<p>Low prevalence of resistance genes in sheltered homeless population in Marseille, France, 2014‚Ä?018</p>
Authors: Tran Duc Anh Ly
Herve Tissot-Dupont
Philippe Gautret
Sekene Badiaga
Linda Hadjadj
Didier Raoult
Thi Loi Dao
Van Thuan Hoang
Jean-Marc Rolain
Meriem Louni
Journal: Infection and Drug Resistance (2019)
Discipline: IMMUNOLOGY
Keywords: antibiotic resistance gene; homeless; potential risk factors; real-time polymerase chain reaction (qPCR).
Affiliations: IRD, AP-HM, SSA, VITROME, Aix Marseille Univ., Marseille, France., IHU-M√©diterran√©e Infection, Marseille, France., MEPHI, Aix Marseille Univ., Marseille, France., Family Medicine Department, Thai Binh University of Medicine and Pharmacy, Th√†nh Ph·ª?Th√°i B√¨nh, Vietnam., Pneumology Department, Thai Binh University of Medicine and Pharmacy, Th√†nh Ph·ª?Th√°i B√¨nh, Vietnam., Emergency Department, North Hospital, AP-HM, Marseille, France.

Abstract:  Objectives: The present study has explored the prevalence and potential factors contributing to the presence of nasal/pharyngeal resistant genes in homeless people. Methods: During the winters 2014-2018, we enrolled sheltered homeless adults and controls and collected nasal/pharyngeal samples. Sixteen antibiotic resistance genes (ARGs), including genes encoding for beta-lactamases and colistin-resistance genes, were searched by real-time polymerase chain reaction (qPCR) performed directly on respiratory samples and followed by conventional PCR and sequencing. Results: Over a 5-year period, using qPCR, we identified in homeless group (n=715) the presence of bla TEM (396/710, 54.7%), blaSHV (27/708, 3.6%), bla OXA-23 (1/708, 0.1%), while other genes including colistin-resistance genes (mcr-1 to mcr-5) were absent. We found a significantly higher proportion of ARG carriage among controls (74.1%) compared to homeless population (57.1%), p=0.038. Tobacco smoking (OR=4.72, p&lt;0.0001) and respiratory clinical signs (OR=4.03, p=0.002) were most prevalent in homeless people, while vaccination against influenza (OR=0.31, p=0.016) was lower compared to controls. Among homeless people, type of housing (shelter A versus B, OR=1.59, p=0.006) and smoking tobacco (smoker versus non-smoker, OR=0.55, p=0.001) were independent factors associated with ARG carriage. By sequencing, we obtained a high diversity of bla TEM and blaSHV in both populations. Conclusion: The lower risk for ARGs in the homeless population could be explained by limited access to health care and subsequently reduced exposure to antibiotics. 

Retracted: No

PubPeer comments:
 In this study, homeless persons in Marseille were recruited from shelters between 2014-2018, examined, and nasal and pharyngeal swabs were obtained. I have a question about the IRB approval for this study, since homeless persons might be considered to be a  vulnerable population (i.e., vulnerable to coercion), similar to veterans or prisoners in the US, although IRB rules might differ per country. Surprisingly, the IRB approval number listed in this paper (2010-A01406-33) is used for at least 17 studies, including this one. Although all of them involve homeless persons recruited from Marseille shelters, the studies themselves vary in terms of study protocols and treatment sample collection. The studies vary from collecting lice, treating subjects with drug-impregnated underwear, filling out questionnaires, medical exams, to nasal and pharyngeal sampling, skin swabbing, blood draw, rectal samples, sputum collection, and chest X rays. Moreover, the studies were performed from 2011 to 2020, spanning almost 10 years. Would the authors be willing to share the original 2010 ethical approval application here? Did they get approval for all these different studies spanning 10 years, in one single application? There is also confusion about which institution or ethical board approved the study. Some papers state that the study was approved by  our institutional review board , suggesting that this was a number referring to IRB approval by the Aix-Marseille Universitu00e9 and or Institut Hospitalo-Universitaire Mu00e9diterranu00e9e Infection, both listed as author affiliations. But in other papers, the IRB approval number appears to be an ANSM RCB authorization ID, as per  Informed consent was obtained from these subjects, and the study was approved by the u2018u2018Comitu00e9 de Protection des Personnes Sud Mediterranu00e9eu2019u2019 on January, 12, 2011 (ID RCB: 2010-A01406-33) , e.g. as mentioned in PLoS ONE 8(2): e58088. Either way, it would be of interest to take away any concern whether studies on this vulnerable populations were all performed within the original IRB approval scope. Here is the list of 17 papers that all appear to share the same ethical approval number: * Rezak Drali et al. - Journal of Clinical Microbiology (2012) p. 2229u20132233 - DOI: 10.1128 JCM.00808-12 * Rezak Drali et al. - PLoS ONE 8(2): e58088 (2013) - DOI: 10.1371 journal.pone.0058088 * Samir Benkouiten et al. - JAMA Dermatol. 2014;150(3):273-279 (2014) - DOI: 10.1001 jamadermatol.2013.6398 * Rezak Drali et al - Infection, Genetics and Evolution 39 (2016) 225u2013231 - DOI: 10.1016 j.meegid.2016.02.008 * Tran Duc Anh Ly et al. - Emerging Infectious Diseases (2017) - DOI: 10.3201 eid2311.170516 * Tran Duc Anh Ly et al. - Clinical Microbiology and Infection 25 (2019) 249.e1e249.e6 - DOI: 10.1016 j.cmi.2018.04.032 * Tran Duc Anh Ly et al. - Front. Cell. Infect. Microbiol. 9:86 (2019) - DOI: 10.3389 fcimb.2019.00086 * Tran Duc Anh Ly et al. - Journal of Epidemiology and Global Health (2019) - DOI: 10.2991 jegh.k.190510.001 * Tran Duc Anh Ly et al. - Infection and Drug Resistance 2019:12 1139u20131151 - DOI: 10.2147 IDR.S202048 * Nadia Amanzougaghene et al. - Parasites Vectors (2020) 13:177 - DOI: 10.1186 s13071-020-04036-y * Tran Duc Anh Ly et al. - European Journal of Clinical Microbiology Infectious Diseases (2020) - DOI: 10.1007 s10096-020-03889-6 * Tran Duc Anh Ly et al. - Travel Medicine and Infectious Disease 36 (2020) 101768 - DOI: 10.1016 j.tmaid.2020.101768 * Tran Duc Anh Ly et al. - Vector-Borne and Zoonotic Diseases (2020) - DOI: 10.1089 vbz.2019.2603 * Tran Duc Anh Ly et al. - Acta Microbiologica et Immunologica Hungarica (2021) - DOI: 10.1556 030.2021.01346 * Tran Duc Anh Ly et al. - Journal of Epidemiology and Global Health (2021) - DOI: 10.2991 jegh.k.201009.001 * Tran Duc Anh Ly et al. - Journal of Infection Volume 82, Issue 1, January 2021, Pages 60-66 - DOI: 10.1016 j.jinf.2020.11.026 * Tran Duc Anh Ly et al. - European Journal of Clinical Microbiology Infectious Diseases (2021) - DOI: 10.1007 s10096-020-04127-9 ,