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Mitchell SW, Moran RA, Elbourne LDH, Chapman B, Bull M, Muscatello G, Coleman NV. Impacts of Domestication and Veterinary Treatment on Mobile Genetic Elements and Resistance Genes in Equine Fecal Bacteria. Appl Environ Microbiol 2023; 89:e0159022. [PMID: 36988354 PMCID: PMC10057962 DOI: 10.1128/aem.01590-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/05/2023] [Indexed: 03/09/2023] Open
Abstract
Antimicrobial resistance in bacteria is a threat to both human and animal health. We aimed to understand the impact of domestication and antimicrobial treatment on the types and numbers of resistant bacteria, antibiotic resistance genes (ARGs), and class 1 integrons (C1I) in the equine gut microbiome. Antibiotic-resistant fecal bacteria were isolated from wild horses, healthy farm horses, and horses undergoing veterinary treatment, and isolates (9,083 colonies) were screened by PCR for C1I; these were found at frequencies of 9.8% (vet horses), 0.31% (farm horses), and 0.05% (wild horses). A collection of 71 unique C1I+ isolates (17 Actinobacteria and 54 Proteobacteria) was subjected to resistance profiling and genome sequencing. Farm horses yielded mostly C1I+ Actinobacteria (Rhodococcus, Micrococcus, Microbacterium, Arthrobacter, Glutamicibacter, Kocuria), while vet horses primarily yielded C1I+ Proteobacteria (Escherichia, Klebsiella, Enterobacter, Pantoea, Acinetobacter, Leclercia, Ochrobactrum); the vet isolates had more extensive resistance and stronger PC promoters in the C1Is. All integrons in Actinobacteria were flanked by copies of IS6100, except in Micrococcus, where a novel IS5 family element (ISMcte1) was implicated in mobilization. In the Proteobacteria, C1Is were predominantly associated with IS26 and also IS1, Tn21, Tn1721, Tn512, and a putative formaldehyde-resistance transposon (Tn7489). Several large C1I-containing plasmid contigs were retrieved; two of these (plasmid types Y and F) also had extensive sets of metal resistance genes, including a novel copper-resistance transposon (Tn7519). Both veterinary treatment and domestication increase the frequency of C1Is in equine gut microflora, and each of these anthropogenic factors selects for a distinct group of integron-containing bacteria. IMPORTANCE There is increasing acknowledgment that a "one health" approach is required to tackle the growing problem of antimicrobial resistance. This requires that the issue is examined from not only the perspective of human medicine but also includes consideration of the roles of antimicrobials in veterinary medicine and agriculture and recognizes the importance of other ecological compartments in the dissemination of ARGs and mobile genetic elements such as C1I. We have shown that domestication and veterinary treatment increase the frequency of occurrence of C1Is in the equine gut microflora and that, in healthy farm horses, the C1I are unexpectedly found in Actinobacteria, while in horses receiving antimicrobial veterinary treatments, a taxonomic shift occurs, and the more typical integron-containing Proteobacteria are found. We identified several new mobile genetic elements (plasmids, insertion sequences [IS], and transposons) on genomic contigs from the integron-containing equine bacteria.
