Recovery Of Pathogens Research Articles

Enabling quantitative comparison of wastewater surveillance data across methods through data standardization without method standardization

Wastewater surveillance for COVID-19 and other pathogens has expanded globally. Rapid development and availability of various assays has facilitated swift adoption of wastewater surveillance in localities with diverse requirements. However, it presents challenges in comparing data due to methodological variations. Using surrogates for recovery control to address quantification biases has limitations as the recovery of surrogates and target pathogens often diverges significantly. Using non-spiked field-obtained wastewater samples as reference samples in an inter-lab study, this article proposes a straightforward, inexpensive, and most representative way of measuring relative quantification biases that occurs in analyzing field wastewater samples. Five labs participated in the study, testing five types of assays, resulting in a total of seven methods of lab-assay combinations. Each method quantified the concentration of SARS-CoV-2 and pepper mild mottle virus (PMMoV) RNAs in two types of reference samples. The results showed significant variations in quantification among methods, but the relative quantification biases were consistent across reference samples. This suggests that relative quantification biases measured with the reference samples are contingent on methods rather than wastewater samples, and that the once-determined method-specific factors can be used to correct for quantification biases in routine wastewater surveillance results. Subsequent data standardization was performed on year-long observational data from seven cities, serving as a preliminary validation of the proposed approach. This process demonstrated the potential for quantitative data comparison through the bias correction factors obtained in this inter-lab study.

Utility of Anaerobic Blood Cultures in Neonatal Sepsis Evaluation.

Clinicians variably obtain anaerobic blood cultures as part of sepsis evaluations in the neonatal intensive care unit (NICU). Our objective was to determine if anaerobic blood culture bottles yielded clinically relevant information by either recovering pathogens exclusively or more rapidly than the concurrently obtained aerobic culture bottle in the NICU. A retrospective cohort study of blood cultures obtained from infants admitted to the NICU from August 01, 2015 to August 31, 2023. Standard practice was to inoculate 2 mL of blood divided equally between an aerobic and an anaerobic culture bottle. We analyzed positive blood cultures where both aerobic and anaerobic bottles were obtained and compared pathogen recovery and time to positivity between the bottles. During the study period, 4599 blood cultures were obtained from 3665 infants, and 265 (5.8%) were positive. Of these, 182 cultures were sent as aerobic-anaerobic pairs and recovered pathogenic organisms. Organisms were recovered exclusively from the anaerobic bottle in 32 (17.6%) cultures. Three organisms were obligate anaerobes; the rest were facultative anaerobes including Coagulase-negative staphylococci (40.6%), Escherichia coli (15.6%), and Staphylococcus aureus (15.6%). Cultures with exclusive recovery in the anaerobic bottle were more frequently obtained ≤3 days after birth, compared to other cultures (31.3% vs 15.3%, P = .03). When both bottles recovered the pathogen (n = 113), the anaerobic bottle had a shorter time to positivity in 76 (67.3%) cultures. Including anaerobic culture bottles could lead to the identification of pathogens not recovered in the aerobic bottle, as well as earlier identification of pathogens.

Determining the Main Infection Courts in Sweet Cherry Trees of the Canker Pathogens Calosphaeria pulchella, Cytospora sorbicola, and Eutypa lata.

The major fungal canker pathogens causing branch dieback of sweet cherry trees in California include Calosphaeria pulchella, Cytospora sorbicola, and Eutypa lata. These pathogens have long been known to infect cherry trees mainly through pruning wounds. However, recent field observations revealed numerous shoots and fruiting spurs exhibiting dieback symptoms with no apparent pruning wounds or mechanical injuries. Accordingly, this study was conducted to assess the incidence of the three pathogens in symptomatic terminal shoots and dying fruiting spurs, in addition to the wood below pruning wounds in branches. Surveys were conducted in five sweet cherry orchards across three counties in California. We also investigated the possibility that leaf scars, bud scars, and wounds resulting from fruit picking could serve as infection courts for Cal. pulchella, Cyt. sorbicola, and E. lata by means of artificial inoculations in the field. Orchard surveys revealed that Cal. pulchella had the highest pathogen incidence below pruning wounds in branch samples, followed by Cyt. sorbicola and E. lata. Among terminal shoots with dieback symptoms and dying fruiting spurs, Cyt. sorbicola was the most prevalent, followed by Cal. pulchella. Results from field inoculations indicated that fruit-picking wounds could serve as important infection courts for Cal. pulchella, Cyt. sorbicola, and E. lata, with average pathogen recovery of 41.5, 63, and 36.2%, respectively. Results also indicated that leaf and bud scars could serve as an entry site for Cyt. sorbicola, although recovery was relatively low. The present study is the first to identify harvest-induced wounds on fruiting spurs of sweet cherry as an important infection court of Cal. pulchella, Cyt. sorbicola, and E. lata.

