Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (501)

Search Parameters:
Keywords = blaOXA

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
13 pages, 1616 KB  
Article
Phylogenetic Relationships and Structural Conservation of blaOXA-48-like Carbapenemase in Multispecies Clinical Strains from an Intensive Care Unit in Pakistan
by Zeb Hussain, Ambreen Fatima, Asad Karim, Muhammad Jahanzaib, Muhammad Sameer Qureshi and Asma Naim
Int. J. Mol. Sci. 2026, 27(12), 5391; https://doi.org/10.3390/ijms27125391 (registering DOI) - 15 Jun 2026
Abstract
The global dissemination of carbapenem resistance is predominantly facilitated by plasmid-mediated carbapenemase genes, notably blaOXA-48-like genes. A comprehensive understanding of their evolutionary relationships and structural conservation is essential for monitoring their spread and informing therapeutic strategies. This study aimed to investigate the [...] Read more.
The global dissemination of carbapenem resistance is predominantly facilitated by plasmid-mediated carbapenemase genes, notably blaOXA-48-like genes. A comprehensive understanding of their evolutionary relationships and structural conservation is essential for monitoring their spread and informing therapeutic strategies. This study aimed to investigate the phylogenetic relationships and structural conservation of blaOXA-48-like carbapenemase genes in multiple Gram-negative bacterial species. We analysed blaOXA-48-like carbapenemase sequences obtained from a hospital in Pakistan and compared them with globally reported variants retrieved from GenBank. Carbapenemase gene sequences (blaOXA-48-like, blaNDM, and blaVIM) were analyzed using maximum-likelihood phylogenetics (MEGA11, Tamura–Nei model, 1000 bootstrap replicates). Comparative global sequences were retrieved from GenBank. Structural modeling of blaOXA-48-like genes was performed using SWISS-MODEL Workspace with the template PDB 3HBR, followed by validation using GMQE, QMEANDisCo, and Ramachandran plot analyses. Phylogenetic analysis revealed a tight clustering of blaOXA-48-like genes across A. baumannii, K. pneumoniae, and E. meningoseptica, showing high similarity to globally distributed plasmid-associated sequences. Structural modeling demonstrated strong conservation of the enzyme, with preserved catalytic residues (Ser70, Lys73, Ser118, Trp157, and Tyr211) and minimal structural deviation (RMSD < 0.3 Å). blaOXA-48-like carbapenemases exhibit strong phylogenetic conservation and structural stability across species and regions, consistent with the horizontal dissemination of blaOXA-48-like genes across bacterial hosts. These findings indicate that blaOXA-48-like carbapenemases have high evolutionary stability. Full article
(This article belongs to the Special Issue Bioinformatics of Gene Regulations and Structure–2025)
18 pages, 2035 KB  
Article
Direct-from-Specimen Detection of Major Carbapenemases by Carbapenem-Resistant K.N.I.V.O. Detection K-Set: Comparative Analysis of Accuracy and Turnaround Time
by Basant Mostafa Gabr, Mona Abd El-Aziz Gadallah, Wafaa Abd Elaziz, Sama Metwally, Raghda Gabr Mashaal, Rasha A. Abd Ellatif, Ahmed G. Elkhouly, Hanan Salem, Amira E. Oraiby, Bsant S. Kasem, Sherif Abdelbaky, Reham M. Elkolaly and Marwa S. Taha
Pathogens 2026, 15(6), 634; https://doi.org/10.3390/pathogens15060634 (registering DOI) - 15 Jun 2026
Abstract
To improve clinical decision-making about Carbapenem-resistant Gram-negative bacteria (CR-GNB) infections and halt the spread of resistant microbes, quicker and less expensive diagnostic techniques are required. Thus, the purpose of this study was to thoroughly evaluate the diagnostic efficiency (sensitivity, specificity, and concordance) of [...] Read more.
To improve clinical decision-making about Carbapenem-resistant Gram-negative bacteria (CR-GNB) infections and halt the spread of resistant microbes, quicker and less expensive diagnostic techniques are required. Thus, the purpose of this study was to thoroughly evaluate the diagnostic efficiency (sensitivity, specificity, and concordance) of direct-from-specimen multiplex lateral flow immunoassay (LFIA) across diverse raw clinical specimens and pathogen types from critically sick patients. A total of 300 non-duplicate samples were tested to detect CR-GNB. Five major Carbapenemase genes were detected directly from the specimen using carbapenem-resistant K.N.I.V.O. detection K-Set and from culture using culture-enhanced multiplex PCR. Turnaround time (TAT) of each method was calculated. The direct LFIA revealed 100% specificity for NDM, KPC, and IMP enzymes in all tested clinical matrices (blood, urine, and respiratory samples). The study demonstrated 100% sensitivity and specificity with perfect categorical agreement (κ = 1.000) for the blaKPC in the Klebsiella pneumoniae and for blaOXA-48 and blaIMP in the Acinetobacter baumannii; however, sensitivity of blaVIM was significantly diminished across all isolates and samples. TAT decreased significantly (p < 0.001) from 30 to 70 h to about 50 min. The tested direct LFIA facilitates the prompt enhancement of lifesaving tailored antibiotic treatment for severe illnesses. Full article
Show Figures

