# Role of Institut Hospitalo-Universitaire Méditerranée Infection in the surveillance of resistance to antibiotics and training of students in the Mediterranean basin and in African countries

L. Peyclit, A. Chanteloup, L. Hadjadj, J.-M. Rolain

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## To cite this version:

L. Peyclit, A. Chanteloup, L. Hadjadj, J.-M. Rolain. Role of Institut Hospitalo-Universitaire Méditerranée Infection in the surveillance of resistance to antibiotics and training of students in the Mediterranean basin and in African countries. New Microbes and New Infections, 2018, 26, pp.S52-S64. 10.1016/j.nmni.2018.06.001. hal-02101062

HAL Id: hal-02101062

https://amu.hal.science/hal-02101062v1

Submitted on 31 Mar 2025

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# Role of Institut Hospitalo-Universitaire Méditerranée Infection in the surveillance of resistance to antibiotics and training of students in the Mediterranean basin and in African countries

L. Peyclit, A. Chanteloup, L. Hadjadj and J.-M. Rolain

Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France

## Abstract

Surveillance of antibiotic resistance has become a public global concern after the rapid worldwide dissemination of several antibiotic resistance genes. Here we report the role of the Institut Hospitalo-Universitaire Méditerranée Infection created in 2011 in the identification and description of multidrug-resistant bacteria thanks to collaborations and training of students from the Mediterranean basin and from African countries. Since the creation of the institute, 95 students and researchers have come from 19 different countries from these areas to characterize 6359 bacterial isolates from 7280 samples from humans (64%), animals (28%) and the environment (8%). Most bacterial isolates studied were Gram-negative bacteria (n = 5588; 87.9%), mostly from Algeria (n = 4190), Lebanon (n = 946), Greece (n = 610), Saudi Arabia (n = 299) and Senegal (n = 278). Antibiotic resistance was diversified with the detection and characterization of extended-spectrum β-lactamases, carbapenemases and resistance to colistin, vancomycin and methicillin. All those studies led to 97 indexed international scientific papers. Over the last 6 years, our institute has created a huge network of collaborations by training students that plays a major role in the surveillance of resistance to antibiotics in these countries.

© 2018 The Author(s). Published by Elsevier Ltd.

**Keywords:** Africa, Antibiotic resistance, IHU Méditerranée Infection, Mediterranean, Multi-drug resistance

**Article published online:** 14 June 2018

**Corresponding author:** J.-M. Rolain, Aix-Marseille Université, IRD, APHM, MEPHI, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.

E-mail: jean-marc.rolain@univ-amu.fr

## Introduction

During the last decade, antibiotic resistance has become one of the major public health priorities in the world [1] because of the emergence of new mechanisms of resistance. Moreover, the massive media coverage has tended to predict of thousands of human deaths every year [2]. However, recent epidemiologic data from our institution demonstrate that the level of anti-biotic resistance for the most common bacterial species of clinical interest did not significantly change over the last 15 years in Marseille, France [3,4]. Similarly, we found a huge disparity between mortality attributable to antibiotic resistance

using simple model estimations and empirical data of true deaths in our institution [5]. Data on the level of antibiotic resistance in Europe show disparities between countries and bacterial species for certain antibiotics; for example, resistance to carbapenems is much more frequent in Romania, Italy and Greece [3]. It appears from those studies that a better understanding and surveillance of antibiotic resistance at the local and national levels is critical to manage antibiotic-resistant bacterial infections in the future [5]. However, data on anti-biotic resistance and surveillance of the emergence and spread of new mechanisms of resistance in the Mediterranean basin and in African countries were lacking in most of those countries until now.

Here we report the specific and unique role of the Institut Hospitalo-Universitaire Méditerranée Infection (IHU-MI), created in November 2011, in the identification, description and surveillance of multidrug-resistant bacteria thanks to collaborations among and training of students coming from the Mediterranean basin and from African countries in our institute. The majority of students who come to our institute for
surveillance and analysis of antibiotic resistance came with their
own bacterial isolates from their countries.

## Methods

This study analyses data collected from 2011 (the date of cre-
ation of the IHU-MI) through the completion of this article in
February 2018. The number of students by level of graduation
and by country of origin per year was sorted from our
administrative database of students and scientific visitors during
the study period from the team dedicated to antibiotic resis-
tance research (JMR team). Students from the Mediterranean
basin and Africa were counted from this primary list and were
sorted by level of graduation (master's degree, PhD, postdoc
and scientific visitors) and by country. Because some students
stayed at our institute both for master's and PhD courses, we
deduplicated the total count. The number of students present
per year in the team was also calculated from this list to show
the student kinetics of reception per year.

All students facing antibiotic resistance in their country came
with their own isolates to analyse them as a course training.
Most of them continued to collaborate with our institute,
resulting in real-time surveillance of antibiotic resistance ac-
cording to their field of research (humans, animals or the
environment). Initially there was no rationale for the recruit-
ment and analysis of the samples because no data existed at the
beginning of this network. Now, however, the follow-up of
antibiotic resistance is mainly focused on the current antibiotic
resistance situation. For each epidemiologic study, the number
and type of samples and/or bacterial isolates and the country of
origin were counted, and data were presented in a single table,
with all data provided by country.

