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JohnJ Lipuma

University of Michigan, Nanotechnology Institute for Medicine and Biological Sciences, Faculty Member

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School of the Art Institute of Chicago

Barry Margulies

Towson University

Tiziano Fantuzzi

UCLouvain (University of Louvain)

Johns Hopkins University

Dr.Yousery Sherif

Mansoura University

Moscow State University

Johannes Sterba

Tu Wien

Professor Dr. Loutfy H . Madkour

Al-Baha University, Kingdom of Saudi Arabia

Nicolas A Karakatsanis

Weill Cornell Medicine

Mumbai University

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Papers by JohnJ Lipuma

The Class A β-Lactamase Produced by Burkholderia Species Compromises the Potency of Tebipenem against a Panel of Isolates from the United States

Antibiotics, May 17, 2022

Tebipenem-pivoxil hydrobromide, an orally bioavailable carbapenem, is currently in clinical devel... more Tebipenem-pivoxil hydrobromide, an orally bioavailable carbapenem, is currently in clinical development for the treatment of extended-spectrum β-lactamaseand AmpC-producing Enterobacterales. Previously, tebipenem was found to possess antimicrobial activity against the biothreat pathogens, Burkholderia pseudomallei and Burkholderia mallei. Thus, herein, tebipenem was evaluated against a panel of 150 curated strains of Burkholderia cepacia complex (Bcc) and Burkholderia gladioli, pathogens that infect people who are immunocompromised or have cystic fibrosis. Using the provisional susceptibility breakpoint of 0.12 mg/L for tebipenem, 100% of the Bcc and B. gladioli tested as being provisionally resistant to tebipenem. Bcc and B. gladioli possess two inducible chromosomal β-lactamases, PenA and AmpC. Using purified PenA1 and AmpC1, model βlactamases expressed in Burkholderia multivorans ATCC 17616, PenA1 was found to slowly hydrolyze tebipenem, while AmpC1 was inhibited by tebipenem with a k 2 /K value of 1.9 ± 0.1 × 10 3 M -1 s -1 . In addition, tebipenem was found to be a weak inducer of bla PenA1 expression. The combination of the slow hydrolysis by PenA1 and weak induction of bla PenA1 likely compromises the potency of tebipenem against Bcc and B. gladioli.

Draft Genome Sequences of Five Pseudomonas fluorescens Subclade I and II Strains, Isolated from Human Respiratory Samples

Genome Announcements, Aug 27, 2015

We report the draft genomes of five Pseudomonas fluorescens strains, isolated from clinical sampl... more We report the draft genomes of five Pseudomonas fluorescens strains, isolated from clinical samples. Phylogenetic analysis places three in subclade I and two in subclade II of the P. fluorescens species complex. The average G؉C content and genomic size are 63% and 7.1 Mbp (subclade I) and 59.6% and 6.14 Mbp (subclade II), respectively.

Potential for Therapeutic Benefit among Cystic Fibrosis Populations Excluded from Clinical Trials or Labeling of Marketed Therapies

Annals of the American Thoracic Society, 2016

Remarkable advances in the management of individuals born with cystic fibrosis (CF) would not hav... more Remarkable advances in the management of individuals born with cystic fibrosis (CF) would not have been realized without empiric trial and error by CF clinicians with treatments developed and available for other purposes. As the testing and registration of CF-specific treatments have increased, so too have associated health care costs, particularly those of chronic medications. The transition of CF from a lethal pediatric disease to a life-shortening one with an adult majority, concurrent with sharp increases in chronic medication costs, has placed many CF treatments under increased scrutiny by third-party payers, particularly when prescribed to individuals from CF subpopulations that may not have been included in registration trials. Despite overall health improvements in the CF cohort and the increasing availability of CF-specific therapies, many physicians remain tasked with managing the health of patients from subpopulations that may be too young, too sick, or too complicated to have been included in clinical trials. An understanding of why particular CF subpopulations may have been excluded from registration trials, as well as consideration of a treatment's described mechanism of action, can support assessment for the potential for benefit (and risk) in these populations and help physicians advocate for patient access to treatments.

