PulseNet Salmonella Isolates Quarterly Report

CDC is working to increase access to foodborne illness data in real time. As an initial step, CDC is publishing data reports from the PulseNet surveillance system. An interactive dashboard is in development and will soon replace these static reports and provide real-time data from Salmonella bacterial isolates in PulseNet. The dashboard will eventually include information on additional pathogens, antibiotic resistance, and epidemiologic data from outbreak investigations. This information will provide industry, public health partners, regulatory agencies, and the public with the most up-to-date data on pathogen trends, including emerging strains, to help inform effective measures to prevent foodborne illness.

PulseNet is a national laboratory network that uses whole genome sequencing (WGS) to connect cases of foodborne illness and detect outbreaks. The network includes public health laboratories in all 50 states, the District of Columbia, and the U.S. territory of Puerto Rico, and food regulatory laboratories within the Food and Drug Administration (FDA) and U.S. Department of Agriculture (USDA). Currently, the PulseNet system includes E. coli (O157 and other Shiga toxin-producing E. coli), Campylobacter, Listeria monocytogenes, Salmonella, Shigella, Vibrio cholerae, Vibrio parahaemolyticus, and Cronobacter isolates.

Data from isolates are submitted through one of two routes. One route is through public health laboratories, which receive isolates from clinical laboratories that process samples from ill patients. Public health laboratories use WGS for bacterial identification and characterization and upload the bacterial DNA sequence data to the national PulseNet databases. A second route is through FDA and USDA regulatory partners that upload data from isolates of environmental and product samples obtained through inspection and surveillance efforts. Notably, when a group of reported illnesses in a specific time frame are genetically similar, an investigation may be launched to determine if there is an outbreak and to identify the source.

While development of an interactive dashboard is underway, CDC will provide interim quarterly reports of PulseNet data. This first report is limited to human Salmonella data. Future reports will contain expanded information to include data on clinical antibiotic resistance, as well as additional pathogens, beginning with clinical samples of Campylobacter.

The data below are from January 1, 2021 through September 30, 2021 (quarters 1-3). Reported dates are the date of isolation from a clinical specimen (not the date the isolate was uploaded to PulseNet). This report is limited to isolates with serotype classification established through WGS. Isolates for which serotype classification required further review at the time of the report were excluded until resolution. The top 15 serotypes identified in the present report were determined by the highest number of uploads in each quarter (January through March; April through June; and July through September, separately). Geographic data are presented by HHS regionexternal icon.

Please note, these data have several limitations:

  • PulseNet data do not reflect the full burden of disease. Information for people with enteric (intestinal) illness who do not seek medical care is not included. Additionally, data for some patients who receive culture-independent diagnostic tests (CIDT) are also unavailable for inclusion in this system.
  • Healthcare-seeking practices, diagnostic testing practices, and laboratory capacity have been heavily impacted by the COVID-19 pandemic. As a result, uploads to PulseNet have decreased compared with previous years. Therefore, 2021 data are compared to averages from 2017–2019 (excluding data from 2020).

Please email pulsenet@cdc.gov using the subject line “PulseNet Static Report” if you have questions or feedback about this report, including additional features that may guide prevention interventions or research activities. Although we may not be able to address all feedback, we welcome comments as we work to make our data accessible and timely to inform prevention of foodborne illnesses.

TABLE 1: Human Salmonella isolate uploads to PulseNet by quarter, in total
Quarter 1 Quarter 2 Quarter 3
2021 4,882 9,833 15,177
Average prior quarterly uploads (2017–2019) 5,525 9,144 13,964
Percent change -12 8 9
TABLE 2: Human Salmonella isolate uploads to PulseNet in quarter 1, top 15 serotypes
Rank Serotype Q1 Uploads (2021) Average Prior Q1 Uploads
(2017–2019)
Percent Change (%)
1 Enteritidis 809 1,033 -22
2 Newport 417 376 11
3 Typhimurium 414 530 -22
4 I 4:I:- 299 204 46
5 Infantis 211 220 -4
6 Javiana 162 165 -1
7 Montevideo 124 119 4
8 Braenderup 114 131 -13
9 Oranienburg 113 114 -1
10 Thompson 112 109 3
11 Saintpaul 111 145 -23
12 Muenchen 99 87 14
13 Hadara 86 21 310
14 Dublin 68 39 74
15 Agona 61 53 15

a: Observed increases in Hadar are driven by a live poultry outbreak beginning in April 2021.

