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WGS based analysis of acquired antimicrobial resistance in human and non-human Acinetobacter baumannii isolates from a German perspective

Abstract

Background

Acinetobacter baumannii ability to develop and acquire resistance makes it one of the most critical nosocomial pathogens globally. Whole-genome sequencing (WGS) was applied to identify the acquired or mutational variants of antimicrobial resistance (AMR) genes in 85 German A. baumannii strains utilizing Illumina technology. Additionally, the whole genome of 104 German isolates deposited in the NCBI database was investigated.

Results

In-silico analysis of WGS data revealed wide varieties of acquired AMR genes mediating resistance mostly to aminoglycosides, cephalosporins, carbapenems, sulfonamides, tetracyclines and macrolides. In the 189 analyzed genomes, the ant (3″)-IIa conferring resistance to aminoglycosides was the most frequent (55%), followed by blaADC.25 (38.6%) conferring resistance to cephalosporin, blaOXA-23 (29%) and the blaOXA-66 variant of the intrinsic blaOXA-51-likes (26.5%) conferring resistance to carbapenems, the sul2 (26%) conferring resistance to sulfonamides, the tet. B (19.5%) conferring resistance to tetracycline, and mph. E and msr. E (19%) conferring resistance to macrolides. blaTEM variants conferring resistance to cephalosporins were found in 12% of genomes. Thirteen variants of the intrinsic blaOXA-51 carbapenemase gene, blaOXA-510 and blaADC-25 genes were found in isolates obtained from dried milk samples.

Conclusion

The presence of strains harboring acquired AMR genes in dried milk raises safety concerns and highlights the need for changes in producing dried milk. Acquired resistance genes and chromosomal gene mutation are successful routes for disseminating AMR determinants among A. baumannii. Identification of chromosomal and plasmid-encoded AMR in the genome of A. baumannii may help understand the mechanism behind the genetic mobilization and spread of AMR genes.

Peer Review reports

Background

Acinetobacter baumannii (A. baumannii) is a member of the ESKAPE pathogens, the leading cause of multidrug-resistant (MDR) and extensively drug-resistant (XDR) nosocomial infections worldwide [1]. The emergence of MDR A. baumannii strains resistant to last-resort antibiotics such as carbapenems and colistin is on the rise in hospital settings globally and complicates the treatment [2]. Therefore, the World Health Organization (WHO) has classified A. baumannii among the most dangerous MDR pathogens worldwide. It is considered one of the critical pathogens that need developing new antibiotics [3, 4]. In Germany, A. baumannii is a ubiquitous pathogen, and several communities and hospital-based outbreaks were reported in 13 out of 16 federal states [5]. Among other sources, the pathogen was also isolated from companion animals [6] and found in dried milk samples [7]. Besides, A. baumannii was released via manure [8] and through wastewater treatment plant (WWTP) effluents [9] into the environment in various districts of Germany. Still, the current knowledge on antibiotic resistance in strains collected from non-humans origin is scarce [10].

Acinetobacter baumannii possesses the ability to develop intrinsic resistance via reducing membrane permeability, efflux pump activity, and the production of wide varieties of ß-lactamases enzymes [11]. However, resistance in this pathogen is frequently associated with mobile genetic elements (MGEs) transferable between bacteria, enabling rapid dissemination and maintenance of resistance genes between different bacterial species [12]. It can also acquire resistance via mutational changes in chromosomal structure and horizontal gene transfer [13], in addition to some different naturally occurring intrinsic resistance genes [14]. Acinetobacter baumannii has an unprecedented ability to acquire resistance against antimicrobial agents from diverse sources and further disseminate and develop new resistance mechanisms [15]. Besides the massive resistance island coding for multiple intrinsic resistance within its genome, it can rapidly acquire further extrinsic resistance during antibiotic therapy by acquiring additional genetic determinants by cross-species horizontal gene transfer [16, 17]. The genome of A. baumannii consists of a chromosome and various plasmids. Most of them have been linked to the acquisition of AMR genes [18]. Comparative genomic analysis of A. baumannii strains revealed that the genome of A. baumannii could acquire a large amount of foreign DNA, which could play a role in antimicrobial resistance and pathogenesis [19, 20]. Thus, the current study is dedicated to collect data on acquired resistance genes in 85 clinical and non-clinical A. baumannii strains originating from Germany. Moreover, the resistance profile in another 104 genomes of German A. baumannii strains deposited in the National Centre for Biotechnology Information (NCBI) database was investigated.

Results

The phenotyping characterization of A. baumannii

The phenotyping characterization of 85 A. baumannii isolates showed a high frequency of resistance for chloramphenicol (100%), followed by fosfomycin in 81 (95%) isolates and the third-generation cephalosporins, cefotaxime in 80 (94%) isolates. Resistance to at least one of the carbapenem compounds was found in 24 (28%) isolates. Resistance to aminoglycosides (amikacin) and tetracycline (tigecycline) was found in 10 (11%) isolates to each. The lowest frequency of resistance was seen for colistin in three isolates (Fig. 1). In parallel, the analysis of the downloaded 104 whole-genome of A. baumannii deposited at the NCBI indicates that the strains harbored genes mediating resistance to ten antimicrobial agent groups, including ß-lactams, (carbapenems and cephalosporins), aminoglycosides, phenicoles, tetracycline, trimethoprim, sulfonamides, macrolides, streptothricin, bleomycin and rifampicin. The frequency of resistance toward aminoglycosides was the highest, followed by carbapenems and cephalosporins. The lowest frequency was seen for streptothricin, bleomycin and rifampicin (Fig. 2).

