Comparative genomics of two Shewanella xiamenensis strains isolated from a pilgrim before and during travels to the Hajj
Authors: Thongpan Leangapichart
Philippe Gautret
Jean-Marc Rolain
Linda Hadjadj
Journal: Gut Pathogens (2021)
Discipline: CLINICAL MEDICINE
Keywords: Comparative genomics; Plasmid; Shewanella; Travelers.
Affiliations: Aix Marseille Univ, IRD, APHM, MEPHI, IHU Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 Boulevard Jean Moulin, 13385, Marseille CEDEX 05, France., IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille CEDEX 05, France., Aix Marseille Univ, IRD, APHM, MEPHI, IHU Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 Boulevard Jean Moulin, 13385, Marseille CEDEX 05, France. ., IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille CEDEX 05, France. .

Abstract:  Background: Shewanella xiamenensis has been reported in water environment and in patients and can act as the originator of oxacillinase in gram-negative bacteria. In order to assess genome plasticity and its functional properties related diarrhea symptoms in pilgrim, comparisons of draft genome sequences of the two isolates were conducted with other closely related genomes. Results: We isolated S. xiamenensis 111B and 111D strains from a pilgrim before travels to the Hajj and during travels with diarrhea symptom, respectively. Whole-genome sequencing showed that draft genome size of 111B strain was 5,008,191 bp, containing 49 kb of a putative plasmid. The genome size of 111D was 4,964,295 bp containing 225 kb of a putative plasmid that shared the backbone sequences with the hospital wastewater strain T17. Comparatively, two Hajj strains are identical at 97.3% identity and 98.7% coverage. They are closely related to river water strain, AS58 by SNPs analysis. Notably, a novel blaOXA-48 allele blaOXA-547 was identified in 111D, sharing 99.5% identity with blaOXA-546 and blaOXA-894. Multiple copies of virulence specific genes, such as capsular polysaccharide biosynthesis, O-antigen and lasB (vibriolysin related gene) have been identified specifically in 111D, but absent in 111B strain. Conclusions: The whole genome sequences of S. xiamenensis strain 111B and 111D, including comparative genomic analysis, highlight here the potential for virulence factors that might be related to the cause of diarrhea in humans and also indicate the possible acquisition of pathogenic bacteria, including antibiotic resistance genes or plasmids during the Hajj. 

Retracted: No

PubPeer comments:
 Several articles have been published in different high impact factor journals concerning the results of the same protocol. This study was performed on muslims who participated in the 2013-2017 Hajj (extended to 2018 in some articles). In all these publications, the same protocol authorized by an IRB under the number 2013-A00961u201344 on July 23, 2013 has been used. But there is serious concern on the compliance of this study to the Helsinki Declaration. Authors mentioned that the study has been approved by IRB in July 23, 2013 and started in September 2013. The protocol was approved by the Aix Marseille Universitu00e9 institutional review board (July 23, 2013; reference no. 2013-A00961u201344). There is several discrepancies in these information. **Did The study start in 2012 before the ethics committee approval ?** In another journal, the Travel Medicine and Infectious Disease journal, certains of the same authors published the results of this protocol, with the same reference number. [Antibiotic use for respiratory infections among Hajj pilgrims: A cohort survey and review of the literature] For information, one of the authors is also Associate Editor in the Travel Medicine and Infectious Disease journal. In article published in Travel Medicine and Infectious Disease journal, you can note that the same protocol started in 2012 before to get the ethics committee approval and then, get the ethics committee approval after (on July 23, 2013). I quote: * Pilgrims from Marseille, France participating in the Hajj from 2012 to 2017 were recruited at a specialized travel agency organizing trips to Mecca. * * The protocol was approved by the Aix-Marseille University institutional review board (**July 23rd, 2013**; reference no. 2013-A00961-44). * This is not a spelling mistake. As mentioned in the study and annexes, 169 pilgrims have been recruited in 2012 and data are provided for this year with the same protocol. As the authors mentioned themselves in the Travel Medicine and Infectious Disease journal that the protocol reference no. 2013-A00961u201344 started in 2012, the Year 2012 should be considered as the study start date for all articles related to the protocol approved under the reference #2013-A00961u201344 A study cannot be published in a scientific journal if it started before to get the proper Ethics Committee approval. Retrospective ethics committee approval is a serious breach of the Helsinski Declaration. Furthermore, I would like to note that only certified IRB (aka CPP in France) can authorize prospective interventional studies in France. Aix Marseille Universitu00e9 Ethics Committee is not a certified IRB in France. The format of the reference # is a RCB ID. This # (2013-A00961u201344) is delivered by the French Health Agency. Not by a certified IRB (CPP). As a consequence, there is a ground for serious and legitimate concerns about the study start date and the ethic committee approval. With regards of the Helsinki Declaration, Editors should consider this matter and clarify this situation asap. **List of articles related to the protocol authorized under the number 2013-A00961u201344 on July 23, 2013** 1 - [Antibiotic use for respiratory infections among Hajj pilgrims: A cohort survey and review of the literature] 2 - [Respiratory Viruses and Bacteria among Pilgrims during the 2013 Hajj] 3 - [Lack of MERS Coronavirus but Prevalence of Influenza Virus in French Pilgrims after 2013 Hajj] 4 - [The dynamics and interactions of respiratory pathogen carriage among French pilgrims during the 2018 Hajj] 5 - [Gastrointestinal symptoms and the acquisition of enteric pathogens in Hajj pilgrims: a 3-year prospective cohort study] 6 - [Acquisition of multidrug-resistant bacteria and encoding genes among French pilgrims during the 2017 and 2018 Hajj] 7 - [Comparative genomics of two Shewanella xiamenensis strains isolated from a pilgrim before and during travels to the Hajj] 8 - [High Prevalence of Mycoplasma faucium DNA in the Human Oropharynx] 9 - [Comparison of nasal swabs with throat swabs for the detection of respiratory viruses by real-time reverse transcriptase PCR in adult Hajj pilgrims] 10 - [Respiratory tract infections among French Hajj pilgrims from 2014 to 2017] ,