Journal of Medical Microbiology

BackgroundThe microbial aetiology of early childhood caries (ECC) in sub-Saharan African populations remains poorly characterised, with most studies focusing on conventional cariogenic pathogens like Streptococcus mutans. This study aimed to characterise the salivary microbial profile of children with ECC in urban Kano, northern Nigeria. MethodsIn this cross-sectional study of 162 children aged 3-5 years in urban Kano, unstimulated saliva samples were collected and analysed using standard bacteriological culture methods. Caries status was assessed using decayed, missing, and filled teeth (dmft) index and International Caries Detection and Assessment System (ICDAS). Microbial isolates were identified through Gram staining, colony morphology, and biochemical tests (catalase, coagulase, oxidase). ResultsOf 32 microbial isolates obtained, Staphylococcus aureus was the most prevalent (43.8%, n=14), followed by Streptococcus species (28.1%, n=9), Klebsiella species (12.5%, n=4), non-aureus staphylococci (6.3%, n=2), yeast (6.3%, n=2), and Pseudomonas species (3.1%, n=1). Only one isolate demonstrated direct association with dmft-detectable caries. Polymicrobial colonisation occurred in four cases (12.5%), predominantly featuring S. aureus-yeast combinations (n=2). White spot lesions (ICDAS 1-2) were associated with S. aureus and Klebsiella species in two separate cases. ConclusionThis study reveals an unexpected predominance of S. aureus in the salivary microbiome of children in northern Nigeria, challenging conventional paradigms of ECC microbiology. The low correlation between microbial isolates and clinical caries suggests complex, multifactorial aetiology. These findings highlight the need for molecular characterisation of oral microbiomes in African populations and reconsideration of caries pathogenesis models in this unique epidemiological context.

Gingival inflammation is associated with dysbiotic oral biofilms characterized by reduced nitrate-reducing capacity and diminished nitric oxide (NO) bioavailability. While dietary nitrate has been shown to influence oral microbial activity, the effects of sustained, localized nitrate delivery on oral biofilm ecology and gingival inflammation remain incompletely defined. In this randomized, double-blind, placebo-controlled trial, 30 adults with gingival bleeding were assigned to receive localized prebiotic nitrate (~0.989 mmol per dose) or placebo for 21 days. The primary outcome was mean bleeding on probing (mBOP). Secondary outcomes included modified Gingival Index (mGI), Quigley-Hein plaque index (QHPI), salivary nitrite (as a proxy for NO bioavailability), oral pH, and microbiome composition assessed by 16S rRNA gene sequencing. Prebiotic nitrate supplementation formulation delivered in a slow-release chewing gum significantly reduced mBOP (25.7% to 15.3%; p = 0.0002) compared to placebo chewing gum. Salivary nitrite levels and oral pH increased, indicating enhanced nitrate metabolism. Microbiome analysis demonstrated enrichment of nitrate-reducing taxa, including Rothia mucilaginosa and Neisseria spp., and a relative reduction in inflammation-associated genera such as Prevotella and Porphyromonas. Localized prebiotic nitrate formula delivered in a functional chewing gum was associated with reduced gingival inflammation and shifts in oral microbiome composition consistent with enhanced nitrate-reducing capacity critical in nitric oxide formation. These findings support a role for biofilm-directed nutritional modulation as a non-antimicrobial approach for managing gingival inflammation and improving nitric oxide bioavailability.

ObjectiveThis study utilizes small-sample periodontitis data to exploratively investigate causal relationships between the oral microbiome and periodontitis in East Asian populations. We aimed to identify specific oral microbial taxa that may drive disease pathogenesis. Given the exploratory nature of the dataset, findings should be interpreted as hypothesis-generating. MethodsWe performed a two-sample Mendelian randomization (MR) analysis using genome-wide association study (GWAS) summary statistics for tongue dorsum and salivary microbiomes alongside periodontitis data in East Asian populations. Primary causal estimates were derived using the inverse-variance weighted (IVW) method, supplemented by MR-Egger, weighted median, weighted mode, and simple mode methods. To ensure robustness, we assessed heterogeneity using Cochrans Q test, evaluated horizontal pleiotropy via the MR-Egger intercept and MR-PRESSO tests, and applied Steiger filtering to rule out reverse causality. ResultsWe identified 60 species-level microbial taxa causally associated with periodontitis, comprising 29 negative and 31 positive associations. These taxa were predominantly enriched within the genera Campylobacter, Pauljensenia, Solobacterium, and Streptococcus. ConclusionThis study provides tentative evidence for causal links between specific species-level oral microbial taxa and periodontitis, highlighting potential targets for prevention and therapeutic intervention.

