Rapid detection of Brucella spp. in blood cultures by fluorescence in situ hybridization

Rapid Identification of Brucella Genus and Species In Silico and On-Site Using Novel Probes with CRISPR/Cas12a

Human brucellosis caused by Brucella is a widespread zoonosis that is prevalent in many countries globally. The high homology between members of the Brucella genus and Ochrobactrum spp. often complicates the determination of disease etiology in patients. The efficient and reliable identification and distinction of Brucella are of primary interest for both medical surveillance and outbreak purposes. A large amount of genomic data for the Brucella genus was analyzed to uncover novel probes containing single-nucleotide polymorphisms (SNPs). GAMOSCE v1.0 software was developed based on the above novel eProbes. In conjunction with clinical requirements, an RPA-Cas12a detection method was developed for the on-site determination of B. abortus and B. melitensis by fluorescence and lateral flow dipsticks (LFDs). We demonstrated the potential of these probes for rapid and accurate detection of the Brucella genus and five significant Brucella species in silico using GAMOSCE. GAMOSCE was validated on different Brucella datasets and correctly identified all Brucella strains, demonstrating a strong discrimination ability. The RPA-Cas12a detection method showed good performance in detection in clinical blood samples and veterinary isolates. We provide both in silico and on-site methods that are convenient and reliable for use in local hospitals and public health programs for the detection of brucellosis.

Microbiological Laboratory Diagnosis of Human Brucellosis: An Overview

Brucella spp. are Gram-negative, non-motile, non-spore-forming, slow-growing, facultative intracellular bacteria causing brucellosis. Brucellosis is an endemic of specific geographic areas and, although underreported, represents the most common zoonotic infection, with an annual global incidence of 500,000 cases among humans. Humans represent an occasional host where the infection is mainly caused by B. melitensis, which is the most virulent; B. abortus; B. suis; and B. canis. A microbiological analysis is crucial to identifying human cases because clinical symptoms of human brucellosis are variable and aspecific. The laboratory diagnosis is based on three different microbiological approaches: (i) direct diagnosis by culture, (ii) indirect diagnosis by serological tests, and (iii) direct rapid diagnosis by molecular PCR-based methods. Despite the established experience with serological tests and highly sensitive nucleic acid amplification tests (NAATs), a culture is still considered the “gold standard” in the laboratory diagnosis of brucellosis due to its clinical and epidemiological relevance. Moreover, the automated BC systems now available have increased the sensitivity of BCs and shortened the time to detection of Brucella species. The main limitations of serological tests are the lack of common interpretative criteria, the suboptimal specificity due to interspecies cross-reactivity, and the low sensitivity during the early stage of disease. Despite that, serological tests remain the main diagnostic tool, especially in endemic areas because they are inexpensive, user friendly, and have high negative predictive value. Promising serological tests based on new synthetic antigens have been recently developed together with novel point-of-care tests without the need for dedicated equipment and expertise. NAATs are rapid tests that can help diagnose brucellosis in a few hours with high sensitivity and specificity. Nevertheless, the interpretation of NAAT-positive results requires attention because it may not necessarily indicate an active infection but rather a low bacterial inoculum, DNA from dead bacteria, or a patient that has recovered. Refined NAATs should be developed, and their performances should be compared with those of commercial and home-made molecular tests before being commercialized for the diagnosis of brucellosis. Here, we review and report the most common and updated microbiological diagnostic methods currently available for the laboratory diagnosis of brucellosis.

NOTIFy (non-toxic lyophilized field)-FISH for the identification of biological agents by Fluorescence in situ Hybridization

The rapid and reliable diagnostics of highly pathogenic bacteria under restricted field conditions poses one of the major challenges to medical biodefense, especially since false positive or false negative reports might have far-reaching consequences. Fluorescence in situ hybridization (FISH) has the potential to represent a powerful microscopy-based addition to the existing molecular-based diagnostic toolbox. In this study, we developed a set of FISH-probes for the fast, matrix independent and simultaneous detection of thirteen highly pathogenic bacteria in different environmental and clinical sample matrices. Furthermore, we substituted formamide, a routinely used chemical that is toxic and volatile, by non-toxic urea. This will facilitate the application of FISH under resource limited field laboratory conditions. We demonstrate that hybridizations performed with urea show the same specificity and comparable signal intensities for the FISH-probes used in this study. To further simplify the use of FISH in the field, we lyophilized the reagents needed for FISH. The signal intensities obtained with these lyophilized reagents are comparable to freshly prepared reagents even after storage for a month at room temperature. Finally, we show that by the use of non-toxic lyophilized field (NOTIFy)-FISH, specific detection of microorganisms with simple and easily transportable equipment is possible in the field.

