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MICROBIAL DRUG RESISTANCE

Volume 25, Number 6, 2019


ª Mary Ann Liebert, Inc.
DOI: 10.1089/mdr.2018.0319

Multidrug-Resistant Bacteria
and Alternative Methods to Control Them:
An Overview

Roberto Vivas,1 Ana Andréa Teixeira Barbosa,1 Silvio Santana Dolabela,1 and Sona Jain1,2

Antibiotic resistance is one of the greatest challenges in the health system nowadays, representing a serious
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problem for public health. Initially, antibiotic-resistant strains were restricted to the hospital environment, but
now they can be found everywhere. Globalization, excessive use of antibiotics in animal husbandry and
aquaculture, use of multiple broad-spectrum agents, and lack of good antimicrobial stewardship can be listed as
the factors most responsible for the spread of antibiotic resistance. The increase in the prevalence of antibiotic-
resistant pathogens implies having fewer antimicrobial agents to treat infections. The estimate is that by 2050,
there will be no effective antibiotic available, if no new drug is developed or discovered. This raises the need to
search for alternative methods of controlling antibiotic-resistant pathogens. Considering this problem, the
objective of this review is to outline the most frequent antibiotic-resistant bacteria and describe the advanta-
geous and limitations of alternative methods that have been proposed to control them.

Keywords: MRSA, VRE, antibiotic resistance, alternative therapies, bacteriocins, phage therapy

Introduction The increase in the prevalence of antibiotic-resistant


pathogens implies having fewer antimicrobial agents to treat
infections caused by these bacteria.5 The estimate is that by
O ne of the greatest challenges in the health system
nowadays is the rise of pathogenic species resistant to
antibiotics. Infections caused by multidrug-resistant (MDR)
2050, there will be no effective antibiotic available to treat
infections if no new drug is developed or discovered.6 This
bacteria are increasingly common and represent a serious raises the need to search for alternative methods of con-
problem for public health. Initially, these species were re- trolling antibiotic-resistant pathogens, and there are in fact
stricted to the hospital environment, but now they can be many research groups around the world actively looking for
found everywhere. Among the gram-positive species, Sta- new solutions. The objective of this review is to list the most
phylococcus aureus, Enterococcus faecium, Enterococcus frequent antibiotic-resistant bacteria and describe alternative
faecalis, and Streptococcus pneumoniae are the most frequent methods that have been proposed to control them.
problem.1 Among the gram-negative strains, Escherichia coli,
Klebsiella pneumoniae, Pseudomonas aeruginosa, and Aci-
Common Antibiotic-Resistant Bacterial Species
netobacter baumannii have been most common.2,3
Antimicrobial resistance in these strains is genetically Health care-associated infections raise morbidity and
determined and most commonly mediated by the acquisition mortality rates worldwide. The increase in mortality is di-
of extra-chromosomal genetic elements via horizontal gene rectly related to antimicrobial resistance which makes
transfer.4 Low permeability of the outer membrane in gram- antibiotic therapy more restrictive, thus also making it dif-
negative bacteria, efflux pumps, production of degrading ficult to treat infections caused by multiresistant microor-
enzymes, and modification of targets are examples of ganisms. At the beginning of the 21st century, infections
mechanisms used by bacteria to resist the toxicity of anti- with carbapenem-resistant gram-negative bacilli, mainly
biotics. Globalization, excessive use of antibiotics in animal Enterobacteria, became a big public health problem.7 MDR
husbandry and aquaculture, use of multiple broad-spectrum gram-negative bacteria including A. baumannii, Pseudomonas
agents, and lack of good antimicrobial stewardship can be aerugionosa, extended-spectrum beta-lactamase (ESBL)-
listed as the factors most responsible for the spread of an- producing Enterobacteria, and carbapenem-resistant En-
tibiotic resistance species.2 terobacteria (CRE) are considered the main causative agents

1
Programa de Pós-Graduação em Biologia Parasitária, Universidade Federal de Sergipe, São Cristóvão, Sergipe, Brasil.
2
Programa de Pós-Graduação em Biotecnologia Industrial, Universidade Tiradentes, Aracaju, Sergipe, Brasil.

890
ANTIBIOTIC RESISTANCE AND ALTERNATIVE METHODS 891

of nosocomial infections.8 Methicillin-resistant S. aureus as evidenced by current scenarios, methicillin-resistant


(MRSA) and vancomycin-resistant Enterococcus (VRE) strains arose quickly.4
have been reported recently to be the most common bacterial Since its emergence in 1961, MRSA has spread world-
pathogens, and besides, hospitals have also been isolated wide, and infections caused by this microorganism are re-
from foods of animal origins, water, and animals (Tables 1 garded as one of three major infectious diseases threatening
and 2). MDR P. aeruginosa, Carbapenem-resistant En- human health. This bacterium apart from causing infections
terobacteriaceae, and A. baumannii have been mainly asso- in cutaneous lesions can result in severe cases of pneumo-
ciated with clinical samples, but some strains have also been nia, meningitis, endocarditis, septicemia, and even systemic
isolated from foods, animals, and water (Tables 3–5). infections, with risk of death.10 Compared to infections
All these strains have been associated with lethal infec- caused by S. aureus strains sensitive to methicillin, those
tions, and in this section, their main characteristics will be caused by MRSA usually have more severe clinical mani-
addressed. festations and are the most difficult to treat, as methicillin
resistance indirectly affects other virulence factors and en-
hances the pathogenesis of the bacterium.11
Methicillin-resistant S. aureus
According to the data published by the Center for Disease
S. aureus is a gram-positive ubiquitous strain known to Control and Prevention (CDC) of the United States, more
produce several virulence factors that facilitate disease than 80,000 illnesses and 11,000 deaths in the hospital set-
causation and help rapidly develop antimicrobial resistance ting were caused by MRSA during 2011.12 The European
against antimicrobial agents used for its control, a feature Centre for Disease Prevention and Control also published in
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that increases the importance of this microorganism as a 2013 that S. aureus is among the most frequently isolated
pathogen.9 Initially, infections caused by S. aureus were pathogen from health care-associated infections. Togneri
easily controlled by penicillin. However, S. aureus acquired et al.10 made a retrospective review for 12 years (2002–
a plasmid-encoded beta-lactamase that conferred resistance 2013) of infections caused by S. aureus in adult patients
to penicillin already in the 1940s, shortly after its intro- (AP) and in pediatric patients (PP) visiting the Hospital
duction for clinical use. To solve this problem, a new, Interzonal General of Treble Evita de Lanús in Argentina
semisynthetic, narrow spectrum, beta-lactamase-resistant and concluded that methicillin resistance increased from
antibiotic named methicillin was developed and introduced 28% to 78% in AP and stayed around 50% in PP. Chmie-
to combat penicillin-resistant strains in 1959. Unfortunately, larczyk et al.13 isolated MRSA strains from patients in 12

