RESUMEN
Legionella infections have a propensity for occurring in HIV-infected individuals, with immunosuppressed individuals tending to present with more severe disease. However, understanding regarding the Legionella host response in immune compromised individuals is lacking. This study investigated the inflammatory profiles associated with Legionella infection in patients hospitalized with HIV and pneumonia in Medellín, Colombia from February 2007 to April 2014, and correlated these profiles with clinical outcomes. Sample aliquots from the Colombian cohort were shipped to Canada where Legionella infections and systemic cytokine profiles were determined using real-time PCR and bead-based technology, respectively. To determine the effect of Legionella coinfection on clinical outcome, a patient database was consulted, comparing laboratory results and outcomes between Legionella-positive and -negative individuals. Principal component analysis revealed higher plasma concentrations of eotaxin, IP-10 and MCP-1 (p = 0.0046) during Legionella infection. Individuals with this immune profile also had higher rates of intensive care unit admissions (adjusted relative risk 1.047 [95% confidence interval 1.027-1.066]). Results demonstrate that systemic markers of monocyte/macrophage activation and differentiation (eotaxin, MCP-1, and IP-10) are associated with Legionella infection and worse patient outcomes. Further investigations are warranted to determine how this cytokine profile may play a role in Legionella pneumonia pathogenesis or immunity.
RESUMEN
CDC group non-oxidizer (NO)-1 is the provisional name designated in 1993 for phenotypically similar, Gram-stain-negative bacilli recovered primarily from human wound infections after animal bites. Otherwise, this group has been rarely alluded to in recent literature. CDC NO-1 strains had been described as non-motile, asaccharolytic, oxidase-negative, catalase-positive, nitrate-reducing bacilli, with predominate cellular fatty acids of C10â:â0 3OH, C16â:â1 ω7c, C16â:â0 and C18â:â1 ω7c. Only one 16S rRNA gene sequence deposited in NCBI (accession no. DQ054782) had been identified as CDC group NO-1 prior to this study. That sequence was closely related (>99â% identity) to sequences called 'Xenophilus species' from canine (JN713339) and feline (KM461961) oral microbiomes as well as to sequences derived from human strains (this study). Some of the 11 isolates delineated here were recovered from human wound infections subsequent to cat/dog bites; others were from wounds (links to animal bites not described) and two were recovered from dialysates. After 16S rRNA and whole genome sequencing, the isolates were found to be most closely related to each other but fell into two distinct genera assignable to the family Comamonadaceae, provisionally discussed here as CDC group NO-1 and CDC group NO-1-like. The genomes of CDC group NO-1 isolates ranged from 3.08 to 3.38 MB with G+C contents of 65.08-66.92â%; genomes derived from CDC group NO-1-like strains were smaller, ranging from 2.72 to 2.82 Mb with G+C contents of 62.87-63.0âmol%. Based on a polyphasic study of these bacteria, we describe Vandammella animalimorsus gen. nov., sp. nov. and Franklinella schreckenbergeri gen. nov., sp. nov. for these clusters.
Asunto(s)
Mordeduras y Picaduras , Comamonadaceae , Filogenia , Animales , Técnicas de Tipificación Bacteriana , Composición de Base , Mordeduras y Picaduras/microbiología , Gatos , Centers for Disease Control and Prevention, U.S. , Comamonadaceae/clasificación , ADN Bacteriano/genética , Perros , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Estados UnidosRESUMEN
Microorganisms that cause foodborne illnesses challenge the food industry; however, environmental studies of these microorganisms on raw grain, prior to food processing, are uncommon. Bacillus cereus sensu lato is a diverse group of bacteria that is common in our everyday environment and occupy a wide array of niches. While some of these bacteria are beneficial to agriculture due to their entomopathogenic properties, others can cause foodborne illness; therefore, characterization of these bacteria is important from both agricultural and food safety standpoints. We performed a survey of wheat and flax grain samples in 2018 (n = 508) and 2017 (n = 636) and discovered that B. cereus was present in the majority of grain samples, as 56.3% and 85.2%, in two years respectively. Whole genome sequencing and comparative genomics of 109 presumptive B. cereus isolates indicates that most of the isolates were closely related and formed two genetically distinct groups. Comparisons to the available genomes of reference strains suggested that the members of these two groups are not closely related to strains previously reported to cause foodborne illness. From the same data set, another, genetically more diverse group of B. cereus was inferred, which had varying levels of similarity to previously reported strains that caused disease. Genomic analysis and PCR amplification of genes linked to toxin production indicated that most of the isolates carry the genes nheA and hbID, while other toxin genes and gene clusters, such as ces, were infrequent. This report of B. cereus on grain from Canada is the first of its kind and demonstrates the value of surveillance of bacteria naturally associated with raw agricultural commodities such as cereal grain and oilseeds.
