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A review of conventional detection and enumeration methods for pathogenic


bacteria in food

Article  in  Canadian Journal of Microbiology · December 2004


DOI: 10.1139/w04-080 · Source: PubMed

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883

REVIEW / SYNTHÈSE

A review of conventional detection and enumeration


methods for pathogenic bacteria in food
Kiev S. Gracias and John L. McKillip

Abstract: With continued development of novel molecular-based technologies for rapid, high-throughput detection of
foodborne pathogenic bacteria, the future of conventional microbiological methods such as viable cell enumeration,
selective isolation of bacteria on commercial media, and immunoassays seems tenuous. In fact, a number of unique
approaches and variations on existing techniques are currently on the market or are being implemented that offer ease
of use, reliability, and low cost compared with molecular tools. Approaches that enhance recovery of sublethally injured
bacteria, differentiation among species using fluorogenics or chromogenics, dry plate culturing, differentiation among
bacteria of interest using biochemical profiling, enumeration using impedence technology, techniques to confirm the
presence of target pathogens using immunological methods, and bioluminescence applications for hygiene monitoring
are summarized here and discussed in relation to their specific advantages or disadvantages when implemented in a
food microbiology setting.
Key words: food pathogen, detection, enumeration methods, food safety.
Résumé : Avec le développement continuel des nouvelles technologies moléculaires permettant la détection rapide et à
haut débit de bactéries alimentaires pathogènes, l’avenir des méthodes microbiologiques conventionnelles comme
l’énumération des cellules viables, l’isolation sélective de bactéries sur milieu commercial, et les essais immunologiques,
semble trouble. En fait, un certain nombre d’approches uniques et de variations de techniques existantes sont actuellement
sur le marché ou sont mises en application afin d’offrir une facilité d’usage, une fiabilité et un coût réduit par rapport
aux outils moléculaires. Cet article résume des approches augmentant la récupération de bactéries endommagées sous le
seuil de la létalité, qui distinguent les espèces d’intérêt à l’aide de profilage biochimique, qui permettent l’énumération
en utilisant la technologie d’impédance, des techniques qui confirment la présence de pathogènes à l’aide de méthodes
immunologiques et des applications de la bioluminescence pour le suivi hygiénique. Nous discutons des avantages et
des désavantages spécifiques à chacune des approches lorsque appliquées dans un contexte de microbiologie alimentaire.
Mots clés : pathogènes alimentaires, détection, méthodes d’énumération, sécurité des produits alimentaires.
[Traduit par la Rédaction] Gracias and McKillip 890

Introduction ment necessitates rapid assay results (Marriott 1999). High


throughput screening of an increasingly diverse array of
Of the more than 200 known diseases transmitted through both fresh and processed foods requires that pre- and
food (in the United States) annually, approximately 8000 postharvest food safety practices be dynamic, sensitive, spe-
deaths are recorded from over 75 million reported cases. cific, as well as versatile and cost-effective for large sample
Surveillance and detection of food-associated pathogenic numbers. No single assay or method will address all of these
bacteria are complicated by emerging strains not routinely criteria optimally, particularly culture-based techniques.
encountered and the unclear route of transmission of many However, these methods do offer certain advantages for
bacteria (Mead et al. 1999). With regard to hygiene monitor- monitoring microbiological quality of foods, including cost-
ing, Hazard Analysis Critical Control Point (HACCP) pro- effectiveness, ease of use, and familiarity among users, as
grams are designed to monitor critical control points for described herein.
potential contamination during food processing. Rigorous
adherence to sanitary practices in a food-processing environ- The last several years have revealed a new generation of
innovative methods and technologies for pathogen enumeration
Received 8 March 2004. Revision received 11 June 2004. and detection in contaminated foods. Molecular approaches
Accepted 30 June 2004. Published on the NRC Research that entail near-time or real-time bacterial detection are rapid,
Press Web site at http://cjm.nrc.ca on 6 January 2005. sensitive, and specific for the target pathogen (Smith et al.
2000; Feng 2001; Rijpens and Herman 2002) or one of the
K.S. Gracias and J.L. McKillip.1 Department of Biology, varied virulence determinants of that pathogen (Fig. 1). The
Ball State University, Muncie, IN 47306, USA.
reliability, cost, and novelty of some of these methods may
1
Corresponding author (e-mail: jlmckillip@bsu.edu). still limit their adoption and scale-up practicality in a food
Can. J. Microbiol. 50: 883–890 (2004) doi: 10.1139/W04-080 © 2004 NRC Canada
884 Can. J. Microbiol. Vol. 50, 2004

