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PubMed2026

Molecular epidemiology of levofloxacin-resistant Klebsiella pneumoniae and the association of plasmid-mediated quinolone resistance genes with key biological phenotypes.

UNLABELLED: Klebsiella pneumoniae is a major opportunistic pathogen in China, yet the molecular epidemiology of quinolone resistance remains poorly characterized. This study analyzed 2,433 clinical isolates from 37 Chinese hospitals (2018-2022). The overall levofloxacin-non-susceptible (NS) rate was 53.60%, with urinary tract isolates showing higher resistance. Whole-genome sequencing identified 12 plasmid-mediated quinolone resistance (PMQR) genes. Among 1,304 NS strains, 74.54% carried at least one PMQR gene (mainly qnrS, qnrB, and aac(6')-Ib-cr), and 60.20% also had quinolone resistance-determining region (QRDR) mutations. Functional studies revealed diverse phenotypic impacts. Most PMQR genes conferred low-level resistance (minimum inhibitory concentration [MIC] = 1 mg/L), while qnrB52 and qnrB91 caused high-level resistance (MIC = 8-16 mg/L). Notably, qnrB91 reduced biofilm formation, indicating a trade-off between resistance and colonization. Growth assays showed that qnrB52, qnrB91, and qnrS1 inhibited normal growth, whereas qepA1 and qnrS1 enhanced growth under ethanol stress. Most PMQR genes (except qnrB6) attenuated bacterial adhesion. qepA1 promoted intracellular survival in macrophages, suggesting a role in chronic infection. Animal models confirmed that qnrB6, qnrB7, qnrVC6, and aac(6')-Ib-cr significantly enhanced virulence. This study is the first in China to report qnrVC6 and novel gyrA mutations (Ser83Ala/Val, Asp87Phe/His) in K. pneumoniae. It systematically reveals how PMQR genes influence infection by modulating resistance, immune evasion, and pathogenicity. These findings highlight that PMQR genes contribute not only to antibiotic resistance but also to virulence, suggesting that treatment strategies should consider specific PMQR genotypes. This research provides the largest-scale molecular epidemiological data and a theoretical basis for controlling quinolone-resistant K. pneumoniae in China. IMPORTANCE: Quinolone-resistant Klebsiella pneumoniae poses a serious threat to public health, yet the role of plasmid-mediated quinolone resistance (PMQR) genes beyond antibiotic resistance remains underexplored. In this largest-scale multicenter study in China, we analyzed 2,433 clinical isolates and discovered that PMQR genes do more than just confer drug resistance-they also influence bacterial growth, stress survival, biofilm formation, and the ability to evade or persist within host immune cells. Some PMQR genes even enhance virulence in an animal model. These findings challenge the traditional view of resistance genes as mere contributors to drug failure, revealing that they can also shape infection outcomes by altering bacterial behavior. Understanding these dual roles may guide more precise treatment strategies targeting specific PMQR genotypes.

Klebsiella pneumoniae↗

PubMed2025

Genomic determinants of antibiotic resistance for Helicobacter pylori treatment: a retrospective phenotypic and genotypic observational study.