Comparison of Three Preharvest Sampling Strategies to Monitor Pathogens in Cattle Lairage Areas

The objective of this study was to compare preharvest monitoring strategies by evaluating three different sampling methods in the lairage area to determine pathogen recovery for each sampling method and incoming pathogen prevalence from the cattle to inform in-plant decision making. Samples were gathered over a 5-month period, from February to June 2022, at a harvesting and processing facility located in Eastern Nebraska. Sampling methods included (i) fecal pats, (ii) boot swabs, and (iii) MicroTally swab. A total of 329 samples were collected over the study period (fecal pats: n = 105, boot swabs: n = 104, and MicroTally swabs: n = 120). Specific media combinations, an incubation temperature of 42°C, and incubation timepoints (18–24 h) were utilized for each matrix and the prevalence of Salmonella, Escherichia coli O157:H7, and six non-O157 Shiga-toxin producing E. coli (STEC) was evaluated using the BAX system Real-Time PCR assay. Overall, results from the study concluded that boot swabs were an effective sampling method for pathogen detection in the cattle lairage area. Boot swabs (97.1%) were statistically more likely to detect for Salmonella (p < 0.05) when compared to fecal pats (67.6%) and MicroTally swab (77.5%) methods. For E. coli O157:H7 and STEC – O26, O121, O45, and O103 prevalence, boot swabs were significantly better at detecting for these pathogens (p < 0.05) than MicroTally swabs (OR = 3.16 – 11.95) and a comparable sampling method to fecal pats (OR = 0.93 – 2.01, p > 0.05). Lastly, all three sampling methods detected a very low prevalence for E. coli O111 and O145; therefore, no further analysis was conducted. The boot swab sampling method was strongly favored because they require little training to implement, are inexpensive, and they do not require much sampling labor; therefore, would be a simple and effective sampling method to implement within the industry to evaluate pathogen prevalence preharvest.

A Review of the Evidence on the Role of Floors and Shoes in the Dissemination of Pathogens in a Healthcare Setting.

Background: It is generally accepted that shoes and floors are contaminated with pathogens including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and Clostridium difficile, yet correlation to clinical infection is not well established. Because floors and shoes are low-touch surfaces, these are considered non-critical surfaces for cleaning and disinfection. The purpose of this review is to assess peer-reviewed literature inclusive of floors and shoe soles as contributors to the dissemination of infectious pathogens within healthcare settings. Methods: Using the Preferred Reporting Items for Systematic Reviews (PRISMA) methodology, PubMed and Medline were searched for articles assessing the presence of pathogens on or the transmission of pathogens between or from floors or shoe soles/shoe covers. Inclusion criteria are the human population within healthcare or controlled experimental settings after 1999 and available in English. Results: Four hundred eighteen articles were screened, and 18 articles documented recovery of bacterial and viral pathogens from both floors and shoes. Seventy-two percent (13/18) of these were published after 2015, showing increased consideration of the transfer of pathogens to high-touch surfaces from shoe soles or floors during patient care. Conclusions: There is evidence that floors and shoes in healthcare settings are contaminated with several different species of health-care-associated pathogens including MRSA, VRE, and Clostridium difficile.

New Antibiotic Binding Resin Bottles Collected from Children Enhances Rapid Microbial Identification.

