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Patel K, Rizzo AN, Bach J, DeVoe W. Suture fixation of traumatic rib fracture flail segment with Klebsiella osteomyelitis. Trauma Case Rep 2024; 51:100996. [PMID: 38633376 PMCID: PMC11021944 DOI: 10.1016/j.tcr.2024.100996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
We report the case of a 71-year-old male who initially presented with urosepsis and was found to have a rib fracture of his right 6th rib with a flail segment and an associated abscess. Given the concern for infection, surgical rib fixation with titanium plating was not pursued during the washout of his abscess and instead, he successfully underwent rib fracture stabilization with bilateral suture transfixation. He was continued on a prolonged course of antibiotics for Klebsiella pneumonia osteomyelitis and was discharged uneventfully with optimal pain control and adequate respiratory effort.
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Affiliation(s)
- Krishna Patel
- Surgery, OhioHealth Riverside Methodist Hospital, Columbus 43214, USA
| | - Anthony N. Rizzo
- Surgery, OhioHealth Riverside Methodist Hospital, Columbus 43214, USA
| | - John Bach
- Surgery, OhioHealth Riverside Methodist Hospital, Columbus 43214, USA
| | - William DeVoe
- Surgery, OhioHealth Riverside Methodist Hospital, Columbus 43214, USA
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Vaquer A, Adrover-Jaume C, Clemente A, Viana J, Rodríguez R, Rojo-Molinero E, Oliver A, de la Rica R. OriPlex: Origami-enabled multiplexed detection of respiratory pathogens. Biosens Bioelectron 2024; 257:116341. [PMID: 38677019 DOI: 10.1016/j.bios.2024.116341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Origami biosensors leverage paper foldability to develop total analysis systems integrated in a single piece of paper. This capability can also be utilized to incorporate additional features that would be difficult to achieve with rigid substrates. In this article, we report a new design for 3D origami biosensors called OriPlex, which leverages the foldability of filter paper for the multiplexed detection of bacterial pathogens. OriPlex immunosensors detect pathogens by folding nanoparticle reservoirs containing different types of nanoprobes. This releases antibody-coated nanoparticles in a central channel where targets are captured through physical interactions. The OriPlex concept was demonstrated by detecting the respiratory pathogens Pseudomonas aeruginosa (PA) and Klebsiella pneumoniae (KP) with a limit of detection of 3.4·103 cfu mL-1 and 1.4·102 cfu mL-1, respectively, and with a turn-around time of 25 min. Remarkably, the OriPlex biosensors allowed the multiplexed detection of both pathogens spiked into real bronchial aspirate (BAS) samples at a concentration of 105 cfu mL-1 (clinical infection threshold), thus demonstrating their suitability for diagnosing lower tract respiratory infections. The results shown here pave the way for implementing OriPlex biosensors as a screening test for detecting superbugs requiring personalized antibiotics in suspected cases of nosocomial pneumonia.
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Affiliation(s)
- Andreu Vaquer
- Multidisciplinary Sepsis Group, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma de Mallorca, Spain; Department of Chemistry, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Cristina Adrover-Jaume
- Multidisciplinary Sepsis Group, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma de Mallorca, Spain; Department of Chemistry, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Antonio Clemente
- Multidisciplinary Sepsis Group, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III Madrid, Spain.
| | - Julia Viana
- Microbiology Department, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma, Spain
| | - Rocío Rodríguez
- Microbiology Department, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma, Spain
| | - Estrella Rojo-Molinero
- Microbiology Department, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III Madrid, Spain
| | - Antonio Oliver
- Microbiology Department, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III Madrid, Spain
| | - Roberto de la Rica
- Multidisciplinary Sepsis Group, Hospital Universitario Son Espases, Health Research Institute of Balearic Islands (IdISBa), Palma de Mallorca, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III Madrid, Spain.
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D, Abulaila S, Mendoza J, Landeta C. Development of a sensor for disulfide bond formation in diverse bacteria. J Bacteriol 2024; 206:e0043323. [PMID: 38493438 PMCID: PMC11025322 DOI: 10.1128/jb.00433-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/19/2024] Open
Abstract
In bacteria, disulfide bonds contribute to the folding and stability of proteins important for processes in the cellular envelope. In Escherichia coli, disulfide bond formation is catalyzed by DsbA and DsbB enzymes. DsbA is a periplasmic protein that catalyzes disulfide bond formation in substrate proteins, while DsbB is an inner membrane protein that transfers electrons from DsbA to quinones, thereby regenerating the DsbA active state. Actinobacteria including mycobacteria use an alternative enzyme named VKOR, which performs the same function as DsbB. Disulfide bond formation enzymes, DsbA and DsbB/VKOR, represent novel drug targets because their inhibition could simultaneously affect the folding of several cell envelope proteins including virulence factors, proteins involved in outer membrane biogenesis, cell division, and antibiotic resistance. We have previously developed a cell-based and target-based assay to identify molecules that inhibit the DsbB and VKOR in pathogenic bacteria, using E. coli cells expressing a periplasmic β-Galactosidase sensor (β-Galdbs), which is only active when disulfide bond formation is inhibited. Here, we report the construction of plasmids that allows fine-tuning of the expression of the β-Galdbs sensor and can be mobilized into other gram-negative organisms. As an example, when expressed in Pseudomonas aeruginosa UCBPP-PA14, which harbors two DsbB homologs, β-Galdbs behaves similarly as in E. coli, and the biosensor responds to the inhibition of the two DsbB proteins. Thus, these β-Galdbs reporter plasmids provide a basis to identify novel inhibitors of DsbA and DsbB/VKOR in multidrug-resistant gram-negative pathogens and to further study oxidative protein folding in diverse gram-negative bacteria. IMPORTANCE Disulfide bonds contribute to the folding and stability of proteins in the bacterial cell envelope. Disulfide bond-forming enzymes represent new drug targets against multidrug-resistant bacteria because inactivation of this process would simultaneously affect several proteins in the cell envelope, including virulence factors, toxins, proteins involved in outer membrane biogenesis, cell division, and antibiotic resistance. Identifying the enzymes involved in disulfide bond formation in gram-negative pathogens as well as their inhibitors can contribute to the much-needed antibacterial innovation. In this work, we developed sensors of disulfide bond formation for gram-negative bacteria. These tools will enable the study of disulfide bond formation and the identification of inhibitors for this crucial process in diverse gram-negative pathogens.
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Affiliation(s)
- Dyotima
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Sally Abulaila
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Jocelyne Mendoza
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Cristina Landeta
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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Sun C, Xu Y, Xu G, Ji X, Jiang P, He Y. Active fractions from Jingfang Baidu Powder alleviate Klebsiella-induced Pneumonia by inhibiting TLR4/Myd88-ERK signaling pathway. J Ethnopharmacol 2024:118067. [PMID: 38636574 DOI: 10.1016/j.jep.2024.118067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/04/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Jingfang Baidu Powder (JFBDP) is a classic traditional Chinese medicine prescription. Although Jingfang Baidu powder obtained a general consensus on clinical efficacy in treating pneumonia, there were many Chinese herbal drugs in formula, complex components, and large oral dosage, which brings certain obstacles to clinical application. AIM OF THE STUDY Therefore, screening of the active fraction that exerts anti-pneumonia helps improve the pharmaceutical preparation, improve the treatment compliance of patients, and further contribute to the clinical application, and the screening of the new active ingredients with anti-pneumonia. The histopathological observation, real-time quantitative PCR, western blotting, and immunofluorescence were applied to evaluate the anti-pneumonia efficacy of active fractions from JFBDP. RESULTS Three fractions from JFBDP inhibit the gene expression of IL-1β, IL-10, CCL3, CCL5, and CCL22 in lung tissue infected by Klebsiella at various degrees, and presented a good dose-response relationship. JF50 showed stronger anti-inflammatory effects among three fractions including JF30, JF50, and JF75. Besides, JF50 significantly reduced the protein expression of TLR4 and Myd88 in lung tissue infected with Klebsiella, and it also significantly inhibited p-ERK and p-NF-κB p65. JF50 significantly inhibits the protein expression of Caspase 3, Caspase 8, and Caspase 9 in lung tissue infected with Klebsiella at the dose of 25 mg/kg and 50 mg/kg. CONCLUSION JF50 improves lung pathological damage in Klebsiella pneumonia mice by inhibiting the TLR4/Myd88/NF-κB-ERK signaling pathway, and inhibiting apoptosis of lung tissue cells. These findings provide a reference for further exploring the active substance basis of Jingfang Baidu Powder in treating bacterial pneumonia.
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Affiliation(s)
- Chuanbo Sun
- College of Biotechnology and Pharmaceutical Engineering of West Anhui University, Lu'an, 237012, China.
| | | | - Guangpei Xu
- College of Biotechnology and Pharmaceutical Engineering of West Anhui University, Lu'an, 237012, China.
| | - Xu Ji
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230001, China.
| | - Ping Jiang
- College of Biotechnology and Pharmaceutical Engineering of West Anhui University, Lu'an, 237012, China.
| | - Yanfei He
- College of Biotechnology and Pharmaceutical Engineering of West Anhui University, Lu'an, 237012, China.
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Fostervold A, Raffelsberger N, Hetland MAK, Bakksjø R, Bernhoff E, Samuelsen Ø, Sundsfjord A, Afset JE, Berntsen CF, Bævre-Jensen R, Ebbesen MH, Gammelsrud KW, Guleng AD, Handal N, Jakovljev A, Johal SK, Marvik Å, Natvik A, Sandnes RA, Tofteland S, Bjørnholt JV, Löhr IH. Risk of death in Klebsiella pneumoniae bloodstream infections is associated with specific phylogenetic lineages. J Infect 2024; 88:106155. [PMID: 38574775 DOI: 10.1016/j.jinf.2024.106155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/22/2024] [Accepted: 03/29/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Klebsiella pneumoniae species complex (KpSC) bloodstream infections (BSIs) are associated with considerable morbidity and mortality, particularly in elderly and multimorbid patients. Multidrug-resistant (MDR) strains have been associated with poorer outcome. However, the clinical impact of KpSC phylogenetic lineages on BSI outcome is unclear. METHODS In an 18-month nationwide Norwegian prospective study of KpSC BSI episodes in adults, we used whole-genome sequencing to describe the molecular epidemiology of KpSC, and multivariable Cox regression analysis including clinical data to determine adjusted hazard ratios (aHR) for death associated with specific genomic lineages. FINDINGS We included 1078 BSI episodes and 1082 bacterial isolates from 1055 patients. The overall 30-day case-fatality rate (CFR) was 12.5%. Median patient age was 73.4, 61.7% of patients were male. Median Charlson comorbidity score was 3. Klebsiella pneumoniae sensu stricto (Kp) (79.3%, n = 858/1082) and K. variicola (15.7%, n = 170/1082) were the dominating phylogroups. Global MDR-associated Kp clonal groups (CGs) were prevalent (25.0%, n = 270/1082) but 78.9% (n = 213/270) were not MDR, and 53.7% (n = 145/270) were community acquired. The major findings were increased risk for death within 30 days in monomicrobial BSIs caused by K. variicola (CFR 16.9%, n = 21; aHR 1.86, CI 1.10-3.17, p = 0.02), and global MDR-associated Kp CGs (CFR 17.0%, n = 36; aHR 1.52, CI 0.98-2.38, p = 0.06) compared to Kp CGs not associated with MDR (CFR 10.1%, n = 46). CONCLUSION Bacterial traits, beyond antimicrobial resistance, have a major impact on the clinical outcome of KpSC BSIs. The global spread of MDR-associated Kp CGs is driven by other mechanisms than antibiotic selection alone. Further insights into virulence determinants, and their association with phylogenetic lineages are needed to better understand the epidemiology of KpSC infection and clinical outcome.
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Affiliation(s)
- Aasmund Fostervold
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway; Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway.
| | - Niclas Raffelsberger
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Marit A K Hetland
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway; Department of Biological Sciences, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - Ragna Bakksjø
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Jan E Afset
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Department of Medical Microbiology, St. Olav's Hospital, Trondheim University hospital, Trondheim, Norway
| | - Christopher F Berntsen
- Department of Internal Medicine, Lovisenberg Diaconal Hospital, Oslo, Norway; Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Roar Bævre-Jensen
- Department of Medical Microbiology, Vestre Viken Hospital Trust, Drammen, Norway
| | - Marit H Ebbesen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Karianne W Gammelsrud
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anja D Guleng
- Centre for Laboratory Medicine, Østfold Hospital Trust, Kalnes, Norway
| | - Nina Handal
- Department of Microbiology and Infection control, Akershus University Hospital, Lørenskog, Norway
| | - Aleksandra Jakovljev
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Department of Medical Microbiology, St. Olav's Hospital, Trondheim University hospital, Trondheim, Norway
| | - Simreen K Johal
- Department of Medical Microbiology, Nordland Hospital Trust, Bodø, Norway
| | - Åshild Marvik
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
| | - Ane Natvik
- Department of Medical Microbiology, Vestre Viken Hospital Trust, Bærum, Norway
| | - Rolf-Arne Sandnes
- Department of Medical Microbiology, Innlandet Hospital Trust, Lillehammer, Norway
| | - Ståle Tofteland
- Department of Microbiology, Hospital of Southern Norway Trust, Kristiansand, Norway
| | - Jørgen V Bjørnholt
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Iren H Löhr
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway; Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
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Kowalski M, Minka Obama B, Catho G, Dewez JE, Merglen A, Ruef M, Andrey DO, Hassoun-Kheir N, de Kraker ME, Combescure C, Emonet S, Galetto-Lacour A, Wagner N. Antimicrobial resistance in Enterobacterales infections among children in sub-Saharan Africa: a systematic review and meta-analysis. EClinicalMedicine 2024; 70:102512. [PMID: 38495519 PMCID: PMC10940950 DOI: 10.1016/j.eclinm.2024.102512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/19/2024] Open
Abstract
Background The burden of antimicrobial resistance (AMR) has been estimated to be the highest in sub-Saharan Africa (SSA). The current study estimated the proportion of drug-resistant Enterobacterales causing infections in SSA children. Methods We searched MEDLINE/PubMed, Embase and the Cochrane Library to identify retrospective and prospective studies published from 01/01/2005 to 01/06/2022 reporting AMR of Enterobacterales causing infections in sub-Saharan children (0-18 years old). Studies were excluded if they had unclear documentation of antimicrobial susceptibility testing methods or fewer than ten observations per bacteria. Data extraction and quality appraisal were conducted by two authors independently. The primary outcome was the proportion of Enterobacterales resistant to antibiotics commonly used in paediatrics. Proportions were combined across studies using mixed-effects logistic regression models per bacteria and per antibiotic. Between-study heterogeneity was assessed using the I2 statistic. The protocol was registered with PROSPERO (CRD42021260157). Findings After screening 1111 records, 122 relevant studies were included, providing data on more than 30,000 blood, urine and stool isolates. Escherichia coli and Klebsiella spp. were the predominant species, both presenting high proportions of resistance to third-generation cephalosporins, especially in blood cultures: 40.6% (95% CI: 27.7%-55%; I2: 85.7%, number of isolates (n): 1032) and 84.9% (72.8%-92.2%; I2: 94.1%, n: 2067), respectively. High proportions of resistance to other commonly used antibiotics were also observed. E. coli had high proportions of resistance, especially for ampicillin (92.5%; 95% CI: 76.4%-97.9%; I2: 89.8%, n: 888) and gentamicin (42.7%; 95% CI: 30%-56.5%; I2: 71.9%, n: 968). Gentamicin-resistant Klebsiella spp. were also frequently reported (77.6%; 95% CI: 65.5%-86.3%; I2: 91.6%, n: 1886). Interpretation High proportions of resistance to antibiotics commonly used for empirical treatment of infectious syndromes were found for Enterobacterales in sub-Saharan children. There is a critical need to better identify local patterns of AMR to inform and update clinical guidelines for better treatment outcomes. Funding No funding was received.
