Search Results (451)

Carbapenem-resistant Enterobacterales (CRE) are a major public health concern, yet genomic data from Bulgaria remain limited. We investigated the genomic epidemiology and genomic characteristics of clinically significant CRE recovered at University Hospital “Lozenetz”, Sofia, between 2022 and 2025. Antimicrobial susceptibility testing, phenotypic carbapenemase characterization, and PCR were combined with whole-genome sequencing of 23 purposively selected isolates chosen to capture temporal, species, carbapenemase, specimen, ward, and resistance-phenotype diversity. The proportion of CRE among all Enterobacterales remained broadly stable over the study period, and Klebsiella pneumoniae was the predominant species throughout. NDM-type carbapenemases were the most frequent overall, although VIM-, KPC-, and OXA-48-like enzymes were also detected. Among the sequenced isolates K. pneumoniae ST6260 (n = 16) was predominant. The remaining isolates included single K. pneumoniae isolates belonging to ST11, ST101, and ST258; two Enterobacter hormaechei ST114; one Proteus mirabilis ST93; and one Providencia stuartii ST46. All ST6260 isolates carried chromosomal blaNDM-5 within a conserved multidrug-resistance module with variable downstream regions, whereas blaOXA-232 was situated on a small ColKP3 plasmid within a defined subcluster. Overall, the data indicate that ST6260 is an emerging hospital-associated multidrug-resistant lineage. Full article

Background/Objectives: Hospital water and wastewater environments are potential reservoirs for antimicrobial resistance genes (ARGs), particularly in high-risk clinical units. This study examined site-specific ARG DNA detection patterns in wet and waste-associated sites of a haematology ward and an intensive care unit (ICU) to identify environmental hotspots that may inform targeted infection prevention and control (IPC) interventions. Methods: A descriptive point-prevalence environmental study was conducted in May 2025 in a tertiary acute-care hospital. Samples were collected after routine cleaning and during usual clinical activity. Real-time PCR assays were used to detect bla_TEM, bla_SHV, bla_CTX-M, bla_OXA-48-like, bla_VIM, bla_NDM, bla_IMP, bla_KPC, and mcr-1. Analytical summaries included samples meeting predefined quality-control criteria. Ct signals were categorised descriptively; Ct values ≤ 40 were considered positive, with Ct values 36–40 classified as very low molecular signals, whereas Ct values > 40 were considered negative. Results: The analytical dataset comprised 60 samples: 31 from haematology and 29 from ICU. At least one included ARG signal was detected in 40/60 samples (66.7%), including 23/31 haematology samples (74.2%) and 17/29 ICU samples (58.6%), bla_TEM (51.7%) and bla_SHV (43.3%) were most frequent. Sink drains showed the broadest multi-gene profiles, especially combinations of ESBL- and carbapenemase-associated genes. Haematology showed broader carbapenemase-associated diversity, whereas ICU detections clustered in patient-room sink drains and sluice-room wastewater infrastructure. Conclusions: ARG DNA signals were unevenly distributed, with sink drains representing most frequently positive sampling sites for multi-gene detection. This molecular, single-timepoint environmental study does not demonstrate viable organisms, colonisation, or transmission; however, point-prevalence environmental assessments may identify wet and wastewater-associated hotspots that can inform targeted IPC interventions against the spread of multidrug-resistant microorganisms. Full article

Background: Bacteria of the genus Providencia are emerging pathogens associated with a wide range of infections, particularly in healthcare settings. In veterinary medicine, infections caused by these organisms are uncommon, and, to date, there have been no reports of carbapenem-resistant Providencia spp. causing infection in companion animals. Methods and Results: This study describes a comprehensive investigation of bacterial endocarditis caused by carbapenem-resistant Providencia rettgeri in a cat, including clinical, imaging, pathological, microbiological, and genomic findings. A 1.5-year-old mixed-breed female cat was admitted to a referral veterinary hospital with an extensive pelvic limb wound and a recent history of laparotomy. During hospitalization, a heart murmur was detected, and echocardiographic examination revealed vegetation-like lesion on the mitral valve. Despite intensive treatment, the patient’s clinical condition progressively deteriorated over a 15-day period, ultimately leading to euthanasia. Necropsy confirmed bacterial endocarditis with evidence of systemic septic embolization. P. rettgeri was isolated from blood collected from both heart ventricles and from an endocardial swab and its identity was confirmed by MALDI-ToF mass spectrometry. Antimicrobial susceptibility testing demonstrated resistance to meropenem. Whole-genome sequencing confirmed the species identification and revealed a Col3M plasmid carrying multiple antimicrobial resistance genes, including the carbapenemase gene bla_NDM-1. Discussion: To the best of our knowledge, this is the first report of carbapenem-resistant Providencia spp. causing infection in a companion animal. This case highlights the emergence of Providencia spp. as potential veterinary pathogens capable of causing severe, invasive and fatal infections. Full article

