Search Results (26)

Introduction: In recent years, antimicrobial resistance (AMR) rates have increased significantly in bacterial pathogens, particularly extended beta-lactam resistance. This study aimed to investigate resistome and phylogenomics of Escherichia coli (E. coli) strains isolated from various sources in Jimma, Ethiopia. Methods: Phenotypic antibiotic resistance patterns of E. coli isolates were determined using automated Kirby–Bauer disc diffusion and minimum inhibitory concentration (MIC). Isolates exhibiting phenotypic resistance to beta-lactam antibiotics were further analyzed with a DNA microarray to confirm the presence of resistance-encoding genes. Additionally, multilocus sequence typing (MLST) of seven housekeeping genes was conducted using PCR and Oxford Nanopore-Technology (ONT) to assess the phylogenetic relationships among the E. coli isolates. Results: A total of 611 E. coli isolates from human, animal, and environmental sources were analyzed. Of these, 41.6% (254) showed phenotypic resistance to at least one of the tested beta-lactams, 96.1% (244) thereof were confirmed genotypically. More than half of the isolates (53.3%) had two or more resistance genes present. The most frequent ESBL-encoding gene was CTX-M-15 (74.2%; 181), followed by TEM (59.4%; 145) and CTX-M-9 (4.1%; 10). The predominant carbapenemase gene was NDM-1, detected in 80% (12 out of 15) of carbapenem-resistant isolates. A phylogenetic analysis revealed clonality among the strains obtained from various sources, with international high-risk clones such as ST131, ST648, ST38, ST73, and ST405 identified across various niches. Conclusions: The high prevalence of CTX-M-15 and NDM-1 in multidrug-resistant E. coli isolates indicates the growing threat of AMR in Ethiopia. The discovery of these high-risk clones in various niches shows possible routes of transmission and highlights the necessity of a One Health approach to intervention and surveillance. Strengthening antimicrobial stewardship, infection prevention, and control measures are crucial to mitigate the spread of these resistant strains. Full article

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a significant opportunistic human pathogen, posing a considerable threat to public health due to its antimicrobial resistance and limited treatment options. The incidence of CRPA is high in the Philippines; however, genomic analysis of CRPA in this setting is limited. Here, we provide the phenotypic and molecular characterization of 35 non-duplicate CRPA obtained from three tertiary hospitals in Metro Manila, Philippines, from August 2022 to January 2023. Six sequence types (STs), including international high-risk clones ST111 and ST357, were identified. This article highlights the first report in the Philippines on the identification of P. aeruginosa harboring Klebsiella pneumoniae Carbapenemase-2 (KPC-2), coproduced with Verona Integron-encoded Metallo-beta-lactamase-2 (VIM-2) and Oxacillinase-74 (OXA-74). Notably, this is also the first report of KPC in the Philippines identified in P. aeruginosa. New Delhi Metallo-beta-lactamase-7 (NDM-7), coproduced with Cefotaxime-Munich-15 (CTX-M-15) and Temoneira-2 (TEM-2), was also identified from a novel ST4b1c. The relentless identification of NDM in the Philippines’ healthcare setting poses a significant global public health risk. The initial detection of the P. aeruginosa strain harboring KPC exacerbated the situation, indicating the inception of potential dissemination of these resistance determinants within P. aeruginosa in the Philippines. Full article

The global dissemination of Klebsiella pneumoniae pathotypes with multidrug-resistant (MDR) and hypervirulent traits poses a threat to public health. The situation in Armenia is unclear, and we performed a comprehensive characterisation of 48 clinical isolates of K. pneumoniae, collected from 2018 to 2024. The majority of the isolates (64.58%) were extensively drug-resistant (XDR) and MDR. Genomic analysis of 21 isolates revealed the presence of international high-risk MDR clones (ST395, ST15, and ST307). The ST395 strains were isolated from children and resisted the first-line drugs such as beta-lactams. These isolates harboured a range of virulence determinants, from capsule polysaccharides to siderophores to regulators of the mucoid phenotype. The ST395 strains are enriched by ICEs, plasmids, and prophages, on which antimicrobial resistance (AMR) and virulence genes are located and which may lead to the convergence of MDR and hypervirulent traits. There is a widespread non-specific AMR mechanism among our K. pneumoniae strains. These are mutations in the porin genes, which reduce permeability to antimicrobials, and mutations in the regulators of efflux pumps, which lead to overexpression of drug efflux pumps such as AcrAB. These mechanisms may contribute to the elevated MICs and confer AMR to strains with no specific AMR genes. Full article

