Comparison of the Copan ESwab system with two Amies agar swab transport systems for maintenance of microorganism viability

What is the prevalence of COVID-19 detection by PCR among deceased individuals in Lusaka, Zambia? A postmortem surveillance study

OBJECTIVES

To determine the prevalence of COVID-19 postmortem setting in Lusaka, Zambia.

DESIGN

A systematic, postmortem prevalence study.

SETTING

A busy, inner-city morgue in Lusaka.

PARTICIPANTS

We sampled a random subset of all decedents who transited the University Teaching Hospital morgue. We sampled the posterior nasopharynx of decedents using quantitative PCR. Prevalence was weighted to account for age-specific enrolment strategies.

INTERVENTIONS

Not applicable-this was an observational study.

PRIMARY OUTCOMES

Prevalence of COVID-19 detections by PCR. Results were stratified by setting (facility vs community deaths), age, demographics and geography and time.

SECONDARY OUTCOMES

Shifts in viral variants; causal inferences based on cycle threshold values and other features; antemortem testing rates.

RESULTS

From 1118 decedents enrolled between January and June 2021, COVID-19 was detected among 32.0% (358/1116). Roughly four COVID-19+ community deaths occurred for every facility death. Antemortem testing occurred for 52.6% (302/574) of facility deaths but only 1.8% (10/544) of community deaths and overall, only ~10% of COVID-19+ deaths were identified in life. During peak transmission periods, COVID-19 was detected in ~90% of all deaths. We observed three waves of transmission that peaked in July 2020, January 2021 and ~June 2021: the AE.1 lineage and the Beta and Delta variants, respectively. PCR signals were strongest among those whose deaths were deemed 'probably due to COVID-19', and weakest among children, with an age-dependent increase in PCR signal intensity.

CONCLUSIONS

COVID-19 was common among deceased individuals in Lusaka. Antemortem testing was rarely done, and almost never for community deaths. Suspicion that COVID-19 was the cause of deaths was highest for those with a respiratory syndrome and lowest for individuals <19 years.

Comparison of the certified Copan eSwab system with commercially available cotton swabs for the detection of multidrug-resistant bacteria in rectal swabs

BACKGROUND

Rectal swabs are well-implemented screening tools for multidrug-resistant bacteria (MDRB). Since certified swabs such as the Copan eSwab system experienced a delivery bottleneck during the COVID-19 pandemic, commercially available alternatives such as commonly used double-tipped cotton swabs had to be investigated, especially considering their similarity to professional cotton swabs for microbiological purposes.

METHODS

Diagnostic properties of commercial cotton swabs (comparable to Q-tips) and Copan eSwabs were qualitatively compared in a prospective single-center study using microbiological standard cultures and PCR methods for the detection of multidrug-resistant Gram-negative bacteria and vancomycin-resistant enterococci (VRE).

RESULTS

A total of 196 swab pairs were collected from 164 participants. MDRB were detected in 36 of 164 cases (22%). There were neither false-negative nor false-positive results using commercial cotton swabs. In 8 of 196 samples (4.1%) MDRB species were detected only by using cotton swabs, including vancomycin-resistant Enterococcus faecium, OXA-48 producing Escherichia coli, ESBL-producing Klebsiella pneumoniae and ESBL-producing Escherichia coli.

DISCUSSION

Commercial cotton swabs turned out to be a reliable alternative to Copan eSwabs. For practical use as a screening tool, relevant storage- and manufacturer-related contamination must be ruled out beforehand.

CONCLUSIONS

Commonly available double-tipped cotton swabs can be used for rectal MDRB screening in the event of supply shortages of certified swabs. Further studies should clarify their suitability as a sampling system for nasopharyngeal MRSA carriage or even for the molecular biological detection of SARS-CoV-2.

A NOVEL VITREOUS CULTURE TECHNIQUE

BACKGROUND/PURPOSE

This is the first case series of a novel method of collecting and transporting a vitreous specimen after a vitreous tap and injection for infectious endophthalmitis.

METHODS

Case series.

RESULTS

Four consecutive cases of presumed infectious endophthalmitis underwent an in-office vitreous tap and antibiotic injection. The vitreous specimen was injected into the ESwab liquid-based collection and transport system for microbiology samples. Three of the four cases had a positive culture.

CONCLUSION

The ESwab is a simple and efficacious method of collecting a vitreous specimen, increasing the probability of a positive culture, particularly when there is a delay between specimen collection and delivery to the laboratory for processing.

Comparison of corneal culture results obtained using the ESwab™ and Amies charcoal swab in canine and feline patients

OBJECTIVE

The objective of the study was to compare corneal culture results using the ESwab™ and Amies charcoal swab.

ANIMALS STUDIED

One hundred fourteen canine and fifteen feline eyes.

PROCEDURES

Retrospective analysis of Dick White Referrals bacterial and fungal corneal culture data was conducted. Results were included from canine and feline patients, which presented with suspected infectious keratitis that had samples taken using an Amies charcoal swab followed by an ESwab™ in the same eye. In respect to positive and negative cultures, a McNemar test was conducted comparing instances of disagreement between swab types, and the Kappa coefficient (κ) was calculated to assess the level of agreement between swab types.

RESULTS

The ESwab™ produced more positive corneal cultures (71/129 [55.0%]) than the Amies charcoal swab (41/129 [31.8%]). 2/129 eyes produced positive fungal cultures. Considering 37/129 eyes in which both swab types detected a positive corneal culture, the same bacterial species were cultured from each swab type in 34/37 (91.9%) eyes, and an additional bacterial species was cultured by the ESwab™ in 3/37 (8.1%) eyes. In 34/38 (89.5%), instances of disagreement between swab types, the ESwab™ showed a positive culture, and the Amies charcoal swab showed a negative culture from the same eye, and this difference was significant (p < 0.0001). There was a moderate level of agreement between results from both swab types (κ = 0.432).

CONCLUSIONS

ESwab™ sampling alone may be superior to Amies charcoal swabs for detecting presence of bacteria in suspected infectious keratitis in cats and dogs.

