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Grodner B, Shi H, Farchione O, Vill AC, Ntekas I, Diebold PJ, Wu DT, Chen CY, Kim DM, Zipfel WR, Brito IL, De Vlaminck I. Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes. Nat Microbiol 2024:10.1038/s41564-024-01735-5. [PMID: 38918467 DOI: 10.1038/s41564-024-01735-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 05/17/2024] [Indexed: 06/27/2024]
Abstract
The exchange of mobile genetic elements (MGEs) facilitates the spread of functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their bacterial hosts in complex microbial communities are currently lacking, limiting our understanding of this process. Here we combined single-molecule DNA fluorescence in situ hybridization (FISH) with multiplexed ribosomal RNA-FISH to enable simultaneous visualization of both MGEs and bacterial taxa. We spatially mapped bacteriophage and antimicrobial resistance (AMR) plasmids and identified their host taxa in human oral biofilms. This revealed distinct clusters of AMR plasmids and prophage, coinciding with densely packed regions of host bacteria. Our data suggest spatial heterogeneity in bacterial taxa results in heterogeneous MGE distribution within the community, with MGE clusters resulting from horizontal gene transfer hotspots or expansion of MGE-carrying strains. Our approach can help advance the study of AMR and phage ecology in biofilms.
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Affiliation(s)
- Benjamin Grodner
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Hao Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Kanvas Biosciences, Inc, Monmouth Junction, NJ, USA
| | - Owen Farchione
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Albert C Vill
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ioannis Ntekas
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - David T Wu
- Division of Periodontology, Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Chia-Yu Chen
- Division of Periodontology, Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - David M Kim
- Division of Periodontology, Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Warren R Zipfel
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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2
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Yokoyama S, Hayashi M, Goto T, Muto Y, Tanaka K. Identification of cfxA gene variants and susceptibility patterns in β-lactamase-producing Prevotella strains. Anaerobe 2023; 79:102688. [PMID: 36580990 DOI: 10.1016/j.anaerobe.2022.102688] [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: 09/07/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 12/28/2022]
Abstract
OBJECTIVES Antimicrobial-resistant isolates of Prevotella species, especially those resistant to β-lactams, have become increasingly common. Here, we aimed to elucidate the underlying mechanisms contributing to the emergence and spread of antimicrobial resistance in Prevotella species. METHODS Prevotella species were isolated from a variety of clinical specimens. β-lactamase production was determined using nitrocefin discs, and the determination of minimum inhibitory concentration (MIC) to ten antimicrobials was done by the agar dilution method. Four resistance genes (cfxA, tetQ, ermF, and nim) and cfxA-flanking regions were detected using polymerase chain reaction. cfxA and the flanking regions were sequenced, and a phylogenetic tree was constructed based on CfxA amino acid sequences using the UPGMA method. RESULTS Among the 45 Prevotella isolates identified, 35 (77.8%) produced β-lactamases and had the cfxA genes. The tetQ, ermF, and nim genes were detected in 53.3%, 17.8%, and 0% of the 45 isolates, respectively. Among the 33 sequenced cfxA alleles, cfxA2 (45.5%) was the most frequent, followed by cfxA3 (42.4%) and a novel variant (cfxA7, 12.1%). The novel CfxA7 β-lactamase had a novel L155F substitution not previously reported in CfxA variants. The MICs of all β-lactam agents tested, excluding cefmetazole and meropenem, were lower among cfxA7-positive isolates than in cfxA2-and cfxA3-positive isolates. CONCLUSIONS Differences in MICs of penicillins and cephalosporins may be due to amino acid substitutions in the CfxA variants, CfxA2, CfxA3, and CfxA7, among Prevotella isolates. Possession of cfxA-mobA, tetQ, and ermF may increase the risks of the emergence and spread of multidrug-resistant Prevotella species.
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Affiliation(s)
- Sodai Yokoyama
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu City, Gifu, Japan
| | - Masahiro Hayashi
- Institute for Glyco-core Research iGCORE, Gifu University, Gifu City, Gifu, Japan; Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu City, Gifu, Japan
| | - Takatsugu Goto
- Institute for Glyco-core Research iGCORE, Gifu University, Gifu City, Gifu, Japan; Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu City, Gifu, Japan
| | - Yoshinori Muto
- Institute for Glyco-core Research iGCORE, Gifu University, Gifu City, Gifu, Japan
| | - Kaori Tanaka
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu City, Gifu, Japan; Institute for Glyco-core Research iGCORE, Gifu University, Gifu City, Gifu, Japan; Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu City, Gifu, Japan.
