Article 1
Article 1
Article 1
Review
A Review of Carbapenem Resistance in Enterobacterales and Its
Detection Techniques
Oznur Caliskan-Aydogan 1,2 and Evangelyn C. Alocilja 1,2, *
Abstract: Infectious disease outbreaks have caused thousands of deaths and hospitalizations, along
with severe negative global economic impacts. Among these, infections caused by antimicrobial-
resistant microorganisms are a major growing concern. The misuse and overuse of antimicrobials
have resulted in the emergence of antimicrobial resistance (AMR) worldwide. Carbapenem-resistant
Enterobacterales (CRE) are among the bacteria that need urgent attention globally. The emergence
and spread of carbapenem-resistant bacteria are mainly due to the rapid dissemination of genes that
encode carbapenemases through horizontal gene transfer (HGT). The rapid dissemination enables
the development of host colonization and infection cases in humans who do not use the antibiotic
(carbapenem) or those who are hospitalized but interacting with environments and hosts colonized
with carbapenemase-producing (CP) bacteria. There are continuing efforts to characterize and
differentiate carbapenem-resistant bacteria from susceptible bacteria to allow for the appropriate
diagnosis, treatment, prevention, and control of infections. This review presents an overview of the
factors that cause the emergence of AMR, particularly CRE, where they have been reported, and then,
it outlines carbapenemases and how they are disseminated through humans, the environment, and
food systems. Then, current and emerging techniques for the detection and surveillance of AMR,
primarily CRE, and gaps in detection technologies are presented. This review can assist in developing
Citation: Caliskan-Aydogan, O.; prevention and control measures to minimize the spread of carbapenem resistance in the human
Alocilja, E.C. A Review of ecosystem, including hospitals, food supply chains, and water treatment facilities. Furthermore,
Carbapenem Resistance in the development of rapid and affordable detection techniques is helpful in controlling the negative
Enterobacterales and Its Detection
impact of infections caused by AMR/CRE. Since delays in diagnostics and appropriate antibiotic
Techniques. Microorganisms 2023, 11,
treatment for such infections lead to increased mortality rates and hospital costs, it is, therefore,
1491. https://doi.org/10.3390/
imperative that rapid tests be a priority.
microorganisms11061491
Academic Editors: Nadezhda Keywords: antibiotic resistance; carbapenem resistance; carbapenem-resistant Enterobacterales (CRE);
Fursova, Olga Khokhlova and carbapenemases; detection technology; surveillance
Angelina Kislichkina
and a cost of EUR 1.5 billion in health expenditures each year [4]. In accordance with
recent estimates, infections by antimicrobial-resistant microorganisms will annually result
in 10 million deaths, along with USD 100 trillion in costs, by the year 2050 [7]. The
problem of AMR is particularly urgent due to the high presence of unregulated antibiotics
in the market [1,3,8]. The misuse and overuse of antibiotics enable the emergence and
spread of resistance in bacteria, leading to more difficulty in controlling and treating such
infections [5].
for adding new genes into the bacterial chromosome and are mostly carried in plasmids,
increasing the horizontal mobility of the antibiotic-resistant genes [13,15,17].
into the bacterial chromosome and are mostly carried in plasmids, increasing the horizontal
mobility of the antibiotic-resistant genes [13,15,17].
1.2. Factors Converging Emergence and Transmission of Antibiotic Resistance
The development
1.2. Factors of antibiotic
Converging Emergence andresistance
Transmission worldwide
of Antibioticis increasing
Resistance due to the misuse
and The
excessive use of antibiotics and antifungals, global
development of antibiotic resistance worldwide is increasing trade networks,due medical
to thetourism,
misuse
poorexcessive
and sanitation useconditions,
of antibioticsimproper waste management
and antifungals, global trade systems, and urbanization
networks, medical tourism, [21–
26]. Remarkably, the overuse and misuse of antibiotics in healthcare,
poor sanitation conditions, improper waste management systems, and urbanization [21–26]. veterinary medicine,
agriculture, the
Remarkably, andoveruse
aquaculture and their
and misuse release to the
of antibiotics environment
in healthcare, contribute
veterinary to the emer-
medicine, agri-
gence and spread of AMR [21,23–26]. Significant sources of antimicrobial-resistant
culture, and aquaculture and their release to the environment contribute to the emergence bacte-
ria include
and spread of healthcare settings Significant
AMR [21,23–26]. and the environment. AMR can be transmitted
sources of antimicrobial-resistant through
bacteria in-
contact
clude with people,
healthcare animals,
settings andenvironment.
and the contaminatedAMR watercan or foods [27]. In addition,
be transmitted throughintestinal
contact
commensal
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animals, have been reportedwater
and contaminated as a or
significant
foods [27]. reservoir of antimicrobial-re-
In addition, intestinal com-
sistant bacteria
mensal bacteria and
havegenes
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reportedDue as atosignificant
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prior use theoffecal carriage the
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animal,
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their emergence example,
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of human fecalworldwide
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ple, animal
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worldwide during In animal
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ment (soilcause
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[1]. Thus, wastewater
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Thus, population-collected
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health-
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Due practices on WWTP
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status and practices
sludge, manure, sediment, and reclaimed water result in their accumulation and spread
on WWTP systems, contaminated urban wastewater, sewage sludge, manure, sediment,
in the
and environment
reclaimed water and community
result [11,26]. As seen
in their accumulation in Figure
and spread 1, everything
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Microorganisms 2023, 11, 1491 4 of 26
acquire structural changes in penicillin-binding proteins (PBPs), (2) show a decrease or loss
of specific outer membrane porins that filter carbapenems from reaching their site of action,
(3) activate the efflux pumps to remove the antibiotics and regulate the intramembrane
environment, and (4) acquire β-lactamases and carbapenemases to degrade or hydrolyze
carbapenems and other β-lactam antibiotics (e.g., penicillins and cephalosporins) [32–34,41].
In addition, carbapenem resistance can be acquired by a combination of CTX-M (activity
against cefotaxime) and AmpC enzymes, allowing low-level carbapenem resistance. Fur-
ther, the combination of the β-lactamase expression and porin gene mutations is associated
with high-level carbapenem resistance, attenuating therapy responses [47].
Overall, CRE can become resistant through chromosomal mutations in the porin gene
(non-carbapenemase-producing CRE) and/or the production of carbapenem hydrolyzing-
enzymes (carbapenemase-producing (CP) CRE) [41]. The presence or expression of the
gene coding carbapenemase is usually sufficient for carbapenem resistance, covering
30% of CRE. Thus, CP-CRE is a subset of all CRE [22,41]. These genes are often on
mobile genetic elements, leading to their rapid spread and resulting in infections and
colonization [1,14,41,48]. Many CRE-colonized individuals do not develop infections;
however, they can still spread the bacteria [41]. Similarly, the transfer of genetic elements
can occur in the food chain and the environment [1,14,41]. Therefore, routine tests for
these carbapenemases through the Antibiotic Resistance Laboratory Network and CDC
laboratories are conducted to prevent and control their emergence and spread [41].
2.1. Carbapenemases
A large variety of carbapenemases have been classified into three groups: Ambler
Classes A, B, and D β-lactamases, based on hydrolytic and inhibitor profiles using active
catalytic substrates of serine or zinc [13,23,32,34,49]. The characteristics of the three most
common classes of carbapenemases are detailed and listed in Table 1 [23,49].
Class A enzymes, serine β-lactamases, hydrolyze a broad variety of β-lactam an-
tibiotics, including carbapenems, cephalosporins, penicillin, and aztreonam [49]. These
enzymes were identified as chromosomally encoded and plasmid-encoded types [49]. Some
of the chromosomally encoded genes are NmcA (not metalloenzyme carbapenemase A),
SME (Serratia marcescencens enzyme), IMI-1 (imipenem hydrolyzing β-lactamase), and
SFC-1 (Serratia fonticola carbapenemase-1). The plasmid-encoded genes are KPC (Kleb-
siella pneumoniae carbapenemase), IMI (Imipenem-hydrolyzing beta-lactamase), and GES
(Guiana extended spectrum) [23,32]. Among these, the KPC type is the most prevalent
enzyme and causes outbreaks in many Asian, African, North American, and European
countries [23,32]. KPC gene is mainly located within a 10-kb length, mobile transposon
Tn4401, frequently established on conjugative plasmids. The link of blaKPC with plasmids
and transposons assists in intraspecies gene transfer and the dissemination of the gene [50].
Several KPC variants have rapidly increased, and 84 KPC alleles have been recorded in
the GenBank database [51]. Of these, KPC-2 and -3 are the most common enzymes world-
wide, and 22 KPC variants have also conferred ESBL-, CTX-M-, or ceftazidime-avibactam
(CZA)-resistance in their gene position. For example, the KPC-2 gene was carried on
the NTEKPC -Ib transposon on plasmids with a 15-bp insertion, which also harbored the
resistance gene, CZA resistance [47,51]. Overall, KPC types are mostly found in Klebsiella
pneumoniae, Klebsiella oxytoca, E. coli, and Serratia marcescens, as well as in Enterobacter,
Salmonella, and Proteus species [13,23,32]. Their rapid spread and diverse variants severely
threaten human health and impact therapeutic efficacy [13,32,51].
Class B enzymes are known as Metallo-β-lactamases (MBL) since they utilize metal
ions (usually Zinc) as a cofactor to attack the enzyme’s active site (β-lactam ring). There
are 10 types of MBLs; the most important ones include New Delhi Metallo-beta-lactamase
(NDM), Verona Integron-Encoded Metallo-beta-lactamase (VIM), and Imipenemase
(IMP) [23,32,41,52]. They hydrolyze all current β-lactam antibiotics, except for monobac-
tams (e.g., aztreonam) [53]. IMP was first reported in Japan in S. marcescens in the early
1990s [13], and over 85 sequence variants have been described [53]. IMP variants are found
Microorganisms 2023, 11, 1491 6 of 26
Table 1. The most common carbapenemases in bacteria with their gene location [23,49,53].
meropenem disk on Mueller Hilton Agar (MHA) that is pre-inoculated with susceptible E.
coli. The plates are incubated overnight, and the cloverleaf-like zone is observed for CP
isolates. The use of this method was recommended by CLSI in 2009. It has good sensitivity
for other carbapenemases (VIM, IMP, and OXA-48), although its performance in detecting
NDM enzymes was found to be lower [108,110]. Overall, its sensitivity and specificity were
found to be 69% [110] and 93–98% [107], respectively.
The carbapenemase inactivation method (CIM) has been recently introduced by
CLSI (2016) with higher accuracy and accessibility [107,108,111]. This method is initiated
by a suspension of bacteria in a broth and incubation with a meropenem disk (2–4 h); if the
isolate produces the enzymes, the meropenem in the disk is degraded. The disk in the broth
can then be placed on MHA streaked with susceptible E. coli and incubated, which detects
carbapenemase activity with no zone or a narrow zone diameter of <19 nm [107,108,111].
This method showed high concordance with results obtained by a PCR test, which is used
in many clinical and public health laboratories [107,108]. The sensitivity and specificity of
the CIM method were over 95% [107,111].
