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Pham NP, Gingras H, Godin C, Feng J, Groppi A, Nikolski M, Leprohon P, Ouellette M. Holistic understanding of trimethoprim resistance in Streptococcus pneumoniae using an integrative approach of genome-wide association study, resistance reconstruction, and machine learning. mBio 2024:e0136024. [PMID: 39120145 DOI: 10.1128/mbio.01360-24] [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: 05/03/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Antimicrobial resistance (AMR) is a public health threat worldwide. Next-generation sequencing (NGS) has opened unprecedented opportunities to accelerate AMR mechanism discovery and diagnostics. Here, we present an integrative approach to investigate trimethoprim (TMP) resistance in the key pathogen Streptococcus pneumoniae. We explored a collection of 662 S. pneumoniae genomes by conducting a genome-wide association study (GWAS), followed by functional validation using resistance reconstruction experiments, combined with machine learning (ML) approaches to predict TMP minimum inhibitory concentration (MIC). Our study showed that multiple additive mutations in the folA and sulA loci are responsible for TMP non-susceptibility in S. pneumoniae and can be used as key features to build ML models for digital MIC prediction, reaching an average accuracy within ±1 twofold dilution factor of 86.3%. Our roadmap of in silico analysis-wet-lab validation-diagnostic tool building could be adapted to explore AMR in other combinations of bacteria-antibiotic. IMPORTANCE In the age of next-generation sequencing (NGS), while data-driven methods such as genome-wide association study (GWAS) and machine learning (ML) excel at finding patterns, functional validation can be challenging due to the high numbers of candidate variants. We designed an integrative approach combining a GWAS on S. pneumoniae clinical isolates, followed by whole-genome transformation coupled with NGS to functionally characterize a large set of GWAS candidates. Our study validated several phenotypic folA mutations beyond the standard Ile100Leu mutation, and showed that the overexpression of the sulA locus produces trimethoprim (TMP) resistance in Streptococcus pneumoniae. These validated loci, when used to build ML models, were found to be the best inputs for predicting TMP minimal inhibitory concentrations. Integrative approaches can bridge the genotype-phenotype gap by biological insights that can be incorporated in ML models for accurate prediction of drug susceptibility.
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Affiliation(s)
- Nguyen-Phuong Pham
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Hélène Gingras
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Chantal Godin
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Alexis Groppi
- Bordeaux Bioinformatics Center and CNRS, Institut de Biochimie et Génétique Cellulaires (IBGC) UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Macha Nikolski
- Bordeaux Bioinformatics Center and CNRS, Institut de Biochimie et Génétique Cellulaires (IBGC) UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
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Schellenberg JJ, Adam HJ, Baxter MR, Karlowsky JA, Golden AR, Martin I, Zhanel GG. Phenotypic and molecular characterization of Streptococcus pneumoniae serotype 3 isolates from blood and respiratory samples in Canada: CANWARD 2007-21. J Antimicrob Chemother 2024:dkae272. [PMID: 39092981 DOI: 10.1093/jac/dkae272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Lower respiratory infections and invasive disease caused by Streptococcus pneumoniae serotype 3 remain major clinical challenges around the world, despite widespread availability of updated vaccines. METHODS As part of CANWARD, antimicrobial susceptibility testing and serotyping were performed on all S. pneumoniae isolates from 2007 to 2021. A subset of 226/264 (85.6%) serotype 3 isolates were selected for WGS to determine sequence type (ST)/clonal cluster (CC) and correspondence of antimicrobial resistance determinants (erm, mefAE, tetM, cat, folA, folP) with resistance phenotype. RESULTS Of the 3,039 S. pneumoniae isolates obtained from 2007 to 2021, 8.7% (n = 264) were serotype 3, with 64.0% of respiratory origin and 36.0% from blood. Of 226 sequenced serotype 3 isolates, 184 (81.4%) were ST180 (GPSC12). The proportion of ST8561 (single locus variant of ST180) increased from 7.2% to 16.6% during the study period. An increasing proportion of serotype 3 isolates had phenotypic resistance (P = 0.0007) and genetic resistance determinants (P = 0.004), comparing 2017-21 to 2007-11, largely due to a recently expanded ST180 clade with cat, tetM and mef determinants. CONCLUSIONS S. pneumoniae serotype 3 from GPSC12 continues to dominate throughout Canada, with an increase in the proportion of ST8561. The proportion of serotype 3 isolates that are phenotypically resistant and with genetic resistance determinants is increasing over time, reflecting a global increase in GPSC12 genotypes with known resistance determinants. Phylogenomic characterization of isolates collected over time and from around the world may facilitate improved treatment and enhanced prevention strategies, including new vaccines with activity against S. pneumoniae serotype 3.