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3
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Ozavci V, Dolgun HTY, Kirkan S. Presence of zoonotic black-pigmented periodontal pathogens in the oral microbiota of pet and stray cats. VET MED-CZECH 2023; 68:62-68. [PMID: 38332760 PMCID: PMC10847818 DOI: 10.17221/59/2022-vetmed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/10/2023] [Indexed: 02/10/2024] Open
Abstract
Black-pigmented bacteria are one of the neglected species to cause periodontal disease in cats, and they are also zoonotic agents that pose an infection risk to humans. In this study, we aimed to determine the presence of Porphyromonas gingivalis, Porphyromonas gulae and Prevotella nigrescens in the oral microbiota of pet and stray cats. Dental swab samples were taken from 25 pet cats and 25 stray cats with symptoms of periodontal disease and then investigated by multiplex polymerase chain reaction using 16S rRNA species-specific primers. As a result of the multiplex PCR analysis, P. gingivalis 3/25 (12%), P. nigrescens 1/25 (4%), P. gingivalis + P. gulae 7/25 (28%), P. gingivalis + P. nigrescens 1/25 (4%), P. gulae + P. nigrescens 1/25 (4%), and P. gingivalis + P. gulae + P. nigrescens 2/25 (8%) were molecularly typed in the pet cats. In addition, 1/25 (4%) of P. gulae and 21/25 (84%) of P. gingivalis + P. gulae were typed in the stray cats. In 10/25 (40%) pet and 3/25 (12%) stray cat samples, no bacteria were detected by molecular typing. In summary, the results provide strong evidence that black-pigmented zoonotic pathogens are associated with cat periodontal disease.
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Affiliation(s)
- Volkan Ozavci
- Department of Microbiology, Faculty of Veterinary Medicine, Dokuz Eylul University, Izmir, Türkiye
| | - Hafize Tugba Yuksel Dolgun
- Department of Microbiology, Faculty of Veterinary Medicine, Aydin Adnan Menderes University, Aydin, Türkiye
| | - Sukru Kirkan
- Department of Microbiology, Faculty of Veterinary Medicine, Aydin Adnan Menderes University, Aydin, Türkiye
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4
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Lebeaux RM, Madan JC, Nguyen QP, Coker MO, Dade EF, Moroishi Y, Palys TJ, Ross BD, Pettigrew MM, Morrison HG, Karagas MR, Hoen AG. Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies. Pediatr Res 2022; 92:1757-1766. [PMID: 35568730 PMCID: PMC9659678 DOI: 10.1038/s41390-022-02104-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/04/2022] [Accepted: 03/29/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Young children are frequently exposed to antibiotics, with the potential for collateral consequences to the gut microbiome. The impact of antibiotic exposures to off-target microbes (i.e., bacteria not targeted by treatment) and antibiotic resistance genes (ARGs) is poorly understood. METHODS We used metagenomic sequencing data from paired stool samples collected prior to antibiotic exposure and at 1 year from over 200 infants and a difference-in-differences approach to assess the relationship between subsequent exposures and the abundance or compositional diversity of microbes and ARGs while adjusting for covariates. RESULTS By 1 year, the abundance of multiple species and ARGs differed by antibiotic exposure. Compared to infants never exposed to antibiotics, Bacteroides vulgatus relative abundance increased by 1.72% (95% CI: 0.19, 3.24) while Bacteroides fragilis decreased by 1.56% (95% CI: -4.32, 1.21). Bifidobacterium species also exhibited opposing trends. ARGs associated with exposure included class A beta-lactamase gene CfxA6. Among infants attending day care, Escherichia coli and ARG abundance were both positively associated with antibiotic use. CONCLUSION Novel findings, including the importance of day care attendance, were identified through considering microbiome data at baseline and post-intervention. Thus, our study design and approach have important implications for future studies evaluating the unintended impacts of antibiotics. IMPACT The impact of antibiotic exposure to off-target microbes and antibiotic resistance genes in the gut is poorly defined. We quantified these impacts in two cohort studies using a difference-in-differences approach. Novel to microbiome studies, we used pre/post-antibiotic data to emulate a randomized controlled trial. Compared to infants unexposed to antibiotics between baseline and 1 year, the relative abundance of multiple off-target species and antibiotic resistance genes was altered. Infants who attended day care and were exposed to antibiotics within the first year had a higher abundance of Escherichia coli and antibiotic resistance genes; a novel finding warranting further investigation.
