Human salmonella isolates

Human salmonella isolates from ESR's enteric reference laboratory.

We welcome the use of this surveillance data with the following acknowledgement, 

New Zealand surveillance data provided by ESR, funded by the Ministry of Health with the cooperation of the diagnostic laboratories.

 

The last five years of data is available below. Human Salmonella isolates data from 2017 - 2002 can be found in the Archive.

 

Human salmonella isolates

  • 2023

     

    Year Month (file linked) Summary
    2023 November

    The number of isolates (n=66) confirmed this month showed a decrease in comparison to the number of isolates confirmed in November 2022 (n=75). Salmonella Typhimurium ST19 (28% in November 2022 vs. 19.7% in November 2023) was the most common serotype confirmed this month. 

    2023 October

    The number of isolates (n=66) confirmed this month showed an increase in comparison to the number of isolates confirmed in October 2022 (n=61). Salmonella Typhimurium ST19 (19.7% in October 2022 vs. 15.2% in October 2023) was the most common serotype confirmed this month. An outbreak of typhoid fever among RSE workers in Tairawhiti. Tairawhiti PHU investigated an outbreak of typhoid fever involving 8 cases (2 confirmed in October). The cases are all RSE workers who live in shared accommodation. The most likely source of the outbreak was an RSE worker who does all the cooking for the group and recently travelled overseas.

    2023 September

    The number of isolates (n=58) confirmed this month showed a slight increase in comparison to the number of isolates confirmed in September 2022 (n=57). Salmonella Typhimurium ST19 (21% in September 2022 vs. 17.2% in September 2023) was the most common serotype confirmed this month. Uncommon serotypes confirmed this month were Salmonella Isangi (18 human cases since it was first confirmed in New Zealand in 1990) and Salmonella Matopeni (2 human cases since it was first confirmed in New Zealand in 1995). An outbreak of typhoid fever among RSE workers in Tairawhiti. Tairawhiti PHU investigated an outbreak of typhoid fever involving 8 cases (6 confirmed in September). The cases are all RSE workers who live in shared accommodation. The most likely source of the outbreak was an RSE worker who does all the cooking for the group and recently travelled overseas.

    2023 August

    The number of isolates (n=65) confirmed this month showed a decrease in comparison to the number of isolates confirmed in August 2022 (n=74). Salmonella Typhimurium ST19 (35.1% in August 2022 vs 12.3% in August 2023) was the most common serotype confirmed this month. Uncommon serotypes confirmed this month was Salmonella Choleraesuis var. Kunzendorf (9 human cases since it was first confirmed in New Zealand in 1989) and Salmonella Kintambo (9 human cases since it was first confirmed in New Zealand in 2022). 

    2023 July

    The total number of isolates (n=40) confirmed this month showed a slight decrease in comparison to the number of isolates confirmed in July 2022 (n=45). Salmonella Agona, Salmonella Brandenburg, Salmonella Enteritidis ST11, Salmonella Monophasic Typhimurium ST34, and Salmonella Typhimurium ST568 (2.2%, 2.2%, 2.2%, 0% and 24.4%, respectively, in July 2022 vs. 7.5% in July 2023) were the most common serotypes confirmed this month. 

    2023 June

    The number of isolates (n=68) confirmed this month showed a slight increase in comparison to the number of isolates confirmed in June 2022 (n=54). Salmonella Typhimurium ST19 (20.4% in June 2022 vs 19.1% in June 2023) was the most common serotype confirmed this month.

    2023 May

    The number of isolates (n=79) confirmed this month showed an increase in comparison to the number of isolates confirmed in May 2022 (n=61). Salmonella Typhimurium ST19 (26.2% in May 2022 vs 16.5% in May 2023) was the most common type confirmed this month. Uncommon serotype confirmed this month was Salmonella Goldcoast (3 human cases since it was first confirmed in New Zealand in 1989).

