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Mohamed HMA, Abd-Elhafeez HH, Al-Jabr OA, El-Zamkan MA. Characterization of Acinetobacter baumannii Isolated from Raw Milk. BIOLOGY 2022; 11:biology11121845. [PMID: 36552354 PMCID: PMC9775129 DOI: 10.3390/biology11121845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Acinetobacter baumannii (A. baumannii) is an opportunistic pathogen associated with nosocomial infections. In this study, 100 raw milk samples were collected from Qena, Egypt, and subjected to conventional and molecular assays to determine the presence of A. baumannii and investigate their antimicrobial resistance and biofilm formation. Our findings revealed that, among the 100 samples, Acinetobacter spp. were found in 13 samples based on CHROM agar results. We further characterized them using rpoB and 16S-23SrRNA sequencing and gyrB multiplex PCR analysis and confirmed that 9 out of the 13 Acinetobacter spp. isolates were A. baumannii and 4 were other species. The A. baumannii isolates were resistant to β-lactam drugs, including cefotaxime (44%), ampicillin-sulbactam and levofloxacin (33.3% for each), imipenem, meropenem and aztreonam (22.2% for each). We observed different antimicrobial resistance patterns, with a multi-antibiotic resistant (MAR) index ranging from 0.2 to 0.3. According to the PCR results, blaOXA-51 and blaOXA-23 genes were amplified in 100% and 55.5% of the A. baumannii isolates, respectively, while the blaOXA-58 gene was not amplified. Furthermore, the metallo-β-lactamases (MBL) genes blaIMP and blaNDM were found in 11.1% and 22.2% of isolates, respectively, while blaVIM was not amplified. Additionally, eight A. baumannii isolates (88.8%) produced black-colored colonies on Congo red agar, demonstrating their biofilm production capacity. These results showed that, besides other foodborne pathogens, raw milk should also be examined for A. baumannii, which could be a public health concern.
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Affiliation(s)
- Hams M. A. Mohamed
- Department of Microbiology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Hanan H. Abd-Elhafeez
- Department of Cells and Tissues, Faculty of Veterinary Medicine, Assiut University, Assiut 71526, Egypt
- Correspondence:
| | - Omar A. Al-Jabr
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Mona A. El-Zamkan
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
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2
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Chen M, Huang D, Chen J, Huang Y, Zheng H, Tang Y, Zhang Q, Chen S, Ai L, Zhou X, Zhang R. Genetic Characterization and Detection of Angiostrongylus cantonensis by Molecular Approaches. Vector Borne Zoonotic Dis 2021; 21:643-652. [PMID: 34242520 DOI: 10.1089/vbz.2020.2734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Angiostrongylus cantonensis constitutes a major etiologic agent of eosinophilic meningoencephalitis. The detection methods for angiostrongyliasis mainly depend on morphology or immunology. A firmer diagnosis could be reached by directly detecting the parasite in the cerebrospinal fluid or through laboratory assays that are specific for Angiostrongylus-induced antibodies or the parasite's DNA. A. cantonensis detection could be carried out by larva release from the tissue upon pepsin digestion. However, the procedure requires live mollusks, which might complicate the analysis of large amounts of samples. Since morphological assays are limited, multiple molecular techniques have been put forward for detecting A. cantonensis, including PCR amplification of targets followed by fragment length or DNA sequence analysis. This allows rapid and accurate identification of A. cantonensis for efficient infection management and epidemiological purposes. In this study, we reviewed the current methods, concepts, and applications of molecular approaches to better understand the genetic characterization, molecular detection methods, and practical application of molecular detection in A. cantonensis.
