Search Results (126)

Background: Neisseria meningitidis (N. meningitidis) is a leading cause of acute meningitis and is classified into 13 serogroups, six of which are predominantly associated with invasive meningococcal disease. This study aimed to investigate the genotype, subgenotype, and antigenic profiles of N. meningitidis serogroup B strains isolated in Vietnam. Methods: Genotyping was performed on 106 N. meningitidis strains isolated from clinical samples from Vietnamese patients and nasopharyngeal swabs of healthy adolescents between 2019 and 2024. The genetic profiles, including the porA, porB, fetA, fHbp, abcZ, adk, aroE, fumC, gdh, pdhC, and pgm genes, were analyzed using Sanger sequencing and bioinformatic methods. Results: We found that 84.9% of the strains carried VR3 families 36 or 35-1, with VR1, VR2, and VR3 families 22-25, 14, and 36 being the most prevalent. Among the 106 serogroup B isolates, 20 variants of the porB allele 3 were identified, with porB 3-1212 being the most frequent (30.2%). Dominant PorB variable loops included L1.6, L4.5, L5.7, L6.6, and L7.13. fHbp variant group 2 was predominant (104/106 strains), and 12 FetA allele variants were identified, with F1-7 being the most common (47.2%). Three clonal complexes were identified, and clonal complex ST-32 was the most predominant. Fifty-five strains (51.9%) belonged to sequence types that have not yet been assigned to any clonal complexes, and 15 strains (14.1%) with allelic profiles were not assigned to STs. The 3-253 and 3-1212 alleles of porB, the F1-7 variant of FetA, the ST-44 and ST-1576 sequence types, and the ST-41/44 complex were observed more frequently in patients compared to asymptomatic carriers, suggesting their association with more virulence. Conclusions: This study showed a high genetic and antigenic diversity of N. meningitidis serogroup B isolates in Vietnam, with VR3 family 36 most common and porB 3-1212 as the predominant allele. fHbp variant group 2 and FetA allele F1-7 were most frequent. ST-32 was the dominant clonal complex, though many strains remained unassigned, highlighting the need for ongoing molecular surveillance. Full article

Background: High-risk Escherichia coli clones, such as sequence type (ST)131 and ST1193, along with multidrug-resistant (MDR) Klebsiella pneumoniae, are globally recognized for their significant role in urinary tract infections (UTIs). This study aimed to provide an overview of the virulence factors, clonal diversity, and antibiotic resistance profiles of extended-spectrum cephalosporin (ESC)-E. coli and K. pneumoniae causing UTIs in humans in the Tebessa region of Algeria. Methods: Forty E. coli and 17 K. pneumoniae isolates exhibiting ESC-resistance were recovered (July 2022–January 2024) from urine samples of patients at three healthcare facilities to be phenotypically and genotypically characterized. Whole genome sequencing (WGS) was performed on the ST1193 clone. Results: Among K. pneumoniae isolates, all except one harbored CTX-M-15, with a single isolate carrying bla_CTX-M-194. Additionally, two K. pneumoniae isolates co-harboring bla_CTX-M-15 and bla_NDM exhibited phenotypic and genotypic hypervirulence traits. Fluoroquinolone resistance (FQR) was detected in 94.1% of K. pneumoniae isolates. The E. coli isolates carried diverse ESC-resistance genes, including CTX-M-15 (87.5%), CTX-M-27 (5%), CTX-M-1, CMY-59, and CMY-166 (2.5% each). Co-carriage of bla_ESC and bla_OXA-48 was identified in three E. coli isolates, while 62.5% exhibited FQR. Phylogenetic analysis revealed that 52.5% of E. coli belonged to phylogroup B2, including the high-risk clonal complex (CC)131 CH40-30 (17 isolates) and ST1193 (one isolate). In silico analysis of the ST1193 genome determined O75:H5-B2 (CH14-64), and the carriage of IncI1-I(Alpha) and IncF [F-:A1:B10] plasmids. Notably, core genome single-nucleotide polymorphism (SNP) analysis demonstrated high similarity between the Algerian ST1193 isolate and a previously annotated genome from a hospital in Northwest Spain. Conclusions: This study highlights the spread and genetic diversity of E. coli CC131 CH40-30 and hypervirulent K. pneumoniae clones in Algeria. It represents the first report of a CTX-M-15-carrying E. coli ST1193 in the region. The findings emphasize the urgent need for antibiotic optimization programs and enhanced surveillance to curb the dissemination of high-risk clones that pose an increasing public health threat in Algeria. A simplified method based on virulence traits for E. coli and K. pneumoniae is proposed here for antimicrobial resistance (AMR) monitoring. Full article

