In the Netherlands, whole-genome sequencing (WGS) was implemented as routine typing tool for Salmonella Enteritidis isolates in 2019. Multiple locus variable-number tandem repeat analyses (MLVA) was ...performed in parallel. The objective was to determine the concordance of MLVA and WGS as typing methods for S. Enteritidis isolates. We included S. Enteritidis isolates from patients that were subtyped using MLVA and WGS-based core-genome Multilocus Sequence Typing (cgMLST) as part of the national laboratory surveillance of Salmonella during January 2019 to March 2020. The concordance of clustering based on MLVA and cgMLST, with a distance of ≤5 alleles, was assessed using the Fowlkes-Mallows (FM) index, and their discriminatory power using Simpson's diversity index. Of 439 isolates in total, 404 (92%) were typed as 32 clusters based on MLVA, with a median size of 4 isolates (range:2 to 141 isolates). Based on cgMLST, 313 (71%) isolates were typed as 48 clusters, with a median size of 3 isolates (range:2 to 39 isolates). The FM index was 0.34 on a scale from 0 to 1, where a higher value indicates greater similarity between the typing methods. The Simpson's diversity index of MLVA and cgMLST was 0.860 and 0.974, respectively. The median cgMLST distance between isolates with the same MLVA type was 27 alleles (interquartile range IQR:17 to 34 alleles), and 2 alleles within cgMLST clusters (IQR:1-5 alleles). This study shows the higher discriminatory power of WGS over MLVA and a poor concordance between both typing methods regarding clustering of S. Enteritidis isolates.
Salmonella is the most frequently reported agent causing foodborne outbreaks and the second most common zoonoses in the European Union. The incidence of the most dominant serotype Enteritidis has increased in recent years. To differentiate between Salmonella isolates, traditional typing methods such as pulsed-field gel electrophoresis (PFGE) and multiple locus variable-number tandem repeat analyses (MLVA) are increasingly replaced with whole-genome sequencing (WGS). This study compared MLVA and WGS-based core-genome Multilocus Sequence Typing (cgMLST) as typing tools for S. Enteritidis isolates that were collected as part of the national Salmonella surveillance in the Netherlands. We found a higher discriminatory power of WGS-based cgMLST over MLVA, as well as a poor concordance between both typing methods regarding clustering of S. Enteritidis isolates. This is especially relevant for cluster delineation in outbreak investigations and confirmation of the outbreak source in trace-back investigations.
A new commercial system based on genetic profiling and aimed at identifying
Salmonella enterica serovars was evaluated by comparing its performance with classical serotyping on 443 strains. Within 62 ...serovars represented, 60 gave unique genetic profiles while 2 were undistinguishable. Results were obtained within 8 h, were reproducible and clear-cut. The system allowed single-tube processing of the samples and required no peculiar technical skill. It showed interesting potential for routine laboratory testing.
Epidemiologically unrelated non-typhoid
Salmonella isolates from humans (
n
=
56) and animal origin (
n
=
241, from faeces, carcasses and meat) in Vietnam were investigated.
Salmonella Typhimurium,
...S. Anatum,
S. Weltevreden,
S. Emek, and
S. Rissen were the most prevalent serovars.
S. Typhimurium phage type 90 was predominant among
S. Typhimurium isolates. The serotype and phage type distribution of the
Salmonella isolates was different from that in Europe and America. Many sero- and phage types found in humans were also found in cattle, pigs, and poultry suggesting that food producing animals are an important source of human non-typhoid
Salmonella infection in Vietnam.
The objective of this study was to investigate the antimicrobial resistance patterns, integron characteristics and gene cassettes as well as the presence of
Salmonella genomic island 1 (SGI1) in ...non-typhoidal
Salmonella (NTS) isolates from human and animal origin. Epidemiologically unrelated Dutch NTS strains (
n
=
237) originating from food-producing animals and human cases of salmonellosis were tested for their susceptibility to 15 antimicrobial agents. Resistance to 14 of these antimicrobials, including the third-generation cephalosporins, was detected. Resistance to sulphonamides, ampicillin, tetracycline, streptomycin, trimethoprim and nalidixic acid was common (≥10% of the strains were resistant). Resistance against three or more antimicrobials was observed in 57 isolates. The same 237 strains were studied for the prevalence of class 1 integrons, their gene cassettes and the presence of SGI1. Thirty-six isolates (15.2%) carried class 1 integrons. These integrons had ten distinct profiles based on the size of the integron and restriction fragment length polymorphism analysis. Integrons were detected for the first time in serovars Indiana and Senftenberg. Multidrug resistance was strongly associated with the presence of class 1 integrons in which the
aadA2,
aadA1,
bla
PSE-1,
dfrA1,
dfrA5,
dfrA14 or
sat genes were present, as determined by nucleotide sequence determination. The presence of gene cassettes or combinations of gene cassettes not previously found in integrons in
Salmonella was observed. SGI1 or its variants (SGI-B, -C and -F) were present in 16 isolates belonging to either serovar Typhimurium, Derby or Albany. Regardless of whether the isolate was of human or animal origin, the same resistance phenotype, integron profile and SGI1 structure could be observed.
