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Abdel-Glil MY, Braune S, Bouwhuis S, Sprague LD. First Description of Mergibacter septicus Isolated from a Common Tern ( Sterna hirundo) in Germany. Pathogens 2023; 12:1096. [PMID: 37764904 PMCID: PMC10536934 DOI: 10.3390/pathogens12091096] [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: 06/27/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Mergibacter septicus (M. septicus), previously known as Bisgaard Taxon 40, is a recently described species within the Pasteurellaceae family. In this study, we present a M. septicus strain isolated from a common tern (Sterna hirundo) chick that died just after fledging from the Banter See in Wilhelmshaven, Germany. The recovered M. septicus strain underwent microbiological phenotypic characterization, followed by whole genome sequencing on Illumina and Nanopore platforms. Phenotypically, M. septicus 19Y0039 demonstrated resistance to colistin, cephalexin, clindamycin, oxacillin, and penicillin G. The genome analysis revealed a circular 1.8 Mbp chromosome without any extrachromosomal elements, containing 1690 coding DNA sequences. The majority of these coding genes were associated with translation, ribosomal structure and biogenesis, followed by RNA processing and modification, and transcription. Genetic analyses revealed that the German M. septicus strain 19Y0039 is related to the American strain M. septicus A25201T. Through BLAST alignment, twelve putative virulence genes previously identified in the M. septicus type strain A25201T were also found in the German strain. Additionally, 84 putative virulence genes distributed across nine categories, including immune modulation, effector delivery system, nutrition/metabolic factors, regulation, stress survival, adherence, biofilm, exotoxin, and motility, were also identified.
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Affiliation(s)
- Mostafa Y. Abdel-Glil
- Institut für Bakterielle Infektionen und Zoonosen (IBIZ), Friedrich-Loeffler-Institut, 07743 Jena, Germany;
- Department of Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Silke Braune
- Niedersächsisches Landesamt für Verbraucherschutz und Lebensmittelsicherheit (LAVES), Lebensmittel- und Veterinärinstitut Braunschweig/Hannover, 30173 Hannover, Germany;
| | | | - Lisa D. Sprague
- Institut für Bakterielle Infektionen und Zoonosen (IBIZ), Friedrich-Loeffler-Institut, 07743 Jena, Germany;
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202
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Liao YC, Huang YT, Tseng CH, Liu CW, Liu PY. Comparative Genomics Identified PenR E151V Substitution Associated with Carbapenem-Resistance Burkholderia cepacia Complex and a Novel Burkholderia cepacia Complex Specific OXA-1043 Subgroup. Infect Drug Resist 2023; 16:5627-5635. [PMID: 37662974 PMCID: PMC10473398 DOI: 10.2147/idr.s418969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
Purpose Burkholderia cepacia complex (Bcc) is a known significant opportunistic pathogen causing morbidity and mortality, particularly in those with cystic fibrosis, chronic granulomatous disease, or immunocompromising host. Mortality of Bcc bloodstream infections among non-cystic fibrosis patients remained high. The antibiotic treatment for Bcc infection is quite challenging due to its intrinsic resistance to most antibiotics, and the resistance to carbapenems was the biggest concern among them. We aimed to realize the mechanism of carbapenem resistance in Bcc. Patients and Methods Ten strains of Bcc were identified by the MALDI-TOF MS, and the drug susceptibility test was using VITEK 2 system. The Burkholderia cepacia complex genomes were sequenced via Nanopore GridIon. We also downloaded another ninety-five strains of Bcc from the National Center for Biotechnology Information database to evaluate the divergence between carbapenem-resistance and carbapenem-sensitive strains. Results The genetic organization between carbapenem-sensitive and carbapenem-resistant strains of Bcc showed no difference. However, in the carbapenem-sensitive strain, E151V substitution in PenR was detected. In addition, a novel specific OXA family subgroup, blaOXA-1043 in Burkholderia cenocepacia was discovered. Conclusion The E151V substitution in PenR may be associated with carbapenem-sensitive in Bcc. Moreover, the V151E mutation in PenR may be related to the activation of PenB, leading to Bcc resistance to carbapenems. Besides, a novel OXA family subgroup, blaOXA-1043, was found in Burkholderia cenocepacia, which differs from the previous OXA family.
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Affiliation(s)
- Ya-Chun Liao
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chia-Wei Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, National Chung Hsing University, Taichung, Taiwan
- Genome Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung, Taiwan
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203
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Raffelsberger N, Buczek DJ, Svendsen K, Småbrekke L, Pöntinen AK, Löhr IH, Andreassen LLE, Simonsen GS, Sundsfjord A, Gravningen K, Samuelsen Ø. Community carriage of ESBL-producing Escherichia coli and Klebsiella pneumoniae: a cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates. mSphere 2023; 8:e0002523. [PMID: 37306968 PMCID: PMC10470604 DOI: 10.1128/msphere.00025-23] [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: 01/17/2023] [Accepted: 04/05/2023] [Indexed: 06/13/2023] Open
Abstract
The global prevalence of infections caused by extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) is increasing, and for Escherichia coli, observations indicate that this is partly driven by community-onset cases. The ESBL-E population structure in the community is scarcely described, and data on risk factors for carriage are conflicting. Here, we report the prevalence and population structure of fecal ESBL-producing E. coli and Klebsiella pneumoniae (ESBL-Ec/Kp) in a general adult population, examine risk factors, and compare carriage isolates with contemporary clinical isolates. Fecal samples obtained from 4,999 participants (54% women) ≥40 years in the seventh survey of the population-based Tromsø Study, Norway (2015, 2016), were screened for ESBL-Ec/Kp. In addition, we included 118 ESBL-Ec clinical isolates from the Norwegian surveillance program in 2014. All isolates were whole-genome sequenced. Risk factors associated with carriage were analyzed using multivariable logistic regression. ESBL-Ec gastrointestinal carriage prevalence was 3.3% [95% confidence interval (CI) 2.8%-3.9%, no sex difference] and 0.08% (0.02%-0.20%) for ESBL-Kp. For ESBL-Ec, travel to Asia was the only independent risk factor (adjusted odds ratio 3.46, 95% CI 2.18-5.49). E. coli ST131 was most prevalent in both collections. However, the ST131 proportion was significantly lower in carriage (24%) versus clinical isolates (58%, P < 0.001). Carriage isolates were genetically more diverse with a higher proportion of phylogroup A (26%) than clinical isolates (5%, P < 0.001), indicating that ESBL gene acquisition occurs in a variety of E. coli lineages colonizing the gut. STs commonly related to extraintestinal infections were more frequent in clinical isolates also carrying a higher prevalence of antimicrobial resistance, which could indicate clone-associated pathogenicity.IMPORTANCEESBL-Ec and ESBL-Kp are major pathogens in the global burden of antimicrobial resistance. However, there is a gap in knowledge concerning the bacterial population structure of human ESBL-Ec/Kp carriage isolates in the community. We have examined ESBL-Ec/Kp isolates from a population-based study and compared these to contemporary clinical isolates. The large genetic diversity of carriage isolates indicates frequent ESBL gene acquisition, while those causing invasive infections are more clone dependent and associated with a higher prevalence of antibiotic resistance. The knowledge of factors associated with ESBL carriage helps to identify patients at risk to combat the spread of resistant bacteria within the healthcare system. Particularly, previous travel to Asia stands out as a major risk factor for carriage and should be considered in selecting empirical antibiotic treatment in critically ill patients.
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Affiliation(s)
- Niclas Raffelsberger
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Dorota Julia Buczek
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kristian Svendsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Lars Småbrekke
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anna Kaarina Pöntinen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Iren H. Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | | | - Gunnar Skov Simonsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Norwegian E. coli ESBL Study Group
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Nordbyhagen, Norway
- Division of Medicine and Laboratory Sciences, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Kirsten Gravningen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Nordbyhagen, Norway
- Division of Medicine and Laboratory Sciences, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
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204
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Karwańska M, Wieliczko A, Bojesen AM, Villumsen KR, Krzyżewska-Dudek E, Woźniak-Biel A. Isolation and characterization of multidrug resistant Gallibacterium anatis biovar haemolytica strains from Polish geese and hens. Vet Res 2023; 54:67. [PMID: 37612766 PMCID: PMC10463661 DOI: 10.1186/s13567-023-01198-2] [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: 04/18/2023] [Accepted: 07/05/2023] [Indexed: 08/25/2023] Open
Abstract
Gallibacterium anatis biovar haemolytica is a bacterium that is frequently associated with infections of the reproductive tract and respiratory system in poultry. To assess the current prevalence and resistance profile of these bacteria in Poland, we collected and investigated 63 strains of Gallibacterium from diseased domestic poultry flocks including geese, laying hens, breeding hens and an ornamental hen. Detailed characterization of the isolates included the analysis of phenotypic antimicrobial resistance profiles and biofilm formation ability. Furthermore, the genetic background of 40 selected isolates regarding the presence of virulence and antimicrobial resistance genes and mobile genetic elements was determined. All investigated isolates were multidrug resistant, most prominently to β-lactams, fluoroquinolones, sulfonamides and macrolides. A total of 48 different resistance profiles were detected. Of all isolates, 50.8% formed a strong biofilm, where strains isolated from geese appeared to be better at biofilm formation than strains isolated from laying and breeding hens. Single-nucleotide polymorphism genotyping revealed that G. anatis bv. haemolytica strains are restricted in host and geographical distribution, and the geese isolates showed greater phylogenetic similarity. Whole genome sequencing enabled identification of 25 different antimicrobial resistance determinants. The most common resistance genes were tetB, blaROB-1, and blaTEM-1 which may be located on mobile genetic elements. All isolates possessed the toxin gene gtxA, and the fimbrial gene flfA was identified in 95% of strains. Our results indicated that all G. anatis bv. haemolytica isolates showed multidrug resistant phenotypes. Strains isolated from geese were characterized by the highest percentage of isolates resistant to selected antimicrobials, probably reflecting host-related adaptations.
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Affiliation(s)
- Magdalena Karwańska
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland.
| | - Alina Wieliczko
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Rømer Villumsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eva Krzyżewska-Dudek
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Anna Woźniak-Biel
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Wrocław, Poland.
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205
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Boutzoukas AE, Komarow L, Chen L, Hanson B, Kanj SS, Liu Z, Salcedo Mendoza S, Ordoñez K, Wang M, Paterson DL, Evans S, Ge L, Giri A, Hill C, Baum K, Bonomo RA, Kreiswirth B, Patel R, Arias CA, Chambers HF, Fowler VG, van Duin D. International Epidemiology of Carbapenemase-Producing Escherichia coli. Clin Infect Dis 2023; 77:499-509. [PMID: 37154071 PMCID: PMC10444003 DOI: 10.1093/cid/ciad288] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Carbapenemase-producing (CP) Escherichia coli (CP-Ec) are a global public health threat. We aimed to describe the clinical and molecular epidemiology and outcomes of patients from several countries with CP-Ec isolates obtained from a prospective cohort. METHODS Patients with CP-Ec were enrolled from 26 hospitals in 6 countries. Clinical data were collected, and isolates underwent whole-genome sequencing. Clinical and molecular features and outcomes associated with isolates with or without metallo-β-lactamases (MBLs) were compared. The primary outcome was desirability of outcome ranking (DOOR) at 30 days after the index culture. RESULTS Of the 114 CP-Ec isolates in Consortium on resistance against carbapenems in Klebsiella and other Enterobacterales-2 (CRACKLE-2), 49 harbored an MBL, most commonly blaNDM-5 (38/49, 78%). Strong regional variations were noted with MBL-Ec predominantly found among patients in China (23/49). Clinically, MBL-Ec were more often from urine sources (49% vs 29%), less often met criteria for infection (39% vs 58%, P = .04), and had lower acuity of illness when compared with non-MBL-Ec. Among patients with infection, the probability of a better DOOR outcome for a randomly selected patient with MBL-Ec as compared with non-MBL-Ec was 62% (95% CI: 48.2-74.3%). Among infected patients, non-MBL-Ec had increased 30-day (26% vs 0%; P = .02) and 90-day (39% vs 0%; P = .001) mortality compared with MBL-Ec. CONCLUSIONS Emergence of CP-Ec was observed with important geographic variations. Bacterial characteristics, clinical presentations, and outcomes differed between MBL-Ec and non-MBL-Ec. Mortality was higher among non-MBL isolates, which were more frequently isolated from blood, but these findings may be confounded by regional variations.