Antibiotic resistance for each sample or bacterial isolates
was studied using the same procedure. Antibiotic resistance
was assessed either directly from samples by PCR or from
bacterial isolates by culture and molecular assays. The first
step consisted of sample culture and isolation of strains on
specific agar media: Columbia agar with 5% sheep's blood,
trypticase soy agar or MacConkey (bioMérieux, Marcy l'Etoile,
France) with or without addition of antibiotics. All collected
strains were subjected to matrix-assisted laser desorption/
ionization time-of-flight mass spectrometry (MALDI-TOF MS)
for identification [6]. Antibiotic susceptibility testing (AST) was
performed using the disc diffusion method on Mueller-Hinton
medium agar for phenotypic characterization of the mecha-
nism of resistance. Specific panels of antibiotics were tested
according to the bacteria species (e.g. Enterobacteriaceae,
nonfermentative Gram-negative bacteria, Gram-positive bac-
teria). Then AST results were interpreted according to

European Committee on Antimicrobial Susceptibility Testing
guidelines [7]. Genotypic identification of resistance genes
were screened by real-time quantitative PCR and confirmed by
standard PCR and sequencing when necessary, and sequences
were analysed using ARG-ANNOT software [8] to identify the
specific antibiotic resistance gene. Multilocus sequence typing
was performed to evaluate genetic relatedness of strains. If
necessary, a whole genome sequence study was performed to
obtain the complete resistome of a strain [9] or to describe
the genetic environment of an antibiotic resistance gene
[10,11].

Each student hosted by our institution received specific
training for the study of antibiotic resistance (MALDI-TOF MS,
AST, molecular training, genomics, bioinformatics) and pre-
sented the progress of their work and their results every week
so that we could prepare tables and figures to be used for
publication. Finally, each student was trained by the senior
member of the team (JMR) to write their scientific papers and
to create their own bibliography on the topic. Most of them
also wrote a review on their topic while writing their PhD
thesis. Weekly seminars or bibliographic sessions were also
provided each Friday to improve students' knowledge in the
field. The number of indexed international scientific papers per
type of sample and per country was also calculated on the basis
of published and submitted papers on antibiotic resistance
during the study period.

## Results

Since the creation of this institute, the JMR team has
welcomed a total of 126 students or visiting scientists,
including 95 deduplicated students (75.4%) from academic
exchanges with 19 countries from the Mediterranean basin,
Africa and Middle East. The number of students present in a
given year has significantly increased during the study period
(ten students in 2011, 15 in 2012, 21 in 2013, 28 in 2014, 27
in 2015, 40 in 2016 and 44 in 2017) to a total of 95 students.
Most of the students are from Algeria (52, 55.3%), followed by
Lebanon (12, 12.8%), Senegal (7, 7.4%) and Tunisia (5, 5.3%).
All these 95 students were from Europe (Spain, 3 students,
3.2%; Italy, 2, 2.1%; Greece, 1, 1.1%), West Africa (Senegal, 7,
7.3%; Benin, Central Africa Republic, Guinea, Ivory Coast,
Mali, Nigeria, Togo, 8, 8.4%), North Africa (Algeria, 52, 55.3%;
Tunisia, 5, 5.3%; Egypt, 1, 1.1%; Morocco, 1, 1.1%), Middle East
(Lebanon, 12, 12.8%; Qatar, Syria, 2, 2.1%) and Madagascar (1,
1.1%).

Each student had a different level of education, including
master's degree (n = 15), PhD students (n = 65), scientific
visitors and postdocs (n = 22). Overall, the number of PhD
students from these countries significantly increased during the study period, from eight in 2011 to 30 in 2017 (2011: 8; 2012: 11; 2013: 16; 2014: 20; 2015: 23; 2016: 28; 2017: 30). The number of postdocs varied from two to four between these different years (2011, 2013, 2015, 2017: 2 students; 2012: 3; 2014, 2016: 4), as did the number of students seeking master's degrees, from one to four (2011, 2012: 1; 2013: 2; 2014, 2015: 3; 2016, 2017: 5). Students trained at the IHU-MI will return to their country of origin and continue to work in this field with

our institute, which is now identified as the core laboratory for surveillance of antibiotic resistance and further analysis of new bacterial isolates from those countries.

A total of 7280 samples from human (n = 4657; 64%), animal (n = 2058; 28%) or environment (n = 565; 8%) from 15 different countries were analysed during the study period (Fig. 1(A)). More than half of those samples came from Algeria (n = 4190; 57.6%), followed by Lebanon (n = 946; 12.9%), Greece (n = 610; 8.4%), Saudi Arabia (n = 299; 4.1%) and

