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1.
Microb Genom ; 10(6)2024 Jun.
Article in English | MEDLINE | ID: mdl-38896471

ABSTRACT

Carbapenems are last-resort antibiotics for treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance is a rising global threat due to the acquisition of carbapenemase genes. Oxacillinase-48 (bla OXA-48)-type carbapenemases are increasing in abundance in Canada and elsewhere; these genes are frequently found on mobile genetic elements and are associated with specific transposons. This means that alongside clonal dissemination, bla OXA-48-type genes can spread through plasmid-mediated horizontal gene transfer. We applied whole genome sequencing to characterize 249 bla OXA-48-type-producing Enterobacterales isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short- and long-read sequencing, we obtained 70 complete and circular bla OXA-48-type-encoding plasmids. Using MOB-suite, four major plasmids clustered were identified, and we further estimated a plasmid cluster for 91.9 % (147/160) of incomplete bla OXA-48-type-encoding contigs. We identified different patterns of carbapenemase mobilization across Canada, including horizontal transmission of bla OXA-181/IncX3 plasmids (75/249, 30.1 %) and bla OXA-48/IncL/M plasmids (47/249, 18.9 %), and both horizontal transmission and clonal transmission of bla OXA-232 for Klebsiella pneumoniae ST231 on ColE2-type/ColKP3 plasmids (25/249, 10.0 %). Our findings highlight the diversity of OXA-48-type plasmids and indicate that multiple plasmid clusters and clonal transmission have contributed to bla OXA-48-type spread and persistence in Canada.


Subject(s)
Bacterial Proteins , Carbapenems , Enterobacteriaceae Infections , Plasmids , Whole Genome Sequencing , beta-Lactamases , beta-Lactamases/genetics , Plasmids/genetics , Canada/epidemiology , Humans , Carbapenems/pharmacology , Bacterial Proteins/genetics , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/epidemiology , Enterobacteriaceae/genetics , Enterobacteriaceae/drug effects , Enterobacteriaceae/classification , Gene Transfer, Horizontal , Anti-Bacterial Agents/pharmacology , Cross Infection/microbiology , Cross Infection/epidemiology
2.
Microbiol Spectr ; 12(5): e0322323, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38526086

ABSTRACT

Gram-negative metallo-ß-lactamase-producing bacteria can be extremely problematic, especially when found to be extensively drug-resistant (XDR). Cefiderocol is a novel antimicrobial that has been shown to overcome most carbapenemases, with very rare resistance reported to date. Within our institution, two multidrug-resistant and one XDR strains were isolated from a patient who recently emigrated from India. Each isolate underwent whole-genome sequencing to resolve plasmids and determine phylogenetics, strain typing, and mechanisms of resistance. The XDR E. coli was ST167, harbored NDM-5, cirA and PBP3 mutations, consistent with cefiderocol resistance. Our study suggests that the NDM region is required in conjunction with cirA and PBP3 mutations. It is not clear why; however, our study did determine a potential novel iron-transport region unique to the cefiderocol-resistant isolate. This is the first characterized cefiderocol-resistant E.coli reported from Canada. Health centers should be on alert for this clone.IMPORTANCEThe development of cefiderocol, a novel siderophore cephalosporin, has provided additional options to the treatment of extensively drug-resistant (XDR) Gram-negative bacteria. Resistance to cefiderocol is poorly understood and only recently described. Here, we describe a case of a patient with recent travel to India harboring three Escherichia coli isolates, one resistant and two susceptible to cefiderocol. Two isolates are highly similar genetically, allowing the mechanism of resistance to be described more closely. The importance of this manuscript contributes both globally to the understanding of cefiderocol resistance in E. coli as well as nationally as this is the first resistant case reported in Canada. This is especially concerning as cefiderocol is not currently approved in Canada. The implications of reporting emerging resistance to new antimicrobials for XDR Gram negatives are impactful to infectious disease specialists, clinical microbiologists, physicians, and public health.