Fig. 1
figure1

Number of resistant and sensitive isolates among 85 A. baumannii strains isolated from human and milk powder samples in Germany. COL, Colistin; T/S, Trimethoprim/Sulfamethoxazole; TGC, Tigecycline; AMK, Amikacin; CAA, Ceftazidime/Avibactam; CEP, Cefepime; MER, Meropenem; IMP, Imipenem; CTA, Ceftolozane/Tazobactam; CAZ, Ceftazidime; PIT, Piperacillin/Tazobactam; PIP, Piperacillin; LEV, Levofloxacin; CIP, Ciprofloxacin; ERT, Ertapenem; CTX, Cefotaxime; FOS, Fosfomycin; CMP, Chloramphenicol

Fig. 2
figure2

Number and frequency of AMR genes harbored within 104 genomes of German A. baumannii isolates obtained from the NCBI database as of September 2020

In-silico detection of acquired AMR genes in A. baumannii strains

The in-silico detection of acquired AMR genes in A. baumannii isolates (n = 85) based on WGS data using the ResFinder database succeeded in identifying 40 acquired AMR genes (Supplementary Table 1). Twenty-two different β-lactamases resistance genes belonging to three different Ambler classes were identified. Thirteen genes were identified in isolates obtained from dried milk samples. Seven genes were identified in clinical isolates obtained from humans, and two genes were shared in isolates obtained from milk samples and humans. At least one, two, and 19 different variants of class C, A, and D β- lactamases were identified, respectively. The Ambler class D β-lactamases were the most predominant genes and represented in 19 blaOXA ß-lactamases variants. Among them, 16 gene variants were belonging to the intrinsic blaOXA-51-like carbapenemase group, of which the blaOXA.430 gene was most frequent, present in 24 (28.2%) isolates obtained from milk powder. All strains harbored blaOXA.430 gene were resistant to cefotaxime, and four of them showed resistance to ertapenem. This was followed by blaOXA.91 and blaOXA.66 genes of the same blaOXA-51-like group and were found in 21 (24.5%) and ten (11.8%) isolates, respectively. Four isolates (4.7%) obtained from milk powder samples harbored blaOXA.343 gene of blaOXA-51-like; however, they showed sensitivity to all tested antibiotics. Additionally, the blaOXA.23 was found in 12 (14%) isolates of human origin, and a single variant of blaOXA-510 and blaOXA-521, each was found in one isolate (Table 1).

Table 1 List of acquired β-lactamases resistance genes identified in A. baumannii isolates (n = 85) from humans and dried milk based on WGS data using ResFinder database

The Ambler class C β-lactamases, Acinetobacter-derived cephalosporinase blaADC.25, was identified in all isolates (100%). Among them, 11 isolates (13%) were carbapenem-resistant, and 80 (94%) isolates were resistant to the third-generation cephalosporin cefotaxime antibiotic. Two acquired AMR genes belonging to the Ambler class A β-lactamases were identified. The blaTEM.1D was found in three isolates (3.8%), and carbenicillin hydrolyzing β-lactamase blaCARB.5 was found in another three isolates. All six isolates were resistant to cephalosporins and carbapenems (Table 1).

On the other hand, 18 non-β-lactamases AMR genes conferring resistance to aminoglycosides, tetracyclines, phenicoles, sulfonamides and macrolides were identified. None of them was found in isolates obtained from milk samples. Eight aminoglycoside-modifying enzymes (AMEs) genes were detected. Among them, three were aminoglycoside acetyltransferase (ACT), which were encoded by plasmids, transposons, and integron in A. baumannii, two were aminoglycoside nucleotidyltransferase (NUT), two were aminoglycoside phosphotransferase (PHT), and one was aminoglycoside methyltransferase (MET). Those eight AMEs genes conferred resistance to amikacin in ten isolates. At least three genes encoding resistance to each tetracycline and phenicoles compounds were identified. The tet. B encoding resistance to tetracycline was identified in nine isolates; among them, eight were resistant to tigecycline. In spite, tet.39 was identified in two isolates, but both were susceptible to tetracycline compounds. All investigated isolates were resistant to chloramphenicol; however, only four isolates harbored three genes (catA, catB and floR) confer resistance to phenicoles were identified. Two genes encoding resistance to each macrolide and sulfonamide antibiotics were identified. The gene sul1 and sul2 variants were found in three and one isolates, respectively, and all were resistant to trimethoprim/sulphamethoxazole. The mph. E and msr. E genes encoding resistance to macrolides were identified in two and three isolates, respectively; however, none of them showed resistance to macrolides (Table 2).

Table 2 List of acquired non-β-lactamases resistance genes identified in A. baumannii isolates from humans (n = 14/85) based on WGS data using ResFinder databases

In-silico analysis of AMR in A. baumannii genomes deposited at the NCBI

In parallel, the frequency and percentage of resistance genes were investigated in 104 whole-genome of A. baumannii strains of German origin deposited at the NCBI. The numbers of resistance genes conferring a specific antibiotic resistance were identified. Additionally, beta-lactamase genes were indicated and divided into their molecular group (class A, B, C, D; based on Ambler), and the plot is separated into chromosomal and plasmid DNA contigs. The identified ß-lactamases and non-ß-lactamases AMR genes in genomes, some are chromosomal-encoded, and some are plasmid-encoded genes (Fig. S1).

