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Fate of Horizontal-Gene-Transfer Markers and Beta-Lactamase Genes during Thermophilic Composting of Human Excreta. Microorganisms 2023; 11:microorganisms11020308. [PMID: 36838273 PMCID: PMC9958827 DOI: 10.3390/microorganisms11020308] [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: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023] Open
Abstract
Thermophilic composting is a suitable treatment for the recycling of organic wastes for agriculture. However, using human excreta as feedstock for composting raises concerns about antibiotic resistances. We analyzed samples from the start and end of a thermophilic composting trial of human excreta, together with green cuttings and straw, with and without biochar. Beta-lactamase genes blaCTX-M, blaIMP, and blaTEM conferring resistance to broad-spectrum beta-lactam antibiotics, as well as horizontal gene transfer marker genes, intI1 and korB, were quantified using qPCR. We found low concentrations of the beta-lactamase genes in all samples, with non-significant mean decreases in blaCTX-M and blaTEM copy numbers and a mean increase in blaIMP copy numbers. The decrease in both intI1 and korB genes from start to end of composting indicated that thermophilic composting can decrease the horizontal spread of resistance genes. Thus, thermophilic composting can be a suitable treatment for the recycling of human excreta.
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2
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Silverio MP, Kraychete GB, Rosado AS, Bonelli RR. Pseudomonas fluorescens Complex and Its Intrinsic, Adaptive, and Acquired Antimicrobial Resistance Mechanisms in Pristine and Human-Impacted Sites. Antibiotics (Basel) 2022; 11:antibiotics11080985. [PMID: 35892375 PMCID: PMC9331890 DOI: 10.3390/antibiotics11080985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/16/2022] Open
Abstract
Pseudomonas spp. are ubiquitous microorganisms that exhibit intrinsic and acquired resistance to many antimicrobial agents. Pseudomonas aeruginosa is the most studied species of this genus due to its clinical importance. In contrast, the Pseudomonas fluorescens complex consists of environmental and, in some cases, pathogenic opportunistic microorganisms. The records of antimicrobial-resistant P. fluorescens are quite scattered, which hinders the recognition of patterns. This review compiles published data on antimicrobial resistance in species belonging to the P. fluorescens complex, which were identified through phylogenomic analyses. Additionally, we explored the occurrence of clinically relevant antimicrobial resistance genes in the genomes of the respective species available in the NCBI database. Isolates were organized into two categories: strains isolated from pristine sites and strains isolated from human-impacted or metal-polluted sites. Our review revealed that many reported resistant phenotypes in this complex might be related to intrinsic features, whereas some of them might be ascribed to adaptive mechanisms such as colistin resistance. Moreover, a few studies reported antimicrobial resistance genes (ARGs), mainly β-lactamases. In-silico analysis corroborated the low occurrence of transferable resistance mechanisms in this Pseudomonas complex. Both phenotypic and genotypic assays are necessary to gain insights into the evolutionary aspects of antimicrobial resistance in the P. fluorescens complex and the possible role of these ubiquitous species as reservoirs of clinically important and transmissible ARGs.
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Affiliation(s)
- Myllena Pereira Silverio
- Laboratório de Ecologia Molecular Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Gabriela Bergiante Kraychete
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Alexandre Soares Rosado
- Laboratório de Ecologia Molecular Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raquel Regina Bonelli
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
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3
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Gonçalves D, Cecílio P, Faustino A, Iglesias C, Branca F, Estrada A, Ferreira H. Intra- and Extra-Hospital Dissemination of IMP-22-Producing Klebsiella pneumoniae in Northern Portugal: The Breach of the Hospital Frontier Toward the Community. Front Microbiol 2022; 12:777054. [PMID: 34970236 PMCID: PMC8713047 DOI: 10.3389/fmicb.2021.777054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/16/2021] [Indexed: 11/18/2022] Open
Abstract
The emergence of infections (and colonization) with Enterobacteriaceae-producing carbapenemases is a threatening public health problem. In the last decades, we watched an isolated case becoming a brutal outbreak, a sporadic description becoming an endemic problem. The present study aims to highlight the dissemination of IMP-22-producing Klebsiella pneumoniae in the North of Portugal, through the phenotypic and genotypic characterization of isolates collected from hospitalized patients (n=5) and out-patients of the emergency ward of the same acute care hospital (n=2), and isolates responsible for the intestinal colonization of residents in a Long-Term Care Facility (n=4). Pulsed-field gel electrophoresis (PFGE) results, associated with conjugation experiments pointed to a pattern of both vertical and horizontal dissemination. Overall, and complementing other studies that give relevance to IMP-22-producing K. pneumoniae in the clinical settings, here we show for the first time the public health threatening breach of the hospital frontier of this resistance threat, toward the community.
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Affiliation(s)
- Daniela Gonçalves
- Microbiology Laboratory - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,UCIBIO - Research Unit on Applied Molecular Biosciences, REQUIMTE, Porto, Portugal.,ISAVE - Instituto Superior de Saúde, Amares, Portugal.,CICS - Interdisciplinary Centre in Health Sciences, Amares, Portugal
| | - Pedro Cecílio
- Microbiology Laboratory - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | | | - Carmen Iglesias
- Clinical Pathology Service - Braga Hospital, Braga, Portugal
| | - Fernando Branca
- Clinical Pathology Service - Braga Hospital, Braga, Portugal
| | | | - Helena Ferreira
- Microbiology Laboratory - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,UCIBIO - Research Unit on Applied Molecular Biosciences, REQUIMTE, Porto, Portugal
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4
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Cheng Q, Zheng Z, Ye L, Chen S. Identification of a Novel Metallo-β-Lactamase, VAM-1, in a Foodborne Vibrio alginolyticus Isolate from China. Antimicrob Agents Chemother 2021; 65:e0112921. [PMID: 34424042 PMCID: PMC8522725 DOI: 10.1128/aac.01129-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/16/2021] [Indexed: 11/20/2022] Open
Abstract
A multidrug-resistant Vibrio alginolyticus isolate recovered from a shrimp sample with reduced carbapenem susceptibility produced a novel metallo-β-lactamase (MBL), VAM-1. That carbapenemase shared 67% to 70% amino acid identity with several VMB family subclass B1 MBLs, which were recently reported among some marine bacteria including Vibrio, Glaciecola, and Thalassomonas. The blaVAM-1 gene was located in a novel conjugative plasmid, namely, pC1579, and multiple copies of blaVAM-1 via an unusual mechanism of gene amplification were detected in pC1579. These findings underline the emergence of marine organisms acting as natural reservoirs for MBL genes and the importance of continuous bacterial antibiotic resistance surveillance.
