Specimen Collection Research Articles

Bee monitoring by community scientists: comparing a collections-based program with iNaturalist.

Bee monitoring, or widespread efforts to document bee community biodiversity, can involve data collection using lethal (specimen collections) or non-lethal methods (observations, photographs). Additionally, data can be collected by professional scientists or by volunteer participants from the general public. Collection-based methods presumably produce more reliable data with fewer biases against certain taxa, while photography-based approaches, such as data collected from public natural history platforms like iNaturalist, can involve more people and cover a broader geographic area. Few efforts have been made to quantify the pros and cons of these different approaches. We established a community science monitoring program to assess bee biodiversity across the state of Pennsylvania (USA) using specimen collections with nets, blue vane traps, and bowl traps. We recruited 26 participants, mostly Master Gardeners, from across the state to sample bees after receiving extensive training on bee monitoring topics and methods. The specimens they collected were identified to species, stored in museum collections, and the data added to public databases. Then, we compared the results from our collections to research-grade observations from iNaturalist during the same time period (2021 and 2022). At state and county levels, we found collections data documented over twice as much biodiversity and novel baseline natural history data (state and county records) than data from iNaturalist. iNaturalist data showed strong biases toward large-bodied and non-native species. This study demonstrates the value of highly trained community scientists for collections-based research that aims to document patterns of bee biodiversity over space and time.

Efficient risk-based collection of biospecimens in cohort studies: Designing a prospective study of diagnostic performance for multicancer detection tests.

In cohort studies, it can be infeasible to collect specimens on an entire cohort. For example, to estimate sensitivity of multiple Multi-Cancer Detection (MCD) assays, we desire an extra 80mL of cell-free DNA (cfDNA) blood, but this much extra blood is too expensive for us to collect on everyone. We propose a novel epidemiologic study design that efficiently oversamples those at highest baseline disease risk from whom to collect specimens, to increase the number of future cases with cfDNA blood collection. The variance reduction ratio from our risk-based subsample versus a simple random (sub)sample (SRS) depends primarily on the ratio of risk model sensitivity to the fraction of the cohort selected for specimen collection subject to constraining the risk model specificity. In a simulation where we chose 34% of Prostate, Lung, Colorectal, and Ovarian Screening Trial cohort at highest risk of lung cancer for cfDNA blood collection, we could enrich the number of lung cancers 2.42-fold and the standard deviation of lung-cancer MCD sensitivity was 31-33% reduced versus SRS. Risk-based collection of specimens on a subsample of the cohort could be a feasible and efficient approach to collecting extra specimens for molecular epidemiology.

Feasibility of Home Collection for Urogenital Microbiome Samples.

Feasibility of home urogenital microbiome specimen collection is unknown. This study aimed to evaluate successful sample collection rates from home and clinical research centers. Adult women participants enrolled in a multicentered cohort study were recruited to an in-person research center evaluation, including self-collected urogenital samples. A nested feasibility substudy evaluated home biospecimen collection prior to the scheduled in-person evaluation using a home collection kit with written instructions, sample collection supplies, and a Peezy™ urine collection device. Participants self-collected samples at home and shipped them to a central laboratory 1 day prior to and the day of the in-person evaluation. We defined successful collection as receipt of at least one urine specimen that was visibly viable for sequencing. Of 156 participants invited to the feasibility substudy, 134 were enrolled and sent collection kits with 89% (119/134) returning at least 1 home urine specimen; the laboratory determined that 79% (106/134) of these urine samples were visually viable for analysis. The laboratory received self-collected urine from the research center visit in 97% (115/119); 76% (91/119) were visually viable for sequencing. Among 401 women who did not participate in the feasibility home collection substudy, 98% (394/401) self-collected urine at the research center with 80% (321/401) returned and visibly viable for sequencing. Home collection of urogenital microbiome samples for research is feasible, with comparable success to clinical research center collection. Sample size adjustment should plan for technical and logistical difficulties, regardless of specimen collection site.