The Use of Flocked Swabs with a Protective Medium Increases the Recovery of Live Brucella spp. and DNA Detection

Brucellosis is a worldwide zoonosis caused by bacteria from the genus Brucella. Once established, it is very hard to eradicate this disease, since it contaminates animals, the environment, and humans, causing problems for veterinary and public health as well as wildlife protection programs. Swabs are used for sampling in bacteriological and/or molecular diagnostics, from seropositive animals with disease symptoms, from genitalia or tissue lesions, as well as from contaminated environments. The aim of this study was to compare main of the commercially used swab types for sampling and diagnostics of Brucella spp. and determine the optimal storage conditions and time frame for testing. To achieve this, we tested bacterial and molecular methods for detection of Brucella abortus, Brucella melitensis, and Brucella suis using nine swab types, all with different tip materials, treated immediately after spiking, after 72 h at +4°C, and after 72 h at −20°C. Flocked swabs showed the highest capacity to preserve bacterial viability and DNA quality, regardless the storage conditions. Flocked swabs immersed in a protective medium provided the best conditions for Brucella survival in all three storage conditions. At the same time, the efficacy of quantitative PCR (qPCR) detection for all swabs, including the positive control, was above 50%, irrespective of the storage conditions, while bacterial survival was significantly lowered when swabs were kept at +4°C or −20°C for 72 h (48.2% and 27.5%, respectively). Compared to the positive control and other types, the flocked swabs maintained higher reproducibility regarding their capacity to preserve live bacteria in all three storage conditions.

IMPORTANCE In order to protect public and veterinary health from highly zoonotic bacteria such as members of the genus Brucella and prevent their dissemination into the environment, direct diagnostics are of utmost importance. However, in addition to the highly specific diagnostic tests, the sampling methods, time necessary for specimens to reach the laboratories, and transport conditions are important factors to consider in order to increase the sensitivity of performed tests, especially bacterial culturing and qPCR. This paper shows how different swab types and storage conditions influence classical bacteriological diagnostics of the most prevalent Brucella species – B. melitensis, B. abortus, and B. suis – but have little impact on molecular methods. The presented results highlight (i) the choice of swab regarding the storage and transport conditions, (ii) the importance of immediate swab treatment upon sampling, and (iii) that molecular methods do not depend on storage conditions, unlike classical bacteriological isolation.

Clinical Relevance of the Microbiome in Odontogenic Abscesses

Simple Summary

Odontogenic infections are very common. The course of disease ranges from mild to severe and sometimes even life-threatening infections. Optimal therapy is based on rapid abscess incision and, especially in severe cases, on adjuvant antibiotic therapy that ideally targets the culprit bacteria. In order to identify these bacteria, clinicians usually perform cultural analysis from smears of pus and aim for antibiotic susceptibility testing. In recent years, using new molecular methods, it has become possible to carry out a much more detailed analysis of the bacterial colonization of different parts of the human body by determining a microbiome. In our study, we have, for the first time, compared such a microbiome of odontogenic abscesses with cultural bacterial determination carried out in the clinical routine of a university hospital. The key finding of the study is not only that considerably more bacteria can be detected in the abscess in this way but also that easily cultivated bacteria dominate over the actual fastidious pathogenic bacteria. Thus, routine clinical culture probably only provides a distorted picture of reality and should be supplemented by molecular methods in the future.

Abstract

Odontogenic abscesses are usually caused by bacteria of the oral microbiome. However, the diagnostic culture of these bacteria is often prone to errors and sometimes fails completely due to the fastidiousness of the relevant bacterial species. The question arises whether additional pathogen diagnostics using molecular methods provide additional benefits for diagnostics and therapy. Experimental 16S rRNA gene analysis with next-generation sequencing (NGS) and bioinformatics was used to identify the microbiome of the pus in patients with severe odontogenic infections and was compared to the result of standard diagnostic culture. The pus microbiome was determined in 48 hospitalized patients with a severe odontogenic abscess in addition to standard cultural pathogen detection. Cultural detection was possible in 41 (85.42%) of 48 patients, while a pus-microbiome could be determined in all cases. The microbiomes showed polymicrobial infections in 46 (95.83%) cases, while the picture of a mono-infection occurred only twice (4.17%). In most cases, a predominantly anaerobic spectrum with an abundance of bacteria was found in the pus-microbiome, while culture detected mainly Streptococcus, Staphylococcus, and Prevotella spp. The determination of the microbiome of odontogenic abscesses clearly shows a higher number of bacteria and a significantly higher proportion of anaerobes than classical cultural methods. The 16S rRNA gene analysis detects considerably more bacteria than conventional cultural methods, even in culture-negative samples. Molecular methods should be implemented as standards in medical microbiology diagnostics, particularly for the detection of polymicrobial infections with a predominance of anaerobic bacteria.

Current status of the lateral flow immunoassay for the detection of SARS-CoV-2 in nasopharyngeal swabs

Early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and diagnosis of coronavirus disease 2019 (COVID-19) are priorities during the pandemic. Symptomatic and suspected asymptomatic individuals should be tested for COVID-19 to confirm infection and to be excluded from social interactions. As molecular testing capacity is overloaded during the pandemic, rapid antigen tests, such as lateral flow immunoassays (LFIAs), can be a useful tool as they allow greater test availability and obtain results in a very short time. This short review aims to present the analytical properties of LFIAs in the detection of SARS-CoV-2 in nasopharyngeal swabs. Lateral flow immunoassay is a method that combines thin-layer chromatography and indirect immunochemical sandwich method and allows the detection of a specific SARS-CoV-2 antigen in nasopharyngeal swabs. Swab specimens should be adequately collected and tested as soon as possible. Users should pay attention to quality control and possible interferences. Antigen tests for SARS-CoV-2 show high sensitivity and specificity in cases with high viral loads, and should be used up to five days after the onset of the first symptoms of COVID-19. False positive results may be obtained when screening large populations with a low prevalence of COVID-19 infection, while false negative results may happen due to improper specimen collection or insufficient amount of antigen in the specimen. So as to achieve reliable results, a diagnostic accuracy study of a specific rapid antigen test should be performed.