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Affiliation(s)
- Qipeng Cheng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong
| | - Zhiwei Zheng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
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5
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Zhang CM, Liang J, Liu WY. Comparative study on the bacterial diversity and antibiotic resistance genes of urban landscape waters replenished by reclaimed water and surface water in Xi'an, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:41396-41406. [PMID: 33786766 DOI: 10.1007/s11356-021-13376-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Pathogenic bacteria and antibiotic resistance genes (ARGs) in urban landscape waters may pose a potential threat to human health. However, the investigation of their occurrence in the urban landscape waters replenished by reclaimed water (RW) and surface water (SW) is still insufficient. The water samples collected from six urban landscape waters replenished by RW or SW were used to analyze bacterial diversity using high-throughput sequencing of 16S rRNA gene and to detect 18 ARGs and 2 integron-integrase genes by means of quantitative PCR array. Results indicated that Proteobacteria was the dominant phylum in all six urban landscape waters. The bacterial species richness was lower in urban landscape waters replenished by RW than that by SW. Sulfonamide resistance genes (sulI and sulIII) were the major ARGs in these urban landscape waters. No significant difference in the relative abundance of sulfonamide resistance genes, tetracycline resistance genes, and most of beta-lactam resistance genes was observed between RW-replenished and SW-replenished urban landscape waters. By contrast, the relative abundance of blaampC gene and qnrA gene in RW-replenished urban landscape waters was significantly higher than that in SW-replenished urban landscape waters (p < 0.05), which suggested that use of RW may increase the amount of specific ARGs to urban landscape waters. Interestingly, among six urban landscape waters, RW-replenished urban landscape waters had a relatively rich variety of ARGs (12-15 of 18 ARGs) but a low relative abundance of ARGs (458.90-1944.67 copies/16S × 106). The RW replenishment was found to have a certain impact on the bacterial diversity and prevalence of ARGs in urban landscape waters, which provide new insight into the effect of RW replenishment on urban landscape waters.
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Affiliation(s)
- Chong-Miao Zhang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an, 710055, China.
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China.
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, Xi'an, 710055, China.
| | - Jie Liang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an, 710055, China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Wan-Ying Liu
- Key Laboratory of Northwest Water Resource, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an, 710055, China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, China
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6
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Antimicrobial Drug-Resistant Gram-Negative Saprophytic Bacteria Isolated from Ambient, Near-Shore Sediments of an Urbanized Estuary: Absence of β-Lactamase Drug-Resistance Genes. Antibiotics (Basel) 2020; 9:antibiotics9070400. [PMID: 32664302 PMCID: PMC7400359 DOI: 10.3390/antibiotics9070400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/05/2020] [Accepted: 07/07/2020] [Indexed: 01/21/2023] Open
Abstract
We assessed the prevalence of antimicrobial resistance and screened for clinically relevant β-lactamase resistance determinants in Gram-negative bacteria from a large urbanized estuary. In contrast to the broad literature documenting potentially hazardous resistance determinants near wastewater treatment discharge points and other local sources of aquatic pollution, we employed a probabilistic survey design to examine ambient, near-shore sediments. We plated environmental samples from 40 intertidal and shallow subtidal areas around San Francisco Bay (California, USA) on drug-supplemented MacConkey agar, and we tested isolates for antimicrobial resistance and presence of clinically relevant β-lactamase resistance determinants. Of the 74 isolates identified, the most frequently recovered taxa were Vibrio spp. (40%), Shewanella spp. (36%), Pseudomonas spp. (11%), and Aeromonas spp. (4%). Of the 55 isolates tested for antimicrobial resistance, the Vibrio spp. showed the most notable resistance profiles. Most (96%) were resistant to ampicillin, and two isolates showed multidrug-resistant phenotypes: V. alginolyticus (cefotaxime, ampicillin, gentamicin, cefoxitin) and V. fluvialis (cefotaxime, ampicillin, cefoxitin). Targeted testing for class 1 integrons and presence of β-lactam-resistance gene variants TEM, SHV, OXA, CTX-M, and Klebsiella pneumonia carbapenemase (KPC) did not reveal any isolates harboring these resistance determinants. Thus, while drug-resistant, Gram-negative bacteria were recovered from ambient sediments, neither clinically relevant strains nor mobile β-lactam resistance determinants were found. This suggests that Gram-negative bacteria in this well-managed, urbanized estuary are unlikely to constitute a major human exposure hazard at this time.
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7
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PFM-Like Enzymes Are a Novel Family of Subclass B2 Metallo-β-Lactamases from Pseudomonas synxantha Belonging to the Pseudomonas fluorescens Complex. Antimicrob Agents Chemother 2020; 64:AAC.01700-19. [PMID: 31685461 DOI: 10.1128/aac.01700-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/25/2019] [Indexed: 12/15/2022] Open
Abstract
A carbapenem-resistant Pseudomonas synxantha isolate recovered from chicken meat produced the novel carbapenemase PFM-1. That subclass B2 metallo-β-lactamase shared 71% amino acid identity with β-lactamase Sfh-1 from Serratia fonticola The bla PFM-1 gene was chromosomally located and likely acquired. Variants of PFM-1 sharing 90% to 92% amino acid identity were identified in bacterial species belonging to the Pseudomonas fluorescens complex, including Pseudomonas libanensis (PFM-2) and Pseudomonas fluorescens (PFM-3), highlighting that these species constitute reservoirs of PFM-like encoding genes.
