AbaR-type genomic islands in non-baumannii Acinetobacter species isolates from South Korea

Interbacterial Transfer of Carbapenem Resistance and Large Antibiotic Resistance Islands by Natural Transformation in Pathogenic Acinetobacter

Acinetobacter baumannii infection poses a major health threat, with recurrent treatment failure due to antibiotic resistance, notably to carbapenems. While genomic analyses of clinical strains indicate that homologous recombination plays a major role in the acquisition of antibiotic resistance genes, the underlying mechanisms of horizontal gene transfer often remain speculative. Our understanding of the acquisition of antibiotic resistance is hampered by the lack of experimental systems able to reproduce genomic observations. We here report the detection of recombination events occurring spontaneously in mixed bacterial populations and which can result in the acquisition of resistance to carbapenems. We show that natural transformation is the main driver of intrastrain but also interstrain recombination events between A. baumannii clinical isolates and pathogenic species of Acinetobacter. We observed that interbacterial natural transformation in mixed populations is more efficient at promoting the acquisition of large resistance islands (AbaR4 and AbaR1) than when the same bacteria are supplied with large amounts of purified genomic DNA. Importantly, analysis of the genomes of the recombinant progeny revealed large recombination tracts (from 13 to 123 kb) similar to those observed in the genomes of clinical isolates. Moreover, we highlight that transforming DNA availability is a key determinant of the rate of recombinants and results from both spontaneous release and interbacterial predatory behavior. In the light of our results, natural transformation should be considered a leading mechanism of genome recombination and horizontal gene transfer of antibiotic resistance genes in Acinetobacter baumannii.

Clinical and molecular characterization of Acinetobacter seifertii in Taiwan

OBJECTIVES

Acinetobacter seifertii, a new member of the Acinetobacter baumannii group, has emerged as a cause of severe infections in humans. We investigated the clinical and molecular characteristics of A. seifertii.

PATIENTS AND METHODS

This retrospective study enrolled 80 adults with A. seifertii bloodstream infection (BSI) at four medical centres over an 8 year period. Species identification was confirmed by MALDI-TOF MS, rpoB sequencing and WGS. Molecular typing was performed by MLST. Clinical information, antimicrobial susceptibility and the mechanisms of carbapenem and colistin resistance were analysed. Transmissibility of the carbapenem-resistance determinants was examined by conjugation experiments.

RESULTS

The main source of A. seifertii BSI was the respiratory tract (46.3%). The 28 day and in-hospital mortality rates of A. seifertii BSI were 18.8% and 30.0%, respectively. High APACHE II scores and immunosuppressant therapy were independent risk factors for 28 day mortality. The most common MLST type was ST553 (58.8%). Most A. seifertii isolates were susceptible to levofloxacin (86.2%), and only 37.5% were susceptible to colistin. Carbapenem resistance was observed in 16.3% of isolates, mostly caused by the plasmid-borne ISAba1-blaOXA-51-like genetic structure. A. seifertii could transfer various carbapenem-resistance determinants to A. baumannii, Acinetobacter nosocomialis and other A. seifertii isolates. Variations of pmrCAB and lpxCAD genes were not associated with colistin resistance of A. seifertii.

CONCLUSIONS

Levofloxacin and carbapenems, but not colistin, have the potential to be the drug of choice for A. seifertii infections. A. seifertii can transfer carbapenem-resistance determinants to other species of the A. baumannii group and warrants close monitoring.

Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications

Acinetobacter baumannii is a highly potent nosocomial pathogen that is associated with increased in-hospital mortality. Here, we investigated the changes in molecular characteristics of carbapenem-resistant A. baumannii (CRAB) isolated from the blood samples of patients admitted to a tertiary hospital in South Korea from January 2009 to July 2015. Whole genome sequencing using the Illumina MiSeq platform and multi-locus sequence typing (MLST) were performed for 98 CRAB clinical isolates. In silico analyses for the prediction of antimicrobial resistance and virulence factor genes were performed. Plasmid sequences, including complete forms, were reconstructed from the sequence reads. Epidemiologic data were collected from the hospital database. MLST using the Oxford scheme revealed 10 sequence types of CRAB, of which ST191 was the dominant type (n = 59). Although bla_OXA-23 was shared by most analysed strains, the compositions of antimicrobial resistance determinants differed among sequence types. ST447 and ST451/ST1809 with a few resistance genes were isolated during the later years of the study period. The number of virulence genes increased, while that of ST191 did not change significantly over the investigation period. Intriguingly MLST types, compositions of antimicrobial resistance genes, and virulence genes had no association with clinical outcomes of CRAB bacteraemia. In conclusion, active changes in or accumulations of antimicrobial resistance determinants and virulence genes in CRAB were not observed during the research period. Molecular characteristics of CRAB had no association with clinical outcomes of CRAB bacteraemia.