BACKGROUND: Rising antimicrobial resistance of Helicobacter pylori is a public health challenge. Genomic-based susceptibility testing allows for the identification of resistance-associated mutations, complementing conventional diagnostics and advancing towards pathogen-based personalised therapies. Our study aimed to identify genes and mutations involved in antimicrobial resistance in H pylori and evaluate the extent to which these markers can be used as predictors of phenotypic resistance against clarithromycin and levofloxacin. METHODS: In this retrospective phenotypic and genotypic observational study, we included 1011 H pylori whole-genome sequences and strains of known geographical origin from the H pylori Genome Project (HpGP) collection. We performed phenotypic clarithromycin and levofloxacin susceptibility testing on a subset of 419 HpGP strains using Etest at a centralised laboratory. A genomic analysis was conducted to identify 23S rRNA and gyrA variants and build a curated catalogue of mutations associated with resistance to clarithromycin (ie, 23S rRNA 2142A→G, 2142A→C, and 2143A→G) and levofloxacin (ie, gyrA A88V or A88P, N87K or N87I, and D91G, D91N, or D91Y). Genotype-phenotype concordance was assessed to estimate sensitivity and specificity, and the curated catalogue of resistance-associated mutations was applied to the complete HpGP set. Region-specific prevalence of resistance-associated mutations was calculated for a combined dataset including the HpGP genomes and 768 whole-genome sequences retrieved from the US National Center for Biotechnology Information Sequence Read Archive repository. Associations between resistance genotypes, H pylori subpopulations, and minimum inhibitory concentrations (MICs) were tested. FINDINGS: Clarithromycin-resistant and levofloxacin-resistant HpGP strains were estimated with a sensitivity and specificity of 100%, with all confidence intervals ranging from 96% to 100%. The combined analysis (n=1779) found the highest prevalence of clarithromycin resistance in the western Pacific region (173 [51·2%] of 338 in southeast Asia and 75 [29·8%] of 252 in eastern Asia), north African region (seven [38·9%] of 18), and western Asian region (12 [31·6%] of 38), whereas the highest prevalence of levofloxacin resistance was found in south Asia (14 [51·85%] of 27), Central America (48 [38·7%] of 124), eastern Europe (four [36·4%] of 11), and southern Africa (three [33·3%] of nine). Similarly, 23S rRNA and gyrA genotypes are variable across H pylori subpopulations. MIC values changed depending on the specific mutation in 23S rRNA (mean clarithromycin MIC 24·61 mg/L [95% CI 12·27-36·96] for 2143A→G and 142·25 mg/L [95% CI 77·88-206·61] for 2142A→G) and gyrA (mean levofloxacin MIC 9·66 mg/L [95% CI 6·75-12·56] for mutations on codon 91, and 27·97 mg/L [95% CI 25·82-30·11] for mutations on codon 87). INTERPRETATION: Mutations in specific genes are reliable indicators to clarithromycin and levofloxacin resistance in H pylori, making them useful markers for the development of diagnostic assays and molecular monitoring. Our results suggest that using clarithromycin and levofloxacin empirically, without previous susceptibility testing, is unsuitable in all geographical regions covered by this study. FUNDING: Intramural Research Program of the US National Cancer Institute, the European Research Council, and the Spanish Ministry of Science and Innovation.

Helicobacter pylori↗

PubMed2026

Molecular characterisation and mutational analysis of antimicrobial resistance genes in Helicobacter pylori isolates in Erbil, Iraq.

BACKGROUND: Antibiotic resistance in Helicobacter pylori poses a significant challenge to the effective eradication of infection worldwide. Understanding molecular mechanisms of resistance is essential for guiding treatment strategies. This study aimed to investigate the molecular basis of antimicrobial resistance in Helicobacter pylori isolates and their associated mutation frequencies. METHODS: In this cross-sectional study, gastric biopsy specimens were collected from 203 patients at Rizgary Hospital in Erbil, Kurdistan Region, Iraq, who underwent endoscopy for dyspepsia-related symptoms. Of the 137 positive patients, 91 Helicobacter pylori isolates were confirmed by colony morphology, Gram staining, and biochemical tests; 63 were successfully subcultured for antimicrobial susceptibility testing (culture success rate: 69.2%). Antimicrobial susceptibility testing was performed by the agar dilution method to determine the minimum inhibitory concentrations. The sequences of specific genes were examined and analysed by next-generation sequencing. Multiple sequence comparisons were performed to identify resistance-related genes and mutations, using 26695 (NC_000915.1) as the reference genome. RESULTS: Only two isolates (3.17%) were susceptible to all antibiotics examined. The frequency of metronidazole resistance was highest (85.71%), followed by levofloxacin (55.55%), clarithromycin (52.38%), amoxicillin (26.98%), tetracycline (6.35%), and rifabutin (4.76%). Mutations in the rdxA and frxA genes correlated with metronidazole resistance, while GyrA protein mutations at positions 87 and 91 were linked to levofloxacin resistance. Clarithromycin resistance was mainly associated with A2142G and A2143G mutations in 23S rRNA. Amoxicillin resistance (26.98%) was associated with mutations in the pbp1A gene, whereas resistance to tetracycline and rifabutin was infrequent. CONCLUSIONS: This study provides the first molecular surveillance data on antimicrobial resistance in Helicobacter pylori in northern Iraq, offering valuable regional evidence to guide local eradication strategies. The relatively high amoxicillin resistance, together with the elevated resistance to metronidazole, levofloxacin, and clarithromycin, underscores the need for susceptibility-guided therapy and continuous local antimicrobial resistance surveillance.

Antibiotic resistance↗

PubMed2026

[Complex therapy of chronic bacterial prostatitis using the immunomodulatory drug sodium aminodihydrophthalazinedione].

