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Smanis G, Avgoustou E, Papadopoulos I, Papadopoulos A, Athanasakos A, Athanasiadis E, Vassilara F. Clostridium paraputrificum Bacteremia and Ectopic Ileal Varices in Underlying Chronic Portal and Superior Mesenteric Vein Thrombosis: Report of a Rare Case. Case Rep Infect Dis 2024; 2024:9443664. [PMID: 39055622 PMCID: PMC11272403 DOI: 10.1155/2024/9443664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/20/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024] Open
Abstract
Ischemic bowel disease is considered a high-risk factor for infection from anaerobic bacteria, as the ischemic bowel is the perfect ground for their development. Herein, we present the case of an advance stage colon cancer patient with a rare cause of gastrointestinal bleeding and bacteremia due to Clostridium paraputrificum, a rare anaerobic Gram-positive bacterium. The patient had presented with several episodes of hematochezia in the context of chronic superior mesenteric-portal vein tumor thrombosis and rupture of ectopic varices, and the bacteremia was an unexpected complication of the bowel ischemia due to a combination of arterial ischemia and venous congestion.
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Affiliation(s)
- Grigorios Smanis
- 5 Department of Internal MedicineHygeia Hospital, Athens, Greece
| | - Eirini Avgoustou
- 5 Department of Internal MedicineHygeia Hospital, Athens, Greece
| | - Ioannis Papadopoulos
- 4 Department of Internal MedicineMedical SchoolUniversity Hospital “ATTIKON”National and Kapodistrian University of Athens, Athens, Greece
| | - Antonios Papadopoulos
- 4 Department of Internal MedicineMedical SchoolUniversity Hospital “ATTIKON”National and Kapodistrian University of Athens, Athens, Greece
| | | | | | - Foula Vassilara
- 5 Department of Internal MedicineHygeia Hospital, Athens, Greece
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2
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Grassi L, Asfahl KL, Van den Bossche S, Maenhout I, Sass A, Vande Weygaerde Y, Van Braeckel E, Verhasselt B, Boelens J, Tunney MM, Dandekar AA, Coenye T, Crabbé A. Antibiofilm activity of Prevotella species from the cystic fibrosis lung microbiota against Pseudomonas aeruginosa. Biofilm 2024; 7:100206. [PMID: 38975276 PMCID: PMC11225020 DOI: 10.1016/j.bioflm.2024.100206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/06/2024] [Accepted: 06/06/2024] [Indexed: 07/09/2024] Open
Abstract
It is increasingly recognized that interspecies interactions may modulate the pathogenicity of Pseudomonas aeruginosa during chronic lung infections. Nevertheless, while the interaction between P. aeruginosa and pathogenic microorganisms co-infecting the lungs has been widely investigated, little is known about the influence of other members of the lung microbiota on the infection process. In this study, we focused on investigating the impact of Prevotella species isolated from the sputum of people with cystic fibrosis (pwCF) on biofilm formation and virulence factor production by P. aeruginosa. Screening of a representative collection of Prevotella species recovered from clinical samples showed that several members of this genus (8 out 10 isolates) were able to significantly reduce biofilm formation of P. aeruginosa PAO1, without impact on growth. Among the tested isolates, the strongest biofilm-inhibitory activity was observed for Prevotella intermedia and Prevotella nigrescens, which caused a reduction of up to 90% in the total biofilm biomass of several P. aeruginosa isolates from pwCF. In addition, a strain-specific effect of P. nigrescens on the ability of P. aeruginosa to produce proteases and pyocyanin was observed, with significant alterations in the levels of these virulence factors detected in LasR mutant strains. Overall, these results suggest that non-pathogenic bacteria from the lung microbiota may regulate pathogenicity traits of P. aeruginosa, and possibly affect the outcome of chronic lung infections.