Prevalence and antibiotic susceptibility trends of periodontal pathogens in the subgingival microbiota of German periodontitis patients: A retrospective surveillance study

OBJECTIVE

This retrospective surveillance study aimed to follow periodontitis-associated bacterial profiles and to identify time-dependent changes in antibiotic susceptibility patterns.

MATERIALS AND METHODS

From 2008 to 2015, bacterial specimen from deep periodontal pockets were collected from a total of 7804 German adults diagnosed with periodontitis. Presence of selected bacteria was confirmed by anaerobic culture and nucleic acid amplification. Antimicrobial susceptibility of clinical isolates was tested by disc diffusion with antibiotics used for the treatment of periodontitis and oral infections. The prevalences of periodontal pathogens were calculated and temporal evolution of antimicrobial susceptibility towards amoxicillin, amoxicillin/clavulanic acid, metronidazole, doxycycline, clindamycin, azithromycin, ciprofloxacin and ampicillin was analysed with logistic regression.

RESULTS

The prevalence of patients harbouring bacteria was 95.9% Fusobacterium nucleatum, 88.0% Tannerella forsythia, 76.4% Treponema denticola, 76.5%, Campylobacter rectus, 76.0% Eikenella corrodens, 75.0% Capnocytophaga spp., 68.2% Porphyromonas gingivalis, 57.7% Peptostreptococcus micros, 43.1% Prevotella intermedia, 30.4% Eubacterium nodatum and 21.5% Aggregatibacter actinomycetemcomitans. In 63.5% of patients, one or more isolates were not susceptible to at least one of the antibiotics tested. The data further revealed a trend towards decreasing susceptibility profiles (p < 0.05) with antibiotic non-susceptibilities in 37% of patients in 2008 and in 70% in 2015.

CONCLUSIONS

The present study confirmed a high prevalence of periodontal pathogens in the subgingival microbiota of German periodontitis patients. The data revealed an incremental increase in isolates displaying resistance to some antibiotics but no relevant change in susceptibility to amoxicillin and metronidazole.

Survival of Staphylococcus aureus on sampling swabs stored at different temperatures

Aims

To understand the impact of storage temperature on recovery of Staphylococcus aureus on sampling swabs. Staphylococcus aureus is a common cause of skin and soft tissue infections, but also causes a variety of life‐threatening diseases. With a large pool of asymptomatic carriers and transmission that can occur even through indirect contact, mitigation efforts have had limited success. Swab sampling, followed by culturing, is a cornerstone of epidemiological studies, however, S. aureus viability on swabs stored at different temperatures has not been characterized.

Methods and Results

We determined survival rates on swabs stored at five different temperatures. Samples stored at −70°C had no decay over time while samples stored at higher temperatures showed an exponential decay in viability. Mortality rates were greatest for swabs stored at 37°C. Survival at intermediate temperatures (−20 to 20·5°C) did not differ significantly, however, we observed more variation at higher temperatures.

Conclusions

To maximize recovery of S. aureus cells, samples should be stored at −70°C or processed for culturing without delay.

Significance and Impact of the Study

Epidemiological studies of bacterial diseases are typically limited to determination of pathogen presence/absence, yet quantitative assessments of pathogen load and genetic diversity can provide insights into disease progression and severity, likelihood of transmission and adaptive evolutionary potential. For studies of S. aureus where time or access to a microbiology laboratory may delay culturing, deep freezing or timely culturing will maximize the degree to which sampling results reflect source status.

Recovery of aerobic gram-negative bacteria from the Copan Eswab transport system after long-term storage

We evaluated the Copan Eswab transport system for the quantitative recovery of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa after 1, 2, 3, 5, and 7 days of storage at room and refrigerator temperatures, and 7 and 30 days of storage at -80 °C and -20 °C using mono- and polymicrobial samples. The study was based on Clinical and Laboratory Standards Institute (CLSI) M40-A2 standard procedures on the quality control of microbiological transport systems. Eswab met the CLSI standards at room and refrigerator temperatures for all (combinations of) bacterial strains tested. At room temperature, after 24 h, bacterial growth was observed. At -80 °C, bacterial viability was maintained in monomicrobial samples; however, in polymicrobial samples, P. aeruginosa recovery was compromised. Storage at -20 °C was unsuitable. We conclude that specimens collected using Eswab should be transported to the laboratory as soon as possible. If transport or processing is delayed, specimens should preferably be stored at refrigerator temperatures.

Investigations into Enhancing Yersinia pestis Cells Viability following Environmental Sampling for Forensic Analysis

Following an intentional or accidental bio-warfare agent (BWA) release, environmental sample analysis is absolutely critical to determine the extent of contamination. When dealing with nonspore forming BWA (e.g., Yersinia pestis), retention of cell viability is central to such analyses. Even though significant advances have been achieved in DNA sequencing technologies, a positive identification of BWAs in environmental samples must be made through the ability of cells to form colony-forming units upon culturing. Inability to revive the cells between collection and analysis renders such studies inconclusive. Commercial kits designed to preserve the viability of pathogens contained within clinical samples are available, but many of them have not been examined for their ability to preserve samples containing suspected BWAs. The study was initiated to examine the applicability of commercial solutions aiding in retention of Y. pestis viability in samples stored under nonpermissive temperatures, that is, 40 and 37°C. While none of the tested solutions sustained cell viability at 40°C, the results show five out of 17 tested preservatives were capable of supporting viability of Y. pestis at 37°C.

Molecular Testing for Detection of Groups A, C, and G β-Hemolytic Streptococci in Pharyngeal Samples from Children

Background

Group A Streptococcus (GAS) and large colony-forming group C (GCS) and G (GGS) β-hemolytic streptococci are important causes of acute pharyngitis in children and adults. Rapid and accurate diagnosis of streptococcal pharyngitis can improve patient care and potentially reduce transmission. In this study, we evaluated the performance of the Lyra Direct Strep (LDS) assay for detection of GAS and GCS/GGS compared with traditional culture methods.

Methods

Pharyngeal samples obtained from 278 children presenting to the emergency department with initial negative GAS rapid antigen detection test (RADT) were used. All samples were cultured as part of routine care and tested in batches using the LDS assay.

