Journal of Medical Microbiology

ObjectivesThe aim of this study was to investigate the potential association between the formation of oral bacterial biofilms and the occurrence of antibiotic resistance among 294 oral bacterial isolates. Study designA total of 100; 25-65year old patients were chosen. Buccal mucosa swabs were collected and cultured in appropriate media, then bacteria were isolated and identified. Then 294 bacterial isolates were assessed for biofilm production by the phenotypic method, i.e., the tissue culture plate method (TCPM). Finally, antibiotic susceptibility patterns of the 294 isolates were done by the Kirby-Bauer disc diffusion method for 7 {beta}-lactam antibiotics (ampicillin, penicillin, amoxicillin, cephalothin, oxacillin, cloxacillin, and cefoxitin) and 7 non-{beta}-lactam antibiotics (tetracycline, co-trimoxazole, ciprofloxacin, clindamycin, erythromycin, lincomycin, and vancomycin). ResultsWhen isolates were exposed to biofilm detection by the TCP method, 9 (3.1%) showed high biofilm formation capacity, 213 (72.4%) showed moderate biofilm formation capacity, while 72 (24.5%) showed weak/no biofilm formation. The isolated bacterial biofilms positively showed that the bacterial isolates that showed high and moderate biofilm formation capacity have a higher rate of resistance to most antibiotics with significant difference (p < 0.0001) than weak/no biofilm formation. ConclusionThe present study demonstrates that aerobic bacteria are still the major bacteria isolates from the oral cavity. Antibiotic resistance in the oral bacterial isolates was found to be associated with bacterial biofilm formation.

BackgroundLower respiratory tract infections (LRTIs) remain a major cause of morbidity and mortality among hospitalized patients.1 However, isolating organisms from respiratory samples often leads to diagnostic uncertainty due to the coexistence of colonizers, commensals, and contaminants.2 To address this challenge, this study employed a structured, stepwise exploratory model to differentiate true pathogens from non-pathogens in aerobic respiratory cultures and Multiplex PCR (Biofire(R) FilmArray) results. MethodsThis prospective, longitudinal time-bound study was conducted over three months (August- October 2024) at a tertiary care center in northern India. Adult patients ([&ge;] 18 years) with positive lower respiratory tract samples (aerobic culture or Multiplex PCR (Biofire(R) FilmArray) were enrolled. Each isolate was independently classified by the treating clinician, microbiologist, and study investigator using a six-step clinical-pathological algorithm that incorporated clinical signs, Sequential Organ Failure Assessment (SOFA) score trends, alternative infection sources, host factors, and outcome data. The final classification was determined by the investigator. Outcomes, including treatment response and mortality at 28 days, were compared across pathogen and non-pathogen groups. FindingsOf the 145 included cases, 131 (90{middle dot}3%) were classified as pathogens and 14 (9{middle dot}7%) as non-pathogens. Cohens Kappa between investigator and microbiologist classifications was 0{middle dot}28, indicating fair agreement. Among pathogen cases, 68 (51{middle dot}9%) responded to treatment, while 63 (48{middle dot}1%) did not respond to treatment in the pathogenic group. In contrast, 12 of 14 non-pathogen cases (85{middle dot}7%) were not treated, with favourable outcomes in most, and only one unrelated death (7{middle dot}1%). InterpretationThe structured clinico -microbiological model strongly correlates with treatment outcomes, making it useful for differentiating infection from colonization. Crucially, microbiological detection alone doesnt determine pathogenicity. Integrating clinical, laboratory, and outcome data is essential for rational antibiotic use and effective antimicrobial stewardship. FundingNone