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Affiliation(s)
- John J Schellenberg
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada R3E 0J9
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada R3E 0J9
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba, Canada R3A 1R9
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada R3E 0J9
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada R3E 0J9
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba, Canada R3A 1R9
| | - Alyssa R Golden
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3R2
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, Canada R3E 3R2
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, Canada R3E 0J9
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Liu Y, Ai H. Current research update on group B streptococcal infection related to obstetrics and gynecology. Front Pharmacol 2024; 15:1395673. [PMID: 38953105 PMCID: PMC11215423 DOI: 10.3389/fphar.2024.1395673] [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: 03/04/2024] [Accepted: 05/31/2024] [Indexed: 07/03/2024] Open
Abstract
Group B streptococcal (GBS) is a Gram-positive bacterium that is commonly found in the gastrointestinal tract and urogenital tract. GBS infestation during pregnancy is a significant contributor to maternal and neonatal morbidity and mortality globally. This article aims to discuss the infectious diseases caused by GBS in the field of obstetrics and gynecology, as well as the challenges associated with the detection, treatment, and prevention of GBS.
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Affiliation(s)
| | - Hao Ai
- Liaoning Provincial Key Laboratory of Follicular Development and Reproductive Health, Jinzhou Medical University, Jinzhou, Liaoning, China
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Rahman MK, Williams RB, Ajulo S, Levent G, Loneragan GH, Awosile B. Predictive Modeling of Phenotypic Antimicrobial Susceptibility of Selected Beta-Lactam Antimicrobials from Beta-Lactamase Resistance Genes. Antibiotics (Basel) 2024; 13:224. [PMID: 38534659 DOI: 10.3390/antibiotics13030224] [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: 01/30/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
The outcome of bacterial infection management relies on prompt diagnosis and effective treatment, but conventional antimicrobial susceptibility testing can be slow and labor-intensive. Therefore, this study aims to predict phenotypic antimicrobial susceptibility of selected beta-lactam antimicrobials in the bacteria of the family Enterobacteriaceae from different beta-lactamase resistance genotypes. Using human datasets extracted from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program conducted by Pfizer and retail meat datasets from the National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS), we used a robust or weighted least square multivariable linear regression modeling framework to explore the relationship between antimicrobial susceptibility data of beta-lactam antimicrobials and different types of beta-lactamase resistance genes. In humans, in the presence of the blaCTX-M-1, blaCTX-M-2, blaCTX-M-8/25, and blaCTX-M-9 groups, MICs of cephalosporins significantly increased by values between 0.34-3.07 μg/mL, however, the MICs of carbapenem significantly decreased by values between 0.81-0.87 μg/mL. In the presence of carbapenemase genes (blaKPC, blaNDM, blaIMP, and blaVIM), the MICs of cephalosporin antimicrobials significantly increased by values between 1.06-5.77 μg/mL, while the MICs of carbapenem antimicrobials significantly increased by values between 5.39-67.38 μg/mL. In retail meat, MIC of ceftriaxone increased significantly in the presence of blaCMY-2, blaCTX-M-1, blaCTX-M-55, blaCTX-M-65, and blaSHV-2 by 55.16 μg/mL, 222.70 μg/mL, 250.81 μg/mL, 204.89 μg/mL, and 31.51 μg/mL respectively. MIC of cefoxitin increased significantly in the presence of blaCTX-M-65 and blaTEM-1 by 1.57 μg/mL and 1.04 μg/mL respectively. In the presence of blaCMY-2, MIC of cefoxitin increased by an average of 8.66 μg/mL over 17 years. Compared to E. coli isolates, MIC of cefoxitin in Salmonella enterica isolates decreased significantly by 0.67 μg/mL. On the other hand, MIC of ceftiofur increased in the presence of blaCTX-M-1, blaCTX-M-65, blaSHV-2, and blaTEM-1 by 8.82 μg/mL, 9.11 μg/mL, 8.18 μg/mL, and 1.04 μg/mL respectively. In the presence of blaCMY-2, MIC of ceftiofur increased by an average of 10.20 μg/mL over 14 years. The ability to predict antimicrobial susceptibility of beta-lactam antimicrobials directly from beta-lactamase resistance genes may help reduce the reliance on routine phenotypic testing with higher turnaround times in diagnostic, therapeutic, and surveillance of antimicrobial-resistant bacteria of the family Enterobacteriaceae.