Background/Objectives: Antimicrobial resistance represents a challenge to public health systems because of the array of resistance and virulence mechanisms that lead to treatment failure and increased mortality rates. Although for years the main driver of carbapenem resistance in Italy has been the Klebsiella pneumoniae KPC carbapenemase, recent years have seen an increase in VIM and NDM metallo-beta-lactamases (MBLs). We conducted a five-year survey of New Delhi Metallo-beta-Lactamase (NDM)-producing Klebsiella pneumoniae (NDM-Kpn) clinical isolates from the Lazio region, Italy; the study aimed to elucidate the molecular mechanisms underpinning their resistant and virulent phenotype. Methods: Antimicrobial susceptibility was evaluated by automated systems and broth microdilution. In silico analysis of acquired resistance and virulence genes was performed using whole-genome sequencing (WGS), molecular typing through MLST, and core genome multi-locus sequence typing (cgMLST). Conclusions: A total of 126 clinical NDM-Kpn isolates were collected from 19 distinct hospitals in the Lazio region. Molecular analysis highlighted the existence of NDM-1 (108/126) and NDM-5 (18/126) variants, 18 Sequence Types (STs), and 15 Cluster Types (CTs). Notably, 31/126 isolates displayed a virulence score of 4, carrying ybt, ICEKp, iuc, and rmp genes. This study identified a variety of NDM-Kpn STs, mainly carrying the bla_NDM-1 gene, with a significant number linked to high-risk clones. Of these isolates, 24.6% showed high-level resistance and virulence, emphasizing the risk of the spread of strains that combine multi-drug-resistance (MDR) and virulence. Proactive surveillance and international collaborations are needed to prevent the spread of high-risk clones, as well as further research into new antimicrobial agents to fight antibiotic resistance. Full article

Background/objectives: Pseudomonas aeruginosa can cause community-acquired infections affecting various body sites. The present retrospective study investigated the genetic diversity of 173 isolates (166 clinical, 7 environmental) of P. aeruginosa collected from clinical pathology laboratories in Abidjan, Côte d’Ivoire (2001–2011). Methods: Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) using 13 loci was applied to all isolates and compared to published MLVA data. The antibiotics status of the isolates was compiled when available and compared to published profiles. Results: Among 95 isolates analyzed for their antibiotics status, 14 displayed concerning resistance profiles: five multidrug-resistant (MDR) and nine extensively drug-resistant (XDR). MLVA typing revealed a high genetic diversity (>130 genotypes), with many genotypes represented by a single strain. Notably, thirteen clusters (≥4 related isolates) were observed. Some clusters displayed close genetic relatedness to isolates from France, Korea, and well-studied strains (ST560, LES and PA14). Comparative analysis suggested the presence of international high-risk MDR clones (CC233, CC111) in Côte d’Ivoire. Importantly, MLVA clustering revealed a close relationship of CC235-MDR strains with a locally identified cluster (group 9). Conclusions: These findings support MLVA as a reliable and cost-effective tool for low-resource settings, allowing the selection of relevant strains for future whole genome sequence analyses. This approach can improve outbreak investigations and public health interventions aimed at curbing MDR P. aeruginosa transmission within hospitals and at the national level. Full article

Here, we report on the emergence and spread of multidrug-resistant NDM-1-producing P. aeruginosa isolates from patients hospitalized in the Attica region, Greece, in 2022 to provide data on their resistome, their virulome, the genetic environment of bla_NDM-1, and their molecular epidemiology. A total of 17 carbapenem-resistant P. aeruginosa isolates identified as NDM-producers by immunochromatography at the hospital level were sent to the Central Public Health Laboratory, in the frame of the laboratory surveillance of carbapenem-resistant pathogens, for further characterization. The initial screening for genetic AMR determinants was carried out by PCR and the MDR Direct Flow Chip assay. Typing was performed by MLST and DLST, the latter in a subset of isolates. Further analysis was performed by whole-genome sequencing (WGS) of six isolates from both hospitals to analyze their entire genomes and elucidate their genetic relatedness. All isolates were allocated to international high-risk clones, sixteen to ST773 and one to ST308. Five ST773 and the sole ST308 isolate were found to harbor the bla_NDM-1 gene, along with various other ARGs integrated into their chromosomes, as well as with a wide variety of virulence genes. The bla_NDM-1 gene was located in the integrative and conjugative elements ICE6600-like and ICE_Tn43716385 in ST773 and ST308 isolates, respectively. Single-nucleotide polymorphism analysis of the five ST773 isolates indicated their clonal spread in both hospitals. These results suggested that two different molecular events contributed to the emergence of NDM-1-producing P. aeruginosa isolates in Athenian hospitals, highlighting the need for ongoing surveillance. Full article

