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Keywords = carbapenem-resistant microorganisms

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25 pages, 596 KB  
Review
AmpC β-Lactamase-Producing Microorganisms in South American Hospitals: A Meta-Regression Analysis, Meta-Analysis, and Review of Prevalence
by Valmir Nascimento Rastely-Junior, Hosanea Santos Nascimento Rocha and Mitermayer Galvão Reis
Trop. Med. Infect. Dis. 2025, 10(10), 280; https://doi.org/10.3390/tropicalmed10100280 - 29 Sep 2025
Viewed by 465
Abstract
AmpC β-lactamases are class C enzymes that hydrolyze penicillins, cephalosporins, and monobactams. The WHO recently classified third-generation cephalosporin-resistant and carbapenem-resistant Enterobacterales as critical pathogens. We conducted a systematic review and meta-analysis to evaluate AmpC prevalence in hospital isolates across South America. We searched [...] Read more.
AmpC β-lactamases are class C enzymes that hydrolyze penicillins, cephalosporins, and monobactams. The WHO recently classified third-generation cephalosporin-resistant and carbapenem-resistant Enterobacterales as critical pathogens. We conducted a systematic review and meta-analysis to evaluate AmpC prevalence in hospital isolates across South America. We searched PubMed/MEDLINE, SciELO, and Google Scholar. We included 69 observational studies that phenotypically or genotypically identified AmpC producers. A random-effects generalized linear mixed model with logit transformation estimated pooled prevalence; heterogeneity and moderators were explored through subgroup analyses and meta-regression. Seventy studies, including 48,801 isolates, were eligible. AmpC β-lactamases were detected in 11.7% of isolates (95% CI 11.4–12.0), with extreme heterogeneity (I2 ≈ 97%). Enterobacter species showed the highest prevalence (~46%), whereas Escherichia spp. had the lowest (~4.5%) prevalence of AmpC positivity within each genus. Meta-regression indicated that studies focusing on a single genus reported higher prevalence and that including pediatric patients was associated with a lower prevalence of AmpC-positive microorganisms among isolates. Quality of evidence was rated low due to inconsistency, moderate risk of bias, and indirectness of data. AmpC producers are entrenched in South American hospitals, and species-aware surveillance and harmonized detection are critical to guide empiric therapy and antimicrobial stewardship. Full article
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16 pages, 610 KB  
Article
Characterization of Carbapenem-Resistant Gram-Negative Bacilli Isolates in Multispecialty Private Hospitals in Lagos, Nigeria
by Moruf Salau, Uraiwan Kositanont, Pirom Noisumdaeng, Folasade Ogunsola, Abdul-Wahab Omo-ope Ettu, Damilola Adewojo, Chinonso Ojimma, Omamode Ojomaikre and Kanjana Changkaew
Infect. Dis. Rep. 2025, 17(5), 119; https://doi.org/10.3390/idr17050119 - 21 Sep 2025
Viewed by 310
Abstract
Background/Objectives: Carbapenem-resistant Gram-negative bacilli (CR-GNB) pose a growing challenge to public health worldwide due to limited treatment options. This cross-sectional study investigated the characteristics of CR-GNB isolated from clinical specimens in Lagos, Nigeria. Methods: Gram-negative bacilli (GNB) and clinical data were obtained from [...] Read more.
Background/Objectives: Carbapenem-resistant Gram-negative bacilli (CR-GNB) pose a growing challenge to public health worldwide due to limited treatment options. This cross-sectional study investigated the characteristics of CR-GNB isolated from clinical specimens in Lagos, Nigeria. Methods: Gram-negative bacilli (GNB) and clinical data were obtained from three multi-specialist private hospitals between March and June 2023. The GNB were identified using the Analytical Profile Index (API) and investigated for CR-GNB by disk diffusion. Antimicrobial resistance patterns and carbapenemase gene data for presumptive carbapenemase-producing Gram-negative bacilli (CP-GNB) were analyzed using Vitek-2 and polymerase chain reaction (PCR). Results: Of 317 GNB, 29.0% (n = 92) were CR-GNB. Significantly higher numbers of CR-GNB were reported from the intensive care unit and oncology department (p = 0.009). Of all CR-GNB, 17 isolates (18.5%) were classified as presumptive CP-GNB. In this subgroup, resistance rates of ampicillin/sulbactam (100.0%) and trimethoprim/sulfamethoxazole (100.0%) were highest. Ten (10) CP-GNB were confirmed, representing 3.15% of all GNB tested. Seven isolates of New Delhi Metallo-β-lactamase (blaNDM) were found among P. aeruginosa, K. pneumoniae, E. coli, and A. baumannii. The blaNDM was identified in strains classified as extensively drug-resistant (XDR) and pandrug-resistant. Conversely, the blaKPC was detected solely in multidrug-resistant and XDR strains. Conclusions: Emerging CR-GNB, specifically CP-GNB, in Nigeria emphasize the need for specific therapeutic management of infected patients. Antimicrobial stewardship and long-term surveillance efforts must be implemented in healthcare settings, as well as improved, accelerated microorganism identification techniques. Full article
(This article belongs to the Section Antimicrobial Stewardship and Resistance)
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26 pages, 748 KB  
Article
Beyond Culture: Real-Time PCR Performance in Detecting Causative Pathogens and Key Antibiotic Resistance Genes in Hospital-Acquired Pneumonia
by Lana Hani Abu Khadija, Shatha M. Alomari, Ahmad R. Alsayed, Heba A. Khader, Andi Dian Permana, Luai Z. Hasoun, Manar Saleh Zraikat, Walaa Ashran and Malek Zihlif
Antibiotics 2025, 14(9), 937; https://doi.org/10.3390/antibiotics14090937 - 17 Sep 2025
Viewed by 1105
Abstract
Introduction: The rise in hospital-acquired pneumonia (HAP) due to antibiotic-resistant bacteria is increasing morbidity, mortality, and inappropriate empirical antibiotic use. This prospective research aimed to evaluate the performance of a real-time polymerase chain reaction (PCR) assay for detecting causative microorganisms and antibiotic-resistance genes [...] Read more.
