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Fu B, Xu J, Yin D, Sun C, Liu D, Zhai W, Bai R, Cao Y, Zhang Q, Ma S, Walsh TR, Hu F, Wang Y, Wu C, Shen J. Transmission of blaNDM in Enterobacteriaceae among animals, food and human. Emerg Microbes Infect 2024; 13:2337678. [PMID: 38629492 PMCID: PMC11034458 DOI: 10.1080/22221751.2024.2337678] [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: 01/24/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
Despite carbapenems not being used in animals, carbapenem-resistant Enterobacterales (CRE), particularly New Delhi metallo-β-lactamase-producing CRE (NDM-CRE), are prevalent in livestock. Concurrently, the incidence of human infections caused by NDM-CRE is rising, particularly in children. Although a positive association between livestock production and human NDM-CRE infections at the national level was identified, the evidence of direct transmission of NDM originating from livestock to humans remains largely unknown. Here, we conducted a cross-sectional study in Chengdu, Sichuan Province, to examine the prevalence of NDM-CRE in chickens and pigs along the breeding-slaughtering-retail chains, in pork in cafeterias of schools, and in colonizations and infections from children's hospital and examined the correlation of NDM-CRE among animals, foods and humans. Overall, the blaNDM increases gradually along the chicken and pig breeding (4.70%/2.0%) -slaughtering (7.60%/22.40%) -retail (65.56%/34.26%) chains. The slaughterhouse has become a hotspot for cross-contamination and amplifier of blaNDM. Notably, 63.11% of pork from the school cafeteria was positive for blaNDM. The prevalence of blaNDM in intestinal and infection samples from children's hospitals was 21.68% and 19.80%, respectively. whole genome sequencing (WGS) analysis revealed the sporadic, not large-scale, clonal spread of NDM-CRE along the chicken and pig breeding-slaughtering-retail chain, with further spreading via IncX3-blaNDM plasmid within each stage of whole chains. Clonal transmission of NDM-CRE is predominant in children's hospitals. The IncX3-blaNDM plasmid was highly prevalent among animals and humans and accounted for 57.7% of Escherichia coli and 91.3% of Klebsiella pneumoniae. Attention should be directed towards the IncX3 plasmid to control the transmission of blaNDM between animals and humans.
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Affiliation(s)
- Bo Fu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jian Xu
- Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People’s Republic of China
| | - Dandan Yin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics (MoH), Shanghai, People’s Republic of China
| | - Chengtao Sun
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Dejun Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Weishuai Zhai
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Rina Bai
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yue Cao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Qin Zhang
- Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People’s Republic of China
| | - Shizhen Ma
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Timothy R. Walsh
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Department of Zoology, Ineos-Oxford Institute of Antimicrobial Research, University of Oxford, Oxford, UK
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics (MoH), Shanghai, People’s Republic of China
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Congming Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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Chen SL, Tiruvayipati S, Tang WY, M S Barkham T. Multilocus sequence typing database for Streptococcus agalactiae contains a spurious allele of the transketolase gene. Microbiol Spectr 2024:e0053724. [PMID: 39052441 DOI: 10.1128/spectrum.00537-24] [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: 02/27/2024] [Accepted: 05/30/2024] [Indexed: 07/27/2024] Open
Abstract
The tkt (transketolase) gene is one of the seven gene fragments used in the multilocus sequence typing (MLST) system for Streptococcus agalactiae. We discovered that the tkt_134 allele is derived from a homologous gene (which we designate tktX) that is not present in all S. agalactiae; all known strains that contain a match to the tkt_134 allele also contain a gene sequence that is much closer in sequence identity to the other non-tkt_134 alleles (i.e., the canonical tkt gene) in the database. Based on these data, the tkt_134 allele has been removed from the MLST database as of September 2021, and all sequence types containing tkt_134 have also been removed.IMPORTANCEMultilocus sequence typing (MLST) databases are a common good and remain important for research, medical, and epidemiological purposes. This remains true even in the context of widespread whole-genome sequencing. We discovered a contaminating allele of the tkt gene in the S. agalactiae MLST database that led to unstable, ambiguous, or erroneous MLST assignment. The allele has since been removed from the public database based on the results presented in this manuscript.
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Affiliation(s)
- Swaine L Chen
- Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore, Singapore
| | - Suma Tiruvayipati
- Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wen Ying Tang
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Timothy M S Barkham
- Department of Laboratory Medicine, Tan Tock Seng Hospital, Singapore, Singapore
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Zhang P, Liu L, Sheng H, Zhang M, Wang T, Chang G, Wang Y, Bai L, Wang X. Antibiotic Resistance and Genomic Analysis of Shiga Toxin-Producing Escherichia coli from Dairy Cattle, Raw Milk, and Farm Environment in Shaanxi Province, China. Foodborne Pathog Dis 2024. [PMID: 39042484 DOI: 10.1089/fpd.2023.0098] [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: 07/25/2024] Open
Abstract
To investigate the epidemiology of Shiga toxin-producing Escherichia coli (STEC) in dairy cattle, 975 samples (185 feces, 34 silage, 36 cattle drinking water, 360 raw milk, and 360 teat skin swabs) were collected from two dairy farms in Baoji and Yangling, Shaanxi Province, China, and were screened for STEC. Whole-genome sequencing was used to analyze the genomic characteristics and potential transmission of STEC isolates. A total of 32 samples were contaminated with STEC, including 4.0% (19/479) in Farm A and 2.6% (13/496) in Farm B. Compared with adult cows (4.5%), nonadult cows had a higher rate (21.3%) of STEC colonization. A total of 14 serotypes and 11 multilocus sequence typing were identified in 32 STEC isolates, among which O55:H12 (25.0%) and ST101 (31.3%) were the most predominant, respectively. Six stx subtypes/combinations were identified, including stx1a (53.1%), stx2g (15.6%), stx2d, stx2a+stx2d, stx1a+stx2a (6.3%, for each), and stx2a (3.1%). Of 32 STEC isolates, 159 virulence genes and 27 antibiotic resistance genes were detected. Overall, STEC isolates showed low levels of resistance to the 16 antibiotics tested (0-40.6%), with most common resistance to ampicillin (40.6%). The phylogenetic analysis confirmed that STEC in the gut of cattle can be transmitted through feces. The results of this study help to improve our understanding of the epidemiological aspects of STEC in dairy cattle and provide early warning and control of the prevalence and spread of the bacterium.
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Affiliation(s)
- Pengfei Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
- College of Food Science, Shanxi Normal University, Taiyuan, Shanxi, China
| | - Lisha Liu
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, Beijing, China
| | - Huanjing Sheng
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Meng Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Ting Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Guanhong Chang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
| | - Yeru Wang
- National Center for Food Safety Risk Assessment, Beijing, China
| | - Li Bai
- National Center for Food Safety Risk Assessment, Beijing, China
| | - Xin Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, China
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Arconada Nuin E, Vilken T, Xavier BB, Doua J, Morrow B, Geurtsen J, Go O, Spiessens B, Sarnecki M, Poolman J, Bonten M, Ekkelenkamp M, Lammens C, Goossens H, Glupczynski Y, Van Puyvelde S. A microbiological and genomic perspective of globally collected Escherichia coli from adults hospitalized with invasive E. coli disease. J Antimicrob Chemother 2024:dkae182. [PMID: 39001716 DOI: 10.1093/jac/dkae182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/14/2024] [Indexed: 07/15/2024] Open
Abstract
OBJECTIVES Escherichia coli can cause infections in the urinary tract and in normally sterile body sites leading to invasive E. coli disease (IED), including bacteraemia and sepsis, with older populations at increased risk. We aimed to estimate the theoretical coverage rate by the ExPEC4V and 9V vaccine candidates. In addition, we aimed at better understanding the diversity of E. coli isolates, including their genetic and phenotypic antimicrobial resistance (AMR), sequence types (STs), O-serotypes and the bacterial population structure. METHODS Blood and urine culture E. coli isolates (n = 304) were collected from hospitalized patients ≥60 years (n = 238) with IED during a multicentric, observational study across three continents. All isolates were tested for antimicrobial susceptibility, O-serotyped, whole-genome sequenced and bioinformatically analysed. RESULTS A large diversity of STs and of O-serotypes were identified across all centres, with O25b-ST131, O6-ST73 and O1-ST95 being the most prevalent types. A total of 45.4% and 64.7% of all isolates were found to have an O-serotype covered by the ExPEC4V and ExPEC9V vaccine candidates, respectively. The overall frequency of MDR was 37.4% and ST131 was predominant among MDR isolates. Low in-patient genetic variability was observed in cases where multiple isolates were collected from the same patient. CONCLUSIONS Our results highlight the predominance of MDR O25b-ST131 E. coli isolates across diverse geographic areas. These findings provide further baseline data on the theoretical coverage of novel vaccines targeting E. coli associated with IED in older adults and their associated AMR levels.
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Affiliation(s)
- Enya Arconada Nuin
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Tuba Vilken
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Joachim Doua
- Janssen Research & Development, Infectious Diseases & Vaccines, Janssen Pharmaceutica, Beerse, Belgium
| | - Brian Morrow
- Janssen Research & Development, Raritan, NJ, USA
| | - Jeroen Geurtsen
- Bacterial Vaccines Discovery & Early Development, Janssen Vaccines & Prevention B.V., Leiden, The Netherlands
| | - Oscar Go
- Janssen Research & Development, Raritan, NJ, USA
| | - Bart Spiessens
- Janssen Research & Development, Infectious Diseases & Vaccines, Janssen Pharmaceutica, Beerse, Belgium
| | - Michal Sarnecki
- Janssen Vaccines, Branch of Cilag GmbH International, Bern, Switzerland
| | - Jan Poolman
- Bacterial Vaccines Discovery & Early Development, Janssen Vaccines & Prevention B.V., Leiden, The Netherlands
| | - Marc Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- ECRAID, Utrecht, The Netherlands
| | - Miquel Ekkelenkamp
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sandra Van Puyvelde
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
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Khan UB, Dyster V, Chaguza C, van Sorge NM, van de Beek D, Man WK, Bentley SD, Bijlsma MW, Jamrozy D. Genetic markers associated with host status and clonal expansion of Group B Streptococcus in the Netherlands. Front Microbiol 2024; 15:1410651. [PMID: 39050634 PMCID: PMC11266191 DOI: 10.3389/fmicb.2024.1410651] [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: 04/01/2024] [Accepted: 06/19/2024] [Indexed: 07/27/2024] Open
Abstract
Objectives Certain Group B Streptococcus (GBS) genotypes are associated with invasive disease in neonates. We conducted a comparative genomic analysis of GBS isolates from neonatal disease and maternal carriage in the Netherlands to determine distribution of genetic markers between the two host groups. Methods Whole genome sequencing was used to characterise 685 neonatal invasive isolates (2006-2021) and 733 maternal carriage isolates (2017-2021) collected in the Netherlands. Results Clonal complex (CC) 17 and serotype III were significantly more common in disease while carriage isolates were associated with serotypes II, IV, V as well as CC1. Previously reported CC17-A1 sub-lineage was dominant among disease isolates and significantly less common in carriage. The phiStag1 phage, previously associated with expansion of invasive CC17 isolates in the Netherlands, was more common among disease isolates compared to carriage isolates overall, however it was equally distributed between CC17 isolates from carriage and disease. Prevalence of antimicrobial resistance genes was overall lower in disease compared to carriage isolates, but increased significantly over time, mediated by rise in prevalence of a multidrug resistance element ICESag37 among disease isolates. Conclusion There is a stable association between certain GBS genotypes and invasive disease, which suggests opportunities for developing more precise disease prevention strategies based on GBS targeted screening. In contrast, GBS mobile genetic elements appear less likely to be correlated with carriage or disease, and instead are associated with clonal expansion events across the GBS population.
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Affiliation(s)
- Uzma Basit Khan
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Victoria Dyster
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, United States
| | - Nina M. van Sorge
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam UMC Location AMC, Amsterdam, Netherlands
| | - Diederik van de Beek
- Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Wing Kit Man
- Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Merijn W. Bijlsma
- Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Paediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Dorota Jamrozy
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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Li X, Hu H, Zhu Y, Wang T, Lu Y, Wang X, Peng Z, Sun M, Chen H, Zheng J, Tan C. Population structure and antibiotic resistance of swine extraintestinal pathogenic Escherichia coli from China. Nat Commun 2024; 15:5811. [PMID: 38987310 PMCID: PMC11237156 DOI: 10.1038/s41467-024-50268-2] [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: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
Extraintestinal Pathogenic Escherichia coli (ExPEC) pose a significant threat to human and animal health. However, the diversity and antibiotic resistance of animal ExPEC, and their connection to human infections, remain largely unexplored. The study performs large-scale genome sequencing and antibiotic resistance testing of 499 swine-derived ExPEC isolates from China. Results show swine ExPEC are phylogenetically diverse, with over 80% belonging to phylogroups B1 and A. Importantly, 15 swine ExPEC isolates exhibit genetic relatedness to human-origin E. coli strains. Additionally, 49 strains harbor toxins typical of enteric E. coli pathotypes, implying hybrid pathotypes. Notably, 97% of the total strains are multidrug resistant, including resistance to critical human drugs like third- and fourth-generation cephalosporins. Correspondingly, genomic analysis unveils prevalent antibiotic resistance genes (ARGs), often associated with co-transfer mechanisms. Furthermore, analysis of 20 complete genomes illuminates the transmission pathways of ARGs within swine ExPEC and to human pathogens. For example, the transmission of plasmids co-harboring fosA3, blaCTX-M-14, and mcr-1 genes between swine ExPEC and human-origin Salmonella enterica is observed. These findings underscore the importance of monitoring and controlling ExPEC infections in animals, as they can serve as a reservoir of ARGs with the potential to affect human health or even be the origin of pathogens infecting humans.
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Affiliation(s)
- Xudong Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huifeng Hu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Yongwei Zhu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Taiquan Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Youlan Lu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiangru Wang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Zhong Peng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Ming Sun
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
| | - Jinshui Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Chen Tan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China.
