Serovar Risk Assessment plus supporting info – CDC

Pathogenic vs non-Pathogenic Science

  1. Risk Assessment of Salmonella Serovars
  2. Serovars of Concern
  3. FDA Data
  1. CDC Data
  1. WHO Data
  2. Host-specific Serovars
  3. Infective Doses

This is from a CDC document and it is a list of every Salmonella Serotype (culture confirmed and partially serotyped) they seem to have identified. There are 1,020 of them listed here.  The numbers reflect the number of illnesses associated with each between 2006-2016.  This document is called National Enteric Disease Surveillance: Salmonella Annual Report, 2016 and is sourced from the CDC. 

Here is a summary of what that looks like as well as considerations for action surrounding the summary… please provide your feedback:

Number of serotypes with 1 case listed – 302

(Consideration: I would like to request FOIA on these cases to determine if these serotypes can indeed be, beyond a reasonable doubt, confirmed as the sole cause of illness or if perhaps the carrier were otherwise ill and, in searching to identify another disease process they found these strains of salmonella which were, in fact, not causing illness)

Number of serotypes with 2 cases listed – 108 (Consideration: same as above)

Number of serotypes with 3 cases listed – 78 (Consideration: same as above) 

Number of serotypes with 4 cases listed – 65 (Consideration: same as above)

Number of serotypes with 5 cases listed – 42 (Consideration: same as above. This is still 1/2 of 1 case per year on average)

Number of serotypes with 6-10 cases listed – 101 – This is an average of .6-1 case per year

Number of serotypes with 11-20 cases listed – 76 – This is an average of 1.1-2 cases per year

Number of serotypes with 21-100 cases listed – 123 – This is an average of 2-10 cases per year

Number of serotypes with 101-500 cases listed – 62 – This is an average of 10.1-50 cases per year

Number of serotypes with less than 1,000 infections in 10 years is 972 out of 1,020.

Number of serotypes with 500-10,000 cases listed – 56 – This is an average of 50.1-1,000 cases per year

Number of serotypes in excess of 10,000 cases listed – 8 – This is 1,007-8,330 cases per year

This document also shows that Salmonella outbreaks are consistently seasonal, being the least likely to cause infection in February, most likely in August.  https://www.cdc.gov/nationalsurveillance/data/salm2016/Figure4.xlsx 

Most infectious strains from worst down:

1) Enteritidis – 83,303 cases 

2) Typhimurium – 63,773 cases

3) Newport – 47,481 cases

4) Javiana – 25,955 cases

5) 4,[5],12:i:- – 18,189 cases

6) Heidelberg – 13,627 cases

7) Montevideo – 11,495 cases

8) Muenchen – 10,379 cases

9) Infantis – 10,077 cases (2012 = 1,106, Diamond Pet Food Recall was 49 of those – Therefore DRY pet food contributed to 0.0048% of cases)

10) Saintpaul – 9,799 cases

11) Oranienburg – 8,012 cases

12) Braenderup – 7,878 cases

13) Thompson – 6,332 cases

14) Mississippi – 5,711 cases

15) Typhi – 4,788 cases

16) Agona – 4,685 cases

17) Paratyphi B var. L(+) tartrate + – 4,486 cases

18) Bareilly – 4,210 cases

19) Poona – 3,844 cases

20) O:4 – 3,547 cases

21) Berta – 3,038 cases

22) Schwarzengrund – 2,934 cases (2007 = 300 infection, Diamond Pet Food Recall was 62 of those) (Mars Pet Care caused CDC regulated outbreak in humans between 2006-2008 of 79. Therefore DRY pet food contributed to 0.048% of cases)

23) Anatum – 2,872 cases

24) Hadar – 2,601 cases

25) Litchfield – 2,499 cases

26) Stanley – 2,370 cases 

27) Hartford – 2,293 cases

28) Mbandaka – 2,284 cases

29) 4, [5], 12:b:- – 2,275 cases

30) Unspecified – 2,210 cases

31) Sandiego – 1,982 cases

32) Panama – 1,980 cases

33) Norwich – 1,935 cases

34) 13,23:b:- 1,921 cases

35) O:7 – 1,203 cases

36) Rubislaw – 1,757 cases

38) Paratyphi A – 1,716 cases

39) Senftenberg – 1,678 cases

40) Dublin – 1,388 cases

41) Tennessee – 1,326 cases

42) Give – 1,309 cases

43) Derby – 1,249 cases

44) O:9 – 1,229 cases

45) Miami – 1,203 cases

46) Kentucky – 1,026 cases

47) Adelaide – 1,001 cases

These are all the cases with more than 1,000 incidence between 2006-2016, or in excess of 100 cases per year. 