Table 1. Methicillin-Resistant Staphylococcus aureus Isolated from Different Sources


and Countries in the World
Frequencya
Source Type Period/year (%) Country Refs.
149
Children and adult patients with skin and soft-tissue CA-MRSA 2009/2011 2.6 China
infections
150
Emergency departments CA-MRSA 2006/2007 2.4 USA
51
Hospital patients CA-MRSA 2011/2012 — Malaysia
HA-MRSA
152
Nasal swabs HA-MRSA — 15.1 Oman
Cell phone swabs HA-MRSA 9.0
153
Pork processing plant LA-MRSA 2010/2011 24.8 Canada
154
Hospital patients HA-MRSA 2010 — Brazil
CA-MRSA
155
Railway stations CA-MRSA 2013/2014 1.58 China
13
Infections from hospitalized patients HA-MRSA 2013 15.1 Poland
CA-MRSA
156
Chicken meat — 2013 6.0 Egypt
157
Milk — — 34 Pakistan
158
Zoo animals LA-MRSA 2013/2016 — United
Kingdom
159
Dairy sheep — 2012 0.7 Italy
160
Pus and blood samples from hospitalized patients HA-MRSA 2009/2012 — Zambia
161
Nasal secretion of healthy children CA-MRSA 2012 15.7 Brazil
162
Nasal secretion of healthy carrier individuals — 2010/2011 1.3 Spain
163
Raw meat products — 2012 1.2 USA
164
Pigs — 2016 99 Portugal
165
Blood samples at a Japanese University Hospital HA-MRSA 2012/2015 — Japan
CA-MRSA
a
AmongStaphylococcus aureus strains.
—, Not reported; MRSA, methicillin-resistant S. aureus; CA-MRSA, community-associated MRSA; LA-MRSA, livestock-associated
MRSA.
892 VIVAS ET AL.

Table 2. Vancomicin-Resistant Enterococcus Isolated from Different Sources


and Countries in the World
Source Period/year Frequencya (%) Country Refs.
166
Wild animals 2014–2015 — Spain
167
Sewage — — Israel
168
Meat preprarations — 23.8 Spain
169
Wastewater effluent and surface water used for 2014 — Netherlands
drinking water production
170
Poultry infections 2011–2014 — Poland
171
Rectal cultures from inpatients 2012–2013 16.3 Taiwan
172
Reclaimed water used for spray irrigation 2009–2010 0.1–42.6 USA
173
Clinical samples 2009–2010 7.9 India
174
Clinical samples 2010–2012 — Brazil
175
Clinical samples of urine, blood, wound swabs and 2014 7 Ethiopia
other body fluids
176
Laundry facility that processes clinical linens 2015 53% in the dirty area and 8% in USA
the clean area.
177
Clinical samples 2015 — Iran
178
Patient with bacteraemia — — Greece
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a
Among Enterococcus strains.

different hospitals in southern Poland and the prevalence of an expanded reservoir of MRSA.15 Consequently, MRSA has
MRSA was higher in patients aged 80 years and more. also been isolated from animal based food products, including
These results are just a few examples that show how com- meat and milk products, such as cheese,16 making it also an
mon and persistent MRSA strains are worldwide. important food-borne microorganism.17
Initially, MRSA was restricted to hospital environment The first case of LA-MRSA from a human source was
(HA-MRSA: health care-associated MRSA), but rapidly, described in 2005, and van Loo et al.18 observed that LA-
since the 1990s, this microorganism has also been found MRSA strains in human population were responsible for
associated with community settings (community associated >20% of all MRSA in the Netherlands. Since then, trans-
MRSA [CA-MRSA]) and has been isolated from the most mission of MRSA from animals to humans and vice-versa
diverse sources worldwide (Table 1). Apart from HA-MRSA has been constantly described.19 These findings show that
and CA-MRSA, livestock-associated MRSA (LA-MRSA) some S. aureus strains might not be strongly host species-
have been isolated from several animals such as cattle, pork, specific, and LA-MRSA can cause infection in humans.20 It
chicken, and horse, among others and associated with zoo- is believed that some LA-MRSA lineages have derived from
notic pneumonia, endocarditis, and necrotizing fasciitis since human strains following genetic adaptation.
1975.10,14 The fact that MRSA has been frequently isolated Molecular and microbiological studies have demonstrated
from livestock animals has been worrying, as it has revealed that HA-MRSA and CA-MRSA strains have distinct genetic

Table 3. Carbapenem-Resistant Enterobacteriaceae Isolated from Different Sources


and Countries in the World
Source Strains Period/year Country Refs.
179
Clinical samples Klebsiella oxytoca 2013–2014 Iran
180
Clinical samples from outpatients Escherichia coli 2013 Italy
Klebsiella pneumoniae
Proteus mirabilis
181
Clinical samples E. coli 2010–2014 China
K. pneumoniae
182
Clinical samples from inpatients K. pneumoniae 2014–2015 Vietnam
183
28 hospitals from Brazil E. coli Brazil
K. pneumoniae
Enterobacter spp.
184
Post-acute-care hospitals K. pneumoniae 2008–2013 Israel
185
Clinical samples K. pneumoniae 2010–2014 Poland
186
Bloodstream isolates at medical centers K. pneumoniae Enterobacter spp. 2013 USA
E. coli
187
Clinical samples from inpatients K. pneumoniae 2007–2014 England
188
Dairy cows E. coli China
189
Beef, pork, and chicken samples E. coli 2013–2014 United Kingdom
190
River water E. coli Algeria
K. pneumoniae
ANTIBIOTIC RESISTANCE AND ALTERNATIVE METHODS 893

