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Leonidou N, Xia Y, Friedrich L, Schütz MS, Dräger A. Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling. PLoS Pathog 2024; 20:e1012528. [PMID: 39312576 DOI: 10.1371/journal.ppat.1012528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 08/26/2024] [Indexed: 09/25/2024] Open
Abstract
With the emergence of multidrug-resistant bacteria, the World Health Organization published a catalog of microorganisms urgently needing new antibiotics, with the carbapenem-resistant Acinetobacter baumannii designated as "critical". Such isolates, frequently detected in healthcare settings, pose a global pandemic threat. One way to facilitate a systemic view of bacterial metabolism and allow the development of new therapeutics is to apply constraint-based modeling. Here, we developed a versatile workflow to build high-quality and simulation-ready genome-scale metabolic models. We applied our workflow to create a metabolic model for A. baumannii and validated its predictive capabilities using experimental nutrient utilization and gene essentiality data. Our analysis showed that our model iACB23LX could recapitulate cellular metabolic phenotypes observed during in vitro experiments, while positive biomass production rates were observed and experimentally validated in various growth media. We further defined a minimal set of compounds that increase A. baumannii's cellular biomass and identified putative essential genes with no human counterparts, offering new candidates for future antimicrobial development. Finally, we assembled and curated the first collection of metabolic reconstructions for distinct A. baumannii strains and analyzed their growth characteristics. The presented models are in a standardized and well-curated format, enhancing their usability for multi-strain network reconstruction.
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Affiliation(s)
- Nantia Leonidou
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
- Quantitative Biology Center (QBiC), Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Yufan Xia
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Lea Friedrich
- Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Monika S Schütz
- Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
- Quantitative Biology Center (QBiC), Eberhard Karl University of Tübingen, Tübingen, Germany
- Data Analytics and Bioinformatics, Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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Wang Z, Li D, Lu L, Xu Z, Ouyang G, Sun Y. Identification of Anncaliia algerae in Ascites in an Immunosuppressed Patient, China. Open Forum Infect Dis 2024; 11:ofae393. [PMID: 39100525 PMCID: PMC11295253 DOI: 10.1093/ofid/ofae393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 07/10/2024] [Indexed: 08/06/2024] Open
Abstract
Anncaliia algerae, a microsporidium, has risen to prominence as an opportunistic pathogen, particularly afflicting individuals who are immunocompromised with conditions such as rheumatoid arthritis, organ transplantation, and hematologic malignancy. Surprisingly, despite its recognized impact, the identification of A algerae in ascitic fluid has not been documented. As such, we pinpointed A algerae as the probable instigator of ascitic accumulation in a patient with a history of acute myeloid leukemia and extended periods of immunosuppressive therapy. For this patient, there were no signs of A algerae-related infections (eg, myositis), vocal cord involvement, or disseminated infection. The presence of A algerae was finally identified by next-generation metagenomic sequencing analysis of the ascitic fluid. Clinical presentation was characterized by elevated C-reactive protein levels (110.7 mg/L), diminished platelet count (48 × 109/L), abdominal distension secondary to ascitic fluid accumulation, and lower limb pain, and it showed marked improvement following a 4-day regimen of sulfamethoxazole/trimethoprim and albendazole. Despite this promising response, the patient succumbed to aspiration of vomitus. This case underscores the importance of considering rarer organisms, such as A algerae infection, in patients who are immunocompromised and present with unexplained ascites accumulation. It highlights the potential effectiveness of sulfamethoxazole/trimethoprim and albendazole in managing such cases. Further research is warranted to elucidate optimal management strategies and improve outcomes in similar clinical scenarios.