Laboratory Diagnosis of Human Brucellosis

The clinical presentation of brucellosis in humans is variable and unspecific, and thus, laboratory corroboration of the diagnosis is essential for the patient's proper treatment. The diagnosis of brucellar infections can be made by culture, serological tests, and nucleic acid amplification assays. Modern automated blood culture systems enable detection of acute cases of brucellosis within the routine 5- to 7-day incubation protocol employed in clinical microbiology laboratories, although a longer incubation and performance of blind subcultures may be needed for protracted cases. Serological tests, though they lack specificity and provide results that may be difficult to interpret in individuals repeatedly exposed to Brucella organisms, nevertheless remain a diagnostic cornerstone in resource-poor countries. Nucleic acid amplification assays combine exquisite sensitivity, specificity, and safety and enable rapid diagnosis of the disease. However, long-term persistence of positive molecular test results in patients that have apparently fully recovered is common and has unclear clinical significance and therapeutic implications. Therefore, as long as there are no sufficiently validated commercial tests or studies that demonstrate an adequate interlaboratory reproducibility of the different homemade PCR assays, cultures and serological methods will remain the primary tools for the diagnosis and posttherapeutic follow-up of human brucellosis.

The NOD-scid IL2rγnull Mouse Model Is Suitable for the Study of Osteoarticular Brucellosis and Vaccine Safety

Osteoarticular brucellosis is the most common complication in Brucella-infected humans regardless of age, sex, or immune status. The mechanism of bone destruction caused by Brucella species remained partially unknown due to the lack of a suitable animal model. Here, to study this complication, we explored the suitability of the use of the NOD-scid IL2rγ^null mouse to study osteoarticular brucellosis and examined the potential use of this strain to evaluate the safety of live attenuated vaccine candidates. Mice were inoculated intraperitoneally with a single dose of 1 × 10⁴, 1 × 10⁵, or 1 × 10⁶ CFU of B. abortus S19 or the vaccine candidate B. abortus S19ΔvjbR and monitored for the development of side effects, including osteoarticular disease, for 13 weeks. Decreased body temperature, weight loss, splenomegaly, and deformation of the tails were observed in mice inoculated with B. abortus S19 but not in those inoculated with S19ΔvjbR Histologically, all S19-inoculated mice had a severe dose-dependent inflammatory response in multiple organs. The inflammatory response at the tail was characterized by the recruitment of large numbers of neutrophils, macrophages, and osteoclasts with marked bone destruction. These lesions histologically resembled what is typically observed in Brucella-infected patients. In contrast, mice inoculated with B. abortus S19ΔvjbR did not show significant bone changes. Immunofluorescence, in situ hybridization, and confocal imaging demonstrated the presence of Brucella at the sites of inflammation, both intra- and extracellularly, and large numbers of bacteria were observed within mature osteoclasts. These results demonstrate the potential use of the NOD-scid IL2rγ^null mouse model to evaluate vaccine safety and further study osteoarticular brucellosis.