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8
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Jung D, Rubin JE. Identification of antimicrobial resistant bacteria from plant-based food products imported into Canada. Int J Food Microbiol 2020; 319:108509. [PMID: 31945714 DOI: 10.1016/j.ijfoodmicro.2020.108509] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/22/2019] [Accepted: 01/06/2020] [Indexed: 02/08/2023]
Abstract
The role of plant-based foods in the epidemiology of antimicrobial resistance has been inadequately studied. In this investigation, resistant organisms from vegetables, fruits and spices imported into Canada were identified and characterized. A total of 143 products imported from primarily Asian and African countries were purchased from international markets in Saskatoon, Saskatchewan. Samples were selectively cultured for bacterial species where resistance is known to be emerging. The proportions of samples positive for each organism were as follows: E. coli (n = 13, 9.1%), Salmonella spp. (n = 2, 1.4%), ESBL producing Enterobacter spp. (n = 2, 1.4%) and K. pneumoniae (n = 2, 1.4%), S. aureus (n = 7, 4.9%) and Enterococcus spp. (n = 66, 46.2%). Antimicrobial minimum inhibitory concentrations were determined by broth micro-dilution and agar-dilution. Based on the susceptibility of each organism, isolates were screened for resistance genes (β-lactamases and plasmid mediated quinolones resistance determinants) by PCR. Extended-spectrum β-lactamase producing Enterobacteriaceae and methicillin resistant S. aureus (MRSA) were identified from 6/143 (4.2%) and 2/143 (1.4%) of samples respectively. The qnrB, qnrS and aac(6')-Ib-cr plasmid mediated quinolone resistance determinants were identified in 2/143 (1.4%) of samples tested. None of the Enterobacteriaceae isolates were resistant to meropenem or colistin. Similarly, all Enterococcus isolates remained susceptible to ampicillin, penicillin and vancomycin. Finding multi-drug resistant bacteria which are frequently isolated from human infections is concerning, although the contribution of the global food trade to the dissemination of resistance remains cryptic. These results suggest that imported plant-based foods may be an underappreciated source of clinically relevant resistant organisms. Further study is required to address these gaps in our understanding of the epidemiology of resistance, and the magnitude of the risk posed to human health by these organisms.
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Affiliation(s)
- Dongyun Jung
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Joseph E Rubin
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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9
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Yu X, Zhang M, Zuo J, Shi X, Tang X, Chen L, Li Z. Evaluation of antibiotic resistant lactose fermentative opportunistic pathogenic Enterobacteriaceae bacteria and bla TEM-2 gene in cephalosporin wastewater and its discharge receiving river. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 228:458-465. [PMID: 30245270 DOI: 10.1016/j.jenvman.2018.09.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
This study investigated the concentration of cephalosporin, the resistant levels of lactose fermentative opportunistic pathogenic Enterobacteriaceae bacteria (LFOPEB) against seven antibiotics and one cephalosporin-resistant gene in cephalosporin wastewater (CPWW) treatment plant and its discharge receiving river. Although large numbers of bacteria have been removed during the CPWW treatment process, the antibiotic resistant rates of the isolates to β-lactam antibiotics significantly increased (p = 0.032) after treatment, while the percentage of resistant LFOPEB to non-β-lactam antibiotics did not change dramatically. Furthermore, the discharge of the effluent of CPWW treatment plant (CPWWeff) led to an obvious increase in the percentages of β-lactam antibiotic-resistant LFOPEB and relative abundance of the blaTEM-2 gene in the downstream receiving river (RWdown) in comparison with those in the upstream receiving river (RWup). The antibiotic resistant phenotypes of isolates in the influent of CPWW treatment plant (CPWWin), CPWWeff and RWdown appeared to be seriously affected by the cephalosporin residues, which suggested that main antibiotic resistance phenotypes in antibiotic contaminated water were closely associated with its antibiotic composition. Therefore, CPWW treatment process has been proved to result in selective growth of ARB and proliferation of ARG. Besides, CPWWeff was also proved to be an important supplier of ARB and ARG to the receiving river.
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Affiliation(s)
- Xin Yu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; China Academy of Urban Planning & Design, Beijing 100044, China
| | - Mengyu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; China Urban Construction Design & Research Institute CO.LTD, Beijing 100120, China
| | - Jiane Zuo
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Xuchuan Shi
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xinyao Tang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Lei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Zaixing Li
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
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10
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Comparative ecology of Escherichia coli in endangered Australian sea lion (Neophoca cinerea) pups. INFECTION GENETICS AND EVOLUTION 2018; 62:262-269. [PMID: 29730275 DOI: 10.1016/j.meegid.2018.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 02/07/2023]
Abstract
The dissemination of human-associated bacteria into the marine environment has the potential to expose wildlife populations to atypical microbes that can alter the composition of the gut microbiome or act as pathogens. The objective of the study was to determine whether endangered Australian sea lion (Neophoca cinerea) pups from two South Australian colonies, Seal Bay, Kangaroo Island and Dangerous Reef, Spencer Gulf, have been colonised by human-associated Escherichia coli. Faecal samples (n = 111) were collected to isolate E. coli, and molecular screening was applied to assign E. coli isolates (n = 94) to phylotypes and detect class 1 integrons; mobile genetic elements that confer resistance to antimicrobial agents. E. coli phylotype distribution and frequency differed significantly between colonies with phylotypes B2 and D being the most abundant at Seal Bay, Kangaroo Island (55% and 7%) and Dangerous Reef, Spencer Gulf (36% and 49%), respectively. This study reports the first case of antimicrobial resistant E. coli in free-ranging Australian sea lions through the identification of class 1 integrons from an individual pup at Seal Bay. A significant relationship between phylotype and total white cell count (WCC) was identified, with significantly higher WCC seen in pups with human-associated phylotypes at Dangerous Reef. The difference in phylotype distribution and presence of human-associated E. coli suggests that proximity to human populations can influence sea lion gut microbiota. The identification of antimicrobial resistance in a free-ranging pinniped population provides crucial information concerning anthropogenic influences in the marine environment.
