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Lerminiaux N, Mitchell R, Katz K, Fakharuddin K, McGill E, Mataseje L. Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010-2021. Microb Genom 2024; 10. [PMID: 38896471 DOI: 10.1099/mgen.0.001257] [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] [Indexed: 06/21/2024] Open
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.
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Affiliation(s)
- Nicole Lerminiaux
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | | | - Kevin Katz
- North York General Hospital, Toronto, Ontario, Canada
| | - Ken Fakharuddin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Erin McGill
- Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Laura Mataseje
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Yao L, Cooper AL, Gill A, Koziol A, Wong A, Blais BW, Carrillo CD. Overcoming Microbial Inhibition of S. Sonnei Through the Exploitation of Genomically Predicted Antibiotic Resistance Profiles for the Development of Food Enrichment Media. J Food Prot 2024; 87:100302. [PMID: 38754553 DOI: 10.1016/j.jfp.2024.100302] [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: 11/30/2023] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024]
Abstract
Linking outbreaks of Shigella spp. to specific foods is challenging due to poor selectivity of current enrichment media. We have previously shown that enrichment media, tailored to the genomically-predicted antimicrobial resistance (AMR) of Shiga toxigenic E. coli strains, enhances their isolation from foods. This study investigates the application of this approach for Shigella isolation. The AMR gene profiles of 21,908 published S. sonnei genomes indicated a high prevalence of genes conferring resistance to streptomycin (aadA, aph(3″)-Ib, aph(6)-Id, 92.8%), sulfonamides (sul1, sul2, 74.8%), and/or trimethoprim (dfrA, 96.2%). Genomic analysis and antibiotic susceptibility testing conducted with a panel of 17 outbreak-associated S. sonnei strains confirmed the correlation of AMR gene detection with resistance phenotypes. Supplementation of Shigella Broth (SB) with up to 400 µg/mL of trimethoprim or sulfadiazine did not suppress the growth of sensitive strains, whereas 100 µg/mL of streptomycin increased the selectivity of this broth. All three antibiotics increased the selectivity of modified Tryptone Soya Broth (mTSB). Based on these results, supplemented media formulations were developed and assessed by measuring the relative growth of S. sonnei in cultures coinoculated with a strain of bacteriocin-producing E. coli that is inhibitory to Shigella growth. S. sonnei was not recovered from cocultures grown in SB or mTSB without antibiotics. In contrast, media supplemented with streptomycin at 50 and 100 µg/mL, trimethoprim at 25 and 50 µg/mL, and sulfadiazine at 100 µg/mL increased the relative proportion of S. sonnei in postenrichment cultures. The enhanced recovery of resistant S. sonnei strains achieved in this study indicates that, in cases where genomic data are available for clinical S. sonnei isolates, customization of selective enrichment media based on AMR gene detection could be a valuable tool for supporting the investigation of foodborne shigellosis outbreaks.
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Affiliation(s)
- Lang Yao
- Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0C6; Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6.
| | - Ashley L Cooper
- Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0C6.
| | - Alex Gill
- Bureau of Microbial Hazards, Health Canada, Ottawa, Ontario, Canada.
| | - Adam Koziol
- Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0C6.
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6.
| | - Burton W Blais
- Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0C6.
| | - Catherine D Carrillo
- Ottawa Laboratory Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0C6.
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Qian W, Ma N, Zeng X, Shi M, Wang M, Yang Z, Tsui SKW. Identification of novel single nucleotide variants in the drug resistance mechanism of Mycobacterium tuberculosis isolates by whole-genome analysis. BMC Genomics 2024; 25:478. [PMID: 38745294 PMCID: PMC11094924 DOI: 10.1186/s12864-024-10390-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) represents a major global health challenge. Drug resistance in Mycobacterium tuberculosis (MTB) poses a substantial obstacle to effective TB treatment. Identifying genomic mutations in MTB isolates holds promise for unraveling the underlying mechanisms of drug resistance in this bacterium. METHODS In this study, we investigated the roles of single nucleotide variants (SNVs) in MTB isolates resistant to four antibiotics (moxifloxacin, ofloxacin, amikacin, and capreomycin) through whole-genome analysis. We identified the drug-resistance-associated SNVs by comparing the genomes of MTB isolates with reference genomes using the MuMmer4 tool. RESULTS We observed a strikingly high proportion (94.2%) of MTB isolates resistant to ofloxacin, underscoring the current prevalence of drug resistance in MTB. An average of 3529 SNVs were detected in a single ofloxacin-resistant isolate, indicating a mutation rate of approximately 0.08% under the selective pressure of ofloxacin exposure. We identified a set of 60 SNVs associated with extensively drug-resistant tuberculosis (XDR-TB), among which 42 SNVs were non-synonymous mutations located in the coding regions of nine key genes (ctpI, desA3, mce1R, moeB1, ndhA, PE_PGRS4, PPE18, rpsA, secF). Protein structure modeling revealed that SNVs of three genes (PE_PGRS4, desA3, secF) are close to the critical catalytic active sites in the three-dimensional structure of the coding proteins. CONCLUSION This comprehensive study elucidates novel resistance mechanisms in MTB against antibiotics, paving the way for future design and development of anti-tuberculosis drugs.
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Affiliation(s)
- Weiye Qian
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Nan Ma
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province and 3D Genomics Research Centre, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mingqiang Wang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, 310018, China.
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Hodges LM, Cooper A, Koziol A, Carrillo CD. Characterization of MLST-99 Salmonella Typhimurium and the monophasic variant I:4,[5],12:i:- isolated from Canadian Atlantic coast shellfish. MICROBIOLOGY (READING, ENGLAND) 2024; 170. [PMID: 38753417 DOI: 10.1099/mic.0.001456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Salmonella enterica subsp. enterica Typhimurium and its monophasic variant I 1;4,[5],12:i:- (MVST) are responsible for thousands of reported cases of salmonellosis each year in Canada, and countries worldwide. We investigated S. Typhimurium and MVST isolates recovered from raw shellfish harvested in Atlantic Canada by the Canadian Food Inspection Agency (CFIA) over the past decade, to assess the potential impact of these isolates on human illness and to explore possible routes of shellfish contamination. Whole-genome sequence analysis was performed on 210 isolates of S. Typhimurium and MVST recovered from various food sources, including shellfish. The objective was to identify genetic markers linked to ST-99, a sequence type specifically associated with shellfish, which could explain their high prevalence in shellfish. We also investigated the genetic similarity amongst CFIA ST-99 isolates recovered in different years and geographical locations. Finally, the study aimed to enhance the molecular serotyping of ST-99 isolates, as they are serologically classified as MVST but are frequently misidentified as S. Typhimurium through sequence analysis. To ensure recovery of ST-99 from shellfish was not due to favourable growth kinetics, we measured the growth rates of these isolates relative to other Salmonella and determined that ST-99 did not have a faster growth rate and/or shorter lag phase than other Salmonella evaluated. The CFIA ST-99 isolates from shellfish were highly clonal, with up to 81 high-quality single nucleotide variants amongst isolates. ST-99 isolates both within the CFIA collection and those isolated globally carried numerous unique deletions, insertions and mutations in genes, including some considered important for virulence, such as gene deletions in the type VI secretion system. Interestingly, several of these genetic characteristics appear to be unique to North America. Most notably was a large genomic region showing a high prevalence in genomes from Canadian isolates compared to those from the USA. Although the functions of the majority of the proteins encoded within this region remain unknown, the genes umuC and umuD, known to be protective against UV light damage, were present. While this study did not specifically examine the effects of mutations and insertions, results indicate that these isolates may be adapted to survive in specific environments, such as ocean water, where wild birds and/or animals serve as the natural hosts. Our hypothesis is reinforced by a global phylogenetic analysis, which indicates that isolates obtained from North American shellfish and wild birds are infrequently connected to isolates from human sources. These findings suggest a distinct ecological niche for ST-99, potentially indicating their specialization and adaptation to non-human hosts and environments, such as oceanic habitats.
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Affiliation(s)
| | | | - Adam Koziol
- Canadian Food Inspection Agency, Ottawa, Canada
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Kalalah AA, Koenig SSK, Bono JL, Bosilevac JM, Eppinger M. Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producing Escherichia coli. Front Microbiol 2024; 15:1364026. [PMID: 38562479 PMCID: PMC10982417 DOI: 10.3389/fmicb.2024.1364026] [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: 01/03/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) of non-O157:H7 serotypes are responsible for global and widespread human food-borne disease. Among these serogroups, O26, O45, O103, O111, O121, and O145 account for the majority of clinical infections and are colloquially referred to as the "Big Six." The "Big Six" strain panel we sequenced and analyzed in this study are reference type cultures comprised of six strains representing each of the non-O157 STEC serogroups curated and distributed by the American Type Culture Collection (ATCC) as a resource to the research community under panel number ATCC MP-9. The application of long- and short-read hybrid sequencing yielded closed chromosomes and a total of 14 plasmids of diverse functions. Through high-resolution comparative phylogenomics, we cataloged the shared and strain-specific virulence and resistance gene content and established the close relationship of serogroup O26 and O103 strains featuring flagellar H-type 11. Virulence phenotyping revealed statistically significant differences in the Stx-production capabilities that we found to be correlated to the strain's individual stx-status. Among the carried Stx1a, Stx2a, and Stx2d phages, the Stx2a phage is by far the most responsive upon RecA-mediated phage mobilization, and in consequence, stx2a + isolates produced the highest-level of toxin in this panel. The availability of high-quality closed genomes for this "Big Six" reference set, including carried plasmids, along with the recorded genomic virulence profiles and Stx-production phenotypes will provide a valuable foundation to further explore the plasticity in evolutionary trajectories in these emerging non-O157 STEC lineages, which are major culprits of human food-borne disease.
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Affiliation(s)
- Anwar A. Kalalah
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - James L. Bono
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
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Lerminiaux N, Mitchell R, Bartoszko J, Davis I, Ellis C, Fakharuddin K, Hota SS, Katz K, Kibsey P, Leis JA, Longtin Y, McGeer A, Minion J, Mulvey M, Musto S, Rajda E, Smith SW, Srigley JA, Suh KN, Thampi N, Tomlinson J, Wong T, Mataseje L. Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021. Antimicrob Agents Chemother 2023; 67:e0086023. [PMID: 37971242 PMCID: PMC10720558 DOI: 10.1128/aac.00860-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/07/2023] [Indexed: 11/19/2023] Open
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.
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Affiliation(s)
| | | | | | - Ian Davis
- QEII Health Sciences Centre, Halifax, Nova Scotia, Canada
| | - Chelsey Ellis
- The Moncton Hospital, Moncton, New Brunswick, Canada
| | - Ken Fakharuddin
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Susy S. Hota
- University Health Network, Toronto, Ontario, Canada
| | - Kevin Katz
- North York General Hospital, Toronto, Ontario, Canada
| | - Pamela Kibsey
- Royal Jubilee Hospital, Victoria, British Columbia, Canada
| | - Jerome A. Leis
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yves Longtin
- Jewish General Hospital, Montréal, Québec, Canada
| | | | - Jessica Minion
- Saskatchewan Health Authority, Regina, Saskatchewan, Canada
| | - Michael Mulvey
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Sonja Musto
- Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - Ewa Rajda
- McGill University Health Centre, Montréal, Québec, Canada
| | | | - Jocelyn A. Srigley
- BC Women’s and BC Children’s Hospital, Vancouver, British Columbia, Canada
| | | | - Nisha Thampi
- Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Titus Wong
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Laura Mataseje
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - on behalf of the Canadian Nosocomial Infection Surveillance Program
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
- Public Health Agency of Canada, Ottawa, Ontario, Canada
- QEII Health Sciences Centre, Halifax, Nova Scotia, Canada
- The Moncton Hospital, Moncton, New Brunswick, Canada
- University Health Network, Toronto, Ontario, Canada
- North York General Hospital, Toronto, Ontario, Canada
- Royal Jubilee Hospital, Victoria, British Columbia, Canada
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Jewish General Hospital, Montréal, Québec, Canada
- Sinai Health, Toronto, Ontario, Canada
- Saskatchewan Health Authority, Regina, Saskatchewan, Canada
- Health Sciences Centre, Winnipeg, Manitoba, Canada
- McGill University Health Centre, Montréal, Québec, Canada
- University of Alberta Hospital, Edmonton, Alberta, Canada
- BC Women’s and BC Children’s Hospital, Vancouver, British Columbia, Canada
- The Ottawa Hospital, Ottawa, Ontario, Canada
- Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
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7
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Islam MR, Sharma MK, KhunKhun R, Shandro C, Sekirov I, Tyrrell GJ, Soualhine H. Whole genome sequencing-based identification of human tuberculosis caused by animal-lineage Mycobacterium orygis. J Clin Microbiol 2023; 61:e0026023. [PMID: 37877705 PMCID: PMC10662373 DOI: 10.1128/jcm.00260-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Abstract
A recently described member of the Mycobacterium tuberculosis complex (MTBC) is Mycobacterium orygis, which can cause disease primarily in animals but also in humans. Although M. orygis has been reported from different geographic regions around the world, due to a lack of proper identification techniques, the contribution of this emerging pathogen to the global burden of zoonotic tuberculosis is not fully understood. In the present work, we report single nucleotide polymorphism (SNP) analysis using whole genome sequencing (WGS) that can accurately identify M. orygis and differentiate it from other members of the MTBC species. WGS-based SNP analysis was performed for 61 isolates from different provinces in Canada that were identified as M. orygis. A total of 56 M. orygis sequences from the public databases were also included in the analysis. Several unique SNPs in the gyrB, PPE55, Rv2042c, leuS, mmpL6, and mmpS6 genes were used to determine their effectiveness as genetic markers for the identification of M. orygis. To the best of our knowledge, five of these SNPs, viz., gyrB 277 (A→G), gyrB 1478 (T→C), leuS 1064 (A→T), mmpL6 486 (T→C), and mmpS6 334 (C→G), are reported for the first time in this study. Our results also revealed several SNPs specific to other species within MTBC. The phylogenetic analysis shows that the studied genomes were genetically diverse and clustered with M. orygis sequences of human and animal origin reported from different geographic locations. Therefore, the present study provides a new insight into the high-confidence identification of M. orygis from MTBC species based on WGS data, which can be useful for reference and diagnostic laboratories.