Table 4. Carbapenem-Resistant Acinetobacter baumannii Isolated from Different Sources


and Countries in the World
Source Period/year Frequencya (%) Country Refs.
191
Dairy cattle 2014 0.3 USA
192
Clinical samples 2008–2014 — French Guiana
193
Clinical samples from hospitalized patients 2015–2016 — Iran
194
Health institutions 2008–2013 — Brazil
195
Hospitals 2008–2010 — Colombia
196
Clinical samples 2012–2014 74 Vietnam
197
Inpatient units of a tertiary hospital 2014–2015 97.7 Nepal
198
Clinical samples 2012–2013 45 China
199
Companion animals 2002–2013 — Germany
200
Meat samples 2013–2014 — Portugal
201
Lettuce and fruit 2013–2014 — Portugal
a
Among A. baumannii strains.

and phenotypic profiles.21,22 HA-MRSA is considered an Vancomycin (VAM) and daptomycin (DAP) are often the
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opportunistic pathogen and CA-MRSA is capable of causing antibiotics of last resort for many S. aureus infections.26
infections in healthy people. Since its inception, CA-MRSA However, MRSA strains have shown a MDR phenotype,
has become the most significant pathogen in several parts of and the most worrying problem is the appearance of strains
the world and its prevalence has surpassed the cases ac- exhibiting resistance or reduced susceptibility to these an-
quired in hospital.10 Moreover, CA-MRSA is also infiltrat- tibiotics. Three classes of vancomycin-resistant S. aureus
ing health care settings and infecting patients in many that differ in vancomycin susceptibilities have emerged:
regions worldwide. There is little evidence of the spread of vancomycin-intermediate S. aureus (VISA), heterogeneous
HA-MRSA outside the hospital setting23 although a HA- VISA (hVISA), and high-level vancomycin-resistant S. au-
MRSA variant strain causing infections in the community reus (VRSA).27
has been reported.24 VRSA species arose due to the acquisition of the vanA
As is well established by several authors, methicillin re- gene from vancomycin-resistant enterococci and have been
sistance in S. aureus is mediated by a penicillin-binding reported in the United States,28 Iran,29 and India.30 The
protein (PBP2A) encoded by the mecA gene, that is carried isolation of VISA and hVISA seems to be a serious emerg-
on a mobile genetic element designated staphylococcal ing problem as they show high spreading potential. After the
cassette chromosome mec (SCCmec). Moreover, methicillin first reports of VISA and hVISA from Japan,31 it did not
resistance determinants are different among HA-MRSA and take long for this resistance phenotype to be recognized
CA-MRSA. HA-MRSA strains present a relatively large around the world.27 The in vivo development of VISA
mobile genetic element known as SCCmec types I, II, or III, and hVISA has led to treatment failures and prolonged
which confers resistance to many classes of non-beta-lactam hospitalization.32
antibiotics. In CA-MRSA, a smaller element, including DAP is bactericidal against MRSA and VISA strains and
SCCmec IV and V, confers resistance, and these strains are was used to treat skin/soft-tissue infections caused by
susceptible to many non-beta-lactam antibiotics.21 In addi- MRSA in 2003 in the United States.33 Syrogiannopoulos
tion, a large numbers of CA-MRSA strains produce the et al.34 showed that DAP alone or in combination with other
Panton Valentine Leukocidin, potent virulence factor that antimicrobial agents was efficacious to control MRSA in-
has greater cytotoxic activity against polymorphonuclear fections in children. However, studies are showing that
cells.25 clinical S. aureus strains have developed DAP resistance

Table 5. Multidrug-Resistant Pseudomonas aeruginosa Isolated from Different Sources


and Countries in the World
Source Period/year Frequencya (%) Country Refs.
202
Burn patients 2013–2014 38 Iran
203
Clinical samples 2011–2013 — France
204
Wastewater collections from a hospital 2012 — Brazil
205
Clincal samples 2011 21.3 Iraq
206
Hospital environment 2015 84.5 Ethiopia
207
Burn patients 2014–2015 48.38 Algeria
208
Cystic fibrosis — — Spain
209
Clinical samples from immunocompetent patients 2007–2013 34 Spain
210
Clinical samples 2014–2016 — India
211
Urine samples 2004–2015 — Hungary
212
Clinical samples — — Pakistan
a
Among P. aeruginosa strains.
894 VIVAS ET AL.

during DAP treatment.35 These findings raise the need to a drug of choice for the treatment of infections caused by
research for alternative methods for the control of MRSA. ESBL producing enterobacteriaceae for years, which is also
one of the main factors responsible for the emergence of
Vancomycin-resistant Enterococcus CREs through selective pressure.44
Among the Enterobacteriacea, K. pneumoniae is the most
Enterococci are indigenous flora of the gastrointestinal
common bacterium exhibiting carbapenem resistance fol-
tracts of animals and humans, and the species E. faecium
lowed by Enterobacter species. Others such as E. coli have
and E. faecalis have heightened interest because of their
been reported less frequently. CREs have emerged in recent
ability to cause serious infections and their intrinsic resis-
decades, but have become one of the major concerns of
tance to antimicrobials, including Vancomycin.36 VRE
hospital infection control services. High prevalence of in-
faecium (VREfm) has disseminated rapidly in hospitals in
fections by these bacteria is present in several countries on
many parts of the world since 2012. In contrast, vancomycin
all continents, leading to an important restriction in treat-
resistance has been reported considerably less frequently in
ment options.45 It is considered endemic in the north-eastern
E. faecalis globally.37
United States (mainly in the state of New York), Puerto
VRE was first isolated in Europe in 1986 from clinical
Rico, Colombia, Greece, Italy, Israel, China, and Brazil, and
samples. One year later, the first VRE isolates were
is also an important cause of nosocomial infections in these
identified in the United States. In Europe, the cases were
countries.46
related to community infections, transmitted by animal-
Early reports of CREs were related to overexpression of
based food products to humans, and associated with the
ampC, and ESBL associated with loss or modifications of
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use of Avorpacina (an antimicrobial of the group of gly-