Classification of Achromobacter genogroups 2, 5, 7 and 14 as Achromobacter insuavis sp. nov., Achromobacter aegrifaciens sp. nov., Achromobacter anxifer sp. nov. and Achromobacter dolens sp. nov., respectively

Systematic and Applied Microbiology, 2013

The phenotypic and genotypic characteristics of seventeen Achromobacter strains representing MLST... more The phenotypic and genotypic characteristics of seventeen Achromobacter strains representing MLST genogroups 2, 5, 7 and 14 were examined. Although genogroup 2 and 14 strains shared a DNA-DNA hybridization level of about 70%, the type strains of both genogroups differed in numerous biochemical characteristics and all genogroup 2 and 14 strains could by distinguished by nitrite reduction, denitrification and growth on acetamide. Given the MLST sequence divergence which identified genogroups 2 and 14 as clearly distinct populations, the availability of nrdA sequence analysis as a single locus identification tool for all Achromobacter species and genogroups, and the differential phenotypic characteristics, we propose to formally classify Achromobacter genogroups 2, 5, 7 and 14 as four novel Achromobacter species for which we propose the names Achromobacter insuavis sp. nov. (with strain LMG 26845 T [= CCUG 62426 T ] as the type strain), Achromobacter aegrifaciens sp. nov. (with strain LMG 26852 T [= CCUG 62438 T ] as the type strain), Achromobacter anxifer sp. nov. (with strain LMG 26857 T [= CCUG 62444 T ] as the type strain), and Achromobacter dolens sp. nov.

In vitro activity and synergy of bismuth thiols and tobramycin against Burkholderia cepacia complex

Journal of Antimicrobial Chemotherapy, 2003

Objectives: To determine the susceptibility of Burkholderia multivorans and Burkholderia cenocepa... more Objectives: To determine the susceptibility of Burkholderia multivorans and Burkholderia cenocepacia to bismuth-thiols (BTs), and to examine the synergistic effects of tobramycin and subinhibitory concentrations of BTs against these organisms. Methods: The susceptibilities of 25 clinical isolates each of B. multivorans and B. cenocepacia to six BTs were measured by broth dilution in accordance with NCCLS protocols. Ten strains were selected to evaluate the antimicrobial interaction between BTs and tobramycin. Fractional inhibitory concentration (FIC) and fractional bactericidal concentration (FBC) indices were calculated to assess synergy. Results: B. multivorans and B. cenocepacia showed a wide range of susceptibilities to BTs. Bismuth ethanedithiol (BisEDT) was one of the more potent BTs against these organisms (MIC 50 7.8 µM), and was selected for synergy studies. Selected strains were highly resistant to tobramycin. The addition of subinhibitory concentrations of BisEDT (2 µM) reduced the MIC and MBC of tobramycin against all strains, achieving synergy in many instances. The FIC index was in the range 0.28-0.66 and the FBC in the range 0.12-0.85. Most strains became susceptible to tobramycin at clinically achievable concentrations in the presence of non-toxic BisEDT levels. Conclusions: Treatment with subinhibitory BisEDT and tobramycin reduces the MICs and MBCs for B. multivorans and B. cenocepacia. BTs may represent an important adjunctive therapy for resistant Burkholderia cepacia complex.

Burkholderia cenocepacia sp. nov.—a new twist to an old story

Research in Microbiology, 2003

DNA-DNA hybridisation experiments between isolates representing Burkholderia cepacia genomovar II... more DNA-DNA hybridisation experiments between isolates representing Burkholderia cepacia genomovar III recA lineages IIIA and IIIB reinforced the classification of both phylogenetic subgroups as a single genospecies, distinct from B. cepacia (genomovar I). A formal classification of B. cepacia genomovar III encompassing the recA lineages IIIA and IIIB, and the new recA lineages IIIC and IIID, as B. cenocepacia sp. nov., with LMG 16656 as the type strain, is proposed.

Changing Epidemiology of the Respiratory Bacteriology of Patients with Cystic Fibrosis

CHEST Journal, 2015

Outbreak of otitis media caused by Burkholderia gladioli infection in immunocompromised mice

Comparative medicine, 2004

An athymic nude mouse with severe head tilt due to otitis media was identified. Within weeks of i... more An athymic nude mouse with severe head tilt due to otitis media was identified. Within weeks of identification of this first case, immune-deficient mice of various genotypes from the same facility were similarly affected, and cases from other facilities were found within two months. Culture of ear exudate specimens from affected mice yielded bacteria that were initially identified as Burkholderia cepacia, a plant pathogen considered an important opportunistic pathogen in persons with cystic fibrosis or chronic granulomatous disease. Several of these isolates, however, were subsequently identified as B. gladioli on the basis of results of biochemical analysis and a species-specific polymerase chain reaction (PCR) assay. Genotyping analysis revealed clonality among the isolates, indicating a shared strain among affected mice. A 16S rDNA-based PCR assay specific for the genera Burkholderia and Ralstonia, and a selective culture medium were used in efforts to characterize the epidemiolo...