    2023 April The number of isolates (n=54) confirmed this month showed a decrease in comparison to the number of isolates confirmed in April 2022 (n=74). Salmonella Typhimurium ST19 (45.9% in April 2022 vs 27.8% in April 2023) was the most common type confirmed this month. Uncommon serotypes confirmed this month was Salmonella Kedougou (15 human cases since it was first confirmed in New Zealand in 1996) and Salmonella Muenster (13 human cases since it was first confirmed in New Zealand in 1994).An isolate was typed as Subsp. (I) ser. 9,12 : m,p : - ST74. This is the first incidence of this isolate in New Zealand. This sequence type has been associated with S. Enteritidis and S. Dublin but has been found to be a novel serotype. Awaiting serotype designation by Institut Pasteur and WHO.
    2023 March The number of isolates (n=100) confirmed this month showed a decrease in comparison to the number of isolates confirmed in March 2022 (n=100). Salmonella Typhimurium ST19 (35.6% in 2022 vs 26% in 2023) was the most common serotypes confirmed this month. Uncommon serotype confirmed this month was Salmonella Uganda (22 human cases since it was first confirmed in New Zealand in 1994).
    2023 February

    The number of isolates (n=96) confirmed this month showed an increase in comparison to the number of isolates confirmed in February 2022 (n=72). Salmonella Typhimurium ST19 (26.3% in 2022 vs 26% in 2023) was the most common serotypes confirmed this month. Uncommon Salmonella serotypes confirmed this month were S. Kintambo (8 human isolates since it was first confirmed in New Zealand in 2022).

    2023 January The number of isolates (n=99) confirmed this month showed an increase in comparison to the number of isolates confirmed in January 2028 (n=64). Salmonella Typhimurium ST19 (20.3% in 2022 vs 27.3% in 2023) was the most common serotypes confirmed this month. Uncommon serotype confirmed this month was Salmonella Johannesburg (16 human cases since it was first confirmed in New Zealand in 1990), Salmonella Kiambu (25 human cases since it was first confirmed in New Zealand in 1990), Salmonella Orion (15 human cases since it was first confirmed in New Zealand in 1993), Salmonella Poona (42 human cases since it was first confirmed in New Zealand in 1998), Salmonella Ruiru (20 human cases since it was first confirmed in New Zealand in 2004) and Salmonella Sandiego (47 human cases since it was first confirmed in New Zealand in 1992).
  • 2022

    Note: Due to COVID-19 effect on overseas travel and habits of the community post lockdown, there has been a downturn in the number of Salmonella samples.

    2022 - Annual summary for human salmonella isolates

    Following the opening of NZ borders, the number of Salmonella isolates confirmed this year (n=738) showed an increase in comparison with 2021 (n= 668). Salmonella Typhimurium ST19 was the predominant sero/genotype, representing 27.4% of total isolates. Salmonella serotypes showing an increase this year in comparison with 2021 included: Salmonella Kintambo (from 0.0% to 0.9%), Salmonella Paratyphi A (from 0.3% to 1.8%), Salmonella Stanley (from 1.4% to 2.4%), S. Typhi (from 0.4% to 3.9%) and S. Infantis (from 0.0% to 1.2%). Salmonella serotypes showing a decrease this year in comparison with 2021 included: S. Enteritidis (from 19.3% to 10.7%).

    • A cluster of 24 cases of Salmonella Typhimurium ST19, locally designated 5-SNP cluster type _2022_C_12, which was detected between July and August 2022 and associated with travel to Fiji. A source was not confirmed.
    • An outbreak of 7 cases of Salmonella Kintambo ST8754, associated with consumption of sesame-based products, which was detected in July and August 2022. This the first time the presence of Salmonella Kintambo has been detected in New Zealand. A consumer level recall was undertaken due to the possible presence of Salmonella https://www.mpi.govt.nz/food-safety-home/food-recalls-and-complaints/recalled-food-products/algota-brand-sesame-tahini/
    • Twelve cases adding to the Salmonella Enteritidis ST11 locally designated 5-SNP cluster type _2019_C_01. The cases were geographically dispersed. The source for the outbreak was confirmed as being from the poultry industry.