Bloodstream infections (BSI) represent a common cause of sepsis and mortality in children. Blood culture (BC) is the gold standard for diagnosis of BSI. The low sensitivity of BC in the pediatric population is usually due to the small volume of blood used for inoculation and to the antibiotics used before sampling. Here, we explore the ways to effectively reduce antibiotic activity to maximize the chances of pathogen recovery, and to enhance the growth of microorganisms in lower blood volume and bacterial counts. The recovery of common pathogens causing blood stream infections was analyzed after exposure to cefo-perazone/sulbactam, vancomycin, and caspofung by using resin-containing or not BacT/Alert PF Plus and BD FX400 peds plus pediatric bottles. The microbial growth in the resin-containing bottles was assessed using 0.5 colony-forming units (CFU) bacterial inoculum to mimic the bacteremia/fungemia condition. The usefulness of a diagnosis to confirm or exclude BSI was evaluated by lower than recommended blood culture sampling (102 CFU/mL, 0.3 mL). Staphylococcus aureus (S. aureus), and Candida glabrata (C. glabrata) were recovered from 100% of two types of resin-containing bottles in the presence of a sufficient antibiotic dose, while Escherichia coli (E. coli) was not restored to 100% in BD FX400 peds plus pediatric bottles. The shorter TTD for S. aureus, C. glabrata, and E. coli were observed in antibiotic-containing BacT/Alert PF Plus bottles. Both the PF Plus and BD resin test bottles showed consistently good TTD performances to Gram-negative, Gram-positive, and yeast species in low inoculum levels, with the exception of S. aureus. The lower volume of blood inoculated into culture bottles hardly affected the growth of most bacteria, but optimized PF Plus resin-bottles accelerated the detection of infectious agents, especially S. aureus, Streptococcus pneumoniae, and C. glabrata. It is possible to enhance recovery from antibiotic-containing pediatric bottles and shorten TTD for the identification of pathogens by using the BacT/Alert blood culture system combination with new resin-containing media.

Effectiveness of solitary and combined use of cover crop species to manage soilborne diseases in woody ornamental nursery production system

The understanding of how solitary and combined use of covercrop species and seeding rates influences soilborne diseases is lacking. Cover crops (crimson clover, triticale and crimson clover + triticale) were seeded in the field plots in September 2019 (Trial 1) and September 2021 (Trial 2) at two seeding rates (low and high) and a no cover cropped fallow served as a control. The soil was collected from all the plots in the following June. Red maple rooted cuttings were planted in nursery containers filled with those soils and plant health was evaluated with and without inoculation with Phytophthora nicotianae, Phytopythium vexans and Rhizoctonia solani. Plant height and fresh weight were measured, and plant roots were assessed for root rot severity (0–100% roots affected) and pathogen recovery. The number of fluorescent Pseudomonads present in soil samples was counted. Root rot severity and pathogen recovery were less with plants grown in cover cropped soil compared to non-cover cropped soil. Root rot severity caused by all three pathogens was least with the plants grown in the crimson clover and mixed cover cropped soil with the mixture being better than crimson clover. Moreover, plants grown in the high rate of cover cropped soil had less root rot severity compared to plants grown in low seeding rate cover cropped soil. Plant fresh weight was greater for plants grown in the high rate of crimson clover cover cropped soil and, in the mixture, compared to the non-cover cropped soil, whereas height was least affected. The Pseudomonad population was greatest in mixed cover cropped as well as in the high rate of cover cropped soil. Our findings suggest that a mixture of cover crop species and high seeding rate provides better service in suppressing root rot diseases likely associated with biological processes and nutrient availability.

Effects of clinically achievable pulmonary antibiotic concentrations on the recovery of bacteria: in vitro comparison of the BioFire FILMARRAY Pneumonia Panel versus conventional culture methods in bronchoalveolar lavage fluid.

