Multicenter evaluation of molecular and culture-dependent diagnostics for Shigella species and Entero-invasive Escherichia coli in the Netherlands

In 1996 and 1997, 2,941 fresh and processed meat products obtained from supermarkets and butcher shops in The Netherlands were examined for the presence of verocytotoxin-producing Escherichia coli of serogroup O157 (O157 VTEC). Additionally, the fate of O157 VTEC in raw meat products stored at low temperatures and the effect of different additives were evaluated. O157 VTEC strains were isolated from 6 (1.1%) of 571 samples of raw minced beef, 2 (0.5%) of 402 samples of raw minced mixed beef and pork, 1 (1.3%) of 76 samples of raw minced pork, 1 (0.3%) of 393 samples of other raw pork products, and 1 (0.3%) of 328 samples of cooked or fermented ready-to-eat meats. Other raw beef products (n = 223) and meat samples originating from poultry (n = 819), sheep or lamb (n = 46), or wild animals (n = 83) were all found to be negative for O157 VTEC. For the survival experiments we used tartaar (minced beef with a fat content of less than 10%) and filet americain (tartaar mixed with a mayonnaise-based sauce [80 to 20%]). The O157 VTEC strain tested was able to survive in tartaar and filet americain stored at −20, 0, 5, or 7°C for 3 days. At both 7 and at 15°C, O157 VTEC counts in tartaar and filet americain remained virtually unchanged throughout a storage period of 5 days. Addition of acetic acid (to pH 4.0), sodium lactate (1 and 2% [wt/wt]), or components of the lactoperoxidase–thiocyanate–hydrogen peroxide system to filet americain did not result in a reduction of viable O157 VTEC cells during storage at 7 or 15°C. It was concluded that raw meat contaminated with O157 VTEC will remain a hazard even if the meat is held at low or freezing temperatures.

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Reclassification of Shigella species as later heterotypic synonyms of Escherichia coli in the Genome Taxonomy Database

10.1101/2021.09.22.461432 ◽

2021 ◽

Author(s):

Donovan H Parks ◽

Maria Chuvochina ◽

Peter R Reeves ◽

Scott A Beatson ◽

Philip Hugenholtz

Keyword(s):

Escherichia Coli ◽

Type Strain ◽

Shigella Flexneri ◽

Laboratory Strain ◽

Single Species ◽

Species Definition ◽

E Coli ◽

Shigella Species ◽

K 12 ◽

Common Laboratory

Members of the genus Shigella have high genomic similarity to Escherichia coli and are often considered to be atypical members of this species. In an attempt to retain Shigella species as recognizable entities, they were reclassified as Escherichia species in the Genome Taxonomy Database (GTDB) using an operational average nucleotide identity (ANI)-based approach nucleated around type strains. This resulted in nearly 80% of E. coli genomes being reclassified to new species including the common laboratory strain E. coli K-12 (to 'E. flexneri') because it is more closely related to the type strain of Shigella flexneri than it is to the type strain of E. coli. Here we resolve this conundrum by treating Shigella species as later heterotypic synonyms of E. coli, present evidence supporting this reclassification, and show that assigning E. coli/Shigella strains to a single species is congruent with the GTDB-adopted genomic species definition.

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Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

10.1101/723734 ◽

2019 ◽

Author(s):

Denise van Hout ◽

Tess D. Verschuuren ◽

Patricia C.J. Bruijning-Verhagen ◽

Thijs Bosch ◽

Anita C. Schürch ◽

...

Keyword(s):

Escherichia Coli ◽

The Netherlands ◽

Resistance Gene ◽

Acquired Resistance ◽

Virulence Gene ◽

Beta Lactamase ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Extended Spectrum ◽

Clonal Distribution

ABSTRACTBackgroundKnowledge on the molecular epidemiology of Escherichia coli causing E. coli bacteremia (ECB) in the Netherlands is mostly based on extended-spectrum beta-lactamase-producing E. coli (ESBL-Ec). We determined differences in clonality and resistance and virulence gene (VG) content between non-ESBL-producing E. coli (non-ESBL-Ec) and ESBL-Ec blood isolates with different epidemiological characteristics.Materials/methodsA random selection of non-ESBL-Ec isolates as well as all available ESBL-Ec blood isolates was obtained from two Dutch hospitals between 2014 and 2016. Whole genome sequencing was performed to infer sequence types (STs), serotypes, acquired antibiotic resistance genes and VG scores, based on presence of 49 predefined putative pathogenic VG.ResultsST73 was most prevalent among the 212 non-ESBL-Ec (N=26, 12.3%) and ST131 among the 69 ESBL-Ec (N=30, 43.5%). Prevalence of ST131 among non-ESBL-Ec was 10.4% (N=22, P value < 0.001 compared to ESBL-Ec). O25:H4 was the most common serotype in both non-ESBL-Ec and ESBL-Ec. Median acquired resistance gene counts were 1 (IQR 1 – 6) and 7 (IQR 4 – 9) for non-ESBL-Ec and ESBL-Ec, respectively (P value < 0.001). Among non-ESBL-Ec, acquired resistance gene count was highest among blood isolates from a primary gastro-intestinal focus (median 4, IQR 1 – 8). Median VG scores were 13 (IQR 9 – 20) and 12 (IQR 8 – 14) for non-ESBL-Ec and ESBL-Ec, respectively (P value = 0.002). VG scores among non-ESBL-Ec from a primary urinary focus (median 15, IQR 11 – 21) were higher compared to non-ESBL-Ec from a primary gastro-intestinal (median 10, IQR 6 – 13) or hepatic-biliary focus (median 11, IQR 5 – 18) (P values = 0.007 and 0.036, respectively). VG content varied between different E. coli STs.ConclusionsNon-ESBL-Ec and ESBL-Ec blood isolates from two Dutch hospitals differed in clonal distribution, resistance gene and VG content. Also, resistance gene and VG content differed between non-ESBL-Ec from different primary foci of ECB.