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7
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Wetzstein N, Diricks M, Anton TB, Andres S, Kuhns M, Kohl TA, Schwarz C, Lewin A, Kehrmann J, Kahl BC, Schmidt A, Zimmermann S, Jansson MK, Baron SA, Schulthess B, Hogardt M, Friesen I, Niemann S, Wichelhaus TA. Clinical and genomic features of Mycobacterium avium complex: a multi-national European study. Genome Med 2024; 16:86. [PMID: 38982539 PMCID: PMC11232273 DOI: 10.1186/s13073-024-01359-8] [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: 01/25/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND The Mycobacterium avium complex (MAC) comprises the most frequent non-tuberculous mycobacteria (NTM) in Central Europe and currently includes twelve species. M. avium (MAV), M. intracellulare subsp. intracellulare (MINT), and M. intracellulare subsp. chimaera (MCH) are clinically most relevant. However, the population structure and genomic landscape of MAC linked with potential pathobiological differences remain little investigated. METHODS Whole genome sequencing (WGS) was performed on a multi-national set of MAC isolates from Germany, France, and Switzerland. Phylogenetic analysis was conducted, as well as plasmids, resistance, and virulence genes predicted from WGS data. Data was set into a global context with publicly available sequences. Finally, detailed clinical characteristics were associated with genomic data in a subset of the cohort. RESULTS Overall, 610 isolates from 465 patients were included. The majority could be assigned to MAV (n = 386), MCH (n = 111), and MINT (n = 77). We demonstrate clustering with less than 12 SNPs distance of isolates obtained from different patients in all major MAC species and the identification of trans-European or even trans-continental clusters when set into relation with 1307 public sequences. However, none of our MCH isolates clustered closely with the heater-cooler unit outbreak strain Zuerich-1. Known plasmids were detected in MAV (325/1076, 30.2%), MINT (62/327, 19.0%), and almost all MCH-isolates (457/463, 98.7%). Predicted resistance to aminoglycosides or macrolides was rare. Overall, there was no direct link between phylogenomic grouping and clinical manifestations, but MCH and MINT were rarely found in patients with extra-pulmonary disease (OR 0.12 95% CI 0.04-0.28, p < 0.001 and OR 0.11 95% CI 0.02-0.4, p = 0.004, respectively) and MCH was negatively associated with fulfillment of the ATS criteria when isolated from respiratory samples (OR 0.28 95% CI 0.09-0.7, p = 0.011). With 14 out of 43 patients with available serial isolates, co-infections or co-colonizations with different strains or even species of the MAC were frequent (32.6%). CONCLUSIONS This study demonstrates clustering and the presence of plasmids in a large proportion of MAC isolates in Europe and in a global context. Future studies need to urgently define potential ways of transmission of MAC isolates and the potential involvement of plasmids in virulence.
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Affiliation(s)
- Nils Wetzstein
- Department of Internal Medicine, Infectious Diseases, Goethe University, University Hospital, Theodor-Stern-Kai 7, FrankfurtFrankfurt Am Main, 60590, Germany.
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
| | - Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thomas B Anton
- Department of Internal Medicine, Infectious Diseases, Goethe University, University Hospital, Theodor-Stern-Kai 7, FrankfurtFrankfurt Am Main, 60590, Germany
| | - Sönke Andres
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Martin Kuhns
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Carsten Schwarz
- Division of Cystic Fibrosis, CF Center Westbrandenburg, Campus Potsdam, Klinikum Potsdam, Potsdam, Germany
| | - Astrid Lewin
- Unit Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Barbara C Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Annika Schmidt
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Zimmermann
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
| | - Moritz K Jansson
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Sophie A Baron
- Faculté de Médecine Et de Pharmacie, IRD, APHM, Aix Marseille Univ, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Bettina Schulthess
- National Reference Laboratory for Mycobacteria, Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, Goethe University, University Hospital, FrankfurtFrankfurt Am Main, Germany
- German National Consiliary Laboratory On Cystic Fibrosis Bacteriology, Frankfurt Am Main, Germany
| | - Inna Friesen
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, Goethe University, University Hospital, FrankfurtFrankfurt Am Main, Germany
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8
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Jia L, Arick MA, Hsu CY, Peterson DG, Evans JD, Robinson K, Sukumaran AT, Ramachandran R, Adhikari P, Zhang L. High-throughput Oxford Nanopore sequencing-based approach for the multilocus sequence typing analysis of large-scale avian Escherichia coli study in Mississippi. Poult Sci 2024; 103:104067. [PMID: 39067129 DOI: 10.1016/j.psj.2024.104067] [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: 05/22/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024] Open
Abstract
Avian pathogenic Escherichia coli (APEC) cause avian colibacillosis and accurately distinguishing infectious isolates is critical for controlling its transmission. Multilocus sequence typing (MLST) is an accurate and efficient strain identification method for epidemiological surveillance. This research aimed to develop a fast and high-throughput workflow that simultaneously sequences the Achtman typing scheme's 7 housekeeping genes of multiple E. coli isolates using the Oxford Nanopore Technologies (ONT) platform for large-scale APEC study. E. coli strains were isolated from poultry farms, the housekeeping genes were amplified, and amplicons were sequenced on an R9.4 MinION flow cell using the Nanopore GridION sequencer (ONT, Oxford, UK) following the initial workflow (ONT-MLST). Moreover, the workflow was revised by introducing large-scale DNA extraction and multiplex PCR into the ONT-MLST workflow and applied to 242 new isolates, 18 isolates from the previous workflow, and 5 ATCC reference strains using Flongle flow cell on the Nanopore MinION Mk1C sequencer (ONT, Oxford, UK). Finally, the sequence type (ST) results of the 308 isolates collected from infected chickens and poultry farm environments were reported and analyzed. Data indicated that E. coli belonging to ST159, ST8578, and ST355 have the potential to infect multiple organs in broiler. In addition, zoonotic STs, ST69, ST10, ST38, and ST131, were detected from poultry farms. With the advantages of the high throughput of ONT, this study provides a rapid workflow for large-scale E. coli typing and identified frequently isolated sequence types related to APEC infection in poultry.
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Affiliation(s)
- Linan Jia
- Department of Poultry Science, Mississippi State University, Mississippi, MS 39762, USA
| | - Mark A Arick
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762, USA
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi, MS 39762, USA
| | - Jeffrey D Evans
- USDA, Agriculture Research Service, Poultry Research Unit, Mississippi, MS 39762, USA
| | - Kelsy Robinson
- USDA, Agriculture Research Service, Poultry Research Unit, Mississippi, MS 39762, USA
| | | | | | - Pratima Adhikari
- Department of Poultry Science, Mississippi State University, Mississippi, MS 39762, USA
| | - Li Zhang
- Department of Poultry Science, Mississippi State University, Mississippi, MS 39762, USA.
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9
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Long MB, Gilmour A, Kehl M, Tabor DE, Keller AE, Warrener P, Gopalakrishnan V, Rosengren S, Crichton ML, McIntosh E, Giam YH, Keir HR, Brailsford W, Hughes R, Belvisi MG, Sellman BR, DiGiandomenico A, Chalmers JD. A Bispecific Monoclonal Antibody Targeting Psl and PcrV Enhances Neutrophil-Mediated Killing of Pseudomonas aeruginosa in Patients with Bronchiectasis. Am J Respir Crit Care Med 2024; 210:35-46. [PMID: 38754132 DOI: 10.1164/rccm.202308-1403oc] [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: 08/11/2023] [Accepted: 05/16/2024] [Indexed: 05/18/2024] Open
Abstract
Rationale: Pseudomonas aeruginosa infection is associated with worse outcomes in bronchiectasis. Impaired neutrophil antimicrobial responses contribute to bacterial persistence. Gremubamab is a bivalent, bispecific monoclonal antibody targeting Psl exopolysaccharide and the type 3 secretion system component PcrV. Objectives: This study evaluated the efficacy of gremubamab to enhance killing of P. aeruginosa by neutrophils from patients with bronchiectasis and to prevent P. aeruginosa-associated cytotoxicity. Methods: P. aeruginosa isolates from a global bronchiectasis cohort (n = 100) underwent whole-genome sequencing to determine target prevalence. Functional activity of gremubamab against selected isolates was tested in vitro and in vivo. Patients with bronchiectasis (n = 11) and control subjects (n = 10) were enrolled, and the effect of gremubamab in peripheral blood neutrophil opsonophagocytic killing (OPK) assays against P. aeruginosa was evaluated. Serum antibody titers to Psl and PcrV were determined (n = 30; 19 chronic P. aeruginosa infection, 11 no known P. aeruginosa infection), as was the effect of gremubamab treatment in OPK and anti-cytotoxic activity assays. Measurements and Main Results: Psl and PcrV were conserved in isolates from chronically infected patients with bronchiectasis. Seventy-three of 100 isolates had a full psl locus, and 99 of 100 contained the pcrV gene, with 20 distinct full-length PcrV protein subtypes identified. PcrV subtypes were successfully bound by gremubamab and the monoclonal antibody-mediated potent protective activity against tested isolates. Gremubamab increased bronchiectasis patient neutrophil-mediated OPK (+34.6 ± 8.1%) and phagocytosis (+70.0 ± 48.8%), similar to effects observed in neutrophils from control subjects (OPK, +30.1 ± 7.6%). No evidence of competition between gremubamab and endogenous antibodies was found, with protection against P. aeruginosa-induced cytotoxicity and enhanced OPK demonstrated with and without addition of patient serum. Conclusions: Gremubamab enhanced bronchiectasis patient neutrophil phagocytosis and killing of P. aeruginosa and reduced virulence.
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Affiliation(s)
- Merete B Long
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Amy Gilmour
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Margaret Kehl
- Vaccine and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - David E Tabor
- Vaccine and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Ashley E Keller
- Vaccine and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Paul Warrener
- Vaccine and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | | | - Sanna Rosengren
- Translational Science and Experimental Medicine, Respiratory & Immunology, Respiratory and Immunology, and
| | - Megan L Crichton
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Eve McIntosh
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Yan Hui Giam
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Holly R Keir
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Wayne Brailsford
- Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden; and
| | - Rod Hughes
- Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Maria G Belvisi
- Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden; and
| | - Bret R Sellman
- Vaccine and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Antonio DiGiandomenico
- Vaccine and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
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10
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Dost I, Abdel-Glil M, Persson S, Conza KL, Oleastro M, Alves F, Maurischat S, Scholtzek A, Mazuet C, Diancourt L, Tenson T, Schmoock G, Neubauer H, Schwarz S, Seyboldt C. Genomic study of European Clostridioides difficile ribotype 002/sequence type 8. Microb Genom 2024; 10. [PMID: 39051872 DOI: 10.1099/mgen.0.001270] [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: 07/27/2024] Open
Abstract
Clostridioides difficile has significant clinical importance as a leading cause of healthcare-associated infections, with symptoms ranging from mild diarrhoea to severe colitis, and possible life-threatening complications. C. difficile ribotype (RT) 002, mainly associated with MLST sequence type (ST) 8, is one of the most common RTs found in humans. This study aimed at investigating the genetic characteristics of 537 C. difficile genomes of ST8/RT002. To this end, we sequenced 298 C. difficile strains representing a new European genome collection, with strains from Germany, Denmark, France and Portugal. These sequences were analysed against a global dataset consisting of 1,437 ST8 genomes available through Enterobase. Our results showed close genetic relatedness among the studied ST8 genomes, a diverse array of antimicrobial resistance (AMR) genes and the presence of multiple mobile elements. Notably, the pangenome analysis revealed an open genomic structure. ST8 shows relatively low overall variation. Thus, clonal isolates were found across different One Health sectors (humans, animals, environment and food), time periods, and geographical locations, suggesting the lineage's stability and a universal environmental source. Importantly, this stability did not hinder the acquisition of AMR genes, emphasizing the adaptability of this bacterium to different selective pressures. Although only 2.4 % (41/1,735) of the studied genomes originated from non-human sources, such as animals, food, or the environment, we identified 9 cross-sectoral core genome multilocus sequence typing (cgMLST) clusters. Our study highlights the importance of ST8 as a prominent lineage of C. difficile with critical implications in the context of One Health. In addition, these findings strongly support the need for continued surveillance and investigation of non-human samples to gain a more comprehensive understanding of the epidemiology of C. difficile.
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Affiliation(s)
- Ines Dost
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
- Present address: Landesuntersuchungsamt Rheinland-Pfalz, Koblenz, Germany
| | - Mostafa Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Søren Persson
- Statens Serum Institut, Dept. Bacteria, Parasites and Fungi, Unit of Foodborne Infections, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Karen Loaiza Conza
- Statens Serum Institut, Dept. Bacteria, Parasites and Fungi, Unit of Foodborne Infections, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Mónica Oleastro
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - Frederico Alves
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
- Chief Scientific Office, European Food Safety Authority (EFSA), Parma, Italy
| | - Sven Maurischat
- German Federal Institute for Risk Assessment, Department Biological Safety, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Anissa Scholtzek
- German Federal Institute for Risk Assessment, Department Biological Safety, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Christelle Mazuet
- Institut Pasteur, Université Paris Cité, Centre National de Référence Bactéries anaérobies et Botulisme, F-75015 Paris, France
| | - Laure Diancourt
- Institut Pasteur, Université Paris Cité, Centre National de Référence Bactéries anaérobies et Botulisme, F-75015 Paris, France
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Gernot Schmoock
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
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11
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Katahira K, Gotoh Y, Kasama K, Yoshimura D, Itoh T, Shimauchi C, Tajiri A, Hayashi T. Mobile genetic element-driven genomic changes in a community-associated methicillin-resistant Staphylococcus aureus clone during its transmission in a regional community outbreak in Japan. Microb Genom 2024; 10. [PMID: 39017043 DOI: 10.1099/mgen.0.001272] [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: 07/18/2024] Open
Abstract
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are now a public health concern in both community and healthcare settings worldwide. We previously identified a suspected case of a maternity clinic-centred outbreak of CA-MRSA skin infection in a regional community in Japan by PFGE-based analysis. In this study, we performed genome sequence-based analyses of 151 CA-MRSA isolates, which included not only outbreak-related isolates that we previously defined based on identical or similar PFGE patterns but also other isolates obtained during the same period in the same region. Our analysis accurately defined 133 isolates as outbreak-related isolates, collectively called the TDC clone. They belonged to a CA-MRSA lineage in clonal complex (CC) 30, known as the South West Pacific (SWP) clone. A high-resolution phylogenetic analysis of these isolates combined with their epidemiological data revealed that the TDC clone was already present and circulating in the region before the outbreak was recognized, and only the isolates belonging to two sublineages (named SL4 and SL5) were directly involved in the outbreak. Long persistence in patients/carriers and frequent intrahousehold transmission of the TDC clone were also revealed by this analysis. Moreover, by systematic analyses of the genome changes that occurred in this CA-MRSA clone during transmission in the community, we revealed that most variations were associated with mobile genetic elements (MGEs). Variant PFGE types were generated by alterations of prophages and genomic islands or insertion sequence (IS)-mediated insertion of a plasmid or a sequence of unknown origin. Dynamic changes in plasmid content, which were linked to changes in antimicrobial resistance profiles in specific isolates, were generated by frequent gain and loss of plasmids, most of which were self-transmissible or mobilizable. The introduction of IS256 by a plasmid (named pTDC02) into sublineage SL5 led to SL5-specific amplification of IS256, and amplified IS256 copies were involved in some of the structural changes of chromosomes and plasmids and generated variations in the repertoire of virulence-related genes in limited isolates. These data revealed how CA-MRSA genomes change during transmission in the community and how MGEs are involved in this process.
