scholarly journals Design of the EPIGENEC Study: Assessing the EPIdemiology and GENetics of Escherichia coli in the Netherlands

2019 ◽  
Author(s):  
Denise van Hout ◽  
Tess D. Verschuuren ◽  
Patricia C.J. Bruijning-Verhagen ◽  
Thijs Bosch ◽  
E. Ascelijn Reuland ◽  
...  
Keyword(s):  
The Netherlands ◽  
Molecular Epidemiology ◽  
Epidemiological Data ◽  
Invasive Disease ◽  
Community Based ◽  
E Coli ◽  
Faecal Samples ◽  
Faecal Carriage ◽  
Population Structures ◽  
Hospital Acquired

Background: Infections caused by E. coli cause considerable disease burden and range from frequently occurring and relatively innocent urinary tract infection (UTI) to severe bloodstream infection (BSI). The incidence of infections caused by ESBL-producing E. coli (ESBL-PEc) is increasing, justifying surveillance and development of preventive strategies in several domains. Faecal carriage is universal and believed to be the most important reservoir for E. coli from which infections can originate. It is currently unknown to what extent Dutch E. coli carriage strains in the community reflect isolates causing disease. In this study, we will perform comparative genomics to infer the population structures of human-derived ESBL-PEc from community- and hospital-acquired infections and from community-based faecal carriage samples in the Netherlands. Furthermore, we will describe the molecular epidemiology of E. coli isolates causing invasive disease (BSI). Methods: This study uses four different microbiological data sources: 1) ESBL-PEc from patients with community-acquired UTI tested in primary care between May and November 2017, 2) ESBL-PEc from urine cultures obtained from patients hospitalized between January 2014 and December 2016, 3) E. coli from blood cultures obtained from patients hospitalized between January 2014 and December 2016, and 4) ESBL-PEc from faecal samples collected in a national population- prevalence study performed between January 2014 and January 2017. Clinical epidemiological data was collected from all patients and all isolates were subjected to whole genome sequencing. Discussion: The EPIGENEC study (EPIdemiology and GENetics of E. coli) will describe the molecular epidemiology of E. coli BSI and assess the genomic population structure of ESBL-PEc strains from community-acquired and nosocomial infections, and of ESBL-PEc reflecting community-based faecal carriage. Information from these studies may assist in optimizing surveillance strategies and determining targets and potential impact of future new preventive measures.

scholarly journals Nationwide prevalence and risk factors for faecal carriage ofEscherichia coliO157 and O26 in very young calves and adult cattle at slaughter in New Zealand

2016 ◽  
Vol 144 (8) ◽  
pp. 1736-1747 ◽  
Author(s):  
P. JAROS ◽  
A. L. COOKSON ◽  
A. REYNOLDS ◽  
D. J. PRATTLEY ◽  
D. M. CAMPBELL ◽  
...  
Keyword(s):  
Risk Factors ◽  
New Zealand ◽  
Real Time ◽  
National Level ◽  
Epidemiological Data ◽  
Cross Sectional Study ◽  
Cross Sectional ◽  
Adult Cattle ◽  
E Coli ◽  
Faecal Carriage

SUMMARYNationwide prevalence and risk factors for faecal carriage ofEscherichia coliO157 and O26 in cattle were assessed in a 2-year cross-sectional study at four large slaughter plants in New Zealand. Recto-anal mucosal swab samples from a total of 695 young (aged 4–7 days) calves and 895 adult cattle were collected post-slaughter and screened with real-time polymerase chain reaction (PCR) for the presence ofE. coliO157 and O26 [Shiga toxin-producingE. coli(STEC) and non-STEC]. Co-infection with either serogroup ofE. coli(O157 or O26) was identified as a risk factor in both calves and adult cattle for being tested real-time PCR-positive forE. coliO157 or O26. As confirmed by culture isolation and molecular analysis, the overall prevalence of STEC (STEC O157 and STEC O26 combined) was significantly higher in calves [6·0% (42/695), 95% confidence interval (CI) 4·4–8·1] than in adult cattle [1·8% (16/895), 95% CI 1·1–3·0] (P< 0·001). This study is the first of its kind in New Zealand to assess the relative importance of cattle as a reservoir of STEC O157 and O26 at a national level. Epidemiological data collected will be used in the development of a risk management strategy for STEC in New Zealand.

scholarly journals Virulence characteristics and the molecular epidemiology of enteroaggregative Escherichia coli isolates from travellers to developing countries

