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Guruge SK, Han Z, Karunaratne SHPP, Chandrajith R, Cooray T, Hu C, Zhang Y, Yang M. Short- and long-read metagenomics uncover the mobile extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater in Sri Lanka. WATER RESEARCH 2025; 283:123831. [PMID: 40412032 DOI: 10.1016/j.watres.2025.123831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2025] [Revised: 05/08/2025] [Accepted: 05/13/2025] [Indexed: 05/27/2025]
Abstract
The antibiotic resistance issue in low- and middle-income countries has drawn global concern. This study presents the first metagenomic investigation of antibiotic resistance genes (ARGs) in hospital and municipal wastewater treatment plants (WWTPs) in Sri Lanka, using Illumina short-read and Nanopore long-read sequencing. Samples from three representative WWTPs receiving hospital and/or municipal wastewater (domestic generated) were collected from four districts in Sri Lanka, and as a comparison, wastewater directly discharged without treatment was also taken. ARG abundance was significantly higher in hospital wastewater (7.22 copies/cell) than in municipal wastewater (2.33 copies/cell), and greatly decreased by 82 % and 93 % after treatment processes, respectively. Similar trends were observed for mobile genetic elements. The prevalent subtypes of clinically relevant extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater were blaOXA, blaGES, blaVEB and blaTEM, whereas blaCTX-M and blaNDM were less dominant, which indicated the potential unique distribution pattern of ESBL and carbapenemase genes in Sri Lanka. Using long-read metagenomics, bacterial host range and genetic locations (plasmid or chromosome) of ARGs in sludge samples were predicted. Diverse pathogenic host taxa (Pseudomonas, Streptococcus, Salmonella and Escherichia) and a higher plasmid proportion were identified in the hospital WWTP (39.8 % vs. 21.5 % in the municipal WWTP). Detected mobile genetic contexts in this study, IS6100-sul1-blaOXA-329-blaGES-5-blaGES-5-intI1 and ISKpn6-blaKPC-2-ISKpn7-ISPsy42, were also common in antibiotic-resistant plasmids in Enterobacteriaceae from different countries. These data will serve to expand the inventory of global ARG epidemiology. Also, the finding emphasizes that the wastewater treatment projects, especially in healthcare facilities, are vital for reducing clinically relevant ARG discharge to the environment. Further monitoring using advanced meta-omics approaches is crucial to assess potential ARG risks and optimize control strategies for improving human and ecosystem health in Sri Lanka.
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Affiliation(s)
- Shashika Kumudumali Guruge
- Key Laboratory of Environmental Aquatic Chemistry, State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, 100049, Beijing, PR China
| | - Ziming Han
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China
| | | | - Rohana Chandrajith
- Faculty of Science, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Titus Cooray
- Faculty of Applied Sciences, Uva Wellassa University, Badulla 90000, Sri Lanka
| | - Chengzhi Hu
- Key Laboratory of Environmental Aquatic Chemistry, State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, 100049, Beijing, PR China
| | - Yu Zhang
- Key Laboratory of Environmental Aquatic Chemistry, State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; University of Chinese Academy of Sciences, 100049, Beijing, PR China.
| | - Min Yang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; University of Chinese Academy of Sciences, 100049, Beijing, PR China.
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Lathakumari RH, Vajravelu LK, Thulukanam J, Narasimhan AK. Next-Gen Nano Biosensor Technologies to Monitor Carbapenem Resistance for Personalized Medicine. Indian J Microbiol 2025; 65:277-296. [PMID: 40371034 PMCID: PMC12069791 DOI: 10.1007/s12088-024-01337-z] [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: 03/31/2024] [Accepted: 06/12/2024] [Indexed: 05/16/2025] Open
Abstract
Carbapenem resistance represents a pressing public health concern, posing significant challenges due to limited treatment options and escalating mortality rates. In India, the prevalence of carbapenem resistance among Enterobacteriaceae ranges between 18 to 31%, causing severe infections such as bloodstream infections, pneumonia, urinary tract infections, and intra-abdominal infections. Accurate and timely diagnosis, particularly for Enterobacteriaceae producing carbapenemase, is crucial for effective clinical prophylaxis of critical care patients as they are considered as a last resort of therapy. Various genotypic and non-genotypic detection methods have been developed over the past decade, their limitations in terms of sensitivity and specificity have led the exploration of innovative technologies. Advanced opportunities for carbapenem resistance detection using microfluidic-based biosensors have miniaturized various biomedical devices. This enables the use of less sample and reagents, cheap pricing, automation, screening, and improved detection. Despite ongoing research and development, the adoption of these biosensors in healthcare settings is limited due to the lack of awareness and understanding of their efficiency. Therefore, this review primarily focuses on the advantages and limitations of all biosensor-based devices over existing methods for the detection of carbapenem resistance in gram negative bacilli. These biosensors represent substantial advancements in combating carbapenem resistance, providing promise for more reliable and accurate diagnostic techniques that may eventually improve patient care and infection control.
