1
|
Pérez-Palacios P, Gual-de-Torrella A, Portillo-Calderón I, Recacha-Villamor E, Franco-Álvarez de Luna F, Lopez-Cerero L, Pascual A. Interhospital Spread of blaVIM-1- and blaCTX-M-15-Producing K. pneumoniae ST15 on an IncR Plasmid in Southern Spain. Antibiotics (Basel) 2023; 12:1727. [PMID: 38136761 PMCID: PMC10740488 DOI: 10.3390/antibiotics12121727] [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: 11/15/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
In 2014-2015, the main CTX-M-15- and OXA-48-producing clone in our region was ST15. Recently, K. pneumoniae ST15 isolates co-producing VIM-1 and CTX-M-15 were detected in several hospitals. The aim was to study the emergence and acquisition of this carbapenemase. Between 2017 and 2019, four hospitals submitted twenty-nine VIM-1- and CTX-M-15-producing K. pneumoniae ST15 isolates to our laboratory. Seven representatives of each XbaI PFGE pulsotype were sequenced using short- and long-read technologies. RAST, CGE databases, and Pathogenwatch were used for resistance determinants and capsule-type analysis. Plasmid comparison was performed with Easyfig2.1. Phylogenetic analysis included other contemporary ST15 isolates from Spain. The 29 isolates were clustered into seven different pulsotypes. The selected genomes, from three hospitals in two different provinces, were clustered together (fewer than 35 alleles) and differed by more than 100 alleles from other ST15 isolates obtained in the region. These seven isolates harbored one IncR plasmid (200-220 kb) with a common backbone and four regions flanked by IS26: one contained blaVIM-1, another contained blaCTX-M-15, the third contained blaOXA-1, and the fourth harbored heavy-metal-tolerance genes. The two initial plasmids, from two different centers, were identical, and rearrangement of four regions was observed in the five subsequent plasmids. Our findings showed the first intercenter dissemination of IncR plasmids carrying blaVIM-1, blaCTX-M-15, and metal-tolerance genes mediated by a new lineage of K. pneumoniae ST15. Two different capture events of the blaVIM-1 gene or different IS26-mediated plasmid rearrangements from a common ancestor may explain plasmid variations.
Collapse
Affiliation(s)
- Patricia Pérez-Palacios
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
- Institute of Biomedicine of Sevilla, 41013 Seville, Spain
| | - Ana Gual-de-Torrella
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
| | - Ines Portillo-Calderón
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
- Institute of Biomedicine of Sevilla, 41013 Seville, Spain
| | - Esther Recacha-Villamor
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
- Institute of Biomedicine of Sevilla, 41013 Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Lorena Lopez-Cerero
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
- Institute of Biomedicine of Sevilla, 41013 Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, 41009 Seville, Spain
| | - Alvaro Pascual
- Division of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, 41009 Seville, Spain; (P.P.-P.)
- Institute of Biomedicine of Sevilla, 41013 Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, 41009 Seville, Spain
| |
Collapse
|
2
|
Furlan JPR, da Silva Rosa R, Ramos MS, Dos Santos LDR, Savazzi EA, Stehling EG. Genomic features of an extensively drug-resistant and NDM-1-positive Klebsiella pneumoniae ST340 isolated from river water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:114678-114684. [PMID: 37845596 DOI: 10.1007/s11356-023-30374-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023]
Abstract
The environmental contamination plays a significant role in the emergence of antimicrobial resistance. In this study, we report a genomic analysis of an extensively drug-resistant and blaNDM-1-producing Klebsiella pneumoniae (EW807) strain recovered from a surface water sample. Strain EW807 belonged to sequence type (ST) 340 and serotype O4:KL15, a high-risk clone of the clonal group 258. This strain carried a broad resistome, including blaNDM-1 and blaCTX-M-15. The core genome multilocus sequence typing phylogenetic analysis revealed that the EW807 strain was most related to strains from Brazil and the USA. An IncX3 plasmid was identified harboring the blaNDM-1 gene, while an IncFIB(K) plasmid was detected carrying the blaCTX-M-15 in addition to multidrug resistance and multimetal tolerance regions. IncX3 and IncFIB(K) plasmids shared high similarity with plasmids from a human in China and a dog in Brazil, respectively. The regions harboring the blaNDM-1 and blaCTX-M-15 genes contained sequences from the Tn3 family. These findings suggest that IncX3 plasmid could play a role in the spread of NDM-1 in a post-pandemic scenario. To the best of our knowledge, this is the first report of blaNDM-1-producing K. pneumoniae ST340 O4:KL15 strain in the environment. Therefore, the presence of high-risk clones of K. pneumoniae carrying carbapenemases in the environment requires strict surveillance.
