Access to this full-text is provided by Frontiers.
Content available from Frontiers in Cellular and Infection Microbiology
This content is subject to copyright.
Deciphering the genetic
network and programmed
regulation of antimicrobial
resistance in
bacterial pathogens
Thandavarayan Ramamurthy
1
*, Amit Ghosh
1
,
Goutam Chowdhury
1
, Asish K. Mukhopadhyay
1
, Shanta Dutta
1
and Shin-inchi Miyoshi
2,3
1
Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,
2
Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National
Institute of Cholera and Enteric Diseases, Kolkata, India,
3
Graduate School of Medicine, Dentistry
and Pharmaceutical Sciences, Okayama University, Okayama, Japan
Antimicrobial resistance (AMR) in bacteria is an important global health
problem affecting humans, animals, and the environment. AMR is considered
as one of the major components in the “global one health”. Misuse/overuse of
antibiotics in any one of the segments can impact the integrity of the others. In
the presence of antibiotic selective pressure, bacteria tend to develop several
defense mechanisms, which include structural changes of the bacterial outer
membrane, enzymatic processes, gene upregulation, mutations, adaptive
resistance, and biofilm formation. Several components of mobile genetic
elements (MGEs) play an important role in the dissemination of AMR. Each
one of these components has a specific function that lasts long, irrespective of
any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion
sequence elements (ISs), and transposons carry the antimicrobial resistance
genes (ARGs) on different genetic backbones. Successful transfer of ARGs
depends on the class of plasmids, regulons, ISs proximity, and type of
recombination systems. Additionally, phage-bacterial networks play a major
role in the transmission of ARGs, especially in bacteria from the environment
and foods of animal origin. Several other functional attributes of bacteria also
get successfully modified to acquire ARGs. These include efflux pumps, toxin-
antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling,
quorum sensing, two-component system, and clustered regularly interspaced
short palindromic repeats (CRISPR) systems. The metabolic and virulence state
of bacteria is also associated with a range of genetic and phenotypic resistance
mechanisms. In spite of the availability of a considerable information on AMR,
the network associations between selection pressures and several of the
components mentioned above are poorly understood. Understanding how a
Frontiers in Cellular and Infection Microbiology frontiersin.org01
OPEN ACCESS
EDITED BY
Mona Mohamed Sobhy,
Animal Production Research Institute
(APRI), Egypt
REVIEWED BY
Barbara Ke˛dzierska,
University of Gdansk, Poland
Laura A. Mike,
University of Toledo, United States
Sameh AbdelGhani,
Beni-Suef University, Egypt
*CORRESPONDENCE
Thandavarayan Ramamurthy
ramamurthy.t@icmr.gov.in
SPECIALTY SECTION
This article was submitted to
Molecular Bacterial Pathogenesis,
a section of the journal
Frontiers in Cellular and
Infection Microbiology
RECEIVED 25 May 2022
ACCEPTED 25 October 2022
PUBLISHED 23 November 2022
CITATION
Ramamurthy T, Ghosh A,
Chowdhury G, Mukhopadhyay AK,
Dutta S and Miyoshi S-i (2022)
Deciphering the genetic network
and programmed regulation of
antimicrobial resistance in
bacterial pathogens.
Front. Cell. Infect. Microbiol. 12:952491.
doi: 10.3389/fcimb.2022.952491
COPYRIGHT
© 2022 Ramamurthy, Ghosh,
Chowdhury, Mukhopadhyay, Dutta and
Miyoshi. This is an open-access article
distributed under the terms of the
Creative Commons Attribution License
(CC BY). The use, distribution or
reproduction in other forums is
permitted, provided the original
author(s) and the copyright owner(s)
are credited and that the original
publication in this journal is cited, in
accordance with accepted academic
practice. No use, distribution or
reproduction is permitted which does
not comply with these terms.
TYPE Review
PUBLISHED 23 November 2022
DOI 10.3389/fcimb.2022.952491
pathogen resists and regulates the ARGs in response to antimicrobials can help
in controlling the development of resistance. Here, we provide an overview of
the importance of genetic network and regulation of AMR in
bacterial pathogens.
KEYWORDS
CRiSPR/Cas, efflux pump, mobile genetic elements, phages, quorum sensing, toxin-
antitoxin, Two- component system, antimicrobial resistance
Introduction
Antimicrobial resistance (AMR) is a major public health
concern, which has been continued to increase primarily due to
inappropriate use of antibiotics in human health and in the
production of food animals. An estimated 4·95 million deaths
were associated with AMR in 2019, which included 1·27 million
deaths directly attributable to pathogenic bacteria (ARC, 2022).
Predictions of the rising magnitude of AMR-associated death
might be around 10 million people by 2050, if no interventions
are applied (Balouiri et al., 2016).
Since their discovery, antimicrobials have been successfully
used in the treatment of different infectious diseases. However,
the efficacy of many antimicrobials is progressively being
compromised with the increase of resistance in disease-
associated bacteria. The rapid emergence and spread of AMR
continue to be a challenging problem, especially in clinical
settings, animal farming, and food manufacturing (Queenan
et al., 2016;Matthiessen et al., 2022). The emergence of
multidrug-resistant (MDR), extensively drug-resistant and
pan-drug-resistant bacterial strains severely limits existing
therapeutic options (Magiorakos et al., 2012;Poulakou et al.,
2014). Besides the development of new drugs, strategies to
prevent the development and spread of resistance are being
extensively explored (Hashempour-Baltork et al., 2019). These
approaches require a clear understanding the mechanisms of
AMR and the role of environmental factors that contribute to
the development of resistance.
The founder effect, fitness costs within the host, and their
ecological association influence the success of AMR
transmission. In the presence of antibiotic selective pressure,
bacteria develop several levels of defense, which include
structural changes of the bacterial outer membrane, enzymatic
mechanisms for antibiotic-inactivation, gene upregulation,
mutations, adaptive resistance, and formation of resistant
phenotypes and biofilm (Abushaheen et al., 2020). Several
such factors, and their interactions between them are shown in
Figure 1. Resistance might occur either through a single
mechanism against multiple antibiotics or multiple
mechanisms against a single antibiotic.
Knowledge on how a pathogen becomes resistant to
antimicrobials by regulating the genes is an important step
towards improving the strategies to tackle the AMR problem.
Antimicrobial resistance genes (ARGs) may form part of mobile
genetic elements (MGEs), which can make the intracellular
transfer onto plasmids or gene cassettes (Baquero et al., 2019).
Gene regulatory networks permit the bacteria to generate a
coordinated response to environmental challenges and shape
the epidemiology of AMR. However, the relationship between
selection pressure and the evolutionary change of these networks
is poorly understood.
