Emergence of ADC-5 Cephalosporinase in environmental Acinetobacter baumannii from a German tank milk with a novel Sequence Type

  1. Ellen M. E. Sykes
  2. Valeria Mateo-Estrada
  3. George Zhanel
  4. Jeremy Dettman
  5. Julie Chapados
  6. Suzanne Gerdis
  7. Ömer Akineden
  8. Izhar I. U. Khan
  9. Santiago Castillo-Ramírez
  10. Ayush Kumar

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Abstract

Bacteria resistant to antibiotics arguably pose the greatest threat to human health in the twenty-first century. One such bacterium that typifies antibiotic resistance is Acinetobacter baumannii . Frequently, hospital strains of A. baumannii display multidrug resistant (MDR) or extensively drug resistant (XDR) phenotypes, often requiring the use of last resort antibiotics for treatment. In addition to hospital settings, A. baumannii has been isolated from many highly divergent sources including wastewater treatment plant effluent, soil, and agricultural run-off with global distribution. However, such isolates remain poorly characterized. In this study, we characterized a strain of A. baumannii, AB341-IK15, isolated from bulk tank milk in Germany that demonstrated resistance to ceftazidime and intermediate resistance to ceftriaxone and piperacillin/tazobactam. Further genetic characterization identified an ADC-5 cephalosporinase, first incidence in an environmental isolate; and an OXA-408 oxacillinase that may contribute to this phenotype. Interestingly, AB341-IK15 is of a novel sequence type. This research underscores the importance of studying isolates of A. baumannii of non-clinical origin to understand the antibiotic resistance and virulence potential of environmental isolates of A. baumannii as well to understand the diversity of this species.

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  1. Version published to 10.1099/acmi.0.000485.v3 on Access Microbiology
  3. Version published to 10.1099/acmi.0.000485.v2 on Access Microbiology
  4. Access Microbiology

    The work presented is clear and the arguments well formed. This is a study that would be of interest to the field and community. The reviewers have highlighted minor concerns with the work presented. Please ensure that you address their comments. Please have a look at the structure, currently it only consists of Abstract, Impact Statement, Data Summary & Introduction. Please introduce Methods, Results and Discussion headers as well to improve readability. The font size in the figures is relatively small, could you increase these and also make the lines wider in the phylogenetic tree to improve readibility?

  5. Access Microbiology

    Comments to Author

    The manuscript presents the report of the analysis of Acinetobacter baumannii strain isolated from bulk tank milk in Germany. The isolate demonstrated resistance to ceftazidime and was genomically analysed. The study presents with methodological rigour the protocols used for the sample preparation, characterisation and the tools used for genomic analysis. The manuscript needs more structure, the title of the section introduction (line 63) is not clear, and other sections are expected also for a short report. This organization would better present the key findings. A few suggestions and points that need clarification are presented below: Line 104 - include how the species identification was predicted using ANI. Line 108 - explain the protocol (tool/software or pipeline) for the "phylogenomic approach". Line 123 - was just one scaffold used for the analysis? The results are well presented, however, some of the details on the characterisation (both phenotypical and genotypical) can be presented in a table. A clarification on the importance of the. nucleotide sequence of ADC-5 and its predicted structure is expected. Is this the key finding of the study? Why is important the alignment of putative ADC-5 cephalosporinase from AB341-IK15 and characterized ADC-5 AJ575184? How are the predicted structures based on the mutations statistically supported? The literature analysis is comprehensive. Please comment on lines 163-164 ( verify the note "Error! Reference source not found").

    Please rate the manuscript for methodological rigour

    Good

    Please rate the quality of the presentation and structure of the manuscript

    Good

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  6. Access Microbiology

    Comments to Author

    Line 163 - there is an error with the reference. It is like: ... which are present in ATCC17978 (Error! Reference source not found.).

    Please rate the manuscript for methodological rigour

    Very good

    Please rate the quality of the presentation and structure of the manuscript

    Very good

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  7. Access Microbiology

    Comments to Author

    1. Methodological rigour, reproducibility and availability of underlying data 2. Presentation of results 3. How the style and organization of the paper communicates and represents key findings 4. Literature analysis or discussion 5. Any other relevant comments

    Please rate the manuscript for methodological rigour

    Good

    Please rate the quality of the presentation and structure of the manuscript

    Good

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  8. Access Microbiology

    Comments to Author

    Dear, I have now reviewed the article entitled: "Emergence of ADC-5 Cephalosporinase in environmental Acinetobacter baumannii from a German tank milk with a novel Sequence Type " for publication in "Access Microbiology". This is a nicely written manuscript describing an environmental isolate of A. baumannii. The authors carried out multiple experiments and analyses to support their claims, in sound methodology. Here are my comments: Can the authors provide the KL and OCL type of the isolate, which could be beneficial and interesting information to provide. L30-2: Frequently, hospital strains of A. baumannii display multidrug resistant (MDR) or extreme drug resistant (XDR) phenotypes, often requiring the use of last resort antibiotics for treatment. - XDR usually refers to extensively drug-resistant. If not the case, what is the definition of an "extreme drug resistant" phenotype? Unusual paragraph sectioning as the "5. Introduction" contains the entire text of the manuscript. L104-6: To evaluate the relatedness of AB341-IK15 to other strains of A. baumannii, ABRicate pipeline (Seeman 2022) and ST classification via the Oxford scheme (Bartual et al. 2005) were used. - More suitable citation of ABRicate is "Seemann T, Abricate, Github https://github.com/tseemann/abricate" as its Github page recommends. The year "2022" is therefore irrelevant since the software is not from 2022. However, the year should be stated when referring to a particular database used via ABRicate, or the version of the database. Which database was employed in order to "evaluate the relatedness of AB341-IK15 to other strains of A. baumannii"? - Employing the Pasteur scheme for MLST would be beneficial as well, since the Oxford scheme detects also targets which are more prone to recombination. How were the representatives of the particular International Clones selected? Have you considered performing a phylogenetic analysis of the available isolates of the same ST (either Oxford or Pasteur if assessed) to see if you isolate clusters with other environmental or clinical isolates? L162-4: Missing reference. L164-5: Considering the degeneration of the genetic code, perhaps BLASTP should be applied on top of the BLASTN. L235: "FAutor"

    Please rate the manuscript for methodological rigour

    Good

    Please rate the quality of the presentation and structure of the manuscript

    Good

    To what extent are the conclusions supported by the data?

    Strongly support

    Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?

    No

    Is there a potential financial or other conflict of interest between yourself and the author(s)?

    No

    If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?

    Yes

  9. Version published to 10.1099/acmi.0.000485.v1 on Access Microbiology