Fig. 1. Targets or features of interest on a general food- Fig. 2. Agar overlay schematic that allows for recovery of
associated pathogenic or spoilage bacterium that are exploited sublethally injured bacteria from food samples using a
for selective isolation, differential media design, or nonselective basal layer (pour plated). Incubation/recovery in this
immunoassays. A few representative virulence determinants are medium for a few hours followed by overlay with the selective
indicated. medium of choice increases the sensitivity of a viable cell count
compared with plating directly onto the selective medium.

dard methods agar, known as the aerobic plate count (APC)


or standard plate count (SPC), is worthy of discussion in
terms of the many offshoot methods that have been designed
to improve upon it.
Increased sensitivity of SPC/APC has been achieved using
a selective agar overlay approach designed to recover a
larger proportion of bacteria from food matrices (compared
with straight plating onto selective media) following
sublethal stressors experienced during processing steps, such
as heat, cold, acid, or osmotic shock (Harrigan 1998; Speck
et al. 1975). Detecting these sublethally damaged bacteria is
of vital significance in the food industry, since the selective
agar overlay technique aids in the resuscitation of bacterial
processing scenario, obligating many laboratories to rely more cells from food, which may still be viable and pose a threat
on traditional microbiological methods for quality control/quality to human health as a result. In this approach, the inoculum is
assurance of foods (Jaykus 2003). These methods are essen- pour-plated with a basal layer of trypticase soy agar, or compa-
tially designed around the recovery and (or) enumeration of rable nonselective medium, and incubated for 1–4 h. During
viable bacteria in the food matrix. Familiarity and accep- this time, sublethally injured bacteria are given a chance to re-
tance among food processors with methods such as the stan- cover and begin growing prior to an overlay with the appropri-
dard plate count or selective and differential media for ate selective medium (Hurst 1977; Ray 1986) (Fig. 2). This
bacterial isolation and detection as well as commercially approach has been demonstrated predominately with enteric
available biochemical profiling systems for identification of bacteria such as Escherichia coli and Salmonella typhimurium,
specific food isolates continue to serve as the basis in many although it has shown promise when modified to enumerate
food microbiology laboratories that lack the necessary re- Gram-positive pathogens such as Listeria monocytogenes,
sources to utilize some of the emerging molecular-based Bacillus cereus, and enterotoxigenic Staphylococcus aureus
technologies. Novel means of detecting and enumerating (Golden et al. 1988; Kang and Siragusa 1999, 2001; Kang
bacteria of interest are continually being reported, and al- and Fung 1999, 2000; Hara-Kudo et al. 2000; Hajmeer et al.
though the majority entail molecular biological approaches, 2001; McKillip 2001; Wu et al. 2001; Sandel et al. 2003).
many fall into the category of conventional techniques. This Slight variations on the resuscitation technique have been
review will present a comparative overview of many con- employed, including a membrane or solid-support-based
ventional approaches in food microbiology for enumeration transfer of E. coli O157:H7 from the trypticase soy agar re-
and (or) detection of bacteria in foods. covery medium onto sorbitol MacConkey agar, which has
been shown to improve recovery of sublethally injured cells
Background on traditional microbiological by a factor of 3 log10 (Blackburn and McCarthy 2000).
methods in food Pre-enrichment of the suspect food sample in a
nonselective or selective broth culture is another strategy to
Standard/aerobic plate counts and relevant variations increase numbers of injured but viable target bacteria to
Detection of viable bacteria is traditionally performed by dectectable levels (Zhao and Doyle 2001), although depend-
implementing a means of culturing/measuring growth of in- ing on the food product being analyzed, the enrichment
dividual microorganisms. Hundreds of commonly used bac- step(s) may require an additional 8–24 h before enumeration
teriological media in the food industry are met with unique or detection can be completed. In the above study applied to
ways of applying them to best monitor for spoilage and (or) heat-injured pathogens, enrichment in the appropriate selec-
pathogenic bacteria in food (Harrigan 1998). The use of rou- tive media was essential to obtain densities of at least 4 log10
tine nonselective media such as trypticase soy agar or stan- to confirm the presence of the pathogen using immunoassay.

