1
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Kim E, Yang SM, Ham JH, Lee W, Jung DH, Kim HY. Integration of MALDI-TOF MS and machine learning to classify enterococci: A comparative analysis of supervised learning algorithms for species prediction. Food Chem 2025; 462:140931. [PMID: 39217752 DOI: 10.1016/j.foodchem.2024.140931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/26/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
This research focused on distinguishing distinct matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral signatures of three Enterococcus species. We evaluated and compared the predictive performance of four supervised machine learning algorithms, K-nearest neighbor (KNN), support vector machine (SVM), and random forest (RF), to accurately classify Enterococcus species. This study involved a comprehensive dataset of 410 strains, generating 1640 individual spectra through on-plate and off-plate protein extraction methods. Although the commercial database correctly identified 76.9% of the strains, machine learning classifiers demonstrated superior performance (accuracy 0.991). In the RF model, top informative peaks played a significant role in the classification. Whole-genome sequencing showed that the most informative peaks are biomarkers connected to proteins, which are essential for understanding bacterial classification and evolution. The integration of MALDI-TOF MS and machine learning provides a rapid and accurate method for identifying Enterococcus species, improving healthcare and food safety.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jun-Hyeok Ham
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Woojung Lee
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Dae-Hyun Jung
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea.
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2
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Nasir SAR, Zeeshan M, Ghanchi N, Saeed N, Ghayas H, Zaka S, Ashraf J, Jabeen K, Farooqi J, Hasan Z, Fatima T, Rezwan F, Mahmood SF, Arshad M, Khan E, Ozer EA, Hasan R. Linezolid-resistant Enterococcus faecium clinical isolates from Pakistan: a genomic analysis. BMC Microbiol 2024; 24:347. [PMID: 39277715 PMCID: PMC11401331 DOI: 10.1186/s12866-024-03491-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024] Open
Abstract
BACKGROUND Linezolid-resistant Enterococcus faecium (LRE) is a global priority pathogen. Thirteen LRE were reported from clinical specimens between November 2021 and April 2023 at two laboratories in Karachi, Pakistan. We aimed to investigate the strain types and genes associated with linezolid resistance among these isolates. Whole genome sequencing (WGS) was performed and analyzed by multilocus sequence typing (MLST). The presence of linezolid resistance genes was identified using ResFinder v4.1.11 and the LRE-finder tool. RESULTS Twelve isolates belonged to clonal complex 17 (CC17); ST80 (n = 10), ST612 (n = 1) and ST1380 (n = 1). Six isolates showed the presence of optrA gene and G2576T mutations in the 23S rRNA gene, while six showed poxtA and cfr(D) genes. One isolate showed the combination of optrA, cfr(D) and poxtA genes. CONCLUSION Our findings show the circulation of CC17 sequence types with a known outbreak potential and we identified molecular mechanisms of resistance that were not previously reported from Pakistan.
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Affiliation(s)
| | | | - Najia Ghanchi
- Aga Khan University Hospital, Karachi, Sindh, Pakistan
- National Institute of Cardiovascular Diseases, Karachi, Sindh, Pakistan
| | - Noureen Saeed
- Aga Khan University Hospital, Karachi, Sindh, Pakistan
| | - Hassan Ghayas
- Aga Khan University Hospital, Karachi, Sindh, Pakistan
| | - Sadaf Zaka
- Aga Khan University Hospital, Karachi, Sindh, Pakistan
| | | | - Kauser Jabeen
- Aga Khan University Hospital, Karachi, Sindh, Pakistan
| | | | - Zahra Hasan
- Aga Khan University Hospital, Karachi, Sindh, Pakistan
| | - Tazeen Fatima
- National Institute of Cardiovascular Diseases, Karachi, Sindh, Pakistan
| | - Faiza Rezwan
- National Institute of Cardiovascular Diseases, Karachi, Sindh, Pakistan
| | | | | | - Erum Khan
- Aga Khan University Hospital, Karachi, Sindh, Pakistan
| | - Egon A Ozer
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rumina Hasan
- Aga Khan University Hospital, Karachi, Sindh, Pakistan.
- Microbiology lab, Sopariwala building, Aga Khan University Hospital, Karachi, Pakistan.
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3
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Soro O, Kigen C, Nyerere A, Gachoya M, Wachira J, Onyonyi V, Georges M, Wataka A, Ondolo S, Cherono K, Odoyo E, Musila L. Complete genome sequences of four lytic bacteriophages against multidrug-resistant Enterococcus faecium. Microbiol Resour Announc 2024:e0068824. [PMID: 39248541 DOI: 10.1128/mra.00688-24] [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: 06/22/2024] [Accepted: 08/05/2024] [Indexed: 09/10/2024] Open
Abstract
We report the genome sequences of four Enterococcus faecium phages isolated from environmental wastewater in Kenya. They are double-stranded DNA phages with genomes varying in length from 42,231 to 43,348 bp, with G+C contents ranging from 34.96% to 35.2%. The genomes contain 78-82 coding sequences.
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Affiliation(s)
- Oumarou Soro
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology, and Innovation, Nairobi, Kenya
| | - Collins Kigen
- Department of Emerging Infectious Diseases, Walter Reed Army Institute of Research-Africa/Kenya Medical Research Institute, Nairobi, Kenya
| | - Andrew Nyerere
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Moses Gachoya
- Department of Emerging Infectious Diseases, Walter Reed Army Institute of Research-Africa/Kenya Medical Research Institute, Nairobi, Kenya
| | - James Wachira
- Department of Emerging Infectious Diseases, Walter Reed Army Institute of Research-Africa/Kenya Medical Research Institute, Nairobi, Kenya
| | - Vanessa Onyonyi
- Department of Emerging Infectious Diseases, Walter Reed Army Institute of Research-Africa/Kenya Medical Research Institute, Nairobi, Kenya
| | - Martin Georges
- Department of Emerging Infectious Diseases, Walter Reed Army Institute of Research-Africa/Kenya Medical Research Institute, Nairobi, Kenya
| | - Allan Wataka
- Department of Emerging Infectious Diseases, Walter Reed Army Institute of Research-Africa/Kenya Medical Research Institute, Nairobi, Kenya
| | - Stephen Ondolo
- Department of Emerging Infectious Diseases, Walter Reed Army Institute of Research-Africa/Kenya Medical Research Institute, Nairobi, Kenya
| | - Karen Cherono
- Department of Emerging Infectious Diseases, Walter Reed Army Institute of Research-Africa/Kenya Medical Research Institute, Nairobi, Kenya
| | - Erick Odoyo
- Department of Emerging Infectious Diseases, Walter Reed Army Institute of Research-Africa/Kenya Medical Research Institute, Nairobi, Kenya
| | - Lillian Musila
- Department of Emerging Infectious Diseases, Walter Reed Army Institute of Research-Africa/Kenya Medical Research Institute, Nairobi, Kenya
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4
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Raddaoui A, Chebbi Y, Frigui S, Latorre J, Ammeri RW, Abdejlil NB, Torres C, Abbassi MS, Achour W. Genetic characterization of vancomycin-resistant Enterococcus faecium isolates from neutropenic patients in Tunisia: spread of the pandemic CC17 clone associated with high genetic diversity in Tn1546-like structures. J Appl Microbiol 2024; 135:lxae225. [PMID: 39210508 DOI: 10.1093/jambio/lxae225] [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: 07/20/2024] [Revised: 08/18/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
AIMS In Tunisia, limited research has focused on characterizing clinical vancomycin-resistant Enterococcus faecium (VREfm). This study aimed to bridge this knowledge gap by molecular characterization of antimicrobial resistance, determining the genetic elements mediating vancomycin-resistance, and whole-genome sequencing of one representative VREfm isolate. METHODS AND RESULTS Over 6 years (2011-2016), a total of eighty VREfm isolates responsible for infection or colonization were identified from hospitalized patients, with the incidence rate increasing from 2% in 2011 to 27% in 2016. All of these strains harbored the vanA gene. The screening for antimicrobial resistance genes revealed the predominance of ermB, tetM, and aac(6')-Ie-aph(2'')-Ia genes and 81.2% of strains harbored the Tn1545. Pulsed-field gel electrophoresis identified seven clusters, with two major clusters (belonging to ST117 and ST80) persisting throughout the study period. Seven Tn1546 types were detected, with type VI (truncated transposon) being the most prevalent (57.5%). Whole-genome sequencing revealed a 3 028 373 bp chromosome and five plasmids. Mobile genetic elements and a type I CRISPR-cas locus were identified. Notably, the vanA gene was carried by the classic Tn1546 transposon with ISL3 insertion on a rep17pRUM plasmid. CONCLUSION A concerning trend in the prevalence of VREfm essentially attributed to CC17 persistence and to horizontal transfer of multiple genetic variants of truncated vanA-Tn1546.
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Affiliation(s)
- Anis Raddaoui
- Laboratory Ward, National Bone Marrow Transplant Center, Tunis 1006, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, Tunis 1006, Tunisia
| | - Yosra Chebbi
- Laboratory Ward, National Bone Marrow Transplant Center, Tunis 1006, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, Tunis 1006, Tunisia
| | - Siwar Frigui
- Laboratory Ward, National Bone Marrow Transplant Center, Tunis 1006, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, Tunis 1006, Tunisia
| | - Javier Latorre
- Area de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño 26006, Spain
| | - Rim Werhani Ammeri
- Laboratory Ward, National Bone Marrow Transplant Center, Tunis 1006, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, Tunis 1006, Tunisia
| | - Nour Ben Abdejlil
- Department of hematology and transplantationtion, National Bone Marrow Transplant Center, Tunis 1006, Tunisia
| | - Carmen Torres
- Area de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño 26006, Spain
| | - Mohamed Salah Abbassi
- Faculty of Medicine of Tunis, Laboratory of Antibiotic Resistance LR99ES09, University of Tunis El Manar, Tunis 1006, Tunisia
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis1006, Tunisia
| | - Wafa Achour
- Laboratory Ward, National Bone Marrow Transplant Center, Tunis 1006, Tunisia
- Faculty of Medicine of Tunis, LR18ES39, University of Tunis El Manar, Tunis 1006, Tunisia
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5
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Gao W, Li H, Yang J, Zhang J, Fu R, Peng J, Hu Y, Liu Y, Wang Y, Li S, Zhang S. Machine Learning Assisted MALDI Mass Spectrometry for Rapid Antimicrobial Resistance Prediction in Clinicals. Anal Chem 2024; 96:13398-13409. [PMID: 39096240 DOI: 10.1021/acs.analchem.4c00741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
Antimicrobial susceptibility testing (AST) plays a critical role in assessing the resistance of individual microbial isolates and determining appropriate antimicrobial therapeutics in a timely manner. However, conventional AST normally takes up to 72 h for obtaining the results. In healthcare facilities, the global distribution of vancomycin-resistant Enterococcus fecium (VRE) infections underscores the importance of rapidly determining VRE isolates. Here, we developed an integrated antimicrobial resistance (AMR) screening strategy by combining matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) with machine learning to rapidly predict VRE from clinical samples. Over 400 VRE and vancomycin-susceptible E. faecium (VSE) isolates were analyzed using MALDI-MS at different culture times, and a comprehensive dataset comprising 2388 mass spectra was generated. Algorithms including the support vector machine (SVM), SVM with L1-norm, logistic regression, and multilayer perceptron (MLP) were utilized to train the classification model. Validation on a panel of clinical samples (external patients) resulted in a prediction accuracy of 78.07%, 80.26%, 78.95%, and 80.54% for each algorithm, respectively, all with an AUROC above 0.80. Furthermore, a total of 33 mass regions were recognized as influential features and elucidated, contributing to the differences between VRE and VSE through the Shapley value and accuracy, while tandem mass spectrometry was employed to identify the specific peaks among them. Certain ribosomal proteins, such as A0A133N352 and R2Q455, were tentatively identified. Overall, the integration of machine learning with MALDI-MS has enabled the rapid determination of bacterial antibiotic resistance, greatly expediting the usage of appropriate antibiotics.
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Affiliation(s)
- Weibo Gao
- Beijing Advanced Innovation Center for Intelligent Robots and Systems, School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Hang Li
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Jingxian Yang
- Department of Clinical Laboratory, Aerospace Center Hospital, Beijing 100039, China
| | - Jinming Zhang
- School of Computer Science & Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Rongxin Fu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, Toronto ON M5S 3H6, Canada
| | - Yechen Hu
- Department of Chemistry, University of Toronto, Toronto ON M5S 3H6, Canada
| | - Yitong Liu
- Department of Chemistry, University of Toronto, Toronto ON M5S 3H6, Canada
| | - Yingshi Wang
- Department of Clinical Laboratory, Aerospace Center Hospital, Beijing 100039, China
| | - Shuang Li
- School of Computer Science & Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Shuailong Zhang
- Beijing Advanced Innovation Center for Intelligent Robots and Systems, School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
- School of Integrated Circuits and Electronics, Beijing Institute of Technology, Beijing, 100081, China
- Zhengzhou Research Institute, Beijing Institute of Technology, Zhengzhou 100081, China
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6
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Kramarska E, Toumi E, Squeglia F, Laverde D, Napolitano V, Frapy E, Autiero I, Sadones O, Huebner J, Skurnik D, Romero-Saavedra F, Berisio R. A rationally designed antigen elicits protective antibodies against multiple nosocomial Gram-positive pathogens. NPJ Vaccines 2024; 9:151. [PMID: 39155280 PMCID: PMC11330964 DOI: 10.1038/s41541-024-00940-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
ESKAPE pathogens are responsible for complicated nosocomial infections worldwide and are often resistant to commonly used antibiotics in clinical settings. Among ESKAPE, vancomycin-resistant Enterococcus faecium (VREfm) and methicillin-resistant Staphylococcus aureus (MRSA) are two important Gram-positive pathogens for which non-antibiotic alternatives are urgently needed. We previously showed that the lipoprotein AdcA of E. faecium elicits opsonic and protective antibodies against E. faecium and E. faecalis. Prompted by our observation, reported here, that AdcA also elicits opsonic antibodies against MRSA and other clinically relevant Gram-positive pathogens, we identified the dominant epitope responsible for AdcA cross-reactive activity and designed a hyper-thermostable and multi-presenting antigen, Sc(EH)3. We demonstrate that antibodies raised against Sc(EH)3 mediate opsonic killing of a wide-spectrum of Gram-positive pathogens, including VREfm and MRSA, and confer protection both in passive and active immunisation models. Our data indicate that Sc(EH)3 is a promising antigen for the development of vaccines against different Gram-positive pathogens.
