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Macori G, Al-Qahtani AA, Koolman L, Althawadi S, Mutabaqani M, Bashtawi R, Aljumaa S, Almaghrabi RS, Fanning S. Stenotrophomonas riyadhensis sp. nov., isolated from a hospital floor swab. Int J Syst Evol Microbiol 2024; 74. [PMID: 38393318 DOI: 10.1099/ijsem.0.006250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024] Open
Abstract
During the analysis of a collection of Pseudomonas strains linked to an outbreak in an intensive care unit at King Faisal Specialist Hospital and Research Center in 2019, one isolate (CFS3442T) was identified phenotypically as Pseudomonas aeruginosa. However, whole-genome sequencing revealed its true identity as a member of the genus Stenotrophomonas, distinct from both P. aeruginosa and Stenotrophomonas maltophilia. The isolate demonstrated: (i) a significant phylogenetic distance from P. aeruginosa; (ii) considerable genomic differences from several S. maltophilia reference strains and other Stenotrophomonas species; and (iii) unique phenotypic characteristics. Based on the combined geno- and phenotypic data, we propose that this isolate represents a novel species within the genus Stenotrophomonas, for which the name Stenotrophomonas riyadhensis sp. nov. is proposed. The type strain is CFS3442T (=NCTC 14921T=LMG 33162T).
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Affiliation(s)
- Guerrino Macori
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Present address: School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Ahmed Ali Al-Qahtani
- Department of infection control and hospital epidemiology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Leonard Koolman
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Ireland
| | - Sahar Althawadi
- Department of Pathology and Laboratory medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maysoon Mutabaqani
- Department of Pathology and Laboratory medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rustom Bashtawi
- Department of infection control and hospital epidemiology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sulaiman Aljumaa
- Department of infection control and hospital epidemiology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Reem Saad Almaghrabi
- Organ transplant center of excellence, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Ireland
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Lee JH, Kim NH, Jang KM, Jin H, Shin K, Jeong BC, Kim DW, Lee SH. Prioritization of Critical Factors for Surveillance of the Dissemination of Antibiotic Resistance in Pseudomonas aeruginosa: A Systematic Review. Int J Mol Sci 2023; 24:15209. [PMID: 37894890 PMCID: PMC10607276 DOI: 10.3390/ijms242015209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Pseudomonas aeruginosa is the primary opportunistic human pathogen responsible for a range of acute and chronic infections; it poses a significant threat to immunocompromised patients and is the leading cause of morbidity and mortality for nosocomial infections. Its high resistance to a diverse array of antimicrobial agents presents an urgent health concern. Among the mechanisms contributing to resistance in P. aeruginosa, the horizontal acquisition of antibiotic resistance genes (ARGs) via mobile genetic elements (MGEs) has gained recognition as a substantial concern in clinical settings, thus indicating that a comprehensive understanding of ARG dissemination within the species is strongly required for surveillance. Here, two approaches, including a systematic literature analysis and a genome database survey, were employed to gain insights into ARG dissemination. The genome database enabled scrutinizing of all the available sequence information and various attributes of P. aeruginosa isolates, thus providing an extensive understanding of ARG dissemination within the species. By integrating both approaches, with a primary focus on the genome database survey, mobile ARGs that were linked or correlated with MGEs, important sequence types (STs) carrying diverse ARGs, and MGEs responsible for ARG dissemination were identified as critical factors requiring strict surveillance. Although human isolates play a primary role in dissemination, the importance of animal and environmental isolates has also been suggested. In this study, 25 critical mobile ARGs, 45 critical STs, and associated MGEs involved in ARG dissemination within the species, are suggested as critical factors. Surveillance and management of these prioritized factors across the One Health sectors are essential to mitigate the emergence of multidrug-resistant (MDR) and extensively resistant (XDR) P. aeruginosa in clinical settings.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Nam-Hoon Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Kyung-Min Jang
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Hyeonku Jin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Kyoungmin Shin
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
| | - Dae-Wi Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin 17058, Republic of Korea; (J.H.L.); (K.-M.J.); (H.J.); (K.S.); (B.C.J.)