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Affiliation(s)
- Morgane Kowalski
- Children’s Hospital, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Basilice Minka Obama
- Paediatric Infectious Diseases Unit, Children’s Hospital, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Regional Hospital Centre for Ebolowa, Ebolowa, Cameroon
| | - Gaud Catho
- Division of Infectious Diseases, Central Institute, Hospital of Valais, Switzerland
- Infection Control Division, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Juan Emmanuel Dewez
- Medical Department, Médecins Sans Frontières, Operational Centre Geneva, Geneva, Switzerland
| | - Arnaud Merglen
- Division of General Paediatrics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Micaela Ruef
- Children’s Hospital, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Diego O. Andrey
- Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Nasreen Hassoun-Kheir
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, WHO Collaborating Centre, Geneva, Switzerland
| | - Marlieke E.A. de Kraker
- Infection Control Programme, Geneva University Hospitals and Faculty of Medicine, WHO Collaborating Centre, Geneva, Switzerland
| | - Christophe Combescure
- Centre for Clinical Research, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Stephane Emonet
- Division of Infectious Diseases, Central Institute, Hospital of Valais, Switzerland
- Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Annick Galetto-Lacour
- Division of Paediatric Emergency Medicine, Children’s Hospital, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Noémie Wagner
- Paediatric Infectious Diseases Unit, Children’s Hospital, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
- Medical Department, Médecins Sans Frontières, Operational Centre Geneva, Geneva, Switzerland
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Ammar A, Singh V, Ilic S, Samiksha F, Marsh A, Rodriguez-Palacios A. Rodent Gut Bacteria Coexisting with an Insect Gut Virus in Parasitic Cysts: Metagenomic Evidence of Microbial Translocation and Co-adaptation in Spatially-Confined Niches. bioRxiv 2024:2024.03.22.585885. [PMID: 38562820 PMCID: PMC10983908 DOI: 10.1101/2024.03.22.585885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In medicine, parasitic cysts or cysticerci (fluid-filled cysts, larval stage of tapeworms) are believed to be sterile (no bacteria), and therein, the treatment of cysticerci infestations of deep extra-intestinal tissues (e.g., brain) relies almost exclusively on the use of antiparasitic medications, and rarely antibiotics. To date, however, it is unclear why common post-treatment complications include abscessation. This study quantified the microbial composition of parasitic cyst contents in a higher-order rodent host, using multi-kingdom shotgun metagenomics, to improve our understanding of gut microbial translocation and adaptation strategies in wild environments. Analysis was conducted on DNA from two hepatic parasitic cysts (Hydatigera (Taeenia) taeniaeformis) in an adult vole mouse (Microtus arvalis), and from feces, liver, and peritoneal fluid of three other vole family members living in a vegetable garden in Ohio, USA. Bacterial metagenomics revealed the presence of gut commensal/opportunistic species, including Parabacteroides distasonis, Klebsiella variicola, Enterococcus faecium, and Lactobacillus acidophilus, inhabiting the cysts. Parabacteroides distasonis and other species were also present outside the cyst in the peritoneal fluid. Remarkably, viral metagenomics revealed various murine viral species, but unexpectedly, it detected an insect-origin virus from the army moth (Pseudaletia/Mythimna unipuncta) known as Mythimna unipuncta granulovirus A (MyunGV-A) in both cysts, and in one fecal and one peritoneal sample from two different voles, indicating survival of the insect virus and adaption in voles. Metagenomics also revealed a significantly lower probability of fungal detection in the cysts compared to other samples (peritoneal fluid, p<0.05; and feces p<0.05), with single taxon detection in each cyst for Malassezia and Pseudophaeomoniella oleicola. The samples with a higher probability of fungi were the peritoneal fluid. In conclusion, commensal/pathobiont bacterial species can inhabit parasitic tapeworm cysts, which needs to be considered during therapeutic decisions of cysticerci or other chronic disease scenarios where immune privileged and spatially restricted ecosystems with limited nutrients and minimal presence of immune cells could facilitate microbial adaptation, such as within gut wall cavitating micropathologies in Crohn's disease.
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Affiliation(s)
- Amro Ammar
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Vaidhvi Singh
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Sanja Ilic
- Department of Human Sciences, Human Nutrition and Food Microbiology, Ohio State University, Columbus, OH, USA
| | - Fnu Samiksha
- Department of Cancer Biology, Learner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Antoinette Marsh
- The Veterinary Medical Center Diagnostic Parasitology, The Ohio State University College of Veterinary Medicine Department of Veterinary Preventive Medicine, Columbus, OH, USA
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center Cleveland, OH 44106, USA
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Neog N, Puzari M, Chetia P. Identification of Potential Inhibitors of Three NDM Variants of Klebsiella Species from Natural Compounds: A Molecular Docking, Molecular Dynamics Simulation, and MM-PBSA Study. Curr Comput Aided Drug Des 2024; 20:CAD-EPUB-139251. [PMID: 38504567 DOI: 10.2174/0115734099294294240311061115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Klebsiella species have emerged as well-known opportunistic pathogens causing nosocomial infections with β-lactamase-mediated resistance as a prevalent antibiotic resistance mechanism. The discovery and emergence of metallo-β-lactamases, mainly new- Delhi metallo-β-lactamases (NDMs), have increased the threat and challenges in healthcare facilities. OBJECTIVE A computational screening was conducted using 570 natural compounds from Dr. Duke's Phytochemical and Ethnobotanical data to discover promising inhibitors for NDM-6, NDM-9, and NDM-23 of the Klebsiella species. METHODS Using homology modeling on the Raptor-X web server, the structures of the three NDM variants were predicted. The structures were validated using various computational tools and MD simulation for 50 ns. Lipinski - Vebers' Filter and ADMET Screening were used to screen 570 compounds, followed by docking in Biovia Discovery Studio 2019 using the CDOCKER module. GROMACS was used to simulate the compounds with the highest scores with the proteins for 50 ns. Using the MM-PBSA method and g_mmpbsa tool, binding free energies were estimated and per-residue decomposition analysis was conducted. RESULTS The three structures predicted were found stable after the 50 ns MD Simulation run. The compounds Budmunchiamine-A and Rhamnocitrin were found to have the best binding energy towards NDM-6, NDM-9, and NDM-23, respectively. From the results of MD Simulation, MM-PBSA binding free energy calculations, and per-residue decomposition analysis, the Protein-ligand complex of NDM-6 with Budmunchiamine A and NDM-9 with Rhamnocitrin was relatively more stable than the complex of NDM-23 and Rhamnocitrin. CONCLUSION The study suggests that Budmunchiamine-A and Rhamnocitrin are potential inhibitors of NDM-6 and NDM-9, respectively, and may pave a path for in-vivo and in-vitro studies in the future.
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Affiliation(s)
- Nakul Neog
- Molecular Plant Taxonomy and Bioinformatics Research Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
- Department of Zoology, Sadiya College, Chapakhowa, Tinsukia, Assam, 786157, India
| | - Minakshi Puzari
- Molecular Plant Taxonomy and Bioinformatics Research Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
| | - Pankaj Chetia
- Molecular Plant Taxonomy and Bioinformatics Research Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam, 786004, India
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9
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Davis KP, Morales Y, Ende RJ, Peters R, McCabe AL, Mecsas J, Aldridge BB. Critical role of growth medium for detecting drug interactions in Gram-negative bacteria that model in vivo responses. mBio 2024; 15:e0015924. [PMID: 38364199 PMCID: PMC10936441 DOI: 10.1128/mbio.00159-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/18/2024] Open
Abstract
The rise in infections caused by multidrug-resistant (MDR) bacteria has necessitated a variety of clinical approaches, including the use of antibiotic combinations. Here, we tested the hypothesis that drug-drug interactions vary in different media, and determined which in vitro models best predict drug interactions in the lungs. We systematically studied pair-wise antibiotic interactions in three different media, CAMHB, (a rich lab medium standard for antibiotic susceptibility testing), a urine mimetic medium (UMM), and a minimal medium of M9 salts supplemented with glucose and iron (M9Glu) with three Gram-negative ESKAPE pathogens, Acinetobacter baumannii (Ab), Klebsiella pneumoniae (Kp), and Pseudomonas aeruginosa (Pa). There were pronounced differences in responses to antibiotic combinations between the three bacterial species grown in the same medium. However, within species, PaO1 responded to drug combinations similarly when grown in all three different media, whereas Ab17978 and other Ab clinical isolates responded similarly when grown in CAMHB and M9Glu medium. By contrast, drug interactions in Kp43816, and other Kp clinical isolates poorly correlated across different media. To assess whether any of these media were predictive of antibiotic interactions against Kp in the lungs of mice, we tested three antibiotic combination pairs. In vitro measurements in M9Glu, but not rich medium or UMM, predicted in vivo outcomes. This work demonstrates that antibiotic interactions are highly variable across three Gram-negative pathogens and highlights the importance of growth medium by showing a superior correlation between in vitro interactions in a minimal growth medium and in vivo outcomes. IMPORTANCE Drug-resistant bacterial infections are a growing concern and have only continued to increase during the SARS-CoV-2 pandemic. Though not routinely used for Gram-negative bacteria, drug combinations are sometimes used for serious infections and may become more widely used as the prevalence of extremely drug-resistant organisms increases. To date, reliable methods are not available for identifying beneficial drug combinations for a particular infection. Our study shows variability across strains in how drug interactions are impacted by growth conditions. It also demonstrates that testing drug combinations in tissue-relevant growth conditions for some strains better models what happens during infection and may better inform combination therapy selection.
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Affiliation(s)
- Kathleen P. Davis
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance Boston, Boston, Massachusetts, USA
| | - Yoelkys Morales
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance Boston, Boston, Massachusetts, USA
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Rachel J. Ende
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance Boston, Boston, Massachusetts, USA
| | - Ryan Peters
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance Boston, Boston, Massachusetts, USA
| | - Anne L. McCabe
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance Boston, Boston, Massachusetts, USA
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences, Albany, New York, USA
| | - Joan Mecsas
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance Boston, Boston, Massachusetts, USA
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Bree B. Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, & Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance Boston, Boston, Massachusetts, USA
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Tufts University School of Engineering, Medford, Massachusetts, USA
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Shi A, Ji X, Li W, Dong L, Wu Y, Zhang Y, Liu X, Zhang Y, Wang S. The Interaction between Human Microbes and Advanced Glycation End Products: The Role of Klebsiella X15 on Advanced Glycation End Products' Degradation. Nutrients 2024; 16:754. [PMID: 38474882 DOI: 10.3390/nu16050754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Previous studies have shown that advanced glycation end products (AGEs) are implicated in the occurrence and progression of numerous diseases, with dietary AGEs being particularly associated with intestinal disorders. In this study, methylglyoxal-beta-lactoglobulin AGEs (MGO-β-LG AGEs) were utilized as the exclusive nitrogen source to investigate the interaction between protein-bound AGEs and human gut microbiota. The high-resolution mass spectrometry analysis of alterations in peptides containing AGEs within metabolites before and after fermentation elucidated the capacity of intestinal microorganisms to enzymatically hydrolyze long-chain AGEs into short-chain counterparts. The 16S rRNA sequencing revealed Klebsiella, Lactobacillus, Escherichia-Shigella, and other genera as dominant microbiota at different fermentation times. A total of 187 potential strains of AGE-metabolizing bacteria were isolated from the fermentation broth at various time points. Notably, one strain of Klebsiella exhibited the most robust growth capacity when AGEs served as the sole nitrogen source. Subsequently, proteomics was employed to compare the changes in protein levels of Klebsiella X15 following cultivation in unmodified proteins and proteins modified with AGEs. This analysis unveiled a remodeled amino acid and energy metabolism pathway in Klebsiella in response to AGEs, indicating that Klebsiella may possess a metabolic pathway specifically tailored to AGEs. This study found that fermenting AGEs in healthy human intestinal microbiota altered the bacterial microbiota structure, especially by increasing Klebsiella proliferation, which could be a key factor in AGEs' role in causing diseases, particularly intestinal inflammation.
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Affiliation(s)
- Aiying Shi
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Xuemeng Ji
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Wanhua Li
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Lu Dong
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Yuekun Wu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Yunhui Zhang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Xiaoxia Liu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Yan Zhang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
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11
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Prinčič L, Orsi RH, Martin NH, Wiedmann M, Trmčić A. Phenotypic and genomic characterizations of Klebsiella pneumoniae ssp. pneumoniae and Rahnella inusitata strains reveal no clear association between genetic content and ropy phenotype. J Dairy Sci 2024; 107:1370-1385. [PMID: 37944807 DOI: 10.3168/jds.2023-23922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 11/12/2023]
Abstract
Ropy defect of pasteurized fluid milk is a type of spoilage which manifests itself by an increased viscosity, slimy body, and string-like flow during pouring. This defect has, among other causes, been attributed to the growth, proliferation and exopolysaccharide production by coliform bacteria, which are most commonly introduced in milk as post-pasteurization contaminants. As we identified both Klebsiella pneumoniae ssp. pneumoniae and Rahnella inusitata that were linked to a ropy defect, the goal of this study was to characterize 3 K. pneumoniae ssp. pneumoniae strains and 2 R. inusitata for (1) their ability to grow and cause ropy defect in milk at 6°C and 21°C and to (2) probe the genetic basis for observed ropy phenotype. Although all K. pneumoniae ssp. pneumoniae and R. inusitata strains showed net growth of >4 log10 over 48 h in UHT milk at 21°C, only R. inusitata strains displayed growth during 28-d incubation period at 6°C (>6 log10). Two out of 3 K. pneumoniae ssp. pneumoniae strains were capable of causing the ropy defect in milk at 21°C, as supported by an increase in the viscosity of milk and string-like flow during pouring; these 2 strains were originally isolated from raw milk. Only one R. inusitata strains was able to cause the ropy defect in milk; this strain was able to cause the defect at both 6°C and 21°C, and was originally isolated from a pasteurized milk. These findings suggest that the potential of K. pneumoniae ssp. pneumoniae and R. inusitata to cause ropy defect in milk is a strain-dependent characteristic. Comparative genomics provided no definitive answer on genetic basis for the ropy phenotype. However, for K. pneumoniae ssp. pneumoniae, genes rffG, rffH, rfbD, and rfbC involved in biosynthesis and secretion of enterobacterial common antigen (ECA) could only be found in the 2 strains that produced ropy defect, and for R. inusitata a set of 2 glycosyltransferase- and flippase genes involved in nucleotide sugar biosynthesis and export could only be identified in the ropy strain. Although these results provide some initial information for potential markers for strains that can cause ropy milk, the relationship between genetic content and ropiness in milk remains poorly understood and merits further investigation.