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Affiliation(s)
- Zanzan Wang
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Dan Li
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co, Ltd, Hangzhou, China
- Hangzhou DA Medical Laboratory, Hangzhou, China
| | - Lingling Lu
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co, Ltd, Hangzhou, China
- Hangzhou DA Medical Laboratory, Hangzhou, China
| | - Zhijuan Xu
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Guifang Ouyang
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yongcheng Sun
- Department of Hematology, The First Affiliated Hospital of Ningbo University, Ningbo, China
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Stege PB, Hordijk J, Sandholt AKS, Zomer AL, Viveen MC, Rogers MRC, Salomons M, Wagenaar JA, Mughini-Gras L, Willems RJL, Paganelli FL. Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition. Microbiol Spectr 2023; 11:e0006323. [PMID: 37404183 PMCID: PMC10434115 DOI: 10.1128/spectrum.00063-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The gut microbiome of humans and animals acts as a reservoir of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC). Dogs are known for having a high prevalence of ESBL-EC in their gut microbiota, although their ESBL-EC carrier status often shifts over time. We hypothesized that the gut microbiome composition of dogs is implicated in ESBL-EC colonization status. Therefore, we assessed whether ESBL-EC carriage in dogs is associated with changes in the gut microbiome and resistome. Fecal samples were collected longitudinally from 57 companion dogs in the Netherlands every 2 weeks for a total of 6 weeks (n = 4 samples/dog). Carriage of ESBL-EC was determined through selective culturing and PCR and in line with previous studies, we observed a high prevalence of ESBL-EC carriage in dogs. Using 16s rRNA gene profiling we found significant associations between detected ESBL-EC carriage and an increased abundance of Clostridium sensu stricto 1, Enterococcus, Lactococcus, and the shared genera of Escherichia-Shigella in the dog microbiome. A resistome capture sequencing approach (ResCap) furthermore, revealed associations between detected ESBL-EC carriage and the increased abundance of the antimicrobial resistance genes: cmlA, dfrA, dhfR, floR, and sul3. In summary, our study showed that ESBL-EC carriage is associated with a distinct microbiome and resistome composition. IMPORTANCE The gut microbiome of humans and animals is an important source of multidrug resistant pathogens, including beta-lactamase-producing Escherichia coli (ESBL-EC). In this study, we assessed if the carriage of ESBL-EC in dogs was associated with changes in gut composition of bacteria and antimicrobial resistant genes (ARGs). Therefore, stool samples from 57 dogs were collected every 2 weeks for a total of 6 weeks. Sixty eight percent of the dogs carried ESBL-EC during at least one of the time points analyzed. By investigating the gut microbiome and resistome composition, we observed specific changes at time points when dogs were colonized with ESBL-EC compared to time points whenESBL-EC were not detected. In conclusion, our study highlights the importance to study the microbial diversity in companion animals, as gut colonization of particular antimicrobial resistant bacteria might be an indication of a changed microbial composition that is associated with the selection of particular ARGs.
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Affiliation(s)
- Paul B. Stege
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joost Hordijk
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Arnar K. S. Sandholt
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Marco C. Viveen
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Malbert R. C. Rogers
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Moniek Salomons
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Rob J. L. Willems
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Fernanda L. Paganelli
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
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Tsai WC, Syue LS, Ko WC, Lo CL, Lee NY. Antimicrobial treatment of monomicrobial phenotypic carbapenem-resistant Klebsiella pneumoniae bacteremia: Two are better than one. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1219-1228. [PMID: 34635426 DOI: 10.1016/j.jmii.2021.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/25/2021] [Accepted: 09/04/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUNDS Infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) are emerging worldwide. The optimal treatment for CRKP infections is challenging for clinicians because therapeutic agents are greatly limited. MATERIAL AND METHODS A retrospective study of CRKP monomicrobial bacteremia was conducted at a medical center between 2010 and 2016. The use of at least one or more drugs with in vitro activity against the blood isolates was defined as appropriate combination therapy. The logistic regression model and propensity score analysis was used to assess clinical effects of therapeutic strategies. The 30-day crude mortality was the primary end point. RESULTS Two hundred and three patients were eligible and the 30-day mortality rate was 37.9% (77 patients). As compared with monotherapy, empirical (11.6 vs. 57.3%, p < .001) or definitive (26.5% vs. 48.6%, p = .001) combination antibiotic therapy showed a lower 30-day mortality rate independently. The propensity score analysis showed that those receiving combination therapy had less clinical (p ≤ .001) or microbiological failure (p = .003) and a lower 30-day mortality rate (p < .001). Among various regimens of definitive therapy, the 30-day mortality rate was the lowest among patients with appropriate combination therapy 23.6%, (p < .001; by log rank test). The primary outcome was similar in those with definitive carbapenem-containing and carbapenem-sparing combination regimens (p = .81). The presence or absence of carbapenemase production did not affect the mortality rate (p = .26). CONCLUSION Combination therapy, regardless of carbapenem-containing or carbapenem-sparing regimens, was associated with a favorable outcome.