IntroductionC-reactive protein (CRP) is an established acute-phase marker for infection and inflammation, which can help guide clinical decision-making in primary and secondary care. Many European guidelines recommend point-of-care (POC) CRP testing to improve antimicrobial stewardship in primary care. This performance evaluation study assessed the equivalence of the quantitative POC LumiraDx CRP Test compared to a laboratory-based reference method. MethodsMethod comparison, matrix equivalency, and precision were evaluated. Plasma samples from secondary care patients presenting with symptoms of infection or inflammation were analyzed centrally using the LumiraDx CRP Test and the reference test (Siemens CRP Extended Range for Dimension(R) Clinical Chemistry System). The method comparison was conducted used Passing-Bablok regression analysis with prespecified criteria of r[&ge;]95 and a slope of 0.95-1.05. The REACT study (NCT05180110) evaluated the equivalence and precision of the testing modalities (fingerstick, venous blood, and plasma samples from the same secondary care patient) using Passing-Bablok regression analysis of the results of the POC LumiraDx CRP Test. ResultsIn analysis of 320 plasma samples from 110 patients, the POC LumiraDx CRP Test demonstrated close agreement with the reference method, meeting the prespecified performance criteria (r=0.99, slope of 1.05, N=110). Paired replicate precision of the testing modalities was high, with mean %CV of 6.4 (plasma), 6.6 (capillary direct), and 8.1 (venous blood). Passing-Bablok regression showed matrix equivalency for all replicate pairs of the testing modalities, with r values across all sample types of 0.97-0.98. ConclusionThe quantitative POC LumiraDx CRP Test showed very close agreement with the established laboratory-based test when using capillary blood, venous blood, or plasma. The use of capillary blood testing in particular is beneficial in both primary and secondary care, with this portable test system providing rapid quantitative results within 4 minutes, potentiating the ability to help guide clinical decision-making. Data from two study collections, the NOVEL study and the REACT study with a trial registration: ClinicalTrials.gov identifier, NCT05180110, were used in this performance evaluation. Key summary pointsO_LIC-reactive protein (CRP) measurements are clinical markers for infection and inflammation, commonly used in primary and secondary care C_LIO_LIPoint-of-care (POC) CRP testing can assist primary care clinicians in making an immediate decision as to whether to prescribe antibiotics while the patient is still at the clinic C_LIO_LIPOC CRP testing that provides quantitative results near to the patient can be useful in emergency care assessment of patients and in hospital monitoring of antibiotic therapy C_LIO_LIThe POC LumiraDx CRP Test has demonstrated quantitative results comparable to those obtained using a recognized laboratory system using plasma C_LIO_LIThe POC LumiraDx CRP Test has also demonstrated matrix equivalence of capillary blood (both direct application and transfer tube), venous blood, and plasma C_LI

BackgroundHypervirulent Klebsiella pneumoniae (hvKp) infections have mainly been described in Asia. Two patients in the age group of 30 to 50 years presented within a two month period to a tertiary referral hospital in Texas with septic shock, hepatic abscess and septic thrombophlebitis. Blood cultures were positive for Klebsiella pneumoniae (isolates 2020CK-00441 and 2021CK-00720 respectively). MethodsWhole genome sequencing was performed using paired-end Illumina MiSeq reads for both isolates. Nanopore sequencing to obtain a closed genome was performed for 2020CK-00441. Results2020CK-00441 belonged to ST23 type while 2021CK-00720 was a ST65 type isolate. Kleborate analyses predicted with high confidence that both the isolates were hvKp. Phylogenetic analyses showed that the two strains are not closely related to each other or to any other known hvKp isolates. Both the isolates had yersiniabactin, colibactin, aerobactin and salmochelin producing loci which likely confer these isolates hvKp phenotype. 2020CK-00441 had a unique pK2044 like plasmid. ConclusionsHvKp strains capable of causing devastating metastatic septic infections have emerged in Texas. These isolates are unique when compared to other hvKp strains of the world. Country wide surveillance and whole genome sequencing of these strains is essential to prevent a major public health emergency in USA.

Background and objectiveDiagnosis of P. jirovecii pneumonia (PJP) is by PCR on lower respiratory tract specimens, the collection of which is not always well-tolerated and requires trained staff and costly equipment not usually available in low-resource settings. We aimed to evaluate P. jirovecii PCR performed on nasopharyngeal swabs (NPS) as a diagnostic test for PJP, as well as the impact of specimen quality on test performance. MethodsPatients with clinically-suspected PJP in public hospitals in Queensland, Australia, who had quantitative P. jirovecii PCR performed on lower respiratory tract specimens from 1 January 2015 to 31 December 2016, and also had NPS collected by healthcare staff within seven days of lower respiratory tract specimen collection were included in this retrospective cohort study. Quantitative P. jirovecii PCR was performed, and sensitivity, specificity, and positive and negative predictive values were calculated. Specimen quality was assessed by quantifying endogenous retrovirus 3 (ERV3) loads, with higher values indicating better specimen quality. ResultsOne hundred and eleven patients were included. The sensitivity of NPS P. jirovecii PCR was 0.66 and specificity was 1.0. The positive predictive value was 1.0 and the negative predictive value was 0.63. Median ERV3 loads in lower respiratory tract specimens and NPS were not significantly different in true positive vs. true negative patients, but was significantly higher in true positives vs. false negatives (7.55x102 vs. 3.67x102; P=0.05). ConclusionP. jirovecii PCR on NPS was highly specific but poorly sensitive. Proper specimen collection is essential to ensure adequate quality and prevent misclassification. Summary at a GlanceUsing nasopharyngeal swabs instead of lower respiratory tract specimens for PCR to diagnose P. jirovecii pneumonia (PJP) may be better tolerated and improve diagnostic accessibility. In this two-year retrospective cohort study of patients with clinically-suspected PJP from Queensland, Australia, P. jirovecii PCR on NPS had high specificity but low sensitivity.