Since bacterial virulence genes can act in tandem with AMR
and MGEs, there is a need to investigate these gene reservoirs
and their mode of transmission. In many findings, it was
reported that the co-selection of AMR takes place frequently
in the presence of heavy metals, environmental toxicants, and
other inorganic agents (Wales and Davies, 2015;Biswas et al.,
2021). Non-antibiotic agents such as detergents and heavy
metals can induce cross-protection against antimicrobials
through the efflux and other systems (Hegstad et al., 2010;
Sistrunk et al., 2016;Vats et al., 2022). This review focuses on
several important aspects of the genetic networks and regulation
of AMR in bacterial pathogens with some known examples.
Mobile genetic elements
MGEs/transposable elements are the genes that can move
within a genome or be transferred from one bacterial species to
another. The gene gain or loss due to MGEs could contribute to
the adaptation to different environments that eventually help to
form a divergent bacterial population (Jørgensen et al., 2015).
The expansion of AMR in bacteria is due to intrinsic or acquired
mechanisms during unstructured de novo mutations and
horizontal gene transfer (HGT). Conjugation, transformation,
and transduction are the three canonical mechanisms of HGT
(Garcıa-Aljaro et al., 2017). MGEs can carry ARGs for different
categories of antibiotics and play a significant role in their spread
within and between bacterial species (Forster et al., 2022). MGEs
successfully transfer ARGs en bloc on the bacterial chromosome
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org02
and/or on the broad-host-range plasmids. The linkage of a well-
organized gene capture and expression systems, together with
the ability for vertical and horizontal transmission of ARGs
signifies a powerful defense machinery used by the bacteria to
resist several antimicrobials (Bencko and Sıma, 2018;Li et al.,
2021). Acquisition of MGEs may have association with fitness
cost and maintained due to antimicrobial selective pressure. The
presence of MGE is generally alleviated by compensatory
mutations in the host chromosome during MGE-host
synchronization and coevolution. In the absence of antibiotic
pressure, the bacteria can be outcompeted by others that do not
carry any MGEs (Depardieu et al., 2007).
Gene clusters gained by HGT in bacterial genomes are
referred to as genomic islands (GIs). They generally carry
essential genes for genome evolution and environmental
adaptation that includes bacterial fitness, metabolism,
pathogenesis, AMR, etc (Juhas et al., 2009). Based on their
structure and functions, GIs are also considered a superfamily
of MGE. GIs have specific features that differentiate them from
the core genome, which include the presence of mobility-related
genes flanked by direct repeats and specific integration sites (e.g.,
tDNA [tRNA/tmRNA] gene) (Juhas et al., 2009). For e.g., the
Salmonella Genomic Island-1 (SGI-1), an MGE found in many
enterobacterial isolates, carries several MDR genes encoding
resistance to ampicillin, chloramphenicol, streptomycin,
sulfonamides, and tetracycline (Amar et al., 2008). However,
the insertion position of SGI-1 might differ among many
bacterial groups (Siebor and Neuwirth, 2022). The macrolide
resistance gene ermB was found to be associated with several
multidrug resistance genomic islands (MDR-GIs) in
Campylobacters(Liu et al., 2019a). In many bacterial species,
tetracycline encoding gene tet(O) acts as a key integration site for
the horizontal transfer of ARGs. During transformation, circular
intermediates are formed owing to the presence of two tet(O)
direct repeats in the terminal parts of MDR-GIs (Friis et al.,
2007). Integrons, insertion sequences, transposons, plasmids,
bacteriophages are some of the important components that carry
several MGEs whose functions including AMR are
described below.
Integrons
Integrons are proficient gene capture and expression system
with several gene cassettes. They play an important role in the
dissemination of AMR, mainly among Gram-negative bacteria
(Cambray et al., 2010). Integrative and conjugative elements
(ICEs, also known as conjugative transposons) are self-
FIGURE 1
Common mechanisms and their interaction in the dissemination of antimicrobial resistance. As shown in different boxes, cellular and molecular
mechanisms as well as mobile genetic elements are responsible for the acquisition and dissemination of AMR. The regulatory factors that prevail
in the environment directly or indirectly influence many of the AMR mechanism.
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org03
transmissible MGEs, which have the combined features of
prophages as well as transposons for integration and excision
from the chromosomes of unrelated bacterial taxa (Akrami et al.,
2019). An ICE generally contains a group of cargo genes that
encodes metabolic adaptation, virulence, and resistance to
antibiotics and/or heavy metals (Johnson and Grossman,
2015). Unlike plasmids, ICEs are not affected by segregational
loss and are stably maintained in the host genome. Integration
can occur at a single attachment site; often a tRNA gene, or in
many locations that are shared by the same class of ICEs to avoid
competition for the limited integration sites between different
co-infecting ICEs (Cambray et al., 2010). The processing of ICE-
DNA for conjugative transfer is similar to that of conjugative
plasmids and rolling-circle replication (Thomas et al., 2013).
This component includes a type IV secretion system, which
makes an intimate contact between the donor and recipient
for propagation.
Many anthropogenic factors induce bacterial gene
arrangements and mutations, thereby contributing to the
dissemination of genes encoding resistance for detergents,
heavy metals and antimicrobials (Ghaly et al., 2017). It is well
known that class 1 integrons (Intl1) are responsible for the global
spread of AMR. The qacE/qacED1 (encoding quaternary
ammonium compound-resistance) gene cassette that confers
resistance to biocides, and the mercury resistance operon
(mer) has been transmitted by Tn21 provide a selective benefit
in several pathogens (Cambray et al., 2010;Akrami et al., 2019).
This resistance mechanism also increases bacterial membrane
permeability and stimulates the production of reactive oxygen
species (ROS), which possibly helps the transfer of plasmids
between bacterial species (Han et al., 2019).
An integron-borne garosamine-specific aminoglycoside
resistance encoding gar gene has been identified in
Pseudomonas aeruginosa,Luteimonas sp., and Salmonella
enterica (Böhm et al., 2020). Integron’sspecificity to
garosamine-containing aminoglycosides may decrease the
efficacy of the semi-synthetic aminoglycoside plazomicin and
evade the aminoglycoside resistance mechanisms. The gene gar
is located within integron and adjacent to aph(3′)-XV,bla
OXA-2
,
and bla
VIM-1
gene cassettes provide resistance to many critically
important antibiotics (Böhm et al., 2020). There are many
excellent reviews on ICEs covering the structure and functions
with reference to the transmission of AMR genes (Johnson and
Grossman, 2015;Burrus, 2017;Delavat et al., 2017;Botelho and
Schulenburg, 2021).
Insertion sequence elements
An insertion sequence encodes a transposase enzyme that
catalyzes the transposition. Generally, the level of transposase
expression influences the frequency of transposition. Insertion
sequence elements (ISs) characteristically have concise
sequences containing terminal inverted repeats at the
boundaries and an open reading frame (ORF) that encodes the
transposase, which is important for its mobility (Britten, 1996).