     

    Monthly summaries:

    Year

    Month (file linked)

    Summary

    2022

    December

    The number of isolates (n=56) confirmed this month showed an increase in comparison to the number of isolates confirmed in December 2021 (n=42). Salmonella Typhimurium ST568 (14.3% in December 2021 vs 21.4% in December 2022) was the most common serotypes confirmed this month. Uncommon Salmonella serotypes confirmed this month were S. Grumpensis (3 human isolates since it was first confirmed in New Zealand in 2000) and S. Liverpool (7 human isolates since it was first confirmed in New Zealand in 1996), S. Nchanga (3 human isolates since it was first confirmed in New Zealand in 2005).

    2022

    November

    The number of isolates (n=75) confirmed this month showed an increase in comparison to the number of isolates confirmed in November 2021 (n=46). Salmonella Typhimurium ST19 (2.2% in November 2021 vs. 28% in November 2022) was the most common serotype confirmed this month. Uncommon serotypes confirmed this month were Salmonella Choleraesuis var. Kunzendorf (7 human cases since it was first confirmed in New Zealand in 1989) and Salmonella Galiema (3 human cases since it was first confirmed in New Zealand in 2000).

    2022

    October

    The number of isolates (n=61) confirmed this month showed an increase in comparison to the number of isolates confirmed in October 2021 (n=33). Salmonella Typhimurium ST568 (15.2% in October 2021 vs. 23% in October 2022) was the most common serotype confirmed this month. Uncommon serotypes confirmed this month were Salmonella Coeln (2 human cases since it was first confirmed in New Zealand in 2017) and Salmonella Kintambo (7 human cases since it was first confirmed in New Zealand in 2022).

    2022

    September

    The number of isolates (n=57) confirmed this month showed an increase in comparison to the number of isolates confirmed in September 2021 (n=40). Salmonella Typhimurium ST568 (12.5% in September 2021 vs. 24.6% in September 2022) was the most common serotype confirmed this month. Uncommon serotypes confirmed this month were Salmonella Bredeney (13 human cases since it was first confirmed in New Zealand in 1991) and Salmonella Minnesota (3 human cases since it was first confirmed in New Zealand in 1998).

    2022

    August

    The number of isolates (n=74) confirmed this month showed an increase in comparison to the number of isolates confirmed in August 2021 (n=34). Salmonella Typhimurium ST19 (35.3% in August 2021 vs 35.1% in August 2022) was the most common serotype confirmed this month. Uncommon serotype confirmed this month was Salmonella Kintambo (5 human cases since it was first confirmed in New Zealand in 2022).

    2022

     July

    The number of isolates (n=45) confirmed this month showed a slight increase in comparison to the number of isolates confirmed in July 2021 (n=42). Salmonella Typhimurium ST19 (7.1% in July 2021 vs. 26.6% in July 2022) was the most common serotype confirmed this month. Uncommon serotype confirmed this month was Salmonella Kintambo (3 human cases since it was first confirmed in New Zealand in 2022). 

    2022 

    June

    The number of isolates (n=54) confirmed this month showed a slight decrease in comparison to the number of isolates confirmed in June 2021 (n=57). Salmonella Typhimurium ST19 (24.6% in June 2021 vs 20.4% in June 2022) was the most common serotype confirmed this month. Uncommon serotype confirmed this month was Salmonella Apeyeme (6 human cases since it was first confirmed in New Zealand in 2011). Salmonella Kintambo was confirmed for the first time in humans in New Zealand this month. 

    2022

    May

    The number of isolates (n=61) confirmed this month showed an increase in comparison to the number of isolates confirmed in May 2021 (n=50). Salmonella Typhimurium ST19 (26% in May 2021 vs 26.2% in May 2022) was the most common type confirmed this month.