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Bacillus cereus/clasificación , Lino/microbiología , Triticum/microbiología , Secuenciación Completa del Genoma/métodos , Bacillus cereus/genética , Bacillus cereus/aislamiento & purificación , Proteínas Bacterianas/genética , Toxinas Bacterianas/genética , Canadá , Grano Comestible/microbiología , Genoma Bacteriano , Genómica , Secuenciación de Nucleótidos de Alto Rendimiento , FilogeniaRESUMEN
Corynebacterium diphtheriae, Corynebacterium belfantii, Corynebacterium rouxii, Corynebacterium ulcerans, Corynebacterium pseudotuberculosis and Corynebacterium silvaticum are the only taxa from among ~121 Corynebacterium species deemed potentially able to harbour diphtheria tox genes. Subsequently tox-gene bearing species may potentially produce diphtheria toxin, which is linked to fatal respiratory distress if a pharyngeal pseudomembrane is formed or toxaemia develops in those unimmunized or under-immunized. Detection of diphtheria toxin-producing species may also invoke a public health response and contact tracing. Recovery of such species from the respiratory tract or other contaminated sources such as non-healing ulcerative wounds are expedited by use of differential and selective media such as modified Tinsdale medium (MTM). This medium is supplemented with potassium tellurite, which supresses most normal flora present in contaminated specimens, as well as l-cystine and thiosulphate. Most diphtheria-tox-gene bearing species grow well on MTM, producing black colonies with a black halo around each colony. This is due to an ability to produce cystinase in the presence of tellurite, cystine and thiosulphate, resulting in black tellurium deposits being observed in the agar. Other Corynebacterium species may/may not be able to grow at all in the presence of tellurite but if able to grow, will have small beige or brownish colonies which do not exhibit black halos. We describe here an unusual non-tox-gene-bearing isolate, NML 93-0612T, recovered from a human wrist granuloma, which produced black colonies with black halos on MTM agar but was otherwise distinguishable from Corynebacterium species which can bear tox genes. Distinctive features included its unusual colony morphology on MTM and sheep blood agar, by proteomic, biochemical and chemotaxonomic properties and by molecular methods. Its genome contained 2â680â694 bytes, a G+C content of 60.65 mol% with features consistent with the genus Corynebacterium and so represents a new species for which we propose the name Corynebacterium hindlerae sp. nov.
Asunto(s)
Corynebacterium/clasificación , Granuloma/microbiología , Filogenia , Técnicas de Tipificación Bacteriana , Composición de Base , Canadá , Corynebacterium/aislamiento & purificación , Corynebacterium diphtheriae/genética , ADN Bacteriano/genética , Ácidos Grasos/química , Humanos , Pigmentación , Proteómica , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
Legionella pneumophila, a Gram-negative bacillus, is the causative agent of Legionnaire's disease, a form of severe community-acquired pneumonia. Infection can have high morbidity, with a high proportion of patients requiring ICU admission, and up to 10% mortality, which is exacerbated by the lack of efficacy of typical empirical antibiotic therapy against Legionella spp. The fastidious nature of the entire Legionellaceae family historically required inclusion of activated charcoal in the solid medium to remove growth inhibitors, which inherently interferes with accurate antimicrobial susceptibility determination, an acknowledged methodological shortfall, now rectified by a new solid medium that gives results comparable to those of microbroth dilution. Here, as an international Legionella community (with authors representing various international reference laboratories, countries and clinical stakeholders for diagnosis and treatment of legionellosis), we set out recommendations for the standardization of antimicrobial susceptibility testing methods, guidelines and reference strains to facilitate an improved era of antibiotic resistance determination.