The infections caused by various bacterial pathogens both in clinical and community settings represent a significant threat to public healthcare worldwide. The growing resistance to antimicrobial drugs acquired by bacterial species causing healthcare-associated infections has already become a life-threatening danger noticed by the World Health Organization. Several groups or lineages of bacterial isolates, usually called ‘the clones of high risk’, often drive the spread of resistance within particular species. Thus, it is vitally important to reveal and track the spread of such clones and the mechanisms by which they acquire antibiotic resistance and enhance their survival skills. Currently, the analysis of whole-genome sequences for bacterial isolates of interest is increasingly used for these purposes, including epidemiological surveillance and the development of spread prevention measures. However, the availability and uniformity of the data derived from genomic sequences often represent a bottleneck for such investigations. With this dataset, we present the results of a genomic epidemiology analysis of 17,546 genomes of a dangerous bacterial pathogen, Acinetobacter baumannii. Important typing information, including multilocus sequence typing (MLST)-based sequence types (STs), intrinsic bla_OXA-51-like gene variants, capsular (KL) and oligosaccharide (OCL) types, CRISPR-Cas systems, and cgMLST profiles are presented, as well as the assignment of particular isolates to nine known international clones of high risk. The presence of antimicrobial resistance genes within the genomes is also reported. These data will be useful for researchers in the field of A. baumannii genomic epidemiology, resistance analysis, and prevention measure development. Full article

The misuse of antibiotics is accelerating antimicrobial resistance (AMR) in Escherichia coli isolated from farm animals. The genomes of ten multidrug-resistant (MDR) E. coli isolates from pigs were analyzed to determine their sequence types, serotypes, virulence, and AMR genes (ARGs). Additionally, the relationship was evaluated adding all the available genomes of Peruvian E. coli from humans using the cgMLST + HierCC scheme. Two aEPEC O186:H11-ST29 were identified, of which H11 and ST29 are reported in aEPEC isolates from different sources. An isolate ETEC-O149:H10-ST100 was identified, considered a high-risk clone that is frequently reported in different countries as a cause of diarrhea in piglets. One ExPEC O101:H11-ST167 was identified, for which ST167 is an international high-risk clone related to urinary infections in humans. We identified many ARGs, including extended-spectrum β-lactamase genes, and one ETEC harboring the mcr-1 gene. CgMLST + HierCC analysis differentiated three clusters, and in two, the human isolates were grouped with those of swine in the same cluster. We observed that Peruvian swine MDR E. coli cluster with Peruvian E. coli isolates from healthy humans and from clinical cases, which is of great public health concern and evidence that AMR surveillance should be strengthened based on the One Health approach. Full article

Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics among K. pneumoniae isolates. The isolates were genetically diverse, consisting of 20 different sequence types (STs) and 34 K-serotype groups. Chromosomal fosA (for fosfomycin) and oqxAB efflux pump genes were detected in all isolates. Two carbapenem resistance genes, blaNDM-5 and blaOXA-181 plus extended-spectrum beta-lactamase (bla_CTX-M-15) gene (68.12%), quinolone-resistant genes qnrS1 (28.99%), qnrB1 (13.04%), and qnrB6 (13.04%) and others were found. All, except three of the isolates, harbored plasmids. While the isolates carried a repertoire of virulence genes, only two isolates carried hypervirulent genes demonstrating a low prevalence (2.90%) of hypervirulent strains. Our study demonstrated genetically diverse populations of K. pneumoniae, low levels of carbapenem resistance among the isolates, and no convergence of MDR and hypervirulence. Emerging high-risk international pandemic clones (ST11, ST14, ST147, ST 86 and ST307) were detected in these healthcare settings which are difficult to treat. Full article