    2022

    April

    The number of isolates (n=74) confirmed this month showed a decrease in comparison to the number of isolates confirmed in April 2021 (n=79). Salmonella Typhimurium ST19 (31.6% in April 2021 vs 45.9% in April 2022) was the most common type confirmed this month. Uncommon serotype confirmed this month was Salmonella Butantan (3 human cases since it was first confirmed in New Zealand in 2004).

    2022

    March

    The number of isolates (n=45) confirmed this month showed a decrease in comparison to the number of isolates confirmed in March 2021 (n=78). Salmonella Typhimurium ST19 (23% in 2021 vs 35.6% in 2022) was the most common serotypes confirmed this month.

    2022

    February

    The number of isolates (n=72) confirmed this month showed a decrease in comparison to the number of isolates confirmed in February 2021 (n=85). Salmonella Typhimurium ST19 (16.6% in 2021 vs 26.3% in 2022) was the most common serotypes confirmed this month.

    2022

    January 

    The number of isolates (n=64) confirmed this month showed a decrease in comparison to the number of isolates confirmed in January 2021 (n=85). Salmonella Typhimurium ST19 (22.4% in 2021 vs 20.3% in 2022) was the most common serotypes confirmed this month.

     

  • 2021

    2021 - Annual Summary for Human Salmonella isolates summary

    2021 - Download the monthly isolates data

    The number of Salmonella isolates confirmed this year (n=668) showed a decrease in comparison with 2020 (n= 726). This decrease is most likely due to a reduction of imported cases as a result of NZ's closed border COVID-19 containment strategy.

    Salmonella Typhimurium ST19 was the predominant type, representing 22.3% of total isolates. 5-SNP clustering of all cases showed this to be a diverse group.

    The main Salmonella serotype showing an increase this year in comparison with 2020 was S. Enteritidis (from 9.9% to 19.3%). This was due to two separate events:

    • A cluster of 28 cases of Salmonella Enteritidis ST183, locally designated 5-SNP cluster type _2021_C_01, which was detected in January and February 2021 and predominantly dispersed within the South Island. A common food source was not confirmed.
    • Forty-nine cases adding to the Salmonella Enteritidis ST11 locally designated 5-SNP cluster type _2019_C_01. The cases were geographically dispersed and a source for the outbreak was confirmed as being from the poultry industry.

    Salmonella serotype showing a decrease this year in comparison with 2020 included: S. Typhi (from 3.6% to 0.4%). This can be wholly attributed to closed borders.

    Monthly detail at a glance available below:

    Year

    Month (file linked)

    Summary

    2021

    December

    The number of isolates (n=42) confirmed this month showed no change in comparison to the number of isolates confirmed in December 2020 (n=42). Salmonella Typhimurium ST19 (28.6% in December 2020 vs 31% in December 2021) was the most common serotypes confirmed this month. Uncommon Salmonella serotypes confirmed this month were S. Bardo (12 human isolates since it was first confirmed in New Zealand in 1989) and S. Kedougou (14 human isolates since it was first confirmed in New Zealand in 1996).

    2021

    November

    The number of isolates (n=46) confirmed this month showed a decrease in comparison to the number of isolates confirmed in November 2020 (n=52). Salmonella Typhimurium ST568 (9.6% in November 2020 vs. 26.1% in November 2021) was the most common serotype confirmed this month. Uncommon Salmonella serotype confirmed this month was S. Orion (14 human isolates since it was first confirmed in New Zealand in 1993).

    2021

    October

    The number of isolates (n=46) confirmed this month showed a decrease in comparison to the number of isolates confirmed in November 2020 (n=52). Salmonella Typhimurium ST568 (9.6% in November 2020 vs. 26.1% in November 2021) was the most common serotype confirmed this month. Uncommon Salmonella serotype confirmed this month was S. Orion (14 human isolates since it was first confirmed in New Zealand in 1993).