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Affiliation(s)
- Wen-Chia Tsai
- Division of Infectious Diseases, Department of Internal Medicine and Tainan, Taiwan
| | - Ling-Shan Syue
- Division of Infectious Diseases, Department of Internal Medicine and Tainan, Taiwan; Center for Infection Control, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Wen-Chien Ko
- Division of Infectious Diseases, Department of Internal Medicine and Tainan, Taiwan; Center for Infection Control, National Cheng Kung University Hospital, Tainan, Taiwan; Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Lung Lo
- Division of Infectious Diseases, Department of Internal Medicine and Tainan, Taiwan; Center for Infection Control, National Cheng Kung University Hospital, Tainan, Taiwan.
| | - Nan-Yao Lee
- Division of Infectious Diseases, Department of Internal Medicine and Tainan, Taiwan; Center for Infection Control, National Cheng Kung University Hospital, Tainan, Taiwan; Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Chia-Wei L, Cheng JF, Tung KC, Hong YK, Lin JH, Lin YH, Tsai CA, Lin SP, Chen YC, Shi ZY, Huang YT, Liu PY. Evolution of trimethoprim/sulfamethoxazole resistance in Shewanella algae from the perspective of comparative genomics and global phylogenic analysis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1195-1202. [PMID: 34732312 DOI: 10.1016/j.jmii.2021.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/22/2021] [Accepted: 09/15/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Shewanella algae is a zoonotic marine bacterium that causes a variety of infections in immunocompromised patients or those who have been exposed to seawater. The development of trimethoprim/sulfamethoxazole (TMP/SMX) resistance in S. algae are found in human and environment isolates during the past ten years, and thus the treatment options are decreasing. METHODOLOGY In the study, we conduct a comparative genomic study to identify the resistant mechanism of TMP/SMX-resistance in S. algae. RESULTS We found the resistance of TMP/SMX in S. algae is associated with the existence of sul1 and dfrA12 within the class 1 integron. The gene cassette dfra12-aadA2-qacEΔ1/sul1 within the class 1 integron is highly conserved. In addition, the class 1 integron and encapsulated sul1 are significantly enriched in Enterobacteriaceae in NCBI and UniProt databases. CONCLUSION Our study suggests that the horizontal transfer of TMP/SMX resistance via class 1 integron is most frequently occurred within Enterobacteriaceae and has spread to a wide range of sources including soil, poultry, and marine water.
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Affiliation(s)
- Liu Chia-Wei
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jan-Fang Cheng
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kwong-Chung Tung
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Kai Hong
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Jyun-Hong Lin
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Yu-Hui Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Che-An Tsai
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shih-Ping Lin
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yung-Chun Chen
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Zhi-Yuan Shi
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan.
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan; Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan.
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Genomic Analysis and Molecular Characteristics in Carbapenem-Resistant Klebsiella pneumoniae Strains. Curr Microbiol 2022; 79:391. [DOI: 10.1007/s00284-022-03093-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
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Setiawan A, Widodo ADW, Endraswari PD. Comparison of ciprofloxacin, cotrimoxazole, and doxycycline on Klebsiella pneumoniae: Time-kill curve analysis. Ann Med Surg (Lond) 2022; 84:104841. [DOI: 10.1016/j.amsu.2022.104841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/26/2022] [Accepted: 10/30/2022] [Indexed: 11/08/2022] Open
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Yang BS. Detection of the Carbapenem Resistance Gene in Gram-negative Rod Bacteria Isolated from Clinical Specimens. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2022. [DOI: 10.15324/kjcls.2022.54.3.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Byoung Seon Yang
- Department of Medical Laboratory Science, JinJu Health College, Jinju, Korea
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El-Defrawy I, Aitta AA, Fam N, Khaled M, Madany N, El Damarawy M, Gamal D, Alkholy MA. In Vitro Activity of Single and Combined Antibiotics against Carbapenem Resistant Enterobacteriaceae Clinical Isolates in Relation to their Resistance Genes. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.10347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background: Mortality due to infection with carbapenem-resistant Enterobacteriaceae (CRE) is reported globally and carbapenemase production is the main mechanism of resistance in these isolates. The detection and treatment of carbapenemase-producing Enterobacteriaceae (CPE) is a major challenge in health care facilities.