porins. However, later they were confirmed to produce a new
copeptides) as a growth promoter in livestock. In the
type of enzymes (carbapenemases) with the capacity to inac-
United States, the predominance of VRE was observed in
tivate any type of beta-lactam, including the carbapenems.47
hospital setting which spread rapidly in the 1990s, prob-
The first carbapenemase was identified more than 20
ably due to the use of vancomycin. A similar situation
years ago in 1982, in Enterobacter cloacae, at a hospital in
occurred in Europe, where the spread of hospital-related
London, England.48 Subsequently, Serratia marcescens en-
VRE occurred a decade later in the 2000.38 VRE has been
zymes (SME) were described in S. marcescens.49 In 1995, in
an emerging problem in some Brazilian hospitals since the
Japan, blaIMP-1 gene was described in a plasmid in Ser-
1990s. The first report of a VRE infection in Brazil oc-
ratia. In 2001, in the United States, first blaKPC-1 gene was
curred in 1996 in Curitiba. Since 1997, the occurrence of
identified in K. Pneumonia.50 Since then, the number of new
outbreaks has been documented in hospitals from other
carbapenemases have increased and proliferated around the
Brazilian cities as well.39
world, generating one of the major therapeutic and epide-
VRE was described as ‘‘serious’’ (the second highest
miological concerns.51
threat level among organisms causing severe human infec-
According to the classification proposed by Ambler, the
tions) by CDC. Among hospitalized patients, over 20,000
betalactamases are divided into four groups (A–D) with
experience an infection due to VRE each year and it is
respect to their functional and molecular properties. Groups
estimated that 1,300 deaths occur directly due to these re-
A, C, and D are serine enzymes, whereas group B are me-
sistant infections in the United States.12 VRE is a common
talloenzymes. Carbapenemases belong mainly to three ma-
cause of nosocomial infections and has also associated with
jor groups of betalactamases A, B, and D, with differences
urinary tract infections, hospital-acquired bloodstream in-
not only in their genetic and biochemical properties but also
fections, endocarditis, abdominal and pelvic abscesses, and
in their clinical characteristics due to difference in their
chronic periodontitis.40
antimicrobial resistance and epidemiological features.52
Resistance to vancomycin is determined by one of nine
Carbapenemases represent the most versatile enzymes in
resistance determinants (vanA, B, C, D, E, G, L, M, and N),
the beta-lactamase family. The group of carbapenemases
but the vanA and vanB genotypes predominate worldwide.
class A includes members of families SME, IMI (Imipene-
These genetic determinants could be carried in the mobile
mase), NMC (Non Metalobetalactamase), GES (extended
genetic element, such as Tn1546, mostly located on con-
spectrum Guyana betalactamase), and K. pneumoniae Car-
jugative plasmids (variants of the vanA and vanB-type) or
bapenemase (KPC). Of these, KPCs are the most predomi-
located on the chromosome (vanC).41 The first case of VRE
nant, found mainly on plasmids in K. Pneumonia.47,49 Since
transmitting the vanA gene to MRSA (VRSA) was reported
its initial recognition, KPC has been also detected in many
in the United States in 2002, increasing the threat of in-
other strains, including Klebsiella oxytoca, Enterobacter
creased colonization and infections by VRE.42
spp., E. coli, Salmonella spp., Serratia spp., Citrobacter
Linezolid is the first-line drug for treatment of VRE in-
freundii, Proteus mirabilis, A. baumannii, P. aeruginosa,
fections, but the first reports of Linezolide-resistant VRE
and Pseudomonas putida.49
have appeared, reducing treatment options.38 Some authors
Class D carbapenemases, known as oxacillinases (OXA),
have also suggested daptomycin as an effective agent in the
consist of OXA derivatives, a family detected in A. bau-
treatment of VRE infections.43
mannii, but already also described in enterobacteria. These
beta-lactamases exhibit activity against carbapenems but do
Carbapenem-resistant enterobacteria
not degrade cephalosporins.47
The emergence of CRE is one of the major public health The metalobetalactamases belong to the families IMP,
problems in the world. Carbapenems are important for the VIM, SPM, GIM, and SIM and were detected mainly in
empirical treatment of critically ill patients at the risk of P. aeruginosa. One of the major threats among this carba-
multiresistant bacterial infection.44 They have been used as penemase group is New Delhi Metalobetalactamase (NDM),
ANTIBIOTIC RESISTANCE AND ALTERNATIVE METHODS 895

which was discovered in 2008 in Sweden in K. pneumoniae lactam antibiotics. Betalactamases are the most impor-
from an Indian patient. NDM has been found to exhibit a tant cause of bacterial resistance, mainly in gram-negative
rapid distribution in hospitalized patients throughout the bacilli.61
world in other enterobacterias as well.53 Resistance to carbapenems may occur by combining
CREs are spread across several countries and have different mechanisms such as change in the affinity to PBPs
emerged as a major threat to hospitalized patients. In the and efflux pumps. However, the main forms of resistance
case of infections caused by K. pneumoniae-producing to carbapenems are the expression of carbapenemases of
carbapenemases, the mortality rate may be as high as 75%, group B and D of Ambler, metallo-b-lactamases, and OXA,
but the associated factors such as age, comorbidities, func- respectively.61
tional status, and underlying disease may influence this
rate.54 Multidrug-resistant Pseudomonas
P. aeruginosa is a nonfermenting gram-negative bacillus,
Carbapenem-resistant A. baumannii widely distributed in nature and in hospital environment.
Responsible for nosocomial infections, it is one of the most
The genus Acinetobacter consists of gram-negative, aer-
important opportunistic pathogen causing bloodstream in-
obic cocobacillus that are ubiquitous, immobile, non-
fection, urinary tract infection, and ventilator-associated
fermenting, catalase positive, and oxidase negative. The A.
pneumonia, especially in critically ill patients receiving in-
calcoaceticus-A. baumannii complex is responsible for most
tensive care.62 Moreover, it is also highly resistant to many
of the community or hospital-acquired infections.55
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currently used drugs making it a major public health con-