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Affiliation(s)
- Md Rashedul Islam
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meenu K. Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Rupinder KhunKhun
- BC Center for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Cary Shandro
- Provincial Laboratory for Public Health, Alberta Precision Labs, Edmonton, Alberta, Canada
| | - Inna Sekirov
- BC Center for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Gregory J. Tyrrell
- Provincial Laboratory for Public Health, Alberta Precision Labs, Edmonton, Alberta, Canada
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
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Mataseje LF, Pitout J, Croxen M, Mulvey MR, Dingle TC. Three separate acquisitions of bla NDM-1 in three different bacterial species from a single patient. Eur J Clin Microbiol Infect Dis 2023; 42:1275-1280. [PMID: 37688673 PMCID: PMC10511597 DOI: 10.1007/s10096-023-04651-4] [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: 05/26/2023] [Accepted: 08/07/2023] [Indexed: 09/11/2023]
Abstract
To investigate the acquisition and relatedness of New Delhi Metallo-beta-lactamase among multiple separate species from one patient. Five isolates from three species (Pseudomonas aeruginosa; Pa, Acinetobacter baumannii; Ab and Proteus mirabilis; Pm) suspected of harbouring a carbapenemase were investigated by phenotype (antimicrobial susceptibilities) and whole genome sequencing. Epidemiological data was collected on this patient. Three different carbapenemase genes were detected; blaVIM-1 (Pa; ST773), blaOXA-23 (Ab, ST499) and blaNDM-1 identified in all isolates. NDM regions were found chromosomally integrated in all isolates. Data showed no evidence of NDM-1 transfer within this patient suggesting the enzyme was acquired in three separate events.
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Affiliation(s)
- L F Mataseje
- National Microbiology laboratory, Winnipeg, MB, Canada
| | - J Pitout
- Alberta Precision Laboratories, Public Health Laboratory, 3030 Hospital Drive N.W, Calgary, AB, T2N 4W4, Canada
- University of Calgary, Calgary, AB, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - M Croxen
- Alberta Precision Laboratories, Public Health Laboratory, 3030 Hospital Drive N.W, Calgary, AB, T2N 4W4, Canada
- University of Alberta, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada
| | - M R Mulvey
- National Microbiology laboratory, Winnipeg, MB, Canada
| | - T C Dingle
- Alberta Precision Laboratories, Public Health Laboratory, 3030 Hospital Drive N.W, Calgary, AB, T2N 4W4, Canada.
- University of Calgary, Calgary, AB, Canada.
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9
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Gao R, Duceppe MO, Chattaway MA, Goodridge L, Ogunremi D. Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure. Front Microbiol 2023; 14:1086198. [PMID: 36937281 PMCID: PMC10020630 DOI: 10.3389/fmicb.2023.1086198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/19/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction Outbreak investigation of foodborne salmonellosis is hindered when the food source is contaminated by multiple strains of Salmonella, creating difficulties matching an incriminated organism recovered from patients with the specific strain in the suspect food. An outbreak of the rare Salmonella Adjame was caused by multiple strains of the organism as revealed by single-nucleotide polymorphism (SNP) variation. The use of highly discriminatory prophage analysis to characterize strains of Salmonella should enable a more precise strain characterization and aid the investigation of foodborne salmonellosis. Methods We have carried out genomic analysis of S. Adjame strains recovered during the course of a recent outbreak and compared them with other strains of the organism (n = 38 strains), using SNPs to evaluate strain differences present in the core genome, and prophage sequence typing (PST) to evaluate the accessory genome. Phylogenetic analyses were performed using both total prophage content and conserved prophages. Results The PST analysis of the S. Adjame isolates showed a high degree of strain heterogeneity. We observed small clusters made up of 2-6 isolates (n = 27) and singletons (n = 11) in stark contrast with the three clusters observed by SNP analysis. In total, we detected 24 prophages of which only four were highly prevalent, namely: Entero_p88 (36/38 strains), Salmon_SEN34 (35/38 strains), Burkho_phiE255 (33/38 strains) and Edward_GF (28/38 strains). Despite the marked strain diversity seen with prophage analysis, the distribution of the four most common prophages matched the clustering observed using core genome. Discussion Mutations in the core and accessory genomes of S. Adjame have shed light on the evolutionary relationships among the Adjame strains and demonstrated a convergence of the variations observed in both fractions of the genome. We conclude that core and accessory genomes analyses should be adopted in foodborne bacteria outbreak investigations to provide a more accurate strain description and facilitate reliable matching of isolates from patients and incriminated food sources. The outcomes should translate to a better understanding of the microbial population structure and an 46 improved source attribution in foodborne illnesses.
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Affiliation(s)
- Ruimin Gao
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
- Department of Food Science and Agricultural Chemistry, McGill University, Ste Anne de Bellevue, QC, Canada
| | - Marc-Olivier Duceppe
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Marie Anne Chattaway
- Gastrointestinal Bacteria Reference Unit, United Kingdom Health Security Agency, London, United Kingdom
| | - Lawrence Goodridge
- Department of Food Science, Canadian Research Institute for Food Safety, University of Guelph, Guelph, ON, Canada
| | - Dele Ogunremi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
- *Correspondence: Dele Ogunremi,
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10
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Prestel C, Moulton-Meissner H, Gable P, Stanton RA, Glowicz J, Franco L, McConnell M, Torres T, John D, Blackwell G, Yates R, Brown C, Reyes K, McAllister GA, Kunz J, Conners EE, Benedict KM, Kirby A, Mattioli M, Xu K, Gualandi N, Booth S, Novosad S, Arduino M, Halpin AL, Wells K, Walters MS. Dialysis Water Supply Faucet as Reservoir for Carbapenemase-Producing Pseudomonas aeruginosa. Emerg Infect Dis 2022; 28:2069-2073. [PMID: 36148936 PMCID: PMC9514332 DOI: 10.3201/eid2810.220731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
During June 2017-November 2019, a total 36 patients with carbapenem-resistant Pseudomonas aeruginosa harboring Verona-integron-encoded metallo-β-lactamase were identified in a city in western Texas, USA. A faucet contaminated with the organism, identified through environmental sampling, in a specialty care room was the likely source for infection in a subset of patients.
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11
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A One Health Genomic Investigation of Gentamicin Resistance in Escherichia coli from Human and Chicken Sources in Canada, 2014 to 2017. Antimicrob Agents Chemother 2022; 66:e0067722. [PMID: 36165686 PMCID: PMC9578425 DOI: 10.1128/aac.00677-22] [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: 11/20/2022] Open
Abstract
We investigated whether gentamicin resistance (Genr) in Escherichia coli isolates from human infections was related to Genr E. coli in chicken and whether resistance may be due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on 483 Genr E. coli isolates isolated between 2014 and 2017. These included 205 human-source isolates collected by the Canadian Ward (CANWARD) program and 278 chicken-source isolates: 167 from live/recently slaughtered chickens (animals) and 111 from retail chicken meat collected by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The predominant Genr gene was different in human and chicken sources; however, both sources carried aac(3)-IId, aac(3)-VIa, and aac(3)-IVa. Forty-one percent of human clinical isolates of Genr E. coli contained a blaCTX-M extended-spectrum beta-lactamase (ESBL) gene (84/205), and 53% of these were sequence type 131 (ST131). Phylogenomic analysis revealed a high diversity of Genr isolates; however, there were three small clusters of closely related isolates from human and chicken sources. Genr and spectinomycin resistance (Specr) genes were colocated in 148/167 (89%) chicken animal isolates, 94/111 (85%) chicken retail meat isolates, and 137/205 (67%) human-source isolates. Long-read sequencing of 23 isolates showed linkage of the Genr and Specr genes on the same plasmid in 14/15 (93%) isolates from chicken(s) and 6/8 (75%) isolates from humans. The use of lincomycin-spectinomycin on farms may be coselecting for gentamicin-resistant plasmids in E. coli in broiler chickens; however, Genr isolates and plasmids were mostly different in chickens and humans.
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12
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Microbiological and Molecular Features Associated with Persistent and Relapsing Staphylococcus aureus Prosthetic Joint Infection. Antibiotics (Basel) 2022; 11:antibiotics11081119. [PMID: 36009988 PMCID: PMC9405193 DOI: 10.3390/antibiotics11081119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/07/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Persistent and relapsing prosthetic joint infection (PJI) due to Staphylococcus aureus presents a clinical challenge. This study aimed to provide an extensive description of phenotypic and genomic changes that could be related to persistence or relapse. Methods: Initial and second S. aureus isolates from 6 cases of persistent and relapsing PJI, along with clinical isolates from 8 cases, with favorable outcome were included. All isolates were studied by phenotypic and genotypic approaches. Results: Recurrent S. aureus isolates exhibited a significant increase in adhesive capacity, invasion and persistence compared to resolved isolates. No association was found for the presence or absence of certain genes with the persistence or relapse of PJI. All sequential isolates showed identical sequence type (ST). Resistance gene loss during the infection and a great diversity of variants in different virulence genes between the pair of strains, mainly in genes encoding adhesins such as fnbA, were observed. Conclusions: S. aureus-caused relapse and persistence PJI is associated with bacterial phenotypical and genotypical adaptation. The main paths of adaptation were persistence in the intracellular compartment, and the loss of antibiotic resistance genes and variant acquisition, especially in genes encoding adhesins.
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13
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Bharat A, Mataseje L, Parmley EJ, Avery BP, Cox G, Carson CA, Irwin RJ, Deckert AE, Daignault D, Alexander DC, Allen V, El Bailey S, Bekal S, German GJ, Haldane D, Hoang L, Chui L, Minion J, Zahariadis G, Reid-Smith RJ, Mulvey MR. One Health Genomic Analysis of Extended-Spectrum β-Lactamase‒Producing Salmonella enterica, Canada, 2012‒2016. Emerg Infect Dis 2022; 28:1410-1420. [PMID: 35731173 PMCID: PMC9239887 DOI: 10.3201/eid2807.211528] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Extended-spectrum β-lactamases (ESBLs) confer resistance to extended-spectrum cephalosporins, a major class of clinical antimicrobial drugs. We used genomic analysis to investigate whether domestic food animals, retail meat, and pets were reservoirs of ESBL-producing Salmonella for human infection in Canada. Of 30,303 Salmonella isolates tested during 2012–2016, we detected 95 ESBL producers. ESBL serotypes and alleles were mostly different between humans (n = 54) and animals/meat (n = 41). Two exceptions were blaSHV-2 and blaCTX-M-1 IncI1 plasmids, which were found in both sources. A subclade of S. enterica serovar Heidelberg isolates carrying the same IncI1-blaSHV-2 plasmid differed by only 1–7 single nucleotide variants. The most common ESBL producer in humans was Salmonella Infantis carrying blaCTX-M-65, which has since emerged in poultry in other countries. There were few instances of similar isolates and plasmids, suggesting that domestic animals and retail meat might have been minor reservoirs of ESBL-producing Salmonella for human infection.