Whole-genome analysis of New Delhi Metallo-Beta-Lactamase-1-producing Acinetobacter haemolyticus from China

OBJECTIVE

Infections caused by multidrug-resistant Acinetobacter spp. have generated worldwide attention. With the increasing isolation of non-baumannii Acinetobacter, the nature of associated infection and resistance needs to be explored. This study aimed to analyse the characteristics of New Delhi Metallo-Beta-Lactamase-1 (NDM-1)-producing Acinetobacter haemolyticus (named sz1652) isolated from Shenzhen city, China.

METHODS

The antibiotic spectrum was analysed after antimicrobial susceptibility testing. Combined disk test (CDT) was used to detect the metallo-beta-lactamases (MBLs). Transferability of carbapenem resistance was tested by filter mating experiments and plasmid transformation assays. Whole-genome sequencing (WGS) was performed using HiSeq 2000 and PacBio RS system.

RESULTS

The Acinetobacter haemolyticus strain sz1652 was resistant to carbapenems and other tested agents except for amikacin, tigecycline and colistin. Production of MBLs was confirmed by CDT. Transfer of carbapenem resistance was unsuccessful. WGS analysis showed that the genome of sz1652 comprised a chromosome and two plasmids; 16 genomic islands (GIs) were predicted. Genes associated with resistance were found in this strain, including the beta-lactamase genes bla_NDM-1, bla_OXA-214 and bla_LRA-18, the fluoroquinolone resistant-related mutations [GyrA subunits (Ser81Ile) and ParC subunits (Ser84Tyr)], and efflux pump genes related to tetracycline and macrolide resistance. Analysis of the genetic environment showed that bla_NDM-1 was embedded in Tn125 transposon. The Tn125 structure was chromosomally located and shared > 99% sequence identity with the previously reported bla_NDM-1 carrying region.

CONCLUSION

The NDM-1-producing Acinetobacter haemolyticus coexisted with multiple drug-resistant determinants. The acquisition of the bla_NDM-1 gene was probably facilitated by Tn125 in this strain. Non-Acinetobacter baumannii species also contained GIs.

Large-Scale Identification of AbaR-Type Genomic Islands in Acinetobacter baumannii Reveals Diverse Insertion Sites and Clonal Lineage-Specific Antimicrobial Resistance Gene Profiles

AbaR-type genomic islands (AbaRs) are important elements responsible for antimicrobial resistance in Acinetobacter baumannii This study performed a large-scale identification of AbaRs to understand their distribution and compositions of antimicrobial resistance genes. We identified 2.89-kb left-end and 1.87-kb right-end conserved sequences (CSs) and developed a bioinformatics approach to identify AbaRs, using the CSs as signatures, in 3,148 publicly available genomes. AbaRs were prevalent in A. baumannii, being found in 2,091 genomes. They were sparse in other Acinetobacter species and confined only to this genus. Results from 111 complete genomes showed that over 85% of AbaRs resided on chromosomes. The external flanks adjacent to the inverted repeats available in all identified CSs were mapped to an AbaR-free chromosome or searched in the NCBI database for empty loci to define insertion sites. Surprisingly, 84 insertion sites with diverse origins were revealed, including 51 scattered on the chromosome, 20 plasmid borne, 12 located on prophages, transposons, ISAba1, complex AbaRs, and genomic islands of other types, and one uncharacterized, and some were strongly associated with clonal lineages. Finally, we found 994 antimicrobial resistance genes covering 28 unique genes from 70.9% (299/422) of intact AbaRs currently available. The resistance gene profiles displayed an apparent clonal lineage-specific pattern, highlighting the distinct features of AbaRs in global clone 1 (GC1) and GC2. The tet(B) gene was highly specific to the AbaRs in GC2. In conclusion, AbaRs have diverse insertion sites on the chromosome and mobile genetic elements (MGEs) and display distinct antimicrobial resistance gene profiles in different clonal lineages.

Molecular Epidemiology of Emerging Carbapenem Resistance in Acinetobacter nosocomialis and Acinetobacter pittii in Taiwan, 2010 to 2014

This study investigated the molecular epidemiology of carbapenem-resistant Acinetobacter nosocomialis and Acinetobacter pittii (ANAP). Clinical isolates of Acinetobacter spp.