Introduction: The rise in hospital-acquired pneumonia (HAP) due to antibiotic-resistant bacteria is increasing morbidity, mortality, and inappropriate empirical antibiotic use. This prospective research aimed to evaluate the performance of a real-time polymerase chain reaction (PCR) assay for detecting causative microorganisms and antibiotic-resistance genes from respiratory specimens compared to traditional methods. Additionally, we aimed to determine the molecular epidemiology of antibiotic resistance genes among HAP patients at The University of Jordan hospital. Methods: Lower respiratory tract samples were collected from HAP patients, including those with ventilator-associated pneumonia (VAP), between May 2024 and October 2024. Clinical data from the medical files were used to collect and analyze demographic and clinical information, including clinical outcomes. Real-time PCR was run to detect causative microbes and antibiotic resistance genes. Results: Among 83 HAP patients (median age 63, 61.45% male), 48.15% died. Culture identified Klebsiella (25.53%), Acinetobacter (22.34%), and Candida (24.47%) as the most common pathogens, while qPCR showed higher detection rates, including for A. baumannii (62.20%, p = 0.02) and K. pneumoniae (45.12%, p < 0.001). Carbapenem resistance was high; A. baumannii showed 100% resistance to most antibiotics except colistin (92.31%). The resistance genes ndm (60%) and oxa-48 (58.46%) were frequently detected and significantly associated with phenotypic resistance (p < 0.001). The qPCR identified resistance genes in all carbapenem-resistant cases. No gene significantly predicted mortality. Conclusions: Real-time PCR diagnostic technique combined with epidemiology of antibiotic resistance genes data may be a rapid and effective tool to improve HAP management. Large, multicenter studies are needed in the future to validate the performance of real-time PCR in HAP diagnosis, and appropriate management is also required. Full article
(This article belongs to the Special Issue Antibiotic Therapy in Respiratory Tract Infections (RTIs))
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21 pages, 888 KB  
Article
Assessment of Factors Contributing to Multidrug Resistance in Urinary Tract Infections: Focus on Carbapenem Resistance
by Carina Alexandra Bandac, Constantin Ristescu, Pavel Onofrei, Ionela-Larisa Miftode, Rodica Radu, Vasile Lucian Boiculese, Ana-Maria Raluca Pauna, Theodor Florin Pantilimonescu, Andreea Luduşanu and Viorel Dragoș Radu
Antibiotics 2025, 14(9), 918; https://doi.org/10.3390/antibiotics14090918 - 11 Sep 2025
Viewed by 610
Abstract
Introduction: Urinary tract infections (UTIs) caused by carbapenem-resistant pathogens are increasingly common and pose serious treatment challenges due to limited antibiotic options and high complication rates. Identifying patients at risk is essential for guiding empirical therapy and improving outcomes. The primary objective of [...] Read more.