Specific media have also been designed for CP strain screening [32,112,113]. For
example, Chromogenic Media and Brilliance CRE Agar are used for the initial detection
of CRE strains in colonized and infected patients, with 76.5% sensitivity. CHROM agar
KPC is used to screen for KPC and VIM-producing Enterobacteriaceae, but it can detect
high-level resistance with 43% sensitivity. SUPERCARBA medium is mainly used for
KPC and OXA-48 producers and is applicable to detect low-level resistance with higher
sensitivity (96.5%) [112–114]. ID Carba and Colorex KPC media were designed for CP
Enterobacteriaceae [112]. All these selective media are directly applicable to patient samples;
however, they have lower specificity (>50%) depending on the enzyme type [112,114,115].
The mentioned culture-based methods are cost-effective and widely applicable. Among
these methods, the CIM has a higher sensitivity and specificity in identifying and typing
carbapenemases. However, they are labor-intensive and require time-consuming steps
to isolate pure cultures, taking days to weeks to determine the resistance profile of the
suspected bacteria [99,102,103].
sure the growth of pure bacteria in the presence of antibiotics for rapid testing [99,103]. An
ultraviolet (UV) spectrophotometric method was developed to measure the carbapenem
imipenem hydrolysis activity of CP bacteria [121]. Lastly, bioluminescence-based detection
assays (BCDA) have also been developed for CP bacteria based on adenosine triphosphate
(ATP) level differences in culture media. Such assays are rapid (<2.5 h) and accurate, with
higher specificity and sensitivity [122]. However, the applicability of this technique in
matrices is low due to reduced sensitivity [108,121–123].
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-
TOF MS) in optical techniques has recently become popular for identifying pathogens
and resistant bacteria due to its distinct fingerprint spectra [104,118]. To determine the
antimicrobial resistant profile in pathogens, MALDI-TOF MS identifies (1) the antimicrobial-
resistant clonal group (e.g., carbapenem-resistant E. coli), the modified antimicrobial drug
(e.g., carbapenemase activity), the modified antimicrobial target (e.g., lipid A modification),
the direct detection of the AMR determinant (e.g., KPC-2 β-lactamases), and biomarkers co-
expressed with the AMR determinants (e.g., blaKPC carrying plasmid) [124]. This technique
identifies specific resistant profiles (e.g., KPC and MBLs) of bacteria at the species and
genus level from single isolated colonies within 1–4 h, with 72.5–100% sensitivity and
98–100% specificity; however, it has issues regarding OXA-48 identification [40,123,124].
Further, the combination of automation and the implementation of a user-friendly interface
recently made MALDI-TOF MS popular in clinical laboratories [123,125–127].
Colorimetric assays have also been developed as rapid, simple, and cost-effective
phenotypic methods for detecting CP bacteria based on their carbapenemase hydrolytic
activity [60,107,108]. The Carba NP test (2 h) measures the hydrolysis of imipenem, leading
to changes in pH and resulting in a color change from red to yellow/orange. The sensitivity
of this test was found to be 73–100% for most carbapenemases, but it performed poorly in
the detection of the OXA-48 enzyme [60,107,108]. The Carba NP test has been recommended
for use as a first-line test for screening carbapenemase activity by the CLSI in the US.
The RAPIDEC Carba NP test (first commercial test), β-CARBA test, Rapid CARB screen,
Rapid Carb Blue kit, and Neo-CARB kit have been used to detect CP bacteria within 2 h,
with varying sensitivity (>70%) and specificity (>89%) from the pure culture [108,123,128].
However, these assays require pure cultures and are dependent on the growth rate of the
bacteria [123].
Many of these rapid phenotypic techniques and automated systems still require
pure cultures; thus, sample preparation and pre-treatment steps require several hours to
days [116,123]. Last but not least, these techniques require costly equipment, complex data
analysis, and skilled personnel, which limits their applicability in low-resource setting
laboratories [99,103,104,118].
detection and quantification of amplified PCR products using fluorescent dyes, eliminating
gel electrophoresis [99,132,133]. Automated systems of PCR or qPCR are commercially
available and automatically purify the sample, concentrate DNA, and amplify and detect
major bacterial genes, confirming antibiotic resistance in less than two hours [99,134].
For two decades, PCR-based techniques have been used as the gold standard for the
detection of β-lactam resistant genes in Enterobacteriaceae. For example, multiplex PCR was
developed to detect 11 acquired genes encoding carbapenemase (blaIMP , blaVIM, blaNDM ,
blaSPM , blaAIM , blaDIM , blaGIM , blaSIM blaKPC, blaBIC , and blaOXA-48 ) using three different
multiplex reaction mixtures [108,123,135]. Several automated systems were also developed
to identify the target genes [108,123,135]. Real-time multiplex PCR or qPCR systems allow
a combination of amplification and detection in a single step, limiting contamination risks.
GeneXpert is an automated real-time PCR platform that uses the Carba-R assay and can
detect and quantify numerous bacterial species and several carbapenemase genes from
rectal samples [123,136]. The Check-Direct assay has a panel of different multiplex real-
time PCR kits using several probes, including narrow and broad-spectrum B-lactamase
genes [108,123,137]. A broad range of multiplex PCR panels was developed to increase their
analytical performance without requiring skilled personnel. However, these PCR-based
tests are expensive, limiting their use in low-resource laboratories [123].
Other molecular methods such as FISH, microarray, WGS, and LAMP assays have
also been used for detecting carbapenem resistance [99,118,138]. FISH is a technique
for detecting specific RNA or DNA sequences using dye-labeled oligonucleotide probes
visualized by fluorescence microscopy [139]. Microarray-based methods utilize multiple
spots on a solid support chip for different oligonucleotides corresponding to resistant genes
to detect labeled DNA fragments in a single assay [140]. In the whole genome sequencing
(WGS) technique, a whole bacterial sequence is screened for antibiotic-resistant genes and
compared with known genes in publicly available databases, allowing the prediction of
existing and emerging phenotypic and genotypic resistance [141]. Lastly, the LAMP assay
is a simple amplification technique that resolves PCR temperature cycling using a single
temperature for target gene amplification. This method produces a large number of DNA
copies in a short period [142,143]. LAMP has been used as an alternative to PCR due to its
simplicity and cost-effectiveness, especially in low-resource setting laboratories. However,
the technique still requires a complex primer design [99,104,138].
Emerging molecular techniques and automated systems have been improved to
reduce costs and the detection system for β-lactam resistant genes [108,123]. Luminex tech,
for example, is a well-established approach based on a colored microsphere-based flow
cytometry assay. The method can detect specific alleles, antibodies, or peptides from a single
colony [144]. The multiplex oligonucleotide ligation-PCR procedure assists in detecting
β-lactam resistant genes and their variations with higher sensitivity and specificity (100%
and 99.4%) within 5 h [123]. Further, the LAMP method, using hydroxy naphtol blue
dye (LAMP-HNB) and microarray techniques, detects genes encoding carbapenemase
with higher specificity and sensitivity at 100% and >90%, respectively [99,108,142,143].
Multiplexed paper-based Bac-PAC is another assay used to categorize the AMR profile of
individual strains of CRE by providing a colorimetric readout [145]. The RNA-targeted
molecular approach, NucliSENS EasyQKPC test, has also been used for detecting blaKPC
variants within 2 h, at a 93.3% sensitivity and 99% specificity [146]. Another technique,
PCR amplification coupled with electrospray ionization mass spectrometry (PCR-ESI-MS),
has been used to accurately measure exact molecular masses. With advanced software,
the sequence of DNA fragments is reconstructed for accurate identification as well as
subtyping of the resistant genes. This technique has been used to identify blaKPC genes
directly from clinical samples in 4–6 h [147]. Lastly, whole genome sequencing methods
have been used as the most reliable technique to detect carbapenemase, but the high cost,
longer turn-around time, and complex data management limit their use [99,108,148].
Genotypic methods generally offer key advantages, including higher sensitivity and
specificity in a short time, increasing their real-world applicability. However, these methods
Microorganisms 2023, 11, 1491 12 of 26
require costly reagents and equipment and need skilled operators [99,103,116,149]. In
addition, their sensitivity and selectivity can be affected by specimen debris, resulting
in the inhibition of the reaction or false positives [99,123]. Another limitation of many
molecular assays is that only known genes can be targeted; phenotypic resistance may
be missed by molecular assays, but WGS can help discover novel genes [99,104,116,129].
Further, the limited number of targeted genes is a challenge in molecular tests due to the
diversity of carbapenemase-encoding genes. Thus, the target gene is mainly based on the
most relevant variant in each geographical area. For example, several commercial kits
stated have been developed to detect blaKPC , the most prevalent carbapenemase in the USA,
and may not be used for other genes [123].
detection of the specific target using cyclic voltammetry [156]. Numerous electrochemical
biosensors have been used to detect antibiotic resistance. Examples include a study that
combined nitrogen-doped graphene with GNPs to detect the human multidrug-resistant
gene MDR1 [157]. In another study, an electrochemical DNA-sensing system identified
MRSA based on a MNP/DNA/AuNP hybridization complex using a chronoamperometric
signal [158]. Another electrochemical sensor utilized an antibody conjugated with MNPs
to detect MRSA from nasal swabs [159]. A label-free electrochemical biosensor detected a
PCR amplified blaNDM gene in carbapenem-resistant Citrobacter freundii using impedance
spectroscopy [160]. In another study, blaKPC detection was achieved in K. pneumoniae and E.
coli using voltammetry techniques and sandwich hybridization assays in 45 min at a level
of 104 CFU/mL [43].
Optical biosensors are widely used platforms for bacterial detection and rely on
measuring absorbance, fluorescence, Raman scattering, surface plasmon resonance (SPR),
and colorimetry [118]. These biosensors are highly sensitive but can be costly. Surface
plasmon resonance (SPR) is the most commonly used assay, which utilizes refractive index
measurements due to the excitation of the surface plasmon waves by the interaction of an
analyte with its ligand [161]. The technique mainly uses antibodies or DNA as a recognition
element. For example, the immobilized single-stranded DNA sequences on the surface bind
to their complementary sequence upon hybridization, resulting in a change in plasmon
resonance [161]. Raman scattering techniques are also common and measure molecular vi-
brational, rotational, and low-frequency modes, providing characteristic information about
carbohydrates, lipids, proteins, and nucleic acids [118,120,138]. However, they require
a higher bacterial concentration and are limited in differentiating closer spectral signals.
Recently, the Surface-Enhanced Raman Scattering technique (SERS) has been developed
using nanoparticles that enhance Raman signals [120]. This assay can differentiate strains
of carbapenem-resistant and susceptible E.coli using silver nanoparticles [120], gold nanos-
tars [162], and gold and silver nanorods [163] by comparing their SERS spectral signature
with higher specificity and sensitivity. However, these optical biosensors require complex
and multivariate data analysis.
The performance of these optical and electrochemical biosensors often depends on the
detection limit, sensitivity, specificity, reproducibility, interference response, response time,
storage, and operational stability [153,154]. These platforms are highly rapid and often
sensitive to their target bacteria. They also reduce or eliminate isolation and culture times,
allowing direct measurements from clinical and biological samples [118,138]. However,
sensitivity at low-level bacterial loads is still challenging for many biosensor platforms,
along with their costly and complex techniques for signal measurements and analysis [118].
