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Hulten KG, Genta RM, Kalfus IN, Zhou Y, Zhang H, Graham DY. Comparison of Culture With Antibiogram to Next-Generation Sequencing Using Bacterial Isolates and Formalin-Fixed, Paraffin-Embedded Gastric Biopsies. Gastroenterology 2021; 161:1433-1442.e2. [PMID: 34293298 PMCID: PMC9047521 DOI: 10.1053/j.gastro.2021.07.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The decline in Helicobacter pylori cure rates emphasizes the need for readily available methods to determine antimicrobial susceptibility. Our aim was to compare targeted next-generation sequencing (NGS) and culture-based H pylori susceptibility testing using clinical isolates and paired formalin-fixed, paraffin-embedded (FFPE) gastric biopsies. METHODS H pylori isolates and FFPE tissues were tested for susceptibility to amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and rifabutin using agar dilution and NGS targeted to 23S rRNA, gyrA, 16S rRNA, pbp1, rpoB and rdxA. Agreement was quantified using κ statistics. RESULTS Paired comparisons included 170 isolates and FFPE tissue for amoxicillin, clarithromycin, metronidazole, and rifabutin and 57 isolates and FFPE tissue for levofloxacin and tetracycline. Agreement between agar dilution and NGS from culture isolates was very good for clarithromycin (κ = 0.90012), good for levofloxacin (κ = 0.78161) and fair for metronidazole (κ = 0.55880), and amoxicillin (κ = 0.21400). Only 1 isolate was resistant to tetracycline (culture) and 1 to rifabutin (NGS). Comparison of NGS from tissue blocks and agar dilution from isolates from the same stomachs demonstrated good accuracy to predict resistance for clarithromycin (94.1%), amoxicillin (95.9%), metronidazole (77%), levofloxacin (87.7%), and tetracycline (98.2%). Lack of resistance precluded comparisons for tetracycline and rifabutin. CONCLUSIONS Compared with agar dilution, NGS reliably determined resistance to clarithromycin, levofloxacin, rifabutin, and tetracycline from clinical isolates and formalin-fixed gastric tissue. Consistency was fair for metronidazole and amoxicillin. Culture-based testing can predict treatment outcomes with clarithromycin and levofloxacin. Studies are needed to compare the relative ability of both methods to predict treatment outcomes for other antibiotics.
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Affiliation(s)
| | - Robert M. Genta
- Inform Diagnostics, Irving, Texas,Department of Pathology, Baylor College of Medicine, Houston, Texas
| | | | - Yi Zhou
- American Molecular Laboratories, Vernon Hills, Illinois
| | - Hongjun Zhang
- American Molecular Laboratories, Vernon Hills, Illinois
| | - David Y. Graham
- Department of Medicine, Michael E. DeBakey VA Medical Center and Baylor College of Medicine, Houston, Texas
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Varghese R, Veeraraghavan B. Decoding the Penicillin Resistance of Streptococcus pneumoniae for Invasive and Noninvasive Infections. Microb Drug Resist 2021; 27:942-950. [DOI: 10.1089/mdr.2020.0233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
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Nzoyikorera N, Diawara I, Fresia P, Maaloum F, Katfy K, Nayme K, Maaloum M, Cornick J, Chaguza C, Timinouni M, Belabess H, Zerouali K, Elmdaghri N. Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco. BMC Genomics 2021; 22:39. [PMID: 33413118 PMCID: PMC7792055 DOI: 10.1186/s12864-020-07316-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/09/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective of this study, which is part of the Pneumococcal African Genome project (PAGe), was to determine the phylogenetic relationships of serotype 1 isolates recovered from children patients in Casablanca (Morocco), compared to these from other African countries; and to investigate the contribution of accessory genes and recombination events to the genetic diversity of this serotype. RESULTS The genome average size of the six-pneumococcus serotype 1 from Casablanca was 2,227,119 bp, and the average content of coding sequences was 2113, ranging from 2041 to 2161. Pangenome analysis of the 80 genomes used in this study revealed 1685 core genes and 1805 accessory genes. The phylogenetic tree based on core genes and the hierarchical bayesian clustering analysis revealed five sublineages with a phylogeographic structure by country. The Moroccan strains cluster in two different lineages, the five invasive strains clusters altogether in a divergent clade distantly related to the non-invasive strain, that cluster with all the serotype 1 genomes from Africa. CONCLUSIONS The whole genome sequencing provides increased resolution analysis of the highly virulent serotype 1 in Casablanca, Morocco. Our results are concordant with previous works, showing that the phylogeography of S. pneumoniae serotype 1 is structured by country, and despite the small size (six isolates) of the Moroccan sample, our analysis shows the genetic cohesion of the Moroccan invasive isolates.
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Affiliation(s)
- Néhémie Nzoyikorera
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco.
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco.
| | - Idrissa Diawara
- Faculty of Sciences and Health Techniques, Mohammed VI University of Health Sciences (UM6SS) of Casablanca, Casablanca, Morocco
| | - Pablo Fresia
- Institut Pasteur de Montevideo, Pasteur + INIA Joint Unit (UMPI), Montevideo, Uruguay
- Institut Pasteur de Montevideo, Microbial Genomics Laboratory, Montevideo, Uruguay
| | - Fakhreddine Maaloum
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Khalid Katfy
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Kaotar Nayme
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Mossaab Maaloum
- Laboratory of Biology and Health, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Jennifer Cornick
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | - Mohammed Timinouni
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Houria Belabess
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Khalid Zerouali
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
| | - Naima Elmdaghri
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco
- Bacteriology-Virology and Hospital Hygiene Laboratory, Ibn Rochd University Hospital Centre, Casablanca, Morocco
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