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Urinary tract infections (UTIs) are among the most common bacterial infections worldwide and are primarily caused by Escherichia coli . While E. coli is known to colonize both humans and food-producing animals, the extent to which zoonotic strains impact human disease remains poorly understood. Emerging evidence suggests that food animals may serve as an underrecognized reservoir for extraintestinal pathogenic E. coli (ExPEC). In this study, we used a genomic attribution model to quantify the contribution of zoonotic strains to UTIs in Southern California. We found that approximately 18% of E. coli UTIs were likely attributable to food animals. Individuals living in high-poverty neighborhoods had a 1.6-fold increased risk of zoonotic UTIs compared to those in low-poverty areas. These findings highlight zoonotic transmission as an important driver of UTIs and suggest that reducing ExPEC in food-animal reservoirs could help lower disease burden and address health disparities.

Background The dogma that urine is sterile in healthy individuals has been overturned by recent studies applying molecular-based methods. Mounting evidences indicate that dysbiosis of the urinary microbiota is associated with several urological diseases. In this study, we aimed to investigate the urinary microbiome of male patients with calcium-based kidney stones and compare it with those of healthy individuals. Results The diversity of the urinary microbiota in kidney stone patients was significantly lower than that of healthy controls based on the Shannon and Simpson index ( P  < 0.001 for both indices). The urinary microbiota structure also significantly differed between kidney stone patients and healthy controls (ANOSIM, R = 0.11, P  < 0.001). Differential representation of inflammation associated bacteria (e.g., Acinetobacter ) and several enriched functional pathways were identified in the urine of kidney stones patients. Meanwhile, we found the species diversity, overall composition of microbiota and predicted functional pathways were similar between bladder urine and renal pelvis urine in kidney stone patients. Conclusions A marked dysbiosis of urinary microbiota in male patients with calcium-based kidney stones was observed, which may be helpful to interpret the association between bacteria and calcium-based kidney stones.

Background The treatment of Enterobacteriaceae family including diarrheagenic E. coli (DEC) has been increasingly complicated due to the emergence of resistant strains. Here we report on the phenotypic resistance profiles and ESBL genotype and virulence profiles of Enteroaggregative E. coli (EAEC) and Enteropathogenic E. coli (EPEC) isolated from children hospitalized with acute gastroenteritis in Qatar (AGE). Results E. coli were isolated and characterized from 76 diarrheagenic stool positive samples, collected from hospitalized children less than 10 years old. Isolates were tested for antibiotic susceptibility against eighteen clinically relevant antibiotics using E-test method. Conventional PCR was performed to detect genes encoding ESBL and virulence factors. Chi-square test was performed to compare the individual antibiotic resistance between EPEC and EAEC. A significant percentage (73.7%) of isolates were resistant to at least one antibiotic. Overall, high resistance (70%) was reported to the first-line antibiotics such as ampicillin, tetracycline (46.4%), and sulfamethoxazole-trimethoprim (42.9%). Further, 39.5% of the isolates were multidrug resistant (MDR), with 22.4% being ESBL producers. On the other hand, all isolates were susceptible to carbapenem, fosfomycin, amikacin and colistin. The incidences of resistance to the 18 antibiotics between EPEC and EAEC were not significantly different by Pearson chi -square test ( P  > 0.05). Genetic analysis revealed that 88.23% of ESBL production was bla CTX-M-G1 ( bla CTX-M-15 , bla CTX-M-3 ) - encoded. Several different combinations of virulence markers were observed, however, there was no specific trend among the isolates apart from absence of the bundle-forming pilus (bfpA ) gene, which encodes the type IV fimbriae in EPEC adherence factor (EAF) plasmid (pEAF), among all EPEC (atypical). 15% of the EAEC strains were positive for a combination of astA , aap & capU , while 10% were positive for three different combinations. The aap , aatA , capU and aggR virulence genes showed the highest frequency of 65, 60, 55 and 55% respectively. Others genes, east , astA , and aai , showed frequencies of 35, 30 and 20% respectively. Conclusions Atypical EPEC and EAEC were the primary etiological agents of diarrhea in children among DEC pathotypes. Our results indicated high rate of antimicrobial resistance pattern of DEC strains, which necessities the development of regulatory programs and reporting systems of antimicrobial resistance in DEC and other AGE-associated bacteria to insure effective control of diarrheal diseases. Results from this study demand a further research on identifying the phenotypic and genotypic profiles of more DEC pathotypes in various clinical samples.

Background Different diagnostic methods have been used for the laboratory confirmation of leptospirosis. Molecular diagnostic techniques are not only faster and more sensitive than culture analysis, but can also detect a Leptospira infection before the appearance of antibodies. The aim of the present study was to analyze and compare two different PCR approaches applied to blood and urine specimens obtained from patients with clinical manifestations that were suggestive of leptospirosis. Furthermore, the results of these different PCR approaches were compared with the results of culture and serology analyses. Results A total of 400 samples (234 blood or 58.5% and 166 urine of 41.5%) from 310 Slovenian patients with clinical manifestations suggestive of leptospirosis were tested using conventional PCR assays targeting the rrs gene and RT-PCR targeting the lipL32 gene. Additionally, culture, serology and sequence analysis were performed for the majority of these samples. The PCR and RT-PCR results were concordant in 376 out of 400 of these samples (94.0%). Conventional PCR was positive for 27 out of 400 samples (6.8%) and RT-PCR was positive for 47 out of 400 samples (11.8%). Culture and microscopic agglutination tests supported these diagnoses. Conclusions A comparison of the two PCR methods indicated that the RT-PCR targeting of the lipL32 gene was faster, more sensitive and more specific for the determination of Leptospira DNA in these clinical samples.