BACKGROUNDAutomated antimicrobial susceptibility testing (AST) systems are crucial for accurate, timely detection of drug-resistant microbial isolates. This meta-analysis assessed the performance of the BD Phoenix ("Phoenix", BD Diagnostic Solutions), Vitek(R) 2 ("Vitek 2", bioMerieux), and DxM MicroScan WalkAway ("MicroScan", Beckman Coulter, Inc.) AST systems relative to common reference methodology. METHODSA systematic literature search in Ovid (MEDLINE and Embase) yielded 275 unique (not duplicated) records, with 44 additional records retrieved from handsearching; 39 studies met inclusion criteria. Categorical agreement (CA), essential agreement (EA), very major errors (VMEs), and major errors (MEs) for the three instruments were compared to a common reference method. Ratios of proportions were analyzed using random-effect meta-regression. RESULTSThe instruments did not differ significantly in CA, EA, or ME. Vitek 2 showed a higher overall VME rate than Phoenix ([~]44% higher; Vitek 2-to-Phoenix ratio = 1.44; p=0.062 [approaching significance]) and MicroScan (74% higher; ratio = 1.74; p=0.045). No appreciable difference was observed for VME between Phoenix and MicroScan. Subgroup analyses should be interpreted cautiously due to limited overall significance indicating varying performance across systems. Vitek 2 generally had higher relative VMEs for gram-negative organisms and lower relative VMEs for gram-positive organisms, whereas Phoenix showed the opposite pattern. MicroScan had relatively low VMEs when stratified by Clinical and Laboratory Standards Institute (CLSI) criteria; no differences in VMEs were observed using European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. CONCLUSIONAlthough some VME differences were noted, overall performance of the three systems was comparable. Organism- and drug-specific VME patterns--and updates to CLSI criteria over time--highlight the importance of continued monitoring of current breakpoints for all three instruments.

BackgroundOral hygiene is linked with dental caries experience. This systematic review and meta-analysis assessed the associations between oral hygiene status, the frequency of tooth brushing, and the prevalence of dental caries in Nigeria. Tools used for maintaining oral hygiene were also identified. MethodsRegistered with PROSPERO (CRD42022367763), this review searched PubMed, Web of Science, Scopus, African Journals Online, African Index Medicus, and Google Scholar in January 2026. Observational studies and clinical trials reporting baseline caries prevalence were included. There was no language restriction. Studies were excluded if they did not provide information on the sample size, had no study outcome data, or featured duplicate samples, and if they were review articles, systematic reviews and meta-analyses, case reports, case series, in vitro studies, commentaries/letters (editorials, opinion pieces) devoid of primary data. Pooled odds ratios (ORs) were estimated using random-effects models. Subgroup analyses were conducted by dentition type, geopolitical zone, study design, publication year, mean age, and sample size. ResultsTwenty-three cross-sectional studies were included, of which 20 (86.9%) were conducted in Southern Nigeria. After removing an influential outlier, poor oral hygiene was associated with a 38% reduction in caries odds (OR 0.62, 95% CI 0.46-0.84). Brushing at least twice daily was strongly associated with reduced caries (OR 0.01, 95% CI 0.00-0.01). No significant association was found between the type of cleaning device and caries prevalence. Subgroup analyses identified dentition type and publication year as significant moderators. Heterogeneity ranged from low to moderate, and no publication bias was detected for primary associations. The most common cleaning tool was a toothbrush with toothpaste, though chewing sticks, cotton wool, and other traditional tools were also reported. ConclusionTwice-daily tooth brushing is strongly associated with lower caries prevalence in Nigeria. Poor oral hygiene was linked to reduced caries odds in pooled analysis, a finding that may reflect socio-economic and dietary confounding. The type of cleaning tool was not significantly associated with caries risk, highlighting the importance of brushing frequency and technique over tool type. Future research should prioritize Northern Nigeria to address the geographic skewness of the data and improve national representativeness.

