIET) & Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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26
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Pseudomonas aeruginosa epidemic high-risk clones and their association with horizontally-acquired β-lactamases: 2020 update. Int J Antimicrob Agents 2020; 56:106196. [DOI: 10.1016/j.ijantimicag.2020.106196] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 07/30/2020] [Accepted: 09/26/2020] [Indexed: 01/17/2023]
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27
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Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach. Sci Rep 2020; 10:13717. [PMID: 32792590 PMCID: PMC7427096 DOI: 10.1038/s41598-020-70581-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that thrives in diverse environments and causes a variety of human infections. Pseudomonas aeruginosa AG1 (PaeAG1) is a high-risk sequence type 111 (ST-111) strain isolated from a Costa Rican hospital in 2010. PaeAG1 has both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases, and it is resistant to β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones. Ciprofloxacin (CIP) is an antibiotic commonly used to treat P. aeruginosa infections, and it is known to produce DNA damage, triggering a complex molecular response. In order to evaluate the effects of a sub-inhibitory CIP concentration on PaeAG1, growth curves using increasing CIP concentrations were compared. We then measured gene expression using RNA-Seq at three time points (0, 2.5 and 5 h) after CIP exposure to identify the transcriptomic determinants of the response (i.e. hub genes, gene clusters and enriched pathways). Changes in expression were determined using differential expression analysis and network analysis using a top–down systems biology approach. A hybrid model using database-based and co-expression analysis approaches was implemented to predict gene–gene interactions. We observed a reduction of the growth curve rate as the sub-inhibitory CIP concentrations were increased. In the transcriptomic analysis, we detected that over time CIP treatment resulted in the differential expression of 518 genes, showing a complex impact at the molecular level. The transcriptomic determinants were 14 hub genes, multiple gene clusters at different levels (associated to hub genes or as co-expression modules) and 15 enriched pathways. Down-regulation of genes implicated in several metabolism pathways, virulence elements and ribosomal activity was observed. In contrast, amino acid catabolism, RpoS factor, proteases, and phenazines genes were up-regulated. Remarkably, > 80 resident-phage genes were up-regulated after CIP treatment, which was validated at phenomic level using a phage plaque assay. Thus, reduction of the growth curve rate and increasing phage induction was evidenced as the CIP concentrations were increased. In summary, transcriptomic and network analyses, as well as the growth curves and phage plaque assays provide evidence that PaeAG1 presents a complex, concentration-dependent response to sub-inhibitory CIP exposure, showing pleiotropic effects at the systems level. Manipulation of these determinants, such as phage genes, could be used to gain more insights about the regulation of responses in PaeAG1 as well as the identification of possible therapeutic targets. To our knowledge, this is the first report of the transcriptomic analysis of CIP response in a ST-111 high-risk P. aeruginosa strain, in particular using a top-down systems biology approach.
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