Background: Staphylococcus aureus constitutes a significant public health threat due to its exceptional adaptability, antimicrobial resistance (AMR), and capacity to form biofilms, all of which facilitate its persistence in clinical and environmental settings. Methods: This study undertook an extensive in silico analysis of 44,069 S. aureus genomic sequences acquired from the NCBI database to assess the global distribution of biofilm-associated and resistance-associated genes. The genomes were categorized into human clinical and environmental groups, with clinical samples representing a predominant 96%. Results: The analysis revealed notable regional discrepancies in sequencing efforts, with Europe and North America contributing 76% of the genomes. Key findings include the high prevalence of the ica locus, which is associated with biofilm formation, and its robust correlation with other genes, such as sasG, which was exclusively linked to SCCmec type IIa. The AMR gene analysis revealed substantial genetic diversity within environmental samples, with genes like vga(E) and erm being identified as particularly prominent. The clonal complex analysis revealed ST8 (USA300) and ST5 as the predominant types in human clinical isolates, while ST398 and ST59 were most frequently observed in environmental isolates. SCCmec type IV was globally prevalent, with subtype Iva being strongly associated with ST8 in North America and subtype IVh with ST239 in Europe. Conclusions: These findings underscore the dynamic evolution of S. aureus via mobile genetic elements and highlight the necessity for standardized metadata in public genomic databases to improve surveillance efforts. Furthermore, they reinforce the critical need for a One Health approach in monitoring S. aureus evolution, particularly concerning the co-dissemination of biofilm and resistance genes across various ecological niches. Full article

Urinary tract infections (UTIs) are a leading cause of illness in children and adults of all ages, with uropathogenic Escherichia coli (UPEC) being the primary agent responsible. During colonization and subsequent infection of the urinary tract (UT), UPEC requires the expression of genes associated with virulence, such as those that encode the fimbrial adhesins FimH, PapG, and CsgA, as well as the presence of the TosA protein and the flagellar appendages of the bacteria. However, for colonization and infection to be successful, UPEC must overcome the host’s immunological barriers, such as physical barriers, expressed peptides and proteins, and immune cells found in the UT. In this context, the UT functions as an integral system where these factors act to prevent the colonization of uropathogens. Significant genetic diversity exists among UPEC strains, and the clonal complex ST131 represents one of the key lineages. This lineage has a high content of virulence genes, multiple mechanisms of antibiotic resistance, and a high frequency of extended-spectrum β-lactamases (ESBLs). New knowledge regarding protein structures known as adhesins and their role in the infection process can help identify therapeutic targets and aid in the design of vaccines. These vaccines could be based on the development of chimeric fusion proteins (FimH + CsgA + PapG), which may significantly reduce the incidence of UTIs in pediatric and adult patients. Full article

Listeria monocytogenes is an important foodborne pathogen, markedly persistent even in harsh environments and responsible for high hospitalization and mortality rates. The aim of the present study was to detect the strains circulating in Sicily over a five-year period and characterize their antimicrobial resistance profiles. The key element of this study was the sharing of data among various entities involved in food control and clinical surveillance of listeriosis in order to develop an integrated approach for this pathogen. A total of 128 isolates were analyzed, including 87 food-source strains and 41 clinical specimens. Whole-genome sequencing (WGS) was performed for sequence type (ST) and clonal complex (CC) identification through multilocus sequence typing (MLST) analysis. Antimicrobial resistance was assessed using the Kirby–Bauer method. The majority of strains belonged to serotype IVb (34/41 and 53/87 of clinical and food-source isolates, respectively) and were subtyped as CC2-ST2 (28/34 and 41/53 of clinical and food-source isolates respectively). Most of the isolates were susceptible to the main antimicrobials recommended for treatment of listeriosis. Resistance (R) and intermediate resistance (I) percentages worthy of attention were found against oxacillin (R: 85.9%) and clindamycin (I: 34.6%) in the food-source isolates and trimethoprim/sulfamethoxazole (R: 29.23%) in the clinical isolates. Also, 7.7% of the food-source isolates were multidrug resistant. Our results highlight how the punctual comparison between food and clinical strains is an essential tool for effectively tracking and preventing foodborne outbreaks. Full article