Empiric antibiotics may affect bacterial pathogen recovery using conventional culture methods (CCMs), while PCR-based diagnostics are likely less affected. Herein, we conducted an in vitro study of bronchoalveolar lavage fluid (BAL) inoculated with bacteria and clinically relevant antibiotic concentrations to compare the recovery between the BioFire FILMARRAY Pneumonia Panel (Pn Panel) and CCMs. Remnant clinical BAL specimens were inoculated to ~105 cfu/mL using 12 clinical isolates. Isolates consisted of one wild-type (WT) and one or more resistant strains of: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus. Piperacillin-tazobactam, cefepime, meropenem, levofloxacin, or vancomycin was added to achieve pulmonary epithelial lining fluid peak and trough concentrations. Post-exposure cfu/mL was quantified by CCMs and simultaneously tested by the PN Panel for identification and semi-quantitative genetic copies/mL. CCM results were categorized as significant growth (SG) (≥1 × 104), no significant growth (NSG) (≥1 × 103, <1 × 104), or no growth (NG) (<1 × 103). The PN Panel accurately identified all isolates, resistance genes, and reported ≥106 genetic copies/mL regardless of antibiotic exposure. The CCM also identified all S. aureus strains exposed to vancomycin. For WT Gram-negative isolates exposed to antibiotics, SG, NSG, and NG were observed in 7/52 (13%), 18/52 (35%), and 27/52 (52%) of CCM experiments, respectively. For resistant Gram-negatives isolates, SG, NSG, and NG were observed in 62/88 (70%), 17/88 (19%), and 9/88 (10%), respectively. These in vitro data demonstrate that the PN Panel is able to identify Gram-negative pathogens in the presence of clinically significant antibiotic concentrations when CCM may not.

Seasonal Susceptibility of Sweet Cherry Pruning Wounds to Calosphaeria pulchella, Cytospora sorbicola, and Eutypa lata.

Fungal canker pathogens commonly infect trees at pruning wounds leading to branch dieback and loss of productivity in sweet cherry orchards. However, the seasonal susceptibility of sweet cherry pruning wounds to Calosphaeria pulchella, Cytospora sorbicola, and Eutypa lata is not well understood. This study compared the susceptibility of sweet cherry pruning wounds made during the dormant season (January) and the postharvest season (late May to June) to infection by main canker pathogens in California. Field trials were conducted in three cherry orchards and trees were pruned at the different periods over 2 years. Fresh pruning wounds were inoculated with spores of each pathogen, and pathogen recovery was assessed through microbiological isolations at 3 to 4 months after inoculations. Pruning wounds made in late May and June resulted in significantly higher infection by Cal. pulchella compared to pruning wounds made in January. Pruning wounds made during both seasons were generally equally susceptible to Cyt. sorbicola and E. lata infections. However, there was one orchard where dormant pruning wounds were more susceptible to infection by E. lata and there was one particularly cold winter where Cyt. sorbicola did not infect pruning wounds. Overall, our findings suggest that Cal. pulchella infections of cherry pruning wounds are more likely to occur during periods of warm temperatures such as late spring and early summer. However, infections by Cyt. sorbicola and E. lata can occur year-round if inoculum is present and if winter temperatures are not abnormally low for California. Finally, our results suggest that the emergence of Cal. pulchella as a major canker pathogen of sweet cherry in California may be the result of a shift from dormant to after-harvest pruning of sweet cherry trees.

Evaluation of temperature, drying time and other determinants for the recovery of Gram-negative bacterial pathogens in disinfectant efficacy testing

In the clinical setting, surface disinfection is an important measure to reduce the risk of cross-transmission of microorganisms and the risk of nosocomial infections. Standardized methods can be used to evaluate said disinfection procedures, as well as the effectiveness of the active ingredients used for disinfection. However, despite standardization, the results of such methodologies are still determined by several factors and incorrect results may lead to invalid assumptions about the effectiveness of a disinfectant, posing significant health risks for patients and health personnel. The objective of this study was to evaluate several determinants for the recovery of Pseudomonas aeruginosa and other test organisms to establish their influence on the results of standardized disinfection methodologies and to find Gram-negative strains that could be used as suitable replacements of P. aeruginosa. The effects of inoculum application, drying times and temperatures as well as surface material on the survival and recovery of the test organisms were evaluated using Student-T test, one-way ANOVA and Tuckey's multiple comparison tests. Our results show that temperature and length of drying as well as application method and the material of germ carriers have significant effects on the recovery of P. aeruginosa cells and therefore influence the outcome of the methodologies used. This study also presents data showing that P. aeruginosa could be replaced with the Gram-negative species Acinetobacter baumannii, a test organism already in many standardized methodologies, which responds better under the same circumstances and has a behavior similar to that of P. aeruginosa in disinfectant efficacy tests.

