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Barmak SM, Mendenhall IH, Sinyavskiy YA, Berdygaliev AB, Sharmanov TS, Sultankulova GT, Tuigunov DN, Zholdybayeva EV. Whole-genome sequence and annotation of Salmonella enterica subsp. enterica strain QazSL-4. Microbiol Resour Announc 2024:e0087623. [PMID: 38624204 DOI: 10.1128/mra.00876-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/09/2024] [Indexed: 04/17/2024] Open
Abstract
Here, we present the whole-genome sequence of Salmonella enterica subsp. enterica strain QazSL-4 isolated from a chicken fillet in 2018, Almaty, Kazakhstan. The genome obtained using Illumina MiSeq technology consists of 49 contigs with a total length of 4,711,816 bp with a GC content of 52.1%.
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Affiliation(s)
- Sabyrkhan M Barmak
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Yuriy A Sinyavskiy
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Aidar B Berdygaliev
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Turegeldy Sh Sharmanov
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Gulmira T Sultankulova
- Department of Pediatric Surgery, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Dilyar N Tuigunov
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Elena V Zholdybayeva
- National scientific shared laboratory of biotechnology, National Center for Biotechnology, Astana, Kazakhstan
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Kyndt JA, Bryantseva IA, Gorlenko VM, F. Imhoff J. Genome of Lamprobacter modestohalophilus ShN Lb02, a moderate halophilic photosynthetic purple bacterium of the Chromatiaceae family. Microbiol Resour Announc 2024; 13:e0012824. [PMID: 38526090 PMCID: PMC11008149 DOI: 10.1128/mra.00128-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/10/2024] [Indexed: 03/26/2024] Open
Abstract
The genome sequence of the moderately halophilic Lamprobacter modestohalophilus ShNLb02 was compared to those of other Lamprobacter and Halochromatium species. It revealed an average nucleotide identity of 94% to Lpb. modestohalophilus DSM 25653 and of 89.7% to Halochromatium roseum DSM 18859, underscoring their close phylogenetic relationship.
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Affiliation(s)
- John A. Kyndt
- College of Science and Technology, Bellevue University, Bellevue, Nebraska, USA
| | - Irina A. Bryantseva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir M. Gorlenko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Wang J, Sun S, Chen D, Gao C, Sang L, Xie X. Pathogenic and genomic characterization of rabbit-sourced Pasteurella multocida serogroup F isolates recovered from dead rabbits with respiratory disease. Microbiol Spectr 2024; 12:e0365423. [PMID: 38385714 DOI: 10.1128/spectrum.03654-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Pasteurella multocida serogroup F can infect a number of animals. However, the pathogenicity and genomic features of this serogroup are still largely unknown. In the present study, the pathogenicity and genomic sequences of 19 rabbit-sourced P. multocida serogroup F isolates were determined. The 19 isolates were highly pathogenic for rabbits causing severe pathologic lesions and high mortality in inoculated rabbits. Nevertheless, the pathologic lesions in rabbits caused by the 19 isolates were distinct from those caused by the previously reported high-virulent serogroup F strains J-4103 (rabbit), P-4218 (turkey), and C21724H3km7 (chicken). Moreover, the 19 isolates were avirulent to white feather broilers. The genomes of the 19 isolates were determined to understand the pathogenicity of these isolates. The finding of a number of functional genes in the 19 isolates by comparison with the low-virulent rabbit-sourced serogroup F strain s4 might contribute to the high virulence of these isolates. Notably, polymorphisms were determined in the lipopolysaccharide outer core biosynthetic genes natC and gatF among the serogroup F strains of different hosts. However, the sequences of natC and gatF from rabbit-sourced strains (except for SD11) were identical, which might be responsible for the host specific of the 19 isolates. The observations and findings in this study would be helpful for the understanding of the pathogenicity variation and host predilection of P. multocida. IMPORTANCE The 19 rabbit-sourced Pasteurella multocida serogroup F isolates showing high virulence to rabbits were avirulent to the broilers. Notably, polymorphisms were determined in the lipopolysaccharide outer core biosynthetic genes natC and gatF among all serogroup F strains of different hosts. However, the sequences of natC and gatF from rabbit-sourced strains (except for SD11) were identical, which might be responsible for the host specific of the 19 isolates.
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Affiliation(s)
- Jinxiang Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Key Laboratory of Animal Genetics and Breeding, Fuzhou, Fujian, China
| | - Shikun Sun
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Key Laboratory of Animal Genetics and Breeding, Fuzhou, Fujian, China
| | - Dongjin Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Key Laboratory of Animal Genetics and Breeding, Fuzhou, Fujian, China
| | - Chenfang Gao
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Key Laboratory of Animal Genetics and Breeding, Fuzhou, Fujian, China
| | - Lei Sang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Key Laboratory of Animal Genetics and Breeding, Fuzhou, Fujian, China
| | - Xiping Xie
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
- Fujian Key Laboratory of Animal Genetics and Breeding, Fuzhou, Fujian, China
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Pozo G, Albuja-Quintana M, Larreátegui L, Gutiérrez B, Fuentes N, Alfonso-Cortés F, Torres MDL. First whole-genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies. G3 (Bethesda) 2024; 14:jkae014. [PMID: 38244218 PMCID: PMC10917520 DOI: 10.1093/g3journal/jkae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered [International union for conservation of nature (IUCN)]. It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are keys for the management of endangered species, but this requires a reference genome, which until now was unavailable for A. f. fusciceps. The present study reports the first whole-genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male, and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable with other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.
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Affiliation(s)
- Gabriela Pozo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
| | - Martina Albuja-Quintana
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Lizbeth Larreátegui
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
| | - Bernardo Gutiérrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Nathalia Fuentes
- Proyecto Washu/Fundación Naturaleza y Arte, Quito 170521, Ecuador
| | | | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito 170901, Ecuador
- Instituto Nacional de Biodiversidad (INABIO), Quito 170135, Ecuador
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Zhou Y, Luo G, Zhang A, Gao S, Tang Y, Du Z, Pan S. Genetic identification of familial hypercholesterolemia within whole genome sequences in 6820 newborns. Clin Genet 2024; 105:308-312. [PMID: 38018368 DOI: 10.1111/cge.14453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023]
Abstract
Familial hypercholesterolemia (FH) is defined as a monogenic disease, characterized by elevated low-density lipoprotein cholesterol (LDL-C) levels. FH remains underdiagnosed and undertreated in Chinese. We whole-genome sequenced 6820 newborns from Qingdao of China to investigate the FH-related gene (LDLR, APOB, PCSK9) mutation types, carrier ratio and genotype-phenotype correlation. In this study, the prevalence of FH in Qingdao of China was 0.47% (95% CI: 0.32%-0.66%). The plasma lipid levels of FH-related gene mutation carriers begin to increase as early as infant. T-CHO and LDL-C of FH infants was higher by 48.1% (p < 0.001) and 42.9% (p < 0.001) relative to non-FH infants. A total of 22 FH infants and their parent participate in further studies. The results indicated that FH infant parent noncarriers have the normal plasma lipid level, while T-CHO and LDL-C increased in FH infants and FH infant parent carriers, but no difference between the groups. This highlights the importance of genetic factors. In conclusion, the spectrum of FH-causing mutations in the newborns of Qingdao, China was described for the first time. These data can serve as a considerable dataset for next-generation sequencing analysis of the Chinese population with FH and potentially helping reform regional policies for early detection and prevention of FH.
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Affiliation(s)
- Yingchao Zhou
- Genetic Testing center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Gang Luo
- Heart Center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Ai Zhang
- Fetal Medicine Center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Shuai Gao
- Heart Center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Yaqi Tang
- Heart Center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Zhanhui Du
- Heart Center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Silin Pan
- Heart Center, Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
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Cardim Falcao R, Edwards MR, Hurst M, Fraser E, Otterstatter M. A Review on Microbiological Source Attribution Methods of Human Salmonellosis: From Subtyping to Whole-Genome Sequencing. Foodborne Pathog Dis 2024; 21:137-146. [PMID: 38032610 PMCID: PMC10924193 DOI: 10.1089/fpd.2023.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Salmonella is one of the main causes of human foodborne illness. It is endemic worldwide, with different animals and animal-based food products as reservoirs and vehicles of infection. Identifying animal reservoirs and potential transmission pathways of Salmonella is essential for prevention and control. There are many approaches for source attribution, each using different statistical models and data streams. Some aim to identify the animal reservoir, while others aim to determine the point at which exposure occurred. With the advance of whole-genome sequencing (WGS) technologies, new source attribution models will greatly benefit from the discriminating power gained with WGS. This review discusses some key source attribution methods and their mathematical and statistical tools. We also highlight recent studies utilizing WGS for source attribution and discuss open questions and challenges in developing new WGS methods. We aim to provide a better understanding of the current state of these methodologies with application to Salmonella and other foodborne pathogens that are common sources of illness in the poultry and human sectors.
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Affiliation(s)
- Rebeca Cardim Falcao
- British Columbia Centre for Disease Control, Vancouver, Canada
- School of Population and Public Health, The University of British Columbia, Vancouver, Canada
| | - Megan R Edwards
- British Columbia Centre for Disease Control, Vancouver, Canada
- School of Population and Public Health, The University of British Columbia, Vancouver, Canada
| | - Matt Hurst
- Public Health Agency of Canada, Guelph, Canada
| | - Erin Fraser
- British Columbia Centre for Disease Control, Vancouver, Canada
- School of Population and Public Health, The University of British Columbia, Vancouver, Canada
| | - Michael Otterstatter
- British Columbia Centre for Disease Control, Vancouver, Canada
- School of Population and Public Health, The University of British Columbia, Vancouver, Canada
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Kang YR, Kim N, Lee Y, Park J, Kang HY, Lee JY, Woo SJ, Kim A, Kim SJ, Kim MS, Cho M, Kim DH. Draft genome sequence of multiple antibiotic-resistant Vibrio harveyi isolated from diseased olive flounder ( Paralichthys olivaceus) farmed in South Korea. Microbiol Resour Announc 2024; 13:e0088623. [PMID: 38189311 PMCID: PMC10868284 DOI: 10.1128/mra.00886-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
Vibrio harveyi strain 22FBVib0145 was isolated from a diseased olive flounder farmed in Jeju, Korea. Here, we report the draft genome sequence of this strain. It is 6,238,277 bp in length with a G + C content of 44.8%.
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Affiliation(s)
- Yu-Ra Kang
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Nameun Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Yoonhang Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Jiyeon Park
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Hyo-Young Kang
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Ju-yeop Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Soo Ji Woo
- Aquaculture Industry Research Division, East Sea Fisheries Research Institute, National Institute of Fisheries Science, Gangneung, South Korea
| | - Ahran Kim
- Pathology Division, National Institute of Fisheries Science, Busan, South Korea
| | - Soo-Jin Kim
- Pathology Division, National Institute of Fisheries Science, Busan, South Korea
| | - Myoung Sug Kim
- Pathology Division, National Institute of Fisheries Science, Busan, South Korea
| | - Miyoung Cho
- Pathology Division, National Institute of Fisheries Science, Busan, South Korea
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
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Li Y, Chen S, Yu Z, Yao J, Jia Y, Liao C, Chen J, Wei Y, Guo R, He L, Ding K. A Novel Bacillus Velezensis for Efficient Degradation of Zearalenone. Foods 2024; 13:530. [PMID: 38397507 PMCID: PMC10888444 DOI: 10.3390/foods13040530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Zearalenone (ZEN) is considered one of the most serious mycotoxins contaminating grains and their by-products, causing significant economic losses in the feed and food industries. Biodegradation pathways are currently considered the most efficient solution to remove ZEN contamination from foods. However, low degradation rates and vulnerability to environmental impacts limit the application of biodegradation pathways. Therefore, the main research objective of this article was to screen strains that can efficiently degrade ZEN and survive under harsh conditions. This study successfully isolated a new strain L9 which can efficiently degrade ZEN from 108 food ingredients. The results of sequence alignment showed that L9 is Bacillus velezensis. Meanwhile, we found that the L9 degradation rate reached 91.14% at 24 h and confirmed that the primary degradation mechanism of this strain is biodegradation. The strain exhibits resistance to high temperature, acid, and 0.3% bile salts. The results of whole-genome sequencing analysis showed that, it is possible that the strain encodes the key enzyme, such as chitinase, carboxylesterases, and lactone hydrolase, that work together to degrade ZEN. In addition, 227 unique genes in this strain are primarily involved in its replication, recombination, repair, and protective mechanisms. In summary, we successfully excavated a ZEN-degrading, genetically distinct strain of Bacillus velezensis that provides a solid foundation for the detoxification of feed and food contamination in the natural environment.
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Affiliation(s)
- Yijia Li
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Songbiao Chen
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, China
| | - Zuhua Yu
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Jie Yao
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Yanyan Jia
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, China
| | - Chengshui Liao
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Jian Chen
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Ying Wei
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Rongxian Guo
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Lei He
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Ke Ding
- Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China; (Y.L.); (S.C.); (Z.Y.); (J.Y.); (Y.J.); (C.L.); (J.C.); (Y.W.); (R.G.); (L.H.)