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Affiliation(s)
- Lucija Prinčič
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria 1190
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Aljoša Trmčić
- Department of Food Science, Cornell University, Ithaca, NY 14853.
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Miki S, Fukamachi H, Itsumi M, Fujiwara N, Takaki T, Kurosawa M, Morisaki H, Suzuki N, Kuwata H. The Klebsiella mannose phosphotransferase system promotes proliferation and the production of extracellular polymeric substances from mannose, facilitating adaptation to the host environment. J Oral Biosci 2024; 66:119-125. [PMID: 38246421 DOI: 10.1016/j.job.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
OBJECTIVES Klebsiella spp., an opportunistic infectious organism, is commensal in the nasal and oral cavities of humans. Recently, it has been reported that oral Klebsiella spp. ectopically colonize the intestinal tract and induce the accumulation of intestinal Th1 cells. For oral bacteria to colonize the intestinal tract, they need to compete for nutrients with indigenous intestinal bacteria. Therefore, we focused on mannose, a mucus-derived sugar, and the mannose phosphotransferase system (PTS) (ManXYZ), a mechanism for mannose uptake, in terms of their effects on intestinal colonization and immune responses to Klebsiella spp. METHODS We generated a Klebsiella manXYZ-deficient strain and investigated whether the utilization of intestinal mucus-derived sugars is associated with the growth. Furthermore, we examine the virulence of this organism in the mouse intestinal tract, especially the ability to colonize the host using competition assay. RESULTS We found that Klebsiella ManXYZ is a PTS that specifically takes up mannose and glucosamine. Through ManXYZ, mannose was used for bacterial growth and the upregulated production of extracellular polymeric substances. In vivo competition assays showed that mannose metabolism promoted intestinal colonization. However, ManXYZ was not involved in Th1 and Th17 induction in the intestinal tract. CONCLUSION The fundamental roles of ManXYZ were to ensure that mannose, which is present in the host, is made available for bacterial growth, to promote the production of extracellular polymeric substances, thus facilitating bacterial adaptation to the host environment.
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Affiliation(s)
- Suguru Miki
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan; Department of Conservative Dentistry, Division of Endodontology, Showa University Graduate School of Dentistry, 2-1-1 Kitasenzoku, Ohta-ku, Tokyo, 145-8515, Japan
| | - Haruka Fukamachi
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan.
| | - Momoe Itsumi
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Nagatoshi Fujiwara
- Department of Food and Nutrition, Tezukayama University, Tezukayama 7-1-1, Nara City, Nara, 631-8585, Japan
| | - Takashi Takaki
- Center for Electron Microscopy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Mie Kurosawa
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Hirobumi Morisaki
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Noriyuki Suzuki
- Department of Conservative Dentistry, Division of Endodontology, Showa University Graduate School of Dentistry, 2-1-1 Kitasenzoku, Ohta-ku, Tokyo, 145-8515, Japan
| | - Hirotaka Kuwata
- Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
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13
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Qin Y, Khan Q, Yan JW, Wang YY, Pan YF, Huang Y, Wei JL, Guo DJ, Li YR, Dong DF, Xing YX. Molecular mechanism of endophytic bacteria DX120E regulating polyamine metabolism and promoting plant growth in sugarcane. Front Plant Sci 2024; 15:1334907. [PMID: 38476689 PMCID: PMC10927768 DOI: 10.3389/fpls.2024.1334907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024]
Abstract
Introduction Sugarcane endophytic nitrogen-fixing bacterium Klebsiella variícola DX120E displayed broad impact on growth, but the exact biological mechanism, especially polyamines (PAs) role, is still meager. Methods To reveal this relationship, the content of polyamine oxidase (PAO), PAs, reactive oxygen species (ROS)-scavenging antioxidative enzymes, phytohormones, 1-aminocyclopropane-1-carboxylic synthase (ACS), chlorophyll content, and biomass were determined in sugarcane incubated with the DX120E strain. In addition, expression levels of the genes associated with polyamine metabolism were measured by transcriptomic analysis. Results Genomic analysis of Klebsiella variícola DX120E revealed that 39 genes were involved in polyamine metabolism, transport, and the strain secrete PAs in vitro. Following a 7-day inoculation period, DX120E stimulated an increase in the polyamine oxidase (PAO) enzyme in sugarcane leaves, however, the overall PAs content was reduced. At 15 days, the levels of PAs, ROS-scavenging antioxidative enzymes, and phytohormones showed an upward trend, especially spermidine (Spd), putrescine (Put), catalase (CAT), auxin (IAA), gibberellin (GA), and ACS showed a significant up-regulation. The GO and KEGG enrichment analysis found a total of 73 differentially expressed genes, involving in the cell wall (9), stimulus response (13), peroxidase activity (33), hormone (14) and polyamine metabolism (4). Discussion This study demonstrated that endophytic nitrogen-fixing bacteria stimulated polyamine metabolism and phytohormones production in sugarcane plant tissues, resulting in enhanced growth. Dual RNA-seq analyses provided insight into the early-stage interaction between sugarcane seedlings and endophytic bacteria at the transcriptional level. It showed how diverse metabolic processes selectively use distinct molecules to complete the cell functions under present circumstances.
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Affiliation(s)
- Ying Qin
- College of Agriculture, Guangxi University, Nanning, China
| | - Qaisar Khan
- Ecology College, Lishui University, Lishui, China
| | - Jia-Wei Yan
- College of Agriculture, Guangxi University, Nanning, China
| | - Yu-Yi Wang
- College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Fei Pan
- College of Agriculture, Guangxi University, Nanning, China
| | - Ying Huang
- College of Agriculture, Guangxi University, Nanning, China
| | - Jiang-Lu Wei
- Centre for Biotechnology Research, Guangxi South Subtropical Agricultural Science Research Institute, Chongzuo, China
| | - Dao-Jun Guo
- College of Life Sciences and Engineering, Hexi University, Zhangye, China
| | - Yang-Rui Li
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
| | - Deng-Feng Dong
- College of Agriculture, Guangxi University, Nanning, China
| | - Yong-Xiu Xing
- College of Agriculture, Guangxi University, Nanning, China
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14
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Kempraj V, Auth J, Cha DH, Mason CJ. Impact of Larval Food Source on the Stability of the Bactrocera dorsalis Microbiome. Microb Ecol 2024; 87:46. [PMID: 38407587 PMCID: PMC10896919 DOI: 10.1007/s00248-024-02352-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
Abstract
Bacterial symbionts are crucial to the biology of Bactrocera dorsalis. With larval diet (fruit host) being a key factor that determines microbiome composition and with B. dorsalis using more than 400 fruits as hosts, it is unclear if certain bacterial symbionts are preserved and are passed on to B. dorsalis progenies despite changes in larval diet. Here, we conducted a fly rearing experiment to characterize diet-induced changes in the microbiome of female B. dorsalis. In order to explicitly investigate the impacts of larval diet on the microbiome, including potential stable bacterial constituents of B. dorsalis, we performed 16S rRNA sequencing on the gut tissues of teneral female flies reared from four different host fruits (guava, mango, papaya, and rose apple) infested using a single cohort of wild B. dorsalis that emerged from tropical almond (mother flies). Although B. dorsalis-associated microbiota were predominantly shaped by the larval diet, some major bacterial species from the mother flies were retained in progenies raised on different larval diets. With some variation, Klebsiella (ASV 1 and 2), Morganella (ASV 3), and Providencia (ASV 6) were the major bacterial symbionts that were stable and made up 0.1-80% of the gut and ovipositor microbiome of female teneral flies reared on different host fruits. Our results suggest that certain groups of bacteria are stably associated with female B. dorsalis across larval diets. These findings provide a basis for unexplored research on symbiotic bacterial function in B. dorsalis and may aid in the development of novel management techniques against this devastating pest of horticultural importance.
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Affiliation(s)
- Vivek Kempraj
- USDA-ARS, Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA
- College of Tropical Agriculture and Human Resources, Komohana Research and Extension Center, University of Hawai'i, Hilo, HI, 96720, USA
| | - Jean Auth
- USDA-ARS, Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA
| | - Dong H Cha
- USDA-ARS, Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA.
| | - Charles J Mason
- USDA-ARS, Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA.
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15
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Liao CH, Kao KL, Wu SI, Yang CJ. Stool microbiota analysis for abundance of genus Klebsiella among adults and children in endemic area for community Klebsiella pneumoniae infection. J Microbiol Immunol Infect 2024:S1684-1182(24)00038-0. [PMID: 38413337 DOI: 10.1016/j.jmii.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/10/2024] [Accepted: 02/13/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Invasive Klebsiella pneumoniae syndrome is a significant endemic disease in Taiwan. Intestinal colonization of virulent clones that cause this phenomenon has been demonstrated in asymptomatic adults. Comparisons of healthy adults and children with stool K. pneumoniae colonization have rarely been reported. We aimed to evaluate the frequency and abundance of K. pneumoniae in the stool of adults and children by stool microbiota analysis. METHODS Healthy volunteers and their children without antibiotic exposure within 3 months were recruited in a Taiwanese medical center. Stool samples were sent for gut microbiota analysis, using amplification of V3-V4 hypervariable regions of 16sRNA followed by high-throughput sequence. Rectal/stool swabs were sent for K. pneumoniae culture and identification by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). RESULTS Fifty-five adults with a mean age of 46.9 years (range, 23.1-72.1 years) and 20 children with a mean age of 2.3 years (range, 0.9-5.8) were enrolled, and 29 adults and 6 children had positive K. pneumoniae swabs. Children had lower microbiota diversity than adults, including higher abundance of phylum Actinobacteria and Proteobacteria, and lower Bacteriodetes. For genus comparison, higher abundance of Escherichia, Streptococcus, Enterococcus and Bifidobacterium were found in children, but the composite abundance of Klebsiella in adults (median: 0.0156, range: 0-0.031) and in children (median: 0.0067, range: 0-0.043) were similar. Klebsiella abundance was significantly higher in participants with positive swabs (p < 0.0001). Klebsiella-positive swabs were strongly negatively correlated with Enterobacter spp. (p < 0.0001), but no known demographic factors correlated with Klebsiella-positive swabs. CONCLUSION Klebsiella species are present in young children, and the abundance is similar in adults and children. Positive swabs correlate strongly with higher abundance in microbiota analysis.
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Affiliation(s)
- Chun-Hsing Liao
- Department of Medicine, Far Eastern Memorial Hospital, Taipei, Taiwan; School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Kai-Liang Kao
- Department of Pediatrics, Far Eastern Memorial Hospital, Taipei, Taiwan; Department of Nursing, Asia Eastern University of Science and Technology, Taipei, Taiwan
| | - Shu-I Wu
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Section of Psychiatry and Suicide Prevention Center, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, Taipei, Taiwan
| | - Chia-Jui Yang
- Department of Medicine, Far Eastern Memorial Hospital, Taipei, Taiwan; School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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16
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Brune JE, Dickenmann M, Sidler D, Walti LN, Golshayan D, Manuel O, Haidar F, Neofytos D, Schnyder A, Boggian K, Mueller TF, Schachtner T, Khanna N, Schaub S, Wehmeier C. Frequency and impact on renal transplant outcomes of urinary tract infections due to extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella species. Front Med (Lausanne) 2024; 11:1329778. [PMID: 38426162 PMCID: PMC10902035 DOI: 10.3389/fmed.2024.1329778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/02/2024] [Indexed: 03/02/2024] Open
Abstract
Background Enterobacterales are often responsible for urinary tract infection (UTI) in kidney transplant recipients. Among these, Escherichia coli or Klebsiella species producing extended-spectrum beta-lactamase (ESBL) are emerging. However, there are only scarce data on frequency and impact of ESBL-UTI on transplant outcomes. Methods We investigated frequency and impact of first-year UTI events with ESBL Escherichia coli and/or Klebsiella species in a prospective multicenter cohort consisting of 1,482 kidney transplants performed between 2012 and 2017, focusing only on 389 kidney transplants having at least one UTI with Escherichia coli and/or Klebsiella species. The cohort had a median follow-up of four years. Results In total, 139/825 (17%) first-year UTI events in 69/389 (18%) transplant recipients were caused by ESBL-producing strains. Both UTI phenotypes and proportion among all UTI events over time were not different compared with UTI caused by non-ESBL-producing strains. However, hospitalizations in UTI with ESBL-producing strains were more often observed (39% versus 26%, p = 0.04). Transplant recipients with first-year UTI events with an ESBL-producing strain had more frequently recurrent UTI (33% versus 18%, p = 0.02) but there was no significant difference in one-year kidney function as well as longer-term graft and patient survival between patients with and without ESBL-UTI. Conclusion First-year UTI events with ESBL-producing Escherichia coli and/or Klebsiella species are associated with a higher need for hospitalization but do neither impact allograft function nor allograft and patient survival.
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Affiliation(s)
- Jakob E. Brune
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Michael Dickenmann
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Daniel Sidler
- Clinic for Nephrology, Bern University Hospital, Bern, Switzerland
| | - Laura N. Walti
- Department of Infectious Diseases, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Déla Golshayan
- Transplantation Center, Lausanne University Hospital, Lausanne, Switzerland
| | - Oriol Manuel
- Transplantation Center, Lausanne University Hospital, Lausanne, Switzerland
- Infectious Diseases Service, Lausanne University Hospital, Lausanne, Switzerland
| | - Fadi Haidar
- Nephrology and Hypertension Service, Division of Medicine, University Hospital Geneva, Geneva, Switzerland
| | - Dionysios Neofytos
- Transplant Infectious Disease Service, Division of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
| | - Aurelia Schnyder
- Clinic for Nephrology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Katia Boggian
- Division of Infectious Diseases and Hospital Epidemiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Thomas F. Mueller
- Clinic for Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Thomas Schachtner
- Clinic for Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Nina Khanna
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Stefan Schaub
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
- Transplantation Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Caroline Wehmeier
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
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17
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Artyszuk D, Jachymek W, Izdebski R, Gniadkowski M, Lukasiewicz J. The OL101 O antigen locus specifies a novel Klebsiella pneumoniae serotype O13 structure. Carbohydr Polym 2024; 326:121581. [PMID: 38142087 DOI: 10.1016/j.carbpol.2023.121581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 12/25/2023]
Abstract
Klebsiella pneumoniae is one of the priority objects for the development of new therapies against infections. The species has been perceived as of limited variety of O antigens (11 O serotypes identified to date). That trait makes lipopolysaccharide an attractive target for protective antibodies. Nowadays, K. pneumoniae O antigens encoding genes are often analysed by bioinformatic tools, such as Kaptive, indicating higher actual diversity of the O antigen loci. One of the novel K. pneumoniae O loci for which the antigen structure has not been elucidated so far is OL101. In this study, four clinical isolates predicted as OL101 were characterized and found to have the O antigen structure composed of β-Kdop-[→3)-α-l-Rhap-(1→4)-α-d-Glcp-(1→]n, representing a novel serotype O13. Identification of the β-Kdop terminus was based on the analysis of the complete LPS molecule by the HR-MAS NMR spectroscopy. The bioinformatic analysis of 71,377 K. pneumoniae genomes from public databases (July 2023) revealed a notable OL101 prevalence of 6.55 %.
