Complete genome sequence of the siphoviral bacteriophage Βϕ-R3177, which lyses an OXA-66-producing carbapenem-resistant Acinetobacter baumannii isolate

Acinetobacter baumannii and Klebsiella pneumoniae Isolates Obtained from Intensive Care Unit Patients in 2024: General Characterization, Prophages, Depolymerases and Esterases of Phage Origin

Acinetobacter baumannii and Klebsiella pneumoniae are significant nosocomial pathogens worldwide. In this study, the general characterization of A. baumannii and K. pneumoniae isolates obtained from the blood of intensive care unit patients of the multidisciplinary scientific and practical center of emergency medicine from January to September 2024 was performed. Prophage regions and prophage-derived tailspike polysaccharide-depolymerizing or -modifying enzymes within these isolates were identified and characterized in detail using a refined workflow. The protocol, encompassing a comprehensive survey of all predicted bacterial proteins, revealed an average of 6.0 prophage regions per Acinetobacter baumannii genome, including regions putatively derived from filamentous phages, and 4.8 prophage regions per Klebsiella pneumoniae isolate. Analysis of these putative prophage regions indicated that most were related to previously isolated, yet unclassified, temperate phages infecting A. baumannii and K. pneumoniae. However, certain identified sequences likely originated from phages representing novel groups comparatively distant from known phages.

Geographic variation in abundance and diversity of Acinetobacter baumannii Vieuvirus bacteriophages

Introduction

Prophages play a crucial role in the genomic diversity of Acinetobacter baumannii, contributing to its pathogenicity and adaptation.

Methods

In this study, we induced and sequenced seven prophages from five isolates of A. baumannii. These were analyzed with 967 prophages identified from various isolates worldwide, plus 21 genomes of other phages infecting A. baumannii previously reported in NCBI. To have an overview of the populations of the prophages infecting A. baumannii.

Results

Our analysis revealed 13 major prophage clusters within the analyzed A. baumannii isolates. Notably, prophages belonging to the Vieuvirus genus were the most prevalent. Specifically, Vieuvirus-related phages were frequently identified in isolates from Thailand, Mexico, China, and South Korea, which show the geographic prevalence of A. baumannii prophages.

Discussion

This study highlights the importance of considering geographic factors to fully understand prophage diversity and their significant role in the evolutionary dynamics of A. baumannii.

Antibiotics-free compounds for managing carbapenem-resistant bacteria; a narrative review

Carbapenem-resistant (CR) Gram-negative bacteria have become a significant public health problem in the last decade. In recent years, the prevalence of CR bacteria has increased. The resistance to carbapenems could result from different mechanisms such as loss of porin, penicillin-binding protein alteration, carbapenemase, efflux pump, and biofilm community. Additionally, genetic variations like insertion, deletion, mutation, and post-transcriptional modification of corresponding coding genes could decrease the susceptibility of bacteria to carbapenems. In this regard, scientists are looking for new approaches to inhibit CR bacteria. Using bacteriophages, natural products, nanoparticles, disulfiram, N-acetylcysteine, and antimicrobial peptides showed promising inhibitory effects against CR bacteria. Additionally, the mentioned compounds could destroy the biofilm community of CR bacteria. Using them in combination with conventional antibiotics increases the efficacy of antibiotics, decreases their dosage and toxicity, and resensitizes CR bacteria to antibiotics. Therefore, in the present review article, we have discussed different aspects of non-antibiotic approaches for managing and inhibiting the CR bacteria and various methods and procedures used as an alternative for carbapenems against these bacteria.

Lytic Capsule-Specific Acinetobacter Bacteriophages Encoding Polysaccharide-Degrading Enzymes

The genus Acinetobacter comprises both environmental and clinically relevant species associated with hospital-acquired infections. Among them, Acinetobacter baumannii is a critical priority bacterial pathogen, for which the research and development of new strategies for antimicrobial treatment are urgently needed. Acinetobacter spp. produce a variety of structurally diverse capsular polysaccharides (CPSs), which surround the bacterial cells with a thick protective layer. These surface structures are primary receptors for capsule-specific bacteriophages, that is, phages carrying tailspikes with CPS-depolymerizing/modifying activities. Phage tailspike proteins (TSPs) exhibit hydrolase, lyase, or esterase activities toward the corresponding CPSs of a certain structure. In this study, the data on all lytic capsule-specific phages infecting Acinetobacter spp. with genomes deposited in the NCBI GenBank database by January 2024 were summarized. Among the 149 identified TSPs encoded in the genomes of 143 phages, the capsular specificity (K specificity) of 46 proteins has been experimentally determined or predicted previously. The specificity of 63 TSPs toward CPSs, produced by various Acinetobacter K types, was predicted in this study using a bioinformatic analysis. A comprehensive phylogenetic analysis confirmed the prediction and revealed the possibility of the genetic exchange of gene regions corresponding to the CPS-recognizing/degrading parts of different TSPs between morphologically and taxonomically distant groups of capsule-specific Acinetobacter phages.

Potential Usefulness of Bacteriophages for the Treatment of Multidrug-Resistant Acinetobacter Infection

Bacteriophages were discovered in early 20th century. However, the interest in bacteriophage research was reduced with the discovery of antibiotics. With the increasing number of infections due to multidrug-resistant (MDR) organisms, the potential usefulness of bacteriophages as therapeutic agents has been re-evaluated. In this review, we found that more than 30 lytic bacteriophages that infect Acinetobacter species have been characterised. These are mainly members of Caudovirales, with genome sizes ranging from 31 kb to 234 kb and G+C contents ranging from 33.5% to 45.5%. The host range can be as low as < 10% of all tested Acinetobacter strains. Fourteen published murine trials indicated positive outcomes in bacteriophage-treated groups. Only two case reports were pertaining to the use of bacteriophages in the treatment of Acinetobacter infections in humans; in both cases, the infections were resolved with bacteriophage therapy. The use of bacteriophages has been associated with reduced Acinetobacter burden in the environment, as shown in two studies. The major limitation of bacteriophage therapy is its highly selective host strain. In conclusion, the potential usefulness of bacteriophage therapy for the treatment of MDR Acinetobacter species has been documented only in limited studies and more research is needed prior to its extensive use in clinical practice.

