Routine Swabs Research Articles

EPS3.01 A comparison of routine cough swabs vs a novel sputum sampling technique in a paediatric population

EPS3.01 A comparison of routine cough swabs vs a novel sputum sampling technique in a paediatric population

P448 An audit to compare bacteria growth in standard routine cough swabs done at annual review compared to an induced sputum in children with cystic fibrosis

P448 An audit to compare bacteria growth in standard routine cough swabs done at annual review compared to an induced sputum in children with cystic fibrosis

Incidence of COVID-19 in general surgery emergency and complications associated in different types of management

Background COVID-19 disease causes complications that are classified according to likelihood to high such as venous thromboembolism, acute kidney injury, and postintensive care syndrome. Other complications are low in likelihood such as cytokine release syndrome, pancreatic injury, gastrointestinal complications, and pregnancy-related complications. Mortality and morbidity are really high when it is combined with surgical intervention especially under general anesthesia. Objectives To evaluate the incidence of COVID-19 in general surgery emergency and complications associated in different types of management. Patient and method This is a retrospective study from June 2020 to January 2021 including all COVID-19 positive cases admitted in general surgery department during previously mentioned period. Before September 2020, screening for COVID was based on swab for only clinically suspected COVID-positive patients. Starting from September 2020, routine swab to all admitted patients was done. All data collected about included cases in study underwent statistical analysis to get results. Results In this study, incidence of COVID-19 is 1.35%, mortality incidence is 26.4% (about 92.9% of mortality cases underwent surgery) and morbidity incidence is 30.2%. About 74% (73.6%) of positive cases improved and discharged. Management of cases is according to guidelines of management to each disease and decision of ER consultant. About 77.4% of cases are managed surgically; about 70.7% of cases operated upon underwent exploration. However, 60.4% of cases are admitted with sepsis and septic shock. Asymptomatic cases for COVID during admission are 26.4%. Conclusion Incidence of COVID-19 in acute general surgery emergency in Kasr Al-Ainy is not that high. However, cases operated upon in the era of COVID are associated with high incidence of mortality. Cases are presented to our institute late, which might be an effect of lock down.

Basidiobolomycosis – An Unsightly Devastating Condition, Ironically Responsive to Inexpensive Medications: A Case Report with Review of Literature

Background: Basidiobolomycosis is an infection which results in an indolent, nonhealing, penetrating, unsightly destruction of subcutaneous tissues, rarely described in children. Clinical Description: A 6-year-old girl with no prior medical illness, presented with low-grade intermittent fever associated with an indurated swelling on the posterior aspect of her right leg, which gradually progressed over a period of 6 months into a deep, spreading, nonhealing ulcer, causing pain and restriction of movement. Management and Outcome: Routine blood investigations and swab cultures ruled out pyogenic infections and tuberculosis. She was negative for HIV. The wound was debrided, but there was poor response to antibiotics, fluconazole, and amphotericin B. Biopsy of debrided tissue revealed subcutaneous basidiobolomycosis. She was then treated with a combination of potassium iodide and cotrimoxazole. Over a 3-month period, the ulcer began granulating, and complete resolution was achieved through split-thickness skin grafting. Conclusion: Although uncommon, basidiobolomycosis may be considered in the evaluation of nonhealing penetrating ulcers, especially in immunocompetent children. Rather than expensive antifungals, potassium iodide and cotrimoxazole yield gratifying results in this condition.

SHOULD WOUND SWABS BE SENT ON ALL PIN SITE INFECTIONS?

