scholarly journals Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

2020 ◽  
Author(s):  
B Constantinides ◽  
KK Chau ◽  
TP Quan ◽  
G Rodger ◽  
M Andersson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Bacterial Infections ◽  
Wide Spectrum ◽  
Klebsiella Oxytoca ◽  
Clinical Disease ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Wide Range

ABSTRACTEscherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonised with diverse populations of E. coli, Klebsiella pneumoniae and Klebsiella oxytoca, including both antimicrobial-resistant and susceptible strains. Using whole genome sequencing (WGS) of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies which may vary as a result of different inputs and selection pressures. WGS of 46 contemporaneous patient isolates identified one (2%; 95% CI 0.05-11%) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10% of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including blaCTX-M, blaSHV and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention.IMPORTANCEEscherichia coli and Klebsiella spp. cause a wide range of bacterial infections, including bloodstream, urine and lung infections. Previous studies have shown that sink drains in hospitals may be part of transmission chains in outbreaks of antimicrobial-resistant E. coli and Klebsiella spp., leading to colonisation and clinical disease in patients. We show that even in non-outbreak settings, contamination of sink drains by these bacteria is common across hospital wards, and that many antimicrobial resistance genes can be found and potentially exchanged in these sink drain sites. Our findings demonstrate that the colonisation of handwashing sink drains by these bacteria in hospitals is likely contributing to some infections in patients, and that additional work is needed to further quantify this risk, and to consider appropriate mitigating interventions.

scholarly journals Antibiotic Resistance Genes and Associated Phenotypes in Escherichia coli and Enterococcus from Cattle at Different Production Stages on a Dairy Farm in Central California

Antibiotics ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1042
Author(s):  
Saharuetai Jeamsripong ◽  
Xunde Li ◽  
Sharif S. Aly ◽  
Zhengchang Su ◽  
Richard V. Pereira ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Wide Spectrum ◽  
Cross Sectional ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Enterococcus Spp ◽  
Production Stages

The objectives of this study were to characterize overall genomic antibiotic resistance profiles of fecal Escherichia coli and Enterococcus spp. from dairy cattle at different production stages using whole-genome sequencing and to determine the association between antimicrobial resistance (AMR) phenotypes and their corresponding genotypes. The Comprehensive Antibiotic Resistance Database (CARD) and ResFinder, two publicly available databases of antimicrobial resistance genes, were used to annotate isolates. Based on the ResFinder database, 27.5% and 20.0% of tested E. coli isolates (n = 40) harbored single and ≥3 antimicrobial resistance genes, respectively; for Enterococcus spp., we observed 87.8% and 8.2%, respectively. The highest prevalence of AMR genes in E. coli was for resistance to tetracycline (27.5%), followed by sulphonamide (22.5%) and aminoglycoside (20.0%); the predominant antimicrobial resistance genes in Enterococcus spp. targeted macrolide drugs (77.6%). Based on the CARD database, resistance to ≥3 antimicrobial classes was observed in all E. coli and 77.6% in Enterococcus spp. isolates. A high degree of agreement existed between the resistance phenotype and the presence of resistance genes for various antimicrobial classes for E. coli but much less so for isolates of Enterococcus. Consistent with prior work, fecal E. coli and Enterococcus spp. isolates from calves harbored a wide spectrum of resistance genes, compared to those from cattle at other production stages, based on the cross-sectional samples from the studied farm.

scholarly journals Impact of UV and Peracetic Acid Disinfection on the Prevalence of Virulence and Antimicrobial Resistance Genes in Uropathogenic Escherichia coli in Wastewater Effluents

2014 ◽  
Vol 80 (12) ◽  
pp. 3656-3666 ◽  
Author(s):  
Basanta Kumar Biswal ◽  
Ramzi Khairallah ◽  
Kareem Bibi ◽  
Alberto Mazza ◽  
Ronald Gehr ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Peracetic Acid ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Municipal Wastewaters ◽  
The Impact

ABSTRACTWastewater discharges may increase the populations of pathogens, includingEscherichia coli, and of antimicrobial-resistant strains in receiving waters. This study investigated the impact of UV and peracetic acid (PAA) disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenicEscherichia coli(UPEC), the most abundantE. colipathotype in municipal wastewaters. Laboratory disinfection experiments were conducted on wastewater treated by physicochemical, activated sludge, or biofiltration processes; 1,766E. coliisolates were obtained for the evaluation. The target disinfection level was 200 CFU/100 ml, resulting in UV and PAA doses of 7 to 30 mJ/cm2and 0.9 to 2.0 mg/liter, respectively. The proportions of UPECs were reduced in all samples after disinfection, with an average reduction by UV of 55% (range, 22% to 80%) and by PAA of 52% (range, 11% to 100%). Analysis of urovirulence genes revealed that the decline in the UPEC populations was not associated with any particular virulence factor. A positive association was found between the occurrence of urovirulence and antimicrobial resistance genes (ARGs). However, the changes in the prevalence of ARGs in potential UPECs were different following disinfection, i.e., UV appears to have had no effect, while PAA significantly reduced the ARG levels. Thus, this study showed that both UV and PAA disinfections reduced the proportion of UPECs and that PAA disinfection also reduced the proportion of antimicrobial resistance gene-carrying UPEC pathotypes in municipal wastewaters.

