Use of shell-vial cell culture assay for isolation of bacteria from clinical specimens: 13 years of experience

A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens

Infection with either Rickettsia prowazekii or Orientia tsutsugamushi is common, yet diagnostic capabilities are limited due to the short window for positive identification. Until now, although targeted enrichment had been applied to increase sensitivity of sequencing-based detection for various microorganisms, it had not been applied to sequencing of R. prowazekii in clinical samples. Additionally, hybridization-based targeted enrichment strategies had only scarcely been applied to qPCR of any pathogens in clinical samples. Therefore, we tested a targeted enrichment technique as a proof of concept and found that it dramatically reduced the limits of detection of these organisms by both qPCR and high throughput sequencing. The enrichment methodology was first tested in contrived clinical samples with known spiked-in concentrations of R. prowazekii and O. tsutsugamushi DNA. This method was also evaluated using clinical samples, resulting in the simultaneous identification and characterization of O. tsutsugamushi directly from clinical specimens taken from sepsis patients. We demonstrated that the targeted enrichment technique is helpful by lowering the limit of detection, not only when applied to sequencing, but also when applied to qPCR, suggesting the technique could be applied more broadly to include other assays and/or microbes for which there are limited diagnostic or detection modalities.

A rapid and low-cost platform for detection of bacterial based on microchamber PCR microfluidic chip

Polymerase chain reaction (PCR) has been considered as the gold standard for detecting nucleic acids. The simple PCR system is of great significance for medical applications in remote areas, especially for the developing countries. Herein, we proposed a low-cost self-assembled platform for microchamber PCR. The working principle is rotating the chamber PCR microfluidic chip between two heaters with fixed temperature to solve the problem of low temperature variation rate. The system consists of two temperature controllers, a screw slide rail, a chamber array microfluidic chip and a self-built software. Such a system can be constructed at a cost of about US$60. The micro chamber PCR can be finished by rotating the microfluidic chip between two heaters with fixed temperature. Results demonstrated that the sensitivity of the temperature controller is 0.1℃. The relative error of the duration for the microfluidic chip was 0.02 s. Finally, we successfully finished amplification of the target gene of Porphyromonas gingivalis in the chamber PCR microfluidic chip within 35 min and on-site detection of its PCR products by fluorescence. The chip consisted of 3200 cylindrical chambers. The volume of reagent in each volume is as low as 0.628 nL. This work provides an effective method to reduce the amplification time required for micro chamber PCR.

Signatures in in vitro infection of NSC-34 mouse neurons and their cell nucleus with Rickettsia helvetica

BACKGROUND

Rickettsia helvetica, a spotted fever rickettsia, is transmitted to humans via ticks in Europe, North Africa, and Asia. The central nervous system is a crucial target for rickettsial diseases, which has been reported for 12 of the 31 species, of which R. helvetica is one. This study aimed, in an experimental model, to identify characteristics of R. helvetica infection in a mouse neuronal cell line, NSC-34.

RESULTS

NSC-34, a fusion cell line of mouse motor spinal cord neurons and neuroblastoma cells, was used as a model. Propagation of R. helvetica in neurons was confirmed. Short actin tails were shown at the polar end of the bacteria, which makes it likely that they can move intracellularly, and even spread between cells. Another protein, Sca4, which with the cell adhesion protein vinculin enables the passage of the cell membrane, was expressed during infection. No significant increase in TNFα levels was seen in the infected neurons, which is of interest because TNFα protects the host cell from infection-induced apoptotic death which is crucial for host cell survival. The bacteria were also shown to invade and grow in the cell nucleus of the neuron.

CONCLUSIONS

The findings suggest that a R. helvetica infection may be harmful to NSC-34 neurons under these in vitro conditions, but the full effects of the infection on the cell need to be studied further, also on human neurons, to also understand the possible significance of this infection in relation to pathogenetic mechanisms.

Limitations of Serological Diagnosis of Typical Cat Scratch Disease and Recommendations for the Diagnostic Procedure

Introduction

Cat scratch disease (CSD) is the most common cause of bacterial infectious lymphadenopathy, especially in children, but its diagnosis still remains challenging. Serological assays are widely applied due to their simplicity and the non-invasive sampling. However, these techniques present several limitations, including not well-defined antigen preparation, assay conditions and cutoff titers, severe cross-reactions with other species and organisms, and the notably ranging seroprevalence in the normal population. The objective of this study is to review the literature in order to determine the best diagnostic procedure for the diagnosis of CSD.

Methods

Databases including PubMed, Medline, Google Scholar, and Google were searched to determine the best diagnostic procedure for the diagnosis of CSD. A total of 437 papers were identified and screened, and after exclusion of papers that did not fulfill the including criteria, 63 papers were used.