- Laboratory of Functional Microbiology and Animal Health, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450000, China
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9
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Rudd Garces G, Letko A, Häfliger IM, Müller J, Herden C, Nesseler A, Wagner H, Schmidt MJ, Drögemüller C, Lühken G. MFSD2A frameshift variant in Kerry Hill sheep with microcephaly. Anim Genet 2024; 55:152-157. [PMID: 37921236 DOI: 10.1111/age.13374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Microcephaly is a rare neurodevelopmental disorder characterized by reduced skull circumference and brain volume that occurs sporadically in farm animals. We investigated an early-onset neurodegenerative disorder observed in seven lambs of purebred Kerry Hill sheep. Clinical signs included inability to stand or severe ataxia, convulsions, and early death. Diagnostic imaging and brain necropsy confirmed microcephaly. The pedigree of the lambs suggested monogenic autosomal recessive inheritance. We sequenced the genome of one affected lamb, and comparison with 115 control genomes revealed a single private protein-changing variant. This frameshift variant, MFSD2A: c.285dupA, p.(Asp96fs*9), represents a 1-bp duplication predicted to truncate 80% of the open reading frame. MFSD2A is a transmembrane protein that is essential for maintaining blood-brain barrier homeostasis and plays a key role in regulating brain lipogenesis. Human MFSD2A pathogenic variants are associated with a neurodevelopmental disorder with progressive microcephaly, spasticity, and brain imaging abnormalities (NEDMISBA, OMIM 616486). Here we present evidence for the occurrence of a recessively inherited form of microcephaly in sheep due to a loss-of-function variant in MFSD2A (OMIA 002371-9940). To the best of our knowledge, this is the first report of a spontaneous MFSD2A variant in domestic animals.
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Affiliation(s)
- Gabriela Rudd Garces
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jana Müller
- Institute for Veterinary Pathology, Justus Liebig University Giessen, Giessen, Germany
| | - Christiane Herden
- Institute for Veterinary Pathology, Justus Liebig University Giessen, Giessen, Germany
- Center for Mind, Brain and Behavior, Justus Liebig University Giessen, Giessen, Germany
| | | | - Henrik Wagner
- Veterinary Clinic for Reproduction and Neonatology, Justus Liebig University, Giessen, Germany
| | - Martin J Schmidt
- Clinic for Small Animals, Neurosurgery, Neuroradiology and Clinical Neurology, Justus Liebig University Giessen, Giessen, Germany
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
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10
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Minhas S, Kashif M, Nisar H, Idrees M, Ansari F. Whole-genome analysis and evolutionary characterization of cervical and oral human papillomavirus 16. Exp Biol Med (Maywood) 2023; 248:2332-2340. [PMID: 38196081 PMCID: PMC10903243 DOI: 10.1177/15353702231211861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 08/24/2023] [Indexed: 01/11/2024] Open
Abstract
High-throughput genome-wide sequencing has revealed high genomic variability of HPV16 in different geographic regions which is the most predominant genotype in human papillomavirus (HPV)-associated malignancies. Analysis of the HPV16 by whole-genome sequence (WGS) is an advanced method for the identification of mutations in the genome. There is limited information about HPV16 diversity in Pakistan, especially at the genomic level. Till now, WGS for HPV16 has not been previously reported in Pakistan. The current study has sequenced three HPV16 viral genomes, from two cervical and one oral cavity positive sample of women presented with general gynecological problems without any evidence of precancerous or cancerous lesions using an ion ampliseq customized panel. Sequencing analysis detected 38 variations, including single-nucleotide polymorphisms (SNPs) and two Indels, across three samples with the highest number of SNPs present in E1, E2, and L2, respectively. A total of 20 non-synonymous and 11 synonymous mutations with amino acid substitutions (T1421C, G1515A, T2223C, T1389C, G1483A, and T2191C) were identified. The phylogenetic analysis revealed the genomes of HPV16 are closely associated with those reported from Thailand and the United States. These are the first HPV16 WGS from Pakistan. However, more research is needed with a large sample size from diversified areas to assess the carcinogenic consequences and impact of HPV vaccinations.
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Affiliation(s)
- Sadia Minhas
- Department of Microbiology, Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan
- Department of Oral Pathology, Akhtar Saeed Medical & Dental College Lahore, Lahore 54000, Pakistan
| | - Muhammad Kashif
- Department of Oral Pathology, Bakhtawar Amin Medical & Dental College, Multan 60000, Pakistan
| | - Haseeb Nisar
- Department of Life Sciences, University of Management and Technology, Lahore 54000, Pakistan
| | - Muhammad Idrees
- Center of Excellence in Molecular Biology, The University of Punjab, Lahore 54000, Pakistan
| | - Farheen Ansari
- Department of Microbiology, Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan
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11
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Lu Y, Wang Z, Wang Y, Chen Y, Tang D, Yu H. Genomic Comparison of Two Species of Samsoniella with Other Genera in the Family Cordycipitaceae. J Fungi (Basel) 2023; 9:1146. [PMID: 38132747 PMCID: PMC10744563 DOI: 10.3390/jof9121146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/12/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023] Open
Abstract
Whole genomes of Samsoniella hepiali ICMM 82-2 and S. yunnanensis YFCC 1527 were sequenced and annotated, as well as compared with whole genome sequences of other species in the family Cordycipitaceae. S. hepiali ICMM 82-2, S. hepiali FENG and S. yunnanensis YFCC 1527 had 54, 57 and 58 putative secondary metabolite biosynthetic gene clusters, respectively. S. hepiali had one unique domain and S. yunnanensis YFCC 1527 six. Both S. hepiali and S. yunnanensis YFCC 1527 had curvupallide-B, fumosorinone and fujikurin putative biosynthetic gene clusters. C. javanica had biosynthetic gene clusters for fumonisin. The 14 genomes had common domains, namely A-P-C-P-C and KS-AT-DH-ER-KR-ACP. The A-P-C-P-C domain may be involved in the biosynthesis of dimethylcoprogen. The maximum likelihood and the Bayesian inference trees of KS-AT-DH-ER-KR-ACP were highly consistent with the multigene phylogenetic tree for the 13 species of Cordycipitaceae. This study facilitates the discovery of novel biologically active SMs from Cordycipitaceae using heterologous expression and gene knockdown methods.
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Affiliation(s)
- Yingling Lu
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, China; (Y.L.); (Z.W.); (Y.C.); (D.T.)
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China
| | - Zhiqin Wang
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, China; (Y.L.); (Z.W.); (Y.C.); (D.T.)
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China
| | - Yi Wang
- Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming 650201, China
| | - Yue Chen
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, China; (Y.L.); (Z.W.); (Y.C.); (D.T.)
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China
| | - Dexiang Tang
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, China; (Y.L.); (Z.W.); (Y.C.); (D.T.)
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China
| | - Hong Yu
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650504, China; (Y.L.); (Z.W.); (Y.C.); (D.T.)
- The International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming 650091, China
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12
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Tambong JT, Xu R, Fleitas MC, Wang L, Hubbard K, Kutcher R. Phylogenomic Insights on the Xanthomonas translucens Complex, and Development of a TaqMan Real-Time Assay for Specific Detection of pv. translucens on Barley. Phytopathology 2023; 113:2091-2102. [PMID: 37097305 DOI: 10.1094/phyto-01-23-0022-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The reemergence and spread of Xanthomonas translucens, the causal agent of bacterial leaf streak in cereal crops and wilt in turfgrass and forage species, is a concern to growers in the United States and Canada. The pathogen is seedborne and listed as an A2 quarantine organism by EPPO, making it a major constraint to international trade and exchange of germplasm. The pathovar concept of the X. translucens group is confusing due to overlapping of plant host ranges and specificity. Here, comparative genomics, phylogenomics, and 81 up-to-date bacterial core gene set (ubcg2) were used to assign the pathovars of X. translucens into three genetically and taxonomically distinct clusters. The study also showed that whole genome-based digital DNA-DNA hybridization unambiguously can differentiate the pvs. translucens and undulosa. Orthologous gene and proteome matrix analyses suggest that the cluster consisting of graminis, poae, arrhenatheri, phlei, and phleipratensis is very divergent. Whole-genome data were exploited to develop the first pathovar-specific TaqMan real-time PCR tool for detection of pv. translucens on barley. Specificity of the TaqMan assay was validated using 62 Xanthomonas and non-Xanthomonas strains as well as growth chamber-inoculated and naturally infected barley leaves. Sensitivity levels of 0.1 pg (purified DNA) and 23 CFUs per reaction (direct culture) compared favorably with other previously reported real-time PCR assays. The phylogenomics data reported here suggest that the clusters could constitute novel taxonomic units or new species. Finally, the pathovar-specific diagnostic tool will have significant benefits to growers and facilitate international exchange of barley germplasm and trade.
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Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Maria Constanza Fleitas
- Department of Plant Sciences & Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lipu Wang
- Department of Plant Sciences & Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Keith Hubbard
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Randy Kutcher
- Department of Plant Sciences & Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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13
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Xie Y, Shi L, Cheng K, Li Y, Yu S. Host Recognition and Specific Infection of Endomelanconiopsis endophytica during Early Infection. J Fungi (Basel) 2023; 9:1040. [PMID: 37888296 PMCID: PMC10607883 DOI: 10.3390/jof9101040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
Coevolution between the pathogen and host plant drives pathogenic effector diversity. However, the molecular mechanism behind host-specific pathogenesis remains to be explored. Here, we present a 43 Mb whole-genome sequence of Endomelanconiopsis endophytica strain LS29, a host-specific pathogen of the common subtropical tree Castanopsis fissa. We described its genome annotations and identified its effector candidates. By performing temporal transcriptome sequencing of E. endophytica on C. fissa during early infection, we found that E. endophytica repressed other microbes in order to attack the tissue of the host by producing antibiotics earlier than 24 h post-inoculation (hpi). Simultaneously, a variety of effectors were secreted to recognize the host plant, but most of them showed a significantly opposing expression regulation trend after 24 hpi, indicating that 24 hpi represents a key time point between host recognition and specific infection. Furthermore, a comparison of isoenzymes showed that only a few effectors were identified as specific effectors, which were involved in hydrolyzing the compounds of the plant cell wall and releasing fatty acids during the early infection of C. fissa. Our results determined host recognition timing and identified a specific catalog of effectors, which are crucial for revealing the molecular mechanism of host-specific pathogenesis.
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Affiliation(s)
- Yan Xie
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Liuqing Shi
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Keke Cheng
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yang Li
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Shixiao Yu
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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14
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Low A, Sheludchenko M, Cheng HE, Koh XQ, Lee JWJ. Complete genome sequences of butyrate producing Anaerostipes hadrus strains BA1 and GIF7 isolated from the terminal ileum of a healthy lean male. Microbiol Resour Announc 2023; 12:e0070123. [PMID: 37772842 PMCID: PMC10586101 DOI: 10.1128/mra.00701-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 08/24/2023] [Indexed: 09/30/2023] Open
Abstract
Anaerostipes hadrus strains BA1 and GIF7 were isolated from a healthy man. The complete genomes' sizes are 2,946,270 bp (BA1) and 2,907,308 bp (GIF7), with high average nucleotide identity (ANIb = 100%) and alignments ≥96.86% between strains. Conversely, both strains share 97.47% (ANIb) identity and ≤77.36% alignments to A. hadrus ATCC 29173T.
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Affiliation(s)
- Adrian Low
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6 Centre for Translational Medicine, Medical Drive, Singapore, Singapore
| | - Maxim Sheludchenko
- ASEAN Microbiome Nutrition Centre, National Neuroscience Institute, Jln Tan Tock Seng, Singapore, Singapore
| | - Huay Ee Cheng
- Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Kent Ridge Crescent, Singapore, Singapore
| | - Xiu Qi Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6 Centre for Translational Medicine, Medical Drive, Singapore, Singapore
| | - Jonathan Wei Jie Lee
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6 Centre for Translational Medicine, Medical Drive, Singapore, Singapore
- Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Kent Ridge Crescent, Singapore, Singapore
- Department of Medicine, Division of Gastroenterology & Hepatology, National University Hospital, Singapore, Singapore
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15
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Ahn S, Jhang SY, Ahn E, Ryu S, Yu J. Complete genome sequence of Pectobacterium brasiliense strain 21PCA_AGRO2 with antimicrobial resistance isolated from napa cabbage. Microbiol Resour Announc 2023; 12:e0006623. [PMID: 37676017 PMCID: PMC10586146 DOI: 10.1128/mra.00066-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/16/2023] [Indexed: 09/08/2023] Open
Abstract
We report a complete genome of Pectobacterium brasiliense strain 21PCA_AGRO2 isolated from napa cabbage, in which the genome consists of a circular chromosome comprising 4,919,671 bp with 4,399 coding DNA sequences, 22 rRNA genes, 77 tRNA genes, and 9 noncoding RNA genes.
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Affiliation(s)
- Sojin Ahn
- eGnome Inc., Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - So Yun Jhang
- eGnome Inc., Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Eunbyeol Ahn
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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16
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Jere KC, Chibwe I, Chaima D, Kasambala W, Mhango C, Bitilinyu-Bangoh J, Mvula B, Kipandula W, Kamng'ona AW, Steele AD, Chauma-Mwale A, Hungerford D, Kagoli M, Nyaga MM, Dube Q, French N, Cunliffe NA, Msefula CL, Chaguza C. Draft genomes of Aeromonas caviae from patients with cholera-like illness during the 2022-2023 cholera outbreak in Malawi. Microbiol Resour Announc 2023; 12:e0058023. [PMID: 37768056 PMCID: PMC10586119 DOI: 10.1128/mra.00580-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Aeromonas caviae is an increasingly recognized etiological agent of acute gastroenteritis. Here, we report five draft genomes of A. caviae isolated from suspected cholera cases during the 2022-2023 cholera outbreak in Malawi.