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Barbu IC, Gheorghe-Barbu I, Grigore GA, Vrancianu CO, Chifiriuc MC. Antimicrobial Resistance in Romania: Updates on Gram-Negative ESCAPE Pathogens in the Clinical, Veterinary, and Aquatic Sectors. Int J Mol Sci 2023; 24:7892. [PMID: 37175597 PMCID: PMC10178704 DOI: 10.3390/ijms24097892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Multidrug-resistant Gram-negative bacteria such as Acinetobacter baumannii, Pseudomonas aeruginosa, and members of the Enterobacterales order are a challenging multi-sectorial and global threat, being listed by the WHO in the priority list of pathogens requiring the urgent discovery and development of therapeutic strategies. We present here an overview of the antibiotic resistance profiles and epidemiology of Gram-negative pathogens listed in the ESCAPE group circulating in Romania. The review starts with a discussion of the mechanisms and clinical significance of Gram-negative bacteria, the most frequent genetic determinants of resistance, and then summarizes and discusses the epidemiological studies reported for A. baumannii, P. aeruginosa, and Enterobacterales-resistant strains circulating in Romania, both in hospital and veterinary settings and mirrored in the aquatic environment. The Romanian landscape of Gram-negative pathogens included in the ESCAPE list reveals that all significant, clinically relevant, globally spread antibiotic resistance genes and carrying platforms are well established in different geographical areas of Romania and have already been disseminated beyond clinical settings.
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Affiliation(s)
- Ilda Czobor Barbu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Irina Gheorghe-Barbu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Georgiana Alexandra Grigore
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- National Institute of Research and Development for Biological Sciences, 060031 Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- Academy of Romanian Scientists, 050044 Bucharest, Romania
- Romanian Academy, 010071 Bucharest, Romania
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Aminoglycoside-Modifying Enzymes Are Sufficient to Make Pseudomonas aeruginosa Clinically Resistant to Key Antibiotics. Antibiotics (Basel) 2022; 11:antibiotics11070884. [PMID: 35884138 PMCID: PMC9312099 DOI: 10.3390/antibiotics11070884] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023] Open
Abstract
Aminoglycosides are widely used to treat infections of Pseudomonas aeruginosa. Genes encoding aminoglycoside-modifying enzymes (AMEs), acquired by horizontal gene transfer, are commonly associated with aminoglycoside resistance, but their effects have not been quantified. The aim of this research was to determine the extent to which AMEs increase the antibiotic tolerance of P. aeruginosa. Bioinformatics analysis identified AME-encoding genes in 48 out of 619 clinical isolates of P. aeruginosa, with ant(2′)-Ia and aac(6′)-Ib3, which are associated with tobramcyin and gentamicin resistance, being the most common. These genes and aph(3′)-VIa (amikacin resistance) were deleted from antibiotic-resistant strains. Antibiotic minimum inhibitory concentrations (MICs) were reduced by up to 64-fold, making the mutated bacteria antibiotic-sensitive in several cases. Introduction of the same genes into four antibiotic-susceptible P. aeruginosa strains increased the MIC by up to 128-fold, making the bacteria antibiotic-resistant in all cases. The cloned genes also increased the MIC in mutants lacking the MexXY-OprM efflux pump, which is an important contributor to aminoglycoside resistance, demonstrating that AMEs and this efflux pump act independently in determining levels of aminoglycoside tolerance. Quantification of the effects of AMEs on antibiotic susceptibility demonstrates the large effect that these enzymes have on antibiotic resistance.
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Antimicrobial resistance determinants in silage. Sci Rep 2022; 12:5243. [PMID: 35347213 PMCID: PMC8960843 DOI: 10.1038/s41598-022-09296-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/21/2022] [Indexed: 11/12/2022] Open
Abstract
Animal products may play a role in developing and spreading antimicrobial resistance in several ways. On the one hand, residues of antibiotics not adequately used in animal farming can enter the human body via food. However, resistant bacteria may also be present in animal products, which can transfer the antimicrobial resistance genes (ARG) to the bacteria in the consumer’s body by horizontal gene transfer. As previous studies have shown that fermented foods have a meaningful ARG content, it is indicated that such genes may also be present in silage used as mass feed in the cattle sector. In our study, we aspired to answer what ARGs occur in silage and what mobility characteristics they have? For this purpose, we have analyzed bioinformatically 52 freely available deep sequenced silage samples from shotgun metagenome next-generation sequencing. A total of 16 perfect matched ARGs occurred 54 times in the samples. More than half of these ARGs are mobile because they can be linked to integrative mobile genetic elements, prophages or plasmids. Our results point to a neglected but substantial ARG source in the food chain.