Results

Of 278 pharyngeal samples with negative GAS RADT, 37 (13.3%) and 63 (22.7%) patients were positive for GAS by culture and LDS assay, respectively. Four (1.4%) patients were positive for GCS or GGS by culture or LDS assay. The LDS assay demonstrated sensitivity and specificity of 97.6% and 89.0%, respectively, compared with culture as the gold standard. Repeat culture and an alternate PCR showed that 85.7% (24 of 28) of discrepant samples agreed with findings of the LDS assay. Since implementation, the LDS assay shows a positivity rate of 21.0% (281 of 1340) compared with 11.7% (246 of 2110) by culture in the previous year.

Conclusions

We successfully implemented the LDS assay at our institution and have observed a significant increase in the positivity rate of GAS compared with culture. The LDS assay alone allowed for the elimination of β-streptococci screening by culture at our institution.

Cross-country transport and isolation and identification of Streptococcus pneumoniae by use of alternate sources of blood supplemented media among laboratories in India

Background

The isolation of S. pneumoniae (Sp) depends on specimen integrity / transport, media and expertise. The non-availability of sheep blood agar poses a challenge in identification of colonial morphology and identification in India.

Methods

Laboratories processed swabs containing either pure Sp or Sp in mixed cultures with a second (confounding) bacterium shipped across the country in cold conditions. Duplicate set of swabs was shipped back to the central laboratory to assess the impact of shipping on culture viability. The identical swab was cultured on sheep, human blood and one additional agar plate used in the laboratory.

Results

46/60(77%) of cultures containing only Sp were correctly identified. In specimens where Sp was present in mixed culture, the proportion of isolates in which Sp was correctly identified varied, with most variability attributed to the particular confounding organism rather than the media. There was no discernible impact of temperature-controlled (4-6°C) transport on the isolation of Sp from culture swabs.

Conclusions

The study clearly elucidates the ability of laboratories for isolation of S. pneumoniae on human blood agar in resource limited settings. The results highlight the difficulties inherent in correctly identifying pathogens in mixed cultures in needs improvement using standardized tests across the study centers. The study also reaffirms the ability to transport biological specimens over long geographical distances without loss.

Culture of Rectal Swab Specimens for Enteric Bacterial Pathogens Decreases Time to Test Result While Preserving Assay Sensitivity Compared to Bulk Fecal Specimens

Diarrheal illness is a major cause of morbidity and mortality throughout the world, yet the etiologic agent of many cases of gastrointestinal illness remains unspecified, often due to the lack of convenient, timely, and sensitive diagnostic testing. Although bulk fecal specimens remain the recommended specimen type for enteric culture, rectal swabs may be an option preferred by clinicians and patients due to the convenience and timing of collection. However, the lack of data evaluating the sensitivity of rectal swabs compared to fecal specimens for detection of enteric pathogens precludes this specimen type from being recommended by national guidelines. In this study, we retrospectively reviewed 480 paired rectal swab and fecal specimens submitted for enteric culture to the Barnes-Jewish Hospital and St. Louis Children's Hospital microbiology laboratories in St. Louis, MO, from 2002 to 2017. We report 32% positivity of paired specimens with an overall agreement of 93% and Cohen's κ of 0.84 (95% confidence interval, 0.78 to 0.89). Additionally, we evaluated the time to result from the time of patient presentation to the health care setting and demonstrate that rectal swabs have a significantly shorter time to an actionable result than bulk fecal specimens (median, 67.4 h versus 78.4 h, respectively; P < 0.001). These findings indicate that rectal swabs facilitate on-demand culture-based testing with a sensitivity comparable to that of fecal specimens and thus should be recommended for enteric bacterial culture when bulk fecal specimens are unavailable.

Assessment of Test Performance and Potential for Environmental Contamination Associated with a Point-of-Care Molecular Assay for Group A Streptococcus in an End User Setting

Although U.S. Food and Drug Administration-approved and CLIA-waived point-of-care (POC) molecular systems are being implemented in routine clinical practice, instrument reliability, test performance in the hands of end users, and the potential for environmental contamination resulting from use of POC molecular systems have not been extensively evaluated. We performed a prospective evaluation of the Roche cobas Liat group A streptococcus (GAS) assay compared to routine real-time PCR. We evaluated test accuracy, instrument failure rate, and monitored for environmental contamination when testing was performed by minimally trained end users in an Express Care Clinic environment. The overall concordance of the Liat GAS assay with routine testing was 97.2% (455/468). The average Liat failure rate across three analyzers was 6.6% (33/501) (range, 3.7 to 11.6%), and no environmental contamination was detected during the course of the study. The cobas Liat platform and GAS assay demonstrated reliable performance in the end user setting and may serve as a rapid, POC option for routine diagnostic testing for certain infectious diseases, including GAS.

Detection and genomic analysis of genital group B streptococcus in pregnant Korean women

AIM

Group B streptococcus (GBS) is a leading cause of life-threatening bacterial infections among newborns, and neonates born to heavily colonized women may be subject to vertical transmission. We sought to determine an appropriate detection method for genital GBS in pregnant women by comparing culture-based methods and real-time polymerase chain reaction (PCR). In addition, we performed molecular serotyping and multilocus sequence typing (MLST) on isolates.

METHODS

A total of 150 pregnant women were enrolled and underwent vaginal-rectal swabbing at 16-40 weeks of gestation. GBS was identified by conventional culture and real-time PCR with or without enrichment. Molecular serotyping and MLST were performed on isolates.

RESULTS

Overall genital GBS positive rate among the 150 study subjects was 17.3%. Direct culture identified 18 (12.0%) positive specimens, enrichment culture 22 (14.6%), direct PCR 24 (16.0%) and enrichment PCR 25 (16.6%). The sensitivity and specificity by direct and enrichment PCR were as follows: for direct PCR, 90.9% and 96.9%, respectively; and for enrichment PCR, 95.5% and 96.9%, respectively. Resistance rates to clindamycin and erythromycin were 33.3% and 19.1%, respectively. Serotype III-1 was the most common (26.3%), followed by serotype Ib (21.1%), III-3 (15.8%), V (15.8%), II (10.5%), IV (5.3%) and VI (5.3%). Most common sequence types (ST) were ST-1, ST-19 and ST-862 (15.8%), followed by ST-2 and ST-654 (10.5%).

