ISSN 0891-4168, Molecular Genetics, Microbiology and Virology, 2019, Vol. 34, No. 1, pp. 16–24. © Allerton Press, Inc., 2019.
Russian Text © The Author(s), 2019, published in Molekulyarnaya Genetika, Mikrobiologiya i Virusologiya, 2019, No. 1, pp. 17–24.
EXPERIMENTAL WORKS
Class 1 and 2 Integrons in Hospital Strains of Gram-Negative
Bacteria Isolated in Moscow and in Regions of the Russian Federation
E. S. Kuzinaa, *, E. I. Astashkina, A. I. Leva, E. N. Ageevaa, N. N. Kartseva,
E. A. Svetocha, and N. K. Fursovaa
a
State Research Center for Applied Microbiology and Biotechnology, Federal Service for Surveillance
on Consumer Rights Protection and Human Well-Being, Obolensk, Moscow oblast, 142279 Russia
*e-mail: e.leonova@mail.ru
Received April 10, 2018; revised April 23, 2018; accepted November 15, 2018
Abstract—Natural systems of cloning and expression of mobile gene cassettes caught by site-specific recombination, class 1 and 2 integrons, play an important role in mobilization and spread of genetic determinants
of antibiotic resistance in gram-negative bacterial human pathogens, especially in a hospital environment.
The gene cassettes localized in variable parts of integrons determine resistance to antibacterial drugs (AD) of
different functional classes. The aim of the work is the detection and characteristic of class 1 and 2 integrons
in gram-negative bacteria isolated in multidisciplinary hospitals of Moscow and other regions of the Russian
Federation in 2003–2015. Clinical strains of gram-negative bacteria (n = 1248) mainly had multidrug resistance phenotype (94%). An amount of 10% of strains were resistant to AD of three functional groups; 19%,
four; 42%, five; 17%, six; and 7%, seven. A high level of resistance of the studied strains to beta-lactams is
associated with the presence of beta-lactamase genes of blaTEM (35% strains), blaSHV (25%), blaCTX-M (38%),
blaOXA (31%), blaVIM (3%), and blaNDM (2%) types; to AD of other functional groups, with the presence of
class 1 integrons (59%) and class 2 integrons (8%). Most class 1 integrons (54%) and class 2 integrons (88%)
contained in its variable part 22 variants of gene cassette arrays in class 1 integrons and 4 variants in class 2
integrons. During the study, 31 types of gene cassettes were identified (including the most widespread, aadB,
aacA4, aacC1, aadA1, aadA2, aadA5, blaVIM-2, dfrA1, dfrA7, dfrA12, orfC, orfE, orfY, and sat1) associated
with the resistance of strains to aminoglycosides, chloramphenicol, sulfonamides, and beta-lactams, as well
as orf cassettes encoding the proteins with unknown functions. New gene cassette arrays were identified:
dfrA12s-orfF-aadA2 (In1249) and dfrA1-IS911-sat1-aadA1 (not numbered).
Keywords: gram-negative bacteria, multidrug resistance, mobile genetic elements, class 1 integrons, class 2
integrons, gene cassettes
DOI: 10.3103/S0891416819010051
accumulating these genes as gene cassettes [9] and
providing their expression from a strong integron promoter [10]. Integrons are widespread in the genomes
of bacteria isolated in different ecological niches: in a
hospital environment, in environmental objects, and
in human and animal organisms [11–14].
To date, based on differences in the primary structure of the integrase gene, five integron classes have
been described; among them, class 1 and 2 integrons
are the most common [15]. A number of 31 078 class 1
integrons and 27 624 class 2 integrons were present in
the GenBank NCBI database on February 14, 2018
(https://www.ncbi.nlm.nih.gov/). More than 130 gene
cassettes and more than 80 gene cassette arrays in class 1
integrons and 6 types of gene cassette arrays in class 2
integrons have been described [16]. In the Russian
Federation, class 1 and 2 integrons are also widespread
in the genomes of multiresistant strains of gram-negative bacteria [17–21].
INTRODUCTION
At present, hospital infections are a large problem
for health care all over the world [1–3]. In Russia, the
portion of isolates of gram-negative bacteria among
bacterial causative agents of nosocomial infections
(NI) was 76.5% in 2013–2014 [4–6]. In the last two
decades, a trend towards an increase in the amount of
multidrug-resistant (MDR), extremely resistant (ER),
and panresistant (PR) bacteria among the causative
agents of NI has been detected [7].
Mobile genetic elements (MGEs) (plasmids, bacteriophages, transposons, IS elements) play a large
role in mobilization and spread of genetic determinants of antibiotic resistance in bacteria [8]. Integrons
(natural systems of cloning and expression of mobile
gene cassettes caught by site-specific recombination)
are spread by means of MGE and play a special role,
since they are an “antibiotic resistance gene depot”
16
CLASS 1 AND 2 INTEGRONS IN HOSPITAL STRAINS OF GRAM-NEGATIVE BACTERIA
The aim of this work is the detection and characterization of class 1 and 2 integrons in the genomes of
gram-negative bacteria isolated in Moscow and other
regions of the Russian Federation in 2003–2015.
MATERIALS AND METHODS
17
formed as instructed by “The European Committee
on Antimicrobial Susceptibility Testing. Breakpoint
Tables for Interpretation of MICs and Vone Diameters.
Version 7.1, 2017-03-10” (http://www.eucast.org/). Susceptible E. coli ATCC 25922 strain and highly resistant
E. coli ATCC 35218 strain were used as internal standards.
Ethical Requirements
Our laboratory had no direct contact with patients
from hospitals. The studied bacterial strains were
obtained in collaboration with the microbiological
laboratories of OOO National Agency for Clinical
Pharmacology and Pharmacy, Moscow; Children’s
Scientific and Clinical Center for Infectious Diseases,
Federal Medical and Biological Agency, St. Petersburg; Burdenko National Medical Research Center
for Neurosurgery, Ministry of Health, Moscow; and
Infectious Clinical Hospital No. 1, Moscow Healthcare Department. In their names, the studied strains
in their contain no personal data about patients, such
as surname, first name, ethnicity, age, religion, or
gender. In accordance with the legislation of Russian
Federation, each patient signed an informed consent
for medical procedures and diagnostic tests upon
admission to the hospital.
Detection of Antibiotic-Resistance Genes
The genes encoding five types of beta-lactamases
(blaCTX-M [22], blaTEM [23], blaSHV [19], blaOXA [24],
blaVIM [25], and blaNDM [26]), as well as class 1 [27]
and class 2 [28] integrases and cassette arrays of class 1
and 2 integrons [29], were determined by the PCR
method with specific primers. The composition of the
reaction mixture and amplification modes corresponded to those previously described for the designated primers. Thermolysates were used as matrices for
amplification [19]. PCR was carried out in GradientPalmCycler (Corbertt Research, Mortlake, Australia)
and Tertsik (DNA Technology, Protvino, Russia) with
subsequent electrophoretic detection of amplification
products in 1.5% agarose gel.
DNA Sequencing
Bacterial Strains and Cultivation
Antibiotic resistant clinical strains of gram-negative bacteria were isolated in Moscow and other
regions of Russia (n = 1248) in 2003–2015, including
strains from the Enterobacteriaceae family (n = 694)
and the group of nonfermenting gram-negative bacteria (n = 552). Bacteria were cultivated at a temperature
of 37°C in a Mueller–Hinton broth and agar nutrient
media (Himedia, Mumbai, India). The species identification of bacteria was conducted on Vitek-2 Compact (Biomerieux, Lyon, France) and MALDI-TOF
Biotyper (Bruker, Karlsruhe, Germany) devices. Bacterial isolates were stored in 40% glycerol at a temperature of –70°C.
Determination of Sensitivity to Antibacterial Drugs
Minimum inhibitory concentrations (MICs) of the
antibacterial drugs: ampicillin (AMP), amoxicillin/clavulanic acid (AMC), amoxicillin–sulbactam (AMS), cefuroxime (CXM), cefoxitin (CEX), cefotaxime (CTX),
ceftriaxone (CRO), ceftazidime (CAZ), cefoperazone–
sulbactam (CFP), cefepime (FEP), imipenem (IPM),
meropenem (MEM), doxycycline (DOC), tigecycline
(TGC), ciprofloxacin (CIP), chloramphenicol (CHL),
gentamicin (GEN), tobramycin (TOB), amikacin
(AMK), trimethoprim (TMP), cotrimoxazole (CTZ),
nitrofurantoin (NIT), and colistin (CST) were determined on a Vitek-2 Compact device (Biomerieux,
Lyon, France). Interpretation of the results was per-
Sequencing reaction was performed by means of an
ABI PRISM BigDyeTM Terminator v. 3.1 kit (Thermo
Fisher Scientific, Waltham, United States) on an
automatic ABI PRISM 3100-Avant DNA sequencer
(SYNTOL, Moscow, Russia).
Bioinformatics Analysis
Computer analysis of DNA sequences was conducted by means of the Vector NTI9 (Invitrogen,
Waltham, United States) and CHROMAS (Technelysium, Pty Ltd., http://technelysium.com.au) programs and the BLAST web resource (http://blast.
ncbi.nlm.nih.gov/Blast.cgi). The analysis of integron
structure was conducted by means of the INTEGRAL
web resource (http://integrall.bio.ua.pt/?).
Counting the number of references to integrones in
GenBank database was conducted on March 10, 2018,
by searching for the gene cassette names in the
“Nucleotide” section of the NCBI web resource
(https://www.ncbi.nlm.nih.gov/).
Deposition of DNA Sequences in the GenBank Database
Ninety-five nucleotide sequences of integron cassette arrays of 22 class 1 integrons and 20 nucleotide
sequences of integron cassette arrays of four class 2
integrons have been deposited in the GenBank database (Table 1).
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KUZINA et al.
Table 1. Gene cassette arrays of class 1 and 2 integrons identified in clinical strains of gram-negative bacteria in the GenBank
database
Integron
(INTEGRAL
database)
Integron
class
Gene cassette array
1
1
1
1
1
aacA4
aacA4-cmlA1j
aacA4-orfD
aacA7-smr2-orfD
aacC1-orfX-orfY-aadA1
In46
In838
ND
In673
In561
1
aadA1
In2
1
1
1
1
1
1
1
1
1
aadA2
aadA7
aadA6-orfD
aadB
aadB-aadA1y
aadB-catB3
blaOXA30-aadA1
blaPSE1
dfrA12-orfF-aadA2
In127
In142
In51
In7
In822
In299
In322
In167
In27
1
1
dfrA12s-orfF-aadA2
dfrA17-aadA5
In1249
In54
1
1
dfrA1-aadA1
dfrA1-orfC
In369
In363
1
1
1
1
dfrA5-ereA2
dfrA7
estX
orfD2-aacA4'-17orfE14-catB8
dfrA12-sat2-aadA1
dfrA1-IS911-sat1-aadA1
dfrA1-sat2
dfrA1-sat2-aadA1
In398
In22
ND
In609
2
2
2
2
In-2-4
ND
In2-3
In-2-4
Number of placed nucleotide sequence
of gene cassette array in GenBank database
Number of references
to integron in GenBank
database on March 10, 2018
HQ832472, HQ832473, JN003857
HM043570, HM043571, HM569733
GQ924771
HQ832478, HQ832479
KM009103, KM009104, KM009105,
KR610434
GQ924774, GQ924775, GQ924776,
GQ924777, KP789949, KP902674,
KU860564
GU001948
—
HQ832477, KP713392, KU870999
GQ924772, GQ924773
HQ914241, KU901703, KY885012
HQ914240
GQ924769, JN003856
HQ832476
GQ924762, GQ924763, GQ924764,
GQ924765, GQ924766, GQ924767,
GU001949, HM043572, HM043573,
HM043574, HM569734, KJ363320,
KM009101, KM236804, KP789948,
KP796139, KP902672, KP965723, KR610433
KT316808
GQ896493, GQ896494, GQ896495,
GQ896496, GQ896497, GQ896498,
GQ896499, GQ896500, GQ896501,
GU055937, KF952266, KJ579283, KM009102,
KM085438, KP713389, KP713390, KP713391,
KP789947, KP789950, KP902673, KR610432,
KT175892, KT175893, KT175894, KT175895,
KT305944, KT305945, KT305943, KT316804,
KT316805, KU860565
GQ924770, KR610435, KT305946
KC862254, KC862255, KC862256,
KF971879
GQ924768
KP789951
KP965724
HM485586
5960
5960
39
3
45
6652
4993
151
39
14597
14597
42
6543
0
196
214
1220
4
77
16
918
3298
482
KJ579284
HM592262
KP796141, KP796142
HM043575, HM043576, HM043577,
KJ633801, KM009106, KM009107,
KM085439, KM085440, KP271998,
KP713393, KP796140, KP965725, KT175896,
KT316806, KT316807, KX274124
13
2
1302
1093
ND, integron number not determined.
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(a)
100
80
60
40
20
0
AMP
AMC
AMS
CXM
CEX
CTX
CRO
CAZ
CPS
FEP
IPM
MEM
DOC
TGC
CIP
CHL
GEN
TOB
AMK
TMP
CTZ
NIT
CST
Portion of resistant strains, %
CLASS 1 AND 2 INTEGRONS IN HOSPITAL STRAINS OF GRAM-NEGATIVE BACTERIA
Portion of resistant strains, %
Antibacterial drugs
25
(b)
20
15
10
5
0
1
2
3
4
5
6
7
Number of AD functional classes, pieces
NGNB
EB
Fig. 1. Antibiotic resistance phenotypes of gram-negative bacterium strains.
(a) Sensitivity to antibacterial drugs: AMP, ampicillin; AMC, amoxicillin/clavulanic acid; AMS, amoxicillin–sulbactam; CXM,
cefuroxime; CEX, cefoxitin; CTX, cefotaxime; CRO, ceftriaxone; CAZ, ceftazidime; CFP, cefoperazone–sulbactam; FEP,
cefepime; IPM, imipenem; MEM, meropenem; DOC, doxycycline; TGC, tigecycline; CIP, ciprofloxacin; CHL, chloramphenicol; GEN, gentamicin; TOB, tobramycin; AMK, amikacin; TMP, trimethoprim; CTZ, cotrimoxazole; NIT, nitrofurantoin;
CST, colistin; (b) portion of strains simultaneously resistant to several functional classes: AD, antibacterial drugs; EB, enterobacteria; NGNB, nonfermenting gram-negative bacteria.
RESULTS AND DISCUSSION
Collection of Studied Strains and Their Sensitivity
to Antibacterial Drugs
Clinical strains of gram-negative bacteria (n = 1248),
including Pseudomonas aeruginosa (n = 320), Klebsiella pneumoniae (n = 271), Acinetobacter baumannii
(n = 232), Escherichia coli (n = 191), Enterobacter spp.
(n = 132), Proteus spp. (n = 67), Citrobacter freundii
(n = 13), Serratia spp. (n = 8), Morganella morganii
(n = 7), Salmonella enterica (n = 2), Achromobacter
xylosoxidans (n = 2), Providencia spp. (n = 2), and Shigella flexneri (n = 1), were isolated from the respiratory
system (n = 493), urinary system (n = 379), surgical
wounds (n = 159), digestive tract (n = 77), blood (n = 60),
nervous system (n = 28), and skin and mucous membranes (n = 15) from patients of multidisciplinary hospitals in Moscow and other regions of the Russian
Federation in 2003–2015, as well as from hospital
environment. The analysis of sensitivity to antimicrobial drugs demonstrated the prevalence of strains
resistant to beta-lactams, including to penicillins (99%
strains), cephalosporins (95%), and carbapenems (20%);
as well as to aminoglycosides (87%), chloramphenicol
(74%), and sulfonamides (72%) (Fig. 1a). Multidrug
resistance (MDR) phenotype (resistance to antimicrobial drugs of 3 and more functional classes according to the classification of A.P. Magiorakos et al. [7])
was detected in 94% strains of the collection. Among
MDR strains, 10% were resistant to 3 functional
groups of drugs; 19%, to 4; 42%, to 5; 17%, to 6; and
7%, to 7 (Fig. 1b).
Genetic Determinants of Resistance to Beta-Lactams
A high level of resistance of the studied strains to
beta-lactams (penicillins, cephalosporins, and car-
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KUZINA et al.
bapenems) is associated with the presence of beta-lactamase genes of blaTEM (35% strains), blaSHV (25%),
blaCTX-M (38%), blaOXA (31%), blaVIM (3%), and
blaNDM (2%) types (Fig. 2). It should be emphasized
that different beta-lactamase genes are typical for different bacterial species. Thus, blaSHV-type genes were
detected only in the K. pneumoniae (92% of strains),
blaVIM-type genes were detected only in the P. aeruginosa (17%), and blaOXA-type genes (blaOXA-40-, blaOXA-23-,
and blaOXA-51-type) were detected only in the A. baumannii (88%).
Class 1 and 2 Integrons
During the study, 842 integrons were detected,
including 737 class 1 integrons (59% strains) and 105
class 2 integrons (8% strains). In addition, integrons
were detected in 43% of strains of enterobacteria and
in 25% of strains of nonfermenting gram-negative
bacteria. The largest number of class 1 integrons was
detected in E. coli, P. aeruginosa, and K. pneumomiae,
and the largest number of class 2 integrons was found
in P. mirabilis (Table 2). Most class 1 integrons (54%)
and class 2 integrons (88%) contained in their variable
part arrays of the gene cassettes associated with strain
resistance to antibacterial drugs of different functional
groups (aminoglycosides, chloramphenicol, sulfonamides, and beta-lactams), as well as orf cassettes
encoding proteins with unknown functions.
Gene Cassette Arrays of Class 1 and 2 Integrons
During the study, 22 variants of gene cassette arrays
in class 1 integrons and 4 variants in class 2 integrons
were detected (Fig. 3). Class I integrons had arrays
consisting of one gene cassette (aacA4, aadA1, aadA2,
aadB, blaPSE1, dfrA7, estX), two gene cassettes
(aacA4-cmlA1j, aacA4-orfD, aadA6-orfD, aadB-aadA1y,
aadB-catB3, bla-OXA30-aadA1, dfrA17-aadA5, dfrA1aadA1, dfrA1-orfC, dfrA5-ereA2), three gene cassettes
(aacA7-smr2-orfD, dfrA12-orfF-aadA2, dfrA12s-orfFaadA2), and four gene cassettes (aacC1-orfX-orfYaadA1; orfD2-aacA4'-17-orfE14-catB8). Class 2 integrons contained arrays out of two gene cassettes
(dfrA1-sat2) and three gene cassettes (dfrA12-sat2aadA1, dfrA1-IS911-sat1-aadA1, dfrA1-sat2-aadA1).
Estimation of the prevalence of the gene cassette
arrays identified in this study based on a representation of annotated integron sequences in bacterial
genomes in the GenBank database demonstrated that
class 1 integrons (n = 62597) are much more common
than class 2 integrons (n = 2410). Among the class 1
integrons that we identified, the integrons carrying
one gene cassette (n = 33120) and two gene cassettes
(n = 28537) were most represented in GenBank database on March 10, 2018, while the integrons with three
cassettes (n = 413) and four cassettes (n = 527) were
Portion of strains, %
20
EB
40
NGNB
30
20
10
0
blaTEM
blaSHV* blaCTX-M blaOXA** blaOXA-48 blaVIM*** blaNDM
Beta-lactamase genes
Fig. 2. Representation of beta-lactamase genes in gramnegative bacterium strains.
*, blaSHV-type genes detected only in K. pneumoniae; **,
blaVIM-type genes detected only in P. aeruginosa; ***, blaOXA (blaOXA-40-, blaOXA-23-, and blaOXA-51-type) genes
detected only in A. baumannii; EB, enterobacteria;
NGNB, nonfermenting gram-negative bacteria.
less represented. The arrays with two gene cassettes
(n = 1302) and with three gene cassettes (n = 1108)
were described in class 2 integrons (Table 1).
Identification of New Integron Gene Arrays
A new class 1 integron, which was assigned the
number In1249 in the INTEGRAL database, was
identified in E. coli I-7433 clinical strain isolated from a
patient’s urine in a Moscow hospital in 2014. Sequencing
of variable part of this integron detected the presence of
three gene cassettes (dfrA12s-orfF-aadA2), and the
dfrA12s gene cassette (GenBank KT316808) is a new
Table 2. Representation of class 1 and 2 integrons in gramnegative bacteria
Number
Species of bacteria of strains,
pcs
Number of strains carrying
integrons (portion, %)
class 1
class 2
E. coli
191
131 (69)
22 (12)
K. pneumoniae
267
140 (52)
10 (4)
64
27 (42)
48 (75)
Other enterobacteria
172
129 (75)
22 (13)
A. baumannii
228
113 (50)
1 (0.4)
P. aeruginosa
320
196 (61)
1 (0.3)
6
1 (17)
0 (0)
1248
737 (59)
105 (8)
P. mirabilis
Other NGNB
Total
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CLASS 1 AND 2 INTEGRONS IN HOSPITAL STRAINS OF GRAM-NEGATIVE BACTERIA
Intl1
attl aacA4
In46
Intl1
attl
aadA1
ND
In2
In127
aadA2
Intl1
attl
Intl1
attl aadA7
aacA4
cmlA1
attC
In673
Intl1
attl
Intl1
attl
Intl1
attl
aacA4
attC orfD
aadB
Intl1
attl
In299
Intl1
attl
Intl1
attl
Intl1
attl
dfrA7
attl
estX∆
In54
In369
In363
In398
Intl1
aadA2
dfrA12s orfF
aadA2
Intl1
attl
Intl1
attl
Intl1
attl
Intl2
attl
Intl2
attl
Intl2
attl
Intl2
attl
attC
attC
attC
orfD
attC
attC
attC
aacA4 orfE
attC
aacC1
attC
catB8
attC
attC
orfC
In561
attC aadA1
drfA7
attl
orfF
attl
blaOXA-1
In322
Intl1
catB3
attC
dfrA12
Intl1
attC
orfD
attC aadA1
aadB
smr
attl
In1249
In609
aadB
aacA7
Intl1
In27
aacA6 attC orfD
In822
In7
ND
attl
In51
In142
In22
Intl1
In838
21
attC
orfY
attC
aadA1
dfrA1
sat1
dfrA1
sat1
aadA1
dfrA12
sat1
aadA1
attC
In2-3
aadA5
attC
attC
In2-4
Intl1
attl
drfA1
attC
aadA1
attC
attC
In2-4
Intl1
drfA1
attl
attC
orfC
dfrA1attC sat1attC aadA1
ND
Intl1
drfA5
attl
attC
ereA2
IS911
Fig. 3. Variants of gene cassette arrays in class 1 and 2 integrons in gram-negative bacterium strains.
attI, primary integron recombination site; attC, gene cassette recombination site.
allele of the gene encoding dehydrofolate reductase,
which provides resistance to trimethoprim. The analysis of the gene primary structure demonstrated the
presence of significant nucleotide substitution T305C, which led to Val102-Ala amino acid substitution in
the composition of the encoded enzyme.
A new class 2 integron, in which the structure of the
dfrA1 gene cassette is damaged by the insertion of
IS911 sequence (1256 bp), was identified in the S. flexneri Y-5 clinical strain isolated during a dysentery outbreak in Yakutsk in 2010. This gene cassette structure
(dfrA1-IS911-sat1-aadA1) was not previously described,
and we deposited it in the GenBank database under
number HM592262. The uniqueness of the structure
and the presence in all S. flexneri isolates isolated with
a dysentery outbreak allowed the class 2 integron to be
used as a molecular genetic marker for epidemiological analysis and to concluded about the clonality of
this outbreak.
Gene Cassettes of Antibiotic Resistance
Gene cassettes of 31 types were identified during
the study. The analysis of representation of these cassette types in GenBank database demonstrated that
the gene cassettes aadB, aacA4, aacC1, aadA1, aadA2,
aadA5, blaVIM-2, dfrA1, dfrA7, dfrA12, orfC, orfE,
orfY, and sat1 were more common in bacteria on
March 10, 2018, while aacA1, aadA6, aadA7, blaPSE1,
dfrB4, ereA2, smr2, and dfrA12s were less common
(Table 3). The following gene cassettes were the most
common in a study by Italian authors in 2009: aadA1
(259 references), aacA4 (204 references), dfrA1
(162 references), aadA2 (150 references), and aadB
(89 references) [16]. Over the past 9 years, representation of these gene cassettes in GenBank database
increased by 25, 40, 27, 34, and 164 times, respectively.
CONCLUSIONS
Class 1 and 2 integrons are an important molecular
genetic mechanism of the formation of MDR phenotype in gram-negative bacteria isolated from patients
and from the hospital environment of multidisciplinary hospitals in Moscow and other regions of the
Russian Federation in 2003–2015. During the study,
generally accepted role of integrons as a kind of
“depot” of genetic determinants of antibiotic resistance and “reserve” for creating new gene cassette
combinations was confirmed. The described new gene
cassette modifications (dfrA12s and dfrA1-IS911) can
be useful molecular genetic markers to track the prevalence of cassettes and evolution of gene cassette
arrays, as well as in epidemiological analysis. The conducted analysis of gene cassettes on the basis of representation in GenBank database and of those identified
during the study indicates the prevalence of class 1 and 2
integrons in the genomes of clinical strains of bacteria
isolated in different regions of the world.
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KUZINA et al.
Table 3. Gene cassettes of antibiotic resistance of class 1 and 2 integrons identified in clinical strains of gram-negative bacteria
Gene
cassette
Synonyms
Encoded enzyme
Resistance
Representation
in GenBank database
on March 10, 2018
aacA1
aac(6')-Ia
Aminoglycoside (6') acetyltransferase
AG
116
aacA4
aac(6')-Ib
Aminoglycoside (6') acetyltransferase
AG
8151
aacA7
aac(6')-II
Aminoglycoside (6') acetyltransferase
AG
666
aacC1
aac(3)-Ia
Aminoglycoside (3) acetyltransferase
AG
1836
aadA1
ant(3'')-Ia
Aminoglycoside (3) adenylyltransferase
STR, SPE
6699
aadA2
–
Aminoglycoside (3) adenylyltransferase
STR, SPE
5092
aadA5
–
Aminoglycoside (3) adenylyltransferase
STR, SPE
1438
Aminoglycoside (3) adenylyltransferase
STR, SPE
261
Aminoglycoside (3) adenylyltransferase
STR, SPE
149
Aminoglycoside (2'') adenylyltransferase STR, SPE
14597
aadA6
aadA11
–
aadA7
aadB
ant(2'')-Ia
blaOXA-1 blaOXA-30
Class D OXA-type beta-lactamase
BL
391
blaPSE1
–
Class B PSE-type metal beta-lactamase
BL
25
blaVIM-2
–
Class B VIM-type metal beta-lactamase BL
7589
catB3
–
Chloramphenicol acetyltransferase
СМ
685
catB8
–
Chloramphenicol acetyltransferase
СМ
700
cmlA1
–
Chloramphenicol exporter
СМ
939
dfrA1
dhfrIb, dfr1, dhfr1
Type A dihydrofolate reductase
THR
4295
dfrA5
dhfrV, dfrV
Type A dihydrofolate reductase
THR
447
dfrA7
dhfrVII, dfrVII, dfrA17
Type A dihydrofolate reductase
THR
2398
dfrA12
dhfrXII, dfr12
Type A dihydrofolate reductase
THR
2666
dfrB4
dhfr2, dfr2b
Type B dihydrofolate reductase
THR
58
Erythromycin esterase
ERI
36
–
ereA2
orfC
gcuC, orfX
Hypothetical protein
UK
6550
orfD
gcuD
Hypothetical protein
UK
952
orfE
gcuE
Hypothetical protein
UK
1556
orfF
gcuF
Hypothetical protein
UK
960
orfY
gcuQ, orfX`, orfXB, orf10 Hypothetical protein
UK
3955
sat1
sat2
Streptomycin acetylase
STT
4632
Esterase
Insecticides
3298
Small multiple resistance protein
BL, AG, CM,
THR, QNL
Type A dihydrofolate reductase
THR
–
estX
smr2
dfrA12s
smr, orfO
–
191
0
AG, aminoglycosides; BL, beta-lactams; CM, chloramphenicol; ERI, erythromycin; UK, unknown; SPE, spectinomycin; STR, streptomycin; STT, streptothricin; THR, trimethoprim; QNL, fluoroquinolones
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CLASS 1 AND 2 INTEGRONS IN HOSPITAL STRAINS OF GRAM-NEGATIVE BACTERIA
ACKNOWLEDGMENTS
We are grateful to A.N. Kruglov, Cand. of Biology, senior scientist (OOO National Agency for Clinical Pharmacology and Pharmacy, Moscow); S.V. Sidorenko, Dr. of Biology, professor (Children’s Scientific and Clinical Center for
Infectious Diseases, Federal Medical and Biological Agency,
St. Petersburg); O.N. Ershova, Dr. of Medicine, associate professor (Burdenko National Medical Research Center for Neurosurgery, Ministry of Health, Moscow); and V.E. Malikov,
Cand. of Medicine (Infectious Clinical Hospital No. 1,
Moscow Healthcare Department).
6.
7.
FUNDING
8.
This work was performed as a part of the Federal Theme
of Research of the Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being “Monitoring and Study of the Properties of Causative Agents of
Food and Hospital Infections, Development of Diagnostic
Tools” (2016–2020).
9.
COMPLIANCE WITH ETHICAL STANDARDS
Conflict of interests. The authors declare that they have
no conflict of interest. Statement on the welfare of animals.
This article does not contain any studies with animals.
Statement of compliance with standards of research involving humans as subjects. All procedures performed in the
study involving human beings complied with the ethical
standards of institutional and/or national research ethics
committees and the Declaration of Helsinki and its subsequent amendments or comparable ethical standards. Informed consent was obtained from each study participant.
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Translated by A. Barkhash
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