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Le HT, Lubian AF, Bowring B, van der Poorten D, Iredell J, George J, Venturini C, Ahlenstiel G, Read S. Using a human colonoid-derived monolayer to study bacteriophage translocation. Gut Microbes 2024; 16:2331520. [PMID: 38517357 PMCID: PMC10962583 DOI: 10.1080/19490976.2024.2331520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
Bacteriophages (phages) are estimated to be the most abundant microorganisms on Earth. Their presence in human blood suggests that they can translocate from non-sterile sites such as the gastrointestinal tract where they are concentrated. To examine phage translocation ex vivo, we adapted a primary colonoid monolayer model possessing cell diversity and architecture, and a thick layer of mucus akin to the colonic environment in vivo. We show that the colonoid monolayer is superior to the Caco-2 cell-line model, possessing intact and organized tight junctions and generating a physiologically relevant mucus layer. We showed, using two different phages, that translocation across the colonoid monolayer was largely absent in differentiated monolayers that express mucus, unlike Caco-2 cultures that expressed little to no mucus. By stimulating mucus production or removing mucus, we further demonstrated the importance of colonic mucus in preventing phage translocation. Finally, we used etiological drivers of gut permeability (alcohol, fat, and inflammatory cytokines) to measure their effects on phage translocation, demonstrating that all three stimuli have the capacity to amplify phage translocation. These findings suggest that phage translocation does occur in vivo but may be largely dependent on colonic mucus, an important insight to consider in future phage applications.
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Affiliation(s)
- Huu Thanh Le
- Blacktown Clinical School, Western Sydney University, Sydney, Australia
- Storr Liver Centre, Westmead Institute for Medical Research, Sydney, Australia
| | - Alicia Fajardo Lubian
- Centre for Infectious Diseases and Microbiology (CIDM), Westmead Institute for Medical Research, Sydney, Australia
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Bethany Bowring
- Centre for Infectious Diseases and Microbiology (CIDM), Westmead Institute for Medical Research, Sydney, Australia
| | - David van der Poorten
- Department of Hepatology and Gastroenterology, Westmead Hospital, Westmead, Australia
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology (CIDM), Westmead Institute for Medical Research, Sydney, Australia
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Sydney, Australia
- Department of Hepatology and Gastroenterology, Westmead Hospital, Westmead, Australia
- School of Medicine, The University of Sydney, Sydney, Australia
| | - Carola Venturini
- Centre for Infectious Diseases and Microbiology (CIDM), Westmead Institute for Medical Research, Sydney, Australia
- Sydney School of Veterinary Science, The University of Sydney, Sydney, Australia
| | - Golo Ahlenstiel
- Blacktown Clinical School, Western Sydney University, Sydney, Australia
- Storr Liver Centre, Westmead Institute for Medical Research, Sydney, Australia
- Blacktown Mt Druitt Hospital, Sydney, Australia
| | - Scott Read
- Blacktown Clinical School, Western Sydney University, Sydney, Australia
- Storr Liver Centre, Westmead Institute for Medical Research, Sydney, Australia
- Blacktown Mt Druitt Hospital, Sydney, Australia
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2
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Noreika A, Stankevičiūtė J, Rutkienė R, Meškys R, Kalinienė L. Exploring the enzymatic activity of depolymerase gp531 from Klebsiella pneumoniae jumbo phage RaK2. Virus Res 2023; 336:199225. [PMID: 37741345 PMCID: PMC10550766 DOI: 10.1016/j.virusres.2023.199225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Klebsiella pneumoniae poses a major global challenge due to its virulence, multidrug resistance, and nosocomial nature. Thus, bacteriophage-derived proteins are extensively being investigated as a means to combat this bacterium. In this study, we explored the enzymatic specificity of depolymerase gp531, encoded by the jumbo bacteriophage vB_KleM_RaK2 (RaK2). We used two different methods to modify the reducing end of the oligosaccharides released during capsule hydrolysis with gp531. Subsequent acidic cleavage with TFA, followed by TLC and HPLC-MS analyses, revealed that RaK2 gp531 is a β-(1→4)-endoglucosidase. The enzyme specifically recognizes and cleaves the capsular polysaccharide (CPS) of the Klebsiella pneumoniae K54 serotype, releasing K-unit monomers (the main product), dimers, and trimers. Depolymerase gp531 remains active from 10 to 50 °C and in the pH 3-8 range, indicating its stability and versatility. Additionally, we demonstrated that gp531's activity is not affected by CPS acetylation, which is influenced by the growth conditions of the bacterial culture. Overall, our findings provide valuable insights into the enzymatic activity of the first characterized depolymerase targeting the capsule of the clinically relevant K54 serotype of K. pneumoniae.