Biochemical Characteristics, Adhesion, and Cytotoxicity of Environmental and Clinical Isolates of Herbaspirillum spp

Journal of Clinical Microbiology, 2014

Herbaspirillumbacteria are best known as plant growth-promoting rhizobacteria but have also been ... more Herbaspirillumbacteria are best known as plant growth-promoting rhizobacteria but have also been recovered from clinical samples. Here, biochemical tests, matrix-assisted laser deionization–time of flight (MALDI-TOF) mass spectrometry, adherence, and cytotoxicity to eukaryotic cells were used to compare clinical and environmental isolates ofHerbaspirillumspp. Discrete biochemical differences were observed between human and environmental strains. All strains adhered to HeLa cells at low densities, and cytotoxic effects were discrete, supporting the view thatHerbaspirillumbacteria are opportunists with low virulence potential.

Updated Version of the Burkholderia cepacia Complex Experimental Strain Panel

Journal of Clinical Microbiology, 2003

Taxonomy and Identification of the Burkholderia cepacia Complex

Journal of Clinical Microbiology, 2001

At the beginning of this review it is essential to clarify the terminology that will be used to r... more At the beginning of this review it is essential to clarify the terminology that will be used to refer to the members of the Burkholderia cepacia complex and their relatives. The name B. cepacia will relate only to B. cepacia genomovar I. Strains resembling B. cepacia may belong to the B. cepacia complex, to other Burkholderia species (for instance, Burkholderia gladioli), or to species from other genera (for instance, Ralstonia pick

An Episodic Outbreak of Genetically Related Burkholderia cepacia Among Non‐Cystic Fibrosis Patients at a University Hospital •

Infection Control and Hospital Epidemiology, 2001

Objective:To investigate an outbreak ofBurkholderia cepacia.Design:Observational study and chart ... more Objective:To investigate an outbreak ofBurkholderia cepacia.Design:Observational study and chart review.Patients:Adult non-cystic fibrosis (CF) patients.Setting:Intensive care units (ICUs) at a university-affiliated teaching hospital.Methods:As part of the epidemiological investigation, we conducted a chart review and collected environmental samples. A review of work schedules of healthcare workers also was performed. We usedB cepaciaselective agar for preliminary screening for all isolates, which subsequently were confirmed as members of theB cepaciacomplex by polyphasic analysis employing conventional biochemical reactions and genus- and species-specific polymerase chain reaction assays. Pulsed-field gel electrophoresis, randomly amplified polymorphic DNA typing, and automated ribotyping were used to genotype the isolates. As part of the intervention, contact isolation precautions were initiated for all patients identified as having had a culture positive forB cepacia.Results:Betw...

Burkholderia anthina sp. nov. and Burkholderia pyrrocinia, two additional Burkholderia cepacia complex bacteria, may confound results of new molecular diagnostic tools

FEMS Immunology and Medical Microbiology, 2002

Nineteen Burkholderia cepacia-like isolates of human and environmental origin could not be assign... more Nineteen Burkholderia cepacia-like isolates of human and environmental origin could not be assigned to one of the seven currently established genomovars using recently developed molecular diagnostic tools for B. cepacia complex bacteria. Various genotypic and phenotypic characteristics were examined. The results of this polyphasic study allowed classification of the 19 isolates as an eighth B. cepacia complex genomovar (Burkholderia anthina sp. nov.) and to design tools for its identification in the diagnostic laboratory. In addition, new and published data for Burkholderia pyrrocinia indicated that this soil bacterium is also a member of the B. cepacia complex. This highlights another potential source for diagnostic problems with B. cepacia-like bacteria.

Environmental Burkholderia cepacia Complex Isolates from Human Infections

Emerging Infectious Diseases, 2007

Identification of DNA Markers for a Transmissible Pseudomonas aeruginosa Cystic Fibrosis Strain

American Journal of Respiratory Cell and Molecular Biology, 2005

A number of transmissible Pseudomonas aeruginosa strains have been identified which potentially c... more A number of transmissible Pseudomonas aeruginosa strains have been identified which potentially constitute an emerging threat to patients with cystic fibrosis (CF). We sought to identify DNA markers that were specific to a transmissible P. aeruginosa CF clone and evaluate these probes on a large collection of genotypically distinct P. aeruginosa strains. Using subtractive DNA hybridization, in combination with analysis using the P. aeruginosa PAO1 genome chip, DNA markers specific for or absent from the Manchester transmissible CF strain (MA) were identified. Five subtractive DNA hybridization markers (MA15, MA18, MA21, MA22, and MA30) were found to be specific to strain MA and were located within a novel 13,318-bp genomic island, designated the MA island. The MA island encoded 18 genes and consisted of two bacteriophage-like regions; one region encoded the MA-specific subtractive hybridization markers, while the other bacteriophage-like region contained a Vibrio cholera-like toxin gene. Probes MA15, MA18, MA21, MA22, and MA30 were all found to be specific to strain MA when a collection of 141 P. aeruginosa strains was examined by hybridization with each DNA marker. In contrast, a previously isolated DNA marker for the Liverpool transmissible CF strain, PS21, was not found to be specific, detecting two additional strain types in the collection screened. Both the Manchester and Liverpool strain types were not encountered in CF populations outside the United Kingdom. The MA genomic island and Vibrio cholera-like toxin gene within it constitute novel genetic factors associated with a transmissible P. aeruginosa strain and their role in pathogenesis remains to be determined.