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Affiliation(s)
- Katsuyuki Katahira
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Respiratory Medicine, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Respiratory Medicine, NHO Omuta Hospital, Tachibana, Omuta City 837-0911, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kentaro Kasama
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Dai Yoshimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Chieko Shimauchi
- Department of Nursing Humanics I, Miyazaki Prefectural Nursing University, Manabino, Miyazaki 880-0929, Japan
| | - Akihiko Tajiri
- Tajiri Dermatology Clinic, Kiyotake, Miyazaki 889-1067, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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12
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Carey ME, Thi Nguyen TN, Tran DHN, Dyson ZA, Keane JA, Pham Thanh D, Mylona E, Nair S, Chattaway M, Baker S. The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi. Commun Biol 2024; 7:775. [PMID: 38942806 PMCID: PMC11213900 DOI: 10.1038/s42003-024-06451-8] [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: 12/22/2023] [Accepted: 06/13/2024] [Indexed: 06/30/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is commonly associated with the H58 lineage, a lineage that arose comparatively recently before becoming globally disseminated. To better understand when and how H58 emerged and became dominant, we performed detailed phylogenetic analyses on contemporary genome sequences from S. Typhi isolated in the period spanning the emergence. Our dataset, which contains the earliest described H58 S. Typhi organism, indicates that ancestral H58 organisms were already multi-drug resistant (MDR). These organisms emerged spontaneously in India in 1987 and became radially distributed throughout South Asia and then globally in the ensuing years. These early organisms were associated with a single long branch, possessing mutations associated with increased bile tolerance, suggesting that the first H58 organism was generated during chronic carriage. The subsequent use of fluoroquinolones led to several independent mutations in gyrA. The ability of H58 to acquire and maintain AMR genes continues to pose a threat, as extensively drug-resistant (XDR; MDR plus resistance to ciprofloxacin and third generation cephalosporins) variants, have emerged recently in this lineage. Understanding where and how H58 S. Typhi originated and became successful is key to understand how AMR drives successful lineages of bacterial pathogens. Additionally, these data can inform optimal targeting of typhoid conjugate vaccines (TCVs) for reducing the potential for emergence and the impact of new drug-resistant variants. Emphasis should also be placed upon the prospective identification and treatment of chronic carriers to prevent the emergence of new drug resistant variants with the ability to spread efficiently.
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
- IAVI, Chelsea & Westminster Hospital, London, UK.
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | | | - Zoe A Dyson
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Elli Mylona
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Satheesh Nair
- United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Unit, London, UK
| | - Marie Chattaway
- United Kingdom Health Security Agency, Gastrointestinal Bacteria Reference Unit, London, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- IAVI, Chelsea & Westminster Hospital, London, UK
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13
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Gianecini RA, Cipolla L, Rocca F, Campos J, Poklepovich T, Prieto M. [Molecular characterization of Listeria monocytogenes isolates from human and food sources in Argentina, 2018-2023]. Rev Argent Microbiol 2024:S0325-7541(24)00042-7. [PMID: 38834434 DOI: 10.1016/j.ram.2024.03.002] [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: 12/19/2023] [Revised: 02/19/2024] [Accepted: 03/04/2024] [Indexed: 06/06/2024] Open
Abstract
Human listeriosis is an infectious disease caused by Listeria monocytogenes. The invasive form of this disease leads to a high rate of hospitalizations and fatality. The main mode of transmission is through contaminated ready-to-eat foods such as dairy, vegetables and meat products. The knowledge of the diversity and population dynamics of isolates collected from human and food sources is essential for the detection of clusters and the identification of common sites of infection. The aim of this study was the molecular characterization of L. monocytogenes isolates in Argentina. We sequenced a total of 63 isolates, 35 from human and 28 from food sources, collected between 2018 and 2023. Our genomic study divided the isolates into two lineages, four serogroups, 17 sequence types and 15 clonal complexes (CCs). The hypervirulent clone CC1 (lineage I; serogroup IVb) predominated in human and food samples. The phylogenomic analysis showed a high and possible epidemiological relationship between isolates from human and/or food sources, suggesting the presence of transmission chains in our country. These findings highlight the need to strengthen genomic surveillance of L. monocytogenes in Argentina. The identification of geographic distribution and characteristics of predominant and emerging clones from human and food sources might help to focus action plans and public health policies better directed at the control and prevention of listeriosis.
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Affiliation(s)
- Ricardo Ariel Gianecini
- Servicio de Bacteriología Especial, Instituto Nacional de Enfermedades Infecciosas - ANLIS «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina.
| | - Lucía Cipolla
- Servicio de Bacteriología Especial, Instituto Nacional de Enfermedades Infecciosas - ANLIS «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
| | - Florencia Rocca
- Servicio de Bacteriología Especial, Instituto Nacional de Enfermedades Infecciosas - ANLIS «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
| | - Josefina Campos
- Unidad de Genómica y Bioinformática, ANLIS «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
| | - Tomás Poklepovich
- Unidad de Genómica y Bioinformática, ANLIS «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
| | - Mónica Prieto
- Servicio de Bacteriología Especial, Instituto Nacional de Enfermedades Infecciosas - ANLIS «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
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14
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Navickaite I, Holmes H, Dondi L, Randall L, Fearnley C, Taylor E, Fullick E, Horton R, Williamson S, AbuOun M, Teale C, Anjum MF. Occurrence and characterization of rmtB-harbouring Salmonella and Escherichia coli isolates from a pig farm in the UK. J Antimicrob Chemother 2024; 79:1329-1336. [PMID: 38629139 DOI: 10.1093/jac/dkae102] [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: 07/19/2023] [Accepted: 03/20/2024] [Indexed: 06/04/2024] Open
Abstract
OBJECTIVES To characterize and elucidate the spread of amikacin-resistant Enterobacteriaceae isolates from environmental samples on a pig farm in the UK, following the previous identification of index Salmonella isolates harbouring the rmtB gene, a 16S rRNA methylase. METHODS Environmental samples were collected during two visits to a pig farm in the UK. Isolates were recovered using selective media (amikacin 128 mg/L) followed by real-time PCR and WGS to analyse rmtB-carrying Salmonella and Escherichia coli isolates. RESULTS Salmonella and E. coli isolates harbouring the rmtB gene were detected at both farm visits. All Salmonella isolates were found to be monophasic S. enterica serovar Typhimurium variant Copenhagen of ST34. rmtB-harbouring E. coli isolates were found to be one of three STs: ST4089, ST1684 and ST34. Long-read sequencing identified the rmtB gene to be chromosomally located in Salmonella isolates and on IncFII-type plasmids in E. coli isolates. The results showed the rmtB gene to be flanked by IS26 elements and several resistance genes. CONCLUSIONS We report on the occurrence of rmtB-harbouring Enterobacteriaceae on a pig farm in the UK. rmtB confers resistance to multiple aminoglycosides and this work highlights the need for surveillance to assess dissemination and risk.
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Affiliation(s)
| | - Harry Holmes
- Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Letizia Dondi
- Animal and Plant Health Agency, Weybridge, Surrey, UK
| | - Luke Randall
- Animal and Plant Health Agency, Weybridge, Surrey, UK
| | | | - Emma Taylor
- Animal and Plant Health Agency, Weybridge, Surrey, UK
| | | | - Robert Horton
- Animal and Plant Health Agency, Weybridge, Surrey, UK
| | | | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, Surrey, UK
| | | | - Muna F Anjum
- Animal and Plant Health Agency, Weybridge, Surrey, UK
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15
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Mylona E, Pham Thanh D, Keane JA, Dongol S, Basnyat B, Dolecek C, Voong Vinh P, Tran Vu Thieu N, Nguyen Thi Nguyen T, Karkey A, Baker S. A retrospective investigation of the population structure and geospatial distribution of Salmonella Paratyphi A in Kathmandu, Nepal. PLoS Negl Trop Dis 2024; 18:e0011864. [PMID: 38889189 PMCID: PMC11216570 DOI: 10.1371/journal.pntd.0011864] [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: 12/14/2023] [Revised: 07/01/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024] Open
Abstract
Salmonella Paratyphi A, one of the major etiologic agents of enteric fever, has increased in prevalence in recent decades in certain endemic regions in comparison to S. Typhi, the most prevalent cause of enteric fever. Despite this increase, data on the prevalence and molecular epidemiology of S. Paratyphi A remain generally scarce. Here, we analysed the whole genome sequences of 216 S. Paratyphi A isolates originating from Kathmandu, Nepal between 2005 and 2014, of which 200 were from patients with acute enteric fever and 16 from the gallbladder of people with suspected chronic carriage. By exploiting the recently developed genotyping framework for S. Paratyphi A (Paratype), we identified several genotypes circulating in Kathmandu. Notably, we observed an unusual clonal expansion of genotype 2.4.3 over a four-year period that spread geographically and systematically replaced other genotypes. This rapid genotype replacement is hypothesised to have been driven by both reduced susceptibility to fluoroquinolones and genetic changes to virulence factors, such as functional and structural genes encoding the type 3 secretion systems. Finally, we show that person-to-person is likely the most common mode of transmission and chronic carriers seem to play a limited role in maintaining disease circulation.
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Affiliation(s)
- Elli Mylona
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Jacqueline A. Keane
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Christiane Dolecek
- The Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nga Tran Vu Thieu
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Program, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - To Nguyen Thi Nguyen
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Abhilasha Karkey
- The Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- IAVI Human Immunology Laboratory, Chelsea and Westminster Hospital, London, United Kingdom
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16
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Nguyen Q, Nguyen YTP, Ha TT, Tran DTN, Voong PV, Chau V, Nguyen PLN, Le NTQ, Nguyen LPH, Nguyen TTN, Trinh TV, Carrique-Mas JJ, Baker S, Thwaites G, Rabaa MA, Choisy M, Chung HT, Pham DT. Genomic insights unveil the plasmid transfer mechanism and epidemiology of hypervirulent Klebsiella pneumoniae in Vietnam. Nat Commun 2024; 15:4187. [PMID: 38760381 PMCID: PMC11101633 DOI: 10.1038/s41467-024-48206-3] [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: 12/29/2023] [Accepted: 04/22/2024] [Indexed: 05/19/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) is a significant cause of severe invasive infections in Vietnam, yet data on its epidemiology, population structure and dynamics are scarce. We screened hvKp isolates from patients with bloodstream infections (BSIs) at a tertiary infectious diseases hospital in Vietnam and healthy individuals, followed by whole genome sequencing and plasmid analysis. Among 700 BSI-causing Kp strains, 100 (14.3%) were hvKp. Thirteen hvKp isolates were identified from 350 rectal swabs of healthy adults; none from 500 rectal swabs of healthy children. The hvKp isolates were genetically diverse, encompassing 17 sequence types (STs), predominantly ST23, ST86 and ST65. Among the 113 hvKp isolates, 14 (12.6%) carried at least one antimicrobial resistance (AMR) gene, largely mediated by IncFII, IncR, and IncA/C plasmids. Notably, the acquisition of AMR conjugative plasmids facilitated horizontal transfer of the non-conjugative virulence plasmid between K. pneumoniae strains. Phylogenetic analysis demonstrated hvKp isolates from BSIs and human carriage clustered together, suggesting a significant role of intestinal carriage in hvKp transmission. Enhanced surveillance is crucial to understand the factors driving intestinal carriage and hvKp transmission dynamics for informing preventive measures. Furthermore, we advocate the clinical use of our molecular assay for diagnosing hvKp infections to guide effective management.
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Affiliation(s)
- Quynh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Tuyen Thanh Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Phat Vinh Voong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Chau
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | | | | | - Tan Van Trinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Juan J Carrique-Mas
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) Department of Medicine, University of Cambridge, Cambridge, UK
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hao The Chung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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17
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Yuu EY, Bührer C, Eckmanns T, Fulde M, Herz M, Kurzai O, Lindstedt C, Panagiotou G, Piro VC, Radonic A, Renard BY, Reuss A, Siliceo SL, Thielemann N, Thürmer A, Vorst KV, Wieler LH, Haller S. The gut microbiome, resistome, and mycobiome in preterm newborn infants and mouse pups: lack of lasting effects by antimicrobial therapy or probiotic prophylaxis. Gut Pathog 2024; 16:27. [PMID: 38735967 PMCID: PMC11089716 DOI: 10.1186/s13099-024-00616-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/13/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Enhancing our understanding of the underlying influences of medical interventions on the microbiome, resistome and mycobiome of preterm born infants holds significant potential for advancing infection prevention and treatment strategies. We conducted a prospective quasi-intervention study to better understand how antibiotics, and probiotics, and other medical factors influence the gut development of preterm infants. A controlled neonatal mice model was conducted in parallel, designed to closely reflect and predict exposures. Preterm infants and neonatal mice were stratified into four groups: antibiotics only, probiotics only, antibiotics followed by probiotics, and none of these interventions. Stool samples from both preterm infants and neonatal mice were collected at varying time points and analyzed by 16 S rRNA amplicon sequencing, ITS amplicon sequencing and whole genome shotgun sequencing. RESULTS The human infant microbiomes showed an unexpectedly high degree of heterogeneity. Little impact from medical exposure (antibiotics/probiotics) was observed on the strain patterns, however, Bifidobacterium bifidum was found more abundant after exposure to probiotics, regardless of prior antibiotic administration. Twenty-seven antibiotic resistant genes were identified in the resistome. High intra-variability was evident within the different treatment groups. Lastly, we found significant effects of antibiotics and probiotics on the mycobiome but not on the microbiome and resistome of preterm infants. CONCLUSIONS Although our analyses showed transient effects, these results provide positive motivation to continue the research on the effects of medical interventions on the microbiome, resistome and mycobiome of preterm infants.
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Affiliation(s)
- Elizabeth Y Yuu
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
| | | | | | - Marcus Fulde
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michaela Herz
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
| | | | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07745, Jena, Germany
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vitor C Piro
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | | | - Bernhard Y Renard
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
| | - Annicka Reuss
- Robert Koch Institute, Berlin, Germany
- Ministry of Justice and Health, Schleswig-Holstein, Kiel , Germany
| | - Sara Leal Siliceo
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraße 11A, 07745 , Jena, Germany
| | - Nadja Thielemann
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | | | - Kira van Vorst
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195, Berlin, Germany
| | - Lothar H Wieler
- Data Analytics & Computational Statistics, Hasso Plattner Institute, University of Potsdam, Prof.-Dr.-Helmert-Straße 2-3, 14482 , Potsdam, Germany
- Robert Koch Institute, Berlin, Germany
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18
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Břinda K, Lima L, Pignotti S, Quinones-Olvera N, Salikhov K, Chikhi R, Kucherov G, Iqbal Z, Baym M. Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.15.536996. [PMID: 37131636 PMCID: PMC10153118 DOI: 10.1101/2023.04.15.536996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Comprehensive collections approaching millions of sequenced genomes have become central information sources in the life sciences. However, the rapid growth of these collections has made it effectively impossible to search these data using tools such as BLAST and its successors. Here, we present a technique called phylogenetic compression, which uses evolutionary history to guide compression and efficiently search large collections of microbial genomes using existing algorithms and data structures. We show that, when applied to modern diverse collections approaching millions of genomes, lossless phylogenetic compression improves the compression ratios of assemblies, de Bruijn graphs, and k -mer indexes by one to two orders of magnitude. Additionally, we develop a pipeline for a BLAST-like search over these phylogeny-compressed reference data, and demonstrate it can align genes, plasmids, or entire sequencing experiments against all sequenced bacteria until 2019 on ordinary desktop computers within a few hours. Phylogenetic compression has broad applications in computational biology and may provide a fundamental design principle for future genomics infrastructure.