Background/Objectives: Acinetobacter baumannii is an increasingly significant nosocomial pathogen causing severe infections globally. The emergence of multidrug-resistant A. baumannii strains has raised concerns about the efficacy of current treatment options. This study aimed to investigate the molecular epidemiology and antimicrobial resistance patterns of A. baumannii isolates from Kazakhstan. Methods: We collected nine A. baumannii isolates in 2022–2023 in Karaganda, Kazakhstan, which were then subjected to whole-genome sequencing (WGS) using the IonTorrent platform for genome characterization. Multilocus sequence typing (MLST) was used to classify the isolates into distinct clonal complexes. In addition, antibiotic susceptibility testing was conducted using the standard methods for a range of antibiotics commonly used against A. baumannii. Results: Our results revealed a high degree of genomic diversity among isolates from Kazakhstan, with multiple distinct classes identified: ST78 (n = 4, 44.4%), ST15 (n = 2, 22.2%), ST2 (n = 2, 22.2%), and ST193 (n = 1, 11%). MLST analysis showed that ST78^Pas/1104^Oxf (harboring blaOXA-72 and blaOXA-90 genes) were prevalent among the multidrug-resistant isolates. Based on the results of MLST, KL, and OCL, the analyzed isolates were assigned to specific international clones: IC2—ST2(Pas)-KL2/168-OCL1, IC4—ST15(Pas)-KL9-OCL7, and IC6—ST78(Pas)-KL49-OCL1. Notably, these isolates exhibited resistance to multiple antibiotics including meropenem, imipenem, gentamicin, amikacin, and ciprofloxacin. Conclusions: This study highlighted the complex molecular epidemiology of A. baumannii in Kazakhstan over a two-year period, underscoring the need for targeted surveillance strategies to monitor antimicrobial resistance patterns. The emergence and dissemination of multidrug-resistant strains within this timeframe emphasizes the importance of whole-genome sequencing as a diagnostic tool and underscores the challenges posed by these infections. Full article

Streptococcus pneumoniae serotype 1 is one of the most prevalent serotypes commonly associated with invasive pneumococcal disease cases and outbreaks worldwide. Several sequence types of this serotype have been identified globally, including those exhibiting both high virulence potential and antimicrobial resistance profiles. This systematic review presents the global distribution of clones of pneumococcal serotype 1, describing their circulating patterns in various regions in the world. A database search was conducted in Google Scholar, PubMed, Scopus, ScienceDirect, and Web of Science using keywords related to Streptococcus pneumoniae serotype 1. The inclusion criteria entailed peer-reviewed studies published in English describing the utilization of at least one molecular genotyping tool to identify S. pneumoniae serotype 1 clones based on their sequence types. Data extracted were managed and analyzed using Microsoft Excel 365 (Version 2108). Forty-three studies were finally included in the systematic review. A total of 103 MLST serotype 1 sequence types were identified in 48 countries. These clones were widely reported to be associated with invasive pneumococcal diseases. Globally, ST217 and ST306 clonal complexes (CC217 and CC306) were the predominant lineages of serotype 1 sequence types, exhibiting distinct continental distribution patterns. CC217, characterized by ST217, ST303, ST612, ST618, and ST3081, was predominant in Africa and Asia. ST306 clonal complex, which is grouped into ST306, ST304, and ST227 were mostly found in Europe, Oceania, North America, and some countries in South America. ST615 was predominant in Chile, Peru, and Argentina. The hypervirulence nature of serotype 1, coupled with its complex genetic diversity, poses a significant public health threat. Our findings emphasize the need for enhanced surveillance and targeted interventions to mitigate the spread of these hypervirulent clones, ultimately informing evidence-based strategies for disease prevention and control. Full article

