Coinfection with Human Norovirus and Escherichia coli O25:H4 Harboring Two Chromosomal blaCTX-M-14 Genes in a Foodborne Norovirus Outbreak in Shizuoka Prefecture, Japan

2020 ◽  
Vol 83 (9) ◽  
pp. 1584-1591
Author(s):  
HIROMI NAGAOKA ◽  
SHINICHIRO HIRAI ◽  
HIROTAKA MORINUSHI ◽  
SHIRO MIZUMOTO ◽  
KANA SUZUKI ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Human Norovirus ◽  
E Coli ◽  
Hospital Acquired Infections ◽  
Antimicrobial Resistance Genes ◽  
Hospital Acquired ◽  
Healthy Persons ◽  
M 14

ABSTRACT Hospital-acquired infections caused by extended-spectrum β-lactamase (ESBL)–producing Escherichia coli are a global problem. Healthy people can carry ESBL-producing E. coli in the intestines; thus, E. coli from healthy people can potentially cause hospital-acquired infections. Therefore, the transmission routes of ESBL-producing E. coli from healthy persons should be determined. A foodborne outbreak of human norovirus (HuNoV) GII occurred at a restaurant in Shizuoka, Japan, in 2018. E. coli O25:H4 was isolated from some of the HuNoV-infected customers. Pulsed-field gel electrophoresis showed that these E. coli O25:H4 strains originated from one clone. Because the only epidemiological link among the customers was eating food from this restaurant, the customers were concurrently infected with E. coli O25:H4 and HuNoV GII via the restaurant food. Whole genome analysis revealed that the E. coli O25:H4 strains possessed genes for regulating intracellular iron and expressing the flagellum and flagella. Extraintestinal pathogenic E. coli often express these genes on the chromosome. Additionally, the E. coli O25:H4 strains had plasmids harboring nine antimicrobial resistance genes. These strains harbored ESBL-encoding blaCTX-M-14 genes on two loci of the chromosome and had higher ESBL activity. Multilocus sequence typing and fimH subtyping revealed that the E. coli O25:H4 strains from the outbreak belonged to the subclonal group, ST131-fimH30R, which has been driving ESBL epidemics in Japan. Because the E. coli O25:H4 strains isolated in the outbreak belonged to a subclonal group spreading in Japan, foods contaminated with ESBL-producing E. coli might contribute to spreading these strains among healthy persons. The isolated E. coli O25:H4 strains produced ESBL and contained plasmids with multiple antimicrobial resistance genes, which may make it difficult to select antimicrobials for treating extraintestinal infections caused by these strains. HIGHLIGHTS

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 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 Antimicrobial Resistance Genes and Diversity of Clones among Faecal ESBL-Producing Escherichia coli Isolated from Healthy and Sick Dogs Living in Portugal

Antibiotics ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1013
Author(s):  
Isabel Carvalho ◽  
Rita Cunha ◽  
Carla Martins ◽  
Sandra Martínez-Álvarez ◽  
Nadia Safia Chenouf ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Genetic Characteristics ◽  
E Coli ◽  
Faecal Samples ◽  
Antimicrobial Resistance Genes ◽  
Healthy Dogs ◽  
Positive Isolate ◽  
Sequence Types ◽  
M 14

The purpose of this study was to analyse the prevalence and genetic characteristics of ESBL and acquired-AmpC (qAmpC)-producing Escherichia coli isolates from healthy and sick dogs in Portugal. Three hundred and sixty-one faecal samples from sick and healthy dogs were seeded on MacConkey agar supplemented with cefotaxime (2 µg/mL) for cefotaxime-resistant (CTXR) E. coli recovery. Antimicrobial susceptibility testing for 15 antibiotics was performed and the ESBL-phenotype of the E. coli isolates was screened. Detection of antimicrobial resistance and virulence genes, and molecular typing of the isolates (phylogroups, multilocus-sequence-typing, and specific-ST131) were performed by PCR (and sequencing when required). CTXRE. coli isolates were obtained in 51/361 faecal samples analysed (14.1%), originating from 36/234 sick dogs and 15/127 healthy dogs. Forty-seven ESBL-producing E. coli isolates were recovered from 32 sick (13.7%) and 15 healthy animals (11.8%). Different variants of blaCTX-M genes were detected among 45/47 ESBL-producers: blaCTX-M-15 (n = 26), blaCTX-M-1 (n = 10), blaCTX-M-32 (n = 3), blaCTX-M-55 (n = 3), blaCTX-M-14 (n = 2), and blaCTX-M-variant (n = 1); one ESBL-positive isolate co-produced CTX-M-15 and CMY-2 enzymes. Moreover, two additional CTXR ESBL-negative E. coli isolates were CMY-2-producers (qAmpC). Ten different sequence types were identified (ST/phylogenetic-group/β-lactamase): ST131/B2/CTX-M-15, ST617/A/CTX-M-55, ST3078/B1/CTX-M-32, ST542/A/CTX-M-14, ST57/D/CTX-M-1, ST12/B2/CTX-M-15, ST6448/B1/CTX-M-15 + CMY-2, ST5766/A/CTX-M-32, ST115/D/CMY-2 and a new-ST/D/CMY-2. Five variants of CTX-M enzymes (CTX-M-15 and CTX-M-1 predominant) and eight different clonal complexes were detected from canine ESBL-producing E. coli isolates. Although at a lower rate, CMY-2 β-lactamase was also found. Dogs remain frequent carriers of ESBL and/or qAmpC-producing E. coli with a potential zoonotic role.

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.

In vitro transduction of antimicrobial resistance genes into Escherichia coli isolates from backyard poultry in Mexico

2021 ◽  
Author(s):  
Juan Martín Talavera-Gonzalez ◽  
Martin Talavera-Rojas ◽  
Edgardo Soriano-Vargas ◽  
JESUS VAZQUEZ-NAVARRETE ◽  
Celene Salgado-Miranda
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Northern Region ◽  
Wild Birds ◽  
Drug Resistant ◽  
E Coli ◽  
Backyard Poultry ◽  
Antimicrobial Resistance Genes

The transmission of multi-drug resistant pathogens and antimicrobial-resistant genes is an arising problem with multiple factors involved (humans, domestic animals, wildlife). The aim of this study was to investigate the presence of Escherichia coli isolates with different antimicrobial resistance genes from backyard poultry and demonstrate the in vitro transduction phenomenon of these genes between phages from migratory wild-birds and poultry E. coli isolates. We collected 197 E. coli isolates from chicken, turkeys, and ducks in backyard production units (northern region of the State of Mexico). Isolates were resistant to ampicillin (80.7%), tetracycline (64.4%), carbenicillin (56.3%), and nalidixic acid and trimethoprim-sulfamethoxazole (both, 26.9%). Moreover, blaTEM (56.3%), tetB (20.8%), tetA (19.2%), sulI (7.6%), sulII (10.1%), qnrA (9.6%) and qnrB (5.5%) genes were found. In vitro transduction using phages from migratory wild birds sampled in the wetland Chimaliapan (State of Mexico) was worked out. It was possible to transduce qnrA, tetB, blaTEM and sulII genes to E. coli isolates from poultry. This is the first report that describes the transduction of antimicrobial resistance genes from phages of migratory wild birds to poultry and suggests the possible transmission in backyard production units.

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