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Affiliation(s)
- Rebecca M Lebeaux
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Juliette C Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Quang P Nguyen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Modupe O Coker
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Erika F Dade
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Yuka Moroishi
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Thomas J Palys
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Benjamin D Ross
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Orthopaedics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Melinda M Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
- Center for Molecular Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Anne G Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
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5
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Castillo Y, Delgadillo NA, Neuta Y, Hernández A, Acevedo T, Cárdenas E, Montaño A, Lafaurie GI, Castillo DM. Antibiotic Susceptibility and Resistance Genes in Oral Clinical Isolates of Prevotella intermedia, Prevotella nigrescens, and Prevotella melaninogenica. Antibiotics (Basel) 2022; 11:antibiotics11070888. [PMID: 35884141 PMCID: PMC9312306 DOI: 10.3390/antibiotics11070888] [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: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
The Prevotella genus is a normal constituent of the oral microbiota, and is commonly isolated from mechanically treated polymicrobial infections. However, antibiotic treatment is necessary for some patients. This study compared the antibiotic susceptibility and the presence of resistance genes in clinical oral isolates of P. intermedia, P. nigrescens, and P. melaninogenica. Antibiotic susceptibility was assessed using the agar dilution method. PCR confirmed the species and resistance gene frequency in the Prevotella species. The frequencies of species P. intermedia, P. nigrescens, and P. melaninogenica were 30.2%, 45.7%, and 24.1%, respectively. No isolates of P. intermedia were resistant to amoxicillin/clavulanic acid, tetracycline, or clindamycin. P. nigrescens and P. melaninogenica were resistant to amoxicillin/clavulanic acid and tetracycline at frequencies of 40% and 20%, respectively. P. intermedia was resistant to metronidazole at a frequency of 30%, P. nigrescens at 20%, and P. melaninogenica at 40%. P. nigrescens and P. melaninogenica were resistant to 50% and 10% clindamycin, respectively. The gene most frequently detected was tetQ, at 43.3%, followed by tetM at 36.6%, blaTEM at 26.6%, ermF at 20%, cfxA, cfxA2, and nimAB at 16.6%, and nimAEFI at 3.3%. P. nigrescens was the species with the highest resistance to antibiotics such as amoxicillin/clavulanic acid, amoxicillin, and clindamycin, in addition to being the species with the largest number of genes compared to P. intermedia and P. melaninogenica.
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Affiliation(s)
- Yormaris Castillo
- Unidad de Investigación Básica Oral-UIBO, Vicerrectoría de Investigaciones, Facultad de Odontología, Universidad El Bosque, 110121 Bogotá, Colombia
| | - Nathaly Andrea Delgadillo
- Unidad de Investigación Básica Oral-UIBO, Vicerrectoría de Investigaciones, Facultad de Odontología, Universidad El Bosque, 110121 Bogotá, Colombia
| | - Yineth Neuta
- Unidad de Investigación Básica Oral-UIBO, Vicerrectoría de Investigaciones, Facultad de Odontología, Universidad El Bosque, 110121 Bogotá, Colombia
| | - Andrés Hernández
- Facultad de Odontología, Universidad El Bosque, 110121 Bogotá, Colombia
| | - Tania Acevedo
- Facultad de Odontología, Universidad El Bosque, 110121 Bogotá, Colombia
| | - Edwin Cárdenas
- Facultad de Odontología, Universidad El Bosque, 110121 Bogotá, Colombia
| | - Andrea Montaño
- Facultad de Odontología, Universidad El Bosque, 110121 Bogotá, Colombia
| | - Gloria Inés Lafaurie
- Unidad de Investigación Básica Oral-UIBO, Vicerrectoría de Investigaciones, Facultad de Odontología, Universidad El Bosque, 110121 Bogotá, Colombia
| | - Diana Marcela Castillo
- Unidad de Investigación Básica Oral-UIBO, Vicerrectoría de Investigaciones, Facultad de Odontología, Universidad El Bosque, 110121 Bogotá, Colombia
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6
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Brooks L, Narvekar U, McDonald A, Mullany P. Prevalence of antibiotic resistance genes in the oral cavity and mobile genetic elements that disseminate antimicrobial resistance: A systematic review. Mol Oral Microbiol 2022; 37:133-153. [DOI: 10.1111/omi.12375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Laura Brooks
- UCL Eastman Dental Institute University College London 47–49 Huntley St London WC1E 6DG UK
| | - Unnati Narvekar
- UCL Eastman Dental Institute University College London 47–49 Huntley St London WC1E 6DG UK
| | - Ailbhe McDonald
- UCL Eastman Dental Institute University College London 47–49 Huntley St London WC1E 6DG UK
| | - Peter Mullany
- UCL Eastman Dental Institute University College London 47–49 Huntley St London WC1E 6DG UK
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7
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Könönen E, Fteita D, Gursoy UK, Gursoy M. Prevotella species as oral residents and infectious agents with potential impact on systemic conditions. J Oral Microbiol 2022; 14:2079814. [DOI: 10.1080/20002297.2022.2079814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Eija Könönen
- Institute of Dentistry, University of Turku, Turku, Finland
| | - Dareen Fteita
- Institute of Dentistry, University of Turku, Turku, Finland
| | - Ulvi K. Gursoy
- Institute of Dentistry, University of Turku, Turku, Finland
| | - Mervi Gursoy
- Institute of Dentistry, University of Turku, Turku, Finland
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8
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Webb KA, Olagoke O, Baird T, Neill J, Pham A, Wells TJ, Ramsay KA, Bell SC, Sarovich DS, Price EP. Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways. Microb Genom 2022; 8. [PMID: 35113778 PMCID: PMC8942031 DOI: 10.1099/mgen.0.000754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterized by increasingly frequent acute pulmonary exacerbations that reduce life quality and length. Human airways are home to a rich polymicrobial environment, which includes members of the obligately anaerobic genus Prevotella. Despite their commonness, surprisingly little is known about the prevalence, role, genomic diversity and antimicrobial resistance (AMR) potential of Prevotella species and strains in healthy and diseased airways. Here, we used comparative genomics to develop a real-time PCR assay to permit rapid Prevotella species identification and quantification from cultures and clinical specimens. Assay specificity was validated across a panel of Prevotella and non-Prevotella species, followed by PCR screening of CF and COPD respiratory-derived cultures. Next, 35 PCR-positive isolates were subjected to whole-genome sequencing. Of eight identified Prevotella species, P. histicola, P. melaninogenica, P. nanceiensis, P. salivae and P. denticola overlapped between participant cohorts. Phylogenomic analysis revealed considerable interhost but limited intrahost diversity, suggesting patient-specific lineages in the lower airways, probably from oral cavity aspirations. Correlation of phenotypic AMR profiles with AMR genes identified excellent correlation between tetQ presence and decreased doxycycline susceptibility, and ermF presence and decreased azithromycin susceptibility and clindamycin resistance. AMR rates were higher in the CF isolates, reflecting greater antibiotic use in this cohort. All tested Prevotella isolates were tobramycin-resistant, providing a potential selection method to improve Prevotella culture retrieval rates. Our addition of 35 airway-derived Prevotella genomes to public databases will enhance ongoing efforts to unravel the role of this diverse and enigmatic genus in both diseased and healthy lungs.