Multilocus Sequence Typing Scheme That Provides Both Species and Strain Differentiation for the Burkholderia cepacia Complex

A single multilocus sequence typing (MLST) scheme was developed for precise characterization of t... more A single multilocus sequence typing (MLST) scheme was developed for precise characterization of the opportunistic pathogens of Burkholderia cepacia complex (BCC), a group composed of at least nine closely related species. Seven conserved housekeeping genes were selected after a comparison of five Burkholderia species, and a collection of strains was subjected to nucleotide sequence analysis using a nested PCR ampli-

Potential for Therapeutic Benefit among Cystic Fibrosis Populations Excluded from Clinical Trials or Labeling of Marketed Therapies

by Donald R VanDevanter and JohnJ Lipuma

Remarkable advances in the management of individuals born with cystic fibrosis (CF) would not hav... more Remarkable advances in the management of individuals born with cystic fibrosis (CF) would not have been realized without empiric trial and error by CF clinicians with treatments developed and available for other purposes. As the testing and registration of CF-specific treatments have increased, so too have associated health care costs, particularly those of chronic medications. The transition of CF from a lethal pediatric disease to a life-shortening one with an adult majority, concurrent with sharp increases in chronic medication costs, has placed many CF treatments under increased scrutiny by third-party payers, particularly when prescribed to individuals from CF subpopulations that may not have been included in registration trials. Despite overall health improvements in the CF cohort and the increasing availability of CF-specific therapies, many physicians remain tasked with managing the health of patients from subpopulations that may be too young, too sick, or too complicated to have been included in clinical trials. An understanding of why particular CF subpopulations may have been excluded from registration trials, as well as consideration of a treatment's described mechanism of action, can support assessment for the potential for benefit (and risk) in these populations and help physicians advocate for patient access to treatments.

In vitro activity and synergy of bismuth thiols and tobramycin against Burkholderia cepacia complex

by Philip Domenico, JohnJ Lipuma, and John LiPuma

Objectives: To determine the susceptibility of Burkholderia multivorans and Burkholderia cenocepa... more

Burkholderia cenocepacia phage BcepMu and a family of Mu-like phages encoding potential pathogenesis factors

Journal of molecular …, Jan 1, 2004

We have isolated BcepMu, a Mu-like bacteriophage whose host range includes human pathogenic Burkh... more We have isolated BcepMu, a Mu-like bacteriophage whose host range includes human pathogenic Burkholderia cenocepacia (formally B. cepacia genomovar III) isolates, and determined its complete 36,748 bp genomic sequence. Like enteric bacteriophage Mu, the BcepMu genomic DNA is flanked by variable host sequences, a result of transposon-mediated replication. The BcepMu genome encodes 53 proteins, including capsid assembly components related to those of Mu, and tail sheath and tube proteins related to those of bacteriophage P2. Seventeen of the BcepMu genes were demonstrated to encode homotypic interacting domains by using a cI fusion system. Most BcepMu genes have close homologs to prophage elements present in the two published Salmonella typhi genomes, and in the database sequences of Photorhabdus luminescens, and Chromobacterium violaceum. These prophage elements, designated SalMu, PhotoMu and ChromoMu, respectively, are collinear with BcepMu through nearly their entire lengths and show only limited mosaicism, despite the divergent characters of their hosts. The BcepMu family of Mu-like phages has a number of notable differences from Mu. Most significantly, the critical left end region of BcepMu is inverted with respect to Mu, and the BcepMu family of transposases is clearly of a distinct lineage with different molecular requirements at the transposon ends. Interestingly, a survey of 33 B. cepacia complex strains indicated that the BcepMu prophage is widespread in human pathogenic B. cenocepacia ET12 lineage isolates, but not in isolates from the PHDC or Midwest lineages. Identified members of the BcepMu family all contain a gene possibly involved in bacterial pathogenicity, a homolog of the type-twosecretion component exeA, but only BcepMu also carries a lipopolysaccharide modification acyltransferase which may also contribute a pathogenicity factor.