IntroductionIntroduction: Pin site infection is a common complication during treatment with a circular frame external fixator and increases time and support patients require from the limb reconstruction team. Wound swabs were not routinely sent by the clinical nurse specialists prior to this study, with most pin site infections treated as Staphylococcus aureus with flucloxacillin (clindamycin in penicillin allergy). The aim of this study was to ascertain whether routine sending of wound swabs in pin site infection would change antibiotic treatment.Materials & MethodsMaterials and Method: Patients presenting at clinic or physiotherapy with clinical signs of pin site infection were assessed using the Maz Oxford Nuffield (MON) Pin Site Infection Grading System© (OUH, 2021). Antibiotics were commenced as per unit guidelines and swabs sent for microscopy, culture and sensitivity.ResultsResults: There were forty patients treated with pin site infections. Swab results showed S. aureus in 60% (N=24), other organisms in 15% (N=6) and no growth or mixed skin organisms in 10% (N=10). Flucloxacillin was prescribed to 77.5% (n=31) of patients with the remaining 22.5% (n=9) of patients receiving clindamycin (due to allergy) or rifampicin and ciprofloxacin (due to a previous MRSA diagnosis). Antibiotic management was subsequently changed in only 5% (n=2) of patients due to one patient with a new MRSA diagnosis and one patient growing Enterobacter in three pin sites tested.ConclusionsConclusion: This study has shown that routine swab testing of pin sites does not usually change antibiotic management but should still be used in multiple, severe or unresolving pin site infections.

Skin swabs in the skin lymphoma clinic: from swab to treatment.

The skin microbiome in cutaneous T-cell lymphoma (CTCL) is a growing area of research. Previous studies have highlighted the possibility of microbial dysbiosis in chronic inflammation and malignant transformation in CTCL. This single, tertiary centre study highlights the importance of routine skin swab use in the management of patients with CTCL and suggests future research developments.

IMPROVING NEONATAL OUTCOME BY STUDYING THE INCIDENCE OF MATERNAL GROUP B STREPTOCOCCUS (GBS) COLONIZATION AMONGST PREGNANT WOMEN: A PROSPECTIVE OBSERVATIONAL STUDY

Background And Objectives: Group B streptococcus (GBS) colonization during pregnancy can lead to invasive infections in neonates including meningitis or sepsis. The major risk factor for the neonatal disease is the rectovaginal colonization of GBS during pregnancy and delivery. The objectives of this study were as follows: 1) To screen antenatal patients at 35-37 weeks of gestation for GBS colonization. 2) To determine the prevalence of GBS among pregnant women. 3) To formulate an antibiotic policy with respect to antepartum antibiotic prophylaxis and empiric choice of antibiotics for early-onset neonatal sepsis. 4) To ascertain the maternal and neonatal outcomes in pregnant women with GBS colonization. Methods: A prospective observational study was conducted among 50 obstetric patients at 35-37 weeks of gestation attending the outpatient and inpatient departments of a tertiary care hospital. High vaginal and rectal swabs were collected and sent for culture and sensitivity testing using the standard culture methods. The incidence of positive cultures was noted and was taken up as a reference for statistical calculations. Results: Out of the 50 vaginal samples, 1 sample showed GBS positivity having a prevalence of 2%. Rectal swabs did not grow GBS for all samples. The mother and the newborn did not show any symptoms or signs due to GBS. GBS grown in vaginal culture was highly sensitive to Penicillin's, Cephalosporins, Clindamycin, Daptomycin, Vancomycin, Meropenem, and Linezolid. Conclusion:Based on our ndings, screening patients with routine rectovaginal swabs may not be necessary for our population. Also, empiric treatment with antibiotics for GBS in symptomatic mothers cannot be justied and hence GBS should be considered an insignicant pathogen

Pre-enriched saline gargle samples for detection of SARS-CoV-2.

A self‑collected gargle sample, which avoids discomfort and largely reduces the dependency on medical resources, is emerging for detection of SARS‑CoV‑2. However, the incomplete usage of starting materials for both routine oropharyngeal swabs (OPS)/nasopharyngeal swabs (NPS) and saline gargle (SG) samples implies sensitivity can be further improved. Presented here is a bead‑based strategy for pre‑enrichment of SG samples, and results revealed that it acquired about 20 times the starting materials obtained from OPS samples for downstream detection of SARS‑CoV‑2. The sensitivity and specificity of this pre‑enrichment strategy were validated in 100 paired pre‑enriched saline gargle (PenSG) and OPS samples and 89 PenSG samples from healthy volunteers. In addition to detection of SARS‑CoV‑2, this pre‑enrichment strategy may also be implemented in more clinical settings to optimize detection of other diseases.

Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples

Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with machine learning-based partial least squares discriminant analysis (PLS-DA) was applied to study if severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be detected from nasopharyngeal swab samples originally collected for polymerase chain reaction (PCR) analysis. Our retrospective study included 558 positive and 558 negative samples collected from Northern Finland. Overall, we found moderate diagnostic performance for ATR-FTIR when PCR analysis was used as the gold standard: the average area under the receiver operating characteristics curve (AUROC) was 0.67–0.68 (min. 0.65, max. 0.69) with 20, 10 and 5 k-fold cross validations. Mean accuracy, sensitivity and specificity was 0.62–0.63 (min. 0.60, max. 0.65), 0.61 (min. 0.58, max. 0.65) and 0.64 (min. 0.59, max. 0.67) with 20, 10 and 5 k-fold cross validations. As a conclusion, our study with relatively large sample set clearly indicate that measured ATR-FTIR spectrum contains specific information for SARS-CoV-2 infection (P < 0.001 for AUROC in label permutation test). However, the diagnostic performance of ATR-FTIR remained only moderate, potentially due to low concentration of viral particles in the transport medium. Further studies are needed before ATR-FTIR can be recommended for fast screening of SARS-CoV-2 from nasopharyngeal swab samples.

Implementation of Chromatic Super CAZ/AVI® medium for active surveillance of ceftazidime-avibactam resistance: preventing the loop from becoming a spiral

Acquired resistance towards ceftazidime-avibactam (CAZ-AVI) is increasingly reported. Several mechanisms can be involved, but mutations in the Ω-loop region of β-lactamases are the most described. Herein, we assessed the implementation of Chromatic Super CAZ/AVI® medium in rectal swab surveillance cultures in a geographic area with endemic distribution of KPC-producing Klebsiella pneumoniae. Routine rectal swabs collected from the intensive care unit (ICU) and non-ICU patients were screened for carbapenemase-producing Enterobacterales (CPE), carbapenem-resistant Gram-negative organisms (CR-GN) and CAZ-AVI-resistant organisms by Chromatic CRE and Super CAZ/AVI® media. Among the 1839 patients screened, 146 (7.9%) were found to be colonized by one or more CPE and/or CR-GN isolates during hospitalization. Overall, among colonized patients the most common bacteria encountered were KPC-producing Enterobacterales (n = 60; 41.1%), carbapenem-resistant Pseudomonas aeruginosa (n = 41; 28.1%) and carbapenem-resistant A. baumannii (n = 34; 23.3%). Among patients colonized by KPC-producing Enterobacterales, thirty-five (58.3%) had CAZ-AVI-resistant strains. A 30.5% rate of faecal carriage of CAZ-AVI-resistant KPC-producing K. pneumoniae, substantially higher than that of susceptible isolates (2.8%), was observed in the COVID-19 ICU. Prevalence of faecal carriage of metallo-β-lactamase-producing organisms was low (0.5% and 0.2% for Enterobacterales and P. aeruginosa, respectively). Chromatic Super CAZ/AVI® medium showed 100% sensitivity in detecting CPE or CR-GN isolates resistant to CAZ-AVI regardless of both MIC values and carbapenemase content. Specificity was 86.8%. The Chromatic Super CAZ/AVI® medium might be implemented in rectal swab surveillance cultures for identification of patients carrying CAZ-AVI-resistant organisms to contain the spread of these difficult-to-treat pathogens.

Candida auris PCR for high-throughput infection control screening.

Candida auris, a difficult to treat yeast-like fungus, has spread through healthcare facilities globally, posing a serious threat to the health of patients. We evaluated a PCR-based method suitable for screening large numbers of patient samples to rapidly and accurately detect C. auris.

Raman Microscopic Analysis of Dry-Surface Biofilms on Clinically Relevant Materials.