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Radu E, Woegerbauer M, Rab G, Oismüller M, Strauss P, Hufnagl P, Gottsberger RA, Krampe J, Weyermair K, Kreuzinger N. Resilience of agricultural soils to antibiotic resistance genes introduced by agricultural management practices. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:143699. [PMID: 33307498 DOI: 10.1016/j.scitotenv.2020.143699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/11/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Antimicrobial resistance (AR) represents a global threat in human and veterinary medicine. In that regard, AR proliferation and dissemination in agricultural soils after manure application raises concerns on the enrichment of endogenous soil bacterial population with allochthonous antibiotic resistance genes (ARGs). Natural resilience of agricultural soils and background concentrations of ARGs play key roles in the mitigation of AR propagation in natural environments. In the present study, we carried out a longitudinal sampling campaign for two crop vegetation periods to monitor spatial and temporal changes in the abundance of seven clinically relevant ARGs (sul1, ermB, vanA, aph(3')-IIa, aph(3')-IIIa, blaTEM-1 and tet(W)) and ribosomal 16S RNA. The absolute and relative abundances of the selected ARGs were quantified in total community DNA extracted from agricultural (manured and non-manured) and forest soils, fresh pig faeces and manure slurry. We observed that ARG concentrations return to background levels after manure-induced exposure within a crop growing season, highlighting the resilience capacity of soil. Naturally occurring high background concentrations of ARGs can be found in forest soil in due distance under low anthropogenic influences. It was observed that pesticide application increases the concentrations of three out of seven ARGs tested (ermB, aph(3')-IIIa and tet(W)). Moreover, we noticed that the absolute abundances of sul1, vanA, ermB and blaTEM-1 resistance genes show an increase by 100- to 10,000- fold, from maturation of fresh pig faeces to manure. Outcomes of our study suggest that agricultural soil environments show a strong capacity to alleviate externally induced disturbances in endogenous ARG concentrations. Naturally occurring high concentrations of ARGs are present also in low human impacted environments represented by the indigenous resistome.
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Affiliation(s)
- Elena Radu
- Institute for Water Quality and Resource Management, University of Technology Vienna, Austria; Austrian Agency for Health and Food Safety AGES, Division of Data, Statistics and Risk Assessment, Department for Integrative Risk Assessment, Vienna, Austria; Institute of Virology Stefan S. Nicolau, Romanian Academy of Science, Bucharest, Romania.
| | - Markus Woegerbauer
- Austrian Agency for Health and Food Safety AGES, Division of Data, Statistics and Risk Assessment, Department for Integrative Risk Assessment, Vienna, Austria
| | - Gerhard Rab
- Institute of Hydraulic Engineering and Water Resources Management, University of Technology Vienna, Austria; Institute for Land and Water Management Research, Federal Agency for Water Management, Petzenkirchen, Austria
| | - Matthias Oismüller
- Institute of Hydraulic Engineering and Water Resources Management, University of Technology Vienna, Austria; Institute for Land and Water Management Research, Federal Agency for Water Management, Petzenkirchen, Austria
| | - Peter Strauss
- Institute for Land and Water Management Research, Federal Agency for Water Management, Petzenkirchen, Austria
| | - Peter Hufnagl
- Austrian Agency for Health and Food Safety AGES, Department for Medical Microbiology and Hygiene, Vienna, Austria
| | - Richard A Gottsberger
- Austrian Agency for Health and Food Safety AGES, Department for Molecular Diagnostic of Plant Diseases, Vienna, Austria
| | - Jörg Krampe
- Institute for Water Quality and Resource Management, University of Technology Vienna, Austria
| | - Karin Weyermair
- Austrian Agency for Health and Food Safety AGES, Division of Data, Statistics and Risk Assessment, Department of Statistics and Analytical Epidemiology, Graz, Austria
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, University of Technology Vienna, Austria