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Affiliation(s)
- Eliza Kramarska
- Institute of Biostructures and Bioimaging, Italian Research Council (CNR), Naples, Italy
| | - Eya Toumi
- CNRS, INSERM, Institut Necker-Enfants Malades, U1151-Equipe 11, Faculté de Médecine, University of Paris City, Paris, France
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, Italian Research Council (CNR), Naples, Italy
| | - Diana Laverde
- Division of Paediatric Infectious Disease, Hauner Children's Hospital LMU, LMU, Munich, Germany
| | - Valeria Napolitano
- Institute of Biostructures and Bioimaging, Italian Research Council (CNR), Naples, Italy
| | - Eric Frapy
- CNRS, INSERM, Institut Necker-Enfants Malades, U1151-Equipe 11, Faculté de Médecine, University of Paris City, Paris, France
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, Italian Research Council (CNR), Naples, Italy
| | - Oceane Sadones
- Division of Paediatric Infectious Disease, Hauner Children's Hospital LMU, LMU, Munich, Germany
| | - Johannes Huebner
- Division of Paediatric Infectious Disease, Hauner Children's Hospital LMU, LMU, Munich, Germany
| | - David Skurnik
- CNRS, INSERM, Institut Necker-Enfants Malades, U1151-Equipe 11, Faculté de Médecine, University of Paris City, Paris, France.
- Department of Clinical Microbiology, Fédération Hospitalo-Universitaire Prématurité (FHU PREMA), Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, University of Paris City, Paris, France.
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Felipe Romero-Saavedra
- Division of Paediatric Infectious Disease, Hauner Children's Hospital LMU, LMU, Munich, Germany.
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, Italian Research Council (CNR), Naples, Italy.
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7
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Yu H, Xu Y, Imani S, Zhao Z, Ullah S, Wang Q. Navigating ESKAPE Pathogens: Considerations and Caveats for Animal Infection Models Development. ACS Infect Dis 2024; 10:2336-2355. [PMID: 38866389 PMCID: PMC11249778 DOI: 10.1021/acsinfecdis.4c00007] [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: 01/04/2024] [Revised: 05/19/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024]
Abstract
The misuse of antibiotics has led to the global spread of drug-resistant bacteria, especially multi-drug-resistant (MDR) ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). These opportunistic bacteria pose a significant threat, in particular within hospitals, where they cause nosocomial infections, leading to substantial morbidity and mortality. To comprehensively explore ESKAPE pathogenesis, virulence, host immune response, diagnostics, and therapeutics, researchers increasingly rely on necessitate suitable animal infection models. However, no single model can fully replicate all aspects of infectious diseases. Notably when studying opportunistic pathogens in immunocompetent hosts, rapid clearance by the host immune system can limit the expression of characteristic disease symptoms. In this study, we examine the critical role of animal infection models in understanding ESKAPE pathogens, addressing limitations and research gaps. We discuss applications and highlight key considerations for effective models. Thoughtful decisions on disease replication, parameter monitoring, and data collection are crucial for model reliability. By meticulously replicating human diseases and addressing limitations, researchers maximize the potential of animal infection models. This aids in targeted therapeutic development, bridges knowledge gaps, and helps combat MDR ESKAPE pathogens, safeguarding public health.
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Affiliation(s)
- Haojie Yu
- Key
Laboratory of Artificial Organs and Computational Medicine in Zhejiang
Province, Key Laboratory of Pollution Exposure and Health Intervention
of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang China
- Stomatology
Hospital, School of Stomatology, Zhejiang University School of Medicine,
Zhejiang Provincial Clinical Research Center for Oral Diseases, Key
Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, China
| | - Yongchang Xu
- Key
Laboratory of Aging and Cancer Biology of Zhejiang Province, School
of Basic Medical Sciences, Hangzhou Normal
University, Hangzhou 311121, China
| | - Saber Imani
- Shulan
International Medical College, Zhejiang
Shuren University, Hangzhou 310015, Zhejiang China
| | - Zhuo Zhao
- Department
of Computer Science and Engineering, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Saif Ullah
- Department
of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
| | - Qingjing Wang
- Key
Laboratory of Artificial Organs and Computational Medicine in Zhejiang
Province, Key Laboratory of Pollution Exposure and Health Intervention
of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, Zhejiang China
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8
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Bonanno Ferraro G, Bonomo C, Brandtner D, Mancini P, Veneri C, Briancesco R, Coccia AM, Lucentini L, Suffredini E, Bongiorno D, Musso N, Stefani S, La Rosa G. Characterisation of microbial communities and quantification of antibiotic resistance genes in Italian wastewater treatment plants using 16S rRNA sequencing and digital PCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173217. [PMID: 38750766 DOI: 10.1016/j.scitotenv.2024.173217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/19/2024]
Abstract
The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in humans, animals and environment is a growing threat to public health. Wastewater treatment plants (WWTPs) are crucial in mitigating the risk of environmental contamination by effectively removing contaminants before discharge. However, the persistence of ARB and ARGs even after treatment is a challenge for the management of water system. To comprehensively assess antimicrobial resistance dynamics, we conducted a one-year monitoring study in three WWTPs in central Italy, both influents and effluents. We used seasonal sampling to analyze microbial communities by 16S rRNA, as well as to determine the prevalence and behaviour of major ARGs (sul1, tetA, blaTEM, blaOXA-48, blaCTX-M-1 group, blaKPC) and the class 1 Integron (int1). Predominant genera included in order: Arcobacter, Acinetobacter, Flavobacterium, Pseudarcobacter, Bacteroides, Aeromonas, Trichococcus, Cloacibacterium, Pseudomonas and Streptococcus. A higher diversity of bacterial communities was observed in the effluents compared to the influents. Within these communities, we also identified bacteria that may be associated with antibiotic resistance and pose a significant threat to human health. The mean concentrations (in gene copies per liter, gc/L) of ARGs and int1 in untreated wastewater (absolute abundance) were as follows: sul1 (4.1 × 109), tetA (5.2 × 108), blaTEM (1.1 × 108), blaOXA-48 (2.1 × 107), blaCTX-M-1 group (1.1 × 107), blaKPC (9.4 × 105), and int1 (5.5 × 109). The mean values in treated effluents showed reductions ranging from one to three log. However, after normalizing to the 16S rRNA gene (relative abundance), it was observed that in 37.5 % (42/112) of measurements, the relative abundance of ARGs increased in effluents compared to influents. Furthermore, correlations were identified between ARGs and bacterial genera including priority pathogens. This study improves our understanding of the dynamics of ARGs and provides insights to develop more effective strategies to reduce their spread, protecting public health and preserving the future efficacy of antibiotics.
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Affiliation(s)
- Giusy Bonanno Ferraro
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy; Department of Biomedical and Biotechnological Science, University of Catania, Italy
| | - Carmelo Bonomo
- Department of Biomedical and Biotechnological Science, University of Catania, Italy
| | - David Brandtner
- Departments of Infectious Disease, Istituto Superiore di Sanità, Rome, Italy
| | - Pamela Mancini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - Carolina Veneri
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - Rossella Briancesco
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - Anna Maria Coccia
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - Luca Lucentini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Dafne Bongiorno
- Department of Biomedical and Biotechnological Science, University of Catania, Italy
| | - Nicolò Musso
- Department of Biomedical and Biotechnological Science, University of Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Science, University of Catania, Italy
| | - Giuseppina La Rosa
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy.
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9
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Pan P, Sun L, Shi X, Huang X, Yin Y, Pan B, Hu L, Shen Q. Analysis of molecular epidemiological characteristics and antimicrobial susceptibility of vancomycin-resistant and linezolid-resistant Enterococcus in China. BMC Med Genomics 2024; 17:174. [PMID: 38951840 PMCID: PMC11218351 DOI: 10.1186/s12920-024-01948-x] [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: 03/07/2024] [Accepted: 06/21/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND This study investigates the distribution and characteristics of linezolid and vancomycin susceptibilities among Enterococcus faecalis (E. faecalis) and Enterococcus faecium (E. faecium) and explores the underlying resistance mechanisms. METHODS A total of 2842 Enterococcus clinical isolates from patients were retrospectively collected, and their clinical data were further analyzed. The minimum inhibitory concentrations (MICs) of vancomycin and linezolid were validated by broth dilution method. The resistance genes optrA, cfr, vanA, vanB and vanM were investigated using polymerase chain reaction (PCR). Housekeeping genes and resistance genes were obtianed through whole-genome sequencing (WGS). RESULTS Of the 2842 Enterococcus isolates, 88.5% (2516) originated from urine, with E. faecium accounted for 60.1% of these. The vanA gene was identified in 27/28 vancomycin resistant Enterococcus (VRE) isolates, 4 of which carried both vanA and vanM genes. The remaining strain was vanM positive. The optrA gene was identified in all E. faecalis isolates among linezolid resistant Enterococcus (LRE). E. faecium showed a higher multiple antibiotic resistance index (MAR index) compared to E. faecalis. The multi-locus sequence typing (MLST) showed the sequence type of E. faecium mainly belongs to clonal complex (CC) 17, nearly E. faecalis isolates analyzed were differentiated into 7 characteristics of sequence types (STs), among which ST16 of CC16 were the major lineage. CONCLUSION Urine was the primary source of VRE and LRE isolates in this study. E. faecium showed higher levels of resistance compared to E. faecalis. OptrA gene was detected in 91.6% of LRE, which could explain linezolid resistance, and van genes were detected in all vancomycin resistant Enterococcus strains, while vanA was a key resistance mechanism in VRE identified in this study.
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Affiliation(s)
- Ping Pan
- Department of Clinical Laboratory, Hangzhou Women's Hospital (Hangzhou Matenal and Child Health Care Hospital), Hangzhou, Zhejiang, 310000, China
| | - Long Sun
- Department of Clinical Laboratory, Hangzhou Women's Hospital (Hangzhou Matenal and Child Health Care Hospital), Hangzhou, Zhejiang, 310000, China
| | - Xinyan Shi
- Department of Clinical Laboratory, Hangzhou Women's Hospital (Hangzhou Matenal and Child Health Care Hospital), Hangzhou, Zhejiang, 310000, China
| | - Xian Huang
- Respiratory department, Zhejiang Provincial General Hospital of Chinese People's Armed Police CN, Hangzhou, Zhejiang, 310051, China
| | - Yiping Yin
- Department of Hospital-acquired infection control, Zhejiang Provincial General Hospital of Chinese People's Armed Police CN, Hangzhou, Zhejiang, 310051, China
| | - Beilei Pan
- Department of Clinical Laboratory, Hangzhou Women's Hospital (Hangzhou Matenal and Child Health Care Hospital), Hangzhou, Zhejiang, 310000, China
| | - Lihua Hu
- Department of Critical Care Medicine, Zhejiang Provincial General Hospital of Chinese People's Armed Police CN, Hangzhou, Zhejiang, 310051, China.
| | - Qiang Shen
- Hangzhou xixi Hospital, Hangzhou, Zhejiang, 310023, China.
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10
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Khazani Asforooshani M, Elikaei A, Abed S, Shafiei M, Barzi SM, Solgi H, Badmasti F, Sohrabi A. A novel Enterococcus faecium phage EF-M80: unveiling the effects of hydrogel-encapsulated phage on wound infection healing. Front Microbiol 2024; 15:1416971. [PMID: 39006751 PMCID: PMC11239553 DOI: 10.3389/fmicb.2024.1416971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 06/13/2024] [Indexed: 07/16/2024] Open
Abstract
Background Enterococcus faecium is one of the members of ESKAPE pathogens. Due to its resistance to antimicrobial agents, treating this bacterium has become challenging. The development of innovative approaches to combat antibiotic resistance is necessary. Phage therapy has emerged as a promising method for curing antibiotic-resistant bacteria. Methods In this study, E. faecium phages were isolated from wastewater. Phage properties were characterized through in vitro assays (e.g. morphological studies, and physicochemical properties). In addition, whole genome sequencing was performed. A hydrogel-based encapsulated phage was obtained and its structure characteristics were evaluated. Wound healing activity of the hydrogel-based phage was assessed in a wound mice model. Results The purified phage showed remarkable properties including broad host range, tolerance to high temperature and pH and biofilm degradation feature as a stable and reliable therapeutic agent. Whole genome sequencing revealed that the genome of the EF-M80 phage had a length of 40,434 bp and harbored 65 open reading frames (ORFs) with a GC content of 34.9% (GenBank accession number is OR767211). Hydrogel-based encapsulated phage represented an optimized structure. Phage-loaded hydrogel-treated mice showed that the counting of neutrophils, fibroblasts, blood vessels, hair follicles and percentage of collagen growth were in favor of the wound healing process in the mice model. Conclusion These findings collectively suggest the promising capability of this phage-based therapeutic strategy for the treatment of infections associated with the antibiotic-resistant E. faecium. In the near future, we hope to expect the presence of bacteriophages in the list of antibacterial compounds used in the clinical settings.
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Affiliation(s)
- Mahshid Khazani Asforooshani
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Sahar Abed
- Department of Microbial Biotechnology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Morvarid Shafiei
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Hamid Solgi
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Aria Sohrabi
- Department of Epidemiology and Biostatistics, Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
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11
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Kopera K, Gromowski T, Wydmański W, Skonieczna-Żydecka K, Muszyńska A, Zielińska K, Wierzbicka-Woś A, Kaczmarczyk M, Kadaj-Lipka R, Cembrowska-Lech D, Januszkiewicz K, Kotfis K, Witkiewicz W, Nalewajska M, Feret W, Marlicz W, Łoniewski I, Łabaj PP, Rydzewska G, Kosciolek T. Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing. Front Microbiol 2024; 15:1342749. [PMID: 38962119 PMCID: PMC11219902 DOI: 10.3389/fmicb.2024.1342749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/20/2024] [Indexed: 07/05/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has led to a wide range of clinical presentations, with respiratory symptoms being common. However, emerging evidence suggests that the gastrointestinal (GI) tract is also affected, with angiotensin-converting enzyme 2, a key receptor for SARS-CoV-2, abundantly expressed in the ileum and colon. The virus has been detected in GI tissues and fecal samples, even in cases with negative results of the reverse transcription polymerase chain reaction in the respiratory tract. GI symptoms have been associated with an increased risk of ICU admission and mortality. The gut microbiome, a complex ecosystem of around 40 trillion bacteria, plays a crucial role in immunological and metabolic pathways. Dysbiosis of the gut microbiota, characterized by a loss of beneficial microbes and decreased microbial diversity, has been observed in COVID-19 patients, potentially contributing to disease severity. We conducted a comprehensive gut microbiome study in 204 hospitalized COVID-19 patients using both shallow and deep shotgun sequencing methods. We aimed to track microbiota composition changes induced by hospitalization, link these alterations to clinical procedures (antibiotics administration) and outcomes (ICU referral, survival), and assess the predictive potential of the gut microbiome for COVID-19 prognosis. Shallow shotgun sequencing was evaluated as a cost-effective diagnostic alternative for clinical settings. Our study demonstrated the diverse effects of various combinations of clinical parameters, microbiome profiles, and patient metadata on the precision of outcome prognostication in patients. It indicates that microbiological data possesses greater reliability in forecasting patient outcomes when contrasted with clinical data or metadata. Furthermore, we established that shallow shotgun sequencing presents a viable and cost-effective diagnostic alternative to deep sequencing within clinical environments.