2007 ◽  
Vol 56 (10) ◽  
pp. 1386-1392 ◽  
Author(s):  
David B. Huang ◽  
Jamal A. Mohamed ◽  
James P. Nataro ◽  
Herbert L. DuPont ◽  
Zhi-Dong Jiang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Developing Countries ◽  
Molecular Epidemiology ◽  
Virulence Genes ◽  
Acute Diarrhoea ◽  
E Coli ◽  
Gene Profiles ◽  
Faecal Samples ◽  
Number Of Genes ◽  
Virulence Properties

Enteroaggregative Escherichia coli (EAEC) is associated with diarrhoea among travellers to developing countries. EAEC virulence properties predisposing to illness are not clear. Sixty-four EAEC strains identified by a HEp-2 cell assay and isolated from faecal samples from US and European travellers to developing countries were studied for the prevalence of 11 putative virulence genes by PCR: 49 EAEC strains from adults with acute diarrhoea and 15 EAEC strains from adults without diarrhoea. E. coli strains from the stools of healthy travellers to the same region were used as controls. EAEC carrying aggR, aap, astA and set1A were identified individually more often in the stools of subjects with diarrhoea compared with those without diarrhoea (P<0.05). EAEC isolates with two or three of these genes were associated with diarrhoea compared with EAEC isolates without the presence of these genes (P<0.05). Subjects with diarrhoea who shed EAEC isolates positive for these genes were more likely than subjects shedding EAEC negative for these genes to pass stools with gross mucus (57 vs 14 %) and faecal leukocytes (40 vs 7 %) (P<0.05). This study shows the heterogeneity of gene profiles of EAEC strains found in the stools of international travellers and suggests that the presence of aggR, aap, astA or set1A, the number of genes present and stool characteristics may be markers for more virulent EAEC strains.

scholarly journals Enhanced surveillance of Clostridium difficile infection occurring outside hospital, England, 2011 to 2013

2016 ◽  
Vol 21 (29) ◽  
Author(s):  
Warren N Fawley ◽  
Kerrie A Davies ◽  
Trefor Morris ◽  
Peter Parnell ◽  
Robin Howe ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Epidemiological Data ◽  
Diversity Indices ◽  
Community Based ◽  
Patient Demographics ◽  
Faecal Samples ◽  
Ribotype 078 ◽  
Discharge From Hospital ◽  
Healthcare Associated ◽  
Care Nursing

There are limited national epidemiological data for community-associated (CA)-Clostridium difficile infections (CDIs). Between March 2011 and March 2013, laboratories in England submitted to the Clostridium difficile Ribotyping Network (CDRN) up to 10 diarrhoeal faecal samples from successive patients with CA-CDI, defined here as C. difficile toxin-positive diarrhoea commencing outside hospital (or less than 48 hours after hospital admission), including those cases associated with community-based residential care, with no discharge from hospital within the previous 12 weeks. Patient demographics and C. difficile PCR ribotypes were compared for CA-CDIs in our study and presumed healthcare-associated (HA) CDIs via CDRN. Ribotype diversity indices, ranking and relative prevalences were very similar in CA- vs HA-CDIs, although ribotypes 002 (p ≤ 0.0001),020 (p = 0.009) and 056 (p < 0.0001) predominated in CA-CDIs; ribotype 027 (p = 0.01) predominated in HA-CDIs. Epidemic ribotypes 027 and 078 predominated in institutional residents with CDI (including care/nursing homes) compared with people with CDI living at home. Ribotype diversity decreased with increasing age in HA-CDIs, but not in CA-CDIs. Ribotype 078 CA-CDIs were significantly more common in elderly people (3.4% (6/174) vs 8.7% (45/519) in those aged < 65 and ≥ 65 years, respectively; p = 0.019). No antibiotics were prescribed in the previous four weeks in about twofold more CA-CDI vs HAs (38.6% (129/334) vs 20.3% (1,226/6,028); p < 0.0001). We found very similar ribotype distributions in CA- and HA-CDIs, although a few ribotypes significantly predominated in one setting. These national data emphasise the close interplay between, and likely common reservoirs for, CDIs, particularly when epidemic strains are not dominant.