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A

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B

<caption>**FIG. 1.** (A) Geographic distribution of samples studied in publications of IHU-MI from 2011 to 2017 (n = 7280). (B) Repartition of bacterial species studied from Mediterranean basin or African countries in IHU-MI from 2011 to 2017 (n = 6359). IHU-MI, Institut Hospitalo-Universitaire Méditerranée Infection.</caption>
<table><caption>TABLE I. Samples and publications studied according to countries in Institut Hospitalo-Universitaire Méditerranée Infection from 2011 to 2017</caption><thead><tr><th>Country</th><th>Year</th><th>Strain type</th><th>Studied strains</th><th>No. of samples</th><th>No. of positive samples with an AR gene detected</th><th>Tested phenotype</th><th>Type of antibiotic resistance genes detected (n)</th><th>Study</th></tr></thead><tbody><tr><td rowspan="10">Algeria</td><td>2008–2011</td><td>Clinical isolates</td><td>Klebsiella pneumoniae</td><td>211</td><td>194</td><td>ESBL<br/>Cephalosporinases<br/>Penicillinase<br/>HLP</td><td>bla<sub>TEM</sub> (146)<br/>bla<sub>SHV</sub> (154)<br/>bla<sub>CTX-M</sub> (130)</td><td>[19]</td></tr><tr><td>2008–2012</td><td>Clinical isolates</td><td>K. pneumoniae</td><td>221</td><td>190</td><td>ESBL<br/>Cephalosporinases<br/>Penicillinase<br/>HLP</td><td>bla<sub>TEM</sub> (146)<br/>bla<sub>SHV</sub> (154)<br/>bla<sub>CTX-M</sub> (130)</td><td>[20]</td></tr><tr><td>2017</td><td>Animal (45) and human (37) isolates</td><td>Salmonella spp.</td><td>92</td><td>18</td><td>ESBL</td><td>bla<sub>CTX-M-1</sub> (12)<br/>bla<sub>CTX-M-15</sub> (5)<br/>bla<sub>TEM</sub> (8)</td><td>[21]</td></tr><tr><td>2011</td><td>Clinical isolates</td><td>Escherichia coli</td><td>1</td><td>1</td><td>Coli R</td><td>mcr-1</td><td>[22]</td></tr><tr><td>2015</td><td>Animal isolates</td><td>E. coli (30)<br/>K. pneumoniae (17)</td><td>47</td><td>47</td><td>Coli R<br/>ESBL</td><td>bla<sub>CTX-M-15</sub> (47)<br/>bla<sub>TEM-1</sub> (25)</td><td>[23]</td></tr><tr><td>2014</td><td>Clinical and environmental isolates</td><td>K. pneumoniae<br/>Enterobacter cloacae<br/>Acinetobacter baumannii<br/>Pseudomonas aeruginosa</td><td>89</td><td>32</td><td>ESBL<br/>Carbapenemases</td><td>bla<sub>OXA-4B</sub> (5)<br/>bla<sub>NDM-1</sub> (7)<br/>bla<sub>OXA-43</sub> (2)<br/>bla<sub>TEM</sub> (6)<br/>bla<sub>SHV</sub> + bla<sub>CTX-M</sub> (7)</td><td>[24]</td></tr><tr><td>2013–2015</td><td>Environmental isolates</td><td>A. baumannii</td><td>1</td><td>1</td><td>Carbapenemases<br/>ESBL<br/>Fluoroquinolones</td><td>bla<sub>NDM-1</sub> (1)</td><td>[25]</td></tr><tr><td>2010–2013</td><td>Clinical isolates</td><td>Enterococcus spp.</td><td>85</td><td>85</td><td>Vanco R</td><td>vanC</td><td>[26]</td></tr><tr><td>2010–2013</td><td>Clinical isolates</td><td>A. baumannii</td><td>43</td><td>43</td><td>Carbapenemases</td><td>bla<sub>NDM-1</sub> (7)<br/>bla<sub>OXA-23</sub> (28)<br/>bla<sub>OXA-24</sub> (1)<br/>bla<sub>OXA-58</sub> (6)<br/>bla<sub>OXA-51</sub> (43)<br/>bla<sub>OXA-23</sub> + bla<sub>NDM-1</sub> (2)<br/>bla<sub>OXA-58</sub> + bla<sub>NDM-1</sub> (1)</td><td>[27]</td></tr><tr><td>2013–2015</td><td>Clinical isolates</td><td>Enterobacteriaceae (161)<br/>P. aeruginosa (18)<br/>A. baumannii (7)</td><td>186</td><td>36</td><td>Carbapenemases<br/>ESBL</td><td>bla<sub>OXA-4B</sub> (2)<br/>bla<sub>VIM-4</sub> (2)<br/>bla<sub>NDM-1</sub> (2)<br/>bla<sub>OXA-23</sub> (5)</td><td>[28]</td></tr><tr><td>2011–2013</td><td>Environmental isolates</td><td>A. baumannii</td><td>67</td><td>61</td><td>Carbapenemases</td><td>bla<sub>OXA-23</sub> (29)<br/>bla<sub>NDM-1</sub> (32)</td><td>[29]</td></tr><tr><td>2013–2014</td><td>Clinical isolates</td><td>Streptococcus agalactiae</td><td>93</td><td>74</td><td>MLSBR</td><td>ermB (18)<br/>ermA<br/>mefA<br/>mefE</td><td>[30]</td></tr><tr><td>2015</td><td>Animal isolates</td><td>E. coli</td><td>1</td><td>1</td><td>Carbapenemase</td><td>bla<sub>NDM-1</sub> (1)</td><td>[31]</td></tr><tr><td>2014–2016</td><td>Animal isolates</td><td>Enterobacteriaceae</td><td>380</td><td>3</td><td>Carbapenemases<br/>ESBL<br/>Cephalosporinases</td><td>bla<sub>OXA-4B</sub> (3)</td><td>[32]</td></tr><tr><td>2012–2014</td><td>Environmental isolates</td><td>K. pneumoniae</td><td>44</td><td>44</td><td>ESBL<br/>Cephalosporinases<br/>Fluoroquinolones<br/>Aminoglycosides</td><td>bla<sub>CTX-M-15</sub> (41)<br/>bla<sub>CTX-M-3</sub> (3)</td><td>[33]</td></tr><tr><td>2014–2015</td><td>Animal isolates</td><td>Samples</td><td>503</td><td>389</td><td>Carbapenemases<br/>ESBL</td><td>bla<sub>TEM</sub> (128)<br/>bla<sub>SHV</sub> (83)<br/>bla<sub>CTX-M</sub> (46)<br/>bla<sub>OXA-58</sub> (132)</td><td>[34]</td></tr><tr><td>2015</td><td>Animal isolates</td><td>Enterobacteriaceae</td><td>32</td><td>32</td><td>Carbapenemases<br/>ESBL</td><td>bla<sub>OXA-4B</sub> (32)<br/>bla<sub>CTX-M-15</sub> (1)<br/>bla<sub>TEM</sub> (2)</td><td>[35]</td></tr><tr><td>2013–2014</td><td>Animal (3) and human (1) isolates</td><td>E. coli</td><td>4</td><td>4</td><td>Coli R</td><td>mcr-1 (4)</td><td>[36]</td></tr><tr><td>2016</td><td>Animal isolates</td><td>E. coli</td><td>8</td><td>8</td><td>Coli R</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2017</td><td>Animal (4) and environmental (5) isolates</td><td>E. coli (8)<br/>E. cloacae (1)</td><td>9</td><td>9</td><td>Coli R</td><td>In progress</td><td>Unpublished results</td></tr></tbody></table>