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Affiliation(s)
- Katarzyna Kopera
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Tomasz Gromowski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Witold Wydmański
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Faculty of Mathematics and Computer Science, Jagiellonian University, Kraków, Poland
| | | | - Agata Muszyńska
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Kinga Zielińska
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | | | - Mariusz Kaczmarczyk
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | - Roland Kadaj-Lipka
- Department of Internal Medicine and Gastroenterology, Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Danuta Cembrowska-Lech
- Department of Biochemical Science, Pomeranian Medical University, Szczecin, Poland
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
| | | | - Katarzyna Kotfis
- Department of Anesthesiology, Intensive Care and Pain Management, Pomeranian Medical University, Szczecin, Poland
| | | | | | - Wiktoria Feret
- Clinical Department of Nephrology, Transplantology and Internal Medicine, Pomeranian Medical University, Szczecin, Poland
| | - Wojciech Marlicz
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - Igor Łoniewski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Biochemical Science, Pomeranian Medical University, Szczecin, Poland
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
| | - Paweł P. Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Grażyna Rydzewska
- Department of Internal Medicine and Gastroenterology, Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Tomasz Kosciolek
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
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12
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Wei Y, Palacios Araya D, Palmer KL. Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01058-6. [PMID: 38890478 DOI: 10.1038/s41579-024-01058-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.
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Affiliation(s)
- Yahan Wei
- School of Podiatric Medicine, The University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - Dennise Palacios Araya
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA.
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13
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Abdel-Raheem SM, Khodier SM, Almathen F, Hanafy AST, Abbas SM, Al-Shami SA, Al-Sultan SI, Alfifi A, El-Tarabili RM. Dissemination, virulence characteristic, antibiotic resistance determinants of emerging linezolid and vancomycin-resistant Enterococcus spp. in fish and crustacean. Int J Food Microbiol 2024; 418:110711. [PMID: 38677237 DOI: 10.1016/j.ijfoodmicro.2024.110711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Enterococci are emerging nosocomial pathogens. Their widespread distribution causes them to be food contaminants. Furthermore, Enterococci can colonize various ecological niches and diffuse into the food chain via contaminated animals and foods because of their remarkable tolerance to unfavorable environmental circumstances. Due to their potential dissemination to humans, antimicrobial-resistant Enterococci in fish are a worldwide health issue. This study characterized AMR, ARGs, VAGs, gelatinase activity, and biofilm formation in Enterococcus spp. recovered from fish and seafood and evaluated potential correlations. 54 Enterococcus spp. strains(32.73 %)were isolated from 165 samples (75 Oreochromis niloticus, 30 Argyrosomus regius, and 60 Shrimp), comprising 30 Enterococcus faecalis (55.6 %) and 24 Enterococcus faecium (44.4 %) with total 32.73 % (54/165), The maximum prevalence rate of Enterococcus spp. was observed in Nile tilapia (34/54; 63 %), followed by shrimp (14/54; 25.9 %) and Argyrosomus regius (6/54; 11.1 %). The maximum prevalence rate of E. faecalis was observed in Nile tilapia (22/30; 73.3 %), followed by shrimp (8/30; 26.7 %) with significant differences. The prevalence rate of E. faecium was observed in Nile tilapia (12/24; 50 %), followed by shrimp (6/24,25 %). E. faecium is only isolated from Argyrosomus regius (6/24,25 %). Isolates exhibited high resistance against both tetracycline (90.7 %) and erythromycin(88.9 %), followed by gentamycin (77.8 %), ciprofloxacin (74.1 %), levofloxacin (72.2 %), penicillin (44.4 %), vancomycin (37 %), and linezolid (20.4 %). 50 strains (92.6 %) exhibited resistance to more than two antibiotics, 5 strains (10 %) were XDR, and the remaining 45 strains (90 %) were classified as MDR. 92.6 % of the isolates had MARindices >0.2, indicating they originated in settings with a high risk of contamination. Additionally, ten ARGs were identified, with tet(M) 92.6 %, followed by erm(B) (88.9 %), aac(6')-Ie-aph(2″)-Ia(77.8 %), tet(K) (75.9 %), gyrA (74.1 %), blaZ (48.1 %), vanA (37 %), vanB (31.5 %), optrA (20.4 %), and catA(3.7 %). Biofilm formation and gelatinase activity were observed in 85.2 %, and 61.1 % of the isolates, respectively. A total of 11 VAGs were detected, with gelE as the most prevalent (83.3 %) followed by agg(79.6 %), pil (74.1 %), both sprE and asa1 (72.2 %), hyl (70.4 %), eps(68.5 %), EF3314 (57.4 %), ace (50 %), and cylA (35.2 %) with no detection of cylB. In conclusion, the emergence of linezolid-resistant -vancomycin-resistant enterococci recovered from Egyptian fish and shrimp, suggests that fish and seafood might participate a fundamental part in the emergence of antimicrobial resistance among humans.
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Affiliation(s)
- Sherief M Abdel-Raheem
- Department of Public Health, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia; Department of Animal Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Assiut University, 71526 Assiut, Egypt.
| | - Sherin M Khodier
- Central lab for marine fish diagnosing and treatment and measuring fish and water quality, Marine Aquaculture Development (MADEӀӀ), Egypt
| | - Faisal Almathen
- Department of Public Health, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia; Camel Research Center, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia.
| | - Al-Shaimaa T Hanafy
- Department of Bacteriology, Animal Health Research Institute, Portsaid laboratory Branch, Egypt
| | - Sarah M Abbas
- Department of Bacteriology, Animal Health Research Institute, Portsaid laboratory Branch, Egypt
| | - Salah Abdulaziz Al-Shami
- Department of Public Health, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia.
| | - Saad Ibrahim Al-Sultan
- Department of Public Health, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia.
| | - Ahmed Alfifi
- Department of Public Health, College of Veterinary Medicine, King Faisal University, P.O. Box 400, Al-Hofuf 31982, Al-Ahsa, Saudi Arabia.
| | - Reham M El-Tarabili
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt.
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14
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Roque-Borda CA, Primo LMDG, Franzyk H, Hansen PR, Pavan FR. Recent advances in the development of antimicrobial peptides against ESKAPE pathogens. Heliyon 2024; 10:e31958. [PMID: 38868046 PMCID: PMC11167364 DOI: 10.1016/j.heliyon.2024.e31958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Multi-drug resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are a global health threat. The severity of the problem lies in its impact on mortality, therapeutic limitations, the threat to public health, and the costs associated with managing infections caused by these resistant strains. Effectively addressing this challenge requires innovative approaches to research, the development of new antimicrobials, and more responsible antibiotic use practices globally. Antimicrobial peptides (AMPs) are a part of the innate immune system of all higher organisms. They are short, cationic and amphipathic molecules with broad-spectrum activity. AMPs interact with the negatively charged bacterial membrane. In recent years, AMPs have attracted considerable interest as potential antibiotics. However, AMPs have low bioavailability and short half-lives, which may be circumvented by chemical modification. This review presents recent in vitro and in silico strategies for the modification of AMPs to improve their stability and application in preclinical experiments.
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Affiliation(s)
- Cesar Augusto Roque-Borda
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, Brazil
- Universidad Católica de Santa María, Vicerrectorado de Investigación, Arequipa, Peru
| | | | - Henrik Franzyk
- University of Copenhagen, Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, Denmark
| | - Paul Robert Hansen
- University of Copenhagen, Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, Denmark
| | - Fernando Rogério Pavan
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, Brazil
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15
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Branda F. The impact of artificial intelligence in the fight against antimicrobial resistance. Infect Dis (Lond) 2024; 56:484-486. [PMID: 38515266 DOI: 10.1080/23744235.2024.2331255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Affiliation(s)
- Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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16
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Denissen J, Havenga B, Reyneke B, Khan S, Khan W. Comparing antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa from environmental and clinical settings. Heliyon 2024; 10:e30215. [PMID: 38720709 PMCID: PMC11076977 DOI: 10.1016/j.heliyon.2024.e30215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa, isolated from water sources collected in informal settlements, were compared to clinical counterparts. Cluster analysis using repetitive extragenic palindromic sequence-based polymerase chain reaction (REP-PCR) indicated that, for each respective species, low genetic relatedness was observed between most of the clinical and environmental isolates, with only one clinical P. aeruginosa (PAO1) and one clinical K. pneumoniae (P2) exhibiting high genetic similarity to the environmental strains. Based on the antibiograms, the clinical E. faecium Ef CD1 was extensively drug resistant (XDR); all K. pneumoniae isolates (n = 12) (except K. pneumoniae ATCC 13883) were multidrug resistant (MDR), while the P. aeruginosa (n = 16) isolates exhibited higher susceptibility profiles. The tetM gene (tetracycline resistance) was identified in 47.4 % (n = 6 environmental; n = 3 clinical) of the E. faecium isolates, while the blaKPC gene (carbapenem resistance) was detected in 52.6 % (n = 7 environmental; n = 3 clinical) and 15.4 % (n = 2 environmental) of the E. faecium and K. pneumoniae isolates, respectively. The E. faecium isolates were predominantly poor biofilm formers, the K. pneumoniae isolates were moderate biofilm formers, while the P. aeruginosa isolates were strong biofilm formers. All E. faecium and K. pneumoniae isolates were gamma (γ)-haemolytic, non-gelatinase producing (E. faecium only), and non-hypermucoviscous (K. pneumoniae only), while the P. aeruginosa isolates exhibited beta (β)-haemolysis and produced gelatinase. The fimH (type 1 fimbriae adhesion) and ugE (uridine diphosphate galacturonate 4-epimerase synthesis) virulence genes were detected in the K. pneumoniae isolates, while the P. aeruginosa isolates possessed the phzM (phenazine production) and algD (alginate biosynthesis) genes. Similarities in antibiotic resistance and virulence profiles of environmental and clinical E. faecium, K. pneumoniae, and P. aeruginosa, thus highlights the potential health risks posed by using environmental water sources for daily water needs in low-and-middle-income countries.
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Affiliation(s)
- Julia Denissen
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Brandon Reyneke
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Sehaam Khan
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
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17
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Grunnvåg JS, Hegstad K, Lentz CS. Activity-based protein profiling of serine hydrolases and penicillin-binding proteins in Enterococcus faecium. FEMS MICROBES 2024; 5:xtae015. [PMID: 38813097 PMCID: PMC11134295 DOI: 10.1093/femsmc/xtae015] [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: 01/26/2024] [Revised: 04/18/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
Enterococcus faecium is a gut commensal bacterium which is gaining increasing relevance as an opportunistic, nosocomial pathogen. Its high level of intrinsic and acquired antimicrobial resistance is causing a lack of treatment options, particularly for infections with vancomycin-resistant strains, and prioritizes the identification and functional validation of novel druggable targets. Here, we use activity-based protein profiling (ABPP), a chemoproteomics approach using functionalized covalent inhibitors, to detect active serine hydrolases across 11 E. faecium and Enterococcus lactis strains. Serine hydrolases are a big and diverse enzyme family, that includes known drug targets such as penicillin-binding proteins (PBPs), whereas other subfamilies are underexplored. Comparative gel-based ABPP using Bocillin-FL revealed strain- and growth condition-dependent variations in PBP activities. Profiling with the broadly serine hydrolase-reactive fluorescent probe fluorophosphonate-TMR showed a high similarity across E. faecium clade A1 strains, but higher variation across A2 and E. lactis strains. To identify these serine hydrolases, we used a biotinylated probe analog allowing for enrichment and identification via liquid chromatography-mass spectrometry. We identified 11 largely uncharacterized targets (α,β-hydrolases, SGNH-hydrolases, phospholipases, and amidases, peptidases) that are druggable and accessible in live vancomycin-resistant E. faecium E745 and may possess vital functions that are to be characterized in future studies.
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Affiliation(s)
- Jeanette S Grunnvåg
- Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT – The Arctic University of Norway, Postboks 6050 Langnes, 9037 Tromsø, Norway
- Centre for New Antibacterial Strategies (CANS), UiT – The Arctic University of Norway, Postboks 6050 Langnes, 9037 Tromsø, Norway
| | - Kristin Hegstad
- Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT – The Arctic University of Norway, Postboks 6050 Langnes, 9037 Tromsø, Norway
- Centre for New Antibacterial Strategies (CANS), UiT – The Arctic University of Norway, Postboks 6050 Langnes, 9037 Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, P.O. Box 56, 9038 Tromsø, Norway
| | - Christian S Lentz
- Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT – The Arctic University of Norway, Postboks 6050 Langnes, 9037 Tromsø, Norway
- Centre for New Antibacterial Strategies (CANS), UiT – The Arctic University of Norway, Postboks 6050 Langnes, 9037 Tromsø, Norway
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18
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Rotsides P, Lee PJ, Webber N, Grasty KC, Beld J, Loll PJ. Diazirine Photoprobes for the Identification of Vancomycin-Binding Proteins. ACS BIO & MED CHEM AU 2024; 4:86-94. [PMID: 38645928 PMCID: PMC11027123 DOI: 10.1021/acsbiomedchemau.3c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 04/23/2024]
Abstract
Vancomycin's interactions with cellular targets drive its antimicrobial activity and also trigger expression of resistance against the antibiotic. Interaction partners for vancomycin have previously been identified using photoaffinity probes, which have proven to be useful tools for exploring vancomycin's interactome. This work seeks to develop diazirine-based vancomycin photoprobes that display enhanced specificity and bear fewer chemical modifications as compared to previous photoprobes. Using proteins fused to vancomycin's main cell-wall target, d-alanyl-d-alanine, we used mass spectrometry to show that these photoprobes specifically label known vancomycin-binding partners within minutes. In a complementary approach, we developed a Western-blot strategy targeting the vancomycin adduct of the photoprobes, eliminating the need for affinity tags and simplifying the analysis of photolabeling reactions. Together, the probes and identification strategy provide a novel and streamlined pipeline for identifying vancomycin-binding proteins.