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Affiliation(s)
- Angelique E Boutzoukas
- Division of Infectious Diseases, Duke University, Durham, North Carolina, USA
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Lauren Komarow
- The Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Blake Hanson
- Center for Infectious Diseases and Microbial Genomics, UTHealth, McGovern School of Medicine at Houston, Houston, Texas, USA
| | - Souha S Kanj
- Division of Infectious Diseases, and Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| | - Zhengyin Liu
- Infectious Disease Section, Department of Internal Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Soraya Salcedo Mendoza
- Servicio de Infectología, Organizacion Clinica General del Norte, Barranquilla, Colombia
| | - Karen Ordoñez
- Department of Infectious Diseases, E.S.E. Hospital Universitario, San Jorge de Pereira, Pereira, Colombia
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - David L Paterson
- ADVANCE-ID, Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Scott Evans
- The Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Lizhao Ge
- The Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Abhigya Giri
- The Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Carol Hill
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Keri Baum
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- VA–Case Center for Antibiotic Resistance and Epidemiology (Case-VA CARES), Cleveland, Ohio, USA
| | - Barry Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Cesar A Arias
- Division of Infectious Diseases and Center for Infectious Diseases, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Henry F Chambers
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Vance G Fowler
- Division of Infectious Diseases, Duke University, Durham, North Carolina, USA
- Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
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206
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Rose R, Nolan DJ, Ashcraft D, Feehan AK, Velez-Climent L, Huston C, Lain B, Rosenthal S, Miele L, Fogel GB, Pankey G, Garcia-Diaz J, Lamers SL. Comparing antimicrobial resistant genes and phenotypes across multiple sequencing platforms and assays for Enterobacterales clinical isolates. BMC Microbiol 2023; 23:225. [PMID: 37596530 PMCID: PMC10436404 DOI: 10.1186/s12866-023-02975-x] [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: 03/15/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
INTRODUCTION Whole genome sequencing (WGS) of bacterial isolates can be used to identify antimicrobial resistance (AMR) genes. Previous studies have shown that genotype-based AMR has variable accuracy for predicting carbapenem resistance in carbapenem-resistant Enterobacterales (CRE); however, the majority of these studies used short-read platforms (e.g. Illumina) to generate sequence data. In this study, our objective was to determine whether Oxford Nanopore Technologies (ONT) long-read WGS would improve detection of carbapenem AMR genes with respect to short-read only WGS for nine clinical CRE samples. We measured the minimum inhibitory breakpoint (MIC) using two phenotype assays (MicroScan and ETEST) for six antibiotics, including two carbapenems (meropenem and ertapenem) and four non-carbapenems (gentamicin, ciprofloxacin, cefepime, and trimethoprim/sulfamethoxazole). We generated short-read data using the Illumina NextSeq and long-read data using the ONT MinION. Four assembly methods were compared: ONT-only assembly; ONT-only assembly plus short-read polish; ONT + short-read hybrid assembly plus short-read polish; short-read only assembly. RESULTS Consistent with previous studies, our results suggest that the hybrid assembly produced the highest quality results as measured by gene completeness and contig circularization. However, ONT-only methods had minimal impact on the detection of AMR genes and plasmids compared to short-read methods, although, notably, differences in gene copy number differed between methods. All four assembly methods showed identical presence/absence of the blaKPC-2 carbapenemase gene for all samples. The two phenotype assays showed 100% concordant results for the non-carbapenems, but only 65% concordance for the two carbapenems. The presence/absence of AMR genes was 100% concordant with AMR phenotypes for all four non-carbapenem drugs, although only 22%-50% sensitivity for the carbapenems. CONCLUSIONS Overall, these findings suggest that the lack of complete correspondence between CRE AMR genotype and phenotype for carbapenems, while concerning, is independent of sequencing platform/assembly method.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA.
- FoxSeq, LLC, Thibodaux, LA, USA.
| | - David J Nolan
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Deborah Ashcraft
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Amy K Feehan
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | | | - Benjamin Lain
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Simon Rosenthal
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
| | - Lucio Miele
- Translational Science and Genetics at Louisiana State University Health Science Center, New Orleans, LA, USA
| | | | - George Pankey
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Julia Garcia-Diaz
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Susanna L Lamers
- BioInfoExperts LLC, 718 Bayou Lane, Thibodaux, LA, 70301, USA
- FoxSeq, LLC, Thibodaux, LA, USA
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207
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Mourão J, Ribeiro-Almeida M, Novais C, Magalhães M, Rebelo A, Ribeiro S, Peixe L, Novais Â, Antunes P. From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production. Microbiol Spectr 2023; 11:e0138623. [PMID: 37428073 PMCID: PMC10434174 DOI: 10.1128/spectrum.01386-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Concerns about colistin-resistant bacteria in animal food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae in the whole poultry production chain needs clarification. We assessed colistin-resistant and copper-tolerant K. pneumoniae occurrence in chickens raised with inorganic and organic copper formulas from 1-day-old chicks to meat (7 farms from 2019 to 2020), after long-term colistin withdrawal (>2 years). Clonal diversity and K. pneumoniae adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken flocks (75%) carried K. pneumoniae at early and preslaughter stages, with a significant decrease (P < 0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative K. pneumoniae were observed among fecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant (81%; silA and pcoD positive and with a MICCuSO4 of ≥16 mM) isolates. WGS revealed accumulation of colistin resistance-associated mutations and F type multireplicon plasmids carrying antibiotic resistance and metal/copper tolerance genes. The K. pneumoniae population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146, and ST392-KL27 and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken production as a reservoir/source of clinically relevant K. pneumoniae lineages and genes with potential risk to humans through food and/or environmental exposure. Despite the limited mcr spread due to the long-term colistin ban, this action was ineffective in controlling colistin-resistant/mcr-negative K. pneumoniae, regardless of feed. This study provides crucial insights into the persistence of clinically relevant K. pneumoniae in the poultry production chain and highlights the need for continued surveillance and proactive food safety actions within a One Health perspective. IMPORTANCE The spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically relevant Klebsiella pneumoniae throughout the poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative K. pneumoniae in chicken flocks, regardless of inorganic and organic copper formulas use and a long-term colistin ban. Despite the high K. pneumoniae isolate diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human K. pneumoniae exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in the food industry and policymakers tasked with regulating food safety.
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Affiliation(s)
- Joana Mourão
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Marisa Ribeiro-Almeida
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Mafalda Magalhães
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
- ESS, Polytechnic of Porto, Porto, Portugal
| | - Sofia Ribeiro
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ângela Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
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208
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Dallman TJ, Neuert S, Fernandez Turienzo C, Berin M, Richardson E, Fuentes-Utrilla P, Loman N, Gharbia S, Jenkins C, Behrens RH, Godbole G, Brown M. Prevalence and Persistence of Antibiotic Resistance Determinants in the Gut of Travelers Returning to the United Kingdom is Associated with Colonization by Pathogenic Escherichia coli. Microbiol Spectr 2023; 11:e0518522. [PMID: 37255437 PMCID: PMC10433802 DOI: 10.1128/spectrum.05185-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
The gut microbiota constitutes an ideal environment for the selection, exchange, and carriage of antibiotic resistance determinants (ARDs), and international travel has been identified as a risk factor for acquisition of resistant organisms. Here, we present a longitudinal metagenomic analysis of the gut resistome in travellers to "high-risk" countries (Gutback). Fifty volunteers, recruited at a travel clinic in London, United Kingdom, provided stool samples before (pre-travel), immediately after (post-travel), and 6 months after their return (follow-up) from a high-risk destination. Fecal DNA was extracted, metagenomic sequencing performed and the resistome profiled. An increase in abundance and diversity of resistome was observed after travel. Significant increases in abundance were seen in antimicrobial genes conferring resistance to macrolides, third-generation cephalosporins, aminoglycosides, and sulfonamides. There was a significant association with increased resistome abundance if the participant experienced diarrhea during travel or took antibiotics, but these two variables were co-correlated. The resistome abundance returned to pre-travel levels by the 6-month sample point but there was evidence of persistence of several ARDs. The post-travel samples had an increase in abundance Escherichia coli which was positively associated with many acquired resistant determinants. Virulence and phylogenetic profiling revealed pathogenic E. coli significantly contributed to this increase abundance. In summary, in this study, foreign travel remains a significant risk factor for acquisition of microbes conferring resistance to multiple classes of antibiotics, often associated with symptomatic exposure to diarrhoeagenic E. coli. IMPORTANCE A future where antimicrobial therapy is severely compromised by the increase in resistant organisms is of grave concern. Given the variability in prevalence and diversity of antimicrobial resistance determinants in different geographical settings, international travel is a known risk factor for acquisition of resistant organisms into the gut microbiota. In this study, we show the utility of metagenomic approaches to quantify the levels of acquisition and carriage of resistance determinants after travel to a "high-risk" setting. Significant modulation to the resistome was seen after travel that is largely resolved within 6 months, although evidence of persistence of several ARDs was observed. Risk factors for acquisition included experiencing a diarrheal episode and the use of antibiotics. Colonization by pathogenic Escherichia coli was correlated with an increase in acquisition of antimicrobial resistance determinants, and as such established public health guidance to travelers on food and water safety remain an important message to reduce the spread of antibiotic resistance.
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Affiliation(s)
- Timothy J. Dallman
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency London, United Kingdom
- Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Saskia Neuert
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency London, United Kingdom
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
| | - Cristina Fernandez Turienzo
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
- Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Michelle Berin
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Emily Richardson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
- MicrobesNG, Birmingham, United Kingdom
| | - Pablo Fuentes-Utrilla
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
- MicrobesNG, Birmingham, United Kingdom
| | - Nicholas Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Saheer Gharbia
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency London, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Genomics and Enabling Data, Warwick University, United Kingdom
| | - Claire Jenkins
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency London, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
| | - Ron H. Behrens
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, United Kingdom
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gauri Godbole
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency London, United Kingdom
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, United Kingdom
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael Brown
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, United Kingdom
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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209
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Laurence Yehouenou C, Bogaerts B, Vanneste K, De Keersmaecker SCJ, Roosens NHC, Kpangon AA, Affolabi D, Simon A, Dossou FM, Dalleur O. Whole-Genome Sequencing-Based Screening of MRSA in Patients and Healthcare Workers in Public Hospitals in Benin. Microorganisms 2023; 11:1954. [PMID: 37630513 PMCID: PMC10459514 DOI: 10.3390/microorganisms11081954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 08/27/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) constitutes a serious public health concern, with a considerable impact on patients' health, and substantial healthcare costs. In this study, patients and healthcare workers (HCWs) from six public hospitals in Benin were screened for MRSA. Strains were identified as MRSA using conventional microbiological methods in Benin, and confirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in Belgium. Whole-genome sequencing (WGS) was used on the confirmed MRSA isolates, to characterize their genomic content and study their relatedness. Amongst the 305 isolates (304 wound swabs and 61 nasal swabs) that were collected from patients and HCWs, we detected 32 and 15 cases of MRSA, respectively. From this collection, 27 high-quality WGS datasets were obtained, which carried numerous genes and mutations associated with antimicrobial resistance. The mecA gene was detected in all the sequenced isolates. These isolates were assigned to five sequence types (STs), with ST8 (55.56%, n = 15/27), ST152 (18.52%, n = 5/27), and ST121 (18.52%, n = 5/27) being the most common. These 27 isolates carried multiple virulence genes, including the genes encoding the Panton-Valentine leukocidin toxin (48.15%, n = 13/27), and the tst gene (29.63%, n = 8/27), associated with toxic shock syndrome. This study highlights the need to implement a multimodal strategy for reducing the risk of the cross-transmission of MRSA in hospitals.
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Affiliation(s)
- Carine Laurence Yehouenou
- Clinical Pharmacy Research Group (CLIP), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain UCLouvain, Avenue Mounier 73, 1200 Brussels, Belgium;
- Laboratoire de Référence des Mycobactéries (LRM), Cotonou BP 817, Benin;
- Faculté des Sciences de la Santé (FSS), Université d’Abomey Calavi (UAC), Cotonou 01 BP 188, Benin
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium; (B.B.); (K.V.); (S.C.J.D.K.); (N.H.C.R.)
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium; (B.B.); (K.V.); (S.C.J.D.K.); (N.H.C.R.)
| | - Sigrid C. J. De Keersmaecker
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium; (B.B.); (K.V.); (S.C.J.D.K.); (N.H.C.R.)
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, 1050 Brussels, Belgium; (B.B.); (K.V.); (S.C.J.D.K.); (N.H.C.R.)
| | - Arsène A. Kpangon
- Ecole Nationale des Techniciens Supérieurs en Santé Publique et Surveillance Épidémiologique, Université de Parakou, Parakou, Benin;
| | - Dissou Affolabi
- Laboratoire de Référence des Mycobactéries (LRM), Cotonou BP 817, Benin;
- Faculté des Sciences de la Santé (FSS), Université d’Abomey Calavi (UAC), Cotonou 01 BP 188, Benin
- Centre National Hospitalier et Universitaire Hubert Koutoukou Maga (CNHU-HKM), Cotonou BP 386, Benin
| | - Anne Simon
- Centres Hospitaliers Jolimont, Prévention et Contrôle des Infections, Groupe Jolimont Asbl, Rue Ferrer 159, 7100 Haine-Saint-Paul, Belgium;
| | - Francis Moise Dossou
- Department of Surgery and Surgical Specialties, Faculty of Health Sciences, Campus Universitaire, Champs de Foire, Cotonou 01 BP 118, Benin;
| | - Olivia Dalleur
- Clinical Pharmacy Research Group (CLIP), Louvain Drug Research Institute (LDRI), Université Catholique de Louvain UCLouvain, Avenue Mounier 73, 1200 Brussels, Belgium;
- Pharmacy, Clinique Universitaire Saint-Luc, Université Catholique de Louvain (UCLouvain), Avenue Hippocrate 10, 1200 Brussels, Belgium
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210
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Ortega-Sanz I, Barbero-Aparicio JA, Canepa-Oneto A, Rovira J, Melero B. CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter. BMC Bioinformatics 2023; 24:291. [PMID: 37474912 PMCID: PMC10357626 DOI: 10.1186/s12859-023-05414-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the growth of data at a faster rate than can be effectively analyzed and critical gaps in bioinformatics knowledge. RESULTS To address both issues, CamPype was developed as a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria, especially Campylobacter, which is the main cause of gastroenteritis worldwide making a negative impact on the economy of the public health systems. CamPype allows fully customization of stages to run and tools to use, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction and identification of nucleotide variants. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation. CONCLUSIONS The minimal user intervention of CamPype makes of this workflow an attractive resource for microbiology laboratories with no expertise in bioinformatics as a first line method for bacterial typing and epidemiological analyses, that would help to reduce the costs of disease outbreaks, or for comparative genomic analyses. CamPype is publicly available at https://github.com/JoseBarbero/CamPype .
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Affiliation(s)
- Irene Ortega-Sanz
- Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain
| | | | | | - Jordi Rovira
- Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain
| | - Beatriz Melero
- Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain.
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211
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Morreale DP, Porsch EA, Kern BK, St Geme JW, Planet PJ. Acquisition, co-option, and duplication of the rtx toxin system and the emergence of virulence in Kingella. Nat Commun 2023; 14:4281. [PMID: 37460464 DOI: 10.1038/s41467-023-39939-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/04/2023] [Indexed: 07/20/2023] Open
Abstract
The bacterial genus Kingella includes two pathogenic species, namely Kingella kingae and Kingella negevensis, as well as strictly commensal species. Both K. kingae and K. negevensis secrete a toxin called RtxA that is absent in the commensal species. Here we present a phylogenomic study of the genus Kingella, including new genomic sequences for 88 clinical isolates, genotyping of another 131 global isolates, and analysis of 52 available genomes. The phylogenetic evidence supports that the toxin-encoding operon rtxCA was acquired by a common ancestor of the pathogenic Kingella species, and that a preexisting type-I secretion system was co-opted for toxin export. Subsequent genomic reorganization distributed the toxin machinery across two loci, with 30-35% of K. kingae strains containing two copies of the rtxA toxin gene. The rtxA duplication is largely clonal and is associated with invasive disease. Assays with isogenic strains show that a single copy of rtxA is associated with reduced cytotoxicity in vitro. Thus, our study identifies key steps in the evolutionary transition from commensal to pathogen, including horizontal gene transfer, co-option of an existing secretion system, and gene duplication.