To accomplish transposition, ISs generally infect the target site
to generate short direct repeats. Some ISs undergo transposition
using a non-replicative or cut-and-paste mechanism, while
others use a replicative copy-and-paste mechanism, where the
first copy remains intact, while the second copy is used at the
target site (Duval-Valentin et al., 2004).
The combination of different incompatibility (InC) groups
of plasmids and MGEs help in the spread of ARGs. There is a
strong interaction between conjugative plasmids and ISs. In
silico analysis exhibited transfer network of about 250 groups,
comprising nearly 60 ARG subtypes and 50 ISs connecting
conjugative plasmids in genetically distinct pathogens (Che
et al., 2021). In this analysis, IS26,ISEcp1, and IS6100 are the
most predominant elements mediating the transfer of ARGs.
ISAba125-bla
NDM-1
,ISEcp1/IS26-bla
CTX-M,
ISApl1-mcr-1 are the
ISs specifically involved in the transfer of New Delhi metallo-b-
lactamase (NDM), extended-spectrum b-lactamase (ESBL) and
mobilized colistin resistance (MCR)-encoding genes with
different genetic backbones. Interspecies transfer mediated by
IS26 and IS6100, both belonging to the IS6family, was widely
identified across many bacteria, involving about 20 genera
belonging to 7 families (Cuzon et al., 2011).
Some of the ISs, specifically carry ESBL encoding genes. For
e.g., homologous recombination mediated by IS26 was found to
be responsible for the spread of several variants of bla
NDM
along
with the other MDR encoding genes (Zhao et al., 2021). ISEcp1
belonging to the IS1380 family is an effective mobilizer of bla
CTX-
M
by a unique transposition process using neighboring
sequences by transposition. In several studies, ISEcp1element
was shown to be associated with bla
CTX-M-15
and other bla
CTX
alleles in both clinical and foodborne pathogens (Ranjbar et al.,
2010;Shawa et al., 2021).
The genetic environment of the mcr-1 structure indicated
that this colistin resistance gene could be mobilized as an ISApl1,
flanked by the composite transposon (Tn6330). However, many
mcr-1 structure sequences have been identified without ISApl or
with a single-ended ISApl, signifying its origin from the ancestral
Tn6330 by a copy-and-paste mechanism (Snesrud et al., 2018).
In most of the bacteria, ISApl1 was identified either upstream or
downstream of mcr with or without other ARGs (Anyanwu et al.,
2020). A novel mobile resistance gene, fexA encoding resistance
for florfenicol (a class of phenicol) has been detected both on the
plasmid and chromosomes of Campylobacter jejuni (Tang et al.,
2020a). The presence of IS1216 around fexA appears to be
important in the integration of the fexA-carrying gene segment
along with tet(L)-fexA-catA-tet(O) gene array.
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org04
Transposons
Transposons are a large and complex version of ISs with
repetitive DNA sequences that can be transposed from one
genome locus to the other (Siguier et al., 2006). This mobility
can result in mutations, alter gene expression and induce
chromosomal rearrangements. Transposons are directly
involved in carrying the cargo genes such as ARGs, MGEs, ISs,
and toxin-antitoxin modules (Babakhani and Oloomi, 2018).
Conjugative transposons integrate into the DNA using different
means of excision and integration compared to the classical
transposons Tn5and Tn10. After excision, the conjugative
transposons form a covalently closed circular intermediate that
can either reintegrate in the genome of the same bacterial cell or
transferred to other bacteria by conjugation (Salyers et al., 1995).
Transposon helps acquisition and spread of ARGs in several
bacterial pathogens. ISChh1-like transposon helps in acquiring
MDR genes in Campylobacter, including the optrA gene that
encodes an ATP-binding cassette F protein. The presence of
optrA has confirmed its role in elevated minimum inhibitory
concentration (MIC) to oxazolidinones and phenicols (Tang
et al., 2020b). Interestingly, ISChh1-like transposon also
integrates with AMR genes such as tet(O),aphA3, and aadE-
sat4-aphA3 gene cluster (Tang et al., 2020b). The function of
ISApl1 transposon in the mobilization of plasmid-borne mcr-1
was first established in the mid-2000s. However, majority of the
sequences reported subsequently had no ISApl1 (Wang et al.,
2018a). This finding suggests that the ISApl1 transposon had
been stabilized over time in the host’s genome background and is
currently spreading mcr-1 through plasmid transfer (Wang et al.,
2018a). The Tn6330 transposon is responsible for the spread of
mcr-1 between various plasmids and chromosomes (Li et al.,
2018). The association between plasmids and the transposon are
further discussed under the section plasmids.
Klebsiella pneumoniae strains carry different type of
transposons with several ARGs. In outbreak-associated K.
pneumoniae strains, the b-lactam resistance encoding genes
bla
TEM-1
and bla
KPC-3
had Tn4401 element located upstream
of the bla
KPC-3
gene (Leavitt et al., 2010). A novel Tn1696-like
composite transposon (designated as Tn6404) has been
identified in a carbapenem-resistant isolate that carried bla
IMP-
4
and bla
SFO-1
genes (Zhou et al., 2017). aac(6’)-Ib, ant(3’)-Ia,
bla
TEM
and bla
OXA-9
genes were found be carried by the Tn1331
(Tolmasky, 2000).
Several Tn7-like transposons have been identified to carry
both an anti-MGE defense system and ARGs, indicating its
multiple impacts on bacteria (Benler et al., 2021). In many
pathogens, tetracycline resistance encoding tet(M) gene that
spreads through Tn916-like elements carry erm(B) with or
without the macrolide efflux genetic operon [mef(E)-msr(D)]
(Marosevic et al., 2017). The conjugative transposon of the
Tn916/Tn1545 family carry several MDR determinants in
Gram-positive pathogens. Most of these transposons
uniformly harbor the tetM gene (Roberts and Mullany, 2011).
An uncommon IS that has 84% homology with ISEc63 of Tn3
family together with the bla
KPC
gene and Tn4401 fragments was
found inserted in the tra operon of outbreak-associated
enterobacterial isolates (Wozniak et al., 2021). These results
indicate the important role of transposons, with stable
integration into the target cell genome and the expression
of AMR.
Plasmids
Transfer of AMR conferring plasmids by conjugation is an
another major factor involved in the dissemination of ARGs.
Plasmid mobilization makes fitness costs in bacteria, which has
been minimized through compensatory mutations. Association
between plasmids and bacteria successfully shapes the
progression of AMR. Normally, conjugative plasmids transfer
AMR determinants using MGEs, including integrons,
transposons, and ISs. Several factors that influence the rate of
plasmid transfer, as well as its functional response have been
identified. In addition, the toxin-antitoxin system (TAS) help in
the maintenance of MDR plasmids that has been discussed in the
section TAS.