INTRODUCTION: Chronic bacterial prostatitis (CBP) is characterized by a recurrent course caused by pathogen persistence and impaired local immunity of the prostate. AIM: To assess the effectiveness of the use of sodium aminodihydrophthalazinedione in the complex therapy of chronic bacterial prostatitis. MATERIALS AND METHODS: The prospective comparative study included 60 men aged 21-50 years with CBP (NIH category II). Patients were randomized into two groups of 30: the comparison group received levofloxacin 500 mg/day for 28 days; the main group additionally received rectal sodium aminodihydrophthalazinedione. NIH-CPSI, IPSS, QoL, uroflowmetry, leukocyte and lecithin body counts in prostatic secretion, and bacteriological examination were assessed at baseline and on day 28, and the recurrence rate over 3 months. RESULTS: By day 28, the main group showed a more pronounced decrease in the total NIH-CPSI score (8.1+/-2.1 vs 13.4+/-2.6; p<0.001), restoration of lecithin bodies (+65.1% vs +24.5%; p<0.05), normalization of uroflowmetry, and pathogen eradication in 86.7% vs 66.7% of patients (p<0.05). The 3-month recurrence rate decreased from 26.7 to 10.0% (p<0.05). No adverse events were registered. DISCUSSION: The advantage of combinationtherapy is due to the combination of anti-inflammatory,immunomodulatory,antioxidantandregenerativeeffects of the drug,which is confirmed by the restoration of the secretoryfunction of the prostateepitheliumaccording to the dynamics of lecithingrains. CONCLUSION: The inclusion of sodium aminodihydrophthalazinedione in the combination therapy of CBP increases the clinical and microbiological efficacy of treatment and reduces the recurrence rate.

Humans↗

PubMed2026

Detection and antimicrobial susceptibility patterns of Salmonella enterica subsp. arizonae and Proteus spp. associated with gastrointestinal disease in rescued hedgehogs (Erinaceus europaeus).

Western European hedgehogs (Erinaceus europaeus) are frequently admitted to wildlife rehabilitation centres, where infectious diseases may affect recovery and raise One Health concerns. This study aimed to identify bacterial isolates recovered from hedgehog samples submitted for suspected gastrointestinal infection and to characterise their antimicrobial susceptibility profiles. Five bacterial isolates were analysed using the MicroScan WalkAway Plus® system with the Neg-Urine-Combo 98 panel, and the results were interpreted in accordance with EUCAST guidelines. The identified bacteria included one isolate of Salmonella enterica subsp. arizonae, three isolates of Proteus mirabilis and one isolate of Proteus penneri. The Salmonella enterica subsp. arizonae isolate was susceptible to all antimicrobials for which a valid result was obtained. Proteus spp. isolates were susceptible to cefotaxime, nalidixic acid, ciprofloxacin, levofloxacin, norfloxacin, amikacin, gentamicin, tobramycin, aztreonam, cefoxitin, ceftazidime and fosfomycin. However, resistance was observed to amoxicillin-clavulanic acid, ampicillin, ertapenem, meropenem, trimethoprim-sulfamethoxazole, cefuroxime, piperacillin-tazobactam, colistin and nitrofurantoin, with the latter two showing resistance in all Proteus spp. The Proteus penneri isolate displayed the broadest resistance profile, including resistance to several β-lactams, carbapenems. As expected, all Proteus spp. showed intrinsic non-susceptibility to colistin and nitrofurantoin. Although the Salmonella enterica subsp. arizonae isolate was susceptible to the tested agents, Proteus spp. from hedgehog samples may display relevant antimicrobial resistance (AMR) patterns. Therefore, continuous bacteriological monitoring and antimicrobial susceptibility testing are important in wildlife rehabilitation settings to guide treatment decisions and support One Health surveillance.

Antimicrobial resistance↗

PubMed2026

wbp-encoded LPS O-antigen architecture as a prognostic and therapeutic target in Pseudomonas aeruginosa keratitis.