CONCLUSION

Direct real-time PCR using vaginal-rectal specimen could be used for detecting GBS in emergent conditions. Molecular serotypes III, Ib and V were most common. MLST analysis frequently presented ST-1, ST-19 and ST-862.

Evaluation of the Use of Rectal Swabs for Laboratory Diagnosis of Clostridium difficile Infection

For the diagnosis of Clostridium difficile infection (CDI), microbiological testing is almost always accomplished through the analysis of stool specimens. We evaluated the performances of rectal swabs with liquid transport medium (FS) and nylon flocked dry swabs for the detection of C. difficile Additionally, the impact on the diagnostic yield of storing swabs at -80°C for up to 3 months was evaluated. Sixty clinical stool samples positive for C. difficile by PCR were used for simulating rectal swabbing. FS and dry swabs were dipped into the stool and tested by PCR directly after swabbing at 1 and 3 months after storage at -80°C. Stool and the liquid medium of FS were additionally tested by a combination of glutamate dehydrogenase antigen (GDH) testing and toxin A/B enzyme immunoassay (EIA), as well as by toxigenic culture (TC). Using dry swabs, the PCR-based detection rate of C. difficile was equal to the rate using stool samples (30/30 [100%]), whereas the detection rate in FS was significantly lower (25/30 [83.2%]; P = 0.019). The sensitivities of FS for detecting C. difficile by PCR, TC, GDH testing, and toxin A/B EIA were 83.3%, 85.7%, 88%, and 68.9%, respectively. Storage of swabs at -80°C had no impact on the detection rate. FS cannot replace stool samples in the two-step laboratory diagnosis of CDI, as the sensitivities were too low, probably due to diluting effects of the fecal sample in the liquid medium. For simple PCR-based detection of C. difficile, dry swabs proved to be a suitable alternative to the use of stool samples.

The intra- and extraluminal appendiceal microbiome in pediatric patients: A comparative study

Intestinal microbiota is involved in metabolic processes and the pathophysiology of various gastrointestinal disorders. We aimed to characterize the microbiome of the appendix in acute pediatric appendicitis comparing extraluminal and intraluminal samples.Between January and June 2015, 29 children (3-17 years, mean age 10.7 ± 3.4 years, sex M:F = 2.6:1) undergoing laparoscopic appendectomy for acute appendicitis were prospectively included in the study. Samples for bacterial cultures (n = 29) and 16S ribosomal desoxyribonucleic acid (rDNA) sequencing (randomly chosen n = 16/29) were taken intracorporeally from the appendiceal surface before preparation ("extraluminal") and from the appendiceal lumen after removal ("intraluminal"). The degree of inflammation was histologically classified into catarrhal, phlegmonous, and gangrenous appendicitis.Seventeen bacterial species were cultivated in 28 of 29 intraluminal samples and 4 species were cultivated in 2 of 29 extraluminal samples. Using 16S rDNA sequencing, 267 species were detected in intraluminal but none in extraluminal samples. Abundance and diversity of detected species differed significantly between histological groups of acute appendicitis in bacterial cultures (P = .001), but not after 16S rDNA sequencing.The appendiceal microbiome showed a high diversity in acute pediatric appendicitis. The intraluminal microbial composition differed significantly depending on the degree of inflammation. As bacteria were rarely found extraluminally by culture and not at all by sequencing, the inflammation in acute appendicitis may start inside the appendix and spread transmurally.

Evaluation of Commercial-off-the-Shelf Materials for the Preservation of Bacillus anthracis Vegetative Cells for Forensic Analysis

Environmental surface sampling is crucial in determining the zones of contamination and overall threat assessment. Viability retention of sampled material is central to such assessments. A systematic study was completed to determine viability of vegetative cells under nonpermissive storage conditions. Despite major gains in nucleic acid sequencing technologies, initial positive identification of threats must be made through direct culture of the sampled material using classical microbiological methods. Solutions have been developed to preserve the viability of pathogens contained within clinical samples, but many have not been examined for their ability to preserve biological agents. The purpose of this study was to systematically examine existing preservation materials that can retain the viability of Bacillus anthracis vegetative cells stored under nonpermissive temperatures. The results show effectiveness of five of seventeen solutions, which are capable of retaining viability of a sporulation deficient strain of B. anthracis Sterne when stored under nonrefrigerated conditions.

Recovery of Neisseria gonorrhoeae from 4 commercially available transport systems

Four commercial transport systems for the recovery of Neisseria gonorrhoeae were evaluated in support of the need to obtain culture isolates for the detection of antimicrobial resistance. Bacterial recovery from the InTray GC system was superior with minimal loss of viability in contrast to non-nutritive transport systems.

Detection of Group B Streptococcus Directly from Collected ESwab Samples by Use of the BD Max GBS Assay

Group B Streptococcus detection directly from Copan ESwab collected samples, using the BD Max GBS assay, was evaluated on receipt in the laboratory and after 24 h at room temperature. Results were compared to those using Lim broth enrichment PCR and culture. No significant difference was observed between 24 h ESwab and Lim broth PCRs.

[Bacterial etiology of acute otitis media in Spain in the post-pneumococcal conjugate vaccine era]

INTRODUCTION

Acute otitis media (AOM) is common in children aged <3 years. A pneumococcal conjugate vaccine (PCV) (PCV7; Prevenar, Pfizer/Wyeth, USA) has been available in Spain since 2001, which has a coverage rate of 50-60% in children aged <5 years.

MATERIALS AND METHODS

Children aged ≥3 to 36 months with AOM confirmed by an ear-nose-throat specialist were enrolled at seven centers in Spain (February 2009-May 2012) (GSK study identifier: 111425). Middle-ear-fluid samples were collected by tympanocentesis or spontaneous otorrhea and cultured for bacterial identification. Culture-negative samples were further analyzed using polymerase chain reaction (PCR).