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide. The growing prevalence of antimicrobial resistance among Enterobacterales, particularly to β-lactam antibiotics, contributes to treatment failures and prolonged hospital stays. This single-center descriptive surveillance study aimed to evaluate the distribution of Enterobacterales recovered from culture-positive urine samples in the Provincial Specialist Hospital in Włocławek, Poland, and to determine the prevalence of β-lactam resistance phenotypes among these isolates. Urine culture results collected between January and December 2025 from all hospital wards and the outpatient urology clinic were retrospectively analyzed in this study, with 1090 positive urine cultures included. For a subset of 85 isolates, microbiological findings were additionally linked with patients’ clinical characteristics. Bacteria of the genus Escherichia were the most frequently isolated (53.8%), followed by Klebsiella (22.9%) and Proteus (14.2%), with the remaining Enterobacterales genera recovered at frequencies ranging from 0.6% to 4.5%. Most isolates presented no detectable β-lactam resistance phenotype; however, resistance mediated by β-lactamase production was observed in some of them. Phenotypic ESBL and AmpC producers accounted for 25.3% and 0.6% of isolates, respectively, whereas phenotypic carbapenemase-producing strains were detected less frequently, with MBL and KPC producers representing 1.4% and 0.3% of isolates, respectively. No clear associations were identified between patient characteristics and the occurrence of specific bacterial isolates or resistance mechanisms, which may be explained by the relatively homogeneous study population, the majority of whom were ≥70 years old (66/85; 77.6%) and had a similar burden of comorbidities. In conclusion, the current level of β-lactam resistance phenotypes among urinary Enterobacterales in our setting can be considered moderate. Nevertheless, continuous surveillance of local urine-derived bacteria and their antimicrobial resistance profiles remains essential for optimizing effective control strategies. Full article

Background/Objectives: The epidemiology of carbapenem-resistant Klebsiella pneumoniae (CR-Kp) in Europe is evolving towards an increasing contribution of metallo-β-lactamases (MBLs). In particular, co-production of New Delhi metallo-β-lactamase (NDM) and OXA-48-like carbapenemases represents a major concern due to limited therapeutic options and epidemic potential. We aimed to describe temporal trends and genomic characteristics of NDM and OXA-48-like co-producing K. pneumoniae within a regional surveillance programme targeting ceftazidime-avibactam (CZA)-resistant carbapenem-resistant Enterobacterales (CRE) in the Latium Region, Italy. Methods: Between January 2019 and December 2025, CZA-resistant CRE isolates were collected through a regional surveillance network. Antimicrobial susceptibility testing and carbapenemase detection were performed, and NDM-producing K. pneumoniae (NDM-Kpn) was analysed by whole-genome sequencing (WGS). Genomic analyses included multi-locus sequence typing, assessment of clonal relatedness, and resistome/virulome profiling. Results: A total of 2752 non-repetitive CZA-resistant CRE were collected. The analysis of CZA-resistant K. pneumoniae isolates submitted to the regional surveillance network showed that the proportion of NDM producers increased markedly from 2023 onwards. In particular, NDM in association with OXA-48-like reached 26.0% in 2024 and 43.6% in 2025, becoming the predominant carbapenemase profile within this selected surveillance population. WGS of 437 NDM-Kpn revealed a structured population dominated by Sequence Type (ST)147 (63.2%), widely disseminated across 24 hospitals and characterised by a predominant NDM-1 variant and OXA-48-like co-producing profile associated with KL10/wzi420 capsular type. A subset of isolates, mainly within the ST147-KL64 subgroup, showed higher virulence scores, indicating a possible convergence of resistance and virulence. Conclusions: Our findings indicate a rapid shift towards NDM-mediated resistance among CZA-resistant K. pneumoniae submitted to the regional surveillance network, with the emergence of NDM and OXA-48-like co-producing isolates associated with a dominant ST147 clone detected across multiple hospitals. These results highlight the urgent need for coordinated genomic surveillance and infection prevention strategies. Full article