Pseudomonas aeruginosa (P. aeruginosa) is one of the most concerning pathogens due to its multidrug resistance. P. aeruginosa can be a part of the normal commensal flora of humans but can also cause a wide range of infections. In this study, we investigated the prevalence of commensal P. aeruginosa in 609 Vietnamese participants (310 females and 299 males, age range of 2 to 73 years) who had no acute infection or disease symptoms at the time of sample collection. Samples were taken from the throat, naris and outer ears. As a result, 19 were positive with P. aeruginosa (3.12%, 95% CI: 0.017-0.045) which came mostly from throat (11/19, 57.89%). Participants with a history of sinusitis were 11.57 times more likely to be colonized with P. aeruginosa than participants without a history of sinusitis (OR: 11.57, 95% CI: 4.08-32.76, p-value< 0.0001). Age and gender were not significantly associated with P. aeruginosa colonization. The commensal P. aeruginosa isolates were tested for biofilm formation, pyocyanin, siderophore, lipase, protease and gelatinase production. Among 16 P. aeruginosa isolates used for these tests, 100% (16/16) were positive for biofilm, pyocyanin and siderophores; 93.75% (15/16) isolates were positive for gelatinase and protease; and 50% (8/16) isolates were positive for lipase. There were no differences in the pattern and range of virulence factors of P. aeruginosa isolates taken from participants with and without sinusitis history. In summary, P. aeruginosa colonized 3.12% of participants, and its presence was clearly associated with sinusitis history. Most commensal P. aeruginosa isolates can produce biofilm, pyocyanin, siderophores, gelatinase and protease. Author summaryP. aeruginosa is both a common opportunistic pathogen which causes various infections in humans, such as blood, lung, and skin infections and a commensal bacterium which can be found normal human flora. In this study, we showed that the P. aeruginosa colonized 3.12% participants and resided mostly in human throat. Interestingly, we found that people with sinusitis history were more likely to be P. aeruginosa carriers. On the other hand, age and gender did not significantly affect P. aeruginosa colonization. Most tested P. aeruginosa isolates expressed various virulence factors, including biofilm, siderophores, pyocyanin, gelatinase, protease, and lipase.

ObjectivesThe study was aimed to determine the predominant bacteria causing Acute Exacerbations of Chronic Obstructive Pulmonary Disease (AECOPD) infection in patients and their antibiotics sensitivity pattern in tertiary care setup. MethodsThis descriptive Cross-sectional study was conducted from September 27th 2023 to December 26th 2023 at Shree Birendra Hospital, chhauni, Kathmandu. Sputum samples that were received in the Microbiology laboratory from in patients for routine diagnosis were included in the study. The samples that were received was subjected to gram staining to assess the quality of the sputum sample, and those samples with good quality (mucoid and muco-purulent) was inoculated onto Blood agar, Chocolate agar and Mac Conkey agar for the isolation of the pathogens, and the media was incubated at 37 degrees Celsius overnight. Culture isolates were identified by standard technique(Cowan and Steels Manual for the Identification of Medical Bacteria, 1993) and Kirby-Bauer method was used to test antibiotic sensitivity of the pathogenic organisms following protocol of (Clinical and Laboratory Standards Institute, 2018) guidelines. ResultsOut of 273 sputum samples, 42/273 (15.4%) showed growth. Five different bacterial species were identified. Among the isolates, Acinetobacter spp. was the most common pathogen 21(44.7%) followed by Pseudomonas aeruginosa 11(23.4%), Klebsiella pneumoniae 10(21.3%), Escherichia coli 4(8.5%) and Citrobacter freundii 1(2.1%). Highest number of AECOPD cases were observed in female 157(57.9%) with 25(15.9%) positivity and highest number of organisms were isolated in age group 56-70(17) and least in age group 40-55(3). All the Acinetobacter spp. (n=21) isolates were resistant to all tested medicine. Almost 90.90% Pseudomonas aeruginosa (n=11) were sensitive to Gentamycin and 81.82% to Meropenem, 70% Klebsiella pneumoniae (n=10) were sensitive to Gentamycin, 75% Escherichia coli (n=4) and 100 % Citrobacter freundii (n=1) to Amikacin. 100% (n=47) isolates were resistant to antibiotic penicillin and 100% Escherichia coli and Citrobacter freundii were resistance to Ceftriazone and Cefepime while 100% (n=47) were found to be multi-drug resistant. ConclusionAcinetobacter spp P. aeruginosa, Klebsiella pneumoniae, and Escherichia coli were the most common bacterial isolates in the current investigation, which revealed a 15.4 % of culture positive. There is a high rate of MDR pattern in all isolated isolates. To further enhance treatment quality and prevent antibiotic resistance, regular surveillance of the etiologies of AECOPD and their pattern of antimicrobial susceptibility is crucial.

