Hazard identification: Summary of Agents

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The agent overview gives data for US populations, where the data could be found and attempts to provide ranges for case fatality ratio (The case fatality ratio is the proportion of infections (or illness) that end in death. It can easily be biased upward if many infections are mild or asymptomatic (and therefore unreported).), burden of disease, and finally incubation time. Source references are listed as well.

You can access the agent overview for each microbe by clicking the name in the following table.

Microbial group Pathogen Case fatality ratio Burden of disease Incubation time
Bacteria Bacillus anthracis Cutaneous with treatment 1%, without treatment 20%. Inhalation 75% despite treatment (CDC) Cutaneous: 0-1 day. Other forms: 1-7 days, rarely up to 60 days (CDC)
Burkholderia pseudomallei and Burkholderia cepacia Melioidosis in Malaysia overall crude mortality rate among the 145 patients with the mean age of 50 years old was 33.8% (Hassan et al, 2010) Melioidosis in Malaysia is at 16.35 per 100,000 population per year (Hassan et al, 2010) 9 days (range 1–21 days) (wikipedia)
Campylobacter jejuni The standardized mortality ratio for cases infected domestically was 2.9 (95% CI: 1.9–4.0) within the first month following the illness (Ternhag et al, 2005) It is estimated to affect over 2.4 million persons every year, or 0.8% of the population (CDC) 3-5 days or up to a week (Medscape)
Coxiella burnetii The estimated case fatality rate is < 2% of hospitalized patients (wikipedia) Between 2000 and 2004, the US saw an average of 51 cases every year. In 2005, 136 cases were reported to the CDC, and 169 in 2006.(Struble, K. 2012). 2-3 weeks (CDC)
Escherichia coli The overall mortality rate for E. coli O157:H7 is <1%. For those who develop hemolytic uremic syndrome, the death rate is between 3-5% (www.azdhs.gov) The incidence of E. coli O157:H7 and non-O157 infection per 100,000 population in 2008 is 1.12 and 0.45 (CDC MMWR) 2 to 8 days, but it usually ranges from 3 to 4 days (www.azdhs.gov)
Francisella tularensis Untreated, tularemia has a mortality rate of 5-15%; this rate is even higher with the typhoidal form. Appropriate antibiotics lower this rate to about 1% (Medscape) 3-4 days (range, 1-14 days) (Medscape)
Legionella pneumophila Legionnaires disease has a 25% mortality rate (Medscape) In the USA about 30 infections with L. pneumophila appear per 100.000 residents per year (Wikipedia) 2 to 10 days (Dose Response Legionella Chapter)
Rickettsia rickettsii For Rocky Mountain Spotted Fever (RMSF), the overall mortality rate is 4%, despite effective antibiotic therapy (Medscape) The average annual RMSF incidence during 1997-2002 was 2.2 cases/million persons (Chapman et al, 2006) 2-14 days (CDC)
Salmonella sp. Nontyphoidal Salmonella cause an estimated between 400 and 600 deaths in the United States annually (Linam and Gerber, 2007) Nontyphoidal Salmonella cause an estimated 1.4 million infections in the United States annually (Linam and Gerber, 2007) A few hours to one day (Wikipedia)
Shigella sp. The overall mortality rate in developed countries is less than 1%. In the Far East and Middle East, the mortality rates for S. dysenteriae infections may be as high as 20-25% (Medscape) The incidence of Shigella infections was 2848 cases per 100,000 population in 2007 (Medscape) 12 hours to 7 days but is typically 2-4 days (Medscape)
Vibrio cholerae Average case fatality rates for Europe and the Americas continue to hover around 1% (Medscape) The incidence in the United States in the age group older than 50 years, which has been around 0.50 cases per 100,000 population from 2003-2008 (Medscape) Four hours to five days with an average of 2-3 days (http://www.azdhs.gov/phs/edc/edrp/es/profcholera.htm)
Yersinia pestis Pneumonic plague (Untreated - 100%, Treated - 50%); Bubonic plague (Untreated - 50%-90%, Treated - 10%-20%); Septicemic plague - 20%-25% (Medscape) The CDC has reported an average of 10-15 cases of yersinia pestis infection annually in the United States.(Siddharth, W. 2009). 2–6 days for Bubonic plague (Wikipedia)