Salmonella Reading is listed as having 858 cases. I point this out as it was blamed for the raw food related illness in humans. Incidence are as follows: 2206 – 50, 2007 – 57, 2008 – 46, 2009 – 53, 2010 – 33, 2011 – 42, 2012 – 58, 2013 – 55, 2014 – 104, 2015 – 139, 2016 – 221 (The primary listed source of this serovar is pre-cut melons)

Surveillance for Foodborne Disease Outbreaks United States Annual Reports are available to show CDC indicated sources of pathogenic infections in humans each year.  2014 (which is the most current summarized document) states the following:

1) From over 13,000 cases and 864 CDC regulated outbreaks only 21 recalls were implemented. 

2) Sources of outbreaks: 

1) Restaurants – 65% of outbreaks and 44% of illnesses

2) Catering and Banquet – 12% of outbreaks and 29% of illnesses

3) Private Home – 12% of outbreaks and 7% of illnesses

4) Institutional Location – 4% of outbreaks and 13% of illnesses

5) Other locations (Grocery, Farm/Dairy, Fair/Festival) – 4% of outbreaks, 4% of illnesses

6) Hospital/Nursing Homes – 1% of outbreaks, 1% of illnesses

7) Private location (place of worship) – 2% of outbreaks, 3% of illnesses

Most common food causes:

1) Seeded vegetables – 16%

2) Fish – 21%

3) Chicken ~ 12%

4) Diary – 10%

5) Beef (comprising 20% of recalls (not outbreaks) and only 20% of those were from Salmonella)

3) Salmonella accounts for 30% of all pathogen infections in the United States https://www.cdc.gov/foodsafety/pdfs/foodborne-outbreaks-annual-report-2014-508.pdf 

This is also an interesting link that shows which states have the highest incidence of Salmonella: https://www.statista.com/statistics/379025/us-salmonella-rate-by-state/

http://www.veterinaryworld.org/Vol.6/Oct-2013/1.pdf Salmonella enterica, the most pathogenic species of the genus Salmonella

The differences observed between serovars in their host preference and clinical manifestations are referred to as “serovar-host specificity” or “serovar-host adaptation”. The genus Salmonella, highly adaptive to vertebrate hosts, has many pathogenic serovars showing host specificity

WAITING ON NATE TO HELP ME MAKE THIS SO I CAN COPY AND PASTE IT… MEANWHILE I BROUGHT IT

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869595/pdf/11117946.pdf The current view of salmonella taxonomy assigns the members of this genus to two species: S. enterica and S. bongori. S. enterica itself is divided into six subspecies, enterica, salamae, arizonae, diarizonae, indica, and houtenae, also known as subspecies I, II, IIIa, IIIb, IV, and VI, respectively [1] .

The pathogenicity of most of the distinct serotypes remains undefined, and even within the most common serotypes, many questions remain to be answered regarding the interactions between the organism and the infected host.

Salmonellosis manifests itself in three major forms: enteritis, septicaemia, and abortion, each of which may be present singly or in combination, depending on both the serotype and the host involved. Although currently over 2300 serovars of Salmonella are recognized, only about 50 serotypes are isolated in any significant numbers as human or animal pathogens [2, 3] and they all belong to subspecies enterica

Only a small number of serotypes typically cause severe systemic disease in man or animals, characterized by septicaemia, fever and}or abortion, and such serotypes are often associated with one or few host species [4–6].

Host-adapted serotypes (Table 1) typically cause systemic disease in a limited number of related species. For example, Typhi, Gallinarum and Abortusovis are almost exclusively associated with systemic disease in humans [7], fowl [8] and ovines [5] respectively

In the past, special attention has been dedicated to nutritional requirements and distinct biochemical characters of Salmonella serotypes. In particular, Salmonella strains had been divided in ‘ ammonium weak’ and ‘ ammonium strong’ strains on the basis of their ability to assimilate nitrogen from ammonia in a defined media that contained simple carbon compounds such as citrate (Simmons citrate agar) or other sugars as sole source of carbon and energy [15]

Serotypes noted as ‘ ammonium weak’ were all host-adapted (Dublin, Rostock, and Choleraesuis) or host-restricted (Paratyphi A, Abortusovis, Typhisuis, Typhi, and Sendai) [15]. . It is important to note that a negative result of this test might be due also to the failure of the organism to grow in absence of other substances that were not provided with such minimal media.