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14
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Zaidi SEZ, Zaheer R, Barbieri R, Cook SR, Hannon SJ, Booker CW, Church D, Van Domselaar G, Zovoilis A, McAllister TA. Genomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum. Front Microbiol 2022; 13:859990. [PMID: 35832805 PMCID: PMC9271880 DOI: 10.3389/fmicb.2022.859990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E. hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.
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Affiliation(s)
- Sani-e-Zehra Zaidi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- University of Lethbridge, Lethbridge, AB, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Ruth Barbieri
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shaun R. Cook
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | | | | | - Deirdre Church
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Calgary Laboratory Services, Calgary, AB, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Tim A. McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- *Correspondence: Tim A. McAllister,
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15
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Clinical and Genomic Investigation of an International Ceftriaxone- and Azithromycin-Resistant Shigella sonnei Cluster among Men Who Have Sex with Men, Montréal, Canada 2017-2019. Microbiol Spectr 2022; 10:e0233721. [PMID: 35647695 PMCID: PMC9241791 DOI: 10.1128/spectrum.02337-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Multidrug-resistant (MDR) Shigella sonnei have become prevalent among men who have sex with men and have become a global public health concern. From June 2017 to April 2019, 32 men were infected with MDR S. sonnei acquired locally, in Montréal, which was suggestive of an outbreak. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), phylogenetic analysis, antimicrobial resistance and virulence characterization, and association to international clusters were performed. The outbreak strain was ceftriaxone- and azithromycin-resistant due to the acquisition of blaCTX-M-27, and mphA and ermB genes, respectively, with reduced susceptibility to ciprofloxacin due to a single point mutation (gyrA S83L). One out of 27 patients treated with a fluoroquinolone experienced microbiological failure. Epidemiological evidence first supported by a rare unique MDR Shigella sonnei documented only in men in 2017 followed by similar pulsed-field gel electrophoresis profiles was confirmed by WGS. A core genome high-quality single-nucleotide variant (hqSNV)-based phylogeny found a median of 6 hqSNV differences among isolates. Virulence gene content was investigated, but no Shiga toxins were detected. An international cluster of highly related isolates was identified (PDS000019750.208) and belonged to the 3.7.29.1.4.1 S. sonnei genotype (Global III VN2.KH1.Aus). Genomic analysis revealed that this Montréal cluster was connected to other documented outbreaks in Australia, the United States, and the United Kingdom. This study highlights the urgent need for public health measures to focus on the prevention and the early detection of S. sonnei, since global transmission patterns of MDR strains is concerning and few antimicrobial treatment options are available. IMPORTANCEShigella sonnei, an important foodborne pathogen, recently became a frequent sexually transmitted agent involved in large and persistent outbreaks globally among men who have sex with men. Most strains also harbor several multidrug-resistant (MDR) determinants of particular concern. This study characterizes an outbreak strain at the source of an important MDR cluster identified in Montréal in 2017. Associations were made to many high-profile international outbreaks, and the causative S. sonnei lineage of these clusters was identified, which was not evident in past reports. The worldwide occurrence of this strain is of concern since treatment with antimicrobials like ceftriaxone and azithromycin may not be effective, and rare microbiological failures have been documented in patients treated with ciprofloxacin. Our investigation highlights the threats of Shigella spp. infection and the necessity for antimicrobial susceptibility monitoring in order to mitigate S. sonnei’s impact on public health and to avoid transmission to other at-risk communities.
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16
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Bernard KA, Pacheco AL, Burdz T, Wiebe D, Bernier AM. 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. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005247] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Kathryn A. Bernard
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ana Luisa Pacheco
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Tamara Burdz
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Deborah Wiebe
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Anne-Marie Bernier
- Department of Biology, Université de Saint-Boniface, Winnipeg, Manitoba, Canada
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17
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Rehman MA, Rempel H, Carrillo CD, Ziebell K, Allen K, Manges AR, Topp E, Diarra MS. Virulence Genotype and Phenotype of Multiple Antimicrobial-Resistant Escherichia coli Isolates from Broilers Assessed from a "One-Health" Perspective. J Food Prot 2022; 85:336-354. [PMID: 34762732 DOI: 10.4315/jfp-21-273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/09/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Extraintestinal pathogenic Escherichia coli (ExPEC) include several serotypes that have been associated with colibacillosis in poultry and with urinary tract infections (UTIs) and newborn meningitis in humans. In this study, 57 antimicrobial-resistant E. coli from apparently healthy broiler chickens were characterized for their health and safety risks. These isolates belonged to 12 serotypes, and isolates of the same serotype were clonal based on single nucleotide variant analysis. Most of the isolates harbored plasmids; IncC and IncFIA were frequently detected. The majority of the resistant isolates harbored plasmid-mediated resistance genes, including aph(3″)-Ib, aph(6)-Id, blaCMY-2, floR, sul1, sul2, tet(A), and tet(B), in agreement with their resistant phenotypes. The class 1 integron was detected in all E. coli serotypes except O124:H25 and O7:H6. Of the 57 broiler E. coli isolates, 27 were avian pathogenic, among which 18 were also uropathogenic E. coli and the remainder were other ExPEC. The two isolates of serotype O161:H4 (ST117) were genetically related to the control avian pathogenic strains and a clinical isolate associated with UTIs. A strain of serotype O159:H45 (ST101) also was closely related to a UTI isolate. The detected virulence factors included adhesins, invasins, siderophores, type III secretion systems, and toxins in combination with other virulence determinants. A broiler isolate of serotype O7:H18 (ST38) carried the ibeA gene encoding a protein involved in invasion of brain endothelium on a 102-kbp genetic island. This isolate moderately adhered and invaded Caco-2 cells and induced mortality (42.5%) in a day-old-chick infection model. The results of this study suggest that multiple antimicrobial-resistant E. coli isolates recovered from apparent healthy broilers can be pathogenic and act as reservoirs for antimicrobial resistance genes, highlighting the necessity of their assessment in a "One-Heath" context. HIGHLIGHTS
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Affiliation(s)
- Muhammad Attiq Rehman
- Guelph Research and Development Center, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada N1G 5C9
| | - Heidi Rempel
- Agassiz Research and Development Center, Agriculture and Agri-Food Canada, Agassiz, British Columbia, Canada V0M 1A2
| | - Catherine D Carrillo
- Canadian Food Inspection Agency, Ottawa Laboratory (Carling), Ottawa, Ontario, Canada K1Y 4K7
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency Canada, Guelph, Ontario, Canada N1G 3W4
| | - Kevin Allen
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Amee R Manges
- School of Population and Public Health, University of British Columbia, British Columbia, Canada V6T 1Z3.,British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada V5Z 4R4
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada N5V 4T3
| | - Moussa S Diarra
- Guelph Research and Development Center, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada N1G 5C9
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18
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Development of Single Nucleotide Polymorphism (SNP)-Based Triplex PCR Marker for Serotype-Specific Escherichia coli Detection. Pathogens 2022; 11:pathogens11020115. [PMID: 35215059 PMCID: PMC8874422 DOI: 10.3390/pathogens11020115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/29/2021] [Accepted: 01/14/2022] [Indexed: 01/27/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are one of the most common forms of genetic variation and as such are powerful tools for the identification of bacterial strains, their genetic diversity, phylogenetic analysis, and outbreak surveillance. In this study, we used 15 sets of SNP-containing primers to amplify and sequence the target Escherichia coli. Based on the combination of the 15-sequence primer sets, each SNP site encompassing forward and reverse primer sequences (620–919 bp) were aligned and an SNP-based marker was designed. Each SNP marker exists in at least two SNP sites at the 3′ end of each primer; one natural and the other artificially created by transition or transversion mutation. Thus, 12 sets of SNP primers (225–488 bp) were developed for validation by amplifying the target E. coli. Finally, a temperature gradient triplex PCR kit was designed to detect target E. coli strains. The selected primers were amplified in three genes (ileS, thrB, and polB), with fragment sizes of 401, 337, and 232 bp for E. coli O157:H7, E. coli, and E. coli O145:H28, respectively. This allele-specific SNP-based triplex primer assay provides serotype-specific detection of E. coli strains in one reaction tube. The developed marker would be used to diagnose, investigate, and control food-borne E. coli outbreaks.
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19
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Increasing azithromycin resistance in
Neisseria gonorrhoeae
due to NG-MAST 12302 clonal spread in Canada, 2015-2018. Antimicrob Agents Chemother 2022; 66:e0168821. [PMID: 34978884 PMCID: PMC8923198 DOI: 10.1128/aac.01688-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Objectives:
Azithromycin resistant (AZIR) gonorrhea has been steadily increasing in Canada over the past decade which is cause for alarm as azithromycin (AZI) has been part of the combination therapy recommended by the Canadian Guidelines on Sexually Transmitted Infections (CGSTI) since 2012.
Method:
Neisseria gonorrhoeae
(NG) with AZI MICs ≥ 1 mg/L collected between 2015 and 2018 as part of the Gonococcal Antimicrobial Surveillance Program-Canada underwent antimicrobial susceptibility testing, molecular typing and whole genome sequencing. Regional, demographic and clinical isolation site comparisons were made to aid in our understanding of AZI susceptibility trending.
Results:
3,447 NG with AZI MICs ≥ 1 mg/L were identified in Canada, increasing from 6.3% in 2015 to 26.5% of isolates in 2018. Central Canada had the highest proportion rising from 9.2% in 2015 to 31.2% in 2018. 273 different NG-MAST sequence types were identified among these isolates with ST-12302 the most prevalent (50.9%). Whole genome sequencing identified the
Neisseria lactamica
-like mosaic
mtr
locus as the mechanism of AZIR in isolates of ST-12302 and isolates genetically similar (differ by ≤ 5 base pairs) designated as the ST-12302 genogroup, accounting for 65.2% of study isolateswhich were originally identified in central Canada but spread to other regions by 2018.
Conclusion:
Genomic analysis indicated that AZIR in Canadian NG expanded rapidly due to clonal spread of the ST-12302 genogroup. The rapid expansion of this AZIR clonal group in all regions of Canada is of concern. CGSTI are currently under review to address the increase in AZIR in Canada.
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20
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Kracalik I, Ham DC, McAllister G, Smith AR, Vowles M, Kauber K, Zambrano M, Rodriguez G, Garner K, Chorbi K, Cassidy PM, McBee S, Stoney RJ, Moser K, Villarino ME, Zazueta OE, Bhatnagar A, Sula E, Stanton RA, Brown AC, Halpin AL, Epstein L, Walters MS. Extensively Drug-Resistant Carbapenemase-Producing Pseudomonas aeruginosa and Medical Tourism from the United States to Mexico, 2018-2019. Emerg Infect Dis 2022; 28:51-61. [PMID: 34932447 PMCID: PMC8714193 DOI: 10.3201/eid2801.211880] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) producing the Verona integron‒encoded metallo-β-lactamase (VIM) are highly antimicrobial drug-resistant pathogens that are uncommon in the United States. We investigated the source of VIM-CRPA among US medical tourists who underwent bariatric surgery in Tijuana, Mexico. Cases were defined as isolation of VIM-CRPA or CRPA from a patient who had an elective invasive medical procedure in Mexico during January 2018‒December 2019 and within 45 days before specimen collection. Whole-genome sequencing of isolates was performed. Thirty-eight case-patients were identified in 18 states; 31 were operated on by surgeon 1, most frequently at facility A (27/31 patients). Whole-genome sequencing identified isolates linked to surgeon 1 were closely related and distinct from isolates linked to other surgeons in Tijuana. Facility A closed in March 2019. US patients and providers should acknowledge the risk for colonization or infection after medical tourism with highly drug-resistant pathogens uncommon in the United States.