Acinetobacter baumannii is a critical WHO priority pathogen due to its multidrug resistance and high mortality in carbapenem-resistant infections. Resistance is predominantly mediated by class D carbapenemase genes bla_OXA-23 and bla_OXA-40, which spread rapidly via horizontal gene transfer in healthcare settings. To address the lack of a rapid assay capable of detecting both blaOXA-23 and blaOXA-40 in a single analytical workflow, we developed a multiplex two-step RPA–CRISPR/Cas12a assay. Since infections caused by strains harboring either gene require identical therapeutic management, their co-detection in a single reaction is clinically justified. Although simultaneous use of two crRNAs within a single CRISPR/Cas12a reaction is often considered technically challenging due to potential inter-crRNA competition, here it advantageously enables dual-target coverage without compromising sensitivity. The assay demonstrated high specificity with no cross-reactivity against a panel of clinically relevant bacterial species, including closely related Acinetobacter spp. Evaluation using genomic DNA extracted from 63 cultured clinical A. baumannii isolates revealed bla_OXA-23 in 19 isolates (30.2%), bla_OXA-40 in 28 (44.4%), and co-carriage of both genes in 9 (14.3%), with at least one resistance gene detected in 60.3% of isolates. The complete workflow was accomplished within 45 min without specialized equipment, offering a rapid, sensitive, and cost-effective solution for point-of-care molecular surveillance of carbapenem-resistant A. baumannii in clinical and resource-limited settings. Full article

Background: The spread of extended-spectrum β-lactamase-producing Klebsiella is an emerging public health concern presenting severe clinical impacts. This problem is particularly severe in developing countries where irrational use of antibiotics makes the treatment of such infections more challenging. Methods: In this cross-sectional study, we investigated antibiotic resistance among clinical Klebsiella pneumoniae isolates from 256 patient specimens from Al-Diwaniyah hospitals, using standard microbiological methods followed by PCR. Antimicrobial susceptibility testing identified resistance rates and proportions of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Carbapenemase genes were detected by multiplex PCR and sequencing. Mutations were characterized, and their functional significance was predicted using in silico prediction tools. Results: Fifty Klebsiella pneumoniae isolates were recovered, exhibiting high resistance rates (42–100%) to penicillins, cephalosporins, fluoroquinolones and carbapenems, with 62% classified as MDR and 38% as XDR. Carbapenemase genes were highly prevalent (blaOXA-48 56%, blaIMP 44%, blaVIM 30%, blaKPC 28%, blaNDM 26%), with 60% of isolates co-harbouring ≥ two genes. Most mutations were predicted to be structurally tolerated, while active-site-proximal substitutions (H120L in NDM-52 and V120L in OXA-48) were predicted to affect enzyme activity. However, docking analysis suggested no significant alteration in carbapenem binding affinity. Conclusions: Our results highlight a very high prevalence of MDR/XDR Klebsiella pneumoniae, associated with diverse carbapenemase genes and resistance-related polymorphisms that may indicate potential functional impacts. To the best of our knowledge, this is the first study in Iraq to combine carbapenemase gene mutation analysis with structural modelling and molecular docking. This study emphasizes the urgent need for effective antimicrobial resistance surveillance in Iraq. Full article