An epidemic Burkholderia cepacia complex strain identified in soil.

RESEARCH LETTERS choreoathetosis, therefore the two loci should be close to each other. 4 Identif... more

The Class A β-Lactamase Produced by Burkholderia Species Compromises the Potency of Tebipenem against a Panel of Isolates from the United States

Antibiotics, May 17, 2022

Tebipenem-pivoxil hydrobromide, an orally bioavailable carbapenem, is currently in clinical devel... more Tebipenem-pivoxil hydrobromide, an orally bioavailable carbapenem, is currently in clinical development for the treatment of extended-spectrum β-lactamaseand AmpC-producing Enterobacterales. Previously, tebipenem was found to possess antimicrobial activity against the biothreat pathogens, Burkholderia pseudomallei and Burkholderia mallei. Thus, herein, tebipenem was evaluated against a panel of 150 curated strains of Burkholderia cepacia complex (Bcc) and Burkholderia gladioli, pathogens that infect people who are immunocompromised or have cystic fibrosis. Using the provisional susceptibility breakpoint of 0.12 mg/L for tebipenem, 100% of the Bcc and B. gladioli tested as being provisionally resistant to tebipenem. Bcc and B. gladioli possess two inducible chromosomal β-lactamases, PenA and AmpC. Using purified PenA1 and AmpC1, model βlactamases expressed in Burkholderia multivorans ATCC 17616, PenA1 was found to slowly hydrolyze tebipenem, while AmpC1 was inhibited by tebipenem with a k 2 /K value of 1.9 ± 0.1 × 10 3 M -1 s -1 . In addition, tebipenem was found to be a weak inducer of bla PenA1 expression. The combination of the slow hydrolysis by PenA1 and weak induction of bla PenA1 likely compromises the potency of tebipenem against Bcc and B. gladioli.

Draft Genome Sequences of Five Pseudomonas fluorescens Subclade I and II Strains, Isolated from Human Respiratory Samples

Genome Announcements, Aug 27, 2015

We report the draft genomes of five Pseudomonas fluorescens strains, isolated from clinical sampl... more We report the draft genomes of five Pseudomonas fluorescens strains, isolated from clinical samples. Phylogenetic analysis places three in subclade I and two in subclade II of the P. fluorescens species complex. The average G؉C content and genomic size are 63% and 7.1 Mbp (subclade I) and 59.6% and 6.14 Mbp (subclade II), respectively.

Potential for Therapeutic Benefit among Cystic Fibrosis Populations Excluded from Clinical Trials or Labeling of Marketed Therapies

Annals of the American Thoracic Society, 2016

Remarkable advances in the management of individuals born with cystic fibrosis (CF) would not hav... more Remarkable advances in the management of individuals born with cystic fibrosis (CF) would not have been realized without empiric trial and error by CF clinicians with treatments developed and available for other purposes. As the testing and registration of CF-specific treatments have increased, so too have associated health care costs, particularly those of chronic medications. The transition of CF from a lethal pediatric disease to a life-shortening one with an adult majority, concurrent with sharp increases in chronic medication costs, has placed many CF treatments under increased scrutiny by third-party payers, particularly when prescribed to individuals from CF subpopulations that may not have been included in registration trials. Despite overall health improvements in the CF cohort and the increasing availability of CF-specific therapies, many physicians remain tasked with managing the health of patients from subpopulations that may be too young, too sick, or too complicated to have been included in clinical trials. An understanding of why particular CF subpopulations may have been excluded from registration trials, as well as consideration of a treatment's described mechanism of action, can support assessment for the potential for benefit (and risk) in these populations and help physicians advocate for patient access to treatments.

Classification of Achromobacter genogroups 2, 5, 7 and 14 as Achromobacter insuavis sp. nov., Achromobacter aegrifaciens sp. nov., Achromobacter anxifer sp. nov. and Achromobacter dolens sp. nov., respectively