© 2004 NRC Canada


Gracias and McKillip 885

Therefore, despite the advantages of these familiar culture posed to long-wave ultraviolet light (Alonso et al. 1998,
methods in detecting viable bacteria, such as ease of use and 1999; Berg and Fiksdal 1988). Enterohemorrhagic E. coli
low cost, assay sensitivity is still relatively low compared O157:H7 is unique in that it is methylumbelliferyl-β-D-
with alternative methods (e.g., molecular-based approaches glucoronidase negative, whereas virtually all other coliforms
such as PCR). In PCR, the enrichment step is crucial in in- are positive for this enzyme (Hartman 1989). This important
creasing bacterial cell numbers, prior to nucleic acid extraction distinction is useful for confirming enterohemorrhagic
(thereby obtaining higher yield and good quality DNA) and E. coli O157:H7 presence in water or food samples (al-
primer-specific amplification, in the highly sensitive and though additional steps are also necessary) (Bettelheim
quick detection of bacterial contaminants in food matrices. It 1998) as growth on solid agar or liquid broth media (Manafi
is important to note that an SPC is done both before and af- 2000).
ter enrichment to enumerate the bacteria in the food sample Chromogenic substrates such as 5-bromo-4-chloro-3-indolyl-
prior to PCR (McKillip et al. 2002; Nakano et al. 2004). β-D-galactopyranoside (XGAL) are useful for coliforms such as E.
Therefore, the time it takes to obtain data prevents the SPC/APC coli as well and produce a distinctive blue colony when this
technique from being considered among the “rapid methods”. compound is cleaved by β-galactosidase produced during cell
In many cases, the food microbiologist may find it neces- growth, particularly if 1-isopropyl-β-D-thiogalactopyranoside is
sary to implement a bacterial concentration or immobiliza- added to the medium to enhance activity of this enzyme.
tion step immediately prior to plating to sequester cells Other fluorogenic or chromogenic media for coliforms are
within an otherwise polluted and heterogenous food matrix. available under various trade names, including Rainbow
Several general approaches have been described for selective agar, BCM O157:H7 (and other coliforms), CHROMagar,
removal of cells from a fluid food system, and each offers and Colilert, all of which have been applied in the clinical or
the potential to greatly increase detection and differentiation food industry to distinguish key species based on coloration
of target bacteria prior to enumeration (Sharpe 1997). Immuno- of suspect colonies.
magnetic separation (IMS) is one such technique that em- For Gram-positive pathogens, fluorogenic and chromogenic
ploys antibodies linked to magnetic beads that are placed in media are also readily available with similar substrates and
the food slurry and allowed to interact with specific epitopes indicator systems. Staphylococcus aureus CHROMagar may
on the bacterial cell surface (Fig. 1). The material is then be supplemented with antibiotics to cross-check for methicillin-
exposed to a magnetic field that essentially pulls the bacteria resistant S. aureus, for example, in clinical applications.
out of suspension for plating or molecular-based (e.g., PCR) Bacillus cereus, as a food-associated pathogen of growing
detection/enumeration (Jinneman et al. 1995; Tomoyasu concern, may produce a phosphatidylinositol-specific phos-
1998). One such commercial application using IMS, pholipase C, the key enzyme reacting with 5-bromo-4-