Background: Carbapenem-resistant Enterobacterales (CRE) are a major therapeutic challenge, particularly in settings where metallo-β-lactamases are prevalent. Aztreonam–avibactam (AZA) may provide activity against metallo-β-lactamase-producing isolates, whereas ceftazidime–avibactam (CZA) has limited activity against the isolates that harbor these enzymes. This study aimed to evaluate the in vitro activity of aztreonam–avibactam and ceftazidime–avibactam against invasive carbapenem-resistant Enterobacterales isolates and to characterize the distribution of carbapenemase genes in a tertiary-care center in Türkiye. Methods: A total of 100 non-duplicate CRE isolates recovered from blood cultures and sterile body fluids between January 2024 and January 2026 were included. Species identification and routine antimicrobial susceptibility testing were performed using MALDI-TOF MS and an automated system. CZA and AZA MICs were determined by gradient diffusion testing, whereas CZA–aztreonam synergy was assessed separately using a disk/gradient diffusion-based method. Carbapenemase genes were detected by real-time PCR. Whole-genome sequencing was performed for the two AZA-resistant Escherichia coli isolates. Results: The isolate collection was dominated by Klebsiella pneumoniae (87.0%), and most isolates were recovered from blood cultures (80.0%). CZA susceptibility was observed in 31.0% of isolates, with MIC_50/90 values of 256/256 mg/L. In contrast, AZA showed high in vitro activity, with 98.0% of isolates categorized as susceptible and MIC_50/90 values of 0.25/0.50 mg/L. CZA–aztreonam synergy was detected in 98.0% of isolates. Qualitative CZA–aztreonam synergy testing did not fully concord with direct AZA MIC-based susceptibility categorization: one AZA-resistant isolate showed a positive synergy result, whereas one synergy-negative isolate remained AZA-susceptible. Carbapenemase genes were detected in 99.0% of isolates; bla_NDM was the most frequent gene (81.0%), followed by bla_OXA-48 (72.0%), bla_KPC (14.0%), and bla_VIM (4.0%). The most common carbapenemase profile was bla_NDM + bla_OXA-48 (62.0%). bla_NDM carriage was strongly associated with CZA resistance, and CZA MICs were significantly higher among bla_NDM-positive isolates. The two AZA-resistant E. coli isolates belonged to ST500 and ST410, and both carried a YRIK insertion in PBP3; one of them additionally showed ompF disruption associated with a 4 bp insertion. Conclusions: AZA demonstrated potent in vitro activity against invasive CRE isolates in this setting, whereas CZA activity was substantially limited, likely reflecting the high prevalence of bla_NDM and frequent carbapenemase co-carriage. These findings support the potential value of AZA in regions with emerging metallo-β-lactamase predominance and highlight the importance of local molecular surveillance to guide antimicrobial strategies. Full article

Background: Acinetobacter baumannii is an important opportunistic pathogen responsible for healthcare-associated infections, particularly among critically ill, intensive care unit (ICU), and post-surgical patients. The emergence of carbapenem-resistant A. baumannii (CRAB) has become a major therapeutic challenge worldwide because of its multidrug-resistant nature and limited treatment options. Despite the increasing prevalence of CRAB in Pakistan, information regarding the molecular characterization of carbapenem resistance genes among isolates recovered from surgical site infections (SSIs) remains limited. Methods: A cross-sectional study was conducted from November 2023 to February 2024 at Khalifa Gul Nawaz Hospital, Bannu, Khyber Pakhtunkhwa, Pakistan. A total of (n = 118) surgical wound specimens were collected from patients with clinically diagnosed SSIs. A. baumannii isolates were identified using standard biochemical tests and confirmed by 16S rRNA gene sequencing. In vitro antimicrobial susceptibility was determined by Kirby–Bauer disk diffusion according to CLSI 2024 guidelines. In addition, the concentration-dependent inhibition-zone response of imipenem and meropenem against carbapenem-resistant isolates was evaluated using an agar well diffusion assay. Molecular detection of blaNDM-1 and blaOXA-23 was performed by polymerase chain reaction (PCR), and representative amplicons were subjected to Sanger sequencing for further analysis. Results: In the current study, the total number of (n = 118) wound specimens from healthcare-associated patients were processed, in which A. baumannii-positive isolates (n = 23, 19.5%) were documented. Its prevalence was higher in males (69.6%) compared to females, and was strongly associated (78.2%) with elderly patients (aged 51–68 years). In vitro susceptibility testing revealed that 91.3% of isolates harbored multidrug-resistant (MDR) attributes. Antimicrobial susceptibility profiling revealed high levels of multidrug resistance, with 82.6% of isolates resistant to imipenem and meropenem, as well as 100% resistance to aztreonam and gentamicin. Colistin showed the highest activity, with 87.0% of isolates remaining susceptible. In the agar well diffusion assay, measurable inhibition of the carbapenem-resistant isolates by imipenem and meropenem occurred only at higher concentrations. Molecular screening of resistance genes identified blaOXA-23 in 60.9% and blaNDM-1 in 30.4% of isolates. Co-expression of both genes was detected in some (n = 4) isolates. Among the selected MDR isolates included in the gene resistance analysis, imipenem and meropenem resistance were recorded in 9/14 blaOXA-23-positive isolates and 5/7 blaNDM-1-positive isolates. Conclusions: This study substantiates an escalated incidence of carbapenem-resistant, MDR A. baumannii in post-surgical infections. blaOXA-23 were documented as the predominant carbapenemase gene, with co-expression of blaNDM-1 in a substantial proportion of isolates. These findings provide an important phenotypic and molecular characterization of selected carbapenemase genes in healthcare-associated infections, highlighting the exigency for strengthened antimicrobial stewardship and infection control strategies in the hospitals of the region. Full article