Challenges, Rewards, and Digital Aspects in Establishing Macau’s First Regional Biobank

Abstract Biobanks have proven to be significant research and reference infrastructures that house collections of specimens and associated data for future biomedical research. The Macau Special Administrative Region government has determined the need to diversify its economy and has set a target ratio for a gross domestic product contribution in the high-tech research industry. This article presents the rewards, challenges, and digital aspects of the potential establishment of a regional biobank in Macau to improve health research capacity and innovative high-tech initiatives while recognizing biosecurity, digital, and public health issues without compromising legal, social, ethical, and/or ethnic boundaries within the region. The development of a regional biobank of biological samples and data, along with additional information from diverse populations for future conducted research projects, is anticipated to stimulate the region’s economic, scientific, and public health growth.

Assessment the Role of Non Invasive Biomarkers as an Early Predictors of Mucosal Healing in Ulcerative Colitis Patients Treated with the Biological Therapy

Abstract Background Ulcerative colitis (UC) is characterized by confluent mucosal inflammation and erosions starting from the anal verge and extending to a variable extent, where patients often complain of diarrhea associated with rectal bleeding, abdominal tenderness, and weight loss. Numerous disease biomarkers have been studied in ulcerative colitis (UC) such as Erythrocyte sedimentation rate(ESR) and C- reactive protein(CRP). On the other hand, fecal calprotectin and Lactoferrin are more specific and sensitive but expensive and still not commonly used in clinical practice due to the need for on demand specimen collection. Objective To evaluate the role of the non-invasive biomarkers as an early predictor of mucosal healing in ulcerative colitis patients treated with biological therapy. Methods Twenty adult patients with ulcerative colitis who received biological therapy (after adequate screening) were included in our study. The patients met the indications for treatment with biological therapy according to European Crohn and Colitis Organization guidelines. The patients were presented to our IBD clinic at tropical medicine department, Ain shams university in the period from 1/2018 to 9/2021. Results There is a strong relationship between clinical response and mucosal healing at 6 months of starting biological therapy as 100% of patients who achieved mucosal healing showed clinical response. Median N/L ratio, median PLT/L ratio and CRP/albumin ratio were 1.58, 425 and 1.19 respectively in patients who achieved mucosal healing at 6 months after 3 months of starting biological therapy with statistical significance (p-value = 0.019, 0.019 and 0.008) respectively in comparison to the patients who didn’t achieve mucosal healing. Both median of L/M ratio and PLT/M ratio were decreased in patients achieved mucosal healing at 6 months after 3 months of starting biological therapy (3.43 and 660) respectively in comparison to patients who didn’t achieve mucosal healing but it didn’t reach any statistical significance. Conclusion Non invasive biomarkers at 3 months like N/L ratio, PLT/L ratio, L/M ratio and PLT/M ratio may be used as non invasive predictors of mucosal healing at 6 months after starting treatment with biological treatment.

Diagnostic Stewardship in Clinical Microbiology: An Indispensable Component of Patient Care.

Emerging infectious diseases and increasing resistance to available antimicrobials are mapping the evolution of clinical microbiology and escalating the nature of undertakings required. Rapid diagnosis has become the need of the hour, which can affect diagnostic algorithms and therapeutic decisions simultaneously. Subsequently, the concept of 'diagnostic stewardship' was introduced into clinical practice for coherent implementation of available diagnostic modalities to ensure that these new rapid diagnostic technologies are conserved, rather than consumed as part of health care resources, with a view to improve the patient care and reduce Turnaround Time (TAT) and treatment expense. The present study highlights the requisite of diagnostic stewardship and outlines the infectious disease diagnostic modalities that can assist in its successful implementation. Diagnostic stewardship promotes precise, timely diagnostics, from the initial specimen collection and identification to reporting with appropriate TAT, so as to enable timely management of the patient. The main aim of diagnostic stewardship is to optimize the right choice of diagnostic test for the right patient to attain clinically significant reports with the least possible TAT for timely management and the least expected adverse effects for the patient, community, and the healthcare system. This underlines the requisite of a multifaceted approach to make technological advancements effective and successful for implementation as a part of diagnostic stewardship for the best patient care.

Molecular Analysis of Volatile Metabolites Synthesized by Candida albicans and Staphylococcus aureus in In Vitro Cultures and Bronchoalveolar Lavage Specimens Reflecting Single- or Duo-Factor Pneumonia.

