Emerging Foodborne Enteric Bacterial Pathogens
SJ Forsythe, Nottingham Trent University, Nottingham, UK
ã 2016 Elsevier Ltd. All rights reserved.
Introduction
Compared to clinical infectious diseases, the number of cur-
rently recognized foodborne pathogens seems small. In part,
this is due to general procedures of food production, for
example, cooking, acidification, and dehydration, which over
the centuries and in different cultures have been refined and
become a self-proved effective means of food preparation.
However, with changes in the sourcing of food ingredients,
the need for large-scale food preparation practices and longer
storage periods along with changes in eating habits has ensured
a continuation of food-related illnesses. Such infections are an
important cause of morbidity and mortality worldwide and
have a major impact on public health. The true worldwide
burden of diseases caused by foodborne pathogens is largely
unknown. At best, we have data indicating trends in infections
for a few pathogens in a few number of developed countries.
The European Food Safety Authority has defined ‘emerging
risk to human, animal and/or plant health’ as a risk resulting
from a newly identified hazard to which a significant exposure
may occur or from an unexpected new or increased significant
exposure and/or susceptibility to a known hazard. Hence, in
order to detect such risks, adequate surveillance and monitor-
ing programs need to be in place. There are many food safety
monitoring systems at national and international levels. These
are summarized in Table 1. Examples are the ‘Rapid Alert
System for Food and Feed’ (RASFF) in Europe and WHO–
INFOSAN. In general, these systems identify problems such
as the increased reported occurrence of a foodborne hazard
retrospectively. Consequently, any intervention is initially reac-
tive instead of predictive.
In order to determine the global health burden of foodborne
illness, the WHO set up the Foodborne Disease Burden Epide-
miology Reference Group. This is composed of internationally
renowned experts in a broad range of disciplines relevant to
global foodborne disease epidemiology; http://www.who.int/
foodsafety/foodborne_disease/ferg/en/index3.html. They have
estimated that in 2005, 1.8 million people died from diarrheal
disease, and these were mainly attributable to contaminated
food and water sources. In the United States, foodborne illnesses
affect up to 80 million people and cost an estimated US$5
billion on an annual basis. Additionally, our understanding of
such infections is changing with the recognition of previously
unrecognized and previously well-recognized pathogens, which
have increased in their prevalence or become associated with
new food vehicles.
The major organisms associated with foodborne disease are
bacteria due to their ease of isolation and identification com-
pared to viruses and fungi. However, with improved global
surveillance systems, as well as improved isolation and identifi-
cation methods, previously unrecognized foodborne infectious
organisms are being recognized. With a global economy and the
Encyclopedia of Food and Health http://dx.doi.org/10.1016/B978-0-12-384947-2.00248-8
international transportation of food, the need to attribute
human infections to food vehicles is warranted for their control.
The study of emerging foodborne enteric pathogens is both
exciting and daunting at the same time. The opportunity to
recognize and define an emergent pathogen leading to its con-
trol and reduced risk is an admirable goal, yet to publicize the
emergence of an enteric pathogen based on limited informa-
tion and initiate action could be regarded as scaremongering
and alarmist. Given the limited number of organisms, which
are routinely monitored in food, it may take considerable time
before there is sufficient body of evidence of its significant
presence such that it might be argued that by the time the link
between the clinical presentations and food as a vector has been
established, the organism will no longer be ‘emerging’ and
therefore outside the scope of the study. The word ‘emerging’
implies the emergence de novo of the pathogen, yet for some, the
term ‘recently recognized’ is more appropriate as the organism
had been previously described, but the link with foodborne
disease may be new. Some organisms in this article are ‘emer-
gent’ or ‘recently recognized’ pathogens for which food has
been established as a vector, but some will not be so strongly
associated but could be foodborne. It may be argued that the
latter should not be included – however, this begs the question
of how will we ever know unless we look. Our powers of
microbial epidemiology are still mainly limited to bacteria as
we are still largely culture-dependent. In time, next-generation
sequencing (NGS) will enable real-time genomic analysis of
infections, but for now, our future predictions remain misty
and unclear.
Illness caused by foodborne pathogens represents an
important economic and public health burden worldwide.
Based on a yearly case estimate and recent US census data, an
estimated 25% of the US population is affected by foodborne
illness each year. Viral foodborne pathogens are thought to
contribute to 50% of all foodborne illness cases in the United
States. Rates of foodborne illness in many developed countries
are similar. While exact numbers are difficult to estimate, it is
thought that the burden of foodborne illness in developing
countries is even higher.
Since 1996 in the United States, FoodNet has been an active
surveillance program for laboratory-confirmed infections due
to seven commonly reported bacterial foodborne pathogens:
Salmonella, shiga toxin-producing Escherichia coli O157, Shigella
spp., Vibrio spp., Yersinia spp., Campylobacter spp., and Listeria
monocytogenes. This surveillance covers 15% of the US popula-
tion. Over the period 1996–2005, there had been 121 536 cases
including 552 deaths, for which 215 and 168 were due to were
among persons infected with Salmonella and Listeria, respec-
tively. Useful as this surveillance is, it does not cover the myriad
of foodborne pathogens and toxigenic agents.
In the United States, there are an estimated 9.4 million cases
of foodborne illness, which can be attributed to 31 known
487
488 Emerging Foodborne Enteric Bacterial Pathogens
Table 1 Early identification systems for emerging foodborne hazards
Country Organization Activity
The United FSA Food Standards Agency
Kingdom (FSA)
The ISIS Day-to-day changes in
Netherlands frequency of all
communicable diseases
European European Centre for Provides a structured and
Disease Prevention systematic approach to
and Control (ECDC) the control of
communicable diseases
and other serious health
threats in partnership
with national health
protection agencies.
Issues warnings to EU
member states through
the early warning and
response system (EWRS)
Rapid alert system on Centralized reporting of
food and feed food hazards (physical,
(RASFF) chemical, biological)
EU: FVO Food and Veterinary Office
(FVO) promotes effective
control systems in food
safety and checks on
compliance
The United CDC: FoodNet Determines the exact
States burden of foodborne
diseases, monitors
foodborne disease
trends in the United
States, and relates
foodborne disease to
specific foods
CDC: eFORS Electronic Foodborne
Outbreak Reporting
System
CDC: PulseNet National network of public
health laboratories that
undertake pulsed-field gel
electrophoresis analysis
of bacteria that may be
foodborne
International WHO: GPHIN Global Public Health
Intelligence Network
WHO: INFOSAN International Network of
Food Safety Authorities
Network disseminates
urgent information
OIE Office International des
Epizooties (OIE) sets
standards for sanitary
practices in the diagnosis
of diseases in animals
and animal products. This
includes the World
Animal Health
Information System
(WAHIS)
After Marvin, H. J. P., Kleter, G. A., Prandini, A., Dekkers, S., and Bolton, D. J. (2009)
Early identification systems for emerging foodborne hazards. Food and Chemical
Toxicology 47, 915–926.
pathogens (2011 data). Of these, 14 pathogens account for
95% of the illnesses and hospitalizations and 98% of deaths.
The associated costs are estimated as $14.0 billion (ranging
from $4.4 to $33.0 billion) of which 90% are attributable to
five pathogens: nontyphoidal Salmonella enteric, Campylobacter
spp., L. monocytogenes, Toxoplasma gondii, and norovirus.
However, there were an additional estimated 38.4 million
cases (80%), which were due to ‘unspecified agents, including
known agents with insufficient data to estimate agent-specific
illness, known agents not yet recognized as causing foodborne
illness, substances known to be in food but of unproven path-
ogenicity, and unknown agents.’ These unattributed cases
resulted in  71 878 hospitalizations and 1686 deaths.
Although this author is not claiming that all these cases are
due to emerging foodborne pathogens, the article illustrates
that there is still scope for previously unrecognized pathogens
to be discovered. Toxin-induced gastroenteritis due to Bacillus
cereus is a well-recognized foodborne pathogen, yet the lack
diagnostic tools means its incidence is highly likely to be
underestimated and not an emergent pathogen as such.
The microbiological safety of food is dependent upon mul-
tiple variable ‘from farm to fork’ along the food chain. The
combined advances in the Internet and culture-independent
(i.e., DNA sequencing) methodologies are enabling improve-
ments in monitoring and surveillance, though the scenario is
constantly changing with increased global transportation of
foods and food ingredients, aging populations, and changes
in eating habits. Against this background, this article reviews
the current situation regarding emergent enteric foodborne
pathogens. In particular, reference will be made to previously
unrecognized vehicles, for example, fresh produce, and serious
issues to public health following the acquisition of antimicro-
bial resistance. Additionally, previously unknown foodborne
pathogens, many of which are zoonotic, are being recognized
through improved methods of surveillance and identification.
This article will not consider well-recognized foodborne
pathogens: Campylobacter jejuni, Salmonella enterica serovars,
E. coli O157 and O104, Vibrio cholerae, V. parahaemolyticus,
Yersinia enterocolitica, Listeria monocytogenes, Clostridium perfrin-
gens, Staphylococcus aureus, and Bacillus cereus. For information
on these organisms, please consult the specific chapters as
listed at the end under ‘See also.’ Such organisms are often
formally controlled via microbiological specifications whether
in international policies or producer–distributor agreements.
Essentially, improvements in the microbiological safety of
foods have been largely driven by public demand in response
to disease outbreaks, and consequently, less-recognized path-
ogens are overlooked. Focussing on a particular potential
source of infection will invariably lead to discoveries, as evi-
denced by the emphasis of bats as vehicles of bacterial disease,
which has opened a whole field of previously unrecognized
bacterial and virus route of transmissions. Awareness and sur-
veillance of viral foodborne pathogens are generally poor and
primarily limited to norovirus, hepatitis A, and rotaviruses.
Although many foodborne parasites are recognized, only Asca-
ris, Cryptosporidia, and Trichinella are effectively monitored in
foods. Their epidemiology of such parasites through the food
chain is poorly understood. The issues of viral and parasitic
foodborne pathogens are not considered in this article due to
the lack of information.