Plasmids are classified based on their incompatibility (Inc),
as they have unique replication and partition systems. Plasmid
and GI-encoded factors are important for the effective AMR-
island excision, mobilization, integration, and regulation in the
host bacteria. In some cases, the mobility of IncC or IncA/C
conjugative plasmid depends on the transcriptional activation of
multiple operons of the plasmid by the master activator AcaCD
regulon (Figure 2). The regulatory network of AcaCD extends to
the chromosomally integrated GIs, and express xis and mobIM
for excision and mobilization, respectively (Figure 2)(Rivard
et al., 2020). This regulon activates the expression of genes
located in the SGI-1 and the MGIVchHai6, which is a GI,
integrated in the trmE on chromosome I of V. cholerae non-
O1/non-O139. Transfer of MGIVchHai6 confers resistance to b-
lactams, sulfamethoxazole, tetracycline, chloramphenicol,
trimethoprim, and streptomycin/spectinomycin (Carraro
et al., 2016).
IncA/C plasmid in various bacterial pathogens shares a
conserved backbone with several MGEs with ARGs. The IncA/
C plasmid with bla
CMY-2
represents a unique lineage that has
been reported in a diverse group of bacteria. Mostly, the basic
structure of this plasmid includes a sul2 module containing the
floR-tetAR-strAB cluster and a Tn21-like element (Fernandez-
Alarcon et al., 2011). As shown in Figure 3, this broad host range
lineage is comprised of three integration hotspots facilitating the
acquisition of additional genes through integrons, IS26,ISEcp1
and ISCR2 elements (Suzuki et al., 2010). ISCR2playsan
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org05
important role in mobilizing the floR-tetA-strAB-sul2 cluster. In
IncA/C plasmid lineage, the sul2 module is steadily maintained,
whereas the bla
CMY-2
and Tn21-like regions vary among
different species. ISEcp1 existed in all the copies of IncA/C-
encoded bla
CMY-2
and was found to be involved in ‘one-ended
transposition’for self-mobilization along with the other ARGs
(Toleman and Walsh, 2011). Transfer and replication of b-
lactamase genes mediated by ISEcp1-like elements have been
identified in the tra1 region on IncA/C plasmids of many
bacterial species (D'Andrea et al., 2011). Plasmids with tra
gene contain several ORFs that encode important proteins
needed for effective conjugation.
Transmission of the bla
NDM-1
gene in E. coli of animal origin is
enhanced due to the presence of IncFII plasmids. IncFII plasmid
with bla
NDM-1
is stably maintained in the animal gut microbiome
even in the absence of carbapenem selection pressure (Lin et al.,
2016). The spread offrequently reported ESBL-encoding bla
CTX-M-
15
appears to be supported by the presence of the IncF plasmid in E.
coli that contains a Tn2-bla
TEM-1
transposon (Branger et al., 2018).
IncX3 plasmid was shown to be important in the emergence and
spread of bla
NDM-5
, which is associated with resistance to most of
the b-lactams (Ma et al., 2020). The transconjugants showed
enhanced growth and biofilm formation. This additional fitness
might be one of the reasons for the global dissemination of IncX3
plasmid with bla
NDM-5
.
Frequently identified genes like mcr are located on the
broad-host-range plasmids and their proximity to different ISs
helps in the effective transmission between different bacterial
species. In a bioinformatic analysis, interspecies transfer of AMR
was found mediated mainly by the conjugative plasmids having
ISs belonging to the IS6family, i.e.,IS26 and IS6100 (Che et al.,
2021). However, such transfers are governed by multiple factors,
including the genetic background of the ARGs, the fitness cost of
the host, etc. Plasmid-mediated colistin resistance is prompted
FIGURE 3
An IncA/C plasmid with defined AMR gene cluster. The basic structure of the IncA/C plasmid carrying the floR-tetAR-strAB cluster is with three
integration hotspots with two IS26,ISCR2 and an unknown ORF (yellow box) in between that facilitate the acquisition of additional genes.
FIGURE 2
The role of plasmid and genomic island-encoded factors in the spread of AMR encoding genes. The mobility of selective Inc conjugative
plasmid carrying the ARGs depends mostly on the master activator AcaCD regulon. The AcaCD supported expression of xis and mobIM helps in
the excision and mobilization of AMR encoding genes, respectively. The fitness costs in bacteria has been minimized through plasmid/
chromosomal compensatory mutations.
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org06
by phosphoethanolamine transferases encoding mcr variants
that are localized on the IncX4 type plasmid. MCR-1 imposes
afitness cost to its host bacterium and hence its spread requires a
high plasmid conjugation frequency. With these features, IncI2,
IncX4, and IncH12 plasmids are epidemiologically successful
genetic vectors that spread mcr-1 globally (Vazquez et al., 2022).
In E. coli, the transcriptional regulator pixR increases plasmid
transmissibility, invasion, and persistence of mcr-1-bearing
plasmids (Yi et al., 2022). Transmission of some of the mcr
alleles from bacterial chromosomes to MGEs seems to occur as
an independent event. For e.g., a novel variant mcr-5 has been
identified in colistin-resistant S. enterica Paratyphi B isolates that
harbored ColE-type plasmids containing transposon of the Tn3
family (Borowiak et al., 2017). An uncommon TnAs3-like
transposon was detected on a self-transmissible IncP plasmid
carried unrelated AGRs, bla
NDM-5
and mcr-3 in MDR clinical
isolates of E. coli (Liu et al., 2017).
The hybrid plasmid of both type-1 and type-2 IncC has been
detected in Vibrio alginolyticus, which displayed resistance to
almost all the b-lactam antibiotics and also had a novel
carbapenemase ‘Vibrio metallo-b-lactamase-1’(Zheng et al.,
2020). The chloramphenicol-florfenicol resistance gene (cfr)and
its alleles that encode an rRNA methyltransferase (ermE), has been
detected in many Gram-positive and Gram-negative pathogens
(Tang et al., 2017). The cfr alleles generally confer resistance to
phenicols, lincosamides, oxazolidinones, pleuromutilins, and
streptogramin-A. The cfrC allele was detected on transferable
plasmids flanked by two copies of IS26. Through homologous
recombination, cfrC can loop out the intervening sequences (Deng
et al., 2014). Transmission of high-level aminoglycoside resistance
(16S-rRNA methylase, rmtB) and a quinolone efflux pump (qepA)
in E. coli are associated with Tn3,IS26, and ISCR3 in an IncFII
plasmid (Deng et al., 2011). Plasmid-mediated qepA2 and multiple
chromosomally-mediated fluoroquinolone resistance determinants
also increases fluoroquinolone resistance to several folds (Machuca
et al., 2015).ThepresenceofqepA2 induces survival cost in E. coli,
but it was counterbalanced by the deletion of multiple antibiotic
resistance (marR)gene(Machuca et al., 2015).
Integrative plasmids play an important role in the stability and
spread of virulence and ARGs. S. Enteritidis-specificvirulence
plasmid, pSEN was found to be integrated into an IncHI2 MDR
plasmid having the cephalosporin and fosfomycin resistance
determinants bla
CTX-M-14
and fosA3,respectively(Wong et al.,
2017). The replicative transposition process has been mediated by
IS26, which is usually identified in many MDR plasmids. In S.