The Application of a Nanomaterial Optical Fiber Biosensor Assay for Identification of Brucella Nomenspecies

Bacteria in the genus Brucella are the cause of brucellosis in humans and many domestic and wild animals. A rapid and culture-free detection assay to detect Brucella in clinical samples would be highly valuable. Nanomaterial optical fiber biosensors (NOFS) are capable of recognizing DNA hybridization events or other analyte interactions with high specificity and sensitivity. Therefore, a NOFS assay was developed to detect Brucella DNA from cultures and in tissue samples from infected mice. An ionic self-assembled multilayer (ISAM) film was coupled to a long-period grating optical fiber, and a nucleotide probe complementary to the Brucella IS711 region and modified with biotin was bound to the ISAM by covalent conjugation. When the ISAM/probe duplex was exposed to lysate containing ≥100 killed cells of Brucella, or liver or spleen tissue extracts from Brucella-infected mice, substantial attenuation of light transmission occurred, whereas exposure of the complexed fiber to non-Brucella gram-negative bacteria or control tissue samples resulted in negligible attenuation of light transmission. Oligonucleotide probes specific for B. abortus, B. melitensis, and B. suis could also be used to detect and differentiate these three nomenspecies. In summary, the NOFS biosensor assay detected three nomenspecies of Brucella without the use of polymerase chain reaction within 30 min and could specifically detect low numbers of this bacterium in clinical samples.

Detection of Acinetobacter spp. in Blood Cultures by an Improved Fluorescent in Situ Hybridization Assay

Fluorescent in situ hybridization (FISH) allows rapid detection of microorganisms. We aimed (i) to evaluate the sensitivity and specificity of FISH for the detection of Acinetobacter spp. in blood culture specimens and (ii) to test the simultaneous application of two genus-specific probes labeled with the same fluorochrome to increase the fluorescent signal intensity and improve the detection of Acinetobacter spp. Three hundred and twenty blood culture specimens were tested via both the conventional laboratory methods and FISH to detect Acinetobacter spp. The specimens were examined separately with each genus-specific probe Aci and ACA, and also using a mixture of the both probes Aci and ACA. In all examinations, probe EUB338 was used accompanied by Aci and ACA. The specificity of FISH was 100% (97.5% confidence interval [CI] = 98.7% – 100%). The sensitivity of FISH by the use of probe Aci was 96.4% (95% CI = 81.7% – 99.9%), whereas, the sensitivity of this technique by the use of probe ACA as well as by the combination of both probes Aci and ACA was 100% (97.5% CI = 87.7% – 100%). Moreover, simultaneous hybridization by probes Aci and ACA increased the fluorescent signal of Acinetobacter spp. cells to 3+ in 13 specimens. In conclusion, FISH, particularly using a combination of Aci and ACA, is a highly accurate method for the detection of Acinetobacter spp. in blood cultures. Furthermore, simultaneous hybridization by the both probes Aci and ACA can increase the fluorescent signal intensity of Acinetobacter spp. cells in some blood culture specimens and facilitate the detection of these microorganisms.

Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review

Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.

Microbiological laboratory diagnostics of neglected zoonotic diseases (NZDs)

This review reports on laboratory diagnostic approaches for selected, highly pathogenic neglected zoonotic diseases, i.e. anthrax, bovine tuberculosis, brucellosis, echinococcosis, leishmaniasis, rabies, Taenia solium-associated diseases (neuro-/cysticercosis & taeniasis) and trypanosomiasis. Diagnostic options, including microscopy, culture, matrix-assisted laser-desorption-ionisation time-of-flight mass spectrometry, molecular approaches and serology are introduced. These procedures are critically discussed regarding their diagnostic reliability and state of evaluation. For rare diseases reliable evaluation data are scarce due to the rarity of samples. If bio-safety level 3 is required for cultural growth, but such high standards of laboratory infrastructure are not available, serological and molecular approaches from inactivated sample material might be alternatives. Multiple subsequent testing using various test platforms in a stepwise approach may improve sensitivity and specificity. Cheap and easy to use tests, usually called "rapid diagnostic tests" (RDTs) may impact disease control measures, but should not preclude developing countries from state of the art diagnostics.