Results

It was revealed that sensitivities of serological assays varied from 10% to 100%. Indeed, more than half of the studies reported a sensitivity lower than 70%, while 71% of them had a sensitivity lower than 80%. Moreover, specificities of serological assays ranged from 15% to 100%, with 25 assays reporting a specificity lower than 90%.

Conclusion

It is considered that molecular assays should be the gold standard technique for CSD confirmation, and physicians are reinforced to proceed to lymph node biopsy in suspicious CSD cases.

Procedure for spotted fever group Rickettsia isolation from limited clinical blood specimens

BACKGROUND

Current isolation techniques for spotted fever group Rickettsia from clinical samples are laborious and are limited to tissue, blood and blood derivatives with volumes ideally greater than 1 mL. We validated the use of simplified methodologies for spotted fever group Rickettsia culture isolation that overcome sample volume limitations and provide utility in clinical diagnostics and research studies.

METHODOLOGY/PRINCIPAL FINDINGS

A modified cell culture method is evaluated for the isolation of Rickettsia ssp. from human diagnostic samples. Culture sampling method, culture platform, and growth phase analysis were evaluated to determine best practices for optimal culture isolation conditions. Rickettsial isolates (R. conorii, R. rickettsii, and R. parkeri) were grown in Vero E6 cells over a course of 5 to 7 days at low inoculum treatments (~40 bacterial copies) to standardize the sampling strategy at a copy number reflective of the bacteremia in acute diagnostic samples. This methodology was verified using small volumes (50 μL) of 25 unprocessed clinical whole blood, plasma, and serum samples from acute samples of patients suspected of having Rocky Mountain Spotted Fever, of which 10 were previously confirmed positive via the PanR8 qPCR assay, 13 had no detectable Rickettsia DNA by the PanR8 qPCR assay, and 2 were not previously tested; these samples resulted in the cultivation of 7 new R. rickettsii isolates.

CONCLUSIONS/SIGNIFICANCE

We observed that rickettsial isolate growth in culture is reproducibly identified by real-time PCR testing of culture media within 72 hours after inoculation. Additionally, specimen sedimentation prior to isolation to remove red blood cells was found to decrease the amount of total organism available in the inoculum. A small volume culture method was established focusing on comparative qPCR detection rather than bacterial visualization, taking significantly shorter time to detect, and requiring less manipulation compared to traditional clinical isolate culture methods.

Mediterranean Spotted Fever: Current Knowledge and Recent Advances

Mediterranean spotted fever (MSF) is an emerging tick-borne rickettsiosis of the spotted fever group (SFG), endemic in the Mediterranean basin. By virtue of technological innovations in molecular genetics, it has been determined that the causative agent of MSF is Rickettsia conorii subspecies conorii. The arthropod vector of this bacterium is the brown dog tick Rhipicephalus sanguineus. The true nature of the reservoir of R. conorii conorii has not been completely deciphered yet, although many authors theorize that the canine population, other mammals, and the ticks themselves could potentially contribute as reservoirs. Typical symptoms of MSF include fever, maculopapular rash, and a characteristic eschar (“tache noire”). Atypical clinical features and severe multi-organ complications may also be present. All of these manifestations arise from the disseminated infection of the endothelium by R. conorii conorii. Several methods exist for the diagnosis of MSF. Serological tests are widely used and molecular techniques have become increasingly available. Doxycycline remains the treatment of choice, while preventive measures are focused on modification of human behavior and vector control strategies. The purpose of this review is to summarize the current knowledge on the epidemiology, pathogenesis, clinical features, diagnosis, and treatment of MSF.

Expansion of Tick-Borne Rickettsioses in the World

Tick-borne rickettsioses are caused by obligate intracellular bacteria belonging to the spotted fever group of the genus Rickettsia. These infections are among the oldest known diseases transmitted by vectors. In the last three decades there has been a rapid increase in the recognition of this disease complex. This unusual expansion of information was mainly caused by the development of molecular diagnostic techniques that have facilitated the identification of new and previously recognized rickettsiae. A lot of currently known bacteria of the genus Rickettsia have been considered nonpathogenic for years, and moreover, many new species have been identified with unknown pathogenicity. The genus Rickettsia is distributed all over the world. Many Rickettsia species are present on several continents. The geographical distribution of rickettsiae is related to their vectors. New cases of rickettsioses and new locations, where the presence of these bacteria is recognized, are still being identified. The variety and rapid evolution of the distribution and density of ticks and diseases which they transmit shows us the scale of the problem. This review article presents a comparison of the current understanding of the geographic distribution of pathogenic Rickettsia species to that of the beginning of the century.