    2021

    September

    The number of isolates (n=40) confirmed this month showed a decrease in comparison to the number of isolates confirmed in September 2020 (n=63). Salmonella Typhimurium ST19 (14.3% in September 2020 vs. 27.5% in September 2021) was the most common serotype confirmed this month. Uncommon serotypes confirmed this month were Salmonella Orion (14 human cases since it was first confirmed in New Zealand in 1993) and Salmonella Uganda (21 human cases since it was first confirmed in New Zealand in 1994).

    2021

    August

    The number of isolates (n=34) confirmed this month showed an increase in comparison to the number of isolates confirmed in August 2020 (n=53). Salmonella Typhimurium ST19 (20.8% in August 2020 vs 35.3% in August 2021) was the most common serotype confirmed this month.

    2021

    July

    The number of isolates (n=42) confirmed this month showed a slight increase in comparison to the number of isolates confirmed in July 2020 (n=39). Salmonella Typhimurium ST568 (28.2% in July 2020 vs. 26.2% in July 2021) was the most common serotype confirmed this month.

    2021

    June

    The number of isolates (n=57) confirmed this month showed a slight increase in comparison to the number of isolates confirmed in June 2020 (n=33). Salmonella Typhimurium ST19 (18.2% in June 2020 vs 24.6% in June 2021) was the most common serotype confirmed this month.

    2021

    May

    The number of isolates (n=50) confirmed this month showed an increase in comparison to the number of isolates confirmed in May 2020 (n=40). S. Typhimurium ST19 (27.5% in May 2020 vs. 26% in May 2021) was the most common serotype confirmed this month. Uncommon serotype confirmed this month was Salmonella Waycross (13 human cases since it was first confirmed in New Zealand in 1996)

    2021

    April

    The number of isolates (n=79) confirmed this month showed an increase in comparison to the number of isolates confirmed in April 2020 (n=26 low due to COVID-19 level 4 restrictions  ). Salmonella Typhimurium ST19 (34.6% in April 2020 vs 31.6% in April 2021) was the most common type confirmed this month. Uncommon serotype confirmed this month was Salmonella Mana (5 human cases since it was first confirmed in New Zealand in 1996).

    2021

    March

    The number of isolates (n=78) confirmed this month showed an increase in comparison to the number of isolates confirmed in March 2020 (n=94). Salmonella Typhimurium ST19 (18% in March 2020 vs 23% in March 2021) was the most common serotypes confirmed this month.

    2021

    February

    ·       The number of isolates (n=78) confirmed this month showed a decrease in comparison to the number of isolates confirmed in February 2020 (n=91). Salmonella Enteritidis ST183 (42.3% in February 2021 vs 5.5% in February 2020) was the most common type confirmed this month. Cases were predominantly in the South Island. (

    2021

    January

    The number of isolates (n=85) confirmed this month showed a decrease in comparison to the number of isolates confirmed in January 2020 (n=136). Salmonella Typhimurium ST19 (25% in 2020 vs 22.4% in 2020) were the most common serotypes confirmed this month. Uncommon serotype confirmed this month was Salmonella Kedougou (13 human cases since it was first confirmed in New Zealand in 1996)

     

  • 2020

    2020 - Annual Human Salmonella isolates summary

    2020 - Download the monthly isolates data

    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.

  • 2019

    2019 - Annual Human Salmonella isolates summary

    2019 - Download the monthly isolates data 

    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.

  • 2018

    2018 - Annual Human Salmonella isolates summary

    2018 - Download the monthly isolates data

    The number of Salmonella isolates confirmed this year (n=1125) showed a decrease in comparison with 2017 (n= 1217). Salmonella Bovismorbificans was the predominant serotype, representing 7.4% of total isolates (4.3% in 2017). Salmonella serotypes showing an increase this year in comparison with 2017 included: S. Agona (from 1.3% to 2.4%) and S. Saintpaul (from 2.2% to 3.5%)