The different species of Acinetobacter present in diverse
cern.63
natural habitats can be isolated from the soil, water, vege-
P. aeruginosa is intrinsically resistant to several antimi-
tables, and animal and human hosts. They are part of the
crobials and has great versatility to acquire new genes that
commensal flora of human skin and mucous membranes. A.
confer resistance to many other drugs. The antibiotic resis-
baumannii can survive in a variety of settings in the hospital
tance of this bacterium is mainly due to the low cell wall
environment: in dialysis machines, mechanical ventilation
permeability of this microorganism, which restricts the up-
systems, water sources, skin and mucous membranes of
take of antibiotics, associated with wide resistance mecha-
health professionals and patients, medicinal preparations,
nisms, such as efflux pumps and enzymes, which modify or
and disinfectants.56
degrade antibiotics and drug targets.64
For a long time Acinetobacter was considered an oppor-
Carbapenems are usually part of the first line of
tunistic agent with low pathogenicity. However, the pres-
therapeutic choice for treatment of Multdrug-resistant
ence of several virulence factors that allow its survival in the
Pseudomonas (MDR) P. aeruginosa infections. Resistance
hospital environment and enhance its capacity to cause
to carbapenems occurs mainly due to the impermeability
disease have resulted in it being one of the main causes of
to the drug, loss of porin, and action of efflux pumps, but
nosocomial infections in many countries.57 Recently, the
the production carbapenemases is the most important
World Health Organization announced this microorganism
mechanism.65
as the first priority pathogen, for which research and de-
The main carbapenemases expressed by P. aeruginosa are
velopment for new antibiotics are urgently needed.58
from class B of Ambler, called metallo-ß-lactamases (IMP,
A. baumannii is increasingly implicated for causing
VIM, SPM, GIM, NDM, and SIM families). These enzymes
health-associated infections, which confer a high risk of
confer resistance to carbapenems and are encoded in plas-
morbidity and mortality to patients. This bacterium can also
mids and integrons of class 1, which are responsible for their
be highly resistant to antimicrobials, especially those iso-
rapid global spread by horizontal transfer.66
lated from the patients in the intensive care units. Infections
P. aeruginosa resistant to carbapenems (PARC) has be-
caused by MDR A. baumannii strains may worsen patient
come one of the major problems for hospitals. Outbreaks of
outcomes due to inadequate initial therapy, limited treat-
infection caused by PARC have been reported by several
ment options, and high toxicity of available therapies. Risk
countries, including Brazil.66 The emergence of antimicro-
factors for infection and colonization by MDR A. baumannii
bial resistance is directly related to an increase in the pa-
include prolonged hospitalization especially in intensive
tient’s hospital stay, increased hospitalization costs, and an
care unit, mechanical ventilation, central venous catheteri-
increase in the mortality rate. In PARC infections, mortality
zation, urinary catheterization, previous antimicrobial ex-
may reach 53.6%.67
posure, increased disease severity, and exposure to surgical
and invasive procedures.59 In the United States, A. bau-
Alternative Methods Proposed for the Control
mannii is responsible for 12,000 cases of health-associated
of Multiresistant Pathogens: Advantages
infections annually, of which 7,200 are multiresistant
and Limitations
causing 500 deaths per year.60
This microorganism has progressively accumulated re- With the emergence of MDR pathogens, alternative
sistance to penicillins, cephalosporins, quinolones, and methods for their control have been studied by several re-
aminoglycosides. Consequently, carbapenems have become search groups. Among these, the use of bacteriocins, es-
the therapy of choice for serious infections. The mecha- sential oils (EOs), antibodies, and phage therapy have been
nisms of resistance of A. baumannii can be intrinsic or ac- reported as promising by several authors. In addition, re-
quired and are mediated by several factors, such as loss of search has also been focused on the use of quorum-sensing
membrane permeability and, more significantly, the pro- inhibitors (QSI) and nanotherapy (Fig. 1). Bacteriocins have
duction of betalactamases, enzymes that degrade beta- been proposed since the 1960s, and antibodies and
896 VIVAS ET AL.

FIG. 1. Published articles to date on the


use of alternative methods in the control of
multidrug-resistant pathogens. Source:
PubMed.

bacteriophages have been present since 1970’s. EOs have struction of the bacterial cell wall and considerably reduced
been studied and proposed to control MDR pathogens since the mortality and weight loss of MRSA-challenged mice.
1990, and more recently (since the year 2000), quorum Many properties of bacteriocins, such as high stability,
sensing inhibitors and nanotherapy have also gained status low toxicity, and both broad and narrow spectra of activity,
as a promising method for the control of these resistant make them good alternative to antibiotics.81 In addition,
strains. A brief review about these alternative methods will some bacteriocins, such as lantibiotics, have a dual mech-
be made in the next subsections addressing their importance anism of action not shared by other therapeutic compounds
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and limitations. in use, which reduces the probability of selecting resistant


