Use of the diagnostic bacteriology laboratory: a practical review for the clinician

Evaluation of InTray Cassettes Directly from Blood Cultures for the Diagnosis of Sepsis in Clinical Bacteriology Laboratories as an Alternative to Classic Culture Media

Culture media is fundamental in clinical bacteriology for the detection and isolation of bacterial pathogens. However, in-house media preparation could be challenging in low-resource settings. InTray^® cassettes (Biomed Diagnostics) could be a valid alternative as they are compact, ready-to-use media preparations. In this study, we evaluate the use of two InTray media as a subculture alternative for the diagnosis of bloodstream infections: the InTray^® Müller-Hinton (MH) chocolate and the InTray^® Colorex™ Screen. The InTray MH chocolate was evaluated in 2 steps: firstly, using simulated positive blood cultures (reference evaluation study), and secondly, using positive blood cultures from a routine clinical laboratory (clinical evaluation study). The Colorex Screen was tested using simulated poly-microbial blood cultures. The sensitivity and specificity of the InTray MH chocolate were respectively 99.2% and 90% in the reference evaluation study and 97.1% and 88.2% in the clinical evaluation study. The time to detection (TTD) was ≤20 h in most positive blood cultures (99.8% and 97% in the two studies, respectively). The InTray^® MH Chocolate agar showed good performance when used directly from clinical blood cultures for single bacterial infections. However, mixed flora is more challenging to interpret on this media than on Colorex™ Screen, even for an experienced microbiologist.

Bedside Diagnostics for Infections: A Guide for Dermatologists

In dermatology, there are many bedside diagnostic tests that may aid in more rapid diagnosis and early initiation of appropriate therapy. When performed correctly, these bedside diagnostic tests can provide both sensitive and specific results. We discuss bedside diagnostic tests, such as the Tzanck smear, potassium hydroxide (KOH) preparation, and mineral oil preparation, with a specific focus on their use in diagnosing infectious dermatoses.

Is Infrared Spectroscopy Ready for the Clinic?

Fourier transform-infrared spectroscopy (FT-IR) represents an attractive molecular diagnostic modality for translation to the clinic, where comprehensive chemical profiling of biological samples may revolutionize a myriad of pathways in clinical settings. Principally, FT-IR provides a rapid, cost-effective platform to obtain a molecular fingerprint of clinical samples based on vibrational transitions of chemical bonds upon interaction with infrared light. To date, considerable research activities have demonstrated competitive to superior performance of FT-IR strategies in comparison to conventional techniques, with particular promise for earlier, accessible disease diagnostics, thereby improving patient outcomes. However, amidst the changing healthcare landscape in times of aging populations and increased prevalence of cancer and chronic disease, routine adoption of FT-IR within clinical laboratories has remained elusive. Hence, this perspective shall outline the significant clinical potential of FT-IR diagnostics and subsequently address current barriers to translation from the perspective of all stakeholders, in the context of biofluid, histopathology, cytology, microbiology, and biomarker discovery frameworks. Thereafter, future perspectives of FT-IR for healthcare will be discussed, with consideration of recent technological advances that may facilitate future clinical translation.

Detection of microbial genes in a single leukocyte by polymerase chain reaction following laser capture microdissection

Although isolation and identification of bacteria in a clinical specimen constitute essential steps for the diagnosis of bacterial infection, positive results of the bacterial culture are not always attained, despite observing the bacteria by Gram staining. As bacteria phagocytosed by the leukocytes are considered as the causative agents of infectious diseases, this study aims to introduce a new approach for the collection of only bacteria phagocytosed by the neutrophils in an animal model using laser capture microdissection (LCM) followed by the DNA identification using polymerase chain reaction (PCR). We inoculated representative bacteria (Escherichia coli and Staphylococcus aureus) into the abdominal cavities of specific pathogen-free C57BL/6 J mice. After 6 h inoculation, we collected the fluid samples from the peritoneal cavities of mice and demonstrated peritonitis by the increase of neutrophils. Then, we smeared the neutrophils on the membrane slides and collected single-cell phagocytosing bacteria by LCM. The supernatant of the cell lysate was supplied for the PCR reaction to amplify the 16S rRNA gene, and we validated the DNA sequences specific for the inoculated bacteria. In addition, PCR using specific primers for E. coli and S. aureus identified each species of bacteria. Hence, this study suggests that the combination of LCM and PCR could be a novel approach to determine bacteria in infectious diseases. Nevertheless, further investigation is warranted to test various additional bacterial taxa to demonstrate the general applicability of this method to clinical samples.