Introduction: Urinary tract infections (UTIs) caused by carbapenem-resistant pathogens are increasingly common and pose serious treatment challenges due to limited antibiotic options and high complication rates. Identifying patients at risk is essential for guiding empirical therapy and improving outcomes. The primary objective of this study was to identify risk factors associated with carbapenem-resistant (CR) UTIs by comparing them with carbapenem-susceptible (CS) UTIs. Secondary objectives included analyzing the types of microorganisms involved in both groups, their antibiotic susceptibility profiles, and the presence of carbapenemase enzymes among CR UTI cases. Method: We conducted a retrospective case-control study involving 127 hospitalized patients with UTIs caused by CR microorganisms and 91 patients with UTIs caused by multidrug-resistant (MDR) strains that retain susceptibility to carbapenems, admitted between 1 October 2023, and 31 March 2025. Results: In univariate analysis, CR UTI patients had significantly higher rates of neoplasia, neurological disorders, urosepsis at admission, septic shock, the presence of urinary catheters at diagnosis, permanent nephrostomy catheters, hospitalizations within the past 180 days, previous antibiotic exposure including carbapenems, and recent urological procedures. Multivariate analysis revealed four independent risk factors for CR UTIs: neoplasia (OR = 2.152; 95% CI: 1.044–4.436; p = 0.038), neurological disorders (OR = 7.427; 95% CI: 2.804–19.674; p < 0.0001), antibiotic use in the previous 180 days (OR = 2.792; 95% CI: 1.487–5.396; p = 0.001), and prior carbapenem treatment OR = 10.313; 95% CI: 1.277–83.248; p = 0.029). Most of the isolated organisms belonged to the Enterobacterales genus, with Klebsiella spp. and Pseudomonas aeruginosa being the most common pathogens in CR UTIs, accounting for over 90% of cases. Among patients tested for carbapenemase production, all but one tested positive for at least one carbapenemase. Conclusions: Neoplasia, neurological disorders, recent antibiotic therapy, and prior carbapenem use were significantly associated with increased risk of developing CR UTIs. Klebsiella spp. and Pseudomonas aeruginosa were the predominant causative organisms, with New Delhi metallo-β-lactamase (NDM) and Klebsiella pneumoniae carbapenemase (KPC) being the most frequently identified resistance mechanisms. Full article
(This article belongs to the Special Issue Antibiotic Resistance in Hospital-Acquired Infections)
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11 pages, 714 KB  
Article
Active Microbiological Surveillance for Contrasting Multi-Drug-Resistant Pathogens: Comparison Between a Multiplex Real-Time PCR Method and Culture
by Gaetano Maugeri, Maddalena Calvo, Guido Scalia and Stefania Stefani
Diagnostics 2025, 15(17), 2128; https://doi.org/10.3390/diagnostics15172128 - 22 Aug 2025
Viewed by 608
Abstract
Background/Objectives. Multi-drug-resistant (MDR) microorganisms pose a significant challenge in healthcare settings, particularly with beta-lactam-resistant Gram-negative bacteria and glycopeptide-resistant enterococci. Culture represents the most reliable technique in determining their presence within surveillance swabs. However, it requires a long time-to-result (TTR) and shows low [...] Read more.
Background/Objectives. Multi-drug-resistant (MDR) microorganisms pose a significant challenge in healthcare settings, particularly with beta-lactam-resistant Gram-negative bacteria and glycopeptide-resistant enterococci. Culture represents the most reliable technique in determining their presence within surveillance swabs. However, it requires a long time-to-result (TTR) and shows low sensitivity. Molecular techniques integrate diagnostic procedures, allowing TTR reduction and precise identification of genes. Methods. During our usual surveillance campaign, we had the opportunity to evaluate the Allplex Entero-DR assay (Seegene Inc., Seoul, Republic of Korea) and the Entero-DR Plus assay (Arrow Diagnostics srl, Genova, Italy) molecular kits for the detection of extended-β-lactamases (ESBL), carbapenem- and vancomycin-resistant genes, as well as Acinetobacter spp. and Pseudomonas aeruginosa spp. identification directly from rectal swabs. A comparison between these tests and the culture-based routine completed the study. Results. The analysis included 300 rectal swabs from the University Hospital Policlinico (Catania, Italy). One hundred and eighty-eight samples (62.6%) resulted as positive for at least one Allplex™ target, reaching optimal sensitivity and negative predictive value (100%). Our results underlined the ubiquitous blaCTX-M and van genes presence and demonstrated the diffusion of double-carbapenemases genes and metallo-β-lactamases-producing strains. In our epidemiological setting, few data were collected about carbapenem-resistant P. aeruginosa and Acinetobacter spp., which require further evaluations on simultaneous respiratory colonization and higher sample numbers. Conclusions. Our analysis highlighted the importance of combining conventional and advanced diagnostic methods in investigating MDR pathogens. The right approach should be based on the prevalence and variability of resistance mechanisms within a specific epidemiological area. Remarkably, molecular screenings may exclude negative samples within high-risk areas due to a significant negative predictive value. Full article
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13 pages, 988 KB  
Article
Identification and Genomic Characterization of Aeromonas dhakensis from a Human Sample
by David Badenas-Alzugaray, Alexander Tristancho-Baró, Juan Manuel García-Lechuz, Natalia Burillo-Navarrete, Sara Sanz-Sanz, Ana María Milagro-Beamonte, Ana Isabel López-Calleja and Antonio Rezusta-López
Acta Microbiol. Hell. 2025, 70(3), 34; https://doi.org/10.3390/amh70030034 - 15 Aug 2025
Viewed by 579
Abstract
Aeromonas is a genus of Gram-negative, facultatively anaerobic bacteria commonly found in aquatic environments and increasingly recognized as opportunistic pathogens. Among them, Aeromonas dhakensis stands out for its high virulence and antimicrobial resistance, but it is often misidentified due to its phenotypic similarity [...] Read more.