Figure 1

19 pages, 2427 KB  
Article
Stenotrophomonas maltophilia Complex: Genomic Characterization, Antimicrobial Resistance and First Report of S. muris from Oman
by Amira ElBaradei, Atika Al-Bimani, Suad A. H. Al-Ubaidani, Amal Al-Hinai, Zainab J. Al-Lawati and Hafidha Al-Hattali
Antibiotics 2026, 15(6), 600; https://doi.org/10.3390/antibiotics15060600 - 12 Jun 2026
Viewed by 163
Abstract
Introduction: Stenotrophomonas maltophilia (S. maltophilia) has emerged as an important opportunistic pathogen. It is resistant to most available antibiotics due to its intrinsic resistance, leaving only some antibacterial agents as possible therapeutic options, which is further complicated by acquired mechanisms [...] Read more.
Introduction: Stenotrophomonas maltophilia (S. maltophilia) has emerged as an important opportunistic pathogen. It is resistant to most available antibiotics due to its intrinsic resistance, leaving only some antibacterial agents as possible therapeutic options, which is further complicated by acquired mechanisms of antimicrobial resistance. This study aimed to provide a comprehensive genomic characterization of clinical S. maltophilia complex (Smc) isolates, focusing on molecular characterization of its resistance and virulence, since studies tackling this are scarce in Oman. Methods: This study is a prospective cross-sectional study, in which a total of 21 clinical isolates of Smc were collected from different clinical samples and further characterized using Whole Genome Sequencing. Results: Besides S. maltophilia, the isolates included S. hibiscicola, S. pavanii, and S. muris for the first time in Oman. All isolates were found to be susceptible to cefiderocol, levofloxacin, and minocycline. Sequence types (STs) were diverse among the isolates, with more than half of the isolates showing new STs with novel alleles. Additionally, blaOXA-2, sul1, and the recently described aac(6′)-Iap and aph(9)-Ic were detected among the isolates. Moreover, virulence-associated genes (smf-1, pilT, pilQ, gpmA, rmlA, spgM, stmPr1, plcN, clpP, and katE) were highly conserved across all isolates. Mobile genetic elements were detected in most of the isolates (76.20%). Conclusions: The collected isolates showed high ST diversity and showed no specific pattern in terms of antibiotic susceptibility and resistance genes. More studies are needed to establish relationships between the different members of the Smc and the different molecular resistome and virulome. Full article
(This article belongs to the Special Issue Genomic Surveillance of Antimicrobial Resistance (AMR))
Show Figures

Figure 1

15 pages, 845 KB  
Article
Comprehensive Molecular Characterization of Extensively Drug-Resistant Acinetobacter baumannii Isolated from Intensive Care Unit Patients: Carbapenemase Genes, Plasmid-Mediated Resistance Determinants, and PFGE-Based Clonal Analysis
by Cihat Öztürk
Pharmaceuticals 2026, 19(6), 862; https://doi.org/10.3390/ph19060862 - 29 May 2026
Viewed by 146
Abstract
Background: Colistin- and carbapenem-resistant Acinetobacter baumannii (CRAB) represent a critical threat in intensive care unit (ICU) settings. This study aimed to provide a comprehensive molecular epidemiological characterization of extensively drug-resistant (XDR) A. baumannii clinical isolates from a tertiary-care hospital in Kırşehir, Central [...] Read more.
Background: Colistin- and carbapenem-resistant Acinetobacter baumannii (CRAB) represent a critical threat in intensive care unit (ICU) settings. This study aimed to provide a comprehensive molecular epidemiological characterization of extensively drug-resistant (XDR) A. baumannii clinical isolates from a tertiary-care hospital in Kırşehir, Central Anatolia, a region previously absent from the national surveillance literature. Methods: A total of 43 non-duplicate XDR A. baumannii isolates recovered from ICU patients between November 2021 and December 2023 were included. Antimicrobial susceptibility testing was performed by automated systems and broth microdilution for colistin. Resistance genes, including OXA-type carbapenemases, extended-spectrum β-lactamases (ESBLs), metallo-β-lactamases, plasmid-mediated colistin resistance (mcr-1 to mcr-5), plasmid-mediated quinolone resistance genes (qnr, qepA, oqxAB, aac(6′)-Ib-cr), and class 1 and 2 integrons, were screened by PCR. Integron gene cassettes were characterized by sequencing. Clonal relatedness was assessed by pulsed-field gel electrophoresis (PFGE) using ApaI digestion. Results: All 43 isolates exhibited the XDR phenotype with universal resistance to carbapenems, colistin, fluoroquinolones, aminoglycosides (except amikacin), piperacillin, cephalosporins, and tobramycin. Amikacin susceptibility was retained in 58.1% of isolates. blaOXA-51 was detected in all isolates (100%), and blaOXA-23 was the predominant acquired carbapenemase (90.7%). Notably, blaOXA-48, a carbapenemase typically associated with Enterobacteriaceae, was identified in 3 isolates (7.0%), each belonging to a distinct pulsotype. No blaOXA-24/40, blaOXA-58, or class B metallo-β-lactamase genes were detected. ESBL genes were found in a subset of isolates, with blaCTX-M group 1 being the most prevalent (20.9%). The aac(6′)-Ib-cr gene was detected in 81.4% of isolates, and oqxA/oqxB in 60.5% and 39.5%, respectively. No mcr or classical qnr genes were identified. Class 1 and 2 integrons were detected in 4.7% and 7.0% of isolates, respectively, carrying dfrA12-DUF1010-aadA2 (class 1) and dfrA1-sat-1 (class 2) gene cassettes. PFGE identified 12 pulsotypes among the typeable isolates; PT4 (n = 20, 47.6%) and PT11 (n = 8, 19.0%) were the dominant clonal clusters, together accounting for 65.1% of typeable isolates. Conclusions: This study presents one of the first comprehensive molecular epidemiological analyses of XDR A. baumannii from Central Anatolia. The dominance of OXA-23-carrying clonal lineages, the detection of blaOXA-48 in A. baumannii distributed across three distinct pulsotypes, the high prevalence of aac(6′)-Ib-cr, and the concurrent distribution of resistance determinants across genetically diverse clonal backgrounds indicate that both clonal expansion and possible horizontal gene transfer contribute to resistance dissemination in this setting. These findings underscore the need for systematic molecular surveillance and reinforced infection control strategies in ICU settings, at both the regional and national levels. Full article
Show Figures