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Affiliation(s)
- Khuzwayo C. Jere
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Malawi-Liverpool-Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre, Malawi
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Innocent Chibwe
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - David Chaima
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Watipaso Kasambala
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - Chimwemwe Mhango
- Malawi-Liverpool-Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Joseph Bitilinyu-Bangoh
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - Bernard Mvula
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - Wakisa Kipandula
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Arox W. Kamng'ona
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - A. Duncan Steele
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
| | - Annie Chauma-Mwale
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - Daniel Hungerford
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Matthew Kagoli
- National Microbiology Reference Laboratory, Public Health Institute of Malawi, Lilongwe, Malawi
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, Free State, South Africa
| | - Queen Dube
- Malawi Ministry of Health, Lilongwe, Malawi
| | - Neil French
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Nigel A. Cunliffe
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, Merseyside, United Kingdom
| | - Chisomo L. Msefula
- NIHR Global Health Research Group on Gastrointestinal Infections, University of Liverpool, Liverpool, Merseyside, United Kingdom
- Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, YaleUniversity, New Haven, Connecticut, USA
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
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17
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Chebotar VK, Gancheva MS, Chizhevskaya EP, Keleinikova OV, Baganova ME, Zaplatkin AN, Husainov KA. Whole-genome sequence of Paenibacillus amylolyticus strain W018, isolated from Triticum aestivum L. seeds, obtained using nanopore sequencing. Microbiol Resour Announc 2023; 12:e0068723. [PMID: 37747250 PMCID: PMC10586160 DOI: 10.1128/mra.00687-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
In this study, we performed nanopore sequencing of the genome of Paenibacillus amylolyticus strain W018, isolated from the seeds of winter wheat, cv. Bezostaya 100. The genome size is 7.07 Mb, with a GC content of 45.8%, and contains 8,190 genes.
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Affiliation(s)
- Vladimir K. Chebotar
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
| | - Maria S. Gancheva
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, St. Petersburg, Russia
| | - Elena P. Chizhevskaya
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
| | - Oksana V. Keleinikova
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
| | - Maria E. Baganova
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
| | - Alexander N. Zaplatkin
- Laboratory of Microbial Technology, All-Russian Research Institute for Agricultural Microbiology, St. Petersburg, Pushkin, Russia
| | - Kharon A. Husainov
- Laboratory of Generic and Selection of Microorganisms, Chechen Research Institute of Agriculture, Chechen Republic, Russia
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18
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Zhao L, Yang C, Chen M, Zhang J, Kong M, Dong L, Gong J, Yang J, Pu J, Lu S, Jin D, Liu L, Wang S, Xu J. Marnyiella aurantia, gen. nov., sp. nov., a novel bacterial species of the family Weeksellaceae that could produce flexirubin type pigments. Int J Syst Evol Microbiol 2023; 73. [PMID: 37906507 DOI: 10.1099/ijsem.0.006020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
Abstract
Two Gram-stain-negative, non-spore-forming, rod-shaped, and obligately aerobic bacteria, designated strains CX-624T and cx-311, were isolated from soil samples in Qinghai Province, China. The two strains grew best at 28 °C on the plate with Tryptone soya agar (TSA). Cells formed circular, convex, translucent, smooth, and orange colonies with approximately 1.0 mm diameter after 2 days of incubation on TSA at 28 °C. The strains were oxidase-negative and catalase-positive. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0, and major polar lipids included phosphatidylethanolamine, an unidentified aminophospholipid, four unidentified lipids and an aminolipid. MK-6 was the sole menaquinone in strain CX-624T. Comparative analysis of the nearly full-length 16S rRNA gene sequences showed strains CX-624T and cx-311 were member of the family Weeksellaceae, with the highest similarity to Kaistella haifensis H38T (96.66 %), Epilithonimonas pallida DSM 18015T (96.59 %), and Chryseobacterium gambrini DSM 18014T (96.53 %). Both phylogenetic analysis of the 16S rRNA gene and 177 core genes revealed that strains CX-624T and cx-311 formed an independent clade. Average nucleotide identity values (< 72.64 %), average amino-acid identity values (<72.61 %) and digital DNA-DNA hybridization (< 21.10 %) indicated that the strains CX-624T and cx-311 should constitute a novel genus. The DNA G+C contents of strains CX-624T and cx-311 were 43.0 mol% and 42.7 mol%. According to the data obtained in this study, strain CX-624T represents a novel species belonging to a novel genus of the Weeksellaceae, for which the name Marnyiella aurantia gen. nov., sp. nov. is proposed. The type strain is CX-624T (=GDMCC 1.1714T = JCM 33925T).
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Affiliation(s)
- Lijun Zhao
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Caixin Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Mengshan Chen
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Zhang
- Marine College, Shandong University, Weihai, PR China
| | - Mimi Kong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lingzhi Dong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jian Gong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
| | - Suping Wang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
| | - Jianguo Xu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi Province 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Institute of Public Health, Nankai University, Tianjin 300350, PR China
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19
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Kumar S, Agyeman-Duah E, Ujor VC. Whole-Genome Sequence and Fermentation Characteristics of Enterobacter hormaechei UW0SKVC1: A Promising Candidate for Detoxification of Lignocellulosic Biomass Hydrolysates and Production of Value-Added Chemicals. Bioengineering (Basel) 2023; 10:1090. [PMID: 37760192 PMCID: PMC10525534 DOI: 10.3390/bioengineering10091090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Enterobacter hormaechei is part of the Enterobacter cloacae complex (ECC), which is widespread in nature. It is a facultative Gram-negative bacterium of medical and industrial importance. We assessed the metabolic and genetic repertoires of a new Enterobacter isolate. Here, we report the whole-genome sequence of a furfural- and 5-hydroxymethyl furfural (HMF)-tolerant strain of E. hormaechei (UW0SKVC1), which uses glucose, glycerol, xylose, lactose and arabinose as sole carbon sources. This strain exhibits high tolerance to furfural (IC50 = 34.2 mM; ~3.3 g/L) relative to Escherichia coli DH5α (IC50 = 26.0 mM; ~2.5 g/L). Furfural and HMF are predominantly converted to their less-toxic alcohols. E. hormaechei UW0SKVC1 produces 2,3-butanediol, acetoin, and acetol, among other compounds of industrial importance. E. hormaechei UW0SKVC1 produces as high as ~42 g/L 2,3-butanediol on 60 g/L glucose or lactose. The assembled genome consists of a 4,833,490-bp chromosome, with a GC content of 55.35%. Annotation of the assembled genome revealed 4586 coding sequences and 4516 protein-coding genes (average length 937-bp) involved in central metabolism, energy generation, biodegradation of xenobiotic compounds, production of assorted organic compounds, and drug resistance. E. hormaechei UW0SKVC1 shows considerable promise as a biocatalyst and a genetic repository of genes whose protein products may be harnessed for the efficient bioconversion of lignocellulosic biomass, abundant glycerol and lactose-replete whey permeate to value-added chemicals.
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Affiliation(s)
| | | | - Victor C. Ujor
- Metabolic Engineering and Fermentation Science Group, Department of Food Science, University of Wisconsin-Madison, Babcock Hall, 1605 Linden Drive, Madison, WI 53706, USA; (S.K.); (E.A.-D.)
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20
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Ankhanbaatar U, Auer A, Ulziibat G, Settypalli TBK, Gombo-Ochir D, Basan G, Takemura T, Tseren-Ochir EO, Ouled Ahmed H, Meki IK, Datta S, Soumare B, Metlin A, Cattoli G, Lamien CE. Comparison of the Whole-Genome Sequence of the African Swine Fever Virus from a Mongolian Wild Boar with Genotype II Viruses from Asia and Europe. Pathogens 2023; 12:1143. [PMID: 37764951 PMCID: PMC10536492 DOI: 10.3390/pathogens12091143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
African swine fever (ASF) is a highly contagious and severe viral hemorrhagic disease in domestic and wild pigs. ASF seriously affects the global swine industry as the mortality rate can reach 100% with highly virulent strains. In 2007, ASF was introduced into the Caucasus and spread to Russia and later into other European and Asian countries. This study reported the first whole-genome sequence (WGS) of the ASF virus (ASFV) that was detected in a Mongolian wild boar. This sequence was then compared to other WGS samples from Asia and Europe. Results show that the ASFV Genotype II from Mongolia is similar to the Asian Genotype II WGS. However, there were three nucleotide differences found between the Asian and European genome sequences, two of which were non-synonymous. It was also observed that the European Genotype II ASFV WGS was more diverse than that of the Asian counterparts. The study demonstrates that the ASFV Genotype II variants found in wild boars and domestic pigs are highly similar, suggesting these animals might have had direct or indirect contact, potentially through outdoor animal breeding. In conclusion, this study provides a WGS and mutation spectrum of the ASFV Genotype II WGS in Asia and Europe and thus provides important insights into the origin and spread of ASFV in Mongolia.
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Affiliation(s)
- Ulaankhuu Ankhanbaatar
- Laboratory of Viral Animal Diseases Diagnostic and Surveillance, State Central Veterinary Laboratory, Ulaanbaatar 17029, Mongolia
- School of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar 17029, Mongolia
| | - Agathe Auer
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre for Nuclear Applications in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Friedenstrasse 1, 2444 Seibersdorf, Austria
- Food and Agriculture Organization of the United Nations (FAO-UN), Viale delle Terme di Caracalla, 00153 Rome, Italy
| | - Gerelmaa Ulziibat
- Laboratory of Viral Animal Diseases Diagnostic and Surveillance, State Central Veterinary Laboratory, Ulaanbaatar 17029, Mongolia
| | - Tirumala B. K. Settypalli
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre for Nuclear Applications in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Friedenstrasse 1, 2444 Seibersdorf, Austria
| | - Delgerzul Gombo-Ochir
- Laboratory of Viral Animal Diseases Diagnostic and Surveillance, State Central Veterinary Laboratory, Ulaanbaatar 17029, Mongolia
| | - Ganzorig Basan
- Laboratory of Viral Animal Diseases Diagnostic and Surveillance, State Central Veterinary Laboratory, Ulaanbaatar 17029, Mongolia
| | - Taichiro Takemura
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre for Nuclear Applications in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Friedenstrasse 1, 2444 Seibersdorf, Austria
| | | | - Hatem Ouled Ahmed
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre for Nuclear Applications in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Friedenstrasse 1, 2444 Seibersdorf, Austria
| | - Irene Kasindi Meki
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre for Nuclear Applications in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Friedenstrasse 1, 2444 Seibersdorf, Austria
| | - Sneha Datta
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre for Nuclear Applications in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Friedenstrasse 1, 2444 Seibersdorf, Austria
| | - Baba Soumare
- Food and Agriculture Organization of the United Nations (FAO-UN), Viale delle Terme di Caracalla, 00153 Rome, Italy
| | - Artem Metlin
- Food and Agriculture Organization of the United Nations (FAO-UN), Viale delle Terme di Caracalla, 00153 Rome, Italy
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre for Nuclear Applications in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Friedenstrasse 1, 2444 Seibersdorf, Austria
| | - Charles E. Lamien
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre for Nuclear Applications in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Friedenstrasse 1, 2444 Seibersdorf, Austria
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21
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Wang BH, Du LF, Zhang MZ, Xia LY, Li C, Lin ZT, Wang N, Gao WY, Ye RZ, Liu JY, Han XY, Shi WQ, Shi XY, Jiang JF, Jia N, Cui XM, Zhao L, Cao WC. Genomic Characterization of Theileria luwenshuni Strain Cheeloo. Microbiol Spectr 2023; 11:e0030123. [PMID: 37260375 PMCID: PMC10434005 DOI: 10.1128/spectrum.00301-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
Theileria, a tick-borne intracellular protozoan, can cause infections of various livestock and wildlife around the world, posing a threat to veterinary health. Although more and more Theileria species have been identified, genomes have been available only from four Theileria species to date. Here, we assembled a whole genome of Theileria luwenshuni, an emerging Theileria, through next-generation sequencing of purified erythrocytes from the blood of a naturally infected goat. We designated it T. luwenshuni str. Cheeloo because its genome was assembled by the researchers at Cheeloo College of Medicine, Shandong University, China. The genome of T. lunwenshuni str. Cheeloo was the smallest in comparison with the other four Theileria species. T. luwenshuni str. Cheeloo possessed the fewest gene gains and gene family expansion. The protein count of each category was always comparable between T. luwenshuni str. Cheeloo and T. orientalis str. Shintoku in the Eukaryote Orthologs annotation, though there were remarkable differences in genome size. T. luwenshuni str. Cheeloo had lower counts than the other four Theileria species in most categories at level 3 of Gene Ontology annotation. Kyoto Encyclopedia of Genes and Genomes annotation revealed a loss of the c-Myb in T. luwenshuni str. Cheeloo. The infection rate of T. luwenshuni str. Cheeloo was up to 81.5% in a total of 54 goats from three flocks. The phylogenetic analyses based on both 18S rRNA and cox1 genes indicated that T. luwenshuni had relatively low diversity. The first characterization of the T. luwenshuni genome will promote better understanding of the emerging Theileria. IMPORTANCE Theileria has led to substantial economic losses in animal husbandry. Whole-genome sequencing data of the genus Theileria are currently limited, which has prohibited us from further understanding their molecular features. This work depicted whole-genome sequences of T. luwenshuni str. Cheeloo, an emerging Theileria species, and reported a high prevalence of T. luwenshuni str. Cheeloo infection in goats. The first assembly and characterization of T. luwenshuni genome will benefit exploring the infective and pathogenic mechanisms of the emerging Theileria to provide scientific basis for future control strategies of theileriosis.