Endophytes of industrial hemp (Cannabis sativa L.) cultivars: identification of culturable bacteria and fungi in leaves, petioles, and seeds

Plant endophytes are a group of microorganisms that reside asymptomatically within the healthy living tissue. The diversity and molecular and biochemical characterization of industrial hemp-associated endophytes have not been previously studied. This study explored the abundance and diversity of culturable endophytes residing in petioles, leaves, and seeds of three industrial hemp cultivars, and examined their biochemical attributes and antifungal potential. A total of 134 bacterial and 53 fungal strains were isolated from cultivars Anka, CRS-1, and Yvonne. The number of bacterial isolates was similarly distributed among the cultivars, with the majority recovered from petiole tissue. Most fungal strains originated from leaf tissue of cultivar Anka. Molecular and phylogenetic analyses grouped the endophytes into 18 bacterial and 13 fungal taxa, respectively. The most abundant bacterial genera were Pseudomonas, Pantoea, and Bacillus, and the fungal genera were Aureobasidium, Alternaria, and Cochliobolus. The presence of siderophores, cellulase production, and phosphorus solubilization were the main biochemical traits. In proof-of-concept experiments, re-inoculation of tomato roots with some endophytes confirmed their migration to aerial tissues of the plant. Taken together, this study demonstrates that industrial hemp harbours a diversity of microbial endophytes, some of which could be used in growth promotion and (or) in biological control designed experiments.

Investigation of bacterial viability from incubated saliva by application of flow cytometry and hyphenated separation techniques

The aim of the study was determination of bacterial viability in saliva samples and finding a correlation between microbiological and volatile profiles of saliva depending on incubation time. Bacteria colonizing healthy oral cavities were also identified. Twelve healthy adults donated unstimulated saliva samples. Flow cytometry, optical density measurements and colony-forming unit (CFU) counting method were employed for analyses of native and inoculated saliva after 0, 1, 2, 24, and 48 h of incubation. Volatile profiles were acquired using headspace-solid phase microextraction-gas chromatography/mass spectrometry (HS-SPME-GC/MS). Oral bacteria were the most viable within 2 h after collection of saliva. Extension of incubation time to 48 h caused considerable decrease in live bacteria counts and sharp increase in dead bacteria counts. The most prevalent strain was Sphingomonas paucimobilis (26.67%). The number of volatiles raised from 5 to 27 with incubation time and most of them were putrefaction products, such as methanethiol, indole and pyrrole. HS-SPME-GC/MS method is insufficient for volatile profiling of "fresh" saliva and should be directed rather to investigation of bacterial metabolites.

Microbiological Zoonotic Emerging Risks, Transmitted Between Livestock Animals and Humans (2007-2015)

As part of the Emerging Risk Identification (ERI) activities of the European Food Safety Authority (EFSA), a literature search was conducted to identify the microbiological agents transmitted between livestock animals and humans that have been suggested as having emerged between 2007 and 2015 in peer-reviewed scientific literature published during the same period (2007-2015). According to the criteria set, the search identified seven such zoonotic agents, namely West Nile Fever virus, Rift Valley Fever virus, Crimean-Congo Haemorrhagic Fever virus, Influenza A H1N1 virus, Coxiella burnetii, Streptococcus suis and livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398. An explanation of the agents' consideration as emerging risks is provided. The experience gained from these emergences has shown that the detection of and response to such risks can be achieved faster and more successfully within a multidisciplinary, collaborative context at the field, local, national and international levels.

