Xiaogang Xu

Antimicrobial resistance (AMR) is a critical global health challenge, demanding rapid and accurate diagnostics to guide timely antimicrobial therapy. Current diagnosis is hindered by prolonged culturing and difficulties detecting low pathogen loads. Here, we present a culture-free diagnostic platform that integrates microfluidics, Raman micro-spectroscopy, and deep learning to deliver “sample-to-report” testing within 20 min. The microfluidic enrichment system employs dialysis-dielectrophoresis (DEP) technology to rapidly isolate pathogens directly from clinical samples with a detection limit as low as <2 colony forming unit (CFU)/ml. Combining a single-cell Raman fingerprint database of 342 clinical isolates from 29 bacterial and 7 fungal species with a 1D ResNet deep learning model, our approach achieved 95.1% accuracy in lab settings. Validated in a 305-patient clinical study involving primary urine and other clinical samples, it demonstrated 95.4% agreement with traditional culture methods and 98.5% sensitivity in diagnosing infections. While broader validation is needed for clinical implementation, the integrated, rapid diagnosis pipeline, as well as broad-spectrum detection, offer a promising solution for next-generation diagnostics for combating AMR.

Group B streptococcus is a leading cause of neonatal invasive diseases. ST12/serotype Ib GBS isolate, the second most prevalent lineage in East Asia, has aroused increasing attention, as a growing body of reports suggests they may be more virulent and fatal than the ST17/serotype III strain. Sag37, an ST12/serotype Ib isolate, was recovered from a fatal neonatal case and exhibited features suggestive of hypervirulence. To define this lineage’s prevalence and virulence, we analyzed 432 non-duplicate GBS isolates collected in Shanghai (2016 ~ 2022), and subtyped them by multilocus sequence typing (MLST) and capsular serotyping via a multiplex polymerase chain reaction. MLST revealed 50 sequence types, with ST10 and ST19 being most common. Nine clonal complexes were identified using the eBURST program, dominated by CC12 and CC19. Among seven serotypes identified, Ib was most prevalent, followed by III, V and Ia. Guided by the epidemiological data, additional clinical ST12/serotype Ib isolates, along with representative strains from other STs/serotypes, were selected for virulence assessment. For survival, 8-week-old CD1 mice were challenged subcutaneously with 1 × 108 CFU and monitored for 7 days. ST12/serotype Ib isolates caused 100% mortality within 48 h, whereas other GBS subtypes resulted in delayed or no mortality. For the median lethal dose (LD50), mice received intraperitoneal doses from 103 to 108 CFU; logistic regression estimated LD50 values ranging from ≤ 103 to ≥ 108 CFU within ST12/serotype Ib, indicating marked intra-lineage heterogeneity. To further investigate the molecular mechanisms underlying the hypervirulence, whole-genome sequencing was conducted on 33 ST12/serotype Ib GBS strains identified herein. A pyseer-based genome-wide association study was performed using LD50 as a quantitative trait. Multiple genetic variations potentially related to virulence were identified, providing insights into the molecular basis of hypervirulence of ST12/serotype Ib GBS. This study underscored the correlation between ST12/serotype Ib GBS isolates and hypervirulence, and further and revealed multiple candidate loci potentially associated with this phenotype. These findings highlighted the need for ongoing surveillance and functional investigation of emerging GBS lineages. Not applicable.

Acinetobacter baumannii is a critical pathogen which can cause hospital-acquired infections, particularly urinary tract infections (UTIs). The antimicrobial resistance (AMR) of A. baumannii is rising which poses a significant challenge to clinical management. Nitroxoline, an old antibiotic for treating uncomplicated UTIs, has gained renewed interest as a potential therapeutic option. Here, we investigates the bactericidal activity of nitroxoline against 34 A. baumannii (17 carbapenem-resistant and 17 carbapenem-sensitive isolates) collected from UTI patients. Nitroxoline exhibited a biphasic bactericidal effect, characterized by enhanced efficacy up to an optimal bactericidal concentration (OBC), followed by declined activity at higher nitroxoline concentrations. The OBCs, minimum bactericidal concentration (MBC), minimum inhibitory concentration (MIC), and time–killing curves were evaluated to elucidate bactericidal activity. Raman deuterium stable isotope probing (Raman-DIP) was employed to validate nitroxoline’s bactericidal effect and its impact on bacterial metabolic activity and survival rates. These results demonstrate that nitroxoline exhibits excellent inhibitory and bactericidal activity against A. baumannii . While nitroxoline exhibits biphasic bactericidal activity with OBC _50/90 values of 4/8 mg/L. Raman spectroscopy identified a decreased C–D ratio as nitroxoline concentration increased, indicating reduced metabolic activity. Notably, an inverse correlation ( r = –0.7594, p <0.0001) was observed between bacterial survival and the ccratio at concentrations above the OBC. These findings underscore the necessity of optimizing dosing regimens to enhance nitroxoline’s therapeutic efficacy and alleviate AMR development. Raman-DIP emerges as a robust tool for assessing nitroxoline’s effects on bacterial metabolism and determining MIC, offering valuable insights for future clinical applications.

The hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) poses a substantial challenge to the global health care. However, the mechanism behind its evolution and transmission remain elusive. Here, four virulence plasmid types were identified from 310 hv-CRKP isolates collected nationwide during 2017–2018, based on their aerobactin ( iuc locus) lineage and IncFIB replicons. Notably, pIUC1-IncFIB(K) ₃₇ and pIUC1-IncFIB(Mar), representing two epidemic virulence plasmids in Asia and Europe, respectively, accounted for >90% of the hv-CRKP episodes. Analysis of 494 K. pneumoniae isolates (376 from 2010–2013; 118 from 2017–2018) and 2578 public K. pneumoniae genomes indicated the notable role of IncFIB(Mar) plasmids in the hv-CRKP emergence and spread. Conjugation assays showed the helper IncFIB(Mar) plasmid could efficiently transfer into a hypervirulent strain and uniquely retromobilize with pIUC1-IncFIB(K) ₃₇ back into CRKP. Thereafter, the IncFIB(Mar) plasmid either lost rapidly or recombined with pIUC1-IncFIB(K) ₃₇ , generating the hybrid pIUC1-IncFIB(Mar) plasmid. Our findings elucidated formation, evolution, and dissemination trajectories of the two major hv-CRKP strains in different regions.

Background and objectives: The antimicrobial nitroxoline is used in treating uncomplicated urinary tract infections (UTIs) in some European countries. In vitro antimicrobial data on uropathogens from China are lacking. To investigate the activity of nitroxoline in vitro against uropathogens isolated from Chinese patients. Methods: MICs of nitroxoline were determined using broth microdilution of 229 bacterial isolates of 10 species including Acinetobacter baumannii derived from urinary sample. The EUCAST susceptibility breakpoint for Escherichia coli (16 mg/L) was applied for all isolates. The MBC for A. baumannii (n = 34) was determined, with the MBC defined as the nitroxoline concentration at which a 99.9% reduction in the initial inoculum was observed. Time-kill curves of the two isolates of A. baumannii were tested over a 24 h period. Results: Except for Pseudomonas aeruginosa, most isolates were susceptible to nitroxoline. The MIC50/90 values of nitroxoline for E. coli, Klebsiella pneumoniae and Proteus mirabilis were 4/8, 8/32 and 8/16 mg/L, respectively. Among the Gram-negative isolates, nitroxoline demonstrated a better inhibitory effect against A. baumannii with an MIC50/90 value of 2/2 mg/L. The MBC of A. baumannii was equal to the MIC or one dilution higher. The time-kill curves of A. baumannii displayed concentration-dependent killing. Conclusions: Nitroxoline showed excellent in vitro activity against uropathogens isolated from China and may be a good option for uncomplicated UTIs caused by A. baumannii, which are more challenging and have few clinical options. Further in vivo efficacy studies are needed.

We first reported the vanM vancomycin resistance gene in enterococci in Shanghai, China in 2006 and later found it to be the predominant van gene in vancomycin-resistant enterococci (VRE). In this study, we successively collected 1292 Enterococcus faecium and Enterococcus faecalis strains from in- and outpatients at Huashan Hospital, Fudan University and found that nearly all of the isolates (1290/1292) were vancomycin-sensitive determined by the VITEK 2 system. However, using a modified macromethod-based disk diffusion test, 10 E. faecium isolates that were previously determined to be vancomycin-sensitive by the VITEK 2 system were found to have colonies in the vancomycin disk inhibition zone. Pulse-field gel electrophoresis results showed that each randomly selected colony in the inhibition zone belonged to the same clone as the original strain. All 10 isolates were later found to be vanM-positive. The disk diffusion-based method may aid in the detection of vanM-positive E. faecium with low vancomycin minimum inhibitory concentrations and prevent missing the detection of vancomycin sensitivity-variable enterococci.

The association between the oral microbiome and mild cognitive impairment (MCI) remains unclear. This study aimed to investigate such an association among Chinese older adults. Participants without dementia were recruited from the community. A battery of neuropsychological tests was administered to evaluate the cognitive function. The diagnosis of MCI was based on Peterson’s criteria. The non-stimulated saliva was collected to extract sequences of the oral microbiome. Forty-seven MCI and 47 cognitively normal participants were included. There was significant difference in alpha diversity and insignificant difference in beta diversity between the two groups of participants. Compared with the cognitively normal group, Gemella haemolysans and Streptococcus gordonii were two significantly decreased species while Veillonella unclassified_Veillonella and Fusobacterium sp._HMT_203 were two significantly increased species in the MCI group. The richness of Gemella haemolysans presented the best discriminate value for MCI with the AUC (Area Under Curve) of 0.707, a cut-off value of 0.008 for relative abundance, the sensitivity of 63.8% and specificity of 70.2%. The dysbiosis of oral microbiome and relative abundance of Gemella haemolysans was significantly associated with MCI. Further studies were needed to develop new treatment strategies targeting the oral microbiome for cognitive impairment.