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Belina D, Gobena T, Kebede A, Chimdessa M, Hald T. Genotypic Antimicrobial Resistance Profiles of Diarrheagenic Escherichia coli and Nontyphoidal Salmonella Strains Isolated from Children with Diarrhea and Their Exposure Environments in Ethiopia. Infect Drug Resist 2024; 17:4955-4972. [PMID: 39539744 PMCID: PMC11559196 DOI: 10.2147/idr.s480395] [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: 05/30/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024] Open
Abstract
Background Antimicrobial resistance (AMR) poses a significant global threat, particularly in low- and middle-income countries, such as Ethiopia, where surveillance is limited. This study aimed to predict and characterize the AMR profiles of diarrheagenic Escherichia coli (DEC) and nontyphoidal Salmonella (NTS) strains isolated from human, animal, food, and environmental samples using whole genome sequencing. Methods A total of 57 NTS and 50 DEC isolates were sequenced on an Illumina NextSeq 550. The ResFinder and PointFinder tools were employed to identify antimicrobial resistance genes (ARGs) and point mutations. Salmonella serotypes were determined using SeqSero. Results The analysis identified at least one ARG in every NTS sample and 78% of the DEC isolates, with 22 distinct ARGs in the NTS samples and 40 in the DEC samples. The most prevalent ARGs were aac(6')-Iaa and aph(3')-Ib, which predict aminoglycoside resistance in 100% of NTS and 54% of DEC isolates, respectively. Other commonly identified ARGs include sul2, aph(6)-Id, blaTEM-1B , and tet(A), which confer resistance to folate inhibitors, aminoglycosides, β-lactams, and tetracycline. Some ARGs predicted phenotypic multidrug resistance in both DEC and NTS isolates. All identified β-lactam ARGs, except for blaTEM -1D, conferred resistance to more than three antibiotics. Interestingly, blaCTX- M-15 was found to confer resistance to nine antibiotics, including third-generation cephalosporins, in 18% of DEC and 3.5% of NTS isolates. DEC isolates from children exhibited the highest ARG diversity. Notably, genes such as aph(3″)-Ib, aph(6)-Id, sul2, and tet(A) were detected across all sample types, including water sources, although some ARGs were exclusive to specific sample types. Point mutations mediating AMR were detected in several genes, with mutations associated with nucleotide substitution being the most frequent. Conclusion This genotypic AMR profiling revealed the presence of widespread drug-resistant NTS and DEC strains in Ethiopia. Robust and sustained AMR surveillance is essential for monitoring the emergence and spread of these resistant pathogens.
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Affiliation(s)
- Dinaol Belina
- College of Veterinary Medicine, Haramaya University, Dire Dawa, Ethiopia
- School of Biological Sciences and Biotechnology, Haramaya University, Dire Dawa, Ethiopia
| | - Tesfaye Gobena
- College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
| | - Ameha Kebede
- School of Biological Sciences and Biotechnology, Haramaya University, Dire Dawa, Ethiopia
| | - Meseret Chimdessa
- School of Biological Sciences and Biotechnology, Haramaya University, Dire Dawa, Ethiopia
| | - Tine Hald
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
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Strateva T, Stratev A, Peykov S. Genomic Insights into Vietnamese Extended-Spectrum β-Lactamase-9-Producing Extensively Drug-Resistant Pseudomonas aeruginosa Isolates Belonging to the High-Risk Clone ST357 Obtained from Bulgarian Intensive Care Unit Patients. Pathogens 2024; 13:719. [PMID: 39338911 PMCID: PMC11435151 DOI: 10.3390/pathogens13090719] [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: 07/27/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 09/30/2024] Open
Abstract