The Isolation of Orientia tsutsugamushi and Rickettsia typhi from Human Blood through Mammalian Cell Culture: a Descriptive Series of 3,227 Samples and Outcomes in the Lao People's Democratic Republic

In the Lao People’s Democratic Republic (Laos), rickettsial infections, including scrub and murine typhus, account for a significant burden of fevers. The Mahosot Hospital Microbiology Laboratory in Vientiane, Laos, routinely performs rickettsial isolation from hospitalized patients with suspected rickettsioses using mammalian cell culture systems. We review the clinical and laboratory factors associated with successful Orientia tsutsugamushi and Rickettsia typhi isolations from this laboratory over a period of 6 years between 2008 and 2014.

In the Lao People’s Democratic Republic (Laos), rickettsial infections, including scrub and murine typhus, account for a significant burden of fevers. The Mahosot Hospital Microbiology Laboratory in Vientiane, Laos, routinely performs rickettsial isolation from hospitalized patients with suspected rickettsioses using mammalian cell culture systems. We review the clinical and laboratory factors associated with successful Orientia tsutsugamushi and Rickettsia typhi isolations from this laboratory over a period of 6 years between 2008 and 2014. The overall isolation success was 7.9% for all samples submitted and 17.3% for samples for which the patient had a positive O. tsutsugamushi or R. typhi rapid diagnostic test (RDT), serology, or PCR. The frequency of successful isolation was highest for samples submitted in November, at the end of the wet season (28.3%). A longer median duration of reported illness, a positive result for a concurrent Orientia or Rickettsia spp. quantitative PCR, and the use of antibiotics by the patient in the week before admission were significantly associated with isolation success (P < 0.05). Buffy coat inoculation and a shorter interval between sample collection and inoculation in the laboratory were associated with a higher frequency of isolation (both P < 0.05). This frequency was highest if cell culture inoculation occurred on the same day as blood sample collection. Factors related to the initial rickettsial bacterial concentration are likely the main contributors to isolation success. However, modifiable factors do contribute to the rickettsial isolation success, especially delays in inoculating patient samples into culture.

Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country

Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries.

High-Content Screening, a Reliable System for Coxiella burnetii Isolation from Clinical Samples

Q fever, caused by Coxiella burnetii, is a worldwide zoonotic disease that may cause severe forms in humans and requires a specific and prolonged antibiotic treatment. Although current serological and molecular detection tools allow a reliable diagnosis of the disease, culture of C. burnetii strains is mandatory to assess their susceptibility to antibiotics and sequence their genome in order to optimize patient management and epidemiological studies. However, cultivating this fastidious microorganism is difficult and restricted to reference centers, as it requires biosafety level 3 laboratories and relies on cell culture performed by experienced technicians. In addition, the culture yield is low, which results in a small number of isolates being available. In this work, we developed a novel high-content screening (HCS) isolation strategy based on optimized high-throughput cell culture and automated microscopic detection of infected cells with specifically designed algorithms targeting cytopathic effects. This method was more efficient than the shell vial assay, at the level of time dependency, when applied to both frozen specimens (7 isolates recovered by HCS only, sensitivity 91% versus 78% for shell vial) and fresh samples (1 additional isolate using HCS, sensitivity 7% versus 5% for shell vial), for which most strains were recovered more rapidly with the new technique. In addition, detecting positive cultures by an automated microscope reduced the need for expertise and saved 24% of technician working time. Application of HCS to antibiotic susceptibility testing of 12 strains demonstrated that it was as efficient as the standard procedure that combines shell vial culture and quantitative PCR.

Coculture at the crossroads of the new microbiology techniques for the isolation of strict intracellular bacteria

Coculture played a major role in clinical microbiology by elucidating strict intracellular bacteria era. Since some of these bacteria are human pathogens, in-depth studies at the strain level are necessary to better understand their pathologies and treatment. Over the last decades, culture-independent tools have taken over the diagnostic procedure at the expense of coculture. These tools, although proven to be rapid and efficient, cannot overcome the need to culture the bacteria, as strain isolation remains a key factor to understanding its epidemiology, virulence and antibiotic susceptibility testing. Moreover, strain availability allows the development of molecular and serological tools, and remains crucial for taxonomy. This review revisits the current status of culture, its advantages, drawbacks and future needs.

