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Lei M, Jiang Z, Xu P, Chang Z, Zhang Y, Zhang S, An L, Li S, Zeng T, Tiselius HG, Zhou Y, Zeng G, Wu W. Characteristics of Bacteria in Urine and Stones from Patients Treated with Percutaneous Nephrolithotomy and Association with Postoperative Infection. Infect Drug Resist 2024; 17:2873-2882. [PMID: 39005855 PMCID: PMC11246033 DOI: 10.2147/idr.s462257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/04/2024] [Indexed: 07/16/2024] Open
Abstract
Background The purpose of this study was to identify bacterial differences between urine cultures (UC) and stone cultures (SC) in patients with complex kidney stones and to determine any correlation with post-percutaneous nephrolithotomy Systemic Inflammatory Response Syndrome (SIRS). Methods Perioperative data of 1055 patients with complex kidney stones treated with first-stage Percutaneous Nephrolithotomy (PCNL) from September 2016 until September 2021 were included. Preoperative mid-stream urine samples and surgically obtained stone material were subjected to bacterial culture and antibiotic sensitivity tests. Preoperatively, antibiotic usage was determined by the UC or local bacterial resistance patterns. After PCNL treatment, antibiotic selection was guided by stone bacterial culture result and clinical symptoms. The effect of different preoperative antibiotic regimens based on urine cultures and postoperative antibiotic treatment based on stone cultures were assessed. Results Positive stone cultures (SC+) were significantly more common than positive urine cultures (UC+) (31.9% vs 20.9%, p < 0.05). Escherichia coli (E. coli) was the most common uropathogen in both urine (54.3%) and stones (43.9%). The difference was statistically significant (p < 0.05). Moreover, UC+SC-, UC-SC+, UC+SC+, and preoperative serum creatinine were independent risk factors of postoperative SIRS. The incidence of SIRS in the UC+SC+ patients with different bacteria in stones and urine (51.6%) was higher than that in other culture groups. The antibiotic resistance of E. coli inside the stone was increased when prolonged preoperative antibiotics were administered to UC+ patients. Conclusion The bacterial spectrum and positive outcome of culture in urine and stones were significantly different. The incidence of postoperative SIRS was highest in patients with UC+SC+ but with different bacteria strains. Prolonged pre-surgical antibiotic treatment apparently induced higher drug resistance for bacteria inside the stone.
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Affiliation(s)
- Min Lei
- Department of Urology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
| | - Zheng Jiang
- Department of Urology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
| | - Peng Xu
- Department of Urology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
| | - Zhenglin Chang
- Department of Urology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Department of Urology, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
| | - Yuyan Zhang
- Guangzhou Institute of Dermatology, Guangzhou, Guangdong, 510095, People’s Republic of China
| | - Shike Zhang
- Department of Urology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
| | - Lingyue An
- Department of Urology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, 550002, People’s Republic of China
| | - Shujue Li
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Department of Urology, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
| | - Tao Zeng
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Department of Urology, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
| | - Hans-Göran Tiselius
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute, Stockholm, 14186, Sweden
| | - Yuhao Zhou
- Department of Urology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
| | - Guohua Zeng
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Department of Urology, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
| | - Wenqi Wu
- Department of Urology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
- Guangdong Key Laboratory of Urology, Guangzhou Medical University, Guangzhou, Guangdong, 510260, People’s Republic of China
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Amábile-Cuevas CF, Lund-Zaina S. Non-Canonical Aspects of Antibiotics and Antibiotic Resistance. Antibiotics (Basel) 2024; 13:565. [PMID: 38927231 PMCID: PMC11200725 DOI: 10.3390/antibiotics13060565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.
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Affiliation(s)
| | - Sofia Lund-Zaina
- Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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3
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Sun Y, Fu X. Comprehensive examination of travel-related antimicrobial resistance and the gut microbiome. THE LANCET. MICROBE 2024; 5:e517. [PMID: 38367634 DOI: 10.1016/s2666-5247(24)00020-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/15/2024] [Indexed: 02/19/2024]
Affiliation(s)
- Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xi Fu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, School of Public Health, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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Gandasegui J, Vergara A, Fleitas P, Rubio E, Fernandez-Pittol M, Aylagas C, Alvarez M, Zancada N, Camprubí-Ferrer D, Vila J, Muñoz J, Petrone P, Casals-Pascual C. Gut microbiota composition in travellers is associated with faecal lipocalin-2, a mediator of gut inflammation. Front Cell Infect Microbiol 2024; 14:1387126. [PMID: 38736752 PMCID: PMC11082338 DOI: 10.3389/fcimb.2024.1387126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction We examined the gut microbiota of travellers returning from tropical areas with and without traveller's diarrhoea (TD) and its association with faecal lipocalin-2 (LCN2) levels. Methods Participants were recruited at the Hospital Clinic of Barcelona, Spain, and a single stool sample was collected from each individual to perform the diagnostic of the etiological agent causing gastrointestinal symptoms as well as to measure levels of faecal LCN2 as a biomarker of gut inflammation. We also characterised the composition of the gut microbiota by sequencing the region V3-V4 from the 16S rRNA gene, and assessed its relation with the clinical presentation of TD and LCN2 levels using a combination of conventional statistical tests and unsupervised machine learning approaches. Results Among 61 participants, 45 had TD, with 40% having identifiable etiological agents. Surprisingly, LCN2 levels were similar across groups, suggesting gut inflammation occurs without clinical TD symptoms. Differential abundance (DA) testing highlighted a microbial profile tied to high LCN2 levels, marked by increased Proteobacteria and Escherichia-Shigella, and decreased Firmicutes, notably Oscillospiraceae. UMAP analysis confirmed this profile's association, revealing distinct clusters based on LCN2 levels. The study underscores the discriminatory power of UMAP in capturing meaningful microbial patterns related to clinical variables. No relevant differences in the gut microbiota composition were found between travellers with or without TD. Discussion The findings suggest a correlation between gut microbiome and LCN2 levels during travel, emphasising the need for further research to discern the nature of this relationship.