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Affiliation(s)
- Kasey A Webb
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Olusola Olagoke
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Timothy Baird
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia.,Sunshine Coast Hospital and Health Service, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Jane Neill
- Sunshine Coast Hospital and Health Service, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Amy Pham
- University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Timothy J Wells
- University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Kay A Ramsay
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Present address: Child Health Research Centre, The University of Queensland, Centre for Children's Health Research, South Brisbane, Queensland, Australia
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Derek S Sarovich
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Erin P Price
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
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9
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Identification of oral anaerobic bacteria and the beta-lactamase resistance genes from Iranian patients with periodontitis. Anaerobe 2022; 75:102515. [DOI: 10.1016/j.anaerobe.2022.102515] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/06/2023]
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10
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Prevotella melaninogenica, a Sentinel Species of Antibiotic Resistance in Cystic Fibrosis Respiratory Niche? Microorganisms 2021; 9:microorganisms9061275. [PMID: 34208093 PMCID: PMC8230849 DOI: 10.3390/microorganisms9061275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 12/31/2022] Open
Abstract
The importance and abundance of strict anaerobic bacteria in the respiratory microbiota of people with cystic fibrosis (PWCF) is now established through studies based on high-throughput sequencing or extended-culture methods. In CF respiratory niche, one of the most prevalent anaerobic genera is Prevotella, and particularly the species Prevotella melaninogenica. The objective of this study was to evaluate the antibiotic susceptibility of this anaerobic species. Fifty isolates of P. melaninogenica cultured from sputum of 50 PWCF have been included. Antibiotic susceptibility testing was performed using the agar diffusion method. All isolates were susceptible to the following antibiotics: amoxicillin/clavulanic acid, piperacillin/tazobactam, imipenem and metronidazole. A total of 96% of the isolates (48/50) were resistant to amoxicillin (indicating beta-lactamase production), 34% to clindamycin (17/50) and 24% to moxifloxacin (12/50). Moreover, 10% (5/50) were multidrug-resistant. A significant and positive correlation was found between clindamycin resistance and chronic azithromycin administration. This preliminary study on a predominant species of the lung “anaerobiome” shows high percentages of resistance, potentially exacerbated by the initiation of long-term antibiotic therapy in PWCF. The anaerobic resistome characterization, focusing on species rather than genera, is needed in the future to better prevent the emergence of resistance within lung microbiota.
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11
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Arredondo A, Blanc V, Mor C, Nart J, León R. Resistance to β-lactams and distribution of β-lactam resistance genes in subgingival microbiota from Spanish patients with periodontitis. Clin Oral Investig 2020; 24:4639-4648. [PMID: 32495224 DOI: 10.1007/s00784-020-03333-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/08/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The aim of this study was to analyze the distribution of β-lactamase genes and the multidrug resistance profiles in β-lactam-resistant subgingival bacteria from patients with periodontitis. MATERIALS AND METHODS Subgingival samples were obtained from 130 Spanish patients with generalized periodontitis stage III or IV. Samples were grown on agar plates with amoxicillin or cefotaxime and incubated in anaerobic and microaerophilic conditions. Isolates were identified to the species level by the sequencing of their 16S rRNA gene. A screening for the following β-lactamase genes was performed by the polymerase chain reaction (PCR) technique: blaTEM, blaSHV, blaCTX-M, blaCfxA, blaCepA, blaCblA, and blaampC. Additionally, multidrug resistance to tetracycline, chloramphenicol, streptomycin, erythromycin, and kanamycin was assessed, growing the isolates on agar plates with breakpoint concentrations of each antimicrobial. RESULTS β-lactam-resistant isolates were found in 83% of the patients. Seven hundred and thirty-seven isolates from 35 different genera were obtained, with Prevotella and Streptococcus being the most identified genera. blaCfxA was the gene most detected, being observed in 24.8% of the isolates, followed by blaTEM (12.9%). Most of the isolates (81.3%) were multidrug-resistant. CONCLUSIONS This study shows that β-lactam resistance is widespread among Spanish patients with periodontitis. Furthermore, it suggests that the subgingival commensal microbiota might be a reservoir of multidrug resistance and β-lactamase genes. CLINICAL RELEVANCE Most of the samples yielded β-lactam-resistant isolates, and 4 different groups of bla genes were detected among the isolates. Most of the isolates were also multidrug-resistant. The results show that, although β-lactams may still be effective, their future might be hindered by the presence of β-lactam-resistant bacteria and the presence of transferable bla genes.