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Affiliation(s)
- Bai-Hui Wang
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Li-Feng Du
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Ming-Zhu Zhang
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Luo-Yuan Xia
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Cheng Li
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Zhe-Tao Lin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Ning Wang
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Wan-Ying Gao
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Run-Ze Ye
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Jin-Yue Liu
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Xiao-Yu Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Wen-Qiang Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Xiao-Yu Shi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
| | - Wu-Chun Cao
- Institute of EcoHealth, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
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22
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Obata S, Hisatsune J, Kawasaki H, Fukushima-Nomura A, Ebihara T, Arai C, Masuda K, Kutsuno S, Iwao Y, Sugai M, Amagai M, Tanese K. Comprehensive Genomic Characterization of Staphylococcus aureus Isolated from Atopic Dermatitis Patients in Japan: Correlations with Disease Severity, Eruption Type, and Anatomical Site. Microbiol Spectr 2023; 11:e0523922. [PMID: 37432109 PMCID: PMC10434064 DOI: 10.1128/spectrum.05239-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/12/2023] [Indexed: 07/12/2023] Open
Abstract
Atopic dermatitis (AD) shows frequent recurrence. Staphylococcus aureus is the primary microbial component in AD and is associated with disease activity. However, traditional typing methods have failed to characterize virulent AD isolates at the clone level. We conducted a comprehensive genomic characterization of S. aureus strains isolated from the skin of AD patients and healthy donors, comparing the whole-genome sequences of the 261 isolates with anatomical and lesional (AD-A)/nonlesional (AD-NL)/healthy sites, eruption types, clinical scores, virulence, and antimicrobial resistance gene repertoires in Japan. Sequence type (ST) diversity was lost with worsening disease activity; ST188 was the most frequently detected ST in AD-A and had the strongest correlation with AD according to the culture rate and proportion with worsening disease activity. ST188 and ST20 isolates inhabited all skin conditions, with significantly higher proportions in AD skin than in healthy skin. ST8, ST15, and ST5 proportions were equivalent for all skin conditions; ST30 was detected only in healthy skin; and ST12 was detected only in AD skin. ST97 detected in AD-A and healthy skin was clearly branched into two subclades, designated ST97A and ST97H. A comparison of two genomes led to the discovery that only ST97A possessed the complete trp operon, enabling bacterial survival without exogenous tryptophan (Trp) on AD skin, where the Trp level was significantly reduced. Primary STs showing an AD skin inhabitation trend (ST188, ST97A, ST20, and ST12) were all trp operon positive. The predominant clones (ST188 and ST97) possessed almost no enterotoxin genes, no mecA gene, and few other antimicrobial resistance genes, different from the trend observed in Europe/North America. IMPORTANCE While Staphylococcus aureus is a member of the normal human skin flora, its strong association with the onset of atopic dermatitis (AD) has been suggested. However, previous studies failed to assign specific clones relevant to disease activities. Enterotoxins produced by S. aureus have been suggested to aggravate and exacerbate the inflammation of AD skin, but their role remains ambiguous. We conducted a nuanced comprehensive characterization of isolates from AD patients and healthy donors, comparing the whole-genome sequences of the isolates with anatomical and lesional/nonlesional/healthy sites, eruption types, clinical scores, virulence, and antimicrobial resistance gene repertoires in Japan. We demonstrate that specific clones are associated with disease severity and clinical manifestations, and the dominant clones are devoid of enterotoxin genes and antimicrobial resistance genes. These findings undermine the established notion of the pathophysiological function of S. aureus associated with AD and introduce a new concept of S. aureus colonization in AD.
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Affiliation(s)
- Shoko Obata
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Junzo Hisatsune
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Kawasaki
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Tamotsu Ebihara
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | - Chika Arai
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Kanako Masuda
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Shoko Kutsuno
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasuhisa Iwao
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keiji Tanese
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
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23
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Damborg P, Pirolo M, Schøn Poulsen L, Frimodt-Møller N, Guardabassi L. Dogs Can Be Reservoirs of Escherichia coli Strains Causing Urinary Tract Infection in Human Household Contacts. Antibiotics (Basel) 2023; 12:1269. [PMID: 37627689 PMCID: PMC10451620 DOI: 10.3390/antibiotics12081269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/06/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
This study aimed to investigate the role played by pets as reservoirs of Escherichia coli strains causing human urinary tract infections (UTIs) in household contacts. Among 119 patients with community-acquired E. coli UTIs, we recruited 19 patients who lived with a dog or a cat. Fecal swabs from the household pet(s) were screened by antimicrobial selective culture to detect E. coli displaying the resistance profile of the human strain causing UTI. Two dogs shed E. coli isolates indistinguishable from the UTI strain by pulsed-field gel electrophoresis. Ten months later, new feces from these dogs and their owners were screened selectively and quantitatively for the presence of the UTI strain, followed by core-genome phylogenetic analysis of all isolates. In one pair, the resistance phenotype of the UTI strain occurred more frequently in human (108 CFU/g) than in canine feces (104 CFU/g), and human fecal isolates were more similar (2-7 SNPs) to the UTI strain than canine isolates (83-86 SNPs). In the other pair, isolates genetically related to the UTI strain (23-40 SNPs) were only detected in canine feces (105 CFU/g). These results show that dogs can be long-term carriers of E. coli strains causing UTIs in human household contacts.
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Affiliation(s)
- Peter Damborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (P.D.); (M.P.); (L.S.P.)
| | - Mattia Pirolo
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (P.D.); (M.P.); (L.S.P.)
| | - Laura Schøn Poulsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (P.D.); (M.P.); (L.S.P.)
| | | | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (P.D.); (M.P.); (L.S.P.)
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24
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Wu N, Wu Y, Chu Y, Ren Z, Li H, Rong C, Yang M, Jiang N, Jiang Y, Chen J, Zhang J, Tian S. The first rare case of Candida palmioleophila infection reported in China and its genomic evolution in a human host environment. Front Microbiol 2023; 14:1165721. [PMID: 37664129 PMCID: PMC10469324 DOI: 10.3389/fmicb.2023.1165721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/13/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Candida palmioleophila is a rare human pathogenic fungus, which has been poorly characterized at the genome level. In this study, we reported the first fatal case of C. palmioleophila infection in China and investigate the microevolution of C. palmioleophila in the human host environment. Methods A series of C. palmioleophila stains were collected from the patient at different time points for routine microbial and drug sensitivity testing. The first C. palmioleophila isolate 07202534 was identified by de novo whole genome sequencing. The in vitro and in vivo genetic evolutionary characteristics of C. palmioleophila were discussed based on the analysis of bioinformatics data. Results The six C. palmioleophila isolates displayed dose-dependent sensitivity to fluconazole. The C. palmioleophila genome contained homologous genes such as CDR1 and MDR1, which were recognized to be related to azole resistance. In addition, amino acid variation was detected at F105L and other important sites of ERG11. In addition, the mean divergence time between C. palmioleophila and Scheffersomyces stipites CBS 6054 was 406.04 million years, indicating that C. palmioleophila originated earlier than its closest relative. In addition, the six strains of C. palmioleophila isolated form the patient had higher homology and fewer mutation sites, which indicated the stability in C. palmioleophila genome. We also found that C. palmioleophila had a wide natural niche and may evolve slowly. Discussion We believe that this study will contribute to improve our understanding of the genetic evolution, pathogenicity, and drug resistance of C. palmioleophila and will aid in the prevention and control of its spread.
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Affiliation(s)
- Na Wu
- Department of Infectious Diseases, The First Hospital of China Medical University, Shenyang, China
| | - Yusheng Wu
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Yunzhuo Chu
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Zhihui Ren
- Department of Intensive Care Unit, Shenyang Fourth People’s Hospital of China Medical University, Shenyang, China
| | - Hailong Li
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Chen Rong
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Min Yang
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Ning Jiang
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Yanyan Jiang
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Jingjing Chen
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Jingping Zhang
- Department of Infectious Diseases, The First Hospital of China Medical University, Shenyang, China
| | - Sufei Tian
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
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25
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Romero-Calle DX, Pedrosa-Silva F, Ribeiro Tomé LM, Fonseca V, Guimarães Benevides R, de Oliveira Santos LTS, de Oliveira T, da Costa MM, Alcantara LCJ, de Carvalho Azevedo VA, Brenig B, Venancio TM, Billington C, Góes-Neto A. Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil. Microorganisms 2023; 11:1837. [PMID: 37513009 PMCID: PMC10384808 DOI: 10.3390/microorganisms11071837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance is increasing despite new treatments being employed, so novel strategies are required to ensure that bacterial infections remain treatable. Bacteriophages (phages; bacteria viruses) have the potential to be used as natural antimicrobial methods to control bacterial pathogens such as Salmonella spp. A Salmonella phage, Wara, was isolated from environmental water samples at the Subaé River Basin, Salvador de Bahia, Brazil. The basin has environmental impacts in its main watercourses arising from the dumping of domestic and industrial effluents and agricultural and anthropological activities. The phage genome sequence was determined by Oxford Nanopore Technologies (ONT) MinION and Illumina HiSeq sequencing, and assembly was carried out by Racon (MinION) and Unicycler (Illumina, Illumina + MinION). The genome was annotated and compared to other Salmonella phages using various bioinformatics approaches. MinION DNA sequencing combined with Racon assembly gave the best complete genome sequence. Phylogenetic analysis revealed that Wara is a member of the Tequintavirus genus. A lack of lysogeny genes, antimicrobial resistance, and virulence genes indicated that Wara has therapeutic and biocontrol potential against Salmonella species in healthcare and agriculture.
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Affiliation(s)
- Danitza Xiomara Romero-Calle
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana 44036-900, Brazil
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana 44036-900, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratory of Chemistry, Function of Proteins and Peptides, Center for Biosciences and Biotechnology, Darcy Ribeiro North Fluminense State University (UENF), Campos dos Goytacazes 28013-602, Brazil
| | - Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vagner Fonseca
- General Coordination of Public Health Laboratories/Secretariat of Health Surveillance, Ministry of Health, Brasília 70800-400, Brazil
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Raquel Guimarães Benevides
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana 44036-900, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana 44036-900, Brazil
| | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mateus Matiuzzi da Costa
- Department of Biological Sciences, Federal University of the São Francisco Valley, Petrolina 56304-917, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
- Flavivirus Laboratory, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, Brazil
| | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, 37073 Göttingen, Germany
| | - Thiago M Venancio
- Laboratory of Chemistry, Function of Proteins and Peptides, Center for Biosciences and Biotechnology, Darcy Ribeiro North Fluminense State University (UENF), Campos dos Goytacazes 28013-602, Brazil
| | - Craig Billington
- Health & Environment Group, Institute of Environmental Sciences and Research, Christchurch 8540, New Zealand
| | - Aristóteles Góes-Neto
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana 44036-900, Brazil
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana 44036-900, Brazil
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Zhao M, Liu K, Zhang Y, Li Y, Zhou N, Li G. Corrigendum: Probiotic characteristics and whole-genome sequence analysis of Pediococcus acidilactici isolated from the feces of adult beagles. Front Microbiol 2023; 14:1235657. [PMID: 37497539 PMCID: PMC10368231 DOI: 10.3389/fmicb.2023.1235657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 06/29/2023] [Indexed: 07/28/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2023.1179953.].
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Affiliation(s)
- Mengdi Zhao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Keyuan Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yuanyuan Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yueyao Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Ning Zhou
- Shandong Chongzhiyoupin Pet Food Co., Ltd., Weifang, China
| | - Guangyu Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
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Sengupta D, Botha G, Meintjes A, Mbiyavanga M, Hazelhurst S, Mulder N, Ramsay M, Choudhury A. Performance and accuracy evaluation of reference panels for genotype imputation in sub-Saharan African populations. Cell Genom 2023; 3:100332. [PMID: 37388906 PMCID: PMC10300601 DOI: 10.1016/j.xgen.2023.100332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 02/11/2023] [Accepted: 05/02/2023] [Indexed: 07/01/2023]
Abstract
Based on evaluations of imputation performed on a genotype dataset consisting of about 11,000 sub-Saharan African (SSA) participants, we show Trans-Omics for Precision Medicine (TOPMed) and the African Genome Resource (AGR) to be currently the best panels for imputing SSA datasets. We report notable differences in the number of single-nucleotide polymorphisms (SNPs) that are imputed by different panels in datasets from East, West, and South Africa. Comparisons with a subset of 95 SSA high-coverage whole-genome sequences (WGSs) show that despite being about 20-fold smaller, the AGR imputed dataset has higher concordance with the WGSs. Moreover, the level of concordance between imputed and WGS datasets was strongly influenced by the extent of Khoe-San ancestry in a genome, highlighting the need for integration of not only geographically but also ancestrally diverse WGS data in reference panels for further improvement in imputation of SSA datasets. Approaches that integrate imputed data from different panels could also lead to better imputation.