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Affiliation(s)
| | | | - Gillian McAllister
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Amanda R. Smith
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Maureen Vowles
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Kelly Kauber
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Melba Zambrano
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Gretchen Rodriguez
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Kelley Garner
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Kaitlyn Chorbi
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - P. Maureen Cassidy
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Shannon McBee
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Rhett J. Stoney
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Kathleen Moser
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Margarita E. Villarino
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Oscar E. Zazueta
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Amelia Bhatnagar
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Erisa Sula
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Richard A. Stanton
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Allison C. Brown
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Alison L. Halpin
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Lauren Epstein
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - Maroya Spalding Walters
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
| | - for the Verona Integron-Encoded Metallo-β-Lactamase–Producing Carbapenem-Resistant Pseudomonas aeruginosa Medical Tourism Investigation Team2
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA (I. Kracalik, D. Cal Ham, G. McAllister, R.J. Stoney, K. Moser, M.E. Villarino, A. Bhatnagar, E. Sula, R.A. Stanton, A.C. Brown, A.L. Halpin, L. Epstein, M. Spalding Walters)
- Utah Department of Health, Salt Lake City, Utah, USA (A.R. Smith, M. Vowles); Washington State Department of Health, Olympia, Washington, USA (K. Kauber)
- Texas Department of State Health Services, Austin, Texas, USA (M. Zambrano, G. Rodriguez)
- Arkansas Department of Health, Little Rock, Arkansas, USA (K. Garner)
- Arizona Department of Health Services, Phoenix, Arizona, USA (K. Chorbi)
- Oregon Health Authority, Portland, Oregon, USA (P.M. Cassidy)
- West Virginia Department of Health and Human Resources, Charleston, West Virginia, USA (S. McBee)
- Secretaría de Salud de Baja California, Mexicali, Mexico (O.E. Zazueta)
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21
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Jamal AJ, Faheem A, Farooqi L, Zhong XZ, Armstrong I, Boyd DA, Borgundvaag E, Coleman BL, Green K, Jayasinghe K, Johnstone J, Katz K, Kohler P, Li AX, Mataseje L, Melano R, Muller MP, Mulvey MR, Nayani S, Patel SN, Paterson A, Poutanen S, Rebbapragada A, Richardson D, Sarabia A, Shafinaz S, Simor AE, Willey BM, Wisely L, McGeer AJ. Household Transmission of Carbapenemase-producing Enterobacterales in Ontario, Canada. Clin Infect Dis 2021; 73:e4607-e4615. [PMID: 32869855 PMCID: PMC8662791 DOI: 10.1093/cid/ciaa1295] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/27/2020] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Data on household transmission of carbapenemase-producing Enterobacterales (CPE) remain limited. We studied risk of CPE household co-colonization and transmission in Ontario, Canada. METHODS We enrolled CPE index cases (identified via population-based surveillance from January 2015 to October 2018) and their household contacts. At months 0, 3, 6, 9, and 12, participants provided rectal and groin swabs. Swabs were cultured for CPE until September 2017, when direct polymerase chain reaction (PCR; with culture of specimens if a carbapenemase gene was detected) replaced culture. CPE risk factor data were collected by interview and combined with isolate whole-genome sequencing to determine likelihood of household transmission. Risk factors for household contact colonization were explored using a multivariable logistic regression model with generalized estimating equations. RESULTS Ninety-five households with 177 household contacts participated. Sixteen (9%) household contacts in 16 (17%) households were CPE-colonized. Household transmission was confirmed in 3/177 (2%) cases, probable in 2/177 (1%), possible in 9/177 (5%), and unlikely in 2/177 (1%). Household contacts were more likely to be colonized if they were the index case's spouse (odds ratio [OR], 6.17; 95% confidence interval [CI], 1.05-36.35), if their index case remained CPE-colonized at household enrollment (OR, 7.00; 95% CI, 1.92-25.49), or if they had at least 1 set of specimens processed after direct PCR was introduced (OR, 6.46; 95% CI, 1.52-27.40). CONCLUSIONS Nine percent of household contacts were CPE-colonized; 3% were a result of household transmission. Hospitals may consider admission screening for patients known to have CPE-colonized household contacts.
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Affiliation(s)
- Alainna J Jamal
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Amna Faheem
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Lubna Farooqi
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Xi Zoe Zhong
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Irene Armstrong
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Communicable Disease Control, Toronto Public Health, Toronto, Ontario, Canada
| | - David A Boyd
- Antimicrobial Resistance and Nosocomial Infections, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Emily Borgundvaag
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Brenda L Coleman
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Karen Green
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | | | - Jennie Johnstone
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Kevin Katz
- Department of Infection Prevention and Control, North York General Hospital, Toronto, Ontario, Canada
| | - Philipp Kohler
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Angel X Li
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Laura Mataseje
- Antimicrobial Resistance and Nosocomial Infections, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Roberto Melano
- Bacteriology, Public Health Ontario Laboratory, Toronto, Ontario, Canada
| | - Matthew P Muller
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Infection Prevention and Control, St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Michael R Mulvey
- Antimicrobial Resistance and Nosocomial Infections, National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Sarah Nayani
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Samir N Patel
- Bacteriology, Public Health Ontario Laboratory, Toronto, Ontario, Canada
| | - Aimee Paterson
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Susan Poutanen
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Anu Rebbapragada
- Scientific Affairs and Market Access, Hologic Inc., Toronto, Ontario, Canada
| | - David Richardson
- Department of Infection Prevention and Control, William Osler Health System, Brampton, Ontario, Canada
| | - Alicia Sarabia
- Department of Infection Prevention and Control, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Shumona Shafinaz
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Andrew E Simor
- Department of Infection Prevention and Control, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Barbara M Willey
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Laura Wisely
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
| | - Allison J McGeer
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Sinai Health System, Toronto, Ontario, Canada
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22
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A One-Health Genomic Investigation of Gentamicin Resistance in Salmonella from Human and Chicken Sources in Canada, 2014 to 2017. Antimicrob Agents Chemother 2021; 65:e0096621. [PMID: 34570642 DOI: 10.1128/aac.00966-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated whether the increased prevalence of gentamicin resistance in Salmonella from human infections was related to a similar increased prevalence in isolates from broiler chickens and whether this increase may have been due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on gentamicin-resistant (Genr) Salmonella isolates from human and chicken sources collected from 2014 to 2017 by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). We determined the genomic relatedness of strains and characterized resistance genes and plasmids. From 2014 to 2017, 247 isolates of Genr Salmonella were identified by CIPARS: 188 were from humans, and 59 were from chicken sources (26 from live animals on farm and 33 from retail meat). The five most common Genr serovars were Salmonella enterica serovars Heidelberg (n = 93; 31.5%), 4,[5],12:i:- (n = 42; 14.2%), Kentucky (n = 37; 12.5%), Infantis (n = 33; 11.2%), and Typhimurium (n = 23; 7.8%). Phylogenomic analysis revealed that for S. Heidelberg and S. Infantis, there were closely related isolates from human and chicken sources. In both sources, resistance to gentamicin and spectinomycin was most frequently conferred by aac(3)-VIa and ant(3'')-Ia, respectively. Plasmid closure confirmed linkages of gentamicin and spectinomycin resistance genes and revealed instances of similar plasmids from both sources. Gentamicin and spectinomycin resistance genes were linked on the same plasmids, and some plasmids and isolates from humans and chickens were genetically similar, suggesting that the use of lincomycin-spectinomycin in chickens may be selecting for gentamicin-resistant Salmonella in broiler chickens and that these resistant strains may be acquired by humans.
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23
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Bernaquez I, Gaudreau C, Pilon PA, Bekal S. Evaluation of whole-genome sequencing-based subtyping methods for the surveillance of Shigella spp. and the confounding effect of mobile genetic elements in long-term outbreaks. Microb Genom 2021; 7. [PMID: 34730485 PMCID: PMC8743557 DOI: 10.1099/mgen.0.000672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Many public health laboratories across the world have implemented whole-genome sequencing (WGS) for the surveillance and outbreak detection of foodborne pathogens. PulseNet-affiliated laboratories have determined that most single-strain foodborne outbreaks are contained within 0–10 multi-locus sequence typing (MLST)-based allele differences and/or core genome single-nucleotide variants (SNVs). In addition to being a food- and travel-associated outbreak pathogen, most
Shigella
spp. cases occur through continuous person-to-person transmission, predominantly involving men who have sex with men (MSM), leading to long-term and recurrent outbreaks. Continuous transmission patterns coupled to genetic evolution under antibiotic treatment pressure require an assessment of existing WGS-based subtyping methods and interpretation criteria for cluster inclusion/exclusion. An evaluation of 4 WGS-based subtyping methods [SNVPhyl, coreMLST, core genome MLST (cgMLST) and whole-genome MLST (wgMLST)] was performed on 9 foodborne-, travel- and MSM-related retrospective outbreaks from a collection of 91
Shigella flexneri
and 232
Shigella sonnei
isolates to determine the methods’ epidemiological concordance, discriminatory power, robustness and ability to generate stable interpretation criteria. The discriminatory powers were ranked as follows: coreMLST<SNVPhyl<cgMLST<wgMLST (range: 0.970–1.000). The genetic differences observed for non-MSM-related
Shigella
spp. outbreaks respect the standard 0–10 allele/SNV guideline; however, mobile genetic element (MGE)-encoded loci caused inflated genetic variation and discrepant phylogenies for prolonged MSM-related
S. sonnei
outbreaks via wgMLST. The
S. sonnei
correlation coefficients of wgMLST were also the lowest at 0.680, 0.703 and 0.712 for SNVPhyl, coreMLST and cgMLST, respectively. Plasmid maintenance, mobilization and conjugation-associated genes were found to be the main source of genetic distance inflation in addition to prophage-related genes. Duplicated alleles arising from the repeated nature of IS elements were also responsible for many false cg/wgMLST differences. The coreMLST approach was shown to be the most robust, followed by SNVPhyl and wgMLST for inter-laboratory comparability. Our results highlight the need for validating species-specific subtyping methods based on microbial genome plasticity and outbreak dynamics in addition to the importance of filtering confounding MGEs for cluster detection.
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Affiliation(s)
- Isabelle Bernaquez
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, H9X 3R5, Canada
| | - Christiane Gaudreau
- Microbiologie médicale et infectiologie, Centre Hospitalier de l’Université de Montréal (CHUM), Montreal, QC, H2X 3E4, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Pierre A. Pilon
- Direction régionale de santé publique, Centre intégré universitaire de santé et de services sociaux du Centre-Sud-de-l’île-de-Montréal, Montreal, QC, H2L 4M1, Canada
- Département de médecine sociale et préventive, Université de Montréal, Montreal, QC, H3N 1X9, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC, H9X 3R5, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montreal, QC, H3C 3J7, Canada
- *Correspondence: Sadjia Bekal,
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Linear regression equations to predict β-lactam, macrolide, lincosamide and fluoroquinolone minimum inhibitory concentrations from molecular antimicrobial resistance determinants in Streptococcus pneumoniae. Antimicrob Agents Chemother 2021; 66:e0137021. [PMID: 34662197 PMCID: PMC8765234 DOI: 10.1128/aac.01370-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance in Streptococcus pneumoniae represents a threat to public health and monitoring the dissemination of resistant strains is essential to guiding health policy. Multiple-variable linear regression modeling was used to determine the contributions of molecular antimicrobial resistance determinants to antimicrobial minimum inhibitory concentration (MIC) for penicillin, ceftriaxone, erythromycin, clarithromycin, clindamycin, levofloxacin, and trimethoprim/sulfamethoxazole. Training data sets consisting of Canadian S. pneumoniae isolated from 1995 to 2019 were used to generate multiple-variable linear regression equations for each antimicrobial. The regression equations were then applied to validation data sets of Canadian (n=439) and USA (n=607 and n=747) isolates. The MIC for β-lactam antimicrobials were fully explained by amino acid substitutions in motif regions of the penicillin binding proteins PBP1a, PPB2b, and PBP2x. Accuracy of predicted MICs within one doubling dilution to phenotypically determined MICs for penicillin was 97.4%, ceftriaxone 98.2%; erythromycin 94.8%; clarithromycin 96.6%; clindamycin 98.2%; levofloxacin 100%; and trimethoprim/sulfamethoxazole 98.8%; with an overall sensitivity of 95.8% and specificity of 98.0%. Accuracy of predicted MICs to the phenotypically determined MICs was similar to phenotype-only MIC comparison studies. The ability to acquire detailed antimicrobial resistance information directly from molecular determinants will facilitate the transition from routine phenotypic testing to whole genome sequencing analysis and can fill the surveillance gap in an era of increased reliance on nucleic acid assay diagnostics to better monitor the dynamics of S. pneumoniae.
