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Human salmonella isolates 2020

05 January 2020

Enteric reference testing

Click to download the isolates data below, or scroll to read the monthly summaries.

Annual summary 2020

The number of Salmonella isolates confirmed this year (n=726) showed a decrease in comparison with 2019 (n= 1153). Salmonella Typhimurium ST19 was the predominant serotype, representing 23% of total isolates. Salmonella serotypes showing an increase this year in comparison with 2019 included: Salmonella Thompson (from 0.8% to 1.9%) and S. Typhimurium (from 36.3% to 48.6%).

Salmonella serotypes showing a decrease this year in comparison with 2019 included: S. Enteritidis (from 14.4% to 9.9%), Salmonella Infantis (from 2.3% to 1.1%), Salmonella Stanley (from 3.6% to 1.7%) and S. Typhi (from 4.6% to 3.6%).

2020 has been at best an unusual year for everyone and the Enteric data for 2020 will always stand apart from other years due the multiple effects of our COVID 19 response on our national data.

When NZ locked down at the end of March 2020, diagnostic laboratories were given over to establishing and performing testing for COVID 19 and were actively discouraging the referral of other, more routine work. This coupled with people staying home in small bubbles; not eating out; and not being able to readily access face-to-face medical assistance meant that for a period of two months there were very few enteric pathogens received at ESR for typing.

Once NZ moved back to Alert Level 2 Enteric testing and isolate referral gradually recommenced. However, with our borders remaining closed for the remainder of the year we have seen an ongoing reduction in some Salmonella serotypes, most particularly Typhoid and Paratyphoid A. Given all of the above the low numbers noted for the year suggest that more Salmonella is associated with overseas travel that previously thought.

No phage typing was undertaken in 2020. Instead, all Typhimurium, Enteritidis, Typhi and Paratyphi A isolates were analysed using whole genome sequencing (WGS) and individual reports only showed the serotype and the 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 single nucleotide polymorphism (SNP) difference level on all of these serotypes. Subsequent to the introduction of WGS, Salmonella Subsp. (I) ser. 4,5,12 : i : - is being reported as monophasic Salmonella Typhimurium.

Twenty-four cases of Salmonella Bovismorbificans were reported during October 2020. An increase compared to the same period in previous years (4 cases in 2019 and 7 cases in 2018). This serotype has been increasingly isolated from sick cattle since 2015 with 218 isolates confirmed to the end of October 2020. It was also detected in canine, feline, and avian sources during 2020. The October human cases were geographically dispersed throughout the North Island, mostly in urban centres and a source for the surge was not confirmed.