A method of recovering the very low concentration of pathogens in river water by combining centrifugation and membrane filtration

Waterborne pathogens present major public health concerns because of the associated high mortality, morbidity and cost of treatment. Consumption of and contact with water contaminated by faeces is a significant risk factor for transmitting these organisms to humans. Their detection in a water sample is critical to ascertain potential risks to humans. They are relatively low in concentrations in surface waters, making their detection a challenge. Campylobacter is targeted here because it is one of the leading causes of enteric diseases globally, and consensus on the superiority of centrifugation over filtration, and vice versa, to recover Campylobacter spp. from river water samples for detection, has yet to be. Therefore, for this study river water sample was processed by combining both methods in a single set-up to concentrate Campylobacter spp. cells from water samples. This method of combining centrifugation and filtration can be expanded to other bacterial waterborne pathogens of public health importance.•Concentrating cells by centrifugation (14,000 × g for 30 min) to collect the pellets, followed by membrane filtration (using 0.45 µm) of the supernatant to trap any remaining suspended cells, and then pooling both pellet and residue presents an effective method for obtaining a satisfactory quantitative recovery of waterborne pathogens, such as Campylobacter spp. from environmental waters.•This is a critical need for quantitative microbial risk assessment studies.

Oak Wilt Fungus (Bretziella fagacearum) Survival in Logs Following Fumigation with Ethanedinitrile

Abstract The phaseout of methyl bromide (MB) fumigation creates an urgent need for an alternative phytosanitary treatment to limit the risk of international spread of the oak wilt fungus, Bretziella fagacearum. Fumigation with ethanedinitrile (EDN) is considered a potential alternative to MB fumigation to eradicate wood-inhabiting pests and pathogens. We evaluated the efficacy of EDN fumigation by comparing the rate of B. fagacearum isolation before and after fumigation of red oak (Quercus rubra or Quercus ellipsoidalis) log sections from oak wilt–affected trees. Logs (range 15.2 to 98.0 cm long; diameter 9.1 to 46.1 cm) were obtained from red oak trees that were naturally infected (NI) or artificially inoculated (AI) with B. fagacearum. The logs were fumigated for 24, 48, and/or 72 hours with 120 g/m3 EDN. Frequencies of pathogen isolation from the sapwood before treatment were higher for AI logs than for NI logs. EDN treatments greatly reduced the frequency of viable pathogen recovery, but eradication occurred only in experiments using the smallest log diameters (9 to 14 cm). Our results suggest that EDN may have limited penetration in oak logs with intact bark, similar to fumigants currently used on wood products, such as MB and sulfuryl fluoride. Results of future work may help in the understanding of the limitations for consistent and full efficacy of EDN against B. fagacearum in logs harvested from diseased trees.

Deciphering Chitosan–Host Plant Interaction in Esca Disease

The production of wine and table grapes is hampered by Phaeomoniella chlamydospora, a fungus related to Petri diseases and Esca, two of the major grapevine trunk diseases causing the death of vines all over the world. This study analyses the effect of a commercial-based substance (chitosan hydrochloride 2.5%) on grapevine–P. chlamydospore interaction. Two experimental scenarios were evaluated: (i) root application in a greenhouse-plant model system and (ii) foliar application in an open-field environment (Tempranillo grape cultivar). Vascular necrosis and pathogen recovery were reduced after chitosan application. The treatment increased root development and the flavonoid index. On open-field application, the treatment did not significantly help decrease the expression of the foliar symptoms of Esca. In symptomatic leaves, the results revealed a lower overexpression of defence-related genes (Chit 1b, CHV5, STS and PR6) in plants treated with chitosan than in nontreated vines. Altogether, this study attempts to provide a first insight into the potential role of chitosan hydrochloride in the treatment of P. chlamydospora and the interaction on the control of the Esca–pathosystem complex. Differences were found between the root and foliar spraying modes of action.