Typhimurium, IncHI2-type plasmid harboring the olaquindox/
quinolone AB-encoding gene oqxAB is responsible for the
ciprofloxacin resistance (Lian et al., 2019). After acquiring this
plasmid, the chromosomal efflux pump genes acrAB,tolC,and
yceE remain upregulated and maintained the survival of
ciprofloxacin exposed S. Typhimurium.
Epigenetic compatibility of quinolone resistance (Qnr)
determinants in the host genome depends on the bacterial
species and other factors. Plasmids carrying the QnrA
determinant are stable in E. coli, whereas the SmQnr, which
was present in a Gram-negative, multidrug resistant,
opportunistic pathogen Stenotrophomonas maltophilia,was
found to be unstable despite both the proteins exhibiting
homologous tertiary structures (Sanchez and Martınez, 2012).
This mechanism signifies that the fitness costs associated with
the acquisition of SmQnr may not be derived from the metabolic
burden, but the acquired gene seems to be important in initiating
specific changes in the host bacterial metabolic and regulatory
network. The plasmid-mediated quinolone resistance
determinant OqxAB-mediates resistance to many
antimicrobials such as chloramphenicol, quinolones,
quinoxalines, trimethoprim, etc., mostly among the members
of the family Enterobacteriaceae. oqxAB flanked by IS26
elements forms a composite transposon Tn6010, which has
been detected mostly in the IncHI2 plasmid (Ruiz et al., 2012;
Wang et al., 2017;Li et al., 2019). This oqxAB has been clustered
with several other resistance genes on the same plasmid,
including aac(6’)-Ib-cr,qnrS,bla
CTX-M-55
,rmtB,fosA3,and
floR (Wang et al., 2017).
Phages
Recent findings suggest that phage-bacterial association play
a substantial role in the transmission of AMR, especially in
bacteria from the environment and foods of animal origin.
Metagenomic analysis of food animals, natural water bodies,
effluents, and soil supplemented with animal manure supported
the view on the spread of ARGs through bacteriophage DNA
and prophage elements (Ross and Topp, 2015;Shousha et al.,
2015;Mohan Raj and Karunasagar, 2019;Balcazar, 2020). ARGs
containing extracellular DNA is protected from the action of
DNase, as they are packed in the phage’s capsid proteins. These
DNA fragments can be safely transferred to bacterial cells,
following their integration into the specificregionsofthe
chromosome through RecA (essential for the repair and
maintenance of DNA)-dependent homologous recombination.
The prophage-containing bacteria can further transfer the ARGs
by HGT. Gaining prophage influences bacterial fitness through
the transfer of several genes, including ARGs. Under in vitro
conditions, it was demonstrated that bacteria confer fitness
benefits by carrying prophage-encoded ARGs (Haaber et al.,
2016;Wachino et al., 2019;Wendling et al., 2021). Findings of in
silico analysis showed that the role of polyvalent-bacteriophages,
that are capable of infecting more than one host, is important in
the intergeneric transmission of ARGs that encode an ESBL
(bla
CTX-M
), ABC-type efflux permease (mel), and ribosomal
protection protein (tetM) loci (Gabashvili et al., 2020).
Analysis of more than thirty viromes from human and non-
human sources (animals and environment) indicated that the
latter group was a reservoir of ARGs (Lekunberri et al., 2017). In
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org07
chicken feces and water samples, bacteriophage genomes carried
several important ARGs (Yang et al., 2020;Zare et al., 2021).
Moreover, several copies of ARGs, including b-lactam,
aminoglycoside, and fluoroquinolone resistance have been
detected in the DNA of E. coli phage YZ1 (Wang et al.,
2018b). Enterotoxigenic E. coli prophage carried several ARGs,
which expressed resistance to sulfamethoxazole-trimethoprim,
chloramphenicol, tetracycline, aminoglycoside and narrow-
spectrum b-lactamase (bla
TEM-1b
). This MDR transmitting
prophage had Tn2transposon with serine recombinase gene
flanking the bla
TEM-1b
and the IntI1 together with the TnAs2
transposon (Wang et al., 2020a). In E. coli isolates of animal
origin, phage-like plasmid with-mcr1 excised and formed a
circular intermediate before integration into plasmids
containing the ISApl1 element (Li et al., 2017a). This event
may be more complex upon translocation into phage-like
vectors, which can be transmitted via transduction events.
Efflux pump system
Efflux pumps are a mechanism of an advanced defense
system in bacteria. Efflux pump systems (EPS) can force out
antibiotics from the bacterial cell to maintain the antibiotic
concentration below the lethal threshold inside the cell. Efflux
pumps can confer resistance to a single or a structurally diverse
class of antibiotics. The distribution of efflux pump genes and
the upregulation of their expression determines the extent of
resistance to many antimicrobial agents. Generally,
chromosomes encode several MDR efflux pumps and their
expression is controlled by point mutations in the regulatory
genes (Nowak et al., 2015). Efflux pumps can be classified into
several categories based on their structure, the number of
transmembrane spanning regions, energy sources, and
substrates. Accordingly, the major subfamilies of efflux pumps
include, i) Resistance Nodulation Division (RND) family, ii)
Major Facilitator Superfamily (MFS), iii) ATP (adenosine
triphosphate)-binding cassette (ABC) superfamily, iv) Small
Multidrug Resistance family and v) Multidrug and Toxic
compound extrusion family. Several coordinated networks of
efflux transporters have been identified in bacteria. Complex
signaling pathways are involved in the EPS-mediated resistance
mechanisms to protect bacteria (Figure 4).
RND is the major mechanism of MDR in Gram-negative
bacteria. This larger efflux transporter is an inner membrane
protein that networks with a periplasmic fusion protein and an
outer membrane channel protein to form a tripartite complex to
directly export antibiotics from the bacterial cells. Members of
Enterobacteriaceae use AcrAB-TolC and OqxAB-TolC efflux
pumps to resist the action of fluoroquinolones, b-lactams,
tetracyclines, macrolides, oxazolidinone, quinolones,
chloramphenicol (Swick et al., 2011). A three-gene operon
FIGURE 4
Diagrammatic representation of shared regulatory network mechanisms involving antibiotic resistance and virulence. Quorum sensing (QS),
toxin-antitoxin (TAS) and two component systems (TCS) upregulate the biofilm formation encoding genes that successively upregulate quorum
sensing molecules. These molecules influence antibiotic resistance genes and virulence. Up-regulated virulence and antibiotic resistance genes
consequently upregulate QS, TAS and TCS.
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org08
cmeABC is the major EPS in Campylobacter and plays a key role
in mediating resistance to structurally dissimilar antimicrobials.