Bovine-associated Klebsiella pneumoniae is an important bacterial species linking animal health, microbial ecology, and One Health-oriented antimicrobial resistance research. In this study, we performed a global genomic analysis of 1291 publicly available bovine-associated K. pneumoniae genomes collected from 18 countries between 2005 and 2024 using data retrieved from NCBI. MLST, core-genome phylogenetic analysis, pangenome analysis, CARD, VFDB, and PlasmidFinder were used to characterize sequence types, genomic diversity, antimicrobial resistance-associated genes, virulence-associated genes, and plasmid replicons. A total of 256 sequence types were identified, among which ST107 was the most common. Core-genome phylogenetic analysis revealed multiple genomic lineages, while pangenome analysis identified 46,325 gene clusters, including 1967 core genes and 40,595 cloud genes, indicating an open pangenome structure and substantial accessory gene diversity. Virulence-associated genes were unevenly distributed, with yagZ/ecpA being the most frequently detected determinant. In total, 138 antimicrobial resistance-associated genes or potential resistance determinants were detected across 16 antimicrobial categories, including clinically important β-lactamase- and carbapenemase-associated genes. IncF-family plasmid replicons, particularly IncFIB(K)_1_Kpn3, were frequently detected, suggesting widespread plasmid replicon-associated genomic backgrounds; however, physical co-localization between resistance genes and specific plasmid backbones could not be confirmed. Overall, this study reveals the genetic diversity, resistance-associated gene reservoir potential, heterogeneity of virulence-associated genes, and plasmid replicon backgrounds of bovine-associated K. pneumoniae. Importantly, the genome-predicted AMR potential identified in this study should not be interpreted as confirmed phenotypic resistance without further experimental validation. These findings provide genomic insights for risk surveillance, candidate control-target screening, and microbiota-oriented intervention research. Full article

Background/Objectives: Klebsiella pneumoniae complex, Escherichia coli, and Enterobacter cloacae complex are considered the most prevalent carbapenemase-producing (CP) Enterobacterales in Spain. However, temporal changes in carbapenemase distribution, clonal diversity, and the mobile genetic elements (MGEs) involved in their dissemination have not been systematically characterised in our region. To address this knowledge gap, this study investigated the epidemiology of these organisms over a seven-year period. Methods: CP Enterobacterales isolates recovered between 2019 and 2025 from rectal screening swabs and clinical specimens (blood, urine, respiratory, wound, and sterile fluid samples) were included. All 297 isolates underwent phenotypic characterisation. Carbapenemase detection and sequence type (ST) assignment were performed for the 282 isolates available for molecular analysis. Following the gradual implementation of long-read whole-genome sequencing (WGS) beginning in 2022, MGEs associated with carbapenemase dissemination were characterised, and selected high-risk clones were analysed by SNP-based phylogenetic analysis. Results: Fifty isolates were recovered from ICU admission rectal screening, and 247 from clinical samples. Although the proportion of CP Enterobacterales among Enterobacterales isolates remained stable throughout the study period, significant changes were observed between 2019 and 2022 and between 2023 and 2025 in carbapenemase types, with a statistically significant increase in metallo-β-lactamases (MBLs) (p < 0.001), as well as in species distribution. Furthermore, predominant plasmid replicons associated with the dissemination of MBL genes were characterised. A K. pneumoniae ST147 clone co-harbouring bla_OXA-48 and bla_NDM-1 emerged and expanded significantly during the study period (p < 0.05). In addition, an ST225 NDM-1 clone was identified. SNP-based phylogenetic analysis revealed distinct genetic clusters within both lineages. Conclusions: Temporal shifts in the epidemiology of CP Enterobacterales, including the emergence and expansion of high-risk clones, were observed. High-resolution genomic analyses provided additional insight into the genetic relationships among circulating lineages. Full article

