The shared NDM-positive strains in the hospital and connecting aquatic environments

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

The spread of antibiotic-resistant priority pathogens outside hospital settings is, both, a significant public health concern and an environmental problem. In recent years, New Delhi Metallo-β-lactamase (NDM)-positive strains have caused nosocomial infections with high mortality and poor prognosis worldwide. Our study investigated the links of NDM-positive strains between the hospital and the connecting river system in Jinan city, Eastern China by using NDM-producing Escherichia coli (NDM-EC) as an indicator via whole genome sequencing. Thirteen NDM-EC isolates were detected from 187 river water and sediment samples, while 9 isolates were identified from patients at the local hospital. All NDM-EC isolates were resistant to imipenem, meropenem, cefotaxime, cefoxitin, ampicillin, tetracycline, fosfomycin, piperacillin-tazobactam. The blaNDM-5 (n = 20) and blaNDM-9 (n = 2) genes were identified, which were predominantly on IncX3 plasmids (n = 13), followed by IncFII plasmids (n = 5) and IncFIA plasmids (n = 2). Conjugation experiments showed that 21 isolates could transfer NDM-harboring plasmids. The well-conserved blaNDM-5 genetic environment (ISAba125-blaNDM-5/9-bleMBL-trpF-dsbD-IS26) of these plasmids suggested a common genetic origin. Nine sequence types (STs) were detected, including three international high-risk clones ST167 (n = 8), ST410 (n = 1), and ST617 (n = 1). Phylogenetic analysis showed ST167 E. coli from the river was genotypically related to clinical isolates recovered from patients. Furthermore, ST167 isolates showed high genetic similarities with other clinical strains from geographically distinct regions. The genetic concordance between isolates from different sampling sites in the same river (ST218 clone), and different rivers (ST448 clone) raises concerns regarding the rapid dissemination of NDM-EC in the aquatic environment. The emergence and spread of the clinically relevant NDM-positive strains, especially for E. coli ST167 clone, an international high-risk clone associated with multi-resistance and virulence capacity, within and between the hospital and aquatic environments were elucidated, highlighting the need for attention and action.

Related collections

Most cited references 70

Record: found
Abstract: found
Article: found

Is Open Access

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

Nabil-Fareed Alikhan, Nicola Petty, Nouri L. Ben Zakour … (2011)

Background Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. Results BLAST Ring Image Generator (BRIG) can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically. Conclusions There is a clear need for a user-friendly program that can produce genome comparisons for a large number of prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. Here we present BRIG, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. BRIG is freely available for all operating systems at http://sourceforge.net/projects/brig/.

0 comments Cited 777 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Occurrence of antibiotics and antibiotic resistance genes in hospital and urban wastewaters and their impact on the receiving river.

Sara Rodriguez-Mozaz, Sara Chamorro, Elisabet Marti … (2015)

Antibiotic resistance has become a major health concern; thus, there is a growing interest in exploring the occurrence of antibiotic resistance genes (ARGs) in the environment as well as the factors that contribute to their emergence. Aquatic ecosystems provide an ideal setting for the acquisition and spread of ARGs due to the continuous pollution by antimicrobial compounds derived from anthropogenic activities. We investigated, therefore, the pollution level of a broad range of antibiotics and ARGs released from hospital and urban wastewaters, their removal through a wastewater treatment plant (WWTP) and their presence in the receiving river. Several antimicrobial compounds were detected in all water samples collected. Among antibiotic families, fluoroquinolones were detected at the highest concentration, especially in hospital effluent samples. Although good removal efficiency by treatment processes was observed for several antimicrobial compounds, most antibiotics were still present in WWTP effluents. The results also revealed that copy numbers of ARGs, such as blaTEM (resistance to β-lactams), qnrS (reduced susceptibility to fluoroquinolones), ermB (resistance to macrolides), sulI (resistance to sulfonamides) and tetW (resistance to tetracyclines), were detected at the highest concentrations in hospital effluent and WWTP influent samples. Although there was a significant reduction in copy numbers of these ARGs in WWTP effluent samples, this reduction was not uniform across analyzed ARGs. Relative concentration of ermB and tetW genes decreased as a result of wastewater treatment, whereas increased in the case of blaTEM, sulI and qnrS genes. The incomplete removal of antibiotics and ARGs in WWTP severely affected the receiving river, where both types of emerging pollutants were found at higher concentration in downstream waters than in samples collected upstream from the discharge point. Taken together, our findings demonstrate a widespread occurrence of antibiotics and ARGs in urban and hospital wastewater and how these effluents, even after treatment, contribute to the spread of these emerging pollutants in the aquatic environment.

0 comments Cited 317 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India.

Dongeun Yong, Mark Toleman, Christian G Giske … (2009)

A Swedish patient of Indian origin traveled to New Delhi, India, and acquired a urinary tract infection caused by a carbapenem-resistant Klebsiella pneumoniae strain that typed to the sequence type 14 complex. The isolate, Klebsiella pneumoniae 05-506, was shown to possess a metallo-beta-lactamase (MBL) but was negative for previously known MBL genes. Gene libraries and amplification of class 1 integrons revealed three resistance-conferring regions; the first contained bla(CMY-4) flanked by ISEcP1 and blc. The second region of 4.8 kb contained a complex class 1 integron with the gene cassettes arr-2, a new erythromycin esterase gene; ereC; aadA1; and cmlA7. An intact ISCR1 element was shown to be downstream from the qac/sul genes. The third region consisted of a new MBL gene, designated bla(NDM-1), flanked on one side by K. pneumoniae DNA and a truncated IS26 element on its other side. The last two regions lie adjacent to one another, and all three regions are found on a 180-kb region that is easily transferable to recipient strains and that confers resistance to all antibiotics except fluoroquinolones and colistin. NDM-1 shares very little identity with other MBLs, with the most similar MBLs being VIM-1/VIM-2, with which it has only 32.4% identity. As well as possessing unique residues near the active site, NDM-1 also has an additional insert between positions 162 and 166 not present in other MBLs. NDM-1 has a molecular mass of 28 kDa, is monomeric, and can hydrolyze all beta-lactams except aztreonam. Compared to VIM-2, NDM-1 displays tighter binding to most cephalosporins, in particular, cefuroxime, cefotaxime, and cephalothin (cefalotin), and also to the penicillins. NDM-1 does not bind to the carbapenems as tightly as IMP-1 or VIM-2 and turns over the carbapenems at a rate similar to that of VIM-2. In addition to K. pneumoniae 05-506, bla(NDM-1) was found on a 140-kb plasmid in an Escherichia coli strain isolated from the patient's feces, inferring the possibility of in vivo conjugation. The broad resistance carried on these plasmids is a further worrying development for India, which already has high levels of antibiotic resistance.