Acinetobacter bereziniae has emerged as a significant human pathogen, acquiring multiple antibiotic resistance genes, including carbapenemases. This study focuses on characterizing the plasmids harboring the bla_NDM-1 and tet(Y) genes in two carbapenem-resistant A. bereziniae isolates (UCO-553 and UCO-554) obtained in Chile during the COVID-19 pandemic. Methods: Antibiotic susceptibility testing was conducted on UCO-553 and UCO-554. Both isolates underwent whole-genome sequencing to ascertain their sequence type (ST), core genome multilocus sequence-typing (cgMLST) profile, antibiotic resistance genes, plasmids, and mobile genetic elements. Conjugation experiments were performed for both isolates. Results: Both isolates exhibited broad resistance, including resistance to carbapenems, third-generation cephalosporins, fluoroquinolones, tetracycline, cotrimoxazole, and aminoglycosides. Both isolates belong to sequence type ST^PAS1761, with a difference of 17 out of 2984 alleles. Each isolate carried a 47,274 bp plasmid with bla_NDM-1 and aph(3′)-VI genes and two highly similar plasmids: a 35,184 bp plasmid with tet(Y), sul2, aph(6)-Id, and aph(3″)-Ib genes, and a 6078 bp plasmid containing the ant(2″)-Ia gene. Quinolone-resistance mutations were identified in the gyrA and parC genes of both isolates. Importantly, bla_NDM-1 was located within a Tn125 transposon, and tet(Y) was embedded in a Tn5393 transposon. Conjugation experiments successfully transferred bla_NDM-1 and tet(Y) into the A. baumannii ATCC 19606 strain, indicating the potential for horizontal gene transfer. Conclusions: This study highlights the critical role of plasmids in disseminating resistance genes in A. bereziniae and underscores the need for the continued genomic surveillance of this emerging pathogen. The findings emphasize the importance of monitoring A. bereziniae for its potential to cause difficult-to-treat infections and its capacity to spread resistance determinants against clinically significant antibiotics.

Antimicrobial resistance (AMR) is a major public health threat that urgently requires alternative strategies to address this challenge. Klebsiella spp. are among the most important clinical pathogens and a leading cause of opportunistic nosocomial infections, with high morbidity and mortality associated with strains resistant to last-line antimicrobials such as carbapenems. Bacteriophages are considered a promising therapeutic option for treating infections caused by Klebsiella strains. Hence, the aim of this work was to isolate and characterize a phage capable of infecting carbapenem-resistant Klebsiella strains. The phage KpCCP1 was isolated using the double layer agar method (DLA), from the influent of a wastewater treatment plant, which was characterized through phenotypic and genomic analyses. Morphological characteristics were determined using TEM, and its host range was evaluated against a collection of 133 Klebsiella strains. Its whole genome was sequenced using the Illumina NovaSeq X Plus platform and then assembled and annotated. VICTOR was used for phylogenetic analysis of the isolated phage, and VIRIDIC to compare its genome with those of its closest relatives. KpCCP1 is a tailed dsDNA lytic phage with a genome size of 177,276 bp and a GC content of 41.82%. It encodes 292 ORFs, including two tRNA genes. Phage KpCCP1 is a member of the Slopekvirus genus in the Straboviridae family. It is capable of infecting 22 carbapenem-resistant Klebsiella strains, including K. pneumoniae and K. michiganensis. Notably, it does not contain virulence or antibiotic resistance genes and harbors putative anti-CRISPR genes, therefore representing a promising candidate for phage therapy against clinically critical Klebsiella strains.

There is an urgent need for alternative solutions to combat multidrug-resistant (MDR) E. coli infections. In recent years, there has been an increase in MDR strains causing urinary tract infections (UTIs), which has resulted in more challenging treatment options, increased healthcare costs and prolonged hospital stays. The utilization of bacteriophages as a prospective modality for the management of bacterial infections has garnered significant attention. The objective of this study was to isolate and describe a phage capable of infecting MDR E. coli strains isolated from the urine of patients affected with UTI. The phage EcoPhCCP1 was isolated using the plaque assay from the influent of a wastewater treatment plant. The phage was characterized by phenotypic and genomic features. Morphological characteristics such as shape and size were determined using electron microscopy, and its host range was determined against multiple MDR strains. The complete genome of the phage was subjected to whole-genome sequencing and then assembled and annotated to search for virulence or antimicrobial resistance gene (ARG). VIRIDIC was employed to compare the closest phage genomes, while VICTOR and taxMyPhage were used to construct its phylogeny. EcoPhCCP1 is a tailed phage capable of infecting and propagating in multiple MDR E. coli strains recovered from UTI. The phage genome is 44,482 bp in length, with a GC content of 50.7 mol%, and encodes 87 ORFs, 33 of which have been previously functionally annotated. Phage EcoPhCCP1 is a Kagunavirus , in the recently created Sarkviridae family. Notably, phage EcoPhCCP1 does not harbour ARGs or virulence genes, thus rendering it a promising candidate for phage therapy against clinically significant MDR E. coli strains. Moreover, phage EcoPhCCP1 possesses putative anti-CRISPR proteins.

Antibiotic-resistant Neisseria gonorrhoeae (Ng) is a WHO priority pathogen and represents a serious public health threat. This study reports the first Chilean Ng ST9363 isolate (GC11/23) exhibiting dual high-level resistance to azithromycin and fluoroquinolone, recovered from a urethral discharge sample in July 2023. Antimicrobial susceptibility was assessed using disk diffusion and MIC strip tests. Whole-genome sequencing (WGS) was performed using a hybrid approach, followed by annotation using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). In silico analyses included Staramr, MLST and NG-STAR. Phylogenetic analysis was performed on the core genome of 2,417 global ST9363 Ng isolates using IQ-TREE and visualized with TreeViewer. GC11/23 exhibited resistance to ciprofloxacin, tetracycline, penicillin, and azithromycin, while remaining susceptible only to ceftriaxone and spectinomycin. The isolate belonged to ST9363 and NG-STAR 3194. Mutations associated with fluoroquinolone resistance were identified in gyrA and parC, while high-level azithromycin resistance (HL-AziR) was linked to mutations in all four copies of the 23S rRNA gene, as well as in mtrD and mtrR. Additional resistance-associated alterations included an insertion (ins346D) in penA and a mutation in rpsJ, conferring resistance to penicillin and tetracycline, respectively. Phylogenetic analysis clustered GC11/23 with isolates from the USA and Europe collected in 2019. GC11/23 represents a multidrug-resistant Ng strain belonging to ST9363/NG-STAR 3194 and carrying mutations conferring resistance to fluoroquinolones, azithromycin, penicillin, and tetracycline. Its phylogenetic placement within a European lineage highlights the global dissemination of HL-AziR and fluoroquinolone-resistant strains.