Deciphering Multidrug-Resistant Acinetobacter baumannii from a Pediatric Cancer Hospital in Egypt

Jalal, Deena; Elzayat, Mariam G; Diab, Aya A.; El-Shqanqery, Hend E; Samir, Omar; Bakry, Usama; Hassan, Reem; Elanany, Mervat; Shalaby, Lobna; Sayed, Ahmed

doi:10.1128/msphere.00725-21

Cited by 16 publications

(27 citation statements)

References 105 publications

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“…In agreement with other studies (Al- Hassan et al, 2019;Fam et al, 2020;Wasfi et al, 2021), MLST analysis revealed the predominance of GC2 isolates in our collection (38.8%). Nevertheless, GC1 strains outweighed those that belonged to GC2 studied by others in our region (Ghaith et al, 2017;Jalal et al, 2021). Less representation (16.6%) was noted for the recently described GC9 (Müller et al, 2019) known to be endemic in Middle East countries (Al-Hassan et al, 2013, 2021Bonnin et al, 2013;Ghaith et al, 2017;Jaidane et al, 2018;Salloum et al, 2018).…”

Section: Discussioncontrasting

confidence: 60%

“…These included the novel clonal complex CC2329 Oxf (CC113 Pas ) represented by M03 (ST113 Pas / 2246 Oxf ) and M14 (ST113 Pas / ST2329 Oxf ). Isolates that belong to this CC were reported from Egypt (Jalal et al, 2021), Saudi Arabia (Lopes et al, 2015), and Brazil (Leal et al, 2020). Another ST identified here, ST164 Pas /1418 Oxf , was reported in the isolates from Myanmar (Tada et al, 2020), Vietnam (Wareth et al, 2021), Brazil (Coelho-Souza et al, 2013, Kenya (Musila et al, 2021), and as a major clone in Thailand (Khuntayaporn et al, 2021).…”

Section: Discussionsupporting

confidence: 54%

“…Updates on the genetic background of MDR and XDR A. baumannii are continuously being published from different parts of the world (Hamidian and Nigro, 2019;Gheorghe et al, 2021;Wareth et al, 2021) and from Egypt as well (Hassan et al, 2021;Jalal et al, 2021;Wasfi et al, 2021). However, reports about the association of resistance genes with RIs are relatively scarce.…”

Section: Discussionmentioning

confidence: 99%

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Genetic Configuration of Genomic Resistance Islands in Acinetobacter baumannii Clinical Isolates From Egypt

et al. 2022

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In Acinetobacter baumannii (A. baumannii), a wide repertoire of resistance genes is often carried within genomic resistance islands (RIs), particularly in high-risk global clones (GCs). As the first in Egypt, the current study aimed at exploring the diversity and genetic configuration of RIs in the clinical isolates of A. baumannii. For this purpose, draft genomes of 18 isolates were generated by Illumina sequencing. Disk diffusion susceptibility profiling revealed multidrug resistance (MDR) and extensive drug resistance (XDR) phenotypes in 27.7 and 72.2%, respectively. The highest susceptibility was noted for tigecycline (100.0%) followed by colistin (94.4%), for which an MIC50 of 0.25 μg/ml was recorded by the broth microdilution assay. Sequence typing (ST) showed that the majority of the isolates belonged to high-risk global clones (GC1, GC2, and GC9). A novel Oxford sequence type (ST2329) that also formed a novel clonal complex was submitted to the PubMLST database. A novel blaADC variant (blaADC−258) was also identified in strain M18 (ST85Pas/1089Oxf). In addition to a wide array of resistance determinants, whole-genome sequencing (WGS) disclosed at least nine configurations of genomic RIs distributed over 16/18 isolates. GC2 isolates accumulated the largest number of RIs (three RIs/isolate) followed by those that belong to GC1 (two RIs/isolate). In addition to Tn6022 (44.4%), the comM gene was interrupted by AbaR4 (5.5%) and three variants of A. baumanniigenomic resistance island 1(AbGRI)-type RIs (44.4%), including AbaR4b (16.6%) and two novel configurations of AbGRI1-like RIs (22.2%). Three of which (AbaR4, AbaR4b, and AbGRI1-like-2) carried blaOXA−23 within Tn2006. With less abundance (38.8%), IS26-bound RIs were detected exclusively in GC2 isolates. These included a short version of AbGRI2 (AbGRI2-15) carrying the genes blaTEM−1 and aphA1 and two variants of AbGRI3 RIs carrying up to seven resistance genes [mphE-msrE-armA-sul1-aadA1-catB8-aacA4]. Confined to GC1 (22.2%), sulfonamide resistance was acquired by an ISAba1 bracketed GIsul2 RI. An additional RI (RI-PER-7) was also identified on a plasmid carried by strain M03. Among others, RI-PER-7 carried the resistance genes armA and blaPER−7. Here, we provided a closer view of the diversity and genetic organization of RIs carried by a previously unexplored population of A. baumannii.