Graphical abstract

28 pages, 1678 KB  
Review
Role of Mobilome in Carbapenem Resistance
by Laiba Hassan, Muhammad Ali Syed, Binghuai Lu, Jiankang Zhao and Bin Cao
Antibiotics 2026, 15(6), 542; https://doi.org/10.3390/antibiotics15060542 - 28 May 2026
Viewed by 322
Abstract
Growing resistance to carbapenem antibiotics is a major public health problem as these antibiotics are considered the last line of therapy for infections caused by multidrug-resistant (MDR) Gram-negative bacteria. The rapid emergence and dissemination of carbapenem-resistant bacterial strains are mainly due to horizontal [...] Read more.
Growing resistance to carbapenem antibiotics is a major public health problem as these antibiotics are considered the last line of therapy for infections caused by multidrug-resistant (MDR) Gram-negative bacteria. The rapid emergence and dissemination of carbapenem-resistant bacterial strains are mainly due to horizontal gene transfer (HGT) within or between bacterial cells via the mobilome. The aim of this article is to discuss the role of mobile genetic elements (MGEs) that capture and disseminate resistance determinants of carbapenem antibiotics, as a comprehensive review integrating the combined role of plasmids, transposons and integrons. It attempts to systematically fill the gap by investigating the role of these MGEs in the acquisition, mobilization and dissemination of genes encoding carbapenemases across clinically important bacteria. Various types of plasmids such as IncF and IncH in Klebsiella pneumoniae, IncL/M in Enterobacter cloacae, IncX3 in Escherichia coli and IncA/C2 in Salmonella enterica carry important genes encoding carbapenemases. The rapid distribution of transposons among bacterial species is one of the main contributing factors in the dissemination of carbapenem-resistant isolates. Transposons including Tn4401 carrying blaKPC in K. pneumoniae and Tn1721 carrying blaKPC in E. coli; Tn2006, Tn2007, Tn2008 and Tn2009 carrying blaOXA-23 in Acinetobacter baumannii; Tn1696 carrying blaIMP-4 in Pseudomonas aeruginosa; Tn125 carrying blaNDM in E. coli; and Tn6306 carrying blaIMI in Raoultella ornithinolytica encode different types of carbapenemases. Integrons mainly belonging to class 1 capture resistance determinants for metallo-carbapenemases such as NDM-, VIM-, SIM- and IMP-type enzymes in P. aeruginosa, A. baumannii, K. pneumoniae and E. coli and can promote the transcription and expression of these determinants. These findings are useful for understanding the genetics of carbapenem resistance and additional knowledge on MGEs may provide avenues for screening of resistance to these antibiotics in clinical settings. Full article
Show Figures

Figure 1

22 pages, 2264 KB  
Review
Advances in CRISPR-Cas for Diagnosis and Treatment of Klebsiella pneumoniae
by Changmei Feng and Jun Yin
Pathogens 2026, 15(6), 570; https://doi.org/10.3390/pathogens15060570 - 26 May 2026
Viewed by 359
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a significant pathogen for both hospital-acquired and community-acquired infections, characterized by its strong epidemic potential and high mortality rate, posing a severe threat to global public health. CRKP spreads widely across the globe through the horizontal transfer of [...] Read more.
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a significant pathogen for both hospital-acquired and community-acquired infections, characterized by its strong epidemic potential and high mortality rate, posing a severe threat to global public health. CRKP spreads widely across the globe through the horizontal transfer of plasmid-mediated resistance genes such as *blaKPC*, *blaNDM*, and *blaOXA-48*. The clinical treatment options for this bacterium are limited, and its resistance has been increasing year by year, urgently necessitating the development of new antimicrobial drugs or alternative strategies. In recent years, the CRISPR-Cas system has shown great potential in the diagnosis and treatment of CRKP, including rapid detection and identification, gene editing, antimicrobial strategies, and resistance inhibition. For instance, CRISPR-Cas12a/13a can be used for the rapid detection and identification of CRKP, while CRISPR-Cas9/Cas3 can target resistance genes to reverse the resistance of strains. With the advancement of delivery and biotechnologies, the CRISPR-Cas system is expected to become an important tool against drug-resistant CRKP. This review focuses on the application of the CRISPR-Cas system in the detection and treatment of CRKP, analyzing its technical advantages, limitations, and future development directions. Full article
(This article belongs to the Section Bacterial Pathogens)
Show Figures