Continued
<table><caption>TABLE I. Continued</caption><thead><tr><th>Country</th><th>Year</th><th>Strain type</th><th>Studied strains</th><th>No. of samples</th><th>No. of positive samples with an AR gene detected</th><th>Tested phenotype</th><th>Type of antibiotic resistance genes detected (n)</th><th>Study</th></tr></thead><tbody><tr><td></td><td>2016</td><td>Clinical isolates</td><td>K. pneumoniae</td><td>3</td><td>3</td><td>Coli R</td><td>In progress</td><td>Unpublished results</td></tr><tr><td></td><td>2015–2016</td><td>Environmental isolates</td><td>Staphylococcus aureus</td><td>200</td><td>153</td><td>Methi R</td><td>In progress</td><td>Unpublished results</td></tr><tr><td></td><td>2011–2013</td><td>Clinical isolates</td><td>A. baumannii</td><td>47</td><td>47</td><td>Carbapenemases<br>Aminoglycosides<br>Fluoroquinolones</td><td>bla<sub>OXA-23</sub> (33)<br>bla<sub>OXA-24</sub> (10)<br>bla<sub>NDM</sub> (11)<br>armA (4)<br>aph(3')VI (24)<br>aadA (6)<br>ant(2')I (10)<br>aac(3)la (33)<br>Mutation in gyrA, parC (45)</td><td>[37]</td></tr><tr><td></td><td>2013–2014</td><td>Clinical isolates</td><td>A. baumannii</td><td>12</td><td>12</td><td>Coli R<br>Carbapenemases</td><td>bla<sub>OXA-24</sub> (4)<br>bla<sub>OXA-23</sub> (6)<br>bla<sub>OXA-51</sub> (12)<br>bla<sub>NDM-1</sub> (2)</td><td>[38]</td></tr><tr><td></td><td>2016–2017</td><td>Animal isolates</td><td>Samples</td><td>200</td><td>4</td><td>ESBL</td><td>In progress</td><td>Unpublished results</td></tr><tr><td></td><td>2013</td><td>Clinical isolates</td><td>Enterococcus hirae</td><td>1</td><td>1</td><td></td><td></td><td>[39]</td></tr><tr><td></td><td>2016</td><td>Clinical isolates</td><td>K. pneumoniae (20)<br>A. baumannii (12)<br>P. aeruginosa (9)<br>E. coli (27)</td><td>68</td><td>68</td><td>Carbapenemases<br>ESBL</td><td>In progress</td><td>Unpublished results</td></tr><tr><td></td><td>2011–2012</td><td>Clinical isolates</td><td>A. baumannii</td><td>30</td><td>24</td><td>Carbapenemases</td><td>bla<sub>OXA-23</sub> (22)<br>bla<sub>OXA-58</sub> (1)<br>bla<sub>OXA-23</sub> + bla<sub>OXA-58</sub> (1)</td><td>[40]</td></tr><tr><td></td><td>2011</td><td>Clinical isolates</td><td>P. aeruginosa</td><td>17</td><td>17</td><td>Carbapenemases</td><td>bla<sub>VIM-2</sub> (14)<br>Mutation in oprD (3)</td><td>[41]</td></tr><tr><td></td><td>2012–2013</td><td>Clinical isolates</td><td>E. coli</td><td>105</td><td>3</td><td>Carbapenemases<br>ESBL<br>Aminoglycosides<br>Fluoroquinolones</td><td>bla<sub>NDM-5</sub> (3)<br>bla<sub>TEM</sub> (3)<br>bla<sub>CTX-M</sub> (3)<br>aadA (3)</td><td>[42]</td></tr><tr><td></td><td>2010–2011</td><td>Clinical isolates</td><td>E. coli (3)<br>K. pneumoniae (24)<br>E. cloacae (11)<br>Serratia marcescens (4)</td><td>42</td><td>39</td><td>ESBL</td><td>bla<sub>CTX-M</sub> (10)<br>bla<sub>TEM</sub> (14)<br>bla<sub>SHV</sub> (15)</td><td>[43]</td></tr><tr><td></td><td>2010–2011</td><td>Clinical isolates</td><td>K. pneumoniae</td><td>100</td><td>100</td><td>ESBL<br>Aminoglycosides<br>Fluoroquinolones</td><td>bla<sub>CTX-M</sub> (76)<br>bla<sub>TEM</sub> (74)<br>bla<sub>SHV</sub> (73)<br>armA (23)<br>aadA (35)<br>aac(6')Ib (50)<br>qnrB (22)</td><td>[44]</td></tr><tr><td></td><td>2013</td><td>Animal isolates</td><td>Acinetobacter spp.</td><td>33</td><td>4</td><td>Carbapenemases</td><td>bla<sub>OXA-23</sub> + bla<sub>OXA-58</sub> + bla<sub>OXA-51</sub> (1)<br>bla<sub>OXA-58</sub> + bla<sub>OXA-51</sub> (1)<br>bla<sub>OXA-58</sub> (2)</td><td>[45]</td></tr><tr><td></td><td>2014–2015</td><td>Clinical isolates</td><td>K. pneumoniae</td><td>7</td><td>7</td><td>ESBL<br>Carbapenemases</td><td>bla<sub>OXA-48</sub> + bla<sub>CTX-M</sub><br>15 + bla<sub>SHV-1</sub> + bla<sub>TEM-1D</sub> (7)</td><td>[46]</td></tr><tr><td></td><td>2015</td><td>Environmental isolates</td><td>Enterobacteriaceae</td><td>12</td><td>9</td><td>Carbapenemases<br>ESBL</td><td>bla<sub>CTX-M-15</sub> (9)<br>bla<sub>OXA-48</sub> (1)<br>bla<sub>TEM</sub> (1)</td><td>[47]</td></tr><tr><td></td><td>2015</td><td>Animal isolates</td><td>Pseudomonas putida</td><td>1</td><td>1</td><td>Carbapenemases<br>ESBL</td><td>bla<sub>VIM-2</sub></td><td>[48]</td></tr><tr><td></td><td>2017</td><td>Clinical isolates</td><td>K. pneumoniae</td><td>1</td><td>1</td><td>Carbapenemases<br>ESBL</td><td>bla<sub>OXA-48</sub> (1)<br>bla<sub>SHV-27</sub> (1)</td><td>[49]</td></tr><tr><td></td><td>2010–2011</td><td>Clinical isolates</td><td>A. baumannii</td><td>71</td><td>71</td><td>Carbapenemases</td><td>bla<sub>OXA-23</sub> (31)<br>bla<sub>OXA-24</sub> (5)<br>bla<sub>OXA-51</sub> (71)</td><td>[50]</td></tr><tr><td></td><td>2010–2011</td><td>Clinical isolates</td><td>A. baumannii</td><td>71</td><td>71</td><td>Carbapenemases<br>ESBL</td><td>bla<sub>TEM</sub> (53)<br>ampC (69)</td><td>[51]</td></tr></tbody></table>
