
==== Front
BMC Microbiol
BMC Microbiol
BMC Microbiology
1471-2180
BioMed Central London

3482
10.1186/s12866-024-03482-3
Research
Whole-genome sequencing of two multidrug-resistant acinetobacter baumannii strains isolated from a neonatal intensive care unit in Egypt: a prospective cross-sectional study
Mohamed Rania Alam Eldin 1
Moustafa Nouran Magdy 12
Mahmoud Fatma Mostafa 1
Elsaadawy Yara Said 1
Aziz Heba Sherif Abdel dr_heba87@cu.edu.eg

3
Gaber Shaimaa Abou Bakr 4
Hussin Abdelrahman Mohamed 5
Seadawy Mohamed G. 6
1 https://ror.org/00cb9w016 grid.7269.a 0000 0004 0621 1570 Medical Microbiology and Immunology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
2 https://ror.org/03myd1n81 grid.449023.8 0000 0004 1771 7446 Basic Medical Science Department, College of Medicine, Dar Al Uloom University, Riyadh, Saudi Arabia
3 https://ror.org/03q21mh05 grid.7776.1 0000 0004 0639 9286 Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
4 https://ror.org/00cb9w016 grid.7269.a 0000 0004 0621 1570 Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
5 https://ror.org/033ttrk34 grid.511523.1 0000 0004 7532 2290 Armed Forces College of Medicine, Cairo, Egypt
6 Biodefense Center for Infectious and Emerging Diseases, Ministry of Defense, Cairo, Egypt
21 9 2024
21 9 2024
2024
24 3621 3 2024
28 8 2024
© The Author(s) 2024
2024
https://creativecommons.org/licenses/by/4.0/ Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Background

Acinetobacter baumannii (A. baumannii) is a life-threatening and challenging pathogen. In addition, it accounts for numerous serious infections, particularly among immunocompromised patients. Resistance to nearly all clinically used antibiotics and their ability to spread this resistance is one of the most important concerns related to this bacterium.

Objectives

This study describes different molecular mechanisms of two multidrug-resistant A. baumannii isolates obtained from endotracheal aspirates collected from the neonatal intensive care unit (NICU), Ain Shams University Hospital, Egypt.

Methods

Following the identification of two isolates, they were examined for susceptibility to antimicrobial agents. This was followed by multilocus sequence typing as well as whole-genome sequence (WGS). Additionally, a Pathosystems Resources Integration Center (PATRIC) analysis was performed.

Results

Two isolates, Ab119 and Ab123, exhibited resistance to all tested antibiotics except for tigecycline and colistin. The WGS analysis of antimicrobial resistance genes (AMR) indicated that both isolates shared beta-lactam, aminoglycoside, macrolides, and sulfonamide resistance genes. Furthermore, each strain revealed different resistance genes such as blaNDM-1, blaNDM-10, OXA-64, aph (3')-VI, Tet-B in Ab119 strain and blaOXA-68, blaPER-1, blaPER-7, Tet-39 in Ab123 strain. Multiple efflux pump genes were detected. Multilocus sequence typing indicated that both isolates belong to the same sequence type (ST931), which belongs to international clone (IC3). Both isolates exhibited the presence of multiple mobile genetic elements (MGEs), but no plasmid was detected in either of them.

Conclusions

A low prevalence of the IC3 sequence type was identified among two A. baumannii isolates obtained from the NICU in Egypt, exhibiting a high resistance level. Healthcare workers must have knowledge regarding the prevalence of A. baumannii among different populations in order to administer suitable treatment, improve patient outcomes, and apply effective infection control practices.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-024-03482-3.

Keywords

Multidrug-resistant a. baumannii
Antibiotic resistance genes
Whole-genome sequencing
Multilocus sequence typing
Cairo UniversityOpen access funding provided by The Science, Technology & Innovation Funding Authority (STDF) in cooperation with The Egyptian Knowledge Bank (EKB).

issue-copyright-statement© BioMed Central Ltd., part of Springer Nature 2024
==== Body
pmcBackground

Acinetobacter baumannii (A. baumannii) is generally a non-pathogenic microorganism. Nevertheless, in the past forty years, it has been discovered to be a severe pathogen in hospitals [1]. Typically, it is associated with hospital-acquired infections like urinary tract infections, bacteremia, lower respiratory tract infections, meningitis, and wound infections [2–5]. Community-acquired infections induced by A. baumannii have been identified, particularly in individuals with comorbidities [6–8]. Neonatal infections caused by A. baumannii are increasing, with a corresponding increase in the frequency of their isolation. In addition, fatality rates due to these infections are more than fatality rates caused by other isolated organisms [9]. Neonates who are born prematurely, have low birth weight, use invasive devices like endotracheal intubation and intravascular catheterization, receive parenteral nutrition, and undergo broad-spectrum antibiotic therapy are more likely to acquire A. baumannii infections [10].

A. baumannii is a significant concern in healthcare facilities globally because it has the capacity to develop and gain resistance to nearly all antibiotics utilized [11]. This risk is significantly amplified amongst patients in intensive care units (ICUs), where death rates can increase up to 40% [12]. A. baumannii has experienced a rapid emergence of antibiotic-resistant strains on a global scale. A. baumannii typically acquires intrinsic resistance by reducing membrane permeability, producing various types of ß-lactamase enzymes, and exhibiting efflux pump activity [13]. The presence of AMR in A. baumannii is typically associated with MGEs that can be transferred between bacteria, facilitating the rapid spread as well as retention of resistance genes across varying bacterial species [14]. Resistance can also be obtained through mutational alterations in the structure of chromosomes, the horizontal transfer of genes [15], and some naturally present intrinsic resistance genes [16].

A. baumannii possesses a remarkable ability to develop AMR from different sources, disseminate it, and evolve novel mechanisms of resistance [17]. Moreover, it can quickly develop extrinsic resistance mechanisms throughout treatment by obtaining additional genetic traits (via cross-species horizontal gene transfer) [18, 19]. The A. baumannii genome comprises a chromosome and numerous plasmids primarily associated with developing AMR genes [20]. A. baumannii strains’ comparative genomic analysis indicated that A. baumannii genome has the ability to incorporate a significant amount of DNA from external sources. This process may contribute to the development of AMR and pathogenesis [21, 22].

Therefore, this study aims to explore, by WGS, different antibiotic resistance mechanisms of A. baumannii strains (isolated from the NICU) at Ain Shams University (ASU) Hospital.

Methods

Ethical approval

The Research Ethical Committee, Faculty of Medicine, Ain Shams University, granted approval for this study under the code No: FMASU R02/2024. Informed consent to participate was obtained from all the legal guardians of the patients.

Settings, study design and isolates selection

The current observational cross-sectional analytic study was performed on two A. baumannii strains. They were isolated from endotracheal aspirates (ETA) from two neonates admitted at the NICU, Ain Shams University Hospital at different times. Both patients presented with clinical signs of pneumonia that required NICU admission and died after short period of admission (Fig. 1).Fig. 1 Workflow of the study

Identification of the organism

ETA collected from patients was sent immediately to the microbiology laboratory for processing. They were cultured on MacConkey agar medium (Oxoid, UK). Bacterial colonies were identified using conventional phenotypic identification including; culture morphology, Gram staining and biochemical reactions. VITEK II compact bacterial system (bioMerieux-Marcy-l’Étoile-France) was used to confirm isolates identification [23].

Antimicrobial susceptibility testing

Antimicrobial susceptibility testing was performed using disc diffusion method (Kirby-Bauer) and minimal inhibitory concentration (MIC) following guidelines of Clinical and Laboratory Standards Institute (CLSI) guidelines [24].

Disc diffusion method (Kirby-Bauer)

Antibiotic discs (delivered from Oxoid, England) containing the subsequent drug concentrations were utilized: Ceftazidime (30 ug), Cefotaxime (30 ug), Cefepime (30 ug), Ceftriaxone (30 ug), Imipenem (10 ug), Aztreonam (30 ug), Piperacillin + Tazobactam (100/10 ug), Meropenem (10 ug), Ampicillin + Sulbactam (10 /10 ug), Gentamicin (10 ug), Tetracycline (30 ug), Amikacin (30 ug), Tigecycline (15 ug), Ciprofloxacin (5 ug), Levofloxacin (5 ug), Trimethoprim + Sulfamethoxazole (1.25/23.75 ug). The results were analyzed utilizing the CLSI breakpoints for all antibiotics (except for tigecycline) [24]. The results of tigecycline were analyzed following the Food and Drug Administration (FDA) breakpoints [25].

Minimal inhibitory concentration

The automated VITEK 2 compact system was utilized to detect MIC of all tested antibiotics, except colistin, following CLSI breakpoints [24]. The broth microdilution technique was used to determine MIC of colistin, following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints [26]. The following concentration range of antibiotics was used; Ampicillin + Sulbactam, Ceftazidime, Cefotaxime, Cefepime, Ceftriaxone, Aztreonam, Tetracycline, Amikacin, Ciprofloxacin, Levofloxacin, Gentamicin (0.5–256 ug/mL), Imipenem and Meropenem (0.06–32 ug/mL), Piperacillin + Tazobactam (0.5–512 ug/mL), Trimethoprim + Sulfamethoxazole (4–128 ug/mL), Tigecycline (0.125 -128 μg/mL), Colistin (0.25- 4 ug/mL).

DNA Extraction and WGS

Two clinical A. baumannii isolates underwent WGS. One milliliter of an overnight bacterial culture was utilized for extracting the total genome including the chromosomal and extrachromosomal entities. MagMAX Microbiome Ultra Nucleic Acid Isolation kit (Applied Biosystems & ThermoFisher Scientific- Monza, Italy) was utilized following the instructions provided by the manufacturer. DNA concentrations have been determined using a Qubit fluorometer (ThermoFisher Scientific) to estimate DNA input.