Routine Culture-Resistant Mycobacterium tuberculosis Rescue and Shell-Vial Assay, France

We used shell-vial assay with a medium that buffered rifampin to isolate routine culture–resistant Mycobacterium tuberculosis bacteria from cerebrospinal fluid and rifampin-containing intervertebral disc and vertebral corpus of a patient in treatment for Pott’s disease and disseminated tuberculosis. Whole-genome sequencing confirmed M. tuberculosis lineage 4 (Euro-American) strain.

Whole-Genome Sequencing of Mycobacterium tilburgii Strain MEPHI

Mycobacterium tilburgii is a fastidious mycobacterium which has previously been reported to cause severe disseminated infections. Genome sequencing of the M. tilburgii MEPHI clinical isolate yielded 3.14 Mb, with 66.3% GC content, and confirmed phylogenetic placement within the Mycobacterium simiae complex.

A Concise Review of the Epidemiology and Diagnostics of Rickettsioses: Rickettsia and Orientia spp

Rickettsioses are globally distributed and caused by the family Rickettsiaceae, which comprise a diverse and expanding list of organisms. These include two genera, Rickettsia and Orientia Serology has been traditionally the mainstay of diagnosis, although this has been limited by cross-reactions among closely related members and diminished sensitivity/utility in the acute phase of illness. Other techniques, such as nucleic acid amplification tests using blood specimens or tissue swabs/biopsy specimens, sequencing, and mass spectrometry, have emerged in recent years for both pathogen and vector identification. This paper provides a concise review of the rickettsioses and the traditional and newer technologies available for their diagnosis.

Culturing the human microbiota and culturomics

The gut microbiota has an important role in the maintenance of human health and in disease pathogenesis. This importance was realized through the advent of omics technologies and their application to improve our knowledge of the gut microbial ecosystem. In particular, the use of metagenomics has revealed the diversity of the gut microbiota, but it has also highlighted that the majority of bacteria in the gut remain uncultured. Culturomics was developed to culture and identify unknown bacteria that inhabit the human gut as a part of the rebirth of culture techniques in microbiology. Consisting of multiple culture conditions combined with the rapid identification of bacteria, the culturomic approach has enabled the culture of hundreds of new microorganisms that are associated with humans, providing exciting new perspectives on host-bacteria relationships. In this Review, we discuss why and how culturomics was developed. We describe how culturomics has extended our understanding of bacterial diversity and then explore how culturomics can be applied to the study of the human microbiota and the potential implications for human health.

Coxiella burnetii Multilevel Disk Space Infection, Epidural Abscess, and Vertebral Osteomyelitis Secondary to Contiguous Spread From Infected Abdominal Aortic Aneurysm or Graft: Report of 4 Cases Acquired in the US and Review of the Literature

Background

Chronic Coxiella burnetii infections such as vertebral osteomyelitis caused by contiguous spread from an infected abdominal aortic graft or aneurysm have been rarely reported and are associated with significant morbidity and mortality.

Methods

We present the first four reported US acquired cases of Coxiella burnetii vertebral osteomyelitis caused by contiguous spread from an infected abdominal aortic graft or aneurysm.

Results

Presenting symptoms included progressive back pain, malaise, and weight loss with recent or remote animal exposure. Typical imaging findings demonstrated a peri-aortic collection with extension to the paraspinal muscles and vertebrae. Antibiotic regimens included doxycycline with either hydroxychloroquine or a quinolone for at least 2 years or as chronic suppression.

Conclusions

C. burnetii vertebral osteomyelitis is rare and can occur by contiguous spread from an abdominal aneurysm or vascular graft infection. It should be suspected in patients where pre-antibiotic cultures are negative with animal/farming exposure.

Case Report: Scalp Eschar and Neck Lymphadenopathy Associated with Bacteremia due to Coxiella-Like Bacteria

Coxiella-like bacteria have been recently proposed as human pathogens. Using molecular techniques, we detected Coxiella-like bacteria in the blood and serum samples of a patient with a scalp eschar, neck lymphadenopathy, severe urticaria, edema, fever, and arthralgia indicating that this organism can provide systemic complications.

Critical Aspects for Detection of Coxiella burnetii

Coxiella burnetii is a globally distributed zoonotic γ-proteobacterium with an obligatory intracellular lifestyle. It is the causative agent of Q fever in humans and of coxiellosis among ruminants, although the agent is also detected in ticks, birds, and various other mammalian species. Requirements for intracellular multiplication together with the necessity for biosafety level 3 facilities restrict the cultivation of C. burnetii to specialized laboratories. Development of a novel medium formulation enabling axenic growth of C. burnetii has facilitated fundamental genetic studies. This review provides critical insights into direct diagnostic methods currently available for C. burnetii. It encompasses molecular detection methods, isolation, and propagation of the bacteria and its genetic characterization. Differentiation of C. burnetii from Coxiella-like organisms is an essential diagnostic prerequisite, particularly when handling and analyzing ticks.