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Affiliation(s)
- Alexandre Arredondo
- Department of Microbiology, Dentaid Research Center, Cerdanyola del Vallès, Spain.,Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Vanessa Blanc
- Department of Microbiology, Dentaid Research Center, Cerdanyola del Vallès, Spain
| | - Carolina Mor
- Department of Periodontology, Universitat Internacional de Catalunya, Barcelona, Spain
| | - José Nart
- Department of Periodontology, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Rubén León
- Department of Microbiology, Dentaid Research Center, Cerdanyola del Vallès, Spain.
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12
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Gasparrini AJ, Wang B, Sun X, Kennedy EA, Hernandez-Leyva A, Ndao IM, Tarr PI, Warner BB, Dantas G. Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome. Nat Microbiol 2019; 4:2285-2297. [PMID: 31501537 PMCID: PMC6879825 DOI: 10.1038/s41564-019-0550-2] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 07/26/2019] [Indexed: 12/29/2022]
Abstract
Hospitalized preterm infants receive frequent and often prolonged exposures to antibiotics because they are vulnerable to infection. It is not known whether the short-term effects of antibiotics on the preterm infant gut microbiota and resistome persist after discharge from neonatal intensive care units. Here, we use complementary metagenomic, culture-based and machine learning techniques to study the gut microbiota and resistome of antibiotic-exposed preterm infants during and after hospitalization, and we compare these readouts to antibiotic-naive healthy infants sampled synchronously. We find a persistently enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug-resistant Enterobacteriaceae and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants that received early-life antibiotics. The collateral damage of early-life antibiotic treatment and hospitalization in preterm infants is long lasting. We urge the development of strategies to reduce these consequences in highly vulnerable neonatal populations.
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Affiliation(s)
- Andrew J Gasparrini
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Elizabeth A Kennedy
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Ariel Hernandez-Leyva
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - I Malick Ndao
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
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13
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Kates AE, Dalman M, Torner JC, Smith TC. The nasal and oropharyngeal microbiomes of healthy livestock workers. PLoS One 2019; 14:e0212949. [PMID: 30861031 PMCID: PMC6413945 DOI: 10.1371/journal.pone.0212949] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/12/2019] [Indexed: 12/26/2022] Open
Abstract
Little information exists on the microbiomes of livestock workers. A cross-sectional, epidemiological study was conducted enrolling 59 participants (26 of which had livestock contact) in Iowa. Participants were enrolled in one of four ways: from an existing prospective cohort study (n = 38), from the Iowa Department of Natural Resources Animal Feeding Operations database (n = 17), through Iowa county fairs (n = 3), and through snowball sampling (n = 1). We collected swabs from the nares and oropharynx of each participant to assess the microbiome via 16s rRNA sequencing. We observed livestock workers to have greater diversity in their microbiomes compared to those with no livestock contact. In the nares, there were 27 operational taxonomic units found to be different between livestock workers and non-livestock workers with the greatest difference seen with Streptococcus and Proteobacteria. In the oropharynx, livestock workers with swine exposure were more likely to carry several pathogenic organisms. The results of this study are the first to characterize the livestock worker nasal and oropharyngeal microbiomes.
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Affiliation(s)
- Ashley E. Kates
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, United States of America
| | - Mark Dalman
- Kent State University, College of Public Health, Kent, OH, United States of America
| | - James C. Torner
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, United States of America
| | - Tara C. Smith
- Kent State University, College of Public Health, Kent, OH, United States of America
- * E-mail:
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14
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Liu Y, Lin Z, Lin Y, Chen Y, Peng XE, He F, Liu S, Yan S, Huang L, Lu W, Xiang Z, Hu Z. Streptococcus and Prevotella are associated with the prognosis of oesophageal squamous cell carcinoma. J Med Microbiol 2018; 67:1058-1068. [PMID: 29923815 DOI: 10.1099/jmm.0.000754] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Oesophageal squamous cell carcinoma (ESCC) is the dominant type of oesophageal cancer among the East Asian population. The role of ESCC tissue bacteria in neoplastic progression has not been fully elucidated. Our goal was to uncover different bacterial communities in pathological staging grouping of ESCC and to identify microorganisms that could predict the likelihood of prognosis. METHODOLOGY Tissue samples were obtained from 45 patients and assessed using 16S ribosomal RNA gene sequencing. Significant bacteria were selected to perform survival analysis and evaluate prognostic biomarker.Results/Key findings. We observed variations in the abundance of oesophageal flora among different pathological characteristics of ESCC. Phylum Bacteroidetes, Firmicutes and Spirochaetes showed significantly higher relative abundances among N+ (positive lymph node) patients when compared to N- (negative lymph node) controls, whereas Proteobacteria showed lower abundances in N+ patients. Both genera Prevotella and Treponema were more abundant in the N+ group. In regard to T stage, the abundance of only Streptococcus in T3-4 was significantly higher than that in T1-2, while the other genera showed no significance. On multivariable analysis adjusted for the effects of standard clinicopathological features, combined Streptococcus and Prevotella abundance retained its association with unfavourable survival (hazard ratio, 6.094; 95 % confidence interval, 1.072-34.646; P=0.042), suggesting that this may be an independent prognostic indicator for ESCC. CONCLUSION Combined Streptococcus and Prevotella abundance is regarded as an independent species prognostic biomarker in ESCC patients.
