Development and evaluation of an artificial intelligence for bacterial growth monitoring in clinical bacteriology.

In clinical bacteriology laboratories, reading and processing of sterile plates remain a significant part of the routine workload (30%-40% of the plates). Here, an algorithm was developed for bacterial growth detection starting with any type of specimens and using the most common media in bacteriology. The growth prediction performance of the algorithm for automatic processing of sterile plates was evaluated not only at 18-24 h and 48 h but also at earlier timepoints toward the development of an early growth monitoring system. A total of 3,844 plates inoculated with representative clinical specimens were used. The plates were imaged 15 times, and two different microbiologists read the images randomly and independently, creating 99,944 human ground truths. The algorithm was able, at 48 h, to discriminate growth from no growth with a sensitivity of 99.80% (five false-negative [FN] plates out of 3,844) and a specificity of 91.97%. At 24 h, sensitivity and specificity reached 99.08% and 93.37%, respectively. Interestingly, during human truth reading, growth was reported as early as 4 h, while at 6 h, half of the positive plates were already showing some growth. In this context, automated early growth monitoring in case of normally sterile samples is envisioned to provide added value to the microbiologists, enabling them to prioritize reading and to communicate early detection of bacterial growth to the clinicians.

Landfill bacteriology: Role in waste bioprocessing elevated landfill gaseselimination and heat management.

This study delves into the critical role of microbial ecosystems in landfills, which are pivotal for handling municipal solid waste (MSW). Within these landfills, a complex interplay of several microorganisms (aerobic/anaerobic bacteria, archaea or methanotrophs), drives the conversion of complex substrates into simplified compounds and complete mineralization into the water, inorganic salts, and gases, including biofuel methane gas. These landfills have dominant biotic and abiotic environments where various bacterial, archaeal, and fungal groups evolve and interact to decompose substrate by enabling hydrolytic, fermentative, and methanogenic processes. Each landfill consists of diverse bio-geochemical environments with complex microbial populations, ranging from deeply underground anaerobic methanogenic systems to near-surface aerobic systems. These kinds of landfill generate leachates which in turn emerged as a significant risk to the surrounding because generated leachates are rich in toxic organic/inorganic components, heavy metals, minerals, ammonia and xenobiotics. In addition to this, microbial communities in a landfill ecosystem could not be accurately identified using lab microbial-culturing methods alone because most of the landfill's microorganisms cannot grow on a culture medium. Due to these reasons, research on landfills microbiome has flourished which has been characterized by a change from a culture-dependent approach to a more sophisticated use of molecular techniques like Sanger Sequencing and Next-Generation Sequencing (NGS). These sequencing techniques have completely revolutionized the identification and analysis of these diverse microbial communities. This review underscores the significance of microbial functions in waste decomposition, gas management, and heat control in landfills. It further explores how modern sequencing technologies have transformed our approach to studying these complex ecosystems, offering deeper insights into their taxonomic composition and functionality.

Does Topical Vancomycin Powder Use in Fracture Surgery Change Bacteriology and Antibiotic Susceptibilities? An Analysis of the VANCO Trial.

OBJECTIVE: To determine whether intrawound vancomycin changes the bacteriology of surgical site infection pathogens and investigate the emergence of antibiotic-resistant pathogens. DESIGN: Secondary analysis of phase III, prospective, randomized clinical trial. SETTING: Thirty-six US trauma centers. PATIENT SELECTION CRITERIA: Patients who became infected after fixation of tibial plateau or pilon fracture. OUTCOME MEASURES AND COMPARISONS: Pathogen types and bacterial susceptibilities as determined from routine clinical culture in the operating room. RESULTS: Seventy-four patients were studied who were 67.5% male with a mean age of 48.6 years. A lower proportion of gram-positive cocci was observed in the vancomycin powder compared with the standard-of-care group (3.7% vs. 8.0%, P = 0.01). Methicillin-resistant Staphylococcus aureus infection incidence was comparable in both the vancomycin powder and the standard-of-care groups, but rates of methicillin-susceptible S. aureus infections were lower in the treatment group (1.4% vs. 4.8%, P = 0.01). The incidence of coagulase-negative Staphylococci and gram-negative rod infections were similar in both groups. There was no significant difference in susceptibilities between groups in rates of vancomycin-resistant enterococcus. CONCLUSIONS: Topical vancomycin powder decreases the likelihood of gram-positive infections consistent with the biologic activity of vancomycin. Fewer methicillin-susceptible S. aureus and coagulase-negative Staphylococci infections were observed in the group treated with vancomycin powder. An effect of vancomycin powder on methicillin-resistant S. aureus infection risk was not detected given the low incidence in both the intrawound vancomycin and the standard-of-care groups. There was no emergence of gram-negative rod infections or increased resistance patterns observed. Use of topical vancomycin powder does not seem to produce infections in these patients with greater antibiotic resistance than would have occurred without its use. LEVEL OF EVIDENCE: Therapeutic Level II. See Instructions for Authors for a complete description of levels of evidence.