strains.82 Unlike most antibiotics, which are secondary
metabolites, bacteriocins are ribosomally synthesized,
Bacteriocins
which allows bioengineering to improve its efficiency.
Bacteriocins are antimicrobial peptides ribosomally syn- Bacteriocins are also sensitive to proteases in the human
thesized by almost all bacterial species and have a varied stomach, not posing any risk of toxicity to the humans or to
mechanism of action and spectrum of activity. A good re- gut flora.73
view on bacteriocin structure, classification, and general Among the lantibiotics, nisin is the most studied bacte-
characteristics can be found in Snyder and Worobo.68 The riocin that has a GRAS status and has been approved by
most studied bacteriocins with known industrial applications Food and Drug Administration (FDA) as food additive since
are those produced by lactic acid bacteria, mainly due to 1988.83 In the last decades, nisin has also been proposed for
their generally recognized as safe (GRAS) status. Since their therapeutic usage.84 Studies have shown that nisin can
discovery, these bacteriocins have been extensively studied prevent the growth of drug-resistant bacterial strains, such as
for their application in food industry and, more recently, MRSA, S. pneumoniae, Enterococci, and C. difficile. It is
their therapeutic potential has been reported by several au- well known that bacteriocins have antimicrobial activities
thors. Bacteriocins have been proposed as potential anti- mainly against gram-positive strains. However, many stud-
cancer69 and anticarcinogenic agent70 and also suggested for ies have demonstrated that nisin in combination with other
the treatment of skin infections71 and many other diseases.72 antibiotics can also be effective against gram-negative
Besides, some authors suggest that bacteriocins may be- pathogens.85
come a potential candidate for replacing antibiotics to treat As described above, bacteriocins have the potential to
MDR pathogens in the future.73 Okuda et al.74 tested the control antibiotic-resistant pathogens and are among the best
effect of three different bacteriocins against MRSA biofilms alternative methods proposed for this purpose. However,
and showed that the bacteriocins formed stable pores on the certain points need to be carefully studied before their
membrane of target cells and were effective to prevent or clinical use: the first being the bacteriocin resistance in vitro.
cure biofilm-associated infections. Duracin 61A was found Resistance to bacteriocin in vitro has been mostly associated
to be effective against Clostridium difficile, VRE, and with physiological adaptation, unlike antibiotic resistance
MRSA, showing synergistic effect when used in combina- that is related to genetic modification.86 Considering that
tion with reuterin or vancomycin. The authors concluded bacteriocins have not yet been used on the same scale as
that durancin 61A alone or in combination with other bac- antibiotics, an existing bacteriocin-resistant population does
teriocins or antibiotics may provide a possible therapeutic not exist. Thus, before the therapeutic use of bacteriocins, it
option for the treatment of infections by these pathogens.75 would be interesting to develop strategies to avoid in the
Shokri et al.76 showed the potential use of a bacteriocin future the current problem with resistance to traditional
produced by an E. faecium strain against VRE. Phumi- antibiotics. The best way to use bacteriocins therapeutically
santiphong et al.77 isolated and characterized a novel bac- could be in combination with traditional antibiotics.
teriocin produced by a strain of Enterococcus faecalis that The second challenge involves development of a better
showed high antibacterial activity against VRE and MDRE way to administer bacteriocin therapeutically, since en-
(MDR enterococci). The lantibiotic NAI-107 also showed zymes present in the gastrointestinal tract inactivate them.
bactericidal activity against MRSA and VRE in animal Topical, intranasal or intravenous use may be an alternative.
models.78 Lacticin 3,147 and nisin were tested against Some preliminary studies87 showed that nisin administered
MRSA and VRE strains and also showed potent activity.79 intranasally inhibited the growth of S. aureus in the respi-
Wang et al.80 tested the efficacy of sublancin for the pre- ratory tract of immunocompromised rats. Heunis et al.71
vention of MRSA-related intraperitoneal infection in mice also demonstrated that nisin-containing nanofiber in wound
and verified that the antimicrobial activity involved the de- dressings has the potential to treat S. aureus skin infections.
ANTIBIOTIC RESISTANCE AND ALTERNATIVE METHODS 897

Nanoparticles (NPs) could also be used as delivery system positive and gram-negative strains related to upper respira-
for bacteriocins.88 tory tract infections. Cardamom oil loaded chitosan nano-
particles also showed excellent antimicrobial potential
against ESBL and MRSA. Rai et al.97 also suggest that the
Essential oils
use of EOs in combination with NPs may exert synergistic
Another alternative tool that has been frequently dis- antimicrobial activity, leading to the development of novel
cussed by several authors as a solution to control MDR approach for treatments of MDR pathogens. Besides, EOs
pathogens are EOs extracted from medicinal plants.89 EOs could also be incorporated into topical creams and nasal
are defined as volatile, natural, and fragrant liquids that can sprays to treat skin wounds and upper respiratory tract in-
be extracted from different parts of the plants especially fections, respectively.102
leaves and flowers, and are produced by plants to protect Bacterial strains showing resistance to EOs are not de-
themselves from diverse pathogenic microbes. Due to their scribed yet. Moreover, Turchi et al.103 showed that the ex-
antimicrobial activities, EOs have been extensively studied posure of S. aureus strains to a subinhibitory concentration
to be used for the treatment of a wide range of microbial of EOs displayed an increased sensitivity in more than 95%
infections.90 EOs have shown antimicrobial activity against of the cases. These results suggest that resistance to EO’s
MRSA,91 MDR strains of K. oxytoca,92 b-lactamases and could be difficult to arise. At the same time, EOs have not
carbapenemases producing E. Coli,90 erythromycin-resistant been used on the same scale as antibiotics, so an existing
Group A streptococci,93 and MDR-A. baumannii89 among EO-resistant population does not exist. Therefore, to avoid
others. emergence of resistant strains, similar to bacteriocins, the
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EOs have shown potential as inhibitory agents for use in best way to use EOs in the control of MDR pathogens could
MRSA biofilm-related infections.94 Lahmar et al.95 showed be in combination with another antimicrobial agents, such as
that three different EOs were effective in reducing the re- commercial antibiotics, bacteriocins, or phage therapy.
sistance of MRSA to amoxicillin, tetracycline, piperacillin,
ofloxacin, and oxacillin, and resistance of A. baumannii to
Phage therapies
amoxicillin and to ofloxacin in interactive manner. They
also showed synergism with the antibiotics ofloxacin and Phage, also known as bacteriophage, is a virus that infects
novobiocin against the ESBL producing E. coli. In another bacteria. Their therapeutic potential in medicine to control
study, the bactericidal activity of herbal volatile oil extract MDR pathogens is due to their specificity and potency in
was tested against MDR A. baumannii and exhibited potent inducing lethal effects in the host bacterium by cell lysis.22
antibacterial activity with minimal bactericidal concentra- Bacteriophage therapy was first utilized in the 1930’s, but
tion (MBC) values around 0.5.89 EOs and nonvolatile the discovery of antibiotics, a more comfortable way to
compounds derived from chamaecyparis obtusa also showed control infectious diseases, led to a rapid decline in the in-
antimicrobial activity against MRSA and VRE strains.96 terests and investments within this field of research. Al-
Cinnamon bark oil was reported to have antimicrobial ac- though phage therapy was given the GRAS status by the
tivity against clinical isolates of MDR P. aeruginosa with FDA in 2006, it is still not approved for use in humans. The
minimum inhibitory concentration (MIC) of 0.0562– key regulatory barriers continue to prevent its approval by
0.225% v/v and MBC of 0.1125–1.8% v/v. Synergistic ef- the US FDA and by the European Medicines Agency.104
fect was also observed when used in combination with co- The worldwide rise of MDR pathogens and the decrease
listin. The authors proposed that this oil could be used as an in research and development of new antibiotics have stim-
alternative for the treatment of infections caused by MDR ulated interest in phage therapy and several studies have
P. aeruginosa.63 shown its efficacy against antibiotic-resistant pathogens.105
Many other studies are showing the beneficial effects of Phage therapy has been shown to be effective against ty-
EOs when two or more EOs are mixed together or when phoid fever and S. aureus bacteremia106 and also against
used in combination with commercial antibiotics.91 When MRSA strains.107 Rasool et al.107 showed that the phages
blended with antimicrobial agents, the constituents of EOs exhibit lytic activity against MRSA both in vivo and in vitro
can unlock the cell membrane channels, thus opening the experiments in another report, Jennes et al.108 described that
passage of antimicrobial agents to reach their internal target phage therapy was effective in the treatment of colistin-
sites.97 This is a great strategy to avoid selection of resistant only-sensitive P. aeruginosa septicemia in a patient with
strains in the future. acute kidney injury. Cheng et al.104 showed a high effi-
Low water-solubility and high vapor pressure are some ciency of a broad host range lytic phage against E. faecalis
characteristics that limit the utilization of EOs in commer- strains, including vancomycin-resistant strains. Chadha
cial applications.98 Consequently, EOs are difficult to be et al.109 showed the potential of liposome entrapped phage
used in aqueous-based products, and they have a tendency to cocktail for treating K. pneumoniae-mediated infections.
volatilize over time, thereby reducing their antimicrobial Gelman et al.110 tested a combination of bacteriophages and
activity. An effective means of overcoming some of these antibiotics against VRE Enterococcus faecalis in a mouse
limitations could be the utilization of EOs vapors, currently model and concluded that this combination imparts an ad-
being studied for decontaminating environment and wound ditional beneficial effect on the treatment success, as a
dressings.99 Moreover, to improve water dispersion and single injection of the bacteriophage cocktail was sufficient
protect EOs from degradation, nanosized formulations to completely reverse the 100% mortality trend caused by
emerge as a viable solution.100 VRE.
Ghaderi et al.101 produced nanoemulsion-based delivery The use of phage therapy has been proposed via intra-
systems containing EOs that were effective against gram- venous106 and oral routes,111 as liposome-entrapped phage
898 VIVAS ET AL.