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Affiliation(s)
- Rahul Harikumar Lathakumari
- Department of Microbiology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Leela Kakithakara Vajravelu
- Department of Microbiology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Jayaprakash Thulukanam
- Department of Microbiology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - Ashwin Kumar Narasimhan
- Advanced Nano-Theranostics (ANTs) Research Group, Biomaterials Lab, Department of Biomedical Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203 India
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Peterle VM, Cardoso JAB, Ferraz CM, Sousa DFD, Pereira N, Nassar AFDC, Castro V, Mathias LA, Cardozo MV, Rossi GAM. Microbiological Quality of Coconut Water Sold in the Grande Vitória Region, Brazil, and Phenogenotypic Antimicrobial Resistance of Associated Enterobacteria. Microorganisms 2024; 12:1883. [PMID: 39338557 PMCID: PMC11434256 DOI: 10.3390/microorganisms12091883] [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: 08/18/2024] [Revised: 09/03/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
This study aimed to evaluate the microbiological quality of coconut water sold from street carts equipped with cooling coils or refrigerated at bakeries in the Grande Vitória Region, Brazil. Additionally, it assessed the phenotypic and genotypic antimicrobial resistance profiles of isolated enterobacteria. The results indicated that coconut water sold at street carts had lower microbiological quality compared to refrigerated samples, as evidenced by significantly higher counts of mesophilic microorganisms. Using MALDI-TOF, the following opportunistic pathogens were identified: Citrobacter freundii, Enterobacter bugandensis, E. kobei, E. roggenkampii, Klebsiella pneumoniae, and Kluyvera ascorbata. Three isolates-E. bugandensis, K. pneumoniae, and K. ascorbata-were classified as multidrug-resistant (MDR). Widespread resistance to β-lactams and cephalosporins was detected, and some isolates were resistant to quinolones, nitrofurans, and phosphonic acids. The gene blaCTX-M-2 was detected in C. freundii, E. bugandensis, E. kobei, and K. ascorbata. However, genes blaNDM, blaKPC, blaCMY-1, and blaCMY-2 were not detected in any isolate. The findings underscore the need to enhance good manufacturing practices in this sector to control the spread of antimicrobial resistance (AMR). To our knowledge, this is the first study documenting the presence of potentially pathogenic enterobacteria in coconut water samples and their associated phenotypic and genotypic AMR profiles.
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Affiliation(s)
- Valéria Modolo Peterle
- Department of Veterinary Medicine, University of Vila Velha (UVV), Vila Velha 29102-920, ES, Brazil
| | | | - Carolina Magri Ferraz
- Department of Veterinary Medicine, University of Vila Velha (UVV), Vila Velha 29102-920, ES, Brazil
| | | | - Natália Pereira
- Department of Pathology, Reproduction and One Health, Sao Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil
| | | | - Vanessa Castro
- Instituto Biológico (IB) de São Paulo, Rua Conselheiro Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil
| | - Luis Antonio Mathias
- Department of Pathology, Reproduction and One Health, Sao Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil
| | - Marita Vedovelli Cardozo
- Department of Pathology, Reproduction and One Health, Sao Paulo State University (UNESP), Jaboticabal 14884-900, SP, Brazil
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Hoarau AOG, Mavingui P, Miltgen G. Comprehensive analysis of antimicrobial resistance in the Southwest Indian Ocean: focus on WHO critical and high priority pathogens. Front Public Health 2024; 12:1357345. [PMID: 38628847 PMCID: PMC11018943 DOI: 10.3389/fpubh.2024.1357345] [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: 12/17/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
The spread of antimicrobial resistance (AMR) is a major global concern, and the islands of the Southwest Indian Ocean (SWIO) are not exempt from this phenomenon. As strategic crossroads between Southern Africa and the Indian subcontinent, these islands are constantly threatened by the importation of multidrug-resistant bacteria from these regions. In this systematic review, our aim was to assess the epidemiological situation of AMR in humans in the SWIO islands, focusing on bacterial species listed as priority by the World Health Organization. Specifically, we examined Enterobacterales, Acinetobacter spp., Pseudomonas spp. resistant to carbapenems, and Enterococcus spp. resistant to vancomycin. Our main objectives were to map the distribution of these resistant bacteria in the SWIO islands and identify the genes involved in their resistance mechanisms. We conducted literature review focusing on Comoros, Madagascar, Maldives, Mauritius, Mayotte, Reunion Island, Seychelles, Sri Lanka, and Zanzibar. Our findings revealed a growing interest in the investigation of these pathogens and provided evidence of their active circulation in many of the territories investigated. However, we also identified disparities in terms of data availability between the targeted bacteria and among the different territories, emphasizing the need to strengthen collaborative efforts to establish an efficient regional surveillance network.