Objectives: The aim of the current study was to evaluate the in-vitro effect of different single and combined antibiotic agents against CRE clinical isolates.
Methodology: Fifty CRE isolates were detected using disk diffusion test as a screening test. Species identification and antibiotic susceptibility testing was done using Vitek 2 system. Carbapenemase enzyme production was confirmed by Carba NP test. Multiplex PCR was done to detect carbapenem resistance genes. Antibiotics were tested in the form of single agents (colistin and tigecycline) and combined (tigecycline/ colistin, doripenem/ colistin and dual carbapenem therapy (ertapenem and doripenem) against CRE isolates using E-test method.
Results: Most of the CRE isolates were K. pneumoniae, 68%, followed by E. coli, 22%, S. marcescens, 4%, E. cloacae, 4% and C. freundii, 2%. CPE was confirmed in 46 isolates by multiplex PCR; blaNDM-like was the main carbapenem resistance gene in (84%) of the isolates, followed by blaOXA-48-like (6%) and blaKPC-like (2%). Carba NP test detected 90% of CPE isolates. Single use of colistin and tigecycline showed 100% sensitivity against all tested CRE isolates except in blaNDM-like (83%). Combination of colistin/tigecycline showed synergetic activity in 18% of CRE that was correlated to their carbapenemase R genes showing a significant increase in blaOXA-48-like and blaKPC-like positive isolates (100%) compared to blaNDM-like (7%). Other combinations showed indifferent effect whereas antagonism was not detected in any of the tested combinations.
Conclusions: blaNDM-like is the main carbapenemase-producing gene detected among our CPE isolates followed by blaOXA-48-like. Colistin and tigecycline are still effective when used as single agents, and may offer effective treatment options when used in combination for CRE infections. Characterization of carbapenemases is crucial in determining treatment options. There is urgent demand for the development of novel therapeutic agents against NDM-producing CPE isolates.
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Jean SS, Harnod D, Hsueh PR. Global Threat of Carbapenem-Resistant Gram-Negative Bacteria. Front Cell Infect Microbiol 2022; 12:823684. [PMID: 35372099 PMCID: PMC8965008 DOI: 10.3389/fcimb.2022.823684] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 02/15/2022] [Indexed: 01/08/2023] Open
Abstract
Infections caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative bacteria (GNB), including carbapenem-resistant (CR) Enterobacterales (CRE; harboring mainly blaKPC, blaNDM, and blaOXA-48-like genes), CR- or MDR/XDR-Pseudomonas aeruginosa (production of VIM, IMP, or NDM carbapenemases combined with porin alteration), and Acinetobacter baumannii complex (producing mainly OXA-23, OXA-58-like carbapenemases), have gradually worsened and become a major challenge to public health because of limited antibiotic choice and high case-fatality rates. Diverse MDR/XDR-GNB isolates have been predominantly cultured from inpatients and hospital equipment/settings, but CRE has also been identified in community settings and long-term care facilities. Several CRE outbreaks cost hospitals and healthcare institutions huge economic burdens for disinfection and containment of their disseminations. Parenteral polymyxin B/E has been observed to have a poor pharmacokinetic profile for the treatment of CR- and XDR-GNB. It has been determined that tigecycline is suitable for the treatment of bloodstream infections owing to GNB, with a minimum inhibitory concentration of ≤ 0.5 mg/L. Ceftazidime-avibactam is a last-resort antibiotic against GNB of Ambler class A/C/D enzyme-producers and a majority of CR-P. aeruginosa isolates. Furthermore, ceftolozane-tazobactam is shown to exhibit excellent in vitro activity against CR- and XDR-P. aeruginosa isolates. Several pharmaceuticals have devoted to exploring novel antibiotics to combat these troublesome XDR-GNBs. Nevertheless, only few antibiotics are shown to be effective in vitro against CR/XDR-A. baumannii complex isolates. In this era of antibiotic pipelines, strict implementation of antibiotic stewardship is as important as in-time isolation cohorts in limiting the spread of CR/XDR-GNB and alleviating the worsening trends of resistance.