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25
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Labbé G, Kruczkiewicz P, Robertson J, Mabon P, Schonfeld J, Kein D, Rankin MA, Gopez M, Hole D, Son D, Knox N, Laing CR, Bessonov K, Taboada EN, Yoshida C, Ziebell K, Nichani A, Johnson RP, Van Domselaar G, Nash JHE. Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel. Microb Genom 2021; 7. [PMID: 34554082 PMCID: PMC8715432 DOI: 10.1099/mgen.0.000651] [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] [Indexed: 11/18/2022] Open
Abstract
Hierarchical genotyping approaches can provide insights into the source, geography and temporal distribution of bacterial pathogens. Multiple hierarchical SNP genotyping schemes have previously been developed so that new isolates can rapidly be placed within pre-computed population structures, without the need to rebuild phylogenetic trees for the entire dataset. This classification approach has, however, seen limited uptake in routine public health settings due to analytical complexity and the lack of standardized tools that provide clear and easy ways to interpret results. The BioHansel tool was developed to provide an organism-agnostic tool for hierarchical SNP-based genotyping. The tool identifies split k-mers that distinguish predefined lineages in whole genome sequencing (WGS) data using SNP-based genotyping schemes. BioHansel uses the Aho-Corasick algorithm to type isolates from assembled genomes or raw read sequence data in a matter of seconds, with limited computational resources. This makes BioHansel ideal for use by public health agencies that rely on WGS methods for surveillance of bacterial pathogens. Genotyping results are evaluated using a quality assurance module which identifies problematic samples, such as low-quality or contaminated datasets. Using existing hierarchical SNP schemes for Mycobacterium tuberculosis and Salmonella Typhi, we compare the genotyping results obtained with the k-mer-based tools BioHansel and SKA, with those of the organism-specific tools TBProfiler and genotyphi, which use gold-standard reference-mapping approaches. We show that the genotyping results are fully concordant across these different methods, and that the k-mer-based tools are significantly faster. We also test the ability of the BioHansel quality assurance module to detect intra-lineage contamination and demonstrate that it is effective, even in populations with low genetic diversity. We demonstrate the scalability of the tool using a dataset of ~8100 S. Typhi public genomes and provide the aggregated results of geographical distributions as part of the tool’s output. BioHansel is an open source Python 3 application available on PyPI and Conda repositories and as a Galaxy tool from the public Galaxy Toolshed. In a public health context, BioHansel enables rapid and high-resolution classification of bacterial pathogens with low genetic diversity.
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Affiliation(s)
- Geneviève Labbé
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | | | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Philip Mabon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Justin Schonfeld
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Daniel Kein
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Marisa A Rankin
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Matthew Gopez
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Darian Hole
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - David Son
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Natalie Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology & Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chad R Laing
- National Centres for Animal Disease Lethbridge Laboratory, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - Kyrylo Bessonov
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Eduardo N Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Catherine Yoshida
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kim Ziebell
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Anil Nichani
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Roger P Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,National Centres for Animal Disease Lethbridge Laboratory, Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - John H E Nash
- National Microbiology Laboratory, Public Health Agency of Canada, Toronto, Ontario, Canada
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26
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Yang C, Rehman MA, Yin X, Carrillo CD, Wang QI, Yang C, Gong J, Diarra MS. Antimicrobial Resistance Phenotypes and Genotypes of Escherichia coli Isolates from Broiler Chickens Fed Encapsulated Cinnamaldehyde and Citral. J Food Prot 2021; 84:1385-1399. [PMID: 33770170 DOI: 10.4315/jfp-21-033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/26/2021] [Indexed: 12/16/2022]
Abstract
ABSTRACT This study was conducted to investigate the effects of in-feed encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination on antimicrobial resistance (AMR) phenotypes and genotypes of Escherichia coli isolates recovered from feces of 6-, 16-, 23-, and 27-day-old broiler chickens. The five dietary treatments including the basal diet (negative control [NC]) and the basal diet supplemented with 55 ppm of bacitracin (BAC), 100 ppm of encapsulated CIN, 100 ppm of encapsulated CIT, or 100 ppm each of encapsulated CIN and encapsulated CIT (CIN+CIT). Antimicrobial susceptibility testing of 240 E. coli isolates revealed that the most common resistance was to β-lactams, aminoglycosides, sulfonamides, and tetracycline; however, the prevalence of AMR decreased (P < 0.05) as birds aged. The prevalence of resistance to amoxicillin-clavulanic acid, ceftiofur, ceftriaxone, cefoxitin, gentamicin, and sulfonamide was lower (P < 0.05) in isolates from the CIN or CIN+CIT groups than in isolates from the NC or BAC groups. Whole genome sequencing of 227 of the 240 isolates revealed 26 AMR genes and 19 plasmids, but the prevalence of some AMR genes and the number of plasmids were lower (P < 0.05) in E. coli isolated from CIN or CIN+CIT birds than in isolates from NC or BAC birds. The most prevalent resistance genes were tet(A) (108 isolates), aac(3)-VIa (91 isolates), aadA1 (86 isolates), blaCMY-2 (78 isolates), sul1 (77 isolates), aph(3)-Ib (58 isolates), aph(6)-Id (58 isolates), and sul2 (24 isolates). The numbers of most virulence genes carried by isolates increased (P < 0.05) in chickens from 6 to 27 days of age. The prevalence of E. coli O21:H16 isolates was lower (P < 0.05) in CIN and CIN+CIT, and the colibacillosis-associated multilocus sequence type (ST117) was most prevalent in isolates from 23-day-old chickens. A phylogenetic tree of whole genome sequences revealed a close relationship between 25 of the 227 isolates and human or broiler extraintestinal pathogenic E. coli strains. These findings indicate that AMR and virulence genotypes of E. coli could be modulated by providing encapsulated CIN or CIN+CIT feed supplements, but further investigation is needed to determine the mechanisms of the effects of these supplements. HIGHLIGHTS
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Affiliation(s)
- Chongwu Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2.,Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada N1G 5C9
| | - Muhammad Attiq Rehman
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada N1G 5C9
| | - Xianhua Yin
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada N1G 5C9
| | - Catherine D Carrillo
- Canadian Food Inspection Agency, Ottawa Laboratory (Carling), Ottawa, Ontario, Canada K1A 0Z2
| | - Q I Wang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada N1G 5C9
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Joshua Gong
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada N1G 5C9
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada N1G 5C9
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27
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Genomic Epidemiology of Carbapenemase-Producing Enterobacterales at a Hospital System in Toronto, Ontario, Canada, 2007 to 2018. Antimicrob Agents Chemother 2021; 65:e0036021. [PMID: 34060902 DOI: 10.1128/aac.00360-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
At a hospital system (H1) in Ontario, Canada, we investigated whether whole-genome sequencing (WGS) altered initial epidemiological interpretation of carbapenemase-producing Enterobacterales (CPE) transmission. We included patients with CPE colonization/infection identified by population-based surveillance from October 2007 to August 2018 who received health care at H1 in the year before/after CPE detection. H1 reported epidemiological transmission clusters. We combined single nucleotide variant (SNV) analysis, plasmid characterization, and epidemiological data. Eighty-five patients were included. H1 identified 7 epidemiological transmission clusters, namely, A to G, involving 24/85 (28%) patients. SNV analysis confirmed transmission clusters C, D, and G and identified two additional cases belonging to cluster A. One was a travel-related case that was the likely index case (0 to 6 SNVs from other isolates); this case stayed on the same unit as the initially presumed index case 4 months prior to detection of the initially presumed index case on another unit. The second additional case occupied a room previously occupied by 5 cluster A cases. Plasmid sequence analysis excluded a case from cluster A and identified clusters E and F as possibly two parts of a single cluster. SNV analysis also identified a case without direct epidemiologic links that was 18 to 21 SNVs away from cluster B, suggesting possible undetected interhospital transmission. SNV and plasmid sequence analysis identified cases belonging to transmission clusters that conventional epidemiology missed and excluded other cases. Implementation of routine WGS to complement epidemiological transmission investigations has the potential to improve prevention and control of CPE in hospitals.
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Kellner JD, Ricketson LJ, Demczuk WHB, Martin I, Tyrrell GJ, Vanderkooi OG, Mulvey MR. Whole-Genome Analysis of Streptococcus pneumoniae Serotype 4 Causing Outbreak of Invasive Pneumococcal Disease, Alberta, Canada. Emerg Infect Dis 2021; 27:1867-1875. [PMID: 34152965 PMCID: PMC8237880 DOI: 10.3201/eid2707.204403] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
After the introduction of pneumococcal conjugate vaccines for children, invasive pneumococcal disease caused by Streptococcus pneumoniae serotype 4 declined in all ages in Alberta, Canada, but it has reemerged and spread in adults in Calgary, primarily among persons who are experiencing homelessness or who use illicit drugs. We conducted clinical and molecular analyses to examine the cases and isolates. Whole-genome sequencing analysis indicated relatively high genetic variability of serotype 4 isolates. Phylogenetic analysis identified 1 emergent sequence type (ST) 244 lineage primarily associated within Alberta and nationally distributed clades ST205 and ST695. Isolates from 6 subclades of the ST244 lineage clustered regionally, temporally, and by homeless status. In multivariable logistic regression, factors associated with serotype 4 invasive pneumococcal disease were being male, being <65 years of age, experiencing homelessness, having a diagnosis of pneumonia or empyema, or using illicit drugs.
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29
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Beukema W, Erens J, Schulz V, Stegen G, Spitzen-van der Sluijs A, Stark T, Laudelout A, Kinet T, Kirschey T, Poulain M, Miaud C, Steinfartz S, Martel A, Pasmans F. Landscape epidemiology of Batrachochytrium salamandrivorans: reconciling data limitations and conservation urgency. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02342. [PMID: 33817953 DOI: 10.1002/eap.2342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 12/01/2020] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Starting in 2010, rapid fire salamander (Salamandra salamandra) population declines in northwestern Europe heralded the emergence of Batrachochytrium salamandrivorans (Bsal), a salamander-pathogenic chytrid fungus. Bsal poses an imminent threat to global salamander diversity owing to its wide host range, high pathogenicity, and long-term persistence in ecosystems. While there is a pressing need to develop further research and conservation actions, data limitations inherent to recent pathogen emergence obscure necessary insights into Bsal disease ecology. Here, we use a hierarchical modeling framework to describe Bsal landscape epidemiology of outbreak sites in light of these methodological challenges. Using model selection and machine learning, we find that Bsal presence is associated with humid and relatively cool, stable climates. Outbreaks are generally located in areas characterized by low landscape heterogeneity and low steepness of slope. We further find an association between Bsal presence and high trail density, suggesting that human-mediated spread may increase risk for spillover between populations. We then use distribution modeling to show that favorable conditions occur in lowlands influenced by the North Sea, where increased survey effort is needed to determine how Bsal impacts local newt populations, but also in hill- and mountain ranges in northeastern France and the lower half of Germany. Finally, connectivity analyses suggest that these hill- and mountain ranges may act as stepping stones for further spread southward. Our results provide initial insight into regional environmental conditions underlying Bsal epizootics, present updated invasibility predictions for northwestern Europe, and lead us to discuss a wide variety of potential survey and research actions needed to advance future conservation and mitigation efforts.
