Assignment of provisionally named CDC group NO-1 strains derived from animal bite wounds and other clinical sources, to genera nova in the family Comamonadaceae: description of Vandammella animalimorsus gen. nov., sp. nov. and Franklinella schreckenbergeri gen. nov., sp. nov.

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 C10 : 0 3OH, C16 : 1 ω7c, C16 : 0 and C18 : 1 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 (>99 % 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 65.08-66.92 %; genomes derived from CDC group NO-1-like strains were smaller, ranging from 2.72 to 2.82 Mb with G+C contents of 62.87-63.0 mol%. 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.

Corynebacterium hindlerae sp. nov., derived from a human granuloma, which forms black colonies and black halos on modified Tinsdale medium but is not closely related to Corynebacterium diphtheriae and related taxa.

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 2 680 694 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.

Pseudoxanthomonas winnipegensis sp. nov., derived from human clinical materials and recovered from cystic fibrosis and other patient types in Canada, and emendation of Pseudoxanthomonas spadix Young et al. 2007.

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 ≥99.4 % similarity to each other but only 97.73-98.29 % 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.

Enemella gen. nov., Enemella evansiae sp. nov., Enemella dayhoffiae sp. nov. and Parenemella sanctibonifatiensis gen. nov., sp. nov., novel taxa assignable to the family Propionibacteriaceae and derived from human clinical samples.

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.

Brevibacterium massiliense (Roux and Raoult 2009) is a later heterotypic synonym of Brevibacterium ravenspurgense (Mages, Frodl, Bernard and Funke 2009), using whole-genome sequence analysis as a comparative tool.

A patient strain derived from urine was found by 16S rRNA gene sequencing to be closely related (99.6 % identity) to sequences derived from both Brevibacterium ravenspurgense CCUG 56047T and Brevibacterium massilienseCCUG 53855T. Those species had been described during the same 11 month period in 2008-2009. Further characterization revealed that those isolates could not be readily distinguished from each other biochemically, by cellular fatty acids, antimicrobial susceptibility, MALDI-TOF MS, 16S rRNA gene sequencing or by whole-genome sequence (WGS) analyses. By WGS comparison, these isolates had an aerage nucleotide identity using blastn (ANIb) scores of 95.7 % or higher to each other, DNA G+C content in the range of 62.3 mol%-62.4 mol%, with genome sizes ranging from 2.28×106 to 2.41×106 bases. Based on these data, we propose that the name B. massiliense is a later heterotypic synonym of B. ravenspurgense and provide an emended description of B. ravenspurgense.

Corynebacterium lowii sp. nov. and Corynebacterium oculi sp. nov., derived from human clinical disease and an emended description of Corynebacterium mastitidis.

Strains of members of the genus Corynebacterium derived from ophthalmologic patients in Japan, Belgium and Switzerland and found to be closely related to-, but distinguishable from Corynebacterium mastitidis by 16S rRNA gene sequencing, were characterized using biochemical, chemotaxonomic, MALDI-TOF mass spectrometry and antimicrobial susceptibility methods and DNA-DNA hybridization as well as by whole-genome sequencing (WGS). Based on this investigation, we describe Corynebacterium lowii sp. nov. and Corynebacterium oculi sp. nov., derived from human ocular specimens, as well as emend the description of Corynebacterium mastitidis. Type strains for these species are: C. lowii R-50085T (=LMG 28276T =CCUG 65815T) and C. oculi R-50187T (=LMG 28277T =CCUG 65816T). DNA G+C content was found to be 62.2 % (by HPLC) and 62.8 % (by WGS) for C. lowii R-50085T, 64.1 % (HPLC) and 64.8 % (WGS) for C. oculi R-50187T and 67.8 % (HPLC) for C. mastitidis LMG 19040T [=S-8T =CCUG 38654T =CECT 4843T =CIP 105509T =DSM 44356T =IFO (NBRC)16160T =JCM 12269T].

Emendation of the description of the species Corynebacterium propinquum to include strains which produce urease.