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Affiliation(s)
- Md Kaisar Rahman
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
| | - Ryan B Williams
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
| | - Samuel Ajulo
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
| | - Gizem Levent
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
| | - Guy H Loneragan
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
| | - Babafela Awosile
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA
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Massacci FR, Cucco L, Panicciá M, Luppi A, Albini E, Peruzzo A, Ferroni L, Ustulin M, Orsini M, Magistrali CF. Streptococcus suis serotype 9 in Italy: genomic insights into high-risk clones with emerging resistance to penicillin. J Antimicrob Chemother 2024; 79:403-411. [PMID: 38153239 PMCID: PMC10832592 DOI: 10.1093/jac/dkad395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Streptococcus suis is an important pig pathogen and an emerging zoonotic agent. In a previous study, we described a high proportion of penicillin-resistant serotype 9 S. suis (SS9) isolates on pig farms in Italy. OBJECTIVES We hypothesized that resistance to penicillin emerged in some SS9 lineages characterized by substitutions at the PBPs, contributing to the successful spread of these lineages in the last 20 years. METHODS Sixty-six SS9 isolates from cases of streptococcosis in pigs were investigated for susceptibility to penicillin, ceftiofur and ampicillin. The isolates were characterized for ST, virulence profile, and antimicrobial resistance genes through WGS. Multiple linear regression models were employed to investigate the associations between STs, year of isolation, substitutions at the PBPs and an increase in MIC values to β-lactams. RESULTS MIC values to penicillin increased by 4% each year in the study period. Higher MIC values for penicillin were also positively associated with ST123, ST1540 and ST1953 compared with ST16. The PBP sequences presented a mosaic organization of blocks. Within the same ST, substitutions at the PBPs were generally more frequent in recent isolates. Resistance to penicillin was driven by substitutions at PBP2b, including K479T, D512E and K513E, and PBP2x, including T551S, while reduced susceptibility to ceftiofur and ampicillin were largely dependent on substitutions at PBP2x. CONCLUSIONS Here, we identify the STs and substitutions at the PBPs responsible for increased resistance of SS9 to penicillin on Italian pig farms. Our data highlight the need for monitoring the evolution of S. suis in the coming years.