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11
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Uyaguari-Díaz MI, Croxen MA, Luo Z, Cronin KI, Chan M, Baticados WN, Nesbitt MJ, Li S, Miller KM, Dooley D, Hsiao W, Isaac-Renton JL, Tang P, Prystajecky N. Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia. Front Microbiol 2018; 9:852. [PMID: 29765365 PMCID: PMC5938356 DOI: 10.3389/fmicb.2018.00852] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/13/2018] [Indexed: 01/08/2023] Open
Abstract
The dissemination of antibiotic resistant bacteria from anthropogenic sources into the environment poses an emerging public health threat. Antibiotic resistance genes (ARGs) and gene-capturing systems such as integron-associated integrase genes (intI) play a key role in alterations of microbial communities and the spread of antibiotic resistant bacteria into the environment. In order to assess the effect of anthropogenic activities on watersheds in southwestern British Columbia, the presence of putative antibiotic resistance and integrase genes was analyzed in the microbiome of agricultural, urban influenced, and protected watersheds. A metagenomics approach and high-throughput quantitative PCR (HT qPCR) were used to screen for elements of resistance including ARGs and intI. Metagenomic sequencing of bacterial genomic DNA was used to characterize the resistome of microbial communities present in watersheds over a 1-year period. There was a low prevalence of ARGs relative to the microbial population (<1%). Analysis of the metagenomic sequences detected a total of 60 elements of resistance including 46 ARGs, intI1, and groEL/intI1 genes and 12 quaternary ammonium compounds (qac) resistance genes across all watershed locations. The relative abundance and richness of ARGs was found to be highest in agriculture impacted watersheds compared to urban and protected watersheds. A downstream transport pattern was observed in the impacted watersheds (urban and agricultural) during dry months. Similar to other reports, this study found a strong association between intI1 and ARGs (e.g., sul1), an association which may be used as a proxy for anthropogenic activities. Chemical analysis of water samples for three major groups of antibiotics was below the detection limit. However, the high richness and gene copy numbers (GCNs) of ARGs in impacted sites suggest that the effects of effluents on microbial communities are occurring even at low concentrations of antimicrobials in the water column. Antibiotic resistance and integrase genes in a year-long metagenomic study showed that ARGs were driven mainly by environmental factors from anthropogenized sites in agriculture and urban watersheds. Environmental factors such as land-use and water quality parameters accounted for 45% of the variability observed in watershed locations.
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Affiliation(s)
- Miguel I Uyaguari-Díaz
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Matthew A Croxen
- Provincial Laboratory for Public Health, Edmonton, AB, Canada.,Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Zhiyao Luo
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Kirby I Cronin
- Laboratory Services, Public Health Ontario, Toronto, ON, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Michael Chan
- BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Waren N Baticados
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | | | - Shaorong Li
- Pacific Biological Station, Nanaimo, BC, Canada
| | | | - Damion Dooley
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - William Hsiao
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Judith L Isaac-Renton
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - Natalie Prystajecky
- Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada.,BC Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada
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12
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Ricci A, Allende A, Bolton D, Chemaly M, Davies R, Girones R, Koutsoumanis K, Herman L, Lindqvist R, Nørrung B, Robertson L, Ru G, Sanaa M, Simmons M, Skandamis P, Snary E, Speybroeck N, Ter Kuile B, Threlfall J, Wahlström H, Cocconcelli PS, Klein Deceased G, Peixe L, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Correia S, Fernández Escámez PS. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 5: suitability of taxonomic units notified to EFSA until September 2016. EFSA J 2017; 15:e04663. [PMID: 32625420 PMCID: PMC7328882 DOI: 10.2903/j.efsa.2017.4663] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
EFSA was requested to assess the safety of a broad range of biological agents in the context of notifications for market authorisation as sources of food and feed additives, enzymes and plant protection products. The qualified presumption of safety (QPS) assessment was developed to provide a harmonised generic pre-assessment to support safety risk assessments performed by EFSA's Scientific Panels. The safety of unambiguously defined biological agents (at the highest taxonomic unit appropriate for the purpose for which an application is intended) and the completeness of the body of knowledge were assessed. Safety concerns identified for a taxonomic unit are, where possible and reasonable in number, reflected as 'qualifications' in connection with a recommendation for a QPS status. A total of 57 biological agents were notified to EFSA between the end of April 2016 and the beginning of September 2016. From these, 34 biological agents already had a QPS status and did not require further evaluation, and 10 were not included in the evaluation as they are filamentous fungi or enterococci, biological groups which have been excluded from QPS evaluation since 2014. Three notifications for Streptomyces violaceoruber, one for Streptomyces albus, one for Bacillus circulans and four for Escherichia coli were not evaluated for QPS status because these species were recently assessed and considered not suitable for QPS status. Therefore, only four notifications related to three taxonomic units were evaluated for QPS status. Of these, Arthrobacter ramosus and Pseudomonas fluorescens are not recommended for the QPS list. Bacillus smithii is recommended for the QPS status.
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13
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Holmgaard DB, Hansen F, Hasman H, Justesen US, Hammerum AM. Characterization of a novel blaIMP gene, blaIMP-58, using whole genome sequencing in a Pseudomonas putida isolate detected in Denmark. Diagn Microbiol Infect Dis 2017; 87:68-70. [DOI: 10.1016/j.diagmicrobio.2016.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/21/2016] [Accepted: 10/04/2016] [Indexed: 11/30/2022]
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Domingues S, Nielsen KM, da Silva GJ. Global dissemination patterns of common gene cassette arrays in class 1 integrons. Microbiology (Reading) 2015; 161:1313-37. [DOI: 10.1099/mic.0.000099] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Hong DJ, Bae IK, Jang IH, Jeong SH, Kang HK, Lee K. Epidemiology and Characteristics of Metallo-β-Lactamase-Producing Pseudomonas aeruginosa. Infect Chemother 2015; 47:81-97. [PMID: 26157586 PMCID: PMC4495280 DOI: 10.3947/ic.2015.47.2.81] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 12/18/2022] Open
Abstract
Metallo-β-lactamase-producing Pseudomonas aeruginosa (MPPA) is an important nosocomial pathogen that shows resistance to all β-lactam antibiotics except monobactams. There are various types of metallo-β-lactamases (MBLs) in carbapenem-resistant P. aeruginosa including Imipenemase (IMP), Verona integron-encoded metallo-β-lactamase (VIM), Sao Paulo metallo-β-lactamase (SPM), Germany imipenemase (GIM), New Delhi metallo-β-lactamase (NDM), Florence imipenemase (FIM). Each MBL gene is located on specific genetic elements including integrons, transposons, plasmids, or on the chromosome, in which they carry genes encoding determinants of resistance to carbapenems and other antibiotics, conferring multidrug resistance to P. aeruginosa. In addition, these genetic elements are transferable to other Gram-negative species, increasing the antimicrobial resistance rate and complicating the treatment of infected patients. Therefore, it is essential to understand the epidemiology, resistance mechanism, and molecular characteristics of MPPA for infection control and prevention of a possible global health crisis. Here, we highlight the characteristics of MPPA.