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Affiliation(s)
- Axel O. G. Hoarau
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Patrick Mavingui
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Guillaume Miltgen
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
- Laboratoire de Bactériologie, CHU Félix Guyon, Saint-Denis, La Réunion, France
- Centre Régional en Antibiothérapie (CRAtb) de La Réunion, Saint-Pierre, La Réunion, France
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Bologna E, Licari LC, Manfredi C, Ditonno F, Cirillo L, Fusco GM, Abate M, Passaro F, Di Mauro E, Crocetto F, Pandolfo SD, Aveta A, Cilio S, Di Filippo I, Barone B, Franco A, Arcaniolo D, La Rocca R, Pinchera B, Napolitano L. Carbapenem-Resistant Enterobacteriaceae in Urinary Tract Infections: From Biological Insights to Emerging Therapeutic Alternatives. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:214. [PMID: 38399502 PMCID: PMC10889937 DOI: 10.3390/medicina60020214] [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: 12/30/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024]
Abstract
Urinary tract infections (UTIs) are the second most frequent type of infection observed in clinical practice. Gram-negative Enterobacteriaceae are common pathogens in UTIs. Excessive antibiotic use in humans and animals, poor infection control, and increased global travel have accelerated the spread of multidrug-resistant strains (MDR). Carbapenem antibiotics are commonly considered the last line of defense against MDR Gram-negative bacteria; however, their efficacy is now threatened by the increasing prevalence of carbapenem-resistant Enterobacteriaceae (CRE). This comprehensive review aims to explore the biological mechanisms underlying carbapenem resistance and to present a focus on therapeutic alternatives currently available for complicated UTIs (cUTIs). A comprehensive bibliographic search was conducted on the PubMed/MEDLINE, Scopus, and Web of Science databases in December 2023. The best evidence on the topic was selected, described, and discussed. Analyzed with particular interest were the clinical trials pivotal to the introduction of new pharmacological treatments in the management of complicated cUTIs. Additional suitable articles were collected by manually cross-referencing the bibliography of previously selected papers. This overview provides a current and comprehensive examination of the treatment options available for CRE infections, offering a valuable resource for understanding this constantly evolving public health challenge.
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Affiliation(s)
- Eugenio Bologna
- Unit of Urology, Department of Maternal-Child and Urological Sciences, Policlinico Umberto I Hospital, “Sapienza” University, 00161 Rome, Italy; (E.B.); (L.C.L.)
| | - Leslie Claire Licari
- Unit of Urology, Department of Maternal-Child and Urological Sciences, Policlinico Umberto I Hospital, “Sapienza” University, 00161 Rome, Italy; (E.B.); (L.C.L.)
| | - Celeste Manfredi
- Unit of Urology, Department of Woman, Child and General and Specialized Surgery, University of Campania “Luigi Vanvitelli”, 80131 Naples, Italy;
| | - Francesco Ditonno
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata, 37100 Verona, Italy;
| | - Luigi Cirillo
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
| | - Giovanni Maria Fusco
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
| | - Marco Abate
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
| | - Francesco Passaro
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
| | - Ernesto Di Mauro
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
| | - Felice Crocetto
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
| | - Savio Domenico Pandolfo
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
- Department of Urology, University of L’Aquila, 67010 L’Aquila, Italy
| | - Achille Aveta
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
| | - Simone Cilio
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
| | - Isabella Di Filippo
- Department of Clinical Medicine and Surgery, Section of Infectious Diseases, University of Naples “Federico II”, 80131 Naples, Italy; (I.D.F.); (B.P.)
| | - Biagio Barone
- Division of Urology, Department of Surgical Sciences, AORN Sant’Anna e San Sebastiano, 81100 Caserta, Italy;
| | - Antonio Franco
- Department of Urology, Sant’Andrea Hospital, “Sapienza” University, 00189 Rome, Italy;
| | - Davide Arcaniolo
- Unit of Urology, Department of Woman, Child and General and Specialized Surgery, University of Campania “Luigi Vanvitelli”, 80131 Naples, Italy;
| | - Roberto La Rocca
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
| | - Biagio Pinchera
- Department of Clinical Medicine and Surgery, Section of Infectious Diseases, University of Naples “Federico II”, 80131 Naples, Italy; (I.D.F.); (B.P.)
| | - Luigi Napolitano
- Department of Neurosciences, Science of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (L.C.); (G.M.F.); (M.A.); (F.P.); (E.D.M.); (F.C.); (S.D.P.); (A.A.); (S.C.); (R.L.R.); (L.N.)
