The study screened adult ICU patients by rectal culture at admission and weekly from July 2022 through August 2025. Rectal CRE colonization was identified in 287 of 3,221 ICU admissions, or 8.9%. Colonization was present at admission in 88 cases (30.7%) and acquired during the ICU stay in 199 (69.3%). Sixteen infections were detected on the colonization date and evaluated separately, leaving 271 admissions for the primary analysis of infection occurring after colonization.

For the risk analysis, time zero was defined as the first documented CRE colonization date. The researchers used competing-risk methods to estimate cumulative incidence, treating ICU death and live ICU discharge before infection as competing events. No evaluated factor was independently associated with subsequent infection in the Fine-Gray model. Prior colistin exposure was borderline but not statistically significant, with a subdistribution hazard ratio of 1.53, a 95% confidence interval of 0.99–2.37 and p = 0.057.

Mortality was higher among patients who developed subsequent infection than among those who did not: 71.2% versus 55.4% (p = 0.007). This was an observed association in a retrospective cohort and does not establish that subsequent infection caused the higher mortality. The findings are limited by the single-center design, retrospective data and the screened adult ICU population, and the available report is an abstract of an accepted article subject to later revision rather than a full assessment of the study.

Subject of Research: Prevalence, timing, outcomes and risk factors for subsequent CRE infection after rectal colonization in adult ICU patients

Article Title: Rectal colonization with Carbapenem-resistant Enterobacterales in intensive care unit patients: prevalence, clinical outcomes, and risk of subsequent infection

Article References: Yüce Yıldırım, D., Şenol, G., Yiş, R., & Gülfidan, Ö. G. (2026). Rectal colonization with Carbapenem-resistant Enterobacterales in intensive care unit patients: prevalence, clinical outcomes, and risk of subsequent infection. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14445-6

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14445-6

Keywords: CRE colonization, rectal culture, intensive care units, subsequent infection, carbapenem resistance, Enterobacterales, cumulative incidence, Fine-Gray model, retrospective cohort, patient mortality, Rectal, colonization

The clinical problem is especially consequential in intensive care, neonatal units and patients who are immunocompromised, hospitalized for prolonged periods or undergoing invasive procedures. S. marcescens is associated with ventilator-associated pneumonia, catheter-related bloodstream infections, complicated urinary tract infections, postoperative wound infections and empyema. Genomic surveillance across 35 countries has identified 12 phylogenetic lineages, with Sm5, Sm6 and Sm7 showing strong associations with human infection and enrichment for high-risk antimicrobial-resistance genes. The organism’s chromosomal ampC gene contributes to intrinsic resistance to several early-generation beta-lactams, although clinically significant AmpC overexpression is uncommon, reported in fewer than approximately 5% of isolates in the evidence summarized by the review. Mobile elements carrying carbapenemase and extended-spectrum beta-lactamase genes have nevertheless reduced the value of many standard beta-lactams, including carbapenems.

The resulting treatment gap has encouraged renewed interest in phages, viruses that infect and lyse bacteria. Their narrow host specificity can distinguish a clinical isolate from much of the surrounding microbiota, while replication at an infection site may increase local exposure. Some anti-Serratia phages also encode depolymerases that degrade capsular or extracellular polymeric material, potentially exposing bacterial receptors and improving access to cells embedded in biofilms. These properties are attractive in principle, but they are not interchangeable with demonstrated human benefit. A retrospective analysis of 242 infected patients reported 28-day all-cause mortality of 50.0% in those with multidrug-resistant isolates, yet the review found insufficient clinical data from which to calculate response rates, comparative efficacy, optimal dosing or reliable treatment durations for phage therapy.

Phage activity begins with recognition of a specific bacterial receptor. In S. marcescens, lipopolysaccharide and its O-antigen are experimentally established receptors for several phages, including kappa, FSB3, FSB55 and phiIF3. Biochemical work with phage kappa identified LPS as its primary receptor, while mutants defective in the LPS O-side chain became resistant to several LPS-dependent phages. In strain Db11, disruption of an O-antigen transporter impaired both productive infection and adsorption by phiIF3; only two of 25 additional Db11 phages retained the ability to infect that mutant. The flagellum provides a mechanistically different route of entry. Deletion of fliC, which encodes flagellin, made S. marcescens ATCC 274 resistant to the flagellotropic phage chi. These observations explain why a phage active against one isolate may fail against another: strain-specific O-antigens, capsule phenotypes and flagellar expression can change receptor availability.

Resistance to phages can also arise after adsorption. S. marcescens strains carry diverse restriction–modification systems, CRISPR–Cas arrays, cyclic-oligonucleotide-based antiphage signaling systems and abortive-infection-associated defenses, although none is present or functionally equivalent in every isolate. A type II restriction–modification system known as SmaI has been characterized, while genomic surveys have found lineage-dependent differences in the wider restriction–modification repertoire. CRISPR systems have been detected in only a subset of strains, and some spacers resemble sequences from Serratia phages, indicating historical interaction without proving current antiviral activity. An S. marcescens CBASS system uses a sequential “cGASylation” mechanism to activate a cyclic antiviral signal and a cell-death-associated response. Abortive infection can also halt phage propagation at the expense of the infected cell. Because the bacterial defense repertoire varies by strain and phages may evolve countermeasures, the genomic presence of a defense locus alone cannot predict susceptibility to a particular therapeutic phage.

Preclinical development is less mature for S. marcescens than for several other multidrug-resistant Gram-negative pathogens. Most studies concern individual phages or small isolate panels, and relatively few evaluate mature biofilms, representative clinical collections, animal infection models or clinically relevant phage–antibiotic combinations. Candidate viruses are typically enriched from sewage, soil, hospital wastewater or clinical material, plaque-purified and characterized phenotypically. Clearing in a spot assay does not prove productive infection, so apparent activity must be confirmed through plaque formation, efficiency-of-plating measurements, viable-count endpoints and evidence of progeny production. Host-range panels should represent contemporary clinical diversity in resistance profile, lineage, O-antigen, capsule, biofilm behavior, infection source, geography and time; the review notes that no international guideline establishes a universal minimum number of isolates. Complete genome sequencing is required to exclude lysogeny, toxin, virulence, antimicrobial-resistance and other undesirable determinants, alongside functional confirmation of a strictly lytic lifecycle.

Biofilm-associated activity is a distinctive target for further testing. The podovirus UFV01, isolated using a clinical S. marcescens strain, carries a tail-fiber-associated depolymerase that degraded extracellular polymeric material and reduced preformed Escherichia coli biofilms without productively infecting the cells. This “bystander” effect demonstrates matrix degradation rather than phage-mediated killing, and it does not establish therapeutic efficacy. A phage such as WSPA, recovered with a multidrug-resistant clinical isolate as enrichment host, showed lytic activity against a panel of contemporary multidrug-resistant strains and no identified virulence or resistance genes, but its tested panel was limited and it had no in vivo or clinical validation. Depolymerase activity, plaque morphology and broad host range are therefore useful screening features, but they cannot substitute for testing under physiological conditions and in infection models.

Direct human evidence remains exceptionally sparse. The review identified a 2025 case report of a 59-year-old patient with persistent postoperative pneumonia and empyema after lung-cancer resection. Pleural fluid remained culture-positive for an extensively drug-resistant S. marcescens strain after 120 days of unsuccessful antibiotic treatment. The strictly lytic phage Spe5P4 was delivered intrapleurally and by nebulization at a reported concentration of 10⁹ PFU/mL, together with meropenem and amikacin, drainage and supportive care. The patient’s dyspnea and chest pain resolved within 72 hours, oxygen saturation normalized, pleural fluid measurements declined and imaging showed lung re-expansion with near-complete resolution of effusion by day 140. No phage-related adverse events were reported, and post-treatment isolates showed reduced fluoroquinolone resistance. However, the uncontrolled single-case design and concurrent antibiotics, drainage and supportive care prevent attribution of improvement to Spe5P4 alone; the report establishes preliminary feasibility in one patient, not efficacy.