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Affiliation(s)
- Scott W. Mitchell
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Robert A. Moran
- Institute of Microbiology and Infection, School of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Liam D. H. Elbourne
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Belinda Chapman
- Quantal Bioscience Pty Ltd, Carlingford, New South Wales, Australia
| | - Michelle Bull
- Quantal Bioscience Pty Ltd, Carlingford, New South Wales, Australia
| | - Gary Muscatello
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Nicholas V. Coleman
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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El-Badawy MF, El-Far SW, Althobaiti SS, Abou-Elazm FI, Shohayeb MM. The First Egyptian Report Showing the Co-Existence of bla NDM-25, bla OXA-23, bla OXA-181, and bla GES-1 Among Carbapenem-Resistant K. pneumoniae Clinical Isolates Genotyped by BOX-PCR. Infect Drug Resist 2020; 13:1237-1250. [PMID: 32425561 PMCID: PMC7196799 DOI: 10.2147/idr.s244064] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/04/2020] [Indexed: 12/18/2022] Open
Abstract
Background and Objective The emergence of carbapenem-resistant K. pneumoniae (CRKP) continues to escalate and is alarming because of the emergence of pan drug-resistant strains. The objective of this study was to investigate the existence of 12 carbapenemase genes among CRKP clinical isolates. Methods Ninety-six Klebsiella spp. clinical isolates were collected. The isolates were identified phenotypically and genotypically. These isolates were screened for susceptibility to 24 different antibiotics. The modified Hodge test (MHT) and the Carba Nordmann/Poirel (NP) test were used to phenotypically screen carbapenem-resistant strains for carbapenemase production. Phenotypic characterization of carbapenemases was performed using the combined disk synergy test (CDST). Additionally, the presence of 12 carbapenemase genes in CRKP isolates was investigated. The DNA sequence of bla NDM and bla GES genes was determined. The BOX-PCR technique was used to determine the clonal relationship between CRKP isolates. Results All carbapenem-resistant isolates were related to K. pneumoniae. Susceptibility testing showed that 19.79% (19/96) of the collected isolates were carbapenem-resistant. Of the CRKP isolates, 68.42% (13/19) tested positive for the MHT and Carba NP test. CDST showed that 42.11% (8/19), 63.16% (12/19), 47.37% (9/19), and 73.68% (14/19) of the CRKP isolates tested positive for the inhibitory effect of clavulanic acid, sulbactam, phenylboronic acid, and tazobactam, respectively, while 84.21% (16/19) and 68.42% (13/16) tested positive for the inhibitory effect of EDTA and mercaptopropionic acid, respectively. It was found that 10.53% (2/19) of the isolates tested positive for the inhibitory effect of sodium chloride. Molecular investigation of carbapenemases showed that 26.32% (5/19), 73.68% (14/19), 21.05% (4/19), 10.53% (2/19), and 5.26% (1/19) of the isolates tested positive for bla NDM, bla OXA-48, bla OXA-181, bla OXA-51, and bla OXA-23, respectively. None of the isolates tested positive for bla OXA-40 and bla OXA-58. Two allelic variants of bla NDM (bla NDM-1 and bla NDM-25) were detected. BOX-PCR revealed high clonal relatedness between CRKP isolates. Conclusion MHT was more sensitive than Carba NP test for evaluating carbapenemase production and class D carbapenemase genes were the most prevalent of the 12 carbapenemase genes that were evaluated.
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Affiliation(s)
- Mohamed F El-Badawy
- Division of Pharmaceutical Microbiology, Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif, Kingdom of Saudi Arabia.,Department of Microbiology and Immunology, Faculty of Pharmacy, Misr University for Science and Technology, 6th of October City, Egypt
| | - Shaymaa W El-Far
- Division of Pharmaceutical Microbiology, Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif, Kingdom of Saudi Arabia
| | | | - Fatma I Abou-Elazm
- Department of Microbiology and Immunology, Faculty of Pharmacy, Misr University for Science and Technology, 6th of October City, Egypt
| | - Mohamed M Shohayeb
- Department of Microbiology and Biotechnology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
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Nagib S, Glaeser SP, Eisenberg T, Sammra O, Lämmler C, Kämpfer P, Schauerte N, Geiger C, Kaim U, Prenger-Berninghoff E, Becker A, Abdulmawjood A. Fatal infection in three Grey Slender Lorises (Loris lydekkerianus nordicus) caused by clonally related Trueperella pyogenes. BMC Vet Res 2017; 13:273. [PMID: 28851356 PMCID: PMC5576266 DOI: 10.1186/s12917-017-1171-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/09/2017] [Indexed: 11/10/2022] Open
Abstract