Corynebacterium propinquum is a Gram-positive rod occasionally recovered from clinical infections which, according to 16S rRNA gene sequencing, is most closely related (>99% sequence similarity) to Corynebacterium pseudodiphtheriticum. The two species are very similar biochemically, commonly differentiated by a single test, the detection of urease, where strains of C. propinquum are described as being urease-non-producing and strains of C. pseudodiphtheriticum are described as urease-producing. In this study, historical and contemporary strains of C. propinquum and C. pseudodiphtheriticum from this laboratory were definitively characterized, which included use of rpoB sequencing. Urease-producing strains of C. propinquum as well as typical urease-non-producing isolates were identified after rpoB sequencing, with six of these being originally identified as C. pseudodiphtheriticum. Based on these observations, we propose emendation of the description of C. propinquum to include strains which produce urease. MALDI-TOF analysis may be a useful tool to differentiate these taxa. Existing commercial databases should be updated to include urease-positive strains of C. propinquum.

Unsatisfactory long-term virological suppression in human immunodeficiency virus-infected children in the Amazonas State, Brazil.

INTRODUCTION: Achieving viral suppression (VS) in children is challenging despite the exponential increase in access to antiretroviral therapy (ART). We evaluated VS in children >1 year of age and adolescents 5 years after they had begun ART, in Manaus, Amazonas state, Brazil. METHODS: HIV-infected, ART-naive children >1 year of age between 1999 and 2016 were eligible. Analysis was stratified by age at ART initiation: 1-5 y, >5-10 y, and >10-19 y. CD4+ T-cell count and viral load were assessed on arrival at the clinic, on ART initiation, and at 6 months, 1 year, 2 years, and 5 years after ART initiation. The primary outcome was a viral load <50 copies/mL 5 years after ART initiation. RESULTS: Ultimately, 121 patients were included. The mean age at diagnosis was 4.8 years (SD 3.5), mean CD4% was 17.9 (SD 9.8), and mean viral load was 4.6 log10 copies/ml (SD 0.8). Five years after ART initiation, the overall VS rate was 46.9%. VS by patient age group was as follows: 36.6% for 1-5 y, 53.3% for >5-10 y, and 30% for >10-19 y. Almost all children (90,4%) showed an increase in CD4%+ T cell count. There were no statistically significant predictors for detecting children who do not achieve VS with treatment. VS remained below 65% in all the evaluated periods. CONCLUSIONS: Considerable immunological improvement is seen in children after ART initiation. Further efforts are needed to maintain adequate long-term VS levels and improve the survival of this vulnerable population.

Legionella quinlivanii strain isolated from a human: A case report and whole genome sequencing analysis.

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.

Molecular Typing of Legionella pneumophila Isolates in the Province of Quebec from 2005 to 2015.

Legionella is found in natural and man-made aquatic environments, such as cooling towers and hot water plumbing infrastructures. Legionella pneumophila serogroup 1 (Lp1) is the most common etiological agent causing waterborne disease in the United States and Canada. This study reports the molecular characterization of Lp strains during a 10 year period. We conducted sequence-based typing (SBT) analysis on a large set of Lp isolates (n = 284) to investigate the province of Quebec sequence types (STs) distribution in order to identify dominant clusters. From 2005 to 2015, 181 clinical Lp isolates were typed by SBT (141 sporadic cases and 40 outbreak related cases). From the same period of time, 103 environmental isolates were also typed. Amongst the 108 sporadic cases of Lp1 typed, ST-62 was the most frequent (16.6%), followed by ST-213 (10.2%), ST-1 (8.3%) and ST-37 (8.3%). Amongst other serogroups (SG), ST-1327 (SG5) (27.3%) and ST-378 (SG10) (12.2%) were the most frequent. From the environmental isolates, ST-1 represent the more frequent SBT type (26.5%). Unweighted pair group method with arithmetic mean (UPGMA) dendrogram from the 108 sporadic cases of SG1 contains 4 major clusters (A to D) of related STs. Cluster B contains the majority of the strains (n = 61) and the three most frequent STs in our database (ST-62, ST-213 and ST-1). During the study period, we observed an important increase in the incidence rate in Quebec. All the community associated outbreaks, potentially or confirmed to be associated with a cooling tower were caused by Lp1 strains, by opposition to hospital associated outbreaks that were caused by serogroups of Lp other than SG1. The recent major Quebec City outbreak caused by ST-62, and the fact that this genotype is the most common in the province supports whole genome sequencing characterization of this particular sequence type in order to understand its evolution and associated virulence factors.