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Affiliation(s)
- Daniel P Morreale
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric A Porsch
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brad K Kern
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph W St Geme
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Planet
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Comparative Genomics, American Museum of Natural History, New York, NY, USA.
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212
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Srednik ME, Perea CA, Giacoboni GI, Hicks JA, Foxx CL, Harris B, Schlater LK. Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study. Int J Mol Sci 2023; 24:11361. [PMID: 37511121 PMCID: PMC10379401 DOI: 10.3390/ijms241411361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6')-aph(2″), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec57395 were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination.
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Affiliation(s)
- Mariela E Srednik
- Postdoctoral Research Participation Program, Office of Research in Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Claudia A Perea
- Postdoctoral Research Participation Program, Office of Research in Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Gabriela I Giacoboni
- Departamento de Microbiología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata 1427, Argentina
| | - Jessica A Hicks
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Christine L Foxx
- Postdoctoral Research Participation Program, Office of Research in Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA
- Transboundary Disease Analytics, Center for Epidemiology and Animal Health, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, CO 80526, USA
| | - Beth Harris
- National Animal Health Laboratory Network, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Linda K Schlater
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
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213
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Ljungquist O, Haldorsen B, Pöntinen AK, Janice J, Josefsen EH, Elstrøm P, Kacelnik O, Sundsfjord A, Samuelsen Ø. Nationwide, population-based observational study of the molecular epidemiology and temporal trend of carbapenemase-producing Enterobacterales in Norway, 2015 to 2021. Euro Surveill 2023; 28:2200774. [PMID: 37410381 PMCID: PMC10370044 DOI: 10.2807/1560-7917.es.2023.28.27.2200774] [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: 09/26/2022] [Accepted: 03/29/2023] [Indexed: 07/07/2023] Open
Abstract
IntroductionNational and regional carbapenemase-producing Enterobacterales (CPE) surveillance is essential to understand the burden of antimicrobial resistance, elucidate outbreaks, and develop infection-control or antimicrobial-treatment recommendations.AimThis study aimed to describe CPE and their epidemiology in Norway from 2015 to 2021.MethodsA nationwide, population-based observational study of all verified clinical and carriage CPE isolates submitted to the national reference laboratory was conducted. Isolates were characterised by antimicrobial susceptibility testing, whole genome sequencing (WGS) and basic metadata. Annual CPE incidences were also estimated.ResultsA total of 389 CPE isolates were identified from 332 patients of 63 years median age (range: 0-98). These corresponded to 341 cases, 184 (54%) being male. Between 2015 and 2021, the annual incidence of CPE cases increased from 0.6 to 1.1 per 100,000 person-years. For CPE-isolates with available data on colonisation/infection, 58% (226/389) were associated with colonisation and 38% (149/389) with clinical infections. WGS revealed a predominance of OXA-48-like (51%; 198/389) and NDM (34%; 134/389) carbapenemases in a diversified population of Escherichia coli and Klebsiella pneumoniae, including high-risk clones also detected globally. Most CPE isolates were travel-related (63%; 245/389). Although local outbreaks and healthcare-associated transmission occurred, no interregional spread was detected. Nevertheless, 18% (70/389) of isolates not directly related to import points towards potentially unidentified transmission routes. A decline in travel-associated cases was observed during the COVID-19 pandemic.ConclusionsThe close-to-doubling of CPE case incidence between 2015 and 2021 was associated with foreign travel and genomic diversity. To limit further transmission and outbreaks, continued screening and monitoring is essential.
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Affiliation(s)
- Oskar Ljungquist
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Bjørg Haldorsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anna Kaarina Pöntinen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jessin Janice
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Ellen Haldis Josefsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Petter Elstrøm
- Department of Antibiotic Resistance and Infection Prevention, Norwegian Institute of Public Health, Oslo, Norway
| | - Oliver Kacelnik
- Department of Antibiotic Resistance and Infection Prevention, Norwegian Institute of Public Health, Oslo, Norway
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
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214
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Ring N, Low AS, Wee B, Paterson GK, Nuttall T, Gally D, Mellanby R, Fitzgerald JR. Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections. Microb Genom 2023; 9:mgen001066. [PMID: 37471128 PMCID: PMC10438823 DOI: 10.1099/mgen.0.001066] [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: 02/16/2023] [Accepted: 06/18/2023] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing typically requires 48-72 h to identify appropriate antibiotics for treatment. In the meantime, broad-spectrum antimicrobials are often used, which may be ineffective or impact non-target commensal bacteria. Here, we present a rapid, culture-free, diagnostics pipeline, involving metagenomic nanopore sequencing directly from clinical urine and skin samples of dogs. We have planned this pipeline to be versatile and easily implementable in a clinical setting, with the potential for future adaptation to different sample types and animals. Using our approach, we can identify the bacterial pathogen present within 5 h, in some cases detecting species which are difficult to culture. For urine samples, we can predict antibiotic sensitivity with up to 95 % accuracy. Skin swabs usually have lower bacterial abundance and higher host DNA, confounding antibiotic sensitivity prediction; an additional host depletion step will likely be required during the processing of these, and other types of samples with high levels of host cell contamination. In summary, our pipeline represents an important step towards the design of individually tailored veterinary treatment plans on the same day as presentation, facilitating the effective use of antibiotics and promoting better antimicrobial stewardship.
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Affiliation(s)
- Natalie Ring
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Alison S. Low
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bryan Wee
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Gavin K. Paterson
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Tim Nuttall
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - David Gally
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Richard Mellanby
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
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215
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Mateo-Estrada V, Tyrrell C, Evans BA, Aguilar-Vera A, Drissner D, Castillo-Ramirez S, Walsh F. Acinetobacter baumannii from grass: novel but non-resistant clones. Microb Genom 2023; 9:mgen001054. [PMID: 37439781 PMCID: PMC10438806 DOI: 10.1099/mgen.0.001054] [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: 03/19/2023] [Accepted: 05/26/2023] [Indexed: 07/14/2023] Open
Abstract
Acinetobacter baumannii is one the most worrisome nosocomial pathogens, which has long been considered almost mainly as a hospital-associated bacterium. There have been some studies about animal and environmental isolates over the last decade. However, little effort has been made to determine if this pathogen dwells in the grass. Here, we aim to determine the evolutionary relationships and antibiotic resistance of clones of A. baumannii sampled from grass to the major human international clones and animal clones. Two hundred and forty genomes were considered in total from four different sources for this study. Our core and accessory genomic epidemiology analyses showed that grass isolates cluster in seven groups well differentiated from one another and from the major human and animal isolates. Furthermore, we found new sequence types under both multilocus sequence typing schemes: two under the Pasteur scheme and seven for the Oxford scheme. The grass isolates contained fewer antibiotic-resistance genes and were not resistant to the antibiotics tested. Our results demonstrate that these novel clones appear to have limited antibiotic resistance potential. Given our findings, we propose that genomic epidemiology and surveillance of A. baumannii should go beyond the hospital settings and consider the environment in an explicit One Health approach.
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Affiliation(s)
- Valeria Mateo-Estrada
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ciara Tyrrell
- Department of Biology, The Kathleen Lonsdale Human Health Institute, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Alejandro Aguilar-Vera
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - David Drissner
- Department of Life Sciences, Albstadt-Sigmaringen University, 72488 Sigmaringen, Germany
| | - Santiago Castillo-Ramirez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Fiona Walsh
- Department of Biology, The Kathleen Lonsdale Human Health Institute, Maynooth University, Maynooth, Co. Kildare, Ireland
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Libuit KG, Doughty EL, Otieno JR, Ambrosio F, Kapsak CJ, Smith EA, Wright SM, Scribner MR, Petit III RA, Mendes CI, Huergo M, Legacki G, Loreth C, Park DJ, Sevinsky JR. Accelerating bioinformatics implementation in public health. Microb Genom 2023; 9:mgen001051. [PMID: 37428142 PMCID: PMC10438813 DOI: 10.1099/mgen.0.001051] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/24/2023] [Indexed: 07/11/2023] Open
Abstract
We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories (PHLs). Bioinformatics implementation for public health requires practitioners to undertake standardized bioinformatic analyses and generate reproducible, validated and auditable results. It is essential that data storage and analysis are scalable, portable and secure, and that implementation of bioinformatics fits within the operational constraints of the laboratory. We address these requirements using Terra, a web-based data analysis platform with a graphical user interface connecting users to bioinformatics analyses without the use of code. We have developed bioinformatics workflows for use with Terra that specifically meet the needs of public health practitioners. These Theiagen workflows perform genome assembly, quality control, and characterization, as well as construction of phylogeny for insights into genomic epidemiology. Additonally, these workflows use open-source containerized software and the WDL workflow language to ensure standardization and interoperability with other bioinformatics solutions, whilst being adaptable by the user. They are all open source and publicly available in Dockstore with the version-controlled code available in public GitHub repositories. They have been written to generate outputs in standardized file formats to allow for further downstream analysis and visualization with separate genomic epidemiology software. Testament to this solution meeting the requirements for bioinformatic implementation in public health, Theiagen workflows have collectively been used for over 5 million sample analyses in the last 2 years by over 90 public health laboratories in at least 40 different countries. Continued adoption of technological innovations and development of further workflows will ensure that this ecosystem continues to benefit PHLs.
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Affiliation(s)
- Kevin G. Libuit
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Emma L. Doughty
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - James R. Otieno
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Frank Ambrosio
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Curtis J. Kapsak
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Emily A. Smith
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Sage M. Wright
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Michelle R. Scribner
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Robert A. Petit III
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
- Wyoming Public Health Laboratory, 208 S College Dr, Cheyenne, WY 82007, USA
| | - Catarina Inês Mendes
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Marcela Huergo
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Gregory Legacki
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
| | - Christine Loreth
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
| | - Daniel J. Park
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
| | - Joel R. Sevinsky
- Theiagen Genomics, Suite 400, 1745 Shea Center Drive, Highlands Ranch, CO, 80129, USA
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217
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Higgs C, Kumar LS, Stevens K, Strachan J, Sherry NL, Horan K, Zhang J, Stinear TP, Howden BP, Gorrie CL. Population structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in Victoria, Australia. Microb Genom 2023; 9:mgen001070. [PMID: 37471116 PMCID: PMC10438814 DOI: 10.1099/mgen.0.001070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Streptococcus pneumoniae is a major human pathogen and can cause a range of conditions from asymptomatic colonization to invasive pneumococcal disease (IPD). The epidemiology and distribution of IPD-causing serotypes in Australia has undergone large changes following the introduction of the 7-valent pneumococcal conjugate vaccine (PCV) in 2005 and the 13-valent PCV in 2011. In this study, to provide a contemporary understanding of the IPD causing population in Victoria, Australia, we aimed to examine the population structure and prevalence of antimicrobial resistance using whole-genome sequencing and comprehensive antimicrobial susceptibility data of 1288 isolates collected between 2018 and 2022. We observed high diversity among the isolates with 52 serotypes, 203 sequence types (STs) and 70 Global Pneumococcal Sequencing Project Clusters (GPSCs) identified. Serotypes contained in the 13v-PCV represented 35.3 % (n=405) of isolates. Antimicrobial resistance (AMR) to at least one antibiotic was identified in 23.8 % (n=358) of isolates with penicillin resistance the most prevalent (20.3 %, n=261 using meningitis breakpoints and 5.1 % n=65 using oral breakpoints). Of the AMR isolates, 28 % (n=101) were multidrug resistant (MDR) (resistant to three or more drug classes). Vaccination status of cases was determined for a subset of isolates with 34 cases classified as vaccine failure events (fully vaccinated IPD cases of vaccine serotype). However, no phylogenetic association with failure events was observed. Within the highly diverse IPD population, we identified six high-risk sub-populations of public health concern characterized by high prevalence, high rates of AMR and MDR, or serotype inclusion in vaccines. High-risk serotypes included serotypes 3, 19F, 19A, 14, 11A, 15A and serofamily 23. In addition, we present our data validating seroBA for in silico serotyping to facilitate ISO-accreditation of this test in routine use in a public health reference laboratory and have made this data set available. This study provides insights into the population dynamics, highlights non-vaccine serotypes of concern that are highly resistant, and provides a genomic framework for the ongoing surveillance of IPD in Australia which can inform next-generation IPD prevention strategies.
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Affiliation(s)
- Charlie Higgs
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Lamali Sadeesh Kumar
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Norelle L. Sherry
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Josh Zhang
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire L. Gorrie
- Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
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218
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Ahlstrom CA, Woksepp H, Sandegren L, Ramey AM, Bonnedahl J. Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches. Appl Environ Microbiol 2023; 89:e0031923. [PMID: 37195171 PMCID: PMC10304903 DOI: 10.1128/aem.00319-23] [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: 02/27/2023] [Accepted: 05/03/2023] [Indexed: 05/18/2023] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in wildlife and human niches, however, remains unclear. We compared wild bird origin E. coli ST38 genome sequences generated by our research group and publicly available genomic data derived from other hosts and environments to (i) understand the frequency of intercontinental dispersal of E. coli ST38 clones isolated from wild birds, (ii) more thoroughly measure the genomic relatedness of carbapenem-resistant isolates from gulls sampled in Turkey and Alaska, USA, using long-read whole-genome sequencing and assess the spatial dissemination of this clone among different hosts, and (iii) determine whether ST38 isolates from humans, environmental water, and wild birds have different core or accessory genomes (e.g., antimicrobial resistance genes, virulence genes, plasmids) which might elucidate bacterial or gene exchange among niches. Our results suggest that E. coli ST38 strains, including those resistant to carbapenems, are exchanged between humans and wild birds, rather than separately maintained populations within each niche. Furthermore, despite close genetic similarity among OXA-48-producing E. coli ST38 clones from gulls in Alaska and Turkey, intercontinental dispersal of ST38 clones among wild birds is uncommon. Interventions to mitigate the dissemination of antimicrobial resistance throughout the environment (e.g., as exemplified by the acquisition of carbapenem resistance by birds) may be warranted. IMPORTANCE Carbapenem-resistant bacteria are a threat to public health globally and have been found in the environment as well as the clinic. Some bacterial clones are associated with carbapenem resistance genes, such as Escherichia coli sequence type 38 (ST38) and the carbapenemase gene blaOXA-48. This is the most frequently reported carbapenem-resistant clone in wild birds, though it was unclear if it circulated within wild bird populations or was exchanged among other niches. The results from this study suggest that E. coli ST38 strains, including those resistant to carbapenems, are frequently exchanged among wild birds, humans, and the environment. Carbapenem-resistant E. coli ST38 clones in wild birds are likely acquired from the local environment and do not constitute an independent dissemination pathway within wild bird populations. Management actions aimed at preventing the environmental dissemination and acquisition of antimicrobial resistance by wild birds may be warranted.