Moist/hydrated biofilms have been well-studied in the medical area, and their association with infections is widely recognized. In contrast, dry-surface biofilms (DSBs) on environmental surfaces in healthcare settings have received less attention. DSBs have been shown to be widespread on commonly used items in hospitals and to harbor bacterial pathogens that are known to cause healthcare-acquired infections (HAI). DSBs cannot be detected by routine surface swabbing or contact plates, and studies have shown DSBs to be less susceptible to cleaning/disinfection products. As DSBs are increasingly reported in the medical field, and there is a likelihood they also occur in food production and manufacturing areas, there is a growing demand for the rapid in situ detection of DSBs and the identification of pathogens within DSBs. Raman microspectroscopy allows users to obtain spatially resolved information about the chemical composition of biofilms, and to identify microbial species. In this study, we investigated Staphylococcus aureus mono-species DSB on polyvinylchloride blanks and stainless steel coupons, and dual-species (S. aureus/Bacillus licheniformis) DSB on steel coupons. We demonstrated that Raman microspectroscopy is not only suitable for identifying specific species, but it also enables the differentiation of vegetative cells from their sporulated form. Our findings provide the first step towards the rapid identification and characterization of the distribution and composition of DSBs on different surface areas.

Universal COVID-19 pre-procedural swabs in children in a developing country: A comparison of findings over two transmission waves

AimThe Coronavirus disease (COVID-19) pandemic has strained healthcare systems worldwide. Some institutions have implemented additional precautionary measures such as pre-procedural swabbing (PPS) to reduce transmission in patients and healthcare workers. We evaluate our experience with universal pre-procedural screening for COVID-19 in low-risk pediatric patients.MethodsWe performed a retrospective review of patients aged 18 years and below who underwent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay swabs in our center over two waves (1st May 2020 to 31st July 2020 and 1st April 2021 to 30th June 2021). We included patients who underwent rRT-PCR for SARS-CoV-2 prior to any procedures requiring general anesthesia and were deemed low risk for COVID-19 according to our institutional screening criteria. All study patients were followed up for 14 days post-procedure.ResultsOf 2065 swabs done for patients aged 18 years and below during the study period, 645 (31.2%) were pre-procedural swabs. Patients were aged 4.2 years (median, interquartile range: 1.6 years–9.8 years). Two patients (0.3%) tested positive for COVID-19 by PPS, detected during Period 2 – both had risk criteria which were overlooked by healthcare workers. Within 14 days post-procedure, 10 patients had unscheduled readmissions and 15 required repeat rRT-PCR, all of which were negative.ConclusionsIn patients deemed low risk for COVID-19 infection according to our screening criteria, routine pre-procedural swabbing returns a low positive rate. Our findings can guide screening protocols at institutions that provide surgical services during the COVID-19 pandemic.

Is Routine Intra-operative Gram Stain, Culture, and Sensitivity during an Appendectomy is Effective in Decreasing the Rate of Post-operative Infective Complications?

BACKGROUND: Organisms blamed in acute appendicitis are right predictable and very susceptible to a wide range of broad-spectrum antibiotics. AIM: The aim of the study was to assess the clinical benefit of the routine intra-operative swab during an appendectomy in guiding antibiotic selection. METHODS: Four hundred and thirty patients underwent appendectomy halved into two groups, each 215. In Group 1, an intra-operative swab was routinely obtained for culture/sensitivity. The results of which were reviewed for helping direct antibiotic selection. No intra-operative swabs were obtained in Group 2. Both groups were given single-dose cefotaxime and metronidazole preoperatively intravenously at the time of induction of anesthesia. RESULTS: In swab group, 63/215 cultures (29.3%) revealed pathogens, while (70.7%) were negative or revealed isolated colonic commensals. Most cultures were negative or isolated colonic commensals. Fifty-two/63 cultures (82.54%) were sensitive to both cefotaxime and metronidazole, and only 11/63 (17.46%) reported resistant organisms to cefotaxime but not to metronidazole. Most pathogens were sensitive to empirical antibiotics. Twenty-two/215 patients (10.23%) developed infective complications, most (63.6%) had their cultures from the infected wound yielded different micro-organisms. Only 8/215 (3.72%) in the swab group needed a change in the empirical antibiotics for treating infective complications. In the non-swab group, 19/215 patients (8.83%) developed infective complications. Only 6/215 patients (2.8%) needed a change in the empirical antibiotics for treating infective complications. Collectively, only 14/430 patients (3.25%) required a change in the empirical antibiotics for treating infected wounds. CONCLUSIONS: Routine peritoneal swabs for culture/sensitivity during appendicectomy are of no clinical value. Such practice is considered a waste of laboratory resources and money. A single prophylactic dose of antibiotics has significant role in preventing surgical site infection.