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Affiliation(s)
- Photis Rotsides
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Paula J. Lee
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Nakoa Webber
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Kimberly C. Grasty
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Joris Beld
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Patrick J. Loll
- Department
of Biochemistry & Molecular Biology and Department of Microbiology &
Immunology, Drexel University College of
Medicine, Philadelphia, Pennsylvania 19102, United States
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19
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Hansen SGK, Klein K, Nymark A, Andersen L, Gradel KO, Lis-Toender J, Oestergaard C, Chen M, Datcu R, Skov MN, Holm A, Rosenvinge FS. Vancomycin-resistant Enterococcus faecium: impact of ending screening and isolation in a Danish University hospital. J Hosp Infect 2024; 146:82-92. [PMID: 38360093 DOI: 10.1016/j.jhin.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/11/2024] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Substantial resources are used in hospitals worldwide to counteract the ever-increasing incidence of vancomycin-resistant and vancomycin-variable Enterococcus faecium (VREfm and VVEfm), but it is important to balance patient safety, infection prevention, and hospital costs. AIM To investigate the impact of ending VREfm/VVEfm screening and isolation at Odense University Hospital (OUH), Denmark, on patient and clinical characteristics, risk of bacteraemia, and mortality of VREfm/VVEfm disease at OUH. The burden of VREfm/VVEfm bacteraemia at OUH and the three collaborative hospitals in the Region of Southern Denmark (RSD) was also investigated. METHODS A retrospective cohort study was conducted including first-time VREfm/VVEfm clinical isolates (index isolates) detected at OUH and collaborative hospitals in the period 2015-2022. The intervention period with screening and isolation was from 2015 to 2021, and the post-intervention period was 2022. Information about clinical isolates was retrieved from microbiological databases. Patient data were obtained from hospital records. FINDINGS At OUH, 436 patients were included in the study, with 285 in the intervention period and 151 in the post-intervention period. Ending screening and isolation was followed by an increased number of index isolates. Besides a change in van genes, only minor non-significant changes were detected in all the other investigated parameters. Mortality within 30 days did not reflect the VREfm/VVEfm-attributable deaths, and in only four cases was VREfm/VVEfm infection the likely cause of death. CONCLUSION Despite an increasing number of index isolates, nothing in the short follow-up period supported a reintroduction of screening and isolation.
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Affiliation(s)
- S G K Hansen
- Department of Clinical Microbiology and Infection Control, Odense University Hospital, Odense, Denmark; Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - K Klein
- Department of Clinical Microbiology and Infection Control, Odense University Hospital, Odense, Denmark; Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - A Nymark
- Department of Clinical Microbiology and Infection Control, Odense University Hospital, Odense, Denmark; Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - L Andersen
- Department of Clinical Microbiology and Infection Control, Odense University Hospital, Odense, Denmark
| | - K O Gradel
- Center for Clinical Epidemiology, Odense University Hospital, Odense, Denmark; Research Unit of Clinical Epidemiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - J Lis-Toender
- Department of Clinical Microbiology, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - C Oestergaard
- Department of Clinical Microbiology, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
| | - M Chen
- Department of Clinical Microbiology, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - R Datcu
- Department of Clinical Microbiology, Esbjerg and Grindsted Hospital, University Hospital of Southern Denmark, Esbjerg, Denmark
| | - M N Skov
- Department of Clinical Microbiology and Infection Control, Odense University Hospital, Odense, Denmark; Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - A Holm
- Department of Clinical Microbiology and Infection Control, Odense University Hospital, Odense, Denmark; Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - F S Rosenvinge
- Department of Clinical Microbiology and Infection Control, Odense University Hospital, Odense, Denmark; Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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Getahun Strobel A, Prasad P, Lane CR, Naidu R, Autar S, Young-Sharma T, Richards M, Suka A, Cameron D, James R, Prasad R, Buising K, Howden BP, Prasad V. The changing epidemiology of antimicrobial resistance in Fiji: a descriptive analysis of antimicrobial susceptibility and trends of endemic and emerging pathogens, 2019-2022. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 45:101036. [PMID: 38516290 PMCID: PMC10955629 DOI: 10.1016/j.lanwpc.2024.101036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/04/2024] [Accepted: 02/19/2024] [Indexed: 03/23/2024]
Abstract
Background There is a paucity of data on antimicrobial resistance in Fiji. The aim of this study was to determine the antimicrobial susceptibility profile of bacterial isolates from clinical samples at Colonial War Memorial Hospital in Fiji. Methods This retrospective study reviewed four-year of data from January 1, 2019, through December 31, 2022. Laboratory testing was carried out using locally approved protocols. Selective antimicrobial susceptibility testing was performed whereby only isolates resistant to first line antimicrobials were tested against second line antimicrobials. Only the first isolate of a given species per patient in a single year were included in the analysis. WHONET software and Microsoft Excel were used for analysis. Findings A total of 29,222 bacterial isolates were included, 62% (n = 18,084) were Gram-negative bacteria. K. pneumoniae was the most common (n = 5363), followed by E. coli (n = 4321). Extended spectrum beta lactamase (ESBL) production increased from 30% in 2019 to 43% in 2022 amongst K. pneumoniae, and 10%-23% in E coli. There were 733 carbapenem-resistant isolates identified from clinical samples, 61% (n = 445) were A. baumannii, 15% (n = 110) E. coli and 14% (n = 101) P. aeruginosa. Amongst the E. coli isolates tested, susceptibility to meropenem declined from 99% (272/274) in 2019 to 79% (255/325) in 2022. The rate of methicillin resistance amongst Staphylococcus aureus was steady, remaining between 11% and 13%. Interpretation This study demonstrated a high rate of MDR amongst Gram-negative bacteria, especially ESBL producing K. pneumoniae and E. coli and carbapenem-resistant A. baumannii. The emergence and rapid spread of carbapenemase producing E. coli in Fiji's largest hospital is of particular concern. There is an urgent need to allocate resources to improve existing capacity and to develop effective multimodal strategies to detect, manage and control the spread of MDR organisms. Funding This study was supported by the Medical Research Future Fund through the Australian government (grant number APP 1200970).
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Affiliation(s)
- Aneley Getahun Strobel
- Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Prinika Prasad
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Courtney R. Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ravi Naidu
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Sanjeshni Autar
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Tracey Young-Sharma
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Matthew Richards
- Infection Prevention and Surveillance Service, The Royal Melbourne Hospital, Melbourne, Australia
| | - Ana Suka
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Donna Cameron
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Rodney James
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ravendra Prasad
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
| | - Kirsty Buising
- Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- The Royal Melbourne Hospital, Melbourne, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vinita Prasad
- Ministry of Health and Medical Services, Colonial War Memorial Hospital, Suva, Fiji
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21
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Yamba K, Mudenda S, Mpabalwani E, Mainda G, Mukuma M, Samutela MT, Lukwesa C, Chizimu J, Kaluba CK, Mutalange M, Chilengi R, Muma JB. Antibiotic prescribing patterns and carriage of antibiotic-resistant Escherichia coli and Enterococcus species in healthy individuals from selected communities in Lusaka and Ndola districts, Zambia. JAC Antimicrob Resist 2024; 6:dlae027. [PMID: 38449515 PMCID: PMC10914442 DOI: 10.1093/jacamr/dlae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
Objectives This study assessed antibiotic prescribing patterns in primary healthcare facilities and antimicrobial resistance (AMR) profiles of commensal Escherichia coli and enterococci isolated from pregnant women and children under 5 years of age. Materials and methods This cross-sectional study was conducted in Lusaka and Ndola districts of Zambia. Prescription pattern data were obtained from hospital pharmacies. Identification and antimicrobial susceptibility profiles of E. coli and enterococci were determined by conventional methods, while confirmation of both pathogens and AMR genes were determined by PCR. Data were analysed using WHONET and SPSS version 25.0. Results Most prescribed antibiotics at the primary healthcare facilities belonged to the Access group of the WHO Access, Watch and Reserve (AWaRe) classification. All the primary healthcare facilities adhered to the AWaRe framework of ≥60% prescribed antibiotics belonging to the Access group. However, resistance was highest in the Access group of antibiotics. E. coli resistance to ampicillin ranged from 71% to 77% and to co-trimoxazole from 74% to 80%, while enterococcal resistance to tetracycline was 59%-64%. MDR was highest in E. coli (75%) isolates, while XDR was highest in enterococcal isolates (97%). The identified AMR genes in E. coli included blaCTX-M, sul2 and qnrA, while those of enterococci included erm(B), erm(C) and erm(A). Conclusions Resistance was highest in the prescribed WHO Access group of antibiotics. These findings highlight the need to use local susceptibility data to formulate country-specific treatment guidelines in line with WHO AWaRe classification and enforce regulations that prohibit easy access to antibiotics.
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Affiliation(s)
- Kaunda Yamba
- Department of Pathology & Microbiology, University Teaching Hospitals, Lusaka, Zambia
- Department of Disease Control University of Zambia, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Antimicrobial Resistance Cluster, Zambia National Public Health Institute, Lusaka, Zambia
| | - Steward Mudenda
- Department of Disease Control University of Zambia, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Evans Mpabalwani
- Department of Paediatrics & Child Health, School of Medicine, University of Zambia, Lusaka, Zambia
| | - Geoffrey Mainda
- Food and Agriculture Organization (FAO) of the United Nations, House No. 5, Chaholi, Off Addis Ababa Drive, Lusaka, Zambia
- Department of Veterinary Services Central Veterinary Research Institute (CVRI), Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Mercy Mukuma
- Department of Food Science, School of Agricultural Sciences and Nutrition, University of Zambia, Lusaka, Zambia
| | - Mulemba Tillika Samutela
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Chileshe Lukwesa
- Department of Pathology & Microbiology, University Teaching Hospitals, Lusaka, Zambia
| | - Joseph Chizimu
- Antimicrobial Resistance Cluster, Zambia National Public Health Institute, Lusaka, Zambia
| | - Ciluvya Kavimba Kaluba
- Department of Disease Control University of Zambia, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Matenge Mutalange
- Department of Disease Control University of Zambia, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Department of Pathology and Microbiology, School of Medicine and Health Sciences, Mulungushi University, Livingstone, Zambia
| | - Roma Chilengi
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia
| | - John Bwalya Muma
- Department of Disease Control University of Zambia, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
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22
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Hourigan D, Stefanovic E, Hill C, Ross RP. Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy. BMC Microbiol 2024; 24:103. [PMID: 38539119 PMCID: PMC10976773 DOI: 10.1186/s12866-024-03243-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/28/2024] [Indexed: 04/19/2024] Open
Abstract
Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections.
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Affiliation(s)
- David Hourigan
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland
| | - Ewelina Stefanovic
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Moorepark West, Fermoy, Co. Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland.
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland.
- Teagasc Food Research Centre, Moorepark, Moorepark West, Fermoy, Co. Cork, Ireland.
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23
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Roer L, Kaya H, Tedim AP, Novais C, Coque TM, Aarestrup FM, Peixe L, Hasman H, Hammerum AM, Freitas AR. VirulenceFinder for Enterococcus faecium and Enterococcus lactis: an enhanced database for detection of putative virulence markers by using whole-genome sequencing data. Microbiol Spectr 2024; 12:e0372423. [PMID: 38329344 PMCID: PMC10913372 DOI: 10.1128/spectrum.03724-23] [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: 10/23/2023] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
Enterococcus faecium (Efm) is a leading cause of hospital-associated (HA) infections, often enriched in putative virulence markers (PVMs). Recently, the Efm clade B was assigned as Enterococcus lactis (Elts), which usually lack HA-Efm infection markers. Available databases for extracting PVM are incomplete and/or present an intermix of genes from Efm and Enterococcus faecalis, with distinct virulence profiles. In this study, we constructed a new database containing 27 PVMs [acm, scm, sgrA, ecbA, fnm, sagA, hylEfm, ptsD, orf1481, fms15, fms21-fms20 (pili gene cluster 1, PGC-1), fms14-fms17-fms13 (PGC-2), empA-empB-empC (PGC-3), fms11-fms19-fms16 (PGC-4), ccpA, bepA, gls20-glsB1, and gls33-glsB] from nine reference genomes (seven Efm + two Elts). The database was validated against these reference genomes and further evaluated using a collection of well-characterized Efm (n = 43) and Elts (n = 7) control strains, by assessing PVM presence/absence and its variants together with a genomic phylogeny constructed as single-nucleotide polymorphisms. We found a high concordance between the phylogeny and in silico findings of the PVM, with Elts clustering separately and mostly carrying Elts-specific PVM gene variants. Based on our validation results, we recommend using the database with raw reads instead of assemblies to avoid missing gene variants. This newly constructed database of 27 PVMs will enable a more comprehensive characterization of Efm and Elts based on WGS data. The developed database exhibits scalability and boasts a range of applications in public health, including diagnostics, outbreak investigations, and epidemiological studies. It can be further used in risk assessment for distinguishing between safe and unsafe enterococci.IMPORTANCEThe newly constructed database, consisting of 27 putative virulence markers, is highly scalable and serves as a valuable resource for the comprehensive characterization of these closely related species using WGS data. It holds significant potential for various public health applications, including hospital outbreak investigations, surveillance, and risk assessment for probiotics and feed additives.
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Affiliation(s)
- Louise Roer
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hülya Kaya
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Carla Novais
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, Denmark
| | - Luísa Peixe
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
| | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anette M. Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ana R. Freitas
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - On behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM)
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, Denmark
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
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24
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McHugh MP, Pettigrew KA, Taori S, Evans TJ, Leanord A, Gillespie SH, Templeton KE, Holden MTG. Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium. J Antimicrob Chemother 2024; 79:656-668. [PMID: 38323373 PMCID: PMC11090465 DOI: 10.1093/jac/dkae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases. OBJECTIVES Determine the impact of within-patient diversity on transmission resolution of VREfm. MATERIALS AND METHODS Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner. RESULTS AND DISCUSSION In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies. CONCLUSIONS Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks.
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Affiliation(s)
- Martin P McHugh
- School of Medicine, University of St Andrews, St Andrews, UK
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | - Surabhi Taori
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Thomas J Evans
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Alistair Leanord
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK
| | | | - Kate E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
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25
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Masuda S, Jinushi R, Imamura Y, Kubota J, Kimura K, Shionoya K, Makazu M, Sato R, Kako M, Kobayashi M, Uojima H, Koizumi K. Association of short-course antimicrobial therapy and bacterial resistance in acute cholangitis: Retrospective cohort study. Endosc Int Open 2024; 12:E307-E316. [PMID: 38420157 PMCID: PMC10901644 DOI: 10.1055/a-2230-8229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/08/2023] [Indexed: 03/02/2024] Open
Abstract
Background and study aims Although the number of resistant bacteria tends to increase with prolonged antimicrobial therapy, no studies have examined the relationship between the duration of antimicrobial therapy and increase in the number of resistant bacteria in acute cholangitis. We hypothesized that the short-term administration of antimicrobial agents in acute cholangitis would suppress bacterial resistance. Patients and methods This was a single-center, retrospective, observational study of patients with acute cholangitis admitted between January 2018 and June 2020 who met the following criteria: successful biliary drainage, positive blood or bile cultures, bacteria identified from cultures sensitive to antimicrobials, and subsequent cholangitis recurrence by January 2022. The patients were divided into two groups: those whose causative organisms at the time of recurrence became resistant to the antimicrobial agents used at the time of initial admission (resistant group) and those who remained susceptible (susceptible group). Multivariate analysis was used to examine risk factors associated with the development of resistant pathogens. Multivariate analysis investigated antibiotics used with the length of 3 days or shorter after endoscopic retrograde cholangiopancreatography (ERCP) and previously reported risk factors for the development of bacterial resistance. Results In total, 89 eligible patients were included in this study. There were no significant differences in patient background or ERCP findings between the groups. The use of antibiotics, completed within 3 days after ERCP, was associated with a lower risk of developing bacterial resistance (odds ratio, 0.17; 95% confidence interval, 0.04-0.65; P =0.01). Conclusions In acute cholangitis, the administration of antimicrobials within 3 days of ERCP may suppress the development of resistant bacteria.