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Affiliation(s)
| | - Lucilla Cucco
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Marta Panicciá
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Andrea Luppi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Parma, Italy
| | - Elisa Albini
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Arianna Peruzzo
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Laura Ferroni
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Martina Ustulin
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
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Higgs C, Kumar LS, Stevens K, Strachan J, Korman T, Horan K, Daniel D, Russell M, McDevitt CA, Sherry NL, Stinear TP, Howden BP, Gorrie CL. Comparison of contemporary invasive and non-invasive Streptococcus pneumoniae isolates reveals new insights into circulating anti-microbial resistance determinants. Antimicrob Agents Chemother 2023; 67:e0078523. [PMID: 37823632 PMCID: PMC10649040 DOI: 10.1128/aac.00785-23] [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: 06/14/2023] [Accepted: 08/23/2023] [Indexed: 10/13/2023] Open
Abstract
Streptococcus pneumoniae is a major human pathogen with a high burden of disease. Non-invasive isolates (those found in non-sterile sites) are thought to be a key source of invasive isolates (those found in sterile sites) and a reservoir of anti-microbial resistance (AMR) determinants. Despite this, pneumococcal surveillance has almost exclusively focused on invasive isolates. We aimed to compare contemporaneous invasive and non-invasive isolate populations to understand how they interact and identify differences in AMR gene distribution. We used a combination of whole-genome sequencing and phenotypic anti-microbial susceptibility testing and a data set of invasive (n = 1,288) and non-invasive (n = 186) pneumococcal isolates, collected in Victoria, Australia, between 2018 and 2022. The non-invasive population had increased levels of antibiotic resistance to multiple classes of antibiotics including beta-lactam antibiotics penicillin and ceftriaxone. We identified genomic intersections between the invasive and non-invasive populations and no distinct phylogenetic clustering of the two populations. However, this analysis revealed sub-populations overrepresented in each population. The sub-populations that had high levels of AMR were overrepresented in the non-invasive population. We determined that WamR-Pneumo was the most accurate in silico tool for predicting resistance to the antibiotics tested. This tool was then used to assess the allelic diversity of the penicillin-binding protein genes, which acquire mutations leading to beta-lactam antibiotic resistance, and found that they were highly conserved (≥80% shared) between the two populations. These findings show the potential of non-invasive isolates to serve as reservoirs of AMR determinants.
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Affiliation(s)
- Charlie Higgs
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lamali Sadeesh Kumar
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Janet Strachan
- Communicable Diseases Branch, Department of Health, Victoria, Australia
| | - Tony Korman
- Department of Microbiology, Monash Health, Clayton, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Diane Daniel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Madeline Russell
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Norelle L. Sherry
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire L. Gorrie
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
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Golden AR, Lefebvre B, Deceuninck G, Brousseau N, De Wals P, Quach C, Demczuk WHB, Martin I. Clonal diversity of Streptococcus pneumoniae serotype 19A collected from children < 5 years old in Québec, Canada, 2016-2021. Vaccine 2023; 41:6612-6618. [PMID: 37758569 DOI: 10.1016/j.vaccine.2023.09.042] [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: 07/21/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023]
Abstract
Streptococcus pneumoniae serotype 19A is a highly diverse, often antimicrobial-resistant Gram-positive bacterium which can cause invasive pneumococcal disease (IPD). In 2021, public health authorities in the Canadian province of Québec observed an increase of serotype 19A IPD in children <5 years. The purpose of this study was to determine the clonal composition of serotype 19A isolates collected from this age group in Québec, from 2016 to 2021. Forty-one and 37 IPD isolates from children <5 years from Québec and the remainder of Canada, respectively, were sequenced using the Illumina NextSeq platform. Phylogenetic analysis using SNVPhyl identified three clusters, corresponding to three common clones of serotype 19A: CC199, CC320 and ST695. CC199, predominantly represented by ST416, accounted for similar proportions of serotype 19A isolates collected from children in Québec (19.5 %) and other Canadian jurisdictions (OCJs, 21.6 %), with significant presence of ermB (62.5 % and 60 % of ST416 isolates, respectively). CC320 was more commonly identified from OCJs in comparison to Québec (18.9 % vs. 7.3 %, respectively), but were highly antimicrobial-resistant regardless of region. ST695 was the most common clone of serotype 19A collected in Québec from children <5 years, representing 65.9 % of isolates collected over the study period (40.5 % of isolates collected in OCJs). Phylogenetic analysis identified geographical differences in ST695 across Canada; including a large clade specific to Québec (with both susceptible and macrolide-resistant [ermB] subclades), and a separate macrolide-resistant (mefA) clade associated with OCJs. The Québec-specific ermB-ST695 clone represented 48.1 % of ST695 collected from the province. Continued genomic surveillance of S. pneumoniae serotype 19A is required to: i) track the prevalence and clonal composition of serotype 19A in Québec in future years; ii) characterize the clonal distribution of serotype 19A in adult populations; and iii) monitor whether the currently geographically restricted ermB-ST695 clone observed in Québec expands to OCJs.