The multidrug efflux CmeDEF interacts with CmeABC and
increases the antimicrobial resistance and the cell viability
(Akiba et al., 2006). In C. jejuni,CmeCfunctionsasa
multidrug efflux transporter, and overexpression of the cmeGH
operon significantly increases its resistance mostly to
fluoroquinolones as well as exogenous hydrogen peroxide
(Jeon et al., 2011). The tripartite protein components of RND
are post-translationally changed to N-linked glycans in C. jejuni.
The multifunctional role of N-linked glycans stabilizes the
protein complexes, by improving their thermostability and
increasing their propensity for protein-protein interaction,
which in turn facilitates AMR through multidrug efflux pump
activity (Abouelhadid et al., 2020).
Involvement of the other RND-type efflux systems such as
AdeABC, AdeFGH, and AdeIJK are important for intrinsic MDR
in several pathogens. Overexpression of AdeABC and AdeFGH
systems in Acinetobacter baumannii induces resistance to
aminoglycosides, b- lactams, chloramphenicol, fluoroquinolones,
macrolides and tetracyclines (Yoon et al., 2015). AdeABC also
alters membrane-associated cellular functions such as the
formation of biofilm and plasmid transfer. Multi-efflux pumps
simultaneously protect the pathogens against several
antimicrobials. In the three multi-drug efflux pump systems
(MacAB-TolC [ABC efflux], MFS drug transport system, and
AcrAB-TolC) of S. Typhi, tolC,macB,acrA,acrB,andmdfA are
involved inmultiple resistance pathways thatprotect the pathogen
from macrolides, chloramphenicol, tetracycline, novobiocin,
quinolones, fluoroquinolones and b-lactams (Debroy et al.,
2020). The genes related to tripartite efflux pumps mdtEF-tolC
and the ABC family efflux pump macAB-tolC are important in
Shiga toxin-producing E. coli (STEC) O157:H7 (Miryala and
Ramaiah, 2019). About 20 genes are involved in multi-efflux
pumps in this pathogen, which are directly orindirectly
associated with the MDR.
Toxin-antitoxin system
Toxin-antitoxin system (TAS) present in the mobile
genetic scaffolds consists of a stable toxin component that
targets an essential cellular process and an antitoxin that
counteracts the activity of the toxin. Recent findings suggest
that the TAS are mostly used to lower bacterial metabolism
during stress, prevent the invasion of phages, stabilize genetic
elements, and support biofilm formation (Song and Wood,
2020). Depending on the molecular nature and their mode of
interaction with the toxins, TAS is classified into several types.
Importantly, in type I TAS, toxin and antitoxin are protein
and RNA, respectively, but in the type II TAS, both toxin and
antitoxin are proteins that may differ greatly among several
bacterial species. TAS can either be on a plasmid or can be
chromosomally encoded, which is generally associated with
bacterial stress adaptation.
In vancomycin- resistant enterococci (VRE), specificTA
pair, the mazEF system located on plasmids is responsible for the
resistance to most major classes of antibiotics (Moritz and
Hergenrother, 2006). In addition, the plasmid replicon types of
pRE25, pRUM, pIP501, and pHT-bin VRE are known to be
linked to glycopeptide resistance and stabilizing TA systems.
Most of the VRE strains belonged to these plasmid replicon
types assigned to the clonal complex 17 (Rosvoll et al., 2010).
The SplTA is widely present in plasmids harboring the
carbapenem resistance gene that helps in the maintenance of
plasmids and provide stability to the transferred genetic
elements. The SplTA and HigBA are the most prevalent
plasmid-associated TAS found in carbapenem resistant A.
baumannii (Jurenaite et al., 2013). Cross-resistance to
chlorhexidine-colistin has also been reported in
carbapenemase-producing K. pneumoniae that has the type II
TAS (Bleriot et al., 2020). In V. cholerae, the mosAT encoded
TAS present within the ICE-SXT (conferring resistance to
sulfamethoxazole and trimethoprim) element helps to
maintain sulfamethoxazole-trimethoprim resistance (Wozniak
and Waldor, 2009). In Staphylococcus aureus TAS, mazEF
encodes the RNase MazF and the antitoxin MazE. This gene
cluster enhances tolerance to several antimicrobials (Ma
et al., 2019a).
In E. coli and Salmonella, ParDE type II TAS that exists in
Inc (I and IncF-type) plasmids not only helps in the plasmid
stability, stress response, and biofilm formation, but also
supports genes encoding resistance to aminoglycoside,
quinolone, and b-lactams (Kamruzzaman and Iredell, 2019).
IncX plasmids are important in the transmission of carbapenem
and colistin resistance. Sequence analysis of IncX plasmids
indicates the existence of RelE/ParE toxin superfamily within
the IncX1 and IncX4 subgroups (Bustamante and Iredell, 2017).
In MDR IncC plasmids, the TAS functions as an effective
addiction module and maintains plasmid stability even in an
antibiotic-free environment (Qi et al., 2021). In K. pneumoniae,
an IncHI2 plasmid has been linked with HipBA and RelBE TAS,
which helps the plasmid to maintain multiple ARGs, including
catA2, aac(6’)-Ib, strB, strA, dfrA19, bla
TEM-1
, bla
SHV-12
, sul1,
qacED1, ereA, arr2, and aac3 along with several other genes
encoding resistance to heavy metals (Zhai et al., 2016).
Influence of small RNAs network
Regulatory small RNAs (sRNA) are important in stabilizing
the configuration of the bacterial envelope and uptake of
antimicrobials by controlling porins and transporters at the
cell surface. The sRNA network that controls several functions
related to AMR is shown in Figure 5. The post-transcriptional
network of sRNA communication is employed to identify the
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org09
network centers and regulatory functions (Mediati et al., 2021).
Though the sRNAs amply exists within the MGEs, their direct
involvement in the regulation of ARGs has not been studied in
detail. The contribution of sRNAs to intrinsic resistance has
been identified in horizontally acquired ARGs. However, their
AMR-related functions are complex in different bacteria. The
sRNA MicF-mediated repression of outer-membrane porin
OmpF in E. coli reduces membrane permeability to inhibit
cephalosporin, norfloxacin, and minocycline uptake (Cohen
et al., 1988). S. aureus sRNA, SprX specifically downregulates
stage-V sporulation protein-G, and SpoVG, which increases
resistance to glycopeptides (Eyraud et al., 2014). Over-
expression of some of the sRNAs (e.g., Sr0161, Sr006) in P.
aeruginosa increased resistance to meropenem and polymyxin-B
(Zhang et al., 2017). A. baumannii fosfomycin efflux (AbaF) is
one of the primary targets of AbsR25, which negatively regulates
the major facilitator superfamily efflux pump gene abaF
(Sharma et al., 2017). Interruption of this abaF indicates that
it contributes to fosfomycin susceptibility, reduction in biofilm
formation, and virulence. SdsR is one of the highly conserved
enterobacterial sRNAs. In S. sonnei, SdsR promotes resistance to
fluoroquinolone by regulating the expression of an efflux pump
TolC (Gan and Tan, 2019).