Aeromonas is a genus of Gram-negative, facultatively anaerobic bacteria commonly found in aquatic environments and increasingly recognized as opportunistic pathogens. Among them, Aeromonas dhakensis stands out for its high virulence and antimicrobial resistance, but it is often misidentified due to its phenotypic similarity with A. hydrophila and A. caviae. In this study, a microorganism was isolated from the peritoneal fluid of a patient with signs of intra-abdominal infection. MALDI-TOF MS initially suggested A. hydrophila or A. caviae, but the identification was confirmed with high confidence only after further molecular analyses and the use of genome-based tools, which identified the organism as A. dhakensis. This was further supported by phylogenomic and ANI analysis. Resistome analysis revealed intrinsic resistance genes, including a chromosomal class C β-lactamase and an imiH-type carbapenemase, consistent with the observed carbapenem resistance. No plasmid-mediated carbapenemases were found. These findings underscore the limitations of MALDI-TOF in identifying Aeromonas species in certain cases and highlight the value of genomic approaches for accurate species determination and resistance profiling, especially for isolates from sterile body fluids. Full article
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20 pages, 869 KB  
Article
Clinical Impact of New Delhi Metallo-Beta-Lactamase-Producing Enterobacterales in Critically Ill Patients: Are We Ready to Face the Challenge?
by Giorgia Montrucchio, Silvia Corcione, Lara Rodigari, Denisa Barganou, Chiara Risso, Riccardo Traversi, Gabriele Sales, Marco Ellena, Andrea Costamagna, Nour Shbaklo, Cecilia Grosso, Carlo Silvestre, Anna Chiara Trompeo, Vito Fanelli, Antonio Curtoni, Cristina Costa, Francesco Giuseppe De Rosa and Luca Brazzi
J. Clin. Med. 2025, 14(16), 5688; https://doi.org/10.3390/jcm14165688 - 12 Aug 2025
Viewed by 677
Abstract
Background: Carbapenem-resistant Enterobacterales infections are frequent in critically ill patients. Outbreaks caused by carbapenemase-producing Enterobacterales, in particular the New Delhi Metallo-beta-lactamase (NDM)-type carbapenemase-producing phenotype, are increasing in Italy. Unfortunately, the clinical impact of this new microorganism is still being defined, as well [...] Read more.
Background: Carbapenem-resistant Enterobacterales infections are frequent in critically ill patients. Outbreaks caused by carbapenemase-producing Enterobacterales, in particular the New Delhi Metallo-beta-lactamase (NDM)-type carbapenemase-producing phenotype, are increasing in Italy. Unfortunately, the clinical impact of this new microorganism is still being defined, as well as the correlation between colonization and invasive infections. The aim of the study is to analyze factors related to the development of NDM infections in colonized patients and to evaluate their impact on patients’ outcome in high-complexity ICUs. Methods: All patients admitted to the General and Cardiac ICUs of ‘Città della Salute e della Scienza’ University Hospital in Turin (Italy) between January and August 2023 were enrolled. Microorganisms were examined by lateral flow immunochromatographic assays or molecular assays on weekly surveillance or clinically requested cultures. Antimicrobial susceptibility was determined by broth microdilution methods and interpreted according to EUCAST breakpoints. Results: Out of a total of 915 patients, 46 (5%) were positive for NDM-producing Enterobacterales and, among them, 13 (28%) developed an invasive infection. All patients were critical (SAPS II 40+/−13). The median times between ICU admission and colonization or infection were 6 and 16 days, respectively. Significant disparities emerged between colonized and infected patients regarding days of mechanical ventilation (1 vs. 28), ICU (7 vs. 39 days), and in-hospital (21 vs. 71 days) length of stay. Renal replacement treatment (OR 8.2461, p = 0.0173, 95% CI [1.3636–65.9114]) and surgery (OR 22.8747, p = 0.0149, CI95% [1.5986–1447.743]) seemed to impact the risk of developing infection. Six patients with invasive infection were treated with Cefiderocol and five with Ceftazidime/Avibactam and Aztreonam. In absence of early identification and appropriate treatment, patients may be at increased risk of colonization spread and potentially worse clinical outcomes. Conclusions: Early identification of the carbapenemase type is clinically relevant in critically ill patients with confirmed or suspected infection, as NDM production necessitates the use of specific agents for effective treatment. Full article
(This article belongs to the Special Issue Key Advances in the Treatment of the Critically Ill: 3rd Edition)
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11 pages, 239 KB  
Article
Carbapenem-Resistant Enterobacteriaceae (CRE) in Children with Cancer: The Impact of Rapid Diagnostics and Targeted Colonization Strategies on Improving Outcomes
by Youssef Madney, Sally Mahfouz, Ahmed Bayoumi, Omayma Hassanain, Omneya Hassanain, Ahmed A. Sayed, Deena Jalal, Maryam Lotfi, May Tolba, Ghada A. Ziad, Mervat Elanany, Mohamed Hashem, Gehad Taha, Lobna Shalaby and Alaa Elhaddad
Microorganisms 2025, 13(7), 1627; https://doi.org/10.3390/microorganisms13071627 - 10 Jul 2025
Viewed by 1957
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) pose an emerging threat, with a high mortality rate among children with cancer. This study aimed to evaluate the impact of routine rectal swab surveillance and rapid PCR-based detection of carbapenemase genes to facilitate the early initiation of appropriate treatment [...] Read more.
