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Podnecky NL, Fredheim EGA, Kloos J, Sørum V, Primicerio R, Roberts AP, Rozen DE, Samuelsen Ø, Johnsen PJ. Conserved collateral antibiotic susceptibility networks in diverse clinical strains of Escherichia coli. Nat Commun 2018; 9:3673. [PMID: 30202004 PMCID: PMC6131505 DOI: 10.1038/s41467-018-06143-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/16/2018] [Indexed: 01/09/2023] Open
Abstract
There is urgent need to develop novel treatment strategies to reduce antimicrobial resistance. Collateral sensitivity (CS), where resistance to one antimicrobial increases susceptibility to other drugs, might enable selection against resistance during treatment. However, the success of this approach would depend on the conservation of CS networks across genetically diverse bacterial strains. Here, we examine CS conservation across diverse Escherichia coli strains isolated from urinary tract infections. We determine collateral susceptibilities of mutants resistant to relevant antimicrobials against 16 antibiotics. Multivariate statistical analyses show that resistance mechanisms, in particular efflux-related mutations, as well as the relative fitness of resistant strains, are principal contributors to collateral responses. Moreover, collateral responses shift the mutant selection window, suggesting that CS-informed therapies may affect evolutionary trajectories of antimicrobial resistance. Our data allow optimism for CS-informed therapy and further suggest that rapid detection of resistance mechanisms is important to accurately predict collateral responses.
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Affiliation(s)
- Nicole L Podnecky
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway.
| | - Elizabeth G A Fredheim
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Julia Kloos
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Vidar Sørum
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Raul Primicerio
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Adam P Roberts
- Department of Parasitology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, PO Box 9505, 2300 RA, Leiden, The Netherlands
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9037, Tromsø, Norway
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway.
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Rhodes KA, Somprasong N, Podnecky NL, Mima T, Chirakul S, Schweizer HP. Molecular determinants of Burkholderia pseudomallei BpeEF-OprC efflux pump expression. Microbiology (Reading) 2018; 164:1156-1167. [PMID: 30024368 DOI: 10.1099/mic.0.000691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Burkholderia pseudomallei, the cause of melioidosis, is intrinsically resistant to many antibiotics. Acquired multidrug resistance, including resistance to doxycycline and co-trimoxazole used for melioidosis eradication phase therapy, is mainly attributed to constitutive expression of the BpeEF-OprC efflux pump. Constitutive expression of this pump is caused by mutations affecting two highly similar LysR-type transcriptional regulators (LTTR), BpeT and BpeS, but their interaction with the regulatory region governing BpeEF-OprC expression has not yet been studied. The bpeE-bpeF-oprC genes are distally located in the llpE-bpeE-bpeF-oprC operon. The llpE gene encodes a putative lipase/esterase of unknown function. We show that in a bpeT mutant llpE is constitutively co-transcribed with bpeE-bpeF-oprC. As expected from previous studies with B. cenocepacia, deletion of llpE does not affect antibiotic efflux. Using transcriptional bpeE'-lacZ fusions, we demonstrate that the 188 bp bpeT-llpE intergenic region located between bpeT and the llpE-bpeE-bpeF-oprC operon contains regulatory elements needed for control of bpeT and llpE-bpeE-bpeF-oprC operon expression. By native polyacrylamide gel electrophoresis and electrophoretic mobility shift assays with purified recombinant BpeT and BpeS proteins, we show BpeT and BpeS form oligomers that share a 14 bp binding site overlapping the essential region required for llpE-bpeE-bpeF-oprC expression. The binding site contains the conserved T-N11-A LTTR box motif involved in binding of LysR proteins, which in concert with two other possible LTTR boxes may mediate BpeT and BpeS regulation of BpeEF-OprC expression. These studies form the basis for further investigation of BpeEF-OprC expression and regulation at the molecular level by yet unknown external stimuli.