Bacterial Enteric Pathogens
Aeromonas Species
Description: Aeromonas genus, composed of 17 hybridization
groups and 14 phenospecies
Phenotypic differentiated groups: A. hydrophila, A. caviae, and A.
sobria
Clinical presentations: Traveler’s diarrhea
Sources: Water, fish, shellfish, meats, dairy products, and fresh
vegetables
Detection methods: Various culture media, for example, starch
ampicillin agar (SAA) and BIBG
The genus Aeromonas was first proposed in 1936 for rod-
shaped Enterobacteriaceae, which possessed a polar flagellum.
Since then, there have been many taxonomic revisions, and
currently, it forms the family Aeromonadaceae. They are Gram-
negative, rod-shaped, facultative anaerobic, nonspore-forming
bacteria, which are widely distributed in the soil and aquatic
environments. Members of the genus are divided into three
phenotypically differentiated groups: Aeromonas hydrophila,
Aeromonas caviae, and Aeromonas sobria. Currently, the genus
is composed of 17 DNA hybridization groups or genomospe-
cies and 14 phenospecies.
The Aeromonas genus includes psychrophiles and
mesophiles and is associated with various diseases of warm-
and cold-blooded animals. They have been isolated from fish,
shellfish, meats, dairy products, and fresh vegetables. However,
only few foodborne outbreaks have been documented. Some
studies have shown that some motile Aeromonas species are
becoming food- and waterborne pathogens of increasing
importance. They have been associated with several foodborne
outbreaks and are progressively being isolated from patients
with traveler’s diarrhea.
A. hydrophilia is present in all freshwater environments and
in brackish water. It has frequently been found in fish and
shellfish and in market samples of red meats (beef, pork, and
lamb) and poultry. The organism is able to grow slowly at 0  C.
It is presumed that given the ubiquity of the organisms, not all
strains are pathogenic. Some strains of A. hydrophila are capable
of causing illness in fish and amphibians as well as in humans
who may acquire infections through open wounds or by inges-
tion of a sufficient number of the organisms in food or water.
A. hydrophila may cause gastroenteritis in healthy individuals or
septicemia in individuals with impaired immune systems or
various malignancies. A. caviae and A. sobria also may cause
enteritis in anyone or septicemia in immunocompromised
persons or those with malignancies.
There is controversy as to whether A. hydrophila is a cause of
human gastroenteritis. The uncertainty occurs because volun-
teer human feeding studies (1011 cell dose) have failed to
demonstrate any associated human illness. However, its pres-
ence in the stools of individuals with diarrhea, in the absence of
other known enteric pathogens, suggests that it has some role in
disease and has been included in this survey of foodborne
pathogens. Similarly, A. caviae and A. sobria are putative patho-
gens associated with diarrheal disease, but as of yet, they are
unproved causative agents. General symptoms of A. hydrophilia
gastroenteritis are diarrhea, abdominal pain, nausea, chills
and headache, dysentery-like illness, and colitis. Additional
Emerging Foodborne Enteric Bacterial Pathogens 489
symptoms may include septicemia, meningitis, endocarditis,
and corneal ulcers.
Two types of gastroenteritis have been associated with A.
hydrophila: a cholera-like illness with severe diarrhea and a
dysenteric illness characterized by loose stools containing
blood and mucus. The infectious dose of this organism is
unknown. A. hydrophila may spread throughout the body in
the bloodstream and cause a general infection in persons with
impaired immune systems. Those at risk are individuals suffer-
ing from leukemia, carcinoma, and cirrhosis and those treated
with immunosuppressive drugs or who are undergoing cancer
chemotherapy.
A. hydrophila produces a cytotonic enterotoxin, hemolysin,
acetyl transferase, and phospholipase. Together, these viru-
lence factors may account for the organism’s pathogenicity.
The detection of genes responsible for Aeromonas virulence is
a vital tool in establishing the potential pathogenicity of the
bacteria, as these virulence genes may act alone or in synergy in
the establishment of infections.
A number of selective and differential isolation media have
been developed for the recovery of Aeromonas species from the
environment, foods, and clinical specimens. Since comparative
studies demonstrate that no single medium results in the opti-
mal recovery of aeromonads, combinations of different isolation
media and methods are used including direct plating, membrane
filtration, and multiple tube tests for determining most probable
numbers. SAA and bile salts–inositol–brilliant green (BIBG)
agar with initial enrichment in alkaline peptone water (APW)
or tryptose broth containing ampicillin (TSB-30, ampicillin
30 mg l 1) are recommended simultaneously with commer-
cially available media such as Aeromonas medium (Ryan’s
medium). Starch glutamate ampicillin penicillin (SGAP-10)
medium has been used to detect aeromonads from foods. The
isolation of aeromonads from contaminated samples such as
feces requires the use of selective and differential media such as
MacConkey agar, cefsulodin–irgasan–novobiocin (CIN) agar,
and blood agar with ampicillin (10 mg l 1 ampicillin). To facil-
itate recovery of aeromonads from highly contaminated samples
such as feces, enrichment broths such as APW are incubated
overnight and subcultured onto CIN agar and blood agar with
ampicillin. Culture plates are then incubated aerobically at 35  C
for 24–48 h. Aeromonas species produce distinctive colonies,
with or without hemolysis on blood agar. Colonies are screened
by carrying out oxidase test and identified using biochemical
methods or commercially available bacterial identification kits.
Arcobacter Species
Description: Arcobacter butzleri, A. cryaerophilus, and A. skirrowii
are the primary species of interest.
Clinical presentations: Persistent and watery diarrhea.
Sources: Contaminated drinking water and food.
Detection methods: mCCDA and CAT.
Campylobacter jejuni and C. coli are well recognized as the major
causes of human gastroenteritis. Meanwhile, a number of other
Campylobacter species and related organisms have also been
recognized as causing animal if not human cases of gastroen-
teritis. These include Campylobacter concisus and Arcobacter spe-