Current microbiological methods for pneumonia diagnosis require invasive specimen collection and time-consuming analytical procedures. There is a need for less invasive and faster methods to detect lower respiratory tract infections. The analysis of volatile metabolites excreted by pathogenic microorganisms provides the basis for developing such a method. Given the synergistic role of Candida albicans in increasing the virulence of pathogenic bacteria causing pneumonia and the cross-kingdom metabolic interactions between microorganisms, we compare the emission of volatiles from Candida albicans yeasts and the bacteria Staphylococcus aureus using single and mixed co-cultures and apply that knowledge to human in vivo investigations. Gas chromatography-mass spectrometry (GC-MS) analysis resulted in the identification of sixty-eight volatiles that were found to have significantly different levels in cultures compared to reference medium samples. Certain volatiles were found in co-cultures that mainly originated from C. albicans metabolism (e.g., isobutyl acetate), whereas other volatiles primarily came from S. aureus (e.g., ethyl 2-methylbutyrate). Isopentyl valerate reflects synergic interactions of both microbes, as its level in co-cultures was found to be approximately three times higher than the sum of its amounts in monocultures. Hydrophilic-lipophilic-balanced (HLB) coated meshes for thin-film microextraction (TFME) were used to preconcentrate volatiles directly from bronchoalveolar lavage (BAL) specimens collected from patients suffering from ventilation-associated pneumonia (VAP), which was caused explicitly by C. albicans and S. aureus. GC-MS analyses confirmed the existence of in vitro-elucidated microbial VOCs in human specimens. Significant differences in BAL-extracted amounts respective to the pathogen-causing pneumonia were found. The model in vitro experiments provided evidence that cross-kingdom interactions between pathogenic microorganisms affect the synthesis of volatile compounds. The TFME meshes coated with HLB particles proved to be suitable for extracting VOCs from human material, enabling the translation of in vitro experiments on the microbial volatilome to the in vivo situation involving infected patients. This indicates the direction that should be taken for further clinical studies on VAP diagnosis based on volatile analysis.

Ten lessons learned from the mass digitisation of a herbarium collection.

Worldwide, herbaria maintain collections of reference specimens representing global plant diversity. These collections are a valuable resource for fundamental botanical research and applied scientific research across various disciplines, and play a significant role in addressing major societal challenges such as biodiversity conservation. The digitisation of herbarium specimens and their online dissemination is one of the most important recent developments in the curation of these collections. Digitisation significantly enhances access to the collections for the research community and facilitates large-scale analysis of biodiversity data. Digitisation also provides a means for preserving the physical specimens, as it reduces the need for handling and transportation. Rapid technological developments have greatly accelerated the rate of databasing and digital imaging of collections. Meise Botanic Garden recently completed a six-year project to mass digitise its herbarium collections of about 3 million specimens mounted on sheets and through this process we have learned valuable lessons. We have captured our experience in 10 recommendations for other collection-holding institutions to take inspiration from as they start planning their own digitisation efforts. We also present case studies where we delve deeper into certain topics as examples.

Assessment of moth diversity in the Zealandia ecosanctuary through a community science initiative

ABSTRACT A collaborative project involving researchers and citizen scientists was conducted in the Zealandia ecosanctuary (Wellington, Aotearoa New Zealand) during 2019–2022 to investigate Lepidoptera biodiversity. Here we present the first results of that project, reporting on the success of the citizen science approach and presenting a checklist of moth species in Zealandia. Sampling efforts took place roughly monthly during the night, and relied heavily on the participation of keen volunteers. Moths were primarily attracted using a mercury vapour light trap, but sweep-netting was also applied. On each trip, a selection of representative specimens was collected, humanely euthanised, prepared, photographed, and deposited as voucher specimens in the entomological collection of the Museum of New Zealand Te Papa Tongarewa. Photos were uploaded to the community science online platform iNaturalist, where experts could help in identifying the species. We report a total of 262 species in Zealandia, belonging to 29 families; of those species, 22 are exotic. Notably, 217 species were found via our sampling, and the remaining 45 were recorded by citizen scientists and posted on iNaturalist. While this is likely an underestimate of the true species count in Zealandia, we consider the project a successful citizen science initiative that has generated valuable data, a fine collection of voucher specimens for the future, considerable public engagement, and positive media attention.