In total, 101 AMR genes were identified in 104 genomes. AMR genes confer resistance to cephalosporin antibiotics were the most frequent genes identified and represented by 37 different gene variants. Among them, 31 blaADC variants were identified, and blaADC-73 was the most frequent gene and was found in 19 (18%) isolates, followed by blaADC-30 in 15 (14.4%), and blaADC-166 in eight (7.7%) isolates, while blaADC-25 was seen only in two isolates (1.9%). Besides, the acquired blaTEM-12 was found in 19 (18%) isolates.

Twenty-four AMR genes conferring resistance to carbapenem compounds were identified. Among them, 19 genes belong to the intrinsic blaOXA-51-like carbapenemase gene; of them, blaOXA-66 was the most frequent and was found in 40 (38.5%) isolates. Additionally, the blaOXA-23 was the most frequent gene found in 43 (41%) isolates, while the blaNDM-1 was found in three (2.9%) isolates. Sixteen AMR genes conferring resistance to aminoglycosides were identified. Aminoglycoside nucleotidyltransferase ant (3″)-IIa conferred resistance to streptomycin and spectinomycin and was found in 104 (100%) genomes. Aminoglycoside O-phosphotransferase aph (3″)-Ib and aph (6)-Id confers resistance to streptomycin were found in 48 (46%), and 45 (43%) of genomes, respectively, followed by aph (3′)-Ia and aph (3′)-VIa that were found in 28 (27%) and 24 (23%) of genomes, respectively (Table 3).

Table 3 Antimicrobial resistance genes detected in 104 whole-genome sequences of A. baumannii originating from Germany and deposited in NCBI

Six AMR genes confer resistance to chloramphenicol antibiotics were found. The catA1 and cmlB1 were the most frequent and found in nine (8.6%) and six (5.8%) genomes, respectively. Three AMR genes confer resistance to tetracycline compounds were identified. The tet. B gene was the most frequent and found in 38 (36.5%) isolates, followed by tet.39 and tet. A. Two AMR genes confer resistance to sulfonamides were identified; the sul1 and sul2 were found in 22 (21%) and 47 (45%) of genomes, respectively. Three genes encoded Trimethoprim resistance were found, and the dfrA1 was the most frequent and found in four (3.8%) isolates, followed by the dfrA7 and dfrA17 genes. Macrolide resistance was predominantly encoded by the mph. E gene in 34 (32.7%) isolates and msr. E in 33 (31.7%) genomes. Rifampicin resistance was encoded by arr-2 and was found in one strain (Table 3).

The frequency and profiling of AMR in genomes of A. baumannii from Germany

As shown in Table 4, the comprehensive analysis of AMR in 189 genomes of A. baumannii of German origin revealed 15 AMR genes with a frequency of more than 10%. The ant (3″)-IIa confers resistance to aminoglycosides was the most prevalent gene with a frequency of 55%, followed by the blaADC.25 confer resistance to cephalosporin with a frequency of 38.6%, and the two genes confer resistance to carbapenems, blaOXA-23 and blaOXA-51-like (blaOXA-66 variant), with a frequency of 29 and 26.5%, respectively. Around a quarter of genomes (26%) harbored sul2 that confer resistance to sulfonamides, while sul1 was found in 13.2% of the genomes. The frequency of tet. B gene confer resistance to tetracycline was 19.5%, and the frequency of mph. E and msr. E confer resistance to macrolide was 19%. The variants of acquired blaTEM were found in 23 genomes with a frequency of 12% (Table 4).

Table 4 The total frequency and percentages of the AMR genes in 189 genomes of A. baumannii isolated from Germany

Discussion

The ability of A. baumannii to survive in adverse environmental conditions and to develop or acquire resistance make it one of the most critical nosocomial pathogens in the hospital’s environment [21]. The presence of various plasmids in the genome of A. baumannii [18] and its ability to acquire foreign DNA [19, 20] enhance the acquisition of AMR genes. Several reports suggested that integrons play significant roles in the horizontal transfer of AMR genes in A. baumannii, particularly genes that confer resistance to aminoglycosides, chloramphenicol and tetracycline [22,23,24]. Identification of acquired AMR genes circulating in A. baumannii is essential for understanding the underlying mechanisms of the acquisition and development of antimicrobial resistance. Next-generation sequence (NGS) technology became available in most routine diagnostic laboratories worldwide, and it is anticipated to substitute the traditional PCR tools for identifying AMR genes. Thus, the current study is focusing on the detection of acquired AMR genes and antimicrobial resistance profiles of 85 A. baumannii strains that were isolated from humans and dried milk samples in Germany and extraction of the relevant information from another 104 genomes of A. baumannii submitted to the NCBI from different laboratories across Germany.

Antimicrobial resistance is on the rise in foods and environmental sources. MDR Acinetobacter strains have been isolated from dried milk in Germany [7], infant milk formulas in Brazil [25] and China [26], as well as from bulk tank milk (BTM) samples and mastitic milk samples of dairy cattle in different districts of Korea [27, 28], representing a significant risk of the transmission of this pathogen to consumers. Inside animal hosts and in the environment, A. baumannii cohabits with several bacterial species. The potential acquisition of horizontal resistance genes from other bacterial species is very high due to the presence of plasmids [18]. In total, 15 AMR genes were identified in strains obtained from powdered milk samples. All milk powder samples were obtained from the end product at the production level. Thus, the origin of A. baumannii in milk samples is unknown because the microbes can enter the dairy supply chain at different stages during milk collection, production and processing [29]. Contamination of dried milk with A. baumannii and the existence of such genes is evidence of a potential threat that should be considered and can affecting human consumers. This highlights the urgent need for strict hygiene measures during the processing of dried milk.