Effects of postage on recovery of pathogens from cystic fibrosis sputum samples

BackgroundRegular surveillance microbiology of sputum is used in cystic fibrosis (CF) to monitor for new pathogens and target treatments. A move to remote clinics has meant greater reliance on samples collected at home and posted back. The impact of delays and sample disruption caused by posting has not been systematically assessed but could have significant implications for CF microbiology. MethodsSputum samples collected from adult CF patients were mixed, split, and either processed immediately or posted back to laboratory. Processing involved a further split into aliquots for culture-dependant and-independent microbiology (quantitative PCR [QPCR] and microbiota sequencing). We calculated retrieval by both approaches for five typical CF pathogens: Pseudomonas aeruginosa, Burkholderia cepacia complex, Achromobacter xylosoxidans, Staphylococcus aureus and Stenotrophomonas maltophilia. Results93 paired samples were collected from 73 CF patients. Median interval between sample posting and receipt was 5 days (range 1–10). For culture, overall concordance for posted and fresh samples was 86% across the five targeted pathogens (ranging from 57 to 100% for different organisms), with no bias towards either sample type. For QPCR, overall concordance was 62% (range 39–84%), again with no bias towards fresh or posted samples. There were no significant differences in culture or QPCR for samples with short (≤3days) versus extended (≥7days) postal delays. Posting had no significant impact on pathogen abundance nor on microbiota characteristics. ConclusionsPosted sputum samples reliably reproduced culture-based and molecular microbiology of freshly collected samples, even after prolonged delays at ambient conditions. This supports use of posted samples during remote monitoring.

COVID-19 bacteremic co-infection is a major risk factor for mortality, ICU admission, and mechanical ventilation

BackgroundRecent single-center reports have suggested that community-acquired bacteremic co-infection in the context of Coronavirus disease 2019 (COVID-19) may be an important driver of mortality; however, these reports have not been validated with a multicenter, demographically diverse, cohort study with data spanning the pandemic.MethodsIn this multicenter, retrospective cohort study, inpatient encounters were assessed for COVID-19 with community-acquired bacteremic co-infection using 48-h post-admission blood cultures and grouped by: (1) confirmed co-infection [recovery of bacterial pathogen], (2) suspected co-infection [negative culture with ≥ 2 antimicrobials administered], and (3) no evidence of co-infection [no culture]. The primary outcomes were in-hospital mortality, ICU admission, and mechanical ventilation. COVID-19 bacterial co-infection risk factors and impact on primary outcomes were determined using multivariate logistic regressions and expressed as adjusted odds ratios with 95% confidence intervals (Cohort, OR 95% CI, Wald test p value).ResultsThe studied cohorts included 13,781 COVID-19 inpatient encounters from 2020 to 2022 in the University of Alabama at Birmingham (UAB, n = 4075) and Ochsner Louisiana State University Health—Shreveport (OLHS, n = 9706) cohorts with confirmed (2.5%), suspected (46%), or no community-acquired bacterial co-infection (51.5%) and a comparison cohort consisting of 99,170 inpatient encounters from 2010 to 2019 (UAB pre-COVID-19 pandemic cohort). Significantly increased likelihood of COVID-19 bacterial co-infection was observed in patients with elevated ≥ 15 neutrophil-to-lymphocyte ratio (UAB: 1.95 [1.21–3.07]; OLHS: 3.65 [2.66–5.05], p < 0.001 for both) within 48-h of hospital admission. Bacterial co-infection was found to confer the greatest increased risk for in-hospital mortality (UAB: 3.07 [2.42–5.46]; OLHS: 4.05 [2.29–6.97], p < 0.001 for both), ICU admission (UAB: 4.47 [2.87–7.09], OLHS: 2.65 [2.00–3.48], p < 0.001 for both), and mechanical ventilation (UAB: 3.84 [2.21–6.12]; OLHS: 2.75 [1.87–3.92], p < 0.001 for both) across both cohorts, as compared to other risk factors for severe disease. Observed mortality in COVID-19 bacterial co-infection (24%) dramatically exceeds the mortality rate associated with community-acquired bacteremia in pre-COVID-19 pandemic inpatients (5.9%) and was consistent across alpha, delta, and omicron SARS-CoV-2 variants.ConclusionsElevated neutrophil-to-lymphocyte ratio is a prognostic indicator of COVID-19 bacterial co-infection within 48-h of admission. Community-acquired bacterial co-infection, as defined by blood culture-positive results, confers greater increased risk of in-hospital mortality, ICU admission, and mechanical ventilation than previously described risk factors (advanced age, select comorbidities, male sex) for COVID-19 mortality, and is independent of SARS-CoV-2 variant.