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19
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Vieira A, Wan Y, Ryan Y, Li HK, Guy RL, Papangeli M, Huse KK, Reeves LC, Soo VWC, Daniel R, Harley A, Broughton K, Dhami C, Ganner M, Ganner MA, Mumin Z, Razaei M, Rundberg E, Mammadov R, Mills EA, Sgro V, Mok KY, Didelot X, Croucher NJ, Jauneikaite E, Lamagni T, Brown CS, Coelho J, Sriskandan S. Rapid expansion and international spread of M1 UK in the post-pandemic UK upsurge of Streptococcus pyogenes. Nat Commun 2024; 15:3916. [PMID: 38729927 PMCID: PMC11087535 DOI: 10.1038/s41467-024-47929-7] [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: 01/12/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
The UK observed a marked increase in scarlet fever and invasive group A streptococcal infection in 2022 with severe outcomes in children and similar trends worldwide. Here we report lineage M1UK to be the dominant source of invasive infections in this upsurge. Compared with ancestral M1global strains, invasive M1UK strains exhibit reduced genomic diversity and fewer mutations in two-component regulator genes covRS. The emergence of M1UK is dated to 2008. Following a bottleneck coinciding with the COVID-19 pandemic, three emergent M1UK clades underwent rapid nationwide expansion, despite lack of detection in previous years. All M1UK isolates thus-far sequenced globally have a phylogenetic origin in the UK, with dispersal of the new clades in Europe. While waning immunity may promote streptococcal epidemics, the genetic features of M1UK point to a fitness advantage in pathogenicity, and a striking ability to persist through population bottlenecks.
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Affiliation(s)
- Ana Vieira
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK
| | - Yu Wan
- Department of Infectious Disease, Imperial College London, London, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK
- Healthcare-Associated Infections, Fungal, AMR, AMU, and Sepsis Division, UK Health Security Agency, London, UK
| | - Yan Ryan
- Reference Services Division, UK Health Security Agency, London, UK
| | - Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Rebecca L Guy
- Healthcare-Associated Infections, Fungal, AMR, AMU, and Sepsis Division, UK Health Security Agency, London, UK
| | - Maria Papangeli
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Kristin K Huse
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Lucy C Reeves
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Valerie W C Soo
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Roger Daniel
- Reference Services Division, UK Health Security Agency, London, UK
| | | | - Karen Broughton
- Reference Services Division, UK Health Security Agency, London, UK
| | - Chenchal Dhami
- Reference Services Division, UK Health Security Agency, London, UK
| | - Mark Ganner
- Reference Services Division, UK Health Security Agency, London, UK
| | | | - Zaynab Mumin
- Reference Services Division, UK Health Security Agency, London, UK
| | - Maryam Razaei
- Reference Services Division, UK Health Security Agency, London, UK
| | - Emma Rundberg
- Reference Services Division, UK Health Security Agency, London, UK
| | - Rufat Mammadov
- Reference Services Division, UK Health Security Agency, London, UK
| | - Ewurabena A Mills
- Department of Infectious Disease, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Vincenzo Sgro
- Department of Infectious Disease, Imperial College London, London, UK
| | - Kai Yi Mok
- Department of Infectious Disease, Imperial College London, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - Nicholas J Croucher
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Theresa Lamagni
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK
- Healthcare-Associated Infections, Fungal, AMR, AMU, and Sepsis Division, UK Health Security Agency, London, UK
| | - Colin S Brown
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK
- Healthcare-Associated Infections, Fungal, AMR, AMU, and Sepsis Division, UK Health Security Agency, London, UK
| | - Juliana Coelho
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK.
- Healthcare-Associated Infections, Fungal, AMR, AMU, and Sepsis Division, UK Health Security Agency, London, UK.
- Reference Services Division, UK Health Security Agency, London, UK.
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK.
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
- NIHR Health Protection Research Unit in Healthcare-associated Infections and AMR, Imperial College London, London, UK.
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20
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Heinz E, Pearse O, Zuza A, Bilima S, Msefula C, Musicha P, Siyabu P, Tewesa E, Graf FE, Lester R, Lissauer S, Cornick J, Lewis JM, Kawaza K, Thomson NR, Feasey NA. Longitudinal analysis within one hospital in sub-Saharan Africa over 20 years reveals repeated replacements of dominant clones of Klebsiella pneumoniae and stresses the importance to include temporal patterns for vaccine design considerations. Genome Med 2024; 16:67. [PMID: 38711148 PMCID: PMC11073982 DOI: 10.1186/s13073-024-01342-3] [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: 10/10/2023] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Infections caused by multidrug-resistant gram-negative bacteria present a severe threat to global public health. The WHO defines drug-resistant Klebsiella pneumoniae as a priority pathogen for which alternative treatments are needed given the limited treatment options and the rapid acquisition of novel resistance mechanisms by this species. Longitudinal descriptions of genomic epidemiology of Klebsiella pneumoniae can inform management strategies but data from sub-Saharan Africa are lacking. METHODS We present a longitudinal analysis of all invasive K. pneumoniae isolates from a single hospital in Blantyre, Malawi, southern Africa, from 1998 to 2020, combining clinical data with genome sequence analysis of the isolates. RESULTS We show that after a dramatic increase in the number of infections from 2016 K. pneumoniae becomes hyperendemic, driven by an increase in neonatal infections. Genomic data show repeated waves of clonal expansion of different, often ward-restricted, lineages, suggestive of hospital-associated transmission. We describe temporal trends in resistance and surface antigens, of relevance for vaccine development. CONCLUSIONS Our data highlight a clear need for new interventions to prevent rather than treat K. pneumoniae infections in our setting. Whilst one option may be a vaccine, the majority of cases could be avoided by an increased focus on and investment in infection prevention and control measures, which would reduce all healthcare-associated infections and not just one.
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Affiliation(s)
- Eva Heinz
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK.
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK.
| | - Oliver Pearse
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Allan Zuza
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Sithembile Bilima
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Patrick Musicha
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Edith Tewesa
- Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Fabrice E Graf
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK
| | - Rebecca Lester
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Division of Infection & Immunity, University College London, London, UK
| | - Samantha Lissauer
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Jennifer Cornick
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Joseph M Lewis
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Kondwani Kawaza
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Nicholas R Thomson
- Parasites and Microbes Program, Wellcome Sanger Institute, Hinxton, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke PlaceLiverpool, L3 5QA, UK.
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.
- School of Medicine, St Andrews University, St Andrews, UK.
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21
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Langelier C, Lu D, Kalantar K, Chu V, Glascock A, Guerrero E, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones A, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani P, Pickering A, Raphenya A, Alcock B, McArthur A. Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline. RESEARCH SQUARE 2024:rs.3.rs-4271356. [PMID: 38746293 PMCID: PMC11092797 DOI: 10.21203/rs.3.rs-4271356/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the CZ ID AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.
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Affiliation(s)
| | - Dan Lu
- Chan Zuckerberg Initiative
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22
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Anggraini D, Siregar FM, Rosdiana D, Kemal RA, Yovi I, Triani ZD, Jasmin N, Dwijelita N, Webb JR, Mayo M, Kaestli M, Currie BJ. Epidemiology and genetic diversity of Burkholderia pseudomallei from Riau Province, Indonesia. PLoS Negl Trop Dis 2024; 18:e0012195. [PMID: 38805481 PMCID: PMC11161056 DOI: 10.1371/journal.pntd.0012195] [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: 09/07/2023] [Revised: 06/07/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024] Open
Abstract
Melioidosis is a bacterial infection caused by Burkholderia pseudomallei, that is common in tropical and subtropical countries including Southeast Asia and Northern Australia. The magnitude of undiagnosed and untreated melioidosis across the country remains unclear. Given its proximity to regions with high infection rates, Riau Province on Sumatera Island is anticipated to have endemic melioidosis. This study reports retrospectively collected data on 68 culture-confirmed melioidosis cases from two hospitals in Riau Province between January 1, 2009, and December 31, 2021, with full clinical data available on 41 cases. We also describe whole genome sequencing and genotypic analysis of six isolates of B. pseudomallei. The mean age of the melioidosis patients was 49.1 (SD 11.5) years, 85% were male and the most common risk factor was diabetes mellitus (78%). Pulmonary infection was the most common presentation (39%), and overall mortality was 41%. Lung as a focal infection (aOR: 6.43; 95% CI: 1.13-36.59, p = 0.036) and bacteremia (aOR: 15.21; 95% CI: 2.59-89.31, p = 0.003) were significantly associated with death. Multilocus sequence typing analysis conducted on six B.pseudomallei genomes identified three sequence types (STs), namely novel ST1794 (n = 3), ST46 (n = 2), and ST289 (n = 1). A phylogenetic tree of Riau B. pseudomallei whole genome sequences with a global dataset of genomes clearly distinguished the genomes of B. pseudomallei in Indonesia from the ancestral Australian clade and classified them within the Asian clade. This study expands the known presence of B. pseudomallei within Indonesia and confirms that Indonesian B. pseudomallei are genetically linked to those in the rest of Southeast Asia. It is anticipated that melioidosis will be found in other locations across Indonesia as laboratory capacities improve and standardized protocols for detecting and confirming suspected cases of melioidosis are more widely implemented.
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Affiliation(s)
- Dewi Anggraini
- Department of Microbiology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
- Arifin Achmad General Hospital, Riau Province, Pekanbaru, Indonesia
- Eka Hospital Pekanbaru, Pekanbaru, Indonesia
| | - Fajri Marindra Siregar
- Arifin Achmad General Hospital, Riau Province, Pekanbaru, Indonesia
- Department of Biochemistry, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Dani Rosdiana
- Arifin Achmad General Hospital, Riau Province, Pekanbaru, Indonesia
- Department of Internal Medicine, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Rahmat Azhari Kemal
- Arifin Achmad General Hospital, Riau Province, Pekanbaru, Indonesia
- Department of Medical Biology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Indra Yovi
- Arifin Achmad General Hospital, Riau Province, Pekanbaru, Indonesia
- Eka Hospital Pekanbaru, Pekanbaru, Indonesia
- Department of Pulmonology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | | | - Novira Jasmin
- Department of Microbiology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Norsila Dwijelita
- Department of Microbiology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Jessica R. Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia
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23
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O’Grady K, Hong S, Putsathit P, George N, Hemphill C, Huntington PG, Korman TM, Kotsanas D, Lahra M, McDougall R, McGlinchey A, Levy A, Moore CV, Nimmo G, Prendergast L, Robson J, Speers DJ, Waring L, Wehrhahn MC, Weldhagen GF, Wilson RM, Riley TV, Knight DR. Defining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia. Microb Genom 2024; 10:001232. [PMID: 38717815 PMCID: PMC11165652 DOI: 10.1099/mgen.0.001232] [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: 01/29/2024] [Accepted: 03/27/2024] [Indexed: 06/13/2024] Open
Abstract
Clostridioides difficile infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of C. difficile ribotypes (RTs) 014/020 (n=169), 002 (n=77) and 056 (n=36), the three most prominent C. difficile strains causing CDI in Australia. Genome scrutiny showed that AMR was uncommon in these lineages, with resistance-conferring alleles present in only 15/169 RT014/020 strains (8.9 %), 1/36 RT056 strains (2.78 %) and none of 77 RT002 strains. Notably, ~90 % of strains were resistant to MLSB agents in vitro, but only ~5.9 % harboured known resistance alleles, highlighting an incongruence between AMR genotype and phenotype. Core genome analyses revealed all three RTs contained genetically heterogeneous strain populations with limited evidence of clonal transmission between CDI cases. The average number of pairwise core genome SNP (cgSNP) differences within each RT group ranged from 23.3 (RT056, ST34, n=36) to 115.6 (RT002, ST8, n=77) and 315.9 (RT014/020, STs 2, 13, 14, 49, n=169). Just 19 clonal groups (encompassing 40 isolates), defined as isolates differing by ≤2 cgSNPs, were identified across all three RTs (RT014/020, n=14; RT002, n=3; RT056, n=2). Of these clonal groups, 63 % (12/19) comprised isolates from the same Australian State and 37 % (7/19) comprised isolates from different States. The low number of plausible transmission events found for these major RTs (and previously documented populations in animal and environmental sources/reservoirs) points to widespread and persistent community sources of diverse C. difficile strains as opposed to ongoing nationwide healthcare outbreaks dominated by a single clone. Together, these data provide new insights into the evolution of major lineages causing CDI in Australia and highlight the urgent need for enhanced surveillance, and for public health interventions to move beyond the healthcare setting and into a One Health paradigm to effectively combat this complex pathogen.