Background/Objective: Vancomycin-resistant enterococci (VRE), particularly Enterococcus faecium (VREfm), are significant healthcare-associated infections, especially bloodstream infections (BSIs). Method: This study explored the genotypic and phenotypic characteristics of 29 VREfm isolates causing BSIs in Thailand. Bacterial species, sequence types (STs), virulence genes, and vancomycin antimicrobial-resistance genes were identified by multiplex PCR, multilocus sequence typing, and whole-genome sequencing (WGS). Antibiotic susceptibility was determined by disk diffusion, while an E-test or broth microdilution were used for daptomycin, teicoplanin, linezolid, and tigecycline. Biofilm formation was assessed using a microtiter plate assay. Results: All isolates harbored the vanA gene and exhibited resistance to ampicillin, erythromycin, norfloxacin, vancomycin, and rifampin. Resistance to ciprofloxacin, tigecycline, and nitrofurantoin was widespread as well. All isolates remained susceptible to chloramphenicol and linezolid. The majority of isolates belonged to clonal complex 17, with ST17 being predominant (21/29, 72.4%), followed by ST80 (6/29, 20.7%), ST761 (1/29, 3.4%), and ST117 (1/29, 3.4%). WGS analysis confirmed the presence of various antimicrobial resistance genes, including aac(6′)-Ii, ant-Ia, erm(B), and vanA. Additionally, virulence genes such as acm (collagen adhesin) and esp (enterococcal surface protein), which are involved in biofilm formation, were detected. Conclusion: This study provides insights into the genomic characteristics and clonal dissemination of invasive VREfm in Thailand, which is crucial for infection control and public health surveillance. Full article

Salmonella is an important foodborne pathogen that can cause a range of illnesses in humans; it has also been a key focus for monitoring in the field of public health, including gastroenteritis, sepsis, and arthritis, and can also cause a decline in egg production in poultry and diarrhea and abortion in livestock, leading to death in severe cases, resulting in huge economic losses. This study aimed to investigate the isolation rate, antimicrobial resistance, serotypes, and genetic diversity of Salmonella isolated from yak feces in various regions on the Qinghai–Tibet Plateau. A total of 1222 samples of yak dung were collected from major cities in the Qinghai–Tibet Plateau area, and the sensitivity of the isolated bacteria to 10 major classes of antibiotics was determined using the K-B paper disk diffusion method for drug susceptibility. Meanwhile, the serotypes of the isolated bacteria were analyzed using the plate agglutination test for serum antigens, and their carriage of drug resistance and virulence genes was determined using PCR and gel electrophoresis experiments. The isolated bacteria were also classified using MLST (Multi-Locus Sequence Typing). The overall isolation rate for Salmonella was 18.25% (223/1222), and the results of the antibiotic susceptibility tests showed that 98.65% (220/223) of the isolated bacteria were resistant to multiple antibiotics. In the 223 isolates of Salmonella, eight classes of 20 different resistance genes, 30 serotypes, and 15 different types of virulence genes were detected. The MLST analysis identified 45 distinct sequence types (STs), including five clonal complexes, of which ST34, ST11, and ST19 were the most common. These findings contribute valuable information about strain resources, genetic profiles, and typing data for Salmonella in the Qinghai–Tibet Plateau area, facilitating improved bacterial surveillance, identification, and control in yak populations. They also provide certain data supplements for animal Salmonella infections globally, filling research gaps. Full article

Listeria monocytogenes is an important foodborne pathogen causing listeriosis. L. monocytogenes, existing in the natural environment, can also contaminate food products, which poses a serious threat to human health and life, especially for high-risk groups: pregnant women, newborn babies, and the elderly. Environmental adaptation of L. monocytogenes refers to the various strategies and mechanisms used by this bacterium to survive and thrive in diverse and often hostile environments that include, among others, toxic heavy metals and disinfectants. The aim of this study was to analyze WGS (whole-genome sequencing) data of 45 L. monocytogenes strains isolated from food to compare the prevalence and types of genetic determinants encoding resistance to toxic metals, such as arsenic and cadmium, as well as quaternary ammonium compounds, like benzalkonium chloride. In L. monocytogenes strains, resistance genes were detected for disinfectants, such as benzalkonium chloride (4.4%), as well as for toxic heavy metals, like cadmium (28.9%) and arsenic (24.4%). The bcrABC cassette was found together with the cadA2C2 genes in two strains: 3855-D (IIc, ST9, CC9) and 4315 (IVb, ST6, CC6). The arsenic cassette, encoded by the genes arsR1D2R2A2B1B2, was co-selected with the cadA4C4 genes. The arsenic cassette was prevalent in nine strains of clonal complex CC2 (82%), one strain of CC3 (9%), and one strain of CC11 (9%). In contrast, the benzalkonium chloride cassette was detected in one strain of CC6 and one strain of CC9. The results of the present study demonstrate the need for further research into the characteristics of L. monocytogenes isolated from other sources in order to understand their spread throughout the food chain. Full article