Community-associated Carbapenem-Resistant Organism Case Investigations in New York City, December 2020-May 2023

Epidemiology of carbapenem-resistant organisms (CRO) has focused on transmission in acute care hospital or long-term care facility (LTCF) settings. Few investigations have examined community-associated (CA)-CRO, with no consensus about common exposures. To explore possible exposures, the New York City (NYC) Department of Health and Mental Hygiene investigated suspected CA-CRO cases through routine surveillance among NYC residents with specimens collected during December 2020-May 2023. CA-CRO cases were defined as urine or skin specimens with bacterial cultures exhibiting carbapenem resistance, among individuals aged ≤70 years with no international travel, hospitalization, or LTCF stays within 12 months before specimen collection. Inclusion was determined by reviewing data from health information exchanges, when available electronic medical records, and telephone screening for those not excluded through record review. We identified 426 suspected cases for review, those not meeting the case definition were excluded; 44 individuals were not reached for screening. A preliminary questionnaire was fielded with 12 individuals and then refined to capture additional potential exposures. Analyses were completed with 23 individuals interviewed with the refined questionnaire. Of the 23, 70% were female; 39% were Hispanic, 17% Black, and 17% White; their median age was 60 years (range: 26-70 years). Further, 83% reported an outpatient appointment, 48% reported an outpatient procedure/surgery, and 9% reported having a hospitalized household member, all within 12 months before specimen collection; 26% had a urinary catheter or indwelling device within 2 days of specimen collection. Additionally, 30% reported taking antibiotics within 3 months of specimen collection, 52% denied taking antibiotics, 9% were unsure about antibiotic use, and 9% did not answer the question. Whole genome sequencing (WGS) was performed on 14 available isolates from CA-CRO cases by the NYC Public Health Laboratory or Wadsworth Center (WC), of which only 7 could be compared with isolates previously sequenced at WC (2017-2023). Six isolates were separated by >50 mutation events, suggesting no close genomic relationship. One isolate from 2021 was 11 mutation events from a 2018 isolate from the same individual, consistent with the expected evolutionary rate. While infrequent, CA-CRO cases occur in NYC. Outpatient healthcare, antibiotic use, and urinary catheters or indwelling devices were common self-reported exposures. Analyses were limited by screening non-response. Increased specimen availability for WGS could enhance investigation of CA-CRO exposure patterns. Health information exchange data were often incomplete and future surveillance could benefit from healthcare and public health partnerships and better documentation for more complete electronic medical histories.

Comparison of Medicare Claims-based Clostridioides difficile infection classification to chart review using a linked cohort

Background: Medicare claims are frequently used to study Clostridioides difficile infection (CDI) epidemiology. Categorizing CDI based on location of onset and potential exposure is critical in understanding transmission patterns and prevention strategies. While claims data are well-suited for identifying prior healthcare utilization exposures, they lack specimen collection and diagnosis dates to assign likely location of onset. Algorithms to classify CDI onset and healthcare association using claims data have been published, but the degree of misclassification is unknown. Methods: We linked patients with laboratory-confirmed CDI reported to four Emerging Infections Program (EIP) sites from 2016-2020 to Medicare beneficiaries using residence, birth date, sex, and hospitalization and/or healthcare exposure dates. Uniquely linked patients with fee-for-service Medicare A/B coverage and complete EIP case report forms were included. Patients with a claims CDI diagnosis code within ±28 days of a positive CDI test reported to EIP were categorized as hospital-onset (HO), long-term care facility onset (LTCFO), or community-onset (CO, either healthcare facility-associated [COHCFA] or community-associated [CA]) using a previously published algorithm based on claim type, ICD-10-CM code position, and duration of hospitalization (if applicable). EIP classifies CDI into these categories using positive specimen collection date and other information from chart review (e.g. admit/discharge dates). We assessed concordance of EIP and claims case classifications using Cohen’s kappa. Results: Of 10,002 eligible EIP-identified CDI cases, 7,064 were linked to a unique beneficiary; 3,451 met Medicare A/B fee-for-service coverage inclusion criteria. Of these, 650 (19%) did not have a claims diagnosis code ±28 days of the EIP specimen collection date (Table); 48% (313/650) of those without a claims diagnosis code were categorized by EIP as CA CDI. Among those with a CDI diagnosis code, concurrence of claims-based and EIP CDI classification was 68% (κ=0.56). Concurrence was highest for HO and lowest for COHCFA CDI. A substantial number of EIP-classified CO CDIs (30%, Figure) were misclassified as HO using the claims-based algorithm; half of these had a primary ICD-10 diagnosis code of sepsis (226/454; 50%). Conclusions: Evidence of CDI in claims data was found for 81% of EIP-reported CDI cases. Medicare classification algorithms concurred with the EIP classification in 68% of cases. Discordance was most common for community-onset CDI patients, many of whom were hospitalized with a primary diagnosis of sepsis. Misclassification of CO-CDI as HO may bias findings of claims-based CDI studies.