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Affiliation(s)
- Sakue Masuda
- Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Ryuhei Jinushi
- Gastroenterology, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Yoshinori Imamura
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University, Kobe, Japan
| | - Jun Kubota
- Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Karen Kimura
- Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Kento Shionoya
- Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Makomo Makazu
- Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Ryo Sato
- Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | - Makoto Kako
- Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
| | | | - Haruki Uojima
- Department of Gastroenterology, Internal Medicine, Kitasato University School of Medicine, Sagamihara, Japan
| | - Kazuya Koizumi
- Gastroenterology, Shonan Kamakura General Hospital, Kamakura, Japan
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Terentjeva M, Ķibilds J, Avsejenko J, Cīrulis A, Labecka L, Bērziņš A. Antimicrobial Resistance in Enterococcus spp. Isolates from Red Foxes ( Vulpes vulpes) in Latvia. Antibiotics (Basel) 2024; 13:114. [PMID: 38391500 PMCID: PMC10885957 DOI: 10.3390/antibiotics13020114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/08/2024] [Accepted: 01/15/2024] [Indexed: 02/24/2024] Open
Abstract
Antimicrobial resistance (AMR) is an emerging public health threat and is one of the One Health priorities for humans, animals, and environmental health. Red foxes (Vulpes vulpes) are a widespread predator species with great ecological significance, and they may serve as a sentinel of antimicrobial resistance in the general environment. The present study was carried out to detect antimicrobial resistance, antimicrobial resistance genes, and genetic diversity in faecal isolates of red foxes (Vulpes vulpes). In total, 34 Enterococcus isolates, including E. faecium (n = 17), E. faecalis (n = 12), E. durans (n = 3), and E. hirae (n = 2), were isolated. Antimicrobial resistance to 12 antimicrobial agents was detected with EUVENC panels using the minimum inhibitory concentration (MIC). The presence of antimicrobial resistance genes (ARGs) was determined using whole-genome sequencing (WGS). Resistance to tetracycline (6/34), erythromycin (3/34), ciprofloxacin (2/34), tigecycline (2/34), and daptomycin (2/34) was identified in 44% (15/34) of Enterococcus isolates, while all the isolates were found to be susceptible to ampicillin, chloramphenicol, gentamicin, linezolid, teicoplanin, and vancomycin. No multi-resistant Enterococcus spp. were detected. A total of 12 ARGs were identified in Enterococcus spp., with the presence of at least 1 ARG in every isolate. The identified ARGs encoded resistance to aminoglycosides (aac(6')-I, ant(6)-Ia, aac(6')-Iih and spw), tetracyclines (tet(M), tet(L) and tet(S)), and macrolide-lincosamide-streptogramin AB (lnu(B,G), lsa(A,E), and msr(C)), and their presence was associated with phenotypical resistance. Core genome multilocus sequence typing (cgMLST) revealed the high diversity of E. faecalis and E. faecium isolates, even within the same geographical area. The distribution of resistant Enterococcus spp. in wild foxes in Latvia highlights the importance of a One Health approach in tackling AMR.
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Affiliation(s)
- Margarita Terentjeva
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
- Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes iela 3, LV-1076 Rīga, Latvia
| | - Juris Ķibilds
- Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes iela 3, LV-1076 Rīga, Latvia
| | - Jeļena Avsejenko
- Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes iela 3, LV-1076 Rīga, Latvia
| | - Aivars Cīrulis
- Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes iela 3, LV-1076 Rīga, Latvia
- Faculty of Biology, University of Latvia, LV-1004 Rīga, Latvia
| | - Linda Labecka
- Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes iela 3, LV-1076 Rīga, Latvia
| | - Aivars Bērziņš
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3001 Jelgava, Latvia
- Institute of Food Safety, Animal Health and Environment "BIOR", Lejupes iela 3, LV-1076 Rīga, Latvia
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Chopjitt P, Boueroy P, Jenjaroenpun P, Wongsurawat T, Hatrongjit R, Kerdsin A, Sunthamala N. Genomic characterization of vancomycin-resistant Enterococcus faecium clonal complex 17 isolated from urine in tertiary hospitals in Northeastern Thailand. Front Microbiol 2024; 14:1278835. [PMID: 38312503 PMCID: PMC10834742 DOI: 10.3389/fmicb.2023.1278835] [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: 08/17/2023] [Accepted: 12/31/2023] [Indexed: 02/06/2024] Open
Abstract
Vancomycin-resistant Enterococci (VREs) have increasingly become a major nosocomial pathogen worldwide, earning high-priority category from the World Health Organization (WHO) due to their antibiotic resistance. Among VREs, vancomycin-resistant Enterococcus faecium (VREfm) is particularly concerning, frequently isolated and resistant to many antibiotics used in hospital-acquired infections. This study investigated VREfm isolates from rural tertiary hospitals in Northeastern Thailand based both antibiotic susceptibility testing and whole-genome sequencing. All isolates showed resistance to vancomycin, ampicillin, erythromycin, tetracycline, ciprofloxacin, norfloxacin, and rifampin. Nitrofurantoin and tigecycline resistance were also observed in nearly all isolates. Conversely, all isolates remained susceptible to chloramphenicol, daptomycin, and linezolid. Genomic characterization revealed that all VREfm isolates belonged to clonal complex 17 (CC17), primarily consisting of sequence type (ST) 80, followed by ST17, ST761, and ST117. Additionally, all isolates harbored numerous antimicrobial-resistant genes, including vanA, tet(L), tet(M), aac(6')-li, ant(6)-Ia, aph(3')-III, aac(6')-aph(2″), aph(2″)-la, ant(9)-la, erm(B), msr(C), erm(T), erm(A), fosB, dfrG, and cfr(B). Notably, all isolates contained virulence genes, for collagen adhesin (acm) and cell wall adhesin (efafm), while hylEfm (glycosyl hydrolase) was detected in VREfm ST80. This study provided important information for understanding the genomic features of VREfm isolated from urine.
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Affiliation(s)
- Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rujirat Hatrongjit
- Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Nuchsupha Sunthamala
- Department of Biology, Faculty of Science, Mahasarakham University, Kantharawichai, Thailand
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Mengesha TH, Ali MM, Mengistu M, Assegu Fenta D. High Gastrointestinal Colonization Rate of Vancomycin-Resistant Enterococci among Hospitalized Patients: Potential Source for Resistant Gene. Int J Microbiol 2024; 2024:6430026. [PMID: 38226181 PMCID: PMC10789508 DOI: 10.1155/2024/6430026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/10/2023] [Accepted: 12/16/2023] [Indexed: 01/17/2024] Open
Abstract
Background Vancomycin-resistant Enterococci (VRE) is a global health problem and responsible for healthcare-associated infections (HAIs) in patients with prolonged hospital stay, severe underlying disease, and previous broad-spectrum antibiotic therapy. These bacteria can cross-resist and transfer drug-resistant genes to other potentially pathogenic bacteria. Therefore; this study was aimed to determine the gastrointestinal colonization rate of VRE, its antimicrobial susceptibility profile, and associated factors among hospitalized patients. Methods Prospective cross-sectional study was conducted using stool samples from 223 patients admitted to different wards at Hawassa University Comprehensive Specialized Hospital, from April 1 to June 30, 2021. Patients admitted to the hospital for more than 48 hours for various medical conditions were included. Sociodemographic and clinical characteristics were collected using a structured questionnaire. Fecal specimens were cultured on Enterococci selective media. Enterococcus species were identified using their growth and mannitol fermentation properties. Vancomycin resistance was screened using both the Kirby-Bauer disk diffusion method and a vancomycin E-test strip. Data were entered and analyzed using SPSS version 25. Descriptive and logistic regressions were used to determine the frequency and association of factors with the VRE colonization rate. A p value of <0.05 was considered statistically significant. Results A total of 223 fecal specimens were collected and processed, and 141 (63.2%) them were positive for Enterococci. The predominant species was E. faecalis 65 (46.1%) followed by E. faecium 76 (53.9%). In this study, the gastrointestinal colonization rate of VRE was 15 (6.7%) and all the species belong to E. faecium. Study participants who had no formal education (AOR = 4.26, 95% CI: 1.01, 18.06), hospitalized patients for >2 weeks (AOR = 4.10, 95% CI: 1.08, 15.57), and those who had a history of treatment with vancomycin (AOR = 4.77, 95% CI: 1.26, 18.09) were more likely to be colonized with vancomycin-resistant Enterococci. More than 95% of Enterococci isolates were susceptible to linezolid, whereas 70.2%, 63.1%, 56.7%, and 53.9% were resistant to tetracycline, erythromycin, penicillin, and ampicillin, respectively. Among the total Enterococci isolated, 141 (54.6%) were multidrug resistant. Conclusions In our study, high proportion of vancomycin-resistant Enterococci was found. Previous exposure to antibiotics and hospital stay were significant factors for VRE gut colonization. The isolated Enterococci showed variable degrees of resistance to commonly prescribed antibiotics which leads to a worldwide problem multidrug resistance. Therefore, periodic surveillance on antimicrobial resistance pattern, adhering to rational use of antibiotics, and implementing infection prevention protocols may reduce colonization by VRE.
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Affiliation(s)
| | - Musa Mohammed Ali
- School of Medical Laboratory Science, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
| | - Mulugeta Mengistu
- School of Medical Laboratory Science, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
| | - Demissie Assegu Fenta
- School of Medical Laboratory Science, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
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Bai Y, Miyanaga K, Yamamoto N. Enhanced tight junction in Caco-2 cells by the pretreatment with Lactobacillus johnsonii strain MG. Biosci Biotechnol Biochem 2023; 87:1532-1536. [PMID: 37704400 DOI: 10.1093/bbb/zbad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/21/2023] [Indexed: 09/15/2023]
Abstract
We investigated roles of Lactobacillus johnsonii MG (MG) isolated from mice with interaction with tight junction on gut barrier function with Caco-2 cell model. Pretreatment with MG enhanced barrier function and showed protective effect against Enterococcus faecium provided damage. MG treatment increased the gene expressions of transcriptional regulator NFKB and major tight junction protein, ZO-1.
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Affiliation(s)
- Yuying Bai
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Kazuhiko Miyanaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
- Department of Infection and Immunity, School of Medicine, Jichi Medical University, 3311-1, Yakushiji, Shimotsuke-Shi, Tochigi, Japan
| | - Naoyuki Yamamoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
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Meschiari M, Kaleci S, Monte MD, Dessilani A, Santoro A, Scialpi F, Franceschini E, Orlando G, Cervo A, Monica M, Forghieri F, Venturelli C, Ricchizzi E, Chester J, Sarti M, Guaraldi G, Luppi M, Mussini C. Vancomycin resistant enterococcus risk factors for hospital colonization in hematological patients: a matched case-control study. Antimicrob Resist Infect Control 2023; 12:126. [PMID: 37957773 PMCID: PMC10644555 DOI: 10.1186/s13756-023-01332-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/05/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Vancomycin-resistant enterococcus (VRE) was the fastest growing pathogen in Europe in 2022 (+ 21%) but its clinical relevance is still unclear. We aim to identify risk factors for acquired VRE rectal colonization in hematological patients and evaluate the clinical impact of VRE colonization on subsequent infection, and 30- and 90-day overall mortality rates, compared to a matched control group. METHODS A retrospective, single center, case-control matched study (ratio 1:1) was conducted in a hematological department from January 2017 to December 2020. Case patients with nosocomial isolation of VRE from rectal swab screening (≥ 48 h) were matched to controls by age, sex, ethnicity, and hematologic disease. Univariate and multivariate logistic regression compared risk factors for colonization. RESULTS A total of 83 cases were matched with 83 controls. Risk factors for VRE colonization were febrile neutropenia, bone marrow transplant, central venous catheter, bedsores, reduced mobility, altered bowel habits, cachexia, previous hospitalization and antibiotic treatments before and during hospitalization. VRE bacteraemia and Clostridioides difficile infection (CDI) occurred more frequently among cases without any impact on 30 and 90-days overall mortality. Vancomycin administration and altered bowel habits were the only independent risk factors for VRE colonization at multivariate analysis (OR: 3.53 and 3.1; respectively). CONCLUSIONS Antimicrobial stewardship strategies to reduce inappropriate Gram-positive coverage in hematological patients is urgently required, as independent risk factors for VRE nosocomial colonization identified in this study include any use of vancomycin and altered bowel habits. VRE colonization and infection did not influence 30- and 90-day mortality. There was a strong correlation between CDI and VRE, which deserves further investigation to target new therapeutic approaches.
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Affiliation(s)
- Marianna Meschiari
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy.
| | - Shaniko Kaleci
- Clinical and Experimental Medicine, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Martina Del Monte
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Andrea Dessilani
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Antonella Santoro
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Francesco Scialpi
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Erica Franceschini
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Gabriella Orlando
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Adriana Cervo
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Morselli Monica
- Section of Hematology, Department of Surgical and Medical Sciences, AOU Policlinico, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabio Forghieri
- Section of Hematology, Department of Surgical and Medical Sciences, AOU Policlinico, University of Modena and Reggio Emilia, Modena, Italy
| | - Claudia Venturelli
- Clinical Microbiology Laboratory, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Enrico Ricchizzi
- Agenzia Sanitaria e Sociale Regionale Emilia-Romagna, Viale Aldo Moro 21, Bologna, 40127, Italy
| | - Johanna Chester
- Department of Dermatology, University of Modena and Reggio Emilia, Modena, 41121, Italy
| | - Mario Sarti
- Clinical Microbiology Laboratory, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Giovanni Guaraldi
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
| | - Mario Luppi
- Section of Hematology, Department of Surgical and Medical Sciences, AOU Policlinico, University of Modena and Reggio Emilia, Modena, Italy
| | - Cristina Mussini
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41122, Italy
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El Zowalaty ME, Lamichhane B, Falgenhauer L, Mowlaboccus S, Zishiri OT, Forsythe S, Helmy YA. Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock. Sci Rep 2023; 13:18609. [PMID: 37903806 PMCID: PMC10616195 DOI: 10.1038/s41598-023-42838-z] [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: 05/17/2023] [Accepted: 09/15/2023] [Indexed: 11/01/2023] Open
Abstract
The emergence of antimicrobial-resistant, livestock-associated Enterococcus faecalis represents a public health concern. Here, we report the isolation, molecular detection of virulence and antimicrobial resistance determinants, in addition to the phylogenetic analyses of 20 Enterococcus species using whole genome sequencing analysis of 15 Enterococcus faecalis strains including six strains of three novel sequence types, three Enterococcus faecium and two Enterococcus durans. All strains were isolated from food chain animals in South Africa. Enterococcus strains were isolated on bile aesculin azide agar, followed by identification using MALDI-TOF MS analysis. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk diffusion method. The genomic DNA of the isolates was extracted and sequencing was performed using the Illumina MiSeq platform. Sequence reads were trimmed and de novo assembled. The assembled contigs were analyzed for antimicrobial resistance genes and chromosomal mutations, extra-chromosomal plasmids, and multi-locus sequence type (MLST). Multidrug antimicrobial resistance genes conferring resistance to aminoglycosides (ant(6)-Ia, aph(3')-IIIa, sat4, and spw), lincosamides (lnu(B), lsa(A), and lsa(E)), macrolides (erm(B)), trimethoprim (dfrG) and tetracyclines (tet(L) and tet(M)) were identified. Plasmid replicons were detected in seven E. faecalis and three E. faecium isolates. The sequence type (ST) of each isolate was determined using the Enterococcus PubMLST database. Ten STs were identified in the collection, three of which (ST1240, ST1241, and ST1242) have not been previously reported and are described in the present study for the first time. To compare the sequenced strains to other previously sequenced E. faecalis strains, assembled sequences of E. faecalis from livestock were downloaded from the PubMLST database. Core genome-based phylogenetic analysis was performed using ParSNP. The detection of multiple drug-resistance in Enterococcus including E. faecalis and E. faecium highlights the significance of genomic surveillance to monitor the spread of antimicrobial resistance in food chain animals. In addition, the genome sequences of Enterococcus strains reported in the present study will serve as a reference point for future molecular epidemiological studies of livestock-associated and antibiotic-resistant E. faecalis in Africa. In addition, this study enables the in-depth analysis of E. faecalis genomic structure, as well as provides valuable information on the phenotypic and genotypic antimicrobial resistance, and the pathogenesis of livestock-associated E. faecalis and E. faecium.