Fierer and colleagues have examined the biochemical features of several Dublin strains and found them all unable to grow in Simmons citrate agar [17]. In the presence of supplemental nicotinic acid, however, all strains were able to utilize citrate. Similarly, we found Abortusovis strains able to utilize citrate in a minimal defined medium only when cystine and nicotinic acid were supplemented (Uzzau and colleagues, unpublished results). Detailed analysis of the nutritional requirement of Salmonella spp. has led to the observation that whereas ubiquitous Typhimurium and Enteritidis were able to grow in relatively simple defined media, certain amino acids and vitamins must be supplied for most strains of Typhi, Typhisuis, Abortusovis, Gallinarum, Paratyphi A, and Dublin [18, 19]. Auxotrophy therefore, seems to be a characteristic of HR and HA serotypes (Table 2).

The taxonomic classification of salmonella has been continually revised over the years. Beyond the level of subspecies, serotyping is used for differentiation, and serotypes have been described within S. enterica subspecies enterica on the basis of somatic (O), flagellar (H), and capsular (Vi) antigens [1]. Within subspecies enterica, some serotypes are polyphyletic; identical serotypes occur among isolates of distantly related clones that also differ in pathogenic potential and host range. This can be attributed to horizontal genetic transfer and recombination of antigen genes between lineages, an event that has been proposed to happen with relatively high frequency [22]. However, overall the subspecies remain clonal [23].

Epithelial cell adhesion and invasion may not be uncoupled in Typhi, since all Typhi invasion mutants isolated in recent studies [47, 52] were also adhesion-defective, whereas mutants obtained from UR serotypes like Typhimurium and Enteritidis were found to adhere to cell monolayers but invaded significantly less [53–55].

Other salmonellae which are primarily or exclusively restricted in host range to humans are Paratyphi A and C and Sendai, all of which cause enteric fever. Some strains of Paratyphi B cause human enteric fever, whereas others, designated as Java, produce gastroenteritis in both humans and animals. Miami, which is serologically related to Sendai, is largely limited to humans but causes gastroenteritis rather than enteric fever in animals [24].

Gallinarum as host-restricted since all reported cases of systemic disease are from avian hosts [8].

Typhisuis This serotype does not naturally infect animals other than the pig and, for this reason, is considered host restricted to swine

Choleraesuis This serotype is defined as host-adapted on the basis that 99% of incidents are associated with pigs. However, it does naturally infect other host species, including man, in which the disease can be severe. Human infections were well known for severity with 10–40% case mortality and the majority of isolates were from non-intestinal sites (i.e. blood-stream, bones, joints)

Dublin is host-adapted to bovine and affects both young and adult cattle causing enteritis and}or systemic disease. In humans Dublin infection generally occurs in patients with underlying chronic diseases, and arises from contact with animals or via the food chain.

Immediately following the invasion of the organisms beyond the intestinal mucosa, more than 90% of the organisms are destroyed at, or close to, the site of inoculation, primarily by resident phagocytic cells. Surviving organisms disseminate, and bacterial growth occurs in the cells of the reticuloendothelial system. The crucial phase occurs when bacterial multiplication is either controlled or continues in an uncontrolled fashion. Polymorphonuclear leukocytes (PMN) are the first phagocytic cells to be attracted towards infected tissues by means of salmonella-induced cytokines secretion [147, 148]. PMNs have been recognized for many years as having a function in the inflammatory response, and recently PMNs have also been implicated in the modulation of the other immune cells [149]. Salmonella has adapted to grow inside macrophages where it is relatively sheltered from PMN [150]. Macrophages play a dual role in the salmonella infection process. Once activated, they can kill salmonella, but macrophages are also the site of bacterial multiplication. Infected macrophages are therefore responsible for the dissemination of the Serotypes of S. enterica 239 infection via the lymphatic ducts to other organs [151]