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Affiliation(s)
- Duck Jin Hong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Il Kwon Bae
- Department of Dental Hygiene, Silla University, Busan, Korea
| | - In-Ho Jang
- Department of Biomedical Laboratory Science, College of Health Sciences, Sangji University, Wonju, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun-Kyung Kang
- Department of Dental Hygiene, Silla University, Busan, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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Potron A, Poirel L, Nordmann P. Emerging broad-spectrum resistance in Pseudomonas aeruginosa and Acinetobacter baumannii: Mechanisms and epidemiology. Int J Antimicrob Agents 2015; 45:568-85. [PMID: 25857949 DOI: 10.1016/j.ijantimicag.2015.03.001] [Citation(s) in RCA: 451] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/05/2015] [Indexed: 02/07/2023]
Abstract
Multidrug resistance is quite common among non-fermenting Gram-negative rods, in particular among clinically relevant species including Pseudomonas aeruginosa and Acinetobacter baumannii. These bacterial species, which are mainly nosocomial pathogens, possess a diversity of resistance mechanisms that may lead to multidrug or even pandrug resistance. Extended-spectrum β-lactamases (ESBLs) conferring resistance to broad-spectrum cephalosporins, carbapenemases conferring resistance to carbapenems, and 16S rRNA methylases conferring resistance to all clinically relevant aminoglycosides are the most important causes of concern. Concomitant resistance to fluoroquinolones, polymyxins (colistin) and tigecycline may lead to pandrug resistance. The most important mechanisms of resistance in P. aeruginosa and A. baumannii and their most recent dissemination worldwide are detailed here.
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Affiliation(s)
- Anaïs Potron
- Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Centre Hospitalier Régional Universitaire, Université de Franche-Comté, Besançon, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland.
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Fribourg, Switzerland; HFR - Hôpital Cantonal de Fribourg, Fribourg, Switzerland
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17
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Power ML, Emery S, Gillings MR. Into the wild: dissemination of antibiotic resistance determinants via a species recovery program. PLoS One 2013; 8:e63017. [PMID: 23717399 PMCID: PMC3661720 DOI: 10.1371/journal.pone.0063017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/27/2013] [Indexed: 11/18/2022] Open
Abstract
Management strategies associated with captive breeding of endangered species can establish opportunities for transfer of pathogens and genetic elements between human and animal microbiomes. The class 1 integron is a mobile genetic element associated with clinical antibiotic resistance in gram-negative bacteria. We examined the gut microbiota of endangered brush-tail rock wallabies Petrogale penicillata to determine if they carried class 1 integrons. No integrons were detected in 65 animals from five wild populations. In contrast, class 1 integrons were detected in 48% of fecal samples from captive wallabies. The integrons contained diverse cassette arrays that encoded resistance to streptomycin, spectinomycin, and trimethoprim. Evidence suggested that captive wallabies had acquired typical class 1 integrons on a number of independent occasions, and had done so in the absence of strong selection afforded by antibiotic therapy. Sufficient numbers of bacteria containing diverse class 1 integrons must have been present in the general environment occupied by the wallabies to account for this acquisition. The captive wallabies have now been released, in an attempt to bolster wild populations of the species. Consequently, they can potentially spread resistance integrons into wild wallabies and into new environments. This finding highlights the potential for genes and pathogens from human sources to be acquired during captive breeding and to be unwittingly spread to other populations.
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Affiliation(s)
- Michelle L Power
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia.
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18
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Gillings MR. Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome. Front Microbiol 2013; 4:4. [PMID: 23386843 PMCID: PMC3560386 DOI: 10.3389/fmicb.2013.00004] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/03/2013] [Indexed: 12/16/2022] Open
Abstract
The widespread use and abuse of antibiotic therapy has evolutionary and ecological consequences, some of which are only just beginning to be examined. One well known consequence is the fixation of mutations and lateral gene transfer (LGT) events that confer antibiotic resistance. Sequential selection events, driven by different classes of antibiotics, have resulted in the assembly of diverse resistance determinants and mobile DNAs into novel genetic elements of ever-growing complexity and flexibility. These novel plasmids, integrons, and genomic islands have now become fixed at high frequency in diverse cell lineages by human antibiotic use. Consequently they can be regarded as xenogenetic pollutants, analogous to xenobiotic compounds, but with the critical distinction that they replicate rather than degrade when released to pollute natural environments. Antibiotics themselves must also be regarded as pollutants, since human production overwhelms natural synthesis, and a major proportion of ingested antibiotic is excreted unchanged into waste streams. Such antibiotic pollutants have non-target effects, raising the general rates of mutation, recombination, and LGT in all the microbiome, and simultaneously providing the selective force to fix such changes. This has the consequence of recruiting more genes into the resistome and mobilome, and of increasing the overlap between these two components of microbial genomes. Thus the human use and environmental release of antibiotics is having second order effects on the microbial world, because these small molecules act as drivers of bacterial evolution. Continued pollution with both xenogenetic elements and the selective agents that fix such elements in populations has potentially adverse consequences for human welfare.
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Affiliation(s)
- Michael R Gillings
- Department of Biological Sciences, Macquarie University Sydney, NSW, Australia
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19
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Chouchani C, Marrakchi R, Henriques I, Correia A. Occurrence of IMP-8, IMP-10, and IMP-13 metallo-β-lactamases located on class 1 integrons and other extended-spectrum β-lactamases in bacterial isolates from Tunisian rivers. ACTA ACUST UNITED AC 2012; 45:95-103. [PMID: 22992193 DOI: 10.3109/00365548.2012.717712] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Antibiotic-resistant bacteria have been surveyed widely in water bodies, but few studies have determined the diversity of antibiotic-resistant bacteria in river waters. This study was undertaken to investigate the origin of resistance among polluted river bacterial isolates in Tunisia. METHODS In this study 128 isolates resistant to β-lactam antibiotics were obtained from 2 polluted rivers in the north of Tunisia. Isolates were identified using Phoenix phenotyping criteria. The occurrence of bla(TEM), bla(SHV), bla(CTX-M), bla(CMY), bla(VIM), and bla(IMP) was studied by polymerase chain reaction (PCR) amplification and sequencing, and the genetic relatedness of the 16 IMP-producing Klebsiella pneumoniae isolates was analyzed by comparison of XbaI pulsed-field gel electrophoresis (PFGE) profiles. RESULTS Using Phoenix phenotyping criteria, diverse genera of bacteria were identified with different rates of prevalence and with different minimum inhibitory concentrations against different antibiotics. The occurrence of bla(TEM), bla(SHV), bla(CTXM), bla(CMY), bla(VIM), and bla(IMP) genes was confirmed. The DNA sequences upstream and downstream of bla(IMP) genes were determined, revealing that all IMP-encoding genes constituted the first cassette of class 1 integrons, followed by aacA gene cassettes encoding aminoglycoside resistance. Comparison of PFGE profiles showed that only 2 of the isolates were clonal, the other 14 displaying unique profiles. The bla(CTX-M) gene was the most dominant of the extended-spectrum β-lactamase (ESBL) genes, while the bla(TEM) gene was the second-most dominant. CONCLUSION The discovery of highly diverse ESBL-producing bacteria and metallo-β-lactamases, particularly bla(IMP), in polluted river water raises alarms with regard to the potential dissemination of antibiotic-resistant bacteria in communities through river environments.