Carbapenem-resistant Enterobacteriaceae (CRE) pose an emerging threat, with a high mortality rate among children with cancer. This study aimed to evaluate the impact of routine rectal swab surveillance and rapid PCR-based detection of carbapenemase genes to facilitate the early initiation of appropriate treatment and assess its effects on outcomes. The study compared two groups of pediatric cancer patients with CRE bloodstream infections: a retrospective cohort of 254 patients from 2013 to 2017, and a prospective cohort of 186 patients from 2020 to 2022, following the implementation of these tools. A rapid diagnostic test in the prospective cohort resulted in the early initiation of proper antibiotics in 85% (165/186) of patients, compared to only 58% (147/254) in the retrospective group. This led to a decrease in the need for ICU admission related to sepsis from CRE and a significant reduction in the 30-day mortality rate (16% vs. 30%, p ≤ 0.01). Genotypic profiling revealed that class B carbapenemases were the most prevalent (69%), with the NDM type being identified in 67% of patients. OXA-48 and KPC enzymes were detected in 59% and 4% of patients, respectively. Multivariate analysis revealed that patients having Klebsiella pneumoniae, NDM genotype carbapenemases, presence of pneumonia, and septic shock requiring ICU admission were predictors of poor outcomes. Rapid diagnostics and targeted colonization lead to the appropriate use of targeted antibiotics, resulting in improved patient outcomes. Understanding carbapenemase-producing microorganisms and administering newer antibiotics may further reduce mortality and enhance treatment strategies for high-risk patients. Full article
(This article belongs to the Special Issue Antimicrobial Resistance: Challenges and Innovative Solutions)
15 pages, 916 KB  
Article
Carbapenem-Resistant Gram-Negative Bacteria in Hospitalized Patients: A Five-Year Surveillance in Italy
by Marcello Guido, Antonella Zizza, Raffaella Sedile, Milva Nuzzo, Laura Isabella Lupo and Pierfrancesco Grima
Infect. Dis. Rep. 2025, 17(4), 76; https://doi.org/10.3390/idr17040076 - 2 Jul 2025
Viewed by 622
Abstract
Background/Objectives: Antibiotic resistance is a significant and escalating challenge that limits available therapeutic options. This issue is further exacerbated by the decreasing number of new antibiotics being developed. Our study aims to describe the epidemiology and pattern of antibiotic resistance in Gram-negative [...] Read more.
Background/Objectives: Antibiotic resistance is a significant and escalating challenge that limits available therapeutic options. This issue is further exacerbated by the decreasing number of new antibiotics being developed. Our study aims to describe the epidemiology and pattern of antibiotic resistance in Gram-negative infections isolated from a cohort of hospitalized patients and to analyze the distribution of infections within the hospital setting. Methods: A retrospective study was conducted on all patients admitted to Vito Fazzi Hospital in Lecce, Italy, who required an infectious disease consultation due to the isolation of Gram-negative bacteria from 1 January 2018 to 31 December 2022. Results: During the study period, 402 isolates obtained from 382 patients (240 men and 142 women) with infections caused by Gram-negative bacteria were identified. Among these isolated, 226 exhibited multidrug resistance, defined as resistance to at least one antimicrobial agent from three or more different classes. In 2018, the percentage of multidrug-resistant isolates peaked at 87.6%, before decreasing to the lowest level (66.2%) in 2021. Overall, of the 402 isolates, 154 (38.3%) displayed resistance to carbapenems, while 73 (18.1%) were resistant to extended-spectrum beta-lactamases (ESBLs). Among the resistant microorganisms, Klebsiella pneumoniae showed the highest resistance to carbapenems, accounting for 85.2% of all resistant strains. Escherichia coli exhibited the greatest resistance to ESBLs, with a rate of 86.7%. Among carbapenem-resistant K. pneumoniae isolates, the following resistance rates were observed: KPC-1 at 98.2%, IMP-1 at 0.9%, VIM-1 at 0.9%, and NDM-1 at 0.9%. Conclusions: Patients with infections caused by multidrug-resistant bacteria have limited treatment options and are therefore at an increased risk of death, complications, and longer hospital stays. Rapid diagnostic techniques and antimicrobial stewardship programs—especially for ESBLs and carbapenemases—can significantly shorten the time needed to identify the infection and initiate appropriate antimicrobial therapy compared to traditional methods. Additionally, enhancing surveillance of antimicrobial resistance within populations is crucial to address this emerging public health challenge. Full article
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14 pages, 1541 KB  
Article
First Report in the Americas of S. enterica Var. Enteritidis Carrying blaNDM-1 in a Putatively New Sub-Lineage of IncC2 Plasmids
by Nicolás F. Cordeiro, Romina Papa-Ezdra, Germán Traglia, Inés Bado, Virginia García-Fulgueiras, María N. Cortinas, Leticia Caiata, Mariana López-Vega, Ana Otero, Martín López, Patricia Hitateguy, Cristina Mogdasy and Rafael Vignoli
Antibiotics 2025, 14(6), 620; https://doi.org/10.3390/antibiotics14060620 - 18 Jun 2025
Viewed by 756
Abstract
Background: Infections caused by carbapenem-resistant Enterobacterales have steadily multiplied over time, becoming a major threat to healthcare systems due to limited therapeutic options and high case-fatality rates. Case report: We studied a patient who, after being discharged from an ICU, developed salmonellosis caused [...] Read more.