Systematic and Applied Microbiology, 2013

The phenotypic and genotypic characteristics of seventeen Achromobacter strains representing MLST... more The phenotypic and genotypic characteristics of seventeen Achromobacter strains representing MLST genogroups 2, 5, 7 and 14 were examined. Although genogroup 2 and 14 strains shared a DNA-DNA hybridization level of about 70%, the type strains of both genogroups differed in numerous biochemical characteristics and all genogroup 2 and 14 strains could by distinguished by nitrite reduction, denitrification and growth on acetamide. Given the MLST sequence divergence which identified genogroups 2 and 14 as clearly distinct populations, the availability of nrdA sequence analysis as a single locus identification tool for all Achromobacter species and genogroups, and the differential phenotypic characteristics, we propose to formally classify Achromobacter genogroups 2, 5, 7 and 14 as four novel Achromobacter species for which we propose the names Achromobacter insuavis sp. nov. (with strain LMG 26845 T [= CCUG 62426 T ] as the type strain), Achromobacter aegrifaciens sp. nov. (with strain LMG 26852 T [= CCUG 62438 T ] as the type strain), Achromobacter anxifer sp. nov. (with strain LMG 26857 T [= CCUG 62444 T ] as the type strain), and Achromobacter dolens sp. nov.

In vitro activity and synergy of bismuth thiols and tobramycin against Burkholderia cepacia complex

Journal of Antimicrobial Chemotherapy, 2003

Objectives: To determine the susceptibility of Burkholderia multivorans and Burkholderia cenocepa... more Objectives: To determine the susceptibility of Burkholderia multivorans and Burkholderia cenocepacia to bismuth-thiols (BTs), and to examine the synergistic effects of tobramycin and subinhibitory concentrations of BTs against these organisms. Methods: The susceptibilities of 25 clinical isolates each of B. multivorans and B. cenocepacia to six BTs were measured by broth dilution in accordance with NCCLS protocols. Ten strains were selected to evaluate the antimicrobial interaction between BTs and tobramycin. Fractional inhibitory concentration (FIC) and fractional bactericidal concentration (FBC) indices were calculated to assess synergy. Results: B. multivorans and B. cenocepacia showed a wide range of susceptibilities to BTs. Bismuth ethanedithiol (BisEDT) was one of the more potent BTs against these organisms (MIC 50 7.8 µM), and was selected for synergy studies. Selected strains were highly resistant to tobramycin. The addition of subinhibitory concentrations of BisEDT (2 µM) reduced the MIC and MBC of tobramycin against all strains, achieving synergy in many instances. The FIC index was in the range 0.28-0.66 and the FBC in the range 0.12-0.85. Most strains became susceptible to tobramycin at clinically achievable concentrations in the presence of non-toxic BisEDT levels. Conclusions: Treatment with subinhibitory BisEDT and tobramycin reduces the MICs and MBCs for B. multivorans and B. cenocepacia. BTs may represent an important adjunctive therapy for resistant Burkholderia cepacia complex.

Burkholderia cenocepacia sp. nov.—a new twist to an old story

Research in Microbiology, 2003

DNA-DNA hybridisation experiments between isolates representing Burkholderia cepacia genomovar II... more DNA-DNA hybridisation experiments between isolates representing Burkholderia cepacia genomovar III recA lineages IIIA and IIIB reinforced the classification of both phylogenetic subgroups as a single genospecies, distinct from B. cepacia (genomovar I). A formal classification of B. cepacia genomovar III encompassing the recA lineages IIIA and IIIB, and the new recA lineages IIIC and IIID, as B. cenocepacia sp. nov., with LMG 16656 as the type strain, is proposed.

Changing Epidemiology of the Respiratory Bacteriology of Patients with Cystic Fibrosis

CHEST Journal, 2015

Outbreak of otitis media caused by Burkholderia gladioli infection in immunocompromised mice

Comparative medicine, 2004

An athymic nude mouse with severe head tilt due to otitis media was identified. Within weeks of i... more An athymic nude mouse with severe head tilt due to otitis media was identified. Within weeks of identification of this first case, immune-deficient mice of various genotypes from the same facility were similarly affected, and cases from other facilities were found within two months. Culture of ear exudate specimens from affected mice yielded bacteria that were initially identified as Burkholderia cepacia, a plant pathogen considered an important opportunistic pathogen in persons with cystic fibrosis or chronic granulomatous disease. Several of these isolates, however, were subsequently identified as B. gladioli on the basis of results of biochemical analysis and a species-specific polymerase chain reaction (PCR) assay. Genotyping analysis revealed clonality among the isolates, indicating a shared strain among affected mice. A 16S rDNA-based PCR assay specific for the genera Burkholderia and Ralstonia, and a selective culture medium were used in efforts to characterize the epidemiolo...