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Affiliation(s)
- Keeley O’Grady
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Stacey Hong
- Communicable Disease Control Directorate, WA Department of Health, East Perth, Western Australia, Australia
| | - Papanin Putsathit
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Narelle George
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | | | - Peter G. Huntington
- Department of Microbiology, NSW Health Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Tony M. Korman
- Monash University, Monash Health, Clayton, Victoria, Australia
| | - Despina Kotsanas
- Monash Infectious Diseases, Monash Health, Monash Medical Centre, Clayton, Victoria, Australia
| | - Monica Lahra
- Department of Microbiology, The Prince of Wales Hospital, Randwick, New South Wales, Australia
| | | | | | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Casey V. Moore
- Microbiology and Infectious Diseases Laboratories, SA Pathology, Adelaide, South Australia, Australia
| | - Graeme Nimmo
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | | | - Jennifer Robson
- Sullivan Nicolaides Pathology, Taringa, Queensland, Australia
| | - David J. Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Medicine, The University of Western Australia, Nedlands, Western Australia, Australia
| | | | | | - Gerhard F. Weldhagen
- Microbiology and Infectious Diseases Laboratories, SA Pathology, Adelaide, South Australia, Australia
| | - Richard M. Wilson
- Australian Clinical Labs, Microbiology Department, Wayville, South Australia, Australia
| | - Thomas V. Riley
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Daniel R. Knight
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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24
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Truong NHM, Nguyen Q, Voong PV, Chau V, Nguyen NHT, Nguyen THM, Vo PH, Nguyen LT, Ha TTP, Nguyen LPH, Le PH, Thanh DP, Nguyen HD. Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam. Microb Genom 2024; 10:001248. [PMID: 38739115 PMCID: PMC11165649 DOI: 10.1099/mgen.0.001248] [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: 02/05/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024] Open
Abstract
Aeromonas spp. are commonly found in the aquatic environment and have been responsible for motile Aeromonas septicemia (MAS) in striped catfish, resulting in significant economic loss. These organisms also cause a range of opportunistic infections in humans with compromised immune systems. Here, we conducted a genomic investigation of 87 Aeromonas isolates derived from diseased catfish, healthy catfish and environmental water in catfish farms affected by MAS outbreaks in eight provinces in Mekong Delta (years: 2012-2022), together with 25 isolates from humans with bloodstream infections (years: 2010-2020). Genomics-based typing method precisely delineated Aeromonas species while traditional methods such as aerA PCR and MALDI-TOF were unable identify A. dhakensis. A. dhakensis was found to be more prevalent than A. hydrophila in both diseased catfish and human infections. A. dhakensis sequence type (ST) 656 followed by A. hydrophila ST251 were the predominant virulent species-lineages in diseased catfish (43.7 and 20.7 %, respectively), while diverse STs were found in humans with bloodstream infections. There was evidence of widespread transmission of ST656 and ST251 on striped catfish in the Mekong Delta region. ST656 and ST251 isolates carried a significantly higher number of acquired antimicrobial resistance (AMR) genes and virulence factors in comparison to other STs. They, however, exhibited several distinctions in key virulence factors (i.e. lack of type IV pili and enterotoxin ast in A. dhakensis), AMR genes (i.e. presence of imiH carbapenemase in A. dhakensis), and accessory gene content. To uncover potential conserved proteins of Aeromonas spp. for vaccine development, pangenome analysis has unveiled 2202 core genes between ST656 and ST251, of which 78 proteins were in either outer membrane or extracellular proteins. Our study represents one of the first genomic investigations of the species distribution, genetic landscape, and epidemiology of Aeromonas in diseased catfish and human infections in Vietnam. The emergence of antimicrobial resistant and virulent A. dhakensis strains underscores the needs of enhanced genomic surveillance and strengthening vaccine research and development in preventing Aeromonas diseases in catfish and humans, and the search for potential vaccine candidates could focus on Aeromonas core genes encoded for membrane and secreted proteins.
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Affiliation(s)
- Nhat Ha Minh Truong
- Center for Bioscience and Biotechnology, VNUHCM-University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Quynh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phat Vinh Voong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Chau
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhi Huynh Thanh Nguyen
- Center for Bioscience and Biotechnology, VNUHCM-University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Tuan Hoa Minh Nguyen
- Center for Bioscience and Biotechnology, VNUHCM-University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Phuong Hong Vo
- Vietnam National University, Ho Chi Minh City, Vietnam
- Research Institute for Aquaculture No.2, Ho Chi Minh City, Vietnam
| | | | | | | | - Phuoc Hong Le
- Research Institute for Aquaculture No.2, Ho Chi Minh City, Vietnam
| | - Duy Pham Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Hoang Duc Nguyen
- Center for Bioscience and Biotechnology, VNUHCM-University of Science, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
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25
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Hala S, Malaikah M, Huang J, Bahitham W, Fallatah O, Zakri S, Antony CP, Alshehri M, Ghazzali RN, Ben-Rached F, Alsahafi A, Alsaedi A, AlAhmadi G, Kaaki M, Alazmi M, AlhajHussein B, Yaseen M, Zowawi HM, Alghoribi MF, Althaqafi AO, Al-Amri A, Moradigaravand D, Pain A. The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years. Genome Med 2024; 16:58. [PMID: 38637822 PMCID: PMC11025284 DOI: 10.1186/s13073-024-01332-5] [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: 10/03/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a major bacterial and opportunistic human pathogen, increasingly recognized as a healthcare burden globally. The convergence of resistance and virulence in K. pneumoniae strains has led to the formation of hypervirulent and multidrug-resistant strains with dual risk, limiting treatment options. K. pneumoniae clones are known to emerge locally and spread globally. Therefore, an understanding of the dynamics and evolution of the emerging strains in hospitals is warranted to prevent future outbreaks. METHODS In this study, we conducted an in-depth genomic analysis on a large-scale collection of 328 multidrug-resistant (MDR) K. pneumoniae strains recovered from 239 patients from a single major hospital in the western coastal city of Jeddah in Saudi Arabia from 2014 through 2022. We employed a broad range of phylogenetic and phylodynamic methods to understand the evolution of the predominant clones on epidemiological time scales, virulence and resistance determinants, and their dynamics. We also integrated the genomic data with detailed electronic health record (EHR) data for the patients to understand the clinical implications of the resistance and virulence of different strains. RESULTS We discovered a diverse population underlying the infections, with most strains belonging to Clonal Complex 14 (CC14) exhibiting dominance. Specifically, we observed the emergence and continuous expansion of strains belonging to the dominant ST2096 in the CC14 clade across hospital wards in recent years. These strains acquired resistance mutations against colistin and extended spectrum β-lactamase (ESBL) and carbapenemase genes, namely blaOXA-48 and blaOXA-232, located on three distinct plasmids, on epidemiological time scales. Strains of ST2096 exhibited a high virulence level with the presence of the siderophore aerobactin (iuc) locus situated on the same mosaic plasmid as the ESBL gene. Integration of ST2096 with EHR data confirmed the significant link between colonization by ST2096 and the diagnosis of sepsis and elevated in-hospital mortality (p-value < 0.05). CONCLUSIONS Overall, these results demonstrate the clinical significance of ST2096 clones and illustrate the rapid evolution of an emerging hypervirulent and MDR K. pneumoniae in a clinical setting.
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Affiliation(s)
- Sharif Hala
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Mohammed Malaikah
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia
- Laboratory of Infectious Disease Epidemiology, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jiayi Huang
- Laboratory of Infectious Disease Epidemiology, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Wesam Bahitham
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Omniya Fallatah
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Samer Zakri
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Chakkiath Paul Antony
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan
| | - Mohammed Alshehri
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Raeece Naeem Ghazzali
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia
| | - Fathia Ben-Rached
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia
| | - Abdullah Alsahafi
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Asim Alsaedi
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Ghadeer AlAhmadi
- King Faisal Specialist Hospital and Research Centre, Jeddah, Saudi Arabia
| | - Mai Kaaki
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Meshari Alazmi
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- College of Computer Science and Engineering, University of Hail, Hail, Saudi Arabia
| | - Baraa AlhajHussein
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Muhammad Yaseen
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Hosam M Zowawi
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
- The University of Queensland, UQ Centre for Clinical Research, Herston, QLD, Australia
| | - Majed F Alghoribi
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Abdulhakeem O Althaqafi
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Abdulfattah Al-Amri
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Danesh Moradigaravand
- Laboratory of Infectious Disease Epidemiology, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia.
- The University of Queensland, UQ Centre for Clinical Research, Herston, QLD, Australia.
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26
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Lu D, Kalantar KL, Chu VT, Glascock AL, Guerrero ES, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones AE, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani PM, Pickering AJ, Raphenya AR, Alcock BP, McArthur AG, Langelier CR. Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589250. [PMID: 38645206 PMCID: PMC11030322 DOI: 10.1101/2024.04.12.589250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.
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Affiliation(s)
- Dan Lu
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | - Victoria T. Chu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Nina Bernick
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | - Kirsty Ewing
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | | | - Erin Hoops
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | - Ann E. Jones
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | - Ryan Lim
- Chan Zuckerberg Initiative, Redwood City, CA, USA
| | | | | | | | | | | | - Peter M. Mourani
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children’s, Little Rock, AR, USA
| | - Amy J. Pickering
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- University of California, Berkeley, Berkeley, CA, USA
| | - Amogelang R. Raphenya
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Brian P. Alcock
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Andrew G. McArthur
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Charles R. Langelier
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
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27
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Hilpipre G, Furfaro LL, Porter M, Blyth CC, Yeoh DK. Characterization of invasive Group B Streptococcus isolates from Western Australian infants, 2004-2020. J Med Microbiol 2024; 73. [PMID: 38567639 DOI: 10.1099/jmm.0.001822] [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: 04/04/2024] Open
Abstract
Background. Invasive Group B Streptococcus (GBS; Streptococcus agalactiae) remains a leading cause of infant morbidity and mortality. Intrapartum antibiotic prophylaxis (IAP) has been implemented in many countries with a reduction in early-onset disease, but an effective vaccine may further reduce the disease burden. Candidate vaccines targeting capsular polysaccharides and surface proteins are now in clinical trials.Methods. Using whole-genome sequencing and phenotypic antimicrobial susceptibility testing, we characterized sterile-site GBS isolates recovered from Western Australian infants between 2004 and 2020. Characteristics were compared between three time periods: 2004-2008, 2009-2015 and 2016-2020.Results. A total of 135 isolates were identified. The proportion of serotype III (22.7 % in Period 1 to 47.9 % in Period 3, P=0.04) and clonal complex 17 (13.6-39.6 %, P=0.01) isolates increased over time. Overall coverage of vaccines currently being trialled was >95 %. No isolates were penicillin resistant (MIC>0.25 mg l-1), but 21.5 % of isolates had reduced penicillin susceptibility (MIC>0.12 mg l-1) and penicillin MIC increased significantly over time (P=0.04). Clindamycin resistance increased over time to 45.8 % in the latest period.Conclusions. Based on comprehensive characterization of invasive infant GBS in Western Australia, we found that coverage for leading capsular polysaccharide and surface protein vaccine candidates was high. The demonstrated changes in serotype and molecular type highlight the need for ongoing surveillance, particularly with regard to future GBS vaccination programmes. The reduced susceptibility to IAP agents over time should inform changes to antibiotic guidelines.
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Affiliation(s)
- Ginger Hilpipre
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine, Perth, Western Australia, Australia
| | - Lucy L Furfaro
- Division of Obstetrics and Gynaecology, School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
| | - Michelle Porter
- Department of Microbiology, PathWest Laboratory Medicine, Perth, Western Australia, Australia
| | - Christopher C Blyth
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine, Perth, Western Australia, Australia
- Department of Infectious Diseases, Perth Children's Hospital, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Daniel K Yeoh
- Department of Infectious Diseases, Perth Children's Hospital, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
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28
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Hu K, Meyer F, Deng ZL, Asgari E, Kuo TH, Münch PC, McHardy AC. Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes. Brief Bioinform 2024; 25:bbae206. [PMID: 38706320 PMCID: PMC11070729 DOI: 10.1093/bib/bbae206] [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: 11/10/2023] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored for this task, but systematic benchmarking is still needed. Here, we evaluated four state-of-the-art ML methods (Kover, PhenotypeSeeker, Seq2Geno2Pheno and Aytan-Aktug), an ML baseline and the rule-based ResFinder by training and testing each of them across 78 species-antibiotic datasets, using a rigorous benchmarking workflow that integrates three evaluation approaches, each paired with three distinct sample splitting methods. Our analysis revealed considerable variation in the performance across techniques and datasets. Whereas ML methods generally excelled for closely related strains, ResFinder excelled for handling divergent genomes. Overall, Kover most frequently ranked top among the ML approaches, followed by PhenotypeSeeker and Seq2Geno2Pheno. AMR phenotypes for antibiotic classes such as macrolides and sulfonamides were predicted with the highest accuracies. The quality of predictions varied substantially across species-antibiotic combinations, particularly for beta-lactams; across species, resistance phenotyping of the beta-lactams compound, aztreonam, amoxicillin/clavulanic acid, cefoxitin, ceftazidime and piperacillin/tazobactam, alongside tetracyclines demonstrated more variable performance than the other benchmarked antibiotics. By organism, Campylobacter jejuni and Enterococcus faecium phenotypes were more robustly predicted than those of Escherichia coli, Staphylococcus aureus, Salmonella enterica, Neisseria gonorrhoeae, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Streptococcus pneumoniae and Mycobacterium tuberculosis. In addition, our study provides software recommendations for each species-antibiotic combination. It furthermore highlights the need for optimization for robust clinical applications, particularly for strains that diverge substantially from those used for training.
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Affiliation(s)
- Kaixin Hu
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Fernando Meyer
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Zhi-Luo Deng
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Ehsaneddin Asgari
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Molecular Cell Biomechanics Laboratory, Department of Bioengineering and Mechanical Engineering, University of California, Berkeley, USA
| | - Tzu-Hao Kuo
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Philipp C Münch
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover Braunschweig, Braunschweig, Germany
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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Wight J, Byrne AS, Tahlan K, Lang AS. Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes. Appl Environ Microbiol 2024; 90:e0180923. [PMID: 38349150 PMCID: PMC10952509 DOI: 10.1128/aem.01809-23] [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: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 03/21/2024] Open
Abstract
Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.
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Affiliation(s)
- Jordan Wight
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Alexander S. Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
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McHugh MP, Pettigrew KA, Taori S, Evans TJ, Leanord A, Gillespie SH, Templeton KE, Holden MTG. Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium. J Antimicrob Chemother 2024; 79:656-668. [PMID: 38323373 PMCID: PMC11090465 DOI: 10.1093/jac/dkae023] [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: 04/27/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases. OBJECTIVES Determine the impact of within-patient diversity on transmission resolution of VREfm. MATERIALS AND METHODS Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner. RESULTS AND DISCUSSION In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies. CONCLUSIONS Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks.
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Affiliation(s)
- Martin P McHugh
- School of Medicine, University of St Andrews, St Andrews, UK
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | - Surabhi Taori
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Thomas J Evans
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Alistair Leanord
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
- Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK
| | | | - Kate E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
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31
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Wetzstein N, Diricks M, Andres S, Kuhns M, Marschall L, Biciusca T, Smaczny C, Friesen I, Niemann S, Wichelhaus TA. Genomic diversity and clinical relevance of Mycobacterium simiae. ERJ Open Res 2024; 10:00773-2023. [PMID: 38500796 PMCID: PMC10945383 DOI: 10.1183/23120541.00773-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/23/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction Mycobacterium simiae is a slow-growing non-tuberculous mycobacterium that can cause non-tuberculous mycobacterium (NTM) pulmonary disease and extrapulmonary infections. Until now, detailed genomic and clinical characteristics, as well as possible transmission routes of this rare pathogen remain largely unknown. Methods We conducted whole genome sequencing of available M. simiae isolates collected at a tertiary care centre in Central Germany from 2006 to 2020 and set them into context with publicly available M. simiae complex sequences through phylogenetic analysis. Resistance, virulence and stress genes, as well as known Mycobacteriaceae plasmid sequences were detected in whole genome raw reads. Clinical data and course were retrieved and correlated with genomic data. Results We included 33 M. simiae sensu stricto isolates from seven patients. M. simiae showed low clinical relevance with only two patients fulfilling American Thoracic Society (ATS) criteria in our cohort and three receiving NTM-effective therapy. The bacterial populations were highly stable over time periods of up to 14 years, and no instances of mixed or re-infections with other strains of M. simiae were observed. Clustering with <12 single nucleotide polymorphisms distance was evident among isolates from different patients; however, proof for human-to-human transmission could not be established from epidemiological data. Conclusion Overall, the available sequence data for M. simiae complex was significantly extended and new insights into its pathogenomic traits were obtained. We demonstrate high longitudinal genomic stability within single patients. Although we cannot exclude human-to-human transmission, we consider it unlikely in the light of available epidemiological data.