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Affiliation(s)
- Lucia Grassi
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Kyle L. Asfahl
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | - Ine Maenhout
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Yannick Vande Weygaerde
- Cystic Fibrosis Reference Centre, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Eva Van Braeckel
- Cystic Fibrosis Reference Centre, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Paediatrics, Ghent University, Ghent, Belgium
| | - Bruno Verhasselt
- Laboratory of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jerina Boelens
- Laboratory of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Michael M. Tunney
- School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Ajai A. Dandekar
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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Bielen A, Babić I, Vuk Surjan M, Kazazić S, Šimatović A, Lajtner J, Udiković-Kolić N, Mesić Z, Hudina S. Comparison of MALDI-TOF mass spectrometry and 16S rDNA sequencing for identification of environmental bacteria: a case study of cave mussel-associated culturable microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:21752-21764. [PMID: 38393570 DOI: 10.1007/s11356-024-32537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used as a rapid and cost-effective method for pathogen identification in clinical settings. In comparison, its performance in other microbiological fields, such as environmental microbiology, is still being tested, although isolates of environmental microbes are essential for in-depth in vivo studies of their biology, including biotechnological applications. We investigated the applicability of MALDI-TOF MS for the identification of bacterial isolates from a highly oligotrophic environment - Dinaric Karst caves, which likely harbor specific microorganisms. We cultured bacteria from the shell surface of the endemic mussel Congeria jalzici, one of the three known cave mussels in the world that lives in the Dinaric karst underground. The bacterial isolates were obtained by swabbing the shell surface of mussels living in microhabitats with different amounts of water: 10 air-exposed mussels, 10 submerged mussels, and 10 mussels in the hygropetric zone. A collection of 87 pure culture isolates was obtained, mostly belonging to the phylum Bacillota (72%), followed by Pseudomonadota (16%), Actinomycetota (11%), and Bacteroidota (1%). We compared the results of MALDI-TOF MS identification (Bruker databases DB-5989 and version 11, v11) with the results of 16S rDNA-based phylogenetic analysis, a standard procedure for bacterial identification. Identification to the genus level based on 16S rDNA was possible for all isolates and clearly outperformed the results from MALDI-TOF MS, although the updated MALDI-TOF MS database v11 gave better results than the DB-5989 version (85% versus 62%). However, identification to the species-level by 16S rDNA sequencing was achieved for only 17% of isolates, compared with 14% and 40% for the MALDI-TOF MS databases DB-5989 and v11 database, respectively. In conclusion, our results suggest that continued enrichment of MALDI-TOF MS libraries will result with this method soon becoming a rapid, accurate, and efficient tool for assessing the diversity of culturable bacteria from different environmental niches.
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Affiliation(s)
- Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia.
| | - Ivana Babić
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Marija Vuk Surjan
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | | | - Ana Šimatović
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Jasna Lajtner
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | | | - Zrinka Mesić
- Oikon Ltd., Trg Senjskih Uskoka 1-2, 10020, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
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Yasir M, Willcox MDP. The use of ultraviolet light generated from light-emitting diodes for the disinfection of transvaginal ultrasound probes. PLoS One 2024; 19:e0298449. [PMID: 38394312 PMCID: PMC10890779 DOI: 10.1371/journal.pone.0298449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Transvaginal ultrasound probes (TVUS) are used for several gynecological procedures. These need to be disinfected between patient use. In the current study we examine whether UVC delivered using light emitting diodes for 90 seconds can provide sufficient disinfection efficacy. A new UVC device that delivers UVC radiation at 265nm-275nm for 90 seconds was used. TVUS probes were swabbed before and after use in an in vitro fertilization clinic. Microbes on the swabs were cultured and identified. In addition, the ability of the UVC device to provided repeated high-level disinfection was analysed by deliberately contaminating probes with spores of Bacillus subtilis and then performing the UVC disinfection and bacterial culture. 50% of probes were contaminated with bacteria, most commonly Bacillus sp., directly after in vivo use. Whereas 97% were sterile after UVC disinfection for 90 seconds. The UVC treatment resulted in no growth of B. subtilis spores after each of five repeated contaminations with 5-9 x 107 spores on the probes. This study has found that UVC delivered via light emitting diodes for only 90 seconds can produce high level disinfection of transvaginal probes.