WGS was performed using Illumina MiSeq (REF SY-410–1003) and Nextera XT-DNA library prep kit per the manufacturer's instructions. The library was sequenced at the Next Generation Sequencing Unit, Biological Prevention Department, Ministry of Defense, Egypt.

Assembly, annotation, antimicrobial resistance, and phylogenic analysis

The two clinical A. baumannii reads were submitted to NCBI, and accession numbers were obtained (SRR26868873, SRR26868872). The comprehensive genome analysis was subsequently done using PATRIC [27] using the annotation statistics, followed by comparing it to other PATRIC genomes with A. baumannii (Tax ID:470). After that, genome annotations were done utilizing the RAST tool kit (RASTtk) [28].

ResFinder and the k-mer-based AMR genes detection method were utilized for the identification of AMR genes. This method uses PATRIC's curated collection of representative AMR gene sequence variants and provides functional annotations and broad antibiotic resistance mechanisms (for each AMR gene).

The phylogenetic analysis was conducted using the closest reference as well as representative genomes that were identified through the Mash/MinHash method [29]. This genome's phylogenetic placement was identified by choosing PATRIC global protein families (PGFams) [30]. These families' protein sequences were aligned using MUSCLE [31], and each sequence's nucleotides were matched to the protein alignment. Subsequently, nucleotide and amino acid alignments were combined to create a data matrix, which was analyzed utilizing RaxML [32]. Fast bootstrapping (100 bootstrap) was also utilized to obtain the support values (in the tree) [33].

MGEs analysis

The identification of AMR genes associated with MGEs was carried out using a CGE server [34], which accurately predicts the mobility and rapid dissemination of these elements within a bacterial community. Mobile Element Finder was developed to rapidly detect MGEs (in addition to their genetic context) in assembled sequence data.

Multilocus sequence typing (MLST)

MLST on genomes of collected A. baumannii was done using the Oxoford scheme. This scheme entails identifying seven internal housekeeping genes: RNA polymerase _70factor (rpoD), glucose-6-phosphate isomerase (gpi), glucose dehydrogenase B (gdhB), DNA gyrase subunit B (gyrB), citrate synthase (gltA), 60-kDa chaperonin(cpn60), and homologous recombination factor (recA) [35].

Results

Two clinical A. baumannii strains (Ab119 and Ab123) were isolated from ETA from two neonates presented with pneumonia and died at NICU at Ain Shams University Hospital.

Antimicrobial susceptibility testing

Both isolates exhibited resistance to all used antibiotics (except for tigecycline & colistin). MIC results showed a remarkable resistance to trimethoprim–sulfamethoxazole, gentamicin, and ciprofloxacin (Table 1).Table 1 MICs of antibiotics used for Ab 119 and Ab 123 isolates

Antibiotics	MIC ug/mL	
Ab119	Ab 123	
Ceftazidime	32	32	
Cefotaxime	128	64	
Ceftriaxone	64	64	
Cefepime	64	32	
Imipenem	8	16	
Meropenem	8	8	
Piperacillin + Tazobactam	128	256	
Ampicillin + Sulbactam	32	64	
Gentamicin	32	64	
Amikacin	32	64	
Tetracycline	16	32	
Ciprofloxacin	128	64	
Levofloxacin	16	32	
Trimethoprim + Sulfamethoxazole	4	8	
Tigecycline	2	1	
Colistin	1	1	

WGS and MLST

According to the annotation statistics and comparing the genome of A. baumannii (Tax ID: 470) in PATRIC. The genomes exhibited excellent quality. The bioinformatics and data analysis of both strains are shown in Table 2 and Fig. 2.Table 2 Genome characteristics of Ab 119 and Ab 123 strains

Strain	Contigs	Genome Length (bp)	GC Content %))	Protein CDS	transfer RNA	ribosomal RNA	
Ab119	92	4,251,654	38.80	4,226	63	3	
Ab123	132	4,097,941	38.84	4,017	63	3	

Fig. 2 Circular graphical display of the genome annotation distribution. The figure includes, from outer to inner rings, the contigs, CDS on the forward strand, CDS on the reverse strand, RNA genes, CDS with homology to known antimicrobial resistance genes, CDS with homology to know virulence factors, GC content and GC skew. The colors of the CDS on the forward and reverse strand indicate the subsystem that these genes belong to

The MLST analysis utilizing the Oxford scheme indicated that both isolates belong to the ST931which is related to IC3.

Phylogenetic analysis

The phylogenetic analysis of the samples showed a close similarity to A. baumannii SDF 509170.6 and A. baumannii ATCC 17978 400,667.7, with the Ab119 and Ab123 strains, respectively (Fig. 3).Fig. 3 Phylogenetic tree of Ab 119 and Ab 123 strains. Phylogenetic analysis was done with closest reference and representative genomes identified by Mash/MinHash. PATRIC global protein families, PGFams were selected from these genomes to determine the phylogenetic placement of this genome. The protein sequences from these families were aligned with MUSCLE and the nucleotides for each of those sequences were mapped to the protein alignment. The joint set of amino acid and nucleotide alignments was concatenated into a data matrix, and RaxML was used to analyze this matrix, with 100 bootstrapping was used to generate the support values in the tree

Antimicrobial Resistance Genes (AMR)

Predicted antimicrobial resistance phenotypes analysis showed multidrug resistance for both isolates. ResFinder analysis revealed different genes as:β-Lactam resistance genes: both isolates harbored molecular class D and class C β-lactamases. In general, bla OXA-23 and bla ADC-25 genes were detected in both isolates with a copresence of bla OXA-64, bla NDM-10, and bla NDM-1 in the AB 119 strain. The presence of bla OXA-68, bla PER-7, and bla PER-1 was detected in the AB 123 strain.

Aminoglycoside resistance genes: The strains exhibited resistance to aminoglycosides because of the detection of the following genes: armA, aph(3')-Via, ant(2'')-Ia, aph(3'')-Ib, and aph(6)-Id. The AB 119 strain exhibited the simultaneous aph(3')-VI gene presence.

Macrolide resistance genes: Both isolates revealed msr E and mph E genes.

Tetracycline resistance genes: Tetracycline resistance is mediated by tet B in the Ab119 strain and tet 39 in the Ab 123 strain.

Other AMR genes: ARP 2 and ARP 3 (rifamycin resistance), Sul 2 and sul1 (sulfonamide resistance), in addition to cmlA1 (chloramphenicol resistance) genes, were found in both isolates (Table 3).

Table 3 AMR genes present in Ab 119 and Ab 123 strains

Strain	B-Lactam resistance genes	Aminoglycoside resistance genes	Macrolide resistance genes	Tetracycline resistance genes	Others:
*Rifamycin
*Sulfamethoxazole
* Chloramphenicol	
Ab 119	blaNDM-1

blaNDM-10

blaADC-25

blaOXA-23

blaOXA-64

	aph(3')-VI

arm A

aph(3')-Via

ant(2'')-Ia

aph(3'')-Ib

aph(6)-Id

	Msr E

Mph E

	Tet B	ARR2

ARR 3

sul2

sul1

cmlA1

	
Ab123	blaOXA-68

blaADC-25

blaOXA-23

blaPER-7

blaPER-1

	ant(2'')-Ia

aph(3'')-Ib

aph(6)-Id

armA

aph(3')-Via

	Msr E

Mph E

	Tet 39	ARR 2

ARR 3

sul2

sul1

cmlA1

	

The CARD platform was utilized to conduct k-mer prediction of the pathogen responsible for AMR genes. This online platform facilitates the examination of metagenomic contigs, genome assemblies, and genomes. CARD’s RGI (Resistance Gene Identifier) allows predictions resistomes from protein or nucleotide data based on homology model with defined criteria ranging from perfect and strict matches to loose similarities [36].

Regarding the Ab119 strain, origin of AMR genes, resistance mechanisms, and drugs were revealed, as shown in (Fig. 4, Table 4). The protein homolog model was found in all genes except for gyr A (S81L), and ParC (V104I and D105E) mutations were detected, as well as the tet R gene overexpression.Fig. 4 Antimicrobial resistance gene origin in Ab119 strain. The figure illustrates the classification of antimicrobial resistance gene origin including three types according to their ordering in genetic identity from high to low (14 genes predicted to be perfect, 15 genes to be strict and none to be loose)

Table 4 AMR genes' origin, drug affected, and resistance mechanisms shown in the Ab 119 strain