A first revision of the Andrena of Iraq (Hymenoptera, Andrenidae), with the description of two new species from Iraqi Kurdistan and additional records from surrounding countries.

Iraq is a large country in the Middle East region that borders both Turkey and Iran, countries known to host two of the largest bee faunas globally, as expected for a group of insects that favour dry to Mediterranean climates. Despite this huge regional species richness, the bee fauna of Iraq is chronically understudied and poorly known, both in relative and absolute terms. This is true for the hyper-speciose bee genus Andrena, for which only 17 species have been previously published for Iraq. This work is the first modern contribution to the revision of the Andrena fauna of Iraq. Based on new specimen collections in Duhok Governorate (Iraqi Kurdistan) during 2023, a revised total of 59 Andrena species for Iraq (42 species recorded for the first time) is presented, including the description of two new species: Andrena (Aciandrena) duhokensis Wood, sp. nov. and Andrena (Notandrena) baiocchii Wood, sp. nov. The unknown males of A. (Micrandrena) elam Wood, 2022, A. (Micrandrena) obsidiana Wood, 2022, and A. (Notandrena) ayna Wood, 2023 are described. Andrenabakrajoensis Amin & Mawlood, 2019, syn. nov. is synonymised with A. (Holandrena) variabilis Smith, 1853. Additional records are presented from nearby Middle Eastern countries, particularly Lebanon. These results highlight the fundamentally understudied nature of the Iraqi Andrena fauna.

Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology.

The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.

Extending the gift—utilizing residual human anatomical materials for training Pathologists’ Assistants in surgical pathology techniques

This study investigates the effectiveness of using residual human anatomical materials, obtained from a gross anatomy course, for training Pathologists' Assistant (PathA) students in surgical pathology techniques. We utilized two surveys to assess the perceived efficacy of this approach: one survey targeted PathA students to evaluate their training experiences with both human and animal tissues, while the other assessed the impact of specimen collection on the educational experiences of gross anatomy course students.

Changes in Antibiotic Use and Disruptions to Antimicrobial Resistance Detection in South Africa and Uganda, 2019 – 2020