Prion Prion Prion-related diseases are relentlessly progressive and invariably lead to death (Medscape) 1 case per million population in the United States (Medscape) Can exceed 50 years (Collinge et al, 2006)
Protozoa Cryptosporidium parvum Mortality rate of 46% in AIDS patients and 29% in patients with other immunodeficiencies (Fayer & Ungar, 1986) In the United States, an estimated 748,000 cases of cryptosporidiosis occur each year (CDC, 2011) 2-10 days, average 7 days
Entamoeba coli Case fatality rates associated with amebic colitis range from 1.9%-9.1% (Aristizábal et al, 1991) The overall prevalence of amebiasis is approximately 4% in the United States (Medscape) 2 days to 4 months (Medscape)
Giardia duodenalis Giardiasis is not associated with mortality except in rare cases of extreme dehydration, primarily in infants or malnourished children (Medscape) National giardiasis cases were 7.5, 7.6 and 7.4 per 100,000 population in 2006, 2007, and 2008 (CDC MMWR) Averages 1-2 weeks, with a mean of 9 days (Medscape)
Naegleria fowleri In the summer of 2007, 6 fatal cases of infection occurred in the United States, all young males (Medscape) 32 reported infections in the U.S. in the 10 years from 2001 to 2010 (CDC) 1-7 days (CDC)
Virus Adenovirus A total of 428 respiratory HAdV infections were studied from 1991 to 2007 in Korean children and the case fatality ratio was 5.1% (Lee et al, 2010) Adenoviruses C in non-hospitalized Mexican children older than five years of age showed a rate of AdV infection of 23% (Rosete et al, 2008) 3-10 days
Echovirus Mortality was higher in infants with severe hepatitis (83%) than in infants with infection of the central nervous system (19%) (Modlin, 1986) 2 days to 2 weeks (Medscape)
Enteroviruses Hand, Foot, and Mouth Disease caused by enterovirus in China between 2008 and 2009 was studied and the case fatality ratio was 0.03% (Zhang et al, 2011) Hand, Foot, and Mouth Disease caused by enterovirus in China between 2008 and 2009 was studied and the incidence rate was 57.9% ([Zhang et al, 2011) 3-10 days (Medscape)
Influenza virus In 2007, influenza caused 411 deaths: 79 of them in persons aged 75-84 years and 139 of them in persons aged 85 years and older (Xu et al, 2007) 18-72 hours (Medscape)
Lassa virus About 15%-20% of hospitalized Lassa fever patients will die from the illness. It is estimated that the overall mortality rate is 1%, however during epidemics mortality can climb as high as 50% (Wikipedia) The number of Lassa virus infections per year in West Africa is estimated at 100,000 to 300,000 (CDC) 1-3 weeks (CDC)
Rhinovirus During a 6-week period in 2003 in a long term care facility for elderly persons, 56 residents and 26 staff developed respiratory illness in a long-term facility; 12 residents died (Louie et al, 2005) Fifty-two percent (615/1192) of patients from October 2009 to December 2009 had a single respiratory virus and 207 had rhinobirus (Chan et al, 2011) 2-4 days (Lessler 2009)
Rotavirus Rotavirus was estimated to be the cause of 37 deaths annually when data were extrapolated to the US population (Fischer et al, 2007) Rotavirus was estimated to be the cause of ~60,000 hospitalizations annually when data were extrapolated to the US population (Fischer et al, 2007) 1-3 days (CDC)
SARS Less than 1% for people aged 24 or younger, 6% for those 25 to 44, 15% for those 45 to 64, and more than 50% for those over 65 (Update 49) In the 2002-2003 outbreak, more than 8,000 cases were identified, mostly in mainland China. North America saw 251 cases during that period (Trivendi, M. 2011). Maximum is 10 days (Update 49)

Besides hazard identification (Hazard identification is the first step in a QMRA. It comprises general information about the agent and its adverse consequences), the other major components of microbial risk assessment are dose response assessment, exposure assessment, risk characterization and risk management.