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Affiliation(s)
- Muxin Chen
- Institute of Pathogenic Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,Health Education and Detection Center, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,Health Education and Detection Center, NHC Key Laboratory for Parasitology and Vector Biology, Shanghai, China.,Health Education and Detection Center, WHO Collaborating Center for Tropical Diseases, Shanghai, China.,Health Education and Detection Center, National Center for International Research on Tropical Diseases, Shanghai, China
| | - Dana Huang
- Institute of Pathogenic Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jiaxu Chen
- Health Education and Detection Center, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,Health Education and Detection Center, NHC Key Laboratory for Parasitology and Vector Biology, Shanghai, China.,Health Education and Detection Center, WHO Collaborating Center for Tropical Diseases, Shanghai, China.,Health Education and Detection Center, National Center for International Research on Tropical Diseases, Shanghai, China.,Health Education and Detection Center, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shenzhen Center for Disease Control and Prevention, Joint Laboratory for Imported Tropical Disease Control, Shanghai, China
| | - Yalan Huang
- Institute of Pathogenic Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Huiwen Zheng
- Institute of Pathogenic Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yijun Tang
- Institute of Pathogenic Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qian Zhang
- Institute of Pathogenic Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Shaohong Chen
- Health Education and Detection Center, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,Health Education and Detection Center, NHC Key Laboratory for Parasitology and Vector Biology, Shanghai, China.,Health Education and Detection Center, WHO Collaborating Center for Tropical Diseases, Shanghai, China.,Health Education and Detection Center, National Center for International Research on Tropical Diseases, Shanghai, China
| | - Lin Ai
- Health Education and Detection Center, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,Health Education and Detection Center, NHC Key Laboratory for Parasitology and Vector Biology, Shanghai, China.,Health Education and Detection Center, WHO Collaborating Center for Tropical Diseases, Shanghai, China.,Health Education and Detection Center, National Center for International Research on Tropical Diseases, Shanghai, China.,Department of One Health, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaonong Zhou
- Health Education and Detection Center, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai, China.,Health Education and Detection Center, NHC Key Laboratory for Parasitology and Vector Biology, Shanghai, China.,Health Education and Detection Center, WHO Collaborating Center for Tropical Diseases, Shanghai, China.,Health Education and Detection Center, National Center for International Research on Tropical Diseases, Shanghai, China.,Health Education and Detection Center, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shenzhen Center for Disease Control and Prevention, Joint Laboratory for Imported Tropical Disease Control, Shanghai, China.,Department of One Health, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Renli Zhang
- Institute of Pathogenic Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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Antibiogram, Prevalence of OXA Carbapenemase Encoding Genes, and RAPD-Genotyping of Multidrug-Resistant Acinetobacter baumannii Incriminated in Hidden Community-Acquired Infections. Antibiotics (Basel) 2020; 9:antibiotics9090603. [PMID: 32942596 PMCID: PMC7558960 DOI: 10.3390/antibiotics9090603] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/10/2020] [Accepted: 09/13/2020] [Indexed: 12/16/2022] Open
Abstract
Acinetobacter spp. has gained fame from their ability to resist difficult conditions and their constant development of antimicrobial resistance. This study aimed to investigate the prevalence, susceptibility testing, OXA carbapenemase-encoding genes, and RAPD-genotyping of multidrug resistant Acinetobacter baumannii incriminated in hidden community-acquired infections in Egypt. The antimicrobial susceptibility testing was assessed phenotypically using Kirby–Bauer disk diffusion method. Also, Modified-Hodge test (MHT) was carried out to detect the carbapenemases production. Multiplex-PCR was used to detect the carbapenemase-encoding genes. Furthermore, the genetic relationship among the isolated strains was investigated using RAPD fingerprinting. The bacteriological examination revealed that, out of 200 Gram-negative non-fermentative isolates, 44 (22%) were identified phenotypically and biochemically as Acinetobacter spp. and 23 (11.5%) were molecularly confirmed as A.baumannii. The retrieved A.baumannii strains were isolated from urine (69%), sputum (22%), and cerebrospinal fluid (csf) (9%). The isolated A. baumannii strains exhibited multidrug resistance and the production rates of carbapenemases were 56.5, 60.9, and 78.3% with meropenem, imipenem, and ertapenem disks, respectively. The blaOXA-24-like genes were the most predominant among the tested strains (65.2%), followed by blaOXA-23 (30.4%) and blaOXA-58 (17.4%), in addition, the examined strains are harbored IMP, VIM, and NDM genes with prevalence of 60.9, 43.5, and 13%, respectively, while KPC and GES genes were not detected. RAPD-PCR revealed that the examined strains are clustered into 11 different genotypes at ≥90% similarity. Briefly, to the best of our knowledge, this study is the first report concerning community-associated A. baumannii infections in Egypt. The high prevalence of hidden multidrug-resistant (MDR) and extensively drug-resistant (XDR) A.baumannii strains associated with non-hospitalized patients raises an alarm for healthcare authorities to set strict standards to control the spread of such pathogens with high rates of morbidity and mortality.