Organism-specific preclinical findings are stronger than the clinical record but remain narrow. In a lethal BALB/c mouse model of S. marcescens infection, immediate administration of phage phiSM9-3Y produced 100% survival, while a 60-minute delay reduced protection to approximately 60% even with a higher phage dose. In a Galleria mellonella model infected with the clinical bloodstream isolate UMH9, a single 10⁷-PFU dose of Sm10b_1 increased six-day survival from 0% to 67% relative to untreated larvae. These models demonstrate in vivo antibacterial activity against S. marcescens, but neither reproduces the full immune, anatomical, physiological and comorbidity complexity of human infection. Phage–antibiotic combinations also cannot be assumed to be synergistic. Some antibiotics can inhibit phage replication by suppressing bacterial metabolism, whereas other combinations enhance killing or biofilm disruption. Each phage, isolate, antibiotic, concentration and treatment sequence therefore requires direct testing, with both bacterial killing and viable phage titers measured.

Translation is additionally constrained by variable pharmacokinetics, bacterial resistance, immune neutralization, manufacturing and regulation. Administered PFU does not reliably predict the active concentration at an infection site because distribution, adsorption, in situ amplification, local clearance and bacterial susceptibility all affect exposure. Local delivery may concentrate phages in pleural or pulmonary compartments, whereas systemic administration can expose them to sequestration and neutralizing immune responses; the clinical significance of anti-phage antibodies remains uncertain. Personalized preparations also require consistent identity, titer, purity, sterility, endotoxin control, potency and storage stability, while cocktails require assessment of component balance, stability and interference. The review’s priorities are standardized isolate-specific susceptibility testing, receptor-informed and diverse phage libraries, quantitative cocktail design, pathogen-specific pharmacokinetic and pharmacodynamic studies, serial monitoring of bacteria and phages, and prospective controlled trials with antibiotic-only and combination comparators. Until those steps are completed, the evidence supports biological plausibility and limited proof of concept, but not reproducible efficacy or generalizable clinical feasibility for multidrug-resistant S. marcescens infections.

Subject of Research: Evaluation of bacteriophage therapy for multidrug-resistant Serratia marcescens infections

Article Title: Phage therapy for multidrug-resistant Serratia marcescens infection: mechanisms, preclinical evidence, and translational challenges

Article References: Zhang, S., Tao, H., Zhao, S., & Wei, Y. (2026). Phage therapy for multidrug-resistant Serratia marcescens infection: mechanisms, preclinical evidence, and translational challenges. Frontiers in Microbiology, 17, Article 1959850. https://doi.org/10.3389/fmicb.2026.1959850

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DOI: 10.3389/fmicb.2026.1959850

Keywords: bacteriophage therapy, Serratia marcescens, multidrug resistance, carbapenem resistance, biofilms, phage receptors, phage-antibiotic synergy, clinical evidence, antiphage defenses, translational research, Phage, therapy

The study screened a library of phytochemicals selected for their reported potential to inhibit resistance enzymes rather than for direct antimicrobial activity. The researchers used ADMET profiling, or assessment of absorption, distribution, metabolism, excretion and toxicity, followed by molecular docking against the NDM-1 and KPC-2 β-lactamase enzymes. Quercetin, eriodictyol and luteolin produced favorable predicted docking scores: −9.1, −8.32 and −8.66 kcal/mol against KPC-2, and −8.74, −8.72 and −8.73 kcal/mol against NDM-1, respectively.

Molecular dynamics simulations were then performed for quercetin complexes with NDM-1 and KPC-2 to examine the predicted conformational behavior of those complexes. These computational findings supported further investigation of quercetin, but the docking and simulation results were predictions rather than direct measurements of enzyme inhibition. The reported in vitro assay showed potentiation of carbapenem activity against the CRKP isolate, while the abstract states that the assays did not directly assess β-lactamase inhibition.

The findings therefore identify quercetin as a preliminary carbapenem-adjuvant candidate under laboratory conditions, with supporting computational analyses and an observed improvement in antibacterial activity. The mechanism responsible for that potentiation remains unconfirmed, and the supplied evidence does not establish whether quercetin directly inhibits NDM-1, KPC-2 or another target. The results are also limited in scope because the reported laboratory testing involved one CRKP isolate; the abstract does not provide evidence about activity against a broader isolate collection or clinical effectiveness in people. The article was published on 12 October 2026 as an open-access, early version of peer-reviewed research and was described as subject to further edits before replacement by the final version of record.

Subject of Research: In vitro and computational evaluation of quercetin as a potential carbapenem adjuvant against a carbapenem-resistant Klebsiella pneumoniae isolate

Article Title: Phytochemical screening as an inhibitor of β-lactamases to overcome the carbapenem-resistant of Klebsiella pneumoniae

Article References: Azmal, M., Paul, J. K., Shohan, M. N. H., Haque, A. N. M. S. N. B., Mrinmoy, M., Talukder, O. F., Mishu, M. A., Mia, M. W., & Ghosh, A. (2026). Phytochemical screening as an inhibitor of β-lactamases to overcome the carbapenem-resistant of Klebsiella pneumoniae. Scientific Reports. https://doi.org/10.1038/s41598-026-68970-0

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DOI: 10.1038/s41598-026-68970-0

Keywords: quercetin, Klebsiella pneumoniae, carbapenem resistance, β-lactamases, NDM-1, KPC-2, molecular docking, ADMET profiling, in vitro assay, Scientific Reports, Phytochemical, screening

The research team used a multi-label framework because an infection episode could contain more than one relevant microorganism or susceptibility profile. The five outcomes were bloodstream infections associated with carbapenem-resistant Gram-negative bacilli, methicillin-resistant staphylococci, third-generation cephalosporin-resistant Enterobacterales, fungal pathogens, and non-multidrug-resistant, non-fungal organisms. Episodes involving more than one applicable group were assigned to each group rather than being forced into mutually exclusive categories. This structure was relevant because 166 episodes, or 11.6% of the cohort, were polymicrobial. The final dataset contained 1,640 microorganisms isolated from the 1,435 episodes.

Most infections occurred early in the treatment course: 60.9% arose during a patient’s first chemotherapy cycle. Non-multidrug-resistant or fungal agents accounted for 1,193 episodes, or 83.1% of the total, while carbapenem-resistant Gram-negative bacilli were identified in 109 episodes, or 7.6%. The most frequently isolated species were Escherichia coli, representing 26.3% of organisms; Klebsiella pneumoniae, 15.5%; and Pseudomonas aeruginosa, 9.0%. Among Enterobacterales isolates, 6.6% were resistant to third-generation cephalosporins and 4.7% were resistant to carbapenems. Across Gram-negative bacteria, carbapenem resistance occurred in 10.8%, equivalent to 114 isolates and 109 episodes. Thirty-day mortality ranged from 30.1% to 40.6% among the infection groups and reached 53.2% in the carbapenem-resistant Gram-negative bacilli group.

Each analytical observation represented one chemotherapy cycle rather than one unique patient, so patients undergoing multiple cycles could contribute more than one record. Candidate explanatory variables included age, sex, cancer type, body measurements, laboratory results, chemotherapy drugs and classes, prior infections, antimicrobial exposure and days spent in hospital. Temporal information was encoded through a first-cycle indicator, cumulative counts of previous infections in each pathogen category, and cumulative antimicrobial and hospitalization exposure during the 90 days preceding the cycle. A binary variable also marked cycles initiated during the COVID-19 pandemic period. The initial collection included 1,505 infected cycles from 1,272 patients. After records with missing age or sex were excluded, extreme height, weight and body-mass-index values were removed, and missing blood-test results were flagged, the analysis retained 1,435 cycles from 1,220 patients.