Aminoglycoside drugs, amikacin, streptomycin, and amikacin liposome inhalation suspension are crucial for treating refractory Mycobacterium avium-intracellulare complex pulmonary disease. In Mycobacterium tuberculosis, cross-resistance occurs between amikacin and kanamycin, but not between amikacin and streptomycin in genetic drug susceptibility testing. However, the occurrence of cross-resistance among aminoglycosides remains unclear in M. avium-intracellulare complex. We aimed to evaluate cross-resistance among aminoglycosides to determine whether streptomycin or kanamycin remains effective after the development of amikacin resistance. This single-center retrospective study included 20 patients with amikacin-resistant M. avium-intracellulare complex harboring rrs mutations. Paired analyses of streptomycin and kanamycin minimum inhibitory concentration values before and after amikacin resistance development were performed. In addition, streptomycin- and kanamycin-resistant strains were generated in vitro and resistance-associated mutations were identified using whole-genome sequencing. No significant increase was observed in streptomycin minimum inhibitory concentration values following amikacin resistance. In contrast, kanamycin values uniformly increased to >256 g/mL after the acquisition of amikacin resistance. Furthermore, amikacin- and kanamycin-resistant isolates shared mutations at position 1408 in the rrs gene, whereas streptomycin-resistant isolates exhibited mutations at position 20 in the rrs gene. These results suggest that amikacin and kanamycin exhibit cross-resistance in M. avium-intracellulare complex, whereas amikacin and streptomycin may not. Two cases in our cohort in which streptomycin treatment was effective after the acquisition of amikacin resistance further support these findings. In conclusion, streptomycin may be a potential therapeutic alternative for amikacin-resistant M. avium-intracellulare complex pulmonary disease. Future studies correlating streptomycin minimum inhibitory concentration values with clinical outcomes are required.

Rationale: Sputum-based testing using Xpert MTB/RIF Ultra (Xpert) is the most common molecular testing method for diagnosing tuberculosis (TB). Objectives: To evaluate whether sputum quality influences Xpert positivity and diagnostic accuracy. Methods: We screened consecutive people for presumptive TB in India, the Philippines, Vietnam, Nigeria, South Africa, Uganda, and Zambia as part of the R2D2 TB Network and ADAPT studies. Participants provided 2-3 sputum samples for Xpert and culture reference testing. The quality of the first sputum sample was graded following standardized procedures by trained research staff and used for Xpert testing. We performed logistic regression to evaluate whether sputum grade was independently associated with Xpert positivity, and calculated sensitivity and specificity of Xpert against a culture-based microbiological reference standard (MRS). Measurements and Main Results: Among 1,855 participants, 798 (43%) were female, 348 (19%) were living with HIV (PLHIV), and 1795 (97%) had a cough of [≥]2 weeks. Overall, 313 (17%) had a positive Xpert result. Most sputum samples were salivary (83%). Xpert positivity was lowest among salivary samples (16.1%) and highest among purulent samples (31.2%). After adjusting for demographic and clinical variables, there was no significant association between any sputum grade and Xpert positivity. Xpert sensitivity (salivary: 89%, mucoid: 91%, mucopurulent: 87%, purulent: 100%) and specificity (>98%) were high across sputum grades. Conclusions: Sputum quality was not independently associated with Xpert positivity and Xpert sensitivity was high across all sputum grades. These findings support molecular testing of all sputum samples for TB diagnosis regardless of macroscopic appearance.