Pseudomonas aeruginosa is a frequent cause of antibiotic-resistant infections. Although P. aeruginosa is intrinsically resistant to many antimicrobial agents, aminoglycosides are active against this organism in the absence of acquired resistance determinants and mutations. However, genes encoding aminoglycoside modifying enzymes (AMEs) are found in many strains that are resistant to these agents. We examined the prevalence of phenotypic resistance to the commonly used aminoglycosides gentamicin, tobramycin, and amikacin in a collection of 227 P. aeruginosa bloodstream isolates collected over two decades from a single U.S. academic medical institution. Resistance to these antibiotics was relatively stable over this time period. High-risk clones ST111 and ST298 were initially common but decreased in frequency over time. Whole genome sequencing identified relatively few AME genes in this collection compared to the published literature; only 14% of isolates contained an AME gene other than the ubiquitous aph(3)-IIb. Of those present, only ant(2")-Ia was associated with phenotypic resistance to gentamicin or to tobramycin. One extensively drug-resistant strain, PS1871, contained 5 AME genes, most of which were part of clusters of antibiotic resistance genes embedded within transposable elements. These findings suggest that AME genes play a relatively minor role in aminoglycoside resistance at our institution but that multidrug-resistant strains remain a problem.

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.

BackgroundStudies have shown that periodontal and periapical diseases are more prevalent among diabetes mellitus (DM) patients. Here, we evaluated the potential relationship between endodontic pathologies and DM through a retrospective analysis of 2,000 electronic health records (EHR) of individuals with/without DM. MethodsRecords of patients treated at UTHealth School of Dentistry presenting with a history of endodontic treatment with and without DM were randomly selected for analysis of 24 treatment- and patient-centric variables to assess for the association between endodontic disease and DM. Data between groups were compared using Chi-square, Fisher Exact tests, and one-way analysis of variance (ANOVA). Significant differences were set at P<0.05. ResultsDiabetic patients had significantly less symptomatic pulpal diagnoses, particularly less symptomatic irreversible pulpitis (P<0.00005); whereas they had significantly more symptomatic apical periodontitis (P=0.01) than non-diabetics. Diabetics had a significantly greater number of endodontically-treated teeth (P=2.2 x 10-16), particularly canines and molars (P<0.002). The frequency of active periapical lesions was higher in non-diabetics, although no differences in lesion size were observed. The frequency of periodontal disease and additional systemic disease(s), and smoking was significantly increased in DM patients with endodontic treatment (P<0.05). No differences were observed between the number of medications taken between groups or upon stratifying analysis by gender (P>0.05). ConclusionsOur results continue to support that DM contributes to increased endodontic disease and highlight the complex relationships between oral and systemic diseases. Practical ImplicationsDental professionals should be cognizant of endodontic pathology as a clinical complication of DM that presents as more chronic in nature, at a greater frequency, and have a tendency toward a nonhealing outcome.