Four algorithms—logistic regression, random forests, multilayer perceptrons and gradient boosting—were implemented in classifier chains. In this arrangement, models predict infection labels sequentially, allowing the output for an earlier label to inform later predictions and thereby representing potential dependencies among infection groups. Hyperparameters were tuned with grid search and empirical refinement within fivefold cross-validation. The researchers reserved one independently partitioned subset for a single final evaluation. To preserve the clinical distribution of uncommon outcomes, no resampling or reweighting was applied. Model selection and overall performance were assessed with a weighted area under the receiver operating characteristic curve, or AUC-ROC, across the five groups. SHapley Additive exPlanations, known as SHAP, were then used on the test set to estimate how individual variables contributed to predictions.

The highest-performing configuration was a classifier chain of 20 random forests, with each forest containing 100 trees and a maximum depth of four. During cross-validation, it produced a weighted mean AUC-ROC of 60.90%, with a standard deviation of 2.52%; on the held-out test set, the weighted average was 66.37%. The model’s highest infection-specific result was for carbapenem-resistant Gram-negative bacilli, for which test-set AUC-ROC reached 83.25%, with a 95% confidence interval of 73.91% to 91.64%. Average precision ranged from 6.40% for third-generation cephalosporin-resistant Enterobacterales to 90.84% for non-multidrug-resistant, non-fungal infections. The neural network and logistic regression each achieved a cross-validation weighted AUC-ROC of 59.96%, with standard deviations of 2.89% and 2.81%, respectively; gradient boosting averaged 56.89%, with a standard deviation of 1.03%. The differences among model families were not large relative to their variability, and the study did not establish the statistical superiority of any algorithm.

SHAP analysis identified days of hospitalization, palliative chemotherapy, hematologic malignancy, monocytopenia and thrombocytopenia as the most influential variables across the infection categories. For carbapenem-resistant Gram-negative bacilli, a previous infection with that group was the leading associated feature, followed by hospitalization duration, hematologic malignancy, thrombocytopenia and low hematocrit. Prominent variables for third-generation cephalosporin-resistant Enterobacterales were previous glycopeptide exposure, hospitalization, acute leukemia, the pandemic-period indicator and antimetabolite treatment. Methicillin-resistant staphylococcal infections were associated with hospitalization duration, hematologic malignancy, lymphopenia, previous fungal infection and male sex. For fungal infections, the leading variables were the pandemic period, male sex, days of glycopeptide use, alkylating-agent treatment and hospitalization duration. These values describe associations encoded by the models rather than independent causal effects.

Chemotherapy classes contributed less overall than hospitalization, prior infection and hematologic disease, but their rankings varied by infection group. Alkylating agents were associated with candidemia, antitumor antibiotics with carbapenem-resistant Gram-negative bacilli, and antimetabolites with third-generation cephalosporin-resistant Enterobacterales. The investigators said these relationships require further study. The pandemic-period indicator was the leading feature associated with fungal infection, which the authors interpreted cautiously: it may have represented changes in healthcare delivery, clinical practice and antimicrobial use rather than a direct effect of SARS-CoV-2 infection. Likewise, prior glycopeptide use may chiefly have marked greater healthcare exposure and susceptibility to infection rather than being a specific risk factor for resistant Enterobacterales or fungi. Palliative chemotherapy was associated with non-multidrug-resistant, non-fungal infection, but that result was relative to the other chemotherapy patients included in the analysis.

The design places important limits on how the findings can be interpreted. Because the dataset was retrospective and restricted to chemotherapy cycles that already had confirmed bloodstream infections, the models estimated the probability of different microbiological profiles among existing infections rather than the risk of developing an infection in all chemotherapy patients. The single-center population may also differ from patients treated elsewhere in their cancer profiles and patterns of bacterial resistance. Relatively few events occurred in uncommon infection groups, especially fungal infections, making their estimates less stable. Although data were partitioned at the chemotherapy-cycle level, partitioning at the patient level would provide a more conservative assessment of performance in previously unseen patients. The wide confidence interval around the strong carbapenem-resistant result also indicates substantial uncertainty, and the retrospective design cannot establish that chemotherapy class, antimicrobial exposure, hospitalization or any other measured factor caused the infections.

Overall, the study shows that multi-label modelling is feasible for exploring several bloodstream-infection profiles within the same chemotherapy cohort while preserving polymicrobial episodes. It also shows that explicitly allowing dependencies among infection labels did not automatically improve predictive performance: the chained random-forest model performed only marginally better during cross-validation than an independent model that fitted separate binary classifiers. The clearest signals involved prior resistant infection, hospitalization duration, hematologic disease, cytopenias and treatment exposures, while chemotherapy classes showed smaller, group-specific associations. Because the study was observational, confined to infected cycles and centered on one Brazilian cancer center, the models are better viewed as a source of hypotheses for larger, externally validated studies than as validated instruments for selecting antimicrobial treatment.

Subject of Research: Multi-label machine learning of bloodstream-infection risk factors in chemotherapy patients

Article Title: Application of machine learning to identify risk factors for bloodstream infections caused by different antimicrobial resistance phenotypes in chemotherapy patients

Article References: Villani Junior, A., Freire, M. P., De Padua Covas Lage, L. A., Lazar Neto, F., Oliveira, M. S., Abdala, E., Nunes, F. L. S., & Levin, A. S. S. (2026). Application of machine learning to identify risk factors for bloodstream infections caused by different antimicrobial resistance phenotypes in chemotherapy patients. Supportive Care in Cancer, 34(11), Article 1127. https://doi.org/10.1007/s00520-026-11379-2

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DOI: 10.1007/s00520-026-11379-2

Keywords: machine learning, bloodstream infections, chemotherapy, antimicrobial resistance, cancer care, carbapenem resistance, fungal infections, clinical prediction, infectious diseases, retrospective cohort, Application, machine

The single-center cohort, which included 100 infected limbs from 98 patients, establishes associations within this hospital population but does not show that particular organisms caused the clinical outcomes. The researchers consecutively enrolled adults with diabetes who were admitted with a foot ulcer and a WIfI foot infection grade from 1 to 3 between February 2017 and March 2019. Deep tissue cultures yielded 133 isolates: 54.1% were Gram-negative, 43.6% Gram-positive and 2.3% fungi.

Staphylococcus aureus was the most frequent species, accounting for 23.3% of isolates. Cultures were monomicrobial in 71 of 100 limbs, meaning that only one species was identified in 71.0% of the sampled infected limbs. Several Enterobacterales were more frequent in grade 3 infection than in grade 2 infection.

Proteus mirabilis had an odds ratio of 15.00, a 95% confidence interval of 1.98 to 112.03 and a p-value of 0.011. Klebsiella pneumoniae and Klebsiella aerogenes each had an odds ratio of 16.78, with p-values of 0.039. The broad confidence interval for Proteus and the small study population indicate substantial uncertainty around these estimates.

When results were grouped by WIfI amputation risk stage, Enterobacterales rose from 13.6% of isolates in the very-low-risk stage to 40.5% in the high-risk stage. Enterococcus faecalis declined from 31.8% to 7.1% across the same stages. The broader decrease in Gram-positive bacteria did not reach statistical significance, so the findings support a species-level pattern rather than a general claim that all Gram-positive organisms became less common as risk increased.