IntroductionAntimicrobial resistance has existed in the environment long before its rapid emergence and detection in clinically relevant pathogens. Studying the resistance of environmental bacterial strains may allow novel resistance mechanisms to be identified before they appear in pathogenic strains. Gap StatementSearching for antimicrobial resistance genes in environmental bacteria represents an understudied research area compared to resistance within clinically relevant pathogens. AimTo evaluate resistance genes present within environmental non-aeruginosa Pseudomonas spp. isolates. MethodologyWe screened a set of bacterial isolates from untreated wastewater from Liverpool, UK, for the presence of extended spectrum {beta}-lactamases and carbapenemases. A sub-set of three resistant Pseudomonas spp. isolates were selected for whole-genome sequencing. We performed minimum inhibitory concentration assays against several {beta}-lactams, and ectopic expression of four novel resistance genes within Escherichia coli. ResultsHere, we report the discovery of novel class C {beta}-lactamase genes blaPFL7, blaPFL8 and blaPFL9, as well as a novel subclass B2 metallo-{beta}-lactamase blaPFM5 present within these strains. The class C genes encoded proteins with between 61-71% amino acid identity to the closest known match, blaPFL-1. These novel {beta}-lactamases degraded the cephalosporin nitrocefin and confer piperacillin and ceftazidime resistance to susceptible Escherichia coli when ectopically expressed. The {beta}-lactamase inhibitor tazobactam was effective at inhibiting these enzymes. The sub-class B2 metallo-{beta}-lactamase had 88% amino acid identity to its closet match blaPFM-1 and conferred carbapenem resistance to susceptible E. coli. The {beta}-lactamase inhibitors relebactam, vaborbactam, xeruborbactam and captopril had no impact on the carbapenem resistance phenotype. Analogues of all these novel genes (>95% nucleotide sequence identity) were identified within publicly available whole-genome sequencing data, suggesting they are found sporadically. ConclusionOur analysis adds to the growing number of {beta}-lactamase genes found from environmental Pseudomonas spp. and suggests that continued surveillance of this environmental reservoir for novel, clinically relevant, {beta}-lactamase genes is warranted.

BackgroundAntimicrobial resistance (AMR) surveillance is essential for quantifying and monitoring the burden of AMR among World Health Organization (WHO) priority pathogens. We analysed Tunisian AMR surveillance system (TARSS) data across five sentinel hospitals from 2014 to 2022. MethodsWe conducted a retrospective isolate-level analysis for Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter spp. Temporal, ward, and specimen associations were quantified using multivariable logistic regression models. Sex and age categories were explored in secondary models due to missingness. Temporal trends were assessed using Cochran-Armitage test, and co-resistance was summarised for third-generation cephalosporin and carbapenem phenotypes. We also evaluated temporal dynamics of 3GCR and CR profiles. ResultsA total of 35,525 E. coli, 14,325 K. pneumoniae, 9,679 P. aeruginosa, and 5,597 Acinetobacter spp. were reported to TARSS between 2014 and 2022. Mean annual MDR prevalence was high for Acinetobacter spp. (85.1%), moderate for K. pneumoniae (45.5%) and for P. aeruginosa (27.1%), and lower for E. coli (17.5%). Adjusted models indicated increased odds of resistance to several antibiotics, whereas E. coli showed decreased odds. Intensive care unit (ICU) and blood isolates were associated with higher odds of resistance in all pathogens. ConclusionThis nine-year multi-hospital analysis reveals a high prevalence of AMR across the four WHO priority pathogens, settings, and specimen types, with increasing resistance for some pathogen-antibiotic combinations. The higher odds of clinically important resistance amongst ICU and blood isolates support the use of ward-level antibiograms and stratified stewardship and infection prevention measures.

IntroductionAcinetobacter is a highly diverse genus which includes a range of common pathogenic species such as A. baumannii, A. lwoffii etc. Acinetobacter species causes bacteremia, pneumonia, wound infections, Urinary tract infections in community as well as hospital settings. A. baumannii is one of the ESKAPE pathogen which makes it even more lethal as antibiotics cannot action on this. AimTo isolate Acinetobacter species from various clinical samples and to check their antimicrobial susceptibility pattern by VITEK {square} Compact in SGT Hospital, Gururam, Haryana. ResultsOut of total 6673 samples 595 were the positive isolates from which 35 were Acinetobacter isolates which were received from various wards of the hospital. Occurrence of Acinetobacter was seen more in males(57.14%) as compare to females (46.8%). A total of 31 strains were A. baumannii, 3 were A. lwoffi and 1 strain was of A. haemolyticus. Prominent presence of Acinetobacter was seen in Blood (48.57%) specimen along with pus(22.85%), endotracheal (22.85%), tracheal (2.85%) and eye swabs (2.85%). All the isolates were resistant to piperacillin/tazobactam (100%), ceftriazone (100%), amikacin (100%), gentamicin (100%) ciprofloxacin (91.42%), ceftazidime (91.42%), cefepime (88.57%), levofloxacin (88.57%) and trimethoprim/sulfamethoxazole (80%). Colistin susceptibility was observed in 88.57% of the isolates. ConclusionAcinetobacter is a common pathogen in hospital acquired as well as in community acquired infections as it is a opportunistic pathogen hence to identify the Acinetobacter species and to understand their antimicrobial resistance pattern this study was conducted.