Background: Infections caused by carbapenem-resistant Enterobacterales have steadily multiplied over time, becoming a major threat to healthcare systems due to limited therapeutic options and high case-fatality rates. Case report: We studied a patient who, after being discharged from an ICU, developed salmonellosis caused by an antibiotic-susceptible S. enteritidis. After undergoing treatment with ciprofloxacin, the patient presented an episode of asymptomatic bacteriuria originated by a carbapenem and ciprofloxacin-resistant S. enteritidis. Results: Whole genome sequencing analysis revealed that both Salmonella isolates belonged to the same strain, and that isolate SEn_T2 acquired a plasmid carrying both blaNDM-1 and qnrA1 genes (pIncCSEn) which was previously present in the patient’s gut in at least one Enterobacter cloacae isolate. Additionally, pIncCSEN was identified as a putatively new sub-lineage of IncC2 plasmids which lacked the first copy of the methyltransferase gene dcm and the rhs gene. The resistance genes blaNDM-1 and qnrA1 were incorporated into a Tn21-derived transposon that included a complex class 1 integron whose genetic arrangement was: intI1- dfrA12- orfF- aadA2- qacEΔ1-sul1-ISCR1- trpF- ble- blaNDM-1 (in reverse direction)- ISAba125-ISCR1- qnrA- cmlA1- qacEΔ1-sul1. Conclusions: Antimicrobial persistence and co-selection of antibiotic resistance play an important role in the dissemination of antimicrobial resistance genes; in this regard, a joint effort involving the infection control team, effective antibiotic stewardship, and genomic surveillance could help mitigate the spread of these multidrug resistant microorganisms. Full article
(This article belongs to the Special Issue Multidrug-Resistance Patterns in Infectious Pathogens)
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25 pages, 1428 KB  
Article
Incidence and Risk Factors of Secondary Infections in Critically Ill SARS-CoV-2 Patients: A Retrospective Study in an Intensive Care Unit
by Mircea Stoian, Leonard Azamfirei, Adina Andone, Anca-Meda Văsieșiu, Andrei Stîngaciu, Adina Huțanu, Sergio Rareș Bândilă, Daniela Dobru, Andrei Manea and Adina Stoian
Biomedicines 2025, 13(6), 1333; https://doi.org/10.3390/biomedicines13061333 - 29 May 2025
Cited by 1 | Viewed by 1011
Abstract
Background/Objectives: The clinical forms of coronavirus disease 2019 (COVID-19) vary widely in severity, ranging from asymptomatic or moderate cases to severe pneumonia that can lead to acute respiratory failure, acute respiratory distress syndrome, multiple organ dysfunction syndrome, and death. Our main objective [...] Read more.
Background/Objectives: The clinical forms of coronavirus disease 2019 (COVID-19) vary widely in severity, ranging from asymptomatic or moderate cases to severe pneumonia that can lead to acute respiratory failure, acute respiratory distress syndrome, multiple organ dysfunction syndrome, and death. Our main objective was to determine the prevalence of bacterial and fungal secondary infections in an intensive care unit (ICU). Secondary objectives included analyzing the impact of these infections on mortality and medical resource utilization, as well as assessing antimicrobial resistance in this context. Methods: We conducted a retrospective cohort study that included critically ill severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients treated in an ICU and analyzed the prevalence of co-infections and superinfections. Results: A multivariate analysis of mortality found that the presence of superinfections increased the odds of death by more than 15-fold, while the Sequential Organ Failure Assessment (SOFA) score and C-reactive protein (adjusted for confounders) increased the odds of mortality by 51% and 13%, respectively. The antibiotic resistance profile of microorganisms indicated a high prevalence of resistant strains. Carbapenems, glycopeptides, and oxazolidinones were the most frequently used classes of antibiotics. Among patients, 27.9% received a single antibiotic, 47.5% received two from different classes, and 24.4% were treated with three or more. Conclusions: The incidence and spectrum of bacterial and fungal superinfections are higher in critically ill ICU patients, leading to worse outcomes in COVID-19 cases. Multidrug-resistant pathogens present significant challenges for ICU and public health settings. Early screening, accurate diagnosis, and minimal use of invasive devices are essential to reduce risks and improve patient outcomes. Full article
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15 pages, 522 KB  
Article
Antibiotic Resistance and Mortality in ICU Patients: A Retrospective Analysis of First Culture Growth Results
by Metin Kilinc
Antibiotics 2025, 14(3), 290; https://doi.org/10.3390/antibiotics14030290 - 11 Mar 2025
Cited by 6 | Viewed by 2960
Abstract
Objectives: This study aimed to analyze the antibiotic resistance patterns of microorganisms isolated from intensive care unit (ICU) patients and evaluate their impact on mortality and length of ICU stay. Given the increasing prevalence of multidrug-resistant (MDR) pathogens in critically ill patients, understanding [...] Read more.