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Affiliation(s)
- Katherine A Rhodes
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,†Present address: University of Arizona BIO5 Institute, Tucson, AZ 85721, USA
| | - Nawarat Somprasong
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Nicole L Podnecky
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,‡Present address: Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Tromsø, 9037 Tromsø, Norway
| | - Takehiko Mima
- 1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.,§Present address: Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Sunisa Chirakul
- 2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Herbert P Schweizer
- 3Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,2Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,1Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
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Kolton CB, Podnecky NL, Shadomy SV, Gee JE, Hoffmaster AR. Bacillus anthracis gamma phage lysis among soil bacteria: an update on test specificity. BMC Res Notes 2017; 10:598. [PMID: 29145870 PMCID: PMC5691394 DOI: 10.1186/s13104-017-2919-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 10/27/2016] [Accepted: 11/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacillus anthracis, which causes anthrax in humans and animals, is enzootic in parts of the U.S. state of Texas where cases are typically reported in animals annually. The gamma phage lysis assay is a common diagnostic method for identification of B. anthracis and is based on the bacterium's susceptibility to lysis. This test has been shown to be 97% specific for B. anthracis, as a small number of strains of other Bacillus spp. are known to be susceptible. In this study, we evaluated the performance of a combination of B. anthracis diagnostic assays on 700 aerobic, spore-forming isolates recovered from soil collected in Texas. These assays include phenotypic descriptions, gamma phage susceptibility, and real-time polymerase chain reaction specific for B. anthracis. Gamma phage-susceptible isolates were also tested using cell wall and capsule direct fluorescent-antibody assays specific for B. anthracis. Gamma phage-susceptible isolates that were ruled out as B. anthracis were identified by 16S rRNA gene sequencing. FINDINGS We identified 29 gamma phage-susceptible isolates. One was confirmed as B. anthracis, while the other 28 isolates were ruled out for B. anthracis by the other diagnostic tests. Using 16S rRNA gene sequencing results, we identified these isolates as members of the B. cereus group, Bacillus sp. (not within B. cereus group), Lysinibacillus spp., and Solibacillus silvestris. Based on these results, we report a specificity of 96% for gamma phage lysis as a diagnostic test for B. anthracis, and identified susceptible isolates outside the Bacillus genus. CONCLUSIONS In this study we found gamma phage susceptibility to be consistent with previously reported results. However, we identified non-B. anthracis environmental isolates (including isolates from genera other than Bacillus) that are susceptible to gamma phage lysis. To date, susceptibility to gamma phage lysis has not been reported in genera other than Bacillus. Though these isolates are not of clinical origin, description of unexpected positives is important, especially as new diagnostic assays for B. anthracis are being developed based on gamma phage lysis or gamma phage proteins.
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Affiliation(s)
- Cari B Kolton
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA.
| | - Nicole L Podnecky
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA.,Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Tromsø, Hansine Hansens veg 18, Tromsø, Norway
| | - Sean V Shadomy
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA.,One Health Office, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.,Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153, Rome, Italy
| | - Jay E Gee
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
| | - Alex R Hoffmaster
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, USA
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Abstract
Several members of the genus Burkholderia are prominent pathogens. Infections caused by these bacteria are difficult to treat because of significant antibiotic resistance. Virtually all Burkholderia species are also resistant to polymyxin, prohibiting use of drugs like colistin that are available for treatment of infections caused by most other drug resistant Gram-negative bacteria. Despite clinical significance and antibiotic resistance of Burkholderia species, characterization of efflux pumps lags behind other non-enteric Gram-negative pathogens such as Acinetobacter baumannii and Pseudomonas aeruginosa. Although efflux pumps have been described in several Burkholderia species, they have been best studied in Burkholderia cenocepacia and B. pseudomallei. As in other non-enteric Gram-negatives, efflux pumps of the resistance nodulation cell division (RND) family are the clinically most significant efflux systems in these two species. Several efflux pumps were described in B. cenocepacia, which when expressed confer resistance to clinically significant antibiotics, including aminoglycosides, chloramphenicol, fluoroquinolones, and tetracyclines. Three RND pumps have been characterized in B. pseudomallei, two of which confer either intrinsic or acquired resistance to aminoglycosides, macrolides, chloramphenicol, fluoroquinolones, tetracyclines, trimethoprim, and in some instances trimethoprim+sulfamethoxazole. Several strains of the host-adapted B. mallei, a clone of B. pseudomallei, lack AmrAB-OprA, and are therefore aminoglycoside and macrolide susceptible. B. thailandensis is closely related to B. pseudomallei, but non-pathogenic to humans. Its pump repertoire and ensuing drug resistance profile parallels that of B. pseudomallei. An efflux pump in B. vietnamiensis plays a significant role in acquired aminoglycoside resistance. Summarily, efflux pumps are significant players in Burkholderia drug resistance.
