Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing

Ludden, Catherine; Reuter, Sandra; Judge, Kim; Gouliouris, Theodore; Blane, Beth; Coll, Francesc Español i; Naydenova, Plamena; Hunt, Martin; Tracey, Alan S.; Hopkins, Katie L.; Brown, Nicholas M.; Woodford, Neil; Parkhill, Julian; Peacock, Sharon J.

doi:10.1099/mgen.0.000114

Cited by 35 publications

(51 citation statements)

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“…There have been many publications of hospital environmental investigations during outbreaks and some during nonoutbreak periods (20,25,27,54,55). Findings from the 2011 bla KPC ϩ K. pneumoniae outbreak investigation at NIHCC led to changes in our infection control policies, such as implementation of environmental surveillance cultures in response to newly identified CPO carriers and surveillance testing of previously positive sites after remediation.…”

Section: Discussionmentioning

confidence: 99%

“…Sources of outbreaks are occasionally linked to aqueous locations such as sinks and drains (9)(10)(11)(12), where the presence of biofilms makes remediation challenging; sink engineering modifications have been proposed to tackle these problems (13,14). Beyond the sink, hospital sewage and wastewater are known reservoirs of CPOs around the world (15)(16)(17)(18)(19)(20). One hypothesis suggests that this reservoir is, in part, due to the use of large quantities of antimicrobial agents in hospitals, which leads to the selection of MDROs and the high likelihood of horizontal gene transfer within the hospital effluent (21).…”

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confidence: 99%

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Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

Weingarten

Johnson

Conlan

et al. 2018

mBio

180

134

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The hospital environment is a potential reservoir of bacteria with plasmids conferring carbapenem resistance. Our Hospital Epidemiology Service routinely performs extensive sampling of high-touch surfaces, sinks, and other locations in the hospital. Over a 2-year period, additional sampling was conducted at a broader range of locations, including housekeeping closets, wastewater from hospital internal pipes, and external manholes. We compared these data with previously collected information from 5 years of patient clinical and surveillance isolates. Whole-genome sequencing and analysis of 108 isolates provided comprehensive characterization of bla KPC /bla NDM -positive isolates, enabling an in-depth genetic comparison. Strikingly, despite a very low prevalence of patient infections with bla KPC -positive organisms, all samples from the intensive care unit pipe wastewater and external manholes contained carbapenemase-producing organisms (CPOs), suggesting a vast, resilient reservoir. We observed a diverse set of species and plasmids, and we noted species and susceptibility profile differences between environmental and patient populations of CPOs. However, there were plasmid backbones common to both populations, highlighting a potential environmental reservoir of mobile elements that may contribute to the spread of resistance genes. Clear associations between patient and environmental isolates were uncommon based on sequence analysis and epidemiology, suggesting reasonable infection control compliance at our institution. Nonetheless, a probable nosocomial transmission of Leclercia sp. from the housekeeping environment to a patient was detected by this extensive surveillance. These data and analyses further our understanding of CPOs in the hospital environment and are broadly relevant to the design of infection control strategies in many infrastructure settings.IMPORTANCE Carbapenemase-producing organisms (CPOs) are a global concern because of the morbidity and mortality associated with these resistant Gramnegative bacteria. Horizontal plasmid transfer spreads the resistance mechanism to new bacteria, and understanding the plasmid ecology of the hospital environment can assist in the design of control strategies to prevent nosocomial infections. A 5-year genomic and epidemiological survey was undertaken to study the CPOs in the patient-accessible environment, as well as in the plumbing system removed from the patient. This comprehensive survey revealed a vast, unappreciated reservoir of CPOs in wastewater, which was in contrast to the low positivity rate in both the patient population and the patient-accessible environment. While there were few patient-environmental isolate associations, there were plasmid backbones common to both populations. These results are relevant to all hospitals for which CPO colonization may not yet be defined through extensive surveillance.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

Weingarten

Johnson

Conlan

et al. 2018

mBio

180

134

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“…The NDM type was first detected in India in tap water and sewage and has now spread to clinical settings worldwide (4,5). Carbapenemase genes are frequently located on plasmids and mobile genetic elements that can be transmitted between species and often coexist with other classes of antibiotic resistance genes, such as aminoglycosides and fluoroquinolones (6).…”

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confidence: 99%

Environmental Presence and Genetic Characteristics of Carbapenemase-Producing Enterobacteriaceae from Hospital Sewage and River Water in the Philippines