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Affiliation(s)
- Wouter Beukema
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, 9820, Belgium
- Naturalis Biodiversity Center, P.O. Box␣9517, Leiden, 2300RA, the Netherlands
| | - Jesse Erens
- Naturalis Biodiversity Center, P.O. Box␣9517, Leiden, 2300RA, the Netherlands
| | - Vanessa Schulz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
- Technische Universität Braunschweig, Division of Evolutionary Biology, Zoological Institute, Mendelssohnstrasse 4, Braunschweig, 38106, Germany
| | - Gwij Stegen
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, 9820, Belgium
| | | | - Tariq Stark
- Reptile, Amphibian & Fish Conservation Netherlands (RAVON), Toernooiveld 1, Nijmegen, 6525ED, the Netherlands
| | - Arnaud Laudelout
- Reptile, Amphibian & Fish Conservation Netherlands (RAVON), Toernooiveld 1, Nijmegen, 6525ED, the Netherlands
| | - Thierry Kinet
- Natagora, Traverse des Muses 1, Namur, 5000, Belgium
| | - Tom Kirschey
- Nature and Biodiversity Conservation Union (NABU), Charitéstrasse 3, Berlin, 10117, Germany
| | - Marie Poulain
- Biogeography and Vertebrate Ecology, CEFE, EPHE-PSL, CNRS, University of Montpellier, Paul Valéry University Montpellier III, 1919 route de Mende, Montpellier, 34293, France
| | - Claude Miaud
- Biogeography and Vertebrate Ecology, CEFE, EPHE-PSL, CNRS, University of Montpellier, Paul Valéry University Montpellier III, 1919 route de Mende, Montpellier, 34293, France
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
| | - An Martel
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, 9820, Belgium
| | - Frank Pasmans
- Wildlife Health Ghent, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, 9820, Belgium
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30
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Gobeille Paré S, Mataseje LF, Ruest A, Boyd DA, Lefebvre B, Trépanier P, Longtin J, Dolce P, Mulvey MR. Arrival of the rare carbapenemase OXA-204 in Canada causing a multispecies outbreak over 3 years. J Antimicrob Chemother 2021; 75:2787-2796. [PMID: 32766684 DOI: 10.1093/jac/dkaa279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/26/2020] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To investigate a persistent multispecies OXA-204 outbreak occurring simultaneously in multiple distant hospitals in the province of Quebec, Canada. METHODS OXA-204 carbapenemase-producing Enterobacterales (CPE) isolated from multiple hospitals between January 2016 and October 2018 were included in the study. An epidemiological inquiry was conducted in order to elucidate possible transmission routes and a putative source. Isolates were characterized by standardized antibiotic susceptibility testing and by WGS, using Illumina short-read data and MinION long-read data. RESULTS The outbreak comprised 65 patients and 82 isolates from four hospital sites. Most patients were ≥65 years old, had multiple comorbidities and had received antibiotics recently. The infection to colonization ratio was 1:20. No persistent environmental reservoir was identified. The most frequent organism was Citrobacter freundii (n = 78), followed by Klebsiella spp. (n = 3) and Escherichia coli (n = 1). WGS analysis showed 77/78 C. freundii isolates differing by 0-26 single nucleotide variants (SNVs). Results of WGS analysis showed blaOXA-204 was present on three plasmids types (IncX1, IncA/C2 and IncFII/FIB/A/C2) and on a prophage. All C. freundii isolates harboured multiple copies of blaOXA-204, both on the chromosome and a plasmid. Plasmid IncFII/FIB/A/C2 was observed in all three species. CONCLUSIONS Transfer of OXA-204 plasmids likely occurred between species within the same patient, highlighting the plasticity of these plasmids and potential for widespread dissemination. OXA-204 carbapenemase has been introduced into Quebec and has rapidly disseminated. Although the infection to colonization ratio was low in this outbreak, this carbapenemase has been associated with severe infection elsewhere.
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Affiliation(s)
- Sarah Gobeille Paré
- Medical Microbiology and Infectious Diseases Department, CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Québec, Canada
| | - Laura F Mataseje
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Annie Ruest
- Medical Microbiology and Infectious Diseases Department, CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Québec, Canada
| | - David A Boyd
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Ste-Anne de Bellevue, Canada
| | - Pascale Trépanier
- Medical Microbiology and Infectious Diseases Department, CHU de Québec-Université Laval, Hôtel-Dieu de Québec, Québec, Canada
| | - Jean Longtin
- Laboratoire de santé publique du Québec, Ste-Anne de Bellevue, Canada
| | | | - Michael R Mulvey
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
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Abstract
Advancements in comparative genomics have generated significant interest in defining applications for healthcare-associated pathogens. Clinical microbiology, however, relies on increasingly automated platforms to quickly identify pathogens, resistance mechanisms, and therapy options within CLIA- and FDA-approved frameworks. Additionally, and most notably, healthcare-associated pathogens, especially those that are resistant to antibiotics, represent a diverse spectrum of genera harboring complex genetic targets including antibiotic, biocide, and virulence determinants that can be highly transmissible and, at least for antibiotic resistance, serve as potential targets for containment efforts. U.S. public health investments have focused on rapidly detecting outbreaks and emerging resistance in healthcare-associated pathogens using reference, culture-based, and molecular methods that are distributed, for example, across national laboratory network infrastructures. Herein we describe the public health applications of genomic science that are built from the top-down for broad surveillance, as well as the bottom-up, starting with identification of infections and infectious clusters. For healthcare-associated, including antimicrobial-resistant, pathogens, we propose a combination of top-down and bottom-up genomic approaches leveraged across the public health spectrum, from local infection control, to regional and national containment efforts, to national surveillance for understanding emerging strain ecology and fitness of healthcare pathogens.
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32
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Gonzales-Luna AJ, Spinler JK, Oezguen N, Khan MAW, Danhof HA, Endres BT, Alam MJ, Begum K, Lancaster C, Costa GP, Savidge TC, Hurdle JG, Britton R, Garey KW. Systems biology evaluation of refractory Clostridioides difficile infection including multiple failures of fecal microbiota transplantation. Anaerobe 2021; 70:102387. [PMID: 34044101 DOI: 10.1016/j.anaerobe.2021.102387] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) aims to cure Clostridioides difficile infection (CDI) through reestablishing a healthy microbiome and restoring colonization resistance. Although often effective after one infusion, patients with continued microbiome disruptions may require multiple FMTs. In this N-of-1 study, we use a systems biology approach to evaluate CDI in a patient receiving chronic suppressive antibiotics with four failed FMTs over two years. METHODS Seven stool samples were obtained between 2016-18 while the patient underwent five FMTs. Stool samples were cultured for C. difficile and underwent microbial characterization and functional gene analysis using shotgun metagenomics. C. difficile isolates were characterized through ribotyping, whole genome sequencing, metabolic pathway analysis, and minimum inhibitory concentration (MIC) determinations. RESULTS Growing ten strains from each sample, the index and first four recurrent cultures were single strain ribotype F078-126, the fifth was a mixed culture of ribotypes F002 and F054, and the final culture was ribotype F002. One single nucleotide polymorphism (SNP) variant was identified in the RNA polymerase (RNAP) β-subunit RpoB in the final isolated F078-126 strain when compared to previous F078-126 isolates. This SNV was associated with metabolic shifts but phenotypic differences in fidaxomicin MIC were not observed. Microbiome differences were observed over time during vancomycin therapy and after failed FMTs. CONCLUSION This study highlights the importance of antimicrobial stewardship in patients receiving FMT. Continued antibiotics play a destructive role on a transplanted microbiome and applies selection pressure for resistance to the few antibiotics available to treat CDI.
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Abstract
In 2018 to 2019, PCR for carbapenemases in routine Gram-negative isolates submitted to the National Microbiology Laboratory revealed an increase in IMP-type metalloenzyme-positive isolates, mostly among Morganellaceae. Whole-genome sequencing revealed that 23 Morganellaceae harbored blaIMP-27 within a chromosomal Tn7 element. Phylogenomics indicated diversity of isolates but also the presence of a few clonal isolates dispersed geographically. These isolates may be difficult to detect due to carbapenem susceptibility and false-negative results in phenotypic testing. IMPORTANCE Over the last decade or so, the frequency of isolation of clinical carbapenemase-producing organisms (CPOs) has increased among health care-associated infections. This may seriously compromise antimicrobial therapy, as carbapenems are considered the last line of defense against these organisms. The ability of carbapenemases to hydrolyze most β-lactams in addition to the co-occurrence of mechanisms of resistance to other classes of antimicrobials in CPOs can leave few options for treating infections. The class B metalloenzymes are globally distributed carbapenemases, and the most commonly found include the NDM, VIM, and IMP types. Our study describes a sudden emergence of IMP-27-harboring Morganellaceae during 2018 to 2019 in Canada. There is a paucity of literature on IMP-27 isolates, and our data bolster the information on the genetic context, antimicrobial profiles, and phylogenomics of this group of CPOs.
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Frost JR, Schulz H, McLachlan E, Hiebert J, Severini A. An enrichment method for capturing mumps virus whole genome sequences directly from clinical specimens. J Virol Methods 2021; 294:114176. [PMID: 33957163 DOI: 10.1016/j.jviromet.2021.114176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/16/2021] [Accepted: 04/24/2021] [Indexed: 10/21/2022]
Abstract
Recently there has been a significant increase in the number of mumps outbreaks occurring in highly vaccinated populations. These outbreaks are often due to a mumps genotype G virus, where sequencing of the SH gene does not reveal enough genetic diversity to sufficient to resolve outbreaks. This has elevated the need to be able to sequence complete mumps viruses from clinical samples without laborious methods. Here we describe a probe enrichment method that allows for whole genome sequencing of the mumps virus directly from clinical specimens. Using 136 clinical samples, we show this method allows for a significant increase in the percentage of viral sequencing reads, resulting in the capture of mumps genomes. This method will be an asset in investigating future mumps outbreaks.
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Affiliation(s)
- Jasmine Rae Frost
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Helene Schulz
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Elizabeth McLachlan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Joanne Hiebert
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Alberto Severini
- Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
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Singh N, Li X, Beshearse E, Blanton JL, DeMent J, Havelaar AH. Molecular Epidemiology of Salmonellosis in Florida, USA, 2017-2018. Front Med (Lausanne) 2021; 8:656827. [PMID: 33968960 PMCID: PMC8100233 DOI: 10.3389/fmed.2021.656827] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 11/21/2022] Open
Abstract
The state of Florida reports a high burden of non-typhoidal Salmonella enterica with approximately two times higher than the national incidence. We retrospectively analyzed the population structure and molecular epidemiology of 1,709 clinical isolates from 2017 and 2018. We found 115 different serotypes. Rarefaction suggested that the serotype richness did not differ between children under 2 years of age and older children and adults and, there are ~22 well-characterized dominant serotypes. There were distinct differences in dominant serotypes between Florida and the USA as a whole, even though S. Enteritidis and S. Newport were the dominant serotypes in Florida and nationally. S. Javiana, S. Sandiego, and S. IV 50:z4, z23:- occurred more frequently in Florida than nationally. Legacy Multi Locus Sequence Typing (MLST) was of limited use for differentiating clinical Salmonella isolates beyond the serotype level. We utilized core genome MLST (cgMLST) hierarchical clusters (HC) to identify potential outbreaks and compared them to outbreaks detected by Pulse Field Gel Electrophoresis (PFGE) surveillance for five dominant serotypes (Enteritidis, Newport, Javiana, Typhimurium, and Bareilly). Single nucleotide polymorphism (SNP) phylogenetic-analysis of cgMLST HC at allelic distance 5 or less (HC5) corroborated PFGE detected outbreaks and generated well-segregated SNP distance-based clades for all studied serotypes. We propose “combination approach” comprising “HC5 clustering,” as efficient tool to trigger Salmonella outbreak investigations, and “SNP-based analysis,” for higher resolution phylogeny to confirm an outbreak. We also applied this approach to identify case clusters, more distant in time and place than traditional outbreaks but may have been infected from a common source, comparing 176 Florida clinical isolates and 1,341 non-clinical isolates across USA, of most prevalent serotype Enteritidis collected during 2017–2018. Several clusters of closely related isolates (0–4 SNP apart) within HC5 clusters were detected and some included isolates from poultry from different states in the US, spanning time periods over 1 year. Two SNP-clusters within the same HC5 cluster included isolates with the same multidrug-resistant profile from both humans and poultry, supporting the epidemiological link. These clusters likely reflect the vertical transmission of Salmonella clones from higher levels in the breeding pyramid to production flocks.