BackgroundThe use of fluoride-containing dentifrices can reduce the risk of dental caries. The systematic review was conducted to address two research questions: (i) the prevalence and frequency of fluoridated toothpaste use among Nigerian children and adolescents across geographic and demographic settings, and (ii) its association with dental caries prevalence, stratified by location and baseline caries risk. MethodsThis systematic review, registered with PROSPERO (CRD42022362116), followed the PRISMA guidelines. A PIO framework was applied to include children and adolescents (6 months-19 years) in Nigeria using fluoridated toothpaste, with caries outcomes measured via dmft/DMFT indices. A comprehensive search of PubMed, Web of Science, Scopus, Embase, AJOL, and Google Scholar was conducted from January 2001 to January 2026, supplemented by reference and grey literature searches. Study selection, data extraction, and risk of bias assessment using an adapted Hoy et al. tool were performed independently by multiple reviewers, with high inter-rater reliability (Kappa=0.90). Data were pooled using a random-effects model, with sensitivity, subgroup, and meta-regression analyses conducted to explore heterogeneity and effect modifiers. Publication bias was assessed using funnel plots and Eggers test. ResultsOf 1,194 identified records, 18 studies (n=12,719 participants) were included. The use of fluoridated toothpaste was widespread (prevalence: 61.9% to 95.8%), yet its association with dental caries varied significantly by location. A meta-analysis of 14 studies indicated a significant 16% reduction in caries odds with fluoridated toothpaste use after removal of an influential outlier (OR = 0.84, 95% CI: 0.71-0.99, p=0.04). Subgroup analyses revealed this protective association was significant in urban and rural settings (p<0.05) but absent in suburban Nigeria. Furthermore, dental caries prevalence and severity (DMFT/dmft) were substantially higher in urban and rural areas, where the association was significant, compared to suburban regions. All studies were assessed as having a low risk of bias, and no significant publication bias was detected. ConclusionFluoridated toothpaste is widely used in Nigeria and associated with a reduction in the prevalence of dental caries in Nigeria. It appears the relationship is moderated by residential location, and the DMFT/dmft. Longitudinal studies are needed to explore the interactions between the DMFT/dmft, use of fluoridated toothpaste, and residential location in Nigeria.

Microbial keratitis is a sight-threatening corneal infection with varying etiological agents, primarily bacteria and fungi. Assessing and contrasting the virulence factors of microorganisms isolated from a non-contact lens-associated keratitis (NCLAK) and contact lens-associated keratitis (CLAK) is the goal of the current investigation. Samples were collected from over 60 patients and analysed using standard microbiological techniques, including culture, Gram staining, KOH mount, biochemical tests, antimicrobial susceptibility testing, and biofilm assays. The results demonstrated that CLAK isolates were predominantly bacterial, especially Pseudomonas aeruginosa, known for strong biofilm production and high multidrug resistance. In contrast, NCLAK showed a higher incidence of fungal infections, particularly Candida albicans. The results highlight the significance of early diagnosis, tailored and improved awareness regarding contact lens hygiene to prevent complications associated with keratitis.

Background Pseudomonas aeruginosa is a major cause of healthcare-associated infections in paediatric settings, where its persistence in moist environments such as hospital water and wastewater systems poses a particular risk to neonates and immunocompromised children. Aim The aim of this study was to showcase the long-term survival and transmission of P. aeruginosa in a large tertiary children's hospital in England which is crucial to develop strategies for water-safe care. Methods Environmental P. aeruginosa isolates were collected from taps, sinks, showers, and baths in augmented care areas of a 330-bed tertiary children's hospital built to NHS water-safety standards. Clinical isolates were classified as invasive (blood, cerebrospinal fluid, and bronchoalveolar lavage) or non-invasive (respiratory, urine, ear, abdominal, and rectal surveillance). Variable number tandem repeat (VNTR) profiles and metadata were extracted from PDF reports, de-identified, deduplicated, and curated using Python and R. Findings This retrospective study analysed nine-locus VNTR profiles of 457 P. aeruginosa isolates submitted to the UK Health Security Agency from a large tertiary children's hospital, identifying 56 isolate clusters (each with [&ge;]2 isolates), of which 19 (34%) contained at least one invasive isolate. The most persistent cluster (Cluster 1, n=20) spanned from July 2016 to September 2024, containing environmental and clinical (invasive and non-invasive) isolates. Conclusion These findings demonstrate long-term persistence of certain genotypes and temporal overlap between environmental and clinical isolates, highlighting the difficulty in detecting and eradicating P. aeruginosa in hospital water and wastewater systems and reinforcing the need for continuous rigorous water system controls.