Carbapenem resistance followed a different and non-linear pattern. Organisms with carbapenem resistance were isolated from 25.7% of limbs with grade 1 infection, 8.3% with grade 2 infection and 40.0% with grade 3 infection. Among the nine carbapenem-resistant isolates from grade 1 limbs, eight were non-fermenting Gram-negative bacilli.

The study authors concluded that this pattern does not indicate that carbapenem resistance was associated with greater infection severity. Clinical outcomes differed across the WIfI amputation risk stages. Major amputation occurred in 15 of the 100 infected limbs, or 15.0%, and the proportion increased from 0.0% in the lowest stage to 32.4% in the highest; the test for trend produced a p-value of 0.003.

Two of the 98 patients died in hospital, corresponding to 2.0%. Overall, the findings offer a detailed microbiological snapshot of infected diabetic foot ulcers treated at one Brazilian tertiary hospital. They should not be assumed to represent every hospital or region, and the observational design, relatively small cohort and low number of deaths limit broader generalization.

Subject of Research: Microbial profiles, antibiotic resistance and clinical outcomes in diabetic foot ulcers stratified by WIfI classification

Article Title: Microbial profiles, resistance patterns, and clinical outcomes in diabetic foot ulcers: a prospective cohort study using the WIfI classification

Article References: Cardoso, N. A., Cisneros, L. D. L., Machado, C. J., Procópio, R. J., Navarro, T. P., & Duani, H. (2026). Microbial profiles, resistance patterns, and clinical outcomes in diabetic foot ulcers: a prospective cohort study using the WIfI classification. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14404-1

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DOI: 10.1186/s12879-026-14404-1

Keywords: diabetic foot ulcers, foot infection, WIfI classification, Enterobacterales, Gram-negative bacteria, carbapenem resistance, amputation, clinical microbiology, prospective cohort, Brazil, Microbial, profiles

Researchers enrolled consecutive adults with clinically diagnosed, culture-positive diabetic foot infections between October 2025 and June 2026 at four centres in three districts of Khyber Pakhtunkhwa. The cross-sectional design characterized pathogens, susceptibility patterns and resistance phenotypes at the time of sampling while assessing factors statistically associated with ulcer severity. IWGDF/IDSA infection-severity criteria were unavailable, so the investigators defined severe ulceration as a Wagner grade of at least 3. Of 190 patients screened, 170 were included. The analysis concerned the enrolled regional population and did not test treatment strategies or determine whether particular management regimens improved clinical outcomes.

Resistance was widespread among the Enterobacterales. A presumptive extended-spectrum beta-lactamase, or ESBL, surrogate phenotype was present in 59 of 76 isolates, representing 77.6%. Carbapenem resistance was organism-restricted in 18 of 99 isolates, or 18.2%, while any recorded resistant carbapenem result occurred in 25 of 110 records, or 22.7%. Among 54 Staphylococcus aureus isolates, 17, or 31.5%, were methicillin-resistant S. aureus, or MRSA. These denominators differed by organism and susceptibility test, reflecting the isolates available for each analysis rather than a single uniform sample of all infections.

Laboratory susceptibility results varied markedly among antimicrobial groups. Meropenem was the most active agent against the 101 Gram-negative primary isolates, with activity against 86 isolates, or 85.1%. Amikacin was active against 66 of 97 tested isolates, or 68.0%, while piperacillin/tazobactam was active against 65 of 101 isolates, or 64.4%. Linezolid and vancomycin were the most active agents against Gram-positive isolates. These figures describe in-vitro susceptibility rather than clinical cure, and the reported denominators reflect the isolates tested for each agent. The investigators supported empirical therapy informed by local microbiology, followed by rapid culture-guided de-escalation and strengthened antimicrobial stewardship, but the cross-sectional study did not compare the effectiveness of management regimens.

Multivariable logistic regression identified two factors associated with severe ulceration. Ischaemia was associated with an adjusted odds ratio of 3.05, with a 95% confidence interval of 1.49–6.23. Each 1-percentage-point increase in HbA1c was associated with an adjusted odds ratio of 1.50 for severe ulceration, with a 95% confidence interval of 1.08–2.09. The ischaemia association remained after ulcers with gangrene were excluded. These estimates represent adjusted associations within the study population, not evidence that impaired perfusion or higher HbA1c caused ulcers to become severe. The culture-positive inclusion criterion also means the sample may not represent all diabetic foot ulcers, particularly infections or ulcers that could not be sampled, and the unavailable IWGDF/IDSA classification limits comparison with studies using that severity framework. Overall, the findings provide a contemporary regional profile of microbiology and resistance in diabetic foot infections, alongside the vascular and glycaemic measures associated with ulcer severity in the four-centre cohort.

Subject of Research: Microbiology, antimicrobial resistance and ulcer severity in diabetic foot infections in Khyber Pakhtunkhwa

Article Title: Microbiological profile, antimicrobial resistance, and factors associated with ulcer severity in diabetic foot infections: a multicentre cross-sectional study from Khyber Pakhtunkhwa, Pakistan

Article References: Atif, E., Ahmad, A., Ullah, R., Ahmad, D., Haq, Y. U., Khan, M. S., Shah, S. I., Farooq, H., Bin Shakoor, M. T., Haidar, Y., Haq, M., & Qazi, S. (2026). Microbiological profile, antimicrobial resistance, and factors associated with ulcer severity in diabetic foot infections: a multicentre cross-sectional study from Khyber Pakhtunkhwa, Pakistan. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14396-y

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DOI: 10.1186/s12879-026-14396-y

Keywords: diabetic foot infections, antimicrobial resistance, Gram-negative bacteria, ESBL, carbapenem resistance, MRSA, ulcer severity, ischaemia, HbA1c, Khyber Pakhtunkhwa, Microbiological, profile

The correspondence responds to a retrospective study by Jafarpour and colleagues, published in the same journal in 2025, which analyzed bloodstream infections over a six-year period at a tertiary teaching hospital in Iran, comparing pre-pandemic and pandemic phases. Bloodstream infections, in which bacteria or fungi circulate in the blood and can seed organs throughout the body, are among the most lethal healthcare-associated infections. The Iranian team found that the etiological profile remained dominated by Gram-negative organisms, a pattern consistent with previous studies from tertiary care settings. Gram-negative bacteria, whose outer membranes make them inherently harder to treat, include some of the most formidable pathogens in modern hospitals.

Yet beneath that stable surface, important changes were underway. The researchers documented an increase in Enterobacterales, the order of Gram-negative bacilli that includes Escherichia coli, Klebsiella species, and Enterobacter species. At the same time, Stenotrophomonas maltophilia, a non-fermenting bacillus that had been a notable player in pre-pandemic bloodstream infections, declined markedly. This redistribution matters clinically because Enterobacterales carry well-characterized resistance mechanisms, including extended-spectrum beta-lactamases and carbapenemases, that can spread rapidly between species and hospitals. A shift toward these organisms, even without a change in overall Gram-negative predominance, can translate into harder-to-treat infections and narrower therapeutic options.

The resistance data accompanying these shifts are the most alarming element of the findings. The Iranian study reported a concerning rise in antimicrobial resistance, particularly among Gram-negative pathogens, with increased resistance spanning multiple antibiotic classes, including carbapenems, often the last reliable line of defense against multidrug-resistant Gram-negative infections. The proportion of methicillin-resistant Staphylococcus aureus, or MRSA, increased substantially, while high rates of vancomycin-resistant enterococci persisted. Collectively, the authors suggest that while the overall epidemiological pattern of bloodstream infections remained stable, the COVID-19 pandemic may have contributed to a shift toward more resistant organisms, effectively raising the resistance floor of the hospital microbiome.