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Affiliation(s)
- Algirdas Noreika
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania.
| | - Jonita Stankevičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania
| | - Laura Kalinienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania.
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3
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Samsing F, Zhang W, Zadoks RN, Whittington R, Venturini C, Giles C, Carson J, Becker JA. Cold temperature stress and damaged skin induced high mortality in barramundi (Lates calcarifer) challenged with Vibrio harveyi. JOURNAL OF FISH DISEASES 2023; 46:751-766. [PMID: 36966382 DOI: 10.1111/jfd.13784] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 06/07/2023]
Abstract
Most diseases in aquaculture are caused by opportunistic pathogens. One of them, Vibrio harveyi, is a widespread Gram-negative bacterium that has become an important pathogen of aquatic species in marine environments. Here, we propose the use of the causal pie model as a framework to conceptualize the causation of vibriosis in juvenile barramundi (Lates calcarifer) and to establish an effective challenge model. In the model, a sufficient cause, or the causal pie, is a constellation of component causes that lead to an outcome (e.g. vibriosis). In the pilot study, a high cumulative mortality (63.3% ± 10.0%, mean ± SE) was observed when V. harveyi was administered by intraperitoneal injection using a high challenge dose [107 colony-forming units (CFU) fish-1 ], but low or no mortality was observed in fish subject to cold stress or fish with intact skin when challenged by immersion. We, therefore, tested the use of a skin lesion (induced with a 4-mm biopsy punch) combined with cold temperature stress to induce vibriosis following the causal pie model. After challenge, fish were immediately subject to cold stress (22°C) or placed at an optimal temperature of 30°C. All groups were challenged with 108 CFU mL-1 for 60 min. A considerably higher mortality level (72.7% ± 13.9%) was observed in fish challenged with both a skin lesion and cold stress compared with mortality in fish only having a skin lesion (14.6% ± 2.8%). V. harveyi was re-isolated from all moribund fish and was detected by species-specific real-time PCR in gills, head kidney and liver, regardless of challenge treatment confirming vibriosis as the cause of disease. Parenchymal tissues had histopathological changes consistent with vibriosis. Whole-genome sequence (WGS) is provided for the Vibrio harveyi isolate examined in this study. Overall, the causal pie model was a useful framework to conceptualize the design of the experimental challenge model, in which both cold stress and skin damage were identified as component causes of vibriosis with high mortality. This conceptual framework can be applied to other opportunistic pathogens in aquaculture or to the study of co-infections in fish.
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Affiliation(s)
- Francisca Samsing
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
| | - William Zhang
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
| | - Ruth N Zadoks
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
| | - Richard Whittington
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
| | - Carola Venturini
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
| | - Carla Giles
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, Tasmania, Australia
| | - Jeremy Carson
- Carson BioConsulting, Launceston, Tasmania, Australia
| | - Joy A Becker
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia
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Tisalema-Guanopatín E, Cabezas-Mera F, Nolivos-Rodríguez K, Fierro I, Pazmiño L, Garzon-Chavez D, Debut A, Vizuete K, Reyes JA. New Bacteriophages Members of the Ackermannviridae Family Specific for Klebsiella pneumoniae ST258. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:99-107. [PMID: 37350993 PMCID: PMC10282792 DOI: 10.1089/phage.2022.0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Background Carbapenem-resistant Klebsiella pneumoniae, particularly isolates classified as sequence-type 258 (ST258), are multidrug-resistant strains that are strongly associated with poor-prognosis nosocomial infections, as current therapeutic options are limited and ineffective. In recent years, phage therapy has emerged as a promising treatment option for these scenarios. Methodology and Results We report the isolation and characterization of three new phages against Klebsiella pneumoniae ST258 strains recovered from Machángara river wastewater. These new members of the Ackermannviridae family showed stability over a wide temperature and pH range and burst sizes ranging from 6 to 44 plaque-forming units per bacteria. Their genomes were about 157 kilobases, with an average guanine-cytosine content of 46.4% and showed presence of several transfer RNAs, which also allowed us to predict in silico a lytic replicative cycle due to the presence of endolysins and lysozymes. Conclusion Three lytic phages of Ackermannviridae family were recovered against Klebsiella pneumoniae ST258 strains from sewage; however, further characterization is needed for future consideration as therapeutic alternatives.