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Affiliation(s)
- Nils Wetzstein
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Infectious Diseases, Frankfurt am Main, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- These authors contributed equally as first authors
| | - Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- These authors contributed equally as first authors
| | - Sönke Andres
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Martin Kuhns
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Lisa Marschall
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Infectious Diseases, Frankfurt am Main, Germany
| | - Teodora Biciusca
- Goethe University Frankfurt, University Hospital, Department of Radiology, Frankfurt am Main, Germany
| | - Christina Smaczny
- Goethe University Frankfurt, University Hospital, Department of Internal Medicine, Pneumology, Frankfurt am Main, Germany
| | - Inna Friesen
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- These authors contributed equally as senior authors
| | - Thomas A. Wichelhaus
- Goethe University Frankfurt, University Hospital, Institute of Medical Microbiology and Infection Control, Frankfurt am Main, Germany
- These authors contributed equally as senior authors
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Guzinski J, Potter J, Tang Y, Davies R, Teale C, Petrovska L. Geographical and temporal distribution of multidrug-resistant Salmonella Infantis in Europe and the Americas. Front Microbiol 2024; 14:1244533. [PMID: 38414709 PMCID: PMC10896835 DOI: 10.3389/fmicb.2023.1244533] [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: 06/22/2023] [Accepted: 12/04/2023] [Indexed: 02/29/2024] Open
Abstract
Recently emerged S. Infantis strains carrying resistance to several commonly used antimicrobials have been reported from different parts of the globe, causing human cases of salmonellosis and with occurrence reported predominantly in broiler chickens. Here, we performed phylogenetic and genetic clustering analyses to describe the population structure of 417 S. Infantis originating from multiple European countries and the Americas collected between 1985 and 2019. Of these, 171 were collected from 56 distinct premises located in England and Wales (E/W) between 2009 and 2019, including isolates linked to incursions of multidrug-resistant (MDR) strains from Europe associated with imported poultry meat. The analysis facilitated the comparison of isolates from different E/W sources with isolates originating from other countries. There was a high degree of congruency between the outputs of different types of population structure analyses revealing that the E/W and central European (Germany, Hungary, and Poland) isolates formed several disparate groups, which were distinct from the cluster relating to the United States (USA) and Ecuador/Peru, but that isolates from Brazil were closely related to the E/W and the central European isolates. Nearly half of the analysed strains/genomes (194/417) harboured the IncFIB(pN55391) replicon typical of the "parasitic" pESI-like megaplasmid found in diverse strains of S. Infantis. The isolates that contained the IncFIB(pN55391) replicon clustered together, despite originating from different parts of the globe. This outcome was corroborated by the time-measured phylogeny, which indicated that the initial acquisition of IncFIB(pN55391) likely occurred in Europe in the late 1980s, with a single introduction of IncFIB(pN55391)-carrying S. Infantis to the Americas several years later. Most of the antimicrobial resistance (AMR) genes were identified in isolates that harboured one or more different plasmids, but based on the short-read assemblies, only a minority of the resistance genes found in these isolates were identified as being associated with the detected plasmids, whereas the hybrid assemblies comprising the short and long reads demonstrated that the majority of the identified AMR genes were associated with IncFIB(pN55391) and other detected plasmid replicon types. This finding underlies the importance of applying appropriate methodologies to investigate associations of AMR genes with bacterial plasmids.
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Affiliation(s)
- Jaromir Guzinski
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Joshua Potter
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Yue Tang
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Rob Davies
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
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El Chaar M, Khoury Y, Douglas GM, El Kazzi S, Jisr T, Soussi S, Merhi G, Moghnieh RA, Shapiro BJ. Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients. Microbiol Spectr 2024; 12:e0312823. [PMID: 38171007 PMCID: PMC10846182 DOI: 10.1128/spectrum.03128-23] [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: 08/21/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
Colonization with multidrug-resistant Escherichia coli strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant E. coli strains in critically ill patients and to identify evolutionary changes and strain replacement events within patients. Patients were admitted to the intensive care unit and hematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on E. coli strains isolated from patients at multiple time points. The E. coli isolates were genetically diverse, with 11 sequence types (STs) identified among 22 isolates sequenced. Five patients were colonized by E. coli sequence type 131 (ST131)-encoding CTX-M-27, an emerging clone not previously observed in clinical samples from Lebanon. Among the eight patients whose resident E. coli strains were tracked over time, five harbored the same E. coli strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different E. coli strains over time. Our study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131-encoding CTX-M-27, which appears to be emerging as a globally important multidrug-resistant E. coli strain, is also prevalent among critical care patients and deserves further monitoring.IMPORTANCEUnderstanding the evolution of bacteria over time in hospitalized patients is of utmost significance in the field of infectious diseases. While numerous studies have surveyed genetic diversity and resistance mechanisms in nosocomial infections, time series of within-patient dynamics are rare, and high-income countries are over-represented, leaving low- and middle-income countries understudied. Our study aims to bridge these research gaps by conducting a longitudinal survey of critically ill patients in Lebanon. This allowed us to track Escherichia coli evolution and strain replacements within individual patients over extended periods. Through whole-genome sequencing, we found extensive strain diversity, including the first evidence of the emerging E. coli sequence type 131 clone encoding the CTX-M-27 beta-lactamase in a clinical sample from Lebanon, as well as likely strain replacement events during hospitalization.
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Affiliation(s)
- Mira El Chaar
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Yaralynn Khoury
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Gavin M. Douglas
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Samir El Kazzi
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Tamima Jisr
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Shatha Soussi
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Georgi Merhi
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Rima A. Moghnieh
- Division of Infectious Diseases, Department of Internal Medicine, Lebanese American University Medical Center, Beirut, Lebanon
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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Li X, Wang Y, Cao R, Xiao F, Wang X, Ye L, Xiao Y, Li D, Zhang T. Antimicrobial Resistance of Clostridioides difficile in Children from a Tertiary Pediatric Hospital in Shanghai, China. Infect Drug Resist 2024; 17:329-339. [PMID: 38293314 PMCID: PMC10826549 DOI: 10.2147/idr.s441312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/13/2023] [Indexed: 02/01/2024] Open
Abstract
Background Our previous study reported a high rate of recurrence in children with Clostridioides difficile (C. difficile) infection (CDI) after conventional antibiotic therapy. Here, we aimed to explore whether metronidazole and vancomycin resistant C. difficile isolates are circulating in pediatric CDI. Methods Antimicrobial susceptibility testing (AST) using the agar dilution method according to the Clinical and Laboratory Standard Institute (CLSI) were performed on C. difficile isolates collected from children with CDI between 2019 and 2022 at the Shanghai Children's Hospital. Whole-genome sequencing (WGS) was performed on all C. difficile isolates, and the presence of antibiotic resistance genes (ARGs) were identified using Resfinder and the Comprehensive Antibiotic Resistance Database (CARD). The presence of plasmid pCD-METRO was detected using SRST2 (v0.2.0) against 8 pCD-METRO coding sequences. Results A total of 50 C. difficile isolates were collected from stools of CDI children. The overall resistance rate on all isolates was 30.00% for metronidazole, 6.00% for vancomycin, 0% for rifaximin, 2.00% for rifampin, 24.00% for meropenem, 100.00% for ceftriaxone and clindamycin, 86.00% for erythromycin, 30.0% for levofloxacin, and 50.0% for tetracycline. Multidrug-resistant (MDR) was presented in 44 isolates (88.00%). Sixteen reported potential ARGs relating with resistance to antibiotic classes of aminoglycoside (AAC(6')-Ie-APH(2")-Ia, aad(6), ANT(6)-Ib, APH(2")-If, APH(3')-IIIa), lincosamide-clindamycin-erythromycin (ErmB, ErmQ), fluoroquinolones (CdeA), glycopeptides (vanRG), nucleoside (SAT-4), tetracycline (tetM, tetA(P), tetB(P), tetO), and trimethoprim (dfrF) were identified. However, the pCD-METRO plasmid and vanA/B were not detected in any isolates. Conclusion C. difficile isolates from children with reduced susceptibility to metronidazole and vancomycin are emerging in pediatric CDI in China. The lack of pCD-METRO plasmid and vanA/B associated with reduced antibiotic susceptibility suggests there are additional mechanisms of resistance.
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Affiliation(s)
- Xiaolu Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yizhong Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Gut Microbiota and Metabolic Research Center, Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Rong Cao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Fangfei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Xufei Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Lin Ye
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yongmei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Dan Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Ting Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Gut Microbiota and Metabolic Research Center, Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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Cooper AL, Low A, Wong A, Tamber S, Blais BW, Carrillo CD. Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools. BMC Microbiol 2024; 24:31. [PMID: 38245666 PMCID: PMC10799530 DOI: 10.1186/s12866-023-03148-6] [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: 08/21/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Although the spread of antimicrobial resistance (AMR) through food and its production poses a significant concern, there is limited research on the prevalence of AMR bacteria in various agri-food products. Sequencing technologies are increasingly being used to track the spread of AMR genes (ARGs) in bacteria, and metagenomics has the potential to bypass some of the limitations of single isolate characterization by allowing simultaneous analysis of the agri-food product microbiome and associated resistome. However, metagenomics may still be hindered by methodological biases, presence of eukaryotic DNA, and difficulties in detecting low abundance targets within an attainable sequence coverage. The goal of this study was to assess whether limits of detection of ARGs in agri-food metagenomes were influenced by sample type and bioinformatic approaches. RESULTS We simulated metagenomes containing different proportions of AMR pathogens and analysed them for taxonomic composition and ARGs using several common bioinformatic tools. Kraken2/Bracken estimates of species abundance were closest to expected values. However, analysis by both Kraken2/Bracken indicated presence of organisms not included in the synthetic metagenomes. Metaphlan3/Metaphlan4 analysis of community composition was more specific but with lower sensitivity than the Kraken2/Bracken analysis. Accurate detection of ARGs dropped drastically below 5X isolate genome coverage. However, it was sometimes possible to detect ARGs and closely related alleles at lower coverage levels if using a lower ARG-target coverage cutoff (< 80%). While KMA and CARD-RGI only predicted presence of expected ARG-targets or closely related gene-alleles, SRST2 (which allows read to map to multiple targets) falsely reported presence of distantly related ARGs at all isolate genome coverage levels. The presence of background microbiota in metagenomes influenced the accuracy of ARG detection by KMA, resulting in mcr-1 detection at 0.1X isolate coverage in the lettuce but not in the beef metagenome. CONCLUSIONS This study demonstrates accurate detection of ARGs in synthetic metagenomes using various bioinformatic methods, provided that reads from the ARG-encoding organism exceed approximately 5X isolate coverage (i.e. 0.4% of a 40 million read metagenome). While lowering thresholds for target gene detection improved sensitivity, this led to the identification of alternative ARG-alleles, potentially confounding the identification of critical ARGs in the resistome. Further advancements in sequencing technologies providing increased coverage depth or extended read lengths may improve ARG detection in agri-food metagenomic samples, enabling use of this approach for tracking clinically important ARGs in agri-food samples.
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Affiliation(s)
- Ashley L Cooper
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Andrew Low
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada
| | - Burton W Blais
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Catherine D Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.
- Department of Biology, Carleton University, Ottawa, ON, Canada.
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Foxall RL, Means J, Marcinkiewicz AL, Schillaci C, DeRosia-Banick K, Xu F, Hall JA, Jones SH, Cooper VS, Whistler CA. Inoviridae prophage and bacterial host dynamics during diversification, succession, and Atlantic invasion of Pacific-native Vibrio parahaemolyticus. mBio 2024; 15:e0285123. [PMID: 38112441 PMCID: PMC10790759 DOI: 10.1128/mbio.02851-23] [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: 10/31/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE An understanding of the processes that contribute to the emergence of pathogens from environmental reservoirs is critical as changing climate precipitates pathogen evolution and population expansion. Phylogeographic analysis of Vibrio parahaemolyticus hosts combined with the analysis of their Inoviridae phage resolved ambiguities of diversification dynamics which preceded successful Atlantic invasion by the epidemiologically predominant ST36 lineage. It has been established experimentally that filamentous phage can limit host recombination, but here, we show that phage loss is linked to rapid bacterial host diversification during epidemic spread in natural ecosystems alluding to a potential role for ubiquitous inoviruses in the adaptability of pathogens. This work paves the way for functional analyses to define the contribution of inoviruses in the evolutionary dynamics of environmentally transmitted pathogens.
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Affiliation(s)
- Randi L. Foxall
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Jillian Means
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Graduate Program in Microbiology, University of New Hampshire, Durham, New Hampshire, USA
| | - Ashely L. Marcinkiewicz
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Graduate Program in Microbiology, University of New Hampshire, Durham, New Hampshire, USA
| | - Christopher Schillaci
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Kristin DeRosia-Banick
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
| | - Feng Xu
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Jeffrey A. Hall
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Stephen H. Jones
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - Vaughn S. Cooper
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Cheryl A. Whistler
- Northeast Center for Vibrio Disease and Ecology, University of New Hampshire, Durham, New Hampshire, USA
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Chu VT, Tsitsiklis A, Mick E, Ambroggio L, Kalantar KL, Glascock A, Osborne CM, Wagner BD, Matthay MA, DeRisi JL, Calfee CS, Mourani PM, Langelier CR. The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients. Nat Commun 2024; 15:92. [PMID: 38168095 PMCID: PMC10762195 DOI: 10.1038/s41467-023-44353-1] [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: 08/30/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Antimicrobial resistant lower respiratory tract infections are an increasing public health threat and an important cause of global mortality. The lung microbiome can influence susceptibility of respiratory tract infections and represents an important reservoir for exchange of antimicrobial resistance genes. Studies of the gut microbiome have found an association between age and increasing antimicrobial resistance gene burden, however, corollary studies in the lung microbiome remain absent. We performed an observational study of children and adults with acute respiratory failure admitted to the intensive care unit. From tracheal aspirate RNA sequencing data, we evaluated age-related differences in detectable antimicrobial resistance gene expression in the lung microbiome. Using a multivariable logistic regression model, we find that detection of antimicrobial resistance gene expression was significantly higher in adults compared with children after adjusting for demographic and clinical characteristics. This association remained significant after additionally adjusting for lung bacterial microbiome characteristics, and when modeling age as a continuous variable. The proportion of adults expressing beta-lactam, aminoglycoside, and tetracycline antimicrobial resistance genes was higher compared to children. Together, these findings shape our understanding of the lung resistome in critically ill patients across the lifespan, which may have implications for clinical management and global public health.