Guanosine pentaphosphate/
tetraphosphate signaling
An alarmone, guanosine pentaphosphate or tetraphosphate
([p]ppGpp) is the effector molecule, which is involved in the up-
regulation of several genes involved in the bacterial response to
extracellular stress, including AMR. (p)ppGpp-mediated
stringent response can support microbes to survive even in the
absence of specific resistance genes due to complex modulation
network activities involving several targets/proteins and other
small signaling molecules (Das and Bhadra, 2020). The relA gene
catalyses the synthesis of (p)ppGpp during antibiotic or other
stresses. In P. aeruginosa, mutations in the spoT and dksA
(involved with the stringent response) induce higher levels of
intracellular ppGpp concentration, which supports tolerance to
quinolones (Viducic et al., 2006). In addition, (p)ppGpp helps in
HGT, including the integron-mediated acquisition of AMR gene
FIGURE 5
A schematic representation showing the interplay of different factors influence in antimicrobial resistance. (p)ppGpp increases the efficiency of
HGT, AMR cassette acquisition through IntlI and upregulates the expression of various components of the efflux pumps. Non-coding small
RNAs (sRNAs) play a major role in post-transcriptional regulation of gene expression. This includes, negatively regulated targets of MgrR involved
in LPS modification (sensitivity to Polymyxin B); SdsR, repress the expression of tolC, the gene encoding the OMP of many multidrug resistance
efflux pumps; SdsR also base-pair with mutS mRNA to repair the DNA after exposure to b-lactams; SprX (a.k.a. RsaOR) influence resistance to
glycopeptides by downregulating the SpoVG; DsrA activates the expression of MdtE, which increases efflux system to antibiotic such as oxacillin,
cloxacillin, erythromycin, novobiocin etc. RybB negatively influences the expression of csgD transcription, which is the master regulator of
biofilm formation. sRNAs strongly interact with the co-factor Hfq, which enhances sRNA stability and facilitates base-pairing of sRNAs with
multiple target mRNAs. Small RNAs are typed in dark brown. Solid arrows indicate activating interactions and T-arrows indicate inhibiting
interactions.
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org10
cassettes (Strugeon et al., 2016). In several pathogens, (p)ppGpp
mediates resistance to vancomycin (Enterococcus faecalis),
aminoglycoside (Salmonella), oxacillin (S. aureus), tetracycline
and erythromycin (V. cholerae)(Abranches et al., 2009;
Koskiniemi et al., 2011;Mwangi et al., 2013;Kim et al., 2018).
Quorum sensing network
The intercellular cell to cell communication mechanism
through quorum-sensing (QS) controls the expression of
several genes through signaling molecules called autoinducers,
which plays a significant role in the adaptation and survival of
bacteria. Regulation of the LuxS/AI-2 QS system has been
identified in many bacterial genomes (Waters and Bassler,
2005). One of its functions is AMR that include quinolones
(inhibition of DNA replication by complexing with DNA and
DNA gyrase and/or topoisomerase IV), sulfonamides
(prevention of tetrahydrofolate synthesis by inhibiting
dihydrofolate reductase and dihydropteroate synthetase),
tetracyclines (preventing aminoacyl-tRNA binding to the
ribosomal-A site), b-lactams (preventing transpeptidation) and
glycopeptides (preventing transpeptidation) (Wang et al., 2019).
In addition, LuxS/AI-2 affects drug resistance through biofilm
formation, MGEs, efflux pumps, VraSR-TCS, folate synthesis
pathway, etc (Wang et al., 2019).
Co-factors and co-selection
In bacteria, many co-factors modulate the activity of AMR.
Several findings now describe about the presence of chemicals,
especially the heavy metal contaminations that enhance the
AMR through co-selection. This section highlights the role of
co-factors and co-selection in the development and
dissemination of AMR.
The b-lactam antibiotics interfere with cell-wall biosynthesis
by inactivating penicillin-binding proteins (PBPs), which are
important for bacterial survival. The interaction between cell-
wall integrity and the resistance mechanisms help in
deactivation of cell-wall-targeting antibiotics through cell-wall
recycling pathway. Several Gram-negative bacteria use DNA-
binding proteins for ampicillin resistance such as the LysR-type
transcriptional regulator (AmpR) system to mobilize resistance
mechanisms in response to b-lactams by changing the
composition of the cell wall-associated peptidoglycan (Dik
et al., 2018). The AmpR system also releases GlcNAc-anhydro-
MurNAc-oligopeptides into the periplasm and the
muropeptides are transported into the cytosol through an
ampG-encoded AmpG transporter (Chahboune et al., 2005).
Further, the activation of the amp genes marks the expression of
AmpC b-lactamase because of its cognate regulator AmpR,
which regulates MDR (Dhar et al., 2018). In addition to
carbapenemases, overexpression of AmpC, efflux pumps, or
porin loss might contribute to the carbapenem resistance in
pathogens like K. aerogenes (D'Souza et al., 2021). The network
of AmpC b-lactamase overexpression has been recognized due
to AmpG in conferring resistance to b-lactam antibiotics,
including cephalosporins and carbapenems. Transposon
insertion mutations in the AmpG b-lactamase expression
pathway make the Klebsiella strains susceptible to extended-
and broad-spectrum cephalosporins (D'Souza et al., 2021).
CpxAR is commonly present in Gram-negative bacteria,
which sense and regulate osmotic pressure and also confer
AMR. In the absence of the AcrB efflux pump, the CpxR is
overexpressed, which lead to resistance to b-lactam antibiotics.
Thus, modifications in the expression of outer membrane
proteins (OMPs) can play an important role in acquiring
resistance to aminoglycosides and b-lactams (Hu et al., 2011).
Phosphoethanolamine (PEtN) transferases (eptA and eptB)
confer one of the mechanisms for colistin resistance. eptA
catalyzes the transfer of PEtN from phosphatidylethanolamine
onto the lipid A of LPS and eptB catalyzes the addition of a PEtN
moiety to the outer 3-deoxy-d-manno-octulosonic acid (Kdo)
residue of a Kdo(2)-lipid A. Presence of mcr-1supplements the
activity of eptB gene in higher transcriptional expression when
the E. coli exposed to a sub-inhibitory concentration of colistin
(Elizabeth et al., 2022).
Several other cofactors have been identified for promoting
MDR. Collateral-resistance/allogenous selection occurs when an
antibiotic induces mutation(s) that express resistance to the
second antibiotic. This form of selection has been described in
aminoglycosides, b-lactams, macrolides, tetracyclines, and
quinolones/fluoroquinolones (Baquero et al., 2021). Many
other interactions between antibiotics and biocides/heavy
metals, may have co-selective or counter-selective
consequences on AMR (Gilbert and McBain, 2003;Ciric et al.,
2011;Rensch et al., 2013). The formation of complexes between
metal cations and certain antibiotics and metal-dependent efflux
induces resistance to b-lactam and tetracycline (Wales and
Davies, 2015). Some of the important non-antimicrobial
agents that induce cross-antimicrobial resistance among
pathogenic bacteria is shown in Table 1.