BACKGROUND: Pseudomonas aeruginosa (P. aeruginosa) keratitis can progress rapidly to vision-threatening disease, even with intensive therapy. Virulence-associated genes are key determinants of ocular-surface pathogenesis. We therefore sought to develop a composite wbp-exo genotyping framework for risk stratification and to guide wbp-dependent, LPS-directed, levofloxacin-polymyxin B (LVX-POL) combination therapy for high-risk corneal infections. METHODS: A well-characterised clinical P. aeruginosa keratitis cohort was integrated with whole-genome sequencing. Based on comprehensive virulence-gene identification and annotation, the relationship between strain-level genetic features and clinical prognosis was analysed. The differences between WBP1 strains and WBP2 strains in adhesion, invasion, and biofilm formation in corneal epithelial cells were further evaluated. To establish biological plausibility, wbp genotypes were correlated with LPS O-antigen electrophoretic profiles and in vivo corneal inflammatory phenotypes in murine infection, including the observation of leucocyte recruitment and cytokine responses. To further confirm the key role of wbp gene status and LPS O-antigen in pathogenicity, wbpL knockout and reconstitution strains were constructed. Their appearances in vitro and in vivo were evaluated. Finally, a mechanistic rationale for an LPS-directed LVX-POL regimen was tested in a high-risk WBP1 P. aeruginosa murine keratitis. FINDINGS: Whole-genome sequencing was performed on 46 clinical P. aeruginosa isolates and identified an average of 332 virulence- and fitness-associated genes per strain. The exo and wbp gene families were significantly associated with patient prognosis. A fusion model (AUC = 0.86) outperformed single-gene-family models (EXO: 0.66; WBP: 0.72) for predicting clinical outcomes. Intact wbp cassettes were enriched in poor-outcome isolates, and electrophoretic LPS profiles indicated that WBP1 strains produce highly polymerised O-antigen associated with sustained neutrophil recruitment and cytokine production. Murine experiments further implicated wbp genes in clinical pathogenesis, showing stronger immune responses and higher expression of TLR4, MyD88, TRAF6, p65, p-p65, IL-6, TNF-α, and IL-1β throughout the inflammatory course. After knocking out wbpL gene, the WBP1 strain got stronger in biofilm formation and adhesion but weaker in inflammation and ocular surface survival. In the high-risk WBP1 P. aeruginosa keratitis model, LVX-POL combinations achieved complete ulcer resolution and markedly improved stromal infiltration and hypopyon, outperforming LVX monotherapy. INTERPRETATION: The wbp gene family was identified as a key genetic factor that contributes to the LPS O-antigen structure, inflammatory intensity, bacterial ocular surface survival and poor prognosis in P. aeruginosa keratitis. A WBP1-targeted, LPS-directed LVX-POL regimen was proposed as a mechanistically informed option for high-risk strains. FUNDING: This research was supported by Beijing Public Health High-level Talent Training Program (Phase III-03-14), Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project (2026ZD01909300) and Beijing Natural Science Foundation "QiYan" Undergraduate Research Fund (QY26496).

Pseudomonas aeruginosa↗

PubMed2024

Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: a multicentre clinical study of two end-to-end commercial workflows.

BACKGROUND: Drug-resistant tuberculosis remains a major obstacle in ending the global tuberculosis epidemic. Deployment of molecular tools for comprehensive drug resistance profiling is imperative for successful detection and characterisation of tuberculosis drug resistance. We aimed to assess the diagnostic accuracy of a new class of molecular diagnostics for drug-resistant tuberculosis. METHODS: We conducted a prospective, cross-sectional, multicentre clinical evaluation of the performance of two targeted next-generation sequencing (tNGS) assays for drug-resistant tuberculosis at reference laboratories in three countries (Georgia, India, and South Africa) to assess diagnostic accuracy and index test failure rates. Eligible participants were aged 18 years or older, with molecularly confirmed pulmonary tuberculosis, and at risk for rifampicin-resistant tuberculosis. Sensitivity and specificity for both tNGS index tests (GenoScreen Deeplex Myc-TB and Oxford Nanopore Technologies [ONT] Tuberculosis Drug Resistance Test) were calculated for rifampicin, isoniazid, fluoroquinolones (moxifloxacin, levofloxacin), second line-injectables (amikacin, kanamycin, capreomycin), pyrazinamide, bedaquiline, linezolid, clofazimine, ethambutol, and streptomycin against a composite reference standard of phenotypic drug susceptibility testing and whole-genome sequencing. FINDINGS: Between April 1, 2021, and June 30, 2022, 832 individuals were invited to participate in the study, of whom 720 were included in the final analysis (212, 376, and 132 participants in Georgia, India, and South Africa, respectively). Of 720 clinical sediment samples evaluated, 658 (91%) and 684 (95%) produced complete or partial results on the GenoScreen and ONT tNGS workflows, respectively, with 593 (96%) and 603 (98%) of 616 smear-positive samples producing tNGS sequence data. Both workflows had sensitivities and specificities of more than 95% for rifampicin and isoniazid, and high accuracy for fluoroquinolones (sensitivity approximately ≥94%) and second line-injectables (sensitivity 80%) compared with the composite reference standard. Importantly, these assays also detected mutations associated with resistance to critical new and repurposed drugs (bedaquiline, linezolid) not currently detectable by any other WHO-recommended rapid diagnostics on the market. We note that the current format of assays have low sensitivity (≤50%) for linezolid and more work on mutations associated with drug resistance is needed. INTERPRETATION: This multicentre evaluation demonstrates that culture-free tNGS can provide accurate sequencing results for detection and characterisation of drug resistance from Mycobacterium tuberculosis clinical sediment samples for timely, comprehensive profiling of drug-resistant tuberculosis. FUNDING: Unitaid.

Humans↗

PubMed2026

The inoculum effect of methicillin-susceptible Staphylococcus aureus on cefazolin and other antimicrobial agents.