scholarly journals Non-human primates in the Gambia harbour human-associated pathogenic Escherichia coli strains

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Ebenezer Foster-Nyarko ◽  
Nabil-Fareed Alikhan ◽  
Anuradha Ravi ◽  
Gaëtan Thilliez ◽  
Nicholas Thomson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
The Gambia ◽  
Public Health Importance ◽  
Software Environment ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Long Read ◽  
Sequence Types

Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between different host species. We have investigated genetic diversity and antimicrobial resistance in Escherichia coli isolates from a range of non-human primates dispersed across the Gambia: patas monkey (n=1), western colobus monkey (n=6), green monkey (n=14) and guinea baboon (n=22). From 43 stools, we recovered 99 isolates. We performed Illumina whole-genome shotgun sequencing on all isolates and nanopore long-read sequencing on isolates with antimicrobial resistance genes. We inferred the evolution of E. coli in this population using the EnteroBase software environment. We identified 43 sequence types (ten of them novel), spanning five of the eight known phylogroups of E. coli. Many of the observed sequence types and phylotypes from non-human primates have been associated with human extra-intestinal infection and carry virulence characteristics associated with disease in humans, particularly ST73, ST217 and ST681. However, we found a low prevalence of antimicrobial resistance genes in isolates from non-human primates. Hierarchical clustering showed that ST442 and ST349 from non-human primates are closely related to isolates from human infections, suggesting recent exchange of bacteria between humans and monkeys. Our results are of public health importance, considering the increasing contact between humans and wild primates.

scholarly journals A Virulence and Antimicrobial Resistance DNA Microarray Detects a High Frequency of Virulence Genes in Escherichia coli Isolates from Great Lakes Recreational Waters

2006 ◽  
Vol 72 (6) ◽  
pp. 4200-4206 ◽  
Author(s):  
Katia Hamelin ◽  
Guillaume Bruant ◽  
Abdel El-Shaarawi ◽  
Stephen Hill ◽  
Thomas A. Edge ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Great Lakes ◽  
Dna Microarray ◽  
Resistance Genes ◽  
Virulence Genes ◽  
Recreational Waters ◽  
E Coli ◽  
Antimicrobial Resistance Genes

ABSTRACT Escherichia coli is generally described as a commensal species with occasional pathogenic strains. Due to technological limitations, there is currently little information concerning the prevalence of pathogenic E. coli strains in the environment. For the first time, using a DNA microarray capable of detecting all currently described virulence genes and commonly found antimicrobial resistance genes, a survey of environmental E. coli isolates from recreational waters was carried out. A high proportion (29%) of 308 isolates from a beach site in the Great Lakes carried a pathotype set of virulence-related genes, and 14% carried antimicrobial resistance genes, findings consistent with a potential risk for public health. The results also showed that another 8% of the isolates had unusual virulence gene combinations that would be missed by conventional screening. This new application of a DNA microarray to environmental waters will likely have an important impact on public health, epidemiology, and microbial ecology in the future.

scholarly journals Occurrence of Virulence and Antimicrobial Resistance Genes in Escherichia coli Isolates from Different Aquatic Ecosystems within the St. Clair River and Detroit River Areas

2006 ◽  
Vol 73 (2) ◽  
pp. 477-484 ◽  
Author(s):  
Katia Hamelin ◽  
Guillaume Bruant ◽  
Abdel El-Shaarawi ◽  
Stephen Hill ◽  
Thomas A. Edge ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Surface Waters ◽  
Aquatic Ecosystems ◽  
Urban Site ◽  
Detroit River ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene

ABSTRACT Although the number of Escherichia coli bacteria in surface waters can differ greatly between locations, relatively little is known about the distribution of E. coli pathotypes in surface waters used as sources for drinking or recreation. DNA microarray technology is a suitable tool for this type of study due to its ability to detect high numbers of virulence and antimicrobial resistance genes simultaneously. Pathotype, phylogenetic group, and antimicrobial resistance gene profiles were determined for 308 E. coli isolates from surface water samples collected from diverse aquatic ecosystems at six different sites in the St. Clair River and Detroit River areas. A higher frequency (48%) of E. coli isolates possessing virulence and antimicrobial resistance genes was observed in an urban site located downstream of wastewater effluent outfalls than in the other examined sites (average of 24%). Most E. coli pathotypes were extraintestinal pathogenic E. coli (ExPEC) pathotypes and belonged to phylogenetic groups B2 and D. The ExPEC pathotypes were found to occur across all aquatic ecosystems investigated, including riverine, estuarine, and offshore lake locations. The results of this environmental study using DNA microarrays highlight the widespread distribution of E. coli pathotypes in aquatic ecosystems and the potential public health threat of E. coli pathotypes originating from municipal wastewater sources.

scholarly journals Development and Validation of an Oligonucleotide Microarray for Detection of Multiple Virulence and Antimicrobial Resistance Genes in Escherichia coli

2006 ◽  
Vol 72 (5) ◽  
pp. 3780-3784 ◽  
Author(s):  
Guillaume Bruant ◽  
Christine Maynard ◽  
Sadjia Bekal ◽  
Isabelle Gaucher ◽  
Luke Masson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Oligonucleotide Microarray ◽  
Genome Plasticity ◽  
E Coli ◽  
Phylogenetic Studies ◽  
Antimicrobial Resistance Genes ◽  
Development And Validation ◽  
Reference Strains

ABSTRACT An oligonucleotide microarray detecting 189 Escherichia coli virulence genes or markers and 30 antimicrobial resistance genes was designed and validated using DNA from known reference strains. This microarray was confirmed to be a powerful diagnostic tool for monitoring emerging E. coli pathotypes and antimicrobial resistance, as well as for environmental, epidemiological, and phylogenetic studies including the evaluation of genome plasticity.

scholarly journals Diverse commensal E. coli clones and plasmids disseminate antimicrobial resistance genes in domestic animals and children in a semi-rural community in Ecuador

2019 ◽  
Author(s):  
Liseth Salinas ◽  
Paúl Cárdenas ◽  
Timothy J. Johnson ◽  
Karla Vasco ◽  
Jay Graham ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Rural Community ◽  
Resistance Genes ◽  
Domestic Animals ◽  
Drug Resistant ◽  
Phenotypic Resistance ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Resistance Patterns

ABSTRACTThe increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts in human medicine. Many of the multi-drug resistant (MDR) Enterobacteriaceae found in humans are community-acquired and linked to food animals (i.e. livestock raised for meat and dairy products). In this study, we examined whether numerically dominant, commensal Escherichia coli strains from humans (n=63 isolates) and domestic animals (n=174 isolates) in the same community and with matching phenotypic AMR patterns, were clonally related or shared the same plasmids. We identified 25 multi-drug resistant isolates (i.e. resistant to 3 or more antimicrobial classes) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes and plasmids carrying the AMR genes using conjugation, replicon typing and whole genome sequencing. None of the MDR E. coli isolates (from children and domestic animals) analyzed were clonal. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. Our findings suggest that nonclonal resistance gene dissemination is common in this community and that diverse plasmids carrying AMR genes presents a significant challenge for understanding the movement of AMR in a community.IMPORTANCEEven though Escherichia coli strains may share nearly identical AMR profiles, AMR genes, and overlap in space and time, the diversity of clones and plasmids challenges to research that aims to identify sources of AMR. Horizontal gene transfer appears to play a much larger role than clonal expansion in the spread of AMR in the community.

scholarly journals Extensive antimicrobial resistance and plasmid-carrying resistance genes in mcr-1-positive E. coli sampled in swine, in Guangxi, South China

2021 ◽  
Author(s):  
Jingzhi Yuan ◽  
Xiaoye Wang ◽  
Dali Shi ◽  
Qiang Ge ◽  
Xingxing Song ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
South China ◽  
Resistance Genes ◽  
Antimicrobial Agents ◽  
Health And Safety ◽  
Drug Resistant ◽  
Potential Threat ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Wide Range