To understand why a viral pandemic would drive bacterial resistance, the Brazilian commentators point to the mechanics of selective pressure. Intensified and often empirical antibiotic use during the COVID-19 pandemic exposed bacterial populations to sustained antimicrobial assault, killing susceptible strains and leaving resistant ones to flourish and spread. In intensive care units, where patients undergo multiple invasive procedures and are managed with broad empirical antimicrobial therapy, this pressure operates at maximum intensity. The commentators note that the situation in Brazil was particularly challenging, given the already high burden of healthcare-associated infections and the clinical complexity of ICU patients, who often require mechanical ventilation, central venous catheters, and urinary devices that serve as gateways for bacterial entry.

The Brazilian team’s own data confirm and expand upon the Iranian observations. In a descriptive, single-center study conducted at a tertiary university hospital, the researchers retrospectively analyzed 474 patients with laboratory-confirmed COVID-19 admitted to a dedicated COVID-19 intensive care unit between June 2020 and December 2021. Clinical data were collected from medical records, and infections were classified as healthcare-associated when symptoms appeared at least 48 hours after admission without evidence of infection at the time of entry. Ventilator-associated pneumonia was defined by the presence of at least 10 to the fifth colony-forming units per milliliter in tracheal aspirate cultures from patients on invasive mechanical ventilation for at least 48 hours, while bloodstream infection required a positive blood culture collected at least 48 hours after hospital or ICU admission.

The results are sobering. The Brazilian team observed a 44.5 percent incidence of secondary healthcare-associated infections diagnosed by microbiological criteria, meaning 211 of 474 critically ill COVID-19 patients developed laboratory-confirmed secondary infections. Of these, 45.3 percent were caused by Gram-negative microorganisms, predominantly involving the lungs and bloodstream. In total, 757 microorganisms were recovered from the 474 patients, and 79.4 percent of those isolates, 601 of 757, were antimicrobial-resistant. Bacterial identification and susceptibility testing were performed using the VITEK 2 automated system, with non-susceptibility classified according to the international expert definitions proposed by Magiorakos and colleagues, based on Clinical and Laboratory Standards Institute interpretive criteria.

Antimicrobial use was high in both the Iranian and Brazilian settings, with the main emphasis on beta-lactams, particularly broad-spectrum agents, though the use of polymyxins and antifungals was unexpectedly high. A trend toward increased prescribing was observed among patients with bloodstream infections, possibly related to the more rapid clinical progression and higher mortality in these cases, which may justify the empirical use of last-resort agents. The commentators report that Escherichia coli showed reduced susceptibility to meropenem, Klebsiella species exhibited significant rises in resistance to tetracycline, ciprofloxacin, and gentamicin, and Enterobacter species demonstrated increased resistance to most evaluated antibiotics, reinforcing the trend of expanding resistance among Gram-negative bacilli. These findings align with Brazilian data from Braga and colleagues and Urzedo and colleagues, which showed that antimicrobial resistance rates and antibiotic consumption were lower before the pandemic, suggesting the pandemic contributed to a worsening resistance scenario.

The convergence of evidence from different geographic regions highlights a critical global issue: the consequences of widespread, intense, and empirical antimicrobial use during the COVID-19 pandemic. Studies across Latin America consistently report high prevalence rates of antimicrobial use, particularly broad-spectrum antibiotics, especially during the pandemic, and the indiscriminate use of these agents exerts selective pressure on microorganisms, promoting acquired resistance mechanisms and limiting therapeutic options. Similar to Brazil, Iran has implemented institutional antimicrobial stewardship programs, but chronic challenges remain, including high use of empirical broad-spectrum antibiotics in hospital and ICU settings. In Brazilian tertiary hospitals, reported healthcare-associated infection prevalence ranges from 44.3 to 79.4 percent, with pneumonia and bloodstream infections among the most frequent, and the microorganisms most often isolated in high-morbidity infections are Gram-negative bacilli, notably the non-fermenting Pseudomonas aeruginosa and Acinetobacter baumannii, alongside Klebsiella pneumoniae and Escherichia coli.

The commentators caution that their study was conducted at a single Brazilian tertiary university hospital during the pandemic, and that comparisons with other cohorts should be interpreted with care due to differences in population characteristics, clinical settings, and study designs, with the retrospective design and sample size potentially limiting some analyses. Nevertheless, the message is clear and urgent. The findings highlight the substantial burden of healthcare-associated infections caused by resistant organisms among critically ill COVID-19 patients, particularly ventilator-associated pneumonia and bloodstream infections, and emphasize the importance of continuous surveillance to guide empirical antibiotic treatment strategies, strengthen infection prevention measures, and optimize antimicrobial stewardship in intensive care settings. Addressing these challenges, the authors argue, is essential to mitigate the impact of antimicrobial resistance during future public health emergencies, because the next pandemic will arrive in hospitals already populated by bacteria shaped by the selective pressures of this one.

Subject of Research: Changes in microbiological characteristics of bloodstream infections before and after the COVID-19 pandemic in a tertiary teaching hospital in Iran

Article Title: Comment on: Changes in microbiological characteristics of bloodstream infections before and after the COVID-19 pandemic in a tertiary teaching hospital in Iran

Article References: Sabino, S. S., Fernandes, A. M., Queiroz, N. L., de Brito, C. S., Queiroz, L. L., Melgarejo, C. R. V., Gontijo Filho, P. P., & Ribas, R. M. (2026). Comment on: Changes in microbiological characteristics of bloodstream infections before and after the COVID-19 pandemic in a tertiary teaching hospital in Iran. BMC Infectious Diseases, 26(1), Article 1668. https://doi.org/10.1186/s12879-026-14075-y

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14075-y

Keywords: bloodstream infection, antimicrobial resistance, COVID-19, Gram-negative bacteria, healthcare-associated infections, MRSA, carbapenem resistance, intensive care unit, antimicrobial stewardship, Enterobacterales, Comment, Changes

The urgency behind the work is hard to overstate. According to the Global Burden of Disease study, drug-resistant bacterial infections were associated with 4.71 million deaths in 2021, including 1.14 million deaths directly attributable to antimicrobial resistance. Projections suggest that by 2050, annual AMR-associated deaths could exceed 8 million. A. baumannii sits at the top of the danger list: the World Health Organization classifies carbapenem-resistant A. baumannii (CRAB) as a critical priority pathogen, and the U.S. Centers for Disease Control and Prevention labels it an urgent threat. The bacterium readily acquires resistance genes, forms stubborn biofilms on medical devices, and has narrowed the therapeutic arsenal to a handful of toxic last-resort drugs.

CIT8 is a derivative of citropin 1.1, a naturally occurring alpha-helical antimicrobial peptide from an Australian tree frog. In an earlier study, the team used a machine learning-guided strategy that mined a database of more than 14,000 experimentally characterized antimicrobial peptides to identify a physicochemically distinct cluster dominated by high hydrophobicity, helicity, and an extended hydrophobic surface. Guided by that analysis, they introduced four amino acid substitutions into a truncated citropin fragment, producing CIT8 with the sequence GLFKVIKKLLKVI. The changes raised the peptide’s net positive charge and hydrophobicity, and the resulting molecule proved highly active against methicillin-resistant Staphylococcus aureus. What remained unknown was how broad its spectrum might be.

The new experiments answered that question decisively. Against a panel of 16 A. baumannii strains, including 14 clinical isolates from the FDA-CDC Antimicrobial Resistance Isolate Bank, CIT8 maintained a minimum inhibitory concentration of 4 micrograms per milliliter against 15 of the 16 strains, including multiple carbapenem-resistant isolates for which meropenem was essentially inactive. Its all-D enantiomer, CIT8-D, performed nearly as well. Time-kill assays revealed just how fast the peptide works: at 20 micrograms per milliliter, five times the MIC, CIT8 drove an initial population of roughly 5 x 10^7 colony-forming units per milliliter of exponential-phase bacteria below the limit of detection within 15 minutes. Polymyxin B, the clinical benchmark membrane-active antibiotic, needed 30 to 120 minutes to achieve the same result, while meropenem alone failed to reduce bacterial counts at all during the four-hour experiment.