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Affiliation(s)
- Yanfang Liu
- 1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China
| | - Zheng Lin
- 1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China.,2Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, 1 Xueyuan Road, Minhou, Fuzhou 350108, PR China
| | - Yingying Lin
- 1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China
| | - Yuanmei Chen
- 3Department of Thoracic Surgery, Fujian Provincial Cancer Hospital affiliated to Fujian Medical University, Fuzhou 350014, PR China
| | - Xian-E Peng
- 1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China.,2Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, 1 Xueyuan Road, Minhou, Fuzhou 350108, PR China
| | - Fei He
- 1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China.,2Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, 1 Xueyuan Road, Minhou, Fuzhou 350108, PR China
| | - Shuang Liu
- 1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China
| | - Siyou Yan
- 1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China
| | - Liping Huang
- 1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China
| | - Wanting Lu
- 1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China
| | - Zhisheng Xiang
- 1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China
| | - Zhijian Hu
- 2Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, 1 Xueyuan Road, Minhou, Fuzhou 350108, PR China.,1Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou 350108, PR China
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15
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Jia S, Zhang XX, Miao Y, Zhao Y, Ye L, Li B, Zhang T. Fate of antibiotic resistance genes and their associations with bacterial community in livestock breeding wastewater and its receiving river water. WATER RESEARCH 2017; 124:259-268. [PMID: 28763642 DOI: 10.1016/j.watres.2017.07.061] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 07/16/2017] [Accepted: 07/23/2017] [Indexed: 05/12/2023]
Abstract
Large amounts of antibiotics are currently used in livestock breeding, which is the main driving factor contributing to the occurrence, spread and proliferation of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the environment. In this study, high-throughput sequencing based metagenomic approaches were employed to characterize the tempo-spacial changes of antibiotic resistome, bacterial community and their correlations in pig farming wastewater and its receiving river. A total of 194 ARG subtypes within 14 ARG types were detectable in all the samples, and their total relative abundance increased in the river water after receiving wastewater discharge, while decreased in the downstream river water. Network analysis showed that 25.26% ARGs within the same type or among the different types showed higher incidences of non-random co-occurrence. The wastewater discharge evidently increased bacterial diversity and induced bacterial community shift in the receiving river water. The genera of Treponema, Prevotella, Pseudomonas, Bacteroides, Oscillibacter and Acholeplasma dominated in the wastewater samples and almost disappeared in the receiving river water, but bacterial pathogens Clostridium difficile and Arcobacter butzleri still occurred in the receiving water. Correlation analysis and host analysis consistently showed that the changes in the abundances of several key genera like Prevotella and Treponema were significantly and positively correlated with the antibiotic resistome alteration. Variation partitioning analysis indicated that bacterial community played a more important role in the resistome alteration than mobile genetic elements. This study may help to understand the correlations among antibiotic resistome, microbiota and environmental conditions in the wastewater-receiving river water.
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Affiliation(s)
- Shuyu Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China.
| | - Yu Miao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Yanting Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Bing Li
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Tong Zhang
- Environmental Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong Special Administrative Region
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Zirk M, Kreppel M, Buller J, Pristup J, Peters F, Dreiseidler T, Zinser M, Zöller JE. The impact of surgical intervention and antibiotics on MRONJ stage II and III – Retrospective study. J Craniomaxillofac Surg 2017; 45:1183-1189. [DOI: 10.1016/j.jcms.2017.05.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/22/2017] [Accepted: 05/29/2017] [Indexed: 01/23/2023] Open
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Binta B, Patel M. Detection of cfxA2, cfxA3, and cfxA6 genes in beta-lactamase producing oral anaerobes. J Appl Oral Sci 2016; 24:142-7. [PMID: 27119762 PMCID: PMC4836921 DOI: 10.1590/1678-775720150469] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/16/2016] [Indexed: 01/06/2023] Open
Abstract
Purpose The aim of this study was to identify β-lactamase-producing oral anaerobic bacteria and screen them for the presence of cfxA and BlaTEM genes that are responsible for β-lactamase production and resistance to β-lactam antibiotics. Material and Methods Periodontal pocket debris samples were collected from 48 patients with chronic periodontitis and anaerobically cultured on blood agar plates with and without β-lactam antibiotics. Presumptive β-lactamase-producing isolates were evaluated for definite β-lactamase production using the nitrocefin slide method and identified using the API Rapid 32A system. Antimicrobial susceptibility was performed using disc diffusion and microbroth dilution tests as described by CLSI Methods. Isolates were screened for the presence of the β-lactamase-TEM (BlaTEM) and β-lactamase-cfxA genes using Polymerase Chain Reaction (PCR). Amplified PCR products were sequenced and the cfxA gene was characterized using Genbank databases. Results Seventy five percent of patients carried two species of β-lactamase-producing anaerobic bacteria that comprised 9.4% of the total number of cultivable bacteria. Fifty one percent of β-lactamase-producing strains mainly Prevotella, Porphyromonas, and Bacteroides carried the cfxA gene, whereas none of them carried blaTEM. Further characterization of the cfxA gene showed that 76.7% of these strains carried the cfxA2 gene, 14% carried cfxA3, and 9.3% carried cfxA6. The cfxA6 gene was present in three Prevotella spp. and in one Porphyromonas spp. Strains containing cfxA genes (56%) were resistant to the β-lactam antibiotics. Conclusion This study indicates that there is a high prevalence of the cfxA gene in β-lactamase-producing anaerobic oral bacteria, which may lead to drug resistance and treatment failure.