This study investigated the molecular epidemiology of carbapenem-resistant Acinetobacter nosocomialis and Acinetobacter pittii (ANAP). Clinical isolates of Acinetobacter spp. collected by the biennial nationwide Taiwan Surveillance of Antimicrobial Resistance program from 2010 to 2014 were subjected to species identification, antimicrobial susceptibility testing, and PCR for detection of carbapenemase genes. Whole-genome sequencing or PCR mapping was performed to study the genetic surroundings of the carbapenemase genes. Among 1,041 Acinetobacter isolates, the proportion of ANAP increased from 11% in 2010 to 22% in 2014. The rate of carbapenem resistance in these isolates increased from 7.5% (3/40) to 22% (14/64), with a concomitant increase in their resistance to other antibiotics. The bla_OXA-72 and bla_OXA-58 genes were highly prevalent in carbapenem-resistant ANAP. Various genetic structures were found upstream of bla_OXA-58 in different plasmids. Among the plasmids found to contain bla_OXA-72 flanked by XerC/XerD, pAB-NCGM253-like was identified in 8 of 10 isolates. Conjugations of plasmids carrying bla_OXA-72 or bla_OXA-58 to A. baumannii were successful. In addition, three isolates with chromosome-located bla_OXA-23 embedded in AbGRI1-type structure with disruption of genes other than comM were detected. Two highly similar plasmids carrying class I integron containing bla_IMP-1 and aminoglycoside resistance genes were also found. The universal presence of bla_{OXA-272/213-like} on A. pittii chromosomes and their lack of contribution to carbapenem resistance indicate its potential to be a marker for species identification. The increase of ANAP, along with their diverse mechanisms of carbapenem resistance, may herald their further spread and warrants close monitoring.

Fluorescence-Based Detection of Natural Transformation in Drug-Resistant Acinetobacter baumannii

Acinetobacter baumannii is a nosocomial agent with a high propensity for developing resistance to antibiotics. This ability relies on horizontal gene transfer mechanisms occurring in the Acinetobacter genus, including natural transformation. To study natural transformation in bacteria, the most prevalent method uses selection for the acquisition of an antibiotic resistance marker in a target chromosomal locus by the recipient cell. Most clinical isolates of A. baumannii are resistant to multiple antibiotics, limiting the use of such selection-based methods. Here, we report the development of a phenotypic and selection-free method based on flow cytometry to detect transformation events in multidrug-resistant (MDR) clinical A. baumannii isolates. To this end, we engineered a translational fusion between the abundant and conserved A. baumannii nucleoprotein (HU) and the superfolder green fluorescent protein (sfGFP). The new method was benchmarked against the conventional antibiotic selection-based method. Using this new method, we investigated several parameters affecting transformation efficiencies and identified conditions of transformability one hundred times higher than those previously reported. Using optimized transformation conditions, we probed natural transformation in a set of MDR clinical and nonclinical animal A. baumannii isolates. Regardless of their origin, the majority of the isolates displayed natural transformability, indicative of a conserved trait in the species. Overall, this new method and optimized protocol will greatly facilitate the study of natural transformation in the opportunistic pathogen A. baumannii IMPORTANCE Antibiotic resistance is a pressing global health concern with the rise of multiple and panresistant pathogens. The rapid and unfailing resistance to multiple antibiotics of the nosocomial agent Acinetobacter baumannii, notably to carbapenems, prompt to understand the mechanisms behind acquisition of new antibiotic resistance genes. Natural transformation, one of the horizontal gene transfer mechanisms in bacteria, was only recently described in A. baumannii and could explain its ability to acquire resistance genes. We developed a reliable method to probe and study natural transformation mechanism in A. baumannii More broadly, this new method based on flow cytometry will allow experimental detection and quantification of horizontal gene transfer events in multidrug-resistant A. baumannii.

Structure and context of Acinetobacter transposons carrying the oxa23 carbapenemase gene

Theoxa23gene encoding the OXA-23 carbapenemase (and several minor variants of it) is widespread inAcinetobacter baumanniiclinical isolates and compromises treatment with carbapenem antibiotics. The gene is derived from the chromosome ofAcinetobacter radioresistenswhere it is an intrinsic gene, here designatedoxaAr InA. baumanniiand otherAcinetobacterspecies,oxa23is usually preceded by an IS, ISAba1, which supplies the strong promoter required for the gene to confer clinically relevant levels of resistance. TheoxaArgene appears to have been mobilized twice creating Tn2008and Tn2008B, both of which consist of a single ISAba1 and anA. radioresistens-derived fragment. Tn2006and Tn2009are clearly derived from Tn2008Band are each made up of Tn2008Bwith an additional segment of unknown origin and an additional ISAba1, creating a compound transposon. Tn2006, Tn2008and possibly Tn2008Bare globally disseminated, while Tn2009has as yet only been found in China. Of the four ISAba1-associated transposons, Tn2006has been most frequently observed worldwide and Tn2006in Tn6022, known as AbaR4, appears to contribute significantly to the dissemination ofoxa23 Moreover, AbaR4, Tn2006, Tn2008and Tn2009have each been found in conjugative plasmids, further facilitating their spread.