The study was undertaken to record the amount of dental aerosol created using 3-in-1 syringe, air rotor, and ultrasonic scaler using high volume suction (HVS) in 5 primary care dental surgeries. The time for the aerosol to dissipate following completion of the procedure was also recorded. The amount of aerosol created above the background level for the surgery corresponding to the operating positions of the nurse, dentist, and patient was recorded using particle meters measuring the number of 2.5{micro}m (PM2.5) and 10{micro}m (PM10) particles respectively. The procedures were recorded in triplicate for each surgery and average change calculated for each procedure, lasting 90 seconds. PM2.5 remained at or very near background readings during all procedures, whereas PM10 increased with use of the air rotor and to a much lower extent with both 3-in-1, and ultrasonic scaler. The means time to return to background reading level was 2.5 minutes. It was concluded that PM2.5 levels did not rise and although PM10 increased for all procedures the increase was low and with a return to background readings within 2m:50s (95% CI: 2:34 to 3:37) of completing the procedures that a minimum fallow period of 5minutes would allow be more than ample to be safe.

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.

A systematic review was performed to answer the following questions: 1) Do dental, oral and maxillofacial (OMF) surgical procedures generate bioaerosols (and if so, which ones), which can result in transmission of COVID-19?; 2) Are aerosolized airborne droplets (and to which extent is splatter) in dental and OMF procedures infective?; 3) Is enhanced personal protective equipment (PPE) an essential to prevent spreading of COVID-19 during dental and OMF aerosol generating procedures (AGPs)? Authors performed a systematic review to retrieve all pertinent literature that assessed effectiveness of surgical mask vs respirators for protecting dental health care workers during dental and OMF AGPs surgical procedures. Additionally, studies which assessed potential aerosolization during dental, OMF and orthopaedic surgeries were retrieved. There is moderate evidence showing that ultrasonic scaling and bone drilling using high speed rotary instruments produces respirable aerosols. Additionally, there is very weak/inconclusive evidence to support the creation of infectious aerosols during dental procedures. According to available very weak/inconclusive evidence, transmission of SARS-CoV-2 via infective aerosol during AGPS, so far, must remain speculative and controversial. As, however, this is a probable opportunistic way of transmission which at least cannot be sufficiently excluded and therefore should not be dismissed out of hand prematurely, proper and equally important properly applied protective equipment (i.e., N95 respirators or FFP-2 masksv or above regarding mouth and nose protection) should always be used during AGPs.

ObjectivesThe objectives were to quantify the contributions of internal (self) and external (familial) sources to the recolonization of the bacterial content of the subgingival plaque following professional prophylaxis and assess the effect of close-contact activities on modifying this contribution. Materials and MethodsFamilies, each consisting of at least one preschool-aged child and at least one sibling, were recruited for this interventional cohort pilot study. Microbial samples were collected from various oral sites, including saliva, buccal mucosa, tongue, supragingival plaque, and subgingival plaque in all family members. Following the childs oral prophylaxis, subgingival plaque samples were collected one week later. DNA from these samples was extracted and sequenced using the 16S rRNA gene and estimation of the sources were quantified using Bayesian source tracking models. Additional analyses using generalized linear mixed models, Phylofactorization, and Spearman correlations. Statistical significance was set at p<0.05. ResultsChilds own subgingival plaque was the primary source of recolonization, contributing 63.7% to the microbial community one-week post-prophylaxis. Siblings contributed approximately 8%, a contribution significantly higher than that from parents, who contributed around 3% each (p<0.05). The analysis revealed a statistically significant positive correlation between the number of siblings and their bacterial contribution to the childs subgingival plaque. Several close contact activities between parents and children were statistically associated with higher contribution (p<0.05, Spearman correlation). Additionally, 110 bacteria were statistically significantly different in their internal contribution compared to external, after accounting for household association, sample type, and family members (p<0.05, Phylofactor) ConclusionThe findings challenge the traditional focus on parent-child transmission of oral microbes, highlighting the importance of studying families as a whole.