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Affiliation(s)
- Victoria T Chu
- Division of Infectious Diseases & Global Health, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Alexandra Tsitsiklis
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Eran Mick
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Division of Pulmonary and Critical Care Medicine, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Lilliam Ambroggio
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
| | | | | | - Christina M Osborne
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
| | - Brandie D Wagner
- Department of Pediatrics, University of Colorado and Children's Hospital Colorado, Aurora, CO, USA
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Michael A Matthay
- Division of Pulmonary and Critical Care Medicine, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Carolyn S Calfee
- Division of Pulmonary and Critical Care Medicine, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Peter M Mourani
- Arkansas Children's Research Institute, Arkansas Children's Hospital, Little Rock, AR, USA
| | - Charles R Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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38
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Parcell BJ, Pettigrew KA, Oravcova K. Application of Pathogen Genomics to Outbreak Investigation. Methods Mol Biol 2024; 2833:161-183. [PMID: 38949710 DOI: 10.1007/978-1-0716-3981-8_16] [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: 07/02/2024]
Abstract
Outbreaks are a risk to public health particularly when pathogenic, hypervirulent, and/or multidrug-resistant organisms (MDROs) are involved. In a hospital setting, vulnerable populations such as the immunosuppressed, intensive care patients, and neonates are most at risk. Rapid and accurate outbreak detection is essential to implement effective interventions in clinical areas to control and stop further transmission. Advances in the field of whole genome sequencing (WGS) have resulted in lowered costs, increased capacity, and improved reproducibility of results. WGS now has the potential to revolutionize the investigation and management of outbreaks replacing conventional genotyping and other discrimination systems. Here, we outline specific procedures and protocols to implement WGS into investigation of outbreaks in healthcare settings.
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Affiliation(s)
- Benjamin J Parcell
- Clinical Senior Lecturer and Honorary Consultant, Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK.
| | - Kerry A Pettigrew
- Lecturer in Biomedical Science, School of Health and Life Sciences, Teesside University, Middlesbrough, UK
| | - Katarina Oravcova
- Lecturer in Bacteriology, School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
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Sánchez-Busó L, Sánchez-Serrano A, Golparian D, Unemo M. pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections. Microb Genom 2024; 10:001189. [PMID: 38288762 PMCID: PMC10868605 DOI: 10.1099/mgen.0.001189] [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: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024] Open
Abstract
Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, multi-locus sequence typing (MLST), Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), allow inter-laboratory and inter-study comparability and reproducibility and provide an approximation to the gonococcal population structure. With whole-genome sequencing (WGS), we obtain a substantially higher and more accurate discrimination between strains compared to previous molecular typing schemes. However, WGS remains unavailable or not affordable in many laboratories, and thus bioinformatic tools that allow the integration of data among laboratories with and without access to WGS are imperative for a joint effort to increase our understanding of global pathogen threats. Here, we present pyngoST, a command-line Python tool for fast, simultaneous and accurate sequence typing of N. gonorrhoeae from WGS assemblies. pyngoST integrates MLST, NG-MAST and NG-STAR, and can also designate NG-STAR clonal complexes, NG-MAST genogroups and penA mosaicism, facilitating multiple sequence typing from large WGS assembly collections. Exact and closest matches for existing alleles and sequence types are reported. The implementation of a fast multi-pattern searching algorithm allows pyngoST to be rapid and report results on 500 WGS assemblies in under 1 min. The mapping of typing results on a core genome tree of 2375 gonococcal genomes revealed that NG-STAR is the scheme that best represents the population structure of this pathogen, emphasizing the role of antimicrobial use and antimicrobial resistance as a driver of gonococcal evolution. This article contains data hosted by Microreact.
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Affiliation(s)
- Leonor Sánchez-Busó
- Joint Research Unit ‘Infection and Public Health’, FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBERESP, ISCIII, Spain
| | - Andrea Sánchez-Serrano
- Joint Research Unit ‘Infection and Public Health’, FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Institute for Global Health, University College London (UCL), London, UK
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40
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Chaguza C, Pöntinen AK, Top J, Arredondo-Alonso S, Freitas AR, Novais C, Torres C, Bentley SD, Peixe L, Coque TM, Willems RJL, Corander J. The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection. Microbiol Spectr 2023; 11:e0020123. [PMID: 37811975 PMCID: PMC10714801 DOI: 10.1128/spectrum.00201-23] [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: 01/13/2023] [Accepted: 08/29/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Enterococcus faecalis causes life-threatening invasive hospital- and community-associated infections that are usually associated with multidrug resistance globally. Although E. faecalis infections cause opportunistic infections typically associated with antibiotic use, immunocompromised immune status, and other factors, they also possess an arsenal of virulence factors crucial for their pathogenicity. Despite this, the relative contribution of these virulence factors and other genetic changes to the pathogenicity of E. faecalis strains remain poorly understood. Here, we investigated whether specific genomic changes in the genome of E. faecalis isolates influence its pathogenicity-infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection and intestinal colonization. Our findings indicate that E. faecalis genetics partially influence the infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection, possibly due to gut-to-bloodstream translocation, highlighting the potential substantial role of host and environmental factors, including gut microbiota, on the opportunistic pathogenic lifestyle of this bacterium.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Anna K. Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sergio Arredondo-Alonso
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Luisa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
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Cho ST, Mills EG, Griffith MP, Nordstrom HR, McElheny CL, Harrison LH, Doi Y, Van Tyne D. Evolution of extended-spectrum β-lactamase-producing ST131 Escherichia coli at a single hospital over 15 years. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571174. [PMID: 38168243 PMCID: PMC10760032 DOI: 10.1101/2023.12.11.571174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Escherichia coli belonging to sequence type ST131 constitute a globally distributed pandemic lineage that causes multidrug-resistant extra-intestinal infections. ST131 E. coli frequently produce extended-spectrum β-lactamases (ESBLs), which confer resistance to many β-lactam antibiotics and make infections difficult to treat. We sequenced the genomes of 154 ESBL-producing E. coli clinical isolates belonging to the ST131 lineage from patients at the University of Pittsburgh Medical Center (UPMC) between 2004 and 2018. Isolates belonged to the well described ST131 clades A (8%), B (3%), C1 (33%), and C2 (54%). An additional four isolates belonged to another distinct subclade within clade C and encoded genomic characteristics that have not been previously described. Time-dated phylogenetic analysis estimated that the most recent common ancestor (MRCA) for all clade C isolates from UPMC emerged around 1989, consistent with previous studies. We identified multiple genes potentially under selection in clade C, including the cell wall assembly gene ftsI, the LPS biosynthesis gene arnC, and the yersiniabactin uptake receptor fyuA. Diverse ESBL genes belonging to the blaCTX-M, blaSHV, and blaTEM families were identified; these genes were found at varying numbers of loci and in variable numbers of copies across isolates. Analysis of ESBL flanking regions revealed diverse mobile elements that varied by ESBL type. Overall, our findings show that ST131 subclades C1 and C2 dominated and were stably maintained among patients in the same hospital and uncover possible signals of ongoing adaptation within the clade C ST131 lineage.
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Affiliation(s)
- Shu-Ting Cho
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Emma G. Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marissa P. Griffith
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hayley R. Nordstrom
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lee H. Harrison
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Unoarumhi Y, Davis ML, Rowe LA, Mathis S, Li Z, Chochua S, Li Y, McGee L, Metcalf BJ, Lee JS, Beall B. A novel invasive Streptococcus pyogenes variant sublineage derived through recombinational replacement of the emm12 genomic region. Sci Rep 2023; 13:21510. [PMID: 38057343 PMCID: PMC10700362 DOI: 10.1038/s41598-023-48035-2] [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: 04/01/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
Group A streptococcal strains potentially acquire new M protein gene types through genetic recombination (emm switching). To detect such variants, we screened 12,596 invasive GAS genomes for strains of differing emm types that shared the same multilocus sequence type (ST). Through this screening we detected a variant consisting of 16 serum opacity factor (SOF)-positive, emm pattern E, emm82 isolates that were ST36, previously only associated with SOF-negative, emm pattern A, emm12. The 16 emm82/ST36 isolates were closely interrelated (pairwise SNP distance of 0-43), and shared the same emm82-containing recombinational fragment. emm82/ST36 isolates carried the sof12 structural gene, however the sof12 indel characteristic of emm12 strains was corrected to confer the SOF-positive phenotype. Five independent emm82/ST36 invasive case isolates comprised two sets of genetically indistinguishable strains. The emm82/ST36 isolates were primarily macrolide resistant (12/16 isolates), displayed at least 4 different core genomic arrangements, and carried 11 different combinations of virulence and resistance determinants. Phylogenetic analysis revealed that emm82/ST36 was within a minor (non-clade 1) portion of ST36 that featured almost all ST36 antibiotic resistance. This work documents emergence of a rapidly diversifying variant that is the first confirmed example of an emm pattern A strain switched to a pattern E strain.
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Affiliation(s)
- Yvette Unoarumhi
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Morgan L Davis
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Lori A Rowe
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Saundra Mathis
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Zhongya Li
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Sopio Chochua
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Yuan Li
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Benjamin J Metcalf
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Justin S Lee
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Bernard Beall
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA.
- Eagle GLobal Scientific, LLC, Atlanta, GA, USA.
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Li X, Li G, Huang H, Wan P, Lu Y, Li Z, Xie L, Xiong W, Zeng Z. The occurrence and contamination of optrA-positive methicillin-resistant Staphylococcus aureus from duck farms in Guangdong, China. J Glob Antimicrob Resist 2023; 35:86-92. [PMID: 37689309 DOI: 10.1016/j.jgar.2023.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023] Open
Abstract
OBJECTIVES Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA), is an important zoonotic microorganism that increasingly causes public health concern worldwide. The objective of this study was to determine the prevalence and transmission of S. aureus in duck farms and evaluate its antimicrobial resistance and genetic characteristics. METHODS The samples associated with ducks, feeders, and the environment were collected on 14 duck farms from four areas in Guangdong, China, from 2020 to 2021. All isolates were subjected to antimicrobial susceptibility testing. A comprehensive epidemiological survey of S. aureus was conducted by S. aureus protein A typing and whole-genome sequencing. RESULTS A total of 560 samples were collected. The prevalence rate of MRSA among ducks (8.1%, 11 of 135) was higher compared with that in environmental samples. OptrA-positive ST398-t034 MRSA were first detected from duck farms in China. A total of 79.3% (34 of 46) S. aureus isolates showed multidrug-resistant phenotypes. Notably, some isolates carried multidrug-resistant genes encoding macrolide-lincosamide-streptogramin B, pleuromutilin-pleuromutilin-streptogramin A, and oxazolidinone. Analysis of the virulence genes revealed that the MRSA isolates carried genes encoding gamma-hemolysin, enterotoxin, and leukocidin. ST9-t899 is a primary clonal lineage among duck- and environment-associated MRSA. Single-nucleotide polymorphism analysis showed the potential contamination relationship of optrA-positive ST2308 MRSA isolates carrying the gamma-hemolysin genes and the leukocidin virulence genes between airborne dust and sick ducks. CONCLUSION The contamination of MRSA, especially optrA-positive MRSA, between food animals and the environment is a growing public health concern worldwide. Based on One Health principles, continuous surveillance of MRSA is urgently needed.
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Affiliation(s)
- Xiaoshen Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Guihua Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Honghao Huang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Peng Wan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Yixing Lu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Zhi Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Longfei Xie
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China.
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Davies TJ, Swann J, Sheppard AE, Pickford H, Lipworth S, AbuOun M, Ellington MJ, Fowler PW, Hopkins S, Hopkins KL, Crook DW, Peto TEA, Anjum MF, Walker AS, Stoesser N. Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli. Microb Genom 2023; 9:001151. [PMID: 38100178 PMCID: PMC10763500 DOI: 10.1099/mgen.0.001151] [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: 06/27/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Several bioinformatics genotyping algorithms are now commonly used to characterize antimicrobial resistance (AMR) gene profiles in whole-genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly Escherichia coli, is of major importance, because this is a common pathogen. However, robust comparisons of different genotyping approaches on relevant simulated and large real-life WGS datasets are lacking. Here, we used both simulated datasets and a large set of real E. coli WGS data (n=1818 isolates) to systematically investigate genotyping methods in greater detail. Simulated constructs and real sequences were processed using four different bioinformatic programs (ABRicate, ARIBA, KmerResistance and SRST2, run with the ResFinder database) and their outputs compared. For simulation tests where 3079 AMR gene variants were inserted into random sequence constructs, KmerResistance was correct for 3076 (99.9 %) simulations, ABRicate for 3054 (99.2 %), ARIBA for 2783 (90.4 %) and SRST2 for 2108 (68.5 %). For simulation tests where two closely related gene variants were inserted into random sequence constructs, KmerResistance identified the correct alleles in 35 338/46 318 (76.3 %) simulations, ABRicate identified them in 11 842/46 318 (25.6 %) simulations, ARIBA identified them in 1679/46 318 (3.6 %) simulations and SRST2 identified them in 2000/46 318 (4.3 %) simulations. In real data, across all methods, 1392/1818 (76 %) isolates had discrepant allele calls for at least 1 gene. In addition to highlighting areas for improvement in challenging scenarios, (e.g. identification of AMR genes at <10× coverage, identifying multiple closely related AMR genes present in the same sample), our evaluations identified some more systematic errors that could be readily soluble, such as repeated misclassification (i.e. naming) of genes as shorter variants of the same gene present within the reference resistance gene database. Such naming errors accounted for at least 2530/4321 (59 %) of the discrepancies seen in real data. Moreover, many of the remaining discrepancies were likely 'artefactual', with reporting of cut-off differences accounting for at least 1430/4321 (33 %) discrepants. Whilst we found that comparing outputs generated by running multiple algorithms on the same dataset could identify and resolve these algorithmic artefacts, the results of our evaluations emphasize the need for developing new and more robust genotyping algorithms to further improve accuracy and performance.