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Zeng Q, Liao C, Terhune J, Wang L. Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysis. MICROBIOME 2019; 7:155. [PMID: 31818316 PMCID: PMC6902485 DOI: 10.1186/s40168-019-0773-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 12/02/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Drug-resistant fish pathogens can cause significant economic loss to fish farmers. Since 2012, florfenicol has become an approved drug for treating both septicemia and columnaris diseases in freshwater fish. Due to the limited drug options available for aquaculture, the impact of the therapeutical florfenicol treatment on the microbiota landscape as well as the resistome present in the aquaculture farm environment needs to be evaluated. RESULTS Time-series metagenomic analyses were conducted to the aquatic microbiota present in the tank-based catfish production systems, in which catfish received standard therapeutic 10-day florfenicol treatment following the federal veterinary regulations. Results showed that the florfenicol treatment shifted the structure of the microbiota and reduced the biodiversity of it by acting as a strong stressor. Planctomycetes, Chloroflexi, and 13 other phyla were susceptible to the florfenicol treatment and their abundance was inhibited by the treatment. In contrast, the abundance of several bacteria belonging to the Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia phyla increased. These bacteria with increased abundance either harbor florfenicol-resistant genes (FRGs) or had beneficial mutations. The florfenicol treatment promoted the proliferation of florfenicol-resistant genes. The copy number of phenicol-specific resistance genes as well as multiple classes of antibiotic-resistant genes (ARGs) exhibited strong correlations across different genetic exchange communities (p < 0.05), indicating the horizontal transfer of florfenicol-resistant genes among these bacterial species or genera. Florfenicol treatment also induced mutation-driven resistance. Significant changes in single-nucleotide polymorphism (SNP) allele frequencies were observed in membrane transporters, genes involved in recombination, and in genes with primary functions of a resistance phenotype. CONCLUSIONS The therapeutical level of florfenicol treatment significantly altered the microbiome and resistome present in catfish tanks. Both intra-population and inter-population horizontal ARG transfer was observed, with the intra-population transfer being more common. The oxazolidinone/phenicol-resistant gene optrA was the most prevalent transferred ARG. In addition to horizontal gene transfer, bacteria could also acquire florfenicol resistance by regulating the innate efflux systems via mutations. The observations made by this study are of great importance for guiding the strategic use of florfenicol, thus preventing the formation, persistence, and spreading of florfenicol-resistant bacteria and resistance genes in aquaculture.
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Affiliation(s)
- Qifan Zeng
- Department of Animal Sciences, Auburn University, Auburn, AL, 36830, USA
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Science, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Chao Liao
- Department of Animal Sciences, Auburn University, Auburn, AL, 36830, USA
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Jeffery Terhune
- Department of Fisheries and Allied Aquacultures, 203 Swingle Hall, Auburn University, Auburn, AL, 36849, USA
| | - Luxin Wang
- Department of Animal Sciences, Auburn University, Auburn, AL, 36830, USA.
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA.
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Belaynehe KM, Shin SW, Hong-Tae P, Yoo HS. Occurrence of aminoglycoside-modifying enzymes among isolates of Escherichia coli exhibiting high levels of aminoglycoside resistance isolated from Korean cattle farms. FEMS Microbiol Lett 2018. [PMID: 28637330 DOI: 10.1093/femsle/fnx129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
This study investigated 247 Escherichia coli isolates collected from four cattle farms to characterize aminoglycoside-modifying enzyme (AME) genes, their plasmid replicons and transferability. Out of 247 isolates a high number of isolates (total 202; 81.78%) were found to be resistant to various antibiotics by disc diffusion. Of the 247 strains, 139 (56.3%) were resistant to streptomycin, and other antibiotic resistances followed as tetracycline (12.15%), ampicillin (7%), chloramphenicol (5.7%) and trimethoprim-sulfamethoxazole (0.8%). Among 247 isolates B1 was the predominant phylogenetic group identified comprising 151 isolates (61.1%), followed by groups A (27.9%), D (7%) and B2 (4%). Out of 139 isolates investigated for AME, 130 (93.5%) isolates carried at least one AME gene. aph3″-1a and aph3″-1b (46%) were the principal genes detected, followed by aac3-IVa (34.5%). ant2″-1a was the least detected gene (2.2%). Nine (6.5%) strains carried no AME genes. Twelve (63.2%) among 19 isolates transferred an AME gene to a recipient and aph3΄-1a was the dominant transferred gene. Transferability mainly occurred via the IncFIB replicon type (52.6%). Pulsed-field gel electrophoresis typing demonstrated a higher degree of diversity with 14 distinct cluster types. This result suggests that commensal microflora from food-producing animals has a tremendous ability to harbor and transfer AME genes, and poses a potential risk by dissemination of resistance to humans through the food chain.