Background: The COVID-19 pandemic disrupted routine health services worldwide, including systems to detect antimicrobial resistance (AR). AR is a mounting global health threat with some studies showing the highest mortality rate from AR infection is in Sub-Saharan Africa (SSA). Antibiotic use is a major contributor to AR. We sought to characterize COVID-19-related changes to antibiotic use and AR detection capacity in two countries in SSA from 2019 to 2020. Methods: Health facilities (HF) in South Africa and Uganda were surveyed as part of a larger study assessing disruptions to essential health services in SSA in the context of COVID-19. Modified stratified random sampling of HF by facility level was conducted in regions with high COVID-19 cumulative prevalence. Hospital pharmacists were surveyed to identify perceived changes in antibiotic use. Among facilities with the capacity to detect AR, surveys were conducted with AR laboratory managers to identify perceived changes in staff, equipment, training, and supplies. Descriptive data analysis was conducted using frequencies and proportions. Results: A total of 39 HFs in South Africa and 45 HFs in Uganda responded to the antibiotic use survey. Increases in total antibiotic use from 2019 to 2020 were reported by 82% (23/28) of HF in South Africa and 68% (27/40) in Uganda. Increased use of antibiotics for multi-drug resistant bacteria (per World Health Organization Reserve classification) was reported by 36% (9/25) and 38% (8/21) of HFs in South Africa and Uganda, respectively. 19 HFs in South Africa and 12 HFs in Uganda responded to the AR detection capacity survey. HFs in both countries reported decreases in laboratory staff responsible for AR (33% [13/40] in South Africa and 31% [11/35] in Uganda). Decreased availability of reagents and consumables for bacteriology and antimicrobial susceptibility testing was reported by 50% (8/16) and 33% (4/12) of HFs, and decreased availability of specimen collection supplies for bacterial cultures was reported by 41% (7/17) and 42% (5/12) of HFs in South Africa and Uganda, respectively. Diversion of laboratory supplies was reported in both countries (32% [6/19] in South Africa and 25% [3/12] of HF in Uganda). Conclusions: HFs in South Africa and Uganda reported increases in antibiotic prescribing, a risk factor for increased AR, concurrently with disruptions in AR detection capacity during the early phases of the COVID-19 pandemic. These findings emphasize the importance of investing in bacteriology and AR testing in SSA and maintaining support during infectious disease pandemics.

Variability of MDRO Reporting Across Tennessee Microbiology Laboratories

Background: Identification and timely reporting of multi-drug resistant organisms (MDROs) drives efficacy of infection prevention efforts. Data on MDRO reporting timeliness and inter-facility variability are limited. Facility-dependent variability in MDRO reporting across Tennessee was examined to identify opportunities for MDRO surveillance improvement. Methods: Data for reported Tennessee MDROs including carbapenem-resistant Enterobacterales (CRE), carbapenem-resistant Acinetobacter baumannii (CRAB), Carbapenem-resistant Pseudomonas aeruginosa (CRPA) and Candida auris, were obtained from the southeast regional Antibiotic Resistance Laboratory Network (ARLN) from 2018-2022, excluding screening and colonization specimens. Variance in days accrued from specimen collection to ARLN receipt was analyzed using one-way analysis of variance (ANOVA) with Tukey’s test (SAS 9.4). Facilities were categorized as fast (1-10 days), slow (11-20 days), or delayed (21-100 days) reporters. Results: There were 9,569 MDRO isolates reported. CRPA was reported faster than other MDROs (p < 0.001), while specimens from West Tennessee compared to other regions (p < 0.001) (Figure) and blood cultures compared to other specimens were reported more slowly (p < 0.001) (Table). There was no difference in reporting times for facilities using on-site microbiology laboratories versus reference laboratories (P = 0.062). Conclusion: MDRO reporting times varied across Tennessee by region, specimen, and organism. Future work to elucidate drivers of variability will consist of surveys and focused interviews with laboratory personnel to identify shared and unique barriers and opportunities for improvement.

Analysis of CAUTIs and Projected Effect of Increasing Pyuria Threshold in Urinalysis with Reflex to Culture