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Affiliation(s)
- Buhle Binta
- School of Oral Health Sciences, Faculty of Health Sciences, University of the Witwatersrand, Gauteng, South Africa
| | - Mrudula Patel
- School of Oral Health Sciences, Faculty of Health Sciences, University of the Witwatersrand, Gauteng, South Africa
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Zirk M, Buller J, Goeddertz P, Rothamel D, Dreiseidler T, Zöller JE, Kreppel M. Empiric systemic antibiotics for hospitalized patients with severe odontogenic infections. J Craniomaxillofac Surg 2016; 44:1081-8. [PMID: 27369813 DOI: 10.1016/j.jcms.2016.05.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 04/16/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022] Open
Abstract
INTRODUCTION Odontogenic infections may lead to severe head and neck infections with potentially great health risk. Age, location of purulent affected sites and beta-lactam allergy are some mentionable factors regarding patients' in-hospital stay and course of disease. Are there new challenges regarding bacteria' antibiotic resistance for empiric treatment and what influences do they have on patients' clinical course? METHODS We analyzed in a 4-year retrospective study the medical records of 294 in-hospital patients with severe odontogenic infections. On a routine base bacteria were identified and susceptibility testing was performed. Length of stay in-hospital was evaluated regarding patients' age, beta-lactam allergy profile, affected sites and bacteria susceptibility to empiric antibiotics. RESULTS Length of stay in-hospital was detected to be associated with affected space and penicillin allergy as well (p < 0.05). Isolates presented large amounts of aerobic gram-positive bacteria (64.2%), followed by facultative anaerobic bacteria (gram+/15.8%, gram-/12.7%). Tested ampicillin in combination with sulbactam (or without) and cephalosporins displayed high susceptibility rates, revealing distinguished results regarding clindamycin (p < 0.05). Co-trimoxazol and moxifloxacin showed high overall susceptibility rates (MOX: 94.7%, COTRIM: 92.6%). DISCUSSION This study demonstrates ampicillin/sulbactam in addition to surgical intervention is a good standard in treatment of severe odontogenic neck infections. Cephalosporins seem to be a considerable option as well. If beta-lactam allergy is diagnosed co-trimoxazol and moxifloxacin represent relevant alternatives. CONCLUSION Age, allergic profile and bacteria' resistance patterns for empiric antibiotics have an influence on patients in-hospital stay. Ampicillin/sulbactam proves itself to be good for empiric antibiosis in severe odontogenic infections. Furthermore cephalosporins could be considered as another option in treatment. However moxifloxacin and co-trimoxazol deserves further investigation as empiric antibiosis in odontogenic infections if beta-lactam allergy is diagnosed.
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Affiliation(s)
- Matthias Zirk
- Department for Oral and Cranio-Maxillo and Facial Plastic Surgery (Head: Prof. Dr. Dr. Joachim E. Zöller), University of Cologne, Germany.