Unsafe water sources contaminated with fecal bacteria and antibiotic-resistant pathogens represent a critical public health challenge in rapidly urbanizing regions. This study investigates the occurrence, distribution, and antimicrobial resistance (AMR) patterns of Escherichia coli across interconnected water sources in Guwahati, India, including river water, wells, municipal supply, and groundwater. A total of 87 samples were analyzed using membrane filtration, biochemical identification, and automated confirmation, followed by antibiotic susceptibility testing and phenotypic detection of β-lactamase production. Total coliforms were detected in 64.4% of samples, while E. coli was confirmed in 51.7%. According to World Health Organization risk thresholds, 93.3% of river water samples and 50% of groundwater samples fell within the very-high-risk category (>1000 CFU/100 mL), indicating widespread fecal contamination in sources used for domestic purposes. Antibiotic-resistant E. coli was identified across all water types, with 14.1% of isolates exhibiting multidrug resistance (MAR index > 0.2). Notably, 20.6% of isolates produced β-lactamases, including one extended-spectrum β-lactamase (ESBL) producer, while no carbapenemase-producing strains were detected. The co-occurrence of multidrug-resistant E. coli across surface and groundwater systems is consistent with the interconnected nature of urban water contamination and suggests the potential for widespread exposure through drinking water pathways, though direct transfer between water systems was not experimentally confirmed in this study. These findings underscore the urgent need for improved wastewater management, protection of groundwater resources, and strengthened antibiotic stewardship within a One Health framework to mitigate the environmental dissemination of AMR. Full article

Background and objectives: Extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae represent an increasing One Health concern because food-producing animals may act as reservoirs of antimicrobial-resistant bacteria with potential transmission to humans. Therefore, this study aimed to assess the prevalence and genomic characteristics of ESBL- and carbapenemase-producing Enterobacteriaceae in livestock and farmers, and to evaluate genomic overlap between animal and human ESBL-producing Escherichia coli to explore potential shared origins and interspecies transmission. Methods: We conducted a cross-sectional study in Osona (Catalonia, Spain), sampling livestock (swine, cattle, poultry, and horses) and farmers. ESBL-, AmpC-, and carbapenemase-producing Enterobacteriaceae were identified and characterized using whole genome sequencing (WGS). Genomic analyses included sequence typing (ST), serotyping, virulence-associated genes, antimicrobial resistance determinants, and plasmid replicon profiling. Results: A total of 945 animals were analysed. ESBL-producing Enterobacteriaceae were predominantly detected in swine, with 63.5% (127/200) of animals testing positive, including four ESBL + AmpC-producing isolates and two carbapenem-resistant Enterobacteriaceae. No ESBL-, AmpC- or carbapenemase-producing isolates were identified in cattle (0/360) or poultry (0/171), and a low prevalence was observed in horses (7.0%, 15/214). A total of 64 farm workers were analysed. ESBL-producing E. coli were detected in 46.7% (7/15) of swine farmers and 8.3% (2/24) of cattle farmers, while no ESBL-producing isolates were found among poultry farmers (0/8) or equine caretakers (0/17). A total of 162 isolates were analyzed by WGS, showing high genetic diversity. Among the 127 Escherichia coli isolates, the most prevalent were ST10 (18/127, 14.2%), followed by ST453 (7/127, 5.5%), ST515 (7/127, 5.5%), and ST10562 (7/127, 5.5%). Virulence-associated gene profiles were heterogeneous, although genes related to stress tolerance and intestinal colonization predominated among ESBL-producing E. coli isolates from swine, including terC (54/127, 42.5%), csgA (41/127, 32.3%), nlpI (41/127, 32.3%), and fimH (39/127, 30.7%). ESBL production among E. coli isolates from swine was primarily mediated by blaCTX-M genes (89/127, 70.1%), with additional contributions from blaSHV (34/127, 26.8%) and blaTEM (40/127, 31.5%). Among swine isolates, IncX1 (100/127, 78.7%), IncFIB(AP001918) (82/127, 64.6%), IncI1-I(Alpha) (69/127, 54.3%), and IncFII (54/127, 42.5%) were the most frequently detected plasmid replicons. Two carbapenem-resistant isolates carrying blaOXA-48 were identified in swine, including E. coli ST58 and K. oxytoca ST145, both associated with IncL plasmids. Conclusions: Swine appear to constitute the primary reservoir of ESBL-producing E. coli. The genomic relatedness observed between animal and human isolates supports shared exposure to a common ecological pool of multidrug-resistant bacteria. The identification of blaOXA-48-producing Enterobacterales associated with IncL plasmids further highlights the public health relevance of livestock-associated antimicrobial resistance. However, the cross-sectional design precludes inference of transmission pathways or transmission directionality. Longitudinal studies are needed to elucidate the dynamics of interspecies transmission. Full article