The high frequency of resistance for carbapenems and cephalosporins was found in both groups of A. baumannii, either sequenced isolates or genomes deposited at NCBI. MDR strains harboring diverse resistance genes confer resistance for carbapenems and cephalosporins were isolated in various hospital outbreaks in Germany [30,31,32]. Broad diversity of OXA-type carbapenemase genes was identified, and the blaOXA-23 and blaOXA-51-like (blaOXA-66 variant) were among the most frequent. Both are ambler class D ß-lactamases, which originally relatively rare and always plasmid-mediated. It is worth mentioning that the OXA β-lactamase group was among the earliest β-lactamases detected, and the variants OXA-23 and OXA-51 are currently spreading on plasmids. Therefore their transmission between different bacterial species can be reasonably assumed [33]. Several studies have shown that the presence of one or both of those genes in A. baumannii is associated with resistance to all β-lactam antibiotics, including carbapenems [34,35,36,37]. The class D carbapenemase blaOXA-66/OXA-51-like contributes to intrinsic resistance to imipenem in clinical strains of A. baumannii [38]. The blaOXA-51 was detected initially in A. baumannii from Argentina in 1996 [39]. It is the largest group of intrinsic OXA-type β-lactamases identified and became an important marker for species identification of A. baumannii. Association of ISAba1 with blaOXA-51-like can increase its expression levels by 50-fold [33]. The oxacillinase blaOXA-23 was identified for the first time in A. baumannii strains isolated from the United Kingdom in 1993. Later, it has been found and linked to the dissemination of carbapenem-resistant in A. baumannii worldwide [40] and is one of the most dominant resistance genes described in A. baumannii in Germany last decade [5].

The ADC beta-lactamases are cephalosporinase with extended-spectrum resistance to cephalosporins. Thirty-one ADC beta-lactamases variants were found in isolates deposited at NCBI, and the blaADC-73 was the most frequent. The blaADC-73 is a novel variant of blaADC and has been detected in A. baumannii isolates in a few studies [41, 42]. Proteogenomic analysis of XDR strains showed that blaADC-73 is one of the significant determinants responsible for antibiotic resistance in A. baumannii [43]. The presence of the ISAba1 element in blaADC–73 gene is responsible for increase the cephalosporinase gene expression [44]. In contrast, blaADC-25_1 was the only variant identified in the 85 sequenced isolates and was found in all isolates (100%). The cephalosporinase-encoding blaADC-25-like gene was uncommon in Germany; however, it has been detected in hospital-acquired A. baumannii infection [31]. It is worth mentioning that the ant (3″)-IIa conferring resistance to aminoglycosides was found in all isolates (n = 104) deposited in the NCBI database. However, none of the 85 sequenced isolates contained this gene by using the ResFinder server. The comprehensive ResFinder server was used for the detection of acquired resistance genes in the sequenced isolates and failed to detect the ant (3″)-IIa. Searching for non-β-lactamases intrinsic resistance genes using CARD and NCBI databases succeeded in detecting this gene in all sequenced isolates [11]. Thus, this study highlights the necessity of combining different databases to determine the resistance profiles of A. baumannii isolates and depending on one database to discriminate the presence of all AMR genes was insufficient [11].

Three tetracycline-encoding genes were identified in A. baumannii, and tet. B was the most frequent in both groups. The tet. B is a tetracycline efflux protein expressed in various Gram-negative bacteria. It is a major facilitator superfamily (MFS) antibiotic efflux pump that confers tetracycline resistance but not tigecycline [45]. In our survey, it was found in nine sequenced isolates; among them, only eight were tigecycline resistant. Tigecycline is a glycylcycline developed to help overcome tetracycline-resistant in microorganisms [46]. In A. baumannii, it was reported that tet. A plays an essential role in tigecycline efflux by removing and transporting tigecycline from the cytoplasm to the periplasm [47]. The tet. A.6 was identified in a tigecycline resistant strain of human origin and was present in 5.8% of genomes deposited in NCBI. Two genes, the sul1 and sul2 mediated resistance to sulfonamides were identified. Both are mediated by transposons and plasmids and are express dihydropteroate synthases in Gram-negative bacteria that confer resistance to sulfonamides [48]. The presence of one or both genes in A. baumannii isolates conferred resistance to trimethoprim/sulfamethoxazole.

In spite, all sequenced A. baumannii isolates (100%) in the current study were chloramphenicol resistant; only four isolates harbored chloramphenicol acetyltransferase encoded variant of the cat genes and chloramphenicol exporter floR gene. It was indicated previously that most A. baumannii isolates are intrinsically resistant to chloramphenicol; however, the mechanism responsible for such resistance is not apparent yet [49]. Three isolates were colistin-resistant; however, none of the plasmid-mediated resistance to colistin (mcr genes) was identified. The mechanism of resistance to colistin in A. baumannii is associated with the mutation in the protein PmrAB [50].

Conclusion

Acinetobacter baumannii is an important opportunistic nosocomial pathogen in healthcare settings in Germany. AMR genes were investigated in the genome of 189 German A. baumannii strains. The spread of MGE is the main driving force in the spread and dissemination of acquired resistance, but a chromosomal gene mutation is a possible route. Three major known resistance mechanisms are associated with MGE, i.e., enzyme inactivation, antibiotics efflux, and antibiotic target sites’ replacement. Acquired AMR belonging to those mechanisms was seen in the current studied group of A. baumannii. Understanding the genetic mobilization of AMR genes in A. baumannii collected from different reservoirs is essential to investigate resistance genes’ interspecies mobility. This is paramount in preventing dissemination and spillover. The presence of A. baumannii strains harboring divers acquired AMR genes in milk powder raises safety and health concerns and highlights the need for a more hygienic environment for the processing of dried milk.