When Salmonella serotypes colonize in the intestinal mucosa of mammals, before progression to a systemic infection in the body, they face to an effective barrier of macrophages that line the lymphatic sinuses of lymph nodes. The granuloma formations caused by the accumulation in inflamed tissue of polynuclear granulocytes in mammals, also exist in avian hosts where it is the heterophiles that are involved, and are morphologically similar to inflammatory lesions in reptiles [160]. Therefore, one of the first steps in the salmonella development towards being a systemic, facultative intracellular pathogen may have been to enter the macrophage in order to escape from the aggressive environment. It is tempting to speculate that it is the ability of HA and HR serotypes to escape cellular defenses that has led to the development of host specificity. That pathogens have adopted different tactics to escape immune systems is well known. Immune evasion of virus and helminth parasites related to cytokine activities is beginning to be explored [161], and also bacteria can be supposed to contain and produce a large number of diverse molecules, which can selectively induce the synthesis of cytokines, as LPS does [162]. Unfortunately, little evidence has been accumulated to date with respect to salmonella.

Salmonella serotypes capable of disseminate in a particular host may utilize alveolar macrophages and pulmonary intravascular macrophages (PIM) for translocation [195]. Calves, sheep, goats, and pigs, but not man or small rodents, possess PIM densities and clearance capacity in the lung parenchyma similar to that of human and murine Kupffer cells in the liver [196]. Pigs rooting behaviour and the ovine and bovine grazing allow salmonella in the environment an easy access to the nasal cavity and thus to the lungs. Salmonella serotypes (i.e. Dublin, Abortusovis, Choleraesuis, and Typhimurium) able to produce systemic infection in these animals might have developed specific mechanisms to take advantage of both the intestinal and the pulmonary route of entry and dissemination. It is worth noting that salmonella infection of these hosts is often characterized by pneumonia and that bovine-adapted Dublin may cause pneumonia as a major sign of infection in sheep

In vitro studies have demonstrated that host-specific pathogenesis of Salmonella serotypes may depend on the selective recognition of complement receptor (CR) types on the macrophages membrane [206]. Typhi and Typhimurium induced their own uptake by micropinocytosis in both human and murine macrophages, but only Typhi was capable of growth in human macrophages. Conversely, Typhimurium survived in murine macrophages whereas Typhi did not. The molecular basis of such restriction has been hypothesized based on the fact that intracellular survival and replication is only made possible by recognition, in the presence of serum opsonin, of the CR type 1 (CR1) but not of CR type 3 (CR3). Strikingly, Typhi and Typhimurium recognized, respectively, CR1 and CR3 on human macrophages, whereas they recognized, respectively, CR3 and CR1 on murine macrophages. Baker and Morona have recently observed that phorbol myristate acetate (PMA) differentiated U937 (PMA-U937, human) cells restricted the net growth of Typhi but not Typhimurium phoP mutants, suggesting that the phoP}Q locus may control expression of genes involved in host specificity, particularly affecting differential effects on Typhi and Typhimurium LPS [206].

At least 11 serotypes are known to carry virulence plasmids, which share common and unique sequences [230]. Typhi does not carry virulence plasmids and not all isolates of those serotypes associated with the plasmids do. The role of the virulence plasmid in pathogenesis has been mainly studied using the mouse model of salmonellosis

https://pdfs.semanticscholar.org/1bd6/123a6ba70af32f68d0f496814d142db1add2.pdf Salmonella is considered to be a ‘universal pathogen’ as it is successfully isolated from all vertebrates and many insects.

Recent studies show that a mechanism making one serovar virulent for one animal species could make the same serovar less or completely avirulent in another animal host [6]. In addition, other factors like the dose of infection, the age during which the host is infected and their immune response contribute equally to a successful infection [7].

Hence, current research is mainly focused on understanding the acquired ability of Salmonella’s host preference by Salmonella.

Out of these 2,500 serovars nearly 1500 belong to the Salmonella subsp. enterica. Figure represents different Salmonella serovars with core genome and with unique genes marked in black [12].

The first group includes serovars which have a broad host range also called as unrestricted serovars as these infect nearly all animals. This group includes serovars like Salmonella Typhimurium and Salmonella Enteritidis.

Although the severity of disease increases in young hosts when compared to adults, this is because of their inability to counter the mature immune responses in older hosts [8].