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Affiliation(s)
- Muhammad Yasir
- School of Optometry and Vision Science, University of New South Wales, Kensington, Australia
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, University of New South Wales, Kensington, Australia
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Jones Severino Vasconcelos QD, Silva Frederico MJ, Sousa Alves RD, Jesus Pinheiro Gomes Bandeira TD, Amaral de Moraes ME, Aragão GF. Effects of whey protein supplementation on gut microbiota of Wistar rats with valproic acid-induced autism symptoms. Future Microbiol 2024; 19:213-226. [PMID: 37934065 DOI: 10.2217/fmb-2023-0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/21/2023] [Indexed: 11/08/2023] Open
Abstract
Aim: To evaluate the effects of whey protein (WP) supplementation (1.24 mg/g, 24 days) in rats with autism spectrum disorder (ASD) induced by valproic acid (400 mg/kg, single dose). Materials & methods: Wistar rats (14 days old) were divided into four groups: control, ASD, ASD plus WP and WP. Results: WP increased bacterial diversity and the number of colonies. Bacteria from the Firmicutes phylum were predominantly found in the supplemented groups (p < 0.05). WP also improved the animals' memory in the Y-maze test and decreased the time that male animals spent in the 'solitary chamber' (p < 0.05). Conclusion: WP supplementation positively influenced gut microbiota, along with memory.
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Affiliation(s)
| | | | - Renata de Sousa Alves
- Department of Clinical and Toxicological Analysis, Federal University of Ceara, 60430-160, Fortaleza, Brazil
| | | | | | - Gislei Frota Aragão
- Health Science Center, State University of Ceara, 60430-275, Fortaleza, Brazil
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Litterio M, Castello L, Venuta ME, Abel S, Fernández-Canigia L, Legaria MC, Rollet R, Vaustat D, Azula N, Fox B, Otero S, Maldonado ML, Mangieri NA, Rossetti MA, Predari SC, Cejas D, Barberis C. Comparison of two MALDI-TOF MS systems for the identification of clinically relevant anaerobic bacteria in Argentina. Rev Argent Microbiol 2024; 56:33-61. [PMID: 38368217 DOI: 10.1016/j.ram.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 10/02/2023] [Accepted: 12/05/2023] [Indexed: 02/19/2024] Open
Abstract
The aim of this study was to compare the performance of two MALDI-TOF MS systems in the identification of clinically relevant strict anaerobic bacteria. The 16S rRNA gene sequencing was the gold standard method when discrepancies or inconsistencies were observed between platforms. A total of 333 isolates were recovered from clinical samples of different centers in Buenos Aires City between 2016 and 2021. The isolates were identified in duplicate using two MALDI-TOF MS systems, BD Bruker Biotyper (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMèrieux, Marcy-l'Etoile, France). Using the Vitek MS system, the identification of anaerobic isolates yielded the following percentages: 65.5% (n: 218) at the species or species-complex level, 71.2% (n: 237) at the genus level, 29.4% (n: 98) with no identification and 5.1% (n: 17) with misidentification. Using the Bruker Biotyper system, the identification rates were as follows: 85.3% (n: 284) at the species or species-complex level, 89.7% (n: 299) at the genus level, 14.1% (n: 47) with no identification and 0.6% (n: 2) with misidentification. Differences in the performance of both methods were statistically significant (p-values <0.0001). In conclusion, MALDI-TOF MS systems speed up microbial identification and are particularly effective for slow-growing microorganisms, such as anaerobic bacteria, which are difficult to identify by traditional methods. In this study, the Bruker system showed greater accuracy than the Vitek system. In order to be truly effective, it is essential to update the databases of both systems by increasing the number of each main spectrum profile within the platforms.
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Affiliation(s)
- Mirta Litterio
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Liliana Castello
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Elena Venuta
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Sofía Abel
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | | | - María Cristina Legaria
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina
| | - Raquel Rollet
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Daniela Vaustat
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Natalia Azula
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno (CEMIC), Buenos Aires, Argentina
| | | | - Silvina Otero
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | | | - Natalia Alejandra Mangieri
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Adelaida Rossetti
- Hospital Interzonal de Agudos Presidente Perón, Avellaneda, Provincia de Buenos Aires, Argentina
| | - Silvia Carla Predari
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - Daniela Cejas
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Buenos Aires, Argentina
| | - Claudia Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina.