DynabeadsTM (Dynal Botech, Oslo, Norway), has proven ef- chloro-3-indoxyl-myoinositol-1-phosphate, giving distinctive
fective for isolation of a variety of food pathogens, includ- turquoise colonies. Analogous indicator systems are
ing L. monocytogenes, E. coli O157:H7, and Salmonella spp. commercially available for Clostridium perfringens, L.
(Hsih and Tsen 2001; Hudson et al. 2001; Ogden et al. 2001; monocytogenes, and Bifidobacterium spp. (Baumgart et al.
Chandler et al. 2001). 1990; Restaino et al. 1999; Chevalier et al. 1991).
An effective alternative to IMS is the use of metal hydroxide Dry plate culturing (e.g., 3M Petrifilm or similar) is yet
based bacterial concentration, which may be used either bound another widely used means of assessing microbiological
to a solid support through which the food slurry passes or quality of a wide range of foods for coliforms, aerobic
applied directly to a liquid food matrix or dilution in floc mesophilic bacteria, psychrotrophs, and staphylococci
form. Titanous, hafnium, or zirconium hydroxide suspen- (Blackburn 1996; Linton 1997; Silbernagel and Lindberg
sions interact with the opposing charge of the bacterial cell 2001; Ellis and Meldrum 2002). This system consists of
(whether viable or dead) and may be separated using low-speed multiple layers of plastic film encasing a dehydrated disk of
centrifugation, resuspended, and directly plated (or used for the appropriate medium. Typically, a single sheet of plastic
molecular-based downstream detection assays). Like IMS, is aseptically peeled back and 1 mL of inoculum is used to
metal hydroxide based concentration has been demonstrated rehydrate the medium while the film is reapplied and
successfully for many common food-associated bacterial patho- pressed flat. In some types of rehydratable films, gas pro-
gens and is useful for removal and detection of spores as duction (e.g., from Enterobacteriaceae) may be detected as
well (Lucore et al. 2000; McKillip et al. 2000; Cullison and bubbles in the film following incubation. Dry media culture
Jaykus 2002; Jaykus 2003). plates have been applied in settings ranging from predicting
For selective isolation and differentiation of food-associated shelf life and monitoring the microbiological quality of milk
spoilage and pathogenic bacteria of interest, a variety of (Hughes and Sutherland 1987; Phillips and Griffiths 1990)
chromogenic and fluorogenic culture media are available. In- to assessing surface contamination of meat and poultry
corporation of enzyme substrates into selective media may (Guthrie et al. 1994; Park et al. 2001; Erdmann et al. 2002)
expedite (or eliminate) followup biochemical confirmation and constitute an AOAC-approved method in food micro-
of bacterial identity. Fluorogenic enzyme substrates consist biology for quality control. Owing to their small size,
of a sugar or amino acid conjugated to a fluorogen (Manafi Petrifilm plates are convenient for larger sample numbers
1996, 2000). A commonly used example, methylumbelliferyl, common in quality control laboratories and require less
has been employed in a wide variety of media and other de- space in a typical incubator but possess the same limitations
tection formats for coliforms (e.g., E. coli O157:H7). When as standard plate counting in terms of poor sensitivity and
cleaved by enzymes produced from specific target species, a the likelihood of encountering false-negative results from
blue fluorescence is observed when suspect colonies are ex- bacteria that may be sublethally injured, precluding accurate