Algerian postcaesarean surgical site infections: A cross-sectional investigation of the epidemiology, bacteriology, and antibiotic resistance profile.

BACKGROUND: Surgical site infections (SSIs) are one of the most common health care-associated infections in low and middle-income countries. The aims of this cross-sectional descriptive study were to estimate the frequency of postcaesarean infection with associated clinical characteristics and the antibiotic resistance profile of bacterial isolates. METHODS: Patients who underwent a cesarean section at the obstetrics and gynecology department of the hospital in Annaba, Algeria were included. Each woman was followed postoperatively for 30 days and sociodemographic data were collected. Culture-based microbiological methods were used to identify the causative bacteria and determine their antibiotic resistance phenotype and molecular characterization. RESULTS: Among 1,810 patients, we recorded 36 (1.9%) SSIs. Most patients had undergone an emergency delivery (75%) and low educational level (72.2%). The most frequent maternal pathologies were Body Mass Index ≥ 30 (63.9%), scarred uteri (58.3%), anemia (55.6%), and an American Society of Anaesthesiologists score between II and III (33.3%). Of the 43 bacteria isolated, Enterobacteriaceae were the most frequent (62.8%), predominated by Escherichia coli strains (43.5%), a majority of which were extended-spectrum ß-lactamases carriers (62.9%). Although gram-positive cocci were less frequent (37.2%), a majority of Enterococcus faecalis (56.2%) were observed and 2 strains of vancomycin-resistant Enterococcus faecium harboring the vanA gene were identified. CONCLUSIONS: Extensive surveillance of at-risk populations should be integrated to prevent the occurrence of SSIs.

Bacteriology of Different Phenotypes of Chronic Rhinosinusitis.

OBJECTIVES: Chronic rhinosinusitis (CRS) reduces the health-related quality of life and subsequently causes a tremendous socio-economic impact. Although many studies have been conducted, few have identified a relationship between bacteriological characteristics and different phenotypes or endotypes. Therefore, this study aimed to elucidate the recent trends in bacterial cultures from different types of CRS in the Asian population. METHODS: This retrospective case-control study recruited patients diagnosed with CRS who underwent functional endoscopic sinus surgery (FESS) at a tertiary hospital in Taiwan. The patients were classified into those with chronic rhinosinusitis with nasal polyps (CRSwNP)/chronic rhinosinusitis without nasal polyps (CRSsNP), eosinophilic chronic rhinosinusitis (eCRS)/non-eosinophilic chronic rhinosinusitis (NECRS), and central compartment atopic disease (CCAD)/lateral-dominant nasal polyp (LDNP) groups. The demographic data and bacteriological characteristics of the groups were analyzed. RESULTS: We included 503 patients, identifying no significant difference between CRSwNP and CRSsNP for several common bacteria in CRS. The number of Staphylococcus epidermidis isolates in culture was significantly higher in the NECRS group (50.46% vs. 32.56%, p = 0.0003) than that in the eCRS group. The number of methicillin-resistant Staphylococcus aureus (MRSA; 8.51% vs. 2.35%, p = 0.0221) positive isolates was significantly higher in the CCAD group than that in the LDNP group. CONCLUSIONS: This was the first study in Asia to analyze the relationship between bacteriological characteristics and CCAD. MRSA is significantly higher in the CCAD group than that in the LDNP group. Recognizing the unique microbiology of CRSwNP, eCRS, and CCAD is crucial when selecting antimicrobial therapy to lessen the socio-economic impact. LEVEL OF EVIDENCE: 3 Laryngoscope, 134:1071-1076, 2024.