Figure 1

21 pages, 1320 KB  
Article
Multiplex PCR-Based Detection of Eight Carbapenemase Genes and Their Clinical Characteristics in Urinary Tract Infections
by Nishadi Jayathilaka, Upeksha Kulasekara, Dilini Nakkawita, Dharshan De Silva, Samanmalee Gunasekara and Thamarasi Senaratne
Antibiotics 2026, 15(6), 529; https://doi.org/10.3390/antibiotics15060529 - 22 May 2026
Viewed by 262
Abstract
Background: The emergence and spread of urinary carbapenem-resistant organisms (CROs) are a major public health concern, particularly in Sri Lanka. Therefore, we aimed to detect and genotypically characterize CROs in urinary tract infections (UTIs) and their clinical outcomes. Methods: Urinary CROs were collected [...] Read more.
Background: The emergence and spread of urinary carbapenem-resistant organisms (CROs) are a major public health concern, particularly in Sri Lanka. Therefore, we aimed to detect and genotypically characterize CROs in urinary tract infections (UTIs) and their clinical outcomes. Methods: Urinary CROs were collected from two hospitals in Sri Lanka from January to December, 2023. Among 7640 urine samples, 100 CROs were identified by disk diffusion method, and 99 were detected by BD PheonixTM automated system. The presence of eight carbapenemase genes; blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-23, blaOXA-48, blaOXA-51, and blaOXA-58, among 97 CROs was detected by a multiplex PCR kit. Results: Out of 99 urinary CROs, K. pneumoniae (33.3%; n = 33/97) was the most common species. Among the 97 isolates tested by PCR, a single carbapenemase gene was detected in 35.05% (34/97), while two or more genes co-occurred in 39.18% (38/97). The most frequently identified gene was blaOXA-51 (47.4%), followed by blaOXA-58 (41.2%). Most patients (95.74%; n = 90/97) showed clinical improvement within seven days of treatment. Among the 93 patients discharged and followed for three months, 74.20% (n = 69/93) experienced at least one mild UTI recurrence. A total of 10 patients died during the study period. Of which, four (40%) during hospitalization and six (60%) during follow-up, though none of the deaths were attributed to UTIs. Conclusions: K. pneumoniae, showed the highest carbapenemase gene diversity. Recurrent UTIs were observed during the follow-up period. Continuous surveillance and implementation of targeted infection control programs are needed to minimize further emergence and spread of carbapenemase genes. Full article
(This article belongs to the Section Mechanism and Evolution of Antibiotic Resistance)
Show Figures

