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Ory J, Bricheux G, Robin F, Togola A, Forestier C, Traore O. Biofilms in hospital effluents as a potential crossroads for carbapenemase-encoding strains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 657:7-15. [PMID: 30530220 DOI: 10.1016/j.scitotenv.2018.11.427] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/09/2018] [Accepted: 11/28/2018] [Indexed: 06/09/2023]
Abstract
Bacterial resistance to carbapenem, which is mainly due to the successful dissemination of carbapenemase-encoding genes, has become a major health problem. Few studies have aimed to characterize the level of resistance in the environment, notably in hospital wastewater, which is a likely hotspot for exchange of antibiotic resistance genes. In this work, we looked for the presence of imipenem-resistant bacteria and imipenem in the effluent of the teaching hospital of Clermont-Ferrand, France. Selective growth of bacteria from 14-day old biofilms formed in the pipe sewer showed that 22.1% of the isolates were imipenem-resistant and identified as Aeromonas (n = 23), Pseudomonas (n = 10), Stenotrophomonas (n = 4) and Acinetobacter (n = 1). Fifteen of these strains harbored acquired carbapenemase-encoding genes blaVIM (n = 11), blaOXA-48 (n = 2), blaGES (n = 1), blaNDM (n = 1). All isolates also harbored associated resistances to aminoglycosides, fluoroquinolones and/or tetracyclin. S1-nuclease pulsed-field gel electrophoresis analysis of eight selected isolates showed that four of them harbored one to two plasmids of molecular weight between 48.5 Kb and 194 Kb. In vitro transformation assays evidenced the presence of blaVIM and blaNDM on plasmids with the blaVIM harboring 80 Kb plasmid having conjugative capacity. The predicted environmental concentration of imipenem in the hospital effluent was 3.16 μg/L, suggesting that biofilm bacteria are subjected to sub-MICs of imipenem within the effluent. However, no imipenem molecule was detected in the hospital effluent, probably owing to its instability: in vitro assays indicated that imipenem's biological activity was no longer detectable after 45 h of storage. However, the predictive value of the hazard quotient relative to the development of resistance was >1.0 (HQr = 28.9 ± 1.9), which indicates a possible risk. The presence of carbapenemase-encoding genes in hospital effluent biofilm strains and their ability to transfer are therefore a potential hazard that should not be neglected and points to the need for monitoring antibiotic resistance in hospital wastewater.
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Affiliation(s)
- J Ory
- Université Clermont Auvergne, CNRS, Laboratoire "Microorganismes: Génome et Environnement", F-63000 Clermont-Ferrand, France; Service d'hygiène hospitalière, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - G Bricheux
- Université Clermont Auvergne, CNRS, Laboratoire "Microorganismes: Génome et Environnement", F-63000 Clermont-Ferrand, France
| | - F Robin
- Laboratoire de Bactériologie & CNR de la Résistance aux Antibiotiques, CHU de Clermont-Ferrand, Clermont-Ferrand, France; Université Clermont Auvergne, Inserm, M2ISH, F-63000 Clermont-Ferrand, France
| | - A Togola
- Bureau de recherches géologiques et minières (BRGM), 3 avenue Claude Guillemin, F-45100 Orléans, France
| | - C Forestier
- Université Clermont Auvergne, CNRS, Laboratoire "Microorganismes: Génome et Environnement", F-63000 Clermont-Ferrand, France
| | - O Traore
- Université Clermont Auvergne, CNRS, Laboratoire "Microorganismes: Génome et Environnement", F-63000 Clermont-Ferrand, France; Service d'hygiène hospitalière, CHU de Clermont-Ferrand, Clermont-Ferrand, France.