BackgroundThe never-ending emergence of superbugs casts a shadow over the victorious age of antibiotics. In fact, the triumph of antibiotics was previously viewed in retrospection as our final victory over bacteria. Bacteria like Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli are now raising an alarming number of infections across hospitals and communities around the globe. The objective was to evaluate the implications for antimicrobial stewardship based on identifying the antibiotic resistance profiles, genotype mechanisms, and trends in common pathogenic bacteria found in various hospitals across Iraq. MethodsWe used a two-fold approach that was comprehensive in scope and involved both efficient multicenter surveillance as well as cutting edge genetic analysis to unravel the complex topography of antibiotic resistance. We provided a geographically heterogeneous but diverse set of clinically obtained isolates to participate in hospitals for a period of 24 months and concentrated our efforts on prioritized pathogens K. pneumoniae, A. baumannii, E. coli, P. aeruginosa, and S. aureus that are well known to pose serious threats. Beginning with clinically obtained isolates sourced across the entire globe, we used standardized techniques such as broth microdilution to first undertake phenotyping in a central reference lab to establish microbial identity based on resistance phenotypes to a set of prioritized antibiotics that include carbapenems, third generation cephalosporins, or fluoroquinolones. Finally, we derived data concerning the emergence patterns and geographic distribution of resistant microbes such as MRSA or CRE. We used genome-wide sequencing to unlock information concerning the genetic blueprints for a set of specifically chosen isolates based on their representational diversity across geographic locales, resistance phenotypes, and specific times. ResultsThe sample was made up of Escherichia coli (n = 225), Klebsiella pneumoniae (n = 185), Staphylococcus aureus (n = 135), Pseudomonas aeruginosa (n= 90), and Acinetobacter baumannii (n = 125). Ceftriaxone resistance was found in 80.4% of E. Coli, ciprofloxacin resistance in 45.6%, and meropenem resistance in 15.1%. K. pneumoniae exhibited 38.9% resistance to aminoglycosides and 70.2% resistance to carbapenems. The percentage of MRSA in S. aureus was 55.5%. P. aeruginosa showed 22.2% resistance to colistin, 37.8% resistance to piperacillin tazobactam, and 50.0% resistance to ceftazidime. Imipenem resistance was found in 85.6% of A. baumannii isolates, whereas colistin resistance was found in 28.8% of isolates. In all, 3.4% of isolates are pan-drug-resistant (PDR), 14.6% are extensively drug-resistant (XDR), and 52.1% are multidrug-resistant (MDR). WGS identified common genes such bla_NDM-1, bla_OXA-48, mcr-1, aac (6)-Ib, and plasmid replicons IncF, IncL/M, and IncI2. Carbapenem resistance in Gram-negative bacteria rose by around 18% over the course of five years. ConclusionsThis study shows that the rapid spread of complex genetic information in bacteria causes antibiotic resistance problems. High-level resistance represents an expected consequence of the spread of resistance genes and successful bacteria within healthcare systems. We demonstrate in our results that our expertise in overcoming resistance at a molecular level will play a crucial role in combating infectious diseases in the coming years.