Plasmonic biosensors that allow colorimetric detection are noteworthy; they offer
rapid and simple visual detection within one hour without the necessity of complex
and costly equipment [164–166]. For example, a study used a plasmonic nanosensor for
the colorimetric detection of CP pathogens using gold nanoparticles (GNP) based on
carbapenemase activity and pH changes [167]. Here, the GNPs changed color in response
to pH and turned to purple, blue, or gray, from red, within 15 min. CRE was detected at a
concentration of more than 105 CFU/mL directly from urine and sputum samples within
2.5–3 h. The results were easily distinguished visually and confirmed quantitatively using
vis-NIR spectroscopy [167]. Further, DNA-based plasmonic biosensors using GNPs have
extensively been used to detect target bacterial DNA. For instance, thiol-capped GNPs were
used to detect Klebsiella pneumoniae within one hour using an amplified K2A gene [165]
and the unamplified DNA of uropathogenic E. coli [168]. Dextrin-coated GNPs were used
earlier to detect the unamplified DNA of E. coli O157:H7 [164], E.coli [169], Salmonella
Enteritidis [170], and Pseudoperonospora cubensis [171] within 30 min. Further, dextrin-
coated GNPs have recently been used to detect KPC-producing bacteria (~103 CFU/mL)
from clinical isolates with 79% sensitivity and 97% specificity [172]. Plasmonic biosensors
allow the detection of pathogens and resistant bacteria in a short time without complex
and costly equipment requirements. However, further attention is needed to detect the
Microorganisms 2023, 11, 1491 14 of 26
resistant genes from clinical and biological samples to improve their accessibility and
applicability [164,172].
Table 2. The advantages and limitations of the current and emerging detection techniques for the most common carbapenemases (carbapenem-hydrolyzing
enzymes).
Among the separation techniques, chemical and biological separation processes have
become popular because of their speed, simplicity, and cost-effectiveness. Within these,
magnetic nanoparticles (MNPs) have commonly been used to rapidly and effectively ex-
tract bacteria from food and clinical samples without centrifugation and filtration [186,187].
MNPs draw attention because of their low-cost, stability, benign nature, biocompatibility,
and functionalization with recognition moieties [149,180,186,187]. Such as many chemical
and biological separation techniques, MNP-bacterial cell adhesion relies on cell surface char-
acteristics, such as surface charge, hydrophobic or hydrophilic interactions, and antibody
or lectin binding sites [180,188,189]. Therefore, cell surface characteristics are important in
understanding cell adhesion mechanisms for bacterial extraction and detection.
Cell surface characteristics of the resistant bacteria were investigated in several stud-
ies. For instance, some studies showed that the biochemical components of antibiotic-
resistant cells are different from those of susceptible bacteria. Raman spectrum is one
example where bacterial differentiation or detection was achieved using unique fingerprint
patterns [190,191]. Further, various studies have shown that alteration in the biosynthesis of
cell wall material, membrane components, and cytoplasmic contents can result in changes in
cell surface characteristics, including cell morphology and surface charge [192–196]. These
cell morphological characteristics are utilized for detecting the bacterial-resistant profile
using AST techniques [102–104]. In addition, cell surface charge characteristics are mostly
utilized for studying cell attachment, bacterial capture, and detection [194,195,197,198].
Research is still ongoing on understanding the cell characteristics of antimicrobial-resistant
bacteria to discover new potential factors. The cell surface properties of carbapenem-
resistant bacteria, in particular, have not been documented well. The changes in cell surface
characteristics can impact their adhesion or attachment to substrate surfaces depending
on their interactions with the environment [194]. Therefore, cell surface characteristics
need further attention in relation to cell adhesion mechanisms for developing or improving
rapid extraction and detection assays.
Author Contributions: O.C.-A. and E.C.A. had the idea for the article and suggested the review
topic. O.C.-A. participated in the collection of data from the literature, critiqued the literature, and
drafting the manuscript. The final manuscript was prepared with contributions from all authors. All
authors have read and agreed to the published version of the manuscript.
Funding: Research related to this article was supported by the Targeted Support Grant for Technology
Development (TSGTD), Michigan State University Foundation, the USDA Hatch project 02782, and
the USDA-NIFA project 2022-67017-36982.
Data Availability Statement: Not applicable.
Acknowledgments: We thank Saad Sharief for many helpful discussions and manuscript reviews.
Furthermore, the Turkish Ministry of Education sponsored O. Caliskan-Aydogan’s Ph.D. program at
Michigan State University.
Conflicts of Interest: The authors declare no conflict of interest.
References
1. Antibiotic Resistance Threats in the United States. 2019. Available online: https://www.cdc.gov/drugresistance/pdf/
threatsreport/2019-ar-threats-report-508.pdf (accessed on 6 September 2022).
2. Ferri, M.; Ranucci, E.; Romagnoli, P.; Giaccone, V. Antimicrobial resistance: A global emerging threat to public health systems.
Crit. Rev. Food Sci. Nutr. 2017, 57, 2857–2876. [CrossRef] [PubMed]
3. Prestinaci, F.; Pezzotti, P.; Pantosti, A. Antimicrobial resistance: A global multifaceted phenomenon. Pathog. Glob. Health 2015,
109, 309–318. [CrossRef] [PubMed]
4. Morehead, M.S.; Scarbrough, C. Emergence of Global Antibiotic Resistance. Prim. Care Clin. Off. Pract. 2018, 45, 467–484.
[CrossRef]
5. World Health Organization (WHO). Antimicrobial Resistance. Available online: https://www.who.int/news-room/fact-sheets/
detail/antimicrobial-resistance (accessed on 10 June 2022).
6. Smith, R.; Coast, J. The true cost of antimicrobial resistance. BMJ 2013, 346, f1493. [CrossRef]
7. Littmann, J.; Buyx, A.; Cars, O. Antibiotic resistance: An ethical challenge. Int. J. Antimicrob. Agents 2015, 46, 359–361. [CrossRef]
[PubMed]
8. Rodríguez-Rojas, A.; Rodríguez-Beltrán, J.; Couce, A.; Blázquez, J. Antibiotics and antibiotic resistance: A bitter fight against
evolution. Int. J. Med. Microbiol. 2013, 303, 293–297. [CrossRef]
9. Hutchings, M.I.; Truman, A.W.; Wilkinson, B. Antibiotics: Past, present and future. Curr. Opin. Microbiol. 2019, 51, 72–80.
[CrossRef]
10. Davies, J.; Davies, D. Origins and Evolution of Antibiotic Resistance. Microbiol. Mol. Biol. Rev. 2010, 74, 417–433. [CrossRef]
11. CDC (Centers for Disease Control and Prevention). “Antimicrobial Resistance”, CDC. Available online: https://www.cdc.gov/
drugresistance/about/how-resistance-happens.html (accessed on 10 September 2022).
12. Moore, D.W. Antibiotic Classification & Mechanism, Ortho Bullets. Available online: https://www.orthobullets.com/basic-
science/9059/antibiotic-classification-and-mechanism (accessed on 10 February 2023).
13. Munita, J.M.; Arias, C.A. Mechanisms of Antibiotic Resistance. Virulence Mech. Bact. Pathog. 2016, 4, 481–511. [CrossRef]
14. Capita, R.; Alonso-Calleja, C. Antibiotic-Resistant Bacteria: A Challenge for the Food Industry. Crit. Rev. Food Sci. Nutr. 2013, 53,
11–48. [CrossRef]
15. Holmes, A.H.; Moore, L.S.P.; Sundsfjord, A.; Steinbakk, M.; Regmi, S.; Karkey, A.; Guerin, P.J.; Piddock, L.J.V. Understanding the
mechanisms and drivers of antimicrobial resistance. Lancet 2016, 387, 176–187. [CrossRef]
16. Corona, F.; Martinez, J.L. Phenotypic Resistance to Antibiotics. Antibiotics 2013, 2, 237–255. [CrossRef] [PubMed]
17. van Hoek, A.H.A.M.; Mevius, D.; Guerra, B.; Mullany, P.; Roberts, A.P.; Aarts, H.J.M. Acquired Antibiotic Resistance Genes: An
Overview. Front. Microbiol. 2011, 2, 203. [CrossRef] [PubMed]
18. Chang, T.-W.; Weinstein, L. Morphological Changes in Gram-Negative Bacilli Exposed To Cephalothin. J. Bacteriol. 1964, 88,
1790–1797. [CrossRef] [PubMed]
19. Toprak, E.; Veres, A.; Michel, J.-B.; Chait, R.; Hartl, D.L.; Kishony, R. Evolutionary paths to antibiotic resistance under dynamically
sustained drug selection. Nat. Genet. 2012, 44, 101–105. [CrossRef] [PubMed]
20. Gullberg, E.; Cao, S.; Berg, O.G.; Ilbäck, C.; Sandegren, L.; Hughes, D.; Andersson, D.I. Selection of Resistant Bacteria at Very Low
Antibiotic Concentrations. PLoS Pathog. 2011, 7, e1002158. [CrossRef] [PubMed]
21. Sandegren, L. Selection of antibiotic resistance at very low antibiotic concentrations. Upsala J. Med. Sci. 2014, 119, 103–107.
[CrossRef]
22. Dankittipong, N.; Fischer, E.A.J.; Swanenburg, M.; Wagenaar, J.A.; Stegeman, A.J.; de Vos, C.J. Quantitative Risk Assessment
for the Introduction of Carbapenem-Resistant Enterobacteriaceae (CPE) into Dutch Livestock Farms. Antibiotics 2022, 11, 281.
[CrossRef]
23. Taggar, G.; Rehman, M.A.; Boerlin, P.; Diarra, M.S. Molecular Epidemiology of Carbapenemases in Enterobacteriales from Humans,
Animals, Food and the Environment. Antibiotics 2020, 9, 693. [CrossRef]
Microorganisms 2023, 11, 1491 19 of 26
24. Andersson, D.I.; Hughes, D. Evolution of antibiotic resistance at non-lethal drug concentrations. Drug Resist. Updat. 2012, 15,
162–172. [CrossRef]
25. Wellington, E.M.H.; Boxall, A.B.A.; Cross, P.; Feil, E.J.; Gaze, W.H.; Hawkey, P.M.; Johnson-Rollings, A.S.; Jones, D.L.; Lee, N.M.;
Otten, W.; et al. The role of the natural environment in the emergence of antibiotic resistance in Gram-negative bacteria. Lancet
Infect. Dis. 2013, 13, 155–165. [CrossRef] [PubMed]
26. Serwecińska, L. Antimicrobials and Antibiotic-Resistant Bacteria: A Risk to the Environment and to Public Health. Water 2020,
12, 3313. [CrossRef]
27. Hu, Y.; Matsui, Y.; Riley, L.W. Risk factors for fecal carriage of drug-resistant Escherichia coli: A systematic review and meta-
analysis. Antimicrob. Resist. Infect. Control 2020, 9, 31. [CrossRef] [PubMed]
28. Mahamat, O.O.; Tidjani, A.; Lounnas, M.; Hide, M.; Benavides, J.; Somasse, C.; Ouedraogo, A.-S.; Sanou, S.; Carrière, C.;
Bañuls, A.-L.; et al. Fecal carriage of extended-spectrum β-lactamase-producing Enterobacteriaceae in hospital and community
settings in Chad. Antimicrob. Resist. Infect. Control 2019, 8, 169. [CrossRef]
29. Band, V.I.; Weiss, D.S. Heteroresistance: A cause of unexplained antibiotic treatment failure? PLoS Pathog. 2019, 15, e1007726.