Background: Catheter-Associated Urinary Tract Infections (CAUTI) are preventable hospital acquired infections that contributes to patient morbidity, prolonged hospital stays and increased healthcare costs. Complete compliance to the CAUTI bundle is critical for preventing infection—not only reducing catheter days, but also ensuring appropriate indications are present for urine culture collection. Methods: This retrospective study included 145 patients diagnosed with CAUTI per NHSN definitions from July 1, 2020 to June 30, 2023. Data collected included laboratory data, catheter duration, catheter indication, urinalysis/culture indication and if foley was appropriately removed/changed prior to specimen collection. A urinary catheter indication order was implemented in February 2021 requiring providers to select specific criteria for catheter placement/maintenance. In July 2023, the threshold for urinalysis to reflex to culture was increased to ≥10 WBCs and this criteria was applied to these cases to estimate the effect on diagnosis of CAUTI. Results: The most common indications for urinary catheters were input and output monitoring 76 (52%) and urinary retention/obstruction 34 (23%). No indication was entered on 22 (15%) patients. No difference was seen in the number of catheters without an indication before or after the 2021 order update. Mean catheter duration was 11.5 days with a median of 7 days. The most common indications for obtaining a urine specimen were leukocytosis/fever/sepsis 91 (63%), urinary symptoms/abdominal/flank pain 13 (9%), urine appearance 6 (4%), and altered mental status 4 (3%). In 31 (21%) patients, no indication was identified. A urinalysis with reflex to culture was completed in 105 (72%) and the catheter was removed prior to culture collection in 68 (47%). Of the 127 patients with a urinalysis and culture, 11 had 0-5 WBCs, 16 had 6-9 WBCs, 15 had 10-20 WBCs and 85 had >20 WBCs. Using the new pyuria criteria for urinalysis to reflex to culture, 27 (19%) CAUTIs could have been avoided. Conclusion: Review of CAUTI cases identified opportunities for improving documentation and education of appropriate indications for urinary catheters and evaluation of urinary tract infection. The majority of urine cultures were obtained due to non-specific symptoms and less than 10% had specific urinary symptoms indicating need for continued education and diagnostic stewardship. Increasing the pyuria threshold needed to reflex to culture has the potential to significantly reduce CAUTIs but additional education is needed to ensure catheters are changed prior culture collection and specimens are only sent when signs and symptoms of urinary tract infection are present.

Optimization and application of bacterial environmental DNA and RNA isolation for qualitative and quantitative studies

AbstractMolecular detection of environmental DNA (eDNA) and RNA (eRNA) allows highly sensitive qualitative (i.e., presence or absence) and quantitative (i.e., abundance) monitoring of aquatic bacteria. However, bacterial molecular diagnostics are limited by low positive predictive values. Protocols for bacterial eDNA and eRNA molecular monitoring have primarily focused on optimizing specimen collection, and the optimal method to purify bacterial nucleic material from postcollection aquatic specimens to maximize the analytical sensitivity of molecular diagnostics remains poorly defined. Accordingly, strategies to isolate bacterial eDNA and eRNA from fresh and saltwater were investigated. We evaluated two filtration and four nucleic acid purification systems as representative of current generation bacterial eDNA and eRNA isolation strategies for capacity to isolate bacterial eDNA and eRNA from prelysed (i.e., free‐nucleic acids) and viable (i.e., colony forming units, CFU) bacterial cells. We also compared the sensitivities of reverse transcription quantitative PCR (RT‐qPCR) and metagenomic shotgun microbiome sequencing. The optimal protocol used 0.7 μm borosilicate glass filters (Whatman plc) followed by extraction with the RNeasy PowerWater kit (Qiagen). The protocol had a very high analytical sensitivity (10−3–100 ng and 102–101 CFU detected in 500 mL) across multiple species of bacteria, when tested with either RTqPCR or metagenomic sequencing. Importantly, this study highlighted several limitations which are restrictive to both qualitative and quantitative bacterial eDNA and eRNA studies. First, a 12‐h time course between sampling and extraction revealed significant species‐specific changes in cell number and free‐nucleic acid concentrations can occur postspecimen collection. Second, we found Gram‐positive bacteria yielded less nucleic material compared to Gram‐negative bacteria suggesting bacterial eDNA and eRNA studies could be biased by microorganism genome stability and extraction efficiency. This study highlights the need to define the species‐specific diagnostic sensitivity of a protocol when monitoring aquatic bacterial eDNA and eRNA with molecular diagnostics.

Reducing Blood Culture Contamination Rates: Introduction of a Combined Education and Skin Antisepsis Intervention.

