<i>Letter to the Editor:</i> Prophages Encode Antibiotic Resistance Genes in <i>Acinetobacter baumannii</i>

López-Leal, Gamaliel; Santamaría, Rosa I.; Cevallos, Miguel A.; González, Víctor; Castillo-Ramírez, Santiago

doi:10.1089/mdr.2019.0362

Cited by 33 publications

(37 citation statements)

References 12 publications

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“…Several genomic data screening studies have been carried out to identify prophages that indeed turn out to be very abundant in A. baumannii genomes [33,61,79]. It is apparent that many of the identified prophages may also be involved in horizontal gene transfer and may carry genes encoding antibiotic resistance or virulence factors [79], however, this was not the case with the prophages identified in this work.…”

Section: Discussionmentioning

confidence: 73%

Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii

Badawy

Pajunen

Haiko

et al. 2020

Viruses

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Acinetobacter baumannii is an opportunistic pathogen that presents a serious clinical challenge due to its increasing resistance to all available antibiotics. Phage therapy has been introduced recently to treat antibiotic-incurable A. baumannii infections. In search for new A. baumannii specific bacteriophages, 20 clinical A. baumannii strains were used in two pools in an attempt to enrich phages from sewage. The enrichment resulted in induction of resident prophage(s) and three temperate bacteriophages, named vB_AbaS_fEg-Aba01, vB_AbaS_fLi-Aba02 and vB_AbaS_fLi-Aba03, all able to infect only one strain (#6597) of the 20 clinical strains, were isolated. Morphological characteristics obtained by transmission electron microscopy together with the genomic information revealed that the phages belong to the family Siphoviridae. The ca. 35 kb genomic sequences of the phages were >99% identical to each other. The linear ds DNA genomes of the phages contained 10 nt cohesive end termini, 52–54 predicted genes, an attP site and one tRNA gene each. A database search revealed an >99% identical prophage in the genome of A. baumannii strain AbPK1 (acc. no. CP024576.1). Over 99% identical prophages were also identified from two of the original 20 clinical strains (#5707 and #5920) and both were shown to be spontaneously inducible, thus very likely being the origins of the isolated phages. The phage vB_AbaS_fEg-Aba01 was also able to lysogenize the susceptible strain #6597 demonstrating that it was fully functional. The phages showed a very narrow host range infecting only two A. baumannii strains. In conclusion, we have isolated and characterized three novel temperate Siphoviridae phages that infect A. baumannii.

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Section: Discussionmentioning

confidence: 73%

Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii

Badawy

Pajunen

Haiko

et al. 2020

Viruses

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“…The carriage of OXA-type carbapenemases in prophages has been observed previously, with oxa58 identified on a prophage in a Proteus mirabilis strain (84) and oxa23 identified on a prophage in A. baumannii strain ANC 4097 (79,80) and on the phage phiOXA in isolate AB5075-UW (59). However, López-Leal et al (85) recently indicated that OXA carbapenemases in prophages may be more widespread, with evidence for potential OXA prophage carriage in approximately 25% of isolates studied. Similarly, we found oxa23 carried on phiOXA in 15% of our isolates.…”

Section: Discussionmentioning

confidence: 71%

Section: Discussionmentioning

confidence: 99%

“…However, recent evidence from studies focusing on A. baumannii have suggested that carriage of both virulence and antibiotic resistance genes by prophages is relatively common in this species and may be a major mechanism of horizontal transfer of these genes (79)(80)(81)(82)(83). It was recently noted that prophages appeared to be more common in IC5 isolates than in those belonging to IC1 or IC2 (81) and it is an intriguing possibility that prophages may be a major factor in the evolution of different international clones. The carriage of OXA-type carbapenemases in prophages has been observed previously, with oxa58 identified on a prophage in a Proteus mirabilis strain (84) and oxa23 identified on a prophage in A. baumannii strain ANC 4097 (79,80) and on the phage phiOXA in isolate AB5075-UW (59).…”

Section: Discussionmentioning

confidence: 99%

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Diversity of carbapenem-resistantAcinetobacter baumanniiand bacteriophage-mediated spread of the Oxa23 carbapenemase