Bacteriology and clinical outcomes of urine mixed bacterial growth in pregnancy.

INTRODUCTION AND HYPOTHESIS: The objective was to analyse the risk of significant bacteriuria in repeat urine cultures from pregnant women, following initial mixed bacterial results. METHODS: This retrospective study examined maternal characteristics and clinical features of women who repeated urine cultures due to previous mixed cultures results. RESULTS: Of 262 women included, 80 (30.5%) had negative cultures and 125 (47.7%) had mixed bacterial growth in their repeat cultures. Positive results (≥104 CFU/ml of a urinary pathogen) were obtained for 57 women (21.8% [95% CI 17.1-27.0]). For 37 (14.1%), the repeat specimen grew 104-105 CFU/ml of microorganisms; whereas for 20 women (7.6% [95% CI 4.9-11.3]), it grew ≥105 CFU/ml. Among women with positive (>104 CFU/ml) compared with those with negative or mixed growth, rates of urinary symptoms were higher (38.6% vs 23.4%, p=0.028), abnormal dipstick results (49.1% vs 21.0%, p<0.001) and hydronephrosis, as demonstrated by renal ultrasound (12.3% vs 2.0, p=0.003). In a multivariate logistic regression analysis, hydronephrosis was associated with the occurrence of a positive repeat culture (aOR = 10.65, 95% CI 2.07-54.90). The sensitivity and specificity for predicting a repeat urine culture with ≥105 CFU/ml were 12.9% and 94.3% respectively, for urinary symptoms; and 19.7% and 97.4% respectively, for abnormal dipstick results. CONCLUSIONS: Mixed bacterial growth might represent a true urinary tract infection in a considerable proportion of women who are symptomatic and have an abnormal dipstick urinalysis.

Veterinary bacteriology in Denmark from the 1880s to 2022.

This paper gives an account of the history of veterinary bacteriology including clinical veterinary bacteriology as well as the area of veterinary public health in Denmark from the 1880s to 2022. We describe key persons, including B. Bang, C.O. Jensen, K.A. Jensen and others who made important contributions to the development of these areas of microbiological expertise, and we discuss how challenges ranging from bovine tuberculosis to bacterial antimicrobial resistance have been met. Further, we describe progress in research on important bacterial pathogens both with regard to animal clinical aspects and zoonotic food-related aspects. Finally, we describe current issues in relation to One Health and research organization.

[ACUTE OTITIS MEDIA BACTERIOLOGY IN CHILDREN YOUNGER THAN THREE MONTHS IN THE LAST 16 YEARS].

BACKGROUND: Only scant information is available regarding the bacteriology of acute otitis media (AOM) in neonates. OBJECTIVES: To investigate the bacteriology of AOM post the introduction of Pneumococcal Conjugate Vaccine (PCV13) in children younger than 3 months and its relation to the mode of delivery. METHODS: Retrospective bacteriological analysis of middle ear fluids taken from children younger than 60 months suffering from AOM. The effect of PCV13 and mode of delivery, caesarian section vs vaginal delivery, on AOM bacteriology was evaluated and compared between children younger than 3 months (group 1) and children aged 3-60 months (group 2). RESULTS: The prevalence of Streptococcus pneumoniae (S.pneumoniae) and Enterobacteriaceae (E.bact) was higher in group 1 compared to group 2, 47.1% vs 35.8% and 12.3% vs 4.3%, respectively (p<0.001), while that of Haemophilus influenza (H. influenzae) and Group A streptococcus (GAS) was higher in group 2 compared to group 1, 40.3% vs 30.1% and 17.5% vs 8.3% respectively (p<0.001). The mode of delivery did not affect AOM bacteriology. The introduction of PCV13 yielded in an increase in the prevalence of GAS (7% to 15%, P<0.001) in group 1. CONCLUSIONS: S. pneumoniae and E. bact are more common AOM pathogens in neonates. Also, the prevalence of GAS was increased in this age group following the introduction of PCV13. DISCUSSION: Our results are applicable towards the formulation AOM treatment guidelines in neonates. This study contributed additional information on a topic that has not been adequately researched so far - neonatal AOM.

Hazards of swine slurry: Heavy metals, bacteriology, and overdosing-Physicochemical models to predict the nutrient value.