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Affiliation(s)
- Daria Artyszuk
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Laboratory of Microbial Immunochemistry and Vaccines, 53-114 Wroclaw, Poland
| | - Wojciech Jachymek
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Laboratory of Microbial Immunochemistry and Vaccines, 53-114 Wroclaw, Poland
| | - Radosław Izdebski
- National Medicines Institute, Department of Molecular Microbiology, 00-725 Warsaw, Poland
| | - Marek Gniadkowski
- National Medicines Institute, Department of Molecular Microbiology, 00-725 Warsaw, Poland
| | - Jolanta Lukasiewicz
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Laboratory of Microbial Immunochemistry and Vaccines, 53-114 Wroclaw, Poland.
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18
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Russo TA, Alvarado CL, Davies CJ, Drayer ZJ, Carlino-MacDonald U, Hutson A, Luo TL, Martin MJ, Corey BW, Moser KA, Rasheed JK, Halpin AL, McGann PT, Lebreton F. Differentiation of hypervirulent and classical Klebsiella pneumoniae with acquired drug resistance. mBio 2024; 15:e0286723. [PMID: 38231533 PMCID: PMC10865842 DOI: 10.1128/mbio.02867-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Distinguishing hypervirulent (hvKp) from classical Klebsiella pneumoniae (cKp) strains is important for clinical care, surveillance, and research. Some combinations of iucA, iroB, peg-344, rmpA, and rmpA2 are most commonly used, but it is unclear what combination of genotypic or phenotypic markers (e.g., siderophore concentration, mucoviscosity) most accurately predicts the hypervirulent phenotype. Furthermore, acquisition of antimicrobial resistance may affect virulence and confound identification. Therefore, 49 K. pneumoniae strains that possessed some combinations of iucA, iroB, peg-344, rmpA, and rmpA2 and had acquired resistance were assembled and categorized as hypervirulent hvKp (hvKp) (N = 16) or cKp (N = 33) via a murine infection model. Biomarker number, siderophore production, mucoviscosity, virulence plasmid's Mash/Jaccard distances to the canonical pLVPK, and Kleborate virulence score were measured and evaluated to accurately differentiate these pathotypes. Both stepwise logistic regression and a CART model were used to determine which variable was most predictive of the strain cohorts. The biomarker count alone was the strongest predictor for both analyses. For logistic regression, the area under the curve for biomarker count was 0.962 (P = 0.004). The CART model generated the classification rule that a biomarker count = 5 would classify the strain as hvKP, resulting in a sensitivity for predicting hvKP of 94% (15/16), a specificity of 94% (31/33), and an overall accuracy of 94% (46/49). Although a count of ≥4 was 100% (16/16) sensitive for predicting hvKP, the specificity and accuracy decreased to 76% (25/33) and 84% (41/49), respectively. These findings can be used to inform the identification of hvKp.IMPORTANCEHypervirulent Klebsiella pneumoniae (hvKp) is a concerning pathogen that can cause life-threatening infections in otherwise healthy individuals. Importantly, although strains of hvKp have been acquiring antimicrobial resistance, the effect on virulence is unclear. Therefore, it is of critical importance to determine whether a given antimicrobial resistant K. pneumoniae isolate is hypervirulent. This report determined which combination of genotypic and phenotypic markers could most accurately identify hvKp strains with acquired resistance. Both logistic regression and a machine-learning prediction model demonstrated that biomarker count alone was the strongest predictor. The presence of all five of the biomarkers iucA, iroB, peg-344, rmpA, and rmpA2 was most accurate (94%); the presence of ≥4 of these biomarkers was most sensitive (100%). Accurately identifying hvKp is vital for surveillance and research, and the availability of biomarker data could alert the clinician that hvKp is a consideration, which, in turn, would assist in optimizing patient care.
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Affiliation(s)
- Thomas A. Russo
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, USA
- The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Cassandra L. Alvarado
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Connor J. Davies
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Zachary J. Drayer
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Ulrike Carlino-MacDonald
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Ting L. Luo
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Melissa J. Martin
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Brendan W. Corey
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Kara A. Moser
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J. Kamile Rasheed
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alison L. Halpin
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Patrick T. McGann
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
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19
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Hu JJ, Lin YS, Zhang JC, Wang YH. Vitamin D Improves Klebsiella-Induced Severe Pneumonia in Rats by Regulating Intestinal Microbiota. Infect Drug Resist 2024; 17:475-484. [PMID: 38348232 PMCID: PMC10860834 DOI: 10.2147/idr.s442330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/17/2024] [Indexed: 02/15/2024] Open
Abstract
Background In the context of progressively uncontrolled drug resistance of bacteria, the difficulty of treating Klebsiella (KP)-induced pneumonia increases. Searching for drugs other than antibiotics has become an urgent task. Vitamin D (VD), meanwhile, is shown to be capable of treating pneumonia. Therefore, we aimed to explore the effects and mechanisms of VD on KP-infected rats. Methods Male Sprague Dawley rats were divided into the Control, VD, KP and KP+VD groups. A rat pneumonia model was induced using an intratracheal drop of 2.4×108 CFU/mL KP. VD treatment was performed by gavage using 5 μg/kg. Subsequently, the survival of the rats was recorded, and the lungs, bronchoalveolar lavage fluid, and feces of the rats were collected 4 days after KP infection. Next, the water content of lung tissues was measured by the wet-to-dry weight ratio. Histopathological changes of lung tissues were observed by Hematoxylin and Eosin staining and the levels of inflammatory factors (TNF-α, IL-1β, MCP1) were detected using ELISA. The feces of rats in each group were also subjected to 16S rDNA gene analysis of intestinal microbiota. Results Compared with the KP group, the KP+VD group showed a significant increase in survival, a significant decrease in water content and bacterial counts in the lungs, a significant improvement in lung injury, and a significant decline in the levels of TNF-α, IL-1β, and MCP1. According to the 16S rDNA sequencing, VD altered the structure of the intestinal bacterial community in the KP-infected rats and made the species richness similar to that of healthy rats. Additionally, the abundance of Anaeroglobus was significantly increased in the KP+VD group. Conclusion VD modulates intestinal microbiota to increase the resistance of rats to pneumonia caused by Klebsiella infection.
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Affiliation(s)
- Jia-Jia Hu
- Medical Intensive Care Unit, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Yu-Sen Lin
- Medical Intensive Care Unit, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Jing-Cong Zhang
- Medical Intensive Care Unit, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Yan-Hong Wang
- Medical Intensive Care Unit, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People’s Republic of China
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20
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Cooper HB, Vezina B, Hawkey J, Passet V, López-Fernández S, Monk JM, Brisse S, Holt KE, Wyres KL. A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex. Microb Genom 2024; 10:001206. [PMID: 38376382 PMCID: PMC10926698 DOI: 10.1099/mgen.0.001206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
The Klebsiella pneumoniae species complex (KpSC) is a major source of nosocomial infections globally with high rates of resistance to antimicrobials. Consequently, there is growing interest in understanding virulence factors and their association with cellular metabolic processes for developing novel anti-KpSC therapeutics. Phenotypic assays have revealed metabolic diversity within the KpSC, but metabolism research has been neglected due to experiments being difficult and cost-intensive. Genome-scale metabolic models (GSMMs) represent a rapid and scalable in silico approach for exploring metabolic diversity, which compile genomic and biochemical data to reconstruct the metabolic network of an organism. Here we use a diverse collection of 507 KpSC isolates, including representatives of globally distributed clinically relevant lineages, to construct the most comprehensive KpSC pan-metabolic model to date, KpSC pan v2. Candidate metabolic reactions were identified using gene orthology to known metabolic genes, prior to manual curation via extensive literature and database searches. The final model comprised a total of 3550 reactions, 2403 genes and can simulate growth on 360 unique substrates. We used KpSC pan v2 as a reference to derive strain-specific GSMMs for all 507 KpSC isolates, and compared these to GSMMs generated using a prior KpSC pan-reference (KpSC pan v1) and two single-strain references. We show that KpSC pan v2 includes a greater proportion of accessory reactions (8.8 %) than KpSC pan v1 (2.5 %). GSMMs derived from KpSC pan v2 also generate more accurate growth predictions, with high median accuracies of 95.4 % (aerobic, n=37 isolates) and 78.8 % (anaerobic, n=36 isolates) for 124 matched carbon substrates. KpSC pan v2 is freely available at https://github.com/kelwyres/KpSC-pan-metabolic-model, representing a valuable resource for the scientific community, both as a source of curated metabolic information and as a reference to derive accurate strain-specific GSMMs. The latter can be used to investigate the relationship between KpSC metabolism and traits of interest, such as reservoirs, epidemiology, drug resistance or virulence, and ultimately to inform novel KpSC control strategies.
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Affiliation(s)
- Helena B. Cooper
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria 3800, Australia
| | - Ben Vezina
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria 3800, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Virginie Passet
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Sebastián López-Fernández
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, California 92093, USA
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria 3800, Australia
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21
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Leite G, Rezaie A, Mathur R, Barlow GM, Rashid M, Hosseini A, Wang J, Parodi G, Villanueva-Millan MJ, Sanchez M, Morales W, Weitsman S, Pimentel M. Defining Small Intestinal Bacterial Overgrowth by Culture and High Throughput Sequencing. Clin Gastroenterol Hepatol 2024; 22:259-270. [PMID: 37315761 DOI: 10.1016/j.cgh.2023.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND& AIMS Despite accelerated research in small intestinal bacterial overgrowth (SIBO), questions remain regarding optimal diagnostic approaches and definitions. Here, we aim to define SIBO using small bowel culture and sequencing, identifying specific contributory microbes, in the context of gastrointestinal symptoms. METHODS Subjects undergoing esophagogastroduodenoscopy (without colonoscopy) were recruited and completed symptom severity questionnaires. Duodenal aspirates were plated on MacConkey and blood agar. Aspirate DNA was analyzed by 16S ribosomal RNA and shotgun sequencing. Microbial network connectivity for different SIBO thresholds and predicted microbial metabolic functions were also assessed. RESULTS A total of 385 subjects with <103 colony forming units (CFU)/mL on MacConkey agar and 98 subjects with ≥103 CFU/mL, including ≥103 to <105 CFU/mL (N = 66) and ≥105 CFU/mL (N = 32), were identified. Duodenal microbial α-diversity progressively decreased, and relative abundance of Escherichia/Shigella and Klebsiella increased, in subjects with ≥103 to <105 CFU/mL and ≥105 CFU/mL. Microbial network connectivity also progressively decreased in these subjects, driven by the increased relative abundance of Escherichia (P < .0001) and Klebsiella (P = .0018). Microbial metabolic pathways for carbohydrate fermentation, hydrogen production, and hydrogen sulfide production were enhanced in subjects with ≥103 CFU/mL and correlated with symptoms. Shotgun sequencing (N = 38) identified 2 main Escherichia coli strains and 2 Klebsiella species representing 40.24% of all duodenal bacteria in subjects with ≥103 CFU/mL. CONCLUSIONS Our findings confirm ≥103 CFU/mL is the optimal SIBO threshold, associated with gastrointestinal symptoms, significantly decreased microbial diversity, and network disruption. Microbial hydrogen- and hydrogen sulfide-related pathways were enhanced in SIBO subjects, supporting past studies. Remarkably few specific E coli and Klebsiella strains/species appear to dominate the microbiome in SIBO, and correlate with abdominal pain, diarrhea, and bloating severities.
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Affiliation(s)
- Gabriela Leite
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California
| | - Ali Rezaie
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California; Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai, Los Angeles, California
| | - Ruchi Mathur
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California; Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai, Los Angeles, California
| | - Gillian M Barlow
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California
| | - Mohamad Rashid
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California
| | - Ava Hosseini
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California
| | - Jiajing Wang
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California
| | - Gonzalo Parodi
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California
| | | | - Maritza Sanchez
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California
| | - Walter Morales
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California
| | - Stacy Weitsman
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California
| | - Mark Pimentel
- Medically Associated Science and Technology Program, Cedars-Sinai, Los Angeles, California; Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai, Los Angeles, California.
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22
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Aleshina Y, Yeleussizova A, Mendybayeva A, Shevchenko P, Rychshanova R. Prevalence and antimicrobial resistance of Enterobacteriaceae in the north of Kazakhstan. Open Vet J 2024; 14:604-616. [PMID: 38549569 PMCID: PMC10970123 DOI: 10.5455/ovj.2024.v14.i2.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/15/2024] [Indexed: 04/02/2024] Open
Abstract
Background An increasing number of drugs are used each year in the treatment of small pets (cats and dogs), including medicines (cephalosporins and fluoroquinolones) used in human therapy. Aim The purpose of this study was to isolate and explore the antibiotic resistance of opportunistic Enterobacteriaceae (Escherichia coli, Klebsiella, Proteus, Ci trobacter, Enterobacter) from cats and dogs, and to isolate resistance genes in the microorganisms. Methods In 2021, 808 samples of biological material from small domestic animals were collected in veterinary clinics in Kostanay. From these, 210 microorganisms were isolated and identified. Results A large majority of the strains sampled belonged to E. coli-149 (70.9%), Enterobacter-11 (5.2%), Klebsiella-28 (13.3%), Proteus-12 (5.7%) and 10 Citrobacter isolates (4.8%). In all isolates identified, antibiotic resistance/sensitivity was determined by disc-diffusion method to ampicillin, cefoxitin, gentamicin, levomycetin, tetracycline, ciprofloxacin, norfloxacin, ofloxacin, cefoperazone, cefpodoxime, streptomycin, kanamycin, doxycycline, gemifloxacin, nalidixic acid, furazolidone, furadonine, amoxicillin, and enrofloxacin. Conclusion The study has demonstrated that the greatest number of Enterobacteriaceae were sensitive to the action of meropenem, which belongs to the group of beta-lactam antibiotics; resistance was demonstrated against tetracycline, doxycycline, ampicillin, amoxicillin, ofloxacin, and cefpodoxime. The most common genes encoding antimicrobial resistance were as follows: BlaTEM and OXA in 41 and 28 isolates, respectively, encoding resistance to beta-lactams; StrA and StrB in 45 and 48 isolates encoding aminoglycosides; and tetA and tetB in 43 and 28 isolates encoding tetracyclines. Obtained data demonstrate that uncontrolled and frequent use of beta-lactam and tetracycline antibacterials, in cats and dogs, results in the spread of genotypic resistance among micro-organisms of the family Enterobacteriaceae.
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Affiliation(s)
- Yuliya Aleshina
- Research Institute of Applied Biotechnology, A. Baitursynov Kostanay Regional University, Kostanay, Republic of Kazakhstan
| | - Anara Yeleussizova
- Department of Veterinary Sanitation, A. Baitursynov Kostanay Regional University, Kostanay, Republic of Kazakhstan
| | - Anara Mendybayeva
- Research Institute of Applied Biotechnology, A. Baitursynov Kostanay Regional University, Kostanay, Republic of Kazakhstan
| | - Pavel Shevchenko
- Research Institute of Applied Biotechnology, A. Baitursynov Kostanay Regional University, Kostanay, Republic of Kazakhstan
| | - Raushan Rychshanova
- Research Institute of Applied Biotechnology, A. Baitursynov Kostanay Regional University, Kostanay, Republic of Kazakhstan
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23
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Malik VK, Sangwan P, Singh M, Kumari P, Shoeran N, Ahalawat N, Kumar M, Deep H, Malik K, Verma P, Yadav P, Kumari S, Aakash, Dhal S. Stem Rot of Pearl Millet Prevalence, Symptomatology, Disease Cycle, Disease Rating Scale and Pathogen Characterization in Pearl Millet- Klebsiella Pathosystem. Plant Pathol J 2024; 40:48-58. [PMID: 38326958 PMCID: PMC10850534 DOI: 10.5423/ppj.oa.09.2023.0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 02/09/2024]
Abstract
The oldest and most extensively cultivated form of millet, known as pearl millet (Pennisetum glaucum (L.) R. Br. Syn. Pennisetum americanum (L.) Leeke), is raised over 312.00 lakh hectares in Asian and African countries. India is regarded as the significant hotspot for pearl millet diversity. In the Indian state of Haryana, where pearl millet is grown, a new and catastrophic bacterial disease known as stem rot of pearl millet spurred by the bacterium Klebsiella aerogenes (formerly Enterobacter) was first observed during fall 2018. The disease appears in form of small to long streaks on leaves, lesions on stem, and slimy rot appearance of stem. The associated bacterium showed close resemblance to Klebsiella aerogenes that was confirmed by a molecular evaluation based on 16S rDNA and gyrA gene nucleotide sequences. The isolates were also identified to be Klebsiella aerogenes based on biochemical assays, where Klebsiella isolates differed in D-trehalose and succinate alkalisation tests. During fall 2021-2023, the disease has spread all the pearl millet-growing districts of the state, extending up to 70% disease incidence in the affected fields. The disease is causing considering grain as well as fodder losses. The proposed scale, consisting of six levels (0-5), is developed where scores 0, 1, 2, 3, 4, and 5 have been categorized as highly resistant, resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible disease reaction, respectively. The disease cycle, survival of pathogen, and possible losses have also been studied to understand other features of the disease.
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Affiliation(s)
- Vinod Kumar Malik
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Pooja Sangwan
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Manjeet Singh
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Pavitra Kumari
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Niharika Shoeran
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Navjeet Ahalawat
- Department of Bioinformatics and Computational Biology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Mukesh Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Harsh Deep
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Kamla Malik
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Preety Verma
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Pankaj Yadav
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Sheetal Kumari
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Aakash
- Department of Plant Pathology, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India
| | - Sambandh Dhal
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77840, USA
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24
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Yu Y, Kim YH, Cho WH, Kim D, So MW, Son BS, Yeo HJ. Unique Changes in the Lung Microbiome following the Development of Chronic Lung Allograft Dysfunction. Microorganisms 2024; 12:287. [PMID: 38399691 PMCID: PMC10893466 DOI: 10.3390/microorganisms12020287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The importance of lung microbiome changes in developing chronic lung allograft dysfunction (CLAD) after lung transplantation is poorly understood. The lung microbiome-immune interaction may be critical in developing CLAD. In this context, examining alterations in the microbiome and immune cells of the lungs following CLAD, in comparison to the lung condition immediately after transplantation, can offer valuable insights. Four adult patients who underwent lung retransplantation between January 2019 and June 2020 were included in this study. Lung tissues were collected from the same four individuals at two different time points: at the time of the first transplant and at the time of the explantation of CLAD lungs at retransplantation due to CLAD. We analyzed whole-genome sequencing using the Kraken2 algorithm and quantified the cell fractionation from the bulk tissue gene expression profile for each lung tissue. Finally, we compared the differences in lung microbiome and immune cells between the lung tissues of these two time points. The median age of the recipients was 57 years, and most (75%) had undergone lung transplants for idiopathic pulmonary fibrosis. All patients were administered basiliximab for induction therapy and were maintained on three immunosuppressants. The median CLAD-free survival term was 693.5 days, and the median time to redo the lung transplant was 843.5 days. Bacterial diversity was significantly lower in the CLAD lungs than at transplantation. Bacterial diversity tended to decrease according to the severity of the CLAD. Aerococcus, Caldiericum, Croceibacter, Leptolyngbya, and Pulveribacter genera were uniquely identified in CLAD, whereas no taxa were identified in lungs at transplantation. In particular, six taxa, including Croceibacter atlanticus, Caldiserium exile, Dolichospermum compactum, Stappia sp. ES.058, Kinetoplastibacterium sorsogonicusi, and Pulveribacter suum were uniquely detected in CLAD. Among immune cells, CD8+ T cells were significantly increased, while neutrophils were decreased in the CLAD lung. In conclusion, unique changes in lung microbiome and immune cell composition were confirmed in lung tissue after CLAD compared to at transplantation.
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Affiliation(s)
- Yeuni Yu
- Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea;
| | - Yun Hak Kim
- Department of Anatomy and Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan 50612, Republic of Korea;
| | - Woo Hyun Cho
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea;
| | - Dohyung Kim
- Department of Thoracic and Cardiovascular Surgery, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea;
| | - Min Wook So
- Division of Rheumatology, Department of Internal Medicine, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea;
| | - Bong Soo Son
- Department of Thoracic and Cardiovascular Surgery, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea;
| | - Hye Ju Yeo
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea;
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
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Mareș C, Petca RC, Popescu RI, Petca A, Mulțescu R, Bulai CA, Ene CV, Geavlete PA, Geavlete BF, Jinga V. Update on Urinary Tract Infection Antibiotic Resistance-A Retrospective Study in Females in Conjunction with Clinical Data. Life (Basel) 2024; 14:106. [PMID: 38255721 PMCID: PMC10820678 DOI: 10.3390/life14010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Urinary tract infections (UTIs) represent a frequent pathology among the female population that has become more and more difficult to treat in the past decade, considering the increase in antibiotic resistance-a serious global public health problem. A cross-sectional retrospective study was conducted for six months to report an update regarding the rates of resistance and susceptibility of uropathogens necessary for optimal treatment. A total of 5487 patients were screened, of which 524 (9.54%) were female patients who met the criteria for inclusion in the study. Escherichia coli was the most common pathogen, representing 290 cases (55.34%), followed by Enterococcus spp. 82 (15.64%). Escherichia coli presented the highest resistance to amoxicillin-clavulanic acid (R = 33.1%), followed by trimethoprim-sulfamethoxazole (R = 32.41%) and levofloxacin (R = 32.06%). The highest sensitivity rates were observed for fosfomycin (S = 96.55%), followed by imipenem (S = 93.1%). Enterococcus spp. showed the highest resistance to levofloxacin (R = 50.0%), followed by penicillin (R = 39.02%). The highest sensitivity was observed for fosfomycin (S = 90.24%), linezolid (S = 89.02%), and nitrofurantoin (S = 86.58%). The second most frequent Gram-negative uropathogen was represented by Klebsiella spp., which had the highest resistance to amoxicillin-clavulanic acid (R = 35.89%), followed by levofloxacin (R = 25.64) and trimethoprim-suflamethoxazole (R = 24.35%). The most frequently associated pathology was an episode of UTI in the previous year, followed by diabetes and chronic kidney disease. Antibiotic resistance is a serious problem for all clinicians who treat UTIs. An up-to-date knowledge of antibiotic resistance rates is a major necessity to stop its evolution. Overall, the highest resistance rates were observed for aminopenicillins, fluoroquinolones, and trimethoprim-sulfamethoxazole. The best susceptibility rates were observed for fosfomycin, nitrofurantoin, and carbapenems. Our report aims to guide clinicians whenever they are forced to prescribe antibiotics empirically.
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Affiliation(s)
- Cristian Mareș
- Department of Urology, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania; (C.M.); (R.-I.P.); (C.A.B.); (C.V.E.); (P.A.G.); (B.F.G.); (V.J.)
- Department of Urology, “Saint John” Clinical Emergency Hospital, 13 Vitan-Barzesti Str., 042122 Bucharest, Romania;
| | - Răzvan-Cosmin Petca
- Department of Urology, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania; (C.M.); (R.-I.P.); (C.A.B.); (C.V.E.); (P.A.G.); (B.F.G.); (V.J.)
- Department of Urology, “Prof. Dr. Th. Burghele” Clinical Hospital, 20 Panduri Str., 050659 Bucharest, Romania
| | - Răzvan-Ionuț Popescu
- Department of Urology, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania; (C.M.); (R.-I.P.); (C.A.B.); (C.V.E.); (P.A.G.); (B.F.G.); (V.J.)
- Department of Urology, “Prof. Dr. Th. Burghele” Clinical Hospital, 20 Panduri Str., 050659 Bucharest, Romania
| | - Aida Petca
- Department of Obstetrics and Gynecology, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania;
- Department of Obstetrics and Gynecology, Elias University Emergency Hospital, 17 Mărăști Blvd., 050474 Bucharest, Romania
| | - Răzvan Mulțescu
- Department of Urology, “Saint John” Clinical Emergency Hospital, 13 Vitan-Barzesti Str., 042122 Bucharest, Romania;
| | - Cătălin Andrei Bulai
- Department of Urology, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania; (C.M.); (R.-I.P.); (C.A.B.); (C.V.E.); (P.A.G.); (B.F.G.); (V.J.)
- Department of Urology, “Saint John” Clinical Emergency Hospital, 13 Vitan-Barzesti Str., 042122 Bucharest, Romania;
| | - Cosmin Victor Ene
- Department of Urology, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania; (C.M.); (R.-I.P.); (C.A.B.); (C.V.E.); (P.A.G.); (B.F.G.); (V.J.)
- Department of Urology, “Saint John” Clinical Emergency Hospital, 13 Vitan-Barzesti Str., 042122 Bucharest, Romania;
| | - Petrișor Aurelian Geavlete
- Department of Urology, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania; (C.M.); (R.-I.P.); (C.A.B.); (C.V.E.); (P.A.G.); (B.F.G.); (V.J.)
- Department of Urology, “Saint John” Clinical Emergency Hospital, 13 Vitan-Barzesti Str., 042122 Bucharest, Romania;
| | - Bogdan Florin Geavlete
- Department of Urology, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania; (C.M.); (R.-I.P.); (C.A.B.); (C.V.E.); (P.A.G.); (B.F.G.); (V.J.)
- Department of Urology, “Saint John” Clinical Emergency Hospital, 13 Vitan-Barzesti Str., 042122 Bucharest, Romania;
| | - Viorel Jinga
- Department of Urology, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd., 050474 Bucharest, Romania; (C.M.); (R.-I.P.); (C.A.B.); (C.V.E.); (P.A.G.); (B.F.G.); (V.J.)
- Department of Urology, “Prof. Dr. Th. Burghele” Clinical Hospital, 20 Panduri Str., 050659 Bucharest, Romania
- Medical Sciences Section, Academy of Romanian Scientists, 050085 Bucharest, Romania
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Shaposhnikov LA, Tishkov VI, Pometun AA. Lactobacilli and Klebsiella: Two Opposites in the Fight for Human Health. Biochemistry (Mosc) 2024; 89:S71-S89. [PMID: 38621745 DOI: 10.1134/s0006297924140050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 04/17/2024]
Abstract
The problem of antibiotic resistance is currently very acute. Numerous research and development of new antibacterial drugs are being carried out that could help cope with various infectious agents. One of the promising directions for the search for new antibacterial drugs is the search among the probiotic strains present in the human gastrointestinal tract. This review is devoted to characteristics of one of these probiotic strains that have been studied to date: Limosilactobacillus reuteri. The review discusses its properties, synthesis of various compounds, as well as role of this strain in modulating various systems of the human body. The review also examines key characteristics of one of the most harmful among the currently known pathogenic organisms, Klebsiella, which is significantly resistant to antibiotics existing in medical practice, and also poses a great threat of nosocomial infections. Discussion of characteristics of the two strains, which have opposite effects on human health, may help in creation of new effective antibacterial drugs without significant side effects.
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Affiliation(s)
- Leonid A Shaposhnikov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir I Tishkov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anastasia A Pometun
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia.
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute of Medicine, Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia
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27
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Guo Y, Kitamoto S, Caballero-Flores G, Kim Y, Watanabe D, Sugihara K, Núñez G, Alteri CJ, Inohara N, Kamada N. Oral pathobiont Klebsiella chaperon usher pili provide site-specific adaptation for the inflamed gut mucosa. Gut Microbes 2024; 16:2333463. [PMID: 38545880 PMCID: PMC10984132 DOI: 10.1080/19490976.2024.2333463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
The ectopic gut colonization by orally derived pathobionts has been implicated in the pathogenesis of various gastrointestinal diseases, including inflammatory bowel disease (IBD). For example, gut colonization by orally derived Klebsiella spp. has been linked to IBD in mice and humans. However, the mechanisms whereby oral pathobionts colonize extra-oral niches, such as the gut mucosa, remain largely unknown. Here, we performed a high-density transposon (Tn) screening to identify genes required for the adaptation of an oral Klebsiella strain to different mucosal sites - the oral and gut mucosae - at the steady state and during inflammation. We find that K. aerogenes, an oral pathobiont associated with both oral and gut inflammation in mice, harbors a newly identified genomic locus named "locus of colonization in the inflamed gut (LIG)" that encodes genes related to iron acquisition (Sit and Chu) and host adhesion (chaperon usher pili [CUP] system). The LIG locus is highly conserved among K. aerogenes strains, and these genes are also present in several other Klebsiella species. The Tn screening revealed that the LIG locus is required for the adaptation of K. aerogenes in its ectopic niche. In particular, we determined K. aerogenes employs a CUP system (CUP1) present in the LIG locus for colonization in the inflamed gut, but not in the oral mucosa. Thus, oral pathobionts likely exploit distinct adaptation mechanisms in their ectopically colonized intestinal niche compared to their native niche.
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Affiliation(s)
- Yijie Guo
- Department of Psychiatry and Center for Brain Science, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sho Kitamoto
- WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Gustavo Caballero-Flores
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Yeji Kim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Daisuke Watanabe
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kohei Sugihara
- WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Gabriel Núñez
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Naohiro Inohara
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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28
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Holmes CL. mSphere of Influence: Coordinating effective clearance of bacterial bloodstream infections. mSphere 2023; 8:e0052123. [PMID: 37874135 PMCID: PMC10732069 DOI: 10.1128/msphere.00521-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023] Open
Abstract
Caitlyn Holmes works in the field of bacterial pathogenesis and host-pathogen interactions. In this mSphere of Influence article, she reflects on how the papers "Innate Lymphocyte/Ly6Chi Monocyte Crosstalk Promotes Klebsiella pneumoniae Clearance" by Xiong et al. (H. Xiong, J. W. Keith, D. W. Samilo, R. A. Carter, et al., Cell 165:679-89, 2016, https://doi.org/10.1016/j.cell.2016.03.017) and "Dual-Track Clearance of Circulating Bacteria Balances Rapid Restoration of Blood Sterility with Induction of Adaptive Immunity" by Broadley et al. (S. P. Broadley, A. Plaumann, R. Coletti, C. Lehmann, et al., Cell Host Microbe 20:36-48, 2016, https://doi.org/10.1016/j.chom.2016.05.023) impacted her research by highlighting the tangled web of immune responses that influence bacterial bloodstream infections.