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Affiliation(s)
- Alyssa R Golden
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Geneviève Deceuninck
- Centre de recherche du Centre hospitalier universitaire de Québec, Équipe de recherche en vaccination, Québec, QC, Canada
| | - Nicholas Brousseau
- Centre de recherche du Centre hospitalier universitaire de Québec, Équipe de recherche en vaccination, Québec, QC, Canada; Institut national de santé publique du Québec, Direction des risques biologiques, Québec, QC, Canada
| | - Philippe De Wals
- Institut national de santé publique du Québec, Direction des risques biologiques, Québec, QC, Canada; Département de médecine sociale et préventive, Université Laval, Québec, QC, Canada
| | - Caroline Quach
- Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Montreal, QC, Canada
| | - Walter H B Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Chung HC, Foxx CL, Hicks JA, Stuber TP, Friedberg I, Dorman KS, Harris B. An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species. PLoS One 2023; 18:e0290473. [PMID: 37616210 PMCID: PMC10449230 DOI: 10.1371/journal.pone.0290473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
Understanding the microbial genomic contributors to antimicrobial resistance (AMR) is essential for early detection of emerging AMR infections, a pressing global health threat in human and veterinary medicine. Here we used whole genome sequencing and antibiotic susceptibility test data from 980 disease causing Escherichia coli isolated from companion and farm animals to model AMR genotypes and phenotypes for 24 antibiotics. We determined the strength of genotype-to-phenotype relationships for 197 AMR genes with elastic net logistic regression. Model predictors were designed to evaluate different potential modes of AMR genotype translation into resistance phenotypes. Our results show a model that considers the presence of individual AMR genes and total number of AMR genes present from a set of genes known to confer resistance was able to accurately predict isolate resistance on average (mean F1 score = 98.0%, SD = 2.3%, mean accuracy = 98.2%, SD = 2.7%). However, fitted models sometimes varied for antibiotics in the same class and for the same antibiotic across animal hosts, suggesting heterogeneity in the genetic determinants of AMR resistance. We conclude that an interpretable AMR prediction model can be used to accurately predict resistance phenotypes across multiple host species and reveal testable hypotheses about how the mechanism of resistance may vary across antibiotics within the same class and across animal hosts for the same antibiotic.
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Affiliation(s)
- Henri C. Chung
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States of America
| | - Christine L. Foxx
- Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Jessica A. Hicks
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States of America
| | - Tod P. Stuber
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States of America
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States of America
| | - Karin S. Dorman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States of America
- Department of Statistics, Iowa State University, Ames, IA, United States of America
| | - Beth Harris
- National Animal Health Laboratory Network, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States of America
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9
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Higgs C, Kumar LS, Stevens K, Strachan J, Sherry NL, Horan K, Zhang J, Stinear TP, Howden BP, Gorrie CL. Population structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in Victoria, Australia. Microb Genom 2023; 9:mgen001070. [PMID: 37471116 PMCID: PMC10438814 DOI: 10.1099/mgen.0.001070] [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: 05/02/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Streptococcus pneumoniae is a major human pathogen and can cause a range of conditions from asymptomatic colonization to invasive pneumococcal disease (IPD). The epidemiology and distribution of IPD-causing serotypes in Australia has undergone large changes following the introduction of the 7-valent pneumococcal conjugate vaccine (PCV) in 2005 and the 13-valent PCV in 2011. In this study, to provide a contemporary understanding of the IPD causing population in Victoria, Australia, we aimed to examine the population structure and prevalence of antimicrobial resistance using