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Affiliation(s)
- Estefanía Tisalema-Guanopatín
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
- Faculty of Engineering and Applied Sciences, Universidad Internacional SEK, Quito, Ecuador
| | - Fausto Cabezas-Mera
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - Karla Nolivos-Rodríguez
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
| | - Isabel Fierro
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
| | - Lourdes Pazmiño
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
| | - Daniel Garzon-Chavez
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud (COCSA), Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - Alexis Debut
- Centro de Nanociencia y Nanotecnología (CENCINAT), Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Karla Vizuete
- Centro de Nanociencia y Nanotecnología (CENCINAT), Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Jorge Aníbal Reyes
- Facultad de Ciencias Químicas, Universidad Central del Ecuador (UCE), Ciudadela Universitaria Avenida América, Quito, Pichincha, Ecuador
- Departamento de Microbiología, Hospital del IESS Quito Sur, Avenida Moraspungo, Quito, Ecuador
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5
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Vitt AR, Sørensen MCH, Bortolaia V, Brøndsted L. A Representative Collection of Commensal Extended-Spectrum- and AmpC-β-Lactamase-Producing Escherichia coli of Animal Origin for Phage Sensitivity Studies. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:35-45. [PMID: 37214655 PMCID: PMC10196081 DOI: 10.1089/phage.2023.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Introduction Extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (AmpC)-producing Escherichia coli from livestock and meat represent a zoonotic risk and biocontrol solutions are needed to prevent transmission to humans. Methods In this study, we established a representative collection of animal-origin ESBL/AmpC E. coli as target to test the antimicrobial potential of bacteriophages. Results Bioinformatic analysis of whole-genome sequence data of 198 ESBL/AmpC E. coli from pigs, broilers, and broiler meat identified strains belonging to all known E. coli phylogroups and 65 multilocus sequence types. Various ESBL/AmpC genes and plasmid types were detected with expected source-specific patterns. Plaque assay using 15 phages previously isolated using the E. coli reference collection demonstrated that Warwickvirus phages showed the broadest host range, killing up to 26 strains. Conclusions 154/198 strains were resistant to infection by all phages tested, suggesting a need for isolating phages specific for ESBL/AmpC E. coli. The strain collection described in this study is a useful resource fulfilling such need.
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Affiliation(s)
- Amira R. Vitt
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - Valeria Bortolaia
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Lone Brøndsted
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
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6
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Beamud B, García-González N, Gómez-Ortega M, González-Candelas F, Domingo-Calap P, Sanjuan R. Genetic determinants of host tropism in Klebsiella phages. Cell Rep 2023; 42:112048. [PMID: 36753420 PMCID: PMC9989827 DOI: 10.1016/j.celrep.2023.112048] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/25/2022] [Accepted: 01/13/2023] [Indexed: 02/08/2023] Open
Abstract
Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show a narrow host range for most phages, with <2% of 6,319 phage-host combinations tested yielding detectable interactions. Bacterial capsule diversity is the main factor restricting phage host range. Consequently, phage-encoded depolymerases are key determinants of host tropism, and depolymerase sequence types are associated with the ability to infect specific capsular types across phage families. However, all phages with a broader host range found do not encode canonical depolymerases, suggesting alternative modes of entry. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences.
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Affiliation(s)
- Beatriz Beamud
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Neris García-González
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Mar Gómez-Ortega
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
| | - Rafael Sanjuan
- Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
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7
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Balcão VM, Moreli FC, Silva EC, Belline BG, Martins LF, Rossi FPN, Pereira C, Vila MMDC, da Silva AM. Isolation and Molecular Characterization of a Novel Lytic Bacteriophage That Inactivates MDR Klebsiella pneumoniae Strains. Pharmaceutics 2022; 14:pharmaceutics14071421. [PMID: 35890314 PMCID: PMC9324672 DOI: 10.3390/pharmaceutics14071421] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 02/07/2023] Open
Abstract
The worldwide increase in serious infections caused by multidrug-resistant (MDR) K. pneumoniae emphasizes the urgent need of new therapeutic strategies for the control of this pathogen. There is growing interest in the use of bacteriophages (or phages) to treat K. pneumoniae infections, and newly isolated phages are needed. Here, we report the isolation and physical/biological/molecular characterization of a novel lytic phage and its efficacy in the control of MDR K. pneumoniae. The phage vB_KpnS_Uniso31, referred to hereafter as phage Kpn31, was isolated from hospital wastewater using K. pneumoniae CCCD-K001 as the host. Phage Kpn31 presents a siphovirus-like morphotype and was classified as Demerecviridae; Sugarlandvirus based on its complete genome sequence. The 113,444 bp Kpn31 genome does not encode known toxins or antimicrobial resistance genes, nor does it encode depolymerases related sequences. Phage Kpn31 showed an eclipse time of 15 min and a burst size of 9.12 PFU/host cell, allowing us to conclude it replicates well in K. pneumoniae CCCD-K001 with a latency period of 30 min. Phage Kpn31 was shown to be effective against at least six MDR K. pneumoniae clinical isolates in in vitro antibacterial activity assays. Based on its features, phage Kpn31 has potential for controlling infections caused by MDR K. pneumoniae.