cies. While there are a relatively few reported cases of infection
490 Emerging Foodborne Enteric Bacterial Pathogens
due to Arcobacter, this is probably due in part to the lack of
routine use of appropriate isolation media.
A number of reviews on Arcobacter spp. have demonstrated
that the organism is a cause of human pathogen and is
associated with food products. One of the first significant
studies of Arcobacter started in 1995 in Belgium where the
WHO Centre for Campylobacter specifically looked for non-
jejuni/Campylobacter coli-like organisms (CLOs) in fecal sam-
ples. It is plausible that A. butzleri and A. cryaerophilus, which
were first isolated from aborted bovine fetuses and later from
porcine fetuses, will in the future be more fully recognized as of
significant human importance. Currently, there is increasing
awareness of their role as veterinary pathogens, but there are
relatively few human cases.
The Arcobacter genus was formerly known as aerotolerant
campylobacters and CLOs. But improved methods of taxo-
nomic evaluation have led to the recognition of the genus
Arcobacter. There are currently 17 recognized Arcobacter species,
and these have been isolated from various sources. Of particu-
lar interest are A. butzleri, A. cryaerophilus, and A. skirrowii, as
these have been associated with human cases of diarrhea, the
probable transmission routes being through the ingestion of
contaminated drinking water and food. These three species are
also veterinary pathogens causing porcine abortions. A. butzleri
serotypes 1 and 5 are regarded as the primary human
pathogens; however, no epidemiological studies have yet
shown the transmission of the organism through the food
chain to humans. The situation is, however, reminiscent of C.
jejuni and L. monocytogenes. These organisms were recognized
as veterinary pathogens many years before the medical micro-
biologists used suitable isolation media to samples from
patients suffering from gastroenteritis. Arcobacter species have
been isolated from a range of food sources (Table 2) using a
range of methods, some of which may favor certain species
more than others. Water may also be a vector of Arcobacter
transmission to animals and humans.
In general, Arcobacter spp. are more aerotolerant and have
lower growth temperature limit than Campylobacter spp. On
blood-based agars, Arcobacter spp. produce round, off-white or
grayish colonies, 2–4 mm in diameter after 3 days of incuba-
tion. The colonies are generally small, nonpigmented, and
Table 2 Incidence of Arcobacter in animals and animal products
Source % n Site
Pigs 0–89.9 299a Ground pork
7 100 Pork
Cows 1.5 68 Minced beef
2.2 90 Beef
Poultry 96.8 125 Chicken carcasses
24.1 220 Turkey meat
Ducks 50 10 Carcasses
52 170 Carcasses
Water 100 10(4)b
a Description: Campylobacter concisus, a fastidious Campylobacter
Only tested for A. butzleri.
b
All samples were positive using FISH, whereas Arcobacter was only isolated from four
samples.
Adapted from Forsythe, S. J. (2006). Arcobacter. In: Motarjemi, Y. and Adams, M.
(eds.), Emerging foodborne pathogens. Cambridge: Woodhead Publishing, references
therein.
convex with entire edges. Swarming has been reported on
fresh agar. Brain Heart Infusion Agar supplemented with
0.6% (w/v) yeast extract and 10% (w/v) blood agar has been
used recently for routine culturing.
Arcobacter isolates can be presumptively identified by their
shape (small comma-shaped or spiral rods) and motility (dart-
ing or corkscrew motility). They can be easily distinguished
from Campylobacter and related genera by their ability to grow
in air at 25  C. The main phenotypic traits used for Arcobacter
species differentiation are catalase activity, nitrate reduction,
cadmium chloride susceptibility, microaerophilic growth at
20  C, and growth on MacConkey agar and in the presence of
3.5% NaCl and 1% glycine. Organic acids and amino acids are
used as carbon sources. Hydrogen is not required for growth.
All Arcobacter isolates hydrolyze indoxyl acetate. A simple diag-
nostic characteristic useful for the presumptive identification of
Campylobacter jejuni, C. coli, and Arcobacter spp. is the cadmium
chloride test.
Arcobacters appear resistant to antimicrobial agents typi-
cally used in the treatment of diarrheal illness caused by Cam-
pylobacter spp., for example, erythromycin, other macrolide
antibiotics, tetracycline, and chloramphenicol. Isolation of
arcobacters requires selective media such as mCCDA and CAT.
Identification can subsequently be achieved using 16S rRNA
probes and genotyped.
The occurrence of arcobacter-related diseases may be under-
estimated due to the lack of surveillance and optimized detec-
tion procedures. Examination of human and veterinary clinical
specimens for the presence of Arcobacter species is rarely per-
formed, and in most cases, suboptimal procedures are used. In
addition, little is known about the risk factors for human
infection. The most extensive study to date on this matter was
undertaken on a total of 67 599 stool samples over an 8-year
period. A. butzleri was the fourth most common CLO isolated.
It was more frequently associated with symptoms of a
persistent and watery diarrhea than C. jejuni.
The isolation of A. butzleri was associated with cases of
persistent and watery diarrhea and less associated with bloody
diarrhea compared to C. jejuni. The pathogenicity and viru-
lence mechanisms of Arcobacter spp. are still poorly understood
and have only been studied in A. butzleri, A. cryaerophilus, A.
skirrowii, and A. cibarius. Analysis of the A. butzleri strain RM
4018 genome shows the presence of several putative virulence
genes in the organism, such as ciaB, cj1349, and cadF. These are
homologous to genes associated with pathogenicity in other
closely related organisms. The ciaB gene encodes an invasion
protein injected directly into the cytoplasm of the host cells
through a secretion system. The cj1349 gene encodes for pro-
teins that enable adhesion to host cells by binding specifically
to fibronectin, and the CadF protein also induces the internal-
ization of bacterial cells by the activation of GTPases.
Campylobacter concisus
species
Clinical presentations: Isolated from healthy and diarrheal
individuals
Sources: Contaminated food and water
Detection method: No specific method available to date
 Emerging Foodborne Enteric Bacterial Pathogens 491