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Affiliation(s)
- Caitlyn L. Holmes
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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29
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Miliotis G, McDonagh F, Singh NK, O'Connor L, Tuohy A, Morris D, Venkateswaran K. Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station. Microbiol Spectr 2023; 11:e0189723. [PMID: 37966203 PMCID: PMC10715203 DOI: 10.1128/spectrum.01897-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/27/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The International Space Station (ISS) is a unique, hermetically sealed environment, subject to environmental pressures not encountered on Earth, including microgravity and radiation (cosmic ionising/UV). While bacteria's adaptability during spaceflight remains elusive, recent research suggests that it may be species and even clone-specific. Considering the documented spaceflight-induced suppression of the human immune system, a deper understanding of the genomics of potential human pathogens in space could shed light on species and lineages of medical astromicrobiological significance. In this study, we used hybrid assembly methods and comparative genomics to deliver a comprehensive genomic characterization of 10 Klebsiella isolates retrieved from the ISS. Our analysis unveiled that Klebsiella quasipneumoniae ST138 demonstrates both spatial and temporal persistence aboard the ISS, showing evidence of genomic divergence from its Earth-based ST138 lineage. Moreover, we characterized plasmids from Klebsiella species of ISS origin, which harbored genes for disinfectant resistance and enhanced thermotolerance, suggestin possible adaptive advantages. Furthermore, we identified a mobile genetic element containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the "high-risk" ST101 clone. Our work provides insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the dynamics of potential pathogenic bacteria in such environments.
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Affiliation(s)
- Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Nitin Kumar Singh
- Biotechnology and Planetary Protection Group, NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Alma Tuohy
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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30
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Concha-Eloko R, Barberán-Martínez P, Sanjuán R, Domingo-Calap P. Broad-range capsule-dependent lytic Sugarlandvirus against Klebsiella sp. Microbiol Spectr 2023; 11:e0429822. [PMID: 37882584 PMCID: PMC10714931 DOI: 10.1128/spectrum.04298-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 09/15/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The emergence of multi-drug resistant bacteria is a global health problem. Among them, Klebsiella pneumoniae is considered a high-priority pathogen, making it necessary to develop new therapeutic tools to reduce the bacterial burden in an effective and sustainable manner. Phages, bacterial viruses, are very promising tools. However, phages are highy specific, rendering large-scale therapeutics costly to implement. This is especially certain in Klebsiella, a capsular bacterium in which phages have been shown to be capsular type dependent, infecting one or a few capsular types through specific enzymes called depolymerases. In this study, we have isolated and characterized novel phages with lytic ability against bacteria from a wide variety of capsular types, representing the Klebsiella phages with the widest range of infection described. Remarkably, these broad-range phages showed capsule dependency, despite the absence of depolymerases in their genomes, implying that infectivity could be governed by alternative mechanisms yet to be uncovered.
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Affiliation(s)
- Robby Concha-Eloko
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | | | - Rafael Sanjuán
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, Paterna, Spain
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31
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Hosny RA, El-Badiea ZA, Elmasry DMA, Fadel MA. Efficacy of ceftiofur N-acyl homoserine lactonase niosome in the treatment of multi-resistant Klebsiella pneumoniae in broilers. Vet Res Commun 2023; 47:2083-2100. [PMID: 37430152 DOI: 10.1007/s11259-023-10161-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
In this study, the efficiency of the ceftiofur N-acyl homoserine lactonase niosome against multi-resistant Klebsiella pneumoniae in broilers was evaluated. Fifty-six K. pneumoniae isolates previously recovered from different poultry and environmental samples were screened for the ahlK gene. The lactonase enzyme was extracted from eight quorum-quenching isolates. The niosome was formulated, characterized, and tested for minimal inhibitory concentration (MIC) and cytotoxicity. Fourteen-day-old chicks were assigned to six groups: groups Ӏ and П served as negative and positive controls, receiving saline and K. pneumoniae solutions, respectively. In groups Ш and IV, ceftiofur and niosome were administrated intramuscularly at a dose of 10 mg/kg body weight for five consecutive days, while groups V and VI received the injections following the K. pneumoniae challenge. Signs, mortality, and gross lesions were recorded. Tracheal swabs were collected from groups П, V, and VI for counting K. pneumoniae. Pharmacokinetic parameters were evaluated in four treated groups at nine-time points. The niosome was spherical and 56.5 ± 4.41 nm in size. The viability of Vero cells was unaffected up to 5 × MIC (2.4 gml-1). The niosome-treated challenged group showed mild signs and lesions with lower mortality and colony count than the positive control group. The maximum ceftiofur serum concentrations in treated groups were observed 2 h following administration. The elimination half-life in niosome-treated groups was longer than that reported in ceftiofur-treated groups. This is the first report of the administration of N-acyl homoserine lactonase for the control of multi-resistant K. pneumoniae infections in poultry.
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Affiliation(s)
- Reham A Hosny
- Reference Laboratory for Veterinary Quality Control On Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt.
| | - Zeinab A El-Badiea
- Reference Laboratory for Veterinary Quality Control On Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Dalia M A Elmasry
- Nanomaterials Research and Synthesis Unit, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Mai A Fadel
- Pharmacology and Pyrogen Unit, Department of Chemistry, Toxicology, and Feed Deficiency, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
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32
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Bell JM, Fajardo Lubian A, Partridge SR, Gottlieb T, Robson J, Iredell JR, Daley DA, Coombs GW. Australian Group on Antimicrobial Resistance (AGAR) Australian Gram-negative Surveillance Outcome Program (GnSOP) Bloodstream Infection Annual Report 2022. Commun Dis Intell (2018) 2023; 47. [PMID: 37968067 DOI: 10.33321/cdi.2023.47.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Indexed: 11/17/2023]
Abstract
The Australian Group on Antimicrobial Resistance (AGAR) performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric gram-negative pathogens. The 2022 survey was the tenth year to focus on blood stream infections caused by Enterobacterales, and the eighth year where Pseudomonas aeruginosa and Acinetobacter species were included. Fifty-five hospitals Australia-wide participated in 2022. The 2022 survey tested 9,739 isolates, comprising Enterobacterales (8,773; 90.1%), P. aeruginosa (840; 8.6%) and Acinetobacter species (126; 1.3%), using commercial automated methods. The results were analysed using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints (January 2023). Key resistances included resistance to the third-generation cephalosporin ceftriaxone in 12.7%/12.7% (CLSI/EUCAST criteria) of Escherichia coli and in 6.6%/6.6% of Klebsiella pneumoniae complex. Resistance rates to ciprofloxacin were 13.7%/13.7% for E. coli; 7.8%/7.8% for K. pneumoniae complex; 5.3%/5.3% for Enterobacter cloacae complex; and 4.3%/10.0% for P. aeruginosa. Resistance rates to piperacillin-tazobactam were 2.8%/5.9%; 2.9%/8.7%; 18.3%/27.2%; and 6.1%/14.7% for the same four species, respectively. Twenty-nine Enterobacterales isolates from 28 patients were shown to harbour a carbapenemase gene: 18 blaIMP-4; four blaNDM-5; three blaNDM-1; one blaOXA-181; one blaOXA-244; one blaNDM-1 + blaOXA-181; and one blaNDM-5 + blaOXA-181. Transmissible carbapenemase genes were also detected among two Acinetobacter baumannii complex isolates (blaOXA-23) and one P. aeruginosa (blaNDM-1) in the 2022 survey.
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Affiliation(s)
- Jan M Bell
- Australian Group on Antimicrobial Resistance, Adelaide, South Australia, Australia
| | - Alicia Fajardo Lubian
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia; University of Sydney, New South Wales, Australia
| | - Sally R Partridge
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia; University of Sydney, New South Wales, Australia; Westmead Hospital, Westmead, New South Wales, Australia
| | - Thomas Gottlieb
- University of Sydney, New South Wales, Australia; Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, New South Wales, Australia .
| | - Jennifer Robson
- Department of Microbiology, Sullivan Nicolaides Pathology, Bowen Hills, Queensland
| | - Jonathan R Iredell
- Westmead Institute for Medical Research, Westmead, New South Wales, Australia; University of Sydney, New South Wales, Australia ; Westmead Hospital, Westmead, New South Wales, Australia
| | - Denise A Daley
- Australian Group on Antimicrobial Resistance, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia; Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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33
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Liang E, Xu L, Su J, Liu Y, Qi S, Li X. Hydrogel bioreactor drives Feammox and synergistically removes composite pollutants: Performance optimization, microbial communities and functional genetic differences. Bioresour Technol 2023; 387:129604. [PMID: 37544543 DOI: 10.1016/j.biortech.2023.129604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/08/2023]
Abstract
Mixed pollutant wastewater has been a difficult problem due to the high toxicity of water bodies and the difficulty of treatment. Rice husk biochar modified with nano-iron tetroxide (RBC-nFe3O4) by polyvinyl alcohol cross-linking internal doping was used to introduce iron-reducing bacteria Klebsiella sp. FC61 to construct a bioreactor. The results of the long-term operation of the bioreactor showed that the removal efficiency of ammonia nitrogen (NH4+-N) and chemical oxygen demand best reached 90.18 and 98.49%, respectively. In addition, in the co-presence of Ni2+, Cd2+, and ciprofloxacin, the bioreactor was still able to remove pollutants efficiently by RBC-nFe3O4 and bio-iron precipitation inside the biocarrier. During the long-term operation, Klebsiella was always the dominant species in the bioreactor. And the sequencing data for functional prediction showed that the biocarrier contained a variety of enzymes and proteins involved in Feammox-related activities to ensure the stable and efficient operation of the bioreactor.
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Affiliation(s)
- Enlei Liang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Liang Xu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Junfeng Su
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Yan Liu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Shangzhe Qi
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xuan Li
- College of Environmental Science & Engineering, Yancheng Institute of Technology, Yancheng 224051, China
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DeLeo FR, Porter AR, Kobayashi SD, Freedman B, Hao M, Jiang J, Lin YT, Kreiswirth BN, Chen L. Interaction of multidrug-resistant hypervirulent Klebsiella pneumoniae with components of human innate host defense. mBio 2023; 14:e0194923. [PMID: 37671860 PMCID: PMC10653787 DOI: 10.1128/mbio.01949-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 09/07/2023] Open
Abstract
IMPORTANCE Klebsiella pneumoniae strains with a combination of multidrug resistance and hypervirulence genotypes (MDR hvKp) have emerged as a cause of human infections. The ability of these microbes to avoid killing by the innate immune system remains to be tested fully. To that end, we compared the ability of a global collection of hvKp and MDR hvKp clinical isolates to survive in human blood and resist phagocytic killing by human neutrophils. The two MDR hvKp clinical isolates tested (ST11 and ST147) were killed in human blood and by human neutrophils in vitro, whereas phagocytic killing of hvKp clinical isolates (ST23 and ST86) required specific antisera. Although the data were varied and often isolate specific, they are an important first step toward gaining an enhanced understanding of host defense against MDR hvKp.
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Affiliation(s)
- Frank R. DeLeo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Adeline R. Porter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Scott D. Kobayashi
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Brett Freedman
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Mingju Hao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, China
| | - Jianping Jiang
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Yi-Tsung Lin
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Emergency and Critical Care Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Barry N. Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
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35
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Kovács ÁT. Colony morphotype diversification as a signature of bacterial evolution. Microlife 2023; 4:uqad041. [PMID: 37901115 PMCID: PMC10608940 DOI: 10.1093/femsml/uqad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/31/2023]
Abstract
The appearance of colony morphotypes is a signature of genetic diversification in evolving bacterial populations. Colony structure highly depends on the cell-cell interactions and polymer production that are adjusted during evolution in an environment that allows the development of spatial structures. Nucci and colleagues describe the emergence of a rough and dry morphotype of a noncapsulated Klebsiella variicola strain during a laboratory evolution study, resembling genetic changes observed in clinical isolates.
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Affiliation(s)
- Ákos T Kovács
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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36
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Laupland KB, Edwards F, Harris PNA, Paterson DL. Significant clinical differences but not outcomes between Klebsiella aerogenes and Enterobacter cloacae bloodstream infections: a comparative cohort study. Infection 2023; 51:1445-1451. [PMID: 36881325 PMCID: PMC10545569 DOI: 10.1007/s15010-023-02010-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/21/2023] [Indexed: 03/08/2023]
Abstract
PURPOSE Although Klebsiella aerogenes (formerly Enterobacter aerogenes) and Enterobacter cloacae share many phenotypic characteristics, controversy exists as to whether they cause clinically distinguishable infections. The objective of this study was to determine the comparative incidence, determinants, and outcomes of K. aerogenes and E. cloacae bloodstream infections (BSI). METHODS Population-based surveillance was conducted among residents aged ≥ 15 years of Queensland, Australia during 2000-2019. RESULTS Overall 695 and 2879 incident K. aerogenes and E. cloacae BSIs were identified for incidence rates of 1.1 and 4.4 per 100,000 population, respectively. There was a marked increase in incidence associated with older age and with males with both species. Patients with K. aerogenes BSIs were older, were more likely male, to have community-associated disease, and to have a genitourinary source of infection. In contrast, E. cloacae were more likely to have co-morbid diagnoses of liver disease and malignancy and be associated with antimicrobial resistance. Enterobacter cloacae were significantly more likely to have repeat episodes of BSI as compared to K. aerogenes. However, no differences in length of stay or all cause 30-day case-fatality were observed. CONCLUSION Although significant demographic and clinical differences exist between K. aerogenes and E. cloacae BSI, they share similar outcomes.
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Affiliation(s)
- Kevin B Laupland
- Department of Intensive Care Services, Royal Brisbane and Women's Hospital, Level 3 Ned Hanlon Building, Butterfield Street, Brisbane, QLD, 4029, Australia.
- Queensland University of Technology (QUT), Brisbane, QLD, Australia.
| | - Felicity Edwards
- Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Patrick N A Harris
- Faculty of Medicine, University of Queensland, UQ Center for Clinical Research, Brisbane, Australia
- Department of Microbiology, Pathology Queensland, Brisbane, Australia
| | - David L Paterson
- Faculty of Medicine, University of Queensland, UQ Center for Clinical Research, Brisbane, Australia
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Brisbane, Australia
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37
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Zhu DH, Nie FH, Song QL, Wei W, Zhang M, Hu Y, Lin HY, Kang DJ, Chen ZB, Chen JJ. Isolation and genomic characterization of Klebsiella Lw3 with polychlorinated biphenyl degradability. Environ Technol 2023; 44:3656-3666. [PMID: 35441572 DOI: 10.1080/09593330.2022.2068381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Bioremediation of sediment organic pollution has been intensely investigated, but the degradation of complex organic compounds, pesticide residues, and polychlorinated biphenyls (PCBs) remains poorly studied. In this study, sediments were collected from Zhanjiang Mangrove Reserve and inoculated in an inorganic salt medium using only biphenyl (BP) and PCBs as the carbon sources to obtain a PCB-degrading strain. A gram-negative bacterium that metabolized PCBs was isolated and identified as Klebsiella Lw3 by 16S rDNA phylogenetic analysis. Genomic sequencing showed that this bacterium possessed genes related to BP/PCB degradation, and its GC content was 58.2%; we identified 3326 cellular pathways. Gas chromatography-mass spectrometry was employed to test the PCB degrading ability; the results showed that the strain had a good degradation effect on PCB3 at concentrations of 5, 10, 20, 40, and 60 mg/L and that the final degradation rate was higher than 97% after 96 h. Interestingly, this strain showed good biodegradability of PCBs despite having no classical PCB degradation pathway, providing a new direction for Klebsiella research with practical significance for in situ bioremediation of PCB contamination. Overall, this study provides valuable insights into the genetic structure of PCB-degrading strains as well as eco-friendly and low-cost PCB degradation and lays a foundation for the discovery of new degradation pathways.