The global repressor, histone-like nucleoid-structuring
protein (H-NS) is a key transcriptional repressor of horizontally
transferred genes in many bacteria. Upregulation and increased
expression of genes associated with aminoglycosides, b-lactams,
chloramphenicol, colistin, sulfonamides, trimethoprim and
quinolones resistance are modulated by the H-NS (Rodgers
et al., 2021). In A. baumannii, H-NS regulates the expression of
genes involved in pathogenesis and resistance to colistin. The
Dhns mutant confirms the role of H-NS as a transcriptional
regulator, ameliorating the A. baumannii transcriptome
associated with AMR.
The SOS response is a conserved regulatory network in
bacteria that has been induced in response to DNA damage.
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org11
SOS response is associated with AMR pathogens. In methicillin-
resistant S. aureus (MRSA), oxacillin is one of the stimulating
factors of a b-lactam-mediated SOS response through lexA/recA
regulators that leads to the increased mutation and development
of resistance. PBP1 also plays an important role in SOS-
mediated recA activation and resistance selection in MRSA
(Plata et al., 2013). Functional analysis showed that PBP1
depletion abolishes both b-lactam-induced recA expression/
activation and increased mutation rates during resistance
selection. Mutations enhancing the AMR involve fitness costs.
However, the specific molecular mechanism of resistance in the
bacterial fitness cost has not been investigated in detail. In P.
aeruginosa, it was shown that the impact of mutations in the
RNA polymerase gene rpoB influences the fitness cost of
rifampin resistance (Qi et al., 2014). This modification occurs
due to alteration in the relative transcript levels of essential genes
that defend against the reduced RNA polymerase activity.
Bacteria recurrently encounter metals in their living
environment, which can either be beneficial or harmful. The
bacteria can use some of the metals as essential micronutrients.
Co-selection of heavy metals and AMR exits as an overlapping
mechanism of physiological intersection (cross-resistance) or
genetic interrelation (co-regulation/co-resistance). An increase
in AMR is associated in part with the co-selection of resistance to
heavy metals and biocides/disinfectants used in livestock
farming. These anthropogenic or non-antimicrobial agents can
induce bacterial adaptations that cause decreased susceptibility
or resistance to one or more antimicrobials even in the absence
of any selection pressure (Table 1). Several cellular mechanisms
are established to support the selection of genetic determinants
associated with AMR. When E. coli strains were exposed to
chlorhexidine digluconate, an increase in resistance to
ampicillin, amoxicillin/clavulanic acid, cefoxitin, cefpodoxime,
and cephalothin has been reported due to an increase in the
RND efflux pump activity and upregulation of genes involved in
cell metabolism (Wesgate et al., 2020).
Presence of plasmid-borne copper resistance genes tcrB and
pcoD are linked with erythromycin, vancomycin, and
tetracycline resistance with the respective encoding genes
ermB, vanA,andtetB in human and animal pathogens
(Hasman and Aarestrup, 2002;Agga et al., 2014). Copper
efflux-associated tcrB and erythromycin resistance erm(B)
genes were transferred by conjugation from the environmental
Enterococcus hirae to E. faecalis (Pasquaroli et al., 2014). Intake
of copper has some influence on AMR. In E. faecalis isolated
from copper-fed pigs, chromosomally located tcrYAZB operon,
tetM,andvanA are identified for copper, tetracycline, and
vancomycin resistance (Zhang et al., 2015a). In livestock
associated MRSA, genes encoding resistance to macrolides
(ermT), tetracyclines (tetL) aminoglycosides (aadT), and
trimethoprim (dfrK) are co-located together with copA,
cadDX,andmco, which encodes resistance to copper and
TABLE 1 Components of non-antimicrobial agents that induce cross-antimicrobial resistance among pathogenic bacteria.
Non-antimicro-
bial agents
Antimicrobial resistance Pathogen Mechanism Reference
As, Cd, Cr, Cu, Hg,
Ni, Pb
Aminoglycoside, Amphenicol,
Cephalosporin, Penicillin, Quinolone, Tetracycline,
Sulphamethoxazole-trimethoprim
E. coli, P.
aeruginosa
Outer membrane
proteins
Choudhury and Kumar, 1996
Co Tetracycline Bacillus subtilis Efflux pumps Cheng et al., 1996
Ag Cephalosporins E. coli Outer membrane
proteins,
efflux pumps
Li et al., 1997
Cd, Zn b-lactams, Erythromycin, Kanamycin, Novobiocin,
Ofloxacin
Burkholderia
cepacia
DsbA–DsbB multidrug efflux
system
Hayashi et al., 2000
Cd, Co, Zn Clindamycin, Erythromycin, Josamycin L. monocytogenes Multidrug efflux system Mata et al., 2000
Vb-lactams, Chloramphenicol, Fluoroquinolones,
Tetracyclines, Ticarcillin, Clavulanic acid
P. aeruginosa MexGHI–OpmD efflux pump,
RND efflux pumps
Aendekerk et al., 2002
BKC Amikacin, Tobramycin P. aeruginosa Efflux pumps Joynson et al., 2002
As, Cr, Cu, Hg, Ni b-lactams, Novobiocin S. Typhimurium Multidrug efflux system Nishino et al., 2007
BKC Ciprofloxacin, Gentamicin L. monocytogenes Efflux pumps Rakic-Martinez et al., 2011
Cu Erythromycin, Tetracycline, Vancomycin Enterococcus spp. Multidrug efflux system Hasman and Aarestrup, 2002;
Agga et al., 2014
TCS Enrofloxacin, Sulphamethoxazole-trimethoprim S. Typhimurium Efflux pumps Gantzhorn et al., 2015
Ag, Cu Aminoglycosides, Macrolides, Tetracyclines,
Trimethoprim
S. Typhimurium Efflux pumps Mourão et al., 2015
As, Cr, Cu, Hg, Ni Chloramphenicol, Cefotaxime Penicillin, Tetracyclines, S. Typhimurium, P.
aeruginosa
Multidrug efflux system Teixeira et al., 2016
Cd Ampicillin, Chloramphenicol, Ceftizoxime, Ciprofloxacin S. Typhi Multidrug efflux system Kaur et al., 2021
Ag, silver; As, arsenic; BKC, benzalkonium chloride; Cd, cadmium; Co, cobalt; Cr, chromium; Cu, copper; Hg, Mercury; Ni, nickel; Pb, lead; TCS, Triclosan; V, vanadium; Zn, Zinc.
Ramamurthy et al. 10.3389/fcimb.2022.952491
Frontiers in Cellular and Infection Microbiology frontiersin.org12