Background. Blood culture contamination (BCC) is an important quality concern in clinical microbiology as it can lead to unnecessary antimicrobial therapy in patients and increased workload for laboratory scientists. The Clinical Laboratory and Standards Institute recommend BCC rates to be <3 % and recently updated guidelines have set a new goal of 1 %. The aim of this project was to design and implement interventions to reduce BCC rates at our institution. Methods. We introduced a combined education and skin antisepsis intervention in a large Model 4 academic teaching hospital in the South of Ireland. BD ChloraPrep skin antisepsis applicators (2 % chlorhexidine gluconate/70 % isopropyl alcohol), licensed for use for blood culture specimen collection, were introduced, replacing Clinell (2 % chlorhexidine gluconate/70 % isopropyl alcohol) wipes. In addition, a multimodal education programme was designed and delivered. This consisted of a video demonstrating the recommended blood culture specimen collection technique using the new applicators as well as simulation training for all interns. The video was uploaded to the intranet as an educational resource available to all staff. Results. The interventions were implemented in July 2022 and BCC rates pre- and post-intervention were calculated. The average BCC rate for the 12 months preceding the intervention (July 2021 to July 2022) was 2.56 % with highest rates in the Emergency Department. This compared to an average rate of 2.2 % in the 12 months post-intervention (July 2022 to July 2023). In comparing the two rates the reduction in BCC rates between the two periods was not statistically significant (P=0.30). Conclusion. Overall BCC rates reduced but the difference between the two periods did not reach statistical significance. The resource-intensive nature of providing regular and timely feedback of contamination rates and the larger impact of in-person education and training over virtual modalities may explain the modest reduction. Further investments in these areas, particularly in the Emergency Department, will be necessary to further reduce rates in line with new recommendations.

Carbapenem-resistant Acinetobacter baumannii and Carbapenem-resistant Enterobacterales in US Dialysis Populations, 2016-2021

Background: Infections lead to high mortality among patients on chronic dialysis; knowledge of multi-drug resistant infections is limited. The Centers for Disease Control and Prevention’s Emerging Infections Program (EIP) conducts laboratory- and population-based surveillance for carbapenem-resistant Enterobacterales (CRE) in 10 U.S. sites and carbapenem-resistant Acinetobacter baumannii (CRAB) in 9 U.S. sites. We investigated clinical characteristics, healthcare exposures, and outcomes of CRE and CRAB cases in persons on chronic dialysis from 2016-2021. Methods: Among EIP catchment-area residents on chronic dialysis, we defined a CRE case as the first isolation of Escherichia coli, Enterobacter cloacae complex, Klebsiella aerogenes (formerly Enterobacter aerogenes), Klebsiella oxytoca, Klebsiella pneumoniae, or Klebsiella variicola resistant to any carbapenem, from a normally sterile site or urine in a 30-day period. A CRAB case was defined as the first isolation of Acinetobacter baumannii complex resistant to any carbapenem (excluding ertapenem), from a normally sterile site or urine (or lower respiratory tract or wound since 2021) in a 30-day period. Medical records were reviewed. A case was considered colonized if the case culture had no associated infection type or colonization was documented in the medical record. Descriptive analyses, including analyses stratified by pathogen, were conducted. Results: Among 426 cases, 314 were CRE, and 112 were CRAB; most cases were male (235, 55.2%), Black (229, 53.8%), and 51-80 years old (320, 75.1%) (Table). An infection was associated with 363 (85.2%) case cultures; bloodstream infections (148; 40.8%), urinary tract infections (134; 36.9%), and pneumonia (17; 4.7%) were the most frequent. Overall, most cases had documented healthcare exposures (excluding outpatient dialysis) in the year before incident specimen collection, including: 366 (85.9%) hospitalizations, 235 (55.2%) surgeries, 209 (49.1%) long-term care facility stays, 54 (12.7%) long-term acute care facility stays. Additionally, 125 (29.3%) had an intensive care unit admission within the 7 days before incident specimen collection. Compared to CRE cases, a higher proportion of CRAB cases (a) had a long-term care facility stay (82/112 [73.2%] versus 127/314 [40.5%], P&lt;.0001) or hospitalization (103/112 [92%] versus 263/314 [83.8%], P = .03) within the preceding year and (b) died within 30 days of incident specimen collection (40/112 [35.7%] versus 64/314 [20.4%], P = .001). Discussion: Among CRE and CRAB cases in persons on chronic dialysis, healthcare exposures were common, and mortality was high. Additional efforts to better describe the burden of these organisms and associated risk factors in the dialysis population are needed for tailoring infection prevention strategies to this vulnerable.