[CrossRef]
30. Rebold, N.; Lagnf, A.M.; Alosaimy, S.; Holger, D.J.; Witucki, P.; Mannino, A.; Dierker, M.; Lucas, K.; Coyne, A.J.K.; El Ghali, A.;
et al. Risk Factors for Carbapenem-Resistant Enterobacterales Clinical Treatment Failure. Microbiol. Spectr. 2023, 11, e02647-22.
[CrossRef]
31. World Health Organization (WHO). WHO Publishes List of Bacteria for Which New Antibiotics Are Urgently Needed. WHO.
Available online: https://www.who.int/news/item/27-02-2017-who-publishes-list-of-bacteria-for-which-new-antibiotics-are-
urgently-needed (accessed on 6 September 2022).
32. Codjoe, F.S.; Donkor, E.S. Carbapenem Resistance: A Review. Med. Sci. 2017, 6, 1. [CrossRef]
33. Papp-Wallace, K.M.; Endimiani, A.; Taracila, M.A.; Bonomo, R.A. Carbapenems: Past, Present, and Future. Antimicrob. Agents
Chemother. 2011, 55, 4943–4960. [CrossRef]
34. Smith, H.Z.; Kendall, B. Carbapenem Resistant Enterobacteriaceae; Statpearls: Tampa, FL, USA, 2021.
35. Bonardi, S.; Pitino, R. Carbapenemase-producing bacteria in food-producing animals, wildlife and environment: A challenge for
human health. Ital. J. Food Saf. 2019, 8, 7956. [CrossRef]
36. Kopotsa, K.; Sekyere, J.O.; Mbelle, N.M. Plasmid evolution in carbapenemase-producing Enterobacteriaceae: A review. Ann. N. Y.
Acad. Sci. 2019, 1457, 61–91. [CrossRef]
37. Michael, G.B.; Freitag, C.; Wendlandt, S.; Eidam, C.; Feßler, A.T.; Lopes, G.V.; Kadlec, K.; Schwarz, S. Emerging issues in
antimicrobial resistance of bacteria from food-producing animals. Future Microbiol. 2015, 10, 427–443. [CrossRef] [PubMed]
38. Woodford, N.; Wareham, D.W.; Guerra, B.; Teale, C. Carbapenemase-producing Enterobacteriaceae and non-Enterobacteriaceae
from animals and the environment: An emerging public health risk of our own making? J. Antimicrob. Chemother. 2014, 69,
287–291. [CrossRef] [PubMed]
39. Mallick, A.; Roy, A.; Sarkar, S.; Mondal, K.C.; Das, S. Customized molecular diagnostics of bacterial bloodstream infections for
carbapenem resistance: A convenient and affordable approach. Pathog. Glob. Health 2023, 1–8. [CrossRef] [PubMed]
40. Liu, Y.-C.; Lu, C.-Y.; Yen, T.-Y.; Chang, L.-Y.; Chen, J.-M.; Lee, P.-I.; Huang, L.-M. Clinical characteristics and outcomes of
carbapenem-resistant Enterobacterales bacteremia in pediatric patients. J. Microbiol. Immunol. Infect. 2023, 56, 84–92. [CrossRef]
[PubMed]
41. CDC (Centers for Disease Control and Prevention). Healthcare-Associated Infections (HAIs): CRE Technical Information. 2019.
Available online: https://www.cdc.gov/hai/organisms/cre/technical-info.html (accessed on 8 June 2022).
42. Liu, B.-T.; Zhang, X.-Y.; Wan, S.-W.; Hao, J.-J.; Jiang, R.-D.; Song, F.-J. Characteristics of Carbapenem-Resistant Enterobacteriaceae
in Ready-to-Eat Vegetables in China. Front. Microbiol. 2018, 9, 1147. [CrossRef]
43. Gordon, N.; Bawa, R.; Palmateer, G. Carbapenem-Resistant Enterobacteriaceae Testing in 45 Minutes Using an Electronic Sensor.
Curr. Issues Med. Diagn. Imaging 2021, 4, 1–18.
44. Rabaan, A.A.; Eljaaly, K.; Alhumaid, S.; Albayat, H.; Al-Adsani, W.; Sabour, A.A.; Alshiekheid, M.A.; Al-Jishi, J.M.; Khamis, F.;
Alwarthan, S.; et al. An Overview on Phenotypic and Genotypic Characterisation of Carbapenem-Resistant Enterobacterales.
Medicina 2022, 58, 1675. [CrossRef]
45. Armin, S.; Azimi, L.; Shariatpanahi, G.; Shirvani, A.; Tehrani, N.A. The Prevalence of Colonization with Carbapenem-resistant
Enterobacteriaceae, E. coli, Klebsiella and Enterobacter, and Related Risk Factors in Children. Arch. Pediatr. Infect. Dis. 2023, in press.
[CrossRef]
46. Zeng, M.; Xia, J.; Zong, Z.; Shi, Y.; Ni, Y.; Hu, F.; Chen, Y.; Zhuo, C.; Hu, B.; Lv, X.; et al. Guidelines for the diagnosis, treatment,
prevention and control of infections caused by carbapenem-resistant gram-negative bacilli. J. Microbiol. Immunol. Infect. 2023,
in press. [CrossRef]
47. Eichenberger, E.M.; Thaden, J.T. Epidemiology and Mechanisms of Resistance of Extensively Drug Resistant Gram-Negative
Bacteria. Antibiotics 2019, 8, 37. [CrossRef]
48. Guerra, B.; Fischer, J.; Helmuth, R. An emerging public health problem: Acquired carbapenemase-producing microorganisms are
present in food-producing animals, their environment, companion animals and wild birds. Vet. Microbiol. 2014, 171, 290–297.
[CrossRef]
Microorganisms 2023, 11, 1491 20 of 26
49. Queenan, A.M.; Bush, K. Carbapenemases: The Versatile beta-Lactamases. Clin. Microbiol. Rev. 2007, 20, 440–458. [CrossRef]
50. Cheruvanky, A.; Stoesser, N.; Sheppard, A.E.; Crook, D.W.; Hoffman, P.S.; Weddle, E.; Carroll, J.; Sifri, C.D.; Chai, W.; Barry, K.;
et al. Enhanced Klebsiella pneumoniae Carbapenemase Expression from a Novel Tn 4401 Deletion. Antimicrob. Agents Chemother.
2017, 61, e00025-17. [CrossRef] [PubMed]
51. Wu, Y.; Yang, X.; Liu, C.; Zhang, Y.; Cheung, Y.C.; Chan, E.W.C.; Chen, S.; Zhang, R. Identification of a KPC Variant Conferring
Resistance to Ceftazidime-Avibactam from ST11 Carbapenem-Resistant Klebsiella pneumoniae Strains. Microbiol. Spectr. 2022,
10, e02655-21. [CrossRef] [PubMed]
52. Farhat, N.; Khan, A.U. Evolving trends of New Delhi Metallo-betalactamse (NDM) variants: A threat to antimicrobial resistance.
Infect. Genet. Evol. 2020, 86, 104588. [CrossRef] [PubMed]
53. Boyd, S.E.; Livermore, D.M.; Hooper, D.C.; Hope, W.W. Metallo-β-Lactamases: Structure, Function, Epidemiology, Treatment
Options, and the Development Pipeline. Antimicrob. Agents Chemother. 2020, 64, 15–22. [CrossRef]
54. Poirel, L.; Héritier, C.; Tolün, V.; Nordmann, P. Emergence of Oxacillinase-Mediated Resistance to Imipenem in Klebsiella
pneumoniae. Antimicrob. Agents Chemother. 2004, 48, 15–22. [CrossRef]
55. Boyd, S.E.; Holmes, A.; Peck, R.; Livermore, D.M.; Hope, W. OXA-48-Like β-Lactamases: Global Epidemiology, Treatment
Options, and Development Pipeline. Antimicrob. Agents Chemother. 2022, 66, e00216-22. [CrossRef]
56. CDC. Tracking Antibiotic Resistance. Available online: https://www.cdc.gov/drugresistance/tracking.html (accessed on
5 May 2022).
57. Nair, D.V.T.; Venkitanarayanan, K.; Kollanoor Johny, A. Antibiotic-Resistant Salmonella in the Food Supply and the Potential Role
of Antibiotic Alternatives for Control. Foods 2018, 7, 167. [CrossRef]
58. Farzana, R.; Jones, L.S.; Rahman, A.; Sands, K.; van Tonder, A.J.; Portal, E.; Criollo, J.M.; Parkhill, J.; Guest, M.F.; Watkins, W.J.;
et al. Genomic Insights Into the Mechanism of Carbapenem Resistance Dissemination in Enterobacterales From a Tertiary Public
Heath Setting in South Asia. Clin. Infect. Dis. 2022, 76, 119–133. [CrossRef]
59. Grundmann, H.; Livermore, D.M.; Giske, C.G.; Cantón, R.; Rossolini, G.M.; Campos, J.; Vatopoulos, A.; Gniadkowski, M.;
Toth, A.; Pfeifer, Y.; et al. Carbapenem-non-susceptible Enterobacteriaceae in Europe: Conclusions from a meeting of national
experts. Eurosurveillance 2010, 15, 19711. [CrossRef]
60. Nordmann, P.; Poirel, L.; Dortet, L. Rapid Detection of Carbapenemase-producing Enterobacteriaceae. Emerg. Infect. Dis. 2012, 18,
1503–1507. [CrossRef]
61. Souli, M.; Galani, I.; Antoniadou, A.; Papadomichelakis, E.; Poulakou, G.; Panagea, T.; Vourli, S.; Zerva, L.; Armaganidis, A.;
Kanellakopoulou, K.; et al. An Outbreak of Infection due to β-Lactamase Klebsiella pneumoniae Carbapenemase 2–Producing K.
pneumoniae in a Greek University Hospital: Molecular Characterization, Epidemiology, and Outcomes. Clin. Infect. Dis. 2010, 50,
364–373. [CrossRef] [PubMed]
62. Raro, O.; Da Silva, R.M.C.; Filho, E.M.R.; Sukiennik, T.C.T.; Stadnik, C.; Dias, C.A.G.; Iglesias, J.O.; Pérez-Vázquez, M.
Carbapenemase-Producing Klebsiella pneumoniae From Transplanted Patients in Brazil: Phylogeny, Resistome, Virulome
and Mobile Genetic Elements Harboring blaKPC–2 or blaNDM–1. Front. Microbiol. 2020, 11, 1563. [CrossRef] [PubMed]
63. Manenzhe, R.I.; Zar, H.J.; Nicol, M.P.; Kaba, M. The spread of carbapenemase-producing bacteria in Africa: A systematic review.