In this work, 124 samples of slurry from 32 commercial farms of three animal categories (lactating sows, nursery piglets, and growing pigs) were studied. The samples were collected in summer and winter over two consecutive years and analyzed for physicochemical properties, macronutrient and micronutrient, heavy metals, and major microbiological indicators. The results were found to be influenced by farm type and to deviate especially markedly in nursery piglets, probably as a consequence of differences in pig age, diet, and management. The main potential hazards of the slurries can be expected to arise from their high contents in heavy metals (Cu and Zn), especially in the nursery piglet group, and from the high proportion of samples testing positive for Salmonella spp. (66%). Linear and nonlinear predictive equations were developed for each animal category and the three as a whole. Dry matter, which was highly correlated with N, CaO, and MgO contents, proved the best predictor of fertilizer value. Using an additional predictor failed to improve the results but nonlinear and farm-specific equations did. Rapid on-site measurements can improve the accuracy of fertilizer value estimates and help optimize the use of swine slurry as a result.

Gasdermins assemble; recent developments in bacteriology and pharmacology.

The discovery of gasdermin D (GSDMD) as the terminal executioner of pyroptosis provided a large piece of the cell death puzzle, whilst simultaneously and firmly putting the gasdermin family into the limelight. In its purest form, GSDMD provides a connection between the innate alarm systems to an explosive, inflammatory form of cell death to jolt the local environment into immunological action. However, the gasdermin field has moved rapidly and significantly since the original seminal work and novel functions and mechanisms have been recently uncovered, particularly in response to infection. Gasdermins regulate and are regulated by mechanisms such as autophagy, metabolism and NETosis in fighting pathogen and protecting host. Importantly, activators and interactors of the other gasdermins, not just GSDMD, have been recently elucidated and have opened new avenues for gasdermin-based discovery. Key to this is the development of potent and specific tool molecules, so far a challenge for the field. Here we will cover some of these recently discovered areas in relation to bacterial infection before providing an overview of the pharmacological landscape and the challenges associated with targeting gasdermins.

The bacteriology of diabetic foot ulcers and infections and incidence of Staphylococcus aureus Small Colony Variants.

Introduction. Uninfected diabetes-related foot ulcer (DFU) progression to diabetes-related foot infection (DFI) is a prevalent complication for patients with diabetes. DFI often progresses to osteomyelitis (DFI-OM). Active (growing) Staphylococcus aureus is the most common pathogen in these infections. There is relapse in 40-60 % of cases even when the initial treatment at the DFI stage apparently clears infection.Hypothesis. S. aureus adopts the quasi-dormant Small Colony Variant (SCV) state during DFU and consequently infection, and when present in DFI cases also permits survival in non-diseased tissues as a reservoir to cause relapse.Aim. The aim of this study was to investigate the bacterial factors that facilitate persistent infections.Methodology. People with diabetes were recruited from two tertiary hospitals. Clinical and bacterial data was taken from 153 patients with diabetes (51 from a control group with no ulcer or infection) and samples taken from 102 patients with foot complications to identify bacterial species and their variant colony types, and then compare the bacterial composition in those with uninfected DFU, DFI and those with DFI-OM, of whom samples were taken both from wounds (DFI-OM/W) and bone (DFI-OM/B). Intracellular, extracellular and proximal 'healthy' bone were examined.Results. S. aureus was identified as the most prevalent pathogen in diabetes-related foot pathologies (25 % of all samples). For patients where disease progressed from DFU to DFI-OM, S. aureus was isolated as a diversity of colony types, with increasing numbers of SCVs present. Intracellular (bone) SCVs were found, and even within uninfected bone SCVs were present. Wounds of 24 % of patients with uninfected DFU contained active S. aureus. All patients with a DFI with a wound but not bone infection had previously had S. aureus isolated from an infection (including amputation), representing a relapse.Conclusion. The presence of S. aureus SCVs in recalcitrant pathologies highlights their importance in persistent infections through the colonization of reservoirs, such as bone. The survival of these cells in intracellular bone is an important clinical finding supporting in vitro data. Also, there seems to be a link between the genetics of S. aureus found in deeper infections compared to those only found in DFU.

Environmental DNA clarifies impacts of combined sewer overflows on the bacteriology of an urban river and resulting risks to public health.