Asunto(s)
Legionella pneumophila , Legionella , Enfermedad de los Legionarios , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Humanos , Enfermedad de los Legionarios/diagnóstico , Enfermedad de los Legionarios/tratamiento farmacológico , Estándares de ReferenciaRESUMEN
Twelve isolates recovered from 10 cystic fibrosis/other patient types and a variety of clinical sources, were referred to Canada's National Microbiology Laboratory over 7 years. These were assignable to the genus Pseudoxanthomonas but were unidentifiable to species level. Patients included five males and five females from two geographically separated provinces, ranging in age from 2 months to 84 years. In contrast, most Pseudoxanthomonas species described to date have been derived from water, plants or contaminated soils. By 16S rRNA gene sequencing, the patient strains had ≥99.4â% similarity to each other but only 97.73-98.29â% to their closest relatives, Pseudoxanthomonas spadix or Pseudoxanthomonas helianthi. Bacteria were studied by whole genome sequencing using average nucleotide identity by Blastn, digital DNA-DNA hybridization, average amino acid identity, core genome and single nucleotide variant analyses, MALDI-TOF, biochemical and cellular fatty acid analyses, and by antimicrobial susceptibility testing. Bacterial structures were assessed using scanning and transmission electron microscopy. Strains were strict aerobes, yellowish-pigmented, oxidative, non-motile, Gram-stain-negative bacilli and generally unable to reduce nitrate. Strains were susceptible to most of the antibiotics tested; some resistance was observed towards carbapenems, several cephems and uniformly to nitrofurantoin. The single taxon group observed by 16S rRNA gene sequencing was supported by whole genome sequencing; genomes ranged in size from 4.36 to 4.73 Mb and had an average G+C content of 69.12 mol%. Based on this study we propose the name Pseudoxanthomonas winnipegensis sp. nov. for this cluster. Pseudoxanthomonas spadix DSM 18855T, acquired for this study, was found to be non-motile phenotypically and by electron microscopy; we therefore propose the emendation of Pseudoxanthomonas spadix Young et al. 2007 to document that observation.
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Fibrosis Quística/microbiología , Filogenia , Xanthomonadaceae/clasificación , Adolescente , Anciano , Anciano de 80 o más Años , Técnicas de Tipificación Bacteriana , Composición de Base , Canadá , Niño , Preescolar , ADN Bacteriano/genética , Ácidos Grasos/química , Femenino , Humanos , Lactante , Masculino , Persona de Mediana Edad , Hibridación de Ácido Nucleico , Pigmentación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Xanthomonadaceae/aislamiento & purificaciónRESUMEN
An elderly patient was admitted with sepsis to a community hospital. The individual was found to have a foot wound infested with maggots, and clinical evidence of cellulitis. A blood culture was positive on day 2 with Ignatzschineria indica . The patient was treated successfully with a combination of antibiotics and manual removal of the maggots. Poor living conditions were central to his presentation.
RESUMEN
Nine Gram-stain-positive cocci, coccobacilli or short, rod-shaped strains recovered from clinical sources from patients located in two Canadian provinces and one environmental source were extensively studied. Clinical sources included blood cultures, cerebral spinal fluid, lymph node, lung biopsy and peritoneal fluid. Through 16S rRNA gene and whole genome sequencing analyses, the strains were found to cluster into three groups, closest to but distinguished from other genera in the family Propionibacteriaceae. The genomes from these bacteria had high G+C content, ranging from 67.8-69.56 mol%, and genome sizes of 3.02-4.52 Mb. Biochemical and chemotaxonomic properties including branched-chain cellular fatty acids, l-lysine diaminopimelic acid (ll-DAP) and cell-wall type A3γ (ll-DAP-gly) containing ll-DAP, alanine, glycine and glutamic acid were found and so the strains were therefore deemed to be consistent with other new genera in this family. Based on this investigation, we propose Enemella gen. nov., Enemella evansiae sp. nov., Enemella dayhoffiae sp. nov. and Parenemella sanctibonifatiensis gen. nov., sp. nov. for these taxa. Misidentified taxon 'Ponticoccus gilvus' was found to be assignable to Enemella evansiae based on this study.