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Affiliation(s)
- Chedly Chouchani
- Université de Carthage, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Technopôle de Borj-Cedria, Hammam-Lif, Tunisia.
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20
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Characterization of a novel IMP-28 metallo-β-lactamase from a Spanish Klebsiella oxytoca clinical isolate. Antimicrob Agents Chemother 2012; 56:4540-3. [PMID: 22668859 DOI: 10.1128/aac.00776-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An isolate of Klebsiella oxytoca carrying a novel IMP metallo-β-lactamase was discovered in Madrid, Spain. The bla(IMP-28) gene is part of a chromosomally located class I integron. The IMP-28 k(cat)/K(m) values for ampicillin, ceftazidime, and cefepime and, to a lesser extent, imipenem and meropenem, are clearly lower than those of IMP-1. The His306Gln mutation may induce important modifications of the L3 loop and thus of substrate accessibility and hydrolysis and be the main reason for this behavior.
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21
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Lin D, Foley S, Qi Y, Han J, Ji C, Li R, Wu C, Shen J, Wang Y. Characterization of antimicrobial resistance of Pseudomonas aeruginosa isolated from canine infections. J Appl Microbiol 2012; 113:16-23. [DOI: 10.1111/j.1365-2672.2012.05304.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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22
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Stalder T, Barraud O, Casellas M, Dagot C, Ploy MC. Integron involvement in environmental spread of antibiotic resistance. Front Microbiol 2012; 3:119. [PMID: 22509175 PMCID: PMC3321497 DOI: 10.3389/fmicb.2012.00119] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 03/13/2012] [Indexed: 11/13/2022] Open
Abstract
The spread of antibiotic-resistant bacteria is a growing problem and a public health issue. In recent decades, various genetic mechanisms involved in the spread of resistance genes among bacteria have been identified. Integrons - genetic elements that acquire, exchange, and express genes embedded within gene cassettes (GC) - are one of these mechanisms. Integrons are widely distributed, especially in Gram-negative bacteria; they are carried by mobile genetic elements, plasmids, and transposons, which promote their spread within bacterial communities. Initially studied mainly in the clinical setting for their involvement in antibiotic resistance, their role in the environment is now an increasing focus of attention. The aim of this review is to provide an in-depth analysis of recent studies of antibiotic-resistance integrons in the environment, highlighting their potential involvement in antibiotic-resistance outside the clinical context. We will focus particularly on the impact of human activities (agriculture, industries, wastewater treatment, etc.).
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23
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Beta-lactams resistance and presence of class 1 integron in Pseudomonas spp. isolated from untreated hospital effluents in Brazil. Antonie van Leeuwenhoek 2012; 102:73-81. [DOI: 10.1007/s10482-012-9714-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 02/20/2012] [Indexed: 10/28/2022]
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24
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Infrequent finding of metallo-β-lactamase VIM-2 in carbapenem-resistant Pseudomonas aeruginosa strains from Croatia. Antimicrob Agents Chemother 2012; 56:2746-9. [PMID: 22371893 DOI: 10.1128/aac.05212-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One hundred sixty-nine nonreplicate imipenem-resistant Pseudomonas aeruginosa strains isolated in a large hospital on the coastal region of Croatia were studied. The most active antibiotics were colistin and amikacin. Most of the isolates were multiresistant. The most prevalent serotype was O12, followed by O11. Six strains carried the bla(VIM-2) gene located in a novel class 1 integron composed in its variable part of the bla(VIM-2)-bla(oxa-10)-ΔqacF-aacA4 genes. Metallo-β-lactamase-producing strains belonged to sequence types ST235 and ST111.
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25
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Maravić A, Skočibušić M, Samanić I, Puizina J. Antibiotic susceptibility profiles and first report of TEM extended-spectrum β-lactamase in Pseudomonas fluorescens from coastal waters of the Kaštela Bay, Croatia. World J Microbiol Biotechnol 2012; 28:2039-45. [PMID: 22806025 DOI: 10.1007/s11274-012-1006-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 01/21/2012] [Indexed: 10/14/2022]
Abstract
The aim of this study was to investigate the antibiotic susceptibility profiles and the presence of extended-spectrum-β-lactamases (ESBLs) in Pseudomonas fluorescens isolates from coastal waters of the Kaštela Bay, Croatia. Twenty-two water samples were collected during 2009. Isolates were tested for susceptibilities to 13 antibiotics by Etest. ESBL production was confirmed by double-disk synergy test carried out on Mueller-Hinton agar plates containing efflux pump inhibitor Phe-Arg-β-naphthylamide dihydrochloride. PCR and DNA sequencing analysis were used to identify ESBL-encoding genes. The transferability of cephalosporin resistance was tested by conjugation experiments. Genetic relatedness of ESBL-producing isolates was determined by random amplified polymorphic DNA (RAPD) analysis. Out of 185 P. fluorescens isolates recovered, 70 (37.8%) demonstrated multiresistance phenotype with highest rates of resistance to tetracycline (61.6%), aztreonam (31.9%), meropenem (17.3%), ceftazidime (15.1%) and cefotaxime (12.4%). Ten (5.4%) isolates were identified as ESBL producers. All isolates carried chromosomally located bla (TEM-116) gene. RAPD analysis identified four different genotypes. Here, we demonstrated a baseline profiles of antimicrobial resistance of P. fluorescens from coastal waters of the Kaštela Bay, Croatia. To our knowledge, this is the first report of the presence of TEM-type ESBL in P. fluorescens, indicating this bacterium as a reservoir of antibiotic resistance genes with clinical relevance.