Fuzzy Logic As A Tool For Estimating Production Potential Of A Sand Layer

In production management, a prior knowledge over production potential of a candidate sand layer (geological complexity in Indonesia has led to existence of stratified reservoirs with a set of layers) to be opened is always desirable. The common practice performed during drilling and completion activities of a production well is through the use of well testing and fluid sampling. From the test, fluid dynamic data such as total liquid rate, water cut, and gas cut are produced. A similar set of data is also required for more mature fields for the purpose of monitoring through the running of routine production and/or swab tests.Although the tests, especially flow tests during drilling and completion, are always regarded as the only source of proof about productive layer(s) production potential, an alternative means that can be used to provide estimates is always desired. The main reason is that flow tests are costly so that only layer(s) considered as the most potential are to be assigned for testing. Layer(s) that are considered less potential are left untested, eventhough in some cases they are also set on production during the well's production phase.The idea of establishing a method that can provide illustration over production potentials of all layer(s) always exists. Certainly, there are approaches to serve the purpose such as productivity index (PI) analogy and petrophysical through fractional flow measurement in a core laboratory. However, those approaches are often considered inadequate in accommodating various factors that may influence production potential.To materialize the idea stated above, the pattern recognition approach was taken. This approach was taken in order to model the relationships between various fac- tors in wellbore and production potential without being trapped by the certain complexity that occurs in any mathematical expressions trying to explain the relationships. For the purpose, fuzzy logie (a branch in ArtificialIntelligence) has been used. The choice is actually based on its ability to accommodate both numeric and non-numeric data. Some non-numeric data such as lithology and pore system also have some degrees of influence on production potential. With a tool that enables us to have production potential estimates of reservoir layers, from which layers with the most promising potential are taken to undergo flow tests. Furthermore, as flow test data has been acquired and used as feedback and calibration by the fuzzy model, production potential of layer(s) with less promising or ambiguous prospect can also be predicted.

Direct RNA Nanopore Sequencing of SARS-CoV-2 Extracted from Critical Material from Swabs

In consideration of the increasing prevalence of COVID-19 cases in several countries and the resulting demand for unbiased sequencing approaches, we performed a direct RNA sequencing (direct RNA seq.) experiment using critical oropharyngeal swab samples collected from Italian patients infected with SARS-CoV-2 from the Palermo region in Sicily. Here, we identified the sequences SARS-CoV-2 directly in RNA extracted from critical samples using the Oxford Nanopore MinION technology without prior cDNA retrotranscription. Using an appropriate bioinformatics pipeline, we could identify mutations in the nucleocapsid (N) gene, which have been reported previously in studies conducted in other countries. In conclusion, to the best of our knowledge, the technique used in this study has not been used for SARS-CoV-2 detection previously owing to the difficulties in the extraction of RNA of sufficient quantity and quality from routine oropharyngeal swabs. Despite these limitations, this approach provides the advantages of true native RNA sequencing and does not include amplification steps that could introduce systematic errors. This study can provide novel information relevant to the current strategies adopted in SARS-CoV-2 next-generation sequencing.

Nasopharyngeal COVID-19 Testing – Simple as ABC(SF Leak)?

Introduction: Routine nasopharyngeal swabbing for Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) testing for SARS-COV-2 (COVID-19) has become the recommended test for safely delivering both emergency and elective patient care. To date over 256 million tests have been conducted in the UK.Whilst the advantages of routine COVID-19 swabbing are evident, it is important to acknowledge the associated common complications as well as unusual ones such as a Cerebrospinal Fluid (CSF) Leak.Methods: We report a case of a 69-year-old female who underwent nasopharyngeal swabbing in preparation for routine elective surgery. At the 8-week follow up the patient complained of a runny nose, which was positive for Beta-2 Transferring thus confirming a CSF leak.The likely area of concern for the CSF leak was in the region of the left fovea ethmoidalis where the bone was extremely thin with a solitary fluid filled air cell. The patient did later report right eye surgery 2 years previously which resulted in postoperative ethmoidal sinusitis managed with antimicrobials. This may have predisposed her to the CSF leak.Results: Nasal swabbing has been shown to be the cause of a CSF leak in a handful of cases, only four thus far have been reported in the literature. This rare but important complication has a significant morbidity with risk of meningitis reaching 19 % in some reports.Conclusions: It is the author’s intention to raise awareness of CSF leak as a potential complication of COVID19 Swabbing to ensure these are recognised promptly and managed in a timely manner.