Objectives: This study aimed to analyze the antibiotic resistance patterns of microorganisms isolated from intensive care unit (ICU) patients and evaluate their impact on mortality and length of ICU stay. Given the increasing prevalence of multidrug-resistant (MDR) pathogens in critically ill patients, understanding their resistance profiles is crucial for optimizing empirical antibiotic therapy and improving patient outcomes. Methods: This retrospective study included 237 ICU patients admitted between 1 July 2022, and 1 January 2024. The initial culture growth results from blood and urine samples were analyzed. Microorganism identification was performed using VITEK 2 Compact and conventional bacteriological methods, while antibiotic susceptibility testing followed CLSI 2022 and EUCAST 2022 guidelines. Results: A total of 237 ICU patients were included in this study. The most frequently isolated microorganisms were Escherichia coli (E. coli) (44.3%), Klebsiella pneumoniae (K. pneumoniae) (35.0%), and Pseudomonas aeruginosa (P. aeruginosa) (25.3%), with Acinetobacter baumannii (A. baumannii) (31.2%) being the most resistant pathogen. Among Gram-positive bacteria, methicillin-resistant Staphylococcus aureus (MRSA) (12.2%) and vancomycin-resistant enterococci (VRE) (21.5%) were the most frequently identified multidrug-resistant (MDR) pathogens. Regarding antimicrobial resistance, carbapenem resistance was highest in A. baumannii (55%), followed by P. aeruginosa (40%) and K. pneumoniae (30%). Additionally, ESBL-producing E. coli (43.2%) and K. pneumoniae (38.5%), as well as carbapenemase-producing K. pneumoniae (18.6%) and E. coli (9.2%), were identified as key resistance mechanisms impacting clinical outcomes. Patients with MDR infections had significantly longer ICU stays (p < 0.05) and higher mortality rates. The Kaplan–Meier survival analysis revealed that A. baumannii infections were associated with the highest mortality risk (HR: 4.6, p < 0.001), followed by MRSA (HR: 3.5, p = 0.005) and P. aeruginosa (HR: 2.8, p = 0.01). Among laboratory biomarkers, elevated procalcitonin (≥2 ng/mL, OR: 2.8, p = 0.008) and CRP (≥100 mg/L, OR: 2.2, p = 0.01) were significantly associated with ICU mortality. Additionally, patients who remained in the ICU for more than seven days had a 1.4-fold increased risk of mortality (p = 0.02), further emphasizing the impact of prolonged hospitalization on adverse outcomes. Conclusions: MDR pathogens, particularly A. baumannii, MRSA, P. aeruginosa, and K. pneumoniae, are associated with longer ICU stays and higher mortality rates. Carbapenem, cephalosporin, fluoroquinolone, and aminoglycoside resistance significantly impact clinical outcomes, emphasizing the urgent need for antimicrobial stewardship programs. ESBL, p-AmpC, and carbapenemase-producing Enterobacterales further worsen patient outcomes, highlighting the need for early infection control strategies and optimized empirical antibiotic selection. Biomarkers such as procalcitonin and CRP, alongside clinical severity scores, serve as valuable prognostic tools for ICU mortality. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Therapy in Intensive Care Unit)
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15 pages, 802 KB  
Article
Seasonal Change in Microbial Diversity: Bile Microbiota and Antibiotics Resistance in Patients with Bilio-Pancreatic Tumors: A Retrospective Monocentric Study (2010–2020)
by Paola Di Carlo, Nicola Serra, Consolato Maria Sergi, Francesca Toia, Emanuele Battaglia, Teresa Maria Assunta Fasciana, Vito Rodolico, Anna Giammanco, Giuseppe Salamone, Adriana Cordova, Angela Capuano, Giovanni Francesco Spatola, Ginevra Malta and Antonio Cascio
Antibiotics 2025, 14(3), 283; https://doi.org/10.3390/antibiotics14030283 - 9 Mar 2025
Viewed by 1423
Abstract
Background: Bilio-pancreatic tumors are a severe form of cancer with a high rate of associated mortality. These patients showed the presence of bacteria such as Escherichia coli and Pseudomonas spp. in the bile-pancreatic tract. Therefore, efficient antibiotic therapy is essential to reduce bacterial [...] Read more.