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Bunnoy A, Na-Nakorn U, Kayansamruaj P, Srisapoome P. Acinetobacter Strain KUO11TH, a Unique Organism Related to Acinetobacter pittii and Isolated from the Skin Mucus of Healthy Bighead Catfish and Its Efficacy Against Several Fish Pathogens. Microorganisms 2019; 7:microorganisms7110549. [PMID: 31717696 PMCID: PMC6920915 DOI: 10.3390/microorganisms7110549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/30/2019] [Accepted: 11/08/2019] [Indexed: 12/20/2022] Open
Abstract
The bacterial strain KU011TH was isolated from the skin mucus of healthy bighead catfish. The strain is a Gram-negative coccobacillus that is nonmotile, aerobic, catalase positive, oxidase negative, and nonhemolytic. Sequence analyses of the housekeeping genes 16S rRNA, gyrB and rpoB indicate that this strain is a new member of the Acb complex of the genus Acinetobacter and is closely related to Acinetobacter pittii and Acinetobacter lactucae. In addition, the genome relatedness-associated ANIb (<95–96%) and in silico DDH (<70%) values clearly supported the new member of the genus Acinetobacter and the Acb complex. The genome of the strain KU011TH was approximately 3.79 Mbp in size, comprising 3619 predicted genes, and the DNA G+C content was 38.56 mol%. The major cellular fatty acids were C18:1ω9c, C16:0, C16:1, C20:2, C18:2ω6c and C18:1ω9t. The whole-genome sequences and phenotypic, phylogenetic, and chemotaxonomic data clearly support the classification of the strain KU011TH as a new member in the genus Acinetobacter which is closest to A. pittii. Additionally, the new bacterial strain exhibited strong activity against a broad range of freshwater fish pathogens in vitro.
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Affiliation(s)
- Anurak Bunnoy
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.B.); (P.K.)
| | - Uthairat Na-Nakorn
- Laboratory of Aquatic Animal Genetics, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, Bangkok 10900, Thailand;
| | - Pattanapon Kayansamruaj
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.B.); (P.K.)
| | - Prapansak Srisapoome
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, Bangkok 10900, Thailand; (A.B.); (P.K.)
- Correspondence:
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5
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Gonzalez E, Pitre FE, Pagé AP, Marleau J, Guidi Nissim W, St-Arnaud M, Labrecque M, Joly S, Yergeau E, Brereton NJB. Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination. MICROBIOME 2018; 6:53. [PMID: 29562928 PMCID: PMC5863371 DOI: 10.1186/s40168-018-0432-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/02/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND One method for rejuvenating land polluted with anthropogenic contaminants is through phytoremediation, the reclamation of land through the cultivation of specific crops. The capacity for phytoremediation crops, such as Salix spp., to tolerate and even flourish in contaminated soils relies on a highly complex and predominantly cryptic interacting community of microbial life. METHODS Here, Illumina HiSeq 2500 sequencing and de novo transcriptome assembly were used to observe gene expression in washed Salix purpurea cv. 'Fish Creek' roots from trees pot grown in petroleum hydrocarbon-contaminated or non-contaminated soil. All 189,849 assembled contigs were annotated without a priori assumption as to sequence origin and differential expression was assessed. RESULTS The 839 contigs differentially expressed (DE) and annotated from S. purpurea revealed substantial increases in transcripts encoding abiotic stress response equipment, such as glutathione S-transferases, in roots of contaminated trees as well as the hallmarks of fungal interaction, such as SWEET2 (Sugars Will Eventually Be Exported Transporter). A total of 8252 DE transcripts were fungal in origin, with contamination conditions resulting in a community shift from Ascomycota to Basidiomycota genera. In response to contamination, 1745 Basidiomycota transcripts increased in abundance (the majority uniquely expressed in contaminated soil) including major monosaccharide transporter MST1, primary cell wall and lamella CAZy enzymes, and an ectomycorrhiza-upregulated exo-β-1,3-glucanase (GH5). Additionally, 639 DE polycistronic transcripts from an uncharacterised Enterobacteriaceae species were uniformly in higher abundance in contamination conditions and comprised a wide spectrum of genes cryptic under laboratory conditions but considered putatively involved in eukaryotic interaction, biofilm formation and dioxygenase hydrocarbon degradation. CONCLUSIONS Fungal gene expression, representing the majority of contigs assembled, suggests out-competition of white rot Ascomycota genera (dominated by Pyronema), a sometimes ectomycorrhizal (ECM) Ascomycota (Tuber) and ECM Basidiomycota (Hebeloma) by a poorly characterised putative ECM Basidiomycota due to contamination. Root and fungal expression involved transcripts encoding carbohydrate/amino acid (C/N) dialogue whereas bacterial gene expression included the apparatus necessary for biofilm interaction and direct reduction of contamination stress, a potential bacterial currency for a role in tripartite mutualism. Unmistakable within the metatranscriptome is the degree to which the landscape of rhizospheric biology, particularly the important but predominantly uncharacterised fungal genetics, is yet to be discovered.