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Nishio M, Morioka H, Takai S, Osada Y, Seki Y, Osugi T, Oba A, Miyaki Y. Bacteraemia and obstructive pyelonephritis caused by Bifidobacterium breve in an elderly woman: a case report and literature review. Access Microbiol 2023; 5:000574.v3. [PMID: 37970080 PMCID: PMC10634491 DOI: 10.1099/acmi.0.000574.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/19/2023] [Indexed: 11/17/2023] Open
Abstract
Bifidobacterium spp. are non-spore-forming Gram-positive anaerobes that are indigenous to the human gastrointestinal tract and vagina. They are believed to be non-pathogenic organisms for humans and thus are widely used as probiotics. An 83-year-old woman taking cephalexin for 4 days was diagnosed with obstructive pyelonephritis. Y-branched Gram-positive rods were found in both anaerobic and aerobic blood culture bottles, and in an anaerobic urine culture. Bifidobacterium breve was finally identified. Ceftriaxone and metronidazole were administered to the patient, and she was discharged after intermittent catheterization for dysuria. Urinary tract infection caused by Bifidobacterium spp. is believed to be rare, but it can develop in patients with underlying urological conditions. Recognition of the characteristic morphology and conducting anaerobic urine culture may help in identifying more cases of Bifidobacterium urinary tract infections.
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Affiliation(s)
- Mitsuru Nishio
- Department of Clinical Laboratory, Komaki City Hospital, Komaki, Aichi, Japan
- Infection Control Team, Komaki City Hospital, Komaki, Aichi, Japan
| | - Hiroshi Morioka
- Infection Control Team, Komaki City Hospital, Komaki, Aichi, Japan
- Department of Infectious Diseases, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Shun Takai
- Department of Urology, Komaki City Hospital, Komaki, Aichi, Japan
| | - Yukari Osada
- Department of Medical Technique, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Yoshie Seki
- Department of Clinical Laboratory, Komaki City Hospital, Komaki, Aichi, Japan
| | - Takato Osugi
- Department of Clinical Laboratory, Komaki City Hospital, Komaki, Aichi, Japan
| | - Airi Oba
- Department of Clinical Laboratory, Komaki City Hospital, Komaki, Aichi, Japan
| | - Yuki Miyaki
- Department of Clinical Laboratory, Komaki City Hospital, Komaki, Aichi, Japan
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Cobo F, Pérez-Carrasco V, Martín-Hita L, García-Salcedo JA, Navarro-Marí JM. Comparative evaluation of MALDI-TOF MS and 16S rRNA gene sequencing for the identification of clinically relevant anaerobic bacteria: critical evaluation of discrepant results. Anaerobe 2023; 82:102754. [PMID: 37321445 DOI: 10.1016/j.anaerobe.2023.102754] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Abstract
OBJECTIVES The main study objective was to evaluate the correlation between matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing results for the identification of anaerobes. METHODS A retrospective study was conducted of all anaerobic bacteria isolated from clinically significant specimens. MALDI-TOF (Bruker Byotyper) and 16S rRNA gene sequencing were performed in all strains. Identifications were considered correct when the concordance with gene sequencing was ≥99%. RESULTS The study included 364 isolates of anaerobic bacteria: 201 (55.2%) Gram-negative and 163 (44.8%) Gram-positive, mostly belonging to the genus Bacteroides. Isolates were largely obtained from blood cultures (128/35.4%) and intra-abdominal samples (116/32.1%). Overall, 87.3% of isolates were identified at species level using the version 9 database (89.5% of Gram-negative and 84.6% of Gram-positive anaerobic bacteria). All isolates belonging to the species B. fragilis sensu stricto were correctly identified by MALDI-TOF MS, but five cases of Phocaeicola (Bacteroides) dorei were misidentified as Phocaeicola (Bacteroides) vulgatus; all Prevotella isolates were correctly identified at the genus level, and most were correctly identified at the species level. Among Gram-positive anaerobes, 12 Anaerococcus species were not identified by MALDI-TOF MS, while six cases identified as Peptoniphilus indolicus were found to belong to other genera/species. CONCLUSIONS MALDI-TOF is a reliable technique for identifying most anaerobic bacteria, although the database needs frequent updating to identify rare, infrequent, and newly discovered species.
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Affiliation(s)
- Fernando Cobo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain.