Figure 1

16 pages, 1704 KB  
Article
Epidemiology and Molecular Profiles of ESBL-Producing Klebsiella pneumoniae in Urinary Tract Infections Across Jordanian Hospitals
by Ayman Alsheikh, Raghad Shanabla, Ahmad Badawi, Hafez Al-Momani, Mohammed Nasser-Ali, Yaqeen Rjoub, Mohammad A. A. Al-Najjar, Montasir Al-Mansi, Iman Aolymat, Lana Al-Shoubaki and Nawal Al-Zaa’q
Microorganisms 2026, 14(5), 1142; https://doi.org/10.3390/microorganisms14051142 - 19 May 2026
Viewed by 517
Abstract
Klebsiella pneumoniae is an opportunistic pathogen associated with both community-acquired and nosocomial infections. Multidrug-resistant (MDR) strains are increasingly implicated in urinary tract infections (UTIs), traveller’s diarrhoea, bacteraemia, and sepsis. β-lactam antibiotics are commonly used for treatment; however, antimicrobial resistance has emerged largely due [...] Read more.
Klebsiella pneumoniae is an opportunistic pathogen associated with both community-acquired and nosocomial infections. Multidrug-resistant (MDR) strains are increasingly implicated in urinary tract infections (UTIs), traveller’s diarrhoea, bacteraemia, and sepsis. β-lactam antibiotics are commonly used for treatment; however, antimicrobial resistance has emerged largely due to the production of extended-spectrum β-lactamases (ESBLs), which confer resistance mainly to penicillins, oxyimino-cephalosporins, and monobactams, while cephamycins and carbapenems usually remain stable to ESBL-mediated hydrolysis and compromise therapeutic efficacy. ESBL-producing strains represent a major cause of severe Gram-negative infections. This study aimed to determine the prevalence of ESBL-producing K. pneumoniae among UTI patients in Jordanian hospitals (Al Mafraq, Ma’an, and Islamic Hospitals), evaluate their antimicrobial susceptibility patterns, and detect antimicrobial resistance genes at the molecular level. A total of 450 urine isolates of K. pneumoniae were collected from UTI patients between November 2023 and May 2024. Isolates were identified in hospital laboratories using standard microbiological methods. Antimicrobial susceptibility testing was performed, and molecular characterisation of ESBL-associated genes was conducted using polymerase chain reaction (PCR). Out of 450 K. pneumoniae isolates collected from UTI patients across three Jordanian regions, 72 (16%) were confirmed as ESBL producers. Among the 72 ESBL-positive K. pneumoniae isolates, 34 (47.2%) were recovered from the Central region, 20 (27.8%) from the North, and 18 (25.0%) from the South. Molecular analysis revealed that 41.7% of ESBL-producing isolates carried the blaCTX-M gene, while 33.3% harboured the blaOXA gene. All ESBL-producing isolates demonstrated antimicrobial resistance to third-generation cephalosporins. A significantly higher proportion of ESBL-producing isolates was identified in female patients (84.7%) compared with males (15.3%). A significant association was observed between blaOXA gene distribution and geographic region (p = 0.016), whereas blaCTX-M gene distribution showed no significant regional association. ESBL-producing K. pneumoniae accounted for a substantial proportion of UTI isolates in Jordan, with blaCTX-M identified as the predominant resistance gene. The higher burden observed in the Central region and among female patients highlights notable distribution patterns in this cohort. These findings emphasise the necessity for sustained molecular surveillance and strengthened antimicrobial stewardship strategies to limit the dissemination of ESBL-producing strains in Jordanian healthcare settings. Full article
(This article belongs to the Section Medical Microbiology)
Show Figures

Figure 1

15 pages, 1207 KB  
Article
Carbapenem-Resistant Acinetobacter baumannii in Zagreb, Croatia, in Post-COVID-19 Pandemic Period: Resistance Trends and Mechanisms
by Branka Bedenić, Marina Nađ, Vesna Bratić, Daniela Bandić Pavlović, Mislav Kasalo, Mirela Dobrić, Rocío Arazo del Pino, Tessa Burgwinkel, Andrea Grisold, Josefa Luxner, Gernot Zarfel and Paul G. Higgins
Microorganisms 2026, 14(5), 1123; https://doi.org/10.3390/microorganisms14051123 - 15 May 2026
Viewed by 372
Abstract
During the COVID-19 pandemic carbapenem-resistant Acinetobacter baumannii (CRAB) was found to be the major pathogen associated with ventilator-associated pneumonia in mechanically ventilated patients. This prompted us to analyze the post-pandemic mechanisms of carbapenem resistance, antibiotic resistance trends, and molecular epidemiology of CRAB in [...] Read more.
During the COVID-19 pandemic carbapenem-resistant Acinetobacter baumannii (CRAB) was found to be the major pathogen associated with ventilator-associated pneumonia in mechanically ventilated patients. This prompted us to analyze the post-pandemic mechanisms of carbapenem resistance, antibiotic resistance trends, and molecular epidemiology of CRAB in Croatia. In total, 94 CRAB isolates from two hospital centers, including outpatient settings, were investigated. Antimicrobial susceptibility testing was performed by broth microdilution. PCR was used to detect genes encoding carbapenemases of group A, B and D and extended-spectrum β-lactamases (ESBL). Randomly selected isolates were subjected to whole resistome analysis by Inter-array CarbaResist Kit and whole-genome sequencing (WGS). Phylogenetic tree and sequence types (STs) were retrieved from WGS. Plasmid incompatibility groups were determined by PCR-based replicon typing (PBRT). All isolates were extensively drug resistant (XDR), showing resistance to ceftazidime, cefepime, piperacillin–tazobactam, imipenem, meropenem, gentamicin, amikacin and ciprofloxacin, and 13% (n = 12) were also resistant to colistin. The Hodge and CIM test exhibited poor sensitivity with only 32 and 30% of isolates being identified as carbapenemase producers, respectively. PCR identified blaOXA-23 as the dominant carbapenemase gene in both hospitals, found in 71% of the isolates (67/94). In an outpatient setting, blaOXA-24/40 was dominant. blaOXA-23 and blaOXA-72 were the only allelic variants. The Inter-array CarbaResist Kit and whole-genome sequencing (WGS) identified a variety of aminoglycoside (armA, ant(3″)-IIa, aph(3″)-Ib, aph(6)-Id) and sulphonamide resistance (sul1 and sul2) genes. The representative blaOXA-23-positive isolates belonged to ST2, while blaOXA-72-positive isolates were allocated to ST492. These data show that there are different populations of XDR A. baumannii between hospital and outpatients. Full article
Show Figures