Suzuki

Nazareno

Nakano

et al. 2020

Appl Environ Microbiol

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This study aimed to evaluate the prevalence and genetic characteristics of carbapenemase-producing Enterobacteriaceae (CPE) in hospital sewage and river water in the Philippines, which has a typical tropical maritime climate. We collected 83 water samples from 7 hospital sewage and 10 river water sites. CPE were identified using CHROMagar mSuperCARBA, and Gram-negative strains were identified using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) or 16S rRNA gene sequencing. Resistance genes in Enterobacteriaceae strains were identified using PCR and DNA sequencing, and transferability of carbapenemase genes from the CPE was investigated with conjugation experiments. Genotyping was performed using multilocus sequence typing (MLST) for Escherichia coli and Klebsiella pneumoniae. Out of 124 Enterobacteriaceae isolates, we identified 51 strains as CPE and divided these into 7 species, 11 E. coli, 14 Klebsiella spp., 15 Enterobacter spp., and 11 others, including 4 additional species. Conjugation experiments via broth mating and using E. coli J53 revealed that 24 isolates can transfer carbapenemase-encoding plasmids. MLST analysis showed that 6 of 11 E. coli isolates belonged to clonal complex 10 (CC10). Of 11 K. pneumoniae strains, 9 unique sequence types (STs) were identified, including ST147. Five types of carbapenemase genes were identified, with the most prevalent being NDM (n = 39), which is epidemic in clinical settings in the Philippines. E. coli CC10 and K. pneumoniae ST147, which are often detected in clinical settings, were the dominant strains. In summary, our results indicate that hospital sewage and river water are contaminated by CPE strains belonging to clinically important clonal groups. IMPORTANCE Carbapenemase-producing Enterobacteriaceae (CPE) cause severe health care-associated infections, and their increasing prevalence is a serious concern. Recently, natural ecosystems have been recognized as important reservoirs of antibiotic resistance genes. We investigated the prevalence and genetic characteristics of CPE isolated from the environment (hospital sewage and river water) in the Philippines and found several CPE, including Escherichia coli and other species, with different carbapenemases. The most prevalent carbapenemase gene type was NDM, which is endemic in clinical settings. This study revealed that isolates belonging to carbapenemase-producing E. coli CC10 and K. pneumoniae sequence type 147 (ST147), which are often detected in clinical settings, were dominant in the natural environment. Our work here provides a report on the presence and characteristics of CPE in the environment in the Philippines and demonstrates that both hospital sewage and river water are contaminated by CPE strains belonging to clinically important clonal groups.

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“…Five samples were from faeces, and one was from blood. These were short-read sequenced in a multiplex run on an Illumina HiSeq 2500 platform and processed as previously outlined [27].…”

Section: Methodsmentioning

confidence: 99%

Complete assembly ofEscherichia coliST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

Decano

Ludden

Feltwell

et al. 2019

Preprint

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22The incidence of infections caused by extraintestinal Escherichia coli (ExPEC) is rising globally, 23 which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been 24 associated with excess mortality, prolonged hospital stays and higher healthcare costs. E. coli ST131 is 25 a major ExPEC clonal group worldwide with variable plasmid composition, and has an array of genes 26 enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genes blaCTX-M-27 14/15/27, which are often rearranged, amplified and translocated by mobile genetic elements (MGEs).28 Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow 29 MGE structures encoding blaCTX-M genes to be fully determined. Here, we performed long read 30 sequencing to decipher the genome structures of six E. coli ST131 isolated from six patients. Most 31 long read assemblies generated entire chromosomes and plasmids as single contigs, contrasting with 32 more fragmented assemblies created with short reads alone. The long read assemblies highlighted 33 diverse accessory genomes with blaCTX-M-15, blaCTX-M-14 and blaCTX-M-27 genes identified in three, one 34 and one isolates, respectively. One sample had no blaCTX-M gene. Two samples had chromosomal 35 blaCTX-M-14 and blaCTX-M-15 genes, and the latter was at three distinct locations, likely transposed by the 36 adjacent MGEs: ISEcp1, IS903B and Tn2. This study showed that AMR genes exist in multiple 37 different chromosomal and plasmid contexts even between closely-related isolates within a clonal 38 group such as E. coli ST131. 39 40 Importance 41 Drug-resistant bacteria are a major cause of illness worldwide and a specific subtype called 42 Escherichia coli ST131 cause a significant amount of these infections. ST131 become resistant to 43 treatment by modifying their DNA and by transferring genes among one another via large packages of 44 genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a 45 better understanding of what plasmids are being exchanged and their exact contents. To achieve this, 46we applied new high-resolution DNA sequencing technology to six ST131 samples from infected 47 patients and compared the output to an existing approach. A combination of methods shows that drug-48 resistance genes on plasmids are highly mobile because they can jump into ST131's chromosomes. We 49 found that the plasmids are very elastic and undergo extensive rearrangements even in closely related 50 samples. This application of DNA sequencing technologies illustrates at a new level the highly 51 dynamic nature of ST131 genomes. 52 53 54 55 56 57 Reported cases of bloodstream and urinary tract infections caused by extraintestinal pathogenic 58 Escherichia coli (ExPEC) are increasing globally at an alarming rate [1]. As a key source of ExPEC 59 isolates worldwide, E. coli sequence type 131 (ST131) is regarded as a serious threat to public health, 60 given its high level of a...

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Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing

Cited by 35 publications

References 61 publications

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

Environmental Presence and Genetic Characteristics of Carbapenemase-Producing Enterobacteriaceae from Hospital Sewage and River Water in the Philippines

Complete assembly ofEscherichia coliST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

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