| | - Virginia Pérez-Carrasco
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - Lina Martín-Hita
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José Antonio García-Salcedo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José María Navarro-Marí
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
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Sabrie NAS, Halani S, Maguire F, Aftanas P, Kozak R, Andany N. Lachnoanaerobaculum orale bacteremia in a patient with acute myeloid leukemia and stomatitis: An emerging pathogen. IDCases 2023; 33:e01837. [PMID: 37645542 PMCID: PMC10461115 DOI: 10.1016/j.idcr.2023.e01837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 08/31/2023] Open
Abstract
Background Lachnoanaerobaculum orale is a newly described, obligately anaerobic gram-positive bacillus. The first report of invasive disease caused by L. orale was described in a patient with acute lymphocytic leukemia following systematic chemotherapy. Here we describe another case of L. orale bacteremia in a patient with a hematologic malignancy following chemotherapy-induced neutropenia. Methods We present a case of a 46-year-old woman with a recent diagnosis of AML who presented to Sunnybrook Health Sciences Center with febrile neutropenia following induction chemotherapy with daunorubicin-cytarabine (3 +7 regimen) with Gemtuzumab and Ozogamycin. Despite being on intravenous pipercillin-tazobactam she remained febrile. Following our clinical assessment and investigations, potential sources of infection included a swollen digit and severe mucositis. Results One blood culture from admission grew Lachnoanaerobaculum orale in the anaerobic bottle, identified by Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF). The isolate also underwent whole-genome sequencing using methods that have been described previously. Results demonstrated the organism was susceptible to cefoxitin, clindamycin, meropenem, metronidazole, penicillin, and piperacillin-tazobactam. We concluded that the source of this patient's bloodstream infection to be chemotherapy-induced stomatitis. Conclusion With the increasing use of intensive immunosuppressive regimens and hematopoietic stem cell transplantation for patients with hematologic malignancies, there has been an increase in the incidence and detection of bloodstream infections due to anaerobic organisms. This is only the second case report of L. orale bacteremia, highlighting its emerging role as an opportunistic pathogen in immunocompromised patients.
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Affiliation(s)
| | | | | | | | - Robert Kozak
- Shared Hospital Laboratory, Canada
- Department of Laboratory Medicine & Pathology, Sunnybrook Health Sciences Centre, Canada
| | - Nisha Andany
- Department of Medicine, University of Toronto, Canada
- Division of Infectious Diseases, Sunnybrook Health Sciences Centre, Canada
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Loy JD, Clawson ML, Adkins PRF, Middleton JR. Current and Emerging Diagnostic Approaches to Bacterial Diseases of Ruminants. Vet Clin North Am Food Anim Pract 2023; 39:93-114. [PMID: 36732002 DOI: 10.1016/j.cvfa.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The diagnostic approaches and methods to detect bacterial pathogens in ruminants are discussed, with a focus on cattle. Conventional diagnostic methods using culture, isolation, and characterization are being replaced or supplemented with new methods. These include molecular diagnostics such as real-time polymerase chain reaction and whole-genome sequencing. In addition, methods such as matrix-assisted laser desorption ionization-time-of-flight mass spectrometry enable rapid identification and enhanced pathogen characterization. These emerging diagnostic tools can greatly enhance the ability to detect and characterize pathogens, but performance and interpretation vary greatly across sample and pathogen types, disease syndromes, assay performance, and other factors.
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Affiliation(s)
- John Dustin Loy
- Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Michael L Clawson
- USDA, Agriculture Research Service US Meat Animal Research Center, Clay Center, NE, USA
| | - Pamela R F Adkins
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - John R Middleton
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
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Fernández Vecilla D, Oiartzabal Elorriaga U, Urrutikoetxea Gutiérrez MJ, Pérez Ramos IS, Díaz de Tuesta Del Arco JL. Jaw osteomielitis and myositis caused by Bacteroides pyogenes. Anaerobe 2023; 79:102670. [PMID: 36423884 DOI: 10.1016/j.anaerobe.2022.102670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/17/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022]
Affiliation(s)
- Domingo Fernández Vecilla
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao, Biscay, Spain; Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Biscay, Spain.
| | - Udane Oiartzabal Elorriaga
- Radiodiagnosis Service of Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao, Biscay, Spain; Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Biscay, Spain.
| | - Mikel Joseba Urrutikoetxea Gutiérrez
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao, Biscay, Spain; Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Biscay, Spain.
| | - Iris Sharon Pérez Ramos
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao, Biscay, Spain; Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Biscay, Spain.
| | - José Luis Díaz de Tuesta Del Arco
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao, Biscay, Spain; Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Biscay, Spain.