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Affiliation(s)
| | - Hanna Woksepp
- Department of Research, Kalmar County Region, Kalmar, Sweden
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Infection Biology, Antimicrobial Resistance and Immunology, Uppsala University, Uppsala, Sweden
| | - Andrew M. Ramey
- Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, USA
| | - Jonas Bonnedahl
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Infectious Diseases, Kalmar County Region, Kalmar, Sweden
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219
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Takeuchi N, Hamada-Zhu S, Suzuki H. Prophages and plasmids can display opposite trends in the types of accessory genes they carry. Proc Biol Sci 2023; 290:20231088. [PMID: 37339743 DOI: 10.1098/rspb.2023.1088] [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: 12/15/2022] [Accepted: 06/01/2023] [Indexed: 06/22/2023] Open
Abstract
Mobile genetic elements (MGEs), such as phages and plasmids, often possess accessory genes encoding bacterial functions, facilitating bacterial evolution. Are there rules governing the arsenal of accessory genes MGEs carry? If such rules exist, they might be reflected in the types of accessory genes different MGEs carry. To test this hypothesis, we compare prophages and plasmids with respect to the frequencies at which they carry antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the genomes of 21 pathogenic bacterial species using public databases. Our results indicate that prophages tend to carry VFGs more frequently than ARGs in three species, whereas plasmids tend to carry ARGs more frequently than VFGs in nine species, relative to genomic backgrounds. In Escherichia coli, where this prophage-plasmid disparity is detected, prophage-borne VFGs encode a much narrower range of functions than do plasmid-borne VFGs, typically involved in damaging host cells or modulating host immunity. In the species where the above disparity is not detected, ARGs and VFGs are barely found in prophages and plasmids. These results indicate that MGEs can differentiate in the types of accessory genes they carry depending on their infection strategies, suggesting a rule governing horizontal gene transfer mediated by MGEs.
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Affiliation(s)
- Nobuto Takeuchi
- School of Biological Sciences, the University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Universal Biology Institute, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sophia Hamada-Zhu
- School of Biological Sciences, the University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
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220
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Alfaray RI, Saruuljavkhlan B, Fauzia KA, Torres RC, Thorell K, Dewi SR, Kryukov KA, Matsumoto T, Akada J, Vilaichone RK, Miftahussurur M, Yamaoka Y. Global Antimicrobial Resistance Gene Study of Helicobacter pylori: Comparison of Detection Tools, ARG and Efflux Pump Gene Analysis, Worldwide Epidemiological Distribution, and Information Related to the Antimicrobial-Resistant Phenotype. Antibiotics (Basel) 2023; 12:1118. [PMID: 37508214 PMCID: PMC10376887 DOI: 10.3390/antibiotics12071118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/15/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023] Open
Abstract
We conducted a global-scale study to identify H. pylori antimicrobial-resistant genes (ARG), address their global distribution, and understand their effect on the antimicrobial resistance (AMR) phenotypes of the clinical isolates. We identified ARG using several well-known tools against extensive bacterial ARG databases, then analyzed their correlation with clinical antibiogram data from dozens of patients across countries. This revealed that combining multiple tools and databases, followed by manual selection of ARG from the annotation results, produces more conclusive results than using a single tool or database alone. After curation, the results showed that H. pylori has 42 ARG against 11 different antibiotic classes (16 genes related to single antibiotic class resistance and 26 genes related to multidrug resistance). Further analysis revealed that H. pylori naturally harbors ARG in the core genome, called the 'Set of ARG commonly found in the Core Genome of H. pylori (ARG-CORE)', while ARG-ACC-the ARG in the accessory genome-are exclusive to particular strains. In addition, we detected 29 genes of potential efflux pump-related AMR that were mostly categorized as ARG-CORE. The ARG distribution appears to be almost similar either by geographical or H. pylori populations perspective; however, some ARG had a unique distribution since they tend to be found only in a particular region or population. Finally, we demonstrated that the presence of ARG may not directly correlate with the sensitive/resistance phenotype of clinical patient isolates but may influence the minimum inhibitory concentration phenotype.
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Affiliation(s)
- Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, Indonesia
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, Indonesia
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Roberto C Torres
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kaisa Thorell
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Selva Rosyta Dewi
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, Indonesia
| | - Kirill A Kryukov
- Biological Networks Laboratory, Department of Informatics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
| | - Ratha-Korn Vilaichone
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Thammasat University Hospital, Khlong Nueng 12120, Pathumthani, Thailand
- Center of Excellence in Digestive Diseases, Thammasat University, Thailand Science Research and Innovation Fundamental Fund, Bualuang ASEAN Chair Professorship at Thammasat University, Khlong Nueng 12121, Pathumthani, Thailand
- Department of Medicine, Chulabhorn International College of Medicine (CICM), Thammasat University, Khlong Nueng 12121, Pathumthani, Thailand
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia
| | - Muhammad Miftahussurur
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60286, Indonesia
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine, Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60286, Indonesia
- The Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Oita 870-1192, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA
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221
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Hounmanou YMG, Wanyana A, Alafi S, Wabwire-Mangen F, Christensen H, Olsen JE, Byarugaba DK. Whole strains vs MGEs in short and longterm transmission of ESBL genes between healthcare and community settings in Uganda. Sci Rep 2023; 13:10229. [PMID: 37353515 PMCID: PMC10290109 DOI: 10.1038/s41598-023-35879-x] [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: 02/18/2023] [Accepted: 05/25/2023] [Indexed: 06/25/2023] Open
Abstract
Multidrug-resistant ESBL-producing Escherichia coli are a leading cause of infections in hospital and community settings. Based on samples from two hospitals in Uganda and households of inpatients we tested the hypothesis that ESBL E. coli and/or their resistance determinants could spread within the healthcare and community settings through discharged patients that were still colonized. We used bacterial culture, susceptibility testing whole genome sequencing and detailed bioinformatics analysis to test the above hypothesis. Genome analysis revealed presence of predominantly blaCTX-M-15 and blaOXA-1 genes with a total resistome with genes belonging to 14 different classes of antimicrobials. Short-term cases of strain sharing were reported within each setting and strains from the two settings were found to cluster together based on their overall resistome. Long-term horizontal transfer of ESBL genes by various IncF and IncY types of plasmids shared between healthcare and community settings was demonstrated. Based on hybrid assembly, plasmid reconstruction and phylogenetic analyses, our study suggests that while the dissemination of AMR between healthcare and community settings in the short-term is possible at whole strain level, the long-term transmission between healthcare and communities is sustained by the transfer of plasmids circulating across niches and disseminating related resistomes.
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Affiliation(s)
- Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Agnes Wanyana
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Stephen Alafi
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Fred Wabwire-Mangen
- School of Public Health, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Denis Karuhize Byarugaba
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda.
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222
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Odih EE, Oaikhena AO, Underwood A, Hounmanou YMG, Oduyebo OO, Fadeyi A, Aboderin AO, Ogunleye VO, Argimón S, Akpunonu VN, Oshun PO, Egwuenu A, Okwor TJ, Ihekweazu C, Aanensen DM, Dalsgaard A, Okeke IN. High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020. mSphere 2023; 8:e0009823. [PMID: 37067411 PMCID: PMC10286719 DOI: 10.1128/msphere.00098-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
Acinetobacter baumannii causes difficult-to-treat infections mostly among immunocompromised patients. Clinically relevant A. baumannii lineages and their carbapenem resistance mechanisms are sparsely described in Nigeria. This study aimed to characterize the diversity and genetic mechanisms of carbapenem resistance among A. baumannii strains isolated from hospitals in southwestern Nigeria. We sequenced the genomes of all A. baumannii isolates submitted to Nigeria's antimicrobial resistance surveillance reference laboratory between 2016 and 2020 on an Illumina platform and performed in silico genomic characterization. Selected strains were sequenced using the Oxford Nanopore technology to characterize the genetic context of carbapenem resistance genes. The 86 A. baumannii isolates were phylogenetically diverse and belonged to 35 distinct Oxford sequence types (oxfSTs), 16 of which were novel, and 28 Institut Pasteur STs (pasSTs). Thirty-eight (44.2%) isolates belonged to none of the known international clones (ICs). Over 50% of the isolates were phenotypically resistant to 10 of 12 tested antimicrobials. The majority (n = 54) of the isolates were carbapenem resistant, particularly the IC7 (pasST25; 100%) and IC9 (pasST85; >91.7%) strains. blaOXA-23 (34.9%) and blaNDM-1 (27.9%) were the most common carbapenem resistance genes detected. All blaOXA-23 genes were carried on Tn2006 or Tn2006-like transposons. Our findings suggest that a 10-kb Tn125 composite transposon is the primary means of blaNDM-1 dissemination. Our findings highlight an increase in blaNDM-1 prevalence and the widespread transposon-facilitated dissemination of carbapenemase genes in diverse A. baumannii lineages in southwestern Nigeria. We make the case for improving surveillance of these pathogens in Nigeria and other understudied settings. IMPORTANCE Acinetobacter baumannii bacteria are increasingly clinically relevant due to their propensity to harbor genes conferring resistance to multiple antimicrobials, as well as their ability to persist and disseminate in hospital environments and cause difficult-to-treat nosocomial infections. Little is known about the molecular epidemiology and antimicrobial resistance profiles of these organisms in Nigeria, largely due to limited capacity for their isolation, identification, and antimicrobial susceptibility testing. Our study characterized the diversity and antimicrobial resistance profiles of clinical A. baumannii in southwestern Nigeria using whole-genome sequencing. We also identified the key genetic elements facilitating the dissemination of carbapenem resistance genes within this species. This study provides key insights into the clinical burden and population dynamics of A. baumannii in hospitals in Nigeria and highlights the importance of routine whole-genome sequencing-based surveillance of this and other previously understudied pathogens in Nigeria and other similar settings.
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Affiliation(s)
- Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anderson O. Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Anthony Underwood
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oyinlola O. Oduyebo
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Abayomi Fadeyi
- Department of Medical Microbiology and Parasitology, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Aaron O. Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Veronica O. Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Silvia Argimón
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | | | - Phillip O. Oshun
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, College of Medicine, University of Lagos, Lagos, Nigeria
| | | | | | | | - David M. Aanensen
- Centre for Genomic pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iruka N. Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
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223
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Bogaerts B, Fraiture MA, Huwaert A, Van Nieuwenhuysen T, Jacobs B, Van Hoorde K, De Keersmaecker SCJ, Roosens NHC, Vanneste K. Retrospective surveillance of viable Bacillus cereus group contaminations in commercial food and feed vitamin B 2 products sold on the Belgian market using whole-genome sequencing. Front Microbiol 2023; 14:1173594. [PMID: 37415815 PMCID: PMC10321352 DOI: 10.3389/fmicb.2023.1173594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
Bacillus cereus is a spore-forming bacterium that occurs as a contaminant in food and feed, occasionally resulting in food poisoning through the production of various toxins. In this study, we retrospectively characterized viable B. cereus sensu lato (s.l.) isolates originating from commercial vitamin B2 feed and food additives collected between 2016 and 2022 by the Belgian Federal Agency for the Safety of the Food Chain from products sold on the Belgian market. In total, 75 collected product samples were cultured on a general medium and, in case of bacterial growth, two isolates per product sample were collected and characterized using whole-genome sequencing (WGS) and subsequently characterized in terms of sequence type (ST), virulence gene profile, antimicrobial resistance (AMR) gene profile, plasmid content, and phylogenomic relationships. Viable B. cereus was identified in 18 of the 75 (24%) tested products, resulting in 36 WGS datasets, which were classified into eleven different STs, with ST165 (n = 10) and ST32 (n = 8) being the most common. All isolates carried multiple genes encoding virulence factors, including cytotoxin K-2 (52.78%) and cereulide (22.22%). Most isolates were predicted to be resistant to beta-lactam antibiotics (100%) and fosfomycin (88.89%), and a subset was predicted to be resistant to streptothricin (30.56%). Phylogenomic analysis revealed that some isolates obtained from different products were closely related or even identical indicating a likely common origin, whereas for some products the two isolates obtained did not show any close relationship to each other or other isolates found in other products. This study reveals that potentially pathogenic and drug-resistant B. cereus s.l. can be present in food and feed vitamin B2 additives that are commercially available, and that more research is warranted to assess whether their presence in these types of products poses a threat to consumers.