The mechanism behind this speed is classic antimicrobial peptide biology. Using the membrane potential-sensitive dye DiSC3(5), the researchers observed rapid, dose-dependent depolarization of the bacterial membrane, with effects visible even at sub-inhibitory concentrations. Sytox Green uptake confirmed that the membrane became permeable to molecules that normally cannot cross it, and a luciferase-based assay showed leakage of intracellular ATP within an hour of exposure. Scanning electron microscopy revealed roughened, indented cell surfaces and extracellular debris in treated bacteria. Together, the data point to a membrane-targeting mode of action in which the cationic peptide binds the negatively charged bacterial surface, accumulates at the membrane interface, and catastrophically disrupts membrane integrity.

Molecular dynamics simulations added atomic-level detail. In two independent one-microsecond simulations using a model membrane of POPE and POPG lipids in a 3:1 ratio, CIT8 bound rapidly to the membrane surface and stayed there, localized in the headgroup region rather than penetrating the hydrophobic core. Potential of mean force calculations confirmed that migration from the membrane interface into the bilayer interior is energetically unfavorable, with a free energy barrier of roughly 28 kilocalories per mole. Crucially, CIT8 held a more stable alpha-helical structure than its weak parent peptide CIT1, retaining a continuous helical core from residue 4 to residue 10. The simulations also showed that CIT8 made substantially more contact with the anionic POPG lipid, particularly through the lysine substitution at position 4, which replaced a negatively charged aspartic acid.

Biofilms, the slimy bacterial communities that make A. baumannii infections so persistent, were another target. When added during biofilm formation, CIT8 reduced biofilm cell viability by more than 95 percent at concentrations of 16 micrograms per milliliter or higher, while CIT8-D achieved the same effect at 4 to 8 micrograms per milliliter. Against established 24-hour biofilms, CIT8 halved biofilm-associated cell viability at roughly 23 micrograms per milliliter in both a reference strain and a CRAB isolate, whereas CIT8-D was roughly three times more potent, achieving the same reduction at 6.6 to 10.8 micrograms per milliliter. Fluorescence microscopy using live-dead staining confirmed that CIT8-D-treated biofilms were almost entirely dead, while meropenem-treated biofilms remained mostly viable. The authors suggest that the superior antibiofilm performance of the D-enantiomer may reflect its resistance to proteolytic degradation, which preserves activity during prolonged exposure.

Safety margins matter as much as potency, and here the results were encouraging. CIT8 showed no detectable effect on the viability of human keratinocyte HaCaT cells or human kidney cortex HKC-8 cells even at 128 micrograms per milliliter, yielding a therapeutic index greater than 32 in both cell lines. CIT8-D was more cytotoxic, with median lethal concentrations of 64.6 and 74.1 micrograms per milliliter in the two cell lines and therapeutic indices of 16.2 and 18.5, but it still retained considerable selectivity for bacterial over mammalian membranes. The peptide’s activity did weaken in the presence of divalent cations such as calcium and magnesium, which stabilize the Gram-negative outer membrane by bridging adjacent lipopolysaccharide molecules, and in the presence of human serum, a reminder that physiological conditions will test any membrane-active candidate.

Perhaps the most clinically intriguing finding involves combination therapy. Standard checkerboard assays detected no synergy between CIT8 and conventional antibiotics, but time-kill assays told a different story. When 4 micrograms per milliliter of CIT8 was combined with 40 micrograms per milliliter of meropenem, viable counts of the carbapenem-resistant isolate AR33 dropped by roughly 4 log10 units relative to the starting inoculum after four hours, an additional 2.7 log10 reduction compared with CIT8 alone. Similar bactericidal synergy, meeting the prespecified threshold of at least a 2 log10 improvement over the most active single agent, was reproduced in two other CRAB isolates. Interestingly, ATP leakage assays showed no additional membrane damage in the combination groups, suggesting the interaction with meropenem is not simply a matter of enhanced permeabilization and may involve the antibiotic gaining better access to its periplasmic targets once the membrane is compromised.

The authors are careful to frame CIT8 as a scaffold rather than a finished drug. Proteolytic stability, pharmacokinetics, resistance potential, and in vivo efficacy all remain to be established, and the reduced activity in serum and in the presence of divalent cations underscores the need for testing in more complex biological matrices. Still, the study makes a compelling case that machine learning-guided sequence optimization, originally aimed at MRSA, can produce molecules with unexpected breadth against Gram-negative priority pathogens. As generative and predictive models for antimicrobial peptide design continue to mature, CIT8 offers a concrete example of how a few rationally chosen amino acid substitutions, validated by rigorous experiments, can transform a modest frog-skin fragment into a candidate worth serious preclinical attention in the fight against one of medicine’s most dangerous bacteria.

Subject of Research: Experimental characterization of the machine learning-optimized antimicrobial peptide CIT8 against carbapenem-resistant Acinetobacter baumannii

Article Title: CIT8, a machine learning-optimized antimicrobial peptide, exhibits potent activity against carbapenem-resistant Acinetobacter baumannii

Article References: Dellis, C., Mishra, B., Zhang, L., Basu, A., Felix, L. O., Shehadeh, F., Ganesan, N., Kolocouris, A., & Mylonakis, E. (2026). CIT8, a machine learning-optimized antimicrobial peptide, exhibits potent activity against carbapenem-resistant Acinetobacter baumannii. Frontiers in Microbiology, 17, Article 1967486. https://doi.org/10.3389/fmicb.2026.1967486

Image Credits: AI Generated

DOI: 10.3389/fmicb.2026.1967486

Keywords: antimicrobial peptides, Acinetobacter baumannii, carbapenem resistance, machine learning, antimicrobial resistance, membrane disruption, biofilm, meropenem synergy, citropin, molecular dynamics, therapeutic index, CRAB

The retrospective multicenter study, led by researchers at the Children’s Hospital of Chongqing Medical University and published in Frontiers in Cellular and Infection Microbiology, analyzed 5,618 pathogenic bacteria isolated from positive urine samples of children under 18 with community-acquired urinary tract infections. Children with congenital urinary tract anomalies, repeated infection episodes, or bacterial colonization without true infection were excluded, sharpening the picture of ordinary community-acquired disease. All susceptibility results were interpreted against the Clinical and Laboratory Standards Institute’s 2024 M100-S34 breakpoints, ensuring a uniform yardstick across the entire study window.

Gram-negative bacteria dominated the landscape, accounting for 71.0 percent of isolates, with Gram-positive organisms making up the remaining 29.0 percent. Escherichia coli was the undisputed leader, representing 37.3 percent of all isolates and ranking first in every age group and in both sexes. Its closest companions were Enterococcus faecium at 12.9 percent, Klebsiella pneumoniae and E. faecalis at 9.0 percent each, and Proteus mirabilis at 5.1 percent. In total, the team identified one hundred distinct uropathogenic species, a reminder that the urinary tract is anything but a single-pathogen disease niche.

The demographic patterns traced familiar developmental biology. Boys accounted for 53.9 percent of infections, with male susceptibility concentrated in the first year of life, where 59.8 percent of cases were male, and in the toilet-training years up to age three. The balance flipped with age: girls predominated from age four onward, likely reflecting the shorter female urethra and its proximity to enteric bacteria. Infancy carries particular risk for boys because of delayed ureteral maturation, congenital obstructive malformations, and physiological phimosis, all of which foster urinary stasis and bacterial colonization near the urethral opening.