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Affiliation(s)
- Shio-Shin Jean
- Department of Emergency and Critical Care Medicine, Min-Sheng General Hospital, Taoyuan, Taiwan
- Department of Pharmacy, College of Pharmacy and Health care, Tajen University, Pingtung, Taiwan
| | - Dorji Harnod
- Division of Critical Care Medicine, Department of Emergency and Critical Care Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Department of Emergency, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
- Ph.D Program for Aging, School of Medicine, China Medical University, Taichung, Taiwan
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
- *Correspondence: Po-Ren Hsueh,
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Cao Z, Yue C, Kong Q, Liu Y, Li J. Risk Factors for a Hospital-Acquired Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infection: A Five-Year Retrospective Study. Infect Drug Resist 2022; 15:641-654. [PMID: 35241916 PMCID: PMC8887613 DOI: 10.2147/idr.s342103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/03/2021] [Indexed: 12/26/2022] Open
Abstract
Purpose This study aimed to describe trends in Klebsiella pneumoniae (KP) resistance in bloodstream infections (BSI) and to identify risk factors for a hospital-acquired carbapenem-resistant Klebsiella pneumoniae (CRKP) BSI and 28-day mortality from a hospital-acquired KP BSI. Patients and Methods We recorded the results of antimicrobial susceptibility testing of 396 KP-positive blood cultures from January 2016 to December 2020. A total of 277 patients with a KP BSI were included in this study, of which 171 had a hospital-acquired infection and 84 had a hospital-acquired CRKP BSI. Multivariate logistic regression analysis was used to identify risk factors for a hospital-acquired CRKP BSI and 28-day mortality from a hospital-acquired KP BSI. Results The proportion of hospital-acquired infections among KP BSI patients increased from 53.1% in 2016 to 72.8% in 2020. The detection rate of CRKP among KP BSI patients increased from 18.8% in 2016 to 37.7% in 2020. Multivariate logistic regression showed that β-lactam/β-lactamase inhibitor combinations (BLBLIs) exposure (P = 0.022, OR 2.863), carbapenems exposure (P = 0.007, OR 3.831) and solid organ transplantation (P <0.001, OR 19.454) were independent risk factors for a hospital-acquired CRKP BSI. Risk factors for a 28-day mortality from hospital-acquired KP BSI were CRKP BSI (P =0.009, OR 5.562), septic shock (P =0.002, OR 4.862), mechanical ventilation>96 hours (P =0.020, OR 8.765), and platelet counts <100×109/L (P =0.003, OR 4.464). Conclusion The incidence of hospital-acquired KP BSI continues to rise and the proportion of CRKP BSI is also increasing. We believe that the use of the BLBLIs needs to be carefully evaluated in hospital-acquired infection. Hospital-acquired KP BSI Patients with CRKP BSI, septic shock, mechanical ventilation and deficiency of platelets are more likely to have a poor prognosis.