UNLABELLED: The inoculum effect (IE) refers to a reduced susceptibility of methicillin-susceptible Staphylococcus aureus (MSSA) to certain antibiotics under high bacterial inocula and may contribute to treatment failure. This exploratory study assessed IE prevalence among 234 nonduplicate MSSA isolates across 11 agents spanning major therapeutic classes, including cefazolin, and characterized IE-positive clones via whole-genome sequencing to inform clinical strategies. Minimum inhibitory concentrations (MICs) were determined by broth microdilution at standard and high inocula. Whole-genome sequencing was performed on IE-positive strains to identify β-lactamase types and conduct multilocus sequence typing. The highest prevalence of IE was observed for trimethoprim-sulfamethoxazole (9.4%), followed by erythromycin (8.8%), linezolid (6.8%), penicillin (6.1%), clindamycin (5.5%), vancomycin (3.8%), cefazolin (3.0%), levofloxacin (1.5%), tetracycline (0.5%), and oxacillin and gentamicin (0.0%). All cefazolin IE-positive strains carried blaZ type A, and ST25 was the most common sequence type (42.9%). For trimethoprim-sulfamethoxazole, erythromycin, and clindamycin IE, ST7 was the most common sequence type (22.7%, 26.7%, and 33.3%, respectively). ST1281 and ST188 were the predominant sequence types among strains exhibiting linezolid IE and vancomycin IE (25.0% and 33.3%, respectively). Among the 234 MSSA strains, 66.7% of ST59, 60.0% of ST25, 58.3% of ST5, and 54.2% of ST7 strains exhibited IE to at least one antimicrobial agent. Cefazolin IE was associated with blaZ type A, and ST5, ST7, ST59, and ST25 were the major sequence types associated with IE across the antimicrobial classes tested. IMPORTANCE: Methicillin-susceptible Staphylococcus aureus (MSSA) can show an inoculum effect on multiple antimicrobial agents, which may reduce antibiotic activity under high-burden conditions. In this study, MSSA isolates from Shanghai exhibited inoculum effects on several commonly used agents, although the overall detection rates were low. Cefazolin inoculum effect was specifically associated with blaZ type A, and several major sequence types were more likely to exhibit this phenotype. These findings improve our understanding of the epidemiology of the inoculum effect in MSSA and may help guide laboratory detection and antimicrobial treatment decisions.

Cefazolin↗

PubMed2026

Genomic analysis of community-associated multidrug-resistant Klebsiella quasipneumoniae subsp. similipneumoniae and the identification of the ST2059-KL1 clone in the U.S.

UNLABELLED: Klebsiella quasipneumoniae subsp. similipneumoniae is an important member of the K. pneumoniae species complex (KpSC) and is increasingly reported as multidrug-resistant (MDR) in healthcare- and community-associated infections. Since clinical laboratories do not routinely distinguish K. quasipneumoniae subsp. similipneumoniae from K. pneumoniae, national prevalence estimates, particularly for MDR, are lacking. In this study, a total of 2,006 community-associated MDR KpSC isolates were collected from 42 U.S. states, with 30 K. quasipneumoniae subsp. similipneumoniae isolates originating from 12 states identified using whole genome sequencing. All isolates were resistant to ceftriaxone and exhibited high rates of resistance to other antimicrobial agents, including ampicillin-sulbactam (56.7%, 17/30), levofloxacin (75.9%, 22/29), and trimethoprim-sulfamethoxazole (53.3%, 16/30). Notably, five isolates were also carbapenem-resistant. Genomic analysis resolved 10 sequence types (STs), with ST2059 (n = 13) and ST414 (n = 9) predominating. Ceftriaxone resistance in most isolates (90%, 27/30) was conferred by an extended-spectrum β-lactamase gene, predominantly blaCTX-M-15 (73.3%, 22/30); the remaining isolates carried either a carbapenemase (blaKPC-3) or an AmpC β-lactamase (blaCMY-2). Nanopore sequencing identified blaCTX-M-15 harbored on two types of IncFIB(Kpn3) antimicrobial resistance (AMR) plasmids, either with or without the conjugative tra gene cluster. Interestingly, the KL1 locus, associated with canonical hypervirulent K. pneumoniae strains, was detected in all ST2059 isolates. Further analysis of public genomic data showed that the KL1 locus is widely distributed across KpSC. KL1 phylogenetic analyses indicated frequent intrasubspecies recombination but limited intersubspecies exchange of KL1. The identification of the dominant MDR K. quasipneumoniae subsp. similipneumoniae KL1-ST2059 clone in the U.S. underscores the importance of ongoing genomic surveillance. IMPORTANCE: Klebsiella quasipneumoniae subsp. similipneumoniae is an underrecognized member of the Klebsiella pneumoniae species complex that is frequently misidentified in clinical laboratories, leading to an incomplete understanding of its role in antimicrobial resistance. In this study, we used large-scale genomic surveillance of community-associated multidrug-resistant isolates across the U.S. to identify this subspecies as a reservoir of clinically relevant resistance plasmids. Notably, we detected a widely distributed ST2059 lineage carrying the K1 capsular locus, a feature traditionally associated with hypervirulent K. pneumoniae. These findings highlight the convergence of resistance and virulence-associated traits in an overlooked species and underscore the need for genomic surveillance to monitor emerging high-risk lineages in community settings.