*RGI Criteria	**ARO Term	Drug class affected	Resistance mechanism	
***Perfect	ADC-57	Cephalosporin	Antibiotic-inactivation	
OXA-64	carbapenem, cephalosporin	Antibiotic-inactivation	
abeS	macrolide, aminocoumarin	Antibiotic-efflux	
adeL	fluoroquinolone, tetracycline	Antibiotic-efflux	
sul1	Sulfonamide	Antibiotic-target replacement	
qacEdelta1	antiseptics & disinfecting agents	Antibiotic-efflux	
cmlA5	Phenicol	Antibiotic-efflux	
arr-2	Rifamycin	Antibiotic-inactivation	
mphE	Macrolide	Antibiotic-inactivation	
msrE	macrolide, streptogramin	Antibiotic-target protection	
armA	Aminoglycoside	Antibiotic-target alteration	
BRP(MBL)	Glycopeptide	Antibiotic-inactivation	
OXA-23	carbapenem, cephalosporin	Antibiotic-inactivation	
sul2	Sulfonamide	Antibiotic-target replacement	
***Strict	LpsB	Peptide	Reduced-permeability to antibiotics	
A. baumannii AmvA	macrolide, disinfecting agents and antiseptics	Antibiotic-efflux	
A. baumannii AbaF	phosphonic acid	Antibiotic-efflux	
adeF	fluoroquinolone, tetracycline	Antibiotic-efflux	
adeR	glycylcycline, tetracycline	Antibiotic-efflux	
ANT(3'')-IIc	Aminoglycoside	Antibiotic-inactivation	
adeN	Macrolide- diaminopyrimidine lincosamide- fluoroquinolone-carbapenem- tetracycline-cephalosporin- rifamycin-phenicol	Antibiotic-efflux	
adeJ	Macrolide- lincosamide- fluoroquinolone-carbapenem-cephalosporin- rifamycin- tetracycline- phenicol- diaminopyrimidine-	Antibiotic-efflux	
APH(6)-Id	Aminoglycoside	Antibiotic-inactivation	
APH(3'')-Ib	Aminoglycoside	Antibiotic-inactivation	
NDM-40	carbapenem, cephalosporin, cephamycin	Antibiotic-inactivation	
tet(B)	Tetracycline	Antibiotic-efflux	
A. baumannii gyrA	Fluoroquinolone	Antibiotic-target alteration	
A. baumannii parC	Fluoroquinolone	Antibiotic-target alteration	
***Strict	tetR	Tetracycline	Antibiotic-target alteration

Antibiotic-efflux

	
*RGI Resistance Gene Identifier

**ARO Antibiotic Resistance Ontology

***Perfect and strict (i.e.; with high confidence and probability)

Regarding the Ab123 strain, the origin of AMR genes, resistance mechanisms, and drugs were revealed and shown in (Fig. 5, Table 5). The protein homolog model was found in all genes except for gyr A (S81L), and ParC (S84L, V104I, and D105E) mutations were detected.Fig. 5 Antimicrobial resistance gene origin in Ab 123 strain. The figure illustrates the classification of antimicrobial resistance gene origin including three types according to their ordering in genetic identity from high to low (18 genes predicted to be perfect, 14 genes to be strict and none to be loose)

Table 5 AMR genes origin, drug affected, and resistance mechanisms shown in Ab123 strain

RGI Criteria	ARO term	Drug class	Resistance mechanisms	
Perfect	A. baumannii AbaF	phosphonic acid	Antibiotic-efflux	
adeI

adeK

	Macrolide-fluoroquinolone-lincosamide- carbapenem- tetracycline- cephalosporin-rifamycin-phenicol- diaminopyrimidine	Antibiotic-efflux	
abeS	macrolide, aminocoumarin	Antibiotic-efflux	
adeG

adeF

	Fluoroquinolone- tetracycline	Antibiotic-efflux	
sul1	sulfonamide	Antibiotic-target replacement	
PER-7	Monobactam-carbapenem- cephalosporin	Antibiotic-inactivation	
sul1	sulfonamide	Antibiotic-target replacement	
qacEdelta1	disinfecting agents and antiseptics	Antibiotic-efflux	
cmlA5	phenicol	Antibiotic-efflux	
arr-2	rifamycin	Antibiotic-inactivation	
OXA-68	carbapenem, cephalosporin	Antibiotic-inactivation	
A. baumannii AbaQ	fluoroquinolone	Antibiotic-efflux	
OXA-23	carbapenem, cephalosporin	Antibiotic-inactivation	
mphE	macrolide	Antibiotic-inactivation	
msrE	macrolide-streptogramin	Antibiotic-target protection	
armA	aminoglycoside	Antibiotic-target alteration	
sul2	sulfonamide	Antibiotic-target replacement	
Strict	adeN

adeJ

	Macrolide- lincosamide- fluoroquinolone- cephalosporin-carbapenem- tetracycline- diaminopyrimidine- rifamycin-phenicol	Antibiotic-efflux	
A. baumannii AmvA	Antiseptics- disinfecting agents- macrolide	Antibiotic-efflux	
LpsB	peptide	Reduced permeability to antibiotics	
ANT(3'')-IIc	aminoglycoside	Antibiotic-inactivation	
adeL

adeH

	fluoroquinolone, tetracycline	Antibiotic-efflux	
ADC-211	Cephalosporin	Antibiotic-inactivation	
APH(3'')-Ib	aminoglycoside antibiotic	Antibiotic-inactivation	
APH(6)-Id	aminoglycoside	Antibiotic-inactivation	
ANT(2'')-Ia	aminoglycoside	Antibiotic-inactivation	
APH(3')-Via	aminoglycoside	Antibiotic-inactivation	
A. baumannii gyrA	fluoroquinolone	Antibiotic-target alteration	
A. baumannii parC	fluoroquinolone	Antibiotic-target alteration	

Mobile Genetic Elements (MGEs)

MGEs were identified by comparing their sequences to a database of (4,452) known elements. This database was enhanced with information about virulence factors, resistance genes, and the identification of plasmids. The analysis of strains indicated the presence of a diverse range of MGE, insertion sequences (ISs) that belong to different IS families. In the Ab119 strain, 14 MGE were detected. Conversely, only 10 MGE were detected in the Ab123 strain. Both strains showed the presence of (ISEc29 related to armA and msrE), (ISEc28 related to sul1, Arr-2 and bla PER-7) and (IS1007, CN-10921-IS1007 related to sul1). In addition, Ab123 strain showed (ISVsa3 that related to aph(3)-Ib and aph(6)-Id). Other ISs that aren't linked to ARG were detected in both strains as (ISAba14, ISAba34, ISAba37, IS1008, ISAca1). Others were detected only in Ab119 strain as (IS Aba10, ISAba33, IS26, ISVsa3). No plasmids were detected in both isolates as shown in Tables 6 and 7.Table 6 Mobile genetic elements (14 MGE) in Ab 119 strain

Table 7 Mobile genetic elements (10 MGE) in Ab123 strain

Discussion

A. baumannii can persist in different environmental circumstances and develop AMR, making it one of hospitals' most life-threatening nosocomial pathogens [37]. MDR nosocomial A. baumannii can cause severe infections in neonates with an increased number of mortalities. The presence of foreign DNA [21, 22] and different plasmids in its genome increase the gaining of AMR genes [20]. Investigating AMR genes among A. baumannii clinical isolates is mandatory for revealing the incriminated mechanisms of AMR development. Specific Egyptian laboratories have access to new methods like NGS technology, which can replace conventional PCR. These methods are used to identify AMR genes. This study focuses on identifying AMR profiles and AMR genes of two clinical isolates of A. baumannii. These isolates were obtained from ETA samples of two neonates admitted to the NICU at ASU Hospital, a large tertiary care hospital in Egypt.

The current investigation demonstrated that both strains exhibited sensitivity to tigecycline and colistin while displaying resistance to all other antibiotics that were tested, encompassing third-generation cephalosporin, carbapenems, aminoglycosides, fluoroquinolones, and trimethoprim/ sulfamethoxazole. The obtained outcomes closely align with the findings of Gaafar et al. (2022), who conducted a study on neonates with sepsis at Zagazig University Hospitals. They reported that Acinetobacter isolates were most sensitive to ciprofloxacin, colistin, and tigecycline, while they were most resistant to trimethoprim/ sulfamethoxazole [38]. In India, a study conducted by Nazir in 2019 found that 95.9% of Acinetobacter strains isolated from the NICU showed resistance to aminoglycosides, cephalosporins, penicillin, and fluoroquinolones. Additionally, 93.68% of the strains exhibited resistance to carbapenems [39].

Carbapenems, even in neonates, are considered first-line therapy for lower respiratory tract infections. However, increased resistance to nearly all existing antimicrobial agents including carbapenems is alarming.

Although our study revealed sensitivity to colistin and tigecycline, studies issued in 2020 reported that about 53% of A. baumannii Egyptian isolates were colistin-resistant [40, 41]. In addition, tigecycline nonsusceptibility was reported in many studies in Egypt [42, 43]. Differences in resistance pattern may be due to restricted usages of colistin and tigecycline at NICU. Moreover, the low isolate number incorporated in our study may cause this difference.

Sequenced-genome analysis indicated that both isolates belonged to the same MLST sequence type (ST931), a representative of the (ST52) pasture scheme, and belongs to international clone 3 (IC3) [44]. A limited number of reports have documented the occurrence of this type globally [45]. It was incriminated in the Netherlands outbreak in 1986 [46]. In 2015, another study documented the occurrence of this type in Nepal [47].

To our knowledge, only one previous study in Egypt reported ST931 in a single isolate among 45 A. baumannii isolates in Tanta University Hospital in 2015. The authors declared that most isolates belonged to IC2 and IC1 [48]. Different studies in various places in the Middle East and Egypt [49–52] reported the spread of IC2. Furthermore, IC1&IC2 were found in all continents, indicating their global distribution, and they frequently contain the acquired carbapenemase genes [53–55].

Nevertheless, IC3 was previously regarded as a prominent clone. However, its occurrence has significantly decreased in the past ten years, and there have been very few documented cases of it originating from non-human sources [56, 57]. IC3 has had limited significance in recent years, with occasional instances reported in Peru [58], South Africa, the USA, and Spain [44].

Our finding that both isolates belonged to the same sequence type (ST931) indicates that this sequence type which belongs to the IC3 group, is likely to start spreading in Egypt and has the potential to become widespread. It is crucial to consider the introduction of a low prevalent sequence type that has a high rate of resistance and transmission into healthcare settings.

A total of 32 and 33 antibiotic resistance genes (ARG) were detected in the Ab119 and Ab123 strains, respectively, through genome sequencing, ResFinder, and CARD platform analysis. Distinct genetic factors that confer resistance to cephalosporins and carbapenems, class A, C, and D β-lactamases, were identified. Neither strain exhibited the presence of KPC nor any other MBLs such as IMP, SPM, VIM, or SIM. Additionally, no other OXA families were detected, including OXA-58. Reporting that each strain carries genes of three classes of beta-lactamase is highly unfavorable to clinicians due to high failure rates of treatment with beta-lactams.