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Affiliation(s)
- Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | - Bram Jacobs
- Foodborne Pathogens, Sciensano, Brussels, Belgium
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | | | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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Behera DU, Dixit S, Gaur M, Mishra R, Sahoo RK, Sahoo M, Behera BK, Subudhi BB, Bharat SS, Subudhi E. Sequencing and Characterization of M. morganii Strain UM869: A Comprehensive Comparative Genomic Analysis of Virulence, Antibiotic Resistance, and Functional Pathways. Genes (Basel) 2023; 14:1279. [PMID: 37372459 DOI: 10.3390/genes14061279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/10/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Morganella morganii is a Gram-negative opportunistic Enterobacteriaceae pathogen inherently resistant to colistin. This species causes various clinical and community-acquired infections. This study investigated the virulence factors, resistance mechanisms, functional pathways, and comparative genomic analysis of M. morganii strain UM869 with 79 publicly available genomes. The multidrug resistance strain UM869 harbored 65 genes associated with 30 virulence factors, including efflux pump, hemolysin, urease, adherence, toxin, and endotoxin. Additionally, this strain contained 11 genes related to target alteration, antibiotic inactivation, and efflux resistance mechanisms. Further, the comparative genomic study revealed a high genetic relatedness (98.37%) among the genomes, possibly due to the dissemination of genes between adjoining countries. The core proteome of 79 genomes contains the 2692 core, including 2447 single-copy orthologues. Among them, six were associated with resistance to major antibiotic classes manifested through antibiotic target alteration (PBP3, gyrB) and antibiotic efflux (kpnH, rsmA, qacG; rsmA; CRP). Similarly, 47 core orthologues were annotated to 27 virulence factors. Moreover, mostly core orthologues were mapped to transporters (n = 576), two-component systems (n = 148), transcription factors (n = 117), ribosomes (n = 114), and quorum sensing (n = 77). The presence of diversity in serotypes (type 2, 3, 6, 8, and 11) and variation in gene content adds to the pathogenicity, making them more difficult to treat. This study highlights the genetic similarity among the genomes of M. morganii and their restricted emergence, mostly in Asian countries, in addition to their growing pathogenicity and resistance. However, steps must be taken to undertake large-scale molecular surveillance and to direct suitable therapeutic interventions.
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Affiliation(s)
- Dibyajyoti Uttameswar Behera
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Mahendra Gaur
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
- Department of Biotechnology & Food Technology, Punjabi University, Patiala 147002, Punjab, India
| | - Rukmini Mishra
- Department of Botany, School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar 761211, Odisha, India
| | - Rajesh Kumar Sahoo
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Maheswata Sahoo
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Bijay Kumar Behera
- College of Fisheries, Rani Lakshmi Bai Central Agricultural University, Gwalior Road, Jhansi 284003, Uttar Pradesh, India
| | - Bharat Bhusan Subudhi
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Sutar Suhas Bharat
- Department of Botany, School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar 761211, Odisha, India
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
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225
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Romero-Martínez R, Maher A, Àlvarez G, Figueiredo R, León R, Arredondo A. Whole Genome Sequencing and Phenotypic Analysis of Antibiotic Resistance in Filifactor alocis Isolates. Antibiotics (Basel) 2023; 12:1059. [PMID: 37370380 DOI: 10.3390/antibiotics12061059] [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: 06/02/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
There is scarce knowledge regarding the antimicrobial resistance profile of F. alocis. Therefore, the objective of this research was to assess antimicrobial resistance in recently obtained F. alocis clinical isolates and to identify the presence of antimicrobial resistance genes. Isolates were obtained from patients with periodontal or peri-implant diseases and confirmed by sequencing their 16S rRNA gene. Confirmed isolates had their genome sequenced by whole genome sequencing and their phenotypical resistance to nine antibiotics (amoxicillin clavulanate, amoxicillin, azithromycin, clindamycin, ciprofloxacin, doxycycline, minocycline, metronidazole, and tetracycline) tested by E-test strips. Antimicrobial resistance genes were detected in six of the eight isolates analyzed, of which five carried tet(32) and one erm(B). Overall, susceptibility to the nine antibiotics tested was high except for azithromycin in the isolate that carried erm(B). Moreover, susceptibility to tetracycline, doxycycline, and minocycline was lower in those isolates that carried tet(32). The genetic surroundings of the detected genes suggested their inclusion in mobile genetic elements that might be transferrable to other bacteria. These findings suggest that, despite showing high susceptibility to several antibiotics, F. alocis might obtain new antimicrobial resistance traits due to its acceptance of mobile genetic elements with antibiotic resistance genes in their genome.
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Affiliation(s)
| | - Anushiravan Maher
- Oral Surgery and Implantology, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Gerard Àlvarez
- Department of Microbiology, DENTAID Research Center, 08290 Barcelona, Spain
| | - Rui Figueiredo
- Oral Surgery and Implantology, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Rubén León
- Department of Microbiology, DENTAID Research Center, 08290 Barcelona, Spain
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226
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Soares GG, Campanini EB, Ferreira RL, Damas MSF, Rodrigues SH, Campos LC, Galvão JD, Fuentes ASDC, Freire CCDM, Malavazi I, Pitondo-Silva A, da Cunha AF, Pranchevicius MCDS. Brevundimonas brasiliensis sp. nov.: a New Multidrug-Resistant Species Isolated from a Patient in Brazil. Microbiol Spectr 2023; 11:e0441522. [PMID: 37067439 PMCID: PMC10269605 DOI: 10.1128/spectrum.04415-22] [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: 11/03/2022] [Accepted: 02/17/2023] [Indexed: 04/18/2023] Open
Abstract
To increase knowledge on Brevundimonas pathogens, we conducted in-depth genomic and phenotypic characterization of a Brevundimonas strain isolated from the cerebrospinal fluid of a patient admitted in a neonatal intensive care unit. The strain was identified as a member of the genus Brevundimonas based on Vitek 2 system results and 16S rRNA gene sequencing and presented a multidrug resistance profile (MDR). Several molecular and biochemical tests were used to characterize and identify the species for in-depth results. The draft genome assembly of the isolate has a total length of 3,261,074 bp and a G+C of 66.86%, similar to other species of the genus. Multilocus sequence analysis, Type (Strain) Genome Server, digital DNA-DNA hybridization, and average nucleotide identity confirmed that the Brevundimonas sp. studied represents a distinct species, for which we propose the name Brevundimonas brasiliensis sp. nov. In silico analysis detected antimicrobial resistance genes (AMRGs) mediating resistance to β-lactams (penP, blaTEM-16, and blaBKC-1) and aminoglycosides [strA, strB, aac(6')-Ib, and aac(6')-Il]. We also found AMRGs encoding the AcrAB efflux pump that confers resistance to a broad spectrum of antibiotics. Colistin and quinolone resistance can be attributed to mutation in qseC and/or phoP and GyrA/GyrB, respectively. The Brevundimonas brasiliensis sp. nov. genome contained copies of type IV secretion system (T4SS)-type integrative and conjugative elements (ICEs); integrative mobilizable elements (IME); and Tn3-type and IS3, IS6, IS5, and IS1380 families, suggesting an important role in the development and dissemination of antibiotic resistance. The isolate presented a range of virulence-associated genes related to biofilm formation, adhesion, and invasion that can be relevant for its pathogenicity. Our findings provide a wealth of data to hinder the transmission of MDR Brevundimonas and highlight the need for monitoring and identifying new bacterial species in hospital environments. IMPORTANCE Brevundimonas species is considered an opportunistic human pathogen that can cause multiple types of invasive and severe infections in patients with underlying pathologies. Treatment of these pathogens has become a major challenge because many isolates are resistant to most antibiotics used in clinical practice. Furthermore, there are no consistent therapeutic results demonstrating the efficacy of antibacterial agents. Although considered a rare pathogen, recent studies have provided evidence of the emergence of Brevundimonas in clinical settings. Hence, we identified a novel pathogenic bacterium, Brevundimonas brasiliensis sp. nov., that presented a multidrug resistance (MDR) profile and carried diverse genes related to drug resistance, virulence, and mobile genetic elements. Such data can serve as a baseline for understanding the genomic diversity, adaptation, evolution, and pathogenicity of MDR Brevundimonas.
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Affiliation(s)
- Gabriela Guerrera Soares
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Roumayne Lopes Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | - Saulo Henrique Rodrigues
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | - Caio César de Melo Freire
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - André Pitondo-Silva
- Programas de Pós-graduação em Odontologia e Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | | | - Maria-Cristina da Silva Pranchevicius
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Centro de Ciências Biológicas e da Saúde, Biodiversidade Tropical - BIOTROP, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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227
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Arredondo-Alonso S, Blundell-Hunter G, Fu Z, Gladstone RA, Fillol-Salom A, Loraine J, Cloutman-Green E, Johnsen PJ, Samuelsen Ø, Pöntinen AK, Cléon F, Chavez-Bueno S, De la Cruz MA, Ares MA, Vongsouvath M, Chmielarczyk A, Horner C, Klein N, McNally A, Reis JN, Penadés JR, Thomson NR, Corander J, Taylor PW, McCarthy AJ. Evolutionary and functional history of the Escherichia coli K1 capsule. Nat Commun 2023; 14:3294. [PMID: 37322051 PMCID: PMC10272209 DOI: 10.1038/s41467-023-39052-w] [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: 01/28/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
Escherichia coli is a leading cause of invasive bacterial infections in humans. Capsule polysaccharide has an important role in bacterial pathogenesis, and the K1 capsule has been firmly established as one of the most potent capsule types in E. coli through its association with severe infections. However, little is known about its distribution, evolution and functions across the E. coli phylogeny, which is fundamental to elucidating its role in the expansion of successful lineages. Using systematic surveys of invasive E. coli isolates, we show that the K1-cps locus is present in a quarter of bloodstream infection isolates and has emerged in at least four different extraintestinal pathogenic E. coli (ExPEC) phylogroups independently in the last 500 years. Phenotypic assessment demonstrates that K1 capsule synthesis enhances E. coli survival in human serum independent of genetic background, and that therapeutic targeting of the K1 capsule re-sensitizes E. coli from distinct genetic backgrounds to human serum. Our study highlights that assessing the evolutionary and functional properties of bacterial virulence factors at population levels is important to better monitor and predict the emergence of virulent clones, and to also inform therapies and preventive medicine to effectively control bacterial infections whilst significantly lowering antibiotic usage.
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Affiliation(s)
- Sergio Arredondo-Alonso
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | - Zuyi Fu
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Rebecca A Gladstone
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Alfred Fillol-Salom
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | | | - Elaine Cloutman-Green
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - François Cléon
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Susana Chavez-Bueno
- University of Missouri Kansas City, Kansas City, USA
- Division of Infectious Diseases, Children's Mercy Hospital Kansas City, UMKC School of Medicine, Kansas City, USA
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Agnieszka Chmielarczyk
- Faculty of Medicine, Chair of Microbiology, Jagiellonian University Medical College, Czysta str. 18, 31-121, Kraków, Poland
| | - Carolyne Horner
- British Society for Antimicrobial Chemotherapy, Birmingham, UK
| | - Nigel Klein
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joice N Reis
- Laboratory of Pathology and Molecular Biology (LPBM), Gonçalo Moniz Research Institute, Oswaldo Cruz Foundation, Salvador, Brazil
- Faculdade de Farmácia, Universidade Federal da Bahia, Salvador, Brazil
| | - José R Penadés
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nicholas R Thomson
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
| | - Peter W Taylor
- School of Pharmacy, University College London, London, UK.
| | - Alex J McCarthy
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
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228
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Raghuram V, Gunoskey JJ, Hofstetter KS, Jacko NF, Shumaker MJ, Hu YJ, Read TD, David MZ. Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonisation cultures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544959. [PMID: 37397999 PMCID: PMC10312683 DOI: 10.1101/2023.06.14.544959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The most common approach to sampling the bacterial populations within an infected or colonised host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. An alternative is to sequence a mixture containing multiple colonies ("pool-seq"), but this has the disadvantage that it is a non-homogeneous sample, making it difficult to perform specific experiments. We compared differences in measures of genetic diversity between eight single-colony isolates (singles) and pool-seq on a set of 2286 S. aureus culture samples. The samples were obtained by swabbing three body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistant S. aureus skin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple Multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.
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Affiliation(s)
- Vishnu Raghuram
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Jessica J. Gunoskey
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katrina S. Hofstetter
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Natasia F. Jacko
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Margot J. Shumaker
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Michael Z. David
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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229
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Cummins ML, Li D, Ahmad A, Bushell R, Noormohammadi AH, Wijesurendra DS, Stent A, Marenda MS, Djordjevic SP. Whole Genome Sequencing of Avian Pathogenic Escherichia coli Causing Bacterial Chondronecrosis and Osteomyelitis in Australian Poultry. Microorganisms 2023; 11:1513. [PMID: 37375015 DOI: 10.3390/microorganisms11061513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
Bacterial chondronecrosis with osteomyelitis (BCO) impacts animal welfare and productivity in the poultry industry worldwide, yet it has an understudied pathogenesis. While Avian Pathogenic Escherichia coli (APEC) are known to be one of the main causes, there is a lack of whole genome sequence data, with only a few BCO-associated APEC (APECBCO) genomes available in public databases. In this study, we conducted an analysis of 205 APECBCO genome sequences to generate new baseline phylogenomic knowledge regarding the diversity of E. coli sequence types and the presence of virulence associated genes (VAGs). Our findings revealed the following: (i) APECBCO are phylogenetically and genotypically similar to APEC that cause colibacillosis (APECcolibac), with globally disseminated APEC sequence types ST117, ST57, ST69, and ST95 being predominate; (ii) APECBCO are frequent carriers of ColV-like plasmids that carry a similar set of VAGs as those found in APECcolibac. Additionally, we performed genomic comparisons, including a genome-wide association study, with a complementary collection of geotemporally-matched genomes of APEC from multiple cases of colibacillosis (APECcolibac). Our genome-wide association study found no evidence of novel virulence loci unique to APECBCO. Overall, our data indicate that APECBCO and APECcolibac are not distinct subpopulations of APEC. Our publication of these genomes substantially increases the available collection of APECBCO genomes and provides insights for the management and treatment strategies of lameness in poultry.