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Affiliation(s)
- Victor M Balcão
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
- Department of Biology and CESAM, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Fernanda C Moreli
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Erica C Silva
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Bianca G Belline
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Layla F Martins
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Fernando P N Rossi
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
| | - Carla Pereira
- Department of Biology and CESAM, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Marta M D C Vila
- PhageLab, Laboratory of Biofilms and Bacteriophages, University of Sorocaba, Sorocaba 18023-000, Brazil
| | - Aline M da Silva
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil
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8
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Venturini C, Bowring B, Partridge SR, Ben Zakour NL, Fajardo-Lubian A, Lopez Ayala A, Qin J, Totsika M, van Galen G, Norris J, Iredell J. Co-Occurrence of Multidrug Resistant Klebsiella pneumoniae Pathogenic Clones of Human Relevance in an Equine Pneumonia Case. Microbiol Spectr 2022; 10:e0215821. [PMID: 35579468 PMCID: PMC9241755 DOI: 10.1128/spectrum.02158-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/13/2022] [Indexed: 11/20/2022] Open
Abstract
The global epidemiology of multidrug resistant Klebsiella pneumoniae, a serious threat to both animal and human health, is dominated by the spread of pathogenic clones, each separately evolving via acquisition of transferable antibiotic resistance or niche-specific virulence determinants. In horses, K. pneumoniae infection can lead to severe respiratory illness. Here, we characterized multiple isolates recovered from bronchial aspirates of a mare with pneumonia refractory to antibiotics. First, we used a combination of standard microbiology, bacteriophage cross-susceptibility and antibiotic resistance testing to profile the infecting K. pneumoniae population. The genomes of isolates with distinct fingerprints (pulsed-field gel electrophoresis) and unique combined bacteriophage/antibiotic profiles were then further analyzed using whole-genome sequencing. Adhesion to human epithelial cells and biofilm production were also measured as virulence indicators. Although it is commonly expected for one clone to dominate an infection episode, we identified five coexisting multidrug resistant K. pneumoniae sharing the same niche. One was a novel sequence type (ST4656), while the other four were all members of emerging human pathogenic clonal groups (ST307, ST628, ST893 and ST392). These isolates did not display significant differences from one another in terms of virulence or resistance and differed only in plasmid content from isolates implicated in severe human infections, with equal potential to prolong duration and severity of infection when sharing the same niche. This study highlights the importance of more precise surveillance and detection measures to uncover bacterial heterogeneity, reminding us that the "single clone" concept is not an absolute in invasive bacterial infections. IMPORTANCE Multidrug resistant Klebsiella pneumoniae are agents of life-threatening infections in animals and humans, with several multidrug resistant clones causing outbreaks of disease worldwide. It is generally accepted that only one clone will be dominant in an infection episode. In this study, we investigated K. pneumoniae isolates from a horse with severe pneumonia and demonstrated co-occurrence of multiple sequence types previously identified as emerging human pathogens. The equine isolates are not significantly different from one another in terms of virulence or resistance, with equal potential to prolong duration and severity of infection, and are indistinguishable from isolates recovered from humans, except for plasmid content. Our study highlights how the "one dominant clone" concept is not an absolute in severe infection, illustrating the need for improved diagnostics to track heterogeneity of infection, and reinforces the importance of cross-monitoring of environmental and human reservoirs of multidrug resistant pathogens.