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Prevalence of phylogroups and O25/ST131 in susceptible and extended-spectrum β-lactamase-producing Escherichia coli isolates, the Netherlands

Clinical Microbiology and Infection ◽

10.1016/j.cmi.2015.02.020 ◽

2015 ◽

Vol 21 (6) ◽

pp. 570.e1-570.e4 ◽

Cited By ~ 5

Author(s):

I.T.M.A. Overdevest ◽

A.M.C. Bergmans ◽

J.J. Verweij ◽

J. Vissers ◽

N. Bax ◽

...

Keyword(s):

Escherichia Coli ◽

The Netherlands ◽

Extended Spectrum

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Disease burden in The Netherlands due to infections with Shiga toxin-producing Escherichia coli O157

Epidemiology and Infection ◽

10.1017/s0950268804001979 ◽

2004 ◽

Vol 132 (3) ◽

pp. 467-484 ◽

Cited By ~ 47

Author(s):

A. H. HAVELAAR ◽

Y. T. H. P. VAN DUYNHOVEN ◽

M. J. NAUTA ◽

M. BOUWKNEGT ◽

A. E. HEUVELINK ◽

...

Keyword(s):

Escherichia Coli ◽

The Netherlands ◽

Shiga Toxin ◽

Disease Burden ◽

Escherichia Coli O157

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Laboratory surveillance of bacterial gastroenteric pathogens in The Netherlands, 1991–2001

Epidemiology and Infection ◽

10.1017/s0950268803008392 ◽

2003 ◽

Vol 130 (3) ◽

pp. 431-441 ◽

Cited By ~ 81

Author(s):

W. van PELT ◽

M. A. S. de WIT ◽

W. J. B. WANNET ◽

E. J. J. LIGTVOET ◽

M. A. WIDDOWSON ◽

...

Keyword(s):

Escherichia Coli ◽

Young Children ◽

The Netherlands ◽

Urban Areas ◽

Annual Number ◽

Dutch Population ◽

Laboratory Surveillance ◽

Bacterial Gastroenteritis ◽

General Practices ◽

The Mean

Results of the Dutch laboratory surveillance of bacterial gastroenteritis between 1991 and 2001 are presented and compared with recent findings in general practices and in the community. Between 1996 and 2000 the mean annual number of stools screened by sentinel laboratories was about 1000 samples/100000 inhabitants, which is 4% of the estimated annual incidence of gastroenteritis in the Dutch population. Campylobacter (36/100000 inhabitants) and salmonella (24/100000 inhabitants) were the main pathogens isolated. Since 1996, the incidence of laboratory confirmed salmonellosis decreased by 30%, predominantly among young children. The incidence of campylobacter was highest in urban areas and Salmonella Enteritidis emerged as the predominant serotype in urban areas. Between 1991 and 2001, multi-resistant Salmonella Typhimurium DT104 emerged to comprise up to 15% of all salmonella isolates in 2001. Reported rates of Shigella spp. and Yersinia spp. varied little, with average annual incidences of 3·2 and 1·2 cases/100000 inhabitants, respectively. Escherichia coli O157 (90% STEC) was scarcely found (0·26/100000).

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The germicidal effect of the open air in different parts of The Netherlands

Journal of Hygiene ◽

10.1017/s0022172400056072 ◽

1977 ◽

Vol 78 (2) ◽

pp. 175-187 ◽

Cited By ~ 12

Author(s):

G. de Mik ◽

Ida de Groot

Keyword(s):

Escherichia Coli ◽

The Netherlands ◽

Wind Direction ◽

Traffic Intensity ◽

Industrial Areas ◽

Different Parts

SUMMARYUsing the microthread technique the survival ofEscherichia coliMRE 162 in open air was measured in different parts of The Netherlands.The presence of bactericidal compounds (open air factor = OAF) could be demonstrated on several days and quantitated in relative units of OAF concentration.In the absence of ozone the OAF concentration was always low. In the presence of ozone the OAF concentration was dependent on wind direction. At the selected microthread exposure sites air from areas with high traffic intensity contributed more to OAF production than air from industrial areas. OAF production is probably related to the nature of hydrocarbons in the air.

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