<table><caption>TABLE I. Continued</caption><thead><tr><th>Country</th><th>Year</th><th>Strain type</th><th>Studied strains</th><th>No. of samples</th><th>No. of positive samples with an AR gene detected</th><th>Tested phenotype</th><th>Type of antibiotic resistance genes detected (n)</th><th>Study</th></tr></thead><tbody><tr><td rowspan="4">Egypt</td><td>2015</td><td>Clinical isolates</td><td>Enterobacteriaceae</td><td>157</td><td>103</td><td>ESBL</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2016</td><td>Clinical isolates</td><td>P. aeruginosa</td><td>3</td><td>3</td><td>Carbapenemases</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2012–2013</td><td>Clinical isolates</td><td>A. baumannii</td><td>150</td><td>150</td><td>Carbapenemases<br>Carbapenemases<br>Aminoglycosides</td><td>bla<sub>NDM-1</sub> (59)<br>bla<sub>OXA-23</sub> (115)<br>armA (141)<br>bla<sub>OXA-51</sub> (150)<br>bla<sub>NDM-1</sub> + bla<sub>OXA-23</sub> (53)<br>armA + bla<sub>NDM-1</sub> + bla<sub>OXA-23</sub> (52)</td><td>[59]</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td></td><td>In progress</td><td>Unpublished results</td></tr><tr><td rowspan="2">Greece</td><td>2013–2017</td><td>Clinical isolates</td><td>P. mirabilis (4)<br>P. putida (1)<br>C. freundii (1)<br>Enterobacter aerogenes (2)<br>Providencia stuartii (8)<br>P. aeruginosa (79)<br>A. baumannii (158)<br>E. cloacae (10)<br>E. coli (33)<br>K. pneumoniae (314)</td><td>610</td><td>610</td><td>Carbapenemases<br>ESBL<br>Coli R<br>Fluoroquinolones</td><td></td><td></td></tr><tr><td></td><td></td><td>Providencia rettgeri</td><td>1</td><td>1</td><td>Carbapenemase</td><td>bla<sub>NDM-1</sub> (1)</td><td>[60]</td></tr><tr><td rowspan="2">Israel</td><td>2011</td><td>Clinical isolates</td><td>K. pneumoniae</td><td>15</td><td>15</td><td>Carbapenemases<br>Coli R<br>Aminoglycosides</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2008–2011</td><td>Clinical isolates</td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td rowspan="2">Ivory Coast</td><td>2010–2011</td><td>Clinical isolates</td><td>K. pneumoniae (1)<br>E. coli (1)<br>P. mirabilis (1)<br>P. rettgeri (1)<br>Morganella morganii (1)</td><td>5</td><td>5</td><td>Carbapenemases</td><td>bla<sub>NDM-1</sub> (5)</td><td>[61]</td></tr><tr><td></td><td></td><td>M. morganii</td><td>1</td><td>1</td><td></td><td></td><td></td></tr><tr><td rowspan="2">Lebanon</td><td>2014</td><td>Clinical isolates</td><td>Enterobacteriaceae</td><td>153</td><td>153</td><td>Carbapenemases</td><td>bla<sub>NDM-1</sub> (1)</td><td>[62]</td></tr><tr><td>2012–2015</td><td>Clinical isolates</td><td></td><td></td><td></td><td>ESBL<br>Aminoglycosides<br>Fluoroquinolones</td><td>In progress</td><td>Unpublished results</td></tr><tr><td rowspan="2">2013</td><td></td><td>Clinical isolates</td><td>P. aeruginosa</td><td>35</td><td>35</td><td>Carbapenemases<br>Cephalosporinases</td><td>bla<sub>VIM-2</sub> (16)<br>bla<sub>IMP-15</sub> (2)<br>ampC (8)</td><td>[14]</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td>ESBL<br>Carbapenemases</td><td>bla<sub>OXA-48</sub> (1)<br>bla<sub>CTX-M-14</sub> (1)<br>bla<sub>TEM-1</sub> (1)</td><td>[63]</td></tr><tr><td rowspan="2">2013</td><td></td><td>Animal isolates</td><td>E. coli</td><td>1</td><td>1</td><td>Carbapenemases</td><td>bla<sub>OXA-23</sub> (4)<br>bla<sub>OXA-58</sub> (1)<br>bla<sub>VIM-2</sub> (4)</td><td>[64]</td></tr><tr><td></td><td></td><td></td><td></td><td></td><td>Carbapenemases<br>Cephalosporinase<br>BLSE<br>MLSBR<br>Chloramphenicol<br>Fluoroquinolones</td><td>bla<sub>OXA-48</sub><br>ampC<br>ampH<br>bla<sub>TEM-166</sub><br>macA<br>macB<br>cmr<br>cat<br>gyrA mutated</td><td>[10]</td></tr><tr><td>2015</td><td>Animal isolates</td><td>E. coli</td><td></td><td>1</td><td>1</td><td>ESBL<br>Coli R<br>Cephalosporinase<br>Coli R</td><td>bla<sub>TEM-135-like</sub> (1)<br>mcr-1 (1)</td><td>[18]</td></tr><tr><td>2015</td><td>Animal isolates</td><td>E. cloacae</td><td></td><td>1</td><td>1</td><td>ESBL<br>Coli R<br>Cephalosporinases</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2015</td><td>Animal isolates</td><td>E. coli (217)<br>K. pneumoniae (8)<br>Escherichia fergusonii (1)</td><td></td><td>235</td><td>235</td><td></td><td>In progress</td><td>Unpublished results</td></tr></tbody></table>