whole-genome sequencing and comprehensive antimicrobial susceptibility data of 1288 isolates collected between 2018 and 2022. We observed high diversity among the isolates with 52 serotypes, 203 sequence types (STs) and 70 Global Pneumococcal Sequencing Project Clusters (GPSCs) identified. Serotypes contained in the 13v-PCV represented 35.3 % (n=405) of isolates. Antimicrobial resistance (AMR) to at least one antibiotic was identified in 23.8 % (n=358) of isolates with penicillin resistance the most prevalent (20.3 %, n=261 using meningitis breakpoints and 5.1 % n=65 using oral breakpoints). Of the AMR isolates, 28 % (n=101) were multidrug resistant (MDR) (resistant to three or more drug classes). Vaccination status of cases was determined for a subset of isolates with 34 cases classified as vaccine failure events (fully vaccinated IPD cases of vaccine serotype). However, no phylogenetic association with failure events was observed. Within the highly diverse IPD population, we identified six high-risk sub-populations of public health concern characterized by high prevalence, high rates of AMR and MDR, or serotype inclusion in vaccines. High-risk serotypes included serotypes 3, 19F, 19A, 14, 11A, 15A and serofamily 23. In addition, we present our data validating seroBA for in silico serotyping to facilitate ISO-accreditation of this test in routine use in a public health reference laboratory and have made this data set available. This study provides insights into the population dynamics, highlights non-vaccine serotypes of concern that are highly resistant, and provides a genomic framework for the ongoing surveillance of IPD in Australia which can inform next-generation IPD prevention strategies.
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Affiliation(s)
- Charlie Higgs
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lamali Sadeesh Kumar
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Norelle L. Sherry
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Josh Zhang
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire L. Gorrie
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
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10
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Golden AR, Adam HJ, Karlowsky JA, Baxter M, Schellenberg J, Martin I, Demczuk W, Minion J, Van Caeseele P, Kus JV, McGeer A, Lefebvre B, Smadi H, Haldane D, Yu Y, Mead K, Mulvey MR, Zhanel GG. Genomic investigation of the most common Streptococcus pneumoniae serotypes causing invasive infections in Canada: the SAVE study, 2011-2020. J Antimicrob Chemother 2023; 78:i26-i36. [PMID: 37130587 DOI: 10.1093/jac/dkad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
OBJECTIVES To investigate the lineages and genomic antimicrobial resistance (AMR) determinants of the 10 most common pneumococcal serotypes identified in Canada during the five most recent years of the SAVE study, in the context of the 10-year post-PCV13 period in Canada. METHODS The 10 most common invasive Streptococcus pneumoniae serotypes collected by the SAVE study from 2016 to 2020 were 3, 22F, 9N, 8, 4, 12F, 19A, 33F, 23A and 15A. A random sample comprising ∼5% of each of these serotypes collected during each year of the full SAVE study (2011-2020) were selected for whole-genome sequencing (WGS) using the Illumina NextSeq platform. Phylogenomic analysis was performed using the SNVPhyl pipeline. WGS data were used to identify virulence genes of interest, sequence types, global pneumococcal sequence clusters (GPSC) and AMR determinants. RESULTS Of the 10 serotypes analysed in this study, six increased significantly in prevalence from 2011 to 2020: 3, 4, 8, 9N, 23A and 33F (P ≤ 0.0201). Serotypes 12F and 15A remained stable in prevalence over time, while serotype 19A decreased in prevalence (P < 0.0001). The investigated serotypes represented four of the most prevalent international lineages causing non-vaccine serotype pneumococcal disease in the PCV13 era: GPSC3 (serotypes 8/33F), GPSC19 (22F), GPSC5 (23A) and GPSC26 (12F). Of these lineages, GPSC5 isolates were found to consistently possess the most AMR determinants. Commonly collected vaccine serotypes 3 and 4 were associated with GPSC12 and GPSC27, respectively. However, a more recently collected lineage of serotype 4 (GPSC192) was highly clonal and possessed AMR determinants. CONCLUSIONS Continued genomic surveillance of S. pneumoniae in Canada is essential to monitor for the appearance of new and evolving lineages, including antimicrobial-resistant GPSC5 and GPSC162.
