Molecular diagnosis and enrichment culture identified a septic pseudoarthrosis due to an infection with Erysipelatoclostridium ramosum

Zakham, Fathiah; Pillonel, Trestan; Brunel, Anne-Sophie; Zambelli, Pierre‐Yves; Greub, Gilbert; Croxatto, Antony; Bertelli, Claire

doi:10.1016/j.ijid.2019.02.001

Cited by 22 publications

(23 citation statements)

References 11 publications

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“…Erysipelatoclostridium ramosum belongs to the human gut microbiota. It is a Gram-positive anaerobic enteric bacterium most widely known as Clostridioides ramosum ( Zakham et al, 2019 ). Hence, the growth of these two bacteria on the culture medium and their disapproval as C. difficile isolates by 16S rRNA sequencing describes the requirement of large scale studies on patients with CDI to differentiate the pathogens and to develop the most appropriate diagnostic tools and treatment strategies.…”

Section: Discussionmentioning

confidence: 99%

Diagnostic deficiencies of C. difficile infection among patients in a tertiary hospital in Saudi Arabia: A laboratory-based case series

Aljindan

AlEraky

Borgio

et al. 2021

Saudi Journal of Biological Sciences

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Clostridioides difficile infection (CDI) has become a threatening public health problem in the developed world. In the kingdom of Saudi Arabia, prevalence of CDI is still unknown due to limited surveillance protocols and diagnostic resources. We used a two-step procedure to study and confirm C. difficile cases. We also studied toxin profiles of these isolates. Stool samples were collected from symptomatic patients and clinically suspected of CDI for almost 12 months. Isolates were confirmed by culture method followed by 16S rRNA sequencing. Multiplex PCR was performed for the identification of toxin A, toxin B and binary toxin genes and compared to Gene Expert results. Out of the 47 collected samples, 27 were successfully grown on culture media. 18 samples were confirmed as C. difficile by both culture and 16S rRNA sequencing. Interestingly, the rest of the isolates (9 species) belonged to different genera. Our results showed 95% of samples were positive for both toxin A and B ( tcdA, tcdB ) and all samples exhibited the toxin gene regulator tcdC . All samples were confirmed negative for the binary toxin gene ctdB and 11% of the isolates were positive for ctdA gene. Interestingly, one isolate harbored the binary toxin gene ( cdtA + ) and tested negative for both toxins A and B. We believe that combining the standard culture method with molecular techniques can make the detection of C. difficile more accurate.

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Section: Discussionmentioning

confidence: 99%

Diagnostic deficiencies of C. difficile infection among patients in a tertiary hospital in Saudi Arabia: A laboratory-based case series

Aljindan

AlEraky

Borgio

et al. 2021

Saudi Journal of Biological Sciences

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“…The published sequencing data were processed in the pipeline of the program DADA2 (Callahan et al, 2016) and the taxonomic assignment of the output amplicon sequence variants (ASVs) was performed with the SILVA reference database v.132 (Quast et al, 2012). Within the list of ASVs, the taxa whose positive effects on host mice/humans were shown in previous studies (e.g., Lactobacillus) (Gorbach, 2000;Bravo et al, 2011;Ritze et al, 2014) and those possibly having negative effects on hosts (e.g., Erysipelatoclostridium) (Zakham et al, 2019) were designated at separate functional layers. Co-occurrence patterns of the ASVs across the 55 samples were analyzed with the SpiecEasi program: ASVs appearing in 15 or more samples were subjected to the analysis.…”

Section: Application 2: Mouse Gut Microbiomementioning

confidence: 99%

Scoring Species for Synthetic Community Design: Network Analyses of Functional Core Microbiomes

et al. 2020

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Constructing biological communities is a major challenge in both basic and applied sciences. Although model synthetic communities with a few species have been constructed, designing systems consisting of tens or hundreds of species remains one of the most difficult goals in ecology and microbiology. By utilizing high-throughput sequencing data of interspecific association networks, we here propose a framework for exploring "functional core" species that have great impacts on whole community processes and functions. The framework allows us to score each species within a large community based on three criteria: namely, topological positions, functional portfolios, and functional balance within a target network. The criteria are measures of each species' roles in maximizing functional benefits at the community or ecosystem level. When species with potentially large contributions to ecosystem-level functions are screened, the framework also helps us design "functional core microbiomes" by focusing on properties of species groups (modules) within a network. When embedded into agroecosystems or human gut, such functional core microbiomes are expected to organize whole microbiome processes and functions. An application to a plantassociated microbiome dataset actually highlighted potential functional core microbes that were known to control rhizosphere microbiomes by suppressing pathogens. Meanwhile, an example of application in mouse gut microbiomes called attention to poorly investigated bacterial species, whose potential roles within gut microbiomes deserve future experimental studies. The framework for gaining "bird's-eye" views of functional cores within networks is applicable not only to agricultural and medical data but also to datasets produced in food processing, brewing, waste water purification, and biofuel production.

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“…(1) Abscess in a case of cerebellar abscess secondary to otitis media in a 5-year-old boy with bilateral chronic suppurative otitis media for 4 years for which he was being treated with no response [21]. 2Prosthetic material in a case of septic pseudarthrosis after an orthopaedic procedure with an allograft in a young female patient with Ewing's sarcoma [48]. 3Peritoneal fluid in a case of peritoneal dialysis-related peritonitis.…”

Section: Case Presentationmentioning

confidence: 99%

“…(13) Synovial fluid and intraoperative samples in a case of knee prosthetic joint infection [39]. Interestingly, 11 of these 14 samples (78 %) yielded C. ramosum in pure culture [17,18,21,28,31,34,39,45,48,49].…”

Section: Case Presentationmentioning

confidence: 99%

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Clostridium ramosum rapidly identified by MALDI-TOF MS. A rare gram-variable agent of bacteraemia.

Legaria

García

Tudanca

et al. 2020

Access Microbiology

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Clostridium ramosum is an enteric anaerobic, endospore-forming, gram-positive rod with a low GC content that is rarely associated with disease in humans. We present a case of C. ramosum bacteraemia. To the best of our knowledge, this is the second case of C. ramosum bacteraemia in an elderly patient presenting with fever, abdominal pain and bilious emesis. We highlight the Gram stain variability, the lack of visualization of spores and the atypical morphology of the colonies that showed C. ramosum in a polymicrobial presentation that initially appeared to show monomicrobial bacteraemia. The microorganism was rapidly identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We present a comprehensive literature review of 32 cases of clinical infections by C. ramosum in which we describe, if available, sex, age, clinical symptoms, predisposing conditions, other organisms present in the blood culture, other samples with C. ramosum, identification methodology, treatment and outcome.

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Molecular diagnosis and enrichment culture identified a septic pseudoarthrosis due to an infection with Erysipelatoclostridium ramosum

Cited by 22 publications

References 11 publications

Diagnostic deficiencies of C. difficile infection among patients in a tertiary hospital in Saudi Arabia: A laboratory-based case series

Diagnostic deficiencies of C. difficile infection among patients in a tertiary hospital in Saudi Arabia: A laboratory-based case series

Scoring Species for Synthetic Community Design: Network Analyses of Functional Core Microbiomes

Clostridium ramosum rapidly identified by MALDI-TOF MS. A rare gram-variable agent of bacteraemia.

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