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Affiliation(s)
- Nicole L Podnecky
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biological Sciences, Colorado State University Fort Collins, CO, USA
| | - Katherine A Rhodes
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biological Sciences, Colorado State University Fort Collins, CO, USA ; Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, Institute for Therapeutic Innovation, University of Florida Gainesville, FL, USA
| | - Herbert P Schweizer
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biological Sciences, Colorado State University Fort Collins, CO, USA ; Department of Molecular Genetics and Microbiology, College of Medicine, Emerging Pathogens Institute, Institute for Therapeutic Innovation, University of Florida Gainesville, FL, USA
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Podnecky NL, Elrod MG, Newton BR, Dauphin LA, Shi J, Chawalchitiporn S, Baggett HC, Hoffmaster AR, Gee JE. Comparison of DNA extraction kits for detection of Burkholderia pseudomallei in spiked human whole blood using real-time PCR. PLoS One 2013; 8:e58032. [PMID: 23460920 PMCID: PMC3583986 DOI: 10.1371/journal.pone.0058032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 01/30/2013] [Indexed: 11/21/2022] Open
Abstract
Burkholderia pseudomallei, the etiologic agent of melioidosis, is endemic in northern Australia and Southeast Asia and can cause severe septicemia that may lead to death in 20% to 50% of cases. Rapid detection of B. pseudomallei infection is crucial for timely treatment of septic patients. This study evaluated seven commercially available DNA extraction kits to determine the relative recovery of B. pseudomallei DNA from spiked EDTA-containing human whole blood. The evaluation included three manual kits: the QIAamp DNA Mini kit, the QIAamp DNA Blood Mini kit, and the High Pure PCR Template Preparation kit; and four automated systems: the MagNAPure LC using the DNA Isolation Kit I, the MagNAPure Compact using the Nucleic Acid Isolation Kit I, and the QIAcube using the QIAamp DNA Mini kit and the QIAamp DNA Blood Mini kit. Detection of B. pseudomallei DNA extracted by each kit was performed using the B. pseudomallei specific type III secretion real-time PCR (TTS1) assay. Crossing threshold (CT) values were used to compare the limit of detection and reproducibility of each kit. This study also compared the DNA concentrations and DNA purity yielded for each kit. The following kits consistently yielded DNA that produced a detectable signal from blood spiked with 5.5×104 colony forming units per mL: the High Pure PCR Template Preparation, QIAamp DNA Mini, MagNA Pure Compact, and the QIAcube running the QIAamp DNA Mini and QIAamp DNA Blood Mini kits. The High Pure PCR Template Preparation kit yielded the lowest limit of detection with spiked blood, but when this kit was used with blood from patients with confirmed cases of melioidosis, the bacteria was not reliably detected indicating blood may not be an optimal specimen.
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Affiliation(s)
- Nicole L. Podnecky
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mindy G. Elrod
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bruce R. Newton
- Bioterrorism Rapid Response and Advanced Technology Laboratory, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Leslie A. Dauphin
- Bioterrorism Rapid Response and Advanced Technology Laboratory, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jianrong Shi
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Henry C. Baggett
- International Emerging Infections Program, Global Disease Detection Regional Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Alex R. Hoffmaster
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jay E. Gee
- Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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