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Affiliation(s)
- Di-Hua Zhu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Fang-Hong Nie
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Qing-Lang Song
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Wan Wei
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Min Zhang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Yao Hu
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Hong-Ying Lin
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Dan-Ju Kang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Zhi-Bao Chen
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Jin-Jun Chen
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
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38
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Demir M, Sigal M. Mucosa-associated microbiota alterations in primary sclerosing cholangitis (PSC) before and after liver transplantation-who is calling the shots? Hepatobiliary Surg Nutr 2023; 12:795-797. [PMID: 37886186 PMCID: PMC10598306 DOI: 10.21037/hbsn-23-335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 10/28/2023]
Affiliation(s)
- Münevver Demir
- Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum and Campus Charité Mitte, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Sigal
- Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum and Campus Charité Mitte, Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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Cuello L, Alvarez Otero J, Greenwood-Quaintance KE, Chen L, Hanson B, Reyes J, Komarow L, Ge L, Lancaster ZD, Gordy GG, Schuetz AN, Patel R. Poor Sensitivity of the MALDI Biotyper ® MBT Subtyping Module for Detection of Klebsiella pneumoniae Carbapenemase (KPC) in Klebsiella Species. Antibiotics (Basel) 2023; 12:1465. [PMID: 37760762 PMCID: PMC10525285 DOI: 10.3390/antibiotics12091465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Rapid detection of Klebsiella pneumoniae carbapenemase (KPC) in the Klebsiella species is desirable. The MALDI Biotyper® MBT Subtyping Module (Bruker Daltonics) uses an algorithm that detects a peak at ~11,109 m/z corresponding to a protein encoded by the p019 gene to detect KPC simultaneously with organism identification by a matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-ToF MS). Here, the subtyping module was evaluated using 795 clinical Klebsiella isolates, with whole genome sequences used to assess for blaKPC and p019. For the isolates identified as KPC positive by sequencing, the overall sensitivity of the MALDI-ToF MS subtyping module was 239/574 (42%) with 100% specificity. For the isolates harboring p019, the subtyping module showed a sensitivity of 97% (239/246) and a specificity of 100%. The subtyping module had poor sensitivity for the detection of blaKPC-positive Klebsiella isolates, albeit exhibiting excellent specificity. The poor sensitivity was a result of p019 being present in only 43% of the blaKPC-positive Klebsiella isolates.
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Affiliation(s)
- Luz Cuello
- Infectious Diseases Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Blake Hanson
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá 110121, Colombia
| | - Lauren Komarow
- The Biostatistics Center, The George Washington University, Rockville, MD 20852, USA
| | - Lizhao Ge
- The Biostatistics Center, The George Washington University, Rockville, MD 20852, USA
| | - Zane D. Lancaster
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Garrett G. Gordy
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Audrey N. Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Robin Patel
- Infectious Diseases Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
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40
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Crawford MA, Lascols C, Lomonaco S, Timme RE, Fisher DJ, Anderson K, Hodge DR, Morse SA, Pillai SP, Sharma SK, Khan E, Allard MW, Hughes MA. Enterobacterales draft genome sequences: 15 historical (1998-2004) and 30 contemporary (2015-2016) clinical isolates from Pakistan. Microbiol Resour Announc 2023; 12:e0016323. [PMID: 37504519 PMCID: PMC10508161 DOI: 10.1128/mra.00163-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/14/2023] [Indexed: 07/29/2023] Open
Abstract
The continued emergence and spread of antimicrobial resistance among pathogenic bacteria are ever-growing threats to health and economy. Here, we report the draft genomes for 45 Enterobacterales clinical isolates, including historical and contemporary drug-resistant organisms, obtained in Pakistan between 1998 and 2016: 5 Serratia, 3 Salmonella, 3 Enterobacter, and 34 Klebsiella.
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Affiliation(s)
- Matthew A. Crawford
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Christine Lascols
- National Center for Emerging and Zoonotic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- IHRC, Inc., Atlanta, Georgia, USA
| | - Sara Lomonaco
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Ruth E. Timme
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Debra J. Fisher
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Kevin Anderson
- Science and Technology Directorate, US Department of Homeland Security, Washington, DC, USA
| | - David R. Hodge
- Science and Technology Directorate, US Department of Homeland Security, Washington, DC, USA
| | | | - Segaran P. Pillai
- Office of the Commissioner, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Shashi K. Sharma
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Erum Khan
- Department of Pathology and Microbiology, Aga Khan University, Karachi, Pakistan
| | - Marc W. Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Molly A. Hughes
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
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41
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Li Y, Santos-Moreno J, Francetic O. The periplasmic coiled coil formed by the assembly platform proteins PulL and PulM is critical for function of the Klebsiella type II secretion system. Res Microbiol 2023; 174:104075. [PMID: 37141929 DOI: 10.1016/j.resmic.2023.104075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
Bacteria use type II secretion systems (T2SS) to secrete to their surface folded proteins that confer diverse functions, from nutrient acquisition to virulence. In the Klebsiella species, T2SS-mediated secretion of pullulanase (PulA) requires assembly of a dynamic filament called the endopilus. The inner membrane assembly platform (AP) subcomplex is essential for endopilus assembly and PulA secretion. AP components PulL and PulM interact with each other through their C-terminal globular domains and transmembrane segments. Here, we investigated the roles of their periplasmic helices, predicted to form a coiled coil, in assembly and function of the PulL-PulM complex. PulL and PulM variants lacking these periplasmic helices were defective for interaction in the bacterial two-hybrid (BACTH) assay. Their functions in PulA secretion and assembly of PulG subunits into endopilus filaments were strongly reduced. Interestingly, deleting the cytoplasmic peptide of PulM nearly abolished the function of variant PulMΔN and its interaction with PulG, but not with PulL, in the BACTH assay. Nevertheless, PulL was specifically proteolyzed in the presence of the PulMΔN variant, suggesting that PulM N-terminal peptide stabilizes PulL in the cytoplasm. We discuss the implications of these results for the T2S endopilus and type IV pilus assembly mechanisms.
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Affiliation(s)
- Yuanyuan Li
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, F-75015 Paris, France.
| | - Javier Santos-Moreno
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, F-75015 Paris, France.
| | - Olivera Francetic
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, F-75015 Paris, France.
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42
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Isler B, Vatansever C, Özer B, Çınar G, Aslan AT, Falconer C, Bauer MJ, Forde B, Şimşek F, Tülek N, Demirkaya H, Menekşe Ş, Akalin H, Balkan İİ, Aydın M, Tigen ET, Demir SK, Kapmaz M, Keske Ş, Doğan Ö, Arabacı Ç, Yağcı S, Hazırolan G, Bakır VO, Gönen M, Saltoğlu N, Azap A, Azap Ö, Akova M, Ergönül Ö, Can F, Paterson DL, Harris PNA. Higher rates of cefiderocol resistance among NDM producing Klebsiella bloodstream isolates applying EUCAST over CLSI breakpoints. Infect Dis (Lond) 2023; 55:607-613. [PMID: 37391868 DOI: 10.1080/23744235.2023.2226709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND Cefiderocol is generally active against carbapenem-resistant Klebsiella spp. (CRK) with higher MICs against metallo-beta-lactamase producers. There is a variation in cefiderocol interpretive criteria determined by EUCAST and CLSI. Our objective was to test CRK isolates against cefiderocol and compare cefiderocol susceptibilities using EUCAST and CLSI interpretive criteria. METHODS A unique collection (n = 254) of mainly OXA-48-like- or NDM-producing CRK bloodstream isolates were tested against cefiderocol with disc diffusion (Mast Diagnostics, UK). Beta-lactam resistance genes and multilocus sequence types were identified using bioinformatics analyses on complete bacterial genomes. RESULTS Median cefiderocol inhibition zone diameter was 24 mm (interquartile range [IQR] 24-26 mm) for all isolates and 18 mm (IQR 15-21 mm) for NDM producers. We observed significant variability between cefiderocol susceptibilities using EUCAST and CLSI breakpoints, such that 26% and 2% of all isolates, and 81% and 12% of the NDM producers were resistant to cefiderocol using EUCAST and CLSI interpretive criteria, respectively. CONCLUSIONS Cefiderocol resistance rates among NDM producers are high using EUCAST criteria. Breakpoint variability may have significant implications on patient outcomes. Until more clinical outcome data are available, we suggest using EUCAST interpretive criteria for cefiderocol susceptibility testing.
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Affiliation(s)
- Burcu Isler
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia
| | - Cansel Vatansever
- Infectious Diseases and Clinical Microbiology, School of Medicine, Koç University, Istanbul, Turkey
| | - Berna Özer
- Infectious Diseases and Clinical Microbiology, School of Medicine, Koç University, Istanbul, Turkey
| | - Güle Çınar
- Infectious Diseases and Clinical Microbiology, School of Medicine, Ankara University Ankara, Turkey
| | - Abdullah Tarık Aslan
- Infectious Diseases and Clinical Microbiology, Hacettepe University School of Medicine, Ankara, Turkey
| | - Caitlin Falconer
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Michelle J Bauer
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Brian Forde
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Funda Şimşek
- Infectious Diseases and Clinical Microbiology, University of Health Sciences, Ministry of Health Prof Dr Cemil Taşçıoğlu City Hospital, Istanbul, Turkey
| | - Necla Tülek
- Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Atilim University, Ankara, Turkey
| | - Hamiyet Demirkaya
- Infectious Diseases and Clinical Microbiology, Ankara Hospital, Başkent University, Ankara, Turkey
| | - Şirin Menekşe
- Infectious Diseases, Koşuyolu Kartal Heart Training and Research Hospital, Istanbul, Turkey
| | - Halis Akalin
- Infectious Diseases and Clinical Microbiology, School of Medicine, Uludağ University, Bursa, Turkey
| | - İlker İnanç Balkan
- Infectious Diseases and Clinical Microbiology, School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Mehtap Aydın
- Infectious Diseases and Clinical Microbiology, Ümraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Elif Tükenmez Tigen
- Infectious Diseases and Clinical Microbiology, Pendik Training and Research Hospital, Marmara University, Istanbul, Turkey
| | - Safiye Koçulu Demir
- Infectious Diseases and Clinical Microbiology, Demiroglu Bilim University, Istanbul, Turkey
| | - Mahir Kapmaz
- Infectious Diseases and Clinical Microbiology, Koç University Hospital, Istanbul, Turkey
| | - Şiran Keske
- Infectious Diseases and Clinical Microbiology, School of Medicine, Koç University, Istanbul, Turkey
- Infectious Diseases, VKV American Hospital, Istanbul, Turkey
| | - Özlem Doğan
- Infectious Diseases and Clinical Microbiology, School of Medicine, Koç University, Istanbul, Turkey
| | - Çiğdem Arabacı
- Clinical Microbiology, Ministry of Health Prof Dr Cemil Taşçıoğlu City Hospital, University of Health Sciences, Istanbul, Turkey
| | - Serap Yağcı
- Clinical Microbiology, Ankara Training and Research Hospital, Ankara, Turkey
| | - Gülşen Hazırolan
- Clinical Microbiology, Hacettepe University School of Medicine, Ankara, Turkey
| | - Veli Oğuzalp Bakır
- Graduate School of Sciences and Engineering, Koç University, Istanbul, Turkey
| | - Mehmet Gönen
- Industrial Engineering, College of Engineering, Koç University, Istanbul, Turkey
| | - Neşe Saltoğlu
- Infectious Diseases and Clinical Microbiology, School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Alpay Azap
- Infectious Diseases and Clinical Microbiology, School of Medicine, Ankara University Ankara, Turkey
| | - Özlem Azap
- Infectious Diseases and Clinical Microbiology, Ankara Hospital, Başkent University, Ankara, Turkey
| | - Murat Akova
- Infectious Diseases and Clinical Microbiology, Hacettepe University School of Medicine, Ankara, Turkey
| | - Önder Ergönül
- Infectious Diseases and Clinical Microbiology, School of Medicine, Koç University, Istanbul, Turkey
- Koç University İş Bank Centre for Infectious Diseases (KUISCID), Istanbul, Turkey
| | - Füsun Can
- Infectious Diseases and Clinical Microbiology, School of Medicine, Koç University, Istanbul, Turkey
- Koç University İş Bank Centre for Infectious Diseases (KUISCID), Istanbul, Turkey
| | - David L Paterson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Patrick N A Harris
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
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43
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Schneider JS, Froböse NJ, Kuczius T, Schwierzeck V, Kampmeier S. Sink Drains in a Neonatal Intensive Care Unit: A Retrospective Risk Assessment and Evaluation. Int J Environ Res Public Health 2023; 20:6692. [PMID: 37681832 PMCID: PMC10487867 DOI: 10.3390/ijerph20176692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Water systems in health care facilities can form reservoirs for Gram-negative bacteria. While planning a new neonatal intensive care unit (NICU), we performed a retrospective evaluation of potential risks from water-diverting systems on the existing NICU of our tertiary care University Hospital. During 2017 to 2023, we recorded nine nosocomial cluster events with bacterial pathogens in our NICU. Of these, three clusters of Gram-negative bacteria were potentially related to sink drains: A Klebsiella oxytoca, a Pseudomonas aeruginosa, and an Enterobacter hormaechei cluster were uncovered by clinical routine screening of patients and breastmilk samples. They were confirmed using whole-genome sequencing and a subsequent core genome multilocus sequence typing (cgMLST) algorithm. Our observations highlight that the implementation of sink drains in a NICU may have negative effects on patients' safety. Construction planning should concentrate on the avoidance of washbasins in patient rooms when redesigning sensitive areas such as NICUs.
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Affiliation(s)
- Julia S. Schneider
- Institute of Hygiene, University Hospital Münster, 48149 Münster, Germany; (J.S.S.); (T.K.); (V.S.)
| | - Neele J. Froböse
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany;
| | - Thorsten Kuczius
- Institute of Hygiene, University Hospital Münster, 48149 Münster, Germany; (J.S.S.); (T.K.); (V.S.)
| | - Vera Schwierzeck
- Institute of Hygiene, University Hospital Münster, 48149 Münster, Germany; (J.S.S.); (T.K.); (V.S.)
| | - Stefanie Kampmeier
- Institute of Hygiene, University Hospital Münster, 48149 Münster, Germany; (J.S.S.); (T.K.); (V.S.)