Our results are comparable to those of various studies conducted in tertiary hospitals in Egypt. A study was conducted on carbapenem-resistant A. baumannii (CR-AB) isolated from multiple clinical units at Kasr Al-Aini Hospital. They reported that the most predominant beta-lactamase gene type among isolates was blaOXA-23, followed by blaNDM-1 and blaKPC. They reported low prevalence of other genes such as bla SPM 6.3%, OXA -58 1.9%, bla VIM 0.5%, and bla SIM 0.5%. The low number of isolates, 18.4%, harbored two or more bla genes [59].

Another study was conducted on carbapenem-insensitive A. baumannii strains isolated from two hospitals, Dar el-Foad and Kasr Al-Aini, Egypt. The bla ADC and blaOXA-51-like genes were observed in all isolates. The prevalence of bla OXA-23, blaPER was 50% and 55%, respectively. However, no isolate carried KPC or MBL-encoding genes [60].

Moreover, a prior study (Zagazig University) stated that 90% and 66.7% of CRAB isolates carried blaOXA-23 and NDM, respectively [61]. Other studies in KSA and Egypt reported that all CRAB isolates harbored blaOXA-23 [62, 63]. They reported different rates 12.1% and 100% of blaNDM and blaVIM [62]. Previous studies in Egypt revealed two variants of NDM (NDM-1 & NDM-2) among A. baumannii clinical isolates [64, 65].

These results denoted a significant prevalence of OXA 23 and NDM in various hospitals in Egypt, particularly in tertiary hospitals. This evidence confirms that class D β-lactamases are the prevailing type of carbapenemases, with MBLs being the second most prevalent. To the best of our knowledge, this is the initial instance of documenting the presence of NDM-10 and NDM-40 in Egyptian hospitals. NDM-positive strains are correlated with severe consequences as well as increased mortalities, especially in neonates and immunosuppressed individuals. Various infections caused by these strains have been documented to have unfavorable outcomes [66], which is alarming for the spread of NDM-harboring isolates in the NICU.

The discrepancies observed in different studies can be attributable to the fact that some authors did not examine all genomes and instead employed multiplex PCR to probe for the detection of particular genes specifically.

The present study uncovered several genes that provide resistance to aminoglycoside in both strains. The armA gene confers resistance to gentamicin, while ant(2'')-Ia mediates resistance to gentamycin, kanamycin, and tobramycin. Aph (3')-VIa and aph(3')-VI seem to confer resistance to amikacin and kanamycin.

Comparable results were reported by ELsheredy et al., who illustrated that A. baumannii clinical isolates from cases in multiple ICUs in Alexandria University Hospital harbored armA and AME genes (aphA6, aphA1). However, they reported other AME genes as aacA4, aacC1, aadA1, and aadB [67]. Another study reported that most isolates carried genes conferring resistance to aminoglycosides (strA, aadA1-pm, armA, strB, aph(3')-VI, aph(3')-Ia, aph(3')-VIa, ant(3")-II, aac(6')-Ib, and ant(3")-IIa) [68].

The combination of these multiple genes limits the usage of nearly all aminoglycosides as an alternative therapy for A. baumannii and makes treatment highly challenging.

In addition, our study revealed that both isolates harbored resistance genes to tetracyclines. Tet B is a tetracycline efflux protein found in various Gram-negative bacteria. The major facilitator superfamily (MFS) antibiotic efflux pump provides resistance to tetracycline, minocycline, and doxycycline (but not tigecycline) [69]. Tet39 confers tetracycline and doxycycline resistance only [70].

Sul1 and Sul2 genes were revealed in both isolates and mediated resistance to sulfonamides. Transposons or plasmids in most Gram-negative bacteria carry these genes, which provide resistance to sulfonamides. Isolates can develop resistance to trimethoprim/sulfamethoxazole through one or both genes [71].

Both isolates in our study carried the cmlA1 gene, which encodes chloramphenicol acetyltransferase and confers resistance to chloramphenicol. Earlier reports indicated that the majority of A. baumannii isolates have inherent resistance to chloramphenicol. However, the mechanisms responsible for this resistance have not been evident until now [72].

Furthermore, both isolates exhibited the presence of mphE and msrE genes, which confer resistance to macrolides, as well as the arr2 gene, which confers resistance to rifamycin. Similar genes were detected by Sa' nchez-Urtaza et al. in Alex; tet39, tetB, sul1, msr.E, sul2, cmlA5, mph.E, and arr-2. However, they reported the presence of other genes, such as catB8 and catA1 that mediate resistance to chloramphenicol and dfrA7 that confer resistance to trimethoprim [68].

Efflux pumps are incriminated into increased antibiotic resistance in A. baumannii. In our study, we revealed different efflux pump coding genesbelonging to the SMR family, the RND family, and the MFS family. Based on our understanding, these genes encode efflux pumps that play a crucial role in increasing resistance to various antibiotics, particularly fluoroquinolones and tetracyclines.

Comparable results were reported by Sánchez-Urtaza et al. in Alex. They declared that most isolates harbored efflux pump encoding genes, as detected in our results, in addition to abeM, adeA, adeB, adeC, and adeS [68].

Both sequenced isolates also detected mutation in gyrA (S81L) and par C (V104I, D105E and S84L). Kumburu et al. reported similar gyr A and par C (S84L) mutations in 50% of the studied isolates. Segatore et al. reported similar mutations in gyrA and parC (V104I, D105E) in A. baumannii isolated from a multicenter in Italy [73].

Different studies from various hospitals in Egypt detected other mutations in gyrA (S83L) and parC (S80L) among fluoroquinolone-resistant A. baumannii isolates. Their prevalence ranged from 100%, as illustrated by Tantawy et al. [74] and Zaki et al. [75], to 23.7%, as reported by Taha et al. [76].

However, the primary mechanism of fluoroquinolone resistance typically involves mutations in the quinolone resistance determining region of (gyrA) that encodes the DNA gyrase A and (parC) that encodes the topoisomerase IV. The isolates with triple and quadruple mutations exhibited a significantly elevated resistance to ciprofloxacin and levofloxacin. To our knowledge, it is the first time these mutations in A. baumannii (isolated from Egyptian hospitals) have been detected.

We observed that specific genes were not identified when using the ResFinder server but were identified when utilizing the CARD databases. Therefore, our findings have confirmed the necessity of utilizing multiple databases to ascertain the resistance profiles of bacterial isolates to prevent the missing of specific resistance genes.

Both isolates show the presence of multiple ISs associated to armA, msrE, and sul1 genes. In addition, the Ab123 isolate harbored ISs associated to aph(3)-Ib and blaPER7 genes. Numerous MGEs have been discovered in different bacteria, including A. baumannii. Nevertheless, the existence of these mobile elements confers a significant degree of resistance to various antibiotics and is implicated in the process of horizontal gene transfer within bacterial cells and between different cells. Furthermore, it is accountable for acquiring new properties, such as antibiotic resistance and pathogenicity [77].

Although various genes such as NDM, some OXA, armA, ant(2'')-Ia, aph(3')-Via, aph(3'')-Ib, aph(6)-Id are known to be plasmid-mediated [78], our results detected these genes on bacterial chromosome not on plasmid. This may be explained by MGEs as ISs and transposon found in plasmids can move and integrate into chromosome of the same or other bacterial cells causing spreading of resistance genes to new bacterial cells. MGEs are crucial in carrying and disseminating resistance genes, with a role comparable to that of plasmids.

Conclusion

We identified a low-frequency strain of A. baumannii clone ST (931) in our clinical environment. This strain carries multiple resistance genes against all antibiotics, with the exception of colistin and tigecycline. The resistant isolates were not linked in terms of their epidemiology. New mutations were revealed gyr A (S81L) and (S84L, V104I and D105E) that did not report yet in Egypt but only in Europe. Isolates harbored multiple MGEs, but no plasmid was detected.

Recommendation

Clinicians and healthcare workers must be aware of A. baumannii populations to implement suitable treatment and infection control protocols. Furthermore, the wide implementation of molecular and genomic technologies is crucial in order to obtain a precise epidemiological picture of A. baumannii and distinguish between different isolates, especially in tertiary health centers and ICUs that treat high-risk patients.

Supplementary Information

Supplementary Material 1.

Supplementary Material 2.

Abbreviations

WGS Whole-genome sequence

AMR Antimicrobial resistance

ST Sequence type

IC International clone

MGEs Mobile genetic elements

NICU Neonatal intensive care unit

A. baumannii Acinetobacter baumannii

ICUs Intensive care units

ASU Ain Shams University

PATRIC Pathosystems Resources Integration Center

ETA Endotracheal aspirates

MIC Minimal inhibitory concentration

EUCAST European Committee on Antimicrobial Susceptibility Testing

PGFams Global protein families

MLST Multilocus sequence typing

rpoD RNA polymerase _70factor

Gpi Glucose-6-phosphate isomerase

gdhB Glucose dehydrogenase B

gyrB DNA gyrase subunit B

gltA Citrate synthase

recA Homologous recombination factor

CDS Protein-coding sequences

rRNA Ribosomal RNA

RGI Resistance Gene Identifier

ARO Antibiotic Resistance Ontology

IS Insertion Sequence

Authors’ contributions

R.A.: substantial contributions to the design of the work; the acquisition, analysis, and interpretation of data; substantively revised the work; have approved the submitted version; and have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. N.M.: substantial contributions to the design of the work; the acquisition, analysis, and interpretation of data; substantively revised the work; have approved the submitted version; and have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. F.M.: substantial contributions to the design of the work; the acquisition, analysis, and interpretation of data; substantively revised the work; have approved the submitted version; and have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. Y.S.: substantial contributions to the design of the work; the acquisition, analysis, and interpretation of data; substantively revised the work; have approved the submitted version; and have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. H.S.: The corresponding author; substantial contributions to the design of the work; the analysis and interpretation of data; have drafted the work; have approved the submitted version; and have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. S.A: substantial contributions to the design of the work; the acquisition, analysis, and interpretation of data; substantively revised the work; have approved the submitted version; and have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. A.M.: the analysis, and interpretation of data; the creation of new software used in the work; have approved the submitted version; and have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. M.G.: the analysis, and interpretation of data; the creation of new software used in the work; have approved the submitted version; and have agreed both to be personally accountable for the author's own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature. All authors reviewed the manuscript.