Extensively drug-resistant P. aeruginosa (XDR-PA) has been highlighted as a serious public health threat. The present study aimed to explore the genomic characteristics of two Vietnamese extended-spectrum β-lactamase-9 (VEB-9)-producing XDR-PA isolates from Bulgaria in comparison to all blaVEB-9-positive strains with available genomes. The isolates designated Pae51 and Pae52 were obtained from tracheobronchial aspirates of intensive care unit (ICU) patients. Antimicrobial susceptibility testing, whole-genome sequencing, RT-qPCR, and phylogenomic analysis were performed. Pae51 and Pae52 were resistant to most antipseudomonal β-lactams including carbapenems, aminoglycosides, and fluoroquinolones but remained susceptible to colistin and cefiderocol. Numerous resistance determinants were detected: blaVEB-9, blaPDC-3, blaOXA-10, blaOXA-50, aac(6')-II, ant(2″)-Ia, ant(3″)-IIa, aph(3')-IIb, cprP, catB7, dfrB2, sul1, fosA, and tet(A). Both isolates carried complex integrons with blaVEB-9 and tet(A) embedded next to the conservative 3' end sequences. A variety of virulence factors were also identified, including the type III secretion system exotoxin U. Pae51 and Pae52 differed by only four SNPs and belonged to the high-risk clone ST357. To our knowledge, this is the first report of blaVEB-9-positive XDR-PA isolates in Bulgaria presenting a detailed genomic analysis. The development of novel antimicrobial strategies for such pathogens should be an essential part of infection control stewardship practices in ICU wards.
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Affiliation(s)
- Tanya Strateva
- Department of Medical Microbiology "Corr. Mem. Prof. Ivan Mitov, MD, DMSc", Faculty of Medicine, Medical University of Sofia, 2 Zdrave Str., 1431 Sofia, Bulgaria
| | - Alexander Stratev
- Intensive Care Unit, University Multiprofile Hospital for Active Treatment 'St. Ivan Rilski', 15 Acad. Ivan Geshov Blvd., 1431 Sofia, Bulgaria
- Department of Anaesthesiology and Intensive Care, Faculty of Medicine, Medical University of Sofia, 1 St. Georgi Sofiyski Str., 1431 Sofia, Bulgaria
| | - Slavil Peykov
- Department of Medical Microbiology "Corr. Mem. Prof. Ivan Mitov, MD, DMSc", Faculty of Medicine, Medical University of Sofia, 2 Zdrave Str., 1431 Sofia, Bulgaria
- Department of Genetics, Faculty of Biology, University of Sofia 'St. Kliment Ohridski', 8 Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
- BioInfoTech Laboratory, Sofia Tech Park, 111 Tsarigradsko Shose Blvd., 1784 Sofia, Bulgaria
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Niharika J, Thakur P, Sengar GS, Deb R, Parihar R, Sonowal J, Chaudhary P, Pegu SR, Das PJ, Rajkhowa S, Gupta VK. Whole genome sequencing-based cataloguing of antibiotic resistant genes in piggery waste borne samples. Gene 2023; 887:147786. [PMID: 37689220 DOI: 10.1016/j.gene.2023.147786] [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: 07/19/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
The growing use of antibiotics in livestock is one of the main causes of the rapid global spread of antimicrobial resistance (AMR). However, extensive research on AMR in animals is currently absent. In this article, we provide the bacterial antibiotic resistance genes (ARGs) from piggery waste samples in West Bengal, India, based on whole genome sequencing (WGS). According to the study, there are alarmingly high levels of Enterobacteriaceae in piggery waste, especially slaughterhouse waste, that are resistant to beta-lactam, aminoglycoside, sulphonamide, and tetracycline. We found several plasmids carrying multidrug-resistant Enterobacteriaceae including resistant to last-resort medications like colistin and carbapenems. Our findings will serve as a guide for developing AMR management policies for livestock in India and aid in understanding the current AMR profiles of pigs. To grasp the actual situation with AMR in the pig sector, large scale sample screening must be done.