Urinary tract infection (UTI) is one of the most common community-acquired bacterial infections mainly caused by extraintestinal pathogenic Escherichia coli (ExPEC) strains. The high-risk Escherichia coli ST131 clone is a major global cause of this disease. The lineage rapid dissemination is associated to multidrug resistance (MDR), production of extended-spectrum beta-lactamase (ESBL), and multiple virulence-associated genes. Although we lack information about ExPEC high-risk clones in Latin America, we recently reported an increase in ST131 dissemination in Rio de Janeiro from 2015 to 2019. The present study aims to characterize virulence and resistance molecular and phenotypic features that may contribute to dissemination of E. coli ST131 in Rio de Janeiro, Brazil. We assessed a 133 E. coli ST131 strains collection obtained from urine of outpatients with suspected UTI, in 2019. We determined antimicrobial susceptibility, fluoroquinolones resistance genes, virulence factors associated genes and biofilm production of all strains and analyzed the frequencies by each clade or subclade. A higher incidence of women (92%) and elderly (65%) subjects was observed. Overall resistance to first- and second-line treatment for UTI antimicrobials ampicillin, ciprofloxacin and sulfamethoxazole-trimethoprim was detected in high rates (40%), with a major impact of subclade C2 strains that were resistant to almost all antimicrobials tested, 52% carry ESBL and 66% of strains harbor the aac(6)-Ib-cr ciprpofloxacin resistance gene. Clade B and subclade C2 showed higher virulence scores among the other clades. They present unique virulence profiles characterized by the presence of papGIII, sfa/focDE, and especially ibeA genes in clade B, and the afa/DrBC, papGII, hlyA, cnf1 genes in subclade C2. Over 50% of our strains are biofilm producers, characterized by weak (24%) and strong producers (32%). ESBL and MDR strains harbor mainly papA, papGII, hlyA, cnf1 and kpsMTII genes that plays a key role in ST131 colonization. Subclade C1 is the major biofilm producer (78%), despite its lower virulence score. We also detected higher incidence of papA (27%), hlyA (19%) genes and the RPAI(malX) marker (84%) in biofilm producer strains with a statistical association of sfa/focDE gene (9%). We can infer that Clade C strains might be responsible for ST131 dissemination and persistence in Rio de Janeiro.

Urinary tract infections (UTIs) are among the most common infectious diseases worldwide, with Escherichia coli being the predominant uropathogen. The increasing prevalence of extended-spectrum beta-lactamase (ESBL)-producing strains and their association with fluoroquinolone resistance pose a significant challenge to empirical therapy, particularly in community settings. The aim of this study was to determine the epidemiology and predictive factors associated with ESBL-producing E. coli and its concomitant fluoroquinolone resistance in community-acquired clinical isolates. A retrospective cross-sectional study was conducted analyzing 244 clinical E. coli isolates. Demographic and microbiological data were collected, including age, sex, sample type, and antibiotic susceptibility. Associations between variables and ESBL production were assessed using Pearsons chi-squared test, and odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. Of the isolates, 165 (68%) were ESBL-producing. A significant association was observed between age group and ESBL production (p < 0.001), with the highest frequency in the 20-39 age group. Most ESBL-positive isolates were obtained from women (73%), although odds ratio (OR) analysis suggested a non-significant trend toward a higher probability in men (OR = 1.29; 95% CI: 0.72-2.31). High rates of fluoroquinolone resistance were identified among the ESBL-producing isolates, with 30% resistance to levofloxacin and 35% to ciprofloxacin (p < 0.001). Urine samples showed the highest concentration of ESBL-positive isolates, with a significant association between sample type and resistance (p < 0.001). The high prevalence of ESBL-producing E. coli and its concomitant resistance to fluoroquinolones highlight a critical challenge for the empirical treatment of urinary tract infections in Mexico, underscoring the need to strengthen antimicrobial use management and local surveillance strategies.

In this study we explored phenotypic resistance using traditional Kirby-Bauer methods in human and animal derived Campylobacter isolates that were concurrently resistant to both azithromycin and ciprofloxacin to an expanded panel of antimicrobials, including clindamycin, fosfomycin, ampicillin sulbactam and tigecycline. Out of 236 Campylobacter isolates, over 85% of C. jejuni and C. coli were resistant to clindamycin, over 60% were resistant to ampicillin sulbactam and over 30% to fosfomycin. Less than 2% of isolates were resistant to tigecycline and there was no observed resistance to Imipenem.

BackgroundThere is a close correlation between neuroendocrine regulation and pulpitis progression. This study aims to identify key neuroendocrine regulation-related genes in pulpitis, providing insights for its treatment. MethodsGSE77459 and GSE92681 datasets were used to validate experimental findings. Key neuroendocrine regulation-related genes were identified via Cytoscape plugin cytoHubba and expression validation. Gene set enrichment analysis, RNA-binding protein regulatory networks, post-translational modifications, molecular regulatory networks, and drug prediction were performed. Key gene expression was experimentally verified in clinical samples. ResultsTop 10 genes were obtained via cytoHubba; 4 (IL6R, OSM, IL1RN, CCL4) with significant differences between pulpitis and control samples and consistent trends in both datasets were identified as key genes. Gene set enrichment analysis showed key genes participate in pathways like cytokine-cytokine receptor interaction. Related RNA-binding proteins were ELAVL1 and HNRNPA1, with phosphorylation as the main post-translational modification. Core regulatory microRNAs included miR-519, miR-765, miR-23, and regulatory factors included FOXC1, PRRX2. Targeted drugs (e.g., sarilumab, haloperidol decanoate, cyclosporine) were predicted, and clinical sample verification confirmed consistent expression trends. Conclusion4 key neuroendocrine regulation-related genes were identified, which may have clinical significance for the diagnosis and treatment of pulpitis.