Pseudomonas aeruginosa ST274 is an international epidemic high-risk clone, mostly associated with hospital settings and appears to colonize cystic fibrosis (CF) patients worldwide. To understand the relevant mechanisms for its success, the biological and genomic characteristics of 11 ST274-P. aeruginosa strains from clinical and non-clinical origins were analyzed. The extensively drug-resistant (XDR/DTR), the non-susceptible to at least one agent (modR), and the lasR-truncated (by ISPsp7) strains showed a chronic infection phenotype characterized by loss of serotype-specific antigenicity and low motility. Furthermore, the XDR/DTR and modR strains presented low pigment production and biofilm formation, which were very high in the lasR-truncated strain. Their whole genome sequences were compared with other 14 ST274-P. aeruginosa genomes available in the NCBI database, and certain associations have been primarily detected: bla_OXA-486 and bla_PDC-24 genes, serotype O:3, exoS⁺/exoU⁻ genotype, group V of type IV pili, and pyoverdine locus class II. Other general molecular markers highlight the absence of vqsM and pldA/tleS genes and the presence of the same mutational pattern in genes involving two-component sensor-regulator systems PmrAB and CreBD, exotoxin A, quorum-sensing RhlI, beta-lactamase expression regulator AmpD, PBP1A, or FusA2 elongation factor G. The proportionated ST274-P. aeruginosa results could serve as the basis for more specific studies focused on better antibiotic stewardship and new therapeutic developments. Full article

The objective of the present study is to report the detection and the molecular characterization of nine bla_NDM-1-positive Pseudomonas aeruginosa isolates, all of which belonged to the epidemic high-risk international clone ST308, and all were isolated from patients in a tertiary care hospital in Central Greece from May to July 2023.The isolates were characterized by whole genome sequencing to obtain multi-locus sequencing typing (MLST) and identify the bla_NDM1-environment and resistome and virulence genes content. In silico MLST analysis showed that all isolates belonged to the high-risk ST308 international clone. All strains possessed 22 different genes, encoding resistance to various antimicrobial agents. Whole genome sequencing revealed that the bla_NDM-1 was chromosomally located within the integrative and conjugative element ICE_Tn43716385 and that it was part of one cassette along with two other resistance genes, floR and msrE. Two additional resistance cassettes were also found in the genome, which included the arrays of aph(6)-Id, aph(3″)-Ib, floR, sul2 and aadA10, qnrVC1, aac(3)-Id, dfrB5, aac(6′)-II. Additionally, the strains possessed various virulence genes, e.g., aprA, exoU, lasA, lasB, toxA, and estA. All of the isolates shared identical genomes, which showed 98% similarity with the P. aeruginosa ST308 genome (acc. no CP020703), previously reported from Singapore. To our knowledge, this is the first report of ST308 bla_NDM-1-positive P. aeruginosa isolation in Europe, which indicates the transmission dynamics of this high-risk clone. Full article

Acinetobacter baumannii is a Gram-negative coccobacillus with exceptional survival skills in an unfavorable environment and the ability to rapidly acquire antibiotic resistance, making it one of the most successful hospital pathogens worldwide, representing a serious threat to public health. The global dissemination of A. baumannii is driven by several lineages named ‘international clones of high risk’ (ICs), two of which were first revealed in the 1970s. Epidemiological surveillance is a crucial tool for controlling the spread of this pathogen, which currently increasingly involves whole genome sequencing. However, the assignment of a particular A. baumannii isolate to some IC based on its genomic sequence is not always straightforward and requires some computational skills from researchers, while the definitions found in the literature are sometimes controversial. In this review, we will focus on A. baumannii typing tools suitable for IC determination, provide data to easily determine IC assignment based on MLST sequence type (ST) and intrinsic bla_OXA-51-like gene variants, discuss the history and current spread data of nine known ICs, IC1-IC9, and investigate the representation of ICs in public databases. MLST and cgMLST profiles, as well as OXA-51-like presence data are provided for all isolates available in GenBank. The possible emergence of a novel A. baumannii international clone, IC10, will be discussed. Full article

Acinetobacter baumannii is one of the significant healthcare-associated meningitis agents characterized by multidrug resistance and a high mortality risk. Thirty-seven A. baumannii strains were isolated from thirty-seven patients of Moscow neuro-ICU with meningitis in 2013–2020. The death rate was 37.8%. Strain susceptibility to antimicrobials was determined on the Vitek-2 instrument. Whole-genome sequencing was conducted using Illumina technology; the sequence types (ST), capsular types (KL), lipooligosaccharide outer core locus (OCL), antimicrobial resistance genes, and virulence genes were identified. The prevalent ST was ST2, belonging to the international clone IC2, and rarer, ST1, ST19, ST45, ST78, ST106, and ST400, with prevalence of KL9 and OCL1. Twenty-nine strains belonged to multidrug-resistant (MDR) and eight extensively drug-resistant (XDR) categories. Genes conferring resistance to beta-lactams (bla_PER, bla_GES, bla_ADC, bla_CARB, bla_CTX-M, bla_TEM, and bla_OXA-types), aminoglycosides (aac, aad, ant, aph, and arm), tetracyclines (tet), macrolides (msr and mph), phenicols (cml, cat, and flo), sulfonamides (dfr and sul), rifampin (arr), and antiseptics (qac) were identified. Virulence genes of nine groups (Adherence, Biofilm formation, Enzymes, Immune evasion, Iron uptake, Regulation, Serum resistance, Stress adaptation, and Antiphagocytosis) were detected. The study highlights the heterogeneity in genetic clones, antimicrobial resistance, and virulence genes variability among the agents of A. baumannii meningitis, with the prevalence of the dominant international clone IC2. Full article