RESULTS

Of 125 confirmed AOM episodes in 124 children, 117 were analyzed (median age: 17 months (range: 3-35); eight AOM episodes were excluded from analyses. Overall, 69% (81/117) episodes were combined culture- and PCR-positive for ≥1 bacterial pathogen; 44% (52/117) and 39% (46/117) were positive for Haemophilus influenzae (Hi) and Streptococcus pneumoniae (Spn), respectively. 77 of 117 episodes were cultured for ≥1 bacteria, of which 63 were culture-positive; most commonly Spn (24/77; 31%) and Hi (32/77; 42%). PCR on culture-negative episodes identified 48% Hi- and 55% Spn-positive episodes. The most common Spn serotype was 19F (4/24; 17%) followed by 19A (3/24; 13%); all Hi-positive episodes were non-typeable (NTHi). 81/117 AOM episodes (69%) occurred in children who had received ≥1 pneumococcal vaccine dose.

CONCLUSIONS

NTHi and Spn were the main etiological agents for AOM in Spain. Impact of pneumococcal vaccination on AOM requires further evaluation in Spain, after higher vaccination coverage rate is reached.

Comparison of the Copan eSwab System with an Agar Swab Transport System for Maintenance of Fastidious Anaerobic Bacterium Viability

We compared the eSwab system to a swab with an anaerobic transport semisolid agar system for their capacities to maintain the viability of 20 species of fastidious anaerobes inoculated on the bench and held at ambient or refrigerator temperature for 24 or 48 h. On average, both systems maintained similar viabilities among analogous groups of organisms at both temperatures, although there were quantitative differences among some species.

Evaluation of Liquid-Based Swab Transport Systems against the New Approved CLSI M40-A2 Standard

Following revised information pertaining to newer swab types and testing protocols in the new CLSI M40-A2 standard, we evaluated three liquid swab transport systems for the recovery of aerobic, anaerobic, and fastidious organisms at room temperature and at 4°C. All tested liquid swab transport systems were fully compliant with the M40-A2 standard, with acceptable performance at both temperatures after the full specified holding period, using both qualitative (roll-plate) and quantitative (swab elution) methods.

Contact lens associated microbial keratitis: practical considerations for the optometrist

Microbial keratitis (MK) is a corneal condition that encompasses several different pathogens and etiologies. While contact lens associated MK is most often associated with bacterial infections, other pathogens (fungi, Acanthamoeba species, etc) may be responsible. This review summarizes the risk factors, microbiology, diagnostic characteristics, and treatment options for all forms of contact lens-related MK.

Does bacteriology laboratory automation reduce time to results and increase quality management?

Due to reductions in financial and human resources, many microbiological laboratories have merged to build very large clinical microbiology laboratories, which allow the use of fully automated laboratory instruments. For clinical chemistry and haematology, automation has reduced the time to results and improved the management of laboratory quality. The aim of this review was to examine whether fully automated laboratory instruments for microbiology can reduce time to results and impact quality management. This study focused on solutions that are currently available, including the BD Kiestra™ Work Cell Automation and Total Lab Automation and the Copan WASPLab(®).

Bacterial Contamination in Tips of Electrocautery Devices During Total Hip Arthroplasty

Surgical equipment can become contaminated during surgery. It is unknown if electrocautery tips can become contaminated in clean orthopedic procedures despite the produced heat. Therefore, we conducted a prospective study to address this concern. The tips from 25 primary and 25 aseptic revision THAs were collected and an additional 5 sterile tips served as negative controls. Aerobic and anaerobic cultures were incubated for a minimum of 3 days. There were 3 positive cultures (6%); one in primary THA (4%) with Lactobacillus and Enterococcus faecalis; two among revisions (8%), one with E. faecalis and another one with alpha hemolytic streptococci and coagulase negative Staphylococcus. The mean exposure time of the contaminated tips was 132.3 minutes. Patients were followed for 90 days postoperatively and none of them developed surgical site infection. This is the first study to demonstrate that electrosurgical devices can become contaminated during THA in laminar flow equipped operating rooms.

In vitro evaluation and comparison of 5 rapid antigen detection tests for the diagnosis of beta-hemolytic group A streptococcal pharyngitis

Streptococcus pyogenes (group A Streptococcus [GAS]) is the leading cause of bacterial pharyngitis. To perform a rapid diagnosis of GAS pharyngitis, rapid antigen detection tests (RADTs) have been developed. In this study, we evaluated and compared the sensitivity and specificity of 5 RADTs (bioNexia Strep A plus™, bioNexia Strep A dipstick™, Clearview Strep A™, QuickVue Strep A plus™, and Streptatest™), using analytical approaches combining dilutions in NaCl 0.9% or in pharyngeal flora. The practicability of each RADT was also determined. Among the 630 RADTs performed in this work, all were specific, as no false positive was found resulting in a specificity of 100%. The 5 RADTs detected GAS at 10(6)CFU/mL in NaCl 0.9% or pooled pharyngeal flora. Regarding the practicability analysis, bioNexia Strep A plus, bioNexia Strep A dipstick and Streptatest RADTs obtained the highest scores for secondary items including kit content and instructions for use information. We concluded that these 5 easy-to-use RADTs are suitable for diagnosis of GAS pharyngitis, as they all detect GAS at a concentration commonly found during pharyngitis.

Emerging technologies for the clinical microbiology laboratory

In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.

Current and past strategies for bacterial culture in clinical microbiology

A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome.

Rectal Carriage of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae in Hospitalized Patients: Selective Preenrichment Increases Yield of Screening

This study evaluated the added value of selective preenrichment for the detection of rectal carriage of extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E). ESBL-E rectal carriage was identified in 4.8% of hospitalized patients, and 25.9% of ESBL-E rectal carriers were identified with selective preenrichment only.

Liquid based microbiological transport systems: conformity assessment of two commercial devices

We compared two types of liquid-based microbiology devices for microorganism viability according to standardized quantitative elution method CLSI M40-A2. The eSwab® met CLSI acceptance criteria of viability maintenance for all microorganisms tested. The Σ-Transwab® failed to meet CLSI acceptance criteria for Peptostreptococcus anaerobius, Prevotella melaninogenica, Fusobacterium nucleatum and Haemophilus influenzae.