Despite considerable efforts in surveillance and improvements

2002 Outbreak at the University of Tennessee investigated
in isolation methods, only about half of the reported intestinal
by CDC and FDA. Fatal case linked to the use of
infectious cases are attributable to a named organism. While a
powdered formula
large number of cases are related to C. jejuni and C. coli
FDA Cronobacter (and then E. sakazakii) detection
infections, there is evidence that other Campylobacter species
method; Bacteriological Analytical Manual
may also be causative agents. Epidemiological evidence is
2004 1st FAO–WHO risk assessment meeting on
poor, but it is reasonable to assume that more fastidious
microbiological safety of PIF
Campylobacter species, such as C. concisus, will not be recovered
Development of first chromogenic differential agar
as efficiently as the better understood C. jejuni. In common with
2006 2nd FAO–WHO risk assessment meeting
other campylobacters, C. concisus is a Gram-negative, curved,
ISO/TS 22964 method released
microaerophilic bacterium. It can be isolated from the human
2008 3rd FAO–WHO risk assessment meeting
oral cavity and fecal samples from healthy and diarrheic
Revised Codex Alimentarius Commission guidelines
patients. As a consequence, its primary pathogenic potential is
for microbiological specifications for PIF released, to
uncertain. In many diarrheal cases, C. concisus is isolated as the
include Cronobacter as a named pathogen
only potential intestinal pathogen, and hence, the need to
Cronobacter genus defined, composed of 5 species
determine its role in human enteric disease is evident.
2009 Open-access seven-loci multilocus sequence typing
Studies to date suggest C. concisus is composed of various
(MLST) scheme established to replace ambiguous 16S
genotypes, which may vary in their pathogenic potential.
rDNA analysis; www.pubMLST.org/cronobacter
However, considerable further work is needed to determine
2010 First whole sequence for C. sakazakii published; isolate
the risk of C. concisus to human health and vehicles of infec-
from the University of Tennessee outbreak
tion. Given the habitat of the organism as being in the
2011 C. sakazakii sequence type 4 (clonal lineage)
intestinal tract of healthy individuals, it is plausible that
association with neonatal meningitis determined
contaminated food and water could be the sources of infec-
C. condimenti and C. universalis recognized
tion. The organism has been included here to raise awareness
2012 First pan-genome analysis of Cronobacter genus based
of this emerging pathogen and its possible contribution to
on 14 genomes
foodborne infections.
Revised FDA method of detection; Bacteriological
Analytical Manual
2013 www.pubMLST.org/cronobacter expanded to include
the following:
Cronobacter spp., Formerly Enterobacter sakazakii
(a) Tax-MLST established, extension of MLST to
Description: Cronobacter genus. Seven recognized species include genotyping of ompA and rpoB
proposed: C. condimenti, C. dublinensis, C. malonaticus, C. (b) Cronobacter BIGSdb searchable repository for all
muytjensii, C. sakazakii, C. turicensis and C. universalis. Gram- published Cronobacter sp. genomes established
negative, frequently motile, facultative aerobic rods; mem-
bers of the Enterobacteriaceae.
Before 1980, yellow-pigmented Enterobacter cloacae-like
Clinical presentations: Infections in all age groups, particularly
strains were called Enterobacter sakazakii. Despite earlier spo-
neonates, infants <6 months of age, and the elderly. Life-
radic cases of neonatal and infant infections, the organism
threatening symptoms in neonates and infants <6 months
was highlighted following an outbreak in a university
of age include meningitis, necrotizing enterocolitis, and
hospital in Tennessee (the United States). One neonate died
respiratory infections.
from meningitis, two died from suspected infections (tracheal
Sources: Infections in neonates associated with contaminated
aspirate-positive), and seven were colonized (six fecal-positive
reconstituted powdered infant formula (PIF). Ubiquitous
and one urine-positive) with the same strain according to
in nature, particularly plant material. Human carriage.
pulsed-field gel electrophoresis (PFCE) profiling. The source
Detection methods: Cultivation on chromogenic agar, followed
was attributed to powdered formula. Since such neonates
by sequencing of fusA or rpoB gene for phylogenetic
only have a limited number of exposure routes, the
analysis.
FAO–WHO instigated three risk assessments that have
Cronobacter is possibly the archetypal recently recognized bac- directly contributed to the 2008 Codex Alimentarius Com-
terial pathogen, which has been associated with foodborne mission revisions in the microbiological specifications of PIF.
infection, albeit via one particular food source: PIF. The con- Prior to this, the number of Enterobacteriaceae (except for
siderable progress in better understanding and control of this Salmonella) permitted in PIF was <100 cfu g 1. These specifi-
organism is undoubtedly due to policy issues. Using seven-loci cations had not been revised since 1979. However, following
multilocus sequence analysis, the close relatedness of the the concern of the serious implications following Cronobacter
Cronobacter species is shown in Figure 1. According to phylo- infections of neonates, the microbiological criteria changed
genetic analysis, these major divisions formed about 41 mil- such that Cronobacter should not be detectable in 10 g test
lion years ago, and further, host adaptation has occurred as will volume quantities of PIF.
be considered later with the specific case of C. sakazakii In order to implement the specifications, improved under-
sequence type 4. standing of the organism and development of detection
Short timeline: Pre-2002, various outbreaks in neonatal methods are needed. The focussed attention showed Enterobac-
intensive care units and sporadic cases reported. ter sakazakii should be regarded as a separate genus and was
492 Emerging Foodborne Enteric Bacterial Pathogens

100 C_sakazakii
99 C_sakazakii-ST4
100 C_malonaticus
C_universalis
100 84 C_turicensis

77 C_muytjensii
C_dublinensis
97
C_condimenti

100 F. pulveris
F. helveticus
S. turicensis

0.01
Figure 1 Maximum likelihood tree of the seven-loci multilocus sequence typing (3036 base pair concatenated length) for the members of
Cronobacter, Franconibacter, and Siccibacter genus, showing the sequence type for each species type strain and the neonatal meningitis-associated
sequence type 4. The tree was drawn using MEGA5.2 (http://www.megasoftware.net) with 1000 bootstrap replicates. Adapted from Holy, O. and
Forsythe, S. J. (2014). Cronobacter species as emerging causes of healthcare-associated infection. Journal of Hospital Infections 86,169–177.