The second group includes serovars which cause highly severe systemic infection in their preferred host and are usually excreted without any clinical symptoms when they accidentally infect hosts others then their most adapted or preferred. Serovars such as Dublin, Choleraesuis fall into this category, as these prove to only cause systemic infection in cattle and pigs respectively [13, 14]; however these upon infection into other hosts like rodents and humans are usually excreted making these hosts as ‘carriers’. Serovars of this group are referred to as the ‘Host-adapted Serovars’.

The third group comprises of serovars which are restricted very strictly with one very specific host only; these serovars are called ‘host–restricted serovars’. They exclusively cause systemic infection, which often proves to be fatal within their host. Serovars such as Typhi, Gallinarum, Abortusequi etc belong to this group.

Salmonella thrives on the Payer’s patches, which is abundant with specialized epithelial M cells, and are considered as the primary site for infection. Upon breaching the mucosal layer, it then translocate to lymphoidal follicles and mesenteric lymph nodes [17]. Salmonella has developed mechanisms to infect and proliferate both in phagocytic and non-phagocytic cells. These include the epithelial cells, macrophages, dendritic cells, enterocytes and neutrophils [18]. The entry of Salmonella within cells is either by phagocytosis, Salmonella mediated through Type Three Secretion System-1 (T3SS1) or T3SS1 independent [10]. The process involves secretion of virulence factors called effector proteins encoded by SPI-1, which bring about actin re-modulation, leading to ruffling and extension of the plasma membrane of the host and hence resulting in invasion of the bacterium [10, 19, 20]. Once inside the epithelial cells, Salmonella develops around it a niche called the Salmonella Containing Vacuole (SCV). These SCVs interact with the endocytic vesicles within the host, thereby accumulating various factors in the process [21]. These include Rho GTPase such as Rab5 and Rab7 and also lysosomal associated membrane protein LAMP-1 [22]. From the SCV, the bacterium secrets another set of effector proteins encoded by SPI-2 genes that are responsible for intracellular replication and survival [23, 24]. After 4-6hrs of invasion the replicating bacteria within the SCV results in formation of tubular network like filaments called the Salmonella induced filaments (Sifs), which helps in maintain the integrity of the SCV [23]. These Sif ’s tend to grow outwards to the plasma membrane accumulating various host constituents. The formation of these Sif ’s is facilitated by TTSS-2 effector protein called SifA [21, 23, 24]. These Sif ’s are highly enriched in cholesterol and LAMP-1. Internalization of Salmonella, also affects other cellular process such as apoptosis, cell division, cytokine production and antigen presentation [25].

Although the precise mechanisms leading to host specificity by Salmonella is not very well understood, however the pathogenicity of Salmonella serovars is influenced by selective pressure within a particular host and its surroundings [5, 8].

Serovars such as a Salmonella Typhimurium, Enteritidis, Pullorum, Gallinarium Dublin and Paratyphi C are a classic example which has undergone gene deletions [13]. As a result, these serovars have lost the ability to replicate in the intestinal lumen of their respective host, although these successfully cause systemic infections [26].

Mannose sensitive pathogenicity determinants like FimH adhesins play an important role in adhesion of Salmonella on its host cell surface [27].

Apart from genetic factors, other paradigms such as physiological state of host cell, availability of amino acids and the ability of one serovar over other to replicate, has a critical role to play in the virulence pattern of a serovar [17].

Regardless of various genetic and physiological parameters effecting host specificity, it is also observed that stress has a significant role to play in pathogenicity and virulence of Salmonella in various hosts leading to its consistent presence in the food chain and environment.

Infective Doses

Infective Dose of Foodborne Pathogens in Volunteers: A Review (Mahendra Kothary) mkothary@cfsan.fda.gov – Division of Virulence Assessment (HFS327) Center for Food Safety and Applied Nutrition, US FDA

“The human infective dose varies depending on the serovar of the organism. Results from the volunteer studies indicated that the infective dose for various serovars was 105 – 1010 organisms. The attack rate depended on the serovar of the organism and ranged from about 16-50%. However, data from outbreaks suggest that infection dose may be as high as 107 – 109 organisms. Various authors of these studies suggested that the high fat and protein content of the food vehicle involved in the outbreaks may have played an important role in protecting the organism from gastric acidity.

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