Figure 1

14 pages, 1172 KB  
Article
Genomic and Phenotypic Insights into Carbapenem-Resistant Pseudomonas aeruginosa in the Aquatic Environments of the Tibetan Plateau
by Dingxiang Lu, Lin Liu, Zhongwei Yang, Tianjiao Chen, Dong Yang, Danyang Shi, Shuqing Zhou, Junwen Li, Haibei Li and Min Jin
Microorganisms 2026, 14(5), 1094; https://doi.org/10.3390/microorganisms14051094 - 12 May 2026
Viewed by 375
Abstract
Carbapenem-resistant Pseudomonas aeruginosa is increasingly becoming a global health threat. However, although aquatic environments are key resistance reservoirs, data obtained from high-altitude ecosystems are scarce. Whole-genome sequencing of eight carbapenem-resistant P. aeruginosa isolates collected from aquatic environments in the Tibetan Plateau identified three [...] Read more.
Carbapenem-resistant Pseudomonas aeruginosa is increasingly becoming a global health threat. However, although aquatic environments are key resistance reservoirs, data obtained from high-altitude ecosystems are scarce. Whole-genome sequencing of eight carbapenem-resistant P. aeruginosa isolates collected from aquatic environments in the Tibetan Plateau identified three sequence types (STs), with ST1420 predominating (62.5%, 5/8). Phylogenetic analysis revealed a close clustering of isolates with those from distant clinical settings, suggesting potential cross-habitat transmission. All studied strains were multidrug-resistant, exhibiting 100% resistance to imipenem, ceftriaxone, and trimethoprim–sulfamethoxazole. This included the PA6 strain, which showed multiple-antibiotic resistance. Eight strains harbored the intrinsic carbapenemase gene blaOXA-50. The diverse virulence-gene profiles of strains PA2, PA4, and PA6 aligned with their high pathogenicity observed both in vitro and in vivo. However, virulence genotypes sometimes did not correlate with phenotypes, revealing the limitations of relying on static genetic information alone. This study highlights the aquatic environments of the Tibetan Plateau as reservoirs of carbapenem-resistant P. aeruginosa with substantial genetic diversity and divergent pathogenic potential, underscoring their public-health relevance. Full article
Show Figures

Figure 1

22 pages, 9922 KB  
Article
Virulence and Antimicrobial Resistance Traits of Escherichia coli Retrieved from Fermented Dairy Products During Ramadan in Egypt: Seasonal Public Health Implications
by Fatma Elzhraa, Gabriella Kiskó and Ágnes Belák
Antibiotics 2026, 15(5), 483; https://doi.org/10.3390/antibiotics15050483 - 9 May 2026
Viewed by 376
Abstract
Background: Rayeb milk and yogurt provide lasting energy and maintain hydration during fasting. The surge in demand during Ramadan (the holiest month of the year across the Islamic world) increases production to meet consumer needs, potentially compromising strict adherence to safety standards. Data [...] Read more.
Background: Rayeb milk and yogurt provide lasting energy and maintain hydration during fasting. The surge in demand during Ramadan (the holiest month of the year across the Islamic world) increases production to meet consumer needs, potentially compromising strict adherence to safety standards. Data on the prevalence and characterization of Escherichia coli (E. coli) in fermented dairy products during Ramadan, a model of increased batch turnover, remain to be investigated. Objectives: This study aimed to identify the AMR profile and molecularly characterize the AMR and virulence traits of E. coli isolates prevalent in fermented milk products. Methods: A total of 34 E. coli isolates, representing eight distinct serotypes, were recovered from 150 fermented milk samples; rayeb milk (n = 75) and yogurt (n = 75) collected from densely populated towns in the Dakahlia Governorate, Egypt. Results: The most prevalent serotypes were O153:H2, O125:H21, and O119:H6, followed by O111:H2, O26:H11, and O127:H6. The virulence genes stx1 and stx2 were detected in 76.47% of isolates, while eaeA and hlyA were found in O26:H11, O119:H6, and O55:H7 serotypes. In total, 73.53% (25/34) of E. coli isolates were classified as MDR, while 26.47% (9/34) exhibited XDR. Resistance was most prevalent against penicillin, tetracycline, ciprofloxacin, ampicillin, kanamycin, chloramphenicol, and trimethoprim. The kan, dfrA, blaOXA-1, tetA(A), and van(A) AMR genes were positive in 70.59%, 67.65%, 61.76%, 100%, and 47.06% of isolates, respectively. Conclusions: Identified E. coli AMR and virulence panels reflect that production pressure can challenge strict adherence to hygiene control measures and cold-chain maintenance. Subsequently, authorities must enforce proper quality assurance protocols to minimize the risk of food poisoning. Full article
(This article belongs to the Special Issue Microbial Resistance Surveillance and Management in Food Systems)
Show Figures