Abouelfetouh

Mattock

Turner

et al. 2020

Preprint

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Carbapenem-resistant A. baumannii are prevalent in low- and middle-income countries such as Egypt, but little is known about the molecular epidemiology and mechanisms of resistance in these settings. Here we characterise carbapenem-resistant A. baumannii from Alexandria, Egypt, and place it in a regional context. 54 carbapenem-resistant isolates from Alexandria Main University Hospital, Egypt, collected between 2010 and 2015 were genome sequenced using Illumina technology. Genomes were de novo assembled and annotated. Genomes for 36 isolates from the Middle East region were downloaded from GenBank. Core gene compliment was determined using Roary, and analyses of recombination were performed in Gubbins. MLST sequence type and antibiotic resistance genes were identified. The majority of Egyptian isolates belonged to one of 3 major clades, corresponding to Pasteur MLST clonal complex (CCPAS) 1, CCPAS2 and sequence type (STPAS) 158. Strains belonging to STPAS158 have been reported almost exclusively from North Africa, the Middle East and Pakistan, and may represent a region-specific lineage. All isolates carried an oxa23 gene, six carried blaNDM-1, and one carried blaNDM-2. The oxa23 gene was located on a variety of different mobile elements, with Tn2006 predominant in CCPAS2 strains, and Tn2008 predominant in other lineages. Of particular concern, in 8 of the 11 CCPAS1 strains, the carbapenemase gene was located in a temperate bacteriophage phiOXA, previously identified only once before in a CCPAS1 clone from the US military. The carbapenem-resistant A. baumannii population in Alexandria Main University hospital is very diverse, and indicates an endemic circulating population, including a region-specific lineage. The major mechanism for oxa23 dissemination in CCPAS1 isolates appears to be a bacteriophage, presenting new concerns about the ability of these carbapenemases to spread throughout the bacterial population.Data SummaryThe whole genome shotgun sequences of the isolates from this study have been deposited at DDBJ/ENA/GenBank under the BioProject accession number PRJNA659545. The individual genome accession numbers for each isolate are as follows: A1a, JACSUC000000000; A2, JACSUB000000000; A4, JACSVQ000000000; A5, JACSUA000000000; A6, JACSTZ000000000; A7-T, JACSVP000000000; A8-T, JACSVO000000000; A8a, JACSTY000000000; A9, JACSTX000000000; A10, JACSTW000000000; A10a, JACSTV000000000; A11a, JACSTU000000000; A13a, JACSTT000000000; A14a, JACSTS000000000; A15, JACSTR000000000; A16, JACSTQ000000000; A18, JACSTP000000000; A21, JACSVN000000000; A22, JACSTO000000000; A27, JACSTN000000000; A30, JACSTM000000000; A31, JACSTL000000000; A34, JACSTK000000000; A35, JACSTJ000000000; A36, JACSTI000000000; A39, JACSTH000000000; A40, JACSTG000000000; A41, JACSTF000000000; A42, JACSTE000000000; A43, JACSTD000000000; A44, JACSTC000000000; A45, JACSTB000000000; A46, JACSTA000000000; A64, JACSSZ000000000; A68, JACSSY000000000; A69, JACSSX000000000; A70, JACSSW000000000; A71, JACSVM000000000; A72, JACSSV000000000; A73, JACSSU000000000; A74, JACSST000000000; A75, JACSSS000000000; A78, JACSSR000000000; A82, JACSSQ000000000; A83, JACSVL000000000; A84, JACSSP000000000; A85, JACSSO000000000; A86, JACSVK000000000; A87, JACSSN000000000; A88, JACSSM000000000; A89, JACSSL000000000; A92, JACSSK000000000; A5910, JACSSJ000000000; A6135, JACSVJ000000000.

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“…In our study, we also investigated antimicrobial resistance (AMR) genes that are embedded in prophage sequences. Previous studies on prophage diversity in A. baumannii had found AMR genes (also called: ARGs) in many prophages that were analysed (Costa et al 2018, López-Leal et al 2020). Yet despite this, it remains to be shown whether prophages confer antimicrobial resistance to its host in A. baumannii .…”

Section: Discussionmentioning

confidence: 99%

A Biological Inventory of Prophages inA. baumanniiGenomes Reveal Distinct Distributions in Classes, Length and Genomic Positions

Loh

Chen

Manohar

et al. 2020

Preprint

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Acinetobacter baumannii is of major clinical importance as the bacterial pathogen often causes hospital acquired infections, further complicated by the high prevalence of antibiotic resistant strains. Aside from natural tolerance to certain antibiotic classes, resistance is often acquired by the exchange of genetic information via conjugation but also by the high natural competence exhibited by A. baumannii. In addition, bacteriophages are able to introduce resistance genes but also toxins and virulence factors via phage mediated transduction. In this work, we analysed the complete genomes of 177 A. baumannii strains for the occurrence of prophages, and analysed their taxonomy, size and positions of insertion. Among all the prophages that were detected, Siphoviridae and Myoviridae were the two most commonly found families, while the average genome size was determined as 3.98 Mbp. Our data shows the wide variation in the number of prophages in A. baumannii genomes and the prevalence of certain prophages within strains that are most successful or potentially beneficial to the host. Our study also revealed that only two specific sites of insertion within the genome of the host bacterium are being used, with few exceptions only. Lastly, we analysed the existence of genes that are encoded in the prophages, which confer antimicrobial resistance (AMR). Several phages carry AMR genes, including OXA-23 and NDM-1, illustrating the importance of lysogenic phages in the acquisition of resistance genes.

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Letter to the Editor: Prophages Encode Antibiotic Resistance Genes in Acinetobacter baumannii

Cited by 33 publications

References 12 publications

Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii

Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii

Diversity of carbapenem-resistantAcinetobacter baumanniiand bacteriophage-mediated spread of the Oxa23 carbapenemase

A Biological Inventory of Prophages inA. baumanniiGenomes Reveal Distinct Distributions in Classes, Length and Genomic Positions

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