Background Trueperella pyogenes is a worldwide known bacterium causing mastitis, abortion and various other pyogenic infections in domestic animals like ruminants and pigs. In this study we represent the first case report of three unusual fatal infections of Grey Slender Lorises caused by Trueperella pyogenes. Meanwhile, this study represents the first in-depth description of the multilocus sequence analysis (MLSA) on T. pyogenes species. Case presentation Three Trueperella pyogenes were isolated from three different Grey Slender Lorises, which died within a period of two years at Frankfurt Zoo (Frankfurt am Main - Germany). The three Grey Slender Loris cases were suffering from severe sepsis and died from its complication. During the bacteriological investigation of the three cases, the T. pyogenes were isolated from different organisms in each case. The epidemiological relationship between the three isolates could be shown by four genomic DNA fingerprint methods (ERIC-PCR, BOX-PCR, (GTG)5-PCR, and RAPD-PCR) and by multilocus sequence analysis (MLSA) investigating four different housekeeping genes (fusA-tuf-metG-gyrA). Conclusion In this study, we clearly showed by means of using three different rep-PCRs, by RAPD-PCR and by MLSA that the genomic fingerprinting of the investigated three T. pyogenes have the same clonal origin and are genetically identical. These results suggest that the same isolate contaminated the animal’s facility and subsequently caused cross infection between the three different Grey Slender Lorises. To the best of our knowledge, this is the first epidemiological approach concentrating on T. pyogenes using MLSA.
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Affiliation(s)
- Samy Nagib
- Institut für Pharmakologie und Toxikologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, D-35392, Gießen, Germany
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 26-32, D-35392, Gießen, Germany
| | - Tobias Eisenberg
- Landesbetrieb Hessisches Landeslabor, Schubertstraße. 60, D-35392, Gießen, Germany
| | - Osama Sammra
- Institut für Pharmakologie und Toxikologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, D-35392, Gießen, Germany
| | - Christoph Lämmler
- Institut für Pharmakologie und Toxikologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, D-35392, Gießen, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 26-32, D-35392, Gießen, Germany
| | - Nicole Schauerte
- Zoologischer Garten Frankfurt am Main, Bernhard-Grzimek-Allee 1, D-60316, Frankfurt, Germany
| | - Christina Geiger
- Zoologischer Garten Frankfurt am Main, Bernhard-Grzimek-Allee 1, D-60316, Frankfurt, Germany
| | - Ute Kaim
- Landesbetrieb Hessisches Landeslabor, Schubertstraße. 60, D-35392, Gießen, Germany
| | - Ellen Prenger-Berninghoff
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, Frankfurter Straße. 85-91, D-35392, Gießen, Germany
| | - André Becker
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173, Hannover, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173, Hannover, Germany.
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Mohan B, Hallur V, Singh G, Sandhu HK, Appannanavar SB, Taneja N. Occurrence of blaNDM-₁ & absence of blaKPC genes encoding carbapenem resistance in uropathogens from a tertiary care centre from north India. Indian J Med Res 2016; 142:336-43. [PMID: 26458351 PMCID: PMC4669870 DOI: 10.4103/0971-5916.166601] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background & objectives: Carbapenem resistance mediated by carbapenemases is increasingly being reported worldwide. This study was conducted to know the occurrence of important carbapenem resistance encoding genes in Gram-negative bacilli (GNB) causing complicated urinary tract infection (CUTI), and to look at the genetic diversity of these isolates. Methods: The study was carried out on 166 consecutive carbapenem resistant uropathogens (CRU) isolated from cases with CUTI during 2008 and 2012. Carbapenemase production was characterized phenotypically and polymerase chain reaction was used to detect blaVIM, blaIMP, blaKPC, and blaNDM-1. BOX- PCR was done on 80 randomly selected isolates for molecular typing. Results: The blaVIM gene was present in 34 (43.6%), blaIMP in five (6.4%) and none of the isolates from 2008 had blaNDM-1 or blaKPC genes. Among the isolates from 2012, blaNDM-1 gene was present in 47 (53.4%), blaVIM in 19 (24.4%), blaIMP in one (1.1%) and none had blaKPC. There were nine isolates during the two years which had multiple genes encoding carbapenemases; while 66 did not have any of the genes tested. Of the 80 isolates subjected to BOX-PCR, 58 could be used for analysis and showed, presence of multiple clusters of carbapenem resistant isolates and absence of a single dominant clone. Interpretation & conclusions: The blaNDM-1 gene was absent in our isolates obtained during 2008 but was present amongst Enterobacteriaceae isolated in 2012. The blaKPC gene was also not found. Nine isolates obtained during the two years had multiple genes encoding carbapenemases confirming the previous reports of emergence of GNB containing genes encoding multiple carbapenemases. Typing using BOX-PCR indicated that this emergence was not because of clonal expansion of a single strain, and multiple strains were circulating at a single point of time.