•Human campylobacteriosis cases mostly originate from poultry and cattle.•Pets and surface water are important non-livestock sources of campylobacteriosis.•Risk factors for campylobacteriosis differ ...according to the original reservoirs.•Effects of frequency and alternative pathways of exposure are significant.•WGS and epidemiological data analyses unveil the origins of campylobacteriosis.
To determine the contributions of several animal and environmental sources of human campylobacteriosis and identify source-specific risk factors.
1417 Campylobacter jejuni/coli isolates from the Netherlands in 2017–2019 were whole-genome sequenced, including isolates from human cases (n = 280), chickens/turkeys (n = 238), laying hens (n = 56), cattle (n = 158), veal calves (n = 49), sheep/goats (n = 111), pigs (n = 110), dogs/cats (n = 100), wild birds (n = 62), and surface water (n = 253). Questionnaire-based exposure data was collected. Source attribution was performed using core-genome multilocus sequence typing. Risk factors were determined on the attribution estimates.
Cases were mostly attributed to chickens/turkeys (48.2%), dogs/cats (18.0%), cattle (12.1%), and surface water (8.5%). Of the associations identified, never consuming chicken, as well as frequent chicken consumption, and rarely washing hands after touching raw meat, were risk factors for chicken/turkey-attributable infections. Consuming unpasteurized milk or barbecued beef increased the risk for cattle-attributable infections. Risk factors for infections attributable to environmental sources were open water swimming, contact with dog faeces, and consuming non-chicken/turkey avian meat like game birds.
Poultry and cattle are the main livestock sources of campylobacteriosis, while pets and surface water are important non-livestock sources. Foodborne transmission is only partially consistent with the attributions, as frequency and alternative pathways of exposure are significant.
In January 2017, an increase in reported
serotype Bovismorbificans cases in the Netherlands was observed since October 2016. We implemented a case-control study to identify the source, including all ...cases after December 2016. Adjusted odds ratios were calculated using logistic regression analysis. We traced back the distribution chain of suspected food items and sampled them for microbiological analysis. Human and food isolates were sequenced using whole genome sequencing (WGS). From October 2016 to March 2017, 54
Bovismorbificans cases were identified. Sequencing indicated that all were infected with identical strains. Twenty-four cases and 37 controls participated in the study. Cases were more likely to have consumed ham products than controls (aOR = 13; 95% CI: 2.0-77) and to have shopped at a supermarket chain (aOR = 7; 95% CI: 1.3-38). Trace-back investigations led to a Belgian meat processor: one retail ham sample originating from this processor tested positive for
Bovismorbificans and matched the outbreak strain by WGS. All ham products related to the same batch were removed from the market to prevent further cases. This investigation illustrates the importance of laboratory surveillance for all
serotypes and the usefulness of WGS in an outbreak investigation.
Fifty-nine
Salmonella enterica serovar Dublin (
Salmonella Dublin) isolates from clinical cases of bovine salmonellosis between 1993 and 2004 were tested for their susceptibility to 15 antimicrobial ...agents and the presence of class 1 integrons. Integrons were further analyzed by conserved segment PCR-RFLP. DNA sequencing was used to identify the inserted gene cassette. Twelve (20.3%) isolates were multidrug-resistant. A combination of resistance against chloramphenicol, streptomycin and sulphonamides was the most common phenotype observed. Multidrug-resistance (MDR) was found to be strongly associated with the presence of integrons, since a class 1 integron with the
aadA1 gene cassette encoding resistance to streptomycin and spectinomycin was found in all 12 multidrug-resistant isolates. The presence of the
aadA1 gene in
Salmonella Dublin has not been reported before. None of the integron carrying
Salmonella Dublin isolates could transfer its antimicrobial resistance to
E. coli K12 by conjugation. Analysis of plasmid profiles and pulsed field gel electrophoresis (PFGE) patterns showed at least some clonality among the
Salmonella Dublin isolates, but 11 different types could be distinguished based on both
XbaI and
BlnI-PFGE patterns. Thus, the Dutch
Salmonella Dublin strains were closely related but not clonal.
The serotypes of 101 faecal bovine necrotoxigenic Escherichia coli (NTEC) producing the cytotoxic necrotizing factor type 2 (CNF2) were determined. Although, NTEC producing CNF2 belonged to 48 ...different O:K:H serotypes, only eleven of them accounted for 54% of strains. The most common serotypes in order of frequency were: O123:K-:H16, O3:K-:H21, O88:K-:H8, O15:K14:H21, O1:K-:H12, O1:K1:H46, O2:K1:H5, O55:H21, O88:K?:H25, O117:K?:H21 and O123:K-:H-. The serotypes of CNF2 NTEC were different from those found in NTEC producing CNF1 and in enterotoxigenic, verotoxigenic, enteropathogenic, enteroinvasive and enteroadherent E. coli strains that cause infections in humans and animals.
PDF