Drug Resistance, Multiple, Bacterial↗

PubMed2026

Clinical Characteristics and Genomic Analysis of Vancomycin-Resistant Enterococcus faecium in a Tertiary Hospital in Huizhou.

OBJECTIVE: To characterize the clinical and genomic features of vancomycin-resistant enterococci (VRE) in a tertiary hospital in Huizhou and identify risk factors to inform local infection control. METHODS: A retrospective study included 58 VRE and 25 vancomycin-susceptible Enterococci (VSE) strains (August 2023-May 2025). Clinical data and antimicrobial susceptibility were analyzed; whole-genome sequencing (WGS) was performed on 54 VRE strains. RESULTS: Midstream urine was the primary VRE-positive specimen. ICU admission, polyantibiotic use (≥3 agents), and urinary catheterization were key risk factors for VRE. All VRE isolates were Enterococcus faecium and showed a predominantly clonal population structure, dominated by CC17/ST80 (68.8%) and CC2/ST106 (64.6%) under the two multilocus sequence typing schemes; five novel STs were ultimately identified in the latter scheme. VRE was universally resistant to ampicillin, with high resistance to penicillin, levofloxacin, and teicoplanin, while linezolid and tigecycline remained effective. Genotypically, 94.8% carried vanA, 100% carried virulence gene esp, and aminoglycoside and macrolide resistance genes were prevalent. A unique VRE strain (VRE48) showed resistance without canonical van genes, harboring a Ddl Ser210Tyr mutation.

Humans↗

PubMed2026

Stenotrophomonas maltophilia in the Antimicrobial Resistance Era: Species-Complex Taxonomy, Pathogenesis, Evolving Therapeutic Priorities, and Genomic Surveillance.

Stenotrophomonas maltophilia is a globally distributed, aerobic, non-fermenting Gram-negative bacillus increasingly recognized as an opportunistic pathogen in hospitalized and immunocompromised patients. Clinical interpretation is challenging because respiratory and device-associated isolates may represent colonization, polymicrobial infection, or true invasive disease. Recent genomic studies further suggest that organisms historically identified as S. maltophilia comprise a genetically diverse species complex, with implications for epidemiology, virulence, resistance surveillance, and susceptibility testing. Treatment is difficult because of biofilm formation, persistence in water-associated healthcare reservoirs, and intrinsic or acquired resistance mediated by L1 and L2 β-lactamases, multidrug efflux pumps, reduced permeability, mobile resistance determinants, and biofilm-associated tolerance. Current IDSA guidance identifies cefiderocol monotherapy as the preferred treatment for invasive S. maltophilia infection, whereas aztreonam-avibactam and agents such as trimethoprim-sulfamethoxazole, levofloxacin, and minocycline occupy alternative or combination-based roles. Nevertheless, the therapeutic evidence base remains uneven, and clinical decisions should integrate infection severity, source control, susceptibility findings, pharmacokinetic/pharmacodynamic (PK/PD) exposure, toxicity, infection site, and host-related factors. This review summarizes advances in taxonomy, epidemiology, pathogenesis, diagnostics, resistance, treatment, infection prevention, and genomic surveillance, and highlights the need for standardized identification, validated breakpoints, prospective comparative-effectiveness studies, and pragmatic or adaptive trial designs.

L1 β-lactamase↗

PubMed2026

Drug-resistant genes, virulence characteristics, and molecular typing of clindamycin-resistant Streptococcus agalactiae in late pregnancy.