Biochemical Characteristics, Adhesion, and Cytotoxicity of Environmental and Clinical Isolates of Herbaspirillum spp

Journal of Clinical Microbiology, 2014

Herbaspirillumbacteria are best known as plant growth-promoting rhizobacteria but have also been ... more Herbaspirillumbacteria are best known as plant growth-promoting rhizobacteria but have also been recovered from clinical samples. Here, biochemical tests, matrix-assisted laser deionization–time of flight (MALDI-TOF) mass spectrometry, adherence, and cytotoxicity to eukaryotic cells were used to compare clinical and environmental isolates ofHerbaspirillumspp. Discrete biochemical differences were observed between human and environmental strains. All strains adhered to HeLa cells at low densities, and cytotoxic effects were discrete, supporting the view thatHerbaspirillumbacteria are opportunists with low virulence potential.

Updated Version of the Burkholderia cepacia Complex Experimental Strain Panel

Journal of Clinical Microbiology, 2003

Taxonomy and Identification of the Burkholderia cepacia Complex

Journal of Clinical Microbiology, 2001

At the beginning of this review it is essential to clarify the terminology that will be used to r... more At the beginning of this review it is essential to clarify the terminology that will be used to refer to the members of the Burkholderia cepacia complex and their relatives. The name B. cepacia will relate only to B. cepacia genomovar I. Strains resembling B. cepacia may belong to the B. cepacia complex, to other Burkholderia species (for instance, Burkholderia gladioli), or to species from other genera (for instance, Ralstonia pick

An Episodic Outbreak of Genetically Related Burkholderia cepacia Among Non‐Cystic Fibrosis Patients at a University Hospital •

Infection Control and Hospital Epidemiology, 2001

Objective:To investigate an outbreak ofBurkholderia cepacia.Design:Observational study and chart ... more Objective:To investigate an outbreak ofBurkholderia cepacia.Design:Observational study and chart review.Patients:Adult non-cystic fibrosis (CF) patients.Setting:Intensive care units (ICUs) at a university-affiliated teaching hospital.Methods:As part of the epidemiological investigation, we conducted a chart review and collected environmental samples. A review of work schedules of healthcare workers also was performed. We usedB cepaciaselective agar for preliminary screening for all isolates, which subsequently were confirmed as members of theB cepaciacomplex by polyphasic analysis employing conventional biochemical reactions and genus- and species-specific polymerase chain reaction assays. Pulsed-field gel electrophoresis, randomly amplified polymorphic DNA typing, and automated ribotyping were used to genotype the isolates. As part of the intervention, contact isolation precautions were initiated for all patients identified as having had a culture positive forB cepacia.Results:Betw...

Burkholderia anthina sp. nov. and Burkholderia pyrrocinia, two additional Burkholderia cepacia complex bacteria, may confound results of new molecular diagnostic tools

FEMS Immunology and Medical Microbiology, 2002

Nineteen Burkholderia cepacia-like isolates of human and environmental origin could not be assign... more Nineteen Burkholderia cepacia-like isolates of human and environmental origin could not be assigned to one of the seven currently established genomovars using recently developed molecular diagnostic tools for B. cepacia complex bacteria. Various genotypic and phenotypic characteristics were examined. The results of this polyphasic study allowed classification of the 19 isolates as an eighth B. cepacia complex genomovar (Burkholderia anthina sp. nov.) and to design tools for its identification in the diagnostic laboratory. In addition, new and published data for Burkholderia pyrrocinia indicated that this soil bacterium is also a member of the B. cepacia complex. This highlights another potential source for diagnostic problems with B. cepacia-like bacteria.

Environmental Burkholderia cepacia Complex Isolates from Human Infections

Emerging Infectious Diseases, 2007

Identification of DNA Markers for a Transmissible Pseudomonas aeruginosa Cystic Fibrosis Strain

American Journal of Respiratory Cell and Molecular Biology, 2005

A number of transmissible Pseudomonas aeruginosa strains have been identified which potentially c... more A number of transmissible Pseudomonas aeruginosa strains have been identified which potentially constitute an emerging threat to patients with cystic fibrosis (CF). We sought to identify DNA markers that were specific to a transmissible P. aeruginosa CF clone and evaluate these probes on a large collection of genotypically distinct P. aeruginosa strains. Using subtractive DNA hybridization, in combination with analysis using the P. aeruginosa PAO1 genome chip, DNA markers specific for or absent from the Manchester transmissible CF strain (MA) were identified. Five subtractive DNA hybridization markers (MA15, MA18, MA21, MA22, and MA30) were found to be specific to strain MA and were located within a novel 13,318-bp genomic island, designated the MA island. The MA island encoded 18 genes and consisted of two bacteriophage-like regions; one region encoded the MA-specific subtractive hybridization markers, while the other bacteriophage-like region contained a Vibrio cholera-like toxin gene. Probes MA15, MA18, MA21, MA22, and MA30 were all found to be specific to strain MA when a collection of 141 P. aeruginosa strains was examined by hybridization with each DNA marker. In contrast, a previously isolated DNA marker for the Liverpool transmissible CF strain, PS21, was not found to be specific, detecting two additional strain types in the collection screened. Both the Manchester and Liverpool strain types were not encountered in CF populations outside the United Kingdom. The MA genomic island and Vibrio cholera-like toxin gene within it constitute novel genetic factors associated with a transmissible P. aeruginosa strain and their role in pathogenesis remains to be determined.