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Affiliation(s)
- Jagana Niharika
- ICAR-National Research Centre on Pig, Guwahati 781131, Assam, India; All India Institute of Hygiene and Public Health, Government of India, Kolkata, West Bengal, India
| | - Priyanka Thakur
- ICAR-National Research Centre on Pig, Guwahati 781131, Assam, India; All India Institute of Hygiene and Public Health, Government of India, Kolkata, West Bengal, India
| | | | - Rajib Deb
- ICAR-National Research Centre on Pig, Guwahati 781131, Assam, India.
| | - Ranjeet Parihar
- ICAR-National Research Centre on Pig, Guwahati 781131, Assam, India
| | - Joyshikh Sonowal
- ICAR-National Research Centre on Pig, Guwahati 781131, Assam, India
| | - Parul Chaudhary
- School of Agriculture, Graphic Era Hill University, Dehradun 248002, Uttarakhand, India
| | - Seema Rani Pegu
- ICAR-National Research Centre on Pig, Guwahati 781131, Assam, India
| | - Pranab Jyoti Das
- ICAR-National Research Centre on Pig, Guwahati 781131, Assam, India
| | - Swaraj Rajkhowa
- ICAR-National Research Centre on Pig, Guwahati 781131, Assam, India
| | - Vivek Kumar Gupta
- ICAR-National Research Centre on Pig, Guwahati 781131, Assam, India.
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Koulenti D, Vandana KE, Rello J. Current viewpoint on the epidemiology of nonfermenting Gram-negative bacterial strains. Curr Opin Infect Dis 2023; 36:545-554. [PMID: 37930069 DOI: 10.1097/qco.0000000000000977] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
PURPOSE OF REVIEW This article aims to review the epidemiology of nonfermenting Gram-negative bacilli (NFGNB) based on recent literature reports, particularly, of the less common, but with emerging clinical significance species. RECENT FINDINGS The reported frequency of multidrug-resistant Acinetobacter baumannii and Pseudomonas aeruginosa is increasing, with very significant variability, however, between different countries. Apart from the major NFGNB, that is, A. baumannii and P. aeruginosa, already recognized as of critical importance healthcare risks, several other NFGNB genera have been increasingly associated with diverse severe infections, such as Stenotrophomonas maltophilia, Burkholderia spp., Elizabethkingia spp., Chryseobacterium spp., Achromobacter spp., Alcaligenes spp., Sphingomonas spp., Shewanella spp. and Ralstonia spp., among others. SUMMARY The exploration of the epidemiology, as well as the pathogenic potential of the of the less frequent, but emerging and increasingly reported NFGNB, is crucial, not only for immunocompromised patients, but also for critically ill patients without overt immunosuppression. As we are heading fast towards a postantibiotic era, such information would contribute to the optimal antimicrobial management, that is, providing prompt, appropriate antimicrobial coverage when needed and, at the same time, avoiding overuse and/or inappropriate use of antimicrobial therapy. Also, it would help to better understand their transmission dynamics and to develop effective prevention strategies.