Successful Combination of Nucleic Acid Amplification Test Diagnostics and Targeted Deferred Neisseria gonorrhoeae Culture

Nucleic acid amplification tests (NAATs) are recommended for the diagnosis of N. gonorrhoeae infections because of their superior sensitivity. Increasing NAAT use causes a decline in crucial antimicrobial resistance (AMR) surveillance data, which rely on culture. We analyzed the suitability of the ESwab system for NAAT diagnostics and deferred targeted N. gonorrhoeae culture to allow selective and efficient culture based on NAAT results. We included patients visiting the STI Clinic Amsterdam, The Netherlands, in 2013. Patient characteristics and urogenital and rectal samples for direct N. gonorrhoeae culture, standard NAAT, and ESwab were collected. Standard NAAT and NAAT on ESwab samples were performed using the Aptima Combo 2 assay for N. gonorrhoeae and C. trachomatis. Two deferred N. gonorrhoeae cultures were performed on NAAT-positive ESwab samples after storage at 4°C for 1 to 3 days. We included 2,452 samples from 1,893 patients. In the standard NAAT, 107 samples were N. gonorrhoeae positive and 284 were C. trachomatis positive. The sensitivities of NAAT on ESwab samples were 83% (95% confidence interval [CI], 75 to 90%) and 87% (95% CI, 82 to 90%), respectively. ESwab samples were available for 98 of the gonorrhea-positive samples. Of these, 82% were positive in direct culture and 69% and 56% were positive in the 1st and 2nd deferred cultures, respectively (median storage times, 27 and 48 h, respectively). Deferred culture was more often successful in urogenital samples or when the patient had symptoms at the sampling site. Deferred N. gonorrhoeae culture of stored ESwab samples is feasible and enables AMR surveillance. To limit the loss in NAAT sensitivity, we recommend obtaining separate samples for NAAT and deferred culture.

Candida colonization as a risk marker for invasive candidiasis in mixed medical-surgical intensive care units: development and evaluation of a simple, standard protocol

Colonization with Candida species is an independent risk factor for invasive candidiasis (IC), but the minimum and most practicable parameters for prediction of IC have not been optimized. We evaluated Candida colonization in a prospective cohort of 6,015 nonneutropenic, critically ill patients. Throat, perineum, and urine were sampled 72 h post-intensive care unit (ICU) admission and twice weekly until discharge or death. Specimens were cultured onto chromogenic agar, and a subset underwent molecular characterization. Sixty-three (86%) patients who developed IC were colonized prior to infection; 61 (97%) tested positive within the first two time points. The median time from colonization to IC was 7 days (range, 0 to 35). Colonization at any site was predictive of IC, with the risk of infection highest for urine colonization (relative risk [RR]=2.25) but with the sensitivity highest (98%) for throat and/or perineum colonization. Colonization of ≥2 sites and heavy colonization of ≥1 site were significant independent risk factors for IC (RR=2.25 and RR=3.7, respectively), increasing specificity to 71% to 74% but decreasing sensitivity to 48% to 58%. Molecular testing would have prompted a resistance-driven decision to switch from fluconazole treatment in only 11% of patients infected with C. glabrata, based upon species-level identification alone. Positive predictive values (PPVs) were low (2% to 4%) and negative predictive values (NPVs) high (99% to 100%) regardless of which parameters were applied. In the Australian ICU setting, culture of throat and perineum within the first two time points after ICU admission captures 84% (61/73 patients) of subsequent IC cases. These optimized parameters, in combination with clinical risk factors, should strengthen development of a setting-specific risk-predictive model for IC.

The corneal ulcer one-touch study: a simplified microbiological specimen collection method

PURPOSE

To determine if a new, single-sample device (ESwab; Copan Diagnostics, Inc) can simplify the traditional multi-sample approach to specimen collection in infectious keratitis.

DESIGN

Prospective, diagnostic test evaluation.

METHODS

In this institutional study, patients with suspected infectious keratitis meeting traditional criteria for diagnostic corneal specimen collection and culture were randomized to the order of first specimen collection method: ESwab or a sample directly plated for growth on chocolate agar. This was followed by standard samples for blood agar, Gram stain, Sabouraud agar, thioglycolate broth, and brain heart infusion broth in all cases. The specimens collected using the 2 approaches were analyzed separately by the laboratory in a masked fashion. The main outcome measure was positive growth on cultured media.

RESULTS

Eighty-one eyes from 80 consecutive patients were sampled. Culture positivity rate for the multi-sample method and ESwab was 70% and 69%, respectively, with a 75% agreement rate. ESwab sensitivity was 84% (95% confidence interval [CI]: 72%-93%), with a specificity of 67% (95% CI: 45%-84%). Positive and negative predictive values of the ESwab were 86% (95% CI: 74%-94%) and 64% (95% CI: 43%-82%), respectively. There was no difference in positive culture reports with respect to the order of specimen collection technique used.

CONCLUSIONS

The single-sample ESwab method is a more accessible and less cumbersome approach to corneal culturing for ophthalmologists, particularly those in the community setting who do not have access to the full set of traditional culture materials. Culture results using this single-sample approach were comparable to the multi-sample method.

ESwab challenges influenza virus propagation in cell cultures

Although the ESwab kit (Copan, Brescia, Italy) is intended for sampling bacteria for culture, this kit is increasingly also used for virus sampling. The effect of ESwab medium on influenza virus detection by real-time reverse transcription-polymerase chain reaction (RT-PCR) or virus propagation in Madin-Darby canine kidney (MDCK) cell culture was investigated. The ESwab medium was suitable for viral RNA detection but not for viral propagation due to cytotoxicity. Sampling influenza viruses with ESwab challenges influenza surveillance by strongly limiting the possibility of antigenic characterisation.

Comparison of flocked and aptima swabs and two specimen transport media in the aptima combo 2 assay

Self-collected vaginal Aptima swabs and flocked swabs in Aptima specimen transport medium and ESwabs in ESwab medium detected all 37 Chlamydia trachomatis-infected patients from 287 women tested by the Aptima Combo assay. Prevalence rates of C. trachomatis, Neisseria gonorrhoeae, and dual infection were 12.8%, 3.1%, and 2.4%, respectively.