ObjectiveTo evaluate the diagnostic efficiency of different methods in detecting COVID-19 to provide preliminary evidence on choosing favourable method for COVID-19 detection. MethodsPubMed, Web of Science and Embase databases were searched for identifing eligible articles. All data were calculated utilizing Meta Disc 1.4, Revman 5.3.2 and Stata 12. The diagnostic efficiency was assessed via these indicators including summary sensitivity and specificity, positive likelihood ratio (PLR), negative LR (NLR), diagnostic odds ratio (DOR), summary receiver operating characteristic curve (sROC) and calculate the AUC. Results18 articles (3648 cases) were included. The results showed no significant threshold exist. EPlex: pooled sensitivity was 0.94; specificity was 1.0; PLR was 90.91; NLR was 0.07; DOR was 1409.49; AUC=0.9979, Q*=0.9840. Panther Fusion: pooled sensitivity was 0.99; specificity was 0.98; PLR was 42.46; NLR was 0.02; DOR was 2300.38; AUC=0.9970, Q*=0.9799. Simplexa: pooled sensitivity was 1.0; specificity was 0.97; PLR was 26.67; NLR was 0.01; DOR was 3100.93; AUC=0.9970, Q*=0.9800. Cobas(R): pooled sensitivity was 0.99; specificity was 0.96; PLR was 37.82; NLR was 0.02; DOR was 3754.05; AUC=0.9973, Q*=0.9810. RT-LAMP: pooled sensitivity was 0.98; specificity was 0.99; PLR was 36.22; NLR was 0.04; DOR was 751.24; AUC=0.9905, Q*=0.9596. Xpert Xpress: pooled sensitivity was 0.99; specificity was 0.97; PLR was 27.44; NLR was 0.01; DOR was 3488.15; AUC=0.9977, Q*=0.9829. ConclusionsThese methods (ePlex, Panther Fusion, Simplexa, Cobas(R), RT-LAMP and Xpert Xpress) bear higher sensitivity and specificity, and might be efficient methods complement to the gold standard.

BackgroundMultidrug resistant (MDR) Pseudomonas aeruginosa isolates harboring genes for virulence and antibiotic resistance, have grown more prevalent lately. These strains pose a major threat to the general population, especially in tertiary care settings. There is a paucity of information on toxigenic and virulence diversity of multidrug resistant P. aeruginosa in Nigeria, hence, the need to characterize and determine the variations of the virulence genes. MethodsSix hundred clinical samples from different anatomical sites were collected aseptically from Lagos University Teaching Hospital (LUTH), University of Medical Sciences, Ondo (UNIMED) and Federal Medical Centre, Abeokuta (FMC). Pseudomonas aeruginosa was isolated using cetrimide agar identified using biochemical tests. Antibiotic sensitivity was done by disc diffusion method. Protease, phospholipase C (lecithinase), caseinase and gelatinase presence were assayed for. Genomic DNA was extracted from P. aeruginosa isolates and screened for the presence of N-Acetylneuraminate synthase (NaN), Elastase B (Las B), Exotoxin A (ExoA), Exoenzyme S (ExoS) and Exoenzyme U (ExoU) virulence genes by PCR. ResultsThree hundred and sixty bacterial isolates identified from clinical samples are as follows: Pseudomonas aeruginosa (11.3%), Escherichia coli (18.0%), Klebsiella pneumoniae (14.3%), Staphylococcus aureus (10.2%), Proteus mirabilis (3.2%), Streptococcus pnuemoniae (2.3%), Enterobacter aerogenes (0.5%) and Acinetobacter baumanni (0.1%). Enzymes detected in the P. aeruginosa isolates were Phospholipase C (77.9%), caseinase (83.9%), gelatinase (98.5%) and protease (88.2%). The P. aeruginosa isolates were all resistant to ampicillin and cloxacillin; 26 (38.2 %) strains exhibited multidrug resistance. Virulence LasB elastase gene was detected in all 14 multi resistant P. aeruginosa, ExoA was detected in 5, ExoS in 4, ExoU in 5 and NaN in 4 isolates: Four (28.6%) ConclusionThe study confirmed presence and variations of toxic genes in Pseudomonas aeruginosa isolated from all the three tertiary hospitals.

The study explores the polymicrobial nature of primary endodontic infections using Illumina Next Generation Sequencing. Samples involved in research have been collected from root canals of the patients suffering from pulp and periapical inflammations with no history of endodontic interventions on affected teeth. The study revealed prevalence of different bacterial phyla, classes, orders, and species. Further work will show potential correlations between individual microbiotas and clinical diagnosis.