There is no reference of microbiological water quality in the European Union's Water Framework Directive, adapted into English law, and consequently microbial water quality is not routinely monitored in English rivers, except for two recently designated bathing water sites. To address this knowledge gap, we developed an innovative monitoring approach for quantitative assessment of combined sewer overflow (CSO) impacts on the bacteriology of receiving rivers. Our approach combines conventional and environmental DNA (eDNA) based methods to generate multiple lines of evidence for assessing risks to public health. We demonstrated this approach by investigating spatiotemporal variation in the bacteriology of the Ouseburn in northeast England for different weather conditions in the summer and early autumn of the year 2021 across eight sampling locations that comprised rural, urban, and recreational land use settings. We characterized pollution source attributes by collecting sewage from treatment works and CSO discharge at the peak of a storm event. CSO discharge was characterized by log10 values per 100 mL (average ± stdev) of 5.12 ± 0.03 and 4.90 ± 0.03 for faecal coliforms and faecal streptococci, and 6.00 ± 0.11 and 7.78 ± 0.04 for rodA and HF183 genetic markers, for E. coli and human host associated Bacteroides, respectively, indicating about 5 % sewage content. SourceTracker analysis of sequencing data attributed 72-77 % of bacteria in the downstream section of the river during a storm event to CSO discharge sources, versus only 4-6 % to rural upstream sources. Data from sixteen summer sampling events in a public park exceeded various guideline values for recreational water quality. Quantitative microbial risk assessment (QMRA) predicted a median and 95th percentile risk of 0.03 and 0.39, respectively, of contracting a bacterial gastrointestinal disease when wading and splashing around in the Ouseburn. We show clearly why microbial water quality should be monitored where rivers flow through public parks, irrespective of their bathing water designation.

Comparison of Bacteriology Between Eosinophilic and Noneosinophilic Chronic Rhinosinusitis With Nasal Polyps.

OBJECTIVE: To compare culture results between eosinophilic chronic rhinosinusitis (CRS) with nasal polyps (ECRSwNP) and noneosinophilic CRS with nasal polyps (nECRSwNP). STUDY DESIGN: Retrospective study. SETTING: Tertiary medical center. METHODS: We retrospectively analyzed a cohort of CRSwNP patients undergoing primary functional endoscopic sinus surgery. Prior to surgery, swab samples for bacterial culture were collected from their middle meatus using cotton tips. After surgery, postoperative specimens were histologically examined for tissue eosinophilia. A tissue eosinophil density of >10 cells at high power magnification was used to discriminate between ECRSwNP and nECRSwNP. RESULTS: A total of 295 patients were studied with polyps present on 471 sides of the nasal cavity. Among them, 236 sides were ECRSwNP, and the remaining 235 sides were nECRSwNP. Bacterial growth was found in 94 ECRSwNP sides, and in 88 nECRSwNP sides. Culture rates were similar between ECRSwNP and nECRSwNP sides (p = .595). However, Gram-negative aerobes were found in 25 of 236 ECRSwNP sides, and in 42 of 235 nECRSwNP sides. The Gram-negative culture rate was significantly higher in nECRSwNP than in ECRSwNP sides (p = .024). CONCLUSION: The bacteriology of CRS was different between ECRSwNP and nECRSwNP. The Gram-negative aerobes were present more in nECRSwNP than in ECRSwNP.

Convergence of flow cytometry and bacteriology. Current and future applications: a focus on food and clinical microbiology.

Since its development in the 1960s, flow cytometry (FCM) was quickly revealed a powerful tool to analyse cell populations in medical studies, yet, for many years, was almost exclusively used to analyse eukaryotic cells. Instrument and methodological limitations to distinguish genuine bacterial signals from the background, among other limitations, have hampered FCM applications in bacteriology. In recent years, thanks to the continuous development of FCM instruments and methods with a higher discriminatory capacity to detect low-size particles, FCM has emerged as an appealing technique to advance the study of microbes, with important applications in research, clinical and industrial settings. The capacity to rapidly enumerate and classify individual bacterial cells based on viability facilitates the monitoring of bacterial presence in foodstuffs or clinical samples, reducing the time needed to detect contamination or infectious processes. Besides, FCM has stood out as a valuable tool to advance the study of complex microbial communities, or microbiomes, that are very relevant in the context of human health, as well as to understand the interaction of bacterial and host cells. This review highlights current developments in, and future applications of, FCM in bacteriology, with a focus on those related to food and clinical microbiology.