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Affiliation(s)
- Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Dmitriy Li
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Aeman Ahmad
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Rhys Bushell
- Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | | | | | - Andrew Stent
- Gribbles Veterinary Pathology, Clayton, VIC 3168, Australia
| | - Marc S Marenda
- Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia
- The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia
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230
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Galgano M, Mrenoshki D, Pellegrini F, Capozzi L, Cordisco M, Del Sambro L, Trotta A, Camero M, Tempesta M, Buonavoglia D, Laricchiuta P, Catella C, Pratelli A, Buonavoglia A, Corrente M. Antibacterial and Biofilm Production Inhibition Activity of Thymus vulgaris L. Essential Oil against Salmonella spp. Isolates from Reptiles. Pathogens 2023; 12:804. [PMID: 37375494 DOI: 10.3390/pathogens12060804] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/10/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Salmonellosis is an infectious disease affecting both animals and humans. Antimicrobial resistant (AMR) and biofilm-producing Salmonella spp., frequently detected in reptiles (who can then act as asymptomatic carriers for warm-blooded animals), have developed resistance to biocides; this represents a warning for the emergence of biocide/antimicrobial cross-resistance. The aim of this study was to evaluate the efficacy of Thymus vulgaris L. essential oil (TEO) in inhibiting bacterial growth and biofilm production of Salmonella spp., which had been isolated from wild reptiles housed in a Zoo in Italy. The resistance profile against different classes of antibiotics showed that all the isolates were susceptible to the tested antibiotics, despite the presence of several AMR genes. All the isolates were also tested with aqueous solutions of TEO at different dilutions (5% to 0.039%). Interestingly, TEO proved effective both in inhibiting bacterial growth at low dilutions, with MIC and MBC values ranging between 0.078% and 0.312%, and in inhibiting biofilm production, with values ranging from 0.039% to 0.156%. TEO demonstrated effective bioactivity against the biofilm producer Salmonella spp., proving to be a valid disinfectant for the prevention of salmonellosis from reptiles, a possible source of infection for humans exposed to the reptiles' environment.
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Affiliation(s)
- Michela Galgano
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Daniela Mrenoshki
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Francesco Pellegrini
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico della Puglia e della Basilicata, Contrada San Pietro Piturno, 70017 Putignano, BA, Italy
| | - Marco Cordisco
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Laura Del Sambro
- Istituto Zooprofilattico della Puglia e della Basilicata, Contrada San Pietro Piturno, 70017 Putignano, BA, Italy
| | - Adriana Trotta
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Michele Camero
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Maria Tempesta
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Domenico Buonavoglia
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
| | | | - Cristiana Catella
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Annamaria Pratelli
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
| | - Alessio Buonavoglia
- Dental School, Department of Biomedical and Neuromotor Sciences, University of Bologna, Via Zamboni 33, 40126 Bologna, BO, Italy
| | - Marialaura Corrente
- Department of Veterinary Medicine, University Aldo Moro of Bari, Sp Casamassima Km 3, 70010 Valenzano, BA, Italy
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Srednik ME, Morningstar-Shaw BR, Hicks JA, Tong C, Mackie TA, Schlater LK. Whole-genome sequencing and phylogenetic analysis capture the emergence of a multi-drug resistant Salmonella enterica serovar Infantis clone from diagnostic animal samples in the United States. Front Microbiol 2023; 14:1166908. [PMID: 37333652 PMCID: PMC10272548 DOI: 10.3389/fmicb.2023.1166908] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/20/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction Salmonella enterica is a major cause of foodborne illness in the United States. A multi-drug resistant (MDR) emergent Salmonella Infantis (ESI) with a megaplasmid (pESI) was first identified in Israel and Italy and subsequently reported worldwide. The ESI clone carrying an extended spectrum β-lactamase blaCTX-M-65 on a pESI-like plasmid and a mutation in the gyrA gene has recently been found in the United States in poultry meat. Methods We analyzed the phenotypic and genotypic antimicrobial resistance, genomics and phylogeny of 200 S. infantis isolates from animal diagnostic samples. Results Of these, 33.5% were resistant to at least one antimicrobial and 19.5% were multi-drug resistant (MDR). Eleven isolates from different animal sources were phenotypically and genetically similar to the ESI clone. These isolates had a D87Y mutation in the gyrA gene conferring reduced susceptibility to ciprofloxacin and harbored a combination of 6-10 resistance genes: blaCTX-M-65, aac(3)-IVa, aadA1, aph(4)-Ia, aph(3')-Ia, floR, sul1, dfrA14, tetA, and fosA. These 11 isolates carried class I and class II integrons and three virulence genes: sinH, involved in adhesion and invasion, ybtQ and ybtP, associated with iron transport. These isolates were also closely related to each other (separated by 7 to 27 SNPs) and phylogenetically related to the ESI clone recently found in the U.S. Discussion This dataset captured the emergence of the MDR ESI clone in multiple animal species and the first report of a pESI-like plasmid in isolates from horses in the U.S.
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Affiliation(s)
- Mariela E. Srednik
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
| | - Brenda R. Morningstar-Shaw
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
| | - Jessica A. Hicks
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
| | - Christopher Tong
- Center for Veterinary Biologics, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
| | - Tonya A. Mackie
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
| | - Linda K. Schlater
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States
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Singh SR, Tang CY, Mao B, Soeng S, Ling CL, Teo JQM, Vonthanak S, Turner P, Hsu LY, Ong RTH. Whole genome sequencing of multidrug resistant Enterobacterales identified in children and their household members within Siem Reap, Cambodia. JAC Antimicrob Resist 2023; 5:dlad067. [PMID: 37325250 PMCID: PMC10265595 DOI: 10.1093/jacamr/dlad067] [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: 02/21/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Objectives To explore the association of recent hospitalization and asymptomatic carriage of multidrug-resistant Enterobacterales (MDRE) and determine the prevailing strains and antibiotic resistance genes in Siem Reap, Cambodia using WGS. Methods In this cross-sectional study, faecal samples were collected from two arms: a hospital-associated arm consisted of recently hospitalized children (2-14 years), with their family members; and a community-associated arm comprising children in the matching age group and their family members with no recent hospitalization. Forty-two families in each study arm were recruited, with 376 enrolled participants (169 adults and 207 children) and 290 stool specimens collected from participants. The DNA of ESBL- and carbapenemase-producing Enterobacterales cultured from the faecal samples was subject to WGS on the Illumina NovaSeq platform. Results Of the 290 stool specimens, 277 Escherichia coli isolates and 130 Klebsiella spp. were identified on CHROMagar ESBL and KPC plates. The DNA of 276 E. coli (one isolate failed quality control test), 89 Klebsiella pneumoniae, 40 Klebsiella quasipneumoniae and 1 Klebsiella variicola was sequenced. CTX-M-15 was the most common ESBL gene found in E. coli (n = 104, 38%), K. pneumoniae (n = 50, 56%) and K. quasipneumoniae (n = 16, 40%). The prevalence of bacterial lineages and ESBL genes was not associated with any specific arm. Conclusions Our results demonstrate that MDRE is likely to be endemic within the Siem Reap community. ESBL genes, specifically blaCTX-M, can be found in almost all E. coli commensals, indicating that these genes are continuously propagated in the community through various unknown channels at present.
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Affiliation(s)
- Shweta R Singh
- Saw Swee Hock School of Public Health, Tahir Foundation Building, National University of Singapore, Singapore
| | - Cheng Yee Tang
- Saw Swee Hock School of Public Health, Tahir Foundation Building, National University of Singapore, Singapore
| | - Bunsoth Mao
- University of Health Sciences, Phnom Penh, Cambodia
| | - Sona Soeng
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Clare L Ling
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | | | | | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Li Yang Hsu
- Saw Swee Hock School of Public Health, Tahir Foundation Building, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, NUHS Tower Block, National University of Singapore, Singapore
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
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Zheng CW, Luo YH, Long X, Gu H, Cheng J, Zhang L, Lai YJS, Rittmann BE. The structure of biodegradable surfactants shaped the microbial community, antimicrobial resistance, and potential for horizontal gene transfer. WATER RESEARCH 2023; 236:119944. [PMID: 37087920 DOI: 10.1016/j.watres.2023.119944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 05/03/2023]
Abstract
While most household surfactants are biodegradable in aerobic conditions, their biodegradability may obscure their environmental risks. The presence of surfactants in a biological treatment process can lead to the proliferation of antimicrobial-resistance genes (ARG) in the biomass. Surfactants can be cationic, anionic, or zwitterionic, and these different classes may have different effects on the proliferation ARG. Cationic hexadecyltrimethyl-ammonium (CTAB), anionic sodium dodecyl sulfate (SDS), and zwitterionic 3-(decyldimethylammonio)-propanesulfonate inner salt (DAPS) were used to represent the three classes of surfactants in domestic household clean-up products. This study focused on the removal of these surfactants by the O2-based Membrane Biofilm Reactor (O2-MBfR) for hotspot scenarios (∼1 mM) and how the three classes of surfactants affected the microbial community's structure and ARG. Given sufficient O2 delivery, the MBfR provided at least 98% surfactant removal. The presence and biodegradation for each surfactant uniquely shaped the biofilms' microbial communities and the presence of ARG. CTAB had by far the strongest impact and the higher ARG abundance. In particular, Pseudomonas and Stenotrophomonas, the two main genera in the biofilm treating CTAB, were highly correlated to the abundance of ARG for efflux pumps and antibiotic inactivation. CTAB also led to more functional genes relevant to the Type-IV secretion system and protection against oxidative stress, which also could encourage horizontal gene transfer. Our findings highlight that the biodegradation of quaternary ammonium surfactants, while beneficial, can pose public health concerns from its ability to promote the proliferation of ARG.
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Affiliation(s)
- Chen-Wei Zheng
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287-5701, United States
| | - Yi-Hao Luo
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287-5701, United States; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Arizona State University, Tempe, AZ, United States
| | - Xiangxing Long
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287-5701, United States; Nanosystems Engineering Research Center for Nanotechnology-Enabled Water Treatment, Arizona State University, Tempe, AZ, United States
| | - Haiwei Gu
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Phoenix, AZ 85004, United States; Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, United States
| | - Jie Cheng
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287-5701, United States
| | - Lei Zhang
- DeepBiome. Co. Ltd., NO.38 Debao Road, China (Shanghai) Pilot Free Trade Zone, Shanghai 200031, China
| | - Yen Jung Sean Lai
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287-5701, United States.
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287-5701, United States
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Tansarli GS, Long DR, Waalkes A, Bourassa LA, Libby SJ, Penewit K, Almazan J, Matsumoto J, Bryson-Cahn C, Rietberg K, Dell BM, Hatley NV, Salipante SJ, Fang FC. Genomic reconstruction and directed interventions in a multidrug-resistant Shigellosis outbreak in Seattle, WA, USA: a genomic surveillance study. THE LANCET. INFECTIOUS DISEASES 2023; 23:740-750. [PMID: 36731480 PMCID: PMC10726761 DOI: 10.1016/s1473-3099(22)00879-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/09/2022] [Accepted: 12/09/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Shigella spp have been associated with community-wide outbreaks in urban settings. We analysed a sustained shigellosis outbreak in Seattle, WA, USA, to understand its origins and mechanisms of antimicrobial resistance, define ongoing transmission patterns, and optimise strategies for treatment and infection control. METHODS We did a retrospective study of all Shigella isolates identified from stool samples at the clinical laboratories at Harborview Medical Center and University of Washington Medical Center (Seattle, WA, USA) from May 1, 2017, to Feb 28, 2022. We characterised isolates by species identification, phenotypic susceptibility testing, and whole-genome sequencing. Demographic characteristics and clinical outcomes of the patients were retrospectively examined. FINDINGS 171 cases of shigellosis were included. 78 (46%) patients were men who have sex with men (MSM), and 88 (52%) were people experiencing homelessness (PEH). Although 84 (51%) isolates were multidrug resistant, 100 (70%) of 143 patients with data on antimicrobial therapy received appropriate empirical therapy. Phylogenomic analysis identified sequential outbreaks of multiple distinct lineages of Shigella flexneri and Shigella sonnei. Discrete clonal lineages (ten in S flexneri and nine in S sonnei) and resistance traits were responsible for infection in different at-risk populations (ie, MSM, PEH), enabling development of effective guidelines for empirical treatment. The most prevalent lineage in Seattle was probably introduced to Washington State via international travel, with subsequent domestic transmission between at-risk groups. INTERPRETATION An outbreak in Seattle was driven by parallel emergence of multidrug-resistant strains involving international transmission networks and domestic transmission between at-risk populations. Genomic analysis elucidated not only outbreak origin, but directed optimal approaches to testing, treatment, and public health response. Rapid diagnostics combined with detailed knowledge of local epidemiology can enable high rates of appropriate empirical therapy even in multidrug-resistant infection. FUNDING None.
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Affiliation(s)
- Giannoula S Tansarli
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Dustin R Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Lori A Bourassa
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Stephen J Libby
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jared Almazan
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jason Matsumoto
- Clinical Microbiology Laboratory, Harborview Medical Center, Seattle, WA, USA
| | - Chloe Bryson-Cahn
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA; Infection Prevention and Control, Harborview Medical Center, Seattle, WA, USA
| | - Krista Rietberg
- Infection Prevention and Control, Harborview Medical Center, Seattle, WA, USA
| | - BreeAnna M Dell
- Public Health-Seattle & King County, Communicable Diseases, Epidemiology, and Immunizations, Seattle, WA, USA
| | - Noël V Hatley
- Public Health-Seattle & King County, Communicable Diseases, Epidemiology, and Immunizations, Seattle, WA, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Ferric C Fang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA; Department of Microbiology, University of Washington School of Medicine, Seattle, WA, USA; Clinical Microbiology Laboratory, Harborview Medical Center, Seattle, WA, USA.
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Joddha HB, Mathakiya RA, Joshi KV, Khant RB, Golaviya AV, Hinsu AT, Desai MR, Jakhesara SJ, Koringa PG. Profiling of Antimicrobial Resistance Genes and Integron from Escherichia coli Isolates Using Whole Genome Sequencing. Genes (Basel) 2023; 14:1212. [PMID: 37372392 DOI: 10.3390/genes14061212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
This study is designed to investigate Escherichia coli for the antibiotic resistance genes (ARGs) and integrons from healthy as well as diarrhoeic/diseased animals/birds' faecal samples. A total of eight samples were selected for the study; from each animal, two samples were taken, one from healthy animals/birds and one from diarrhoeic/diseased animals/birds. Antibiotic sensitivity testing (AST) and whole genome sequencing (WGS) was performed for selected isolates. The E. coli isolates showed resistance to moxifloxacin, followed by erythromycin, ciprofloxacin, pefloxacin, tetracycline, levofloxacin, ampicillin, amoxicillin, and sulfadiazine (4/8, 50.00% each). The E. coli isolates were 100% sensitive to amikacin, followed by chloramphenicol, cefixime, cefoperazone, and cephalothin. A total of 47 ARGs from 12 different antibiotic classes were detected among the eight isolates by WGS. The different classes of antibiotics included aminoglycoside, sulphonamide, tetracycline, trimethoprim, quinolone, fosfomycin, phenicol, macrolide, colistin, fosmidomycin, and multidrug efflux. The class 1 integrons were detected in 6/8 (75.00%) isolates with 14 different gene cassettes.