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Affiliation(s)
- Mohamed E El Zowalaty
- Veterinary Medicine and Food Security Research Group, Medical Laboratory Sciences Program, Faculty of Health Sciences, Abu Dhabi Women's Campus, Higher Colleges of Technology, Abu Dhabi, 41012, UAE.
| | - Bibek Lamichhane
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Biomedical Research Center Seltersberg, Schubertstrasse 81, 35392, Giessen, Germany
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases Research Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine-WA, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Oliver T Zishiri
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Private Bag X54001, Westville, Durban, 4000, South Africa
| | - Stephen Forsythe
- Foodmicrobe.com Ltd., Adams Hill, Keyworth, Nottingham, NG12 5GY, UK
| | - Yosra A Helmy
- Department of Veterinary Science, Martin-Gatton College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY, 40546, USA.
- Department of Zoonoses, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt.
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Yang J, Chen Y, Dong Z, Zhang W, Liu L, Meng W, Li Q, Fu K, Zhou Z, Liu H, Zhong Z, Xiao X, Zhu J, Peng G. Distribution and association of antimicrobial resistance and virulence characteristics in Enterococcus spp. isolates from captive Asian elephants in China. Front Microbiol 2023; 14:1277221. [PMID: 37954234 PMCID: PMC10635408 DOI: 10.3389/fmicb.2023.1277221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
Enterococcus spp., as an opportunistic pathogen, are widely distributed in the environment and the gastrointestinal tracts of both humans and animals. Captive Asian elephants, popular animals at tourist attractions, have frequent contact with humans. However, there is limited information on whether captive Asian elephants can serve as a reservoir of antimicrobial resistance (AMR). The aim of this study was to characterize AMR, antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), gelatinase activity, hemolysis activity, and biofilm formation of Enterococcus spp. isolated from captive Asian elephants, and to analyze the potential correlations among these factors. A total of 62 Enterococcus spp. strains were isolated from fecal samples of captive Asian elephants, comprising 17 Enterococcus hirae (27.4%), 12 Enterococcus faecalis (19.4%), 8 Enterococcus faecium (12.9%), 7 Enterococcus avium (11.3%), 7 Enterococcus mundtii (11.3%), and 11 other Enterococcus spp. (17.7%). Isolates exhibited high resistance to rifampin (51.6%) and streptomycin (37.1%). 50% of Enterococcus spp. isolates exhibited multidrug resistance (MDR), with all E. faecium strains demonstrating MDR. Additionally, nine ARGs were identified, with tet(M) (51.6%), erm(B) (24.2%), and cfr (21.0%) showing relatively higher detection rates. Biofilm formation, gelatinase activity, and α-hemolysin activity were observed in 79.0, 24.2, and 14.5% of the isolates, respectively. A total of 18 VAGs were detected, with gelE being the most prevalent (69.4%). Correlation analysis revealed 229 significant positive correlations and 12 significant negative correlations. The strongest intra-group correlations were observed among VAGs. Notably, we found that vancomycin resistance showed a significant positive correlation with ciprofloxacin resistance, cfr, and gelatinase activity, respectively. In conclusion, captive Asian elephants could serve as significant reservoirs for the dissemination of AMR to humans.
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Affiliation(s)
- Jinpeng Yang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanshan Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhiyou Dong
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wenqing Zhang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lijuan Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wanyu Meng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qianlan Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keyi Fu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ziyao Zhou
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haifeng Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhijun Zhong
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiao Xiao
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jieyao Zhu
- Xishuangbanna Vocational and Technical College, Yunnan, China
| | - Guangneng Peng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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Qu Q, Chen T, He P, Geng H, Zeng P, Luan G. Isolation and characterization of a novel lytic bacteriophage vB_Efm_LG62 infecting Enterococcus faecium. Virus Genes 2023; 59:763-774. [PMID: 37422898 DOI: 10.1007/s11262-023-02016-9] [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: 02/22/2023] [Accepted: 06/11/2023] [Indexed: 07/11/2023]
Abstract
Enterococcus faecium has been classified as a "high priority" pathogen by the World Health Organization. Enterococcus faecium has rapidly evolved as a global nosocomial pathogen with adaptation to the nosocomial environment and the accumulation of resistance to multiple antibiotics. Phage therapy is considered a promising strategy against difficult-to-treat infections and antimicrobial resistance. In this study, we isolated and characterized a novel virulent bacteriophage, vB_Efm_LG62, that specifically infects multidrug-resistant E. faecium. Morphological observations suggested that the phage has siphovirus morphology, with an optimal multiplicity of infection of 0.001. One-step growth tests revealed that its latent growth was at 20 min, with a burst size of 101 PFU/cell. Phage vB_Efm_LG62 was verified to have a double-stranded genome of 42,236 bp (35.21% GC content), containing 66 predicted coding sequences as determined by whole genomic sequencing. No genes were predicted to have functions associated with virulence factors or antibiotic resistance, indicating that the phage vB_Efm_LG62 has good therapeutic potential. Our isolation and characterization of this highly efficient phage aids in expanding our knowledge of E. faecium-targeting phages, and provides additional options for phage cocktail therapy.
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Affiliation(s)
- Qianyu Qu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Tao Chen
- Medical Laboratory, Xindu District People's Hospital of Chengdu, Chengdu, China
| | - Penggang He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huaixin Geng
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Peibin Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
| | - Guangxin Luan
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China.
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Borgio JF, AlJindan R, Alghourab LH, Alquwaie R, Aldahhan R, Alhur NF, AlEraky DM, Mahmoud N, Almandil NB, AbdulAzeez S. Genomic Landscape of Multidrug Resistance and Virulence in Enterococcus faecalis IRMC827A from a Long-Term Patient. BIOLOGY 2023; 12:1296. [PMID: 37887006 PMCID: PMC10604365 DOI: 10.3390/biology12101296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
We report on a highly virulent, multidrug-resistant strain of Enterococcus faecalis IRMC827A that was found colonizing a long-term male patient at a tertiary hospital in Khobar, Saudi Arabia. The E. faecalis IRMC827A strain carries several antimicrobial drug resistance genes and harbours mobile genetic elements such as Tn6009, which is an integrative conjugative element that can transfer resistance genes between bacteria and ISS1N via an insertion sequence. Whole-genome-sequencing-based antimicrobial susceptibility testing on strains from faecal samples revealed that the isolate E. faecalis IRMC827A is highly resistant to a variety of antibiotics, including tetracycline, doxycycline, minocycline, dalfopristin, virginiamycin, pristinamycin, chloramphenicol, streptomycin, clindamycin, lincomycin, trimethoprim, nalidixic acid and ciprofloxacin. The isolate IRMC827A carries several virulence factors that are significantly associated with adherence, biofilm formation, sortase-assembled pili, manganese uptake, antiphagocytosis, and spreading factor of multidrug resistance. The isolate also encompasses two mutations (G2576T and G2505A) in the 23S rRNA gene associated with linezolid resistance and three more mutations (gyrA p.S83Y, gyrA p.D759N and parC p.S80I) of the antimicrobial resistance phenotype. The findings through next-generation sequencing on the resistome, mobilome and virulome of the isolate in the study highlight the significance of monitoring multidrug-resistant E. faecalis colonization and infection in hospitalized patients. As multidrug-resistant E. faecalis is a serious pathogen, it is particularly difficult to treat and can cause fatal infections. It is important to have quick and accurate diagnostic tests for multidrug-resistant E. faecalis, to track the spread of multidrug-resistant E. faecalis in healthcare settings, and to improve targeted interventions to stop its spread. Further research is necessary to develop novel antibiotics and treatment strategies for multidrug-resistant E. faecalis infections.
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Affiliation(s)
- J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
| | - Reem AlJindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Lujeen H. Alghourab
- Summer Research Program, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Rahaf Alquwaie
- Master Program of Biotechnology, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Razan Aldahhan
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
| | - Norah F. Alhur
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
| | - Doaa M. AlEraky
- Department of Biomedical Dental Science, Microbiology and Immunology Division, Collage of Dentistry, Dammam 31441, Saudi Arabia
| | - Nehal Mahmoud
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
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Ullah MA, Islam MS, Rana ML, Ferdous FB, Neloy FH, Firdous Z, Hassan J, Rahman MT. Resistance Profiles and Virulence Determinants in Biofilm-Forming Enterococcus faecium Isolated from Raw Seafood in Bangladesh. Pathogens 2023; 12:1101. [PMID: 37764909 PMCID: PMC10535238 DOI: 10.3390/pathogens12091101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/29/2023] Open
Abstract
Pathogenic, antibiotic-resistant, and biofilm-forming bacteria can be transferred to humans through the consumption of contaminated seafood. The present study was carried out to determine antibiotic resistance profiles and virulence determinants in biofilm-forming Enterococcus faecium isolated from seafood in Bangladesh. A total of 150 seafood samples, including shrimp (n = 50), crabs (n = 25), and marine fish (n = 75), were screened using cultural, staining, biochemical, polymerase chain reaction (PCR), Congo red (CR), and disk diffusion (DD) assays. In PCR, E. faecium was detected in 27.3% (41/150; CI95% 20.8; 34.9) of samples, where marine fish (34.7%, CI95% 24.9; 45.9) had the highest prevalence (p < 0.05) compared to crabs (32%, CI95% 17.2; 51.6) and shrimp (14%, CI95% 7.0; 26.1). Thirty-two (78.1%, CI95% 63.3; 88.0) of the E. faecium isolates were determined to be biofilm formers in the CR test, where 43.9% (18/41, CI95% 29.9; 59.0) and 34.2% (14/41, CI95% 21.6; 49.5) of the isolates were strong and intermediate biofilm formers, respectively. In PCR, virulence genes, i.e., pil (100%), ace (92.7%), agg (68.3%), fsrA (65.9%), gelE (63.4%), sprE (53.7%), fsrB (51.2%), and fsrC (43.9%), were detected in E. faecium isolates. All the E. faecium isolates were phenotypically resistant to ≥3 antimicrobial categories and ≥3 antibiotics, including WHO-classified reserve antibiotics linezolid (70.7%) and fosfomycin (19.5%). Moreover, the multiple antibiotic resistance index ranged up to 0.8, showing resistance to ten antibiotics and eight antibiotic classes. In this study, the prevalence of virulence genes and antibiotic resistance was significantly greater (p < 0.05) in strong biofilm-forming E. faecium strains as compared to strains with intermediate and non-biofilm-forming abilities. As far as we know, this study, for the first time in Bangladesh, determined antibiotic resistance and detected virulence genes in biofilm-forming E. faecium isolated from seafood samples. The data from this study could play a significant role in evaluating potential health hazards linked to the ingestion of uncooked or minimally processed seafood.
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Affiliation(s)
| | | | | | | | | | | | | | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.A.U.); (M.S.I.); (M.L.R.); (F.B.F.); (F.H.N.); (Z.F.); (J.H.)
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Gregory KS, Hall PR, Onuh JP, Mojanaga OO, Liu SM, Acharya KR. Crystal Structure of the Catalytic Domain of a Botulinum Neurotoxin Homologue from Enterococcus faecium: Potential Insights into Substrate Recognition. Int J Mol Sci 2023; 24:12721. [PMID: 37628902 PMCID: PMC10454453 DOI: 10.3390/ijms241612721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Clostridium botulinum neurotoxins (BoNTs) are the most potent toxins known, causing the deadly disease botulism. They function through Zn2+-dependent endopeptidase cleavage of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, preventing vesicular fusion and subsequent neurotransmitter release from motor neurons. Several serotypes of BoNTs produced by Clostridium botulinum (BoNT/A-/G and/X) have been well-characterised over the years. However, a BoNT-like gene (homologue of BoNT) was recently identified in the non-clostridial species, Enterococcus faecium, which is the leading cause of hospital-acquired multi-drug resistant infections. Here, we report the crystal structure of the catalytic domain of a BoNT homologue from Enterococcus faecium (LC/En) at 2.0 Å resolution. Detailed structural analysis in comparison with the full-length BoNT/En AlphaFold2-predicted structure, LC/A (from BoNT/A), and LC/F (from BoNT/F) revealed putative subsites and exosites (including loops 1-5) involved in recognition of LC/En substrates. LC/En also appears to possess a conserved autoproteolytic cleavage site whose function is yet to be established.
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Affiliation(s)
- Kyle S. Gregory
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (K.S.G.); (P.-R.H.); (J.P.O.); (O.O.M.)
| | - Peter-Rory Hall
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (K.S.G.); (P.-R.H.); (J.P.O.); (O.O.M.)
| | - Jude Prince Onuh
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (K.S.G.); (P.-R.H.); (J.P.O.); (O.O.M.)
| | - Otsile O. Mojanaga
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (K.S.G.); (P.-R.H.); (J.P.O.); (O.O.M.)
| | - Sai Man Liu
- Protein Sciences Department, Ipsen Bioinnovation Limited, 102 Park Drive, Milton Park, Abingdon OX14 4RY, UK;
| | - K. Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (K.S.G.); (P.-R.H.); (J.P.O.); (O.O.M.)