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Affiliation(s)
- Timothy J. Davies
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Anna E. Sheppard
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Hayleigh Pickford
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Samuel Lipworth
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Manal AbuOun
- Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - Matthew J. Ellington
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Division, UK Health Security Agency, London, UK
| | | | - Susan Hopkins
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Division, UK Health Security Agency, London, UK
| | - Katie L. Hopkins
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Derrick W. Crook
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Timothy E. A. Peto
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Muna F. Anjum
- Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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45
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Heydecke A, Yin H, Tano E, Sütterlin S. Limitations in predicting reduced susceptibility to third generation cephalosporins in Escherichia coli based on whole genome sequence data. PLoS One 2023; 18:e0295233. [PMID: 38033151 PMCID: PMC10688838 DOI: 10.1371/journal.pone.0295233] [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: 01/23/2023] [Accepted: 11/19/2023] [Indexed: 12/02/2023] Open
Abstract
Prediction of antibiotic resistance from whole genome sequence (WGS) data has been proposed. However, the performance of WGS data analysis for this matter may be influenced by the resistance mechanism's biology. This study compared traditional antimicrobial susceptibility testing with whole genome sequencing for identification of extended-spectrum beta-lactamases (ESBL) in a collection of 419 Escherichia coli isolates. BLASTn-based prediction and read mapping with srst2 gave matching results, and in 381/419 (91%) isolates WGS was congruent with phenotypic testing. Incongruent results were grouped by potential explanations into biological-related and sequence analysis-related results. Biological-related explanations included weak ESBL-enzyme activity (n = 4), inconclusive phenotypic ESBL-testing (n = 4), potential loss of plasmid during subculturing (n = 7), and other resistance mechanisms than ESBL-enzymes (n = 2). Sequence analysis-related explanations were cut-off dependency for read depth (n = 5), too stringent (n = 3) and too loose cut-off for nucleotide identity and coverage (n = 13), respectively. The results reveal limitations of both traditional antibiotic susceptibility testing and sequence-based resistance prediction and highlight the need for evidence-based standards in sequence analysis.
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Affiliation(s)
- Anna Heydecke
- Center for Research and Development Gävleborg, Uppsala University, Gävle, Sweden
| | - Hong Yin
- Department of Clinical Microbiology, Falun Hospital, Falun, Sweden
| | - Eva Tano
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Susanne Sütterlin
- Department of Women’s and Child’s Health, International Maternal and Child Health, Uppsala University, Uppsala, Sweden
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Lutgring JD, Kent AG, Bowers JR, Jasso-Selles DE, Albrecht V, Stevens VA, Pfeiffer A, Barnes R, Engelthaler DM, Johnson JK, Gargis AS, Rasheed JK, Limbago BM, Elkins CA, Karlsson M, Halpin AL. Comparison of carbapenem-susceptible and carbapenem-resistant Enterobacterales at nine sites in the USA, 2013-2016: a resource for antimicrobial resistance investigators. Microb Genom 2023; 9. [PMID: 37987646 DOI: 10.1099/mgen.0.001119] [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: 11/22/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) are an urgent public health threat. Genomic sequencing is an important tool for investigating CRE. Through the Division of Healthcare Quality Promotion Sentinel Surveillance system, we collected CRE and carbapenem-susceptible Enterobacterales (CSE) from nine clinical laboratories in the USA from 2013 to 2016 and analysed both phenotypic and genomic sequencing data for 680 isolates. We describe the molecular epidemiology and antimicrobial susceptibility testing (AST) data of this collection of isolates. We also performed a phenotype-genotype correlation for the carbapenems and evaluated the presence of virulence genes in Klebsiella pneumoniae complex isolates. These AST and genomic sequencing data can be used to compare and contrast CRE and CSE at these sites and serve as a resource for the antimicrobial resistance research community.
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Affiliation(s)
- Joseph D Lutgring
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alyssa G Kent
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Goldbelt C6, LLC, Chesapeake, Virginia, USA
| | - Jolene R Bowers
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Daniel E Jasso-Selles
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Valerie Albrecht
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Present address: Office of the Director, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Valerie A Stevens
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ashlyn Pfeiffer
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Riley Barnes
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - David M Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amy S Gargis
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Kamile Rasheed
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Brandi M Limbago
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Present address: Office of Science, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher A Elkins
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria Karlsson
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Goldbelt C6, LLC, Chesapeake, Virginia, USA
| | - Alison L Halpin
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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47
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De Silva PM, Bennett RJ, Kuhn L, Ngondo P, Debande L, Njamkepo E, Ho B, Weill FX, Marteyn BS, Jenkins C, Baker KS. Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins. EBioMedicine 2023; 97:104822. [PMID: 37806286 PMCID: PMC10579285 DOI: 10.1016/j.ebiom.2023.104822] [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: 04/11/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Shigella sp. are enteric pathogens which causes >125 million cases of shigellosis annually. S. sonnei accounts for about a quarter of those cases and is increasingly prevalent in industrialising nations. Being an enteric pathogen, S. sonnei benefits from outcompeting gut commensals such as Escherichia coli to establish itself and cause disease. There are numerous mechanisms that bacterial pathogens use to outcompete its rivals including molecules called colicins. A Type 6 Secretion System (T6SS) was recently described as contributing to E. coli killing in S. sonnei. METHODS We used Bulk Phenotyping of Epidemiological Replicates (BPER) which combined bacterial Genome Wide Association Studies (bGWAS) and high throughput phenotyping on a collection of S. sonnei surveillance isolates to identify the genetic features associated with E. coli killing and explore their relationship with epidemiological behaviour. We further explored the presence of colicins and T6SS components in the isolates using genomics, laboratory experimentation, and proteomics. FINDINGS Our bGWAS analysis returned known and novel colicin and colicin related genes as significantly associated with E. coli killing. In silico analyses identified key colicin clusters responsible for the killing phenotype associated with epidemiologically successful sub-lineages. The killing phenotype was not associated with the presence of a T6SS. Laboratory analyses confirmed the presence of the key colicin clusters and that killing was contact-independent. INTERPRETATION Colicins are responsible for E. coli killing by S. sonnei, not a T6SS. This phenotype contributes to shaping the observed epidemiology of S. sonnei and may contribute to its increasing prevalence globally. BPER is an epidemiologically relevant approach to phenotypic testing that enables the rapid identification of genetic drivers of phenotypic changes, and assessment of their relevance to epidemiology in natural settings. FUNDING Biotechnology and Biological Sciences Research Council, Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship, Wellcome Trust, Medical Research Council (UK), French National Research Agency.
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Affiliation(s)
- P Malaka De Silva
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Rebecca J Bennett
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Patryk Ngondo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Lorine Debande
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Elisabeth Njamkepo
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Brian Ho
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, UK
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Benoît S Marteyn
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000, Strasbourg, France
| | - Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, Colindale, London, UK
| | - Kate S Baker
- Department of Clinical Infection, Microbiology, and Immunology, Institute for Infection, Veterinary, and Ecological Sciences (IVES), University of Liverpool, Liverpool, United Kingdom; Department of Genetics, University of Cambridge, Downing Place, Cambridge, UK.
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48
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Nagano DS, Taniguchi I, Ono T, Nakamura K, Gotoh Y, Hayashi T. Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes. Microb Genom 2023; 9. [PMID: 37966169 DOI: 10.1099/mgen.0.001135] [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: 11/16/2023] Open
Abstract
Plasmids play important roles in bacterial genome diversification. In the Serratia marcescens complex (SMC), a notable contribution of plasmids to genome diversification was also suggested by our recent analysis of >600 draft genomes. As accurate analyses of plasmids in draft genomes are difficult, in this study we analysed 142 closed genomes covering the entire complex, 67 of which were obtained in this study, and identified 132 plasmids (1.9-244.4 kb in length) in 77 strains. While the average numbers of plasmids in clinical and non-clinical strains showed no significant difference, strains belonging to clade 2 (one of the two hospital-adapted lineages) contained more plasmids than the others. Pangenome analysis revealed that of the 28 954 genes identified, 12.8 % were plasmid-specific, and 1.4 % were present in plasmids or chromosomes depending on the strain. In the latter group, while transposon-related genes were most prevalent (31.4 % of the function-predicted genes), genes related to antimicrobial resistance and heavy metal resistance accounted for a notable proportion (22.7 %). Mash distance-based clustering separated the 132 plasmids into 23 clusters and 50 singletons. Most clusters/singletons showed notably different GC contents compared to those of host chromosomes, suggesting their recent or relatively recent appearance in the SMC. Among the 23 clusters, 17 were found in only clinical or only non-clinical strains, suggesting the possible preference of their distribution on the environmental niches of host strains. Regarding the host strain phylogeny, 16 clusters were distributed in two or more clades, suggesting their interclade transmission. Moreover, for many plasmids, highly homologous plasmids were found in other species, indicating the broadness of their potential host ranges, beyond the genus, family, order, class or even phylum level. Importantly, highly homologous plasmids were most frequently found in Klebsiella pneumoniae and other species in the family Enterobacteriaceae, suggesting that this family, particularly K. pneumoniae, is the main source for plasmid exchanges with the SMC. These results highlight the power of closed genome-based analysis in the investigation of plasmids and provide important insights into the nature of plasmids distributed in the SMC.
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Affiliation(s)
- Debora Satie Nagano
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tomoyuki Ono
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
- Department of Cardiovascular Surgery, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
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49
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Cuénod A, Agnetti J, Seth-Smith HMB, Roloff T, Wälchli D, Shcherbakov D, Akbergenov R, Tschudin-Sutter S, Bassetti S, Siegemund M, Nickel CH, Moran-Gilad J, Keys TG, Pflüger V, Thomson NR, Egli A. Bacterial genome-wide association study substantiates papGII of Escherichia coli as a major risk factor for urosepsis. Genome Med 2023; 15:89. [PMID: 37904175 PMCID: PMC10614358 DOI: 10.1186/s13073-023-01243-x] [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: 06/06/2023] [Accepted: 10/02/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Urinary tract infections (UTIs) are among the most common bacterial infections worldwide, often caused by uropathogenic Escherichia coli. Multiple bacterial virulence factors or patient characteristics have been linked separately to progressive, more invasive infections. In this study, we aim to identify pathogen- and patient-specific factors that drive the progression to urosepsis by jointly analysing bacterial and host characteristics. METHODS We analysed 1076 E. coli strains isolated from 825 clinical cases with UTI and/or bacteraemia by whole-genome sequencing (Illumina). Sequence types (STs) were determined via srst2 and capsule loci via fastKaptive. We compared the isolates from urine and blood to confirm clonality. Furthermore, we performed a bacterial genome-wide association study (bGWAS) (pyseer) using bacteraemia as the primary clinical outcome. Clinical data were collected by an electronic patient chart review. We concurrently analysed the association of the most significant bGWAS hit and important patient characteristics with the clinical endpoint bacteraemia using a generalised linear model (GLM). Finally, we designed qPCR primers and probes to detect papGII-positive E. coli strains and prospectively screened E. coli from urine samples (n = 1657) at two healthcare centres. RESULTS Our patient cohort had a median age of 75.3 years (range: 18.00-103.1) and was predominantly female (574/825, 69.6%). The bacterial phylogroups B2 (60.6%; 500/825) and D (16.6%; 137/825), which are associated with extraintestinal infections, represent the majority of the strains in our collection, many of which encode a polysaccharide capsule (63.4%; 525/825). The most frequently observed STs were ST131 (12.7%; 105/825), ST69 (11.0%; 91/825), and ST73 (10.2%; 84/825). Of interest, in 12.3% (13/106) of cases, the E. coli pairs in urine and blood were only distantly related. In line with previous bGWAS studies, we identified the gene papGII (p-value < 0.001), which encodes the adhesin subunit of the E. coli P-pilus, to be associated with 'bacteraemia' in our bGWAS. In our GLM, correcting for patient characteristics, papGII remained highly significant (odds ratio = 5.27, 95% confidence interval = [3.48, 7.97], p-value < 0.001). An independent cohort of cases which we screened for papGII-carrying E. coli at two healthcare centres further confirmed the increased relative frequency of papGII-positive strains causing invasive infection, compared to papGII-negative strains (p-value = 0.033, chi-squared test). CONCLUSIONS This study builds on previous work linking papGII with invasive infection by showing that it is a major risk factor for progression from UTI to bacteraemia that has diagnostic potential.
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Affiliation(s)
- Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, UK.
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland.
- Department of Microbiology and Immunology, McGill University, Montréal, Canada.
| | - Jessica Agnetti
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Helena M B Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Denise Wälchli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Dimitri Shcherbakov
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Rashid Akbergenov
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sarah Tschudin-Sutter
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Stefano Bassetti
- Division of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Martin Siegemund
- Department of Clinical Research, University of Basel, Basel, Switzerland
- Intensive Care Unit, University Hospital Basel, Basel, Switzerland
| | - Christian H Nickel
- Emergency Department, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Timothy G Keys
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | | | - Nicholas R Thomson
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland.
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50
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Salamzade R, McElheny CL, Manson AL, Earl AM, Shaikh N, Doi Y. Genomic epidemiology and antibiotic susceptibility profiling of uropathogenic Escherichia coli among children in the United States. mSphere 2023; 8:e0018423. [PMID: 37581436 PMCID: PMC10597468 DOI: 10.1128/msphere.00184-23] [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: 04/10/2023] [Accepted: 06/15/2023] [Indexed: 08/16/2023] Open
Abstract
Escherichia coli is the most common cause of urinary tract infections (UTIs) in children, and yet the underlying mechanisms of virulence and antibiotic resistance and the overall population structure of the species is poorly understood within this age group. To investigate whether uropathogenic E. coli (UPEC) from children who developed pyelonephritis carried specific genetic markers, we generated whole-genome sequence data for 96 isolates from children with UTIs. This included 57 isolates from children with either radiologically confirmed pyelonephritis or cystitis and 27 isolates belonging to the well-known multidrug-resistant sequence type ST131, selected to investigate their population structure and antibiotic resistance characteristics. We observed a UPEC population structure that is similar to those reported in adults. In comparison with prior investigations, we found that the full pap operon was more common among UPEC from pediatric cases of pyelonephritis. Further, in contrast with recent reports that the P-fimbriae adhesin-encoding papGII allele is substantially more prevalent in invasive UPEC from adults, we found papGII was common to both invasive and non-invasive UPEC from children. Among the set of ST131 isolates from children with UTIs, we found antibiotic resistance was correlated with known genetic markers of resistance, as in adults. Unexpectedly, we observed that fimH30, an allele of the fimbrial gene fimH often used as a proxy to type ST131 isolates into the most drug-resistant subclade C, was carried by some of the subclade A and subclade B isolates, suggesting that the fimH30 allele could confer a selective advantage for UPEC. IMPORTANCE Urinary tract infections (UTIs), which are most often caused by Escherichia coli, are not well studied in children. Here, we examine genetic characteristics that differentiate UTI-causing bacteria in children that either remain localized to the bladder or are involved in more serious kidney infections. We also examine patterns of antibiotic resistance among strains from children that are part of E. coli sequence type 131, a group of bacteria that commonly cause UTIs and are known to have high levels of drug resistance. This work provides new insight into the virulence and antibiotic resistance characteristics of the bacteria that cause UTIs in children.
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Affiliation(s)
- Rauf Salamzade
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Abigail L. Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Nader Shaikh
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Fujita Health University School of Medicine, Aichi, Japan
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