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Affiliation(s)
- Carola Venturini
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Bethany Bowring
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Sally R. Partridge
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Medicine, University of Sydney, Sydney, New South Wales, Australia
- Westmead Hospital, Western Sydney Local Health District (WSLHD), Westmead, New South Wales, Australia
| | - Nouri L. Ben Zakour
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Alicia Fajardo-Lubian
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Ariana Lopez Ayala
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Jilong Qin
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Gaby van Galen
- Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jacqueline Norris
- Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Medicine, University of Sydney, Sydney, New South Wales, Australia
- Westmead Hospital, Western Sydney Local Health District (WSLHD), Westmead, New South Wales, Australia
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9
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Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL, Holt KE. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun 2021; 12:4188. [PMID: 34234121 PMCID: PMC8263825 DOI: 10.1038/s41467-021-24448-3] [Citation(s) in RCA: 368] [Impact Index Per Article: 122.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/16/2021] [Indexed: 12/14/2022] Open
Abstract
Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.
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Affiliation(s)
- Margaret M C Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Stephen C Watts
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Louise T Cerdeira
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
- London School of Hygiene & Tropical Medicine, London, UK
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10
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Identification of a Depolymerase Specific for K64-Serotype Klebsiella pneumoniae: Potential Applications in Capsular Typing and Treatment. Antibiotics (Basel) 2021; 10:antibiotics10020144. [PMID: 33535705 PMCID: PMC7912862 DOI: 10.3390/antibiotics10020144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 01/08/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP), one of the major nosocomial pathogens, is increasingly becoming a serious threat to global public health. There is an urgent need to develop effective therapeutic and preventive approaches to combat the pathogen. Here, we identified and characterized a novel capsule depolymerase (K64-ORF41) derived from Klebsiella phage SH-KP152410, which showed specific activities for K. pneumoniae K64-serotype. We showed that this depolymerase could be used in the identification of K64 serotypes based on the capsular typing, and the results agreed well with those from the conventional serotyping method using antisera. From this study, we also identified K64 mutant strains, which showed typing discrepancy between wzi-sequencing based genotyping and depolymerase-based or antiserum-based typing methods. Further investigation indicated that the mutant strain has an insertion sequence (IS) in wcaJ, which led to the alteration of the capsular serotype structure. We further demonstrated that K64-ORF41 depolymerase could sensitize the bacteria to serum or neutrophil killing by degrading the capsular polysaccharide. In summary, the identified K64 depolymerase proves to be an accurate and reliable tool for capsular typing, which will facilitate the preventive intervention such as vaccine development. In addition, the polymerase may represent a potential and promising therapeutic biologics against CRKP-K64 infections.
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Effects of Antibiotic Treatment with Piperacillin/Tazobactam versus Ceftriaxone on the Composition of the Murine Gut Microbiota. Antimicrob Agents Chemother 2021; 65:AAC.01504-20. [PMID: 33168609 DOI: 10.1128/aac.01504-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
Effective antimicrobial stewardship requires a better understanding of the impact of different antibiotics on the gut microflora. Studies with humans are confounded by large interindividual variability and difficulty in identifying control cohorts. However, controlled murine models can provide valuable information. In this study, we examined the impact of a penicillin-like antibiotic (piperacillin-tazobactam [TZP]) or a third-generation cephalosporin (ceftriaxone [CRO]) on the murine gut microbiota by analysis of changes in fecal microbiome composition by 16S rRNA amplicon sequencing and standard microbiology. Resistance to colonization by multidrug-resistant Escherichia coli sequence type 131 (ST131) and Klebsiella pneumoniae ST258 was also tested. Changes in microbiome composition and a significant (P < 0.05) decrease in diversity occurred in all treated mice, but dysbiosis was more marked and prolonged after CRO exposure, with a persistent rise in Proteobacteria Enterobacteriaceae blooms occurred in all antibiotic-treated mice, but for TZP, unlike CRO, these were significant only under direct antibiotic pressure. At the height of dysbiosis after antibiotic termination, the murine gut was highly susceptible to colonization with both multidrug-resistant enterobacterial pathogens. Cohabitation of treated mice with untreated individuals had a notable mitigating effect on dysbiosis of treated guts. The administration of a third-generation cephalosporin caused a more severe imbalance in the murine fecal microflora than that caused by a penicillin/β-lactam inhibitor combination with comparable activity against medically important virulent bacteria. At the height of dysbiosis, both antibiotic treatments equally led to microbial instability associated with loss of resistance to gut colonization by antibiotic-resistant pathogens.
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