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Vilcarromero S, Small M, Lizarzaburu A, Rivadeneyra-Rodriguez A. Pleural empyema by Parvimonas micra in an immunocompetent patient: a case report. Rev Peru Med Exp Salud Publica 2023; 40:99-104. [PMID: 37377244 PMCID: PMC10953646 DOI: 10.17843/rpmesp.2023.401.11956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/30/2022] [Indexed: 06/29/2023] Open
Abstract
We present the case of a young immunocompetent patient, with a history of pulmonary tuberculosis, who attended the hospital with a subacute clinical picture of persistent fever, weight loss, dyspnea and abolition of vesicular murmur. Chest CT scan showed an extensive empyema in the left hemithorax. Samples were taken for detection of common germs. Then, a chest drainage tube was placed and antibiotic therapy started. The MALDI-TOF MS test identified Parvimonas micra, an anaerobic bacterium, commensal to the oral flora, associated with severe periodontitis, but rarely reported in cases of pleural empyema, especially in immunocompetent patients. Gingivitis and pericoronaritis of the third molar were diagnosed during oral evaluation. The patient progressed favorably. Parvimonas micra should be considered as a possible etiological agent in cases of subacute or chronic pleural empyema, in addition to mycobacteria. Tests such as MALDI-TOF MS or 16S rRNA sequencing, chest tube placement, empirical antibiotic coverage and an adequate oral evaluation should be considered in these cases.
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Affiliation(s)
- Stalin Vilcarromero
- Infectious Diseases Service of the Hospital Edgardo Rebagliati Martins, EsSalud, Lima, Peru.nfectious Diseases Service of the Hospital Edgardo Rebagliati MartinsEsSaludLimaPeru
| | - Max Small
- Pneumology Service of the Hospital Edgardo Rebagliati Martins , EsSalud, Lima, Peru.Servicio de Neumología del Hospital Edgardo Rebagliati MartinsEsSaludLimaPeru
| | - Alexis Lizarzaburu
- Pneumology Service of the Hospital Edgardo Rebagliati Martins , EsSalud, Lima, Peru.Servicio de Neumología del Hospital Edgardo Rebagliati MartinsEsSaludLimaPeru
| | - Abel Rivadeneyra-Rodriguez
- Odontostomatology Service of the Hospital Edgardo Rebagliati Martins, EsSalud, Lima, Peru.Odontostomatology Service of the Hospital Edgardo Rebagliati MartinsEsSaludLimaPeru
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Sepsityper ® Kit versus In-House Method in Rapid Identification of Bacteria from Positive Blood Cultures by MALDI-TOF Mass Spectrometry. Life (Basel) 2022; 12:life12111744. [PMID: 36362899 PMCID: PMC9693840 DOI: 10.3390/life12111744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/16/2022] Open
Abstract
In order to further accelerate pathogen identification from positive blood cultures (BC), various sample preparation protocols to identify bacteria with MALDI-TOF MS directly from positive BCs have been developed. We evaluated an in-house method in comparison to the Sepsityper® Kit (Bruker Daltonics, Bremen, Germany) as well as the benefit of an on-plate formic acid extraction step following positive signal by the BACTECTM FX system. Confirmation of identification was achieved using subcultured growing biomass used for MALDI-TOF MS analysis. A total of 113 monomicrobial positive BCs were analyzed. The rates of Gram-positive bacteria correctly identified to the genus level using in-house method and Sepsityper® Kit were 63.3% (38/60) and 81.7% (49/60), respectively (p = 0.025). Identification rates at species level for Gram-positive bacteria with in-house method and Sepsityper® kit were 30.0% (18/60) and 66.7% (40/60), respectively (p < 0.001). Identification rates of Gram-negative bacteria were similar with the in-house method and Sepsityper® Kit. Additional on-plate formic acid extraction demonstrated significant improvement in the identification rate of Gram-positive bacteria at both genus and species level for both in-house (p = 0.001, p < 0.001) and Sepsityper® Kit methods (p = 0.007, p < 0.001). Our in-house method is a candidate for laboratory routines with Sepsityper® Kit as a back-up solution when identification of Gram-positive bacteria is unsuccessful.