TABLE 3: Human Salmonella isolate uploads to PulseNet in quarter 2, top 15 serotypes
Rank Serotype Q2 Uploads (2021) Average Prior Q2 Uploads
(2017–2019)
Percent Change (%)
1 Enteritidis 1,703 1,741 -2
2 Newport 917 667 37
3 Typhimurium 818 816 0
4 Infantis 606 389 56
5 I 4:I:- 450 309 46
6 Javiana 385 340 13
7 Muenchen 260 194 34
8 Braenderup 251 305 -18
9 Hadara 233 65 258
10 Saintpaul 230 249 -8
11 Mississippi 217 163 33
12 Bareilly 199 105 90
13 Montevideo 195 223 -13
14 Thompson 185 175 6
15 Oranienburg 180 149 21

a: Observed increases in Hadar are driven by a live poultry outbreak beginning in April 2021.

TABLE 4: Human Salmonella isolate uploads to PulseNet in quarter 3, top 15 serotypes
Rank Serotype Q3 Uploads (2021) Average Prior Q3 Uploads
(2017–2019)
Percent Change (%)
1 Newport 1,951 1,751 11
2 Enteritidis 1,880 1,816 4
3 Typhimurium 1,511 1,376 10
4 Javiana 1,200 1,103 9
5 Oranienburga 1,097 265 314
6 I 4:I:- 658 420 57
7 Infantis 589 525 12
8 Thompson 397 328 21
9 Muenchen 382 290 32
10 Saintpaul 368 360 2
11 Mississippi 358 264 36
12 Montevideo 322 330 -2
13 Braenderup 304 378 -13
14 Bareilly 192 172 12
15 Poona 153 85 80

a: Observed increases in Oranienburg are driven by an outbreak beginning in April 2021.

TABLE 5: Human Salmonella isolate uploads to PulseNet, by HHS region
Q1 Uploads (2021) Average Prior Q1 Uploads (2017–2019) Q1 Percent Change (%) Q2 Uploads (2021) Average Prior Q2 Uploads (2017–2019) Q2 Percent Change (%) Q3 Uploads (2021) Average Prior Q3 Uploads (2017–2019) Q3 Percent Change (%)
Region 1
(CT, ME, MA, NH, RI, VT)
233 243 -4 452 419 8 676 634 7
Region 2
(NJ, NY, PR, VI)
336 416 -19 698 617 13 1,152 1,135 1
Region 3
(DE, DC, MD, PA, VA, WV)
396 419 -5 641 753 -15 1,149 1,182 -3
Region 4
(AL, FL, GA, KY, MS, NC, SC, TN)
1,205 1,261 -4 2,793 2,442 14 3,937 3,955 0
Region 5
(IL, IN, MI, MN, OH, WI)
721 842 -14 1,508 1,402 8 2,314 1,910 21
Region 6
(AR, LA, NM, OK, TX)
633 741 -15 1,227 1,258 -2 2,495 1,931 29
Region 7
(IA, KS, MO, NE)
257 343 -25 521 490 6 806 688 17
Region 8
(CO, MT, ND, SD, UT, WY)
170 224 -24 347 289 20 527 422 25
Region 9
(AZ, CA, HI, NV, AS, MP, FSM, GU, MH, ROP)
712 806 -12 1,339 1,159 16 1,766 1,715 3
Region 10
(AK, ID, OR, WA)
163 198 -18 281 288 -2 335 371 -10