Evaluation of two types of swabs for sampling allograft musculoskeletal tissue

BACKGROUND

Allograft musculoskeletal tissue is commonly sampled by a swab for bioburden screening. To determine if bioburden recovery could be improved at the pre-analytical stage, two swab systems were evaluated: the Amies gel swab and the ESwab.

METHODS

In vitro studies were performed to determine the recovery of each swab system with <100 colony-forming unit of challenge organisms using inoculated swabs and by sampling inoculated femoral heads. The standard culture protocol used in this laboratory was also evaluated after sampling of inoculated femoral heads. A prospective study was performed with both swab systems used in parallel to sample cadaveric allograft musculoskeletal tissue.

RESULTS

The challenge organisms could be recovered from the in vitro inoculated studies. The standard culture protocol in this laboratory recovered all challenge organisms from both swab systems. One hundred and six paired Amies and ESwabs were collected from eight cadaveric donors with skin commensals the predominant isolates.

CONCLUSIONS

The sampling of an inoculated femoral head was included to reflect routine swab sampling practice as was the inclusion of the standard method used in this laboratory. This appears to be the first study to compare Amies gel swabs with ESwabs to sample allograft femoral heads and in a prospective study with cadaveric allograft musculoskeletal tissue. Other comparative studies of swab systems have used a much higher inoculum to mimic an infection; however, sepsis is an exclusion criterion for allograft donors. It was found that the Amies gel swab and ESwab are both suitable sampling devices for bioburden testing of allograft musculoskeletal tissue.

Comparison of ESwab with traditional swabs for detection of methicillin-resistant Staphylococcus aureus using two different walk-away commercial real-time PCR methods

The ESwab system (Copan Diagnostics) was evaluated as a nasopharyngeal specimen collection device to be used for methicillin-resistant Staphylococcus aureus (MRSA) detection by the GeneXpert and BD Max MRSA assays. Different MRSA strains and dilutions of each strain were tested in triplicate. ESwabs proved to be a suitable collection system for the two assays tested.

Comparison of FecalSwab and ESwab devices for storage and transportation of Diarrheagenic bacteria

Using a collection (n = 12) of ATCC and known stock isolates, as well as 328 clinical stool specimens, we evaluated the ESwab and the new FecalSwab liquid-based microbiology (LBM) devices for storing and transporting diarrheagenic bacteria. The stock isolates were stored in these swab devices up to 48 h at refrigeration (4°C) or room (∼25°C) temperature and up to 3 months at -20°C or -70°C. With the clinical stool specimens, the performances of the ESwab and FecalSwab were compared to those of routinely used transport systems (Amies gel swabs and dry containers). At a refrigeration temperature, all isolates survived in FecalSwab up to 48 h, while in ESwab, only 10 isolates (83.3%) out of 12 survived. At -70°C, all isolates in FecalSwab were recovered after 3 months of storage, whereas in ESwab, none of the isolates were recovered. At -20°C, neither of the swab devices preserved the viability of stock isolates after 2 weeks of storage, and at room temperature, 7 (58.3%) of the stock isolates were recovered in both transport devices after 48 h. Of the 328 fecal specimens, 44 (13.4%) were positive for one of the common diarrheagenic bacterial species with all transport systems used. Thus, the suitability of the ESwab and FecalSwab devices for culturing fresh stools was at least equal to those of the Amies gel swabs and dry containers. Although the ESwab was shown to be an option for collecting and transporting fecal specimens, the FecalSwab device had clearly better preserving properties under different storage conditions.

Automation in the clinical microbiology laboratory

Imagine a clinical microbiology laboratory where a patient's specimens are placed on a conveyor belt and sent on an automation line for processing and plating. Technologists need only log onto a computer to visualize the images of a culture and send to a mass spectrometer for identification. Once a pathogen is identified, the system knows to send the colony for susceptibility testing. This is the future of the clinical microbiology laboratory. This article outlines the operational and staffing challenges facing clinical microbiology laboratories and the evolution of automation that is shaping the way laboratory medicine will be practiced in the future.

Clinical evaluation of the walk-away specimen processor and ESwab for recovery of Streptococcus agalactiae isolates in prenatal screening specimens

Rectal/vaginal specimens (n = 97) were collected in parallel using ESwab and Liquid Stuart (LS) rayon fiber wrapped swab collection devices. Each collection device was used to directly inoculate culture medium and LIM broth. Medium inoculation by ESwab was conducted using the Walk-Away specimen processor (WASP). Medium inoculation by the LS device was conducted manually. The sensitivities of ESwab and LS upon direct plating were 93.8% and 87.5%, respectively, and increased to 96.9% and 90.6%, respectively, following broth enrichment.

Swab or biopsy samples for bioburden testing of allograft musculoskeletal tissue?

Swab and biopsy samples of allograft musculoskeletal tissue are most commonly collected by tissue banks for bacterial and fungal bioburden testing. An in vitro study was performed using the National Committee for Clinical Laboratory Standards standard 'Quality control of microbiological transport systems' (2003) to validate and evaluate the recovery of six challenge organisms from swab and biopsy samples of allograft musculoskeletal tissue. On average, 8.4 to >100 and 7.2 to >100 % of the inoculum was recovered from swab and biopsy samples respectively. A retrospective review of donor episodes was also performed, consisting of paired swab and biopsy samples received in this laboratory during the period 2001-2012. Samples of allograft femoral heads were collected from living donors during hip operations. From the 3,859 donor episodes received, 21 paired swab and biopsy samples each recovered an isolate, 247 swab samples only and 79 biopsy samples only were culture positive. Low numbers of challenge organisms were recovered from inoculated swab and biopsy samples in the in vitro study and validated their use for bioburden testing of allograft musculoskeletal tissue. Skin commensals were the most common group of organisms isolated during a 12-year retrospective review of paired swab and biopsy samples from living donor allograft femoral heads. Paired swab and biopsy samples are a suitable representative sample of allograft musculoskeletal tissue for bioburden testing.