Asunto(s)
Líquidos Corporales/microbiología , Filogenia , Propionibacteriaceae/clasificación , Técnicas de Tipificación Bacteriana , Composición de Base , Canadá , ADN Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Grasos/química , Tamaño del Genoma , Genoma Bacteriano , Humanos , Propionibacteriaceae/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
The Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella (HACEK) group genus Eikenella contained a single species, Eikenella corrodens, for many years. In November 2019, Eikenella exigua was described after recovery from a brain abscess and blood culture in Norway. Coincidentally, characterization of 22 Gram-negative bacteria resembling Eikenella from 17 Canadian patients had been underway. Seven isolates from five patients were conclusively identifiable as E. corrodens. One (NML 120819) was deemed to represent a species of the genus Eikenella most closely related to E. corrodens. Fourteen isolates had 97.6 to 98.8% similarities to E. corrodens by 16S rRNA gene sequencing, forming three distinct groups by genome analyses. The largest contained ten anaerobic isolates from eight patients recovered from blood, brain, bone and other abscesses; upon re-evaluation, this group was found to be most consistent with E. exigua. A second facultatively anaerobic clade consisted of two ocular isolates from one patient and a sinus isolate from a second patient. The third taxon consisted of a single strictly anaerobic blood culture isolate. The novel taxa, like E. corrodens, were poorly reactive biochemically and difficult to discern from each other phenotypically and chemotaxonomically, including by cellular fatty acids. MALDI-TOF (Bruker) and whole-genome sequencing were used to further characterize isolates. Draft genomes for the strains had similar DNA G+C contents (55.38-58.53 mol%) while sizes varied from 1.82 Mb to 2.54 Mb. We propose here emendations of the genus Eikenella and the species Eikenella exigua, as well as describing Eikenella halliae sp. nov. NML 130454T (=LMG 30894T=NCTC 14180T) and Eikenella longinqua sp. nov. NML 02-A-017T (=LMG 30896T=NCTC 14179T), on the basis of these findings.
Asunto(s)
Sangre/microbiología , Eikenella/clasificación , Filogenia , Bacterias Anaerobias/clasificación , Técnicas de Tipificación Bacteriana , Composición de Base , Cultivo de Sangre , Canadá , ADN Bacteriano/genética , Eikenella/aislamiento & purificación , Ácidos Grasos/química , Humanos , Noruega , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
We describe a strain of Legionella quinlivanii isolated from a bronchoalveolar lavage specimen from an 83-year-old patient in the province of Québec. Identification was done using 16S rRNA sequencing. The strain could replicate efficiently in human THP-1 macrophages and maintained a low level of cytotoxicity. Upon analyzing the whole genome sequencing data, the icm/dot secretion system was present, but the strain lacked some effector genes known to express proteins toxic to cells. The pathogenicity of this Legionella species should be investigated further.
Les auteurs décrivent une souche de Legionella quinlivanii isolée dans le prélèvement de lavage bronchoalvéolaire d'une patiente de 83 ans de la province de Québec. Ils ont identifié la souche par séquençage de l'ARN ribosomal 16S. Cette souche, qui pouvait se répliquer en toute efficacité dans les macrophages humains THP-1, maintenait une faible cytotoxicité. L'analyse des données de séquençage complet du génome de la souche a révélé la présence du système de sécrétion icm/dot, mais l'absence de certains gènes effecteurs connus pour exprimer les protéines cytotoxiques. Il faudra étudier plus en profondeur la pathogénicité de cette espèce de Legionella.