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Affiliation(s)
| | | | | | | | | | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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Pan Y, Kong KF, Tsang JSH. Complete genome sequence and characterization of the haloacid-degrading Burkholderia caribensis MBA4. Stand Genomic Sci 2015; 10:114. [PMID: 26629309 PMCID: PMC4665904 DOI: 10.1186/s40793-015-0109-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 11/20/2015] [Indexed: 11/11/2022] Open
Abstract
Burkholderia caribensis MBA4 was isolated from soil for its capability to grow on haloacids. This bacterium has a genome size of 9,482,704 bp. Here we report the genome sequences and annotation, together with characteristics of the genome. The complete genome sequence consists of three replicons, comprising 9056 protein-coding genes and 80 RNA genes. Genes responsible for dehalogenation and uptake of haloacids were arranged as an operon. While dehalogenation of haloacetate would produce glycolate, three glycolate operons were identified. Two of these operons contain an upstream glcC regulator gene. It is likely that the expression of one of these operons is responsive to haloacetate. Genes responsible for the metabolism of dehalogenation product of halopropionate were also identified.
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Affiliation(s)
- Yanling Pan
- Molecular Microbiology Laboratory, School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR China
| | - Ka Fai Kong
- Molecular Microbiology Laboratory, School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR China
| | - Jimmy S H Tsang
- Molecular Microbiology Laboratory, School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR China
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Korona-Glowniak I, Malm A. Characteristics of Streptococcus pneumoniae strains colonizing upper respiratory tract of healthy preschool children in Poland. ScientificWorldJournal 2012; 2012:732901. [PMID: 22927787 PMCID: PMC3419415 DOI: 10.1100/2012/732901] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 05/27/2012] [Indexed: 01/04/2023] Open
Abstract
Antibiotic resistant and invasive pneumococci may spread temporally and locally in day care centers (DCCs). We examined 267 children attending four DCCs located in the same city and 70 children staying at home in three seasons (autumn, winter, and spring) to determine prevalence, serotype distribution, antibiotic resistance patterns, and transmission of pneumococcal strains colonizing upper respiratory tract of healthy children without antipneumococcal vaccination. By pheno- and genotyping, we determined clonality of pneumococci, including drug-resistant strains. The average carriage of pneumococci in three seasons was 38.2%. 73.4% and 80.4% of the isolates belonged to serotypes present in 10- and 13-valent conjugate vaccine, respectively. Among the pneumococcal strains, 33.3% were susceptible to all antimicrobial tested and 39.2% had decreased susceptibility to penicillin. Multidrug resistance was common (35.7%); 97.5% of drug-resistant isolates represented serotypes included to 10- and 13-valent conjugate vaccine. According to BOX-PCR, clonality definitely was observed only in case of serotype 14. Multivariate analysis determined DCC attendance as strongly related to pneumococcal colonization in all three seasons, but important seasonal differences were demonstrated. In children attending DCCs, we observed dynamic turnover of pneumococcal strains, especially penicillin nonsusceptible and multidrug resistant, which were mostly distributed among serotypes included to available pneumococcal conjugate vaccines.
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Affiliation(s)
- Izabela Korona-Glowniak
- Department of Pharmaceutical Microbiology, Medical University of Lublin, Chodzki 1, Lublin, Poland.
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