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Affiliation(s)
- Nitya Singh
- Animal Sciences Department, Emerging Pathogens Institute, Food Systems Institute, University of Florida, Gainesville, FL, United States
| | - Xiaolong Li
- Department of Environmental and Global Health, Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Elizabeth Beshearse
- Animal Sciences Department, Emerging Pathogens Institute, Food Systems Institute, University of Florida, Gainesville, FL, United States
| | - Jason L Blanton
- Bureau of Public Health Laboratories, Florida Department of Health, Jacksonville, FL, United States
| | - Jamie DeMent
- Independent Researcher, Orlando, FL, United States.,Food and Waterborne Disease Program, Florida Department of Health, Tallahassee, FL, United States
| | - Arie H Havelaar
- Animal Sciences Department, Emerging Pathogens Institute, Food Systems Institute, University of Florida, Gainesville, FL, United States
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Resistance determinants and their genetic context in enterobacteria from a longitudinal study of pigs reared under various husbandry conditions. Appl Environ Microbiol 2021; 87:AEM.02612-20. [PMID: 33514521 PMCID: PMC8091121 DOI: 10.1128/aem.02612-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. Cefotaxime-resistant bacteria were quantified and isolated from feed, feces, manures and carcasses of pigs reared with penicillin-using or antibiotic-free husbandries. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays. The extended spectrum β-lactamase (ESBL) phenotype was more frequent in isolates originating from antibiotic-free animals, while the bacteria isolated from penicillin-using animals were on average resistant to a greater number of antibiotics. The ESBL-encoding genes identified were bla CTX-M-1, bla CTX-M-15 and bla CMY-2 and they co-localised on plasmids with various genes encoding resistance to ß-lactams, co-trimoxazole, phenicols and tetracycline, all antibiotics used in pig production. Groups of genes conferring the observed resistance and the mobile elements disseminating multidrug resistance were determined. The observed resistance to ß-lactams was mainly due to the complementary actions of penicillin-binding proteins, an efflux pump and ß-lactamases. Most resistance determinants were shared by animals raised with or without antimicrobials. This suggests a key contribution of indigenous enterobacteria maternally transmitted along the sow lineage, regardless of antimicrobial use. It is unclear if the antimicrobial resistance observed in the enterobacteria populations of the commercial pig herds studied were present before the use of antibiotics, or the extent to which historical antimicrobial use exerted a selective pressure defining the resistant bacterial populations in farms using penicillin prophylaxis.Importance: Antimicrobial resistance is a global threat that needs to be fought on numerous fronts along the One Health continuum. Vast quantities of antimicrobials are used in agriculture to ensure animal welfare and productivity, and are arguably a driving force for the persistence of environmental and food-borne resistant bacteria. This study evaluated the impact of conventional, organic and other antibiotic-free husbandry practices on the frequency and nature of antimicrobial resistance genes and multidrug resistant enterobacteria. It provides knowledge about the relative contribution of specific resistance determinants to observed antibiotic resistance. It also showed the clear co-selection of genes coding for extended-spectrum beta-lactamases and genes coding for the resistance to antibiotics commonly used for prophylaxis or in curative treatments in pig operations.
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Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands. Antibiotics (Basel) 2021; 10:antibiotics10030267. [PMID: 33807748 PMCID: PMC8000398 DOI: 10.3390/antibiotics10030267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 12/24/2022] Open
Abstract
Salmonella Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR S. Infantis strains recovered from poultry house environments in Santa Cruz Island of the Galapagos showing extended-spectrum β-lactamase (ESBL) resistance and reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed the presence of the ESBL-conferring blaCTX-M-65 gene in an IncFIB-like plasmid in three S. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the S. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1–3 SNP difference) to blaCTX-M-65-containing clinical and veterinary S. Infantis isolates from the United States and Latin America. Furthermore, phylogenetic analysis of SNPs following core-genome alignment (i.e., ParSNP) inferred close relatedness between the S. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos S. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR blaCTX-M-65-containing S. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens.
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Cooper AL, Carrillo CD, DeschÊnes M, Blais BW. Genomic Markers for Quaternary Ammonium Compound Resistance as a Persistence Indicator for Listeria monocytogenes Contamination in Food Manufacturing Environments. J Food Prot 2021; 84:389-398. [PMID: 33038236 DOI: 10.4315/jfp-20-328] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022]
Abstract
ABSTRACT Persistent contamination of food manufacturing environments by Listeria monocytogenes is an important public health risk, because such contamination events defy standard sanitization protocols, for example, the application of quaternary ammonium compounds such as benzalkonium chloride (BC), providing a source for prolonged dissemination of the bacteria in food products. We performed whole genome sequencing analyses of 1,279 well-characterized L. monocytogenes isolates from various foods and food manufacturing environments and identified the bcrABC gene cassette associated with BC resistance in 531 (41.5%) isolates. The bcrABC cassette was significantly associated with L. monocytogenes isolates belonging to clonal complex (CC) 321, CC155, CC204, and CC199, which are among the 10 most prevalent genotypes recovered from foods and food production environments. All but 1 of the 177 CC321 isolates harbored the bcrABC cassette. In addition, 384 (38.6%) of the 994 isolates recovered from foods representing 67 different CCs and 119 (59.2%) of isolates from food manufacturing environmental samples representing 26 different CCs were found to harbor the intact bcrABC cassette. A representative set of 69 isolates with and without bcrABC was assayed for the ability to grow in the presence of BC, and 34 of 35 isolates harboring the bcrABC cassette exhibited MICs of ≥10 μg/mL BC. Determination of bcrABC in isolates could be achieved using both PCR and whole genome sequencing techniques, providing food testing laboratories with options for the characterization of isolates. The ability to determine markers of quaternary ammonium compound resistance such as bcrABC and epidemiologic lineage may provide risk managers with a tool to assess the potential for persistent contamination of the food manufacturing environment and the need for more targeted surveillance to ensure the efficacy of mitigation actions. HIGHLIGHTS
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Affiliation(s)
- Ashley L Cooper
- Research and Development Section, Ottawa Laboratory Carling, Science Branch, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0Y9
| | - Catherine D Carrillo
- Research and Development Section, Ottawa Laboratory Carling, Science Branch, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0Y9
| | - MylÈne DeschÊnes
- Research and Development Section, Ottawa Laboratory Carling, Science Branch, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0Y9
| | - Burton W Blais
- Research and Development Section, Ottawa Laboratory Carling, Science Branch, Canadian Food Inspection Agency, Ottawa, Ontario, Canada K1A 0Y9
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Haim MS, Zaheer R, Bharat A, Di Gregorio S, Di Conza J, Galanternik L, Lubovich S, Golding GR, Graham MR, Van Domselaar G, Cardona ST, Mollerach M. Comparative genomics of ST5 and ST30 methicillin-resistant Staphylococcus aureus sequential isolates recovered from paediatric patients with cystic fibrosis. Microb Genom 2021; 7:mgen000510. [PMID: 33599606 PMCID: PMC8190608 DOI: 10.1099/mgen.0.000510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/21/2020] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus aureus chronic airway infection in patients with cystic fibrosis (CF) allows this pathogen to adapt over time in response to different selection pressures. We have previously shown that the main sequence types related to community-acquired methicillin-resistant S. aureus (MRSA) infections in Argentina - ST5 and ST30 - are also frequently isolated from the sputum of patients with CF, but in these patients they usually display multi-drug antimicrobial resistance. In this study, we sequenced the genomes of MRSA from four paediatric CF patients with the goal of identifying mutations among sequential isolates, especially those possibly related to antimicrobial resistance and virulence, which might contribute to the adaptation of the pathogen in the airways of patients with CF. Our results revealed genetic differences in sequential MRSA strains isolated from patients with CF in both their core and accessory genomes. Although the genetic adaptation of S. aureus was distinct in different hosts, we detected independent mutations in thyA, htrA, rpsJ and gyrA - which are known to have crucial roles in S. aureus virulence and antimicrobial resistance - in isolates recovered from multiple patients. Moreover, we identified allelic variants that were detected in all of the isolates recovered after a certain time point; these non-synonymous mutations were in genes associated with antimicrobial resistance, virulence, iron scavenging and oxidative stress resistance. In conclusion, our results provide evidence of genetic variability among sequential MRSA isolates that could be implicated in the adaptation of these strains during chronic CF airway infection.
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Affiliation(s)
- María Sol Haim
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Rahat Zaheer
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Sabrina Di Gregorio
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - José Di Conza
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Silvina Lubovich
- Hospital de Niños 'Dr Ricardo Gutiérrez', Buenos Aires, Argentina
| | - George R. Golding
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Morag R. Graham
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Silvia T. Cardona
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Marta Mollerach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Valiente-Mullor C, Beamud B, Ansari I, Francés-Cuesta C, García-González N, Mejía L, Ruiz-Hueso P, González-Candelas F. One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads. PLoS Comput Biol 2021; 17:e1008678. [PMID: 33503026 PMCID: PMC7870062 DOI: 10.1371/journal.pcbi.1008678] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 02/08/2021] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species were selected as reference sequences, and read alignment statistics, SNP calling, recombination rates, dN/dS ratios, and phylogenetic trees were evaluated depending on the mapping reference. The choice of different reference genomes proved to have an impact on almost all the parameters considered in the five species. In addition, these biases had potential epidemiological implications such as including/excluding isolates of particular clades and the estimation of genetic distances. These findings suggest that the single reference approach might introduce systematic errors during mapping that affect subsequent analyses, particularly for data sets with isolates from genetically diverse backgrounds. In any case, exploring the effects of different references on the final conclusions is highly recommended. Mapping consists in the alignment of reads (i.e., DNA fragments) obtained through high-throughput genome sequencing to a previously assembled reference sequence. It is a common practice in genomic studies to use a single reference for mapping, usually the ‘reference genome’ of a species—a high-quality assembly. However, the selection of an optimal reference is hindered by intrinsic intra-species genetic variability, particularly in bacteria. It is known that genetic differences between the reference genome and the read sequences may produce incorrect alignments during mapping. Eventually, these errors could lead to misidentification of variants and biased reconstruction of phylogenetic trees (which reflect ancestry between different bacterial lineages). To our knowledge, this is the first work to systematically examine the effect of different references for mapping on the inference of tree topology as well as the impact on recombination and natural selection inferences. Furthermore, the novelty of this work relies on a procedure that guarantees that we are evaluating only the effect of the reference. This effect has proved to be pervasive in the five bacterial species that we have studied and, in some cases, alterations in phylogenetic trees could lead to incorrect epidemiological inferences. Hence, the use of different reference genomes may be prescriptive to assess the potential biases of mapping.
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Affiliation(s)
- Carlos Valiente-Mullor
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Beatriz Beamud
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- * E-mail: (BB); (FG-C)
| | - Iván Ansari
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Carlos Francés-Cuesta
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Neris García-González
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Lorena Mejía
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Paula Ruiz-Hueso
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBER in Epidemiology and Public Health, Valencia, Spain
- * E-mail: (BB); (FG-C)
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A Bioinformatic Pipeline for Improved Genome Analysis and Clustering of Isolates during Outbreaks of Legionnaires' Disease. J Clin Microbiol 2021; 59:JCM.00967-20. [PMID: 33239371 DOI: 10.1128/jcm.00967-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 11/19/2020] [Indexed: 11/20/2022] Open
Abstract
Legionnaires' disease, a severe lung infection caused by the bacterium Legionella pneumophila, occurs as single cases or in outbreaks that are actively tracked by public health departments. To determine the point source of an outbreak, clinical isolates need to be compared to environmental samples to find matching isolates. One confounding factor is the genome plasticity of L. pneumophila, making an exact sequence comparison by whole-genome sequencing (WGS) challenging. Here, we present a WGS analysis pipeline, LegioCluster, that is designed to circumvent this problem by automatically selecting the best matching reference genome prior to mapping and variant calling. This approach reduces the number of false-positive variant calls, maximizes the fraction of all genomes that are being compared, and naturally clusters the isolates according to their reference strain. Isolates that are too distant from any genome in the database are added to the list of candidate references, thereby creating a new cluster. Short insertions or deletions are considered in addition to single-nucleotide polymorphisms for increased discriminatory power. This manuscript describes the use of this automated and "locked down" bioinformatic pipeline deployed at the New York State Department of Health's Wadsworth Center for investigating relatedness between clinical and environmental isolates. A similar pipeline has not been widely available for use to support these critically important public health investigations.
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Fagorzi C, Checcucci A. A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists. Methods Mol Biol 2021; 2242:233-243. [PMID: 33961228 DOI: 10.1007/978-1-0716-1099-2_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Making use of mathematics and statistics, bioinformatics helps biologists to quickly obtain information from a huge amount of experimental data. Nowadays, a large number of web- and computer-based tools are available, allowing more unskilled scientists to be familiar with data analysis techniques. The present chapter gives an overview of the most easy-to-use tools and software packages for bacterial genes and genome analysis present on the Web, with the aim to mainly help wet-lab researcher at undergraduate and postgraduate levels to introduce them to bioinformatics analysis of biological data.
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Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Florence, Italy
| | - Alice Checcucci
- Department of Agricultural and Food Science, University of Bologna, Bologna, Italy.
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43
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Investigation of Two Mycobacterium abscessus Outbreaks in Quebec Using Whole Genome Sequencing. BIOMED RESEARCH INTERNATIONAL 2020. [DOI: 10.1155/2020/7092053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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.