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Affiliation(s)
- Zubai Cao
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
| | - Chengcheng Yue
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
| | - Qinxiang Kong
- Department of Infectious Diseases, The Chaohu Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
| | - Yanyan Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
- Anhui Center for Surveillance of Bacterial Resistance, Anhui Medical University, Hefei, Anhui, People’s Republic of China
- Institute of Bacterial Resistance, Anhui Medical University, Hefei, Anhui, People’s Republic of China
| | - Jiabin Li
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
- Anhui Center for Surveillance of Bacterial Resistance, Anhui Medical University, Hefei, Anhui, People’s Republic of China
- Institute of Bacterial Resistance, Anhui Medical University, Hefei, Anhui, People’s Republic of China
- Correspondence: Jiabin Li Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Jixi road 218, Hefei, Anhui, 230022, People’s Republic of ChinaTel +86-551-62922713Fax +86-551-62922281 Email
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Hassan MA, Abd El-Aziz S, Elbadry HM, El-Aassar SA, Tamer TM. Prevalence, antimicrobial resistance profile, and characterization of multi-drug resistant bacteria from various infected wounds in North Egypt. Saudi J Biol Sci 2022; 29:2978-2988. [PMID: 35531185 PMCID: PMC9073052 DOI: 10.1016/j.sjbs.2022.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 11/30/2022] Open
Abstract
Multi-drug resistant (MDR) bacteria associated with wounds are extremely escalating. This study aims to survey different wounds in Alexandria hospitals, North Egypt, to explore the prevalence and characteristics of MDR bacteria for future utilization in antibacterial wound dressing designs. Among various bacterial isolates, we determined 22 MDR bacteria could resist different classes of antibiotics. The collected samples exhibited the prevalence of mono-bacterial infections (60%), while 40% included poly-bacterial species due to previous antibiotic administration. Moreover, Gram-negative bacteria showed dominance with a ratio of 63.6%, while Gram-positive bacteria reported 36.4%. Subsequently, the five most virulent bacteria were identified following the molecular approach by 16S rRNA and physiological properties using the VITEK 2 automated system. They were deposited in GenBank as Staphylococcus haemolyticus MST1 (KY550377), Pseudomonas aeruginosa MST2 (KY550378), Klebsiella pneumoniae MST3 (KY550379), Escherichia coli MST4 (KY550380), and Escherichia coli MST5 (KY550381). In terms of isolation source, S. haemolyticus MST1 was isolated from a traumatic wound, while P. aeruginosa MST2 and E. coli MST4 were procured from hernia surgical wounds, and K. pneumoniae MST3 and E. coli MST5 were obtained from diabetic foot ulcers. Antibiotic sensitivity tests exposed that K. pneumoniae MST3, E. coli MST4, and E. coli MST5 are extended-spectrum β-lactamases (ESBLs) bacteria. Moreover, S. haemolyticus MST1 belongs to the methicillin-resistant coagulase-negative staphylococcus (MRCoNS), whereas P. aeruginosa MST2 exhibited resistance to common empirical bactericidal antibiotics. Overall, the study provides new insights into the prevalent MDR bacteria in Egypt for further use as specific models in formulating antibacterial wound dressings.
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Affiliation(s)
- Mohamed A. Hassan
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, P.O. Box: 21934, Alexandria, Egypt
- Corresponding authors.
| | - Sarah Abd El-Aziz
- Polymer Materials Research Department, Advanced Technology and New Materials Research Institute (ATNMRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, P.O. Box: 21934, Alexandria, Egypt
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Horeya M. Elbadry
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Samy A. El-Aassar
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Tamer M. Tamer
- Polymer Materials Research Department, Advanced Technology and New Materials Research Institute (ATNMRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, P.O. Box: 21934, Alexandria, Egypt
- Corresponding authors.
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Carbapenemase-producing Enterobacterales infections: Recent advances in diagnosis and treatment. Int J Antimicrob Agents 2022; 59:106528. [DOI: 10.1016/j.ijantimicag.2022.106528] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 11/19/2022]
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Mitra SD, Irshad P, Anusree M, Rekha I, Shailaja S, Suresh J, Aishwarya G, Shrestha S, Shome BR. Whole genome global insight of antibiotic resistance gene repertoire and virulome of high - risk multidrug-resistant Uropathogenic Escherichiacoli. Microb Pathog 2021; 161:105256. [PMID: 34695556 DOI: 10.1016/j.micpath.2021.105256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/06/2021] [Accepted: 10/14/2021] [Indexed: 12/17/2022]
Abstract