Funding

Open access funding provided by The Science, Technology & Innovation Funding Authority (STDF) in cooperation with The Egyptian Knowledge Bank (EKB). No fund was obtained from any institution or any organization.

Availability of data and materials

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. Data for both isolates were submitted on NCBI as SRA and accession numbers were obtained for ab119 isolate was SRR26868873 and ab 123 isolate was SRR26868872.

Declarations

Ethics approval and consent to participate

The Research Ethical Committee, Faculty of Medicine, Ain Shams University, granted approval for this study under the code No: FMASU R02/2024. Informed consent to participate was obtained from all the legal guardians of the patients.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
==== Refs
References

1. Howard A O'Donoghue M Feeney A Sleator R Acinetobacter baumannii: an emerging opportunistic pathogen Virulence 2012 3 243 250 10.4161/viru.19700 22546906
Howard A, O’Donoghue M, Feeney A, Sleator R. Acinetobacter baumannii: an emerging opportunistic pathogen. Virulence. 2012;3:243–50.22546906
2. Andersen C Langendorf C Garba S Sayinzonga-Makombe N Mambula C Mouniaman I Hanson K Grais R Isanaka S Risk of community- and hospital-acquired bacteremia and profile of antibiotic resistance in children hospitalized withsevere acute malnutrition in Niger Int J Infect Dis 2022 119 163 171 10.1016/j.ijid.2022.03.047 35346836
Andersen C, Langendorf C, Garba S, Sayinzonga-Makombe N, Mambula C, Mouniaman I, Hanson K, Grais R, Isanaka S. Risk of community- and hospital-acquired bacteremia and profile of antibiotic resistance in children hospitalized withsevere acute malnutrition in Niger. Int J Infect Dis. 2022;119:163–71.35346836
3. Wu D Huang Y Ding J Jia Y Liu H Xiao J Peng J Impact of carbapenem-resistant Acinetobacter baumannii infections on acute pancreatitis patients Pancreatology 2022 22 194 199 10.1016/j.pan.2021.12.004 34924296
Wu D, Huang Y, Ding J, Jia Y, Liu H, Xiao J, Peng J. Impact of carbapenem-resistant Acinetobacter baumannii infections on acute pancreatitis patients. Pancreatology. 2022;22:194–9.34924296
4. Rao S Betancourt-Garcia M Kare-Opaneye Y Swierczewski B Bennett J Horne B Fackler J Suazo Hernandez L Brownstein M Critically ill patient with multidrug-resistant Acinetobacter baumannii respiratory infection successfully treated with intravenous and nebulized bacteriophage therapy Antimicrob Agents Chemother 2022 66 e0082421 10.1128/AAC.00824-21 34662188
Rao S, Betancourt-Garcia M, Kare-Opaneye Y, Swierczewski B, Bennett J, Horne B, Fackler J, Suazo Hernandez L, Brownstein M. Critically ill patient with multidrug-resistant Acinetobacter baumannii respiratory infection successfully treated with intravenous and nebulized bacteriophage therapy. Antimicrob Agents Chemother. 2022;66:e0082421.34662188
5. Martinez J Razo-Gutierrez C Le C Courville R Pimentel C Liu C Fung S Tuttobene M Phan K Vila A Cerebrospinal fluid (CSF) augments metabolism and virulence expression factors in Acinetobacter baumannii Sci Rep 2021 11 4737 10.1038/s41598-021-81714-6 33637791
Martinez J, Razo-Gutierrez C, Le C, Courville R, Pimentel C, Liu C, Fung S, Tuttobene M, Phan K, Vila A, et al. Cerebrospinal fluid (CSF) augments metabolism and virulence expression factors in Acinetobacter baumannii. Sci Rep. 2021;11:4737.33637791
6. Xu A Zhu H Gao B Weng H Ding Z Li M Weng X He G Diagnosis of severe community-acquired pneumonia caused by Acinetobacter baumannii through next-generation sequencing: a case report BMC Infect Dis 2020 20 45 10.1186/s12879-019-4733-5 31941459
Xu A, Zhu H, Gao B, Weng H, Ding Z, Li M, Weng X, He G. Diagnosis of severe community-acquired pneumonia caused by Acinetobacter baumannii through next-generation sequencing: a case report. BMC Infect Dis. 2020;20:45.31941459
7. Chen C Wang Y Kuo S Shih F Chen T How C Yang Y Lee Y Community-acquired bloodstream infections caused by Acinetobacter baumannii: a matched case-control study J Microbiol Immunol Infect 2018 51 629 635 10.1016/j.jmii.2017.02.004 28701266
Chen C, Wang Y, Kuo S, Shih F, Chen T, How C, Yang Y, Lee Y. Community-acquired bloodstream infections caused by Acinetobacter baumannii: a matched case-control study. J Microbiol Immunol Infect. 2018;51:629–35.28701266
8. Wong D Nielsen T Bonomo R Pantapalangkoor P Luna B Spellberg B Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges Clin Microbiol Rev 2017 30 409 447 10.1128/CMR.00058-16 27974412
Wong D, Nielsen T, Bonomo R, Pantapalangkoor P, Luna B, Spellberg B. Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges. Clin Microbiol Rev. 2017;30:409–47.27974412
9. Jeyamurugan T Ragulganesh R Sucilathangam G Acinetobacter spp.: an emerging pathogen in neonatal septicaemia JCDR. 2012 6 5 805 806
Jeyamurugan T, Ragulganesh R, Sucilathangam G, et al. Acinetobacter spp.: an emerging pathogen in neonatal septicaemia. JCDR. 2012;6(5):805–6.
10. Wei H Hsu Y Lin H Multidrugresistant Acinetobacter baumannii infection among neonates in a neonatal intensive care unit at a medical center in central Taiwan J Microbiol Immunol Infect 2015 48 5 531 539 10.1016/j.jmii.2014.08.025 25442873
Wei H, Hsu Y, Lin H, et al. Multidrugresistant Acinetobacter baumannii infection among neonates in a neonatal intensive care unit at a medical center in central Taiwan. J Microbiol Immunol Infect. 2015;48(5):531–9.25442873
11. Vázquez-López R Solano-Gálvez SG Juárez Vignon-Whaley JJ Abello Vaamonde JA Padró Alonzo LA Rivera RA Muleiro ÁM Vega López EN Franyuti-Kelly G Álvarez-Hernández DA Acinetobacter baumannii resistance: a real challenge for clinicians Antibiotics 2020 9 205 10.3390/antibiotics9040205 32340386
Vázquez-López R, Solano-Gálvez SG, Juárez Vignon-Whaley JJ, Abello Vaamonde JA, Padró Alonzo LA, Rivera RA, Muleiro ÁM, Vega López EN, Franyuti-Kelly G, Álvarez-Hernández DA, et al. Acinetobacter baumannii resistance: a real challenge for clinicians. Antibiotics. 2020;9:205.32340386
12. Asif M Alvi IA Rehman SU Insight into Acinetobacter baumannii: pathogenesis, global resistance, mechanisms of resistance, treatment options, and alternative modalities Infect Drug Resist 2018 11 1249 10.2147/IDR.S166750 30174448
Asif M, Alvi IA, Rehman SU. Insight into Acinetobacter baumannii: pathogenesis, global resistance, mechanisms of resistance, treatment options, and alternative modalities. Infect Drug Resist. 2018;11:1249.30174448
13. Wareth G Linde J Hammer P Nguyen NH Nguyen TNM Splettstoesser WD Phenotypic and WGS-derived antimicrobial resistance profiles of clinical and non-clinical Acinetobacter baumannii isolates from Germany and Vietnam Int J Antimicrob Agents 2020 56 4 106127 10.1016/j.ijantimicag.2020.106127 32750418
Wareth G, Linde J, Hammer P, Nguyen NH, Nguyen TNM, Splettstoesser WD, et al. Phenotypic and WGS-derived antimicrobial resistance profiles of clinical and non-clinical Acinetobacter baumannii isolates from Germany and Vietnam. Int J Antimicrob Agents. 2020;56(4):106127.32750418
14. Brovedan MA Cameranesi MM Limansky AS Morán-Barrio J Marchiaro P Repizo GD What do we know about plasmids carried by members of the Acinetobacter genus? World J Microbiol Biotechnol 2020 36 8 109 10.1007/s11274-020-02890-7 32656745
Brovedan MA, Cameranesi MM, Limansky AS, Morán-Barrio J, Marchiaro P, Repizo GD. What do we know about plasmids carried by members of the Acinetobacter genus? World J Microbiol Biotechnol. 2020;36(8):109.32656745
15. Pagano M Martins AF Barth AL Mobile genetic elements related to carbapenem resistance in Acinetobacter baumannii Brazilian J Microbiol 2016 47 4 785 792 10.1016/j.bjm.2016.06.005
Pagano M, Martins AF, Barth AL. Mobile genetic elements related to carbapenem resistance in Acinetobacter baumannii. Brazilian J Microbiol. 2016;47(4):785–92.
16. Brandt C Braun SD Stein C Slickers P Ehricht R Pletz MW In silico serine β-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species Sci Rep 2017 7 1 43232 10.1038/srep43232 28233789
Brandt C, Braun SD, Stein C, Slickers P, Ehricht R, Pletz MW, et al. In silico serine β-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species. Sci Rep. 2017;7(1):43232.28233789