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Affiliation(s)
- Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerrit Botha
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ayton Meintjes
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Mamana Mbiyavanga
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Zhao M, Liu K, Zhang Y, Li Y, Zhou N, Li G. Probiotic characteristics and whole-genome sequence analysis of Pediococcus acidilactici isolated from the feces of adult beagles. Front Microbiol 2023; 14:1179953. [PMID: 37256049 PMCID: PMC10225567 DOI: 10.3389/fmicb.2023.1179953] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
The beneficial effects of lactic acid bacteria are well known and recognized as functional foods that are health benefits for companion animals. This study, for the first time, reports the probiotic properties, safety, and whole-genome sequence of Pediococcus acidilactici GLP06 isolated from feces of beagles. In this study, candidate probiotic bacteria P. acidilactici GLP02 and GLP06 were morphologically characterized and tested for their antimicrobial capacity, tolerance to different conditions (low pH, bile salts, an artificial gastrointestinal model, and high temperature), antibiotic sensitivity, hemolytic activity, cell surface hydrophobicity, autoaggregation activity, and adhesion to Caco-2 cells. P. acidilactici GLP06 showed better probiotic potential. Therefore, P. acidilactici GLP06 was evaluated for in vivo safety in mice and whole-genome sequencing. The results showed, that the supplemented MG06 group (1010 cfu/mL), GLP06 was not only nontoxic to mice, but also promoted the development of the immune system, improved resistance to oxidative stress, and increased the diversity of intestinal microorganisms and the abundance of Lactobacillus. Whole-genome sequencing showed that P. acidilactici GLP06 was 2,014,515 bp and contained 1,976 coding sequences, accounting for 86.12% of the genome, with no drug resistance genes and eight CRISPR sequences. In conclusion, the newly isolated canine-derived P. acidilactici GLP06 had good probiotic potential, was nontoxic to mice and promoted the development of immune organs, improved the biodiversity of the intestinal flora, and had no risk of drug-resistant gene transfer, indicating that P. acidilactici GLP06 can be used as a potential probiotic for the prevention and treatment of gastrointestinal diseases in companion animals.
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Affiliation(s)
- Mengdi Zhao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Keyuan Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yuanyuan Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yueyao Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Ning Zhou
- Shandong Chongzhiyoupin Pet Food Co., Ltd., Weifang, China
| | - Guangyu Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
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Peng Y, Jiang L, Jiang Y, Seo J, Jeon D, Kim YM, Li Z, Lee J. Gymnodinialimonas phycosphaerae sp. nov., a phycosphere bacterium isolated from Karlodinium veneficum. Int J Syst Evol Microbiol 2023; 73. [PMID: 37141117 DOI: 10.1099/ijsem.0.005874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
A facultative anaerobic, Gram-negative, non-motile, rod-shaped bacterial strain, designated N5T, was obtained from the phycosphere microbiota of the marine planktonic dinoflagellate, Karlodinium veneficum. Strain N5T showed growth on marine agar at 25 °C, pH 7 and 1 % (w/v) NaCl and produced a yellow colour. According to a phylogenetic study based on 16S rRNA gene sequences, strain N5T has a lineage within the genus Gymnodinialimonas. The G+C content in the genome of strain N5T is 62.9 mol% with a total length of 4 324 088 bp. The NCBI Prokaryotic Genome Annotation Pipeline revealed that the N5T genome contained 4230 protein-coding genes and 48 RNA genes, including a 5S rRNA, 16S rRNA, 23S rRNA, 42 tRNA, and three ncRNAs. Genome-based calculations (genome-to-genome distance, average nucleotide identity and DNA G+C content) clearly indicated that the isolate represents a novel species within the genus Gymnodinialimonas. The predominant fatty acids were C19 : 0 cyclo ω8c and feature 8 (comprising C18 : 1 ω6c and/or C18 : 1 ω7c). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The main respiratory quinone was Q-10. Based on its phenotypic, phylogenetic, genomic and chemotaxonomic features, strain N5T represents a novel species of the genus Gymnodinialimonas, for which the name Gymnodinialimonas phycosphaerae sp. nov. is proposed. The type strain is N5T (=KCTC 82362T=NBRC 114899T).
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Affiliation(s)
- Yuxin Peng
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Lingmin Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Yue Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jiyoon Seo
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Doeun Jeon
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Young-Min Kim
- Department of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Zhun Li
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- University of Science and Technology (UST), Yuseong, Daejeon 34113, Republic of Korea
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Aljohani RH, ElFeky DS, Alswaji AA, Alrashidi E, Okdah L, Alalwan B, Aljohani SM, Balkhy HH, Redhwan A, Alghoribi MF. Genomic Characterization of Uropathogenic Escherichia coli Isolates from Tertiary Hospitals in Riyadh, Saudi Arabia. Int J Mol Sci 2023; 24:7582. [PMID: 37108743 PMCID: PMC10141978 DOI: 10.3390/ijms24087582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infections (UTIs) in hospitalised and non-hospitalised patients. Genomic analysis was used to gain further insight into the molecular characteristics of UPEC isolates from Saudi Arabia. A total of 165 isolates were collected from patients with UTIs between May 2019 and September 2020 from two tertiary hospitals in Riyadh, Saudi Arabia. Identification and antimicrobial susceptibility testing (AST) were performed using the VITEK system. Extended-spectrum β-lactamase (ESBL)-producing isolates (n = 48) were selected for whole genome sequencing (WGS) analysis. In silico analysis revealed that the most common sequence types detected were ST131 (39.6%), ST1193 (12.5%), ST73 (10.4%), and ST10 (8.3%). Our finding showed that blaCTX-M-15 gene was detected in the majority of ESBL isolates (79.2%), followed by blaCTX-M-27 (12.5%) and blaCTX-M-8 (2.1%). ST131 carried blaCTX-M-15 or blaCTX-M-27, and all ST73 and ST1193 carried blaCTX-M-15. The relatively high proportion of ST1193 in this study was notable as a newly emerged lineage in the region, which warrants further monitoring.
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Affiliation(s)
- Rawan H. Aljohani
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
| | - Dalia S. ElFeky
- Department of Basic Medical Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo 12613, Egypt
| | - Abdulrahman A. Alswaji
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Eisa Alrashidi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Liliane Okdah
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Bassam Alalwan
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
| | - Sameera M. Aljohani
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 14611, Saudi Arabia
| | | | - Alya Redhwan
- Department of Health, College of Health and Rehabilitation Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
| | - Majed F. Alghoribi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 14611, Saudi Arabia
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Xie QP, Zhan W, Shi JZ, Liu F, Niu BL, He X, Liu M, Wang J, Liang QQ, Xie Y, Xu P, Wang X, Lou B. Whole-genome assembly and annotation for the little yellow croaker (Larimichthys polyactis) provide insights into the evolution of hermaphroditism and gonochorism. Mol Ecol Resour 2023; 23:632-658. [PMID: 36330680 DOI: 10.1111/1755-0998.13731] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 10/17/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
The evolutionary direction of gonochorism and hermaphroditism is an intriguing mystery to be solved. The special transient hermaphroditic stage makes the little yellow croaker (Larimichthys polyactis) an appealing model for studying hermaphrodite formation. However, the origin and evolutionary relationship between of L. polyactis and Larimichthys crocea, the most famous commercial fish species in East Asia, remain unclear. Here, we report the sequence of the L. polyactis genome, which we found is ~706 Mb long (contig N50 = 1.21 Mb and scaffold N50 = 4.52 Mb) and contains 25,233 protein-coding genes. Phylogenomic analysis suggested that L. polyactis diverged from the common ancestor, L. crocea, approximately 25.4 million years ago. Our high-quality genome assembly enabled comparative genomic analysis, which revealed several within-chromosome rearrangements and translocations, without major chromosome fission or fusion events between the two species. The dmrt1 gene was identified as the male-specific gene in L. polyactis. Transcriptome analysis showed that the expression of dmrt1 and its upstream regulatory gene (rnf183) were both sexually dimorphic. Rnf183, unlike its two paralogues rnf223 and rnf225, is only present in Larimichthys and Lates but not in other teleost species, suggesting that it originated from lineage-specific duplication or was lost in other teleosts. Phylogenetic analysis shows that the hermaphrodite stage in male L. polyactis may be explained by the sequence evolution of dmrt1. Decoding the L. polyactis genome not only provides insight into the genetic underpinnings of hermaphrodite evolution, but also provides valuable information for enhancing fish aquaculture.
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Affiliation(s)
- Qing-Ping Xie
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wei Zhan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian-Zhi Shi
- Novogene Bioinformatics Institute, Beijing, China
| | - Feng Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Bao-Long Niu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xue He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing, China
| | - Jing Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Qi-Qi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Yue Xie
- Novogene Bioinformatics Institute, Beijing, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA.,Alabama Agricultural Experiment Station, Auburn, Alabama, USA.,The HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Bao Lou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Beutler J, Li T, Roman-Reyna V, Fleitas MC, Bamrah R, Jacobs JM, Kutcher HR, Tambong JT, Brar GS. First Report of Bacterial Leaf Streak of Barley ( Hordeum vulgare) Caused by Xanthomonas translucens pv. translucens in British Columbia, Canada. Plant Dis 2023. [PMID: 36723957 DOI: 10.1094/pdis-09-22-2112-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Bacterial leaf streak (BLS) of barley is caused by the Gram-negative bacterial pathogen Xanthomonas translucens (Sapkota et al. 2020). In 2021, we observed multiple hill plots with BLS symptomatic plants in a barley stripe rust nursery in Vancouver, BC, Canada. We collected 29 leaf samples showing typical BLS symptoms (e.g. necrotic lesions; Fig. S1) and stored at 4 oC until bacterial isolation. Samples were surface-sterilized in 10% NaOCl for 20 sec and rinsed twice. About 1 cm2 of leaf tissue containing BLS characteristic lesions was macerated in 200 μL sterile H2O on a petri dish, incubated for 15 min, and 10 μl of the homogenates was streaked onto Wilbrink's - Boric Acid - Cephalexin (WBC) agar medium. Plates were incubated at 28-30 oC for 48 hrs. Four single colonies were obtained: BC10-1-2a (USask BC10-2a), BC10-1-2b (USask BC10-2b), UBC026 and UBC028. Colonies were grown in WBC broth and gDNA was extracted using E.Z.N.A. Bacterial DNA Kit (Omega Bio-Tek) or DNeasy Plant Pro Kit® (Qiagen) following manufacturer protocols. Genus-level identification was achieved using 16S rRNA sequencing with 27F/1492R primers (Lane 1991) of UBC026 (1,399 bp; NCBI # OP327375) and UBC028 (1,415 bp; NCBI #OP327376). Complete 16S rRNA sequences (1,533bp) of BC10-2a and BC10-2b (1,533 bp) were extracted from the draft whole-genome sequences (WGS) generated in this study. The 16S rRNA sequence homology values of 99.0-100% were recorded between the 4 strains. BLAST analyses of the 16S rRNA sequences to GenBank entries exhibited 99.5-100% similarity values (100% coverage) with the pathotype strains of Xtt DSM 18974T (LT604072) and X. translucens pv. undulosa (Xtu) CFBP 2055 (CP074361). Whole genomes of BC10-2a (JANUQY01) and BC10-2b (JANUQZ01) were sequenced (150-bp; reads 33.1 million; mean coverage 2125x) using NovaSeq Illumina, assembled (Unicycler v0.4.8; Wick et al. 2017) and analyzed to identify the strains to the species-level (Tambong et al. 2021). WGS of strains USask BC10-2a and USask BC10-2b exhibited genome-based DNA-DNA hybridization (dDDH; Meier-Kolthoff et al. 2013) and BLAST-based average nucleotide identity (ANIb; Richter et al. 2015) of 100%. The two strains also showed dDDH and ANIb of 90.4% (species-leel cut-off of 70%) and 98.780% and 98.80% (cut-off of 96%), respectively, with Xtt DSM 18974T (LT604072). In contrast, the WGS of BC10-2a and BC10-2b exhibited only 78.2% dDDH homology values with Xtu CFBP 2055T, suggesting that the strains are genetically more similar to Xtt. The assignment of these strains to Xtt is corroborated by phylogenomic analysis (Fig. S2; Meier-Kolthoff and Göker 2019) that showed the two strains clustering together (100% bootstrap) with the type strain DSM 18974T. These data suggest that these strains are taxonomically members of Xtt. Identification was also confirmed to the genus-level by LAMP assay using published X. translucens primers (Langlois et al. 2017). Pathovar-level identification was confirmed using a cbsA and S8.pep multiplex PCR diagnostic assay (Roman-Reyna et al. 2022). Koch's postulates were verified by greenhouse inoculation via leaf infiltration of UBC026 and UBC028 on 21-day old barley plants (line HB522) using an inoculum of 108 CFU ml-1 followed by re-isolation of the bacteria on WBC. The inoculated plants showed typical BLS symptoms similar to those observed in the field (Fig. S1). Water-inoculated plants had no symptoms. To our knowledge, this is the first published report of BLS of barley in British Columbia.