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Tuo H, Yang Y, Tao X, Liu D, Li Y, Xie X, Li P, Gu J, Kong L, Xiang R, Lei C, Wang H, Zhang A. The Prevalence of Colistin Resistant Strains and Antibiotic Resistance Gene Profiles in Funan River, China. Front Microbiol 2018; 9:3094. [PMID: 30619173 PMCID: PMC6305280 DOI: 10.3389/fmicb.2018.03094] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/29/2018] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic activities near urban rivers may have significantly increased the acquisition and dissemination of antibiotic resistance. In this study, we investigated the prevalence of colistin resistant strains in the Funan River in Chengdu, China. A total of 18 mcr-1-positive isolates (17 Escherichia coli and 1 Enterobacter cloacae) and 6 mcr-3-positive isolates (2 Aeromonas veronii and 4 Aeromonas hydrophila) were detected, while mcr-2, mcr-4 and mcr-5 genes were not detected in any isolates. To further explore the overall antibiotic resistance in the Funan River, water samples were assayed for the presence of 15 antibiotic resistance genes (ARGs) and class 1 integrons gene (intI1). Nine genes, sul1, sul2, intI1, aac(6')-Ib-cr, bla CTX-M, tetM, ermB, qnrS, and aph(3')-IIIa were found at high frequencies (70-100%) of the water samples. It is worth noting that mcr-1, bla KPC, bla NDM and vanA genes were also found in water samples, the genes that have been rarely reported in natural river systems. The absolute abundance of selected antibiotic resistance genes [sul1, aac(6')-Ib-cr, ermB, blaCTX-M, mcr-1, and tetM] ranged from 0 to 6.0 (log10 GC/mL) in water samples, as determined by quantitative polymerase chain reaction (qPCR). The sul1, aac(6')-Ib-cr, and ermB genes exhibited the highest absolute abundances, with 5.8, 5.8, and 6.0 log10 GC/mL, respectively. The absolute abundances of six antibiotic resistance genes were highest near a residential sewage outlet. The findings indicated that the discharge of resident sewage might contribute to the dissemination of antibiotic resistant genes in this urban river. The observed high levels of these genes reflect the serious degree of antibiotic resistant pollution in the Funan River, which might present a threat to public health.
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Affiliation(s)
- Hongmei Tuo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yanxian Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xi Tao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dan Liu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yunxia Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xianjun Xie
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ping Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ju Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Linghan Kong
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Rong Xiang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Zurfluh K, Stevens MJ, Stephan R, Nüesch-Inderbinen M. Complete and assembled genome sequence of an NDM-5- and CTX-M-15-producing Escherichia coli sequence type 617 isolated from wastewater in Switzerland. J Glob Antimicrob Resist 2018; 15:105-106. [DOI: 10.1016/j.jgar.2018.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 10/28/2022] Open
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Characteristics of Carbapenemase-Producing Enterobacteriaceae in Wastewater Revealed by Genomic Analysis. Antimicrob Agents Chemother 2018; 62:AAC.02501-17. [PMID: 29483120 DOI: 10.1128/aac.02501-17] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/22/2018] [Indexed: 12/19/2022] Open
Abstract
Wastewater is considered a major source of antibiotic-resistant bacteria released into the environment. Here, we characterized carbapenemase-producing Enterobacteriaceae (CPE) in wastewater by whole-genome analysis. Wastewater samples (n = 40) were collected from municipal wastewater treatment plants and hospital wastewater in Japan and Taiwan. Samples were screened for CPE using selective media, and the obtained isolates were sequenced using an Illumina MiSeq. The isolates (n = 45) included the following microorganisms: Klebsiella quasipneumoniae (n = 12), Escherichia coli (n = 10), Enterobacter cloacae complex (n = 10), Klebsiella pneumoniae (n = 8), Klebsiella variicola (n = 2), Raoultella ornithinolytica (n = 1), Citrobacter freundii (n = 1), and Citrobacter amalonaticus (n = 1). Among the 45 isolates, 38 harbored at least one carbapenemase-encoding gene. Of these, the blaGES (blaGES-5, blaGES-6, and blaGES-24) genes were found in 29 isolates. The genes were situated in novel class 1 integrons, but the integron structures were different between the Japanese (In1439 with blaGES-24 and In1440 with blaGES-5) and Taiwanese (In1441 with blaGES-5 and In1442 with blaGES-6) isolates. Other carbapenemase-encoding genes (blaVIM-1, blaNDM-5, blaIMP-8, blaIMP-19, and blaKPC-2) were found in one to three isolates. Notably, class 1 integrons previously reported among clinical isolates obtained in the same regions as the present study, namely, In477 with blaIMP-19 and In73 with blaIMP-8, were found among the Japanese and Taiwanese isolates, respectively. The results indicate that CPE with various carbapenemase-encoding genes in different genetic contexts were present in biologically treated wastewater, highlighting the need to monitor for antibiotic resistance in wastewater.