Guidelines for the Detection of Rickettsia spp

The genus Rickettsia (Rickettsiales: Rickettsiaceae) includes Gram-negative, small, obligate intracellular, nonmotile, pleomorphic coccobacilli bacteria transmitted by arthropods. Some of them cause human and probably also animal disease (life threatening in some patients). In these guidelines, we give clinical practice advices (microscopy, serology, molecular tools, and culture) for the microbiological study of these microorganisms in clinical samples. Since in our environment rickettsioses are mainly transmitted by ticks, practical information for the identification of these arthropods and for the study of Rickettsia infections in ticks has also been added.

Bartonella henselae is usually not viable in lymph nodes of patients with cat scratch disease

Bartonella henselae, the agent of cat scratch disease (CSD), appears to be a common organism responsible for lymphadenitis in both adults and children. There is a very low isolation rate for B. henselae from lymph nodes of patients with CSD. Our objective was to evaluate B. henselae viability in a large series of lymph nodes from patients with CSD. From January to November 2016, we analyzed lymph node biopsy samples from patients diagnosed with CSD. We used reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect B. henselae RNA, as well as cultures, histological analyses, and fluorescence in situ hybridization (FISH). We tested 87 lymph nodes positive for B. henselae DNA but only 8 (9%) presented with B. henselae RNA. We did not find a significant difference for the pap threshold cycle (C_T) values between RNA-positive and RNA-negative lymph nodes (p = 0.5). Cultures, histological analyses, and FISH were negative for all the tested samples. We provide evidence that B. henselae are not or are rarely viable in most cases in the lymph nodes of patients with CSD.

From Q Fever to Coxiella burnetii Infection: a Paradigm Change

Coxiella burnetii is the agent of Q fever, or "query fever," a zoonosis first described in Australia in 1937. Since this first description, knowledge about this pathogen and its associated infections has increased dramatically. We review here all the progress made over the last 20 years on this topic. C. burnetii is classically a strict intracellular, Gram-negative bacterium. However, a major step in the characterization of this pathogen was achieved by the establishment of its axenic culture. C. burnetii infects a wide range of animals, from arthropods to humans. The genetic determinants of virulence are now better known, thanks to the achievement of determining the genome sequences of several strains of this species and comparative genomic analyses. Q fever can be found worldwide, but the epidemiological features of this disease vary according to the geographic area considered, including situations where it is endemic or hyperendemic, and the occurrence of large epidemic outbreaks. In recent years, a major breakthrough in the understanding of the natural history of human infection with C. burnetii was the breaking of the old dichotomy between "acute" and "chronic" Q fever. The clinical presentation of C. burnetii infection depends on both the virulence of the infecting C. burnetii strain and specific risks factors in the infected patient. Moreover, no persistent infection can exist without a focus of infection. This paradigm change should allow better diagnosis and management of primary infection and long-term complications in patients with C. burnetii infection.

Rickettsia sibirica mongolitimonae Infection, France, 2010-2014

To further characterize human infections caused by Rickettsia sibirica mongolitimonae, we tested skin biopsy and swab samples and analyzed clinical, epidemiologic, and diagnostic characteristics of patients with a rickettsiosis. The most common (38%) indigenous species was R. sibirica mongolitimonae. Significantly more cases of R. sibirica mongolitimonae infection occurred during spring and summer.

Candidatus Coxiella massiliensis Infection

Bacteria genetically related to Coxiella burnetii have been found in ticks. Using molecular techniques, we detected Coxiella-like bacteria, here named Candidatus Coxiella massiliensis, in skin biopsy samples and ticks removed from patients with an eschar. This organism may be a common agent of scalp eschar and neck lymphadenopathy after tick bite.

Treatment and Prophylactic Strategy for Coxiella burnetii Infection of Aneurysms and Vascular Grafts: A Retrospective Cohort Study