J. Antimicrob. Chemother. 2014, 70, 23–40. [CrossRef] [PubMed]
64. Tula, M.Y.; Enabulele, O.I.; Ophori, E.A.; Aziegbemhin, A.S.; Iyoha, O.; Filgona, J. A systematic review of the current status of
carbapenem resistance in Nigeria: Its public health implication for national intervention. Niger. Postgrad. Med. J. 2023, 30, 1–11.
[CrossRef]
65. Taha, M.S.; Hagras, M.M.; Shalaby, M.M.; Zamzam, Y.A.; Elkolaly, R.M.; Abdelwahab, M.A.; Maxwell, S.Y. Genotypic Characteri-
zation of Carbapenem-Resistant Klebsiella pneumoniae Isolated from an Egyptian University Hospital. Pathogens 2023, 12, 121.
[CrossRef]
66. Munny, N.N.; Shamsuzzaman, S.M.; Hossain, T.; Khatun, S.; Johora, F.T. Prevalence and Phenotypic Detection of Carbapenem-
Resistant Enterobacter Species from the Clinical Specimens of a Tertiary Care Hospital in Bangladesh. Updat. Dent. Coll. J. 2023,
13, 17–22. [CrossRef]
67. Huang, Y.; Li, J.; Wang, Q.; Tang, K.; Cai, X.; Li, C. Detection of carbapenem-resistant hypervirulent Klebsiella pneumoniae
ST11-K64 co-producing NDM-1 and KPC-2 in a tertiary hospital in Wuhan. J. Hosp. Infect. 2022, 131, 70–80. [CrossRef]
68. Cuzon, G.; Naas, T.; Demachy, M.C.; Nordmann, P. Plasmid-Mediated Carbapenem-Hydrolyzing β-Lactamase KPC-2 in Klebsiella
pneumoniae Isolate from Greece. Antimicrob. Agents Chemother. 2008, 52, 796–797. [CrossRef]
69. Naas, T.; Nordmann, P.; Vedel, G.; Poyart, C. Plasmid-Mediated Carbapenem-Hydrolyzing β-Lactamase KPC in a Klebsiella
pneumoniae Isolate from France. Antimicrob. Agents Chemother. 2005, 49, 4423–4424. [CrossRef]
70. Kumarasamy, K.K.; Toleman, M.A.; Walsh, T.R.; Bagaria, J.; Butt, F.; Balakrishnan, R.; Chaudhary, U.; Doumith, M.; Giske, C.G.;
Irfan, S.; et al. Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: A molecular, biological, and
epidemiological study. Lancet Infect. Dis. 2010, 10, 597–602. [CrossRef]
71. van der Bij, A.K.; Pitout, J.D.D. The role of international travel in the worldwide spread of multiresistant Enterobacteriaceae. J.
Antimicrob. Chemother. 2012, 67, 2090–2100. [CrossRef] [PubMed]
72. Peirano, G.; Bradford, P.A.; Kazmierczak, K.M.; Badal, R.E.; Hackel, M.; Hoban, D.J.; Pitout, J.D. Global Incidence of
Carbapenemase-Producing Escherichia coli ST131. Emerg. Infect. Dis. 2014, 20, 1928–1931. [CrossRef] [PubMed]
Microorganisms 2023, 11, 1491 21 of 26
73. Pitout, J.D.D.; Nordmann, P.; Poirel, L. Carbapenemase-Producing Klebsiella pneumoniae, a Key Pathogen Set for Global
Nosocomial Dominance. Antimicrob. Agents Chemother. 2015, 59, 5873–5884. [CrossRef] [PubMed]
74. Poirel, L.; Barbosa-Vasconcelos, A.; Simões, R.R.; Da Costa, P.M.; Liu, W.; Nordmann, P. Environmental KPC-Producing
Escherichia coli Isolates in Portugal. Antimicrob. Agents Chemother. 2012, 56, 1662–1663. [CrossRef] [PubMed]
75. Zhang, X.; Lü, X.; Zong, Z. Enterobacteriaceae producing the KPC-2 carbapenemase from hospital sewage. Diagn. Microbiol. Infect.
Dis. 2012, 73, 204–206. [CrossRef]
76. Isozumi, R.; Yoshimatsu, K.; Yamashiro, T.; Hasebe, F.; Nguyen, B.M.; Ngo, T.C.; Yasuda, S.P.; Koma, T.; Shimizu, K.; Arikawa, J.
blaNDM-1 –positive Klebsiella pneumoniae from Environment, Vietnam. Emerg. Infect. Dis. 2012, 18, 1383–1385. [CrossRef]
77. Lepuschitz, S.; Schill, S.; Stoeger, A.; Pekard-Amenitsch, S.; Huhulescu, S.; Inreiter, N.; Hartl, R.; Kerschner, H.; Sorschag, S.;
Springer, B.; et al. Whole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella
pneumoniae isolates from Austrian rivers and clinical isolates from hospitals. Sci. Total Environ. 2019, 662, 227–235. [CrossRef]
78. Tanner, W.D.; VanDerslice, J.A.; Goel, R.K.; Leecaster, M.K.; Fisher, M.A.; Olstadt, J.; Gurley, C.M.; Morris, A.G.; Seely, K.A.;
Chapman, L. Multi-state study of Enterobacteriaceae harboring extended-spectrum beta-lactamase and carbapenemase genes in
U.S. drinking water. Sci. Rep. 2019, 9, 3938. [CrossRef]
79. Hoelle, J.; Johnson, J.R.; Johnston, B.D.; Kinkle, B.; Boczek, L.; Ryu, H.; Hayes, S. Survey of US wastewater for carbapenem-resistant
Enterobacteriaceae. J. Water Health 2019, 17, 219–226. [CrossRef]
80. Miriagou, V.; Tzouvelekis, L.S.; Rossiter, S.; Tzelepi, E.; Angulo, F.J.; Whichard, J.M. Imipenem Resistance in a Salmonella Clinical
Strain Due to Plasmid-Mediated Class A Carbapenemase KPC-2. Antimicrob. Agents Chemother. 2003, 47, 1297–1300. [CrossRef]
81. Chagas, T.; Seki, L.; da Silva, D.; Asensi, M. Occurrence of KPC-2-producing Klebsiella pneumoniae strains in hospital wastewater.
J. Hosp. Infect. 2011, 77, 281. [CrossRef] [PubMed]
82. Hamza, D.; Dorgham, S.; Ismael, E.; El-Moez, S.I.A.; ElHariri, M.; Elhelw, R.; Hamza, E. Emergence of β-lactamase- and
carbapenemase-producing Enterobacteriaceae at integrated fish farms. Antimicrob. Resist. Infect. Control 2020, 9, 67. [CrossRef]
[PubMed]
83. Fischer, J.; Schmoger, S.; Jahn, S.; Helmuth, R.; Guerra, B. NDM-1 carbapenemase-producing Salmonella enterica subsp. enterica
serovar Corvallis isolated from a wild bird in Germany. J. Antimicrob. Chemother. 2013, 68, 2954–2956. [CrossRef] [PubMed]
84. Shaheen, B.W.; Nayak, R.; Boothe, D.M. Emergence of a New Delhi Metallo-β-Lactamase (NDM-1)-Encoding Gene in Clinical
Escherichia coli Isolates Recovered from Companion Animals in the United States. Antimicrob. Agents Chemother. 2013, 57,
2902–2903. [CrossRef]
85. Stolle, I.; Prenger-Berninghoff, E.; Stamm, I.; Scheufen, S.; Hassdenteufel, E.; Guenther, S.; Bethe, A.; Pfeifer, Y.; Ewers, C.
Emergence of OXA-48 carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in dogs. J. Antimicrob. Chemother.
2013, 68, 2802–2808. [CrossRef]
86. Fischer, J.; Rodríguez, I.; Schmoger, S.; Friese, A.; Roesler, U.; Helmuth, R.; Guerra, B. Escherichia coli producing VIM-1
carbapenemase isolated on a pig farm. J. Antimicrob. Chemother. 2012, 67, 1793–1795. [CrossRef]
87. Fischer, J.; Rodríguez, I.; Schmoger, S.; Friese, A.; Roesler, U.; Helmuth, R.; Guerra, B. Salmonella enterica subsp. enterica producing
VIM-1 carbapenemase isolated from livestock farms. J. Antimicrob. Chemother. 2012, 68, 478–480. [CrossRef]
88. Vikram, A.; Schmidt, J.W. Functional blaKPC-2 Sequences Are Present in U.S. Beef Cattle Feces Regardless of Antibiotic Use.
Foodborne Pathog. Dis. 2018, 15, 444–448. [CrossRef]
89. Sugawara, Y.; Hagiya, H.; Akeda, Y.; Aye, M.M.; Win, H.P.M.; Sakamoto, N.; Shanmugakani, R.K.; Takeuchi, D.; Nishi, I.;
Ueda, A.; et al. Dissemination of carbapenemase-producing Enterobacteriaceae harbouring blaNDM or blaIMI in local market
foods of Yangon, Myanmar. Sci. Rep. 2019, 9, 14455. [CrossRef]
90. Roschanski, N.; Guenther, S.; Vu, T.T.T.; Fischer, J.; Semmler, T.; Huehn, S.; Alter, T.; Roesler, U. VIM-1 carbapenemase-producing
Escherichia coli isolated from retail seafood, Germany 2016. Eurosurveillance 2017, 22, 17-00032. [CrossRef]
91. Wang, J.; Yao, X.; Luo, J.; Lv, L.; Zeng, Z.; Liu, J.H. Emergence of Escherichia coli coproducing NDM-1 and KPC-2 carbapenemases
from a retail vegetable, China. J. Antimicrob. Chemother. 2018, 73, 252–254. [CrossRef] [PubMed]
92. Touati, A.; Mairi, A.; Baloul, Y.; Lalaoui, R.; Bakour, S.; Thighilt, L.; Gharout, A.; Rolain, J.-M. First detection of Klebsiella
pneumoniae producing OXA-48 in fresh vegetables from Béjaïa city, Algeria. J. Glob. Antimicrob. Resist. 2017, 9, 17–18. [CrossRef]
93. Yao, X.; Doi, Y.; Zeng, L.; Lv, L.; Liu, J.-H. Carbapenem-resistant and colistin-resistant Escherichia coli co-producing NDM-9 and
MCR-1. Lancet Infect. Dis. 2016, 16, 288–289. [CrossRef] [PubMed]
94. Chaalal, N.; Touati, A.; Bakour, S.; Aissa, M.A.; Sotto, A.; Lavigne, J.-P.; Pantel, A. Spread of OXA-48 and NDM-1-Producing
Klebsiella pneumoniae ST48 and ST101 in Chicken Meat in Western Algeria. Microb. Drug Resist. 2021, 27, 492–500. [CrossRef]
[PubMed]
95. Fernández, J.; Guerra, B.; Rodicio, M.R. Resistance to Carbapenems in Non-Typhoidal Salmonella enterica Serovars from Humans,
Animals and Food. Vet. Sci. 2018, 5, 40. [CrossRef] [PubMed]
96. Morrison, B.J.; Rubin, J.E. Carbapenemase Producing Bacteria in the Food Supply Escaping Detection. PLoS ONE 2015, 10, e0126717.