17. Chakravarty B Genetic mechanisms of antibiotic resistance and virulence in Acinetobacter baumannii: background, challenges and future prospects Mol Biol Rep 2020 47 5 4037 4046 10.1007/s11033-020-05389-4 32303957
Chakravarty B. Genetic mechanisms of antibiotic resistance and virulence in Acinetobacter baumannii: background, challenges and future prospects. Mol Biol Rep. 2020;47(5):4037–46.32303957
18 Blackwell GA Hamidian M Hall RM IncM plasmid R1215 is the source of chromosomally located regions containing multiple antibiotic resistance genes in the globally disseminated Acinetobacter baumannii GC1 and GC2 clones mSphere. 2016 1 3 e00117 16 10.1128/mSphere.00117-16 27303751
Blackwell GA, Hamidian M, Hall RM. IncM plasmid R1215 is the source of chromosomally located regions containing multiple antibiotic resistance genes in the globally disseminated Acinetobacter baumannii GC1 and GC2 clones. mSphere. 2016;1(3):e00117-16.27303751
19. Wong D Nielsen TB Bonomo RA Pantapalangkoor P Luna B Spellberg B Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges Clin Microbiol Rev 2017 30 1 409 447 10.1128/CMR.00058-16 27974412
Wong D, Nielsen TB, Bonomo RA, Pantapalangkoor P, Luna B, Spellberg B. Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges. Clin Microbiol Rev. 2017;30(1):409–47.27974412
20. Salgado-Camargo AD Castro-Jaimes S Gutierrez-Rios RM Lozano LF Altamirano-Pacheco L Silva-Sanchez J Structure and evolution of Acinetobacter baumannii plasmids Front Microbiol 2020 11 1283 10.3389/fmicb.2020.01283 32625185
Salgado-Camargo AD, Castro-Jaimes S, Gutierrez-Rios RM, Lozano LF, Altamirano-Pacheco L, Silva-Sanchez J, et al. Structure and evolution of Acinetobacter baumannii plasmids. Front Microbiol. 2020;11:1283.32625185
21. Krizova L Dijkshoorn L Nemec A Diversity and evolution of AbaR genomic resistance islands in Acinetobacter baumannii strains of European clone I Antimicrob Agents Chemother 2011 55 7 3201 3206 10.1128/AAC.00221-11 21537009
Krizova L, Dijkshoorn L, Nemec A. Diversity and evolution of AbaR genomic resistance islands in Acinetobacter baumannii strains of European clone I. Antimicrob Agents Chemother. 2011;55(7):3201–6.21537009
22. Lin MF Lan CY Antimicrobial resistance in Acinetobacter baumannii: from bench to bedside World J Clin Cases 2014 2 12 787 814 10.12998/wjcc.v2.i12.787 25516853
Lin MF, Lan CY. Antimicrobial resistance in Acinetobacter baumannii: from bench to bedside. World J Clin Cases. 2014;2(12):787–814.25516853
23. Gupta N Gandham N Jadhav S Mishra RN Isolation and identification of Acinetobacter species with special reference to antibiotic resistance J Nat Sci Biol Med 2015 6 1 159 162 10.4103/0976-9668.149116 25810655
Gupta N, Gandham N, Jadhav S, Mishra RN. Isolation and identification of Acinetobacter species with special reference to antibiotic resistance. J Nat Sci Biol Med. 2015;6(1):159–62.25810655
24. CLSI. Performance Standards for Antimicrobial Susceptibility Testing. 32nd ed. CLSI supplement M100. Clinical and Laboratory Standards Institute; 2022.
25. Babaei S Haeili M Evaluating the performance characteristics of different antimicrobial susceptibility testing methodologies for testing susceptibility of gram-negative bacteria to tigecycline BMC Infect Dis 2021 21 709 10.1186/s12879-021-06338-7 34315422
Babaei S, Haeili M. Evaluating the performance characteristics of different antimicrobial susceptibility testing methodologies for testing susceptibility of gram-negative bacteria to tigecycline. BMC Infect Dis. 2021;21:709.34315422
26. European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters. 2021;Version 11.0.
27. Wattam AR Davis JJ Assaf R Boisvert S Brettin T Bun C Conrad N Dietrich EM Disz T Gabbard JL Improvements to PATRIC, the all-bacterial Bioinformatics database and analysis resource center Nucleic Acids Res 2017 45 D535 D542 10.1093/nar/gkw1017 27899627
Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T, Bun C, Conrad N, Dietrich EM, Disz T, Gabbard JL, et al. Improvements to PATRIC, the all-bacterial Bioinformatics database and analysis resource center. Nucleic Acids Res. 2017;45:D535–42.27899627
28. Brettin T Davis JJ Disz T Edwards RA Gerdes S Olsen GJ Olson R Overbeek R Parrello B Pusch GD RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes Sci Rep 2015 5 8365 10.1038/srep08365 25666585
Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5:8365.25666585
29. Ondov BD Treangen TJ Melsted P Mallonee AB Bergman NH Koren S Phillippy AM Mash: fast genome and metagenome distance estimation using MinHash Genome Biol 2016 17 132 10.1186/s13059-016-0997-x 27323842
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016;17:132.27323842
30. Davis JJ Gerdes S Olsen GJ Olson R Pusch GD Shukla M Vonstein V Wattam AR Yoo H PATtyFams: protein families for the microbial genomes in the PATRIC database Front Microbiol 2016 7 118 10.3389/fmicb.2016.00118 26903996
Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch GD, Shukla M, Vonstein V, Wattam AR, Yoo H. PATtyFams: protein families for the microbial genomes in the PATRIC database. Front Microbiol. 2016;7:118.26903996
31. Edgar RC MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.15034147
32. Stamatakis A RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Bioinformatics 2014 30 1312 1313 10.1093/bioinformatics/btu033 24451623
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.24451623
33. Stamatakis A Hoover P Rougemont J A rapid bootstrap algorithm for the RAxML web servers Syst Biol 2008 57 758 771 10.1080/10635150802429642 18853362
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 2008;57:758–71.18853362
34. Johansson MHK Bortolaia V Tansirichaiya S Aarestrup FM Roberts AP Petersen TN Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder J Antimicrob Chemother 2021 76 1 101 109 10.1093/jac/dkaa390 33009809
Johansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP, Petersen TN. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother. 2021;76(1):101–9.33009809
35. Bartual SG Seifert H Hippler C Luzon MA Wisplinghoff H Rodriguez-Valera F Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii J Clin Microbiol 2005 43 4382 4390 10.1128/JCM.43.9.4382-4390.2005 16145081
Bartual SG, Seifert H, Hippler C, Luzon MA, Wisplinghoff H, Rodriguez-Valera F. Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii. J Clin Microbiol. 2005;43:4382–90.16145081
36. Alcock et al. CARD 2023: Expanded Curation, Support for Machine Learning, and Resistome Prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research. 2023; 51, D690-D699 Nowak P, Paluchowska P. Acinetobacter baumannii: biology and drug resistance - role of carbapenemases. Folia Histochem Cytobiol. 2016;54(2): 61–74.
37. Nowak P Paluchowska P Acinetobacter baumannii: biology and drug resistance - role of carbapenemases Folia Histochem Cytobiol 2016 54 2 61 74 27270503
Nowak P, Paluchowska P. Acinetobacter baumannii: biology and drug resistance - role of carbapenemases. Folia Histochem Cytobiol. 2016;54(2):61–74.27270503
38. Gaafar M Khalil A Shaheen A Kamel E Multidrug resistant acinetobacter species infection among neonatal sepsis Egypt J Hosp Med 2022 86 541 547 10.21608/ejhm.2022.215101
Gaafar M, Khalil A, Shaheen A, Kamel E. Multidrug resistant acinetobacter species infection among neonatal sepsis. Egypt J Hosp Med. 2022;86:541–7.
39. Nazir A Multidrug-resistant Acinetobacter septicemia in neonates: a study from a teaching hospital of Northern India J Lab Physicians 2019 11 1 23 28 10.4103/JLP.JLP_129_18 30983798
Nazir A. Multidrug-resistant Acinetobacter septicemia in neonates: a study from a teaching hospital of Northern India. J Lab Physicians. 2019;11(1):23–8.30983798
40. Fam N Gamal D Mohamed S Wasfy R Soliman M El-Kholy A Molecular characterization of Carbapenem/Colistin-resistant Acinetobacter baumannii clinical isolates from Egypt by whole-genome sequencing Infect Drug Resist 2020 13 4487 4493 10.2147/IDR.S288865 33364795
Fam N, Gamal D, Mohamed S, Wasfy R, Soliman M, El-Kholy A, et al. Molecular characterization of Carbapenem/Colistin-resistant Acinetobacter baumannii clinical isolates from Egypt by whole-genome sequencing. Infect Drug Resist. 2020;13:4487–93.33364795