BACKGROUND: Streptococcus agalactiae increases the risk of adverse pregnancy outcomes and neonatal infections. Clindamycin is a key alternative for intrapartum prophylaxis in penicillin-allergic women, but the prevalence of clindamycin-resistant S. agalactiae is increasing, posing a significant clinical challenge. METHODS: A total of 178 strains isolated from tertiary hospitals in Jinan and Qingdao, Shandong Province, China, were characterized using antimicrobial susceptibility testing, whole-genome sequencing, multilocus sequence typing, serotyping, and analysis of resistance and virulence genes. RESULTS: All strains were susceptible to penicillin, ampicillin, linezolid, vancomycin, and tigecycline. In contrast, resistance rates to erythromycin, levofloxacin, and tetracycline were 95.5%, 60.1%, and 56.7%, respectively. Six serotypes and 15 sequence types belonging to eight clonal complexes were identified. Notable regional differences were observed. The Ib-ST10-CC12 lineage dominated in Jinan, whereas V-ST529-CC327 was predominant in Qingdao. The resistance gene mreA was ubiquitous (100%), followed by ermB (80.3%). The key virulence genes cylE, hylB, and pavA, were detected in all strains. fbsA (99.4%), the alpha protein family (98.9%), cfb (98.3%), the Pilus Island gene cluster (94.9%), and lmb (92.7%) were also highly prevalent. The two major clindamycin resistance genes, erm and lnuB, exhibited distinctly different enrichment patterns among S. agalactiae clonal complexes, despite a certain overlap in CC19 and CC327. Specifically, erm was significantly enriched in CC12 (serotype Ib), CC19 (III/V), and CC327 (III/V). In contrast, lnuB was predominantly restricted to CC19 and CC327, where it defined a unique phylogenetic subcluster. Significant differences in resistance and virulence gene profiles were observed across different clonal complexes. CONCLUSION: Clindamycin-resistant S. agalactiae in late-pregnancy women in Shandong Province, China exhibits a broad resistance spectrum, diverse molecular types, and significant regional heterogeneity. These findings underscore the need for continued surveillance and region-specific strategies for preventing neonatal S. agalactiae infections.

Humans↗

PubMed2026

EprX associates with concurrent shifts in antimicrobial resistance and virulence in clinical bloodstream E. coli: a putative adaptive node for bacterial fitness.

Bloodstream infections (BSIs) caused by E. coli represent a growing global threat, driven by escalating antimicrobial resistance (AMR) and sustained virulence. However, the regulatory mechanisms linking these two phenotypes remain poorly understood. Here, we identify EprX, a previously uncharacterized YjbI-type pentapeptide repeat protein (PRP), a locus that our data suggest may influence metabolic and transcriptional profiles in clinical BSI E. coli isolates. Genomic screening of 85 clinical BSI strains reveals that eprX is present in 21.2% of isolates, often within distinct genomic contexts suggestive of mobile acquisition. Using λ-Red recombineering, we constructed eprX knockout mutants. Loss of eprX is associated with altered antimicrobial resistance profiles, increasing susceptibility to gentamicin, ciprofloxacin, and levofloxacin. This phenotype is consistent with upregulation of outer membrane porin genes (ompC, ompF) and downregulation of multidrug efflux pump genes (macB, mdtC, emrB) and two-component regulatory system genes. eprX deficiency also appears to correlate with attenuated virulence in our assays, as evidenced by improved survival of Galleria mellonella larvae (65-95% at 72 h post-infection vs. 40-60% for wild-type strains) and reduced adhesion to and invasion of human HeLa cells. Transcriptomic profiling reveals that eprX carriage is associated with broad, coordinated shifts in the expression of genes involved in LPS transport (lptG/lptF), type ;II secretion system components (gspD/gspE/gspF), autotransporter adhesins (ag43), and flagellar assembly, suggesting potential disruptions in outer-membrane integrity, biofilm formation, and virulence programs. Our data suggests that eprX is a genetic locus whose presence correlates with concurrent shifts in resistance maintenance and virulence traits, representing a putative adaptive node within the E. coli fitness landscape.

Animals↗

PubMed2026

Non-invasive management of severe chlamydia psittaci pneumonia presenting with hypoxemia and diarrhea: a case report.

This case report describes a rare presentation of severe Chlamydia psittaci pneumonia in a 43-year-old female patient with prominent hypoxemia and gastrointestinal symptoms, and evaluates the efficacy of standardized non-invasive integrated management for critically ill patients with this atypical phenotype. The patient was admitted with lumbago, persistent high fever, progressive dyspnea, severe hypoxemia, and intractable non-bloody watery diarrhea. Chest computed tomography (CT) revealed extensive bilateral pulmonary ground-glass opacities and consolidation. Rapid and precise etiological diagnosis was achieved via targeted metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF), which identified high-load Chlamydia psittaci infection, with 227,155 normalized reads and a genomic coverage of 98.6%. Comprehensive non-invasive multidisciplinary management was implemented throughout the disease course, including high-flow nasal cannula (HFNC) oxygen therapy, dual anti-infective therapy with omadacycline combined with levofloxacin, symptomatic supportive care, and standardized stepwise early rehabilitation training. Dynamic monitoring of clinical and laboratory indicators showed a gradual and sustained decline in inflammatory biomarkers (C-reactive protein,procalcitonin, interleukin-6),accompanied by progressive absorption of pulmonary lesions and recovery of respiratory function. The patient avoided invasive mechanical ventilation throughout hospitalization, was successfully weaned from HFNC on day 14 of admission, and achieved completeclinical, laboratory and radiological recovery at the 1-month follow-up. This case conforms to the CARE (CAse REports) reporting guidelines. It highlights that severe psittacosis pneumonia can present with atypical dominant manifestations of combined hypoxemia and severe gastrointestinal diarrhea, which is easily misdiagnosed clinically. Targeted mNGS enables rapid etiological confirmation of atypical severe psittacosis, and individualized non-invasive integrated management can achieve favorable prognosis in eligible critically ill patients, providing a valuable clinical reference for the standardized diagnosis and treatment of similar rare cases.