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Cimen C, Berends MS, Bathoorn E, Lokate M, Voss A, Friedrich AW, Glasner C, Hamprecht A. Vancomycin-resistant enterococci (VRE) in hospital settings across European borders: a scoping review comparing the epidemiology in the Netherlands and Germany. Antimicrob Resist Infect Control 2023; 12:78. [PMID: 37568229 PMCID: PMC10422769 DOI: 10.1186/s13756-023-01278-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
The rising prevalence of vancomycin-resistant enterococci (VRE) is a matter of concern in hospital settings across Europe without a distinct geographical pattern. In this scoping review, we compared the epidemiology of vancomycin-resistant Enterococcus spp. in hospitals in the Netherlands and Germany, between 1991 and 2022. We searched PubMed and summarized the national antibiotic resistance surveillance data of the two countries. We included 46 studies and summarized national surveillance data from the NethMap in the Netherlands, the National Antimicrobial Resistance Surveillance database in Germany, and the EARS-Net data. In total, 12 studies were conducted in hospitals in the Netherlands, 32 were conducted in German hospitals, and an additional two studies were conducted in a cross-border setting. The most significant difference between the two countries was that studies in Germany showed an increasing trend in the prevalence of VRE in hospitals, and no such trend was observed in studies in the Netherlands. Furthermore, in both Dutch and German hospitals, it has been revealed that the molecular epidemiology of VREfm has shifted from a predominance of vanA towards vanB over the years. According to national surveillance reports, vancomycin resistance in Enterococcus faecium clinical isolates fluctuates below 1% in Dutch hospitals, whereas it follows an increasing trend in German hospitals (above 20%), as supported by individual studies. This review demonstrates that VRE is more frequently encountered in German than in Dutch hospitals and discusses the underlying factors for the difference in VRE occurrence in these two neighboring countries by comparing differences in healthcare systems, infection prevention control (IPC) guidelines, and antibiotic use in the Netherlands and Germany.
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Affiliation(s)
- Cansu Cimen
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Matthijs S Berends
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Medical Epidemiology, Certe Medical Diagnostics and Advice Foundation, Groningen, The Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Andreas Voss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Corinna Glasner
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Axel Hamprecht
- Institute for Medical Microbiology and Virology, University of Oldenburg, Oldenburg, Germany
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Canli K, Bozyel ME, Turu D, Benek A, Simsek O, Altuner EM. Biochemical, Antioxidant Properties and Antimicrobial Activity of Steno-Endemic Origanum onites. Microorganisms 2023; 11:1987. [PMID: 37630547 PMCID: PMC10457892 DOI: 10.3390/microorganisms11081987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/29/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023] Open
Abstract
Origanum onites (Lamiaceae) is an Eastern Mediterranean plant that is widely used in Turkish traditional medicine. This study aimed to investigate the biochemical composition, antimicrobial activity, and antioxidant potential of O. onites. In this study, the biochemical composition of the O. onites ethanol extract (OOEt) was analyzed using GC-MS. The antimicrobial activity was investigated using a disk diffusion test and determining minimum inhibitory concentrations (MIC) against 30 microorganism strains, including 28 bacteria (some multidrug-resistant) and 2 fungi. Additionally, the antioxidant activity was evaluated using the DPPH method. The main component identified was carvacrol. OOEt demonstrated antimicrobial activity against a wide range of tested microorganism strains. OOEt displayed the highest activity against E. faecium (a Gram-positive bacterium) at 100 µL with a 52 mm inhibition zone. Additionally, P. aeruginosa DSMZ 50071 and P. fluorescens P1, which are Gram-negative bacteria, were the most sensitive strains with a 24 mm inhibition zone in 100 µL of OOEt. The data obtained from A. baumannii (a multidrug-resistant strain) is particularly striking, as higher activity was observed compared to all positive controls. All tested fungal strains showed more effective results than positive controls. The antioxidant activity of OOEt was found to be stronger than that of the positive control, ascorbic acid. This study determined that O. onites has significant antimicrobial and antioxidant potential.
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Affiliation(s)
- Kerem Canli
- Department of Biology, Faculty of Science, Dokuz Eylül University, Izmir 35390, Türkiye
- Fauna and Flora Research and Application Center, Dokuz Eylül University, Izmir 35390, Türkiye
| | - Mustafa Eray Bozyel
- Department of Biology, Faculty of Science, Dokuz Eylül University, Izmir 35390, Türkiye
| | - Dilay Turu
- Department of Biology, Graduate School of Natural and Applied Science, Dokuz Eylül University, Izmir 35390, Türkiye
| | - Atakan Benek
- Department of Biology, Graduate School of Natural and Applied Sciences, Kastamonu University, Kastamonu 37150, Türkiye
| | - Ozcan Simsek
- Department of Forestry, Yenice Vocational School, Çanakkale Onsekiz Mart University, Çanakkale 17950, Türkiye
| | - Ergin Murat Altuner
- Department of Biology, Faculty of Science, Kastamonu University, Kastamonu 37150, Türkiye
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Pongchaikul P, Romero R, Mongkolsuk P, Vivithanaporn P, Wongsurawat T, Jenjaroenpun P, Nitayanon P, Thaipisuttikul I, Kamlungkuea T, Singsaneh A, Santanirand P, Chaemsaithong P. Genomic analysis of Enterococcus faecium strain RAOG174 associated with acute chorioamnionitis carried antibiotic resistance gene: is it time for precise microbiological identification for appropriate antibiotic use? BMC Genomics 2023; 24:405. [PMID: 37468842 DOI: 10.1186/s12864-023-09511-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Preterm labor syndrome is associated with high perinatal morbidity and mortality, and intra-amniotic infection is a cause of preterm labor. The standard identification of causative microorganisms is based on the use of biochemical phenotypes, together with broth dilution-based antibiotic susceptibility from organisms grown in culture. However, such methods could not provide an accurate epidemiological aspect and a genetic basis of antimicrobial resistance leading to an inappropriate antibiotic administration. Hybrid genome assembly is a combination of short- and long-read sequencing, which provides better genomic resolution and completeness for genotypic identification and characterization. Herein, we performed a hybrid whole genome assembly sequencing of a pathogen associated with acute histologic chorioamnionitis in women presenting with PPROM. RESULTS We identified Enterococcus faecium, namely E. faecium strain RAOG174, with several antibiotic resistance genes, including vancomycin and aminoglycoside. Virulence-associated genes and potential bacteriophage were also identified in this genome. CONCLUSION We report herein the first study demonstrating the use of hybrid genome assembly and genomic analysis to identify E. faecium ST17 as a pathogen associated with acute histologic chorioamnionitis. The analysis provided several antibiotic resistance-associated genes/mutations and mobile genetic elements. The occurrence of E. faecium ST17 raised the awareness of the colonization of clinically relevant E. faecium and the carrying of antibiotic resistance. This finding has brought the advantages of genomic approach in the identification of the bacterial species and antibiotic resistance gene for E. faecium for appropriate antibiotic use to improve maternal and neonatal care.
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Affiliation(s)
- Pisut Pongchaikul
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital Mahidol University, Samut Prakan, Thailand
- Integrative Computational BioScience Center, Mahidol University, Nakhon Pathom, Thailand
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Roberto Romero
- Pregnancy Research Branch (formerly The Perinatology Research Branch, NICHD/NIH/DHHS, in Detroit, Michigan, USA, has been renamed as the Pregnancy Research Branch, NICHD/NIH/DHHS), Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
- Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, United States Department of Health and Human Services, Detroit, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Paninee Mongkolsuk
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital Mahidol University, Samut Prakan, Thailand
| | - Pornpun Vivithanaporn
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital Mahidol University, Samut Prakan, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Perapon Nitayanon
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Iyarit Thaipisuttikul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Threebhorn Kamlungkuea
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Arunee Singsaneh
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Piya Chaemsaithong
- Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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Sundar S, Piramanayagam S, Natarajan J. A comprehensive review on human disease-causing bacterial proteases and their impeding agents. Arch Microbiol 2023; 205:276. [PMID: 37414902 DOI: 10.1007/s00203-023-03618-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/20/2023] [Accepted: 06/24/2023] [Indexed: 07/08/2023]
Abstract
Proteases are enzymes that catalyze the amide bond dissociation in polypeptide and protein peptide units. They are categorized into seven families and are responsible for a wide spectrum of human ailments, such as various types of cancers, skin infections, urinary tract infections etc. Specifically, the bacterial proteases cause a huge impact in the disease progression. Extracellular bacterial proteases break down the host defense proteins, while intracellular proteases are essential for pathogens virulence. Due to its involvement in disease pathogenesis and virulence, bacterial proteases are considered to be potential drug targets. Several studies have reported potential bacterial protease inhibitors in both Gram-positive and Gram-negative disease causing pathogens. In this study, we have comprehensively reviewed about the various human disease-causing cysteine, metallo, and serine bacterial proteases as well as their potential inhibitors.
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Affiliation(s)
- Shobana Sundar
- Department of Biotechnology, PSG College of Technology, Coimbatore, India
| | | | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
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Monteiro Marques J, Coelho M, Santana AR, Pinto D, Semedo-Lemsaddek T. Dissemination of Enterococcal Genetic Lineages: A One Health Perspective. Antibiotics (Basel) 2023; 12:1140. [PMID: 37508236 PMCID: PMC10376465 DOI: 10.3390/antibiotics12071140] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Enterococcus spp. are commensals of the gastrointestinal tracts of humans and animals and colonize a variety of niches such as water, soil, and food. Over the last three decades, enterococci have evolved as opportunistic pathogens, being considered ESKAPE pathogens responsible for hospital-associated infections. Enterococci's ubiquitous nature, excellent adaptative capacity, and ability to acquire virulence and resistance genes make them excellent sentinel proxies for assessing the presence/spread of pathogenic and virulent clones and hazardous determinants across settings of the human-animal-environment triad, allowing for a more comprehensive analysis of the One Health continuum. This review provides an overview of enterococcal fitness and pathogenic traits; the most common clonal complexes identified in clinical, veterinary, food, and environmental sources; as well as the dissemination of pathogenic genomic traits (virulome, resistome, and mobilome) found in high-risk clones worldwide, across the One Health continuum.
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Affiliation(s)
- Joana Monteiro Marques
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Mariana Coelho
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Andressa Rodrigues Santana
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Daniel Pinto
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Teresa Semedo-Lemsaddek
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
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Kwentoh I, Henry T. Look Beyond Syncope: A Positive Outcome in the Management of Multiple Bladder Diverticuli-Associated Enterococcus faecium Urinary Tract Infection. Cureus 2023; 15:e42361. [PMID: 37525864 PMCID: PMC10387183 DOI: 10.7759/cureus.42361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2023] [Indexed: 08/02/2023] Open
Abstract
Enterococcus faecium is a Gram-positive flora bacterium home to the gastrointestinal tracts of humans. A true ubiquitous pathogen and a member of the intestinal microbiome, formerly known as group D streptococci, this pathogen has been around for over 10 centuries. Enterococcus faecium thrives in the presence of stool and sewage. The ability to cause endocarditis and urinary tract infections (UTIs) has led to morbidity and mortality in the adult population. We report a case of an elderly woman who presented with multiple falls to our trauma bay area. She was initially managed as trauma during multiple visits with superficial scalp lacerations. However, with multiple falls, she was subsequently transferred to medicine to rule out cardiogenic versus neurogenic syncope. She was admitted to the telemetry unit, and a cardiologist was consulted. Orthostatic vitals were negative, and she had no fever or leukocytosis. Abdominal computed tomography (CT) done as part of the standard trauma workup revealed an interesting finding of multiple bladder diverticula.
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Affiliation(s)
- Ifeoma Kwentoh
- Medicine, Columbia University, New York, USA
- Internal Medicine, Harlem Hospital Center, New York, USA
| | - Terrence Henry
- Internal Medicine, Harlem Hospital Center, New York, USA
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Wammes LJ, Voor In 't Holt AF, Klaassen CHW, Vos MC, Verkaik NJ, Severin JA. Contact tracing for vancomycin-resistant Enterococcus faecium (VRE): evaluation of the Dutch policy of quintuple screening cultures. Eur J Clin Microbiol Infect Dis 2023:10.1007/s10096-023-04632-7. [PMID: 37351725 DOI: 10.1007/s10096-023-04632-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Abstract
Detection of vancomycin-resistant Enterococcus faecium (VRE) is hampered by low sensitivity of rectal swab cultures. This study aimed to define the number of screening cultures needed to increase sensitivity to detect VRE transmission, and to determine time from presumed exposure to detectable colonization. In a tertiary care setting, we retrospectively analyzed data from 9 VRE outbreaks. As a proxy or estimation for time to detectable colonization, the time between first positive culture of the presumed index patient and that of their contacts was determined. Only 64% of secondary cases were positive in the first out of five cultures. By using the first three out of five rectal swabs, 89% (95%CI: 78-95%) of all secondary cases would have been identified. The median number of days between the positive culture of the index patient and the first positive culture of secondary cases was 9 days. Eleven percent of secondary cases would have been missed if only three rectal samples would have been obtained. Furthermore, our results show that one or more rectal swabs taken around day 9 after presumed exposure should at least be included in the screening approach. In our setting, obtaining a fourth and a fifth rectal swab showed a relevant additional value compared to only one to three swabs. Our findings are useful for determining the most effective VRE contact tracing approach to prevent transmission.
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Affiliation(s)
- Linda J Wammes
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
- Present address: Department of Medical Microbiology, LUMC Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Anne F Voor In 't Holt
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Corné H W Klaassen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Nelianne J Verkaik
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Juliëtte A Severin
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
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Udaondo Z, Abram K, Kothari A, Jun SR. Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas. Microbiol Spectr 2023; 11:e0490122. [PMID: 36995227 PMCID: PMC10269635 DOI: 10.1128/spectrum.04901-22] [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: 11/28/2022] [Accepted: 03/10/2023] [Indexed: 03/31/2023] Open
Abstract
Control of hospital-associated Enterococcus faecium infection is a strenuous task due to the difficulty of identifying transmission routes and the persistence of this nosocomial pathogen despite the implementation of infection control measures that have been successful with other important nosocomial pathogens. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from 66 cancer patients at the University of Arkansas for Medical Sciences (UAMS) between June 2018 and May 2019. In the top-down approach used in this study, we employed, in addition to the 106 E. faecium UAMS isolates, a filtered set of 2,167 E. faecium strains from the GenBank database to assess the current population structure of E. faecium species and, consequently, to identify the lineages associated with our clinical isolates. We then evaluated the antibiotic resistance and virulence profiles of hospital-associated strains from the species pool, focusing on antibiotics of last resort, to establish an updated classification of high-risk and multidrug-resistant nosocomial clones. Further investigation of the clinical isolates collected from UAMS patients using whole-genome sequencing analytical methodologies (core genome multilocus sequence typing [cgMLST], core single nucleotide polymorphism [coreSNP] analysis, and phylogenomics), with the addition of patient epidemiological data, revealed a polyclonal outbreak of three sequence types occurring simultaneously in different patient wards. The integration of genomic and epidemiological data collected from the patients increased our understanding of the relationships and transmission dynamics of the E. faecium isolates. Our study provides new insights into genomic surveillance of E. faecium to assist in monitoring and further limiting the spread of multidrug-resistant E. faecium. IMPORTANCE Enterococcus faecium is a member of the gastrointestinal microbiota. Although its virulence is low in healthy, immunocompetent individuals, E. faecium has become the third leading cause of health care-associated infections in the United States. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from cancer patients at the University of Arkansas for Medical Sciences (UAMS). We employed a top-down analytical approach (from population genomics to molecular biology) to classify our clinical isolates into their genetic lineages and thoroughly evaluate their antibiotic resistance and virulence profiles. The addition of patient epidemiological data to the whole-genome sequencing analytical methodologies performed in the study allowed us to increase our understanding of the relationships and transmission dynamics of the E. faecium isolates. This study provides new insights into genomic surveillance of E. faecium to help monitor and further limit the spread of multidrug-resistant E. faecium.