Coxiella burnetii vascular infections continue to be very severe diseases and no guidelines exist about their prevention. In terms of treatment, the benefit of the surgical removal of infected tissues has been suggested by 1 retrospective study.We present a case of a C burnetii abdominal aortic graft infection for which we observed a dramatic clinical and biological recovery after surgery. We thus performed a retrospective cohort study to evaluate the impact of surgery on survival and serological outcome for patients with Q fever vascular infections diagnosed in our center.Between 1986 and February 2015, 100 patients were diagnosed with Q fever vascular infections. The incidence of these infections has significantly increased over the past 5 years, in comparison with the mean annual incidence over the preceding 22 years (8.83 cases per year versus 3.14 cases per year, P = 0.001). A two-and-a-half-year follow-up was available for 66 patients, of whom 18.2% died. We observed 6.5% of deaths in the group of patients who were operated upon at 2 and a half years, in comparison with 28.6% in the group which were not operated upon (P = 0.02). Surgery was the only factor that had a positive impact on survival at 2 and a half years using univariate analysis [hazard ratio: 0.17 [95% CI]: [0.039-0.79]; P = 0.024]. Surgery was also associated with a good serological outcome (74.1% vs 57.1% of patients, P = 0.03). In the group of patients with vascular graft infections (n = 47), surgery had a positive impact on serological outcome at 2 and a half years (85.7% vs 42.9%, P < 0.001) [hazard ratio: 0.40 [95% CI]: [0.17-098]; P = 0.046] and tended to be associated with lower although not statistically significant mortality (11.1% vs 27.6% of deaths, P = 0.19).Surgical treatment confers a benefit in terms of survival following C burnetii vascular infections. However, given the high mortality of these infections and their rising incidence, we propose a strategy that consists of screening for vascular graft and aneurysms in the context of primary Q fever, to decide when to start prophylactic treatment, similar to the strategy recommended for the prophylaxis of Q fever endocarditis.

Strategies for detecting rickettsiae and diagnosing rickettsial diseases

Rickettsial diseases and scrub typhus constitute a group of the oldest known vector-borne diseases. The cosmopolitan distribution of the vectors that transmit rickettsiae and orientiae leads to a worldwide prevalence of these diseases. Despite their significant historical status, detection and diagnosis of these diseases are still evolving today. Serological methods remain among the most prevalent techniques used for the detection/diagnosis of rickettsial diseases and scrub typhus. Molecular techniques have been instrumental in increasing the sensitivity/specificity of diagnosis, identifying new Rickettsia and Orientia species and have enhanced epidemiological capabilities when used in combination with serological methods. In this review, we discuss these techniques and their associated pros and cons.

A comprehensive repertoire of prokaryotic species identified in human beings

The compilation of the complete prokaryotic repertoire associated with human beings as commensals or pathogens is a major goal for the scientific and medical community. The use of bacterial culture techniques remains a crucial step to describe new prokaryotic species. The large number of officially acknowledged bacterial species described since 1980 and the recent increase in the number of recognised pathogenic species have highlighted the absence of an exhaustive compilation of species isolated in human beings. By means of a thorough investigation of several large culture databases and a search of the scientific literature, we built an online database containing all human-associated prokaryotic species described, whether or not they had been validated and have standing in nomenclature. We list 2172 species that have been isolated in human beings. They were classified in 12 different phyla, mostly in the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. Our online database is useful for both clinicians and microbiologists and forms part of the Human Microbiome Project, which aims to characterise the whole human microbiota and help improve our understanding of the human predisposition and susceptibility to infectious agents.

The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota

Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.

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.

Looking in ticks for human bacterial pathogens

Ticks are considered to be second worldwide to mosquitoes as vectors of human diseases and the most important vectors of disease-causing pathogens in domestic and wild animals. A number of emerging tick-borne pathogens are already discovered; however, the proportion of undiagnosed infectious diseases, especially in tropical regions, may suggest that there are still more pathogens associated with ticks. Moreover, the identification of bacteria associated with ticks may provide new tool for the control of ticks and tick-borne diseases. Described here molecular methods of screening of ticks, extensive use of modern culturomics approach, newly developed artificial media and different cell line cultures may significantly improve our knowledge about the ticks as the agents of human and animal pathology.

Bacterial lymphadenitis at a major referral hospital in France from 2008 to 2012

Lymph node enlargement is a common medical problem, and in a large number of patients, the causes of lymphadenopathy remain undiagnosed. We report a thorough microbiological analysis of 1,688 lymph node biopsy specimens collected in our bartonellosis reference center. We studied lymph node biopsy samples from patients with suspected regional infectious lymph node enlargement from January 2008 to December 2012. To evaluate a useful strategy for the diagnosis of infectious lymphadenitis, specimens were cultured and subjected to molecular assays. Histologic analysis was done when possible. A total of 642 (38%) biopsy specimens were infected with a bacterial agent, and quantitative PCR (qPCR) was significantly better than 16S rRNA gene PCR (rrs) for the detection of Bartonella henselae (P = 0.05), Mycobacterium tuberculosis (P = 0.05), and Mycobacterium avium (P = 0.007). Molecular assays were significantly better than bacterial cultures for the diagnosis of Francisella tularensis (P = 0.017) but were less effective for detecting M. tuberculosis (P = 0.004) and M. avium (P = 0.001). Histologic analysis was done for 412 lymph nodes, and 20% of these were compatible with an infectious lymphadenitis, whereas a neoplasm was found in 29% of these lymph nodes. M. tuberculosis was detected significantly more in female than in male patients (P = 0.01), and patients with cat scratch disease (CSD) were younger than patients with M. tuberculosis, Tropheryma whipplei, and F. tularensis. Negative rrs PCR does not exclude the diagnosis of infectious lymphadenitis. Histologic analysis of lymph node biopsy specimens is critical, as a diagnosis of infectious lymphadenitis does not preclude other concurrent diseases.