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Khadka C, Shyaula M, Syangtan G, Bista S, Tuladhar R, Singh A, Joshi DR, Pokhrel LR, Dawadi P. Extended-spectrum β-lactamases producing Enterobacteriaceae (ESBL-PE) prevalence in Nepal: A systematic review and meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166164. [PMID: 37572913 DOI: 10.1016/j.scitotenv.2023.166164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/09/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
An alarming increase in the occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-PE) has threatened the treatment and management of bacterial infections. This systematic review and meta-analysis aimed to provide a quantitative estimate of the prevalence of ESBL among the members of the Enterobacteriaceae family by analyzing the community-based and clinical studies published between 2011 and 2021 from Nepal and determine if ESBL-PE correlates with multidrug resistance (MDR). The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines were followed for systematic review and meta-analysis and the articles' quality was assessed using the Newcastle-Ottawa scale. Of the 2529 articles screened, 65 articles were systematically reviewed, data extracted, and included in in-depth meta-analysis. The overall pooled prevalence of ESBL-producers in Enterobacteriaceae was 29 % (95 % CI: 26-32 %) with high heterogeneity (I2 = 96 %, p < 0.001). Escherichia coli was the predominant ESBL-producing member of the Enterobacteriaceae family, followed by Citrobacter spp. and Klebsiella spp. The prevalence of ESBL-PE increased from 18.7 % in 2011 to 29.5 % in 2021. A strong positive correlation (r = 0.98) was observed between ESBL production and MDR in Enterobacteriaceae. ESBL-PE isolates showed high resistance to ampicillin, cephalosporins, and amoxicillin-clavulanic acid, and blaCTX-M type was the most reported gene variant among ESBL-PE. In conclusion, this study demonstrated an increased prevalence of ESBL-PE in Nepal over the last decade, and such isolates showed a high level of MDR against the β-lactams and non-β-lactam antibiotics. Tackling the rising antibiotic resistance (AR) and MDR in ESBL-PE would require concerted efforts from all stakeholders to institute effective infection control programs in the community and clinical settings.
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Affiliation(s)
- Christina Khadka
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Manita Shyaula
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Gopiram Syangtan
- Shi-Gan International College of Science and Technology, Tribhuvan University, Kathmandu, Nepal
| | - Shrijana Bista
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Reshma Tuladhar
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Anjana Singh
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal; Faculty of Science, Nepal Academy of Science and Technology, Khumaltar, Lalitpur, Nepal
| | - Dev Raj Joshi
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Lok R Pokhrel
- Department of Public Health, The Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA.
| | - Prabin Dawadi
- Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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Belouad EM, Benaissa E, El Mrimar N, Bssaibis F, Maleb A, Elouennass M. Predominance of OXA-48 Carbapenemase-Producing Enterobacterales in a Moroccan Hospital. Int J Microbiol 2023; 2023:8581883. [PMID: 37250920 PMCID: PMC10219769 DOI: 10.1155/2023/8581883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 02/23/2023] [Accepted: 05/06/2023] [Indexed: 05/31/2023] Open
Abstract
Objective The emergence of carbapenemase-producing Enterobacterales (CPE) is a major concern that is increasingly reported worldwide. Our study aimed at investigating the resistance of CPE isolates in a Moroccan teaching hospital using phenotypic and genotypic methods. Methods Enterobacterales strains from March to June 2018 were collected from different clinical samples. The Enterobacterales isolates resistant to third-generation cephalosporins (3GC) and/or carbapenems were subjected to the Carba NP test and an immunochromatographic test for phenotypic detection. Detection of extended-spectrum β-lactamases (ESBL) was also performed following standards. Molecular screening of carbapenemases genes (OXA-48, NDM, blaKPC, blaIMP, blaVIM, and blaOXA-24, blaOXA-23, OXA-51, OXA-58) using conventional multiplex PCR assays was also performed on 143 isolates. Results Enterobacterales represented 52.7% with a proportion of 21.8% of bacteria resistant to 3GC and/or carbapenems. Within 143 isolates MDR to 3GC, K. pneumoniae, E. coli, and E. cloacae represent 53.1%, 40.6%, and 6.3%, respectively. These strains were isolated mainly from urinary samples (74.8%) in patients admitted to emergency and surgical units. 81.1% of strains are producing ESBL and 29% are carbapenemase producers as confirmed by the Carba NP test, immunochromatographic test, and molecular testing. OXA-48 carriers represent 83.3% of these strains, followed by NDM with 16.7%. blaKPC, blaIMP, blaVIM, and blaOXA-24, blaOXA-23, OXA-51, OXA-58 were not detected in any of these bacteria. Conclusions A high rate of CPE carrying OXA-48 among Enterobacterales resistant to 3GC and/or carbapenems isolates was found. Strict observance of hospital hygiene measures and more rational use of antibiotics are mandatory. Implantation of carbapenemases detection should be encouraged in our hospital settings to estimate the true burden of the CPE.