| | - Johannes Buller
- Department for Oral and Cranio-Maxillo and Facial Plastic Surgery (Head: Prof. Dr. Dr. Joachim E. Zöller), University of Cologne, Germany
| | - Peter Goeddertz
- Department for Oral and Cranio-Maxillo and Facial Plastic Surgery (Head: Prof. Dr. Dr. Joachim E. Zöller), University of Cologne, Germany
| | - Daniel Rothamel
- Department for Oral and Cranio-Maxillo and Facial Plastic Surgery (Head: Prof. Dr. Dr. Joachim E. Zöller), University of Cologne, Germany
| | - Timo Dreiseidler
- Dreifaltigkeits-Krankenhaus Wesseling, University Teaching Hospital, Germany
| | - Joachim E Zöller
- Department for Oral and Cranio-Maxillo and Facial Plastic Surgery (Head: Prof. Dr. Dr. Joachim E. Zöller), University of Cologne, Germany
| | - Matthias Kreppel
- Department for Oral and Cranio-Maxillo and Facial Plastic Surgery (Head: Prof. Dr. Dr. Joachim E. Zöller), University of Cologne, Germany
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Liu L, Zhang Q, Lin J, Ma L, Zhou Z, He X, Jia Y, Chen F. Investigating Oral Microbiome Profiles in Children with Cleft Lip and Palate for Prognosis of Alveolar Bone Grafting. PLoS One 2016; 11:e0155683. [PMID: 27191390 PMCID: PMC4871547 DOI: 10.1371/journal.pone.0155683] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/03/2016] [Indexed: 11/29/2022] Open
Abstract
In this study, we sought to investigate the oral microbiota structure of children with cleft lip and palate (CLP) and explore the pre-operative oral bacterial composition related to the prognosis of alveolar bone grafting. In total, 28 patients (19 boys, 9 girls) with CLP who were scheduled to undergo alveolar bone grafting for the first time were recruited. According to the clinical examination of operative sites at the third month after the operation, the individuals were divided into a non-inflammation group (n = 15) and an inflammation group (n = 13). In all, 56 unstimulated saliva samples were collected before and after the operation. The v3-v4 hypervariable regions of the 16S rRNA gene were sequenced using an Illumina MiSeq sequencing platform. Based on the beta diversity of the operational taxonomic units (OTUs) in the inflammation and non-inflammation samples, the microbial variation in the oral cavity differed significantly between the two groups before and after the operation (P < 0.05). Analysis of the relative abundances of pre-operative OTUs revealed 26 OTUs with a relative abundance higher than 0.01%, reflecting a significant difference of the relative abundance between groups (P < 0.05). According to a principal component analysis of the pre-operative samples, the inflammation-related OTUs included Tannerella sp., Porphyromonas sp., Gemella sp., Moraxella sp., Prevotella nigrescens, and Prevotella intermedia, most of which were enriched in the inflammation group and showed a significant positive correlation. A cross-validated random forest model based on the 26 different OTUs before the operation was able to fit the post-operative status of grafted sites and yielded a good classification result. The sensitivity and specificity of this classified model were 76.9% and 86.7%, respectively. These findings show that the oral microbiota profile before alveolar bone grafting may be related to the risk of post-operative inflammation at grafted sites.
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Affiliation(s)
- Luwei Liu
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, P.R. China
| | - Qian Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, P.R. China
| | - Jiuxiang Lin
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, P.R. China
| | - Lian Ma
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, P.R. China
| | - Zhibo Zhou
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, P.R. China
| | - Xuesong He
- School of Dentistry, University of California Los Angeles, Los Angeles, United States of America
| | - Yilin Jia
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, P.R. China
- * E-mail: (YJ); (FC)
| | - Feng Chen
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, P.R. China
- * E-mail: (YJ); (FC)
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Tamanai-Shacoori Z, Monfort C, Oliviero N, Gautier P, Bonnaure-Mallet M, Jolivet-Gougeon A. cfxA expression in oral clinical Capnocytophaga isolates. Anaerobe 2015. [PMID: 26204794 DOI: 10.1016/j.anaerobe.2015.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Capnocytophaga spp. are commensal bacteria involved in oral and systemic diseases, with a variable susceptibility to beta-lactams. The cfxA gene expression level was assessed using quantitative RT-PCR, and reasons of the observed misexpression were discussed, as insertion of foreign genetic material, contributing to dissemination and evolution of antibiotic resistance genes.
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Affiliation(s)
- Zohreh Tamanai-Shacoori
- Equipe de Microbiologie, EA 1254, Université de Rennes 1, Université Européenne de Bretagne, 2, avenue du Professeur Léon Bernard, 35043 Rennes, France
| | - Clarisse Monfort
- Equipe de Microbiologie, EA 1254, Université de Rennes 1, Université Européenne de Bretagne, 2, avenue du Professeur Léon Bernard, 35043 Rennes, France
| | - Nolwenn Oliviero
- Equipe de Microbiologie, EA 1254, Université de Rennes 1, Université Européenne de Bretagne, 2, avenue du Professeur Léon Bernard, 35043 Rennes, France
| | - Philippe Gautier
- Pole Biologie, Rennes Teaching Hospital, 2 rue Henri Le Guilloux, 35033 Rennes, France
| | - Martine Bonnaure-Mallet
- Equipe de Microbiologie, EA 1254, Université de Rennes 1, Université Européenne de Bretagne, 2, avenue du Professeur Léon Bernard, 35043 Rennes, France; Pole Odontologie, Rennes Teaching Hospital, 2 rue Henri Le Guilloux, 35033 Rennes, France
| | - Anne Jolivet-Gougeon
- Equipe de Microbiologie, EA 1254, Université de Rennes 1, Université Européenne de Bretagne, 2, avenue du Professeur Léon Bernard, 35043 Rennes, France; Pole Biologie, Rennes Teaching Hospital, 2 rue Henri Le Guilloux, 35033 Rennes, France.
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