Modern clinical microbiology: new challenges and solutions

In the twenty-first century, the clinical microbiology laboratory plays a central part in optimizing the management of infectious diseases and surveying local and global epidemiology. This pivotal role is made possible by the adoption of rational sampling, point-of-care tests, extended automation and new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and versatile and permissive culture systems. When balanced with cost, these developments can improve the workflow and output of clinical microbiology laboratories and, by identifying and characterizing microbial pathogens, provide significant input to scientific discovery.

Cell extract-containing medium for culture of intracellular fastidious bacteria

The culture of fastidious microorganisms is a critical step in infectious disease studies. As a proof-of-concept experiment, we evaluated an empirical medium containing eukaryotic cell extracts for its ability to support the growth of Coxiella burnetii. Here, we demonstrate the exponential growth of several bacterial strains, including the C. burnetii Nine Mile phase I and phase II strains, and C. burnetii isolates from humans and animals. Low-oxygen-tension conditions and the presence of small hydrophilic molecules and short peptides were critical for facilitating growth. Moreover, bacterial antigenicity was conserved, revealing the potential for this culture medium to be used in diagnostic tests and in the elaboration of vaccines against C. burnetii. We were also able to grow the majority of previously tested intracellular and fastidious bacterial species, including Tropheryma whipplei, Mycobacterium bovis, Leptospira spp., Borrelia spp., and most putative bioterrorism agents. However, we were unable to culture Rickettsia africae and Legionella spp. in this medium. The versatility of this medium should encourage its use as a replacement for the cell-based culture systems currently used for growing several facultative and putative intracellular bacterial species.

Coxiella burnetii DNA, but not viable bacteria, in dairy products in France

Transmission by the oral route of Coxiella burnetii is controversial. Our objective was to evaluate dairy products in the transmission of Q fever. Pasteurized, unpasteurized, and thermized dairy products were tested for C. burnetii by using a quantitative polymerase chain reaction specific for IS1111 and IS30A spacers, culturing in human embryonic lung fibroblasts cells, and inoculation into BALB/c mice. We tested 201 products and C. burnetii was identified in 64%. Cow milk origin products were more frequently positive than goat or ewe products (P = 0.006 and P = 0.0001, respectively), and industrial food was more frequently positive than artisanal food (P < 0.0001). Food made from unpasteurized milk contained higher bacteria concentrations than food made from pasteurized milk (P = 0.02). All cultures were negative and mice did not show signs of illness. Farm animals are highly infected in France but consumption of cheese and yogurt does not seem to pose a public health risk for transmission of Q fever.

A case of Q fever prosthetic joint infection and description of an assay for detection of Coxiella burnetii

We present the first published case of Coxiella burnetii prosthetic joint infection. Diagnosis was established with PCR and culture of periprosthetic tissue and synovial fluid (and serology). A novel PCR assay is described herein. Q fever should be considered in patients with prosthetic joint infection without an identified pathogen.

Comparison of real-time quantitative PCR and culture for the diagnosis of emerging Rickettsioses

Background

Isolation of Rickettsia species from skin biopsies may be replaced by PCR. We evaluated culture sensitivity compared to PCR based on sampling delay and previous antibiotic treatment.

Methodology/Principal Findings

Skin biopsies and ticks from patients with suspected Rickettsia infection were screened for Rickettsia spp. using qPCR, and positive results were amplified and sequenced for the gltA and ompA genes. Immunofluorescence for spotted fever group rickettsial antigens was done for 79 patients. All skin biopsies and only ticks that tested positive using qPCR were cultured in human embryonic lung (HEL) fibroblasts using the centrifugation-shell vial technique. Patients and ticks were classified as definitely having rickettsioses if there was direct evidence of infection with a Rickettsia sp. using culture or molecular assays or in patients if serology was positive. Data on previous antibiotic treatments were obtained for patients with rickettsiosis. Rickettsia spp. infection was diagnosed in 47 out of 145 patients (32%), 41 by PCR and 12 by culture, whereas 3 isolates were obtained from PCR negative biopsies. For 3 of the patients serology was positive although PCR and culture were negative. Rickettsia africae was the most common detected species (n = 25, [17.2%]) and isolated bacterium (n = 5, [3.4%]). The probability of isolating Rickettsia spp. was 12 times higher in untreated patients and 5.4 times higher in patients from our hometown. Rickettsia spp. was amplified in 24 out of 95 ticks (25%) and we isolated 7 R. slovaca and 1 R. raoultii from Dermacentor marginatus.