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Affiliation(s)
| | - Andrea Vergara
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto Salud Carlos III, Madrid, Spain
| | - Pedro Fleitas
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Elisa Rubio
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Mariana Fernandez-Pittol
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Cristian Aylagas
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Míriam Alvarez
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Noelia Zancada
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Daniel Camprubí-Ferrer
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Tropical Medicine and International Health Department, Hospital Clínic, Barcelona, Spain
| | - Jordi Vila
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto Salud Carlos III, Madrid, Spain
| | - José Muñoz
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto Salud Carlos III, Madrid, Spain
- Tropical Medicine and International Health Department, Hospital Clínic, Barcelona, Spain
| | - Paula Petrone
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
| | - Climent Casals-Pascual
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Department of Clinical Microbiology, Biomedical Diagnostic Center (CDB), Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto Salud Carlos III, Madrid, Spain
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Shen C, Luo L, Zeng J, Zhou H, Huang B, Chen C. Dynamics and persistence of antimicrobial resistance genes and gut microbiome after travel. THE LANCET. MICROBE 2024; 5:e314. [PMID: 38244552 DOI: 10.1016/s2666-5247(23)00394-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/22/2023] [Indexed: 01/22/2024]
Affiliation(s)
- Cong Shen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Research on Emergency in TCM, Guangzhou, China
| | - Li Luo
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China
| | - Jinxiang Zeng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China
| | - Hongyun Zhou
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China
| | - Bin Huang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China; Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Cha Chen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, State Key Laboratory of Traditional Chinese Medicine Syndrome, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou 510006, China.
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Blake KS, Schwartz DJ, Paruthiyil S, Wang B, Ning J, Isidean SD, Burns DS, Whiteson H, Lalani T, Fraser JA, Connor P, Troth T, Porter CK, Tribble DR, Riddle MS, Gutiérrez RL, Simons MP, Dantas G. Gut microbiome and antibiotic resistance effects during travelers' diarrhea treatment and prevention. mBio 2024; 15:e0279023. [PMID: 38085102 PMCID: PMC10790752 DOI: 10.1128/mbio.02790-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 10/30/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE The travelers' gut microbiome is potentially assaulted by acute and chronic perturbations (e.g., diarrhea, antibiotic use, and different environments). Prior studies of the impact of travel and travelers' diarrhea (TD) on the microbiome have not directly compared antibiotic regimens, and studies of different antibiotic regimens have not considered travelers' microbiomes. This gap is important to be addressed as the use of antibiotics to treat or prevent TD-even in moderate to severe cases or in regions with high infectious disease burden-is controversial based on the concerns for unintended consequences to the gut microbiome and antimicrobial resistance (AMR) emergence. Our study addresses this by evaluating the impact of defined antibiotic regimens (single-dose treatment or daily prophylaxis) on the gut microbiome and resistomes of deployed servicemembers, using samples collected during clinical trials. Our findings indicate that the antibiotic treatment regimens that were studied generally do not lead to adverse effects on the gut microbiome and resistome and identify the relative risks associated with prophylaxis. These results can be used to inform therapeutic guidelines for the prevention and treatment of TD and make progress toward using microbiome information in personalized medical care.
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Affiliation(s)
- Kevin S. Blake
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Drew J. Schwartz
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for Women’s Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Srinand Paruthiyil
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jie Ning
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sandra D. Isidean
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
- Naval Medical Research Command, Silver Spring, Maryland, USA
| | - Daniel S. Burns
- Academic Department of Military Medicine, UK Defence Medical Directorate, Birmingham, United Kingdom
| | - Harris Whiteson
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tahaniyat Lalani
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Jamie A. Fraser
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Patrick Connor
- Academic Department of Military Medicine, UK Defence Medical Directorate, Birmingham, United Kingdom
| | - Tom Troth
- Academic Department of Military Medicine, UK Defence Medical Directorate, Birmingham, United Kingdom
| | - Chad K. Porter
- Naval Medical Research Command, Silver Spring, Maryland, USA
| | - David R. Tribble
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Mark S. Riddle
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | | | - Mark P. Simons
- Naval Medical Research Command, Silver Spring, Maryland, USA
- Infectious Disease Clinical Research Program, Preventive Medicine and Biostatistics Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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