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Affiliation(s)
- Ana Maravić
- Department of Biology, Faculty of Science, University of Split, N. Tesle 12, 21000 Split, Croatia.
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26
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Sahai S. Dissemination of NDM-1. THE LANCET. INFECTIOUS DISEASES 2012; 12:100-102. [PMID: 22281137 DOI: 10.1016/s1473-3099(11)70334-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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27
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IMP-29, a novel IMP-type metallo-β-lactamase in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2012; 56:2187-90. [PMID: 22290960 DOI: 10.1128/aac.05838-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of two clonally related multiresistant Pseudomonas aeruginosa isolates led to the identification of a novel IMP-type metallo-β-lactamase. IMP-29 was significantly different from the other IMP variants (the closest variant being IMP-5 with 93% amino acid identity). The bla(IMP-29) gene cassette was carried by a class 1 integron in strain 10.298, while in strain 10.266 it was located in a rearranged DNA region on a 30-kb conjugative plasmid. Biochemical analysis confirmed that IMP-29 efficiently hydrolyzed carbapenems.
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28
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Lupo A, Coyne S, Berendonk TU. Origin and evolution of antibiotic resistance: the common mechanisms of emergence and spread in water bodies. Front Microbiol 2012; 3:18. [PMID: 22303296 PMCID: PMC3266646 DOI: 10.3389/fmicb.2012.00018] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 01/10/2012] [Indexed: 11/25/2022] Open
Abstract
The environment, and especially freshwater, constitutes a reactor where the evolution and the rise of new resistances occur. In water bodies such as waste water effluents, lakes, and rivers or streams, bacteria from different sources, e.g., urban, industrial, and agricultural waste, probably selected by intensive antibiotic usage, are collected and mixed with environmental species. This may cause two effects on the development of antibiotic resistances: first, the contamination of water by antibiotics or other pollutants lead to the rise of resistances due to selection processes, for instance, of strains over-expressing broad range defensive mechanisms, such as efflux pumps. Second, since environmental species are provided with intrinsic antibiotic resistance mechanisms, the mixture with allochthonous species is likely to cause genetic exchange. In this context, the role of phages and integrons for the spread of resistance mechanisms appears significant. Allochthonous species could acquire new resistances from environmental donors and introduce the newly acquired resistance mechanisms into the clinics. This is illustrated by clinically relevant resistance mechanisms, such as the fluoroquinolones resistance genes qnr. Freshwater appears to play an important role in the emergence and in the spread of antibiotic resistances, highlighting the necessity for strategies of water quality improvement. We assume that further knowledge is needed to better understand the role of the environment as reservoir of antibiotic resistances and to elucidate the link between environmental pollution by anthropogenic pressures and emergence of antibiotic resistances. Only an integrated vision of these two aspects can provide elements to assess the risk of spread of antibiotic resistances via water bodies and suggest, in this context, solutions for this urgent health issue.
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Affiliation(s)
- Agnese Lupo
- Institute of Hydrobiology, Department of Hydrosciences, Technical University Dresden Dresden, Germany
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29
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Bush K, Fisher JF. Epidemiological expansion, structural studies, and clinical challenges of new β-lactamases from gram-negative bacteria. Annu Rev Microbiol 2012; 65:455-78. [PMID: 21740228 DOI: 10.1146/annurev-micro-090110-102911] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
β-Lactamase evolution presents to the infectious disease community a major challenge in the treatment of infections caused by multidrug-resistant gram-negative bacteria. Because over 1,000 of these naturally occurring β-lactamases exist, attempts to correlate structure and function have become daunting. Although new enzymes in the extended-spectrum β-lactamase (ESBL) families are frequently identified, the older CTX-M-14 and CTX-M-15 enzymes have become the most prevalent ESBLs in global surveillance. Carbapenemases with either serine-based or zinc-facilitated hydrolysis mechanisms are posing some of the most critical problems. Most geographical regions now report KPC serine carbapenemases and the metallo-β-lactamases VIM, IMP, and NDM-1, even though NDM-1 was only recently identified. The rapid emergence of these newer enzymes, with multiple β-lactamases appearing in a single organism, makes the design of new β-lactamase inactivators or β-lactamase-stable β-lactams all the more difficult. Combination therapy will likely be required to counteract the continuing evolution of these insidious enzymes in multidrug-resistant pathogens.
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Affiliation(s)
- Karen Bush
- Biology Department, Indiana University, Bloomington, Indiana 47401, USA.
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30
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Ma L, Zhang XX, Cheng S, Zhang Z, Shi P, Liu B, Wu B, Zhang Y. Occurrence, abundance and elimination of class 1 integrons in one municipal sewage treatment plant. ECOTOXICOLOGY (LONDON, ENGLAND) 2011; 20:968-973. [PMID: 21431316 DOI: 10.1007/s10646-011-0652-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/23/2011] [Indexed: 05/30/2023]
Abstract
Integrons are elements that encode a site-specific recombination system that recognizes and captures mobile gene cassettes and are closely related to multiple resistances of environmental microorganisms. This study was undertaken to determine the efficiency of an activated sludge process to remove integrons. The prevalence and characteristics of class 1 integrons were investigated for bacterial species isolated from the activated sludge of Nanjing Jiangxinzhou sewage treatment plant (STP, China). A total of 189 bacterial strains were isolated from influent water, activated sludge and effluent water, and PCR-RFLP (Polymerase chain reaction--restriction fragment length polymorphism) of 16S rRNA gene showed that the isolated bacteria were Escherichia coli, Aeromonas veronii, Klebsiella spp., Aeromonas salmonicida and Aeromonas media. PCRs showed that 57 isolates contained class 1 integronase gene intI1. The integron detection frequency in the isolated strains was 20.4% for influent, 30.9% for activated sludge and 38.9% for effluent. Quantitative real-time PCR assay showed that the abundance of integrons in effluent was higher than that in influent. This study indicates that class 1 integrons are wide-spread in STPs which might be involved in multiple resistances in the activated sludge characterized by high biomass and biodiversity.
