Human salmonella isolates 2019

Annual summary 2019

The number of Salmonella isolates confirmed this year (n=1153) showed an increase in comparison with 2018 (n= 1125). Salmonella Typhimurium phage type 108/170 was the predominant serotype, representing 7.2% of total isolates (0.4% in 2018). Salmonella serotypes showing an increase this year in comparison with 2017 included: S. Enteritidis phage type 8 (from 0.4% to 1.6%), S. Enteritidis phage type 26 (from 0.5% to 1.8%), S. Typhimurium phage type 2 (from 0% to 1.6%) and S. Subsp. (I) ser. 4,5,12 : i : - (from 2020 referred to as monophasic Typhimurium) (from 2.3% to 4.2%)

From 1st November 2019, all phage typing ceased. From this time serotypes that were historically phage typed – Typhi, Typhimurium and Enteritidis; along with Paratyphi A and B (but not Paratyphi B var java) have all been fine typed using whole genome sequencing. Individual reports only show the serotype and Achtman 7-gene ST type – which does not discriminate to a fine level within a serotype. However, each week a full cluster comparison is done at SNP difference level on all of these isolates. Subsequent to the introduction of WGS, Salmonella Subsp. (I) ser. 4,5,12 : i : - is being reported as monophasic Salmonella Typhimurium.

To note: There is no direct correlation between phage type and genomic SNP cluster type. A phage type – such as 108/170 may comprise a number of SNP cluster types and are therefore not all related (illustrated in the sprout outbreak below). Conversely, sometimes SNP clusters comprise isolates of different phage types. This is not an error as phage type susceptibility for a given isolate is determined by its accessory genome which is not used in SNP analysis..

During 2019 we experienced a national outbreak of Salmonella Typhimurium phage type 108/170 including 65 confirmed cases, all with the same unique Multiple Locus Variable-number Tandem Repeat Analysis (MLVA) profiles. (The MLVA profile of the outbreak strain had not previously been detected in New Zealand prior to this outbreak). Investigation found that the New Zealand outbreak MLVA profile had been rarely detected overseas. Whole genome sequencing was performed on a number of the clinical isolates which confirmed the cases were part of a cluster. The outbreak strain's sequence profile had not been detected overseas where data were available. Detailed epidemiological investigation implicated alfalfa sprouts and subsequent culture of the implicated brand yielded Salmonella Typhimurium phage type 108/170 genetically indistinguishable from the cluster type

NZ normally sees on average a single case of Salmonella Paratyphi B each year with all having a recent South American travel history. In 2019 there were five cases, three of whom had no history of overseas travel. These three cases clustered together by SNP analysis and were significantly different from our background dataset of other recent isolates. As this background group is small, conclusions are not well substantiated. Epidemiological investigation of the three cases did not implicate a common link.