Background: Bilio-pancreatic tumors are a severe form of cancer with a high rate of associated mortality. These patients showed the presence of bacteria such as Escherichia coli and Pseudomonas spp. in the bile-pancreatic tract. Therefore, efficient antibiotic therapy is essential to reduce bacterial resistance and adverse events in cancer patients. Recent studies on the seasonality of infectious diseases may aid in developing effective preventive measures. This study examines the seasonal impact on the bile microbiota composition and the antibiotic resistance of its microorganisms in patients with hepato-pancreatic-biliary cancer. Methods: We retrospectively evaluated the effect of the seasonally from 149 strains isolated by 90 Italian patients with a positive culture of bile samples collected through endoscopic retrograde cholangiopancreatography between 2010 and 2020. Results: Across all seasons, the most frequently found bacteria were E. coli, Pseudomonas spp., and Enterococcus spp. Regarding antibiotic resistance, bacteria showed the highest resistance to 3GC, fluoroquinolones, aminoglycosides, fosfomycin, and piperacillin-tazobactam in the summer and the lowest resistance in the spring, except for carbapenems and colistin. Conclusions: Antibiotic resistance has negative effects in cancer patients who rely on antibiotics to prevent and treat infections. Knowing whether bacterial and fungal resistance changes with the seasons is key information to define adequate and more effective antibiotic therapy. Full article
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11 pages, 1500 KB  
Article
Impact of Antibiotic Therapy with Ceftazidime Avibactam vs. Best Available Therapy in Adult Patients with Bacteremia Caused by Carbapenem-Resistant Enterobacterales
by Daniel Arboleda, Camilo Buitrago, Erika Paola Vergara, Laura Cristina Nocua-Báez, Carlos Humberto Saavedra and Jorge Alberto Cortés
Antibiotics 2025, 14(3), 226; https://doi.org/10.3390/antibiotics14030226 - 24 Feb 2025
Viewed by 1616
Abstract
Background/Objectives: Carbapenem-resistant Enterobacterales (CRE) infection is associated with a higher mortality rate. The purpose of this study was to evaluate the effect of ceftazidime avibactam (CZA) for treating bacteremia caused by CRE compared to the best available therapy in an area where these [...] Read more.
Background/Objectives: Carbapenem-resistant Enterobacterales (CRE) infection is associated with a higher mortality rate. The purpose of this study was to evaluate the effect of ceftazidime avibactam (CZA) for treating bacteremia caused by CRE compared to the best available therapy in an area where these microorganisms are endemic. Methods: A retrospective cohort study of patients with CRE bacteremia was conducted. We included adults with CRE bacteremia who were treated with CZA or the best available therapy (BAT) for more than 48 h, and the hospitalization time was recorded. The outcomes included death during hospitalization, relapse, and microbiological cure. Confounders were adjusted using propensity score-derived stabilized inverse probability of treatment weighting (IPTW). Results: A total of 169 patients with CRE bacteremia were included. About 72.6% of isolates had a class A serin carbapenamase, and 20.4% had metallo-β-lactamase co-production. A total of 107 patients were treated with CZA, 63% in monotherapy and 32% with aztreonam (ATM). Crude mortality during hospitalization was 36 (34.5%) in patients treated with CZA and 21 (33.2%) with BAT. No difference was observed between death rates (HR 0.86: IC 95% 0.40–1.83), microbiological cure (OR 1.31 IC 95% 0.46–3.67), clinical response (OR 1.39 IC 95% 0.35–5.43), acute kidney injury (OR 0.56 IC 95% 0.11–2.80) or relapse (OR 0.99 IC 95% 0.17–5.51) during the hospitalization after the adjustment. Conclusions: Among adult patients with CRE, no differences were observed between treatments with CZA and BAT after adjustment with IPTW. Full article
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15 pages, 582 KB  
Article
Sequencing Analysis of Invasive Carbapenem-Resistant Klebsiella pneumoniae Isolates Secondary to Gastrointestinal Colonization
by Gaetano Maugeri, Maddalena Calvo, Dafne Bongiorno, Dalida Bivona, Giuseppe Migliorisi, Grete Francesca Privitera, Guido Scalia and Stefania Stefani
Microorganisms 2025, 13(1), 89; https://doi.org/10.3390/microorganisms13010089 - 5 Jan 2025
Cited by 4 | Viewed by 1877
Abstract
Klebsiella pneumoniae represent a common invasive infection etiological agent, whose potential carbapenem-resistance and hypermucoviscosity complicate the patient’s management. Infection development often derives from gastrointestinal colonization; thus, it is fundamental to monitor asymptomatic K. pneumoniae colonization through surveillance protocols, especially for intensive care and [...] Read more.
Klebsiella pneumoniae represent a common invasive infection etiological agent, whose potential carbapenem-resistance and hypermucoviscosity complicate the patient’s management. Infection development often derives from gastrointestinal colonization; thus, it is fundamental to monitor asymptomatic K. pneumoniae colonization through surveillance protocols, especially for intensive care and immunocompromised patients. We described a six-month routine screening protocol from the Policlinico of Catania (Italy), while blood samples were collected from the same patients only in cases of a systemic infection suspicion. All the patients who had dissemination episodes were furtherly investigated through next-generation sequencing, analyzing both colonizing and disseminating strains. This study documents emerging invasive sequence types such as ST101, ST307, and ST395, mainly revealing blaNDM or blaKPC genes, along with siderophores and hyperproduction capsule markers as virulence factors. Most of the detected factors are presumably related to a specific plasmid content, which are extremely varied and rich. In conclusion, active surveillance through sequencing is essential to enhance awareness of local epidemiology within high-risk multi-drug resistance areas. A random sequencing analysis on the most warning microorganisms could enhance sequence typing (ST) awareness within specific settings, allowing for better prevention control strategies on their eventual persistence or diffusion. Full article
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