Infections caused by carbapenem-resistant Enterobacterales (CRE) pose significant threats to patients and public health worldwide. Carbapenem resistance can occur through several molecular mechanisms, including enzymatic hydrolysis by carbapenemases and reduced influx via porin mutations. Identifying carbapenemase-producing isolates could enable tailored antibiotic selection to improve patient outcomes and infection control measures to prevent further carbapenemase transmission. In a large collection of CRE isolates, we found that only carbapenemase-producing CRE exhibited an inoculum effect, in which their measured resistance varies markedly with cell density, which risks misdiagnosis. Further, this inoculum effect occurred under conditions where bacteria released carbapenemases to the community upon exposure to antibiotics that resulted in cell death. Measuring this inoculum effect, or integrating other data from routine antimicrobial susceptibility testing, enhanced carbapenem resistance detection, paving the way for more effective strategies to combat this growing public health crisis.

GBS remains a major cause of neonatal sepsis, pneumonia, and meningitis despite the common use of IAP that aims to eradicate maternal colonization, the main risk factor for neonatal disease. Although IAP has reduced the incidence of early-onset neonatal infections, it has had no impact on late-onset infections in babies between 7 days and 3 months of age. Since colonization is intermittent and GBS has been shown to persist in the genitourinary tract despite antibiotic exposure, more research is needed to understand mechanisms of adaptation. By comparing the genomes of GBS strains recovered before (prenatal) and after (postpartum) IAP and childbirth, this study demonstrates how selective pressures shape GBS evolution, favoring traits that promote survival and persistence. Understanding adaptive traits is essential for improving diagnostics, refining prophylaxis strategies, and guiding the development of more effective prevention practices that can reduce the likelihood of GBS transmission to neonates.

Nationwide multicenter surveillance demonstrates a substantial burden of antimicrobial resistance among ocular bacterial pathogens. In the 2009-2018 ARMOR collection, methicillin-resistant (MRSA) accounted for 34.9% of ocular isolates, and methicillin resistance was strongly associated with fluoroquinolone resistance. Ocular infections can destroy tissue within hours; timely microbiologic diagnosis and treatment adjustment are essential; however, culture is constrained by small specimen volumes, low inoculum, and prior antimicrobial exposure. To tackle multidrug-resistant (MDR) infections, we propose that phenotypic testing could be complemented with targeted whole-genome sequencing in cases of severe or persistent eye infections, to provide lineage characterization, resistance and virulence determinants, and critical features of pathogenic MDR bacteria that are clinically relevant to predict patient outcomes. A genome-informed workflow, sequencing from pure culture, and integration with phenotypic data could refine empiric therapy, enable earlier de-escalation, and strengthen surveillance of high-risk lineages to reduce vision-threatening treatment failures and save patients' vision.

Although β-lactamases have always been considered enzymes involved in resistance to β-lactam antibiotics, they also have to be considered as playing a role in reshaping bacterial physiology. By studying a series of class C β-lactamases, we uncovered an unexpected dual role. Besides conferring resistance to β-lactams, they also impact bacterial growth, motility, and pathogenicity through modulation of flagellar biosynthesis. Strikingly, while CMY-42- and CMY-145-producing recombinant Escherichia coli strains showed enhanced in vitro fitness growth by reducing energy-costly flagellar production, production of CMY-2 (the most commonly identified acquired AmpC β-lactamase identified in Enterobacterales) restored flagella and increased virulence in vivo . This work reframes β-lactamases as metabolic regulators influencing ecological success, offering new insight into how resistance determinants promote the spread and clinical impact of Enterobacterales.

Carbapenem-resistant Enterobacterales are defined as Enterobacterales which are resistant in vitro to any carbapenem antimicrobial or are documented to produce a carbapenemase. They are a serious public health threat and are listed as critical pathogens on the World Health Organization’s (WHO) list of priority pathogens. Critical pathogens are antibiotic resistant pathogens which pose the highest threat to public health due to limited treatment options, high disease burden, high rates of treatment failure, high transmissibility, increased healthcare costs and increasing trends in antibiotic resistance, with few or no promising antibiotic candidates in the research and development pipeline. When treatment failure due to CRE occurs, physicians are left with few antibiotic alternatives, most of which have high toxicity profiles. While CRE are of public health importance, globally, their problem is exacerbated in Low and Middle Income Countries (LMICs) due to reasons such as poor diagnostic microbiology capacity, data gaps due to poor surveillance structures, inadequate antibiotic treatment options and poor infection prevention and control protocols and ultimately poor patient outcomes. Also, rising rates of CRE infections and infections caused by other multidrug resistant (MDR) organisms could result in a failure to achieve the health related sustainable development goals, due to increased healthcare costs, poverty and reduced productivity. Efforts to adequately combat CRE infections in LMICs must therefore involve context specific and sustainable solutions. The aim of this review, therefore, is to discuss the challenge of CRE in LMICs and offer recommendations to curb the menace posed by CRE.

Chronic otitis media (COM) is a common and often persistent ear disease, especially when complicated by Eustachian tube dysfunction (ETD). By profiling microbiota at both Eustachian tube openings, this study links upper-airway microbial ecology with middle-ear microbial states in COM and helps clarify where clinically relevant signals may arise along the Eustachian tube pathway. The paired nasopharyngeal–middle ear design revealed that nasopharyngeal microbes may be linked to middle-ear community shifts in COM with obstructive ETD, consistent with a potential upper airway contribution to the middle-ear microbiota, generating testable hypotheses about microbial exchange and persistence. These findings highlight the upper airway microbiome as a potential target for developing new preventive and therapeutic strategies in COM.