Phage-Enzybiotic: dealing with critical pathogenic antibiotic-resistant bacteria

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Draft Genome Sequences of 29 Helicobacter pylori Strains Isolated from Colombia

Publication . Muñoz, Angela B.; Stepanian, Johanna; Acosta, Carmen; Solano-Gutierrez, Juan S.; Vale, Filipa F.; Trespalacios-Rangel, Alba Alicia

Here, we present the draft genome sequences of 29 Colombian Helicobacter pylori strains. These strains were isolated in Bogotá, Colombia, from patients diagnosed with chronic gastritis. The genomic characterization of these strains will provide more information on the genetic composition of H. pylori strains from Colombia.

2021-05-13Journal article

Open access

Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates

Publication . Marques, Andreia T.; Tanoeiro, Luis; Duarte, Aida; Gonçalves, Luisa; Vítor, Jorge M. B.; Vale, Filipa F.

Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion sites and phylogenetic analysis of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored at least one prophage and we identified 104 intact prophages (69.3%). The prophage size ranges from 29.7 to 50.6 kbp, coding between 32 and 78 putative genes. The prophage GC content is 51.2%, lower than the average GC content of 57.1% in K. pneumoniae. Complete prophages were classified into three families in the order Caudolovirales: Myoviridae (59.6%), Siphoviridae (38.5%) and Podoviridae (1.9%). In addition, an alignment and phylogenetic analysis revealed nine distinct clusters. Evidence of recombination was detected within the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) were maintained. These results support the knowledge that prophages are diverse and widely disseminated in K. pneumoniae genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified K. pneumoniae prophages in a set of endolysin genes, which were found to code for proteins with lysozyme activity, cleaving the β-1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in the peptidoglycan network and thus representing genes with the potential for lysin phage therapy.

2021-10-28Journal article

Open access

An American lineage of Helicobacter pylori prophages found in Colombia

Publication . Muñoz, Angela B.; Trespalacios Rangel, Alba Alicia; Vale, Filipa F.

Background Helicobacter pylori is a human gastric carcinogen that is highly prevalent in Latin American. The prophages of H. pylori show a structured population and contribute to the diversity of this bacterium. However, H. pylori prophages present in American strains have not been described to date. In this study, we identified, characterized, and present the phylogenetic analysis of the prophages present in Colombian H. pylori strains. Methods To characterize Colombian H. pylori strains and their prophages, a Multilocus Sequences Typing (MLST) and a Prophage Sequences Typing (PST), using the integrase and holin genes, were performed. Furthermore, five Colombian H. pylori had their full genome sequenced, and six Colombian H.pylori retrieved from databases, allowing to determine the prophage complete genome and insertion site. Results The integrase gene frequency was 12.6% (27/213), while both integrase and holin genes were present in 4.2% (9/213) of the samples analyzed. The PST analysis showed that Colombian prophages belong to different populations, including hpSWEurope, hpNEurope, hpAfrica1, and a new population, named hpColombia. The MLST analysis classified most of the Colombia strains in the hpEurope population. Conclusions The new H. pylori prophage population revealed that Colombian prophages follow a unique evolutionary trajectory, contributing to bacterial diversity. The global H. pylori prophage phylogeny highlighted five phylogenetic groups, one more than previously reported. After the arrival of Europeans, the Colombian H. pylori bacteria and their prophages formed an independent evolutionary line to adapt to the new environment and new human hosts.

2021-04-05Journal article

Restricted access

Cryptic Prophages Contribution for Campylobacter jejuni and Campylobacter coli Introgression

Publication . Tanoeiro, Luis; Oleastro, Mónica; Nunes, Alexandra; Marques, Andreia T.; Duarte, Sílvia Vaz; Gomes, João Paulo; Matos, António Pedro Alves; Vítor, Jorge M. B.; Vale, Filipa

Campylobacter coli and C. jejuni, the causing agents of campylobacteriosis, are described to be undergoing introgression events, i.e., the transference of genetic material between different species, with some isolates sharing almost a quarter of its genome. The participation of phages in introgression events and consequent impact on host ecology and evolution remain elusive. Three distinct prophages, named C. jejuni integrated elements 1, 2, and 4 (CJIE1, CJIE2, and CJIE4), are described in C. jejuni. Here, we identified two unreported prophages, Campylobacter coli integrated elements 1 and 2 (CCIE1 and CCIE2 prophages), which are C. coli homologues of CJIE1 and CJIE2, respectively. No induction was achieved for both prophages. Conversely, induction assays on CJIE1 and CJIE2 point towards the inducibility of these prophages. CCIE2-, CJIE1-, and CJIE4-like prophages were identified in a Campylobacter spp. population of 840 genomes, and phylogenetic analysis revealed clustering in three major groups: CJIE1-CCIE1, CJIE2-CCIE2, and CJIE4, clearly segregating prophages from C. jejuni and C. coli, but not from human- and nonhuman-derived isolates, corroborating the flowing between animals and humans in the agricultural context. Punctual bacteriophage host-jumps were observed in the context of C. jejuni and C. coli, and although random chance cannot be fully discarded, these observations seem to implicate prophages in evolutionary introgression events that are modulating the hybridization of C. jejuni and C. coli species.

2022-02-26Journal article

Open access

Diagnosis of Helicobacter pylori infection

Publication . Vale, Filipa F.; Oleastro, Mónica

Several studies addressed the usefulness of using molecular techniques for the diagnosis of Helicobacter pylori, pointing to the emerging paradigm change for clinical microbiology laboratories. During the last year, new variations of PCR-based approaches (formats, probes), new targets, as well as non-PCR based methods were described. In most cases, molecular methods combine detection of H. pylori with antimicrobial susceptibility testing, to predict antibiotic treatment outcome and guide clinicians in their choice of therapy. Macrolides and fluoroquinolones, for which resistance determinants are well known and are a major cause of treatment failure, remain the main targets of the classical molecular methods. Several other non-molecular methods, based on different technologies, were described for direct or indirect detection of H. pylori in different biological samples. Newly described endoscopic technologies offer advantages in the identification of patients at high risk of developing gastric cancer. Regarding serology, the importance of using optimised serological assays in specific geographical regions, employing local H. pylori strains for preparing antigens was highlighted. Next Generation Sequencing (NGS) based methods appear as a powerful tool to predict antibiotic resistance and will soon lead to a paradigm shift in the transition from culture-based to molecular-based susceptibility testing. In this context, due to the complexity of the resistance mechanisms and to allow the inclusion of further antibiotics, more comprehensive genotypic-phenotypic comparisons are needed. Additionally, the review of papers on H. pylori diagnosis published last year provided information concerning current prevalence of infection and antibiotic resistance in distinct geographies, indicating a tendency towards declining prevalence and rising antibiotic resistance.

2022Journal article

Open access