[CrossRef]
97. Mills, M.C.; Lee, J. The threat of carbapenem-resistant bacteria in the environment: Evidence of widespread contamination of
reservoirs at a global scale. Environ. Pollut. 2019, 255, 113143. [CrossRef]
98. Bedos, J.; Daikos, G.; Dodgson, A.; Pan, A.; Petrosillo, N.; Seifert, H.; Vila, J.; Ferrer, R.; Wilson, P. Early identification and optimal
management of carbapenem-resistant Gram-negative infection. J. Hosp. Infect. 2020, 108, 158–167. [CrossRef]
Microorganisms 2023, 11, 1491 22 of 26
99. Sutherland, J.B.; Rafii, F.J.O.L., Jr.; Williams, A.J. Rapid Analytical Methods to Identify Antibiotic-Resistant Bacteria. Antibiot.
Drug Resist. 2019, 533–566. [CrossRef]
100. Alizadeh, M.; Wood, R.L.; Buchanan, C.M.; Bledsoe, C.G.; Wood, M.E.; McClellan, D.S.; Blanco, R.; Ravsten, T.V.; Husseini, G.A.;
Hickey, C.L.; et al. Rapid separation of bacteria from blood—Chemical aspects. Colloids Surf. B Biointerfaces 2017, 154, 365–372.
[CrossRef]
101. Buehler, S.S.; Madison, B.; Snyder, S.R.; Derzon, J.; Cornish, N.E.; Saubolle, M.A.; Weissfeld, A.S.; Weinstein, M.P.; Liebow, E.B.;
Wolk, D.M. Effectiveness of Practices To Increase Timeliness of Providing Targeted Therapy for Inpatients with Bloodstream
Infections: A Laboratory Medicine Best Practices Systematic Review and Meta-analysis. Clin. Microbiol. Rev. 2016, 29, 59–103.
[CrossRef] [PubMed]
102. McLain, J.E.; Cytryn, E.; Durso, L.M.; Young, S. Culture-based Methods for Detection of Antibiotic Resistance in Agroecosystems:
Advantages, Challenges, and Gaps in Knowledge. J. Environ. Qual. 2016, 45, 432–440. [CrossRef] [PubMed]
103. Syal, K.; Mo, M.; Yu, H.; Iriya, R.; Jing, W.; Guodong, S.; Wang, S.; Grys, T.; Haydel, S.; Tao, N. Current and emerging techniques
for antibiotic susceptibility tests. Theranostics 2017, 7, 1795–1805. [CrossRef] [PubMed]
104. Khan, Z.A.; Siddiqui, M.F.; Park, S. Current and Emerging Methods of Antibiotic Susceptibility Testing. Diagnostics 2019, 9, 49.
[CrossRef]
105. Al-Zahrani, I.A. Routine detection of carbapenem-resistant gram-negative bacilli in clinical laboratories. Saudi Med. J. 2018, 39,
861–872. [CrossRef] [PubMed]
106. Cusack, T.; Ashley, E.; Ling, C.; Rattanavong, S.; Roberts, T.; Turner, P.; Wangrangsimakul, T.; Dance, D. Impact of CLSI and
EUCAST breakpoint discrepancies on reporting of antimicrobial susceptibility and AMR surveillance. Clin. Microbiol. Infect. 2019,
25, 910–911. [CrossRef] [PubMed]
107. Lutgring, J.D.; Limbago, B.M. The Problem of Carbapenemase-Producing-Carbapenem-Resistant-Enterobacteriaceae Detection. J.
Clin. Microbiol. 2016, 54, 529–534. [CrossRef]
108. Cui, X.; Zhang, H.; Du, H. Carbapenemases in Enterobacteriaceae: Detection and Antimicrobial Therapy. Front. Microbiol. 2019,
10, 1823. [CrossRef]
109. Takayama, Y.; Adachi, Y.; Nihonyanagi, S.; Okamoto, R. Modified Hodge test using Mueller–Hinton agar supplemented with
cloxacillin improves screening for carbapenemase-producing clinical isolates of Enterobacteriaceae. J. Med. Microbiol. 2015, 64,
774–777. [CrossRef]
110. Amjad, A.; Ia, M.; Sa, A.; Farwa, U.; Malik, N.; Zia, F. Modified Hodge Test: A Simple and Effective Test for Detection of
Carbapenemase Production The Isolates Which Showed Intermediate or Susceptible Zones for Imipenem Were Tested for
Carbapenemase Modified Hodge Test, as CL Recommends the MHT to Be Perform. Iran. J. Microbiol. 2011, 3, 189–193.
111. Saito, K.; Nakano, R.; Suzuki, Y.; Nakano, A.; Ogawa, Y.; Yonekawa, S.; Endo, S.; Mizuno, F.; Kasahara, K.; Mikasa, K.; et al.
Suitability of Carbapenem Inactivation Method (CIM) for Detection of IMP Metallo-β-Lactamase-Producing Enterobacteriaceae.
J. Clin. Microbiol. 2017, 55, 1220–1222. [CrossRef]
112. Alizadeh, N.; Rezaee, M.A.; Kafil, H.S.; Barhaghi, M.H.S.; Memar, M.Y.; Milani, M.; Hasani, A.; Ghotaslou, R. Detection of
carbapenem-resistant Enterobacteriaceae by chromogenic screening media. J. Microbiol. Methods 2018, 153, 40–44. [CrossRef]
[PubMed]
113. Nordmann, P.; Poirel, L. Strategies for identification of carbapenemase-producing Enterobacteriaceae. J. Antimicrob. Chemother.
2012, 68, 487–489. [CrossRef]
114. Nordmann, P.; Girlich, D.; Poirel, L. Detection of Carbapenemase Producers in Enterobacteriaceae by Use of a Novel Screening
Medium. J. Clin. Microbiol. 2012, 50, 2761–2766. [CrossRef] [PubMed]
115. Girlich, D.; Poirel, L.; Nordmann, P. Comparison of the SUPERCARBA, CHROMagar KPC, and Brilliance CRE screening media
for detection of Enterobacteriaceae with reduced susceptibility to carbapenems. Diagn. Microbiol. Infect. Dis. 2013, 75, 214–217.
[CrossRef] [PubMed]
116. Somily, A.M.; Garaween, G.A.; Abukhalid, N.; Absar, M.M.; Senok, A.C. Comparison of Molecular and Phenotypic Methods for
the Detection and Characterization of Carbapenem Resistant Enterobacteriaceae. Acta Microbiol. Immunol. Hung. 2016, 63, 69–81.
[CrossRef]
117. Maugeri, G.; Lychko, I.; Sobral, R.; Roque, A.C.A. Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial
Agents: A Review of Current and Future Trends. Biotechnol. J. 2018, 14, e1700750. [CrossRef]
118. Reynoso, E.C.; Laschi, S.; Palchetti, I.; Torres, E. Advances in Antimicrobial Resistance Monitoring Using Sensors and Biosensors:
A Review. Chemosensors 2021, 9, 232. [CrossRef]
119. Silva, A.P.; Faria-Ramos, I.; Ricardo, E.; Miranda, I.M.; Espinar, M.J.; Costa-De-Oliveira, S.; Cantón, R.; Rodrigues, A.G.;
Pina-Vaz, C. Rapid Flow Cytometry Test for Identification of Different Carbapenemases in Enterobacteriaceae. Antimicrob. Agents
Chemother. 2016, 60, 3824–3826. [CrossRef]
120. Bashir, S.; Nawaz, H.; Majeed, M.I.; Mohsin, M.; Abdullah, S.; Ali, S.; Rashid, N.; Kashif, M.; Batool, F.; Abubakar, M.; et al.
Rapid and sensitive discrimination among carbapenem resistant and susceptible E. coli strains using Surface Enhanced Raman
Spectroscopy combined with chemometric tools. Photodiagn. Photodyn. Ther. 2021, 34, 102280. [CrossRef]
121. Bernabeu, S.; Poirel, L.; Nordmann, P. Spectrophotometry-based detection of carbapenemase producers among Enterobacteriaceae.
Diagn. Microbiol. Infect. Dis. 2012, 74, 88–90. [CrossRef] [PubMed]
Microorganisms 2023, 11, 1491 23 of 26
122. van Almsick, V.; Ghebremedhin, B.; Pfennigwerth, N.; Ahmad-Nejad, P. Rapid detection of carbapenemase-producing Acineto-
bacter baumannii and carbapenem-resistant Enterobacteriaceae using a bioluminescence-based phenotypic method. J. Microbiol.
Methods 2018, 147, 20–25. [CrossRef] [PubMed]
123. Decousser, J.-W.; Poirel, L.; Nordmann, P. Recent advances in biochemical and molecular diagnostics for the rapid detection
of antibiotic-resistant Enterobacteriaceae: A focus on ß-lactam resistance. Expert. Rev. Mol. Diagn. 2017, 17, 327–350. [CrossRef]
[PubMed]
124. Bianco, G.; Comini, S.; Boattini, M.; Ricciardelli, G.; Guarrasi, L.; Cavallo, R.; Costa, C. MALDI-TOF MS-Based Approaches for
Direct Identification of Gram-Negative Bacteria and BlaKPC -Carrying Plasmid Detection from Blood Cultures: A Three-Year
Single-Centre Study and Proposal of a Diagnostic Algorithm. Microorganisms 2022, 11, 91. [CrossRef]
125. Knox, J.; Jadhav, S.; Sevior, D.; Agyekum, A.; Whipp, M.; Waring, L.; Iredell, J.; Palombo, E.; Cillo, A.R.; Vagratian, D.; et al.
Phenotypic Detection of Carbapenemase-Producing Enterobacteriaceae by Use of Matrix-Assisted Laser Desorption Ionization–
Time of Flight Mass Spectrometry and the Carba NP Test. J. Clin. Microbiol. 2014, 52, 4075–4077. [CrossRef]
126. Gato, E.; Anantharajah, A.; Arroyo, M.J.; Artacho, M.J.; Caballero, J.D.D.; Candela, A.; Chudějová, K.; Constanso, I.P.; Elías, C.;
Fernández, J.; et al. Multicenter Performance Evaluation of MALDI-TOF MS for Rapid Detection of Carbapenemase Activity in
Enterobacterales: The Future of Networking Data Analysis With Online Software. Front. Microbiol. 2022, 12, 4145. [CrossRef]
127. Yu, J.; Lin, Y.-T.; Chen, W.-C.; Tseng, K.-H.; Lin, H.-H.; Tien, N.; Cho, C.-F.; Huang, J.-Y.; Liang, S.-J.; Ho, L.-C.; et al. Direct
prediction of carbapenem-resistant, carbapenemase-producing, and colistin-resistant Klebsiella pneumoniae isolates from routine
MALDI-TOF mass spectra using machine learning and outcome evaluation. Int. J. Antimicrob. Agents 2023, 61, 106799. [CrossRef]
128. Eltahlawi, R.A.; Jiman-Fatani, A.; Gad, N.M.; Ahmed, S.H.; Al-Rabia, M.W.; Zakai, S.; Kharaba, A.; El-Hossary, D. Detection of
Carbapenem-resistance in CRE by Comparative Assessment of RAPIDEC®CARBA NP and Xpert™Carba-R Assay. Infect. Drug
Resist. 2023, 16, 1123–1131. [CrossRef]
129. Woodford, N.; Sundsfjord, A. Molecular detection of antibiotic resistance: When and where? J. Antimicrob. Chemother. 2005, 56,
259–261. [CrossRef]
130. Rijpens, N.P.; Herman, L.M.F. Molecular Methods for Identification and Detection of Bacterial Food Pathogens. J. AOAC Int. 2002,
85, 984–995. [CrossRef]
131. Smiljanic, M.; Kaase, M.; Ahmad-Nejad, P.; Ghebremedhin, B. Comparison of in-house and commercial real time-PCR based
carbapenemase gene detection methods in Enterobacteriaceae and non-fermenting gram-negative bacterial isolates. Ann. Clin.