cocktail,109 and for vaccine development.112 Some advan- 20% based on early treatment. QS system from this bacte-
tages of using phage therapy instead of antibiotic include rium was also inhibited by bioactive molecules extracted
lower developmental costs; 100% bactericidal nature; high from leaves of Kalanchoe blossfeldiana.124 D’Angelo
specificity thus also preventing secondary infections; and the et al.125 tested FDA-approved drugs as antivirulence agents
requirement of only a single dose or phage multiplication at targeting the pqs QS system of P. aeruginosa and found that
the infection site compared to antibiotics that require several clofoctol (approved for clinical treatment of pulmonary in-
doses. In addition, phage therapy can be used in combination fections caused by gram-positive bacteria) has considerable
with traditional antibiotics, or a combination of diverse clinical potential as an antivirulence agent for the treatment
phages as a cocktail to increase its antibacterial spectrum.113 of P. aeruginosa lung infections. Anti-QS system against
The use of whole phage to treat infection could have P. aeruginosa was also observed in a study with EOs derived
some disadvantages, as the genetic material in temperate from Ferula (Ferula asafoetida L.) and Dorema (Dorema
phage could increase the virulence of certain species of aucheri Bioss.), exhibiting anti-QS activity at 25 mg/mL of
bacteria through transduction of virulence genes. An ex- concentration.126
ample is the acquisition of the gene encoding the Panton In the last 20 years, various QSI from plants, animals, and
Valentine Leucocidin toxin, causing ‘‘scalded skin syn- microorganisms have been characterized and animal and
drome,’’114 common in CA-MRSA strains that increase their plant infection models have demonstrated their antibacterial
pathogenicity. In this way, instead of the whole phage, some efficacy against QS pathogens.119 QSI could thus serve as a
studies have proposed the use of bacteriophage-encoded en- good alternative to treat infections caused by MDR pathogens.
dolysins that destroy the bacterial cell wall, resulting in cell However, its application in clinical medicine still requires
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death through lysis.105 Some advantages of using endolysins more research. According to Baldry et al.121 application of QSI
as pointed by Fischetti et al.115 include their ability to retain might have adverse interactions with host factors in favour of
specificity without affecting commensal flora, rapid bacterial host colonization.
lysis, genetically nontransducible nature, and lesser proba-
bility of acquiring resistance due to the essential bacterial
Antibodies
binding sites. These endolysins have demonstrated antibac-
terial activity against gram-positive and gram-negative strains The use of antibodies has also been proposed as a prom-
and also against MDR pathogens such as MRSA.116 ising strategy for the containment of MDR bacterial strains,
as they can enhance phagocytosis or activation of comple-
ment proteins. To maximize antibody action, some authors
Quorum-sensing inhibitors
have proposed the use of more than one isotype, generally a
QSI are another alternative method to control MDR path- mix of Immunoglobulin M (IgM), Immunoglobulin G (IgG),
ogens proposed in the last years. Quorum sensing (QS) is an and Immunoglobulin A (IgA).127,128 A polyclonal prepara-
intercellular bacterial communication used to coordinate tion enriched with IgM immunoglobulins commercially
group behaviours in a cell density-dependent manner. At high available is Pentaglobin (Biotest AG, Dreieich, Germany),
concentrations, pathogens can switch their transcription pro- which contains 76% IgG, 12% IgA, and 12% IgM (IgGAM).
files to an invasive phenotype, including genes related to To date, there are at least three other licensed monoclonal
antibiotic tolerance and virulence determinants, and cause antibodies products against infectious targets: Palivizu-
disease.117 In this way, QS systems constitute important an- mab,129 Raxibacumab,130 and Panobacumab.131
tivirulence targets, as they often regulate the expression of Several studies have shown the effectiveness of this al-
several virulence genes simultaneously.118 QSI act by in- ternative treatment, which is also one of the most studied
hibiting cell-to-cell communications and, consequently, dis- methods (Fig. 1). Lu et al.132 tested Panobacumab, a fully
ease evolution, enabling the host immune system to prevent human monoclonal antibody of the IgM/k isotype directed
bacterial colonization and/or to clear an established infection. against the lipopolysaccharide (LPS) O-polysaccharide moi-
This antimicrobial control relies on reducing the burden of ety of P. aeruginosa, which enhances the phagocytosis of
virulence rather than killing the bacteria.119 this pathogen. The authors concluded that this therapy is
Hansen et al.120 tested the use of lactam hybrid analogs of safe and is associated with high clinical cure and survival
solonamide B and autoinducing peptides to inhibit the Agr rates in patients developing nosocomial P. aeruginosa infec-
QS system, which is a major inducer of virulence in CA- tion. Rossmann et al.128 demonstrated that IgGAM induces
MRSA. The authors concluded that this and closely related in vitro killing of MDR clinical isolates of K. pneumoniae
compounds were 20- to 40-fold more potent in AgrC inhi- through enhancement of phagocytosis. Results obtained by
bition than the starting hit compound. Baldry et al.121 also Giamarellos-Bourboulis et al.127 also showed that IgGAM
showed that solonamide B and analogs alter immune re- was effective as an adjunct to antimicrobial treatment for the
sponses to S. aureus, but do not exhibit adverse effects on management of septic shock caused by MDR gram-negative
immune cell functions. However, the authors also stated that bacteria. Diago-Navarro et al.133 observed that anticapsular
application of compounds inducing an Agr-negative state antibodies promoted extracellular processes killing, comple-
may have adverse interactions with host factors in favour of ment deposition, deployment of neutrophil extracellular traps,
host colonization. RNAIII-inhibiting peptide was also ap- and opsonophagocytosis of carbapenem-resistant Klebsiella
pointed by Simonetti et al.122 as useful for the control of pneumonia. The author concluded that the tested antibodies
MRSA in infected wounds by inhibiting QS systems. could ultimately treat or protect patients infected or at risk of
Hraiech et al.123 have shown that a lactonase isolated infection by this MDR bacterium.
from Sulfolobus solfataricus efficiently inhibited QS in Antibody conjugates with antimicrobial agents have also
P. aeruginosa, reducing the mortality in rats from 75% to been shown to be effective to control MDR strains by
ANTIBIOTIC RESISTANCE AND ALTERNATIVE METHODS 899