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Affiliation(s)
- Despoina Koulenti
- Second Critical Care Department, Attikon University Hospital, Athens, Greece
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Kalwaje Eswhara Vandana
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Jordi Rello
- Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain
- FOREVA Research Unit, CHU Nîmes, Nîmes, France
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Li Y, Liu X, Chen L, Shen X, Wang H, Guo R, Li X, Yu Z, Zhang X, Zhou Y, Fu L. Comparative genomics analysis of Stenotrophomonas maltophilia strains from a community. Front Cell Infect Microbiol 2023; 13:1266295. [PMID: 38089814 PMCID: PMC10715271 DOI: 10.3389/fcimb.2023.1266295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
Background Stenotrophomonas maltophilia is a multidrug-resistant (MDR) opportunistic pathogen with high resistance to most clinically used antimicrobials. The dissemination of MDR S. maltophilia and difficult treatment of its infection in clinical settings are global issues. Methods To provide more genetic information on S. maltophilia and find a better treatment strategy, we isolated five S. maltophilia, SMYN41-SMYN45, from a Chinese community that were subjected to antibiotic susceptibility testing, biofilm formation assay, and whole-genome sequencing. Whole-genome sequences were compared with other thirty-seven S. maltophilia sequences. Results The five S. maltophilia strains had similar antibiotic resistance profiles and were resistant to β-lactams, aminoglycosides, and macrolides. They showed similar antimicrobial resistance (AMR) genes, including various efflux pumps, β-lactamase resistance genes (blaL1/2), aminoglycoside resistance genes [aac(6'), aph(3'/6)], and macrolide-resistant gene (MacB). Genome sequencing analysis revealed that SMYN41-SMYN45 belonged to sequence type 925 (ST925), ST926, ST926, ST31, and ST928, respectively, and three new STs were identified (ST925, ST926, and ST928). Conclusion This study provides genetic information by comparing genome sequences of several S. maltophilia isolates from a community of various origins, with the aim of optimizing empirical antibiotic medication and contributing to worldwide efforts to tackle antibiotic resistance.
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Affiliation(s)
- Yini Li
- Department of Ultrasound, Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China
| | - Xin Liu
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Lingzhi Chen
- Department of Ultrasound, Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China
| | - Xiao Shen
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Haihong Wang
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Ruiyu Guo
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Xiang Li
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Zehui Yu
- Laboratory Animal Center, Southwest Medical University, Luzhou, China
| | - Xiaoli Zhang
- Department of Allergy, Jiangnan University Medical Center, Wuxi, China
| | - Yingshun Zhou
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, China
| | - Li Fu
- Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China
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Fernández M, Garcias B, Duran I, Molina-López RA, Darwich L. Current Situation of Bacterial Infections and Antimicrobial Resistance Profiles in Pet Rabbits in Spain. Vet Sci 2023; 10:vetsci10050352. [PMID: 37235435 DOI: 10.3390/vetsci10050352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Research on antimicrobial resistance (AMR) in pet rabbits is very scarce. The aim of this study was to provide an overview of the current state of AMR in rabbits attended to in veterinary clinics distributed in Spain. Records of 3596 microbiological results of clinical cases submitted from 2010 to 2021 were analyzed. Staphylococcus spp. (15.8%), Pseudomonas spp. (12.7%), Pasteurella spp. (10%), Bordetella spp. (9.6%) and Streptococcus spp. (6.8%) were the most frequently diagnosed agents. Enterobacteriaceae, principally Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae, accounted for about 18% of the cases and showed the highest proportion of multi-drug resistance (MDR) isolates, with 48%, 57.5% and 36% of MDR, respectively. Regarding the antimicrobial susceptibility testing for a number of antimicrobial categories/families, the largest proportion of isolates showing resistance to a median of five antimicrobial categories was observed in P. aeruginosa, Stenotrophomonas maltophilia and Burkolderia spp. In contrast, infections caused by Staphylococcus, Streptococcus spp. and Pasteurella multocida were highly sensitive to conventional antimicrobials authorized for veterinary use (categories D and C). The emergence of AMR major nosocomial opportunistic pathogens such as P. aeruginosa, S. maltophilia and K. pneumoniae in pet rabbits can represent a serious public health challenge. Consequently, collaboration between veterinarians and human health professionals is crucial in the fight against antimicrobial resistance, to optimize, rationalize and prudently use antimicrobial therapies in domestic animals and humans.
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Affiliation(s)
- Mercedes Fernández
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - Biel Garcias
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
| | - Inma Duran
- Departamento Veterinaria de Laboratorio Echevarne, S.A., 08037 Barcelona, Spain
| | - Rafael A Molina-López
- Catalan Wildlife Service, Centre de Fauna Salvatge de Torreferrussa, 08130 Santa Perpètua de Mogoda, Spain
| | - Laila Darwich
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), 08193 Cerdanyola del Vallès, Spain
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