Materials and methods

Molecular characterization and phenotyping of A. baumannii strains

Eighty-five A. baumannii strains isolated between 2005 and 2018 in Germany were received by the Institute of Bacterial Infections and Zoonoses (IBIZ, Jena) for confirmation and typing. Fourteen clinical strains were isolated from humans between 2017 and 2018, and 71 non-clinical strains were obtained from powdered milk samples produced in Germany. All milk powder samples investigated in the current study were isolated from the end product of three different companies in Germany between 2005 and 2012 at the production level. The strains were identified at species level using a combination of Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-TOF MS) with a score value > 2.300 and the intrinsic blaOXA-51-like-PCR [51]. The identity and non-clonality of all isolates were confirmed using the WGS data. Antimicrobial susceptibility testing (AST) for 18 antibiotics was carried out via the broth microdilution method using an automated MICRONAUT-S system (Micronaut, MERLIN Diagnostics GmbH, Bornheim-Hersel Germany) according to the manufacturer’s instructions. The minimum inhibitory concentration (MIC) was determined according to the Clinical and Laboratory Standards Institute (CLSI) breakpoint guidelines available for A. baumannii, as previously described [11].

WGS based detection of acquired AMR genes in A. baumannii strains

DNA was extracted using the High Pure PCR Template Preparation Kit (Roche Diagnostics GmbH, Mannheim, Germany) according to the manufacturer’s instructions. The sequencing library was prepared, followed by paired-end sequencing on an Illumina MiSeq sequencer (Illumina, USA). The raw sequencing data were assembled and analyzed as previously described [11]. The comprehensive ResFinder server [52] was used to identify the acquired AMR genes among A. baumannii strains. Known acquired resistance genes relevant to ß-lactams (including carbapenems and cephalosporins), aminoglycosides, phenicoles, macrolide-lincosamide-streptogramin B, quinolones, sulfonamides, and tetracyclines were included in the analysis. The β-lactamase and non-β-lactamase gene variants were determined with a 100% identity using the A. baumannii reference genome (Accession ASM74664v1) as input. Reference sequences for acquired resistance genes were curated from those described in the ResFinder (https://cge.cbs.dtu.dk/services/data.php) datasets.

WGS based detection of AMR genes in A. baumannii genomes

In parallel, 104 out of 9.579 available genomes of A. baumannii were downloaded from the NCBI database https://www.ncbi.nlm.nih.gov/genome/browse/#!/ prokaryotes/403/ (access date 10.09.2020). Acinetobacter baumannii genomes with the Genbank tag (/country=), which contained “Germany” were eligible for inclusion. In this way, we extracted 104 out of 195 German A. baumannii. The extracted isolates were mostly clinical isolates from 2012 to 2019, and in 88 out of 104 isolates, an isolation source was specified as the following: 19 groins, 12 wounds, 10 wound swab, 9 rectal swabs, 7 tracheal secretions, 4 respiratory, 3 blood, 3 clinical material, 2 bronchial secretions, 2 screening swab, 1 catheter swab, 1 catheter urine, 1 cerebrospinal fluid, 1 conjunctivitis, 1 drainage liquid, 1 groin swab, 1 perianal swab, 1 pleural drainage, 1 respiratory tract, 1 sterile tissue, 1 stoma swab, 1 throat, 1 tracheal secretion, 1 urine, 2 water and 1 eggshell. These sequences were annotated with ABRicate v.1.0.1 (https://github.com/tseemann/abricate). The NCBI AMR Finder Plus [53], the ResFinder database [52], the CARD database [54] and the ARG-ANNOT [55] were used for the identification of resistance genes. Only resistance genes with a coverage of > 80 and > 75% identity (proportion of exact nucleotide matches) were accepted. The following information was extracted from the data: the gene’s names, frequency within 104 genomes, percentage, predicted phenotype and accession number for each gene. DNA contigs were separated via plasflow (v1.1.0) into chromosomal and plasmid contigs. Gene detection was performed via abricate and fargene (https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0670-1), and plotted via ggplot2.

Availability of data and materials

All data generated or analyzed during this study are included in this published article and its supplementary information files.

Abbreviations

AMR:

Antimicrobial resistance

MDR:

Multidrug-resistant

XDR:

Extensively drug-resistant

PDR:

Pan-drug resistant

AST:

Antimicrobial susceptibility testing

MGEs:

Mobile genetic elements

NGS:

Next-generation sequencing

WGS:

Whole-genome sequencing

MIC:

Minimal inhibitory concentration

A. baumannii :

Acinetobacter baumannii

CRAB:

Carbapenem-resistant Acinetobacter baumannii

TEM:

Temoneira

SHV:

Sulfhydryl variable

CTX-M:

Cefotaxime hydrolyzing capabilities

OXA:

Oxacillinase

References

  1. 1.

    Santajit S, Indrawattana N. Mechanisms of antimicrobial resistance in ESKAPE pathogens. Biomed Res Int. 2016;2016:2475067.

    Article  Google Scholar 

  2. 2.

    Ayobami O, Willrich N, Harder T, Okeke IN, Eckmanns T, Markwart R. The incidence and prevalence of hospital-acquired (carbapenem-resistant) Acinetobacter baumannii in Europe, eastern Mediterranean and Africa: a systematic review and meta-analysis. Emerg Microbes Infect. 2019;8(1):1747–59. https://doi.org/10.1080/22221751.2019.1698273.