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Affiliation(s)
- El Mehdi Belouad
- Department of Clinical Bacteriology, Mohammed V Military Teaching Hospital, Rabat, Morocco
- Research Team of Epidemiology and Bacterial Resistance, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Elmostafa Benaissa
- Department of Clinical Bacteriology, Mohammed V Military Teaching Hospital, Rabat, Morocco
- Research Team of Epidemiology and Bacterial Resistance, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Nadia El Mrimar
- Research Team of Epidemiology and Bacterial Resistance, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Fatna Bssaibis
- Department of Clinical Bacteriology, Mohammed V Military Teaching Hospital, Rabat, Morocco
| | - Adil Maleb
- Research Team of Epidemiology and Bacterial Resistance, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Mostafa Elouennass
- Department of Clinical Bacteriology, Mohammed V Military Teaching Hospital, Rabat, Morocco
- Research Team of Epidemiology and Bacterial Resistance, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
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Ariyawansa S, Gunawardana KN, Hapudeniya MM, Manelgamage NJ, Karunarathne CR, Madalagama RP, Ubeyratne KH, Wickramasinghe D, Tun HM, Wu P, Lam TTY, Chan OSK. One Health Surveillance of Antimicrobial Use and Resistance: Challenges and Successes of Implementing Surveillance Programs in Sri Lanka. Antibiotics (Basel) 2023; 12:antibiotics12030446. [PMID: 36978313 PMCID: PMC10044479 DOI: 10.3390/antibiotics12030446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/09/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Background: Sri Lanka is a low-income country, as defined by the World Bank. The country suffered further economic downturn during the COVID-19 pandemic. This situation adversely affected the prioritization of policies and programs around healthcare and public health. In particular, inflation, fuel prices, and shortage of food supplies increased struggles to implement antimicrobial resistance (AMR) programs. However, in the long run, it is crucial to gather data and evidence to plan AMR policies and track interventions. (1) Aim: To establish and reiterate the importance of prioritizing AMR programs in the One Health framework, the Fleming Fellows collected and studied antimicrobial use/consumption (AMU/AMC) and resistance (AMR) in humans, food-producing animals, and the environment. (2) Methods: A systematic and cross-sectional study was conducted between 2019 and 2021. By way of coordinating an AMU/AMC and AMR prevalence study across six agencies from human health and food-producing animal sectors, the authors established a field epidemiology study, laboratory testing, and data processing at their institutions. AMU/AMC patterns were surveyed using questionnaires and interviews, while AMR samples were collected for antibiotic susceptibility tests and genomic tests. Samples were tested for phenotypic and genotypic resistance. (3) Results: In human samples, resistance was highest to beta-lactam antibiotics. In non-human samples, resistance was highest to erythromycin, a highest-priority, critically important antibiotic defined by the World Health Organization. From government records, tylosin was sold the most in the food-producing animal sector. (4) Conclusions: Sri Lanka AMU and AMR trends in human and non-human sectors can be ascertained by a One Health framework. Further coordinated, consistent, and sustainable planning is feasible, and can help implement an AMU/AMR surveillance system in Sri Lanka.
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Affiliation(s)
- Sujeewa Ariyawansa
- National Aquatic Resources Research and Development Agency, Crow Island, Colombo 01500, Sri Lanka
| | | | | | - Nimal J. Manelgamage
- Department of Animal Production and Health, No. 13, Getambe, Peradeniya, Kandy 20400, Sri Lanka
| | - Chinthana R. Karunarathne
- Department of Animal Production and Health, Veterinary Investigation Centre, Court Road, Wariyapola 60400, Sri Lanka
| | | | | | | | - Hein M. Tun
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peng Wu
- The School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 7 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Tommy T. Y. Lam
- The School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 7 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Olivia S. K. Chan
- The School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 7 Sassoon Road, Pokfulam, Hong Kong SAR, China
- Correspondence: or
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9