Microbiol. Antimicrob. 2017, 16, 48. [CrossRef]
132. Probst, K.; Boutin, S.; Späth, I.; Scherrer, M.; Henny, N.; Sahin, D.; Heininger, A.; Heeg, K.; Nurjadi, D. Direct-PCR from rectal
swabs and environmental reservoirs: A fast and efficient alternative to detect blaOXA-48 carbapenemase genes in an Enterobacter
cloacae outbreak setting. Environ. Res. 2021, 203, 111808. [CrossRef] [PubMed]
133. Naas, T.; Ergani, A.; Carrër, A.; Nordmann, P. Real-Time PCR for Detection of NDM-1 Carbapenemase Genes from Spiked Stool
Samples. Antimicrob. Agents Chemother. 2011, 55, 4038–4043. [CrossRef] [PubMed]
134. Hlousek, L.; Voronov, S.; Diankov, V.; Leblang, A.B.; Wells, P.J.; Ford, D.M.; Nolling, J.; Hart, K.W.; Espinoza, P.A.; Bristol, M.R.;
et al. Automated high multiplex qPCR platform for simultaneous detection and quantification of multiple nucleic acid targets.
Biotechniques 2012, 52, 316–324. [CrossRef] [PubMed]
135. Poirel, L.; Walsh, T.R.; Cuvillier, V.; Nordmann, P. Multiplex PCR for detection of acquired carbapenemase genes. Diagn. Microbiol.
Infect. Dis. 2011, 70, 119–123. [CrossRef] [PubMed]
136. Dortet, L.; Fusaro, M.; Naas, T. Improvement of the Xpert Carba-R Kit for the Detection of Carbapenemase-Producing Enterobac-
teriaceae. Antimicrob. Agents Chemother. 2016, 60, 3832–3837. [CrossRef]
137. Lau, A.F.; Fahle, G.A.; Kemp, M.A.; Jassem, A.N.; Dekker, J.P.; Frank, K.M. Clinical Performance of Check-Direct CPE, a Multiplex
PCR for Direct Detection of bla KPC , bla NDM and/or bla VIM , and bla OXA-48 from Perirectal Swabs. J. Clin. Microbiol. 2015, 53,
3729–3737. [CrossRef]
138. Wu, S.; Hulme, J.P. Recent Advances in the Detection of Antibiotic and Multi-Drug Resistant Salmonella: An Update. Int. J. Mol.
Sci. 2021, 22, 3499. [CrossRef] [PubMed]
139. Frickmann, H.; Zautner, A.E.; Moter, A.; Kikhney, J.; Hagen, R.M.; Stender, H.; Poppert, S. Fluorescence in situ hybridization
(FISH) in the microbiological diagnostic routine laboratory: A review. Crit. Rev. Microbiol. 2017, 43, 263–293. [CrossRef]
140. Frye, J.G.; Jesse, T.; Long, F.; Rondeau, G.; Porwollik, S.; McClelland, M.; Jackson, C.R.; Englen, M.; Cray, P. DNA microarray
detection of antimicrobial resistance genes in diverse bacteria. Int. J. Antimicrob. Agents 2006, 27, 138–151. [CrossRef]
141. Marimuthu, K.; Venkatachalam, I.; Koh, V.; Harbarth, S.; Perencevich, E.; Cherng, B.P.Z.; Fong, R.K.C.; Pada, S.K.; Ooi, S.T.;
Smitasin, N.; et al. Whole genome sequencing reveals hidden transmission of carbapenemase-producing Enterobacterales. Nat.
Commun. 2022, 13, 3052. [CrossRef] [PubMed]
142. Nakano, R.; Nakano, A.; Ishii, Y.; Ubagai, T.; Kikuchi-Ueda, T.; Kikuchi, H.; Tansho-Nagakawa, S.; Kamoshida, G.; Mu, X.; Ono, Y.
Rapid detection of the Klebsiella pneumoniae carbapenemase (KPC) gene by loop-mediated isothermal amplification (LAMP). J.
Infect. Chemother. 2014, 21, 202–206. [CrossRef] [PubMed]
143. Wu, B.; Tong, X.; Chen, B.; Yuan, W.; Fu, M.; Yang, X.; Chen, H.; Zhang, G.; Wu, G.; Xu, B. Development of Microfluidic Chip-Based
Loop-Mediated Isothermal Amplification (LAMP) Method for Detection of Carbapenemase Producing Bacteria. Microbiol. Spectr.
2022, 10, e00322-22. [CrossRef]
Microorganisms 2023, 11, 1491 24 of 26
144. Ceyssens, P.-J.; Garcia-Graells, C.; Fux, F.; Botteldoorn, N.; Mattheus, W.; Wuyts, V.; De Keersmaecker, S.; Dierick, K.; Bertrand, S.
Development of a Luminex xTAG® assay for cost-effective multiplex detection of β-lactamases in Gram-negative bacteria. J.
Antimicrob. Chemother. 2016, 71, 2479–2483. [CrossRef] [PubMed]
145. Oeschger, T.; Kret, L.; Erickson, D. Multiplexed Paper-Based Assay for Personalized Antimicrobial Susceptibility Profiling of
Carbapenem-Resistant Enterobacteriaceae Performed in a Rechargeable Coffee Mug. Sci. Rep. 2022, 12, 11990. [CrossRef]
[PubMed]
146. McEwan, A.S.; Derome, A.; Meunier, D.; Burns, P.J.; Woodford, N.; Dodgson, A.R. Evaluation of the NucliSENS EasyQ KPC Assay
for Detection of Klebsiella pneumoniae Carbapenemase-Producing Enterobacteriaceae. J. Clin. Microbiol. 2013, 51, 1948–1950.
[CrossRef]
147. Laffler, T.G.; Cummins, L.L.; McClain, C.M.; Quinn, C.D.; Toro, M.A.; Carolan, H.E.; Toleno, D.M.; Rounds, M.A.; Eshoo, M.W.;
Stratton, C.W.; et al. Enhanced Diagnostic Yields of Bacteremia and Candidemia in Blood Specimens by PCR-Electrospray
Ionization Mass Spectrometry. J. Clin. Microbiol. 2013, 51, 3535–3541. [CrossRef]
148. Zankari, E.; Hasman, H.; Kaas, R.S.; Seyfarth, A.M.; Agersø, Y.; Lund, O.; Larsen, M.V.; Aarestrup, F.M. Genotyping using
whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J.
Antimicrob. Chemother. 2012, 68, 771–777. [CrossRef]
149. Bohara, R.A.; Pawar, S.H. Innovative Developments in Bacterial Detection with Magnetic Nanoparticles. Appl. Biochem. Biotechnol.
2015, 176, 1044–1058. [CrossRef] [PubMed]
150. Wareham, D.W.; Shah, R.; Betts, J.W.; Phee, L.M.; Momin, M.H.F.A. Evaluation of an Immunochromatographic Lateral Flow
Assay (OXA-48 K -SeT) for Rapid Detection of OXA-48-Like Carbapenemases in Enterobacteriaceae. J. Clin. Microbiol. 2016, 54,
471–473. [CrossRef]
151. Hu, S.; Niu, L.; Zhao, F.; Yan, L.; Nong, J.; Wang, C.; Gao, N.; Zhu, X.; Wu, L.; Bo, T.; et al. Identification of Acinetobacter
baumannii and its carbapenem-resistant gene blaOXA-23-like by multiple cross displacement amplification combined with lateral
flow biosensor. Sci. Rep. 2019, 9, 17888. [CrossRef] [PubMed]
152. Greissl, C.; Saleh, A.; Hamprecht, A. Rapid detection of OXA-48-like, KPC, NDM, and VIM carbapenemases in Enterobacterales
by a new multiplex immunochromatographic test. Eur. J. Clin. Microbiol. Infect. Dis. 2018, 38, 331–335. [CrossRef] [PubMed]
153. Perumal, V.; Hashim, U. Advances in biosensors: Principle, architecture and applications. J. Appl. Biomed. 2014, 12, 1–15.