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Affiliation(s)
- Kuastros Mekonnen Belaynehe
- Department of infectious diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung Won Shin
- Department of infectious diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | | | - Han Sang Yoo
- Department of infectious diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
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Occurrence and characterisation of ESBL-encoding plasmids among Escherichia coli isolates from fresh vegetables. Vet Microbiol 2018; 219:63-69. [PMID: 29778206 DOI: 10.1016/j.vetmic.2018.03.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/22/2018] [Accepted: 03/28/2018] [Indexed: 01/11/2023]
Abstract
Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates have been increasingly reported in different reservoirs. The aims of this study were to investigate the presence of ESBL-producing E. coli in fresh vegetables and to characterise their ESBL gene-carrying plasmids. Among the 245 samples from vegetables investigated during 2011-2013, seven putative ESBL-producing E. coli (salad n = 2, sprouts n = 5) were found. They were subjected to ESBL phenotypic confirmatory tests, detection/sequencing of ESBL genes, antimicrobial susceptibility testing (AST), phylotyping, XbaI-macrorestriction analysis, multilocus sequence typing and transformation. Transformants were characterised by AST, S1-nuclease PFGE, replicon typing, conjugation and investigated for co-located antimicrobial resistance genes. Two ESBL gene-carrying plasmids were sequenced using a HiSeq 2500 system. The seven isolates were confirmed as ESBL producers, displayed unrelated XbaI-patterns and unique sequence types (STs) and belonged to the phylogroups A, B1 or D. The ESBL genes were located on plasmids. Two plasmids carrying blaCTX-M-14 genes (incompatibility group IncK or IncHI2) were seen in isolates from salad (ST973) and sprout (ST527). Two blaCTX-M-15- (IncFIB; non-typeable) and the IncN blaCTX-M-65- and IncHI2 blaCTX-M-125-carrying plasmids were found in isolates from sprouts (ST410, ST847, ST10, ST542). All plasmids were conjugative, except for the IncFIA-FIB blaCTX-M-2-carrying plasmid. Sequence analysis of two plasmids identified the ESBL genes in close location to other resistance genes: sulfonamide resistance gene sul2, streptomycin resistance genes strA and strB, the plasmid-mediated quinolone resistance gene qnrS1 and blaTEM-1 (sul2-strA-strB-IS66-blaTEM-1-tnpR-ΔtnpA-ISEcp1-blaCTX-M-15-Δorf477-ΔtnpA-qnrS1) or the fosfomycin resistance gene fosA3 (ΔISEcp1-blaCTX-M-125-ΔIS903B-fosA3). These observations underline the importance of vegetables as reservoirs for multidrug resistant ESBL-producing E. coli.
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Abstract
Phylogenetic relationships between species in the genus Photobacterium have been poorly studied despite pathogenic and ecological relevance of some of its members. This is the first phylogenetic study that includes new species of Photobacterium (validated or not) that have not been included in any of the previously described clades, using 16S rRNA sequences and multilocus sequence analysis (MLSA) in concatenated sequences of gyrB, gapA, topA, ftsZ and mreB housekeeping genes. Sequence analysis has been implemented using Maximum-parsimony (MP), Neighbour-joining (NJ) and Maximum likelihood (ML) treeing methods and the predicted evolutionary relationship between the Photobacterium clades was established on the basis of bootstrap values of >75% for 16S rRNA sequences and MLSA. We have grouped 22 species of the genus Photobacterium into the following 5 clades: Phosphoreum (comprises P. aquimaris, “P. carnosum,” P. iliopiscarium, P. kishitanii, P. phosphoreum, “P. piscicola” and “P. toruni”); clade Profundum (composed of P. aestuarii, P. alginatilyticum, P. frigidiphilum, P. indicum, P. jeanii, P. lipolyticum, “P. marinum,” and P. profundum); clade Damselae (two subspecies of P. damselae, damselae and piscicida); and two new clades: clade Ganghwense (includes P. aphoticum, P. aquae, P. galatheae, P. ganghwense, P. halotolerans, P. panuliri and P. proteolyticum); and clade Leiognathi (composed by P. angustum, P. leiognathi subsp. leiognathi and “P. leiognathi subsp. mandapamensis”). Two additional clades, Rosenbergii and Swingsii, were formed using a phylogenetic method based on 16S rRNA gene, although they are not confirmed by any MLSA methods. Only P. aplysiae could not be included in none of the established clade, constituting an orphan clade.