In the absence of data on the reporting of L. monocytogenes resistance to antibiotics, we sought to determine which clonal complexes (CCs)/sequence types (STs) circulate in the food chain in Kosovo and to determine their antibiogram profiles to a panel of 18 antibiotics. From a total of 114 isolates, 21 different typical STs were identified by multilocus sequence typing (MLST). Each isolate derived from the food categories was subjected to tests to verify its susceptibility to the selected antibiotics according to the designed Sensititre GPN3F panel. Among the different STs that were identified, CC9-ST9 was more abundant in meat products (38.75%) while CC29-ST29 was more abundant (24.0%) in dairy products. Moreover, these isolates showed marked resistance against levofloxacin (22.8%), gentamicin and rifampicin (17.5%), quinupristin/dalfopristin (14.9%), erythromycin (11.4%), penicillin (7.89%), tetracycline (1.75%), and streptomycin (0.88%). A total of 27 multiple antibiotic resistance (MAR) phenotypes were observed amongst the isolates, which ranged from 3 to 12. The ARI of the food category including meat and meat products (MMP, 0.22) and fish meat products (FMP, 0.26) were >0.2, the permissible Krumperman threshold. The number of strains with MAR values >0.2 was 34, (29.8%). The identification of typical multidrug-resistant STs among L. monocytogenes isolates in Kosovo constitutes a potential threat to food safety and public health, which requires a continuous and expanded surveillance system to prevent the further spread of antimicrobial resistant (AMR) isolates. Full article

Background/Objectives: Intestinal colonization by multidrug-resistant (MDR) bacteria is considered one of the main risk factors for invasive infections in the hematopoietic stem-cell transplant (HSCT) setting, associated with hard-to-eradicate microorganisms. The aim of this study was to assess the rate of intestinal colonization by MDR bacteria and their microbial spectrum in a group of post-HSCT patients to study the genetic determinants of beta-lactam and glycopeptide resistance in the recovered isolates, as well as to determine the epidemiological relation between them. Methods: The intestinal colonization status of 74 patients admitted to the transplantation center of University Hospital “St. Marina”—Varna in the period January 2019 to December 2021 was investigated. Stool samples/rectal swabs were screened for third-generation cephalosporin and/or carbapenem-resistant Gram-negative bacteria, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and Stenotrophomonas maltophilia. Identification and antimicrobial susceptibility testing were performed by Phoenix (BD, Sparks, MD, USA) and MALDI Biotyper sirius (Bruker, Bremen, Germany). Molecular genetic methods (PCR, DNA sequencing) were used to study the mechanisms of beta-lactam and glycopeptide resistance in the collected isolates, as well as the epidemiological relationship between them. Results: A total of 28 patients (37.8%) were detected with intestinal colonization by MDR bacteria. Forty-eight non-duplicate MDR bacteria were isolated from their stool samples. Amongst them, the Gram-negative bacteria prevailed (68.8%), dominated by ESBL-producing Escherichia coli (30.3%), and followed by carbapenem-resistant Pseudomonas sp. (24.2%). The Gram-positive bacteria were represented exclusively by Enterococcus faecium (31.2%). The main beta-lactam resistance mechanisms were associated with CTX-M and VIM production. VanA was detected in all vancomycin-resistant enterococci. A clonal relationship was observed among Enterobacter cloacae complex and among E. faecium isolates. Conclusions: To the best of our knowledge, this is the first Bulgarian study that presents detailed information about the prevalence, resistance genetic determinants, and molecular epidemiology of MDR gut-colonizing bacteria in HSCT patients. Full article

