CENTRE FOR DISEASE CONTROL AND PREVENTION :Disease outbreak data set

require(ggplot2)
require(dplyr)
#library(plyr)
library(knitr)
library(DT)
library(xtable)
getwd()
ou<-read.csv("C:/Users/vivek/Documents/foodborne-diseases/outbreaks.csv", header = T)
kable(ou[5:10,c(1:5,8,10:12)])
Year Month State Location Food Serotype.Genotype Illnesses Hospitalizations Fatalities
5 1998 January California Private Home/Residence Lasagna, Unspecified; Eggs, Other Enteritidis 26 3 0
6 1998 January California Restaurant 25 3 0
7 1998 January California Restaurant 8 0 0
8 1998 January California Restaurant Stuffing, Unspecified; Sandwich, Turkey Enteritidis 4 3 0
9 1998 January Colorado Restaurant Salad, Unspecified 21 NA NA
10 1998 January Colorado Restaurant Peppers, Chili 3 NA 0

How the number of cases of Food borne illnesses varied between 1998-2015

Year n
1998 1317
1999 1337
2000 1405
2001 1248
2002 1320
2003 1089
2004 1328
2005 959
2006 1255
2007 1088
2008 1029
2009 669
2010 853
2011 796
2012 833
2013 824
2014 872
2015 897

Food borne diseases/outbreaks trend 1998-2015

## `geom_smooth()` using method = 'loess'

Monthly trend of food borne sickness 1998-2015

Months in which people fell sick the most, 1998-2015

top_mons <- bymonth[order(-(bymonth$n)),]
kable(top_mons)
Month n
May 1898
June 1819
December 1816
April 1725
March 1724
July 1538
August 1533
January 1515
November 1509
February 1448
October 1347
September 1247

Top places where people fell sick after eating

kable(ord_by_count_loc[1:20, ])
Location counts
Restaurant 10448
2166
Private Home/Residence 1681
Catering Service 1089
Banquet Facility 367
Fast Food Restaurant 366
Unknown 355
School/College/University 354
Grocery Store 301
Restaurant; Private Home/Residence 205
Prison/Jail 193
Nursing Home/Assisted Living Facility 184
Restaurant; Catering Service 164
Camp 120
Religious Facility 110
Office/Indoor Workplace 97
Private Home/Residence; Grocery Store 97
Private Home/Residence; Catering Service 83
Fair/Festival 80
Restaurant; Grocery Store 59

1998-2015 Contaminant/Species that was behind ‘most’ food borne illnesses

Species n
6619
Norovirus genogroup I 2744
Salmonella enterica 2303
Norovirus genogroup II 1424
Norovirus unknown 790
Clostridium perfringens 732
Staphylococcus aureus 532
Escherichia coli, Shiga toxin-producing 485
Scombroid toxin 389
Norovirus 334
Bacillus cereus 299
Campylobacter jejuni 280
Ciguatoxin 270
Chemical or toxin 156
Bacillus cereus; Clostridium perfringens 139
Shigella sonnei 130
Vibrio parahaemolyticus 120
Bacterium 114
Virus 101
Campylobacter unknown 90
Hepatitis A 88
Clostridium perfringens; Bacillus cereus 82
Listeria monocytogenes 58
Clostridium botulinum 57
Salmonella enterica; Salmonella enterica 49

Contaminant/Species that caused most number of fatalities 1998-2015

Species Fatalities
11 Listeria monocytogenes 121
18 Salmonella enterica 82
9 Escherichia coli, Shiga toxin-producing 35
1 26
7 Clostridium perfringens 12
6 Clostridium botulinum 10
12 Mycotoxins 7
17 Rotavirus 7
15 Norovirus genogroup II 6
10 Hepatitis A 5
16 Norovirus unknown 4
19 Salmonella enterica; Salmonella enterica 4
21 Staphylococcus aureus 3
8 Clostridium perfringens; Bacillus cereus 2
14 Norovirus genogroup I 2
20 Shigella sonnei 2
2 Bacillus cereus; Clostridium perfringens 1
3 Campylobacter jejuni 1
4 Chemical or toxin 1
5 Ciguatoxin 1
13 Norovirus 1
22 Unknown 1
23 Vibrio cholerae 1
24 Vibrio vulnificus 1
25 Yersinia enterocolitica 1
For t he above table, please note that the ’numbe r of fatalities’ and the ‘number of illnesses’ attributed to Listeria monocytogenes significantly differ because in the data set the ‘state’ column had one value ‘Multi-State’ which doesn’t mention which set of US states it refers to for a particular illness.

So the total number of Lysteria monocytogenes related fatalities were 121. if you were to exclude the data points from ‘Multistate’ then the total number of ‘illnesses’ caused by ‘Lysteria Monocytogenes’ would be 58.

1998-2015 Top 15 states where people fell sick due to food

State n
Florida 2409
California 2293
Ohio 1288
Illinois 1133
New York 909
Michigan 882
Minnesota 842
Washington 824
Maryland 816
Colorado 510
Oregon 504
Pennsylvania 480
Wisconsin 428
Georgia 375
Texas 367

1998-2015 States where food borne illness/outbreaks were the least

State n
Delaware 13
South Dakota 26
Washington DC 35
Nebraska 36
West Virginia 39
Montana 41
Vermont 41
Mississippi 43
Kentucky 44
Arkansas 54
New Mexico 55
Wyoming 57
Oklahoma 58
Rhode Island 62
Nevada 64

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