- Institute for Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany
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Yuan T, Qazi IH, Li J, Yang P, Yang H, Zhang X, Liu W, Liu J. Analysis of changes in bacterial diversity in healthy and bacterial wilt mulberry samples using metagenomic sequencing and culture-dependent approaches. Front Plant Sci 2023; 14:1206691. [PMID: 37680359 PMCID: PMC10481342 DOI: 10.3389/fpls.2023.1206691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/21/2023] [Indexed: 09/09/2023]
Abstract
Introduction Mulberry bacterial wilt is a serious destructive soil-borne disease caused by a complex and diverse group of pathogenic bacteria. Given that the bacterial wilt has been reported to cause a serious damage to the yield and quality of mulberry, therefore, elucidation of its main pathogenic groups is essential in improving our understanding of this disease and for the development of its potential control measures. Methods In this study, combined metagenomic sequencing and culture-dependent approaches were used to investigate the microbiome of healthy and bacterial wilt mulberry samples. Results The results showed that the healthy samples had higher bacterial diversity compared to the diseased samples. Meanwhile, the proportion of opportunistic pathogenic and drug-resistant bacterial flora represented by Acinetobacter in the diseased samples was increased, while the proportion of beneficial bacterial flora represented by Proteobacteria was decreased. Ralstonia solanacearum species complex (RSSC), Enterobacter cloacae complex (ECC), Klebsiella pneumoniae, K. quasipneumoniae, K. michiganensis, K. oxytoca, and P. ananatis emerged as the main pathogens of the mulberry bacterial wilt. Discussion In conclusion, this study provides a valuable reference for further focused research on the bacterial wilt of mulberry and other plants.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiping Liu
- South China Agriculture University, College of Animal Science, Regional Sericulture Training Center for Asia-Pacific, Guangzhou, Guangdong, China
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Rose R, Nolan DJ, Ashcraft D, Feehan AK, Velez-Climent L, Huston C, Lain B, Rosenthal S, Miele L, Fogel GB, Pankey G, Garcia-Diaz J, Lamers SL. Comparing antimicrobial resistant genes and phenotypes across multiple sequencing platforms and assays for Enterobacterales clinical isolates. BMC Microbiol 2023; 23:225. [PMID: 37596530 PMCID: PMC10436404 DOI: 10.1186/s12866-023-02975-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
INTRODUCTION Whole genome sequencing (WGS) of bacterial isolates can be used to identify antimicrobial resistance (AMR) genes. Previous studies have shown that genotype-based AMR has variable accuracy for predicting carbapenem resistance in carbapenem-resistant Enterobacterales (CRE); however, the majority of these studies used short-read platforms (e.g. Illumina) to generate sequence data. In this study, our objective was to determine whether Oxford Nanopore Technologies (ONT) long-read WGS would improve detection of carbapenem AMR genes with respect to short-read only WGS for nine clinical CRE samples. We measured the minimum inhibitory breakpoint (MIC) using two phenotype assays (MicroScan and ETEST) for six antibiotics, including two carbapenems (meropenem and ertapenem) and four non-carbapenems (gentamicin, ciprofloxacin, cefepime, and trimethoprim/sulfamethoxazole). We generated short-read data using the Illumina NextSeq and long-read data using the ONT MinION. Four assembly methods were compared: ONT-only assembly; ONT-only assembly plus short-read polish; ONT + short-read hybrid assembly plus short-read polish; short-read only assembly. RESULTS Consistent with previous studies, our results suggest that the hybrid assembly produced the highest quality results as measured by gene completeness and contig circularization. However, ONT-only methods had minimal impact on the detection of AMR genes and plasmids compared to short-read methods, although, notably, differences in gene copy number differed between methods. All four assembly methods showed identical presence/absence of the blaKPC-2 carbapenemase gene for all samples. The two phenotype assays showed 100% concordant results for the non-carbapenems, but only 65% concordance for the two carbapenems. The presence/absence of AMR genes was 100% concordant with AMR phenotypes for all four non-carbapenem drugs, although only 22%-50% sensitivity for the carbapenems. CONCLUSIONS Overall, these findings suggest that the lack of complete correspondence between CRE AMR genotype and phenotype for carbapenems, while concerning, is independent of sequencing platform/assembly method.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA.
- FoxSeq, LLC, Thibodaux, LA, USA.
| | - David J Nolan
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Deborah Ashcraft
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Amy K Feehan
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | | | - Benjamin Lain
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Simon Rosenthal
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Lucio Miele
- Translational Science and Genetics at Louisiana State University Health Science Center, New Orleans, LA, USA
| | | | - George Pankey
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Julia Garcia-Diaz
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Susanna L Lamers
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
- FoxSeq, LLC, Thibodaux, LA, USA
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Nale JY, McEwan NR. Bacteriophage Therapy to Control Bovine Mastitis: A Review. Antibiotics (Basel) 2023; 12:1307. [PMID: 37627727 PMCID: PMC10451327 DOI: 10.3390/antibiotics12081307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Bovine mastitis is a polymicrobial disease characterised by inflammation of the udders of dairy and beef cattle. The infection has huge implications to health and welfare of animals, impacting milk and beef production and costing up to EUR 32 billion annually to the dairy industry, globally. Bacterial communities associated with the disease include representative species from Staphylococcus, Streptococcus, Enterococcus, Actinomyces, Aerococcus, Escherichia, Klebsiella and Proteus. Conventional treatment relies on antibiotics, but antimicrobial resistance, declining antibiotic innovations and biofilm production negatively impact therapeutic efficacy. Bacteriophages (phages) are viruses which effectively target and lyse bacteria with extreme specificity and can be a valuable supplement or replacement to antibiotics for bovine mastitis. In this review, we provide an overview of the etiology of bovine mastitis, the advantages of phage therapy over chemical antibiotics for the strains and research work conducted in the area in various model systems to support phage deployment in the dairy industry. We emphasise work on phage isolation procedures from samples obtained from mastitic and non-mastitic sources, characterisation and efficacy testing of single and multiple phages as standalone treatments or adjuncts to probiotics in various in vitro, ex vivo and in vivo bovine mastitis infection models. Furthermore, we highlight the areas where improvements can be made with focus on phage cocktail optimisation, formulation, and genetic engineering to improve delivery, stability, efficacy, and safety in cattle. Phage therapy is becoming more attractive in clinical medicine and agriculture and thus, could mitigate the impending catastrophe of antimicrobial resistance in the dairy sector.
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Affiliation(s)
- Janet Y. Nale
- Centre for Epidemiology and Planetary Health, Scotland’s Rural College (SRUC), Inverness IV2 5NA, Scotland, UK
| | - Neil R. McEwan
- School of Veterinary Medicine, Scotland’s Rural College (SRUC), Aberdeen AB21 9YA, Scotland, UK;
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Hapsari BDA, Melita M, Ismail AR, Djatmika FNT. A large primary lung abscess due to Klebsiella oxytoca: How critical the combination between early antibiotic therapy and bronchoscopy? Narra J 2023; 3:e169. [PMID: 38450261 PMCID: PMC10916413 DOI: 10.52225/narra.v3i2.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 08/13/2023] [Indexed: 03/08/2024]
Abstract
Lung abscess is a microbial infection that can cause necrosis of the lung tissue and formation of cavities. Antibiotics and bronchoscopy are needed in the management of large lung abscess to prevent further complications. However, some of the cases have poor clinical improvement. The aim of this case report was to describe a patient with large lung abscess who had well responded to antibiotic therapy combined with bronchoscopy drainage. We reported a 55-year-old man with a lung abscess presented with initial symptom of acute productive cough for two weeks. Chest computed tomography (CT) scan with contrast of patient indicated a massive abscess on the right lung segment with a size of 10.9 × 10.41 × 8 cm. Laboratory examination showed leukocytosis. Bronchoscopy was performed as a diagnostic and therapeutic procedure. Antibiotic resistance test was conducted from bronchoalveolar lavage sample to determine the most suitable antibiotics for the patient. The culture yielded a positive for Klebsiella oxytoca that was resistant to ampicillin and cefazolin. The bacterium was sensitive to piperacillin-tazobactam, aztreonam, ceftazidime, ceftriaxone, ertapenem, cefepime, nitrofurantoin, meropenem, amikacin, gentamicin, ciprofloxacin, tigecycline, trimethoprim- sulfamethoxazole, and levofloxacin. Levofloxacin 750 mg injection was given for 14 days followed with oral levofloxacin 500 mg once a day for four weeks and bronchoscopy to stop the microbial infection process in the lung tissues. Lung abscess reduced significantly and the patient was followed until recovered. In conclusion, early combination therapy of adequate antibiotics and bronchoscopy is effective in treating a massive lung abscess caused by Klebsiella oxytoca.
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Affiliation(s)
- Brigitta DA. Hapsari
- Department of Pulmonology and Respiratory Medicine Faculty of Medicine, Universitas Sebelas Maret, Surakarta,Indonesia
| | - Melita Melita
- Department of Pulmonology and Respiratory Medicine Faculty of Medicine, Universitas Sebelas Maret, Surakarta,Indonesia
| | - Affan R. Ismail
- Faculty of Medicine, Universitas Sebelas Maret, Surakarta, Indonesia
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Root-Bernstein R, Huber J, Ziehl A, Pietrowicz M. SARS-CoV-2 and Its Bacterial Co- or Super-Infections Synergize to Trigger COVID-19 Autoimmune Cardiopathies. Int J Mol Sci 2023; 24:12177. [PMID: 37569555 PMCID: PMC10418384 DOI: 10.3390/ijms241512177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Autoimmune cardiopathies (AC) following COVID-19 and vaccination against SARS-CoV-2 occur at significant rates but are of unknown etiology. This study investigated the possible roles of viral and bacterial mimicry, as well as viral-bacterial co-infections, as possible inducers of COVID-19 AC using proteomic methods and enzyme-linked immunoadsorption assays. BLAST and LALIGN results of this study demonstrate that SARS-CoV-2 shares a significantly greater number of high quality similarities to some cardiac protein compared with other viruses; that bacteria such as Streptococci, Staphylococci and Enterococci also display very significant similarities to cardiac proteins but to a different set than SARS-CoV-2; that the importance of these similarities is largely validated by ELISA experiments demonstrating that polyclonal antibodies against SARS-CoV-2 and COVID-19-associated bacteria recognize cardiac proteins with high affinity; that to account for the range of cardiac proteins targeted by autoantibodies in COVID-19-associated autoimmune myocarditis, both viral and bacterial triggers are probably required; that the targets of the viral and bacterial antibodies are often molecularly complementary antigens such as actin and myosin, laminin and collagen, or creatine kinase and pyruvate kinase, that are known to bind to each other; and that the corresponding viral and bacterial antibodies recognizing these complementary antigens also bind to each other with high affinity as if they have an idiotype-anti-idiotype relationship. These results suggest that AC results from SARS-CoV-2 infections or vaccination complicated by bacterial infections. Vaccination against some of these bacterial infections, such as Streptococci and Haemophilus, may therefore decrease AC risk, as may the appropriate and timely use of antibiotics among COVID-19 patients and careful screening of vaccinees for signs of infection such as fever, diarrhea, infected wounds, gum disease, etc.
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Affiliation(s)
- Robert Root-Bernstein
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; (J.H.); (A.Z.); (M.P.)
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Tsui CKM, Ben Abid F, Al Ismail K, McElheny CL, Al Maslamani M, Omrani AS, Doi Y. Genomic Epidemiology of Carbapenem-Resistant Klebsiella in Qatar: Emergence and Dissemination of Hypervirulent Klebsiella pneumoniae Sequence Type 383 Strains. Antimicrob Agents Chemother 2023; 67:e0003023. [PMID: 37310284 PMCID: PMC10353355 DOI: 10.1128/aac.00030-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/23/2023] [Indexed: 06/14/2023] Open
Abstract
The emergence of carbapenem-resistant, hypervirulent Klebsiella pneumoniae is a new threat to health care. We studied the molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae isolates in Qatar using whole-genome sequence data. We also characterized the prevalence and genetic basis of hypervirulent phenotypes and established the virulence potential using a Galleria mellonella model. Of 100 Klebsiella isolates studied, NDM and OXA-48 were the most common carbapenemases. Core genome single-nucleotide polymorphism (SNP) analysis indicated the presence of diverse sequence types and clonal lineages; isolates belonging to Klebsiella quasipneumoniae subsp. quasipneumoniae sequence type 196 (ST196) and ST1416 may be disseminated among several health care centers. Ten K. pneumoniae isolates carried rmpA and/or truncated rmpA2, and 2 isolates belonged to KL2, indicating low prevalence of classical hypervirulent isolates. Isolates carrying both carbapenem resistance and hypervirulence genes were confined mainly to ST231 and ST383 isolates. One ST383 isolate was further investigated by MinION sequencing, and the assembled genome indicated that blaNDM was located on an IncHI1B-type plasmid (pFQ61_ST383_NDM-5) which coharbored several virulence factors, including the regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD and iutA), likely resulting from recombination events. Comparative genomics indicated that this hybrid plasmid may be present in two additional Qatari ST383 isolates. Carbapenem-resistant, hypervirulent K. pneumoniae ST383 isolates pose an emerging threat to global health due to their simultaneous hypervirulence and multidrug resistance.
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Affiliation(s)
- Clement Kin-Ming Tsui
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Weill Cornell Medicine—Qatar, Doha, Qatar
| | - Fatma Ben Abid
- Weill Cornell Medicine—Qatar, Doha, Qatar
- Communicable Diseases Center, Hamad Medical Corporation, Doha, Qatar
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Khalil Al Ismail
- Communicable Diseases Center, Hamad Medical Corporation, Doha, Qatar
| | - Christi Lee McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Muna Al Maslamani
- Communicable Diseases Center, Hamad Medical Corporation, Doha, Qatar
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Ali S. Omrani
- Communicable Diseases Center, Hamad Medical Corporation, Doha, Qatar
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
- College of Medicine, Qatar University, Doha, Qatar
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Japan
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50
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Schluter J, Djukovic A, Taylor BP, Yan J, Duan C, Hussey GA, Liao C, Sharma S, Fontana E, Amoretti LA, Wright RJ, Dai A, Peled JU, Taur Y, Perales MA, Siranosian BA, Bhatt AS, van den Brink MRM, Pamer EG, Xavier JB. The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia. Cell Host Microbe 2023; 31:1126-1139.e6. [PMID: 37329880 PMCID: PMC10527165 DOI: 10.1016/j.chom.2023.05.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/28/2022] [Accepted: 05/24/2023] [Indexed: 06/19/2023]
Abstract
Longitudinal microbiome data provide valuable insight into disease states and clinical responses, but they are challenging to mine and view collectively. To address these limitations, we present TaxUMAP, a taxonomically informed visualization for displaying microbiome states in large clinical microbiome datasets. We used TaxUMAP to chart a microbiome atlas of 1,870 patients with cancer during therapy-induced perturbations. Bacterial density and diversity were positively associated, but the trend was reversed in liquid stool. Low-diversity states (dominations) remained stable after antibiotic treatment, and diverse communities had a broader range of antimicrobial resistance genes than dominations. When examining microbiome states associated with risk for bacteremia, TaxUMAP revealed that certain Klebsiella species were associated with lower risk for bacteremia localize in a region of the atlas that is depleted in high-risk enterobacteria. This indicated a competitive interaction that was validated experimentally. Thus, TaxUMAP can chart comprehensive longitudinal microbiome datasets, enabling insights into microbiome effects on human health.
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Affiliation(s)
- Jonas Schluter
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA.
| | - Ana Djukovic
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Bradford P Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jinyuan Yan
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Caichen Duan
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Grant A Hussey
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Sneh Sharma
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Emily Fontana
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Luigi A Amoretti
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Roberta J Wright
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Anqi Dai
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan U Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Ying Taur
- Department of Immunology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | | | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA; Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcel R M van den Brink
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
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