RESUMEN
BACKGROUND: Whipple's disease is a clinically relevant multi-system disorder that is often undiagnosed given its elusive nature. We present an atypical case of Whipple's disease involving pan-valvular endocarditis and constrictive pericarditis, requiring cardiac intervention. A literature review was also performed assessing the prevalence of atypical cases of Whipple's disease. CASE PRESENTATION: A previously healthy 56-year-old male presented with a four-year history of congestive heart failure with weight loss and fatigue. Notably, he had absent gastrointestinal symptoms. He went on to develop pan-valvular endocarditis and constrictive pericarditis requiring urgent cardiac surgery. A clinical diagnosis of Whipple's disease was suspected, prompting duodenal biopsy sampling which was unremarkable, Subsequently, Tropheryma whipplei was identified by 16S rDNA PCR on the cardiac valvular tissue. He underwent prolonged antibiotic therapy with recovery of symptoms. CONCLUSIONS: Our study reports the first known case of Whipple's disease involving pan-valvular endocarditis and constrictive pericarditis. A literature review also highlights this presentation of atypical Whipple's with limited gastrointestinal manifestations. Duodenal involvement was limited and the gold standard of biopsy was not contributory. We also highlight the Canadian epidemiology of the disease from 2012 to 2016 with an approximate 4% prevalence rate amongst submitted samples. Routine investigations for Whipple's disease, including duodenal biopsy, in this case may have missed the diagnosis. A high degree of suspicion was critical for diagnosis of unusual manifestations of Whipple's disease.
Asunto(s)
Endocarditis Bacteriana/microbiología , Enfermedades de las Válvulas Cardíacas/microbiología , Miocarditis/microbiología , Pericarditis Constrictiva/microbiología , Tropheryma/aislamiento & purificación , Enfermedad de Whipple/microbiología , Antibacterianos/uso terapéutico , Endocarditis Bacteriana/diagnóstico , Endocarditis Bacteriana/tratamiento farmacológico , Endocarditis Bacteriana/cirugía , Insuficiencia Cardíaca/microbiología , Enfermedades de las Válvulas Cardíacas/diagnóstico , Enfermedades de las Válvulas Cardíacas/tratamiento farmacológico , Enfermedades de las Válvulas Cardíacas/cirugía , Implantación de Prótesis de Válvulas Cardíacas , Humanos , Masculino , Persona de Mediana Edad , Anuloplastia de la Válvula Mitral , Miocarditis/diagnóstico , Miocarditis/tratamiento farmacológico , Pericardiectomía , Pericarditis Constrictiva/diagnóstico , Pericarditis Constrictiva/tratamiento farmacológico , Pericarditis Constrictiva/cirugía , Ribotipificación , Resultado del Tratamiento , Tropheryma/genética , Enfermedad de Whipple/diagnóstico , Enfermedad de Whipple/tratamiento farmacológicoRESUMEN
Due to poor diagnostics and increased co-infections, HIV-associated Legionella infections are underreported. We aimed to retrospectively determine the frequency of Legionella infections in bronchoalveolar lavage (BAL) from HIV-associated pneumonia patients hospitalized in Medellin, Colombia, between February 2007 and April 2014. Although culture was negative, 17 BAL (36%) were positive for Legionella by quantitative polymerase chain reaction, most of which were in the Mycobacterium tuberculosis or Pneumocystis jirovecii co-infected patients, and included L. anisa (nâ¯=â¯6), L. bozemanae (nâ¯=â¯4), L. pneumophila (nâ¯=â¯3), and L. micdadei (nâ¯=â¯2). All L. bozemanae and L. micdadei associated with Pneumocystis, while all L. pneumophila associated with M. tuberculosis. Legionella probable cases had more complications and higher mortality rates (Pâ¯=â¯0.02) and were rarely administered empirical anti-Legionella therapy while in hospital. Clinicians should be aware of the possible presence of Legionella in HIV and M. tuberculosis or P. jirovecii co-infected patients.
Asunto(s)
Infecciones Oportunistas Relacionadas con el SIDA/microbiología , Coinfección/microbiología , Legionella/fisiología , Legionelosis/microbiología , Neumonía/microbiología , Infecciones Oportunistas Relacionadas con el SIDA/epidemiología , Adulto , Líquido del Lavado Bronquioalveolar/microbiología , Coinfección/epidemiología , Colombia/epidemiología , Femenino , Humanos , Legionella/genética , Legionelosis/epidemiología , Masculino , Persona de Mediana Edad , Mycobacterium tuberculosis/fisiología , Pneumocystis carinii/aislamiento & purificación , Neumonía/epidemiología , Reacción en Cadena de la Polimerasa , Estudios Retrospectivos , RiesgoRESUMEN
Draft genome sequences of two strains of the rarely isolated organism Legionella jordanis, NML 060502 (from a patient with a lower respiratory infection) and NML 130005 (from water), were assembled and studied. Respectively, the genome sizes obtained were 2,927,328 bp and 3,101,130 bp, with G+C contents of 41.9% and 41.7%.