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Phenotypic and genotypic distribution of ESBL, AmpC β-lactamase and carbapenemase-producing Enterobacteriaceae in community acquired (CA-UTI) and hospital acquired urinary tract infections (HA-UTI) in Sri Lanka. J Glob Antimicrob Resist 2022; 30:115-122. [PMID: 35667644 DOI: 10.1016/j.jgar.2022.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/25/2022] [Accepted: 05/25/2022] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Although Sri Lanka belongs to a region with a high prevalence of extended-spectrum β-lactamase (ESBL), AmpC β-lactamase and carbapenemase-producing Enterobacteriaceae, data regarding antimicrobial resistance (AMR) is limited. We studied the prevalence and diversity of β-lactamases produced by Enterobacteriaceae urinary pathogens from two hospitals in the Western Province of Sri Lanka. METHODS ESBL, AmpC β-lactamase and carbapenemase production was detected by phenotypic testing followed by genotyping. RESULTS The species responsible for urinary tract infections (UTI) were Escherichia coli (69%), Klebsiella pneumoniae (16%) and Enterobacter sp (6%). The prevalence of ESBL (50%), AmpC β-lactamase (19%) and carbapenemase (11%) phenotypes was high, and greater in hospital acquired (HA-UTI) (75%) than community acquired UTI (CA-UTI) (42%). Identification of CA-UTI caused by carbapenemase-producing Enterobacteriaceae (5%) is alarming. Only one ESBL gene, blaCTX- M-15, was detected. AmpC β-lactamase genes found in E. coli and K. pneumoniae were blaCMY-2, blaCMY-42 and blaDHA-1while Enterobacter sp. carried blaACT-1. Carbapenemase genes were blaNDM-1, blaNDM-4, blaOXA-181 and blaOXA-232 while blaKPC, blaIMP and blaVIM were absent. Co-occurrence of multiple bla genes, with some isolates harbouring 6 different bla genes, was common. Carbapenem resistant isolates without carbapenemase genes displayed mutations in the outer membrane porin genes, ompF of E. coli and omp36 of K. pneumoniae. Factors associated with UTI with β-lactamase-producing Enterobacteriaceae were age ≥50 years, previous hospitalization, presence of an indwelling urinary catheter, history of diabetes mellitus or other chronic illness and recurrent urinary tract infections. CONCLUSIONS This study adds to the currently scarce data on AMR in Sri Lanka.
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Metagenomic Approaches Reveal Strain Profiling and Genotyping of Klebsiella pneumoniae from Hospitalized Patients in China. Microbiol Spectr 2022; 10:e0219021. [PMID: 35319275 PMCID: PMC9045201 DOI: 10.1128/spectrum.02190-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae is a leading cause of highly drug-resistant infections in hospitals worldwide. Strain-level bacterial identification on the genetic determinants of multidrug resistance and high pathogenicity is critical for the surveillance and treatment of this clinically relevant pathogen. In this study, metagenomic next-generation sequencing was performed for specimens collected from August 2020 to May 2021 in Ruijin Hospital, Ningbo Women and Children’s Hospital, and the Second Affiliated Hospital of Harbin Medical University. Genome biology of K. pneumoniae prevalent in China was characterized based on metagenomic data. Thirty K. pneumoniae strains derived from 14 sequence types were identified by multilocus sequence typing. The hypervirulent ST11 K. pneumoniae strains carrying the KL64 capsular locus were the most prevalent in the hospital population. The phylogenomic analyses revealed that the metagenome-reconstructed strains and public isolate genomes belonging to the same STs were closely related in the phylogenetic tree. Furthermore, the pangenome structure of the detected K. pneumoniae strains was analyzed, particularly focusing on the distribution of antimicrobial resistance genes and virulence genes across the strains. The genes encoding carbapenemases and extended-spectrum beta-lactamases were frequently detected in the strains of ST11 and ST15. The highest numbers of virulence genes were identified in the well-known hypervirulent strains affiliated to ST23 bearing the K1 capsule. In comparison to traditional cultivation and identification, strain-level metagenomics is advantageous to understand the mechanisms underlying resistance and virulence of K. pneumoniae directly from clinical specimens. Our findings should provide novel clues for future research into culture-independent metagenomic surveillance for bacterial pathogens. IMPORTANCE Routine culture and PCR-based molecular testing in the clinical microbiology laboratory are unable to recognize pathogens at the strain level and to detect strain-specific genetic determinants involved in virulence and resistance. To address this issue, we explored the strain-level profiling of K. pneumoniae prevalent in China based on metagenome-sequenced patient materials. Genome biology of the targeted bacterium can be well characterized through decoding sequence signatures and functional gene profiles at the single-strain resolution. The in-depth metagenomic analysis on strain profiling presented here shall provide a promising perspective for culture-free pathogen surveillance and molecular epidemiology of nosocomial infections.