[CrossRef]
154. Ahmed, A.; Rushworth, J.V.; Hirst, N.A.; Millner, P.A. Biosensors for Whole-Cell Bacterial Detection. Clin. Microbiol. Rev. 2014, 27,
631–646. [CrossRef]
155. Ahmed, M.U.; Zourob, M.; Tamiya, E. Introduction to Food Biosensors. In Food Biosens; Food Chemistry, Function and Analysis;
Royal Society of Chemistry, 2017; pp. 1–21. ISBN 978-1-5231-2621-7. Available online: https://books.rsc.org/books/edited-
volume/571/chapter/245460/Introduction-to-Food-Biosensors (accessed on 23 May 2023). [CrossRef]
156. Drummond, T.G.; Hill, M.G.; Barton, J.K. Electrochemical DNA sensors. Nat. Biotechnol. 2003, 21, 1192–1199. [CrossRef]
157. Chen, M.; Hou, C.; Huo, D.; Bao, J.; Fa, H.; Shen, C. An electrochemical DNA biosensor based on nitrogen-doped graphene/Au
nanoparticles for human multidrug resistance gene detection. Biosens. Bioelectron. 2016, 85, 684–691. [CrossRef]
158. Watanabe, K.; Kuwata, N.; Sakamoto, H.; Amano, Y.; Satomura, T.; Suye, S.-I. A smart DNA sensing system for detecting
methicillin-resistant Staphylococcus aureus using modified nanoparticle probes. Biosens. Bioelectron. 2015, 67, 419–423. [CrossRef]
159. Nemr, C.R.; Smith, S.J.; Liu, W.; Mepham, A.H.; Mohamadi, R.M.; Labib, M.; Kelley, S.O. Nanoparticle-Mediated Capture and
Electrochemical Detection of Methicillin-Resistant Staphylococcus aureus. Anal. Chem. 2019, 91, 2847–2853. [CrossRef]
160. Huang, J.M.-Y.; Henihan, G.; Macdonald, D.; Michalowski, A.; Templeton, K.; Gibb, A.P.; Schulze, H.; Bachmann, T.T. Rapid
Electrochemical Detection of New Delhi Metallo-beta-lactamase Genes To Enable Point-of-Care Testing of Carbapenem-Resistant
Enterobacteriaceae. Anal. Chem. 2015, 87, 7738–7745. [CrossRef]
161. Homola, J. Present and future of surface plasmon resonance biosensors. Anal. Bioanal. Chem. 2003, 377, 528–539. [CrossRef]
162. Wong, Y.L.; Kang, W.C.M.; Reyes, M.; Teo, J.W.P.; Kah, J.C.Y. Rapid Detection of Carbapenemase-Producing Enterobacteriacae
Based on Surface-Enhanced Raman Spectroscopy with Gold Nanostars. ACS Infect. Dis. 2020, 6, 947–953. [CrossRef]
163. Li, J.; Wang, C.; Kang, H.; Shao, L.; Hu, L.; Xiao, R.; Wang, S.; Gu, B. Label-free identification carbapenem-resistant Escherichia coli
based on surface-enhanced resonance Raman scattering. RSC Adv. 2018, 8, 4761–4765. [CrossRef] [PubMed]
164. Dester, E.; Kao, K.; Alocilja, E.C. Detection of Unamplified E. coli O157 DNA Extracted from Large Food Samples Using a Gold
Nanoparticle Colorimetric Biosensor. Biosensors 2022, 12, 274. [CrossRef] [PubMed]
165. Ahmadi, S.; Kamaladini, H.; Haddadi, F.; Sharifmoghadam, M.R. Thiol-Capped Gold Nanoparticle Biosensors for Rapid and
Sensitive Visual Colorimetric Detection of Klebsiella pneumoniae. J. Fluoresc. 2018, 28, 987–998. [CrossRef] [PubMed]
166. Quintela, I.A.; de los Reyes, B.G.; Lin, C.-S.; Wu, V.C.H. Simultaneous Colorimetric Detection of a Variety of Salmonella spp. in
Food and Environmental Samples by Optical Biosensing Using Oligonucleotide-Gold Nanoparticles. Front. Microbiol. 2019,
10, 1138. [CrossRef]
167. Santopolo, G.; Rojo-Molinero, E.; Clemente, A.; Borges, M.; Oliver, A.; de la Rica, R. Bedside Detection of Carbapenemase-
Producing Pathogens with Plasmonic Nanosensors. Sens. Actuators B Chem. 2020, 329, 129059. [CrossRef]
168. Bakthavathsalam, P.; Rajendran, V.K.; Mohammed, J.A.B. A direct detection of Escherichia coli genomic DNA using gold
nanoprobes. J. Nanobiotechnol. 2012, 10, 8. [CrossRef]
Microorganisms 2023, 11, 1491 25 of 26
169. Sharief, S.A.; Caliskan-Aydogan, O.; Alocilja, E. Carbohydrate-coated magnetic and gold nanoparticles for point-of-use food
contamination testing. Biosens. Bioelectron. X 2023, 13, 100322. [CrossRef]
170. Sharief, S.A.; Caliskan-Aydogan, O.; Alocilja, E.C. Carbohydrate-coated nanoparticles for PCR-less genomic detection of Salmonella
from fresh produce. Food Control 2023, 150, 109770. [CrossRef]
171. Baetsen-Young, A.M.; Vasher, M.; Matta, L.L.; Colgan, P.; Alocilja, E.C.; Day, B. Direct colorimetric detection of unamplified
pathogen DNA by dextrin-capped gold nanoparticles. Biosens. Bioelectron. 2018, 101, 29–36. [CrossRef]
172. Caliskan-Aydogan, O.; Sharief, S.A.; Alocilja, E.C. Nanoparticle-Based Plasmonic Biosensor for the Unamplified Genomic
Detection of Carbapenem-Resistant Bacteria. Diagnostics 2023, 13, 656. [CrossRef] [PubMed]
173. World Health Organization (WHO). Global Antimicrobial Resistance and Use Surveillance System (GLASS). Available online:
https://www.who.int/initiatives/glass (accessed on 15 January 2023).
174. FDA. The National Antimicrobial Resistance Monitoring System, NARMS FDA. Available online: https://www.fda.gov/animal-
veterinary/antimicrobial-resistance/national-antimicrobial-resistance-monitoring-system (accessed on 20 June 2022).
175. ECDC: EARS-Net, Annual Report of The European Antimicrobial Resistance Surveillance Network (EARS-Net) Surveill. Re-
port; ECDC. 2017. Available online: https://www.ecdc.europa.eu/en/publications-data/surveillance-antimicrobial-resistance-
europe-2017 (accessed on 20 October 2022).
176. FDA. Clinical Laboratory Improvement Amendments (CLIA). Available online: https://www.fda.gov/medical-devices/ivd-
regulatory-assistance/clinical-laboratory-improvement-amendments-clia (accessed on 15 July 2022).
177. CDC. Foodborne Diseases Active Surveillance Network (FoodNet). Available online: https://www.cdc.gov/foodnet/index.html
(accessed on 22 May 2022).
178. CDC. Culture-Independent Diagnostic Tests. Available online: https://www.cdc.gov/foodsafety/challenges/cidt.html (accessed
on 13 December 2022).
179. CDC. CDC’s Antibiotic Resistance (AR) Laboratory Networks. Available online: https://www.cdc.gov/drugresistance/
laboratories.html (accessed on 12 March 2023).
180. Dester, E.; Alocilja, E. Current Methods for Extraction and Concentration of Foodborne Bacteria with Glycan-Coated Magnetic
Nanoparticles: A Review. Biosensors 2022, 12, 112. [CrossRef] [PubMed]
181. Suh, S.; Jaykus, L.-A.; Brehm-Stecher, B. Advances in Separation and Concentration of Microorganisms from Food Samples; Woodhead
Publishing Ltd.: Shaston, UK, 2013. [CrossRef]
182. Pitt, W.G.; Alizadeh, M.; Husseini, G.A.; McClellan, D.S.; Buchanan, C.M.; Bledsoe, C.G.; Robison, R.A.; Blanco, R.; Roeder, B.L.;
Melville, M.; et al. Rapid separation of bacteria from blood-review and outlook. Biotechnol. Prog. 2016, 32, 823–839. [CrossRef]
183. Li, Z.; Ma, J.; Ruan, J.; Zhuang, X. Using Positively Charged Magnetic Nanoparticles to Capture Bacteria at Ultralow Concentration.
Nanoscale Res. Lett. 2019, 14, 195. [CrossRef] [PubMed]
184. Kearns, H.; Goodacre, R.; Jamieson, L.E.; Graham, D.; Faulds, K. SERS Detection of Multiple Antimicrobial-Resistant Pathogens
Using Nanosensors. Anal. Chem. 2017, 89, 12666–12673. [CrossRef] [PubMed]
185. Wang, J.; Yang, W.; Peng, Q.; Han, D.; Kong, L.; Fan, L.; Zhao, M.; Ding, S. Rapid detection of carbapenem-resistant Enterobacteri-
aceae using pH response based on vancomycin-modified Fe3 O4 @Au nanoparticle enrichment and the carbapenemase hydrolysis
reaction. Anal. Methods 2019, 12, 104–111. [CrossRef]
186. Krishna, V.D.; Wu, K.; Su, D.; Cheeran, M.C.; Wang, J.-P.; Perez, A. Nanotechnology: Review of concepts and potential application
of sensing platforms in food safety. Food Microbiol. 2018, 75, 47–54. [CrossRef]
187. Lv, M.; Liu, Y.; Geng, J.; Kou, X.; Xin, Z.; Yang, D. Engineering nanomaterials-based biosensors for food safety detection. Biosens.
Bioelectron. 2018, 106, 122–128. [CrossRef]
188. Frank, J.F. Microbial Attachment to Food and Food Conctact Surfaces. In Advances Innnnnnnn Food and Nutrition Research;
Academic Press: Cambridge, MA, USA, 2001; Volume 43, ISBN 0-12-016443-4.
189. Payne, M.J.; Kroll, R.G. Methods for the separation and concentration of bacteria from foods. Trends Food Sci. Technol. 1991, 2,
315–319. [CrossRef]
190. Wang, K.; Li, S.; Petersen, M.; Wang, S.; Lu, X. Detection and Characterization of Antibiotic-Resistant Bacteria Using Surface-
Enhanced Raman Spectroscopy. Nanomaterials 2018, 8, 762. [CrossRef]
191. Galvan, D.D.; Yu, Q. Surface-Enhanced Raman Scattering for Rapid Detection and Characterization of Antibiotic-Resistant
Bacteria. Adv. Health Mater. 2018, 7, e1701335. [CrossRef] [PubMed]
192. Cushnie, T.P.T.; O’Driscoll, N.H.; Lamb, A.J. Morphological and ultrastructural changes in bacterial cells as an indicator of
antibacterial mechanism of action. Cell. Mol. Life Sci. 2016, 73, 4471–4492. [CrossRef] [PubMed]
193. Yang, D.C.; Blair, K.M.; Salama, N.R. Staying in Shape: The Impact of Cell Shape on Bacterial Survival in Diverse Environments.
Microbiol. Mol. Biol. Rev. 2016, 80, 187–203. [CrossRef] [PubMed]
194. Nishino, M.; Matsuzaki, I.; Musangile, F.Y.; Takahashi, Y.; Iwahashi, Y.; Warigaya, K.; Kinoshita, Y.; Kojima, F.; Murata, S.-I.
Measurement and visualization of cell membrane surface charge in fixed cultured cells related with cell morphology. PLoS ONE
2020, 15, e0236373. [CrossRef]
195. Maillard, A.P.F.; Espeche, J.C.; Maturana, P.; Cutro, A.C.; Hollmann, A. Zeta potential beyond materials science: Applications to
bacterial systems and to the development of novel antimicrobials. Biochim. et Biophys. Acta (BBA)-Biomembr. 2021, 1863, 183597.
[CrossRef] [PubMed]
Microorganisms 2023, 11, 1491 26 of 26
196. Soon, R.L.; Nation, R.L.; Cockram, S.; Moffatt, J.H.; Harper, M.; Adler, B.; Boyce, J.D.; Larson, I.; Li, J. Different surface charge of
colistin-susceptible and -resistant Acinetobacter baumannii cells measured with zeta potential as a function of growth phase and
colistin treatment. J. Antimicrob. Chemother. 2010, 66, 126–133. [CrossRef]
197. Wilson, W.; Wade, M.M.; Holman, S.C.; Champlin, F.R. Status of methods for assessing bacterial cell surface charge properties
based on zeta potential measurements. J. Microbiol. Methods 2001, 43, 153–164. [CrossRef]
198. Kumar, N.; Wang, W.; Ortiz-Marquez, J.C.; Catalano, M.; Gray, M.; Biglari, N.; Hikari, K.; Ling, X.; Gao, J.; van Opijnen, T.; et al.
Dielectrophoresis assisted rapid, selective and single cell detection of antibiotic resistant bacteria with G-FETs. Biosens. Bioelectron.
2020, 156, 112123. [CrossRef]
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