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Affiliation(s)
- E Gonzalez
- Canadian Center for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montréal, H3A 1A4, Canada
- Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada
| | - F E Pitre
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - A P Pagé
- Aquatic and Crop Resource Development (ACRD), National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - J Marleau
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
| | - W Guidi Nissim
- Department of Agri-food and Environmental Science, University of Florence, Viale delle Idee, Sesto Fiorentino, FI, Italy
| | - M St-Arnaud
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - M Labrecque
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - S Joly
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada
- Montreal Botanical Garden, Montreal, QC, H1X 2B2, Canada
| | - E Yergeau
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - N J B Brereton
- Institut de recherche en biologie végétale, University of Montreal, Montreal, QC, H1X 2B2, Canada.
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Lv S, Zhang Y, Steinmann P, Utzinger J, Zhou XN. The genetic variation of Angiostrongylus cantonensis in the People's Republic of China. Infect Dis Poverty 2017; 6:125. [PMID: 28859686 PMCID: PMC5579933 DOI: 10.1186/s40249-017-0341-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/26/2017] [Indexed: 01/13/2023] Open
Abstract
Background The People’s Republic of China (P.R. China) is the presumptive home range of the rat lungworm Angiostrongylus cantonensis, a major aetiological agent of human eosinophilic meningitis. We present a study of the genetic variation of A. cantonensis in P.R. China. Our aim was to deepen the current knowledge pertaining to its origin and global spread from a molecular perspective. Methods Adult A. cantonensis were collected in the frame of a national survey and identified based on morphological criteria. Polymerase chain reaction (PCR) was employed to amplify the target DNA sequences (cytochrome c oxidase subunit I (cox1), nicotinamide adenine dinucleotide dehydrogenase subunit 1 (nad1) and internal transcribed spacer (ITS)). The PCR product of cox1 was directly submitted to sequencing, while clone sequencing was used for nad1 and ITS. The identity of the samples was verified by comparing the sequences to those of accepted A. cantonensis specimens. The specific composition of substitutions in each gene was analysed, and the genotypes were compared based on the complete cox1, nad1 and ITS genes. Results We characterised the complete mitochondrial genes cox1 and nad1 of 130 specimens and obtained 357 nuclear sequences containing two complete ITS (ITS1 and ITS2) and 5.8S rRNA of the same samples. All specimens were genetically confirmed as A. cantonensis. Two major groups (i.e. I and II) were identified according to the phylogeny of cox1 sequences. Group I could be further categorised into six distinct clades. Almost half of the specimens (47.7%) belong to the clade Ia and 22.3% to the group II. The former was widely distributed across the study region. A variable number of repeat units in three microsatellites was observed, resulting in considerable length variation in ITS. Intragenomic variation of ITS sequences was found in a large proportion of the samples. Genotyping showed a striking difference between mitochondrial DNA and ITS. Conclusions Our results demonstrate that A. cantonensis is the only rat lungworm species in P.R. China and shows high genetic diversity. Results of diversity and genotyping of A. cantonensis can be impacted by the sequencing strategy and biomarker. Although ITS may be a valuable marker for interspecific identification, it is not suitable for studying the intraspecific variation of A. cantonensis due to its high intragenomic variation and current challenges for direct sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s40249-017-0341-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shan Lv
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China. .,Swiss Tropical and Public Health Institute, P.O. Box, CH-4002, Basel, Switzerland. .,University of Basel, P.O. Box, CH-4003, Basel, Switzerland.