Collapse
Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | | | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil.
| |
Collapse
|
3
|
Rebelo A, Almeida A, Peixe L, Antunes P, Novais C. Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain. Antibiotics (Basel) 2023; 12:1474. [PMID: 37760770 PMCID: PMC10525130 DOI: 10.3390/antibiotics12091474] [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: 07/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.
Collapse
Affiliation(s)
- Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- ESS, Polytechnic of Porto, 4200-072 Porto, Portugal
| | - Agostinho Almeida
- LAQV/REQUIMTE, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, 4150-180 Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| |
Collapse
|
4
|
Pedrosa-Silva F, Venancio TM. Comparative Genomics Reveals Novel Species and Insights into the Biotechnological Potential, Virulence, and Resistance of Alcaligenes. Genes (Basel) 2023; 14:1783. [PMID: 37761923 PMCID: PMC10530903 DOI: 10.3390/genes14091783] [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: 08/03/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Alcaligenes is a cosmopolitan bacterial genus that exhibits diverse properties which are beneficial to plants. However, the genomic versatility of Alcaligenes has also been associated with the ability to cause opportunistic infections in humans, raising concerns about the safety of these microorganisms in biotechnological applications. Here, we report an in-depth comparative analysis of Alcaligenes species using all publicly available genomes to investigate genes associated with species, biotechnological potential, virulence, and resistance to multiple antibiotics. Phylogenomic analysis revealed that Alcaligenes consists of at least seven species, including three novel species. Pan-GWAS analysis uncovered 389 species-associated genes, including cold shock proteins (e.g., cspA) and aquaporins (e.g., aqpZ) found exclusively in the water-isolated species, Alcaligenes aquatilis. Functional annotation of plant-growth-promoting traits revealed enrichment of genes for auxin biosynthesis, siderophores, and organic acids. Genes involved in xenobiotic degradation and toxic metal tolerance were also identified. Virulome and resistome profiles provide insights into selective pressures exerted in clinical settings. Taken together, the results presented here provide the grounds for more detailed clinical and ecological studies of the genus Alcaligenes.
Collapse
Affiliation(s)
| | - Thiago M. Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes 28013-602, Brazil;
| |
Collapse
|
5
|
Li X, Yang Z, Zhang G, Si S, Wu X, Cai L. Plasmid Genomes Reveal the Distribution, Abundance, and Organization of Mercury-Related Genes and Their Co-Distribution with Antibiotic Resistant Genes in Gammaproteobacteria. Genes (Basel) 2022; 13:2149. [PMID: 36421823 PMCID: PMC9690531 DOI: 10.3390/genes13112149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/13/2022] [Accepted: 11/13/2022] [Indexed: 09/29/2023] Open
Abstract
Mercury (Hg) pollution poses human health and environmental risks worldwide, as it can have toxic effects and causes selective pressure that facilitates the spread of antibiotic resistant genes (ARGs) among microbes. More and more studies have revealed that numerous Hg-related genes (HRGs) can help to resist and transform Hg. In the present study, we systematically analyzed the HRG distribution, abundance, organization, and their co-distribution with ARGs, using 18,731 publicly available plasmid genomes isolated from a Gammaproteobacteria host. Our results revealed that there were many Hg-resistant (mer) operon genes but they were not extensively distributed across plasmids, with only 9.20% of plasmids harboring HRGs. Additionally, no hgcAB genes (which methylate Hg to create methylmercury) were identified in any of the analyzed plasmids. The host source significantly influenced the number of HRGs harbored by plasmids; plasmids isolated from humans and animals harbored a significantly smaller number of HRGs than plasmids isolated from the wastewater and sludge. HRG clusters displayed an extremely high organizational diversity (88 HRG cluster types), though incidences of more than half of the HRG cluster types was <5. This indicates the frequent rearrangement among HRGs in plasmids. The 1368 plasmids harboring both HRGs and ARGs, were dominated by Klebsiella, followed by Escherichia, Salmonella, and Enterobacter. The tightness of the HRG and ARG co-distribution in plasmids was affected by the host sources but not by pathogenicity. HRGs were more likely to co-occur with specific ARG classes (sulfonamide, macrolide-lincosamide-streptogramin, and aminoglycoside resistance genes). Collectively, our results reveal the distribution characteristics of HRGs in plasmids, and they have important implications for further understanding the environmental risks caused by the spread of ARGs through the plasmid-mediated co-transfer of ARGs and HRGs.