Diversity of culturable bacterial endophytes of saffron in Kashmir, India

Saffron (Crocus sativus) is a medicinally important plant. The Kashmir valley (J&K, India) emblematizes one of the major and quality saffron producing areas in the world. Nonetheless, the area has been experiencing a declining trend in the production of saffron during the last decade. Poor disease management is one of the major reasons for declining saffron production in the area. Endophytes are known to offer control against many diseases of host plant. During the present study, culturable bacterial endophytes were isolated from saffron plant, identified and assessed for plant growth promoting activities. Molecular and phylogenetic analysis grouped the fifty-four bacterial isolates into eleven different taxa, viz. Bacillus licheniformis, B. subtilis, B. cereus, B. humi, B. pumilus, Paenibacillus elgii, B. safensis, Brevibacillus sp., Pseudomonas putida, Staphylococcus hominis and Enterobacter cloacae. The results were also supported with the identification based on BIOLOG system. B. licheniformis was the dominant endophyte in both leaves and corms of saffron. 81 % isolates showed lipase activity, 57 % cellulase, 48 % protease, 38 % amylase, 33 % chitinase and 29 % showed pectinase activity. 24 % of the isolates were phosphate solublizers, 86 % showed siderophore production and 80 % phytohormone production potential. The present repository of well characterized bacterial endophytes of saffron, have plant growth promoting potential which can be explored further for their respective roles in the biology of the saffron plant.

No Outbreak of Vancomycin and Linezolid Resistance in Staphylococcal Pneumonia over a 10-Year Period

BACKGROUND

Staphylococci can cause wound infections and community- and nosocomial-acquired pneumonia, among a range of illnesses. Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) have been rapidly increasing as a cause of infections worldwide in recent decades. Numerous reports indicate that S. aureus and MRSA are becoming resistant to many antibiotics, which makes them very dangerous. Therefore, this study retrospectively investigated the resistance to antimicrobial agents in all hospitalized patients suffering from community- or nosocomial-acquired pneumonia due to S. aureus and MRSA.

METHODS

Information from the study groups suffering from either community- or nosocomial-acquired pneumonia caused by S. aureus or MRSA was gathered by searching records from 2004 to 2014 at the HELIOS Clinic Wuppertal, Witten/Herdecke University, Germany. The findings of antibiotic resistance were analyzed after the evaluation of susceptibility testing for S. aureus and MRSA.

RESULTS

Total of 147 patients (63.9%, 95% CI 57.5%-69.8%), mean age 67.9 ± 18.5 years, with pneumonia triggered by S. aureus, and 83 patients (36.1%, 95% CI 30.2%-42.5%), mean age 72.3 ± 13.8 years, with pneumonia due to MRSA. S. aureus and MRSA developed no resistance to vancomycin (P = 0.019 vs. < 0.0001, respectively) or linezolid (P = 0.342 vs. < 0.0001, respectively). MRSA (95.3%) and S. aureus (56.3%) showed a high resistance to penicillin. MRSA (87.7%) was also found to have a high antibiotic resistance against ß-lactam antibiotics, compared to S. aureus (9.6%). Furthermore, MRSA compared to S. aureus, respectively, had increased antibiotic resistance to ciprofloxacin (90.1% vs. 17.0%), cefazolin (89.7% vs. 10.2%), cefuroxime (89.0% vs. 9.1%), levofloxacin (88.2% vs. 18.4%), clindamycin (78.0% vs. 14.7%), and erythromycin (76.5% vs. 20.8%).

CONCLUSION

No development of resistance was found to vancomycin and linezolid in patients with pneumonia caused by S. aureus and MRSA.

Pasteurella multocida: from zoonosis to cellular microbiology

In a world where most emerging and reemerging infectious diseases are zoonotic in nature and our contacts with both domestic and wild animals abound, there is growing awareness of the potential for human acquisition of animal diseases. Like other Pasteurellaceae, Pasteurella species are highly prevalent among animal populations, where they are often found as part of the normal microbiota of the oral, nasopharyngeal, and upper respiratory tracts. Many Pasteurella species are opportunistic pathogens that can cause endemic disease and are associated increasingly with epizootic outbreaks. Zoonotic transmission to humans usually occurs through animal bites or contact with nasal secretions, with P. multocida being the most prevalent isolate observed in human infections. Here we review recent comparative genomics and molecular pathogenesis studies that have advanced our understanding of the multiple virulence mechanisms employed by Pasteurella species to establish acute and chronic infections. We also summarize efforts being explored to enhance our ability to rapidly and accurately identify and distinguish among clinical isolates and to control pasteurellosis by improved development of new vaccines and treatment regimens.