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Affiliation(s)
- Alyssa R Golden
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Heather J Adam
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba, R3A 1R9, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - James A Karlowsky
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba, R3A 1R9, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Melanie Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - John Schellenberg
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Jessica Minion
- Roy Romanow Provincial Laboratory, Saskatchewan Health Authority, 5 Research Drive, Regina, Saskatchewan, S4S 0A4, Canada
| | - Paul Van Caeseele
- Cadham Provincial Laboratory, Shared Health, 750 William Avenue, Winnipeg, Manitoba, R3E 3J7, Canada
| | - Julianne V Kus
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, Ontario, M5G 1M1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle-6th Floor, Toronto, Ontario, M5S 1A8, Canada
| | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network (TIBDN), Department of Microbiology, Mount Sinai Hospital. 600 University Avenue-Suite 171, Toronto, Ontario, M5G 1X5, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, 20045 Ch Ste-Marie, Ste-Anne-de-Bellevue, Québec, H9X 3R5, Canada
| | - Hanan Smadi
- Epidemiology and Surveillance Branch, New Brunswick Department of Health, 520 King Street, Fredericton, New Brunswick, E3B 5G8, Canada
| | - David Haldane
- Department of Pathology and Laboratory Medicine, Queen Elizabeth II Health Science Centre, 1276 South Park Street, Halifax, Nova Scotia, B3H 2Y9, Canada
| | - Yang Yu
- Newfoundland and Labrador Public Health Laboratory, Dr. Leonard A. Miller Centre-Suite 1, 100 Forest Road, St. John's, Newfoundland and Labrador, A1A 1E3, Canada
| | - Kristen Mead
- Provincial Laboratory Services, Queen Elizabeth Hospital, 60 Riverside Drive, Charlottetown, Prince Edward Island, C1A 8T5, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
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11
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Zhanel GG, Lynch JP, Adam HJ. Streptococcus pneumoniae serotyping and antimicrobial susceptibility: assessment for vaccine efficacy in Canada after the introduction of PCV13. J Antimicrob Chemother 2023; 78:i2-i7. [PMID: 37130585 DOI: 10.1093/jac/dkad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Streptococcus pneumoniae continues to be an important bacterial pathogen associated with invasive (e.g. bacteraemia, meningitis) and non-invasive (e.g. community-acquired respiratory tract) infections worldwide. Surveillance studies conducted nationally and globally assist in determining trends over geographical areas and allow comparisons between countries. OBJECTIVES To characterize invasive isolates of S. pneumoniae in terms of their serotype, antimicrobial resistance, genotype and virulence and to use the serotype data to determine the level of coverage by different generations of pneumococcal vaccines. METHODS SAVE (Streptococcus pneumoniae Serotyping and Antimicrobial Susceptibility: Assessment for Vaccine Efficacy in Canada) is an ongoing, annual, national collaborative study between the Canadian Antimicrobial Resistance Alliance (CARE) and the National Microbiology Laboratory, focused on characterizing invasive isolates of S. pneumoniae obtained across Canada. Clinical isolates from normally sterile sites were forwarded by participating hospital public health laboratories to the Public Health Agency of Canada-National Microbiology Laboratory and CARE for centralized phenotypic and genotypic investigation. RESULTS The four articles in this Supplement provide a comprehensive examination of the changing patterns of antimicrobial resistance and MDR, serotype distribution, genotypic relatedness and virulence of invasive S. pneumoniae obtained across Canada over a 10 year period (2011-2020). CONCLUSIONS The data highlight the evolution of S. pneumoniae under pressure by vaccination and antimicrobial usage, as well as vaccine coverage, allowing both clinicians and researchers nationally and globally to view the current status of invasive pneumococcal infections in Canada.
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Affiliation(s)
- George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745, Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Joseph P Lynch
- Division of Pulmonary, Critical Care Medicine, Allergy, and Clinical Immunology Department of Medicine, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave, Room 37-131 CHS, Los Angeles, CA 90095, USA
| | - Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745, Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
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