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Affiliation(s)
- Jonathan Beutler
- University of California, Plant Pathology, One Shields Avenue, Davis, California, United States, 95616
- The University of British Columbia, 8166, Faculty of Land and Food Systems, 2357 Main Mall, #214 Macmillan Building, Vancouver, British Columbia, Canada, V6J 2N6;
| | - Tiffany Li
- The University of British Columbia, 8166, Vancouver, British Columbia, Canada;
| | - Veronica Roman-Reyna
- Ohio State University, 2647, Department of Plant Pathology, 201 Kottman Hall, 2021 Coffey Rd, Columbus, Ohio, United States, 43210;
| | | | | | - Jonathan Michael Jacobs
- Ohio State University, 2647, Department of Plant Pathology, 2021 Coffey Road, 201C Kottman Hall, Columbus, Ohio, United States, 43210-1132
- United States;
| | - Hadley R Kutcher
- University of Saskatchewan College of Agriculture and Bioresources, 98627, Plant Sciences, 51 Campus Drive, Saskatoon, Saskatchewan, Canada, S7N 5A8;
| | - James T Tambong
- Agriculture & Agri-Food Canada, 960 carling Avenue, Ottawa, Ontario, Canada, K1A0C6;
| | - Gurcharn Singh Brar
- The University of British Columbia, 8166, Plant Sciences, 231-2357 Main Mall, H.R. MacMillan Building, Vancouver, British Columbia, Canada, V6T 1Z4;
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Mazloum A, van Schalkwyk A, Shotin A, Zinyakov N, Igolkin A, Chernishev R, Debeljak Z, Korennoy F, Sprygin AV. Whole-genome sequencing of African swine fever virus from wild boars in the Kaliningrad region reveals unique and distinguishing genomic mutations. Front Vet Sci 2023; 9:1019808. [PMID: 36686186 PMCID: PMC9849583 DOI: 10.3389/fvets.2022.1019808] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/30/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction Since the first report of outbreaks of African swine fever (ASF) in Georgia in 2007, the disease has expanded into Europe, Russia, and Asia, spreading rapidly via contact with infected animals including domestic pigs and wild boars. The vast expansion of this Genotype II African swine fever virus (ASFV) across wide-ranging territories and hosts inevitably led to the acquisition of novel mutations. These mutations could be used to track the molecular epidemiology of ASFV, provided that they are unique to strains restricted within a certain area. Whilst whole-genome sequencing remains the gold standard for examining evolutionary changes, sequencing of a single locus with significant variation and resolution power could be used as a rapid and cost-effective alternative to characterize multiple isolates from a single or related outbreak. Material and methods ASFVs obtained during active ASF outbreaks in the Russian region of Kaliningrad between 2017 and 2019 were examined. Since all of the viruses belonged to Genotype II and no clear differentiation based on central variable region (CVR) sequencing was observed, the whole-genome sequences of nine ASFV isolates from this region were determined. To obtain insights into the molecular evolution of these isolates, their sequences were compared to isolates from Europe, Asia, and Africa. Results Phylogenetic analysis based on the whole-genome sequences clustered the new isolates as a sister lineage to isolates from Poland and Germany. This suggests a possible shared origin followed by the addition of novel mutations restricted to isolates from this region. This status as a sister lineage was mirrored when analyzing polymorphisms in MGF-505-5R and MGF-110-7L, whilst a polymorphism unique to sequences from Kaliningrad was identified at locus K145R. This newly identified mutation was able to distinguish the isolates obtained from Kaliningrad with sequences of Genotype II ASFVs available on GenBank. Discussion The findings of this study suggest that ASFVs circulating in Kaliningrad have recently obtained this mutation providing an additional marker to the mutations previously described.
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Affiliation(s)
- Ali Mazloum
- Reference Laboratory for African Swine Fever Virus, FGBI “Federal Centre for Animal Health” (FGBI “ARRIAH”), Vladimir, Russia,*Correspondence: Ali Mazloum ✉
| | - Antoinette van Schalkwyk
- Agricultural Research Council - Onderstepoort Veterinary Institute, Pretoria, South Africa,Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Andrey Shotin
- Reference Laboratory for African Swine Fever Virus, FGBI “Federal Centre for Animal Health” (FGBI “ARRIAH”), Vladimir, Russia
| | - Nikolay Zinyakov
- Reference Laboratory for African Swine Fever Virus, FGBI “Federal Centre for Animal Health” (FGBI “ARRIAH”), Vladimir, Russia
| | - Alexey Igolkin
- Reference Laboratory for African Swine Fever Virus, FGBI “Federal Centre for Animal Health” (FGBI “ARRIAH”), Vladimir, Russia
| | - Roman Chernishev
- Reference Laboratory for African Swine Fever Virus, FGBI “Federal Centre for Animal Health” (FGBI “ARRIAH”), Vladimir, Russia
| | - Zoran Debeljak
- Department of Epizoology, Veterinary Specialist Institute “Kraljevo”, Kraljevo, Serbia
| | - Fedor Korennoy
- Reference Laboratory for African Swine Fever Virus, FGBI “Federal Centre for Animal Health” (FGBI “ARRIAH”), Vladimir, Russia
| | - Alexander V. Sprygin
- Reference Laboratory for African Swine Fever Virus, FGBI “Federal Centre for Animal Health” (FGBI “ARRIAH”), Vladimir, Russia
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Jackson N, Belmont CR, Tarlton NJ, Allegretti YH, Adams-Sapper S, Huang YY, Borges CA, Frazee BW, Florence-Petrovic D, Hufana C, Parker A, Mastrangelo CF, Awasthi S, Kane I, Coralic Z, Miller S, Diaz J, Fee C, Bittencourt CE, Garner O, Chandrasekaran S, Crandall C, Marcha JC, Noorbakhsh MH, Rodrigues-Wong P, deBoer TR, Riley LW. Genetic Predictive Factors for Nonsusceptible Phenotypes and Multidrug Resistance in Expanded-Spectrum Cephalosporin-Resistant Uropathogenic Escherichia coli from a Multicenter Cohort: Insights into the Phenotypic and Genetic Basis of Coresistance. mSphere 2022; 7:e0047122. [PMID: 36377882 DOI: 10.1128/msphere.00471-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance in urinary tract infections (UTIs) is a major public health concern. This study aims to characterize the phenotypic and genetic basis of multidrug resistance (MDR) among expanded-spectrum cephalosporin-resistant (ESCR) uropathogenic Escherichia coli (UPEC) causing UTIs in California patient populations. Between February and October 2019, 577 ESCR UPEC isolates were collected from patients at 6 clinical laboratory sites across California. Lineage and antibiotic resistance genes were determined by analysis of whole-genome sequence data. The lineages ST131, ST1193, ST648, and ST69 were predominant, representing 46%, 5.5%, 4.5%, and 4.5% of the collection, respectively. Overall, 527 (91%) isolates had an expanded-spectrum β-lactamase (ESBL) phenotype, with blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, and blaCTX-M-14 being the most prevalent ESBL genes. In the 50 non-ESBL phenotype isolates, 40 (62%) contained blaCMY-2, which was the predominant plasmid-mediated AmpC (pAmpC) gene. Narrow-spectrum β-lactamases, blaTEM-1B and blaOXA-1, were also found in 44.9% and 32.1% of isolates, respectively. Among ESCR UPEC isolates, isolates with an ESBL phenotype had a 1.7-times-greater likelihood of being MDR than non-ESBL phenotype isolates (P < 0.001). The cooccurrence of blaCTX-M-15, blaOXA-1, and aac(6')-Ib-cr within ESCR UPEC isolates was strongly correlated. Cooccurrence of blaCTX-M-15, blaOXA-1, and aac(6')-Ib-cr was associated with an increased risk of nonsusceptibility to piperacillin-tazobactam, cefepime, fluoroquinolones, and amikacin as well as MDR. Multivariate regression revealed the presence of blaCTX-M-55, blaTEM-1B, and the ST131 genotype as predictors of MDR. IMPORTANCE The rising incidence of resistance to expanded-spectrum cephalosporins among Escherichia coli strains, the most common cause of UTIs, is threatening our ability to successfully empirically treat these infections. ESCR E. coli strains are often MDR; therefore, UTI caused by these organisms often leads to treatment failure, increased length of hospital stay, and severe complications (D. G. Mark, Y.-Y. Hung, Z. Salim, N. J. Tarlton, et al., Ann Emerg Med 78:357-369, 2021, https://doi.org/10.1016/j.annemergmed.2021.01.003). Here, we performed an in-depth analysis of genetic factors of ESCR E. coli associated with coresistance and MDR. Such knowledge is critical to advance UTI diagnosis, treatment, and antibiotic stewardship.
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Cheng S, Fleres G, Chen L, Liu G, Hao B, Newbrough A, Driscoll E, Shields RK, Squires KM, Chu TY, Kreiswirth BN, Nguyen MH, Clancy CJ. Within-Host Genotypic and Phenotypic Diversity of Contemporaneous Carbapenem-Resistant Klebsiella pneumoniae from Blood Cultures of Patients with Bacteremia. mBio 2022; 13:e0290622. [PMID: 36445082 PMCID: PMC9765435 DOI: 10.1128/mbio.02906-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 12/02/2022] Open
Abstract
It is unknown whether bacterial bloodstream infections (BSIs) are commonly caused by single organisms or mixed microbial populations. We hypothesized that contemporaneous carbapenem-resistant Klebsiella pneumoniae (CRKP) strains from blood cultures of individual patients are genetically and phenotypically distinct. We determined short-read whole-genome sequences of 10 sequence type 258 (ST258) CRKP strains from blood cultures in each of 6 patients (Illumina HiSeq). Strains clustered by patient by core genome and pan-genome phylogeny. In 5 patients, there was within-host strain diversity by gene mutations, presence/absence of antibiotic resistance or virulence genes, and/or plasmid content. Accessory gene phylogeny revealed strain diversity in all 6 patients. Strains from 3 patients underwent long-read sequencing for genome completion (Oxford Nanopore) and phenotypic testing. Genetically distinct strains within individuals exhibited significant differences in carbapenem and other antibiotic responses, capsular polysaccharide (CPS) production, mucoviscosity, and/or serum killing. In 2 patients, strains differed significantly in virulence during mouse BSIs. Genetic or phenotypic diversity was not observed among strains recovered from blood culture bottles seeded with index strains from the 3 patients and incubated in vitro at 37°C. In conclusion, we identified genotypic and phenotypic variant ST258 CRKP strains from blood cultures of individual patients with BSIs, which were not detected by the clinical laboratory or in seeded blood cultures. The data suggest a new paradigm of CRKP population diversity during BSIs, at least in some patients. If validated for BSIs caused by other bacteria, within-host microbial diversity may have implications for medical, microbiology, and infection prevention practices and for understanding antibiotic resistance and pathogenesis. IMPORTANCE The long-standing paradigm for pathogenesis of bacteremia is that, in most cases, a single organism passes through a bottleneck and establishes itself in the bloodstream (single-organism hypothesis). In keeping with this paradigm, standard practice in processing positive microbiologic cultures is to test single bacterial strains from morphologically distinct colonies. This study is the first genome-wide analysis of within-host diversity of Klebsiella pneumoniae strains recovered from individual patients with bloodstream infections (BSIs). Our finding that positive blood cultures comprised genetically and phenotypically heterogeneous carbapenem-resistant K. pneumoniae strains challenges the single-organism hypothesis and suggests that at least some BSIs are caused by mixed bacterial populations that are unrecognized by the clinical laboratory. The data support a model of pathogenesis in which pressures in vivo select for strain variants with particular antibiotic resistance or virulence attributes and raise questions about laboratory protocols and treatment decisions directed against single strains.
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Affiliation(s)
- Shaoji Cheng
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Guojun Liu
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Binghua Hao
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | | | - Ryan K. Shields
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | - Ting-yu Chu
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Barry N. Kreiswirth
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - M. Hong Nguyen
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Cornelius J. Clancy
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
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Chen XF, Hou X, Zhang H, Jia XM, Ning LP, Cao W, Fan X, Huang JJ, Yang WH, Zhang G, Zhang JJ, Kang W, Xiao M, Xu YC. First two fungemia cases caused by Candida haemulonii var. vulnera in China with emerged antifungal resistance. Front Microbiol 2022; 13:1036351. [PMID: 36466633 PMCID: PMC9710277 DOI: 10.3389/fmicb.2022.1036351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/17/2022] [Indexed: 11/11/2022] Open
Abstract
Candida haemulonii var. vulnera is a rare variant of C. haemulonii, which has been previously reported to cause human infections. Owing to the close kinship between C. haemulonii sensu stricto and C. haemulonii var. vulnera, accurate identification of C. haemulonii var. vulnera relied on DNA sequencing assay targeting, for example, rDNA internal transcribed spacer (ITS) region. In this work, two strains of C. haemulonii var. vulnera were collected from the China Hospital Invasive Fungal Surveillance Net (CHIF-NET). The identification capacity of three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and VITEK 2 YST ID biochemical methods were evaluated against ITS sequencing. In addition, antifungal susceptibility testing was performed using Sensititre YeastOne. Moreover, we comprehensively screened drug-resistant related genes by whole-genome sequencing. The two strains were not correctly identified to species variant level using MALDI-TOF MS and YST ID cards. Both strains were resistant to amphotericin B (minimum inhibitory concentration [MIC] > 2 μg/ml). Moreover, strain F4564 and F4584 exhibited high MIC to fluconazole (>256 μg/ml) and 5-flucytosine (>64 μg/ml), respectively, which were supposed to result from key amino acid substitutions Y132F and G307A in Erg11p and V58fs and G60K substitutions in Fur1p. The rare species C. haemulonii var. vulnera has emerged in China, and such drug-resistant fungal species that can cause invasive diseases require further close attention.