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Bernard KA, Vachon A, Pacheco AL, Burdz T, Wiebe D, Beniac DR, Hiebert SL, Booth T, Doyle DA, Lawson P, Bernier AM. 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. Int J Syst Evol Microbiol 2020; 70:6313-6322. [PMID: 33118921 DOI: 10.1099/ijsem.0.004533] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Kathryn A Bernard
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Alicia Vachon
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Ana Luisa Pacheco
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Tamara Burdz
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Deborah Wiebe
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Daniel R Beniac
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Shannon L Hiebert
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Tim Booth
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- National Microbiology Laboratory-CSCHAH, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Dena Annie Doyle
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Paul Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Anne-Marie Bernier
- Department of Biology, Université de Saint-Boniface, Winnipeg, Manitoba, Canada
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Labuda SM, Garner K, Cima M, Moulton-Meissner H, Laufer Halpin A, Charles-Toney N, Yu P, Bolton E, Pierce R, Crist MB, Gomes D, Gable P, McAllister G, Lawsin A, Houston H, Patil N, Wheeler JG, Bradsher R, Vyas K, Haselow D. Bloodstream Infections With a Novel Nontuberculous Mycobacterium Involving 52 Outpatient Oncology Clinic Patients-Arkansas, 2018. Clin Infect Dis 2020; 71:e178-e185. [PMID: 31872853 PMCID: PMC7938859 DOI: 10.1093/cid/ciz1120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/12/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND In July 2018, the Arkansas Department of Health (ADH) was notified by hospital A of 3 patients with bloodstream infections (BSIs) with a rapidly growing nontuberculous Mycobacterium (NTM) species; on 5 September 2018, 6 additional BSIs were reported. All were among oncology patients at clinic A. We investigated to identify sources and to prevent further infections. METHODS ADH performed an onsite investigation at clinic A on 7 September 2018 and reviewed patient charts, obtained environmental samples, and cultured isolates. The isolates were sequenced (whole genome, 16S, rpoB) by the Centers for Disease Control and Prevention to determine species identity and relatedness. RESULTS By 31 December 2018, 52 of 151 (34%) oncology patients with chemotherapy ports accessed at clinic A during 22 March-12 September 2018 had NTM BSIs. Infected patients received significantly more saline flushes than uninfected patients (P < .001) during the risk period. NTM grew from 6 unused saline flushes compounded by clinic A. The identified species was novel and designated Mycobacterium FVL 201832. Isolates from patients and saline flushes were highly related by whole-genome sequencing, indicating a common source. Clinic A changed to prefilled saline flushes on 12 September as recommended. CONCLUSIONS Mycobacterium FVL 201832 caused BSIs in oncology clinic patients. Laboratory data allowed investigators to rapidly link infections to contaminated saline flushes; cooperation between multiple institutions resulted in timely outbreak resolution. New state policies being considered because of this outbreak include adding extrapulmonary NTM to ADH's reportable disease list and providing more oversight to outpatient oncology clinics.
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Affiliation(s)
- Sarah M Labuda
- Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Kelley Garner
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Michael Cima
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Heather Moulton-Meissner
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alison Laufer Halpin
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- US Public Health Service, Rockville, Maryland, USA
| | - Nadege Charles-Toney
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Peter Yu
- Jefferson Regional Medical Center, Pine Bluff, Arkansas, USA
| | - Erin Bolton
- Jefferson Regional Medical Center, Pine Bluff, Arkansas, USA
| | - Reid Pierce
- Jefferson Regional Medical Center, Pine Bluff, Arkansas, USA
| | - Matthew B Crist
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Danica Gomes
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Paige Gable
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gillian McAllister
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Adrian Lawsin
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hollis Houston
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Naveen Patil
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - J Gary Wheeler
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Robert Bradsher
- University of Arkansas for the Medical Sciences, Little Rock, Arkansas, USA
| | - Keyur Vyas
- University of Arkansas for the Medical Sciences, Little Rock, Arkansas, USA
| | - Dirk Haselow
- Arkansas Department of Health, Little Rock, Arkansas, USA
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46
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Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa. J Clin Microbiol 2020; 58:JCM.00214-20. [PMID: 32493782 DOI: 10.1128/jcm.00214-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that frequently causes health care-associated infections (HAIs). Due to its metabolic diversity and ability to form biofilms, this Gram-negative nonfermenting bacterium can persist in the health care environment, which can lead to prolonged HAI outbreaks. We describe the creation of a core genome multilocus sequence typing (cgMLST) scheme to provide a stable platform for the rapid comparison of P. aeruginosa isolates using whole-genome sequencing (WGS) data. We used a diverse set of 58 complete P. aeruginosa genomes to curate a set of 4,440 core genes found in each isolate, representing ∼64% of the average genome size. We then expanded the alleles for each gene using 1,991 contig-level genome sequences. The scheme was used to analyze genomes from four historical HAI outbreaks to compare the phylogenies generated using cgMLST to those of other means (traditional MLST, pulsed-field gel electrophoresis [PFGE], and single-nucleotide variant [SNV] analysis). The cgMLST scheme provides sufficient resolution for analyzing individual outbreaks, as well as the stability for comparisons across a variety of isolates encountered in surveillance studies, making it a valuable tool for the rapid analysis of P. aeruginosa genomes.
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47
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Clark CG, Landgraff C, Robertson J, Pollari F, Parker S, Nadon C, Gannon VPJ, Johnson R, Nash J. Distribution of heavy metal resistance elements in Canadian Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype. PLoS One 2020; 15:e0236436. [PMID: 32716946 PMCID: PMC7384650 DOI: 10.1371/journal.pone.0236436] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/06/2020] [Indexed: 12/02/2022] Open
Abstract
Salmonella 4,[5],12:i:- are monophasic S. Typhimurium variants incapable of producing the second-phase flagellar antigen. They have emerged since the mid-1990s to become one of the most prevalent Salmonella serotypes causing human disease world-wide. Multiple genetic events associated with different genetic elements can result in the monophasic phenotype. Several jurisdictions have reported the emergence of a Salmonella 4,[5],12:i:- clone with SGI-4 and a genetic element (MREL) encoding a mercury resistance operon and antibiotic resistance loci that disrupts the second phase antigen region near the iroB locus in the Salmonella genome. We have sequenced 810 human and animal Canadian Salmonella 4,[5],12:i:- isolates and determined that isolates with SGI-4 and the mercury resistance element (MREL; also known as RR1&RR2) constitute several global clades containing various proportions of Canadian, US, and European isolates. Detailed analysis of the data provides a clearer picture of how these heavy metal elements interact with bacteria within the Salmonella population to produce the monophasic phenotype. Insertion of the MREL near iroB is associated with several deletions and rearrangements of the adjacent flaAB hin region, which may be useful for defining human case clusters that could represent outbreaks. Plasmids carrying genes encoding silver, copper, mercury, and antimicrobial resistance appear to be derived from IS26 mediated acquisition of these genes from genomes carrying SGI-4 and the MREL. Animal isolates with the mercury and As/Cu/Ag resistance elements are strongly associated with porcine sources in Canada as has been shown previously for other jurisdictions. The data acquired in these investigations, as well as from the extensive literature on the subject, may aid source attribution in outbreaks of the organism and interventions to decrease the prevalence of this clone and reduce its impact on human disease.
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Affiliation(s)
- Clifford G Clark
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Chrystal Landgraff
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - James Robertson
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Frank Pollari
- FoodNet Canada, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Stephen Parker
- FoodNet Canada, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Celine Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- PulseNet Canada, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Victor P J Gannon
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Canada
| | - Roger Johnson
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - John Nash
- Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
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48
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Nadin-Davis S, Pope L, Chmara J, Duceppe MO, Burke T, Devenish J, Andrievskaia O, Allain R, Ogunremi D. An Unusual Salmonella Enteritidis Strain Carrying a Modified Virulence Plasmid Lacking the prot6e Gene Represents a Geographically Widely Distributed Lineage. Front Microbiol 2020; 11:1322. [PMID: 32625191 PMCID: PMC7311658 DOI: 10.3389/fmicb.2020.01322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/25/2020] [Indexed: 12/02/2022] Open
Abstract
This study identifies a strain of Salmonella enterica subspecies enterica serovar Enteritidis that harbors a highly unusual virulence plasmid. During the characterisation of a group of S. Enteritidis isolates, 10 isolates recovered from Canadian duck production facilities, of which seven were phage type 9b and three were closely related atypical phage types, failed detection by a PCR targeting the prot6e gene, a marker located on the virulence plasmid often employed for identification of this serovar. Comparison to prot6e+ isolates by several standard genetic typing tools, further revealed their distinctive genomic makeup. Both short read and long read whole genome sequencing were completed on six of these isolates. In addition to loss of the prot6e gene, the virulence plasmid of each isolate was found to be exceptionally large (86.5 Kb) due to a 28 Kb insertion of S. Typhimurium plasmid sequence that encodes multiple genes of the incF operon. Interrogation of the chromosome sequence data of these isolates using a SNP-based typing tool and MLST both indicated their close genetic relatedness. One additional isolate carrying this plasmid was identified in an in-house collection of S. Enteritidis isolates. Finally, the identification of this unusual plasmid sequence in additional isolates submitted to public repositories of Salmonella sequence data was explored. All these analyses indicated that a very distinctive but rarely reported strain of S. Enteritidis was widely distributed across North America and the United Kingdom with one additional report involving a case from Brazil. With increased use of genetic methods for Salmonella identification, the loss of the prot6e sequence may confound correct identification of this serovar while also potentially altering the mode of transmission to humans given the gene’s role in facilitating propagation of this bacterium in eggs. Accordingly, this strain may present certain challenges with respect to public health investigations. Our studies also suggest this strain is often associated with duck hosts thereby providing a possible mechanism by which this strain has spread over an extensive geographical area.
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Affiliation(s)
- Susan Nadin-Davis
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Louise Pope
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Chmara
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Marc-Olivier Duceppe
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Teresa Burke
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - John Devenish
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Olga Andrievskaia
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Ray Allain
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Dele Ogunremi
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
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49
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Yousfi K, Usongo V, Berry C, Khan RH, Tremblay DM, Moineau S, Mulvey MR, Doualla-Bell F, Fournier E, Nadon C, Goodridge L, Bekal S. Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012. Front Microbiol 2020; 11:1317. [PMID: 32625190 PMCID: PMC7311582 DOI: 10.3389/fmicb.2020.01317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
Whole-genome sequencing (WGS) is the method of choice for bacterial subtyping and it is rapidly replacing the more traditional methods such as pulsed-field gel electrophoresis (PFGE). Here we used the high-resolution core genome single nucleotide variant (cgSNV) typing method to characterize clinical and food from Salmonella enterica serovar Heidelberg isolates in the context of source attribution. Additionally, clustered regularly interspaced short palindromic repeats (CRISPR) analysis was included to further support this method. Our results revealed that cgSNV was highly discriminatory and separated the outbreak isolates into distinct clusters (0-4 SNVs). CRISPR analysis was also able to distinguish outbreak strains from epidemiologically unrelated isolates. Specifically, our data clearly demonstrated the strength of these two methods to determine the probable source(s) of a 2012 epidemiologically characterized outbreak of S. Heidelberg. Using molecular cut-off of 0-10 SNVs, the cgSNV analysis of 246 clinical and food isolates of S. Heidelberg collected in Québec, in the same year of the outbreak event, revealed that retail and abattoir chicken isolates likely represent an important source of human infection to S. Heidelberg. Interestingly, the isolates genetically related by cgSNV also harbored the same CRISPR as outbreak isolates and clusters. This indicates that CRISPR profiles can be useful as a complementary approach to determine source attribution in foodborne outbreaks. Use of the genomic analysis also allowed to identify a large number of cases that were missed by PFGE, indicating that most outbreaks are probably underestimated. Although epidemiological information must still support WGS-based results, cgSNV method is a highly discriminatory method for the resolution of outbreak events and the attribution of these events to their respective sources. CRISPR typing can serve as a complimentary tool to this analysis during source tracking.
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Affiliation(s)
- Khadidja Yousfi
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.,Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Valentine Usongo
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.,Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Rufaida H Khan
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.,Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Denise M Tremblay
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Florence Doualla-Bell
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Celine Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Lawrence Goodridge
- Department of Food Science and Agricultural Chemistry, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
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50
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Van Rossum T, Ferretti P, Maistrenko OM, Bork P. Diversity within species: interpreting strains in microbiomes. Nat Rev Microbiol 2020; 18:491-506. [PMID: 32499497 DOI: 10.1038/s41579-020-0368-1] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 02/06/2023]
Abstract
Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.
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Affiliation(s)
- Thea Van Rossum
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Pamela Ferretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany. .,Max Delbrück Centre for Molecular Medicine, Berlin, Germany. .,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany. .,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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