    Article  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Sleiman A, Fayad AGA, Banna H, Matar GM. Prevalence and molecular epidemiology of carbapenem-resistant Gram-negative Bacilli and their resistance determinants in the Eastern Mediterranean region over the last decade. J Glob Antimicrob Resist. 2021;25:209–21. https://doi.org/10.1016/j.jgar.2021.02.033.

  4. 4.

    Babu Rajendran N, Mutters NT, Marasca G, Conti M, Sifakis F, Vuong C, et al. Mandatory surveillance and outbreaks reporting of the WHO priority pathogens for research & discovery of new antibiotics in European countries. Clin Microbiol Infect. 2020;26(7):943.e1-.e6.

    Article  Google Scholar 

  5. 5.

    Wareth G, Brandt C, Sprague LD, Neubauer H, Pletz MW. Spatio-temporal distribution of Acinetobacter baumannii in Germany-a comprehensive systematic review of studies on resistance development in humans (2000–2018). Microorganisms. 2020;8(3):375. https://doi.org/10.3390/microorganisms8030375.

  6. 6.

    Ewers C, Klotz P, Leidner U, Stamm I, Prenger-Berninghoff E, Göttig S, et al. OXA-23 and ISAba1-OXA-66 class D β-lactamases in Acinetobacter baumannii isolates from companion animals. Int J Antimicrob Agents. 2017;49(1):37–44. https://doi.org/10.1016/j.ijantimicag.2016.09.033.

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Cho GS, Li B, Rostalsky A, Fiedler G, Rösch N, Igbinosa E, et al. Diversity and antibiotic susceptibility of Acinetobacter strains from milk powder produced in Germany. Front Microbiol. 2018;9:536. https://doi.org/10.3389/fmicb.2018.00536.

    Article  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Pulami D, Schauss T, Eisenberg T, Wilharm G, Blom J, Goesmann A, et al. Acinetobacter baumannii in manure and anaerobic digestates of German biogas plants. FEMS Microbiol Ecol. 2020;96(10):fiaa176. https://doi.org/10.1093/femsec/fiaa176.

  9. 9.

    Alexander J, Hembach N, Schwartz T. Evaluation of antibiotic resistance dissemination by wastewater treatment plant effluents with different catchment areas in Germany. Sci Rep. 2020;10(1):8952. https://doi.org/10.1038/s41598-020-65635-4.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Wareth G, Neubauer H, Sprague LD. Acinetobacter baumannii - a neglected pathogen in veterinary and environmental health in Germany. Vet Res Commun. 2019;43(1):1–6. https://doi.org/10.1007/s11259-018-9742-0.

    Article  PubMed  Google Scholar 

  11. 11.

    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. https://doi.org/10.1016/j.ijantimicag.2020.106127.

  12. 12.

    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. https://doi.org/10.1007/s11274-020-02890-7.

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    Pagano M, Martins AF, Barth AL. Mobile genetic elements related to carbapenem resistance in Acinetobacter baumannii. Brazilian J Microbiol. 2016;47(4):785–92. https://doi.org/10.1016/j.bjm.2016.06.005.

    CAS  Article  Google Scholar 

  14. 14.

    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. https://doi.org/10.1038/srep43232.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. 15.

    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. https://doi.org/10.1007/s11033-020-05389-4.

    CAS  Article  PubMed  Google Scholar 

  16. 16.

    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. https://doi.org/10.1128/mSphere.00117-16.

  17. 17.

    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. https://doi.org/10.1128/CMR.00058-16.

    CAS  Article  PubMed  Google Scholar 

  18. 18.

    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. https://doi.org/10.3389/fmicb.2020.01283.

    Article  PubMed  PubMed Central  Google Scholar 

  19. 19.

    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. https://doi.org/10.1128/AAC.00221-11.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. 20.

    Lin MF, Lan CY. Antimicrobial resistance in Acinetobacter baumannii: from bench to bedside. World J Clin Cases. 2014;2(12):787–814. https://doi.org/10.12998/wjcc.v2.i12.787.

    Article  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Nowak P, Paluchowska P. Acinetobacter baumannii: biology and drug resistance - role of carbapenemases. Folia Histochem Cytobiol. 2016;54(2):61–74. https://doi.org/10.5603/FHC.a2016.0009.

    CAS  Article  PubMed  Google Scholar 

  22. 22.

    Lin MF, Chang KC, Yang CY, Yang CM, Xiao CC, Kuo HY, et al. Role of integrons in antimicrobial susceptibility patterns of Acinetobacter baumannii. Jpn J Infect Dis. 2010;63(6):440–3.

    CAS  PubMed  Google Scholar 

  23. 23.

    Huang LY, Chen TL, Lu PL, Tsai CA, Cho WL, Chang FY, et al. Dissemination of multidrug-resistant, class 1 integron-carrying Acinetobacter baumannii isolates in Taiwan. Clin Microbiol Infect. 2008;14(11):1010–9. https://doi.org/10.1111/j.1469-0691.2008.02077.x.

    CAS  Article  PubMed  Google Scholar 

  24. 24.

    Rabea RA, Zaki MES, Fahmy EM, Fathelbab A. Molecular study of nodulation division genes and integron genes in Acinetobacter baumannii. Clin Lab. 2020;66(9). https://doi.org/10.7754/Clin.Lab.2020.200124.

  25. 25.