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Affiliation(s)
- Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Xin Hou
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Han Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Xin-Miao Jia
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China,Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li-Ping Ning
- Department of Laboratory Medicine, No.908 Hospital of Joint Logistics Support Force, Nanchang, Jiangxi, China
| | - Wei Cao
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hubei, China
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jing-Jing Huang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Wen-Hang Yang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ge Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Jing-Jia Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Wei Kang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China,*Correspondence: Meng Xiao,
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China,Ying-Chun Xu,
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Brito BP, Koong J, Wozniak A, Opazo-Capurro A, To J, Garcia P, Hamidian M. Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Strains Recovered from Chilean Hospitals Reveals Lineages Specific to South America and Multiple Routes for Acquisition of Antibiotic Resistance Genes. Microbiol Spectr 2022; 10:e0246322. [PMID: 36154439 PMCID: PMC9602995 DOI: 10.1128/spectrum.02463-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/09/2022] [Indexed: 01/04/2023] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAb) is a public health threat accounting for a significant number of hospital-acquired infections. Despite the importance of this pathogen, there is scarce literature on A. baumannii molecular epidemiology and evolutionary pathways relevant to resistance emergence in South American strains. We analyzed the genomic context of 34 CRAb isolates recovered from clinical samples between 2010 and 2013 from two hospitals in Santiago, Chile, using whole-genome sequencing. Several Institut Pasteur scheme sequence types (STs) were identified among the 34 genomes studied here, including ST1, ST15, ST79, ST162, and ST109. No ST2 (the most widespread sequence type) strain was detected. Chilean isolates were phylogenetically closely related, forming lineages specific to South America (e.g., ST1, ST79, and ST15). The genomic contexts of the resistance genes were diverse: while genes were present in a plasmid in ST15 strains, all genes were chromosomal in ST79 strains. Different variants of a small Rep_3 plasmid played a central role in the acquisition of the oxa58 carbapenem and aacC2 aminoglycoside resistance genes in ST1, ST15, and ST79 strains. The aacC2 gene along with blaTEM were found in a novel transposon named Tn6925 here. Variants of Tn7 were also found to play an important role in the acquisition of the aadA1 and dfrA1 genes. This work draws a detailed picture of the genetic context of antibiotic resistance genes in a set of carbapenem-resistant A. baumannii strains recovered from two Chilean hospitals and reveals a complex evolutionary picture of antibiotic resistance gene acquisition events via multiple routes involving several mobile genetic elements. IMPORTANCE Treating infections caused by carbapenem-resistant A. baumannii (CRAb) has become a global challenge given that CRAb strains are also often resistant to a wide range of antibiotics. Analysis of whole-genome sequence data is now a standard approach for studying the genomic context of antibiotic resistance genes; however, genome sequence data from South American countries are scarce. Here, phylogenetic and genomic analyses of 34 CRAb strains recovered from 2010 to 2013 from two Chilean hospitals revealed a complex picture leading to the generation of resistant lineages specific to South America. From these isolates, we characterized several mobile genetic elements, some of which are described for the first time. The genome sequences and analyses presented here further our understanding of the mechanisms leading to multiple-drug resistance, extensive drug resistance, and pandrug resistance phenotypes in South America. Therefore, this is a significant contribution to elucidating the global molecular epidemiology of CRAb.
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Affiliation(s)
- Barbara P. Brito
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Jonathan Koong
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Aniela Wozniak
- Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Andres Opazo-Capurro
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Laboratorio de Investigación en Agentes Antibacterianos, Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Joyce To
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Patricia Garcia
- Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Mehrad Hamidian
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
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Zhang N, Tang Y, Yang X, Jin M, Chen J, Qin S, Liu F, Liu X, Guo J, Wang C, Chen Y. Genomic Evolution of ST11 Carbapenem-Resistant Klebsiella pneumoniae from 2011 to 2020 Based on Data from the Pathosystems Resource Integration Center. Genes (Basel) 2022; 13. [PMID: 36140792 DOI: 10.3390/genes13091624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/19/2022] Open
Abstract
(1) Objective: ST11 carbapenem-resistant Klebsiella pneumoniae (CRKP) is widespread throughout the world, and the mechanisms for the transmission and evolution of major serotypes, ST11-KL47 and ST11-KL64, were analyzed to investigate the global distribution and evolutionary characteristics of ST11 CRKP; (2) Methods: The Pathosystems Resource Integration Center (PATRIC) database was downloaded and all K. pneumoniae from 2011 to 2020 were screened to obtain ST11 CRKP genome assemblies with basic information. The relationship of serotype evolution between KL47 and KL64 was then investigated using statistical and bioinformatic analysis; (3) Results: In total, 386 ST11 CRKP isolates were included for analysis. Blood (31.09%, 120/386), respiratory tract (23.06%, 89/386), and feces (20.21%, 78/386) were the major sources of samples. China was the leading country where ST11 CRKP was isolated. KL47 and KL64 were found to be the most prevalent serotypes. ST11-KL64 CRKP [median 78(P25~P75: 72~79.25)] had remarkably more virulence genes than the KL47 [median 63(P25~P75: 63~69)], and the distinction was statistically significant (p < 0.001). A differential comparison of virulence genes between KL47 and KL64 revealed 35 differential virulence genes, including rmpA/rmpA2, iucABCD, iutA, etc. The comparison of the recombination of serotype-determining regions between the two serotypes revealed that KL64 CRKP carried more nucleotide sequences in the CD1-VR2-CD2 region than KL47 CRKP. More nucleotide sequences added approximately 303 base pairs (bp) with higher GC content (58.14%), which might facilitate the evolution of the serotype toward KL64; (4) Conclusions: KL47 and KL64 have become the predominant serotypes of ST11 CRKP. KL64 CRKP carries more virulence genes than KL47 and has increased by approximately 303 bp through recombinant mutations, thus facilitating the evolution of KL47 to KL64. Stricter infection prevention and control measures should be developed to deal with the epidemic transmission of ST11-KL64 CRKP.
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Nishu SD, No JH, Lee TK. Transcriptional Response and Plant Growth Promoting Activity of Pseudomonas fluorescens DR397 under Drought Stress Conditions. Microbiol Spectr 2022; 10:e0097922. [PMID: 35863006 PMCID: PMC9430913 DOI: 10.1128/spectrum.00979-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/23/2022] [Indexed: 11/20/2022] Open
Abstract
Drought is one of the most vulnerable factors that affect crop productivity. Little is known about plant-associated microbiomes and their functional roles in assisting plant growth under drought. We investigated the genetic and transcriptomic characteristics of opportunistic beneficial microorganisms that selectively alleviate stress through plant-bacteria interactions under drought. Pseudomonas fluorescens DR397 was isolated from the drought-prone rhizospheric soil of soybean and showed high metabolic activity at -1.25 Mpa. The genome of DR397 possesses several genes related to the synthesis of compatible solutes (choline and glycine-betaine), exopolysaccharides (alginate and cellulose), and secretion systems (type II, III, IV, and VI), as well as genes related to plant growth promotion (indole-3-acetic acid, transketolase, and thiamine phosphate synthesis). The expression of these genes was significantly upregulated (8- to 263-fold change) only under drought conditions with plant root exudate treatment, whereas subtle transcriptomic changes were observed under solely root exudate treatment. When DR397 was placed on both legume cultivars (Pisum sativum and Phaseolus vulgaris), growth was hardly affected under well-watered conditions, but the shoot and root growths were increased by up from 62.0% to 149.1% compared with the control group under drought conditions. These results provide fundamental insight on the plant-bacterial interactions that alleviate plant stress as an important ecological strategy for improving drought tolerance. IMPORTANCE Drought is a serious abiotic stress on plants as wells as the microbes that coexist with plants, which significantly lowers their fitness. The plant-bacterial interaction is an important strategy to enhance their fitness under drought. However, many knowledge gaps still exist in our understanding of transcriptomic features of bacteria interacting with plant under drought. Here, by investigating the transcriptomic profiles and pot cultivation with legume, we show that the interactions of Pseudomonas fluorescens DR397 with plants change with drought. We, therefore, provide a fundamental evidence of a hidden hero in the soil that promote plant fitness from external stress.
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Affiliation(s)
- Susmita Das Nishu
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Jee Hyun No
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
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Shi S, Shao D, Yang L, Liang Q, Han W, Xue Q, Qu L, Leng L, Li Y, Zhao X, Dong P, Walugembe M, Kayang BB, Muhairwa AP, Zhou H, Tong H. Whole Genome Analyses Reveal Novel Genes Associated with Chicken Adaptation to Tropical and Frigid Environments. J Adv Res 2022; 47:13-25. [PMID: 35907630 PMCID: PMC10173185 DOI: 10.1016/j.jare.2022.07.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Accepted: 07/17/2022] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION Investigating the genetic footprints of historical temperature selection can get insights to the local adaptation and feasible influences of climate change on long-term population dynamics. OBJECT Chicken is a significative species to study genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties. Yet, few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments. METHOD Here, we generated whole genome resequencing of 119 domesticated chickens in China including the following breeds which are in order of breeding environmental temperature from more tropical to more frigid: Wenchang chicken (WCC), green-shell chicken (GSC), Tibetan chicken (TBC), and Lindian chicken (LDC). RESULTS Our results showed WCC branched off earlier than LDC with an evident genetic admixture between WCC and LDC, suggesting their closer genetic relationship. Further comparative genomic analyses solute carrier family 33 member 1 (SLC33A1) and thyroid stimulating hormone receptor (TSHR) genes exhibited stronger signatures for positive selection in the genome of the more tropical WCC. Furthermore, genotype data from about 3,000 African local ecotypes confirmed that allele frequencies of single nucleotide polymorphisms (SNPs) in these 2 genes appeared strongly associated with tropical environment adaptation. In addition, the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) gene exhibited a strong signature for positive selection in the LDC genome, and SNPs with marked allele frequency differences indicated a significant relationship with frigid environment adaptation. CONCLUSION Our findings partially clarify how selection footprints from environmental temperature stress can lead to advantageous genomic adaptions to tropical and frigid environments in poultry and provide a valuable resource for selective breeding of chickens.
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Affiliation(s)
- Shourong Shi
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Dan Shao
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Lingyun Yang
- Novogene Bioinformatics Institute, Beijing 10089, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 10089, China
| | - Wei Han
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Qian Xue
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Liang Qu
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Li Leng
- College of Animal Science and technology, Northeast Agricultural University, Harbin, Heilongjiang, 150038, China
| | - Yishu Li
- Tropical Crop Germplasm Research Institute, Haikou, Hainan, 571101, China
| | - Xiaogang Zhao
- Agriculture and Animal Husbandry Rural and Science and Technology Bureau, Xiangcheng County, Ganzi Tibetan Autonomous Prefecture, Sichuan, 626000, China
| | - Ping Dong
- Agriculture and Animal Husbandry Rural and Science and Technology Bureau, Xiangcheng County, Ganzi Tibetan Autonomous Prefecture, Sichuan, 626000, China
| | - Muhammed Walugembe
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| | - Boniface B Kayang
- Department of Animal Science, University of Ghana, Legon, Accra 233, Ghana
| | - Amandus P Muhairwa
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3000 Chuo Kikuu, Morogoro, Tanzania
| | - Huaijun Zhou
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
| | - Haibing Tong
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China.
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Pightling AW, Rand H, Pettengill J. Using Evolutionary Analyses to Refine Whole-Genome Sequence Match Criteria. Front Microbiol 2022; 13:797997. [PMID: 35875579 PMCID: PMC9301902 DOI: 10.3389/fmicb.2022.797997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Whole-genome sequence databases continue to grow. Collection times between samples are also growing, providing both a challenge for comparing recently collected sequence data to historical samples and an opportunity for evolutionary analyses that can be used to refine match criteria. We measured evolutionary rates for 22 Salmonella enterica serotypes. Based upon these measurements, we propose using an evolutionary rate of 1.97 single-nucleotide polymorphisms (SNPs) per year when determining whether genome sequences match.
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Affiliation(s)
- Arthur W Pightling
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Hugh Rand
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - James Pettengill
- Biostatistics and Bioinformatics Staff, Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
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Lo KH, Lu CW, Liu FG, Kao CM, Chen SC. Draft genome sequence of Pseudomonas sp. A46 isolated from mercury-contaminated wastewater. J Basic Microbiol 2022; 62:1193-1201. [PMID: 35849092 DOI: 10.1002/jobm.202200106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/07/2022] [Accepted: 06/30/2022] [Indexed: 11/08/2022]
Abstract
Pseudomonas sp. A46 was first isolated from mercury-contaminated groundwater in Taiwan. This study is the first to report the draft whole-genome sequence of Pseudomonas sp. A46. Its genome consists of 126 contigs, with a total length of 6,782,516 bp and a GC content of 64.7%. Phylogenetic analysis based on 16 S rRNA gene sequences revealed that Pseudomonas sp. A46 is closely related to Pseudomonas citronellolis. Assessment of the draft genome sequence revealed that Pseudomonas sp. A46 harbors sets of genes conferring resistance to heavy metals, such as mercury, zinc, lead, copper, cadmium, chromate, and arsenate. These identified genes enable this bacterium to tolerate heavy metal stress.