several other authors. Lehar et al.134 verified that an anti- showed that this NP enhanced bacterial activity of the an-
body–antibiotic conjugate eliminates intracellular S. aur- tibiotic against MSRA. For in vivo application, the stability
eus01, and this conjugate was superior to vancomycin for of this formulation remains to be improved.145 Combination
treatment of bacteraemia. Antibody-directed photodynamic of metal oxide NPs with ciprofloxacin, erythromycin,
therapy was very effective in killing different MRSA strains, methicillin, and vancomycin was reported to effectively
in all growth phases and may be a good candidate for a reduce the MICs of these antibiotics against VRE.146 Khan
novel treatment of MRSA infections.135 et al.147 tested the photo inactivation of MDR strains of
As stated by Szijártó et al.,136 passive immunization was a E. coli and K. pneumoniae by monomeric methylene blue
standard treatment option in the preantibiotic era, and as we conjugated gold NPs and obtained 97% killing of MDR
move toward a possible postantibiotic era, it may be prudent bacteria. They put forward the possibility of this NP-based
to reconsider the merits of this therapy. The actual advances photodynamic therapy as a potential therapeutic approach
in the research and biopharmaceutical manufacturing capa- against MDR infections. Similarly in another report, tri-
cities enable the development of highly purified humanized methyl chitosan-capped silver NPs were shown to have high
antibodies against a range of pathogenic microorganisms. antibacterial activity with a MIC of £12.25 mg/mL against
Moreover, MAbs are directed against nonhuman targets and clinically isolated MDR A. Baumannii.148 NPs thus seem to
in general have an excellent safety record. Similar to other be a good alternative with high potential to solve the
alternative methods, antibodies can complement antibiotic emerging bacterial MDR.
therapy. A challenge of this therapy is to find molecular de-
terminants of the pathogens that are accessible on the cell
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Concluding Remarks
surface.136
Antibiotic resistance is one of the greatest health prob-
lems we will have to face in the coming years. Considering
Nanotherapeutics that little advancement has been made in the discovery of
Besides the methods described above, some authors have novel antibiotics especially those effective against drug-
also proposed the use of nanotechnology in the control of resistant strains, use of alternative methods could be the best
MDR strains. Some of the NPs proposed are silver NPs,137 way to resolve this problem. As discussed in this review,
Gold NPs,138 Photoexcited Quantum dots,139 anf Core–shell there are several promising alternatives to circumvent this
Magnetic Nanoparticle (MNP)140 among others. As stated problem. It is up to the competent authorities to accelerate
by Singh et al.141 ‘‘Nanomaterials possess unique proper- and encourage further research and release appropriate fi-
ties, and multiple bactericidal mechanisms render them nancial support for the successful implementation of these
more effective than conventional drugs.’’ In addition, Zaidi methods. The alternative methods listed in this review
et al.88 also affirm that NPs have potential to overcome the probably will be successfully used in combination with the
problem of antibiotic resistance in the present days and ‘‘to antibiotics available and not completely replace antibiotics
revolutionize the diagnosis and treatment of bacterial in- as treatment agents.
fections.’’
The use of NPs can enhance the antimicrobial activity of Acknowledgments
available drugs by functioning as drug delivery systems that
can be targeted precisely.88 NPs material could be metallic The authors thank the Conselho de Desenvolvimento
or organic and has been found to synergize the killing effect Cientıfico e Tecnologico (CNPq), Brasılia, Brazil, the
of antibiotics142 and could also have the same effect in Fundação de Apoio a Pesquisa a InovaçãoTecnologica do
combination with other antimicrobial agents, such as bac- Estado de Sergipe (FAPITEC), Sergipe, Brazil, for provid-
teriocins and EOs.100,105 Generally, the antimicrobial ac- ing fellowships and financial support, which support the
tivity of NP involves a triple mechanism of action: oxidative research with bacteriocins, essential oils, and antibiotic-
stress, metal ion release, and nonoxidative stress,143 together resistant pathogens in our laboratory.
with the effect of any other antimicrobial that can be com- This research did not receive any specific grant from
bined with NPs. This multiple mechanism of action makes it funding agencies in the public, commercial, or nonprofit
more difficult to acquire resistance. Moreover, NPs enhance sectors.
drug solubility, concurrent delivery of multiple drugs, and
prolonged systemic circulation.144 Disclosure Statement
Yuan et al.137 used silver NPs to control drug-resistant
No competing financial interests exist.
strains of S. aureus and P. aeruginosa and showed that it
induced cell death of these strains. Niemirowicz et al.139
anslyzed the synergistic effects of core–shell MNPs when References
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