    Araújo BC, Moraes MS, Costa LE, Nascimento JS. Short communication: multidrug-resistant Acinetobacter baumannii-calcoaceticus complex isolated from infant milk formula and utensils in a nursery in Rio de Janeiro, Brazil. J Dairy Sci. 2015;98(4):2303–6. https://doi.org/10.3168/jds.2014-8825.

    CAS  Article  PubMed  Google Scholar 

  26. 26.

    Wu S, Jiang Y, Lou B, Feng J, Zhou Y, Guo L, et al. Microbial community structure and distribution in the air of a powdered infant formula factory based on cultivation and high-throughput sequence methods. J Dairy Sci. 2018;101(8):6915–26. https://doi.org/10.3168/jds.2017-13968.

    CAS  Article  PubMed  Google Scholar 

  27. 27.

    Gurung M, Nam HM, Tamang MD, Chae MH, Jang GC, Jung SC, et al. Prevalence and antimicrobial susceptibility of Acinetobacter from raw bulk tank milk in Korea. J Dairy Sci. 2013;96(4):1997–2002. https://doi.org/10.3168/jds.2012-5965.

    CAS  Article  PubMed  Google Scholar 

  28. 28.

    Nam HM, Lim SK, Kim JM, Joo YS, Jang KC, Jung SC. In vitro activities of antimicrobials against six important species of gram-negative bacteria isolated from raw milk samples in Korea. Foodborne Pathog Dis. 2010;7(2):221–4. https://doi.org/10.1089/fpd.2009.0406.

    CAS  Article  PubMed  Google Scholar 

  29. 29.

    McHugh AJ, Feehily C, Fenelon MA, Gleeson D, Hill C, Cotter PD. Tracking the dairy microbiota from farm bulk tank to skimmed milk powder. mSystems. 2020;5(2):e00226–20. https://doi.org/10.1128/mSystems.00226-20.

  30. 30.

    Katchanov J, Asar L, Klupp EM, Both A, Rothe C, König C, Rohde H, Kluge S, Maurer FP. Carbapenem-resistant gram-negative pathogens in a German university medical center: prevalence, clinical implications and the role of novel β-lactam/β-lactamase inhibitor combinations. Plos One. 2018;13(4):e0195757. https://doi.org/10.1371/journal.pone.0195757.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Wendel AF, Malecki M, Otchwemah R, Tellez-Castillo CJ, Sakka SG, Mattner F. One-year molecular surveillance of carbapenem-susceptible A. baumannii on a German intensive care unit: diversity or clonality. Antimicrob Resist Infect Control. 2018;7(1):145.

    Article  Google Scholar 

  32. 32.

    Rieber H, Frontzek A, Pfeifer Y. Molecular Investigation of carbapenem-resistant Acinetobacter spp. from hospitals in North Rhine-Westphalia, Germany. Microbial Drug Resist (Larchmont). 2017;23(1):25–31.

    CAS  Article  Google Scholar 

  33. 33.

    Evans BA, Amyes SG. OXA β-lactamases. Clin Microbiol Rev. 2014;27(2):241–63. https://doi.org/10.1128/CMR.00117-13.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Khurshid M, Rasool MH, Ashfaq UA, Aslam B, Waseem M, Xu Q, et al. Dissemination of Bla (OXA-23)-harbouring carbapenem-resistant Acinetobacter baumannii clones in Pakistan. J Glob Antimicrob Resist. 2020;21:357–62. https://doi.org/10.1016/j.jgar.2020.01.001.

    Article  PubMed  Google Scholar 

  35. 35.

    Hu S, Niu L, Zhao F, Yan L, Nong J, Wang C, et al. Identification of Acinetobacter baumannii and its carbapenem-resistant gene Bla (OXA-23-like) by multiple cross displacement amplification combined with lateral flow biosensor. Sci Rep. 2019;9(1):17888. https://doi.org/10.1038/s41598-019-54465-8.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Rao M, Rashid FA, Shukor S, Hashim R, Ahmad N. Detection of antimicrobial resistance genes associated with carbapenem resistance from the whole-genome sequence of Acinetobacter baumannii isolates from Malaysia. Can J Infect Dis Med Microbiol. 2020;2020:5021064. https://doi.org/10.1155/2020/5021064.

  37. 37.

    Chen CM, Liu PY, Ke SC, Wu HJ, Wu LT. Investigation of carbapenem-resistant Acinetobacter baumannii isolates in a district hospital in Taiwan. Diagn Microbiol Infect Dis. 2009;63(4):394–7. https://doi.org/10.1016/j.diagmicrobio.2008.12.011.

    CAS  Article  PubMed  Google Scholar 

  38. 38.

    Hu WS, Yao S-M, Fung C-P, Hsieh Y-P, Liu C-P, Lin J-F. An OXA-66/OXA-51-like carbapenemase and possibly an efflux pump are associated with resistance to imipenem in Acinetobacter baumannii. Antimicrob Agents Chemother. 2007;51(11):3844–52. https://doi.org/10.1128/AAC.01512-06.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Brown S, Young HK, Amyes SG. Characterisation of OXA-51, a novel class D carbapenemase found in genetically unrelated clinical strains of Acinetobacter baumannii from Argentina. Clin Microbiol Infect. 2005;11(1):15–23. https://doi.org/10.1111/j.1469-0691.2004.01016.x.

    CAS  Article  PubMed  Google Scholar 

  40. 40.