Multidrug-resistant (MDR) Klebsiella pneumoniae represents a major clinical and public health challenge worldwide, particularly in regions with limited genomic surveillance. This study investigated the clinical, phenotypic, and genomic characteristics of clinical K. pneumoniae isolates recovered from a tertiary-care hospital in Peshawar, Pakistan. A total of 2400 non-duplicate clinical specimens were processed, and antimicrobial susceptibility testing was performed according to CLSI guidelines. Whole-genome sequencing (WGS) was conducted on a purposively selected subset of 18 isolates representing diverse resistance and phenotypic profiles. Genomic analyses included multilocus sequence typing, resistome and virulome profiling, identification of resistance-associated chromosomal mutations, plasmid replicon typing, and phylogenomic comparison with publicly available international genomes. K. pneumoniae was identified in 256/2400 (10.7%) specimens, predominantly from urine samples. MDR and extensively drug-resistant (XDR) phenotypes were detected in 83.2% and 13.3% of isolates, respectively. WGS revealed substantial genomic heterogeneity, with ST147 identified as the most frequent lineage among sequenced isolates. Extended-spectrum β-lactamase genes, particularly bla_CTX-M-15, together with carbapenemase genes including bla_OXA-48-like and bla_NDM-5, were identified in multiple isolates alongside resistance-associated chromosomal alterations in gyrA, parC, ompK36, mgrB, pmrB, and ramR. Yersiniabactin-associated loci were detected in all sequenced isolates, whereas canonical hypervirulence-associated determinants (rmpA, iuc, iro) were absent. These findings highlight the complex genomic landscape of MDR K. pneumoniae in Pakistan and underscore the need for continued genomic surveillance and antimicrobial stewardship. Full article

Background/Objectives: Urinary tract infections (UTIs) represent the most common infectious complication following kidney transplantation. An increasing number of UTIs are caused by multidrug-resistant organisms (MDROs). The role of intestinal MDRO colonisation in complicated urinary tract infections (cUTIs) among kidney transplant recipients is not fully understood. Methods: We conducted a retrospective, single-centre study of kidney or kidney–pancreas transplant recipients hospitalised for infectious diseases. Each hospitalisation was analysed as a separate event. Routine rectal screening targeted carbapenem-resistant Enterobacterales and vancomycin-resistant/vancomycin-variable enterococci. Results: The study included 65 hospitalisations from 52 kidney transplant recipients, with some patients contributing multiple admissions. cUTIs accounted for 63.1% of admissions, and 22.0% of cUTIs were associated with concomitant bloodstream infection (BSI). The most frequently isolated pathogens were Klebsiella pneumoniae (58.8%) and Escherichia coli (41.2%). Extended-spectrum β-lactamase (ESBL) production was detected in 50% of E. coli isolates, while carbapenemase production was identified in 60% of K. pneumoniae isolates. MDRO rectal carriage was detected in 43.1% of cases and was more frequent in cUTI than in other infections (53.7% vs. 25.0%, p = 0.024). Carbapenemase-producing K. pneumoniae (CP-KP) rectal carriage was also more frequent in cUTI (31.7% vs. 4.2%, p = 0.011), but did not remain statistically significant after adjustment for urinary stent presence (odds ratio 7.1, 95% CI 0.7–66.2; p = 0.087). Nevertheless, CP-KP rectal carriage was associated with CP-KP cUTI aetiology (PPV 75.0%; NPV 86.4%). The median length of hospital stay (LoS) was 15 days. In multivariable analysis, a longer median LoS was associated with BSI (12.2 days; 95% CI: 0.8–23.6; p = 0.037), urinary stent presence (6.8 days; 95% CI: 1.5–12.2; p = 0.014), and older age (2.3 days; 95% CI: 0.7–4.0; p = 0.007). Conclusions: Rectal CP-KP colonisation may represent a potential marker of cUTI risk, although its independent association was not confirmed after adjustment. These findings should be interpreted with caution, given the study design and sample size and require confirmation in larger prospective studies. Rectal screening may contribute to early risk stratification, whereas its role in guiding empirical therapy remains to be prospectively evaluated. Full article