COVID-19 has emerged as a highly contagious and debilitating disease caused by the SARS-CoV-2 virus and has claimed the lives of over 6.8 million people worldwide. Bacterial co-infections are one of many co-morbidities that have been suggested to impact the outcome of COVID-19 in patients. The primary goal of this study was to assess the prevalence of bacterial co-infections and to describe any trends observed during the height of the COVID-19 pandemic. To do this, we investigated SARS-CoV-2 and bacterial co-infections from outpatient RT-PCR testing in Texas. The results indicate Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae were the most frequently detected bacterial pathogens in both SARS-CoV-2 positive and SARS-CoV-2 negative patients and that these bacterial pathogens were present in these two patient populations at similar proportions. We also detected Staphylococcus aureus in a significantly larger proportion of males relative to females and people under 65 years of age relative to those 65 and over. Finally, we found that Hispanics were 75% more likely to be SARS-CoV-2 positive than non-Hispanics. The results suggest that COVID-19 patients may benefit from rapid diagnostic tests for bacterial pathogens and that this information could help delineate targeted antimicrobial therapy.

Pseudomonas aeruginosa is an opportunistic pathogen with high clinical relevance in intensive care units (ICU) due to its elevated resistance to various antimicrobials, which lead to high morbidity and mortality in patients in critical situations. In this study, we aimed to detect variants of genes encoding {beta}-lactamases and efflux pumps in P. aeruginosa isolates resistant to {beta}-lactams, fluoroquinolones and aminoglycosides. All genes belonging to the subfamilies were included in this study: blaSHV, blaTEM, blaNDM, blaKPC, blaGES, blaCTX-M. In addition, we investigated the most relevant variants of the blaOXA subfamily and genes belonging to the efflux pumps of the Mex family. We tested 54 isolates of P. aeruginosa with a high prevalence of resistance to the antimicrobials piperacillin/tazobactam, ceftazidime, cefepime, imipenem and meropenem. Resistance genes related to carbapenems and spectrum {beta}-lactamases extended were found, which included blaKPC genes (81.49%), blaCTXM-2 (72.22%) and blaCTXM-1 (66.66%). In relation to the presence of Mex family efflux pumps genes, 100% of positivity were detected. These findings suggest that P. aeruginosa isolates exhibit an arsenal of genes encoding {beta}-lactamases able to induce phenotypic patterns of resistance to several antimicrobials commonly used as first-line treatment. Author SummarySince the introduction of the use of antimicrobials, resistance to antimicrobials has been growing and becoming a global public health problem, as it leads to ineffective treatment and an increased risk of mortality. P. aeruginosa is included in the World Health Organization (WHO) critical list of bacteria that have a higher rate of resistance to antimicrobials, requiring constant epidemiological investigation of the strains, especially in hospital environments, to correctly approach them. In this work, we used a methodology that detects 740 variants of different classes of {beta}-lactamases to evaluate the genotype of the study strains against the phenotype found. We evidenced a high prevalence of strains carrying genes related to carbapenems and extended-spectrum {beta}-lactamases, demonstrating a correlation with the phenotypes. Furthermore, we found a 100% positivity rate among the efflux pumps tested belonging to the MEX family.

Introduction & ObjectivesThe COVID-19 pandemic has been raging across the globe since early January 2020. India has reported over 27 million cases and more than 3, 00,000 deaths. This study was planned to analyze the differences in demographic, clinical features and oral manifestations of COVID 19 patients hospitalized during COVID-19 pandemic. MethodsThis observational pilot study had total 36 participants, 12 each of mild, moderate and severe RT-PCR positive COVID cases hospitalized during COVID 19 pandemic. All demographic, clinical features, treatment details and oral manifestations were noted from first day of admission to hospital till treatment completion with follow up of minimum 7 days. ResultsMean age of the patients was 39.44 {+/-}9.13 years with M: F ratio of 5:4. Most common clinical presentation was fever, shortness of breath and treatment involved was symptomatic with supplemental oxygen & mechanical ventilation. Most common oral site involved was tongue & oral lesions observed were herpes labialis, mucositis, burning sensation, dryness of oral cavity, angular chelitis, aphthous ulcers, geographic tongue, fissuring of tongue, candidiasis, coated tongue, sublingual varicosity, & scalloped tongue. Interpretation and ConclusionAll demographic, clinical and oral manifestations were significantly different in mild, moderate and severe cases of covid hospitalized patients. Though clinical symptoms were improved, oral lesions were worsened. Oral Lesions seen in covid patients were associated with multiple drug therapy for illness along with poor oral hygiene, but further etiology for lesions needs to be evaluated. Sublingual varicosity was observed in our hospitalised covid patients, but large sample observation is required for confirmation of findings and may be an early oral feature for covid detection. Prevention is always better than cure, so all patients positive for Covid should have a full mouth examination. Oral health should be priority during overall management of COVID patients and dentists should be a part of Covid management team.