Table 3 Isolation of Cronobacter spp. from throat swabs of outpatients according to age groups

Patient age (years)

Year <1 1–4 5–9 10–14 15–44 45–64 65–74 >75 Total

2005 1 5 1 1(1) 2 0 2 0 12(1)

2006 (1)a 1(2) 0 5 2 0 (3) (2) 8(8)
2007 2 9 0 2 2(1) (1) (1) (1) 15(4)
2008 0 1(1) 2 2(1) 0 0 (2) (1) 5(5)
2009 (2) 4 1 2 1 (2) 1 (1) 9(5)
2010 0 5 2(1) 0 (2) 1(1) (2) 2 10(6)
2011 (1) 0 2 0 0 0 0 0 2(1)
Total number of Cronobacter isolates 3(4) 25(3) 8(1) 12(2) 7(3) 1(4) 3(8) 2(5) 61(30)
% of isolates/age group 4.9 41 13.1 19.7 11.5 1.6 4.9 3.3 100.0
Number of patients sampledb 808 3404 2651 1867 18 223 10 744 3888 3538 45 123
Incidence of Cronobacter isolates/1000 patients sampled 8.7 8.2 3.4 7.5 0.5 0.5 2.8 2.0 2.0
a
Numbers in parentheses indicate additional isolates from normally sterile sites, sampled according to the clinical presentation of the patient.
b
Total number during the period 2005–2011.
Reproduced from Holy and Forsythe (2014).

named Cronobacter; in 2013, there were seven recognized spe-
cies. Only four of which are associated with human infections:
C. sakazakii, C. malonaticus, C. turicensis, and C. universalis. It is
highly probable that the number of infections has probably
been unreported due to misidentification. The species can be
grouped, with the mostly clinically relevant being group 1
(C. sakazakii and C. malonaticus, which form the majority of
clinical isolates in all age groups) and group 2 (C. turicensis and
C. universalis, which have been less frequently reported). The
other species are primarily environmental commensals and are
probably of little clinical significance. Table 3 shows an age
profile of Cronobacter isolated using throat swabs from over
45 000 outpatients during the period 2005–2011. The organ-
ism was isolated from every age group, with a higher frequency
from children < 14 years of age.
In 2011, Joseph and Forsythe announced the strong associ-
ation between neonatal meningitis cases and the clonal lineage
of C. sakazakii ST4. This was established using retrospective
study of 41 clinical strains from 1953 to 2008, collected from
seven countries. This association was confirmed later in the
year by the analysis of a number of highly publicized cases in
the United States. The reason for the association of one
sequence type out of >200 STs in the genus is unclear as no
particular virulence traits have been determined in C. sakazakii
ST4. However, it is known that this sequence type is frequently
(24% of strains) isolated from the infant formula and milk
powder manufacturing plants in Australia, Germany, Switzer-
land, and Ireland and therefore may represent a particularly
persistent clonal variant, resulting in increased neonatal
exposure.
Cronobacter can invade human intestinal cells, replicate in
macrophages, and invade the blood–brain barrier. The route of
infection is probably through attachment and invasion of the
intestinal cells. Whole genome sequencing has revealed a large
 Emerging Foodborne Enteric Bacterial Pathogens 493