Age stratification also shifted the microbial cast. E. coli peaked at 45.7 percent of pathogens in the four-to-six-year group, while E. faecium took second place in infants at 22.5 percent, and K. pneumoniae clustered most prominently in the youngest children. Notably, resistance to the fluoroquinolones ciprofloxacin and levofloxacin differed significantly across age groups for both E. coli and K. pneumoniae, reinforcing the authors’ argument that empirical treatment decisions should be calibrated to a child’s developmental stage rather than applied uniformly.

The resistance trends over time painted a mixed and sometimes counterintuitive portrait. E. coli resistance to sulbactam/ampicillin fell significantly from 57.9 percent in 2019 to 36.5 percent in 2024, and resistance to amikacin, gentamicin and nitrofurantoin also declined. Yet ciprofloxacin resistance climbed from 36.5 to 50.2 percent over the same period, and carbapenem-resistant E. coli rose from 2.7 to 4.9 percent. K. pneumoniae moved in the opposite direction on some fronts: its carbapenem resistance fell from a peak of 23.1 percent in 2019 to 18.9 percent in 2024, while its resistance to amikacin, the fluoroquinolones and nitrofurantoin rose significantly.

The enzymes that confer much of this resistance also diverged. The proportion of ESBL-producing E. coli, bacteria carrying extended-spectrum beta-lactamases that destroy penicillin-class drugs, crept upward from 54.0 percent to 62.2 percent, while ESBL-producing K. pneumoniae fell sharply from 66.2 to 52.7 percent. ESBL-producing strains of both species were consistently more resistant than their non-ESBL counterparts to nearly every agent tested, and carbapenem-resistant isolates showed broad resistance across the panel. For the enterococci, penicillin resistance averaged a striking 91.5 percent in E. faecium and 63.7 percent in E. faecalis, but no vancomycin- or linezolid-resistant E. faecalis was found anywhere in the cohort.

The pandemic’s influence emerged most clearly when the years were split into pre-COVID (2019), pandemic (2020 to 2022) and post-COVID (2023 to 2024) periods. Detection of E. coli, E. faecium and K. pneumoniae all declined after the pandemic, with E. coli dropping from 45.3 percent of isolates before COVID to 35.0 percent afterward, possibly reflecting more enduring hygiene habits. At the same time, resistance of E. coli and K. pneumoniae to piperacillin/tazobactam, cefepime, ciprofloxacin and levofloxacin rose post-pandemic, while penicillin resistance increased significantly in both enterococcal species. The authors suggest that reduced antibiotic consumption and altered healthcare-seeking behavior during the pandemic years plausibly drove these shifting dynamics.

A particularly subtle finding concerned the minimum inhibitory concentrations, the drug doses needed to halt bacterial growth. Vancomycin MIC values for the enterococci did not drift over the six years, but linezolid MICs did, with the proportion of isolates requiring concentrations of at least 2 micrograms per milliliter falling significantly in both species. The downward drift was more pronounced in E. faecalis, beginning around 2022, and by 2024 only 44.5 percent of E. faecalis isolates sat at or above that threshold, down from 93.3 percent in 2019. That vancomycin and linezolid remained fully effective against E. faecalis offers a rare reassuring note in the resistance literature.

The study’s practical message is sharpened by its limits: it covers only the Chongqing region, and its retrospective design could not confirm resistance mechanisms through molecular analysis. Even so, the surveillance data carry clear clinical guidance. Nitrofurantoin, with just 2.0 percent E. coli resistance, stands out as the only oral option below the 5 percent threshold recommended for empiric use, though it is suitable only for simple bladder infections since it penetrates kidney tissue poorly. Fluoroquinolone resistance rates well above 10 percent rule them out as first-line agents, and the authors argue that carbapenems, vancomycin and linezolid should be preserved as effective last-line options. Above all, they conclude, continued monitoring and age-stratified treatment strategies are essential, because the pandemic has shown that pediatric urinary infections are a moving target.

Subject of Research: Epidemiology and antibiotic resistance of pediatric urinary tract infections before, during and after the COVID-19 pandemic in China

Article Title: Changes in epidemiology and antibiotic resistance patterns isolated from paediatric urinary tract infections: a multicenter study in China pre-, during and post-COVID-19

Article References: Tang, L., Tian, R., Wei, X., Yu, X., Xiong, Z., Xiang, Y., Liu, F., & Jing, C. (2026). Changes in epidemiology and antibiotic resistance patterns isolated from paediatric urinary tract infections: a multicenter study in China pre-, during and post-COVID-19. Frontiers in Cellular and Infection Microbiology, 16, Article 1923862. https://doi.org/10.3389/fcimb.2026.1923862

Image Credits: AI Generated

DOI: 10.3389/fcimb.2026.1923862

Keywords: urinary tract infections, antibiotic resistance, pediatrics, COVID-19, Escherichia coli, Klebsiella pneumoniae, enterococci, ESBL, carbapenem resistance, surveillance, Chongqing, nitrofurantoin

Pseudomonas aeruginosa is an opportunistic pathogen renowned for its arsenal of virulence factors and its extraordinary capacity to adapt to hostile environments. It is the third most common Gram-negative bacillus isolated from intensive care units globally, and it disproportionately strikes immunocompromised patients, including those with cystic fibrosis, chronic obstructive pulmonary disease, and bronchiectasis. The bacterium deploys quorum sensing activation and biofilm formation to colonise the lungs and persist on moist hospital equipment such as mechanical ventilators, where it resists certain antiseptics and causes ventilator-associated pneumonia, a leading cause of mortality in critically ill patients. Its lipopolysaccharide chain mediates attachment to host cells while its flagellum drives motility, and it excretes exotoxins that disrupt host cell functions alongside enzymes that facilitate tissue invasion and immune suppression. Treatment difficulties stem principally from efflux pumps that expel antibiotics from the bacterial cell and enzymes that inactivate them, and the pathogen acquires further resistance through horizontal gene transfer and mutation. Multidrug-resistant strains are defined as those resistant to three or more categories of antipseudomonal agents, while extensively drug-resistant strains remain susceptible to only two or fewer categories, and the difficult-to-treat designation introduced in 2018 refers to strains resistant to nearly all antipseudomonal agents including all first-line options.

The study’s methodology was straightforward but rigorous. Researchers analysed de-identified secondary data from the main hub of a private laboratory group with 250 laboratories throughout Gauteng province, capturing results in an Excel spreadsheet after ethical approval was granted in February 2025. Isolates were identified using Gram staining, colony morphology, rapid bench tests, and MALDI-TOF mass spectrometry, while antimicrobial susceptibility testing employed the Kirby-Bauer disk diffusion method and the automated VITEK-2 system. All zone of inhibition diameters and breakpoints were interpreted according to Clinical and Laboratory Standards Institute guidelines, with the laboratory updating its breakpoints annually across the M100 editions from Ed29 in 2019 through Ed33 in 2023. Notably, in 2023 the CLSI ceased to recommend gentamicin as a treatment option for Pseudomonas aeruginosa, and the laboratory stopped reporting susceptibility results for that antibiotic. Each requisition number was treated as an individual sample, and isolates were classified as multidrug-resistant if they showed resistance to four or more antibiotics from the testing panel, ensuring that three or more antipseudomonal categories were represented.