Collapse
Affiliation(s)
- Xiangyang Li
- School of Life and Health Science, Kaili University, Kaili 556011, China
- Bacterial Genome Data Mining & Bioinformatic Analysis Center, Kaili University, Kaili 556011, China
| | - Zilin Yang
- School of Sciences, Kaili University, Kaili 556018, China
| | - Guohui Zhang
- School of Life and Health Science, Kaili University, Kaili 556011, China
| | - Shengli Si
- School of Life and Health Science, Kaili University, Kaili 556011, China
| | - Xianzhi Wu
- School of Life and Health Science, Kaili University, Kaili 556011, China
| | - Lin Cai
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China
| |
Collapse
|
6
|
Prasad M, Shetty SK, Nair BG, Pal S, Madhavan A. A novel and improved selective media for the isolation and enumeration of Klebsiella species. Appl Microbiol Biotechnol 2022; 106:8273-8284. [PMID: 36380193 PMCID: PMC9726774 DOI: 10.1007/s00253-022-12270-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022]
Abstract
Bacterial pathogens are fostered in and transmitted through wastewater. Hence, monitoring their impact on sanitation and hygiene is imperative. As part of the monitoring process, culture-based methodologies are primarily used, which centre on the use of selective and differential media. Media available today are, at best, difficult to formulate and, at worst, prohibitively expensive. To address this lacuna, the study proposes a selective and differential medium for Klebsiella spp. Klebsiella blue agar (KBA) is completely selective against selected gram-positive bacteria (Bacillus spp., Staphylococcus aureus) and a few gram-negative bacteria (Acinetobacter baumanii, Serratia marcescens). On the other hand, it supports the growth of the chosen members of the Klebsiella pneumoniae species-complex with a characteristic green colouration. Methylene blue, tryptophan, and bile salt make up the selective components of KBA. Moreover, methylene blue, 0.6% NaCl, and glycerol render it differential. KBA was more selective than HiCrome™ Klebsiella Selective Agar Base (KSA) in replica plating experiments. KBA promoted only 157 CFUs against 209 CFUs in KSA when stamped with 253 CFUs grown on LB. The colonies so isolated were predominantly Klebsiella spp., on identification through colony polymerase chain reaction. Moreover, the differential nature of KBA distinguished Klebsiella aerogenes from other species. On the contrary, KSA lodged colonies indistinguishable from each other and Klebsiella spp. Due to its ease of formulation, high selectivity, differential nature, and cost-effective composition, KBA is a viable option for the routine culture of Klebsiella spp. in environmental and clinical settings. KEY POINTS: • Formulated a novel selective and differential media for Klebsiella spp., named Klebsiella Blue agar • Facile formulation methodology • Can be employed to isolate Klebsiella spp. from complex sources such as wastewater.
Collapse
Affiliation(s)
- Megha Prasad
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kerala, 690525, India
| | - Sindhu K Shetty
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kerala, 690525, India
| | - Bipin G Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kerala, 690525, India
| | - Sanjay Pal
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kerala, 690525, India.
| | - Ajith Madhavan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kerala, 690525, India.
| |
Collapse
|