Nationwide Molecular Surveillance of Pandemic H1N1 Influenza A Virus Genomes: Canada, 2009

BACKGROUND: In April 2009, a novel triple-reassortant swine influenza A H1N1 virus ("A/H1N1pdm"; also known as SOIV) was detected and spread globally as the first influenza pandemic of the 21(st) century. Sequencing has since been conducted at an unprecedented rate globally in order to monitor the diversification of this emergent virus and to track mutations that may affect virus behavior. METHODOLOGY/PRINCIPAL FINDINGS: By Sanger sequencing, we determined consensus whole-genome sequences for A/H1N1pdm viruses sampled nationwide in Canada over 33 weeks during the 2009 first and second pandemic waves. A total of 235 virus genomes sampled from unique subjects were analyzed, providing insight into the temporal and spatial trajectory of A/H1N1pdm lineages within Canada. Three clades (2, 3, and 7) were identifiable within the first two weeks of A/H1N1pdm appearance, with clades 5 and 6 appearing thereafter; further diversification was not apparent. Only two viral sites displayed evidence of adaptive evolution, located in hemagglutinin (HA) corresponding to D222 in the HA receptor-binding site, and to E374 at HA2-subunit position 47. Among the Canadian sampled viruses, we observed notable genetic diversity (1.47 x 10⁻³ amino acid substitutions per site) in the gene encoding PB1, particularly within the viral genomic RNA (vRNA)-binding domain (residues 493-757). This genome data set supports the conclusion that A/H1N1pdm is evolving but not excessively relative to other H1N1 influenza A viruses. Entropy analysis was used to investigate whether any mutated A/H1N1pdm protein residues were associated with infection severity; however no virus genotypes were observed to trend with infection severity. One virus that harboured heterozygote coding mutations, including PB2 D567D/G, was attributed to a severe and potentially mixed infection; yet the functional significance of this PB2 mutation remains unknown. CONCLUSIONS/SIGNIFICANCE: These findings contribute to enhanced understanding of Influenza A/H1N1pdm viral dynamics

Investigation of Two Mycobacterium abscessus Outbreaks in Quebec Using Whole Genome Sequencing

In recent decades, nontuberculous mycobacteria (NTM) infections are of emerging public health concern and have contributed towards significant clinical and economic burden globally. One such rapid growing mycobacteria, Mycobacterium abscessus, can cause clonal outbreaks, and these bacteria exhibit a highly resistant antimicrobial susceptibility profile. Here, we present an investigation of two small outbreaks of M. abscessus: first in a pediatric clinic setting and second in a tattoo parlour from Quebec. Two whole genome sequencing approaches were utilized for genotyping: MAB-MLST, a multilocus sequencing typing scheme containing housekeeping, identification, and antimicrobial resistance genes, and SNVPhyl that uses phylogenetics to determine single nucleotide variations between strains. MAB-MLST results showed that the pediatric outbreak strains had two distinct sequence types, demonstrating that one strain did not belong to the outbreak, while all tattoo outbreak isolates belonged to the same sequence type. SNVPhyl results were similar to MAB-MLST results and showed that the pediatric outbreak strains tightly clustered together with 0-1 SNVs between isolates, a sharp contrast between unrelated strains used as controls. Similar results were seen for tattoo outbreak cases with 3-11 SNVs between isolates. NTM infections can be difficult to identify, and outbreak investigations can be complicated. Thus, WGS tools can be used in public health outbreak investigations as they provide high discriminatory power

VanG-Type Vancomycin-Resistant Enterococcus faecalis Strains Isolated in Canada

Enterococcus faecalis G1-0247 (vancomycin MIC, 16 μg/ml) was found to harbor a vanG operon 99% identical to the vanG operon in E. faecalis BM4518. E. faecalis N03-0233 (vancomycin MIC, 16 μg/ml) was found to harbor a novel vanG operon, vanG2, on an element in a different chromosomal location than the vanG-harboring elements in G1-0247 and BM4518

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-50085(T) (=LMG 28276(T) =CCUG65815(T)) and C. oculi R-50187(T) (=LMG 28277(T) =CCUG65816(T)). DNA G+C content was found to be 62.2%(by HPLC) and 62.8%(by WGS) for C. lowii R-50085(T), 64.1%(HPLC) and 64.8%(WGS) for C. oculi R-50187(T) and 67.8%(HPLC) for C. mastitidis LMG 19040(T) [=S-8(T) =CCUG38654(T) =CECT 4843(T) =CIP 105509(T) =DSM44356(T) =IFO (NBRC) 16160(T) =JCM 12269(T)]

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-50085(T) (=LMG 28276(T) =CCUG65815(T)) and C. oculi R-50187(T) (=LMG 28277(T) =CCUG65816(T)). DNA G+C content was found to be 62.2%(by HPLC) and 62.8%(by WGS) for C. lowii R-50085(T), 64.1%(HPLC) and 64.8%(WGS) for C. oculi R-50187(T) and 67.8%(HPLC) for C. mastitidis LMG 19040(T) [=S-8(T) =CCUG38654(T) =CECT 4843(T) =CIP 105509(T) =DSM44356(T) =IFO (NBRC) 16160(T) =JCM 12269(T)]