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11
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Sri Ranganathan S, Wanigatunge C, Senadheera GPSG, Beneragama BVSH. A national survey of antibacterial consumption in Sri Lanka. PLoS One 2021; 16:e0257424. [PMID: 34520501 PMCID: PMC8439449 DOI: 10.1371/journal.pone.0257424] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/31/2021] [Indexed: 01/21/2023] Open
Abstract
INTRODUCTION Optimizing the use of antibacterial medicines is an accepted strategy to combat the antibacterial resistance. Availability of reliable antibacterial consumption (ABC) data is a prerequisite to implement this strategy. OBJECTIVES To quantify and describe the national ABC in Sri Lanka and to examine any differences in the consumption between public and private sector. METHODS The methodology for this survey was adapted from World Health Organization (WHO) methodology for a global programme on surveillance of antimicrobial consumption. Aggregate data on national consumption of systemic antibacterials (J01- Anatomical Therapeutic Chemical Classification (ATC) for 2017 were retrospectively extracted from all available data sources and classified using ATC classification. Quantity of consumption was converted to Defined Daily Doses (DDDs). Data are presented as total consumption and comparison between the public and private sector. Selected key quality indicators of ABC were compared between these two sectors. FINDINGS From the available data sources, the total ABC in 2017 was 343.46 million DDDs. Private sector consumption accounted for 246.76 million DDDs compared to 97.96 million DDDs distributed to entire public sector by the Ministry of Health. Beta-lactam-penicillins antibacterial group accounted for 58.79% in public sector compared to 27.48% in private sector while macrolides, quinolones and other beta-lactam antibacterials accounted for 60.51% in the private compared to 28.41% in public sector. Consumption of Reserve group antibacterials was negligible, and limited to private sector. Watch category antibacterials accounted for 46%, 24% and 54% of the total, public and private sector consumption, respectively. CONCLUSIONS A disproportionately higher use of broad spectrum and Watch category antibacterials was observed in the private sector which needs further study. This national consumption survey highlights the need and provides the opening for establishment of ABC surveillance in Sri Lanka.
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Affiliation(s)
| | - Chandanie Wanigatunge
- Department of Pharmacology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Sri Jayewardenepura, Sri Lanka
| | - G. P. S. G. Senadheera
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Allied Health Sciences, University of Sri Jayewardenepura, Sri Jayewardenepura, Sri Lanka
| | - B. V. S. H. Beneragama
- National focal point for combating antimicrobial resistance in Sri Lanka, Ministry of Health, Colombo, Sri Lanka
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12
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Li Z, Ding Z, Yang J, Liu Y, Jin X, Xie J, Li T, Ding Y, Zeng Z, Liu J. Carbapenem-Resistant Klebsiella pneumoniae in Southwest China: Molecular Characteristics and Risk Factors Caused by KPC and NDM Producers. Infect Drug Resist 2021; 14:3145-3158. [PMID: 34413658 PMCID: PMC8370685 DOI: 10.2147/idr.s324244] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/04/2021] [Indexed: 12/19/2022] Open
Abstract
Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) infection has attracted worldwide concern and became a serious challenge for clinical treatment. The aims of this study were to evaluate the molecular characteristics and risk factors for CRKP infection. Methods All the CRKP strains were screened for antimicrobial resistance genes, virulence genes, and integron by polymerase chain reaction (PCR). Plasmid typing was performed by plasmid conjugation assay and PCR-based replicon typing (PBRT). The genetic environments of blaKPC-2 and blaNDM-1 were analyzed by using overlapping PCR and molecular typing was performed by multi-locus sequence typing (MLST). Risk factors for CRKP infection were analyzed by logistic regression model. Results All the 66 CRKP isolates were multidrug-resistant, but all of them were susceptible to tigecycline and polymyxin B. Among the CRKP isolates, 42 blaKPC-2-positive strains were identified carrying IncFII plasmids. Meanwhile, 24 blaNDM-positive strains were found on lncX3 plasmids, including 20 blaNDM-1 isolates and 4 blaNDM-5 isolates. Most of CRKP isolates contained several virulence genes and the class I integron (intl1). The genetic environments of blaKPC-2 and blaNDM-1 revealed that the conserved regions (tnpA-tnpR-ISkpn8-blaKPC-2) and (blaNDM-1-bleMBL-trpF-tat) were associated with the dissemination of KPC-2 and NDM-1. ST11 was the most common type in this work. Hematological disease, tracheal cannula, and use of β-lactams and β-lactamase inhibitor combination were identified as independent risk factors for CRKP infection. Conclusion This study established the resistance pattern, molecular characteristics, clonal relatedness, and risk factors of CRKP infection. The findings of the novel strain that co-harboring blaNDM-5 and blaIMP-4, and the novel ST4495 indicated that the brand-new types have spread in Southwest China, emphasizing the prevent and control the further dissemination of CRKP isolates are highly needed.