| | - Yi Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China
| | - Peter Steinmann
- Swiss Tropical and Public Health Institute, P.O. Box, CH-4002, Basel, Switzerland.,University of Basel, P.O. Box, CH-4003, Basel, Switzerland
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, P.O. Box, CH-4002, Basel, Switzerland.,University of Basel, P.O. Box, CH-4003, Basel, Switzerland
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, 200025, People's Republic of China
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Khowal S, Siddiqui MZ, Ali S, Khan MT, Khan MA, Naqvi SH, Wajid S. A report on extensive lateral genetic reciprocation between arsenic resistant Bacillus subtilis and Bacillus pumilus strains analyzed using RAPD-PCR. Mol Phylogenet Evol 2016; 107:443-454. [PMID: 27956257 DOI: 10.1016/j.ympev.2016.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/26/2016] [Accepted: 12/08/2016] [Indexed: 12/16/2022]
Abstract
The study involves isolation of arsenic resistant bacteria from soil samples. The characterization of bacteria isolates was based on 16S rRNA gene sequences. The phylogenetic consanguinity among isolates was studied employing rpoB and gltX gene sequence. RAPD-PCR technique was used to analyze genetic similarity between arsenic resistant isolates. In accordance with the results Bacillus subtilis and Bacillus pumilus strains may exhibit extensive horizontal gene transfer. Arsenic resistant potency in Bacillus sonorensis and high arsenite tolerance in Bacillus pumilus strains was identified. The RAPD-PCR primer OPO-02 amplified a 0.5kb DNA band specific to B. pumilus 3ZZZ strain and 0.75kb DNA band specific to B. subtilis 3PP. These unique DNA bands may have potential use as SCAR (Sequenced Characterized Amplified Region) molecular markers for identification of arsenic resistant B. pumilus and B. subtilis strains.
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Affiliation(s)
- Sapna Khowal
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi 110 062, India
| | - Md Zulquarnain Siddiqui
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi 110 062, India
| | - Shadab Ali
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi 110 062, India
| | - Mohd Taha Khan
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi 110 062, India
| | - Mather Ali Khan
- 247, Bond Life Sciences Centre, 1201 Rollins Street, University of Missouri-Columbia, Columbia, MO 65211, USA
| | | | - Saima Wajid
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi 110 062, India.
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Gurtler V, Grando D, Kumar BK, Maiti B, Karunasagar I, Karunasagar I. The Use of Recombined Ribosomal RNA Operon (rrn) Type-Specific Flanking Genes to Investigate rrn Differences Between Vibrio parahaemolyticus Environmental and Clinical Strains. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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ConStrains identifies microbial strains in metagenomic datasets. Nat Biotechnol 2015; 33:1045-52. [PMID: 26344404 PMCID: PMC4676274 DOI: 10.1038/nbt.3319] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 07/16/2015] [Indexed: 01/21/2023]
Abstract
An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived datasets provides insights into microbial community dynamics.