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Section: Discussioncontrasting

confidence: 60%

Section: Discussionsupporting

confidence: 54%

Section: Discussionmentioning

confidence: 99%

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Genetic Configuration of Genomic Resistance Islands in Acinetobacter baumannii Clinical Isolates From Egypt

et al. 2022

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“…Accordingly, the higher biofilm-forming ability of strain #36 in comparison with strain #150 could be explained by the absence of a conserved Bap protein in this strain; vice versa, the presence of Omp33–36 could account for the enhanced adhesion to pulmonary cells of strain #150 with respect to strain #36 [ 13 ]. Accordingly, previous studies revealed the absence of the bap gene in a number of A. baumannii isolates that displayed a reduced biofilm-forming ability [ 80 , 81 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity of Antimicrobial Resistance and Key Virulence Features in Two Extensively Drug-Resistant Acinetobacter baumannii Isolates

Migliori

Scribano

Sarshar

et al. 2022

IJERPH

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In recent decades, Acinetobacter baumannii emerged as a major infective menace in healthcare settings due to scarce therapeutic options to treat infections. Therefore, undertaking genome comparison analyses of multi-resistant A. baumannii strains could aid the identification of key bacterial determinants to develop innovative anti-virulence approaches. Following genome sequencing, we performed a molecular characterization of key genes and genomic comparison of two A. baumannii strains, #36 and #150, with selected reference genomes. Despite a different antibiotic resistance gene content, the analyzed strains showed a very similar antibiogram profile. Interestingly, the lack of some important virulence determinants (i.e., bap, ata and omp33–36) did not abrogate their adhesive abilities to abiotic and biotic surfaces, as reported before; indeed, strains retained these capacities, although to a different extent, suggesting the presence of distinct vicarious genes. Conversely, secretion systems, lipopolysaccharide (LPS), capsule and iron acquisition systems were highly similar to A. baumannii reference strains. Overall, our analyses increased our knowledge on A. baumannii genomic content and organization as well as the genomic events occurring in nosocomial isolates to better fit into changing healthcare environments.

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“…Advances in whole-genome sequencing technology have facilitated bacterial whole-genome characterization, enhancing the ability to elucidate the antibiotic-resistant mechanism and pathogenesis in Acinetobacter baumannii [ 33 , 34 ]. However, data concerning genome analysis on colistin resistance of Acinetobacter baumannii isolated from Thailand is currently limited in the literature [ 35 ].…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequence of pan drug-resistant clinical isolate of Acinetobacter baumannii ST1890

et al. 2022

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Acinetobacter baumannii is an opportunistic gram-negative bacteria typically attributed to hospital-associated infection. It could also become multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan drug-resistant (PDR) during a short period. Although A. baumannii has been documented extensively, complete knowledge on the antibiotic-resistant mechanisms and virulence factors responsible for pathogenesis has not been entirely elucidated. This study investigated the drug resistance pattern and characterized the genomic sequence by de novo assembly of PDR A. baumannii strain VJR422, which was isolated from a catheter-sputum specimen. The results showed that the VJR422 strain was resistant to any existing antibiotics. Based on de novo assembly, whole-genome sequences showed a total genome size of 3,924,675-bp. In silico and conventional MLST analysis of sequence type (ST) of this strain was new ST by Oxford MLST scheme and designated as ST1890. Moreover, we found 10,915 genes that could be classified into 45 categories by Gene Ontology (GO) analysis. There were 1,687 genes mapped to 34 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The statistics from Clusters of Orthologous Genes (COG) annotation identified 3,189 genes of the VJR422 strain. Regarding the existence of virulence factors, a total of 59 virulence factors were identified in the genome of the VJR422 strain by virulence factors of pathogenic bacteria databases (VFDB). The drug-resistant genes were investigated by searching in the Comprehensive Antibiotic Resistance Database (CARD). The strain harbored antibiotic-resistant genes responsible for aminoglycoside, β-lactam-ring-containing drugs, erythromycin, and streptogramin resistance. We also identified resistance-nodulation-cell division (RND) and the major facilitator superfamily (MFS) associated with the antibiotic efflux pump. Overall, this study focused on A. baumannii strain VJR422 at the genomic level data, i.e., GO, COG, and KEGG. The antibiotic-resistant genotype and phenotype as well as the presence of potential virulence associated factors were investigated.

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Deciphering Multidrug-Resistant Acinetobacter baumannii from a Pediatric Cancer Hospital in Egypt

Cited by 16 publications

References 105 publications

Genetic Configuration of Genomic Resistance Islands in Acinetobacter baumannii Clinical Isolates From Egypt

Genetic Configuration of Genomic Resistance Islands in Acinetobacter baumannii Clinical Isolates From Egypt

Genetic Diversity of Antimicrobial Resistance and Key Virulence Features in Two Extensively Drug-Resistant Acinetobacter baumannii Isolates

Whole genome sequence of pan drug-resistant clinical isolate of Acinetobacter baumannii ST1890

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