41. Makharita R El-Kholy I Hetta H Abdelaziz M Hagagy F Ahmed A Antibiogram and genetic characterization of carbapenem-resistant gram-negative pathogens incriminated in healthcare-associated infections Infect Drug Resist 2020 13 3991 4002 10.2147/IDR.S276975 33177849
Makharita R, El-Kholy I, Hetta H, Abdelaziz M, Hagagy F, Ahmed A, et al. Antibiogram and genetic characterization of carbapenem-resistant gram-negative pathogens incriminated in healthcare-associated infections. Infect Drug Resist. 2020;13:3991–4002.33177849
42. Hamed SM Elkhatib WF Brangsch H Gesraha AS Moustafa S Khater DF Acinetobacter baumannii global clone-specific resistomes explored in clinical isolates recovered from Egypt Antibiotics 2023 12 1149 10.3390/antibiotics12071149 37508245
Hamed SM, Elkhatib WF, Brangsch H, Gesraha AS, Moustafa S, Khater DF, et al. Acinetobacter baumannii global clone-specific resistomes explored in clinical isolates recovered from Egypt. Antibiotics. 2023;12:1149.37508245
43. ALTabbakh AlsM, Saied SA, Shahat A. Detection of Genes of Efflux Pumps (adeB, adeJ and adeG) in Tigecycline Resistant Acinetobacter baumannii Isolated from Benha University Hospital. Egypt J Med Microbiol. 2022;(31):131–139.
44. Gaiarsa S Batisti Biffignandi G Esposito E Castelli M Jolley K Brisse S Sassera D Zarrilli R Comparative analysis of the two Acinetobacter baumannii Multilocus Sequence Typing (MLST) Schemes Front Microbiol 2019 3 10 930 10.3389/fmicb.2019.00930
Gaiarsa S, Batisti Biffignandi G, Esposito E, Castelli M, Jolley K, Brisse S, Sassera D, Zarrilli R. Comparative analysis of the two Acinetobacter baumannii Multilocus Sequence Typing (MLST) Schemes. Front Microbiol. 2019;3(10):930.
45. Zarrilli R Pournaras S Giannouli M Tsakris A Global evolution of multidrugresistant Acinetobacter baumannii clonal lineages Int J Antimicrob Agents 2013 41 11 19 10.1016/j.ijantimicag.2012.09.008 23127486
Zarrilli R, Pournaras S, Giannouli M, Tsakris A. Global evolution of multidrugresistant Acinetobacter baumannii clonal lineages. Int J Antimicrob Agents. 2013;41:11–9.23127486
46 Diancourt L Passet V Nemec A Dijkshoorn L Brisse S The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool PLoS One. 2010 5 4 e10034 10.1371/journal.pone.0010034 20383326
Diancourt L, Passet V, Nemec A, Dijkshoorn L, Brisse S. The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. PLoS One. 2010;5(4):e10034.20383326
47. Shrestha S Tada T Miyoshi-Akiyama T Ohara H Shimada K Satou K Teruya K Nakano K Shiroma A Sherchand J Rijal B Hirano T Kirikae T Pokhrel B Molecular epidemiology of multidrug-resistant Acinetobacter baumannii isolates in a university hospital in Nepal reveals the emergence of a novel epidemic clonal lineage Int J Antimicrob Agents 2015 46 5 526 531 10.1016/j.ijantimicag.2015.07.012 26362951
Shrestha S, Tada T, Miyoshi-Akiyama T, Ohara H, Shimada K, Satou K, Teruya K, Nakano K, Shiroma A, Sherchand J, Rijal B, Hirano T, Kirikae T, Pokhrel B. Molecular epidemiology of multidrug-resistant Acinetobacter baumannii isolates in a university hospital in Nepal reveals the emergence of a novel epidemic clonal lineage. Int J Antimicrob Agents. 2015;46(5):526–31.26362951
48 Al-Hassan L Al-Madboly L Molecular characterisation of an Acinetobacter baumannii outbreak Infect Prev Pract. 2020 2 2 100040 10.1016/j.infpip.2020.100040 34368692
Al-Hassan L, Al-Madboly L. Molecular characterisation of an Acinetobacter baumannii outbreak. Infect Prev Pract. 2020;2(2):100040.34368692
49. Fouad M Attia A Tawakkol W Hashem A Emergence of carbapenemresistant Acinetobacter baumannii harboring the OXA-23 carbapenemase in intensive care units of Egyptian hospitals Int J Infect Dis 2013 17 e1252 e1254 10.1016/j.ijid.2013.07.012 24084245
Fouad M, Attia A, Tawakkol W, Hashem A. Emergence of carbapenemresistant Acinetobacter baumannii harboring the OXA-23 carbapenemase in intensive care units of Egyptian hospitals. Int J Infect Dis. 2013;17:e1252–4.24084245
50. Al-Hassan L, El Mehallawy H, Amyes SG. Diversity in Acinetobacter baumannii isolates from paediatric cancer patients in Egypt. Clin Microbiol Infect. 2013;19(11):1082-8. 10.1111/1469-0691.12143.
51. Lopes B Al-Agamy M Ismail M Shibl A Al-Qahtani A Al-Ahdal M The transferability of blaOXA-23 gene in multidrug-resistant Acinetobacter baumannii isolates from Saudi Arabia and Egypt Int J Med Microbiol 2015 305 581 588 10.1016/j.ijmm.2015.07.007 26253451
Lopes B, Al-Agamy M, Ismail M, Shibl A, Al-Qahtani A, Al-Ahdal M, et al. The transferability of blaOXA-23 gene in multidrug-resistant Acinetobacter baumannii isolates from Saudi Arabia and Egypt. Int J Med Microbiol. 2015;305:581–8.26253451
52. Al-Hassan L Zafer M El-Mahallawy H Multiple sequence types responsible for healthcare-associated Acinetobacter baumannii dissemination in a single centre in Egypt BMC Infect Dis 2019 19 829 10.1186/s12879-019-4433-1 31590644
Al-Hassan L, Zafer M, El-Mahallawy H. Multiple sequence types responsible for healthcare-associated Acinetobacter baumannii dissemination in a single centre in Egypt. BMC Infect Dis. 2019;19:829.31590644
53. Hamidian M Nigro S Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii Microb Genomics 2019 5 e000306 10.1099/mgen.0.000306
Hamidian M, Nigro S. Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii. Microb Genomics. 2019;5:e000306.
54. Müller C, Stefanik D, Wille J, Hackel M, Higgins PG, Seifert H. Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii clinical isolates and identification of the novel international clone IC9: results from a worldwide surveillance study (2012 – 2016). In Proceedings of the Abstract Book of the 29th European Congress of Clinical Microbiology and Infectious Diseases, P0947. Amsterdam: 2019.
55. Tomaschek F Higgins P Stefanik D Wisplinghoff H Seifert H Hatcher J Head-to-Head comparison of two multilocus sequence typing (MLST) schemes for characterization of Acinetobacter baumannii outbreak and sporadic isolates PLoS One 2019 11 e0153014 10.1371/journal.pone.0153014
Tomaschek F, Higgins P, Stefanik D, Wisplinghoff H, Seifert H, Hatcher J, et al. Head-to-Head comparison of two multilocus sequence typing (MLST) schemes for characterization of Acinetobacter baumannii outbreak and sporadic isolates. PLoS One. 2019;11:e0153014.
56. Rafei R Hamze M Pailhories H Eveillard M Marsollier L Joly-Guillou M Dabboussi F Kempf M Extrahuman epidemiology of Acinetobacter baumannii in Lebanon Appl Environ Microbiol 2015 81 2359 2367 10.1128/AEM.03824-14 25616788
Rafei R, Hamze M, Pailhories H, Eveillard M, Marsollier L, Joly-Guillou M, Dabboussi F, Kempf M. Extrahuman epidemiology of Acinetobacter baumannii in Lebanon. Appl Environ Microbiol. 2015;81:2359–67.25616788
57. Klotz P Higgins P Schaubmar A Failing K Leidner U Seifert H Scheufen S Semmler T Ewers C Seasonal occurrence and carbapenem susceptibility of bovine Acinetobacter baumannii in Germany Front Microbiol 2019 10 272 10.3389/fmicb.2019.00272 30853949
Klotz P, Higgins P, Schaubmar A, Failing K, Leidner U, Seifert H, Scheufen S, Semmler T, Ewers C. Seasonal occurrence and carbapenem susceptibility of bovine Acinetobacter baumannii in Germany. Front Microbiol. 2019;10:272.30853949
58. Levy-Blitchtein S Roca I Plasencia-Rebata S Vicente-Taboada W Velásquez-Pomar J Muñoz L Moreno-Morales J Pons M del Valle-Mendoza J Vila J Emergence and spread of carbapenem-resistant Acinetobacter baumannii international clones II and III in Lima Peru Emerg Microbes Infect 2018 7 1 9 10.1038/s41426-018-0127-9
Levy-Blitchtein S, Roca I, Plasencia-Rebata S, Vicente-Taboada W, Velásquez-Pomar J, Muñoz L, Moreno-Morales J, Pons M, del Valle-Mendoza J, Vila J. Emergence and spread of carbapenem-resistant Acinetobacter baumannii international clones II and III in Lima. Peru Emerg Microbes Infect. 2018;7:1–9.
59. Hassan R Salem S Hassan S Hegab A Elkholy Y Molecular characterization of carbapenem-resistant Acinetobacter baumannii clinical isolates from Egyptian patients PLoS One 2021 16 6 e0251508 10.1371/journal.pone.0251508 34166384
Hassan R, Salem S, Hassan S, Hegab A, Elkholy Y. Molecular characterization of carbapenem-resistant Acinetobacter baumannii clinical isolates from Egyptian patients. PLoS One. 2021;16(6):e0251508.34166384