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Affiliation(s)
- Alejandro M Labella
- Department of Microbiology, Faculty of Sciences, Universidad de Malaga, 29071 Malaga, Spain.
| | - M Dolores Castro
- Department of Microbiology, Faculty of Sciences, Universidad de Malaga, 29071 Malaga, Spain.
| | - Manuel Manchado
- Puerto de Santa María, Junta de Andalucía, IFAPA Centro El Toruño, 11500 Cadiz, Spain.
| | - Juan J Borrego
- Department of Microbiology, Faculty of Sciences, Universidad de Malaga, 29071 Malaga, Spain.
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Oruganty K, Talevich EE, Neuwald AF, Kannan N. Identification and classification of small molecule kinases: insights into substrate recognition and specificity. BMC Evol Biol 2016; 16:7. [PMID: 26738562 PMCID: PMC4702295 DOI: 10.1186/s12862-015-0576-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/21/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Many prokaryotic kinases that phosphorylate small molecule substrates, such as antibiotics, lipids and sugars, are evolutionarily related to Eukaryotic Protein Kinases (EPKs). These Eukaryotic-Like Kinases (ELKs) share the same overall structural fold as EPKs, but differ in their modes of regulation, substrate recognition and specificity-the sequence and structural determinants of which are poorly understood. RESULTS To better understand the basis for ELK specificity, we applied a Bayesian classification procedure designed to identify sequence determinants responsible for functional divergence. This reveals that a large and diverse family of aminoglycoside kinases, characterized members of which are involved in antibiotic resistance, fall into major sub-groups based on differences in putative substrate recognition motifs. Aminoglycoside kinase substrate specificity follows simple rules of alternating hydroxyl and amino groups that is strongly correlated with variations at the DFG + 1 position. CONCLUSIONS Substrate specificity determining features in small molecule kinases are mostly confined to the catalytic core and can be identified based on quantitative sequence and crystal structure comparisons.
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Affiliation(s)
- Krishnadev Oruganty
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Eric E Talevich
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA.
| | - Andrew F Neuwald
- Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, 21201, USA.
| | - Natarajan Kannan
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
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Woegerbauer M, Zeinzinger J, Gottsberger RA, Pascher K, Hufnagl P, Indra A, Fuchs R, Hofrichter J, Kopacka I, Korschineck I, Schleicher C, Schwarz M, Steinwider J, Springer B, Allerberger F, Nielsen KM, Fuchs K. Antibiotic resistance marker genes as environmental pollutants in GMO-pristine agricultural soils in Austria. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 206:342-351. [PMID: 26232739 DOI: 10.1016/j.envpol.2015.07.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 07/15/2015] [Accepted: 07/18/2015] [Indexed: 06/04/2023]
Abstract
Antibiotic resistance genes may be considered as environmental pollutants if anthropogenic emission and manipulations increase their prevalence above usually occurring background levels. The prevalence of aph(3')-IIa/nptII and aph(3')-IIIa/nptIII - frequent marker genes in plant biotechnology conferring resistance to certain aminoglycosides - was determined in Austrian soils from 100 maize and potato fields not yet exposed to but eligible for GMO crop cultivation. Total soil DNA extracts were analysed by nptII/nptIII-specific TaqMan real time PCR. Of all fields 6% were positive for nptII (median: 150 copies/g soil; range: 31-856) and 85% for nptIII (1190 copies/g soil; 13-61600). The copy-number deduced prevalence of nptIII carriers was 14-fold higher compared to nptII. Of the cultivable kanamycin-resistant soil bacteria 1.8% (95% confidence interval: 0-3.3%) were positive for nptIII, none for nptII (0-0.8%). The nptII-load of the studied soils was low rendering nptII a typical candidate as environmental pollutant upon anthropogenic release into these ecosystems.
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Affiliation(s)
- Markus Woegerbauer
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria.
| | - Josef Zeinzinger
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Richard Alexander Gottsberger
- Division for Food Security, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Kathrin Pascher
- Department of Integrative Biology and Biodiversity Research (DIB), Institute of Zoology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Hufnagl
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Alexander Indra
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Reinhard Fuchs
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Johannes Hofrichter
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Ian Kopacka
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | | | - Corina Schleicher
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Michael Schwarz
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Johann Steinwider
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
| | - Burkhard Springer
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Franz Allerberger
- Division for Public Health, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna, Austria
| | - Kaare M Nielsen
- GenØk - Centre for Biosafety and Department of Pharmacy, University of Tromsø, Norway
| | - Klemens Fuchs
- Division for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit), Vienna and Graz, Austria
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