Azithromycin resistance in Escherichia coli and Salmonella from food-producing animals and meat in Europe.

OBJECTIVES: To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014-18 and the Danish AMR surveillance programme in 2016-19. METHODS: WGS data of 1007 E. coli [165 azithromycin resistant (MIC > 16 mg/L)] and 269 Salmonella [29 azithromycin resistant (MIC > 16 mg/L)] were screened for acquired macrolide resistance genes and mutations in rplDV, 23S rRNA and acrB genes using ResFinder v4.0, AMRFinder Plus and custom scripts. Genotype-phenotype concordance was determined for all isolates. Transferability of mef(C)-mph(G)-carrying plasmids was assessed by conjugation experiments. RESULTS: mph(A), mph(B), mef(B), erm(B) and mef(C)-mph(G) were detected in E. coli and Salmonella, whereas erm(C), erm(42), ere(A) and mph(E)-msr(E) were detected in E. coli only. The presence of macrolide resistance genes, alone or in combination, was concordant with the azithromycin-resistant phenotype in 69% of isolates. Distinct mph(A) operon structures were observed in azithromycin-susceptible (n = 50) and -resistant (n = 136) isolates. mef(C)-mph(G) were detected in porcine and bovine E. coli and in porcine Salmonella enterica serovar Derby and Salmonella enterica 1,4, [5],12:i:-, flanked downstream by ISCR2 or TnAs1 and associated with IncIγ and IncFII plasmids. CONCLUSIONS: Diverse azithromycin resistance genes were detected in E. coli and Salmonella from food-producing animals and meat in Europe. Azithromycin resistance genes mef(C)-mph(G) and erm(42) appear to be emerging primarily in porcine E. coli isolates. The identification of distinct mph(A) operon structures in susceptible and resistant isolates increases the predictive power of WGS-based methods for in silico detection of azithromycin resistance in Enterobacterales.

Whole genome sequencing data used for surveillance of Campylobacter infections: detection of a large continuous outbreak, Denmark, 2019.

BackgroundCampylobacter is one of the most frequent causes of bacterial gastroenteritis. Campylobacter outbreaks are rarely reported, which could be a reflection of a surveillance without routine molecular typing. We have previously shown that numerous small outbreak-like clusters can be detected when whole genome sequencing (WGS) data of clinical Campylobacter isolates was applied.AimTyping-based surveillance of Campylobacter infections was initiated in 2019 to enable detection of large clusters of clinical isolates and to match them to concurrent retail chicken isolates in order to react on ongoing outbreaks.MethodsWe performed WGS continuously on isolates from cases (n = 701) and chicken meat (n = 164) throughout 2019. Core genome multilocus sequence typing was used to detect clusters of clinical isolates and match them to isolates from chicken meat.ResultsSeventy-two clusters were detected, 58 small clusters (2-4 cases) and 14 large clusters (5-91 cases). One third of the clinical isolates matched isolates from chicken meat. One large cluster persisted throughout the whole year and represented 12% of all studied Campylobacter cases. This cluster type was detected in several chicken samples and was traced back to one slaughterhouse, where interventions were implemented to control the outbreak.ConclusionOur WGS-based surveillance has contributed to an improved understanding of the dynamics of the occurrence of Campylobacter strains in chicken meat and the correlation to clusters of human cases.

Assessing the value of bacteriological examination as a diagnostic tool in relation to meat inspection in cattle.

In Denmark, lesions indicating acute generalised infection identified at meat inspection will result in total condemnation. An official bacteriological examination (BU) protocol can be used for slaughtered animals with lesions such as endocarditis and endophlebitis as an assisting diagnostic tool to confirm whether the condition is local or generalised. If local, the carcass can be approved after condemnation of the relevant organs. The BU involves cultivating samples from the spleen and muscle. The aim of this study was to assess the value of the BU protocol. The study was conducted from February to May 2019 at a Danish cattle abattoir. Three groups of slaughtered cattle were included: 24 cases consisting of cattle with endocarditis and endophlebitis, 25 control animals consisting of cattle fully approved at inspection and 16 animals condemned at inspection due to endocarditis and endophlebitis with complications. Samples were taken from the heart, liver, kidney, lung, spleen and muscles of each animal. The BU protocol was used for cultivation. Different types of colonies were identified using MALDI-TOF-MS analysis. One or more samples with bacterial growth were found in all condemned animals - in 16 out of the 24 case animals and in two out of 25 control animals. In all three groups, Trueperella pyogenes was the most frequently isolated bacterium (60%) followed by Fusobacterium necrophorum (10%). For the case animals, the organ most commonly found with bacterial growth was the liver (46%), followed by the lung (38%) and the kidney (38%), while 96% of the muscle samples were negative. For the condemned group, bacterial growth was found in 75% of the spleen samples, 56% of liver and lung samples, and 50% of the muscle samples. A statistical analysis of the samples from cases and controls showed strong pair-wise associations for the presence of bacteria between organs, but no pair-wise associations between presence of bacteria in the muscle and any of the organs. Hence, if bacteria are found e.g. in the liver, they are likely to be found in other organs, but not in the muscle. In total, 20 of the 24 case animals were fully or partly approved in accordance with the current rules for judgement. It was concluded that the BU protocol using spleen and muscle samples would be suitable as a diagnostic tool for the judgement of slaughtered animals in cases where there is doubt about the stage of the lesions observed.