Aim: To comprehensively characterize the salivary proteome in periodontitis using Orbitrap Astral data-independent acquisition mass spectrometry (DIA-MS), identify an atlas of differentially expressed proteins (DEPs), and develop a machine learning-derived multi-protein biomarker panel for non-invasive diagnosis of stage III/IV periodontitis. Materials and Methods: Unstimulated saliva samples from 199 participants (periodontal health/gingivitis, n=120; stage III/IV periodontitis, n=79) were analyzed by Orbitrap Astral DIA-MS. DEPs were identified, and pathway enrichment analysis was performed. A two-tier machine learning pipeline, integrating pathway-based feature selection with cross-validated evaluation, was applied to identify the optimal diagnostic panel. Results: Orbitrap Astral DIA-MS quantified 5,597 salivary proteins and 1,966 DEPs (|log2FC|>0.5, FDR<0.05). Pathway analysis identified 14 periodontitis-relevant KEGG pathways, including Th17 cell differentiation, IL-17 signaling, neutrophil extracellular trap formation, and complement and coagulation cascades. A four-protein panel (TEC, RAC1, MAPK14, KRT17) achieved an area under the curve (AUC) of 0.985 plus-or-minus sign 0.010, with 83% sensitivity and 100% specificity. The panel was corroborated using public datasets. Conclusions: To our knowledge, this study represents the first application of Orbitrap Astral DIA mass spectrometry in periodontitis research, establishing a disease-specific DEPs atlas and a salivary biomarker panel with high diagnostic accuracy for stage III/IV periodontitis, providing a foundation for future external validation studies.

Background: Metronidazole (MTZ) is a first-line antibiotic for several enteric infections. Its use is common in low-income countries, where most primary-care consultations are conducted by nurses. However, increasing resistance among some enteric pathogens is a growing concern. Using WHO guidelines, we conducted a register-based cross-sectional study to assess MTZ prescribing practices and their determinants in public and private primary healthcare facilities in South Benin. Methods: We performed a register-based cross-sectional study covering the year 2020 in 11 primary healthcare facilities (5 public and 6 private) in Abomey-Calavi, South Benin, following WHO recommendations. In total, 200 visits per facility were selected using systematic random sampling. The primary outcome was the prevalence of MTZ prescription. Determinants of MTZ prescription were identified using multivariable logistic regression analysis. Results: In total, 2,200 medical visits were analyzed. The median age of patients was 19 years, and 57% were female. Antimalarials were prescribed in 52% of visits. Antibacterial agents were prescribed in the majority of visits, with MTZ being the second most frequently prescribed antibiotic (18%), after aminopenicillins (27%). In multivariable analysis, digestive symptoms (adjusted odds ratio [aOR], 8.65; 95% confidence interval [CI], 6.49-11.6), genitourinary symptoms (aOR, 6.84; 95% CI, 3.18-15.0), and skin lesions (aOR, 2.39; 95% CI, 1.58-3.60) were independently associated with increased odds of MTZ prescription. In contrast, fever (aOR, 0.66; 95% CI, 0.49-0.87), respiratory symptoms (aOR, 0.44; 95% CI, 0.26-0.71), and malaria (aOR, 0.21; 95% CI, 0.15-0.28) were associated with decreased odds. Visits in the private sector were also associated with higher odds of MTZ prescription compared with the public sector (aOR, 2.31; 95% CI, 1.78-3.02). Conclusion: MTZ is the second most commonly prescribed antibiotic in primary care in the study area, with its use largely driven by digestive symptoms. Further studies are needed to assess the appropriateness of this prescription. Additionally, research is warranted to understand better the determinants of higher antimicrobial prescribing in the private healthcare sector.