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Complete and assembled genome sequence of an NDM-9- and CTX-M-15-producing Klebsiella pneumoniae ST147 wastewater isolate from Switzerland. J Glob Antimicrob Resist 2018; 13:53-54. [PMID: 29551728 DOI: 10.1016/j.jgar.2018.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/03/2018] [Accepted: 03/07/2018] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES Carbapenem-resistant Klebsiella pneumoniae have emerged worldwide and represent a major threat to human health. Here we report the genome sequence of K. pneumoniae 002SK2, an NDM-9- and CTX-M-15-producing strain isolated from wastewater in Switzerland and belonging to the international high-risk clone sequence type 147 (ST147). METHODS Whole-genome sequencing of K. pneumoniae 002SK2 was performed using Pacific Biosciences (PacBio) single-molecule, real-time (SMRT) technology RS2 reads (C4/P6 chemistry). De novo assembly was performed using Canu assembler, and sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). RESULTS The genome of K. pneumoniae 002SK2 consists of a 5.4-Mbp chromosome containing blaSHV-11 and fosA6, a 159-kb IncFIB(K) plasmid carrying the heavy metal resistance genes ars and sil, and a 77-kb IncR plasmid containing blaCTX-M-15, blaNDM-9, blaOXA-9 and blaTEM-1. CONCLUSIONS Multidrug-resistant K. pneumoniae harbouring blaNDM-9 and blaCTX-M-15 are spreading into the environment, most probably via wastewater from clinical settings.
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Haller L, Chen H, Ng C, Le TH, Koh TH, Barkham T, Sobsey M, Gin KYH. Occurrence and characteristics of extended-spectrum β-lactamase- and carbapenemase- producing bacteria from hospital effluents in Singapore. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 615:1119-1125. [PMID: 29751417 DOI: 10.1016/j.scitotenv.2017.09.217] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/17/2017] [Accepted: 09/20/2017] [Indexed: 05/09/2023]
Abstract
One of the most important resistance mechanisms in Gram-negative bacteria today is the production of enzymes causing resistance to cephalosporin and carbapenem antibiotics. The spread of extended-spectrum β-lactamases (ESBL)- and carbapenemase- producing Gram-negative bacteria is an emerging global public health problem. The aim of the present study was to (i) assess the prevalence of carbapenem-resistant bacteria (CRB) and ESBL-producing strains in sewage effluents from two major hospitals in Singapore, (ii) characterize the isolated strains and (iii) identify some of the ESBL and carbapenemase genes responsible for the resistance. CHROMagar ESBL and KPC plates were used to rapidly screen for ESBL-producing bacteria and those expressing reduced susceptibility to carbapenems, respectively. The abundance of ESBL-producers and CRB in hospital wastewater ranged between 103 and 106CFU/mL. Out of the 66 isolates picked from ESBL and KPC plates, 95%, 82%, 82% and 76% were resistant to ceftriaxone, ceftazidime (3rd generation cephalosporin family), ertapenem and meropenem (carbapenem family), respectively. Among the resistant isolates, the most predominant taxa identified were Pseudomonas spp. (28.2%), Klebsiella spp. (28.2%), Enterobacter spp. (18.3%) and Citrobacter spp. (11.3%). PCR and sequencing analysis showed that the predominant β-lactamase genes were blaSHV (41.1%) followed by blaNDM-1 (35.6%), blaCTX (35.6%) and blaKPC (28.8%). The results of this study show a high prevalence of bacteria resistant to modern extended-spectrum cephalosporins and carbapenems and the presence of ESBL- and carbapenemase producers in hospital effluents. These findings support the need to improve management of hospital wastewater in order to minimize the spread of antimicrobial resistant microorganisms from this source.