Bacteriological Analysis of Bronchoalveolar Lavage Fluid in Patients with Respiratory Tract Infections

Background and Aim: Bacterial respiratory infections are most commonly causes of illness for all age group patientsin ICU. Most of the patients suffer from urosepsis, postoperative disease and lower respiratory infection whenadmitted in ICU’s. Broncho alveolar lavage (BAL) is an ideal sample that allows the recovery of pathogens cellularand noncellular components from the epithelial surface of lower respiratory tract. This study was performed todetect pathogenic organisms by microscopy of BAL fluid and isolate and identify various bacteria and fungi fromBAL fluid in culture and analyze their antibiogram.Material and Methods: The cross-sectional prospective study was conducted in the Department of Microbiology,tertiary care teaching hospital, India. The study included 200 BAL samples taken from all consecutive patientsreferred with suspicion of pneumonia. Bronchial wash was done with the help of fibreoptic bronchoscope underlocal anaesthesia. All BAL samples were cultured on three bacteriological media agar plates using a sterile 4mmnichrome loop (0.01ml), and incubated at 37 C for 72 hours for quantitative bacterial culture using standardlaboratory techniques. Bacterial isolates were identified by performing standard microbiological procedures suchas study of colony morphology, Gram staining and standard biochemical tests.Results: Out of the total 200 samples, 120 (60%) were from males, and 80 (40%) were female patients. Thepredominant GNB was Klebsiella pneumoniae 45 (61%), followed by Pseudomonas aeruginosa 22(30%), Esch.coli 6(8%) and the fungal isolate was Aspergillus niger 5(1%). Klebsiella &amp; Pseudomonas were highly sensitive toamikacin, piperacillin-tazobactam, imipenem, gentamycin, followed by tobramycin.Conclusion: Results of the present study demonstrate the high incidence of gram-negative isolates. The study alsosuggests that regular antimicrobial sensitivity monitoring should be done as most isolates are highly resistant tocephalosporin and other commonly used antimicrobials

Perpetuation of Phoma naikii in the crop debris of pigeonpea

Infected debris such as leaves, stem, petiole and twig could be an important source of survival for the pathogens and source of inoculum for the subsequent spreads from one season to the next and from one area to another area. This study was conducted to determine the length of survival of Phoma naikii in the infected pigeonpea debris under different storage conditions viz., room, refrigerator, pot and field conditions. Under pot conditions, the samples were buried under 5 and 7.5 cm and one set were placed on surface of the soil. These samples were subjected for isolation at 15 days interval incubated at 25 ±2 oC. The observations were recorded for growth and development of pathogen in the tissues after a week. The results revealed that frequency of recovery of pathogen decreased over time and the fungus was capable of overwintering for 23 weeks (% reduction was 86.66-6.66) in infected debris buried in sterilized soil regardless of burial depth. It has survived for 27 weeks (% reduction was 93.33-13.33) in field conditions, 30 weeks (% reduction was 100.0-20.0) on surface of soil, 34 weeks (% reduction was 100.0-20.0) in room conditions and 36 weeks (% reduction was 100.00-26.66) in the refrigerated conditions. Hence, the present study indicates the variation in the viability of the pathogen in the infected debris stored ate six different conditions.

Improved Recovery of Captured Airborne Bacteria and Viruses with Liquid-Coated Air Filters.