60. Al-Agamy M Khalaf N Tawfick M Shibl A Kholy A Molecular characterization of carbapenem-insensitive Acinetobacter baumannii in Egypt Int J Infect Dis 2014 22 49 54 10.1016/j.ijid.2013.12.004 24607428
Al-Agamy M, Khalaf N, Tawfick M, Shibl A, Kholy A. Molecular characterization of carbapenem-insensitive Acinetobacter baumannii in Egypt. Int J Infect Dis. 2014;22:49–54.24607428
61. Ramadan R Gebriel M Kadry H Mosallem A Carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa: characterization of carbapenemase genes and E-test evaluation of colistin-based combinations Infect Drug Resist 2018 11 1261 1269 10.2147/IDR.S170233 30197524
Ramadan R, Gebriel M, Kadry H, Mosallem A. Carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa: characterization of carbapenemase genes and E-test evaluation of colistin-based combinations. Infect Drug Resist. 2018;11:1261–9.30197524
62. Kamel NA, El-Tayeb WN, El-Ansary MR, Mansour MT, Aboshanab KM. Phenotypic screening and molecular characterization of carbapenemase-producing Gram-negative bacilli recovered from febrile neutropenic pediatric cancer patients in Egypt. PLoS One. 2018;13(8):e0202119. 10.1371/journal.pone.0202119.
63. Alkasaby NM, El Sayed Zaki M. Molecular Study of Acinetobacter baumannii Isolates for Metallo-β-Lactamases and Extended-Spectrum-β-Lactamases Genes in Intensive Care Unit, Mansoura University Hospital, Egypt. Int J Microbiol. 2017;2017:3925868. 10.1155/2017/3925868.
64. Hraba'k J Sˇtolbova' M Sˇtudentova' V Fridrichova' M Chuda´čkova´ E Zemlickova H NDM-1 producing Acinetobacter baumannii isolated from a patient repatriated to the Czech Republic from Egypt, July 2011 Eurosurveillance 2012 17 7 1 3
Hraba’k J, Sˇtolbova’ M, Sˇtudentova’ V, Fridrichova’ M, Chuda´čkova´ E, Zemlickova H. NDM-1 producing Acinetobacter baumannii isolated from a patient repatriated to the Czech Republic from Egypt, July 2011. Eurosurveillance. 2012;17(7):1–3.
65. Kaase M Nordmann P Wichelhaus TA Gatermann SG Bonnin RA Poirel L NDM-2 carbapenemase in Acinetobacter baumannii from Egypt J Antimicrob Chemother 2011 66 6 1260 1262 10.1093/jac/dkr135 21427107
Kaase M, Nordmann P, Wichelhaus TA, Gatermann SG, Bonnin RA, Poirel L. NDM-2 carbapenemase in Acinetobacter baumannii from Egypt. J Antimicrob Chemother. 2011;66(6):1260–2.21427107
66. Guducuoglu H Gursoy N Yakupogullari Y Parlak M Karasin G Sunnetcioglu M Hospital outbreak of a colistin-resistant, NDM-1- and OXA-48-producing Klebsiella pneumoniae: high mortality from pandrug resistance Microb Drug Resist 2018 24 966 972 10.1089/mdr.2017.0173 29265963
Guducuoglu H, Gursoy N, Yakupogullari Y, Parlak M, Karasin G, Sunnetcioglu M, et al. Hospital outbreak of a colistin-resistant, NDM-1- and OXA-48-producing Klebsiella pneumoniae: high mortality from pandrug resistance. Microb Drug Resist. 2018;24:966–72.29265963
67. El Sheredy A Yousif Z Elghazzawi E Elmenshawy A Ghazal A Prevalence of genes encoding aminoglycoside-modifying enzymes and armA among Acinetobacter baumannii clinical isolates in Alexandria Egypt. Infect. Disord. Drug Targets. 2021 21 8 e300821191828 10.2174/1871526521666210225113041 33632111
El Sheredy A, Yousif Z, Elghazzawi E, Elmenshawy A, Ghazal A. Prevalence of genes encoding aminoglycoside-modifying enzymes and armA among Acinetobacter baumannii clinical isolates in Alexandria. Egypt Infect Disord Drug Targets. 2021;21(8):e300821191828.33632111
68. Sa' nchez-Urtaza S Ocampo-Sosa A Molins-Bengoetxea A El-Kholy MA Hernandez M Abad D Shawky SM Alkorta I Gallego L Molecular characterization of multidrug resistant Acinetobacter baumannii clinical isolates from Alexandria, Egypt Front Cell Infect Microbiol 2023 13 1208046 10.3389/fcimb.2023.1208046 37545857
Sa’ nchez-Urtaza S, Ocampo-Sosa A, Molins-Bengoetxea A, El-Kholy MA, Hernandez M, Abad D, Shawky SM, Alkorta I, Gallego L. Molecular characterization of multidrug resistant Acinetobacter baumannii clinical isolates from Alexandria, Egypt. Front Cell Infect Microbiol. 2023;13:1208046.37545857
69. Roberts MC Update on acquired tetracycline resistance genes FEMS Microbiol Lett 2005 245 2 195 203 10.1016/j.femsle.2005.02.034 15837373
Roberts MC. Update on acquired tetracycline resistance genes. FEMS Microbiol Lett. 2005;245(2):195–203.15837373
70. Rumbo C Gato E López M Ruiz De Alegría C Fernández-Cuenca F Martínez-Martínez L Vila J Pachón J Cisneros J Rodríguez-Baño J Contribution of efflux pumps, porins, and β-lactamases to multidrug resistance in clinical isolates of Acinetobacter baumannii Antimicrob Agents Chemother 2013 57 5247 5257 10.1128/AAC.00730-13 23939894
Rumbo C, Gato E, López M, Ruiz De Alegría C, Fernández-Cuenca F, Martínez-Martínez L, Vila J, Pachón J, Cisneros J, Rodríguez-Baño J, et al. Contribution of efflux pumps, porins, and β-lactamases to multidrug resistance in clinical isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 2013;57:5247–57.23939894
71. Sköld O Resistance to trimethoprim and sulfonamides Vet Res 2001 32 3–4 261 273 10.1051/vetres:2001123 11432417
Sköld O. Resistance to trimethoprim and sulfonamides. Vet Res. 2001;32(3–4):261–73.11432417
72. Roca I Marti S Espinal P Martínez P Gibert I Vila J CraA, a major facilitator superfamily efflux pump associated with chloramphenicol resistance in Acinetobacter baumannii Antimicrob Agents Chemother 2009 53 9 4013 4014 10.1128/AAC.00584-09 19581458
Roca I, Marti S, Espinal P, Martínez P, Gibert I, Vila J. CraA, a major facilitator superfamily efflux pump associated with chloramphenicol resistance in Acinetobacter baumannii. Antimicrob Agents Chemother. 2009;53(9):4013–4.19581458
73. Kumburu HH Sonda T van Zwetselaar M Leekitcharoenphon P Lukjancenko O Mmbaga BT Alifrangis M Lund O Aarestrup FM Kibiki GS Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania J Antimicrob Chemother 2019 74 6 1484 1493 10.1093/jac/dkz055 30843063
Kumburu HH, Sonda T, van Zwetselaar M, Leekitcharoenphon P, Lukjancenko O, Mmbaga BT, Alifrangis M, Lund O, Aarestrup FM, Kibiki GS. Using WGS to identify antibiotic resistance genes and predict antimicrobial resistance phenotypes in MDR Acinetobacter baumannii in Tanzania. J Antimicrob Chemother. 2019;74(6):1484–93.30843063
74. Tantawy EA El-Sayed HM Matar HM ElAzhary BA Multi- and Extensive-Drug resistant Acinetobacter baumannii in ICUs, Risk factors, antimicrobial resistance profiles, and co-harboring of gyrA and parC mutations Egypt J Med Microbiol 2020 29 109 116 10.51429/EJMM29414
Tantawy EA, El-Sayed HM, Matar HM, ElAzhary BA. Multi- and Extensive-Drug resistant Acinetobacter baumannii in ICUs, Risk factors, antimicrobial resistance profiles, and co-harboring of gyrA and parC mutations. Egypt J Med Microbiol. 2020;29:109–16.
75. Zaki MES Abou ElKheir N Mofreh M Molecular study of quinolone resistance determining regions of gyrA gene and parC genes in clinical isolated of Acinetobacter baumannii resistant to fluoroquinolones Open Microbiol J 2018 12 116 122 10.2174/1874285801812010116 29785218
Zaki MES, Abou ElKheir N, Mofreh M. Molecular study of quinolone resistance determining regions of gyrA gene and parC genes in clinical isolated of Acinetobacter baumannii resistant to fluoroquinolones. Open Microbiol J. 2018;12:116–22.29785218
76. Taha M Shoeib S Abdelwahab M Mutations in gyrA and parC genes in fluoroquinolone-resistant Acinetobacter baumannii that causes hospital acquired infection Microbes Infect Dis 2023 4 2 590 600
Taha M, Shoeib S, Abdelwahab M. Mutations in gyrA and parC genes in fluoroquinolone-resistant Acinetobacter baumannii that causes hospital acquired infection. Microbes Infect Dis. 2023;4(2):590–600.
77. Partridge SR Kwong SM Firth N Jensen SO Mobile genetic elements associated with Antimicrobial resistance Clin Microbiol Rev 2018 31 4 e00088 e117 10.1128/CMR.00088-17 30068738
Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile genetic elements associated with Antimicrobial resistance. Clin Microbiol Rev. 2018;31(4):e00088-e117.30068738
78. Kyriakidis I Vasileiou E Pana ZD Tragiannidis A Acinetobacter baumannii Antibiotic resistance mechanisms Pathogens 2021 10 3 373 10.3390/pathogens10030373 33808905
Kyriakidis I, Vasileiou E, Pana ZD, Tragiannidis A. Acinetobacter baumannii Antibiotic resistance mechanisms. Pathogens. 2021;10(3):373.33808905