An ion-exchange nanomembrane sensor for detection of nucleic acids using a surface charge inversion phenomenon

We present a novel low-cost biosensor for rapid, sensitive and selective detection of nucleic acids based on an ionic diode feature of an anion exchange nanoporous membrane under DC bias. The ionic diode feature is associated with external surface charge inversion on the positively charged anion exchange nanomembrane upon hybridization of negatively charged nucleic acid molecules to single-stranded oligoprobes functionalized on the membrane surface resulting in the formation of a cation selective monolayer. The resulting bipolar membrane causes a transition from electroconvection-controlled to water-splitting controlled ion conductance, with a large ion current signature that can be used to accurately quantify the hybridized nucleic acids. The platform is capable of distinguishing two base-pair mismatches in a 22-base pairing segment of microRNAs associated with oral cancer, as well as serotype-specific detection of dengue virus. We also show the sensor' capability to selectively capture target nucleic acids from a heterogeneous mixture. The limit of detection is 1 pM for short 27 base target molecules in a 15-min assay. Similar hybridization results are shown for short DNA molecules as well as RNAs from Brucella and Escherichia coli. The versatility and simplicity of this low-cost biosensor should enable point-of-care diagnostics in food, medical and environmental safety markets.

Developments for improved diagnosis of bacterial bloodstream infections

Bloodstream infections (BSIs) are associated with high mortality and increased healthcare costs. Optimal management of BSI depends on several factors including recognition of the disease, laboratory tests and treatment. Rapid and accurate identification of the etiologic agent is crucial to be able to initiate pathogen specific antibiotic therapy and decrease mortality rates. Furthermore, appropriate treatment might slow down the emergence of antibiotic resistant strains. Culture-based methods are still considered to be the "gold standard" for the detection and identification of pathogens causing BSI. Positive blood cultures are used for Gram-staining. Subsequently, positive blood culture material is subcultured on solid media, and (semi-automated) biochemical testing is performed for species identification. Finally, a complete antibiotic susceptibility profile can be provided based on cultured colonies, which allows the start of pathogen-tailored antibiotic therapy. This conventional workflow is extremely time-consuming and can take up to several days. Furthermore, fastidious and slow-growing microorganisms, as well as antibiotic pre-treated samples can lead to false-negative results. The main aim of this review is to present different strategies to improve the conventional laboratory diagnostic steps for BSI. These approaches include protein-based (MALDI-TOF mass spectrometry) and nucleic acid-based (polymerase chain reaction [PCR]) identification from subculture, blood cultures, and whole blood to decrease time to results. Pathogen enrichment and DNA isolation methods, to enable optimal pathogen DNA recovery from whole blood, are described. In addition, the use of biomarkers as patient pre-selection tools for molecular assays are discussed.

Beacon-based (bbFISH®) technology for rapid pathogens identification in blood cultures

BACKGROUND

Diagnosis and treatment of bloodstream infections (BSI) are often hampered by the delay in obtaining the final results of blood cultures. Rapid identification of pathogens involved in BSI is of great importance in order to improve survival of septic patients. Beacon-based fluorescent in situ hybridization (hemoFISH® Gram positive and hemoFISH® Gram negative test kits, miacom diagnostics GmbH Düsseldorf, Germany) accelerates the identification of most frequent bacterial pathogens of sepsis.

RESULTS

In this study a total of 558 blood culture (377 blood culture positive and 181 negative) were tested with the hemoFISH® method and the results were evaluated in comparison with the traditional culture based methods. The overall sensitivity and specificity of the hemoFISH® tests were 94.16% and 100%, while, the PPV and NPV were 100 and 89.16%, respectively. As the hemoFISH® results were obtained within 45 mins, the time difference between the final results of the traditional culture method and the hemoFISH® assay was about two days.

CONCLUSIONS

Considering the good sensitivity and specificity of the hemoFISH® assays as well as the significant time saving in obtaining the final results (p-value 0.0001), the introduction of the system could be rialable in the microbiology laboratories, even alongside the traditional systems.

Molecular diagnosis of sepsis

INTRODUCTION

Current management of sepsis relies on the early detection and early administration of antimicrobials. This requires detection of pathogens earlier than conventional blood cultures and recognition of the immune status of the host earlier than the conventional biomarkers. This can be achieved by molecular techniques.

AREAS COVERED

Molecular diagnosis of pathogens is based on either rapid detection of pathogens grown in blood cultures or direct use of whole blood and blood products. Molecular diagnosis of the constellation of activations and inhibitions of pathways implicated in cellular processes can be achieved by gene profiling of a large array of genes.