Genome diversity of domesticated Acinetobacter baumannii ATCC 19606T strains

Acinetobacter baumannii has emerged as an important opportunistic pathogen worldwide, being responsible for large outbreaks for nosocomial infections, primarily in intensive care units. A. baumannii ATCC 19606^T is the species type strain, and a reference organism in many laboratories due to its low virulence, amenability to genetic manipulation and extensive antibiotic susceptibility. We wondered if frequent propagation of A. baumannii ATCC 19606^T in different laboratories may have driven micro- and macro-evolutionary events that could determine inter-laboratory differences of genome-based data. By combining Illumina MiSeq, MinION and Sanger technologies, we generated a high-quality whole-genome sequence of A. baumannii ATCC 19606^T, then performed a comparative genome analysis between A. baumannii ATCC 19606^T strains from several research laboratories and a reference collection. Differences between publicly available ATCC 19606^T genome sequences were observed, including SNPs, macro- and micro-deletions, and the uneven presence of a 52 kb prophage belonging to genus Vieuvirus. Two plasmids, pMAC and p1ATCC19606, were invariably detected in all tested strains. The presence of a putative replicase, a replication origin containing four 22-mer direct repeats, and a toxin-antitoxin system implicated in plasmid stability were predicted by in silico analysis of p1ATCC19606, and experimentally confirmed. This work refines the sequence, structure and functional annotation of the A. baumannii ATCC 19606^T genome, and highlights some remarkable differences between domesticated strains, likely resulting from genetic drift.

A novel vieuvirus from multidrug-resistant Acinetobacter baumannii

Bacteriophages are considered the most abundant biological entities on earth, and they are able to modulate the populations of their bacterial hosts. Although the potential of bacteriophages has been accepted as an alternative strategy to combat multidrug-resistant pathogenic bacteria, there still exists a considerable knowledge gap regarding their genetic diversity, which hinders their use as antimicrobial agents. In this study, we undertook a genomic and phylogenetic characterization of the phage Ab11510-phi, which was isolated from a multidrug-resistant Acinetobacter baumannii strain (Ab11510). We found that Ab11510-phi has a narrow host range and belongs to a small group of transposable phages of the genus Vieuvirus that have only been reported to infect Acinetobacter bacteria. Finally, we showed that Ab11510-phi (as well as other vieuvirus phages) has a high level of mosaicism. On a broader level, we demonstrate that comparative genomics and phylogenetic analysis are necessary tools for the proper characterization of phage diversity.

Structure of an Acinetobacter Broad-Range Prophage Endolysin Reveals a C-Terminal α-Helix with the Proposed Role in Activity against Live Bacterial Cells

Proteins that include enzymatic domain degrading the bacterial cell wall and a domain providing transport through the bacterial outer membrane are considered as prospective compounds to combat pathogenic Gram-negative bacteria. This paper presents an isolation and study of an enzyme of this class naturally encoded in the prophage region of Acinetobacter baumannii AB 5075 genome. Recombinant protein expressed in E. coli exhibits an antimicrobial activity with respect to live cultures of Gram-negative bacteria reducing the population of viable bacteria by 1.5⁻2 log colony forming units (CFU)/mL. However the protein becomes rapidly inactivated and enables the bacteria to restore the population. AcLys structure determined by X-ray crystallography reveals a predominantly &alpha;&mdash;helical fold similar to bacteriophage P22 lysozyme. The С-terminal part of AcLys polypeptide chains forms an &alpha;&mdash;helix enriched by Lys and Arg residues exposed outside of the protein globule. Presumably this type of structure of the C-terminal &alpha;&mdash;helix has evolved evolutionally enabling the endolysin to pass the inner membrane during the host lysis or, potentially, to penetrate the outer membrane of the Gram-negative bacteria.

Comparative Analysis of 37 Acinetobacter Bacteriophages

Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades.

Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki

Acinetobacter baumannii has emerged as an important nosocomial pathogen in healthcare and community settings. While over 100 of Acinetobacter phages have been described in the literature, relatively few have been sequenced. This work describes the characterisation and genome annotation of a new lytic Acinetobacter siphovirus, vB_AbaS_Loki, isolated from activated sewage sludge. Sequencing revealed that Loki encapsulates a 41,308 bp genome, encoding 51 predicted open reading frames. Loki is most closely related to Acinetobacter phage IME_AB3 and more distantly related to Burkholderia phage KL1, Paracoccus phage vB_PmaS_IMEP1 and Pseudomonas phages vB_Pae_Kakheti25, vB_PaeS_SCH_Ab26 and PA73. Loki is characterised by a narrow host range, among the 40 Acinetobacter isolates tested, productive infection was only observed for the propagating host, A. baumannii ATCC 17978. Plaque formation was found to be dependent upon the presence of Ca2+ ions and adsorption to host cells was abolished upon incubation with a mutant of ATCC 17978 encoding a premature stop codon in lpxA. The complete genome sequence of vB_AbaS_Loki was deposited in the European Nucleotide Archive (ENA) under the accession number LN890663.