Isolation of post operative hospital acquired infections in a private hospital of Bangladesh and identification of clonal relatedness of E. coli by using Pulse filed gel electrophoresis

2012 ◽  
Vol 6 (2) ◽  
pp. 7-10
Author(s):  
Mohammad Murshed ◽  
Sabeena Shahnaz ◽  
Md. Abdul Malek
Keyword(s):  
Private Hospital ◽  
Isolation And Identification ◽  
College Hospital ◽  
Hospital Acquired Infection ◽  
E Coli ◽  
Hospital Acquired Infections ◽  
Medical College ◽  
Clonal Relatedness ◽  
Hospital Acquired ◽  
Dressing Materials

Isolation and identification of post operative hospital acquired infection was carried out from July 2008 to December 2008 in Holy Family Red Crescent Medical College Hospital (private hospital). The major pathogen of wound infection was E. coli. A total; of 120 samples were collected from the surrounding environment of post operative room like floor, bed sheets, instruments, dressing materials, catheter, nasogastric and endotracheal tube. E. coli (40%) was the predominant organism followed by S. aureus (24%). DNA fingerprinting analysis using pulsed field gel electreopheresis of XbaI restriction digested genomic DNA showed that clonal relatedness between the two clinical nd environmental isolates were 100%.DOI: http://dx.doi.org/10.3329/bjmm.v6i2.19369 Bangladesh J Med Microbiol 2012; 06(02): 7-10

scholarly journals Clonal Clusters, Molecular Resistance Mechanisms and Virulence Factors of Gram-Negative Bacteria Isolated from Chronic Wounds in Ghana

Antibiotics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 339
Author(s):  
Denise Dekker ◽  
Frederik Pankok ◽  
Thorsten Thye ◽  
Stefan Taudien ◽  
Kwabena Oppong ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Virulence Factors ◽  
Iron Uptake ◽  
Chronic Wounds ◽  
Sub Saharan Africa ◽  
Gram Negative Bacteria ◽  
Beta Lactamase ◽  
Secretion Systems ◽  
Gram Negative ◽  
E Coli

Wound infections are common medical problems in sub-Saharan Africa but data on the molecular epidemiology are rare. Within this study we assessed the clonal lineages, resistance genes and virulence factors of Gram-negative bacteria isolated from Ghanaian patients with chronic wounds. From a previous study, 49 Pseudomonas aeruginosa, 21 Klebsiellapneumoniae complex members and 12 Escherichia coli were subjected to whole genome sequencing. Sequence analysis indicated high clonal diversity with only nine P. aeruginosa clusters comprising two strains each and one E. coli cluster comprising three strains with high phylogenetic relationship suggesting nosocomial transmission. Acquired beta-lactamase genes were observed in some isolates next to a broad spectrum of additional genetic resistance determinants. Phenotypical expression of extended-spectrum beta-lactamase activity in the Enterobacterales was associated with blaCTX-M-15 genes, which are frequent in Ghana. Frequently recorded virulence genes comprised genes related to invasion and iron-uptake in E. coli, genes related to adherence, iron-uptake, secretion systems and antiphagocytosis in P. aeruginosa and genes related to adherence, biofilm formation, immune evasion, iron-uptake and secretion systems in K. pneumonia complex. In summary, the study provides a piece in the puzzle of the molecular epidemiology of Gram-negative bacteria in chronic wounds in rural Ghana.

scholarly journals Molecular Epidemiology of Group A Streptococcus Infections in The Gambia

Vaccines ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 124
Author(s):  
Sona Jabang ◽  
Annette Erhart ◽  
Saffiatou Darboe ◽  
Aru-Kumba Baldeh ◽  
Valerie Delforge ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Vaccine Development ◽  
Group A Streptococcus ◽  
Epidemiological Data ◽  
The Gambia ◽  
Strain Diversity ◽  
Group A ◽  
Considerable Strain

Molecular epidemiological data on Group A Streptococcus (GAS) infection in Africa is scarce. We characterized the emm-types and emm-clusters of 433 stored clinical GAS isolates from The Gambia collected between 2004 and 2018. To reduce the potential for strain mistyping, we used a newly published primer for emm-typing. There was considerable strain diversity, highlighting the need for vaccine development offering broad strain protection.

scholarly journals Multidrug Resistance Dissemination in Escherichia coli Isolated from Wild Animals: Bacterial Clones and Plasmid Complicity

2021 ◽  
Vol 12 (1) ◽  
pp. 123-137
Author(s):  
Carolina Sabença ◽  
Gilberto Igrejas ◽  
Patrícia Poeta ◽  
Frédéric Robin ◽  
Richard Bonnet ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Epidemiological Data ◽  
Generation Cephalosporin ◽  
Wild Animals ◽  
Variable Regions ◽  
E Coli ◽  
Wild Fauna ◽  
Long Read ◽  
Sequence Types ◽  
Animal Isolates