EXPERT OPINION

Molecular microbial diagnosis enables rapid identification and precedes results obtained by conventional culture methods. Its role can be proved more useful in sepsis caused by specific microorganisms such as fungi performed by PMA-FISH and MALDI-TOF MS. Molecular techniques using blood aim for rapid pathogen identification. However, the provided information regarding the antimicrobial susceptibility of the pathogen is limited. Gene profiling in sepsis provides individualized information for the activation or inhibition of pathways of a variety of cellular processes. The transcriptome information is difficult to interpret in everyday clinical practice particularly on how information translates to patient needs.

Implications of laboratory diagnosis on brucellosis therapy

Brucellosis is a worldwide zoonosis with a huge economic impact on animal husbandry and public health. The diagnosis of human brucellosis can be protracted because the disease primarily presents as fever of unknown origin with unspecific clinical signs and symptoms. The isolation rate of the fastidious etiologic agent from blood cultures is low, and therefore laboratory diagnosis is mainly based on serologic and molecular testing. However, seronegative brucellosis patients have been described, and antibody titers of diagnostic significance are difficult to define. Whether the molecular detection of Brucella DNA in clinical samples should be followed by long-term antibiotic treatment or not is also a matter of debate. The aim of this article is to review and discuss the implications of laboratory test results in the diagnosis of human brucellosis on disease therapy.

Evaluation of the recombinant 10-kilodalton immunodominant region of the BP26 protein of Brucella abortus for specific diagnosis of bovine brucellosis

Brucellosis is a disease with worldwide distribution affecting animals and human beings. Brucella abortus is the causative agent of bovine brucellosis. The cross-reactions of currently available diagnostic procedures for B. abortus infection result in false-positive reactions, which make the procedures unreliable. These tests are also unable to differentiate Brucella-infected and -vaccinated animals. The present work is focused on the use of a nonlipopolysaccharide (LPS) diagnostic antigen, a recombinant 10-kDa (r10-kDa) protein of B. abortus, for specific diagnosis of brucellosis. The purified recombinant protein was used as a diagnostic antigen in plate enzyme-linked immunosorbent assay (p-ELISA) format to screen 408 bovine serum samples (70 presumptively negative, 308 random, and 30 vaccinated), and the results were compared with those of the Rose Bengal plate agglutination test (RBPT) and the standard tube agglutination test (STAT). Statistical analysis in presumptive negative samples revealed 100 and 98.41% specificity of p-ELISA with RBPT and STAT, and an agreement of 91.43% with the tests using Cohen's kappa statistics. In random samples, the agreement of p-ELISA was 77.92% and 80.52% with RBPT and STAT, respectively. p-ELISA investigation of vaccinated samples reported no false-positive results, whereas RBPT and STAT reported 30% and 96.6% false-positive results, respectively. The data suggest that p-ELISA with r10-kDa protein may be a useful method for diagnosis of bovine brucellosis. Furthermore, p-ELISA may also be used as a tool for differentiating Brucella-vaccinated and naturally infected animals.

Rapid identification of pathogens in blood culture with fluorescent in situ hybridization (FISH)

Rapid identification of pathogens in bloodstream infections is of utmost importance to improve survival of septic patients. Fluorescent in situ hybridization (FISH) accelerates the identification of most frequent bacterial and yeast pathogens of sepsis. In this study, 210 positive blood cultures were tested with FISH method and the results were evaluated comparing to the traditional cultivation based results. Overall agreement between FISH and conventional identification was 91.4%, with better results for Gram-negative bacteria than for Gram-positives (100% and 89.5%, respectively). FISH results were obtained within 1 hour. FISH may serve as a useful tool to supplement traditional microbiological methods for rapid, provisional identification of sepsis pathogens.

Rapid differentiation of Francisella species and subspecies by fluorescent in situ hybridization targeting the 23S rRNA

Background

Francisella (F.) tularensis is the causative agent of tularemia. Due to its low infectious dose, ease of dissemination and high case fatality rate, F. tularensis was the subject in diverse biological weapons programs and is among the top six agents with high potential if misused in bioterrorism. Microbiological diagnosis is cumbersome and time-consuming. Methods for the direct detection of the pathogen (immunofluorescence, PCR) have been developed but are restricted to reference laboratories.