Abstract Background: The discovery of the superbug mcr-1-positive Escherichia coli (MCRPEC) has attracted worldwide attention. Swine-origin multi-drug resistant MCRPEC is a potential threat to public health and safety. To date, few detailed studies have been reported on swine MCRPEC in Guangxi, South China.Results: In this study, thirty-three MCRPEC strains were identified from 142 E. coli strains isolated from 116 samples in Guangxi in 2018. All MCRPEC isolates were classified into eight unique STs and a total of six incompatibility plasmid groups (IncFI, IncHI1, IncY, IncN, IncI1 and IncX1) were found. Then, susceptibility of MCRPEC isolates to 27 antimicrobial agents belonging to 17 antimicrobial categories was tested. There were nineteen 3rd and 4th generation cephalosporins resistant E. coli and twelve carbapenem resistant E. coli among the 33 MCRPEC strains. Importantly, the MCRPEC were highly resistant to two carbapenem antibiotics, imipenem and meropenem, which were not permitted for use in livestock production. Three MCRPEC strains were further identified to be extensively drug-resistant (XDR), and the other isolates were recognized as multi-drug-resistant (MDR). Moreover, we detected whether the plasmid-carrying resistance genes coexist with the mcr-1 gene of the MCRPEC isolates. At last, β-lactamase antimicrobial resistance genes such as ESBL genes (blaCTX-M14, blaCTX-M24, blaCTX-M123, blaOXA-1), plasmid-mediated AmpC (pAmpC) gene (blaCMY-2), and the carbapenem gene blaNDM-5 were detected. In addition, non-β-lactamase antimicrobial resistance genes such as qnrA, qnrB, qnrS, aac(6’)-Ib-cr, tetA, tetB, sul1, sul2, floR, aadA were also detected.Conclusion: Thirty-three mcr-1-positive E. coli isolates in Guangxi had a wide range of antimicrobial resistance. Plasmid-carrying resistance genes might be the main cause of MCRPEC multidrug resistance. This study highlighted the necessity for long-term surveillance of mcr-1-positive E. coli in pigs.

scholarly journals Extensive antimicrobial resistance and plasmid-carrying resistance genes in mcr-1-positive E. coli sampled in swine, in Guangxi, South China

2020 ◽  
Author(s):  
Jingzhi Yuan ◽  
Xiaoye Wang ◽  
Dali Shi ◽  
Qiang Ge ◽  
Xingxing Song ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
South China ◽  
Resistance Genes ◽  
Antimicrobial Agents ◽  
Health And Safety ◽  
Drug Resistant ◽  
Potential Threat ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
Wide Range

Abstract Background: The discovery of the superbug mcr-1 -positive Escherichia coli (MCRPEC) has attracted worldwide attention. Swine-origin multi-drug resistant MCRPEC is a potential threat to public health and safety. To date, few detailed studies have been reported on swine MCRPEC in Guangxi, South China. Results: In this study, thirty-three MCRPEC strains were identified from 142 E. coli strains isolated from 116 samples in Guangxi in 2018. All MCRPEC isolates were classified into eight unique STs and a total of six incompatibility plasmid groups (IncFI, IncHI1, IncY, IncN, IncI1 and IncX1) were found. Then, susceptibility of MCRPEC isolates to 27 antimicrobial agents belonging to 17 antimicrobial categories was tested. There were nineteen 3rd and 4th generation cephalosporins resistant E. coli and twelve carbapenem resistant E. coli among the 33 MCRPEC strains. Importantly, the MCRPEC were highly resistant to two carbapenem antibiotics, imipenem and meropenem, which were not permitted for use in livestock production. Three MCRPEC strains were further identified to be extensively drug-resistant (XDR), and the other isolates were recognized as multi-drug-resistant (MDR). Moreover, we detected whether the plasmid-carrying resistance genes coexist with the mcr-1 gene of the MCRPEC isolates. At last, β-lactamase antimicrobial resistance genes such as ESBL genes ( bla CTX-M14 , bla CTX-M24 , bla CTX-M123 , bla OXA-1 ), plasmid-mediated AmpC (pAmpC) gene ( bla CMY-2 ), and the carbapenem gene bla NDM-5 were detected. In addition, non-β-lactamase antimicrobial resistance genes such as qnrA , qnrB , qnrS , aac(6’)-Ib-cr , tetA , tetB , sul1 , sul2 , floR , aadA were also detected. Conclusion: Thirty-three mcr-1 -positive E. coli isolates in Guangxi had a wide range of antimicrobial resistance. Plasmid-carrying resistance genes might be the main cause of MCRPEC multidrug resistance. This study highlighted the necessity for long-term surveillance of mcr-1 -positive E. coli in pigs.

Mobilization of tet (X4) by IS 1 family elements in porcine Esc herichia coli isolates

2021 ◽  
Author(s):  
Runhao Yu ◽  
Zheng Chen ◽  
Stefan Schwarz ◽  
Hong Yao ◽  
Xiang-Dang Du
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Suicide Plasmid ◽  
E Coli ◽  
Antimicrobial Resistance Genes ◽  
High Level

The dissemination mechanism of the high-level tigecycline resistance gene tet (X4) in porcine Escherichia coli was investigated . tet (X4) and other antimicrobial resistance genes were located on the plasmids p1919D3-1 and p1919D62-1 and flanked by two or three copies of IS 1 family elements, which can form one to three translocatable units (TUs). Using a reduced transposition model, IS 1A was experimentally demonstrated to mediate the transposition of tet (X4) from a suicide plasmid into the E. coli chromosome.

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