Delafloxacin is a novel fluoroquinolone agent that is approved for clinical application. In this study, we analyzed the antibacterial efficacy of delafloxacin in a collection of 47 Escherichia coli strains. Antimicrobial susceptibility testing was performed by the broth microdilution method and minimum inhibitory concentration (MIC) values were determined for delafloxacin, ciprofloxacin, levofloxacin, moxifloxacin, ceftazidime, cefotaxime, and imipenem. Two multidrug-resistant E. coli strains, which exhibited delafloxacin and ciprofloxacin resistance as well as extended-spectrum beta-lactamase (ESBL) phenotype, were selected for whole-genome sequencing (WGS). In our study, delafloxacin and ciprofloxacin resistance rates were 47% (22/47) and 51% (24/47), respectively. In the strain collection, 46 E. coli were associated with ESBL production. The MIC50 value for delafloxacin was 0.125 mg/L, while all other fluoroquinolones had an MIC50 value of 0.25 mg/L in our collection. Delafloxacin susceptibility was detected in 20 ESBL positive and ciprofloxacin resistant E. coli strains; by contrast, E. coli strains that exhibited a ciprofloxacin MIC value above 1 mg/L were delafloxacin-resistant. WGS analysis on the two selected E. coli strains (920/1 and 951/2) demonstrated that delafloxacin resistance is mediated by multiple chromosomal mutations, namely, five mutations in E. coli 920/1 (gyrA S83L, D87N, parC S80I, E84V, and parE I529L) and four mutations in E. coli 951/2 (gyrA S83L, D87N, parC S80I, and E84V). Both strains carried an ESBL gene, bla_CTX-M-1 in E. coli 920/1 and bla_CTX-M-15 in E. coli 951/2. Based on multilocus sequence typing, both strains belong to the E. coli sequence type 43 (ST43). In this paper, we report a remarkable high rate (47%) of delafloxacin resistance among multidrug-resistant E. coli as well as the E. coli ST43 international high-risk clone in Hungary. Full article

We report on the case of prenatal detection of trisomy 2 in placental biopsy and further algorithm of genetic counseling and testing. A 29-year-old woman with first-trimester biochemical markers refused chorionic villus sampling and preferred targeted non-invasive prenatal testing (NIPT), which showed low risk for aneuploidies 13, 18, 21, and X. A series of ultrasound examinations revealed increased chorion thickness at 13/14 weeks of gestation and fetal growth retardation, a hyperechoic bowel, challenging visualization of the kidneys, dolichocephaly, ventriculomegaly, increase in placental thickness, and pronounced oligohydramnios at 16/17 weeks of gestation. The patient was referred to our center for an invasive prenatal diagnosis. The patient’s blood and placenta were sampled for whole-genome sequencing-based NIPT and array comparative genomic hybridization (aCGH), respectively. Both investigations revealed trisomy 2. Further prenatal genetic testing in order to confirm trisomy 2 in amniocytes and/or fetal blood was highly questionable because oligohydramnios and fetal growth retardation made amniocentesis and cordocentesis technically unfeasible. The patient opted to terminate the pregnancy. Pathological examination of the fetus revealed internal hydrocephalus, atrophy of brain structure, and craniofacial dysmorphism. Conventional cytogenetic analysis and fluorescence in situ hybridization revealed chromosome 2 mosaicism with a prevalence of trisomic clone in the placenta (83.2% vs. 16.8%) and a low frequency of trisomy 2, which did not exceed 0.6% in fetal tissues, advocating for low-level true fetal mosaicism. To conclude, in pregnancies at risk of fetal chromosomal abnormalities that refuse invasive prenatal diagnosis, whole-genome sequencing-based NIPT, but not targeted NIPT, should be considered. In prenatal cases of trisomy 2, true mosaicism should be distinguished from placental-confined mosaicism using cytogenetic analysis of amniotic fluid cells or fetal blood cells. However, if material sampling is impossible due to oligohydramnios and/or fetal growth retardation, further decisions should be based on a series of high-resolution fetal ultrasound examinations. Genetic counseling for the risk of uniparental disomy in a fetus is also required. Full article