Figure 1

13 pages, 763 KB  
Article
Antimicrobial Susceptibility and Characterization of Extended-Spectrum β-Lactamases in Escherichia coli Isolated from Buffalo Mastitis Milk in Guangdong Province, China
by Yunchen Zhou, Rong Xi, Siran Wang, Ban Li, Yue Wu, Chengbo Wen and Dexian Zhang
Microorganisms 2026, 14(5), 1055; https://doi.org/10.3390/microorganisms14051055 - 8 May 2026
Viewed by 383
Abstract
Antimicrobial resistance (AMR) in Escherichia coli (E. coli) from food-producing animals constitutes a substantial public health concern. This study characterized antimicrobial resistance profiles, phylogenetic diversity, virulence-gene distribution, and plasmid-borne extended-spectrum β-lactamase (ESBL) determinants of E. coli isolates recovered from water buffaloes [...] Read more.
Antimicrobial resistance (AMR) in Escherichia coli (E. coli) from food-producing animals constitutes a substantial public health concern. This study characterized antimicrobial resistance profiles, phylogenetic diversity, virulence-gene distribution, and plasmid-borne extended-spectrum β-lactamase (ESBL) determinants of E. coli isolates recovered from water buffaloes with subclinical mastitis. Among the 54 ESBL-producing E. coli isolates, all were resistant to ampicillin and cefotaxime. High resistance rates were also observed for cephalothin (75.9%), trimethoprim–sulfamethoxazole (74.0%), ceftiofur (70.4%), florfenicol (68.5%), and cefazolin (63.0%). Lower resistance was recorded for colistin sulfate (40.7%), enrofloxacin (33.3%), and gentamicin (25.9%). Phylogenetic analysis of ESBL producers identified phylogroup B1 (42.6%) as predominant, followed by groups A (29.6%) and D (25.9%). Multilocus sequence typing (MLST) revealed that ST50 (20.4%) was the most common sequence type, and serogroup O150 was dominant (70.4%). Virulence genes, such as iss (81.5%), astA (59.3%), and espP (38.9%), were frequently detected among ESBL isolates. ESBL genes were predominantly blaCTX-M-1 (27.8%) in all isolates, while the narrow-spectrum β-lactamase genes blaTEM-1 (55.6%) and blaOXA-10 (14.8%) were also commonly co-detected. Bioinformatic analysis predicted that all ESBL genes were associated with plasmid-derived contigs, with the predicted plasmid size ranging from approximately 32 to 187 kb and belonging to IncFIB, IncFIA, IncI1, IncFIA + I1, and IncFII replicon types. Conjugation frequencies ranged from 4.8 × 10−7 to 4.1 × 10−2, and plasmids were predicted to carry additional resistance genes mediating resistance to chloramphenicol (floR), sulfonamides (sul1, sul3), tetracyclines (tet(A) and tet(B)), and trimethoprim (dfrA1, dfrA12). The co-carriage of ESBL genes with additional antimicrobial resistance and virulence determinants suggests the potential role of water buffaloes as reservoirs of clinically relevant resistance traits that may disseminate through horizontal gene transfer. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
Show Figures

Figure 1

21 pages, 2188 KB  
Article
High-Resolution Genomic Surveillance of Carbapenem-Resistant Acinetobacter baumannii: IC-2 Clonal Diversity, Resistance Determinants, and Virulence Signatures
by Arianna Basile, Valentina Antonelli, Claudia Rotondo, Michele Properzi, Francesco Messina, Silvia D’Arezzo, Valentina Dimartino, Ivano Petriccione, Laura Loiacono, Maria Grazia Bocci, Giulia Capecchi, Alessia Arcangeli, Alessandra Marani, Filippo Pasquale Riggio, Massimiliano Lucidi, Francesco Imperi, Paolo Visca and Carla Fontana
Antibiotics 2026, 15(5), 464; https://doi.org/10.3390/antibiotics15050464 - 4 May 2026
Viewed by 717
Abstract
Background/Objectives: Acinetobacter baumannii is a critical opportunistic pathogen causing severe healthcare-associated infections, particularly in intensive care units. The global dissemination of carbapenem-resistant A. baumannii (CRAB) and its environmental persistence necessitate continuous genomic surveillance to monitor high-risk clones. Methods: We conducted whole-genome sequencing [...] Read more.
Background/Objectives: Acinetobacter baumannii is a critical opportunistic pathogen causing severe healthcare-associated infections, particularly in intensive care units. The global dissemination of carbapenem-resistant A. baumannii (CRAB) and its environmental persistence necessitate continuous genomic surveillance to monitor high-risk clones. Methods: We conducted whole-genome sequencing (WGS), core genome multi-locus sequence typing (cgMLST), and phylogenomic analyses on 26 CRAB isolates collected at the National Institute for Infectious Diseases (INMI) “Lazzaro Spallanzani” IRCCS (September 2023–September 2024). Antimicrobial resistance determinants, virulence-related genes, and capsular (KL) and lipooligosaccharide outer core (OCL) loci were characterized by interrogation of comprehensive bioinformatic pipelines. Results: All CRAB isolates displayed an extensively drug-resistant (XDR) phenotype, with a shared resistance pattern to carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and sulfonamides, while being susceptible only to colistin and cefiderocol. The carbapenemase gene blaOXA-23 was detected in all CRAB isolates, together with clone-specific blaOXA-51-like variants. For all isolates, the resistome profile fully matched the observed resistance phenotype. All isolates belonged to the International Clonal Lineage II (ICL II), Pasteur Sequence Type (ST) 2, and Oxford ST369, ST208, and ST455. Integration of cgMLST data with phylogenomic analyses and genome-based classification of KL and OCL loci revealed five distinct clusters, each one including nearly identical isolates, indicating both intra-hospital dissemination and possible inter-hospital transmission. Virulome profiling revealed heterogeneous repertoires of virulence-associated genes, resulting in cluster-specific patterns, while patristic analysis identified phylogenetic clusters linking the study isolates to other Italian and other European lineages. Conclusions: This study underscores the complex genomic landscape of CRAB in our setting, driven by the circulation of different ICL II clonal types, and reinforces the urgency of integrated genomic surveillance and robust antimicrobial stewardship to mitigate the spread of high-risk XDR A. baumannii clones. Full article
(This article belongs to the Special Issue Antibiotic Resistance Genes: Mechanisms, Evolution and Dissemination)
Show Figures