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Affiliation(s)
- Zhaoyinqian Li
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Zixuan Ding
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jia Yang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Yao Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Xinrui Jin
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jingling Xie
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Tingting Li
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Yinhuan Ding
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Zhangrui Zeng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
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Munasinghe T, Vidanapathirana G, Kuthubdeen S, Ekanayake A, Angulmaduwa S, De Silva K, Subhasinghe S, Kalupahana R, Liyanapathirana V, Ip M. Colonization with selected antibiotic resistant bacteria among a cohort of Sri Lankan university students. BMC Infect Dis 2021; 21:578. [PMID: 34130629 PMCID: PMC8207576 DOI: 10.1186/s12879-021-06289-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/04/2021] [Indexed: 11/30/2022] Open
Abstract
Background Antibiotic Resistance is an imminent global public health threat. Antibiotic resistance emerged in healthcare settings and has now moved on to the community settings. This study was conducted to identify the rates of asymptomatic colonization with selected antibiotic resistant organisms, (Methicillin Resistant Staphylococcus aureus (MRSA), Extended Spectrum Beta Lactamase (ESBL) producing Escherichia coli and Klebsiella spp and carbapenem resistant E.coli and Klebsiella spp) - among a group of university students in Sri Lanka. Identification of genetic determinants of MRSA and ESBL was an additional objective of the study. Methods A self - collected nasal swab and a peri-rectal swab collected after passing stools were obtained. Routine microbiological methods were used for the isolation S.aureus from the nasal swab and E.coli and Klebsiella species from the peri-rectal swab. Antibiotic sensitivity testing was performed as recommended by clinical and laboratory standard institute (CLSI). Three (3) genes that are responsible for ESBL production; blaCTX-M, blaSHV, and blaTEM were tested using previously described primers and PCR procedures. Identification of MecA and PVL genes attributed to MRSA was also done with PCR. Results A total of 322 participants between 21 and 28 years were recruited representing 5 different faculties of study. Seventy one (22.0%) were colonized with S.aureus and 14 among them with MRSA, making the MRSA colonization rate of 4.3%. Forty five (15%) of the participants were colonized with an ESBL producing E.coli or Klebsiella spp. No one was colonized with carbapenem resistant E.coli or Klebsiella species. Of the 45 ESBL producers the commonest genetic determinant identified was blaCTX-M (n = 36), while 16 isolates had blaTEM and 7 had blaSHV. Similarly, of the 14 isolates identified as MRSA, 3 (21.4%) were found to be PVL positive while 11 (78.6%) were MecA positive. Conclusions A high rate of colonization with ESBL producing E.coli and Klebsiella species was noted in our study group.
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Affiliation(s)
- Thilini Munasinghe
- Postgraduate Institute of Science, University of Peradeniya, Kandy, Sri Lanka
| | | | - Shahlina Kuthubdeen
- Postgraduate Institute of Science, University of Peradeniya, Kandy, Sri Lanka
| | - Asela Ekanayake
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Kandy, Sri Lanka
| | - Sacheera Angulmaduwa
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Kandy, Sri Lanka
| | - Kunchana De Silva
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Kandy, Sri Lanka
| | | | - Ruwani Kalupahana
- Department of Veterinary Public Health and Pharmacology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Kandy, Sri Lanka
| | - Veranja Liyanapathirana
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Kandy, Sri Lanka.
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
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Kumudunie WGM, Wijesooriya LI, Wijayasinghe YS. Comparison of four low-cost carbapenemase detection tests and a proposal of an algorithm for early detection of carbapenemase-producing Enterobacteriaceae in resource-limited settings. PLoS One 2021; 16:e0245290. [PMID: 33434203 PMCID: PMC7802922 DOI: 10.1371/journal.pone.0245290] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/25/2020] [Indexed: 01/27/2023] Open
Abstract
Rapidly progressing antibiotic resistance is a great challenge in therapy. In particular, the infections caused by carbapenem-resistant Enterobacteriaceae (CRE) are exceedingly difficult to treat. Carbapenemase production is the predominant mechanism of resistance in CRE. Early and accurate identification of carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) is extremely important for the treatment and prevention of such infections. In the present study, four phenotypic carbapenemase detection tests were compared and an algorithm was developed for rapid and cost-effective identification of CP-CRE. A total of 117 Enterobacteriaceae (54 CP-CRE, 3 non-CP-CRE, and 60 non-CRE) isolates were tested for carbapenemase production using modified Hodge test (MHT), modified carbapenem inactivation method (mCIM), Carba NP test (CNPt), and CNPt-direct test. The overall sensitivity/specificity values were 90.7%/92.1% for MHT, 100%/100% for mCIM, 75.9%/100% for CNPt, and 83.3%/100% for CNPt-direct. OXA-48-like enzymes were detected with 93.2% sensitivity by MHT and >77.3% sensitivity by two Carba NP tests. MHT could only detect half of the NDM carbapenemase producers. CNPt-direct exhibited enhanced sensitivity compared to CNPt (100% vs 25%) for detection of NDM producers. Considering these findings we propose CNPt-direct as the first test followed by mCIM for rapid detection of CP-CRE. With this algorithm >80% of the CP-CRE could be detected within 24 hours from the time the sample is received and 100% CP-CRE could be detected in day two. In conclusion, mCIM was the most sensitive assay for the identification of CP-CRE. CNPt-direct performed better than CNPt. An algorithm consisting CNPt-direct and mCIM allows rapid and reliable detection of carbapenemase production in resource-limited settings.
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