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Maslunka C, Gürtler V, Seviour R. The impact of horizontal gene transfer on targeting the internal transcribed spacer region (ITS) to identify Acinetobacter junii
strains. J Appl Microbiol 2015; 118:1435-43. [DOI: 10.1111/jam.12800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/24/2015] [Accepted: 03/12/2015] [Indexed: 11/30/2022]
Affiliation(s)
- C. Maslunka
- Biotechnology Research Centre; La Trobe University; Bendigo Vic. Australia
| | - V. Gürtler
- School of Applied Science; RMIT University; Bundoora Vic. Australia
| | - R.J. Seviour
- Biotechnology Research Centre; La Trobe University; Bendigo Vic. Australia
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Maslunka C, Gürtler V, Seviour R. Unusual features of the sequences of copies of the 16S-23S rRNA internal transcribed spacer regions of Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi arise from horizontal gene transfer events. MICROBIOLOGY-SGM 2014; 161:322-329. [PMID: 25505188 DOI: 10.1099/mic.0.083600-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The highly variable nature of the internal transcribed spacer region (ITS) has been claimed to represent an ideal target for designing species-specific probes/primers capable of differentiating between closely related Acinetobacter species. However, several Acinetobacter species contain multiple ITS copies of variable lengths, and these include Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi. This study shows these length variations result from inter-genomic insertion/deletion events (indels) involving horizontal transfer of ITS fragments of other Acinetobacter species and possibly unrelated bacteria, as shown previously by us. In some instances, indel incorporation results in the loss of probe target sites in the recipient cell ITS. In other cases, some indel sequences contain target sites for probes designed from a single ITS sequence to target other Acinetobacter species. Hence, these can generate false positives. The largest of the indels that remove probe sites is 683 bp (labelled bay/i1-0), and it derives from the horizontal transfer of a complete ITS between A. bereziniae BCRC15423(T) and A. baylyi strain ADP1. As a consequence, ITS sequencing or fingerprinting cannot be used to distinguish between the 683 bp ITS in these two strains.
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Affiliation(s)
- Christopher Maslunka
- Biotechnology Research Centre, La Trobe University, Bendigo, Victoria 3552, Australia
| | - Volker Gürtler
- School of Applied Science, RMIT University, Bundoora, Victoria 3152, Australia
| | - Robert Seviour
- Department of Microbiology, La Trobe University, Bundoora, Victoria 3152, Australia.,Biotechnology Research Centre, La Trobe University, Bendigo, Victoria 3552, Australia
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12
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Gifford B, Tucci J, McIlroy SJ, Petrovski S. Isolation and characterization of two plasmids in a clinical Acinetobacter nosocomialis strain. BMC Res Notes 2014; 7:732. [PMID: 25326196 PMCID: PMC4210605 DOI: 10.1186/1756-0500-7-732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/10/2014] [Indexed: 11/11/2022] Open
Abstract
Background Acinetobacter species are recognised as important nosocomial pathogens that have become a major cause of invasive opportunistic infections in hospitalised patients. Their clinical significance is largely due to the rapid development of antimicrobial resistance among strains. The development of antibiotic resistance among bacterial strains occurs frequently by the acquisition of resistance genes by gene transfer systems such as bacterial plasmids. Method Multi-antibiotic resistant Acinetobacter nosocomialis strain 178 was isolated from a hospital in Melbourne, Australia. This strain was screened for the presence of plasmids. The two plasmids isolated were sequenced and annotated. Results Two plasmids isolated from a single clinical Acinetobacter nosocomialis strain were sequenced. One plasmid, designated pRAY*-v3, appears to have evolved via the same lineage as the pRAY plasmid isolated from an Acinetobacter baumannii in South Africa. The other plasmid, designated pAB49-v1, appears to be an evolutionary descendent from a cryptic plasmid isolated from an A. baumannii almost 20 years ago. Both of the plasmid sequences here share a high level of sequence similarity with their ancestors, however differences are noted. Conclusion The isolation of these plasmid-lineages across different decades and continents suggests their global dissemination.
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Affiliation(s)
| | | | | | - Steve Petrovski
- La Trobe Institute for Molecular Sciences, La Trobe University, Bendigo, Australia.
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