atypical clinical manifestation↗

PubMed2026

Molecular epidemiology and antimicrobial resistance of human Streptococcus suis isolates in Guangxi, China, 2015-2021.

BACKGROUND: Streptococcus suis (S. suis) is an important zoonotic pathogen and a common colonizer of the upper respiratory tract of pigs. Human infections have been reported in several regions of China, including Guangxi, but genomic and antimicrobial resistance data from this region remain limited. This study investigated the molecular epidemiology, antimicrobial susceptibility, and genomic characteristics of human S. suis isolates collected in Baise City, Guangxi, from 2015 to 2021. METHODS: This retrospective study included 39 non-duplicate clinical isolates confirmed as S. suis by whole-genome analysis. Antimicrobial susceptibility testing was performed using a broth microdilution-based system and interpreted according to the Clinical and Laboratory Standards Institute guidelines. Serotypes were determined by agglutination using type-specific antisera. Whole-genome sequencing was used for species confirmation, multilocus sequence typing, detection of antimicrobial resistance and virulence-associated genes, and core-protein phylogenetic analysis. RESULTS: The median patient age was 55 years, and 36/39 (92.3%) patients were male. Meningitis was documented in 34/39 (87.2%) patients, and hearing impairment occurred in 21/39 (53.8%). Pig- or pork-related exposure was recorded in 15/39 (38.5%) patients. Resistance was highest to tetracycline (38/39, 97.4%), followed by erythromycin and clindamycin (26/39, 66.7% each). Four isolates (10.3%) showed intermediate susceptibility to penicillin, but none were resistant. All isolates remained susceptible to ampicillin, ceftriaxone, levofloxacin, linezolid, vancomycin, and meropenem. Serotype 2 predominated (32/39, 82.1%), followed by serotype 14 (7/39, 17.9%), while ST1 (29/39, 74.4%) and ST7 (7/39, 17.9%) were the two major sequence types. Resistance genes were mainly associated with tetracyclines, macrolides, lincosamides, and aminoglycosides. All ST1 isolates carried mrp and lacked tet(40), while all ST7 isolates showed the reverse pattern. CONCLUSION: Serotype 2 and ST1 predominated among the human S. suis isolates collected at this center. Resistance to tetracycline, erythromycin, and clindamycin was common, while susceptibility to the β-lactams tested was largely preserved. Differences in virulence- and resistance-associated gene profiles were also observed between the major lineages, indicating distinct genetic characteristics among the locally circulating isolates.

Streptococcus suis↗

PubMed2026

[Genomic characteristics of multi-drug resistant of non-O1/non-O139 Vibrio cholerae ST1565 from sepsis cases].

To analyze the genomic characteristics of multi-drug resistant of non-O1/non-O139 Vibrio cholerae ST1565 from sepsis cases. An 88 years old male patient admitted to Huashan Hospital in Shanghai on July 2, 2025, who was retrospectively analyzed. The clinical diagnosis was severe bacterial enteritis and secondary NOVC sepsis. Blood culture confirmed the presence of non-O1/non-O139 group Vibrio cholerae. The strain was a multidrug-resistant isolated of ST1565 as determined by whole-genome sequencing. The ResFinder database predicted 11 resistance genes for 6 classes of antibiotics: qnrVC5, sul2, floR, tet(59), aph(6)-Id, aph(3'')-Ib, dfrA15, dfrA31, almE, almF, and almG. Except for the quinolone qnrVC5, which was not expressed, the other resistance genes were consistent matched the phenotypic results. Additionally, 8 insertion sequences were identified: ISVch1, ISVvu4, ISVch6, ISVvu8, ISVpa3, ISVpa4, ISVsa3, and ISShfr9. Important virulence factors included 3 secreted protein toxin genes: Vibrio cholerae hemolysin, repeat toxin, and Vibrio parahaemolyticus thermostable direct hemolysin. The patient was cured after sequential treatment with meropenem, levofloxacin, and doxycycline. NOVC/ST1565 is a newly identified sequence type in China, which exhibits multidrug-resistant and hypervirulent phenotypes.

Drug Resistance, Multiple, Bacterial↗