Sequence-type 5 (ST5) of methicillin-resistant Staphylococcus aureus (MRSA), harboring the staphylococcal chromosomal cassette mec type IV (SCCmecIV), was first detected in Portugal. It emerged as a significant cause of healthcare-associated (HA) infection in pediatric units and was hence named the pediatric clone. Another ST5 lineage, which carries SCCmecII, also prevailed in the USA and Japan for multiple years. More recently, another MRSA lineage, ST105-SCCmecII, part of the evolution of clonal complex 5 (CC5) MRSA, has emerged as the cause of hospital-acquired bloodstream infection outbreaks in countries including Portugal, the USA, and Brazil. This article reviews studies on the epidemiology and evolution of these newly emerging pathogens. To this end, a search of PUBMED from inception to 2024 was performed to find articles reporting the occurrence of ST105 MRSA in epidemiologic studies. A second search was performed to find studies on MRSA, CC5, ST5, and SCCmecII. A search of PUBMED from 1999 to 2024 was also performed to identify studies on the genomics and evolution of ST5, CC5, and ST105 MRSA. Further studies were identified by analyzing the references of the previously selected articles from PUBMED. Most articles on ST105 MRSA were included in this review. Only articles written in English were included. Furthermore, only studies that used a reliable genotyping method (e.g., whole genome sequencing, or MLST) to classify the CC5 lineages were selected. The quality and selection of articles were based on the consensus assessment of the three authors in independent evaluations. In conclusion, ST105-SCCmecII is an emerging MRSA in several countries, being the second/third most important CC5 lineage, with a relatively high frequency in bloodstream infections. Of concern is the increased mortality from BSI in patients older than 15 years and the higher prevalence of ST105-SCCmecII in the blood of patients older than 60 years reported in some studies. Full article

Acute myeloid leukemia (AML) is an aggressive hematologic neoplasia with a complex polyclonal architecture. Among driver lesions, those involving the FLT3 gene represent the most frequent mutations identified at diagnosis. The development of tyrosine kinase inhibitors (TKIs) has improved the clinical outcomes of FLT3-mutated patients (Pt). However, overcoming resistance to these drugs remains a challenge. To unravel the molecular mechanisms underlying therapy resistance and clonal selection, we conducted a longitudinal analysis using a single-cell DNA sequencing approach (MissionBioTapestri® platform, San Francisco, CA, USA) in two patients with FLT3-mutated AML. To this end, samples were collected at the time of diagnosis, during TKI therapy, and at relapse or complete remission. For Pt #1, disease resistance was associated with clonal expansion of minor clones, and 2nd line TKI therapy with gilteritinib provided a proliferative advantage to the clones carrying NRAS and KIT mutations, thereby responsible for relapse. In Pt #2, clonal architecture was less complex, and 1st line TKI therapy with midostaurin was able to eradicate the leukemic clones. Our results corroborate previous findings about clonal selection driven by TKIs, highlighting the importance of a deeper characterization of individual clonal architectures for choosing the best treatment plan for personalized approaches aimed at optimizing outcomes. Full article

Our whole-genome sequencing analysis of sixteen uropathogenic E. coli isolates revealed a concerning picture of multidrug resistance and potentially virulent bacteria. All isolates belonged to four distinct clonal groups, with the highly prevalent ST131 lineage being associated with extensive antibiotic resistance and virulence factors. Notably, all isolates exhibited multidrug resistance, with some resistant to as many as 12 antibiotics. Fluoroquinolone resistance stemmed primarily from efflux pumps and mutations in gyrase and topoisomerase genes. Additionally, we identified genes encoding resistance to extended-spectrum cephalosporins, trimethoprim/sulfamethoxazole, and various heavy metals. The presence of diverse plasmids and phages suggests the potential for horizontal gene transfer and the dissemination of virulence factors. All isolates harbored genomic islands containing virulence factors associated with adhesion, biofilm formation, and invasion. Genes essential for iron acquisition, flagella biosynthesis, secretion systems, and toxin production were also prevalent. Adding further complexity to understanding the isolates’ genetic makeup, we identified CRISPR-Cas systems. This study underscores the need for continued genomic surveillance in understanding the pathogenic mechanisms and resistance profiles of uropathogenic E. coli to aid in developing targeted therapeutic strategies. Full article