RESUMEN
A rod-shaped, motile anaerobic bacterium, designated CCRI-22567T, was isolated from a vaginal sample of a woman diagnosed with bacterial vaginosis and subjected to a polyphasic taxonomic study. The novel strain was capable of growth at 30-42 °C (optimum, 42 °C), at pH 5.5-8.5 (optimum, pH 7.0-7.5) and in the presence of 0-1.5â% (w/v) NaCl (optimally at 0.5â% NaCl). The phylogenetic trees based on 16S rRNA gene sequences showed that strain CCRI-22567T forms a distinct evolutionary lineage independent of other taxa in the family Peptostreptococcaceae. Strain CCRI-22567T exhibited 90.1â% 16S rRNA gene sequence similarity to Peptoanaerobacter stomatis ACC19aT and 89.7â% to Eubacterium yurii subsp. schtitka ATCC 43716. The three closest organisms with an available whole genome were compared to strain CCRI-22567T for genomic relatedness assessment. The genomic average nucleotide identities (OrthoANIu) obtained with Peptoanaerobacter stomatis ACC19aT, Eubacterium yurii subsp. margaretiae ATCC 43715 and Filifactor alocis ATCC 35896T were 71.8, 70.3 and 69.6â%, respectively. Strain CCRI-22567T contained C18â:â1 ω9c and C18â:â1 ω9c DMA as the major fatty acids. The DNA G+C content of strain CCRI-22567T based on its genome sequence was 33.8âmol%. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain CCRI-22567T is considered to represent a new genus and species within the family Peptostreptococcaceae, for which the name Criibacterium bergeronii gen. nov., sp. nov., is proposed. The type strain of Criibacterium bergeronii is CCRI-22567T (=LMG 31278T=DSM 107614T=CCUG 72594T).
RESUMEN
Draft genome sequences of Corynebacterium macginleyi CCUG 32361T and clinical isolates NML 080212 and NML 120205 were assembled and studied. Genome sizes ranged from 2.35 Mb to 2.42 Mb, with G+C contents ranging from 57.1% to 57.2%.
RESUMEN
Draft genome sequences of Propionibacterium australiense isolates NML 98A072T and NML 98A078, derived from granulomatous lesions of infected bovines, were assembled and studied. Respectively, the genome sizes were 2.99 and 3.01 Mb, with G+C contents of 68.4% and 68.5%.
RESUMEN
A description of an outbreak of necrotizing enterocolitis among neonates, linked to the putative novel species Clostridium neonatale and assignable to the genus Clostridium, was previously reported in brief but that name had never been validly published (Alfa et al. Clin Inf Dis 2002;35:S101-S105). Features of this taxon group and its phylogenetic position with respect to contemporary species in the genus Clostridium were recently reviewed and still found to be unique. Therefore, we provide here a description based on biochemical, chemotaxonomic and antimicrobial susceptibility testing (AST), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, 16S rRNA gene sequencing as well as information obtained by whole genome sequencing (WGS) for strains 99A005T and 99A006. Those two C. neonatale strains were essentially identical to each other, with genome sizes of 4â658â596-4â705â520 bp and G+C content of 28.4-28.5âmol% (WGS). AST inferred susceptibility to 14 antibiotics. MALDI-TOF spectra were unique and could potentially be used for identification. The type strain is (NML) LCDC 99A005T [=ATCC BAA-265T=CCUG 46077T=St. Boniface Hospital 30686T]. While performing this review, we found that the names of 24 validly published species assignable to the genus Clostridium had been omitted from the emended description of the genus (Lawson and Rainey Int J Syst Evol Microbiol 2016;66â:1009-1016). Those species are listed in brief here. Lastly, based on this review, we also propose that Eubacterium budayi, Eubacterium nitritogenes and Eubacterium combesii be transferred to the emended genus Clostridium, as Clostridium budayi comb. nov., Clostridium nitritogenes comb. nov. and Clostridium combesii comb. nov., respectively.