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Affiliation(s)
- Kai-Hung Lo
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Che-Wei Lu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan, Taiwan
| | - Fu-Guo Liu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan, Taiwan
| | - Chih-Ming Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Ssu Ching Chen
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan, Taiwan
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43
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Heidaritabar M, Carney V, Groenen MAM, Plastow G. Assessing the genomic diversity and relatedness in 10 Canadian heritage chicken lines using whole-genome sequence data. J Anim Breed Genet 2022; 139:556-573. [PMID: 35579203 DOI: 10.1111/jbg.12720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/01/2022] [Indexed: 11/29/2022]
Abstract
In the past 50 years, there has been a steep increase in the demand for poultry products, met by increasing production along with genetic selection for improved growth, efficiency, health and reproduction. The selection tends to reduce the number and type of genetic resources contributing to the majority of production. The University of Alberta maintains 10 heritage chicken lines (Brown Leghorn (BL), Light Sussex (LS), New Hampshire (NH), Saskatchewan Barred Rock (SaskBR), Shaver Barred Rock (ShaverBR), Shaver Rhode Island Red (RIR), White Leghorn (WL) and three commercial crosses called Alberta Meat Control strains 1957 (AMC-1957), 1978 sire line (AMC-1978-20S) and 1978 dam line (AMC-1978-30D), that played a large role in the evolution of the poultry industry in Canada. Since these lines have not been subjected to the same intensive selection pressures as commercial counterparts, they may contain unique genetic variants lost in commercial lines. Thus, for conservation management of these lines, the first step is to assess their genetic diversity. 71 male samples from across 10 lines were analysed using whole-genome sequencing and patterns of genetic diversity and relatedness among these lines were explored. AMC-1978-30D showed the highest genetic diversity as reflected in observed and expected heterozygosity (0.327 and 0.250), percentage of polymorphic markers (~ 65%) and average recent inbreeding coefficient (-0.039), followed by AMC-1978-20S and AMC-1957. BL showed the lowest genetic diversity as reflected in observed and expected heterozygosity (0.130 and 0.116), percentage of polymorphic markers (~31%) and average recent inbreeding coefficient (0.577), followed by LS, WL and NH. Our findings highlight the need for special attention for the populations of BL, WL, LS and NH, with the largest levels of inbreeding. Our results can be used to develop a breeding strategy to optimize and conserve the genetic variation present in heritage lines.
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Affiliation(s)
- Marzieh Heidaritabar
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
| | - Valerie Carney
- Poultry Innovation Partnership, University of Alberta, Edmonton, Alberta, Canada
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
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Liu Y, Li H, Wang M, Zhang X, Yang L, Zhao C, Wu C. Genetic architectures and selection signatures of body height in Chinese indigenous donkeys revealed by next-generation sequencing. Anim Genet 2022; 53:487-497. [PMID: 35535569 DOI: 10.1111/age.13211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/18/2022] [Accepted: 04/13/2022] [Indexed: 01/02/2023]
Abstract
Donkeys are widely distributed labour animals in the world. During the process of the domestication and artificial selection of domestic donkeys, body sizes show significant differences among different breeds of donkeys. Based on the genome resequencing data of 103 Chinese indigenous donkeys from 11 breeds (Biyang, Dezhou, Guangling, Hetian, Jiami, Kulun, Qingyang, Turfan, Tibetan, Xinjiang, and Yunnan), seven Spanish donkeys from two breeds (Zamorano~Leonés and Andalusian), and three wild donkeys, we investigated the population structures of Chinese domestic donkeys with different body sizes. We used FST and XP-EHH analyses to explore the selected regions related to body sizes. The results showed that Chinese indigenous donkeys have a closer relationship with African wild donkeys than with Asian wild donkeys. LCORL/NCAPG, FAM184B, TBX3, and IHH were identified as genes with strong signals in analysis of selection signature (FST and XP-EHH) in large and small donkeys. The seven identified variants can be served as candidate loci affecting the body size of Chinese donkeys. Five of seven loci were located in intron 9 of FAM184B and were in a haplotype block, and one of the identified variants (Chr03:112664848) located in the CDS region of the LCORL gene was found to cause stop-loss. These candidate genes and variants shed new light on the molecular basis of donkey body size and will facilitate the breeding activities of donkeys.
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Affiliation(s)
- Yu Liu
- Equine Center, China Agricultural University, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haijing Li
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd, Liaocheng, China
| | - Min Wang
- Equine Center, China Agricultural University, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xinhao Zhang
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd, Liaocheng, China
| | - Li Yang
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd, Liaocheng, China
| | - Chunjiang Zhao
- Equine Center, China Agricultural University, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China
| | - Changxin Wu
- Equine Center, China Agricultural University, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
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Li Z, Li Y, Liu T, Zhang C, Xiao D, Hou X. Non-Heading Chinese Cabbage Database: An Open-Access Platform for the Genomics of Brassica campestris (syn. Brassica rapa) ssp. chinensis. Plants (Basel) 2022; 11:1005. [PMID: 35448733 PMCID: PMC9029197 DOI: 10.3390/plants11081005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
The availability of a high-quality genome sequence of Brassica campestris ssp. chinensis NHCC001 has paved the way for deep mining of genome data. We used the B. campestris NHCC001 draft genome to develop a comprehensive database, known as the non-heading Chinese cabbage database, which provides access to the B. campestris NHCC001 genome data. The database provides 127,347 SSR, from which 382,041 pairs of primers were designed. NHCCDB contains information on 105,360 genes, which were further classified into 63 transcription factor families. Furthermore, NHCCDB provides eight kinds of tools for biological or sequencing data analyses, including sequence alignment tools, functional genomics tools, comparative genomics tools, motif analysis tools, genome browser, primer design, and SSR analysis tools. In addition, eight kinds of graphs, including a box plot, Venn diagram, corrplot, Q-Q plot, Manhattan plot, seqLogo, volcano plot, and a heatmap, can be generated rapidly using NHCCDB. We have incorporated a search system for efficient mining of transcription factors and genes, along with an embedded data submit function in NHCCDB. We believe that the NHCCDB database will be a useful platform for non-heading Chinese cabbage research and breeding.
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Affiliation(s)
| | | | | | | | | | - Xilin Hou
- Correspondence: ; Tel.: +86-13705166115
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46
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Liu Z, Zhao Y, Sossah FL, Okorley BA, Amoako DG, Liu P, Sheng H, Li D, Li Y. Characterization, Pathogenicity, Phylogeny, and Comparative Genomic Analysis of Pseudomonas tolaasii Strains Isolated from Various Mushrooms in China. Phytopathology 2022; 112:521-534. [PMID: 34293910 DOI: 10.1094/phyto-12-20-0550-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Since 2016, devastating bacterial blotch affecting the fruiting bodies of Agaricus bisporus, Cordyceps militaris, Flammulina filiformis, and Pleurotus ostreatus in China has caused severe economic losses. We isolated 102 bacterial strains and characterized them polyphasically. We identified the causal agent as Pseudomonas tolaasii and confirmed the pathogenicity of the strains. A host range test further confirmed the pathogen's ability to infect multiple hosts. This is the first report in China of bacterial blotch in C. militaris caused by P. tolaasii. Whole-genome sequences were generated for three strains: Pt11 (6.48 Mb), Pt51 (6.63 Mb), and Pt53 (6.80 Mb), and pangenome analysis was performed with 13 other publicly accessible P. tolaasii genomes to determine their genetic diversity, virulence, antibiotic resistance, and mobile genetic elements. The pangenome of P. tolaasii is open, and many more gene families are likely to emerge with further genome sequencing. Multilocus sequence analysis using the sequences of four common housekeeping genes (glns, gyrB, rpoB, and rpoD) showed high genetic variability among the P. tolaasii strains, with 115 strains clustered into a monophyletic group. The P. tolaasii strains possess various genes for secretion systems, virulence factors, carbohydrate-active enzymes, toxins, secondary metabolites, and antimicrobial resistance genes that are associated with pathogenesis and adapted to different environments. The myriad of insertion sequences, integrons, prophages, and genome islands encoded in the strains may contribute to genome plasticity, virulence, and antibiotic resistance. These findings advance understanding of the determinants of virulence, which can be targeted for the effective control of bacterial blotch disease.
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Affiliation(s)
- Zhenghui Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
- Department of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yitong Zhao
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Frederick L Sossah
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Benjamin A Okorley
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
- Crop Science Department, University of Ghana, Legon, Accra, Ghana
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Peibin Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Hongyan Sheng
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Dan Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Ministry of Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Ministry of Science and Technology, Jilin Agricultural University, Changchun 130118, China
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Masuda S, Yaeno T, Shibata H, Yorozu S, Yamamoto S, Shirasu K. High-Quality Genome Sequence Resource of the Taro Pathogen Phytophthora colocasiae. Mol Plant Microbe Interact 2022; 35:297-299. [PMID: 35139662 DOI: 10.1094/mpmi-05-21-0120-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Sachiko Masuda
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Takashi Yaeno
- Department of Agriculture, Ehime University, Matsuyama, 790-8566, Japan
| | - Hideaki Shibata
- Ehime Research Institute of Agriculture, Forestry and Fisheries, Matsuyama, 799-2405, Japan
| | - Shuuhei Yorozu
- Agriculture and Horticulture Division, Agriculture, Forestry and Fisheries Department, Ehime Prefectural Government, Matsuyama, 790-0001, Japan
| | - Satoki Yamamoto
- Agriculture and Horticulture Division, Agriculture, Forestry and Fisheries Department, Ehime Prefectural Government, Matsuyama, 790-0001, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
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Wang L, Guo S, Zeng B, Wang S, Chen Y, Cheng S, Liu B, Wang C, Wang Y, Meng Q. Draft Genome Assembly and Annotation for Cutaneotrichosporon dermatis NICC30027, an Oleaginous Yeast Capable of Simultaneous Glucose and Xylose Assimilation. Mycobiology 2022; 50:69-81. [PMID: 35291590 PMCID: PMC8890563 DOI: 10.1080/12298093.2022.2038844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.
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Affiliation(s)
- Laiyou Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Shuxian Guo
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Bo Zeng
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Shanshan Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Yan Chen
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Shuang Cheng
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Bingbing Liu
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Chunyan Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Yu Wang
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Qingshan Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Jiang F, Kong Z, Liu K, Cheng C, Jiang T, Ma P, Li R. Phenotypic and Genotypic Characterization of Linezolid Resistance Coagulase-negative Staphylococci Possessing cfr-Carrying Plasmid. J Glob Antimicrob Resist 2022; 28:226-232. [PMID: 35041999 DOI: 10.1016/j.jgar.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES Linezolidine-dependent growth contributed to wide dissemination of Staphylococcus epidermidis throuthout hospitals. This study aimed to characterize 13 linezolid resistant coagulase-negative Staphylococci (CoNS) isolates and possibility of dependence on linezolid in China. METHODS Resistance phenotypic and genotypic of thirteen CoNS isolates were investigated by antimicrobial susceptibility testing and polymerase chain reaction (PCR). Similarity of isolates was estimated by pulsed field gel electrophoresis (PFGE). Characterization of cfr plasmid was carried out by S1 nuclease-PFGE, southern blotting and whole-genome sequencing (WGS). Phylogenetic analysis was conducted by constructing a maximum-likelihood phylogenetic tree. Growth curve analysis was conducted with and without linezolid to determinate possibility contribution of linezolid dependence to linezolid resistance CoNS isolates dissemination. RESULTS Thirteen CoNS isolates showed linezolid MICs of 8mg/L to >256mg/L and were typed into three PFGE profiles. Southern blotting and WGS indicated that cfr gene was located on a plasmid of 39.5 kb, revealing 99% identity to the sequence of the cfr-harbouring plasmid pSR01, pLRSA417 and pH46-29. The cfr gene was flanked by two copies of an IS256-like element ISEnfa4 family transposase, indicating the transferability of linezolid resistance conferred by the cfr gene. Comparative phylogenetic analysis revealed that S. capitis XZ03 share high similarity with linezolid-resistant S.capitis isolates (17-758, 17-396, 18-857, 15-72 and 15-101) in Huashan Hospital, Shanghai. Thirteen CoNS isolates did not exhibit linezolid-dependent upon exposure from 8mg/L to 32mg/L. CONCLUSIONS The endemic CoNS clone carrying cfr gene in our hospital showed high level of linezolid resistance, which threatened the utilization of linezolid. Linezolidine-dependent growth under linezolid selective pressure was not observed in our study, indicating that it may be not a common phenotype in Staphylococcus spp. at present.
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Affiliation(s)
- Fei Jiang
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China; School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Ziyan Kong
- Department of Laboratory Medicine, Changzhou Hospital of Traditional Chinese Medicine, Changzhou, China
| | - Ke Liu
- Xuzhou Administration for Market Regulation, Xuzhou, China
| | - Chen Cheng
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tingting Jiang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Ping Ma
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Rongpeng Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
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50
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Ruperao P, Gandham P, Rathore A. Construction of Practical Haplotype Graph (PHG) with the Whole-Genome Sequence Data. Methods Mol Biol 2022; 2443:273-284. [PMID: 35037212 DOI: 10.1007/978-1-0716-2067-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With the emerging sequencing technologies and cost reduction, the sequence data generation has accelerated from a single individual to multiple (thousands of) individuals of a species. The terabytes of sequence data generated from thousands of individuals include the majority of the redundant sequence which depends on the level of sequence similarity within the population of individuals. Managing large datasets and creating the unique catalogue sequence from such a large population is challenging to analyze, store, and retrieve the information. In this chapter, we discuss the practical haplotype graph (PHG) which addresses the above said challenges and also able to retrieve required information such as variants and sequences more efficiently, which enable researchers to manage and assess large genomic data.
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Affiliation(s)
- Pradeep Ruperao
- Statistics, Bioinformatics and Data Management, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India.
| | - Prasad Gandham
- Statistics, Bioinformatics and Data Management, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Abhishek Rathore
- Statistics, Bioinformatics and Data Management, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
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