Graphical abstract

9 pages, 1748 KB  
Data Descriptor
Draft Genome Sequence Data of Multidrug-Resistant Pseudomonas aeruginosa, Strain ASK-80
by Shilippreet Kour, Shilpa Sharma, Achhada Ujalkaur Avatsingh, Prem Prashant Chaudhary and Nasib Singh
Data 2026, 11(5), 96; https://doi.org/10.3390/data11050096 - 26 Apr 2026
Cited by 1 | Viewed by 538
Abstract
In this study, we report the draft genome sequence of Pseudomonas aeruginosa strain ASK-80, a multidrug-resistant bacterium isolated from municipal wastewater in Baddi, district Solan, Himachal Pradesh, India. The whole genome was sequenced through Illumina MiSeq sequencing (150 bp paired-end). The size of [...] Read more.
In this study, we report the draft genome sequence of Pseudomonas aeruginosa strain ASK-80, a multidrug-resistant bacterium isolated from municipal wastewater in Baddi, district Solan, Himachal Pradesh, India. The whole genome was sequenced through Illumina MiSeq sequencing (150 bp paired-end). The size of the assembled genome was 6,261,345 bp, and the genome annotation revealed 5834 genes, including 5778 CDSs, 5748 protein-coding genes, 56 RNA genes and 30 pseudo genes. Genomic characterization revealed the occurrence of multiple antibiotic resistance genes (blaOXA-396, blaOXA-486, blaOXA-494, blaPAO, blaPDC-8, aph(3)-IIb, catB7, fosA and others), virulence genes (algB, chpA, clpV1, exsA, flgA, pilB, pvcA, toxA, tse1, and waaA), insertion sequences, transposable elements and phage sequences. This genome data may serve as a valuable resource for comparative genomics of P. aeruginosa and research on the antibiotic resistance surveillance of wastewater. Full article
(This article belongs to the Special Issue Benchmarking Datasets in Bioinformatics, 3rd Edition)
Show Figures

Figure 1

8 pages, 692 KB  
Article
Multiplex Lateral Flow Immunochromatographic Assay Is an Effective Method to Detect Carbapenemases in Non-Susceptible Acinetobacter baumannii
by Ilay Pinto, Talya Finn, Svetlana Paikin and Jonathan Lellouche
J. Clin. Med. 2026, 15(9), 3232; https://doi.org/10.3390/jcm15093232 - 23 Apr 2026
Viewed by 340
Abstract
Objectives: This study evaluated the diagnostic performance of the lateral flow immunochromatographic assay (RESIST-ACINETO, Coris BioConcept) for the rapid detection of the major carbapenemases in Acinetobacter baumannii. Methods: Blood culture isolates collected between 2014 and 2024 with meropenem MIC ≥ 4 mg/L [...] Read more.
Objectives: This study evaluated the diagnostic performance of the lateral flow immunochromatographic assay (RESIST-ACINETO, Coris BioConcept) for the rapid detection of the major carbapenemases in Acinetobacter baumannii. Methods: Blood culture isolates collected between 2014 and 2024 with meropenem MIC ≥ 4 mg/L were retrieved, re-identified by MALDI-TOF MS, and susceptibility was confirmed by broth microdilution. Carbapenemase genes (blaOXA-23, blaOXA-40, blaNDM) were detected using multiplex PCR, which served as the reference standard. All isolates were tested using the RESIST ACINETO assay, and diagnostic accuracy parameters were calculated. Results: A total of 114 isolates were recovered and confirmed as A. baumannii. Among 93 carbapenem-non-susceptible isolates, 97.8% (91/93) were correctly identified by the assay. The test showed 99.1% sensitivity and 99.1% specificity, with most positive results appearing within 3–10 min. Two discrepant results were observed (one false positive, one false negative), while all meropenem-susceptible isolates tested negative. Conclusions: The RESIST ACINETO assay provides rapid, accurate detection of carbapenemases in A. baumannii, significantly reducing turnaround time compared with conventional workflows. Its performance supports integration into routine diagnostics to enhance timely resistance confirmation and infection-control interventions. Full article
Show Figures

Figure 1

Back to TopTop