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Affiliation(s)
- Laurence Haller
- Department of Civil & Environmental Engineering, National University of Singapore, E1A-07-03, 1 Engineering Drive 2, 117576, Singapore
| | - Hongjie Chen
- Department of Civil & Environmental Engineering, National University of Singapore, E1A-07-03, 1 Engineering Drive 2, 117576, Singapore
| | - Charmaine Ng
- Department of Civil & Environmental Engineering, National University of Singapore, E1A-07-03, 1 Engineering Drive 2, 117576, Singapore
| | - Thai Hoang Le
- Department of Civil & Environmental Engineering, National University of Singapore, E1A-07-03, 1 Engineering Drive 2, 117576, Singapore
| | - Tse Hsien Koh
- Department of Pathology, Singapore, General Hospital, Outram Road, Singapore 169608
| | - Timothy Barkham
- Department of Laboratory Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433
| | - Mark Sobsey
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina CB# 7431, Chapel Hill, N.C. 27599, USA
| | - Karina Yew-Hoong Gin
- Department of Civil & Environmental Engineering, National University of Singapore, E1A-07-03, 1 Engineering Drive 2, 117576, Singapore; NUS Environmental Research Institute (NERI), National University of Singapore, T-Lab Building (#02-01), 5A Engineering Drive 1, 117411, Singapore.
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Complete Genome Sequence of Escherichia coli ABWA45, an rmtB-Encoding Wastewater Isolate. GENOME ANNOUNCEMENTS 2017; 5:5/34/e00844-17. [PMID: 28839027 PMCID: PMC5571413 DOI: 10.1128/genomea.00844-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We present the complete genome sequence of Escherichia coli ABWA45, a 16S rRNA methyltransferase-producing wastewater isolate. Assembly and annotation resulted in a 5,094,639-bp circular chromosome and four closed plasmids of 145,220 bp, 113,793 bp, 57,232 bp, and 47,900 bp in size. Furthermore, a small open plasmid (7,537 bp in size) was assembled.
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Draft Genome Sequence of Klebsiella pneumoniae 704SK6, an OXA-48- and CTX-M-15-Encoding Wastewater Isolate. GENOME ANNOUNCEMENTS 2017; 5:5/33/e00831-17. [PMID: 28818913 PMCID: PMC5604786 DOI: 10.1128/genomea.00831-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The Swiss wastewater isolate
Klebsiella pneumoniae
704SK6, encoding OXA-48 and CTX-M-15 β-lactamases, was fully sequenced. The assembly resulted in an open chromosome of 5,208,104 bp in size (G+C content, 57.6%) and four closed plasmid sequences of 209,651, 197,670, 65,998, and 63,605 bp in size.
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Complete Genome Sequence of Citrobacter freundii 705SK3, an OXA-48-Encoding Wastewater Isolate. GENOME ANNOUNCEMENTS 2017; 5:5/33/e00842-17. [PMID: 28818914 PMCID: PMC5604787 DOI: 10.1128/genomea.00842-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We present the genome sequence of Citrobacter freundii 705SK3, a wastewater isolate harboring an IncL OXA-48-encoding plasmid. Assembly of the genome resulted in a 5,242,839-bp circular chromosome (GC content, 52%) and two closed plasmids of 296,175 bp and 63, 458 bp in size.
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Complete Genome Sequence of Enterobacter cloacae 704SK10, an OXA-48-Encoding Wastewater Isolate. GENOME ANNOUNCEMENTS 2017; 5:5/33/e00830-17. [PMID: 28818912 PMCID: PMC5604785 DOI: 10.1128/genomea.00830-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Here we present the complete genome sequence of Enterobacter cloacae 704SK10, a Swiss wastewater isolate encoding an OXA-48 carbapenemase. Assembly resulted in closed sequences of the 4,876,946-bp chromosome, a 111,184-bp IncF plasmid, and an OXA-48-encoding IncL plasmid (63,458 bp) nearly identical to the previously described plasmid pOXA-48.
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