<table><tbody><tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>2017</td><td>Animal isolates</td><td>A. baumannii (1)<br/>P. mirabilis (3)<br/>E. cloacae (2)<br/>E. coli (105)<br/>E. fergusonii (2)<br/>K. pneumoniae (4)</td><td>111</td><td>111</td><td>ESBL<br/>Cephalosporinase<br/>Coli R</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2017</td><td>Animal (346)<br/>Environmental (53)<br/>Human (11) isolates</td><td>E. coli (341)<br/>K. pneumoniae (31)<br/>Enterobacter asburiae (1)<br/>Stenotrophomonas<br/>maltophilia (4)<br/>Serratia rubidae (1)<br/>A. baumannii (4)<br/>Acinetobacter<br/>genomospecies (4)<br/>Pseudomonas spp. (8)<br/>Ochrobactrum spp. (1)<br/>E. cloacae (4)</td><td>399</td><td>399</td><td>ESBL<br/>Cephalosporinase<br/>Coli R</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2016–2017</td><td>Clinical isolates</td><td>Enterobacter faecium</td><td>4</td><td>4</td><td>Glycopeptides</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2016</td><td>Clinical isolates</td><td>A. baumannii</td><td>31</td><td>31</td><td>ESBL<br/>Carbapenemases</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2016</td><td>Clinical isolates</td><td>Campylobacter jejuni</td><td>1</td><td>1</td><td>ESBL<br/>Carbapenemases</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2010–2016</td><td>Clinical isolates</td><td>E. coli</td><td>43</td><td>43</td><td>ESBL</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2015</td><td>Clinical isolates</td><td>K. pneumoniae</td><td>3</td><td>3</td><td>ESBL<br/>Coli R</td><td>In progress<br/>bla<sub>CTX-M-15</sub> + bla<sub>TEM-12</sub> + bla<sub>SHV-5</sub> (2)<br/>bla<sub>SHV-5</sub> (1)<br/>Mutation mgb (2)<br/>phoQ (1)<br/>pmrA (1)</td><td>[65]</td></tr><tr><td>2016–2017</td><td>Clinical isolates</td><td>Enterobacteriaceae (8)<br/>P. aeruginosa (1)</td><td>9</td><td>9</td><td>ESBL<br/>Carbapenemases<br/>Coli R</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2012</td><td>Clinical isolates</td><td>A. baumannii</td><td>4</td><td>4</td><td>Carbapenemases</td><td>bla<sub>NDM-1</sub> (4)<br/>bla<sub>OXA-94</sub> (4)</td><td>[15]</td></tr><tr><td>2016</td><td>Clinical isolates</td><td>Neisseria meningitidis</td><td>58</td><td>1</td><td>In progress</td><td>In progress</td><td>Unpublished results</td></tr><tr><td>2013–2014</td><td>Clinical isolates</td><td>P. aeruginosa (24)<br/>A. baumannii (25)</td><td>49</td><td>43</td><td>Carbapenemases</td><td>bla<sub>OXA-24</sub> (3)<br/>bla<sub>OXA-23</sub> (19)<br/>bla<sub>VIM-2</sub> (19)</td><td>[66]</td></tr><tr><td>2015</td><td>Clinical isolates</td><td>A. baumannii</td><td>36</td><td>36</td><td>Carbapenemases</td><td>bla<sub>OXA-23</sub> (29)<br/>bla<sub>NDM-1</sub> (8)<br/>bla<sub>NDM-1</sub> (36)</td><td>[67]</td></tr><tr><td>Nigeria</td><td>2012<br/>2012–2013<br/>2012</td><td>Clinical isolates<br/>Clinical isolates<br/>Animal (2) and human (1)<br/>isolates</td><td>A. baumannii<br/>Klebsiella spp.<br/>E. coli</td><td>3<br/>139<br/>3</td><td>3<br/>1<br/>1</td><td>Carbapenemases<br/>Coli R<br/>Coli R</td><td>bla<sub>OXA-23</sub> (3)<br/>mgb (1)<br/>mcr-1 (1)</td><td>[68]<br/>[69]<br/>[70]</td></tr><tr><td>Qatar<br/>Saudi Arabia</td><td>2011–2012<br/>2013–2014</td><td>Clinical isolates<br/>Clinical isolates</td><td>A. baumannii<br/>E. coli (10)<br/>K. pneumoniae (1)</td><td>48<br/>11</td><td>48<br/>11</td><td>Carbapenemases<br/>Coli R<br/>ESBL</td><td>bla<sub>OXA-23</sub> (48)<br/>mcr-1 (10)<br/>bla<sub>TEM-1</sub> (10)<br/>bla<sub>SHV-1</sub> (1)<br/>bla<sub>CTX-M-15</sub> (1)<br/>oxa-72 (1)</td><td>[68]<br/>[71]</td></tr><tr><td>2014</td><td>Clinical isolates</td><td>A. baumannii</td><td>42</td><td>28</td><td>Carbapenemases<br/>ESBL<br/>Aminoglycosides</td><td>bla<sub>NDM-5</sub> (1)<br/>bla<sub>NDM-1</sub> (1)<br/>bla<sub>OXA-48</sub> (1)<br/>bla<sub>OXA-58</sub> (22)<br/>bla<sub>OXA-51</sub> + bla<sub>OXA-72</sub> (1)<br/>bla<sub>NDM-5</sub> + bla<sub>CTX-M-15</sub> + bla<sub>TEM-1</sub> + aadA2 (1)<br/>bla<sub>NDM-5</sub> + bla<sub>TEM-1</sub> + aadA2 (1)</td><td>[72]</td></tr><tr><td>2013–2014</td><td>Clinical isolates</td><td>E. coli (23)<br/>K. pneumoniae (5)</td><td>28</td><td>28</td><td>ESBL</td><td>bla<sub>CTX-M</sub> (27)<br/>bla<sub>TEM</sub> (19)<br/>bla<sub>SHV</sub> (4)</td><td>[73]</td></tr><tr><td>2013–2014</td><td>Clinical isolates</td><td>Samples</td><td>218</td><td>73</td><td>ESBL</td><td>bla<sub>CTX-M</sub> (73)</td><td>[74]<br/>[75]</td></tr></tbody></table>