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Church DL, Griener T, Gregson D. Multi-year comparison of VITEK® MS and 16S rRNA gene sequencing performance for the identification of rarely encountered anaerobes causing invasive human infections in a large Canadian region: can our laboratory abandon 16S rRNA gene sequencing? Anaerobe 2022; 78:102640. [PMID: 36126828 DOI: 10.1016/j.anaerobe.2022.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/13/2022] [Accepted: 09/07/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND Our large regional laboratory routinely provides a definitive identification (ID) for 800-1,200 anaerobic bacteria per annum that cause invasive human infections. An increasing number of isolates (i.e., 10-13%) recovered from clinical specimens from these cases were more unusual or rarely isolated genera and/or species (i.e., ≤5 individual cases/annum). METHODS VITEK® MS (MALDI-TOF MS)is done initially on all anaerobic bacteria, but rare isolates undergo in-house PCR/sequencing when proteomics provides a wrong ID or no results despite repeat testing. A clinical microbiologist in consultation with the Infectious Diseases service approves molecular analyses. This multi-year comparison (2014-19) of the performance of MALDI-TOF MS and 16S rRNA gene sequencing using the IDNS Smart Gene bacterial dataset shows both method's abilities to provide a genus-level and/or species-level ID for rare isolates. RESULTS 489 rare anaerobes were recovered from a variety of clinical specimens: 57% blood cultures, 19% other sterile fluids, 14% sterile tissues, 8% deep wounds/abscesses, and 2% prosthetic implants. 16S rRNA gene sequencing gave an accurate genus-vs. species level ID for 487/489 (99.6%) and 401/489 (82.0%) of isolates respectively. Accurate genus-vs species-level ID were obtained by MALDI-TOF MS for 269/489 (53.4%) and 187/489 (37.3%) of isolates respectively. MALDI-TOF MS gave wrong or no results for 35.1% of Gram-negative anaerobic cocci (GNAC), 62% of Gram-negative anaerobic bacilli (GNAB), 30.8% of Gram-positive anaerobic cocci (GPAC) and 46.3% of Gram-positive anaerobic bacilli (GPAB). Neither method gave an ID for one GNAB and one GPAC isolate. MALDI-TOF MS genus-level ID of GNAC and genus/species-level ID of GPAB improved during the study but its performance remained stable for genus- or species-level ID of other organism groups. CONCLUSIONS MALDI-TOF MS provides accurate ID for most common anaerobes, but molecular analyses need to be available for rare isolates. Large complex laboratories should have a workflow for sending rare isolates for 16S rRNA gene sequencing in invasive cases where a definitive ID is clinically required.
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Affiliation(s)
- D L Church
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Department of Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada.
| | - T Griener
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada
| | - D Gregson
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Department of Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada
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Bacteremia due to Prevotella oris of probable hepatic origin. Anaerobe 2022; 76:102586. [DOI: 10.1016/j.anaerobe.2022.102586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/25/2022]
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Sunil krishna, Shenoy PA, Priyanka KS, Vishwanath S. “Breast abscess in a male patient due to Finegoldia magna and Bifidobacterium scardovii: An unusual entity”. Anaerobe 2022; 75:102536. [DOI: 10.1016/j.anaerobe.2022.102536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 11/16/2022]
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Investigation of MALDI-TOF Mass Spectrometry for Assessing the Molecular Diversity of Campylobacter jejuni and Comparison with MLST and cgMLST: A Luxembourg One-Health Study. Diagnostics (Basel) 2021; 11:diagnostics11111949. [PMID: 34829296 PMCID: PMC8621691 DOI: 10.3390/diagnostics11111949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 11/17/2022] Open
Abstract
There is a need for active molecular surveillance of human and veterinary Campylobacter infections. However, sequencing of all isolates is associated with high costs and a considerable workload. Thus, there is a need for a straightforward complementary tool to prioritize isolates to sequence. In this study, we proposed to investigate the ability of MALDI-TOF MS to pre-screen C. jejuni genetic diversity in comparison to MLST and cgMLST. A panel of 126 isolates, with 10 clonal complexes (CC), 21 sequence types (ST) and 42 different complex types (CT) determined by the SeqSphere+ cgMLST, were analysed by a MALDI Biotyper, resulting into one average spectra per isolate. Concordance and discriminating ability were evaluated based on protein profiles and different cut-offs. A random forest algorithm was trained to predict STs. With a 94% similarity cut-off, an AWC of 1.000, 0.933 and 0.851 was obtained for MLSTCC, MLSTST and cgMLST profile, respectively. The random forest classifier showed a sensitivity and specificity up to 97.5% to predict four different STs. Protein profiles allowed to predict C. jejuni CCs, STs and CTs at 100%, 93% and 85%, respectively. Machine learning and MALDI-TOF MS could be a fast and inexpensive complementary tool to give an early signal of recurrent C. jejuni on a routine basis.
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