Objectives. Epidemiological data concerning third-generation cephalosporin (3GC) resistance in wild fauna are scarce. The aim of this study was to characterize the resistance genes, their genetic context, and clonal relatedness in 17 Escherichia coli resistant to 3GC isolated from wild animals. Methods. The isolates were characterized by short-read whole genome sequencing, and long-read sequencing was used for the hybrid assembly of plasmid sequences. Results. The 3GC resistance gene most identified in the isolates was the extended-spectrum β-lactamases (ESBL)-encoding gene blaCTX-M-1 (82.3%), followed by blaCTX-M-32 (5.9%), blaCTX-M-14 (5.9%), and blaSHV-12 (5.9%). E. coli isolates mainly belonged to the sequence types (STs) rarely reported from humans. The single nucleotide polymorphism (SNP)-based typing showed that most E. coli genomes from wild animals (wild boars, birds of prey, and buzzards) formed clonal clusters (<5 SNPs), showing a clonal dissemination crossing species boundaries. blaCTX-M-1-harboring IncI1-ST3 plasmid was the predominant ESBL-encoding plasmid (76.4%) in wild animal isolates. Plasmid comparison revealed a 110-kb self-transferable plasmid consisting of a conserved backbone and two variable regions involved in antimicrobial resistance and in interaction with recipient cells during conjugation. Conclusion. Our results highlighted the unexpected clonal dissemination of blaCTX-M-1-encoding clones and the complicity of IncI1-ST3 plasmid in the spread of blaCTX-M-1 within wild fauna.

Faecal samples reveal the diet of breeding adult Sandwich terns Thalasseus sandvicensis in Belgium and the southern part of the Netherlands

2017 ◽  
Vol 127 ◽  
pp. 182-193 ◽  
Author(s):  
W. Courtens ◽  
H. Verstraete ◽  
N. Vanermen ◽  
M. Van de walle ◽  
E.W.M. Stienen
Keyword(s):  
The Netherlands ◽  
Faecal Samples

scholarly journals Independent Behavior of Commensal Flora for Carriage of Fluoroquinolone-Resistant Bacteria in Patients at Admission

2010 ◽  
Vol 54 (12) ◽  
pp. 5193-5200 ◽  
Author(s):  
Victoire de Lastours ◽  
Françoise Chau ◽  
Florence Tubach ◽  
Blandine Pasquet ◽  
Etienne Ruppé ◽  
...  
Keyword(s):  
Risk Factors ◽  
Bacterial Resistance ◽  
Care Facility ◽  
Health Care Facility ◽  
Epidemiological Data ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
E Coli ◽  
Commensal Flora ◽  
Resistant Strains

ABSTRACT The important role of commensal flora as a natural reservoir of bacterial resistance is now well established. However, whether the behavior of each commensal flora is similar to that of other floras in terms of rates of carriage and risk factors for bacterial resistance is unknown. During a 6-month period, we prospectively investigated colonization with fluoroquinolone-resistant bacteria in the three main commensal floras from hospitalized patients at admission, targeting Escherichia coli in the fecal flora, coagulase-negative Staphylococcus (CNS) in the nasal flora, and α-hemolytic streptococci in the pharyngeal flora. Resistant strains were detected on quinolone-containing selective agar. Clinical and epidemiological data were collected. A total of 555 patients were included. Carriage rates of resistance were 8.0% in E. coli, 30.3% in CNS for ciprofloxacin, and 27.2% in streptococci for levofloxacin; 56% of the patients carried resistance in at least one flora but only 0.9% simultaneously in all floras, which is no more than random. Risk factors associated with the carriage of fluoroquinolone-resistant strains differed between fecal E. coli (i.e., colonization by multidrug-resistant bacteria) and nasal CNS (i.e., age, coming from a health care facility, and previous antibiotic treatment with a fluoroquinolone) while no risk factors were identified for pharyngeal streptococci. Despite high rates of colonization with fluoroquinolone-resistant bacteria, each commensal flora behaved independently since simultaneous carriage of resistance in the three distinct floras was uncommon, and risk factors differed. Consequences of environmental selective pressures vary in each commensal flora according to its local specificities (clinical trial NCT00520715 [http://clinicaltrials.gov/ct2/show/NCT00520715 ]).

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