Results

The complete 23S rRNA genes of representative strains of F. philomiragia and all subspecies of F. tularensis were sequenced. Single nucleotide polymorphisms on species and subspecies level were confirmed by partial amplification and sequencing of 24 additional strains. Fluorescent In Situ Hybridization (FISH) assays were established using species- and subspecies-specific probes.

Different FISH protocols allowed the positive identification of all 4 F. philomiragia strains, and more than 40 F. tularensis strains tested. By combination of different probes, it was possible to differentiate the F. tularensis subspecies holarctica, tularensis, mediasiatica and novicida. No cross reactivity with strains of 71 clinically relevant bacterial species was observed. FISH was also successfully applied to detect different F. tularensis strains in infected cells or tissue samples. In blood culture systems spiked with F. tularensis, bacterial cells of different subspecies could be separated within single samples.

Conclusion

We could show that FISH targeting the 23S rRNA gene is a rapid and versatile method for the identification and differentiation of F. tularensis isolates from both laboratory cultures and clinical samples.

The era of molecular and other non-culture-based methods in diagnosis of sepsis

Sepsis, a leading cause of morbidity and mortality throughout the world, is a clinical syndrome with signs and symptoms relating to an infectious event and the consequent important inflammatory response. From a clinical point of view, sepsis is a continuous process ranging from systemic inflammatory response syndrome (SIRS) to multiple-organ-dysfunction syndrome (MODS). Blood cultures are the current "gold standard" for diagnosis, and they are based on the detection of viable microorganisms present in blood. However, on some occasions, blood cultures have intrinsic limitations in terms of sensitivity and rapidity, and it is not expected that these drawbacks will be overcome by significant improvements in the near future. For these principal reasons, other approaches are therefore needed in association with blood culture to improve the overall diagnostic yield for septic patients. These considerations have represented the rationale for the development of highly sensitive and fast laboratory methods. This review addresses non-culture-based techniques for the diagnosis of sepsis, including molecular and other non-culture-based methods. In particular, the potential clinical role for the sensitive and rapid detection of bacterial and fungal DNA in the development of new diagnostic algorithms is discussed.

Rapid methods for diagnosis of bloodstream infections

Direct detection technologies for pathogenic microorganisms are emerging to be applied in the diagnosis of serious bloodstream infections and infections at sterile body sites, as well as for quality control measures prior to the release of sterile blood products and to ascertain microbial safety of food. Standard blood cultures as the current gold standard for detection of bacteraemia/sepsis and other culture-based microbiological identification procedures are comparatively slow and have limited sensitivity for fastidious or slow-growing microorganisms. Rapid nucleic acid-based technologies with PCR amplification or hybridisation probes for specific pathogens, broad-range bacterial or fungal assays, flow cytometry, as well as protein-based characterisation by mass spectrometry, aim at identification of pathogenic microorganisms within minutes to hours. Interpretation of direct detection of panbacterial or panfungal nucleic acids instead of living microorganisms in blood is complex, given the risk of contamination, the ubiquitous presence of bacterial and fungal DNA, and the lack of a gold standard. Since many of the infections at sterile sites, particularly sepsis, are medical emergencies requiring immediate therapeutic responses, rapid technologies could contribute to reduction of morbidity, mortality, and of the economic burden. This review summarises the currently available data on rapid non-culture-based technologies and outlines the potential clinical usefulness in infectious disease diagnosis.

Rapid identification of Fusobacterium nucleatum and Fusobacterium necrophorum by fluorescence in situ hybridization

Identification of clinically relevant Fusobacterium spp. is hampered by their slow growth, their frequent occurrence in polymicrobial culture, and the low reliability of biochemical differentiation methods. A newly developed fluorescence in situ hybridization (FISH) assay allowed reliable and rapid identification of Fusobacterium necrophorum and Fusobacterium nucleatum from culture. Preliminary results show that the method offers the perspective for direct detection of these pathogens in blood cultures and abscess aspirates.