© 2004 NRC Canada


886 Can. J. Microbiol. Vol. 50, 2004

enumeration from suspect foods. This and other methods for must operate under the assumption that such observations are
food-associated pathogen detection are summarized in Feng likely the rule rather than the exception and design and imple-
(1998). ment detection methodologies with this in mind. Regardless,
the myriad of commercially available kit/strip-based bio-
Other means of measuring cell growth chemical systems allow for confirmation of isolated bacteria
from food, particularly during the development of faster and
Impedance microbiology more sensitive molecular assays. The utility and evolution of
The use of the impedance allows for detection of microbes many of these miniaturized biochemical systems have been
directly through metabolite accumulation in surrounding reported (Cox et al. 1987; Dziezak 1987; Fung et al. 1988;
substrate or indirectly by carbon dioxide liberation (Silley Feng 1996, 1997, 1998; Shi and Fung 2000).
and Forsythe 1996; Marshall 1999). Direct impedance detec- As is common with identification strategies, many of the
tion is measured by the increase in the conductivity of the rapid kit-based systems commercially available were first in-
medium as a function of continually accumulating organic troduced in the clinical arena and were then eventually
acids, ammonium ions, and other compounds that are pro- adapted for use in food microbiology (Stager and Davis
duced from growth of a pure isolate. Whether direct or indi- 1992). The majority of the biochemical test kits currently
rect measurements are used, the time required for detectable sold assess fermentation of a battery of carbohydrates via
changes to occur depends on inoculum size, although detec- pH indicators and (or) specific amino acid or alternative sub-
tion limits here are theoretically a single cell, if conditions strate utilization. Most are designed for the differentiation
are permissible for growth. Conductance assays are widely and putative identification of Gram-negative bacteria, although
used in food microbiology for prediction of shelf life and a a few are sold for use on Gram-positives such as staphylo-
variety of bacterial growth modeling studies for specific cocci and Bacillaceae, although with greater variability
pathogens, including E. coli (Madden and Gilmour 1995; (Feng 2001; Murtiningsih 1997).
Edmiston 1998, 2000) and Campylobacter spp. (Moore and Each of these systems requires a pure culture for inocula-
Madden 2002). This technique requires specialized instru- tion and 16–24 h for incubation to obtain results. If used
mentation with significant up-front costs, however, and ne- with a standardized inoculum, accuracy of identification
cessitates the establishment of stringently reproducible may exceed 95%, particularly if one uses some of the latest
growth curve profiles of isolated strains under each tempera- kits on the market that are compatible with instruments de-
ture or culture condition of interest (Duran and Marshall signed to facilitate data acquisition and quantitation (Feng
2002). Variability may ensue from different food matrices 1996, 1998). However, the higher sample throughput af-
containing inconsistent levels of interfering organic material forded by this automatability increases cost significantly.
and, as with the SPC, stressed bacteria may introduce an ad- Commercially available miniaturized assays are overviewed
ditional element of variability into experimental runs, mak- in Russell et al. (1997) and in tabular format in Feng (1998).
ing reproducibility difficult to achieve. Once impedance
curves are established for specific isolates under standard Molecular-based semi-automated detection
sample preparation regimes, high throughput is possible with formats
relative ease.
Immunoassays
Miniaturized assays Among the widely accepted molecular methods in use for
Frequently, bacteria isolated from contaminated food are a battery of food pathogens is the enzyme-linked immuno-
identified to the species level after growth on (or in) the ap- sorbent assay (ELISA), which potentially offers much greater
propriate selective medium. Selective enrichment steps in specificity compared with SPC owing to the antibody–target
broth are sometimes employed to increase the density of a interaction (although contaminants and food matrix debris
target microbe or population suspected to be present. As may interfere). This process essentially consists of the addi-
mentioned above, this regime is both time- and labor- tion of the suspect antigen (food slurry or diluted extract) to
intensive and may not directly correlate with the presence of the sample wells in a microtiter plate containing a (primary)
pathogenic strains of interest if one simply relies on match- antibody with specificity to the target molecule. This mole-
ing the biochemical profile of the food isolate with a data set cule may be a component of the pathogen, such as a cell or
from a type strain. Since bacterial virulence factors may be flagellar antigen, or a product of the bacteria (e.g., enterotoxin)
shared among a wide variety of species, or conversely may (Notermans and Wernars 1991). Following an incubation step,
be absent in an otherwise correctly identified strain, the no- unbound material is rinsed away and the secondary anitibody
tion of using species identification as a hallmark of obliga- is added to form a “sandwich” of the antigen between the 2
tory pathogenicity is an obsolescent design strategy. For antibody molecules. After a second rinse, the assay is devel-
example, the flagship food-associated pathogen within oped per the conjugate or tag bound to the secondary anti-
Bacillaceae, B. cereus, frequently produces enterotoxins that body (Fig. 3). If serial dilutions of the suspect antigen (e.g.,
elicit toxicoinfection-related illness (Granum and Lund food sample) are made, one may glean relative quantitative,
1997; McKillip 2000). Of course, not all B. cereus strains high-throughput data if a spectrophotometer with microtiter
are enterotoxigenic, and many species outside the B. cereus plate capabilities is employed for data collection. ELISA has
phylogenetic group may harbor enterotoxin genes and express been successfully used to detect either whole-cell antigen
them in varied growth environments (Hoult and Tuxford targets or products (e.g., virulence determinants) of pathogens
1991; Damgaard 1995; Beattie and Williams 1999; Pruß et such as Salmonella spp., E. coli O157:H7, Campylobacter
al. 1999; Phelps and McKillip 2002). Food microbiologists spp., B. cereus, and L. monocytogenes, among others (Peplow