The COVID-19 pandemic has revealed the importance of the detection of airborne pathogens. Here, we present composite air filters featuring a bioinspired liquid coating that facilitates the removal of captured aerosolized bacteria and viruses for further analysis. We tested three types of air filters: commercial polytetrafluoroethylene (PTFE), which is well known for creating stable liquid coatings, commercial high-efficiency particulate air (HEPA) filters, which are widely used, and in-house-manufactured cellulose nanofiber mats (CNFMs), which are made from sustainable materials. All filters were coated with omniphobic fluorinated liquid to maximize the release of pathogens. We found that coating both the PTFE and HEPA filters with liquid improved the rate at which Escherichia coli was recovered using a physical removal process compared to uncoated controls. Notably, the coated HEPA filters also increased the total number of recovered cells by 57%. Coating the CNFM filters did not improve either the rate of release or the total number of captured cells. The most promising materials, the liquid-coated HEPA, filters were then evaluated for their ability to facilitate the removal of pathogenic viruses via a chemical removal process. Recovery of infectious JC polyomavirus, a nonenveloped virus that attacks the central nervous system, was increased by 92% over uncoated controls; however, there was no significant difference in the total amount of genomic material recovered compared to that of controls. In contrast, significantly more genomic material was recovered for SARS-CoV-2, the airborne, enveloped virus, which causes COVID-19, from liquid-coated filters. Although the amount of infectious SARS-CoV-2 recovered was 58% higher, these results were not significantly different from uncoated filters due to high variability. These results suggest that the efficient recovery of airborne pathogens from liquid-coated filters could improve air sampling efforts, enhancing biosurveillance and global pathogen early warning.

Control of Phytophthora and Rhizoctonia Root Rot on Red Maple Using Fungicides and Biofungicides

Phytophthora nicotianae and Rhizoctonia solani are the well-described soilborne pathogens of concern causing Phytophthora and Rhizoctonia root rot, respectively, of red maple plants (Acer rubrum L.), resulting in substantial economic losses to nursery growers. The management of root and crown rot disease of red maple is a big challenge. The objective of this study was to test the efficacy of several fungicide and biofungicide products to control Phytophthora and Rhizoctonia root rot on red maple plants in greenhouse conditions. Treatments, including fungicides and biofungicides, and nontreated and inoculated and nontreated and noninoculated as controls were arranged in a completely randomized design with six replications. Red maples planted in number 1 nursery containers were artificially inoculated with P. nicotianae or R. solani. Plant height, plant width, total fresh weight, and root fresh weight were measured and roots were assessed for root rot disease severity based on a scale of 0% to 100% root damaged. The pathogen recovery percentage of plant roots was determined by culturing ten randomly selected root pieces (≈1 cm long) cut from the root tips on Phytophthora selective medium (PARPH-V8) or Rhizoctonia semi-selective medium. All tested fungicides and biofungicides reduced Phytophthora and Rhizoctonia root rot on red maple plants compared with the nontreated and inoculated control. Likewise, pathogen recovery was lower for fungicide-treated and biofungicide-treated plants. Fungicides, such as mefenoxam, oxathiapiprolin, pyraclostrobin plus boscalid, and pyraclostrobin provided the most effective control of Phytophthora root rot. Pyraclostrobin plus boscalid and pyraclostrobin followed by biofungicides Bacillus amyloliquefaciens strain F727 and Trichoderma harzianum Rifai strain T-22 plus T. virens strain G-41 were most effective for suppressing Rhizoctonia root rot. There were no differences in plant height, plant width, plant fresh weight, and root fresh weight among the treatments. These findings will help nursery producers make decisions while formulating soilborne disease management strategies for red maple production.

Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis

ObjectiveTo investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual Materials14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 th century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis. MethodsShotgun sequencing data from was examined to determine the presence of Brucella DNA. ResultsThree of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7−169), but for many the data quality was insufficient to withstand our identification and authentication criteria. ConclusionsWe identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification. SignificanceOur results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease. LimitationsStudy focuses on pathogen recovery in a single individual. Suggestions for further researchFurther analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples