Paleoserological detection of Coronavirus antigens in dental calculus of human remains dating from the beginning of the 19th century, French Ardennes

OBJECTIVE

Vanishing viral RNA restricts our ability to detect ancient pathogens, so, we used paleo serological approaches to trace the dynamics of the Coronavirus in ancient populations.

MATERIALS AND METHODS

We investigated 10 ancient dental calculus samples collected from a cemetery dated to the beginning of the 19th century and excavated in Charleville-Mézières. After paleoserum samples were extracted from dental calculus, paleoserology using mini-line-blot incorporating one alpha-Coronavirus (Coronavirus 229 E) and two beta-Coronavirus (Coronavirus OC 43, SARS-CoV-2) antigens and controls was completed by an automated Western blotting assay.

RESULTS

Once appropriate controls had validated the data, mini-line-blot detected antibodies against the two beta-Coronavirus antigens in individuals US1300 and US1339, automated Western blotting confirming one beta-Coronavirus antigen for individual US1300 and an additional individual US1326.

DISCUSSION

Combing mini-line blot and automated Western blot assays made it possible to detect immunoreactive immunoglobulin tracing circulation of Coronavirus in France at the very beginning of the 19th century.

PPE Barcoding Identifies Biclonal Mycobacterium ulcerans Buruli Ulcer, Côte d'Ivoire

Mycobacterium ulcerans, an environmental opportunistic pathogen, causes necrotic cutaneous and subcutaneous lesions, named Buruli ulcers, in tropical countries. PCR-derived tests used to detect M. ulcerans in environmental and clinical samples do not allow one-shot detection, identification, and typing of M. ulcerans among closely related Mycobacterium marinum complex mycobacteria. We established a 385-member M. marinum/M. ulcerans complex whole-genome sequence database by assembling and annotating 341 M. marinum/M. ulcerans complex genomes and added 44 M. marinum/M. ulcerans complex whole-genome sequences already deposited in the NCBI database. Pangenome, core genome, and single-nucleotide polymorphism (SNP) distance-based comparisons sorted the 385 strains into 10 M. ulcerans taxa and 13 M. marinum taxa, correlating with the geographic origin of strains. Aligning conserved genes identified one PPE (proline-proline-glutamate) gene sequence to be species and intraspecies specific, thereby genotyping the 23 M. marinum/M. ulcerans complex taxa. PCR sequencing of the PPE gene correctly genotyped nine M. marinum/M. ulcerans complex isolates among one M. marinum taxon and three M. ulcerans taxa in the African taxon (T2.4). Further, successful PPE gene PCR sequencing in 15/21 (71.4%) swabs collected from suspected Buruli ulcer lesions in Côte d'Ivoire exhibited positive M. ulcerans IS2404 real-time PCR and identified the M. ulcerans T2.4.1 genotype in eight swabs and M. ulcerans T2.4.1/T2.4.2 mixed genotypes in seven swabs. PPE gene sequencing could be used as a proxy for whole-genome sequencing for the one-shot detection, identification, and typing of clinical M. ulcerans strains, offering an unprecedented tool for identifying M. ulcerans mixed infections. IMPORTANCE We describe a new targeted sequencing approach that characterizes the PPE gene to disclose the simultaneous presence of different variants of a single pathogenic microorganism. This approach has direct implications on the understanding of pathogen diversity and natural history and potential therapeutic implications when dealing with obligate and opportunistic pathogens, such as Mycobacterium ulcerans presented here as a prototype.

CRISPR-Based Detection, Identification and Typing of Mycobacterium tuberculosis Complex Lineages

The polymerase chain reaction (PCR)-based detection of Mycobacterium tuberculosis (M. tuberculosis) complex (MTC) in clinical samples is a first-line approach by which to diagnose tuberculosis in clinical microbiology laboratories. In this study, the genome-wide profiling of 3,156 mycobacterial genomes using Roary determined the CRISPR-csm4 gene as specific for MTB. Real time (RT)-PCR and the PCR-sequencing of CRISPR-csm4, tested on a collection of 20 MTC and 5 nontuberculous mycobacteria, confirmed the 20 MTC isolates, whereas the 5 nontuberculous isolates were not detected. Further, 65 of the leftover clinical samples, including 25 GeneXpert-positive and 40 GeneXpert-negative samples, that were used to evaluate the CRISPR-csm4-MTB assay in the clinical microbiology laboratory setting yielded expected results in every case, further allowing for the identification of the M. tuberculosis Beijing lineage. RT-PCR and the PCR-sequencing of CRISPR-csm4 could be implanted in the clinical microbiology laboratory to complement the currently used assays, with the potential of increasing the specification of the MTC pathogens responsible for tuberculosis. IMPORTANCE The whole-genome sequence comparison of the Mycobacterium tuberculosis complex (MTC) genomic sequences that are available in the NCBI database identified a unique, specific gene to be used directly on clinical diagnostic samples to detect MTC against all species of mycobacteria and to differentiate between MTC species, lineages, and sublineages.

Introducing clinical nanorachaeaology: Isolation by co-culture of Nanopusillus massiliensis sp. nov

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The first ever detection in human microbiota of nanoarchaea.

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Detection and co-isolation of nanoarchaea new species in human oral microbiota.

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These data suggest the contribution of methanogens to the perinatal development of intestinal microbiota and physiology.

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Extended our knowledge of human microbiota diversity.

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Opening a new field of research in clinical microbiology here referred to as clinical nanoarchaeology.

Background

Nanoarchaeota, obligate symbiont of some environmental archaea with reduced genomes, have been described in marine thermal vent environments, yet never detected in hosts, including humans.

Methods

Here, using laboratory tools geared towards the detection of nanoarchaea including PCR-sequencing, WGS, microscopy and culture.

Results

We discovered a novel nanoarchaea, Nanopusillus massiliensis, detected in dental plate samples by specific PCR-based assays. Combining fluorescent in situ hybridization (FISH) with scanning electron microscopy disclosed close contacts between N. massiliensis and the archaea Methanobrevibacter oralis in these samples. Culturing one sample yielded co-isolation of M. oralis and N. massiliensis with a 606,935-bp genome, with 23.6% GC encoded 16 tRNA, 3 rRNA and 942 coding DNA sequences, of which 400 were assigned to clusters of orthologous groups.

Conclusion

The discovery of N. massiliensis, made publicly available in collection, extended our knowledge of human microbiota diversity, opening a new field of research in clinical microbiology here referred to as clinical nanoarchaeology.

Detection of methanogens in peri-appendicular abscesses: Report of four cases

The aetiology of appendicular abscess is predominantly microbial with aerobic and anaerobic bacteria from gut flora. In this study, by using specific laboratory tools, we co-detected Methanobrevibacter oralis and Methanobrevibacter smithii among a mixture of enterobacteria including Escherichia coli, Enterococcus faecium and Enterococcus avium in four unrelated cases of postoperative appendiceal abscesses. These unprecedented observations raise a question on the role of methanogens in peri-appendicular abscesses, supporting antibiotics as an alternative therapeutic option for appendicitis, including antibiotics active against methanogens such as metronidazole or fusidic acid.

Methanobrevibacter smithii tonsillar phlegmon: a case report

Untreated tonsillar phlegmon is a life-threatening condition commonly caused by Streptococcus pyogenes and Fusobacterium necrophorum, among other pathogens. Here, using specific laboratory tools, we detected Methanobrevibacter smithii in addition to S. pyogenes. This unprecedented observation questions the role of methanogens in phlegmon and the optimal treatment of this mixed infection.

The puzzle of the evolutionary natural history of tuberculosis

Several pieces of the puzzle of the natural history of tuberculosis are assembled in this review to illustrate the potential reservoirs and sources of the Mycobacterium tuberculosis complex (MTBC) mycobacteria, their transmission to animals and humans, and their fate in populations, in a co-evolutionary perspective. Millennia-old companions of mammalian and human populations, MTBC are detected in the soil, in which they infect and survive within vegetative amoebae and cysts, except for Mycobacterium canettii. Never detected in the sphere of plants, they are transmissible by transcutaneous, digestive and respiratory routes and cause an infection of the lymphatic system with secondary dissemination in most tissues, in which they determine a specific and non-pathognomonic granulomatous inflammatory reaction; in which MTBC survives in dormant form irrespective of MTBC species and mammalian species; indicating that the current epidemiology in mammalian populations is essentially governed by the probabilities of contact between mammalian species and MTBC species. Individual variabilities in clinical expression of tuberculosis are related to MTBC species, strain and inoculum; host genetic factors; acquired modulations of the inflammatory response; and probably human microbiota. This review of the literature suggests an evolutionary natural history of telluric environmental mycobacteria, satellites of unicellular eukaryotes, transmissible to mammals via the digestive and then respiratory tracts, in which they determine a fatal contagious infection that is primarily lymphatic and a quiescence-mimicking encysted form. This review opens perspectives for microbiological and translational medical research.

Preventing contamination of PCR-based multiplex assays including the use of a dedicated biosafety cabinet

We retrospectively investigated cases of false-positive diagnoses using the BIOFIRE® FilmArray® meningitis/encephalitis (ME) panel to measure the impact of using a dedicated biosafety cabinet combined with preventive measures to reduce the prevalence of false-positive diagnoses due to pre-analytical in-laboratory contamination. False-positive results were identified by reviewing clinical data, biological parameters and cytology results of cerebrospinal fluid (CSF) samples showing discrepant results between the FilmArray ME panel and routine PCR assays. A total of 327 CSF were analysed over 16 weeks in point-of-care (POC) A and B, over two 8-week periods, periods 1 and 2. The analysis yielded 30 (9·17%) detection of at least one pathogen including 21/30 (70%) viruses and 9/30 (30%) bacteria. During period 1, POC-A and POC-B manipulated CSF under a non-dedicated hood featuring laminar flow, whereas during period 2, CSFs were manipulated under a dedicated biosafety cabinet without any airflow in POC-A. During period 1, false positives were detected in 3/114 CSF (2·63%) in POC-A and 1/36 (2·77%) in POC-B (P = 0·97); during period 2, false positives were detected in 0/139 CSF (0%) in POC-A and 1/38 (2·63%) in POC-B (P = 0·23). All false positives were bacterial. The use of a dedicated cabinet without ventilation along with preventive measures during period 2 in POC-A significantly reduced the number of false-positive results (P = 0·05). Preventive measures described in this study can mitigate false positives when using PCR-based multiplex assays such as the BIOFIRE FilmArray ME Panel for the diagnosis of meningitis and other infectious diseases.

Yersinia pestis: the Natural History of Plague

The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.

Digestive tract methanodrome: Physiological roles of human microbiota-associated methanogens

Methanogens are the archaea most commonly found in humans, in particular in the digestive tract and are an integral part of the digestive microbiota. They are present in humans from the earliest moments of life and represent the only known source of methane production to date. They are notably detected in humans by microscopy, fluorescent in situ hybridization, molecular biology including PCR-sequencing, metagenomics, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and culture. Methanogens present in the human digestive tract play major roles, in particular the use of hydrogen from the fermentation products of bacteria, thus promoting digestion. They are also involved in the transformation of heavy metals and in the use of trimethylamine produced by intestinal bacteria, thus preventing major health problems, in particular cardiovascular diseases. Several pieces of evidence suggest their close physical contacts with bacteria support symbiotic metabolism. Their imbalance during dysbiosis is associated with many pathologies in humans, particularly digestive tract diseases such as Crohn's disease, ulcerative colitis, diverticulosis, inflammatory bowel disease, irritable bowel syndrome, colonic polyposis, and colorectal cancer. There is a huge deficit of knowledge and partially contradictory information concerning human methanogens, so much remains to be done to fully understand their physiological role in humans. It is necessary to develop new methods for the identification and culture of methanogens from clinical samples. This will permit to isolate new methanogens species as well as their phenotypic characterization, to explore their genome by sequencing and to study the population dynamics of methanogens by specifying in particular their exact role within the complex flora associated with the mucous microbiota of human.

Enorma burkinafasonensis sp. nov., a new bacterium isolated from a human gut microbiota

Strain Marseille-P9525^T is a Gram-positive, obligatory anaerobic and non-motile bacterium isolated from a human faecal micobiota. Its phenotypic pattern, including mass spectrometry peptide profile and genome sequence, support the proposal of a new species for which the name Enorma burkinafasonensis sp. nov. is proposed. The type strain has been deposited in a public collection.

333018F-Fluorodeoxyglucose Positron Emission Tomography Computed Tomography (PET/CT) for the diagnosis of prosthetic valve infective endocarditis (PVIE): a prospective multicenter study

Background and objectives

18F-FDG PET/CT has recently been added as a major criterion in the ESC 2015 infective endocarditis (IE) guidelines, but the value of this new diagnostic algorithm has never been prospectively assessed.

Purposes

1. Primary objective: to assess the value of the new ESC criteria including 18F-FDG PET/CT in prosthetic valve infective endocarditis (PVIE).

2. Secondary objectives: to determine the reproducibility of 18F-FDG PET/CT; to assess its ability to predict embolic events.

Methods

Between 2014 and 2017, 175 patients with suspected PVIE were prospectively included in 3 French centers. After exclusion of patients with uninterpretable or not feasible PET/CT,115 patients were finally included in the analysis, including 91 definite IE and 24 rejected IE, as defined by an expert Consensus of Endocarditis Team after 3-month follow-up as Gold Standard

Nuclear data were blindly analyzed by two independent nuclear medicine physicians.

Patients follow-up was scheduled at one and three months after hospitalization

Results

Significant cardiac uptake by PET/CT (major criterion) was observed in 67 among 91 patients with definite PVIE and 6 patients with rejected IE (sensitivity 73.6%, specificity 75%, positive predictive value 91%, negative predictive value 42%). Considering cardiac uptake as a major criterion, the ESC 2015 classification increased the sensitivity of Duke criteria from 57 to 84% (p<0.001) but decreased its specificity from 84 to 70% (p<0.001).

Intraobserver reproducibility of cardiac uptake evaluation was good (kappa = 0.84) but inter observer reproductibility was less satisfactory (kappa = 0.63).

Embolic events occurred in 31 patients (27%) and were correlated with vegetation size by ECHO (p<0.001), Staphylococcus infection (p=0.003), and PET/CT cardiac uptake (p=0.02).

Conclusion

1. the value of PET CT and ESC criteria is confirmed and may allow earlier diagnosis of PVIE

2. PET CT is associated with an increased risk of false positive results probably related to the technical improvements

3. Reproducibility of nuclear measurements seems unsatisfactory, justifying efforts to standardize PET studies interpretation

4. Our study describes for the first time a positive correlation between a positive PET/Ct and occurrence of embolic events, warranting additional studies.

P2760Prognostic value of 18-fluorodeoxyglucose positron emission tomography/computed tomography in infective endocarditis

Background

18-Fluorodeoxyglucose Positron emission tomography (18F-FDG PET/CT) has been shown to be useful for the diagnosis of IE, but its prognostic value is unknown.

Objectives

This study sought to assess the prognostic value of 18F-FDG PET/CT in prosthetic (PVE) and native valve endocarditis (NVE).

Methods

We prospectively studied 173 consecutive patients (109 PVE and 64 NVE) with definite IE who underwent a 18F-FDG PET/CT study and were follow-up for one year. Primary end-point was a composite of major cardiac events i.e. death, recurrence of IE, acute cardiac failure, non-scheduled hospitalization for cardiovascular reason, and new embolic event

Results

18F-FDG PET/CT was positive in 98 (57%) patients, 82% (n=88/109) in the PVE and 16% (n=10/64) in the NVE group. At a mean follow of 225±18 days, the primary end-point occurred in 94 (55%) patients, 63 (58%) in the PVE group and 31 (48%) in the NVE group. In the PVE group, positive 18F-FDG PET/CT was significantly associated with higher rate of primary end-point (OR=2.6, IC95%=1.04 to 6.6; p=0.04). Moderate to intense 18F-FDG valvular uptake was also associated with worse outcome (OR=2.1; IC95%=1.1 to 4.0; p=0.03) and to new embolic events, (OR: 8.8; IC95%= 1.1 to 69.5; p=0.02). In the NVE group, 18F-FDG PET/CT was not associated with occurrence of the primary end-point.

Conclusion

In addition to be an accurate diagnostic tool, 18F-FDG PET/CT is predictive of major cardiac events in PVE and to embolic events during the first year following IE episode

Naming microorganisms: the contribution of the IHU Méditerranée Infection, Marseille, France

The number of isolated new microorganisms has dramatically increased after the readaption of culture using the culturomics approach. Each of these microorganisms is deposited in an international strain collection institute, with its name being attributed and published by the scientist who isolated it. The attributed name is of Latin or Latinized origin and chosen on the basis of the geographical location of the sample collection, the institute or geographical region where the project was being performed, the name of a concerned scientist, and characteristics of the sample or the microorganism. Our institution has played an important role in the isolation of new microorganisms, with the first effort reporting 468 new bacterial species (3% of the bacterial species isolated at least once worldwide) and 327 species isolated for the first time from human beings, which in turn resulted in an increase of 30% of the total number of microorganisms isolated. Additionally, more than 100 giant viruses, including seven new species, have been isolated at our institute. In the present work, after recalling the rules of nomenclature, we detail the naming of the new microorganisms chosen at our laboratory. The most common species name was massiliensis, attributed 161 times. We consider it imperative for the cultivators, who have frequently made considerable efforts in the field of microbial culture, to be the ones who name the newly isolated microorganisms, taking into consideration the Latinized nomenclature standards.

MALDI-TOF MS and point of care are disruptive diagnostic tools in Africa

We review reviewing our experience of point-of-care and mass spectrometry in Senegal as two disruptive technologies promoting the rapid diagnosis of infection, permitting better medical management of patients.

Two thousand years of epidemics in Marseille and the Mediterranean Basin

Marseille has been exposed to epidemics for two millennia, including plague, cholera and yellow fever. This long-standing exposure to epidemics has given the people of Marseilles a particular expertise in fighting epidemics. Lazarets and other quarantine measures were implemented as a response to preventing the further spread of the disease in the community. The Institut Hospitalier Universitaire Méditerranée Infection is paving the way today, with its responses built on the region's long history and knowledge of epidemics, infectious diseases and medical microbiology.

Mycobacterium terramassiliense, Mycobacterium rhizamassiliense and Mycobacterium numidiamassiliense sp. nov., three new Mycobacterium simiae complex species cultured from plant roots

Three slowly growing mycobacteria named strain AB308, strain AB215 and strain AB57 were isolated from the tomato plant roots. The 16S rRNA and rpoB gene sequence analyses suggested that each strain was representative of one hitherto unidentified slowly-growing Mycobacterium species of the Mycobacterium simiae complex. Genome sequencing indicated that each strain contained one chromosome of 6.015-6.029 Mbp. A total of 1,197, 1,239 and 1,175 proteins were found to be associated with virulence and 107, 76 and 82 proteins were associated with toxin/antitoxin systems for strains AB308, AB215 and AB57, respectively. The three genomes encode for secondary metabolites, with 38, 33 and 46 genes found to be associated with polyketide synthases/non-ribosomal peptide synthases and nine, seven and ten genes encoding for bacteriocins, respectively. The genome of strain AB308 encodes for one questionable prophage and three incomplete prophages, while only incomplete prophages were predicted in AB215 and AB57 genomes. Genetic and genomic data indicate that strains AB308, AB215 and AB57 are each representative of a new Mycobacterium species that we respectively named Mycobacterium terramassiliense, Mycobacterium numidiamassiliense and Mycobacterium rhizamassiliense.

"Mycobacterium massilipolynesiensis" sp. nov., a rapidly-growing mycobacterium of medical interest related to Mycobacterium phlei

In French Polynesia, respiratory tract clinical isolate M26, displayed unusual phenotype and contradictory phylogenetic affiliations, suggesting a hitherto unidentified rapidly-growing Mycobacterium species. The phenotype of strain M26 was further characterized and its genome sequenced. Strain M26 genome consists in a 5,732,017-bp circular chromosome with a G + C% of 67.54%, comprising 5,500 protein-coding genes and 52 RNA genes (including two copies of the 16 S rRNA gene). One region coding for a putative prophage was also predicted. An intriguing characteristic of strain M26’s genome is the large number of genes encoding polyketide synthases and nonribosomal peptide synthases. Phylogenomic analysis showed that strain M26’s genome is closest to the Mycobacterium phlei genome with a 76.6% average nucleotide identity. Comparative genomics of 33 Mycobacterium genomes yielded 361 genes unique to M26 strain which functional annotation revealed 84.21% of unknown function and 3.88% encoding lipid transport and metabolism; while 48.87% of genes absent in M26 strain have unknown function, 9.5% are implicated in transcription and 19% are implicated in transport and metabolism. Strain M26’s unique phenotypic and genomic characteristics indicate it is representative of a new species named “Mycobacterium massilipolynesiensis”. Looking for mycobacteria in remote areas allows for the discovery of new Mycobacterium species.

Molecular history of plague

Plague, a deadly zoonose caused by the bacterium Yersinia pestis, has been firmly documented in 39 historical burial sites in Eurasia that date from the Bronze Age to two historical pandemics spanning the 6th to 18th centuries. Palaeomicrobiologic data, including gene and spacer sequences, whole genome sequences and protein data, confirmed that two historical pandemics swept over Europe from probable Asian sources and possible two-way-ticket journeys back from Europe to Asia. These investigations made it possible to address questions regarding the potential sources and routes of transmission by completing the standard rodent and rodent-flea transmission scheme. This suggested that plague was transmissible by human ectoparasites such as lice, and that Y. pestis was able to persist for months in the soil, which is a source of reinfection for burrowing mammals. The analyses of seven complete genome sequences from the Bronze Age indicated that Y. pestis was probably not an ectoparasite-borne pathogen in these populations. Further analyses of 14 genomes indicated that the Justinian pandemic strains may have formed a clade distinct from the one responsible for the second pandemic, spanning in Y. pestis branch 1, which also comprises the third pandemic strains. Further palaeomicrobiologic studies must tightly connect with historical and anthropologic studies to resolve questions regarding the actual sources of plague in ancient populations, alternative routes of transmission and resistance traits. Answering these questions will broaden our understanding of plague epidemiology so we may better face the actuality of this deadly infection in countries where it remains epidemic.

Direct matrix-assisted laser desorption ionisation time-of-flight mass spectrometry identification of mycobacteria from colonies

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) identification of mycobacteria requires a standard acetonitrile/formic acid pre-MALDI-TOF-MS. We prospectively compared this standard protocol with direct deposit with matrix for the identification of mycobacteria cultured on solid media. We first verified that Mycobacterium tuberculosis was killed after it was mixed with matrix. Then, 111 Mycobacterium isolates previously identified by partial rpoB gene sequencing were tested in parallel by the two protocols. An identification score >1.7 was obtained in 86/111 (77.5 %) isolates after protein extraction versus 97/111 (87.4 %) isolates after direct deposit (p = 0.039, Chi-squared test). In a third step, we determined that direct deposit achieved identification for as few as 2.10⁴ M. tuberculosis organisms. In a fourth step, we evaluated direct deposit of one colony for 116 solid medium-cultured clinical isolates finally identified as representative of 12 species (63.8 % M. tuberculosis). For 114/116 (98.3 %) isolates with an identification score >1.2, the MALDI-TOF-MS identification was in complete agreement with the reference rpoB gene sequencing identification. One isolate with a MALDI-TOF-MS identification score of 1.22 for M. fortuitum was identified as M. avium by partial rpoB gene sequencing. One other isolate with a MALDI-TOF-MS identification score of 1.22 for M. tuberculosis was identified as M. tuberculosis by genotyping. All the original MALDI-TOF-MS spectra reported here have been deposited in a public database. Direct deposit of one colony on a MALDI-TOF-MS plate allows for an accurate identification of mycobacteria for an identification score >1.3.

Formulation of a flush solution of heparin, vancomycin, and colistin for implantable access systems in oncology

Introduction: Because of the increased use of im plantable access systems, the incidence of blood stream and catheter infections associated with these systems has concomitantly increased. Classically, he parin-lock flush solutions were used to prevent thrombosis; more recently, vancomycin was added to the solution to prevent infections caused by Gram- positive bacteria, particularly coagulase-negative Staphylococci. Disorders due to Gram-negative organ isms have now appeared in oncologic patients. We therefore tested the addition of colistin to heparin- vancomycin solutions. Colistin was chosen for its good activity against Gram-negative bacteria (98% susceptibility in our hospital), its good tolerance due to low systemic passage, and its low cost.

Methods: We developed formulations contain ing heparin (100 IU/mL) and various concentrations of vancomycin (10-500 μg/mL) and colistin (10-100 μg/mL) in 0.9% NaCl. Each sterile solution was tested for physical and chemical compatibility (spectropho tometry, nuclear magnetic resonance, and pH mea surements) and its antibacterial activity (against ox acillin-resistant Staphylococcus aureus, Enterococcus faecium, Klebsiella pneumoniae exhibiting broad- spectrum betalactamase (BSBL), imipenem-resistant Pseudomonas aeruginosa) for 2 months at 4°C and at room temperature.

Results: The most suitable combination of drugs is heparin (100 IU/mL), vancomycin (100 μg/mL), and colistin (100 μg/mL). This flush solution main tains activity when stored at 4°C for up to 1 month.

Conclusions: We feel that the combination of heparin, vancomycin, and colistin can be used as a flush solution for indwelling catheters.

Colonization of Hospital Water Networks by Gemmata massiliana, a New Planctomycetes Bacterium

Planctomycetes have been isolated from various hydric environments. These fastidious bacteria are overlooked by routine 16S rRNA gene-based PCR detection in hospital laboratories, and their presence has not been documented in the health-care environment. Using a specific culture protocol, we recently isolated a new, non-filterable Planctomycetes species, Gemmata massiliana, from one hospital water network. The goal of the study was to monitor the presence of G. massiliana in two hospital water networks. We developed a G. massiliana-specific real-time PCR system and monitored the presence of the Planctomycetes for 12 months in two hospital water networks, in filtered water collected at the intensive care unit and in non-filtered water collected from dental chairs, tanks, and usage points. Four of 180 (2.2%) filtered water samples tested positive versus 23 of 204 (11.3%) non-filtered points (p < 0.05), including 18 of 128 (14.1%) dental chairs, 3 of 51 (5.9%) usage points, and two of 25 (8%) tank specimens. There was no significant difference in the prevalence of G. massiliana between the two hospitals (p > 0.05). However, this organism was detected significantly more frequently during April and September than the 10 other months. Because G. massiliana is deeply entrenched in the hospitalized patient's environment, evaluating this organism as a new opportunistic, health-care-associated pathogen is warranted.

Steps towards the discovery of Mycobacterium tuberculosis by Robert Koch, 1882

Palaeomicrobiology has detected the tuberculosis agent in animal and human skeletons that are thousands of years old. The German doctor Robert Koch was the first microbiologist to report in 1882 the successful isolation of the causative agent of tuberculosis, named 1 year later as Mycobacterium tuberculosis. This immense discovery, however, was not made from scratch, but involved the combining of previous scientific knowledge, chiefly the previous demonstration by the French doctor Jean-Antoine Villemin that tuberculosis was a transmissible disease, and two innovations--a new staining procedure that allowed R. Koch to consistently observe the new organism in tuberculous lesions, and use of a solidified, serum-based medium instead of broths for the culture. These innovations allowed R. Koch not only to isolate M. tuberculosis from animal and patient specimens for the first time, but also to reproduce the disease in experimentally inoculated guinea pigs. It is thanks to R. Koch that one of the most lethal diseases in human history could be diagnosed, could be treated and cured after the discovery of streptomycin 65 years later, and could be efficiently prevented by isolation of cases. His microbiological innovations are now being renewed with molecular and improved culture-based detection being the twenty-first century weapons in the fight against this disease, which remains a major killer.

Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases

Molecular tools have shown an added value in the diagnosis of infectious diseases, in particular for those caused by fastidious intracellular microorganisms, or in patients receiving antibiotics before sampling. If 16S rDNA amplification had been gradually implemented in microbiology laboratories, specific real-time polymerase chain reaction (PCR) would have permitted an increase in the sensitivity of molecular methods and a reduction of contamination. Herein, we report our experience in the diagnosis of infectious diseases over two years, during which 32,948 clinical samples from 18,056 patients were received from France and abroad. Among these samples, 81,476 PCRs were performed, of which 1,192 were positive. Molecular techniques detected intracellular microorganisms in 31.3 % of respiratory samples, 27.8 % of endocarditis samples and 51.9 % of adenitis samples. Excluding intracellular bacteria, 25 % of the positive samples in this series were sterile in culture. Conventional broad-range PCR permitted the identification of fastidious and anaerobic microorganisms, but specific real-time PCR showed a significant superiority in the diagnosis of osteoarticular infections, in particular for those caused by Kingella kingae and Staphylococcus aureus, and for endocarditis diagnosis, specifically when Streptococcus gallolyticus and Staphylococcus aureus were involved. The sensitivity of conventional broad-range PCR was 62.9 % concerning overall diagnoses for which both techniques had been performed. These findings should lead microbiologists to focus on targeted specific real-time PCR regarding the clinical syndrome. Finally, syndrome-driven diagnosis, which consists of testing a panel of microorganisms commonly involved for each syndrome, permitted the establishment of 31 incidental diagnoses.

Potential changes to French recommendations about peri-prosthetic infections based on the international consensus meeting (ICMPJI)

BACKGROUND

Despite the large volume of studies on the prevention, diagnosis, and treatment of peri-prosthetic infections, surgical practice often rests on limited scientific evidence in this field. The vast International Consensus Meeting on Peri-prosthetic Joint Infection (ICMPJI) held in 2013 produced robust recommendations.

HYPOTHESIS

French consensus conference recommendations show no major differences with ICMPJI recommendations.

MATERIALS AND METHODS

The 207 recommendations developed by 300 experts at the ICMPJI were translated, and the translation was then examined by four reviewers, including 2 having participated in the consensus conference. The reviewers looked for any differences with French practices and recommendations.

RESULTS

Twenty-three major differences or innovations were identified compared to French recommendations and standard practice. Among them, pre-operative screening for nasal or urinary micro-organisms is performed routinely in France but should be reserved according to the ICMPJI for symptomatic patients and/or patients at high risk for infection. The ICMPJI emphasizes the role for the operating room environment as a vector for infection; more specifically, the operating lamp handle and suction cannula deserve close attention. A wound discharge persisting longer than 5-7 days requires irrigation and debridement. This procedure is effective only within the first 3 post-operative months and/or the first 3 weeks after symptom onset and must include exchange of all modular implants. The ICMPJI warns against both irrigation-debridement in fungal infections (suggesting two-stage prosthesis replacement) and one-stage replacement in patients with sinus tracts. The use of spacers (articulating at the knee) is recommended in the event of two-stage prosthesis replacement.

DISCUSSION

The ICMPJI recommendations differed in many ways with French recommendations and standard practice. They can be expected to impact practices in France, although a point worth noting is that only 1 of the 207 recommendations received unanimous agreement by the conference experts (keeping operating room traffic to a minimum).

Looking in amoebae as a source of mycobacteria

Mycobacteria exhibit various relationships with amoebae, ranging from the killing of one partner by the other one, to amoebae hosting mycobacteria in trophozoites and cysts. This observation indicates that poorly described biological factors affect the relationships, including mycobacterial cell-wall glycolipids and the size of the mycobacteria. Experimental observations indicate that a majority of environmental, opportunistic mycobacteria but also obligate pathogens including Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium ulcerans are inter-amoebal organisms. Amoebae may give opportunities for genetic exchanges between mycobacteria, sympatric intra-amoebal organisms and the amoebae themselves. Amoebae clearly protect opportunistic mycobacterial pathogens during their environmental life but their role for obligate mycobacterial infection remains to be established. Accordingly, water was the source for emerging, community-acquired and health care-associated infection with amoeba-resisting mycobacteria of the Mycobacterium avium, Mycobacterium abscessus and Mycobacterium fortuitum groups, among others. Amoebae are organisms where mycobacteria can be found and, accordingly, amoeba co-culture can be used for the isolation of mycobacteria from environmental and clinical specimens. Looking in amoebae may help recovering new species of mycobacteria.

Relation between nasal carriage of Staphylococcus aureus and surgical site infection in orthopedic surgery: the role of nasal contamination. A systematic literature review and meta-analysis

Staphylococcus aureus is the pathogen most frequently implicated in infection on orthopedic hardware; various strategies are deployed to limit the risk of transmission and surgical infection.

OBJECTIVES

The present study is based on a meta-analysis assessing firstly the relationship between nasal carriage of S. aureus and the development of osteo-articular infection and secondly current methods of decolonization.

RESULTS

The meta-analysis showed increased risk of surgical site infection in case of nasal carriage of S. aureus: OR=5.92, 95% CI [1.15-30.39]; P=0.033. For cross-transmission, a scientifically proven reduction in surgical site S. aureus levels is ensured by associated mupirocin and 2% chlorhexidine antiseptic solution in subjects with positive nasal screening results for all surgical procedures taken together; the reduction was not, however, significant in the orthopedic surgery subgroup. The meta-analysis confirmed these findings: OR=0.60, 95% CI [0.34-1.06]; P=0.08.

CONCLUSION

The literature review confirmed that nasal carriage of S. aureus is a major risk factor for surgical site infection. The efficacy of eradication could not be demonstrated for orthopedic surgery as samples were too small. The positive trend found, however, should encourage further studies with sufficient power and risk/benefit should meanwhile be assessed on a case-by-case basis.

LEVEL OF EVIDENCE

Level 2. Meta-analysis.