© 2004 NRC Canada


Gracias and McKillip 887

Fig. 3. Schematic of ELISA for high-throughput screening of include steps to either segregate microbial from somatic
food pathogens using any one of a number of target antigens. A ATP (filtration step in the protocol) or destroy the somatic
bound capture antibody may be used to immobilize or remove ATP so that all that remains in the sample is that that is as-
the target microbe or molecule from a heterogeneous matrix such sociated with microbial contaminants, although these steps
as a food slurry; following a rinse step, a labeled secondary anti- extend assay time and decrease sensitivity.
body is added, and detection ensues via an enzyme–substrate In the ATP bioluminescence approach, luciferase is added
(e.g., colorimetric) reaction. Alternatively, the secondary antibody to a sample, along with luciferin, in a magnesium-containing
may be conjugated to a fluorophore and read as fluorescence fol- buffer. As the luciferin is oxidized to oxyluciferin, the pho-
lowing excitation. tons of light emitted may be measured using a luminometer.
Once a standard curve is established with dilutions of bacte-
ria at known densities, the level of contamination may be as-
sessed in the food sample or on the contact surface (Poulis et
al. 1993; de Boer and Beumer 1999). Although ATP assays
do not require an enrichment step, the sensitivity is typically
on the order of 104 CFU/mL. Bioluminescence lends itself
well to rapid spot monitoring, as the results are obtained in
less than 15 min (Feng 2001). This technique has been used
on a diverse array of foods, including raw and pasteurized
dairy products (Webster et al. 1988; Kyriakides 1992;
Brovko et al. 1999; Niza-Ribeiro et al. 2000; Samkutty et al.
2001), meat and poultry products (Bautista et al. 1994, 1995;
Siragusa and Cutter 1995; Chen 2000), beer (Dowhanick
et al. 1999; Chen et al. 2001; Valdivieso-Garcia et al. 2001; and Sobczak 1994), and fruit (Ukuku et al. 2001).
Daly et al. 2002; de Paula et al. 2002; Yeh et al. 2002;
Bolton et al. 2002), in a more user-friendly format than re- Perspectives
verse passive latex agglutination assays (explained below).
ELISA is automatable, however, and is convenient for large In order for any conventional or molecular-based detec-
sample numbers with relative ease. Despite these advan- tion format to be a feasible tool in the food industry for hy-
tages, ELISA methods may still suffer in terms of desired giene monitoring or quality control, it must demonstrate
sensitivity, with a typical detection limit of 104 CFU/mL, reproducible sensitivity (ability to detect target cells or mol-
depending on the food being analyzed (Cox et al. 1987; ecules at very low levels), marked specificity (ability to ex-
Hartman et al. 1992). hibit positive results in a high background of nontarget
A less quantitative means of confirming the presence of a molecules or cells), speed in obtaining results, low cost per
pure culture of a specific pathogen following isolation could assay, acceptability and ease of use by the scientific commu-
entail the use of reverse passive latex agglutination. This nity and food microbiology laboratory staff, and standard-
rapid test is performed by mixing a suspension of test cells ized protocols and data interpretation (Fung 2002; Malorny
(usually following enrichment) with sensitized latex beads et al. 2003). Since no single approach satisfies all or even
containing antibodies specific for the target pathogen under most of these criteria, the user must prioritize the features of
study. After several minutes, visible clumping is observed in each available format against the needs of the facility and
a positive reaction compared with control samples. This pro- implement the most practical method(s) accordingly.
cedure is typically performed from components sold com-
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