Elucidation of genetic determinants via whole genome sequence (WGS) analyses can help understand the high risk multidrug-resistant (MDR) Uropathogenic Escherichia coli (UPEC) associated with urinary tract infections (UTI) and its evasion strategies from treatment. We investigated the WGS of 30 UPEC strains from UTI samples across the world (2016-2019) and found 25 UPEC strains carrying 2-23 antibiotic resistance genes (ARGs) scattered across 1-3 plasmids per strain. Different ARGs (blaTEM, blaCTXM, blaNDM, blaOXA, blaCMY) encoding extended-spectrum beta-lactamases (TEM, CTXM, CMY) and carbapenemases (NDM, OXA) were found in 24/30, ARGs encoding aminoglycoside modifying enzymes (AAC, APH, AAD) variants in 23/30, trimethoprim ARGs (dfrA17, dfrA12, dfrA5, dfrB4 variants) encoding dihydrofolate reductase in 19/30 and sulfonamide ARGs (sul1, sul2, sul3) encoding dihydropteroate synthase and macrolide ARGs (mph1) encoding macrolide 2' phosphotransferase in 15/30 UPEC strains. Collectively the ARGs were distributed in different combinations in 40 plasmids across UPEC strains with 20 plasmids displaying co-occurrence of multiple ARGs conferring resistance to beta lactam, aminoglycoside, sulfonamide, trimethoprim and macrolide antibiotics. These resistance plasmids belonged to seven incompatibility groups (IncF, IncI, IncC, IncH, IncN, IncB and Col), with IncFI and IncFII being the predominant resistance plasmids. Additionally, we observed co-occurrence of specific mutation pattern in quinolone resistance determining region (QRDR) viz., DNA gyrase (gyrA: S83L, D87N), and topoisomerase IV (parC: S80I, E84V; parE: I529L) in 18/30 strains. The strains also harbored diverse virulence genes, such as fimH, gad, iss, iha, ireA, iroN, cnf1 and san. Multilocus sequence typing (MLST) reconfirmed ST131(n = 10) as the predominant global high-risk clonal strain causing UTI. In summary, our findings contribute to better understand the plasmid mediated ARGs and its encoded enzymes that may contribute in antibiotic inactivation/modification or alteration in the antibiotic target site in high risk MDR hypervirulent UPEC strains causing UTI. The study reinforces the need to characterize and design appropriate inhibitors to counterattack different enzymes and devise strategies to curtail resistance plasmid.
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Affiliation(s)
- Susweta Das Mitra
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India.
| | - Pir Irshad
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - M Anusree
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Injeti Rekha
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - S Shailaja
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Janshi Suresh
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - G Aishwarya
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Smeeta Shrestha
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Bibek Ranjan Shome
- ICAR- National Institute of Veterinary Epidemiology & Disease Informatics, Bangalore, India
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High Prevalence of Multidrug-Resistant Klebsiella pneumoniae in a Tertiary Care Hospital in Ethiopia. Antibiotics (Basel) 2021; 10:antibiotics10081007. [PMID: 34439057 PMCID: PMC8388856 DOI: 10.3390/antibiotics10081007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/12/2021] [Accepted: 05/25/2021] [Indexed: 11/24/2022] Open
Abstract
Klebsiella pneumoniae poses an urgent public health threat, causing nosocomial outbreaks in different continents. It has been observed to develop resistance to antimicrobials more easily than most bacteria. These days, multidrug-resistant strains are being increasingly reported from different countries. However, studies on the surveillance of multidrug-resistant Klebsiella pneumoniae are very rare in Ethiopia. This study aimed to determine the antimicrobial resistance patterns and magnitude of MDR K. pneumoniae isolates from patients attending or admitted to Tikur Anbessa Specialized Hospital (TASH). A cross-sectional study was conducted from September 2018 to February 2019 at TASH, Addis Ababa, Ethiopia. Identification of K. pneumoniae was done by examining the Gram stain, colony characteristics on MacConkey agar and 5% sheep blood agar, as well as using a series of biochemical tests. Antimicrobial susceptibility testing of the isolates for 21 antimicrobials was done by the Kirby–Bauer disc diffusion technique. Data were double entered using Epidata 3.1 and exported to SPSS version 25 software for analysis. Among the total K. pneumoniae isolates (n = 132), almost all 130 (98.5%) were MDR. Two (1.5%) isolates showed complete non-susceptibility to all antimicrobial agents tested. Moreover, a high rate of resistance was observed to cefotaxime and ceftriaxone 128 (97%), trimethoprim-sulfamethoxazole 124 (93.9%), and cefepime 111 (84.1%). High susceptibility was recorded to amikacin 123 (93.2%), imipenem 107 (81.1%), meropenem 96 (72.7%), and ertapenem 93 (70.5%). K. pneumoniae isolates showed a high rate of resistance to most of the tested antimicrobials. The magnitude of MDR K. pneumoniae was very alarming. Therefore, strengthening antimicrobial stewardship programs and antimicrobial surveillance practices is strongly recommended in TASH.
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