Continued
<table><caption>TABLE I. Continued</caption><thead><tr><th>Country</th><th>Year</th><th>Strain type</th><th>Studied strains</th><th>No. of samples</th><th>No. of positive samples with an AR gene detected</th><th>Tested phenotype</th><th>Type of antibiotic resistance genes detected (n)</th><th>Study</th></tr></thead><tbody><tr><td rowspan="3">Senegal</td><td>2011</td><td>Clinical isolates</td><td>A. baumannii</td><td>5</td><td>3</td><td>Carbapenemases</td><td>bla<sub>OXA-23</sub> (3)</td><td>[76]</td></tr><tr><td>2014</td><td>Clinical isolates</td><td>M. morganii</td><td>112</td><td>112</td><td>ESBL</td><td>bla<sub>CTX</sub> (1/2)</td><td>[77]</td></tr><tr><td>2015–2017</td><td>Clinical isolates</td><td>Enterobacteriaceae</td><td>161</td><td>120</td><td>Carbapenemases<br>ESBL<br>Aminoglycosides<br>Fluoroquinolones</td><td>bla<sub>TEM</sub> (86)<br>bla<sub>SUV</sub> (63)<br>In progress</td><td>Unpublished results</td></tr><tr><td rowspan="3">Spain</td><td>2015</td><td>Clinical isolates</td><td>Acinetobacter nosocomialis</td><td>1</td><td>1</td><td>Coli R</td><td>bla<sub>OXA-51</sub> + bla<sub>OXA-23</sub> (25)</td><td>[78]</td></tr><tr><td>2013–2016</td><td>Clinical isolates</td><td>A. baumannii</td><td>25</td><td>25</td><td>Coli R</td><td>bla<sub>CTX</sub> (47)</td><td>[79]</td></tr><tr><td>2015</td><td>Clinical isolates</td><td>E. coli (51)<br>K. pneumoniae (36)</td><td>87</td><td>68</td><td>Carbapenemases<br>ESBL</td><td>bla<sub>TEM-1</sub> (31)<br>bla<sub>SUV</sub> (18)<br>bla<sub>OXA</sub> (10)</td><td>[80]</td></tr><tr><td rowspan="2">Yemen</td><td rowspan="2">2013</td><td rowspan="2">Clinical isolates</td><td rowspan="2">A. baumannii</td><td rowspan="2">3</td><td rowspan="2">3</td><td>Carbapenemases<br>Aminoglycosides<br>Fluoroquinolones</td><td>bla<sub>OXA-23</sub> (3)<br>armA (3)<br>aac(6')Ib (1)<br>Mutated gyrA (3)</td><td rowspan="2">[81]</td></tr><tr><td>Total studied samples</td><td>7280</td><td>Total studied strains</td><td>6359</td><td>Total no. of publications</td><td>97</td></tr></tbody></table>