Unsatisfactory long-term virological suppression in human immunodeficiency virus-infected children in the Amazonas State, Brazil

Abstract INTRODUCTION: Achieving viral suppression (VS) in children is challenging despite the exponential increase in access to antiretroviral therapy (ART). We evaluated VS in children >1 year of age and adolescents 5 years after they had begun ART, in Manaus, Amazonas state, Brazil. METHODS: HIV-infected, ART-naive children >1 year of age between 1999 and 2016 were eligible. Analysis was stratified by age at ART initiation: 1-5 y, >5-10 y, and >10-19 y. CD4+ T-cell count and viral load were assessed on arrival at the clinic, on ART initiation, and at 6 months, 1 year, 2 years, and 5 years after ART initiation. The primary outcome was a viral load <50 copies/mL 5 years after ART initiation. RESULTS: Ultimately, 121 patients were included. The mean age at diagnosis was 4.8 years (SD 3.5), mean CD4% was 17.9 (SD 9.8), and mean viral load was 4.6 log10 copies/ml (SD 0.8). Five years after ART initiation, the overall VS rate was 46.9%. VS by patient age group was as follows: 36.6% for 1-5 y, 53.3% for >5-10 y, and 30% for >10-19 y. Almost all children (90,4%) showed an increase in CD4%+ T cell count. There were no statistically significant predictors for detecting children who do not achieve VS with treatment. VS remained below 65% in all the evaluated periods. CONCLUSIONS: Considerable immunological improvement is seen in children after ART initiation. Further efforts are needed to maintain adequate long-term VS levels and improve the survival of this vulnerable population.

Isolation and characterization of Pigmentiphaga-like isolates from human clinical material.

Species in the genus Pigmentiphaga are Gram-negative, catalase- and oxidase-positive rods derived exclusively to date from environmental sources. Features of strains most like Pigmentiphaga daeguensis or Pigmentiphaga kullae from a case of suppurative otitis media in a 6-year-old female post-transplant recipient and in a human stool sample are described.

Staphylococcus lugdunensis: low prevalence and clinical significance in a pediatric microbiology laboratory.

Staphylococcus lugdunensis is reported to be a highly virulent coagulase-negative Staphylococcus species, but whether it is an important pediatric pathogen is uncertain. At our pediatric center, only 2.1% (7/347) of coagulase-negative Staphylococcus isolates were found to be S. lugdunensis, and only 1 isolate was considered possibly clinically significant.S. lugdunensis does not appear to be a common pathogen in children.

Assignment of Brevibacterium stationis (ZoBell and Upham 1944) Breed 1953 to the genus Corynebacterium, as Corynebacterium stationis comb. nov., and emended description of the genus Corynebacterium to include isolates that can alkalinize citrate.

Brevibacterium stationis ATCC 14403(T), Corynebacterium ammoniagenes ATCC 6872 and two clinical isolates were found to form a single taxon group consistent with the genus Corynebacterium, designated here as Corynebacterium stationis comb. nov. The type strain of Corynebacterium stationis is ATCC 14403(T) =CCUG 43497( T) =CIP 104228(T) =DSM 20302(T) =NBRC 12144(T) =JCM 11611(T) =VKM B-1228(T). These strains can utilize citrate; therefore, inclusion of C. stationis requires that the description of the genus Corynebacterium be amended to include citrate-positive strains.

Síntomas tempranos de neurotoxicidad por exposición prolongada a plaguicidas / Early symptoms of neurotoxicity by lengthy exposure to pesticides

Es un diseño descriptivo de corte transversal, clínico epidemiológico, realizado entre diciembre 2000 - septiembre 2001. Con una muestra no probabilística, 28 agricultores voluntarios, género masculino, una edad promedio de 29 años, habitantes de la comunidad Gabante, Municipio Tovar, Estado Aragua, Venezuela. Un proceso de trabajo similar, dedicados al cultivo de durazno diez (10) horas diarias, lunes a sábado. Exposición a plaguicidas de 11 a 15 años. Un nivel de escolaridad (42.9 por ciento) de primaria incompleta. La entrevista clínico psicológica comprendió: historia de salud, historia laboral, antecedentes patológicos - neurológicos y antecedentes patológicos - psiquiátricos. Los resultados mostraron que los síntomas padecidos en los últimos tres meses mareos un 39 por ciento. Los hábitos psicobiológicos, alcohol (100 por ciento) y tabaco (42 por ciento) arrojaron porcentajes resaltantes. Las pruebas neuropsicológicas, Benton, PFN y destreza manual calificaron con resultados apreciables. El análisis estadístico se realizó con el PSICOTOX que clasificó el 72 por ciento tipo 2 o dudosos y el EPI-INFO 2000.