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Affiliation(s)
- Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Kaleb Abram
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Atul Kothari
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Se-Ran Jun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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Romanescu M, Oprean C, Lombrea A, Badescu B, Teodor A, Constantin GD, Andor M, Folescu R, Muntean D, Danciu C, Dalleur O, Batrina SL, Cretu O, Buda VO. Current State of Knowledge Regarding WHO High Priority Pathogens-Resistance Mechanisms and Proposed Solutions through Candidates Such as Essential Oils: A Systematic Review. Int J Mol Sci 2023; 24:9727. [PMID: 37298678 PMCID: PMC10253476 DOI: 10.3390/ijms24119727] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Combating antimicrobial resistance (AMR) is among the 10 global health issues identified by the World Health Organization (WHO) in 2021. While AMR is a naturally occurring process, the inappropriate use of antibiotics in different settings and legislative gaps has led to its rapid progression. As a result, AMR has grown into a serious global menace that impacts not only humans but also animals and, ultimately, the entire environment. Thus, effective prophylactic measures, as well as more potent and non-toxic antimicrobial agents, are pressingly needed. The antimicrobial activity of essential oils (EOs) is supported by consistent research in the field. Although EOs have been used for centuries, they are newcomers when it comes to managing infections in clinical settings; it is mainly because methodological settings are largely non-overlapping and there are insufficient data regarding EOs' in vivo activity and toxicity. This review considers the concept of AMR and its main determinants, the modality by which the issue has been globally addressed and the potential of EOs as alternative or auxiliary therapy. The focus is shifted towards the pathogenesis, mechanism of resistance and activity of several EOs against the six high priority pathogens listed by WHO in 2017, for which new therapeutic solutions are pressingly required.
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Affiliation(s)
- Mirabela Romanescu
- Doctoral School, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania; (M.R.); (A.L.); (B.B.); (A.T.); (G.D.C.)
- Faculty of Medicine, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania; (M.A.); (R.F.); (D.M.)
| | - Camelia Oprean
- Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania
- OncoGen Centre, County Hospital ‘Pius Branzeu’, Blvd. Liviu Rebreanu 156, 300723 Timisoara, Romania
| | - Adelina Lombrea
- Doctoral School, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania; (M.R.); (A.L.); (B.B.); (A.T.); (G.D.C.)
| | - Bianca Badescu
- Doctoral School, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania; (M.R.); (A.L.); (B.B.); (A.T.); (G.D.C.)
| | - Ana Teodor
- Doctoral School, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania; (M.R.); (A.L.); (B.B.); (A.T.); (G.D.C.)
| | - George D. Constantin
- Doctoral School, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania; (M.R.); (A.L.); (B.B.); (A.T.); (G.D.C.)
| | - Minodora Andor
- Faculty of Medicine, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania; (M.A.); (R.F.); (D.M.)
| | - Roxana Folescu
- Faculty of Medicine, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania; (M.A.); (R.F.); (D.M.)
| | - Delia Muntean
- Faculty of Medicine, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania; (M.A.); (R.F.); (D.M.)
- Multidisciplinary Research Center on Antimicrobial Resistance, “Victor Babes” University of Medicine and Pharmacy, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Corina Danciu
- Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluation, “Victor Babes” University of Medicine and Pharmacy, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Olivia Dalleur
- Louvain Drug Research Institute, Université Catholique de Louvain, Avenue Emmanuel Mounier 73, 1200 Brussels, Belgium
| | - Stefan Laurentiu Batrina
- Faculty of Agriculture, University of Life Sciences “King Mihai I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
| | - Octavian Cretu
- Faculty of Medicine, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania; (M.A.); (R.F.); (D.M.)
| | - Valentina Oana Buda
- Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy, 2 Eftimie Murgu Street, 300041 Timisoara, Romania
- Research Center for Pharmaco-Toxicological Evaluation, “Victor Babes” University of Medicine and Pharmacy, 2 Eftimie Murgu Square, 300041 Timisoara, Romania
- Ineu City Hospital, 2 Republicii Street, 315300 Ineu, Romania
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Huch S, Nersisyan L, Ropat M, Barrett D, Wu M, Wang J, Valeriano VD, Vardazaryan N, Huerta-Cepas J, Wei W, Du J, Steinmetz LM, Engstrand L, Pelechano V. Atlas of mRNA translation and decay for bacteria. Nat Microbiol 2023:10.1038/s41564-023-01393-z. [PMID: 37217719 DOI: 10.1038/s41564-023-01393-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
Regulation of messenger RNA stability is pivotal for programmed gene expression in bacteria and is achieved by a myriad of molecular mechanisms. By bulk sequencing of 5' monophosphorylated mRNA decay intermediates (5'P), we show that cotranslational mRNA degradation is conserved among both Gram-positive and -negative bacteria. We demonstrate that, in species with 5'-3' exonucleases, the exoribonuclease RNase J tracks the trailing ribosome to produce an in vivo single-nucleotide toeprint of the 5' position of the ribosome. In other species lacking 5'-3' exonucleases, ribosome positioning alters endonucleolytic cleavage sites. Using our metadegradome (5'P degradome) sequencing approach, we characterize 5'P mRNA decay intermediates in 96 species including Bacillus subtilis, Escherichia coli, Synechocystis spp. and Prevotella copri and identify codon- and gene-level ribosome stalling responses to stress and drug treatment. We also apply 5'P sequencing to complex clinical and environmental microbiomes and demonstrate that metadegradome sequencing provides fast, species-specific posttranscriptional characterization of responses to drug or environmental perturbations. Finally we produce a degradome atlas for 96 species to enable analysis of mechanisms of RNA degradation in bacteria. Our work paves the way for the application of metadegradome sequencing to investigation of posttranscriptional regulation in unculturable species and complex microbial communities.
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Affiliation(s)
- Susanne Huch
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Lilit Nersisyan
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
| | - Maria Ropat
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Donal Barrett
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Mengjun Wu
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Jing Wang
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Valerie D Valeriano
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Nelli Vardazaryan
- Armenian Bioinformatics Institute, Yerevan, Armenia
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
| | - Jaime Huerta-Cepas
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo-UPM, Madrid, Spain
| | - Wu Wei
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Juan Du
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden.
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47
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Pereira KE, Deslouches JT, Deslouches B, Woodley SK. In Vitro Investigation of the Antibacterial Activity of Salamander Skin Peptides. Curr Microbiol 2023; 80:214. [PMID: 37195436 DOI: 10.1007/s00284-023-03320-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 05/02/2023] [Indexed: 05/18/2023]
Abstract
Given the current and future costs of antibiotic-resistant bacteria to human health and economic productivity, there is an urgent need to develop new antimicrobial compounds. Antimicrobial peptides are a promising alternative to conventional antibiotics and other antimicrobials. Amphibian skin is a rich source of bioactive compounds, but the antibacterial properties of salamander skin peptides have been neglected. Here, we examined the in vitro ability of skin peptides from 9 species of salamander representing 6 salamander families to inhibit the growth of ESKAPE pathogens, which are bacteria that have developed resistance to conventional antibiotics. We also examined whether the skin peptides caused lysis of human red blood cells. Skin peptides from Amphiuma tridactylum had the greatest antimicrobial properties, completely inhibiting the growth of all bacterial strains except for Enterococcus faecium. Likewise, skin peptides from Cryptobranchus alleganiensis completely inhibited the growth of several of the bacterial strains. In contrast, skin peptide mixtures from Ambystoma maculatum, Desmognathus fuscus, Eurycea bislineata, E. longicauda, Necturus beyeri, N. maculosus, and Siren intermedia did not completely inhibit bacterial growth even at the highest concentrations. Finally, none of the skin peptide mixtures caused lysis of human red blood cells. Together, we demonstrate that salamander skin produces peptides with potent antibacterial properties. It remains to elucidate the peptide sequences and their antibacterial mechanisms.
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Affiliation(s)
- Kenzie E Pereira
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA, USA
| | | | - Berthony Deslouches
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah K Woodley
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA, USA.
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48
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Boschert AL, Arndt F, Hamprecht A, Wolke M, Walker SV. Comparison of Five Different Selective Agar for the Detection of Vancomycin-Resistant Enterococcus faecium. Antibiotics (Basel) 2023; 12:antibiotics12040666. [PMID: 37107028 PMCID: PMC10135216 DOI: 10.3390/antibiotics12040666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Five commercially available selective agar were evaluated regarding sensitivity and specificity to detect vancomycin-resistant Enterococcus (E.) faecium. Altogether 187 E. faecium strains were included, comprising 119 van-carrying strains (phenotypically vancomycin-resistant n = 105; phenotypically vancomycin-susceptible VVE-B n = 14) and 68 vancomycin-susceptible isolates. Limit of detection was calculated for each selective agar for pure cultures, stool suspensions and artificial rectal swabs. After 24-h incubation sensitivity ranged between 91.6% and 95.0%. It increased in 2 out of 5 agar after 48-h incubation. Specificity ranged between 94.1% and 100% and was highest after 24 h in 4 out of the 5 agar. Sensitivity of van-carrying phenotypically vancomycin-resistant strains was higher after 24 h (97.1–100%) and 48 h (99.1–100%) when compared to van-carrying strains that tested vancomycin-susceptible (50.0–57.1% after both incubation periods). Overall, chromID VRE, CHROMagar VRE and Brilliance VRE demonstrated the highest detection rates after 24 h. Detection rates of Chromatic VRE and VRESelect improved after 48 h. Adjustment of incubation time depending on the applied media may be advised. As detection of VVE-B was impeded with all selective agar, screening for vancomycin-resistant enterococci relying solely on selective media would not be recommended for critical clinical samples, but rather in combination with molecular methods to improve detection of these strains. Furthermore, stool samples were demonstrated to be superior to rectal swabs and should be favoured, if possible, in screening strategies.
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Affiliation(s)
- Alessa L. Boschert
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, 50935 Cologne, Germany
| | - Franca Arndt
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, 50935 Cologne, Germany
- German Aerospace Center (DLR), Institute of Aerospace Medicine, 51147 Cologne, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, 50935 Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 50441 Cologne, Germany
- Institute for Medical Microbiology and Virology, University of Oldenburg, 26001 Oldenburg, Germany
| | - Martina Wolke
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, 50935 Cologne, Germany
| | - Sarah V. Walker
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, 50935 Cologne, Germany
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, 50441 Cologne, Germany
- Institute for Clinical Microbiology and Hospital Hygiene, Klinikum Ludwigsburg, 71634 Ludwigsburg, Germany
- Correspondence:
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49
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Khan K, Jalal K, Uddin R. Pangenome profiling of novel drug target against vancomycin-resistant Enterococcus faecium. J Biomol Struct Dyn 2023; 41:15647-15660. [PMID: 36935100 DOI: 10.1080/07391102.2023.2191134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/07/2023] [Indexed: 03/20/2023]
Abstract
Enterococcus faecium is a frequent causative agent of nosocomial infection mainly acquired from outgoing hospital patients (Hospital Acquired Infection-HAIs). They are largely involved in the outbreaks of bacteremia, UTI, and endocarditis with a high transmissibility rate. The recent emergence of VRE strain (i.e. vancomycin resistant enterococcus) turned it into high priority pathogen for which new drug research is of dire need. Therefore, in current study, pangenome and resistome analyses were performed for available antibiotic-resistant genomes (n = 216) of E. faecium. It resulted in the prediction of around 5,059 genes as an accessory gene, 1,076 genes as core and 1,558 genes made up a unique genome fraction. Core genes common to all strains were further used for the identification of potent drug targets by applying subtractive genomics approach. Moreover, the COG functional analysis showed that these genomes are highly enriched in metabolic pathways such as in translational, ribosomal, proteins, carbohydrates and nucleotide transport metabolism. Through subtractive genomics it was observed that 431 proteins were non-homologous to the human proteome, 166 identified as essential for pathogen survival while 26 as potential and unique therapeutic targets. Finally, 3-dehydroquinate dehydrogenase was proposed as a potent drug target for further therapeutic candidate identification. Moreover, the molecular docking and dynamic simulation technique were applied to performed a virtual screening of natural product libraries (i.e., TCM and Ayurvedic compounds) along with 3-amino-4,5-dihydroxy-cyclohex-1-enecarboxylate (DHS) as a standard compound to validate the study. Consequently, Argeloside I, Apigenin-7-O-gentiobioside (from Ayurvedic library), ZINC85571062, and ZINC85570908 (TCM library) compounds were identified as potential inhibitors of 3-dehydroquinate dehydrogenase. The study proposed new compounds as novel therapeutics, however, further experimental validation is needed as a follow-up.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Khurshid Jalal
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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50
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Chen P, An L, Zhang Z. Sequential Therapy of Linezolid and Contezolid to Treat Vancomycin-Resistant Enterococcus faecium Pneumonia in a Centenarian Patient: Case Report. Infect Drug Resist 2023; 16:1573-1578. [PMID: 36969942 PMCID: PMC10032165 DOI: 10.2147/idr.s401533] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Enterococcus faecium (E. faecium) is one of the core components of enterococci and causes serious illnesses in the elderly and immunocompromised patients. Due to its adaptive traits and antibiotic resistance, E. faecium has evolved as a worldwide hospital-associated pathogen, especially vancomsycin-resistant Enterococcus faecium (VREfm). Pneumonia caused by VREfm is quite rare in clinical settings, and optimal treatment has not yet been determined. Here, we present a case of nosocomial VREfm pneumonia with lung cavitation following adenovirus infection, which was successfully treated with linezolid and contezolid.
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Affiliation(s)
- Pengzhi Chen
- Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Li An
- Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Zhijian Zhang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, People’s Republic of China
- Correspondence: Zhijian Zhang, Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, People’s Republic of China, Tel +86 17701090515, Email
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