    Mugnier PD, Poirel L, Naas T, Nordmann P. Worldwide dissemination of the blaOXA-23 carbapenemase gene of Acinetobacter baumannii. Emerg Infect Dis. 2010;16(1):35–40. https://doi.org/10.3201/eid1601.090852.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Karah N, Dwibedi CK, Sjöström K, Edquist P, Johansson A, Wai SN, et al. Novel aminoglycoside resistance transposons and transposon-derived circular forms detected in carbapenem-resistant Acinetobacter baumannii clinical isolates. Antimicrob Agents Chemother. 2016;60(3):1801–18. https://doi.org/10.1128/AAC.02143-15.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. 42.

    Hadjadj L, Shoja S, Diene SM, Rolain JM. Dual infections of two carbapenemase-producing Acinetobacter baumannii clinical strains isolated from the same blood culture sample of a patient in Iran. Antimicrob Resist Infect Control. 2018;7(1):39. https://doi.org/10.1186/s13756-018-0329-x.

    Article  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Lee SY, Oh MH, Yun SH, Choi CW, Park EC, Song HS, et al. Genomic characterization of extensively drug-resistant Acinetobacter baumannii strain, KAB03 belonging to ST451 from Korea. Infect Genet Evol. 2018;65:150–8. https://doi.org/10.1016/j.meegid.2018.07.030.

    CAS  Article  PubMed  Google Scholar 

  44. 44.

    Héritier C, Poirel L, Nordmann P. Cephalosporinase over-expression resulting from insertion of ISAba1 in Acinetobacter baumannii. Clin Microbiol Infect. 2006;12(2):123–30. https://doi.org/10.1111/j.1469-0691.2005.01320.x.

    Article  PubMed  Google Scholar 

  45. 45.

    Roberts MC. Update on acquired tetracycline resistance genes. FEMS Microbiol Lett. 2005;245(2):195–203. https://doi.org/10.1016/j.femsle.2005.02.034.

    CAS  Article  PubMed  Google Scholar 

  46. 46.

    Greer ND. Tigecycline (Tygacil): The first in the glycylcycline class of antibiotics. Proc (Baylor Univ Med Cent). 2006;19(2):155–61. https://doi.org/10.1080/08998280.2006.11928154.

  47. 47.

    Foong WE, Wilhelm J, Tam HK, Pos KM. Tigecycline efflux in Acinetobacter baumannii is mediated by TetA in synergy with RND-type efflux transporters. J Antimicrob Chemother. 2020;75(5):1135–9. https://doi.org/10.1093/jac/dkaa015.

    CAS  Article  PubMed  Google Scholar 

  48. 48.

    Sköld O. Resistance to trimethoprim and sulfonamides. Vet Res. 2001;32(3–4):261–73. https://doi.org/10.1051/vetres:2001123.

    Article  PubMed  Google Scholar 

  49. 49.

    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. https://doi.org/10.1128/AAC.00584-09.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  50. 50.

    Adams MD, Nickel GC, Bajaksouzian S, Lavender H, Murthy AR, Jacobs MR, et al. Resistance to colistin in Acinetobacter baumannii associated with mutations in the PmrAB two-component system. Antimicrob Agents Chemother. 2009;53(9):3628–34. https://doi.org/10.1128/AAC.00284-09.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Turton JF, Woodford N, Glover J, Yarde S, Kaufmann ME, Pitt TL. Identification of Acinetobacter baumannii by detection of the blaOXA-51-like carbapenemase gene intrinsic to this species. J Clin Microbiol. 2006;44(8):2974–6. https://doi.org/10.1128/JCM.01021-06.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  52. 52.

    Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–4. https://doi.org/10.1093/jac/dks261.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, et al. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother. 2019;63(11):e00483-19. https://doi.org/10.1128/AAC.00483-19.

  54. 54.

    Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2017;45(D1):D566–d73. https://doi.org/10.1093/nar/gkw1004.

    CAS  Article  PubMed  Google Scholar 

  55. 55.

    Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M, Landraud L, et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother. 2014;58(1):212–20. https://doi.org/10.1128/AAC.01310-13.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

We thank Dr. Philipp Hammer and Dr. Wolf D. Splettstoesser for providing the samples, Dr. Jörg Linde for bioinformatics analysis, Dr. Gernot Schmoock, Johannes Solle and Claudia Grosser for excellent technical assistance in susceptibility testing and WGS.

Funding

This work received no external fund. Open Access funding enabled and organized by Projekt DEAL.

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GW created the idea, identified and analyzed the AMR in the sequenced isolates, and wrote the manuscript. CB downloaded the sequences from NCBI and performed bioinformatics analysis. LDS, HN and MWP supervised the work and validated the data. All authors read and approved the final manuscript.

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Correspondence to Gamal Wareth.

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Supplementary Information

Additional file 1: Figure S1

. A. baumannii genomes are listed at the x-axis. Resistance against antibiotics is indicated on the y-axis. The circle sizes and colours represent the number of resistance genes identified, conferring a specific antibiotic resistance. Additionally, beta-lactamase genes are also indicated and are divided into their molecular group (class A, B, C, D; based on Ambler) due to their importance. The plot is separated into chromosomal and plasmid DNA contigs.

Additional file 2: Supplementary Table 1.

List of sequenced 85 A. baumannii strains showing ID, year of isolation and source of each strain, and the full details of acquired resistance genes that have been identified by ResFinder server.

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Wareth, G., Brandt, C., Sprague, L.D. et al. WGS based analysis of acquired antimicrobial resistance in human and non-human Acinetobacter baumannii isolates from a German perspective. BMC Microbiol 21, 210 (2021). https://doi.org/10.1186/s12866-021-02270-7

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Keywords

  • A. baumannii
  • Acquired resistance
  • WGS
  • NCBI
  • Germany