number of plausible virulence factors, though many require 2013, they were reclassified as Cronobacter and therefore
further laboratory studies for confirmation. These are should have been positively detected, however in 2014 there
summarized in the succeeding text, and further details can be were removed from the genus and formed the new genera
obtained from the original publications. Due to the increasing Franconibacter and Siccibacter (Figure 1).
number of Cronobacter genomes being sequenced, for up-to- It should be noted that the emphasis of controlling Crono-
date information, the reader should consult the Cronobacter bacter spp. in PIF has given the false impression that this is the
BIGSdb, which is a searchable (BLAST) repository of all pub- only route of infection. In fact, the C. malonaticus type strain
lished Cronobacter genomes (see ‘Relevant Websites’). was isolated from breast abscess, there is human carriage and
A number of fimbria clusters have been identified in the the organism is recovered from a wide range of foods (Table 4),
genomes of Cronobacter species. Many fimbria clusters are and the organism has been isolated from the nasogastric feed-
common to all species, though there are two interesting excep- ing tubes of neonates not receiving reconstituted infant
tions. C. sakazakii is the only Cronobacter species encoding for formula.
b-fimbriae, whereas the genomes of the other species encode
for curli fimbriae. This may reflect evolution to the host eco-
system. A number of iron assimilation mechanisms have been
Enteroaggregative Escherichia coli
found in Cronobacter species, which might enable the organism
to utilize iron from breast milk and infant formula. Five puta- Description: The enteroaggregative Escherichia coli (EAEC) are a
tive type VI secretion system clusters have been identified pathotype within the E. coli species. Gram-negative, facul-
Cronobacter sp. genomes. These may be involved in adherence, tative rods. The genus is a member of the Enterobacteria-
cytotoxicity, host-cell invasion, growth inside macrophages, ceae family.
and survival within the host. It has been proposed that the Source: Contaminated food.
outer membrane proteins ompA and ompX have roles in Cro- Clinical presentations: Watery diarrhea with or without blood
nobacter penetrating the blood–brain barrier. The mechanism and mucus, abdominal pain, nausea, vomiting, and low-
(s) leading to the destruction of the brain cells is unknown and grade fever can be persistent.
could in part be a host response. The organism also encodes for Detection methods: No specific isolation procedures are
a number of hemolysins. available.
C. sakazakii is unique in the Cronobacter genus in its utiliza-
tion of exogenous sialic acid, and this may have clinical signif-
Table 4 Survey of dry food products and food ingredients from
icance. The ability to utilize sialic acid could be a major
which Cronobacter spp. have been isolated
evolutionary host adaptation since the compound is found in
breast milk, mucin, and gangliosides. Sialic acid is also an Food product or Number of Total number of
ingredient in PIF due to its association with brain develop- ingredient positive samples samples %
ment. C. sakazakii is also able to grow on the ganglioside
GM1 as a sole carbon source. Levels of endotoxin due to the Powdered infant 2 82 2
presence of heat-stable lipopolysaccharide (LPS) have been formula
Follow-up formula 3 91 3
measured in infant formula. In rat pups, LPS enhances the
Dry infant food 24 199 12
translocation of Cronobacter across both the intestines and the Milk powder 3 72 4
blood–brain barrier and therefore indicates that its presence in Milk powder and 1 55 2
infant formula could increase the risk of bacteremia in neo- derived products
nates. It has been speculated that frequent LPS contamination Starches 40 1389 3
of PIF (known to disrupt tight junctions) might contribute to Corn, soy, wheat, and 14 78 18
the invasiveness of Cronobacter across the blood–brain barrier. rice
The organism also has a number of heavy metal resistance Rice flour 6 16 38
factors and biofilm formation, which might enable it to resist Saengsik 41 86 48
disinfectants in food production environments. Dry food ingredients 15 66 23
Herbs and spices 40 122 33
Due to the high profile and changes in microbiological
Spices 14 71 20
specifications for PIF for target age <6 months, a number of Nuts 2 2 100
isolation and identification methods were developed Instant soups 2 13 15
post-2002. Tea 3 5 60
Isolation of the organism from PIF largely resembles that Confectionary 3 42 7
for Salmonella, with the use of stages for preenrichment, enrich- Chocolate products 11 37 30
ment, presumptive isolation, and confirmatory tests. It should Seeds 14 34 41
be noted that the FDA and ISO methods for the detection of Dried fish (inc. 13 50 26
Cronobacter are not up to date with respect to the taxonomy of shrimp)
the genus and not all species will necessarily be recovered by Sunsik 17 36 47
Tofu 4 11 36
these techniques. In fact, a well-known phenotyping kit man-
Desiccated foods 18 115 16
ufacturer still retains the name Enterobacter sakazakii instead of
Cronobacter spp. in its online database. In addition, E. helveti- Adapted from Forsythe, S. J., Dickins, B., and Jolley, K. A. (2014). Cronobacter, the
cus, E. pulveris, and E. turicensis have been used as negative emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole
control cultures as they were regarded as close relatives. In genome sequence analysis. BMC Genomics 15, 1121 and references therein.
494 Emerging Foodborne Enteric Bacterial Pathogens
The well-known gastrointestinal bacterium Escherichia coli
includes a number of pathotypes defined according to their
clinical presentation or adherence pattern on Hep-2 cell line.
EAEC self-aggregate and form a biofilm on intestinal mucosa
cells (Hep-2 cell line) with a ‘stacked-brick’ adherence pheno-
type. The first EAEC infection case was described in 1987 in a
child with acute diarrhea in Lima, Peru. These days, EAEC is
estimated to be the second most common cause of traveler’s
diarrhea. Unconfirmed reports have linked EAEC with the
development of irritable bowel syndrome. EAEC is a heteroge-
neous cluster of E. coli strains, which is an important cause
worldwide of acute or persistent diarrhea in children and
adults. The reason for its inclusion in this article is that since
the late 1990s, EAEC has received increasing attention as a
cause of acute, often persistent, and watery diarrhea and
malnutrition in children and HIV-infected persons living in
developed countries.
EAEC outbreaks have been described in children and adults
in the United Kingdom and France. The carriage of the organ-
ism by children < 5 years of age was higher in those with a
history of diarrhea. Similarly in Brazil, EAEC was found to be
more frequently associated with diarrhea in children < 2 years
of age. There has been an increasing rise in the proportion of
childhood diarrheal cases in which EAEC are implicated, and
this indicates that EAEC are important emerging agents of
pediatric diarrhea. It is believed that EAEC not only may be
causing acute and persistent diarrheal disease but also may
be persisting in the human intestine subclinically, inducing
chronic inflammation in the absence of dysentery. This persis-
tent infection could result in chronic disruption of gut function
resulting in malnutrition and restricted childhood
development.
EAEC route of transmission can be through contaminated
food. In Italy, two consecutive EAEC outbreaks (affecting 24
individuals) were linked to contaminated unpasteurized
cheese. A study of Mexican tabletop sauces identified 44% of
sauces from Guadalajara (Mexico) contained viable EAEC cells,
compared to 0% of sauces in restaurants in Houston (the
United States). In the largest reported outbreak so far, 2697
(40.6%) Japanese children who consumed infected school
lunches had severe diarrhea, and EAEC was found in 10% of
cases. Serotyping of EAEC is not applicable in the diagnosis of
diarrheagenic E. coli infections. In the United Kingdom, 97
EAEC strains were serotyped to 40 different O types, and in
another study, 93 out of 143 EAEC strains could be serotyped
to 47 different serotypes. Finally, many of the EAEC strains
autoagglutinate and so are described as nontypable or O
rough.
EAEC pathogenesis involves three stages: (1) adherence to
the intestinal mucosa by aggregative adherence fimbriae and
adherence factors, (2) increased production of mucus that
enhances EAEC adherence to the surface of enterocytes, and
(3) the release of toxins and elicitation of an inflammatory
response, mucosal toxicity, and intestinal secretion. The best-
studied virulence factor is AggR. This is a transcription activator
carried on pAA, a large 60 MDa plasmid. AggR controls the
expression of fimbriae (adherence factors), a dispersin protein,
and at least two pathogenicity islands on the EAEC chromo-
some. Dispersin is an antigenic antiaggregative protein, which
is encoded by the aap gene in the pAA plasmid. It is regulated
by aggR, modulates fimbrial adhesion, and facilitates penetra-
tion of the microorganism through intestinal mucus by bind-
ing to LPS and altering the electrostatic properties of the EAEC
outer membrane surface. Although several other virulence
factors are detectable using PCR probes, none exhibit 100%
specificity to EAEC strains. Other putative virulence factors
include a yersiniabactin system, a complex carbohydrate-
specific lectin, enterotoxins, and cytotoxins. The large E. coli
O104 outbreak in 2011 was due to a hybrid EAEC.
Escherichia albertii
Description: Escherichia albertii, species closely related to E. coli.
Gram-negative, facultative nonmotile rods. The genus is a
member of the Enterobacteriaceae family.
Sources: Human feces, birds, animals, and environment.
Clinical presentation: Diarrhea.
Detection methods: No specific isolation procedures are avail-
able. May originally be identified by routine diagnostic
protocols as enteropathogenic E. coli (EPEC) or enteroh-
emorrhagic E. coli (EHEC).
Little is known about the host or geographic distribution of
E. albertii; however, it is carried by 1% of wild birds and is
associated with mass mortality events among birds in the
Northern Hemisphere and the cause of mortality in captive
birds and poultry. The author does not know of any confirmed
cases of foodborne infections due to this organism or even
isolation from food. Nevertheless, the organism has been
tentatively included in this article as an emerging enteric food-
borne pathogen based on its association with poultry and
misidentification with EPEC and EHEC in order to raise
awareness.
The recognition of Escherichia albertii as an emerging
human enteric pathogen typifies the value in reevaluating pre-
vious identification schemes and anomalies. The organism has
previously been misidentified as eae-positive Hafnia alvei, as
well as strains of eae-positive E. coli, E. coli serotype O86, EPEC,
and EHEC.
In 1991, clinical isolates of H. alvei were found to differ
from representative H. alvei strains by phenotypic and geno-
typic assays. This variation included the carriage of an intimin
gene homologous to the eae gene encoding for the attaching-
effacing phenotype of EPEC. Following the use of 16S rDNA
sequence analysis and DNA–DNA hybridization, the new
Escherichia species, Escherichia albertii, was proposed for the
previously eae-positive H. alvei strains. In addition to the pos-
session of intimin, E. albertii also produces a cytolethal dis-
tending toxin. Using MLST and virulence gene sequences (eae
and cdt), it is proposed that the E. albertii lineage includes
Shigella boydii (serotype 13) and other previously nontypable
clinical isolates. This lineage shared a common ancestor with
E. coli and Shigella pathogenic groups 28 million years ago
(mya), and also the E. albertii lineage was established before
the radiation of pathogenic E. coli and Shigella. In essence, E.
albertii is not a newly emerged pathogenic variant of E. coli–
Shigella, but a previously unrecognized pathogen, which was
confused with other more familiar, closely related organisms.
E. albertii strains are nonmotile, fermented D-glucose (with
gas), D-mannitol, and D-mannose, but does not ferment lactose