Routine bacterial culture of proximal bone specimens during minor amputation in patients with diabetes-related foot infections has little clinical utility in predicting re-operation or ulcer healing

BackgroundTrans-phalangeal and trans-metatarsal amputation, collectively termed ‘minor amputations’ are important procedures for managing infections of diabetes-related foot ulcers (DFU). Following minor amputation, international guidelines recommend a prolonged course of antibiotics if residual infected bone on intra-operative bone samples are identified, but the quality of the evidence underpinning these guidelines is low. In this study, we examined the concordance of microbiological results from proximal bone cultures compared to results from superficial wound swabs in relation to patient outcomes; with the aim of determining the utility of routinely obtaining marginal bone specimens.MethodsData was retrospectively collected on 144 individuals who underwent minor amputations for infected DFU at a large Australian tertiary hospital. Concordance was identified for patients with both superficial wound swabs and intra-operative bone samples available. Patient outcomes were monitored up to 6 months post-amputation. The primary outcome was complete healing at 6 months; and secondary outcome measures included further surgery and death. Mann Whitney U testing was performed for bivariate analyses of continuous variables, Chi-Squared testing used for categorical variables and a logistic regression was performed with healing as the dependent variable.ResultsA moderate-high degree of concordance was observed between microbiological samples, with 38/111 (35%) of patients having discordant wound swab and bone sample microbiology. Discordant results were not associated with adverse outcomes (67.2% with concordant results achieved complete healing compared with 68.6% patients with discordant results; P = 0.89). Revascularisation during admission (0.37 [0.13–0.96], P = 0.04) and amputation of the 5th ray (0.45 [0.21–0.94], P = 0.03) were independent risk factors for non-healing.ConclusionThere was a moderate-high degree of concordance between superficial wound swab results and intra-operative bone sample microbiology in this patient cohort. Discordance was not associated with adverse outcomes. These results suggest there is little clinical utility in routinely collecting proximal bone as an adjunct to routine wound swabs for culture during minor amputation for an infected DFU.

A challenging case of tracheal foreign body retrieval following COVID-19 swabbing.

The COVID-19 pandemic has resulted in a significant increase in the number of tracheostomised patients in hospitals requiring ventilatory support. These patients require highly specialist care, but overwhelmed hospital systems with stretched human resources potentially leave these patients cared for by undertrained healthcare professionals. We describe a rare complication where a routine COVID-19 swab done incorrectly via a tracheostomy tube, resulted in a snapped-off swab in the trachea. We outline the events and our method of removal using rigid bronchoscopy through the tracheostomy stoma as endo-tracheal bronchoscopy was impossible due to significant sub-glottic stenosis. This case highlights the paramount importance of the unique care needed to safely manage tracheostomies during this ongoing pandemic.

Unexplained worsening of parkinsonian symptoms in a patient with advanced Parkinson\u2019s disease as the sole initial presentation of COVID-19 infection: a case report

BackgroundParkinson’s disease (PD) is a neurodegenerative condition that has been reported following viral infections in rare occasions. Several neurological complications have emerged in association with coronavirus disease 2019 (COVID-19), since its declaration as a pandemic. Herein, we present a novel case of unexplained worsening of PD as the sole initial presentation of COVID-19, in the absence of fever or respiratory symptoms.Case presentationA 56-year-old male with advanced PD presented with severe rigidity, dystonic posturing of both feet, and confusion of 4 days duration. His condition progressed to an akinetic-rigid state and confusion during the following week, and a routine nasopharyngeal swab tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the 9th day of onset. He developed fever and dyspnea later and was intubated on the 10th day.ConclusionTo our knowledge, worsening of PD symptoms as the sole initial manifestation of SARS-CoV-2 infection, in the absence of other cardinal features of COVID-19, has not been reported in the literature. We suggest testing for COVID-19 infection in patients with PD, especially advanced cases, who present with unexplained worsening of symptoms, even in the absence of COVID-19 cardinal features.