The demographic picture that emerged is striking. Among the 16,167 positive samples, the predominant age group was patients over 60 years, accounting for 50.8 percent of isolates with a mean age of 74 years, while the 11-to-20-year age group contributed the fewest isolates. This concentration in the elderly aligns with a 2023 Saudi Arabian study reporting that the age group most affected by multidrug-resistant Pseudomonas aeruginosa is 50 years and older, and it resonates with recent Gauteng research on urinary samples from long-term care facilities suggesting that higher antimicrobial resistance rates in older patients may stem from empirical urinary tract infection treatment. The clinical specimen distribution was equally revealing: urine samples yielded the highest proportion of isolates at 30.7 percent, respiratory samples followed at 28.7 percent, and tissue samples accounted for 21.1 percent, while ear swabs at 0.9 percent and fluids at 2.4 percent contributed minimally. A Kuwaiti study reported similar findings, with respiratory samples at 42.5 percent and urine at 20.3 percent, whereas other international studies have found ESKAPE pathogens more commonly in urine and blood cultures.

When researchers compared sensitive versus multidrug-resistant isolates across each year, the chi-square result of 184.704 with a p-value below 0.001 indicated a high level of statistical significance over time, confirming that the year of collection was genuinely associated with changes in susceptibility. The cumulative rise in multidrug-resistant isolates amounted to a 2.9 percent increase from 2019 to 2023, with a pronounced surge between 2019 and 2021. Blood culture samples carried the highest proportion of multidrug-resistant isolates in 2019 at 32.3 percent, 2020 at 31.5 percent, and 2023 at 33.3 percent, with a 7.3 percent increase between 2019 and 2022 followed by a 6.3 percent decline in 2023. Pus fluid samples led in 2021 and 2022, peaking at 41.3 percent multidrug resistance in 2022. Respiratory samples showed a 6 percent surge in multidrug-resistant isolates from 2020 to 2021 and an overall 5.5 percent increase across the five-year period. The researchers suggest that the blood culture increase could reflect prolonged intensive care unit stays during South Africa’s COVID-19 waves, when glucocorticoids used to treat severe cases have been independently associated with the development of bacteraemia in Japanese studies.

The antibiotic-level trends are perhaps the most alarming technical finding. In 2019, only three antibiotics—ciprofloxacin, imipenem, and meropenem—showed resistance above 20 percent. By 2021 that number had grown to five, adding doripenem and ceftazidime-avibactam. In 2022, six antibiotics exceeded the 20 percent threshold, adding cefepime and ceftolozane-tazobactam. By 2023, seven antibiotics showed resistance above 20 percent, adding aztreonam. Carbapenems consistently presented the highest resistance rates, with imipenem and meropenem exceeding 20 percent in all five years and doripenem crossing that threshold from 2021 onward. Resistance to amikacin rose by 2.4 percent, tobramycin by 0.9 percent, ceftazidime by 3.8 percent, cefepime by 3.3 percent, piperacillin-tazobactam by 3.9 percent, imipenem by 3.6 percent, meropenem by 2.3 percent, and doripenem by 6.1 percent over the study period. Gentamicin resistance declined by 4.5 percent, though the researchers attribute this partly to reduced reporting following EUCAST discouragement in 2020 and CLSI guideline updates in 2023 rather than a true biological reversal. Ciprofloxacin, the only fluoroquinolone tested, declined by 4.7 percent, a decrease the researchers suggest could reflect reduced use and the possibility of resistance reversal in antibiotic-free environments where selective pressure for nfxB gene mutations driving efflux pump overexpression is absent.

Perhaps most concerning is the resistance observed against the newest antipseudomonal agents. Ceftazidime-avibactam was tested against 666 multidrug-resistant isolates, of which 454 showed resistance, yielding a rate of 71.7 percent in 2021, 66.7 percent in 2022, and 63.2 percent in 2023. Ceftolozane-tazobactam was tested against 559 multidrug-resistant isolates, with 379 showing resistance, producing rates of 73.4 percent in 2022 and 63.4 percent in 2023. Aztreonam, tested against only 14 multidrug-resistant isolates with 5 showing resistance, registered 33.3 percent in 2023. The researchers caution that because these newer antibiotics were largely restricted to multidrug-resistant isolates and registered in South Africa only towards the end of the study period, the generalisability of these findings to the broader isolate population is limited. Colistin, a last-line polymyxin reserved for extensively drug-resistant infections, showed a 7.8 percent resistance increase from 2019 to 2020 followed by a 10 percent decline from 2020 to 2021, and its resistance presence is troubling for critically ill patients because chromosomal mutations or plasma-mediated spread of the mcr gene can eliminate this final option.

Sample-type analysis revealed where resistance concentrates most heavily. Respiratory samples presented the highest prevalence of carbapenem resistance at 42.1 percent and beta-lactam resistance at 37.7 percent, with urine samples second at 23.8 percent and 28.9 percent respectively, and tissue samples third at 14.1 percent and 14.6 percent. For aminoglycosides, urine samples led at 38.8 percent, respiratory samples followed at 30.6 percent, and tissue samples registered 12.8 percent. This pattern correlates with Iranian findings reporting tobramycin resistance of 45 percent and amikacin resistance of 43 percent among aminoglycoside-resistant isolates. The respiratory concentration is particularly worrying given that a 2024 Norwegian cohort study found that 70 percent of hospitalised patients with respiratory viral infections and positive PCR tests but no evidence of bacterial infection were nonetheless administered antibiotic therapy, and a 2024 systematic review concluded that the COVID-19 pandemic influenced Pseudomonas aeruginosa resistance patterns through intense antibiotic use. Patients with severe respiratory viral infections frequently required intensive care admission and invasive mechanical ventilation for prolonged periods, creating ideal conditions for ventilator-associated pneumonia and the spread of resistant strains within hospital settings.

The study’s authors conclude that antibiotic stewardship, together with infection control, plays a decisive role in preventing the development and spread of resistant strains. Stewardship programmes aim to reduce misuse and overuse by promoting narrow-spectrum antibiotics and discouraging empirical broad-spectrum therapy, which can accelerate resistance before culture results identify the true pathogen. World Health Organisation infection control recommendations—including rigorous hand hygiene, glove and gown use, patient isolation, environmental disinfection, and surveillance—are particularly critical in intensive care units prone to nosocomial infections. The researchers acknowledge limitations: the retrospective data came from a single private laboratory and may represent only the private sector epidemiology rather than the public sector, patient clinical records were absent so previous antibiotic exposure could not be assessed, and de-identified datasets made it impossible to determine whether multiple requisition numbers belonged to the same patient, especially among intensive care patients who may submit repeated samples. Despite these constraints, the findings provide crucial insight into the antimicrobial patterns of a WHO priority pathogen in Johannesburg and underscore the urgent demand for new antipseudomonal drugs and expanded surveillance of Pseudomonas aeruginosa and other ESKAPE pathogens in the clinical setting, contributing to the global antimicrobial resistance discourse and supporting future treatment decisions.

Subject of Research: Carbapenem Resistance Climbs in Johannesburg Pseudomonas aeruginosa Isolates

Article Title: ESKAPE pathogen alert: resistance trends in Pseudomonas aeruginosa from clinical isolates in Johannesburg (2019–2023)

Article References: Chaggan, S., & Mieta, S. I. K. (2026). ESKAPE pathogen alert: resistance trends in Pseudomonas aeruginosa from clinical isolates in Johannesburg (2019–2023). Frontiers in Bacteriology, 5, Article 1869638. https://doi.org/10.3389/fbrio.2026.1869638

Image Credits: AI Generated

DOI: 10.3389/fbrio.2026.1869638

Keywords: Pseudomonas aeruginosa, antimicrobial resistance, ESKAPE pathogens, carbapenem resistance, Johannesburg, South Africa, multidrug-resistant, nosocomial infections, antibiotic stewardship, infection control, COVID-19 pandemic, clinical isolates