Conclusions/Significance

We found a positive correlation between the bacteria copies and the isolation success in skin biopsies and ticks. Culture remains critical for strain analysis but is less sensitive than serology and PCR for the diagnosis of a Rickettsia infection.

Diagnosis of Rickettsia infection would benefit by use of the more rapid and sensitive method of quantitative real-time PCR than the time-intensive and less sensitive method of culturing Rickettsia species from skin biopsies. We evaluated culture sensitivity compared to PCR according to sampling delay and previous antibiotic treatment. We found that skin biopsies can be positive even when molecular tests were negative, and a negative result using molecular assays did not exclude the diagnosis of Rickettsia spp. infection. Rickettsia africae was the most common species in skin biopsies and R. slovaca was most common in ticks. We found a positive correlation between the number of bacteria copies and the isolation success in skin biopsies and ticks. The probability of isolating Rickettsia spp. was higher in untreated patients and in patients from our hometown. To increase the sensitivity of culture, skin biopsies should be sampled before treatment early in the course of the disease and should be inoculated as soon as possible.

Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology

Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.

Isolation from animal tissue and genetic transformation of Coxiella burnetii are facilitated by an improved axenic growth medium

We recently described acidified citrate cysteine medium (ACCM), which supports host cell-free (axenic) growth of Coxiella burnetii. After 6 days of incubation, greater than 3 logs of growth was achieved with the avirulent Nine Mile phase II (NMII) strain. Here, we describe modified ACCM and culture conditions that support improved growth of C. burnetii and their use in genetic transformation and pathogen isolation from tissue samples. ACCM was modified by replacing fetal bovine serum with methyl-β-cyclodextrin to generate ACCM-2. Cultivation of NMII in ACCM-2 with moderate shaking and in 2.5% oxygen yielded 4 to 5 logs of growth over 7 days. Similar growth was achieved with the virulent Nine Mile phase I and G isolates of C. burnetii. Colonies that developed after 6 days of growth in ACCM-2 agarose were approximately 0.5 mm in diameter, roughly 5-fold larger than those formed in ACCM agarose. By electron microscopy, colonies consisted primarily of the C. burnetii small cell variant morphological form. NMII was successfully cultured in ACCM-2 when medium was inoculated with as little as 10 genome equivalents contained in tissue homogenates from infected SCID mice. A completely axenic C. burnetii genetic transformation system was developed using ACCM-2 that allowed isolation of transformants in about 2 1/2 weeks. Transformation experiments demonstrated clonal populations in colonies and a transformation frequency of approximately 5 × 10(-5). Cultivation in ACCM-2 will accelerate development of C. burnetii genetic tools and provide a sensitive means of primary isolation of the pathogen from Q fever patients.

Shell vial cell culture as a tool for Streptobacillus moniliformis "resuscitation"

Streptobacillus moniliformis is a fastidious growing Gram-negative bacillus responsible of rat-bite fever. We describe here the first report of this disease in la Réunion and the first isolation using shell vial cell culture from a blood culture bottle with a bacterium suspected to be dead.

Bartonella henselae in skin biopsy specimens of patients with cat-scratch disease

During the past 2 years, we identified live Bartonella henselae in the primary inoculation sites of 3 patients after a cat scratch. Although our data are preliminary, we report that a cutaneous swab of the skin lesion from a patient in the early stage of cat-scratch disease can be useful for diagnosis of the infection.

Combining culture techniques for Bartonella: the best of both worlds

In this study we compared some common Bartonella culturing methodologies using four diverse species causing human illnesses. Based on a review of the literature, we focused on three major inconsistencies between protocols: base medium, cell coculture, and temperature. Our data showed that Bartonella tamiae demonstrated temperature-dependent growth limitations between common culturing conditions only 2°C apart. Additionally, growth of B. quintana was significantly enhanced by the presence of mammalian cell coculture under mammalian cell culture conditions; however, when the medium was modified to incorporate insect cell culture-based medium, coculturing with mammalian cells was no longer needed. In this study, we were able to overcome these temperature- and cell-dependent limitations and accommodate all of the strains tested by combining mammalian cell culture-based medium with insect cell culture-based medium.