Asunto(s)
Clostridium/clasificación , Enterocolitis Necrotizante/microbiología , Filogenia , Técnicas de Tipificación Bacteriana , Composición de Base , Clostridium/genética , ADN Bacteriano/genética , Humanos , Recién Nacido , Pruebas de Sensibilidad Microbiana , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Espectrometría de Masa por Láser de Matriz Asistida de Ionización DesorciónRESUMEN
BACKGROUND AND AIMS: We aimed to determine whether monitoring of duodenoscope cleaning by rapid adenosine triphosphate (ATP) combined with channel-purge storage could eliminate high-concern microorganisms. METHODS: In a simulated-use study, suction channels, as well as lever recesses, from 2 duodenoscopes models and the unsealed elevator guidewire (EGW) channel from 1 of these 2 duodenoscopes (the other model has a sealed EGW) were perfused with ATS2015 containing approximately 8 Log10 colony-forming units (CFU)/mL of both Enterococcus faecalis and Escherichia coli. Pump-assisted cleaning was monitored by rapid ATP testing. Duodenoscopes exceeding 200 relative light units (RLUs) were recleaned. Clean duodenoscopes were processed through an automated endoscope reprocessor and then stored in a channel-purge storage cabinet for 1 to 3 days. Cultures of EGW channel and instrument channel combined with the lever recess (IC-LR) were taken after storage. The impacts of extended cleaning and alcohol flush were evaluated. RESULTS: E coli was reliably eliminated in IC-LR and EGW channels of 119 duodenoscope tests (59 with sealed EGW and 60 with nonsealed EGW). However, actionable levels of E faecalis and environmental bacteria persisted. Neither alcohol flush nor extended cleaning resulted in a reduction of actionable levels for these organisms. Identification of isolates indicated that residual organisms in duodenoscope channels were hardy Gram-positive bacteria (often spore formers) that likely originated from environmental sources. CONCLUSIONS: These data indicate that high-concern Gram-negative bacteria but not E faecalis or environmental bacteria can be reliably eliminated by use of the manufacturer's instructions for reprocessing with ATP monitoring of cleaning and channel-purge storage conditions.
Asunto(s)
Desinfección/métodos , Desinfección/normas , Duodenoscopios/microbiología , Control de Calidad , Adenosina Trifosfato/análisis , Enterococcus faecalis/aislamiento & purificación , Contaminación de Equipos , Escherichia coli/aislamiento & purificaciónRESUMEN
Features from two Pigmentiphaga isolates referred to Canada's National Microbiology Laboratory from human clinical materials were described previously (N. Bridger, S. Drews, T. Burdz, D. Wiebe, A. L. Pacheco, B. Ng, and K. Bernard, J Med Microbiol 62:708-711, 2013, https://doi.org/10.1099/jmm.0.051615-0). Whole-genome sequencing was performed on strains NML030171 and NML080357; the sequences were found to have 5.86 and 5.73 Mb of clean data and G+C contents of 67.5 and 66.74 mol%, respectively.
RESUMEN
Eisenbergiella gen. nov. was proposed in 2014 to describe an obligate anaerobic, structurally Gram-positive but Gram-stain-negative-appearing bacillus recovered from the blood culture of an elderly Israeli man. Here, we describe features for eight blood culture isolates as well one appendix-derived isolate, recovered from seven patients located in two Canadian provinces, which by 16S rRNA gene sequencing, were identifiable as Eisenbergiella tayi, the sole validly- named species in this genus. After whole genome sequencing, isolates were found to be essentially identical (96.8-98.7% identity) to each other and to E. tayi DSM 26961T, after comparison using the ANIb tool and in silico DNA-DNA hydridization. All isolates were observed to have remarkably large genomes (7.1-8.3 Mb) with a G + C content of 46.5%-46.9%.