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Affiliation(s)
- Harshrajsinh B Joddha
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Rafiyuddin A Mathakiya
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Kuldip V Joshi
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Ravindra B Khant
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Akash V Golaviya
- Department of Veterinary Microbiology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Mansi R Desai
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and A H, Kamdhenu University, Anand 388001, Gujarat, India
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Hu Y, Yang Y, Feng Y, Fang Q, Wang C, Zhao F, McNally A, Zong Z. Prevalence and clonal diversity of carbapenem-resistant Klebsiella pneumoniae causing neonatal infections: A systematic review of 128 articles across 30 countries. PLoS Med 2023; 20:e1004233. [PMID: 37339120 DOI: 10.1371/journal.pmed.1004233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 04/04/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae is the most common pathogen causing neonatal infections, leading to high mortality worldwide. Along with increasing antimicrobial use in neonates, carbapenem-resistant K. pneumoniae (CRKP) has emerged as a severe challenge for infection control and treatment. However, no comprehensive systematic review is available to describe the global epidemiology of neonatal CRKP infections. We therefore performed a systematic review of available data worldwide and combined a genome-based analysis to address the prevalence, clonal diversity, and carbapenem resistance genes of CRKP causing neonatal infections. METHODS AND FINDINGS We performed a systematic review of studies reporting population-based neonatal infections caused by CRKP in combination with a genome-based analysis of all publicly available CRKP genomes with neonatal origins. We searched multiple databases (PubMed, Web of Science, Embase, Ovid MEDLINE, Cochrane, bioRxiv, and medRxiv) to identify studies that have reported data of neonatal CRKP infections up to June 30, 2022. We included studies addressing the prevalence of CRKP infections and colonization in neonates but excluded studies lacking the numbers of neonates, the geographical location, or independent data on Klebsiella or CRKP isolates. We used narrative synthesis for pooling data with JMP statistical software. We identified 8,558 articles and excluding those that did not meet inclusion criteria. We included 128 studies, none of which were preprints, comprising 127,583 neonates in 30 countries including 21 low- and middle-income countries (LMICs) for analysis. We found that bloodstream infection is the most common infection type in reported data. We estimated that the pooled global prevalence of CRKP infections in hospitalized neonates was 0.3% (95% confidence interval [CI], 0.2% to 0.3%). Based on 21 studies reporting patient outcomes, we found that the pooled mortality of neonatal CRKP infections was 22.9% (95% CI, 13.0% to 32.9%). A total of 535 neonatal CRKP genomes were identified from GenBank including Sequence Read Archive, of which 204 were not linked to any publications. We incorporated the 204 genomes with a literature review for understanding the species distribution, clonal diversity, and carbapenemase types. We identified 146 sequence types (STs) for neonatal CRKP strains and found that ST17, ST11, and ST15 were the 3 most common lineages. In particular, ST17 CRKP has been seen in neonates in 8 countries across 4 continents. The vast majority (75.3%) of the 1,592 neonatal CRKP strains available for analyzing carbapenemase have genes encoding metallo-β-lactamases and NDM (New Delhi metallo-β-lactamase) appeared to be the most common carbapenemase (64.3%). The main limitation of this study is the absence or scarcity of data from North America, South America, and Oceania. CONCLUSIONS CRKP contributes to a considerable number of neonatal infections and leads to significant neonatal mortality. Neonatal CRKP strains are highly diverse, while ST17 is globally prevalent and merits early detection for treatment and prevention. The dominance of blaNDM carbapenemase genes imposes challenges on therapeutic options in neonates and supports the continued inhibitor-related drug discovery.
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Affiliation(s)
- Ya Hu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Yongqiang Yang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Feng
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Qingqing Fang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Chengcheng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Feifei Zhao
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
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Fang P, Elena AX, Kunath MA, Berendonk TU, Klümper U. Reduced selection for antibiotic resistance in community context is maintained despite pressure by additional antibiotics. ISME COMMUNICATIONS 2023; 3:52. [PMID: 37258727 PMCID: PMC10232432 DOI: 10.1038/s43705-023-00262-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 05/15/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
Selection for antibiotic resistance at very low antibiotic concentrations has been demonstrated for individual antibiotics in single species experiments. Furthermore, selection in these focal strains is reduced when taking place in complex microbial community context. However, in the environment, bacteria are rarely exposed to single, but rather complex mixtures of selective agents. Here, we explored how the presence of a second selective agent affects selection dynamics between isogenic pairs of focal E. coli strains, differing exclusively in a single resistance determinant, in the absence and presence of a model wastewater community across a gradient of antibiotics. An additional antibiotic that exclusively affects the model wastewater community, but to which the focal strains are resistant to, was chosen as the second selective agent. This allowed exploring how inhibition alters the community's ability to reduce selection. In the presence of the community, the selection coefficient at specific antibiotic concentrations was consistently decreased compared to the absence of the community. While pressure through the second antibiotic significantly decreased the activity and diversity of the community, its ability to reduce selection was consistently maintained at levels comparable to those recorded in absence of the second antibiotic. This indicates that the observed effects of community context on selection dynamics are rather based on competitive or protective effects between the focal strains and a small proportion of bacteria within the community, than on general competition for nutrients. These findings have implications for our understanding of the evolution and selection for multi-drug resistant strains.
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Affiliation(s)
- Peiju Fang
- Technische Universität Dresden, Institute of Hydrobiology, Zellescher Weg 40, Dresden, Germany
| | - Alan Xavier Elena
- Technische Universität Dresden, Institute of Hydrobiology, Zellescher Weg 40, Dresden, Germany
| | - Maxi Antonia Kunath
- Technische Universität Dresden, Institute of Hydrobiology, Zellescher Weg 40, Dresden, Germany
| | - Thomas U Berendonk
- Technische Universität Dresden, Institute of Hydrobiology, Zellescher Weg 40, Dresden, Germany
| | - Uli Klümper
- Technische Universität Dresden, Institute of Hydrobiology, Zellescher Weg 40, Dresden, Germany.
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Stubhaug TT, Giske CG, Justesen US, Kahlmeter G, Matuschek E, Sundsfjord A, Skaare D. Antimicrobial susceptibility testing of Bacteroides species by disk diffusion: The NordicAST Bacteroides study. Anaerobe 2023:102743. [PMID: 37253399 DOI: 10.1016/j.anaerobe.2023.102743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
OBJECTIVES - Antimicrobial susceptibility testing (AST) of anaerobic bacteria has until recently been done by MIC methods. We have carried out a multi-centre evaluation of the newly validated EUCAST disk diffusion method for AST of Bacteroides spp. METHODS - A panel of 30 Bacteroides strains was assembled based on reference agar dilution MICs, resistance gene detection and quantification of cfiA carbapenemase gene expression. Nordic clinical microbiology laboratories (n = 45) performed disk diffusion on Fastidious Anaerobe Agar with 5% mechanically defibrinated horse blood (FAA-HB) for piperacillin-tazobactam, meropenem and metronidazole. RESULTS - A total of 43/45 (95.6%) laboratories carried out disk diffusion per protocol. Intraclass correlation coefficients were 0.87 (0.80-0.93) for piperacillin-tazobactam, 0.95 (0.91-0.97) for meropenem and 0.89 (0.83-0.94) for metronidazole. For metronidazole, one media lot yielded smaller zones and higher variability than another. Piperacillin-tazobactam and meropenem zone diameters correlated negatively with cfiA expression. A meropenem zone diameter of <28 mm in B. fragilis indicated presence of cfiA. Piperacillin-tazobactam had the most false susceptible results. Categorical errors for this antimicrobial were particularly prevalent in cfiA-positive strains, and piperacillin-tazobactam had the highest number of comments describing zone reading difficulties. CONCLUSIONS - Inter-laboratory agreement by disk diffusion was good or very good. The main challenges were media-related variability for metronidazole and categorical disagreement with the reference method for piperacillin-tazobactam in some cfiA-positive strains. An area of technical uncertainty specific for such strains may be warranted.
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Affiliation(s)
- Tore Taksdal Stubhaug
- Vestfold Hospital Trust, Department of Microbiology, Tønsberg, Norway; University of Oslo, Institute of Clinical Medicine, Oslo, Norway.
| | - Christian G Giske
- Karolinska University Hospital, Department of Clinical Microbiology, Stockholm, Sweden; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ulrik S Justesen
- Odense University Hospital, Department of Clinical Microbiology, Odense, Denmark
| | | | | | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance (K-res), University Hospital of North Norway, Tromsø, Norway; UiT the Arctic University of Norway, Department of Medical Biology, Tromsø, Norway
| | - Dagfinn Skaare
- Vestfold Hospital Trust, Department of Microbiology, Tønsberg, Norway
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Rödel J, Pfeifer Y, Fischer MA, Edel B, Stoll S, Pfister W, Löffler B. Screening of Klebsiella pneumoniae Isolates for Carbapenemase and Hypervirulence-Associated Genes by Combining the Eazyplex ® Superbug CRE and hvKp Assays. Antibiotics (Basel) 2023; 12:959. [PMID: 37370278 DOI: 10.3390/antibiotics12060959] [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: 04/28/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The acquisition of hypervirulence-associated genes by carbapenemase-producing Klebsiella pneumoniae is being increasingly observed, and easy-to-use diagnostic tests are needed for the surveillance of the hypervirulent K. pneumoniae (hvKp). In this pilot study, 87 K. pneumoniae isolates from invasive infections collected in 2022 and 2023 were analysed using the LAMP-based eazyplex® Superbug CRE and hvKp assays for the simultaneous identification of carbapenemases and virulence genes (rmpA/A2, iuC, iroC, ybt, clb). Nine isolates showed a Kleborate virulence score of 4 or 5 (10.3%). The time for the results of the eazyplex® assays ranged from 6.5 to 13 min, and the total turnaround time, including sample preparation, was less than 30 min. Five isolates, three of which produced New Delhi metallo-beta lactamase (NDM), were subjected to whole-genome sequencing (WGS) analysis for further characterisation. The eazyplex® test results for beta-lactamase and virulence genes were confirmed. The eazyplex® hvKp, currently only available as a Research Use Only assay, may be a useful tool for the rapid identification of hvKp without significant additional workload when combined with the eazyplex® Superbug CRE assay for the detection of carbapenemases.
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Affiliation(s)
- Jürgen Rödel
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07747 Jena, Germany
| | - Yvonne Pfeifer
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany
| | - Martin A Fischer
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany
| | - Birgit Edel
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07747 Jena, Germany
| | - Sylvia Stoll
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07747 Jena, Germany
| | - Wolfgang Pfister
- Department of Hospital Hygiene, Sophien-und Hufeland-Klinikum, 99425 Weimar, Germany
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, 07747 Jena, Germany
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240
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Papp M, Tóth AG, Valcz G, Makrai L, Nagy SÁ, Farkas R, Solymosi N. Antimicrobial resistance gene lack in tick-borne pathogenic bacteria. Sci Rep 2023; 13:8167. [PMID: 37210378 DOI: 10.1038/s41598-023-35356-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/16/2023] [Indexed: 05/22/2023] Open
Abstract
Tick-borne infections, including those of bacterial origin, are significant public health issues. Antimicrobial resistance (AMR), which is one of the most pressing health challenges of our time, is driven by specific genetic determinants, primarily by the antimicrobial resistance genes (ARGs) of bacteria. In our work, we investigated the occurrence of ARGs in the genomes of tick-borne bacterial species that can cause human infections. For this purpose, we processed short/long reads of 1550 bacterial isolates of the genera Anaplasma (n = 20), Bartonella (n = 131), Borrelia (n = 311), Coxiella (n = 73), Ehrlichia (n = 13), Francisella (n = 959) and Rickettsia (n = 43) generated by second/third generation sequencing that have been freely accessible at the NCBI SRA repository. From Francisella tularensis, 98.9% of the samples contained the FTU-1 beta-lactamase gene. However, it is part of the F. tularensis representative genome as well. Furthermore, 16.3% of them contained additional ARGs. Only 2.2% of isolates from other genera (Bartonella: 2, Coxiella: 8, Ehrlichia: 1, Rickettsia: 2) contained any ARG. We found that the odds of ARG occurrence in Coxiella samples were significantly higher in isolates related to farm animals than from other sources. Our results describe a surprising lack of ARGs in these bacteria and suggest that Coxiella species in farm animal settings could play a role in the spread of AMR.
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Affiliation(s)
- Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, 1078, Hungary
| | - Adrienn Gréta Tóth
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, 1078, Hungary
| | - Gábor Valcz
- Translational Extracellular Vesicle Research Group, Eötvös Loránd Research Network-Semmelweis University, Budapest, 1089, Hungary
- Department of Image Analysis, 3DHISTECH Ltd., Budapest, 1141, Hungary
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, 1143, Hungary
| | - Sára Ágnes Nagy
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, 1078, Hungary
| | - Róbert Farkas
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, 1078, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, 1078, Hungary.
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, 1117, Hungary.