or other sugars. All strains are positive for the eaeA gene, but the
presence of other virulence-related genes is variable, namely,
cdtB, phoE, ehxA, and stx2f. Therefore, there is variability within
this lineage, which may cause confusion and hinder accurately
identifying E. albertii from other members of the Escherichia
genus. Although the number of accurately recorded outbreaks
due to E. albertii is uncertain, it is plausible that some outbreaks
have been misattributed to E. coli as shown in the reassessment
of a food poisoning outbreak of gastroenteritis.
Plesiomonas shigelloides
Description: Plesiomonas shigelloides is the only recognized spe-
cies in the genus Plesiomonas. Gram-negative, facultative
aerobic rods; oxidase-positive. The genus is a member of
the Enterobacteriaceae family.
Clinical presentations: Three forms of gastroenteritis, (i) a secre-
tory, watery type; (ii) an invasive, dysentery-like type; and
(iii) a subacute or chronic form, lasting between 2 weeks
and 3 months.
Sources: Freshwater and estuarine water. Wide range of hosts:
amphibians, birds, fish, and animals.
Detection methods: No specific isolation procedures are
available.
P. shigelloides is the only species in the genus Plesiomonas and is
the only oxidase-positive member of the Enterobacteriaceae
family. It is recognized as an emerging water- and foodborne
enteric pathogen and a major cause of traveler’s diarrhea in
China and Japan. The organism can cause three types of gas-
troenteritis: (i) a secretory, watery type; (ii) an invasive,
dysentery-like type; and (iii) a subacute or chronic form lasting
between 2 weeks and 3 months. There are additional reports of
extraintestinal infections: meningitis in neonates, bacteremia,
sepsis, and septic shock with high fatality rates. The natural
environment for the organism is freshwater and estuarine
water. It is also found in amphibians, birds, fish, and animals.
Outbreaks are generally related to the consumption of contam-
inated seafood (crabs, oysters, and fish) or untreated water.
The pathogenicity of P. shigelloides is poorly understood,
although there are reports of secreted toxins in vitro: cholera-
like toxin, thermostable and thermolabile toxins, b-hemolysins,
and cytotoxin complex. The somatic antigen of P. shigelloides
may also play a role in pathogenicity, since the gene encoding
the most common type, O17, shares almost complete identity
with the smooth antigen gene of Shigella sonnei. An acute food-
borne outbreak in Cameroon was postulated to be due to a
preformed toxin in the food, due to the short incubation period.
There is no specific medium for the direct isolation of
P. shigelloides. In general Enterobacteriaceae media, the organism
produces nonlactose-, nonsucrose-fermenting colonies. The
organism does not grow on thiosulfate–citrate–bile salts–
sucrose medium, but does grow on CIN medium (normally
used to isolate Yersinia and Aeromonas species), producing opa-
que colonies without a pink center indicating that mannitol is
not fermented. It has a minimum growth temperature of 8  C.
Providencia alcalifaciens
Description: Gram-negative rods. The genus is a member of the
Enterobacteriaceae family.
Emerging Foodborne Enteric Bacterial Pathogens 495
Clinical presentation: Traveler’s diarrhea.
Sources: Contaminated food and water.
Detection method: A selective medium has been formulated but
possibly not evaluated.
Providencia alcalifaciens is primarily recognized as possible
cause of traveler’s diarrhea in developing countries. But in
1996, there was a large outbreak of foodborne infection caus-
ing acute gastroenteritis, involving 290 patients, in Fukui,
Japan. No previously recognized enteropathogens were
detected in the fecal samples of the patients. However, PFGE-
indistinguishable P. alcalifaciens strains were recovered from 7
of 18 samples. Additionally, a specific antibody against the
isolated strain was found to be elevated in the patients’ sera.
In vitro virulence studies of the strains using the Caco-2 cell line
showed strains could invade human intestinal cells and fluid
accumulation in rabbit ileal loop experiments. Together, these
results indicate that P. alcalifaciens was probably the causative
agent of the outbreak.
A selective medium for the recovery of the organism from
feces has been published. But to the author’s knowledge, no
large-scale trials of method evaluations have been undertaken.
Shigella sonnei
Description: Gram-negative facultative aerobic rods. The
Shigella genus is a member of the Enterobacteriaceae family.
Clinical presentations: Dysentery, fever, and stomach cramps.
Sources: Water and food contaminated with feces and flies.
Detection methods: No specific isolation procedures are available.
Shigella spp. can be regarded as pathotypes of Escherichia coli
with the ability to invade the human gut mucosa and cause
dysentery. Infection is due to the ingestion of the organism via
fecally contaminated food or water and can be due to poor
personal hygiene by food handlers. S. sonnei is well known as a
primary cause of dysentery in developed countries and is now
emerging as a problem in the developing world. It is replacing
the more diverse Shigella species S. flexneri in areas that are
undergoing economic development and improvements in
water quality.
Whole genome sequence analysis shows that the current S.
sonnei population descends from the most recent common
ancestor <500 years ago. Evidence to date indicates the species
primarily diversified in Europe into four distinct lineages with
unique characteristics. This was followed by the spread and
establishment of a single, rapidly evolving, multidrug-resistant
lineage into Asia, Africa, and America, termed ‘pandemic line-
age III.’ This lineage is now a dominant cause of dysentery in
many endemic areas of the world.
The emergence of S. sonnei has been attributed to the acqui-
sition of virulence plasmid pINV B, encoding the Plesiomonas
shigelloides-related O antigen. This has been difficult to confirm
since the plasmid is easily lost during laboratory subculturing
prior to analysis. Similarly, it has been proposed that previous
exposure to P. shigelloides (via contaminated water) may offer
some protection from S. sonnei infection since the O antigens
are indistinguishable and cross-react. This could account for
the increased incidence in S. sonnei infections following
improvements in water quality due to the reduced passive
cross protection by exposure to P. shigelloides.
496 Emerging Foodborne Enteric Bacterial Pathogens
Ones to Watch
Antibiotic Resistance of Recognized Foodborne Bacterial
Pathogens
A detailed consideration of antibiotic resistance and their wide-
spread use in human and veterinary medicine, agriculture, and
aquaculture animal husbandry and veterinary usage are out-
side the scope of this article. Nevertheless, antibiotic-resistant
enteric foodborne pathogens are an emerging public risk. Anti-
microbial resistance has been described in well-known patho-
gens, some of which are foodborne: Salmonella, Campylobacter,
Shigella, and Vibrio spp., methicillin-resistant Staphylococcus
aureus, E. coli, and enterococci. The resistance of animal- and
food-associated bacteria to antimicrobial agents has been
repeatedly reported. Bacterial resistance inevitably develops to
each new class of antibiotics. A variety of different antimicro-
bial resistance phenotypes result from the acquisition of exter-
nal genes that can provide resistance to an entire class of
antimicrobials. These genes are frequently associated with
large transferable extrachromosomal DNA elements, plasmids,
on which there may be other mobile DNA elements such as
transposons and integrons.
Plasmids in the incompatibility group IncA/C are of con-
siderable interest with respect to multiple antibiotic resistance
in enteric pathogens of humans and animals. Although these
large, low-copy number plasmids have been known for over 40
years, they appear to be of increasing relevance in the spread of
antibiotic resistance. The plasmids have at least three hotspots
for the integration of mobile genetic elements. They were first
identified from multidrug-resistant Aeromonas hydrophila and
Vibrio spp. in cultured fish. This coincided with the use of
antibiotics for cultured fish. A survey of clinical isolates of
Salmonella newport from 1940 to 2000 revealed that IncA/C
plasmids and their multiresistance phenotype emerged after
1980, the reservoir being environmental bacteria, followed by
the acquisition of antibiotic gene modules according to anti-
biotic exposure. IncA/C plasmids which have acquired the
blaNDM-1 gene encoding the New Dehli metallo-b-lactamase
have been disseminated in clinical E. coli and K. pneumoniae.
Another issue with increasing antibiotic resistance is the
coresistance to microbiocides, such as triclosan and quaternary
compounds. It has been reported that exposure of Salmonella
enterica and Escherichia coli O157 to sublethal concentrations
of antibacterial agents contributed to their development of
adaptive resistance to both biocides and antibiotics. Benzalk-
onium chloride-resistant Salmonella enterica serovar Virchow
showed elevated resistance to chlorhexidine. E. coli O157
Table 5 Foodborne outbreaks investigated using whole genome sequencing, genomic epidemiology
Organism Source Size of outbreak
Salmonella Seven egg farms 193 cases
Typhimurium
Salmonella Spiced salami 300 people in 44 US states
Montevideo
E. coli O104 Bean sprouts >3600 infections and >40 deaths in Germany and >100 in
other countries
L. monocytogenes Ready-to-eat meat 22 deaths and at least 57 illnesses
1/2a products
acquired high levels of resistance to triclosan after only two
sublethal exposures and, when adapted, repeatedly demon-
strated decreased susceptibilities to various antimicrobial
agents, including chloramphenicol, erythromycin, imipenem,
tetracycline, and trimethoprim. However, the specific mecha-
nisms of such coresistance remain poorly understood.
Revelations from Whole Genome Sequencing
Clinical and food microbiology is moving from being culture-
dependent to culture-independent. This gives the promise of
earlier recognition of attributable organisms. In order to
achieve this, there needs to be (a) accessibility to centralized
information and (b) consistent interpretation of the DNA
sequence. From mid-2013, the FDA has started to sequence
100 000 foodborne pathogens, with 30 completed in Decem-
ber 2013. The genome sequence data will have open access and
are being deposited in the National Center for Biotechnology
Information and hence shared with other countries for inter-
national surveillance.
The major advantages of culture-independent testing are
that it is usually faster than culture-based methods and can
simultaneously provide subtyping information as required for
epidemiological studies and accessible for further analysis.
MLST can be predicted from the genome sequence and is not
limited to the conventional seven loci. BIGSdb has been imple-
mented for a number of bacterial pathogens such as Campylo-
bacter jejuni and Cronobacter spp. A number of retrospective
foodborne outbreaks have been studied using NGS although
as yet few in real time (Table 5).
Conclusions and Future Studies
Compared to clinical infectious diseases, the number of cur-
rently recognized foodborne pathogens seems small. In part,
this is due to general procedures of food production, which
over the centuries have been refined and self-proved effective
means of food preparation, for example, cooking, acidification,
and dehydration. However, with changes in sourcing of food
ingredients, large-scale food preparation practices, longer
storage, and changes in eating habits have ensured a continued
of food-related illnesses. The major organisms associated with
foodborne disease are bacteria due to the ease of isolation and
identification compared to viruses and fungi. However, with
improved global surveillance systems, as well as improved iso-
lation and identification methods, previously unrecognized
Comment References
Retrospective Hawkey et al.
Retrospective Allard et al. and
Lienau et al.
Real time Mellmann et al.
Retrospective Gilmour et al.