Subject(s)
Anti-Bacterial Agents , Drug Resistance, Multiple, Bacterial , Escherichia coli Infections , Humans , Male , Anti-Bacterial Agents/pharmacology , beta-Lactamases/genetics , beta-Lactamases/metabolism , Canada , Cefiderocol , Cephalosporins/pharmacology , Drug Resistance, Multiple, Bacterial/genetics , Escherichia coli/genetics , Escherichia coli/drug effects , Escherichia coli/isolation & purification , Escherichia coli Infections/microbiology , Escherichia coli Infections/drug therapy , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , India , Microbial Sensitivity Tests , Mutation , Phylogeny , Plasmids/genetics , Whole Genome Sequencing , Aged
3.
Can J Microbiol ; 70(5): 178-189, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38354391

ABSTRACT

The best whole genome assemblies are currently built from a combination of highly accurate short-read sequencing data and long-read sequencing data that can bridge repetitive and problematic regions. Oxford Nanopore Technologies (ONT) produce long-read sequencing platforms and they are continually improving their technology to obtain higher quality read data that is approaching the quality obtained from short-read platforms such as Illumina. As these innovations continue, we evaluated how much ONT read coverage produced by the Rapid Barcoding Kit v14 (SQK-RBK114) is necessary to generate high-quality hybrid and long-read-only genome assemblies for a panel of carbapenemase-producing Enterobacterales bacterial isolates. We found that 30× long-read coverage is sufficient if Illumina data are available, and that more (at least 100× long-read coverage is recommended for long-read-only assemblies. Illumina polishing is still improving single nucleotide variants (SNVs) and INDELs in long-read-only assemblies. We also examined if antimicrobial resistance genes could be accurately identified in long-read-only data, and found that Flye assemblies regardless of ONT coverage detected >96% of resistance genes at 100% identity and length. Overall, the Rapid Barcoding Kit v14 and long-read-only assemblies can be an optimal sequencing strategy (i.e., plasmid characterization and AMR detection) but finer-scale analyses (i.e., SNV) still benefit from short-read data.


Subject(s)
Genome, Bacterial , High-Throughput Nucleotide Sequencing , High-Throughput Nucleotide Sequencing/methods , Gram-Negative Bacteria/genetics , Whole Genome Sequencing/methods , beta-Lactamases/genetics , Nanopore Sequencing/methods , Gene Library , Sequence Analysis, DNA/methods
4.
Antimicrob Agents Chemother ; 67(12): e0086023, 2023 12 14.
Article in English | MEDLINE | ID: mdl-37971242

ABSTRACT

Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.


Subject(s)
Klebsiella Infections , beta-Lactamases , Humans , Canada/epidemiology , beta-Lactamases/genetics , beta-Lactamases/metabolism , Plasmids/genetics , Bacterial Proteins/genetics , Klebsiella pneumoniae , Anti-Bacterial Agents/pharmacology , Carbapenems/pharmacology , Genomics , Klebsiella Infections/epidemiology , Microbial Sensitivity Tests
5.
Microb Drug Resist ; 29(2): 47-50, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36802273

ABSTRACT

This study investigated the mechanism of carbapenem resistance in an Enterobacter cloacae complex positive by the modified carbapenem inactivation method (mCIM) but negative by the Rosco Neo-Rapid Carb Kit, ß CARBA, and conventional PCR for common carbapenemase genes (KPC, NDM, OXA-48, IMP, VIM, GES, and IMI/NMC). Using whole genome sequencing (WGS) data we confirmed the identification of Enterobacter asburiae (ST1639) and the presence of blaFRI-8 located on a 148kb IncFII(Yp) plasmid. This is the first occurrence of a clinical isolate harboring the FRI-8 carbapenemase and the second occurrence of FRI in Canada. This study highlights the need to use both WGS and phenotypic screening methods for detection of carbapenemase-producing strains if we consider the growing diversity of carbapenemases.


Subject(s)
Anti-Bacterial Agents , Carbapenems , Anti-Bacterial Agents/pharmacology , Carbapenems/pharmacology , Canada , Microbial Sensitivity Tests , Bacterial Proteins/analysis , beta-Lactamases , Sensitivity and Specificity
6.
Emerg Infect Dis ; 19(6): 999-1001, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23735312

ABSTRACT

We report emergence of ciprofloxacin-resistant Salmonella enterica serovar Kentucky in Canada during 2003-2009. All isolates had similar macrorestriction patterns and were multilocus sequence type ST198, which has been observed in Europe and Africa. Ciprofloxacin-resistant S. enterica serovar Kentucky represents 66% of all ciprofloxacin-resistant nontyphoidal Salmonella sp. isolates observed in Canada since 2003.


Subject(s)
Anti-Infective Agents/pharmacology , Ciprofloxacin/pharmacology , Drug Resistance, Bacterial , Salmonella enterica/drug effects , Adolescent , Adult , Aged , Canada/epidemiology , Drug Resistance, Bacterial/genetics , Humans , Microbial Sensitivity Tests , Middle Aged , Multilocus Sequence Typing , Salmonella Infections/epidemiology , Salmonella Infections/microbiology , Salmonella Infections/transmission , Salmonella enterica/classification , Salmonella enterica/genetics , Young Adult
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