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241
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Jiang T, Li G, Huang L, Ding D, Ruan Z, Yan J. Genomic and Phylogenetic Analysis of a Multidrug-Resistant blaNDM-carrying Klebsiella michiganensis in China. Infect Drug Resist 2023; 16:3109-3116. [PMID: 37228660 PMCID: PMC10202706 DOI: 10.2147/idr.s409544] [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: 03/12/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
Objective Klebsiella michiganensis is an emerging hospital-acquired bacterial pathogen. However, there is a dearth of knowledge on the antimicrobial resistance and transmission of K. michiganensis. Here, we characterized the microbiological and genomic features of a carbapenem-resistant K. michiganensis strain harboring the blaNDM-1 gene in China. Methods K. michiganensis strain 2563 was recovered from the sputum sample of a hospitalized patient with pulmonary infection. Whole-genome sequencing of K. michiganensis strain 2563 was conducted using both the short-read Illumina and long-read MinION platforms to thoroughly characterize the genetic context of blaNDM-carrying plasmid in K. michiganensis 2563. Furthermore, BacWGSTdb server was utilized to perform in silico multilocus sequence typing (MLST), identify antimicrobial resistance genes, and conduct genomic epidemiological analyses of the closely related isolates deposited in the public database. Results K. michiganensis 2563 was resistant to piperacillin, aztreonam, meropenem, imipenem, amoxicillin-clavulanic acid, ampicillin, cefotaxime, cefazolin, ampicillin/sulbactam, cefepime, piperacillin-tazobactam, and ceftazidime. It belonged to sequence type (ST) 43, and the blaNDM-1 gene was found to be located on the plasmid p2563_NDM (54,035 bp). This plasmid showed remarkable similarity to other blaNDM-1-encoding plasmids found in various Enterobacterium species in the public database. The occurrence of global ST43 K. michiganensis was primarily sporadic, and the closest relative of K. michiganensis 2563 was another ST43 isolate 12,084 recovered from China in 2013, which differed by 171 SNPs. Conclusion Our study reports the genome characteristics of a carbapenem-resistant K. michiganensis strain carrying the blaNDM-1 gene in China, highlighting the need for ongoing surveillance of this pathogen in clinical settings.
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Affiliation(s)
- Tian Jiang
- Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, People’s Republic of China
| | - Guoli Li
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Linyao Huang
- Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, People’s Republic of China
| | - Ding Ding
- Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, People’s Republic of China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Jianxin Yan
- Department of Clinical Laboratory, The Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, People’s Republic of China
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242
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Du S, Tong X, Lai ACK, Chan CK, Mason CE, Lee PKH. Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution. Nat Commun 2023; 14:2676. [PMID: 37160974 PMCID: PMC10169181 DOI: 10.1038/s41467-023-38400-0] [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: 11/02/2022] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
Viruses in built environments (BEs) raise public health concerns, yet they are generally less studied than bacteria. To better understand viral dynamics in BEs, this study assesses viromes from 11 habitats across four types of BEs with low to high occupancy. The diversity, composition, metabolic functions, and lifestyles of the viromes are found to be habitat dependent. Caudoviricetes species are ubiquitous on surface habitats in the BEs, and some of them are distinct from those present in other environments. Antimicrobial resistance genes are identified in viruses inhabiting surfaces frequently touched by occupants and in viruses inhabiting occupants' skin. Diverse CRISPR/Cas immunity systems and anti-CRISPR proteins are found in bacterial hosts and viruses, respectively, consistent with the strongly coupled virus-host links. Evidence of viruses potentially aiding host adaptation in a specific-habitat manner is identified through a unique gene insertion. This work illustrates that virus-host interactions occur frequently in BEs and that viruses are integral members of BE microbiomes.
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Affiliation(s)
- Shicong Du
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, P. R. China
| | - Alvin C K Lai
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Chak K Chan
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
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243
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Calderón-Franco D, van Loosdrecht MCM, Abeel T, Weissbrodt DG. Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01834-z. [PMID: 37156983 DOI: 10.1007/s10482-023-01834-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L-1). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L-1). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.
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Affiliation(s)
| | | | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway.
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244
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Ikhimiukor OO, Souza SSR, Marcovici MM, Nye GJ, Gibson R, Andam CP. Leaky barriers to gene sharing between locally co-existing coagulase-negative Staphylococcus species. Commun Biol 2023; 6:482. [PMID: 37137974 PMCID: PMC10156822 DOI: 10.1038/s42003-023-04877-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/26/2023] [Indexed: 05/05/2023] Open
Abstract
Coagulase-negative Staphylococcus (CoNS) are opportunistic pathogens implicated in many human and animal infections. The evolutionary history of CoNS remains obscure because of the historical lack of recognition for their clinical importance and poor taxonomic sampling. Here, we sequenced the genomes of 191 CoNS isolates representing 15 species sampled from diseased animals diagnosed in a veterinary diagnostic laboratory. We found that CoNS are important reservoirs of diverse phages, plasmids and mobilizable genes encoding antimicrobial resistance, heavy metal resistance, and virulence. Frequent exchange of DNA between certain donor-recipient partners suggests that specific lineages act as hubs of gene sharing. We also detected frequent recombination between CoNS regardless of their animal host species, indicating that ecological barriers to horizontal gene transfer can be surmounted in co-circulating lineages. Our findings reveal frequent but structured patterns of transfer that exist within and between CoNS species, which are driven by their overlapping ecology and geographical proximity.
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Affiliation(s)
- Odion O Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
| | - Stephanie S R Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Michael M Marcovici
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Griffin J Nye
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | - Robert Gibson
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
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245
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Edalatmand A, McArthur AG. CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database. Database (Oxford) 2023; 2023:7133783. [PMID: 37079891 PMCID: PMC10118295 DOI: 10.1093/database/baad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/01/2023] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
Scientific literature is published at a rate that makes manual data extraction a highly time-consuming task. The Comprehensive Antibiotic Resistance Database (CARD) utilizes literature to curate information on antimicrobial resistance genes and to enable time-efficient triage of publications we have developed a classification algorithm for identifying publications describing first reports of new resistance genes. Trained on publications contained in the CARD, CARD*Shark downloads, processes and identifies publications recently added to PubMed that should be reviewed by biocurators. With CARD*Shark, we can minimize the monthly scope of articles a biocurator reviews from hundreds of articles to a few dozen, drastically improving the speed of curation while ensuring no relevant publications are overlooked. Database URL http://card.mcmaster.ca.
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Affiliation(s)
- Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Andrew G McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
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246
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Avershina E, Khezri A, Ahmad R. Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics (Basel) 2023; 12:antibiotics12040781. [PMID: 37107143 PMCID: PMC10135054 DOI: 10.3390/antibiotics12040781] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
- Institute of Clinical Medicine, Faculty of Health Science, UiT The Arctic University of Norway, Hansine Hansens veg, 189019 Tromsø, Norway
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247
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Sundermann AJ, Srinivasa VR, Mills EG, Griffith MP, Waggle KD, Ayres AM, Pless L, Snyder GM, Harrison LH, Van Tyne D. Two artificial tears outbreak-associated cases of XDR Pseudomonas aeruginosa detected through whole genome sequencing-based surveillance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.11.23288417. [PMID: 37131775 PMCID: PMC10153325 DOI: 10.1101/2023.04.11.23288417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We describe two cases of XDR Pseudomonas aeruginosa infection caused by a strain of public health concern recently associated with a nationwide outbreak of contaminated artificial tears. Both cases were detected through database review of genomes in the Enhanced Detection System for Hospital-Associated Transmission (EDS-HAT), a routine genome sequencing-based surveillance program. We generated a high-quality reference genome for the outbreak strain from one of the case isolates from our center and examined the mobile elements encoding bla VIM-80 and bla GES-9 carbapenemases. We then used publicly available P. aeruginosa genomes to explore the genetic relatedness and antimicrobial resistance genes of the outbreak strain.
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Affiliation(s)
- Alexander J. Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vatsala Rangachar Srinivasa
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emma G. Mills
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marissa P. Griffith
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kady D. Waggle
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ashley M. Ayres
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania, USA
| | - Lora Pless
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Graham M. Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania, USA
| | - Lee H. Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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248
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Neidhöfer C, Sib E, Neuenhoff M, Schwengers O, Dummin T, Buechler C, Klein N, Balks J, Axtmann K, Schwab K, Holderried TAW, Feldmann G, Brossart P, Engelhart S, Mutters NT, Bierbaum G, Parčina M. Hospital sanitary facilities on wards with high antibiotic exposure play an important role in maintaining a reservoir of resistant pathogens, even over many years. Antimicrob Resist Infect Control 2023; 12:33. [PMID: 37061726 PMCID: PMC10105422 DOI: 10.1186/s13756-023-01236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/29/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Hospitals with their high antimicrobial selection pressure represent the presumably most important reservoir of multidrug-resistant human pathogens. Antibiotics administered in the course of treatment are excreted and discharged into the wastewater system. Not only in patients, but also in the sewers, antimicrobial substances exert selection pressure on existing bacteria and promote the emergence and dissemination of multidrug-resistant clones. In previous studies, two main clusters were identified in all sections of the hospital wastewater network that was investigated, one K. pneumoniae ST147 cluster encoding NDM- and OXA-48 carbapenemases and one VIM-encoding P. aeruginosa ST823 cluster. In the current study, we investigated if NDM- and OXA-48-encoding K. pneumoniae and VIM-encoding P. aeruginosa isolates recovered between 2014 and 2021 from oncological patients belonged to those same clusters. METHODS The 32 isolates were re-cultured, whole-genome sequenced, phenotypically tested for their antimicrobial susceptibility, and analyzed for clonality and resistance genes in silico. RESULTS Among these strains, 25 belonged to the two clusters that had been predominant in the wastewater, while two others belonged to a sequence-type less prominently detected in the drains of the patient rooms. CONCLUSION Patients constantly exposed to antibiotics can, in interaction with their persistently antibiotic-exposed sanitary facilities, form a niche that might be supportive for the emergence, the development, the dissemination, and the maintenance of certain nosocomial pathogen populations in the hospital, due to antibiotic-induced selection pressure. Technical and infection control solutions might help preventing transmission of microorganisms from the wastewater system to the patient and vice versa, particularly concerning the shower and toilet drainage. However, a major driving force might also be antibiotic induced selection pressure and parallel antimicrobial stewardship efforts could be essential.
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Affiliation(s)
- Claudio Neidhöfer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany.
| | - Esther Sib
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Marcel Neuenhoff
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Tobias Dummin
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Christian Buechler
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Niklas Klein
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, Koblenz, Germany
| | - Julian Balks
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Katharina Axtmann
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Katjana Schwab
- Department of Oncology, Hematology, and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Tobias A W Holderried
- Department of Oncology, Hematology, and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Georg Feldmann
- Department of Oncology, Hematology, and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Peter Brossart
- Department of Oncology, Hematology, and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Steffen Engelhart
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Nico T Mutters
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Marijo Parčina
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
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Tseng CH, Huang YT, Mao YC, Lai CH, Yeh TK, Ho CM, Liu PY. Insight into the Mechanisms of Carbapenem Resistance in Klebsiella pneumoniae: A Study on IS26 Integrons, Beta-Lactamases, Porin Modifications, and Plasmidome Analysis. Antibiotics (Basel) 2023; 12:antibiotics12040749. [PMID: 37107111 PMCID: PMC10135210 DOI: 10.3390/antibiotics12040749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The emergence of carbapenem-resistant Klebsiella pneumoniae poses a significant threat to public health. In this study, we aimed to investigate the distribution and genetic diversity of plasmids carrying beta-lactamase resistance determinants in a collection of carbapenem-resistant K. pneumoniae blood isolates. Blood isolates of carbapenem-resistant K. pneumoniae bacteremia were collected and identified. Whole-genome sequencing, assembly and analysis were performed for the prediction of antimicrobial resistance determinants. Plasmidome analysis was also performed. Our plasmidome analysis revealed two major plasmid groups, IncFII/IncR and IncC, as key players in the dissemination of carbapenem resistance among carbapenem-resistant K. pneumoniae. Notably, plasmids within the same group exhibited conservation of encapsulated genes, suggesting that these plasmid groups may serve as conservative carriers of carbapenem-resistant determinants. Additionally, we investigated the evolution and expansion of IS26 integrons in carbapenem-resistant K. pneumoniae isolates using long-read sequencing. Our findings revealed the evolution and expansion of IS26 structure, which may have contributed to the development of carbapenem resistance in these strains. Our findings indicate that IncC group plasmids are associated with the endemic occurrence of carbapenem-resistant K. pneumoniae, highlighting the need for targeted interventions to control its spread. Although our study focuses on the endemic presence of carbapenem-resistant K. pneumoniae, it is important to note that carbapenem-resistant K. pneumoniae is indeed a global problem, with cases reported in multiple regions worldwide. Further research is necessary to better understand the factors driving the worldwide dissemination of carbapenem-resistant K. pneumoniae and to develop effective strategies for its prevention and control.
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Affiliation(s)
- Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 62102, Taiwan
| | - Yan-Chiao Mao
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
- School of Medicine, National Defense Medical Center, Taipei 11490, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Hsu Lai
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, Kaohsiung 82445, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 82445, Taiwan
| | - Ting-Kuang Yeh
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
- Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Chung-Mei Ho
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung 40705, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
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250
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Mason LCE, Greig DR, Cowley LA, Partridge SR, Martinez E, Blackwell GA, Chong CE, De Silva PM, Bengtsson RJ, Draper JL, Ginn AN, Sandaradura I, Sim EM, Iredell JR, Sintchenko V, Ingle DJ, Howden BP, Lefèvre S, Njampeko E, Weill FX, Ceyssens PJ, Jenkins C, Baker KS. The evolution and international spread of extensively drug resistant Shigella sonnei. Nat Commun 2023; 14:1983. [PMID: 37031199 PMCID: PMC10082799 DOI: 10.1038/s41467-023-37672-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023] Open
Abstract
Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant S. sonnei was reported in the United Kingdom. Here, we aimed to identify the genetic basis, evolutionary history, and international dissemination of the outbreak strain. Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a most recent common ancestor in 2018 carrying a low-fitness cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri. Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data.
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Affiliation(s)
- Lewis C E Mason
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - David R Greig
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, UK
| | | | - Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Elena Martinez
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Grace A Blackwell
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Charlotte E Chong
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - P Malaka De Silva
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Rebecca J Bengtsson
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Jenny L Draper
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Andrew N Ginn
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
- Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia
| | - Indy Sandaradura
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
| | - Eby M Sim
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
- Western Sydney Local Health District, Westmead, NSW, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney, NSW, Australia
- New South Wales Health Pathology, Dee Why, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Microbiology Research, Westmead Hospital, Westmead, NSW, Australia
| | - Danielle J Ingle
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sophie Lefèvre
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - Elisabeth Njampeko
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Paris, F-75015, France
| | - 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
| | | | - Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, UK
| | - Kate S Baker
- NIHR HPRU in Gastrointestinal Infections at University of Liverpool, Liverpool, UK.
- Department of Clinical Infection, Microbiology, and Immunology; Institute for Infection, Veterinary and Ecological Sciences, Liverpool, UK.
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