Multilocus Sequence Typing Scheme That Provides Both Species and Strain Differentiation for the Burkholderia cepacia Complex

A single multilocus sequence typing (MLST) scheme was developed for precise characterization of t... more A single multilocus sequence typing (MLST) scheme was developed for precise characterization of the opportunistic pathogens of Burkholderia cepacia complex (BCC), a group composed of at least nine closely related species. Seven conserved housekeeping genes were selected after a comparison of five Burkholderia species, and a collection of strains was subjected to nucleotide sequence analysis using a nested PCR ampli-

Potential for Therapeutic Benefit among Cystic Fibrosis Populations Excluded from Clinical Trials or Labeling of Marketed Therapies

by Donald R VanDevanter and JohnJ Lipuma

Remarkable advances in the management of individuals born with cystic fibrosis (CF) would not hav... more Remarkable advances in the management of individuals born with cystic fibrosis (CF) would not have been realized without empiric trial and error by CF clinicians with treatments developed and available for other purposes. As the testing and registration of CF-specific treatments have increased, so too have associated health care costs, particularly those of chronic medications. The transition of CF from a lethal pediatric disease to a life-shortening one with an adult majority, concurrent with sharp increases in chronic medication costs, has placed many CF treatments under increased scrutiny by third-party payers, particularly when prescribed to individuals from CF subpopulations that may not have been included in registration trials. Despite overall health improvements in the CF cohort and the increasing availability of CF-specific therapies, many physicians remain tasked with managing the health of patients from subpopulations that may be too young, too sick, or too complicated to have been included in clinical trials. An understanding of why particular CF subpopulations may have been excluded from registration trials, as well as consideration of a treatment's described mechanism of action, can support assessment for the potential for benefit (and risk) in these populations and help physicians advocate for patient access to treatments.

In vitro activity and synergy of bismuth thiols and tobramycin against Burkholderia cepacia complex

by Philip Domenico, JohnJ Lipuma, and John LiPuma

Objectives: To determine the susceptibility of Burkholderia multivorans and Burkholderia cenocepa... more

Burkholderia cenocepacia phage BcepMu and a family of Mu-like phages encoding potential pathogenesis factors

Journal of molecular …, Jan 1, 2004

We have isolated BcepMu, a Mu-like bacteriophage whose host range includes human pathogenic Burkh... more We have isolated BcepMu, a Mu-like bacteriophage whose host range includes human pathogenic Burkholderia cenocepacia (formally B. cepacia genomovar III) isolates, and determined its complete 36,748 bp genomic sequence. Like enteric bacteriophage Mu, the BcepMu genomic DNA is flanked by variable host sequences, a result of transposon-mediated replication. The BcepMu genome encodes 53 proteins, including capsid assembly components related to those of Mu, and tail sheath and tube proteins related to those of bacteriophage P2. Seventeen of the BcepMu genes were demonstrated to encode homotypic interacting domains by using a cI fusion system. Most BcepMu genes have close homologs to prophage elements present in the two published Salmonella typhi genomes, and in the database sequences of Photorhabdus luminescens, and Chromobacterium violaceum. These prophage elements, designated SalMu, PhotoMu and ChromoMu, respectively, are collinear with BcepMu through nearly their entire lengths and show only limited mosaicism, despite the divergent characters of their hosts. The BcepMu family of Mu-like phages has a number of notable differences from Mu. Most significantly, the critical left end region of BcepMu is inverted with respect to Mu, and the BcepMu family of transposases is clearly of a distinct lineage with different molecular requirements at the transposon ends. Interestingly, a survey of 33 B. cepacia complex strains indicated that the BcepMu prophage is widespread in human pathogenic B. cenocepacia ET12 lineage isolates, but not in isolates from the PHDC or Midwest lineages. Identified members of the BcepMu family all contain a gene possibly involved in bacterial pathogenicity, a homolog of the type-twosecretion component exeA, but only BcepMu also carries a lipopolysaccharide modification acyltransferase which may also contribute a pathogenicity factor.

An epidemic Burkholderia cepacia complex strain identified in soil.

RESEARCH LETTERS choreoathetosis, therefore the two loci should be close to each other. 4 Identif... more