foodborne infectious organisms are being recognized. With a
global economy and transportation of food, the need to con-
tinue to attribute human infections to food vehicles is war-
ranted for their control. This article considers a range of viral
and bacterial enteric pathogens, which may be foodborne.
Some like Cronobacter are currently associated with one food
product, reconstituted infant formula, and was previously
unrecognized as a bacterial genus, whereas others such as Shi-
gella are far better understood. Some recently recognized enteric
pathogens are due to increased awareness (such as Cronobacter);
others are adaptations of existing pathogens. Selective pressures
due to the use of antibiotics will drive further changes in the
microbiota, which may have severe consequences yet in the
future. Being able to predict the future emergence of foodborne
enteric pathogens is not possible at this time because of their
diversity in virulence and pathogenicity properties, their ability
to adapt, the diversity of foods, and the variation in suscepti-
bility to infection by the human population. The best available
approach to recognizing the emergence of a foodborne enteric
pathogen emergence is through improved surveillance schemes
leading to prompt, informed, and appropriate level of control.
In part, this will be met by the expansion of genomic epidemi-
ology whereby cases and outbreaks are investigated using whole
genome sequencing.
The recognition, control, and monitoring of potential
enteric pathogens require a reliable and robust detection sys-
tem. It is probable that as newly described enteric pathogen is
studied, then its description and taxonomy are likely to change
as hitherto, it was poorly described and any strains in culture
collections could be the more easily recovered variants and
only a subpopulation of the taxonomic unit.
It is clear that the major challenge ahead is to establish
effective communication between public health, veterinary,
and food safety experts, which will bring together multidisci-
plinary skills and multipathogen expertise. Such collaboration
is essential to monitor changing trends in foodborne infec-
tions, in order to detect emerging pathogens and to predict
their risk to human health such that appropriate control mea-
sures can be implemented.
Emerging Foodborne Enteric Bacterial Pathogens 497
See also: Clostridium: Food Poisoning by Clostridium perfringens;
Clostridium: Occurrence and Detection of Clostridium botulinum and
Botulinum Neurotoxin; Clostridium: Occurrence and Detection of
Clostridium perfringens; Escherichia coli and Other Enterobacteriaceae:
Occurrence and Detection; Food Poisoning: Classification; Food
Poisoning: Epidemiology; Food Poisoning: Tracing Origins and
Testing; Foodborne Pathogens; Salmonella: Detection; Salmonella:
Properties and Occurrence; Salmonella: Salmonellosis.
Further Reading
Allard MW, Luo Y, Strain E, et al. (2012) High resolution clustering of Salmonella
enterica serovar Montevideo strains using a next-generation sequencing approach.
BMC Genomics 13: 32.
Forsythe SJ (2008) Other Gram-negative bacterial pathogens. In: Blackburn C and
McClure P (eds.) Foodborne pathogens: Hazards, risk analysis and control.
Cambridge: Woodhead Publishing.
Forsythe SJ (2006) Arcobacter. In: Motarjemi Y and Adams M (eds.) Emerging
foodborne pathogens. Cambridge: Woodhead Publishing.
Forsythe SJ (2010) The microbiology of safe food, 2nd ed. Chichester: Wiley-Blackwell.
Gilmour MW, Graham M, Van Domselaar G, et al. (2010) High-throughput genome
sequencing of two Listeria monocytogenes clinical isolates during a large foodborne
outbreak. BMC Genomics 11: 120.
Hawkey J, Edwards DJ, Dimovski K, Hiley L, Billman-Jacobe H, Hogg G, and Holt KE
(2013) Evidence of microevolution of Salmonella Typhimurium during a series
of egg-associated outbreaks linked to a single chicken farm. BMC Genomics
14: 800.
Lieneau EK, Strains E, Wang C, et al. (2011) Identification of a salmonellosis outbreak
by means of molecular sequencing. The New England Journal of Medicine
364: 981–982.
Mellmann A, Harmsen D, Cummings CA, et al. (2011) Prospective genomic
characterization of the German enterohemorrhagic Escherichia coli O104:H4
outbreak by rapid next generation sequencing technology. PLoS One 6: e22751.
Relevant Websites
www.pubMLST.org/cronobacter – Searchable (BLAST) repository of all published
Cronobacter genomes.