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Affiliation(s)
- Liping Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Road, Nanjing, 210046, China
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31
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Stokes HW, Gillings MR. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol Rev 2011; 35:790-819. [PMID: 21517914 DOI: 10.1111/j.1574-6976.2011.00273.x] [Citation(s) in RCA: 372] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance continues to become worse, despite the ever-increasing resources devoted to combat the problem. One of the most important factors in the development of resistance to antibiotics is the remarkable ability of bacteria to share genetic resources via Lateral Gene Transfer (LGT). LGT occurs on a global scale, such that in theory, any gene in any organism anywhere in the microbial biosphere might be mobilized and spread. With sufficiently strong selection, any gene may spread to a point where it establishes a global presence. From an antibiotic resistance perspective, this means that a resistance phenotype can appear in a diverse range of infections around the globe nearly simultaneously. We discuss the forces and agents that make this LGT possible and argue that the problem of resistance can ultimately only be managed by understanding the problem from a broad ecological and evolutionary perspective. We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans.
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Affiliation(s)
- Hatch W Stokes
- The i3 Institute, University of Technology, Broadway 2007, Sydney, NSW, Australia.
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32
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Isolation of Pseudomonas aeruginosa coproducing metallo-β-lactamase SPM-1 and 16S rRNA methylase RmtD1 in an urban river. Antimicrob Agents Chemother 2011; 55:3063-4. [PMID: 21464240 DOI: 10.1128/aac.00138-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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33
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Zhao WH, Hu ZQ. IMP-type metallo-β-lactamases in Gram-negative bacilli: distribution, phylogeny, and association with integrons. Crit Rev Microbiol 2011; 37:214-26. [PMID: 21707466 DOI: 10.3109/1040841x.2011.559944] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Twenty-nine IMP-type β-lactamases (IMPs) have been identified in at least 26 species of clinically important Gram-negative bacilli from more than 24 countries/regions. Most of bla(IMP) genes are harbored by class 1 integrons that are usually embedded in transposons and/or plasmids, footnoting their horizontal transfer and worldwide distribution. bla(IMP) genes usually co-exist with other resistance genes, such as aacA, catB, and bla(OXA), resulting in multi-drug resistance. Compared to other gene cassettes, 76.3% of the bla(IMP) gene cassettes are located adjacent to Pc promoter of the class 1 integrons, indicating that the bla(IMP) genes are readily expressed in most of bacterial hosts.
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Affiliation(s)
- Wei-Hua Zhao
- Department of Microbiology and Immunology, Showa University School of Medicine, Shinagawa-ku, Tokyo, Japan.
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Miki K, Takegawa H, Etoh M, Hayashi M, Haruta T, Yamane K, Arakawa Y. [First outbreak report of VIM-1 metallo-beta-lactamase producing Pseudomonas aeruginosa in Japan]. ACTA ACUST UNITED AC 2011; 84:721-6. [PMID: 21226324 DOI: 10.11150/kansenshogakuzasshi.84.721] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
VIM-1 metallo-beta-lactamase (MBL) producing Pseudomonas aeruginosa was isolated from 35 Kobe City Medical Center General Hospital patients from September 2007 to July 2008. All but one were highly resistant to all beta-lactams, aminoglycoside, and fluoroquinolone, and one susceptible to amikacin. Strains negative to a disk diffusion screening test using sodium mercaptoacetate for detecting MBL numbered 35. PCR for MBL indicated all strains were positive for bla(VIWM-1). These strains were indistinguishable by pulsed-field gel electrophoresis, indicating an outbreak of infections caused by VIM-1 MBL producing Pseudomonas aeruginosa. After intervention to control contact, the outbreak was controlled.
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Affiliation(s)
- Kanji Miki
- Department of Clinical Laboratory, Kobe City Medical Center General Hospital
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35
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Pellegrini C, Celenza G, Segatore B, Bellio P, Setacci D, Amicosante G, Perilli M. Occurrence of class 1 and 2 integrons in resistant Enterobacteriaceae collected from a urban wastewater treatment plant: first report from central Italy. Microb Drug Resist 2011; 17:229-34. [PMID: 21268680 DOI: 10.1089/mdr.2010.0117] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The purpose of this study was to investigate the presence and distribution of integron-carrying isolates among Enterobacteriaceae resistant to β-lactam antibiotics collected from a wastewater effluent of the city of L'Aquila (Italy). A total of 471 Enterobacteriaceae were collected during a period of 2 years (2005-2006). The presence and distribution of class 1 and 2 integrons was investigated by colony blot hybridization using specific probes labelled with dUTP-fluoresceine kit. The variable region of class 1 and 2 integrons was analyzed by polymerase chain reaction and DNA sequencing in 24 isolates with different random amplified polymorphic DNA profile. The characterization of class 1 and 2 integrons gene cassettes of 24 nonrelated strains showed the presence of four different arrays: dfr17-aadA5; aadA10; dfr1-sat1; dfr1-sat1-aadA1. This is the first report from Italy in which the authors confirm the presence of Enterobacteriaceae carrying class 1 and 2 integrons in a wastewater treatment plant that collects the urban and hospital discharges.
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Affiliation(s)
- Cristina Pellegrini
- Department of Biomedical Sciences and Technologies, University of L'Aquila, L'Aquila, Italy
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36
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Nicolau CJ, Oliver A. Carbapenemasas en especies del género Pseudomonas. Enferm Infecc Microbiol Clin 2010; 28 Suppl 1:19-28. [DOI: 10.1016/s0213-005x(10)70004-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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37
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Novel ambler class A carbapenem-hydrolyzing beta-lactamase from a Pseudomonas fluorescens isolate from the Seine River, Paris, France. Antimicrob Agents Chemother 2009; 54:328-32. [PMID: 19901091 DOI: 10.1128/aac.00961-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Pseudomonas fluorescens isolate (PF-1) resistant to carbapenems was recovered during an environmental survey performed with water from the Seine River (Paris). It expressed a novel Ambler class A carbapenemase, BIC-1, sharing 68 and 59% amino acid identities with beta-lactamases SFC-1 from Serratia fonticola and the plasmid-encoded KPC-2, respectively. beta-Lactamase BIC-1 hydrolyzed penicillins, carbapenems, and cephalosporins except ceftazidime and monobactams. The bla(BIC-1) gene was chromosomally located and was also identified in two other P. fluorescens strains isolated from the Seine River 3 months later.
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