Samples' indicates that no strains were isolated but samples were directly tested by PCR. Coli R, colistin resistance; ESBL, extended-spectrum β-lactamase; HLP, high-level penicillinase; Methi R, methicillin resistance; MLSB, macrolide-lincosamide-streptogramin B phenotype; Vanco R, vancomycin resistance.

Senegal (n = 278; 3.8%) (Fig. 1(A)). From those 7280 samples, 6359 bacterial isolates were cultured and analysed phenotypically (bacterial identification by MALDI-TOF MS and AST) and genetically (molecular detection of antibiotic resistance genes).

Bacterial genera studied included Enterobacteriaceae (1296 Klebsiella and 1053 Escherichia), followed by Acinetobacter (n = 1176) or other Gram-negative organisms (n = 1774 including bacteria of the genera Serratia, Salmonella, Enterobacter, Salmonella, Raoultella and Shewanella) and Pseudomonas (n = 289) (Fig. 1(B)). Gram-positive strains were represented with 771 strains (12%), including bacteria of the genera Enterococcus, Staphylococcus or Streptococcus (Fig. 1(B)).

All these studies allowed the detection and characterization of specific antibiotic resistance genes in multidrug-resistant bacteria from these genera and led to 97 scientific international indexed publications. Table 1 lists the publications and findings of specific antibiotic resistance determinants by country and bacterial species.

The main antibiotic resistance determinants detected and characterized were extended-spectrum β-lactamases (ESBLs) and carbapenemases including bla<sub>CTX-M</sub>, bla<sub>SHV</sub>, bla<sub>TEM</sub> [12], bla<sub>OXA-48</sub> [13], bla<sub>NDM</sub> [82] and bla<sub>VIM</sub> [14] genes. Genes encoding for resistance to aminoglycosides were also reported, including, for example, armA or aac(6')-Ib in Acinetobacter baumannii [81]. Resistance to colistin mediated by the newly plasmid-mediated mcr-1 gene in human and animal isolates has been tested to date in 21 studies from eight countries (Algeria, Greece, Israel, Lebanon, Nigeria, Saudi Arabia, Senegal and Spain), leading to ten scientific publications (Table 1). An overview of the global distribution of the main findings of antibiotic resistance determinants in the 7280 samples studied per country and type of samples is provided in the map in Fig. 2.

Discussion

Here we show the unique role of IHU-MI in training about 100 students working in the field of antibiotic resistance from the Mediterranean basin and Africa over the last 6 years. This has led to the description and surveillance of new mechanisms of resistance to antibiotics in 15 various countries reported in 97 scientific publications, including 24 different peer-reviewed journals. The majority of the publications have reported the first detection of antibiotic resistance genes, mainly ESBLs [47], carbapenemases [15,16,31] and the mcr-1 plasmid-mediated colistin resistance gene [17,18,22] in these countries in both humans and animals. One of the main contributions in the field is the description of a strong link between antibiotic consumption in animals and emergence and spread of antibiotic resistance genes in animals as well as the transfer to humans [83].
<figure><img src="image_5.png" /><figcaption>FIG. 2. Global distribution of samples in Mediterranean basin and African countries.</figcaption></figure>

Antibiotics are widely used in agricultural settings in these countries, without clear control policies; this situation has affected human health and is implicated in the evolution of new mechanisms of resistance [84]. Epidemiologic descriptions are essential, and our results confirmed that surveillance should continue in Africa and in the Mediterranean basin to monitor and control the emergence and spread of antibiotic resistance genes. Thanks to these students and their training at the IHU-MI, the institute has created a unique collaborative network for surveillance and study of antibiotic resistance in Africa and in the Mediterranean basin because most of these students returned to their country of origin and created microbiology laboratories to study and survey antibiotic resistance in collaboration with the IHU-MI institute. Further engagements with key individuals are ongoing to create new partnerships to study antibiotic resistance in humans and animals in Italy, Morocco, Turkey and in the Balkans, and should be reinforced in Egypt and Libya as well as the Middle East, although the political situation is currently complex. The current migrant crisis in Europe should prompt us to survey antibiotic resistance in humans and animals from these countries, including Syria and Iraq, to avoid the possible spreading of specific clones, as previously reported in Greece [85,86] and Israel [87] for Klebsiella pneumoniae carbapenemase producers.

Because of its special location as a seaport in the Mediterranean basin, Marseille has historically always been a critical place for the entrance of infectious diseases such as plague or cholera [88]. Because antibiotic-resistant bacteria and antibiotic resistance genes that could spread in the Mediterranean basin do not have borders, the IHU-MI in Marseille plays a critical role in the surveillance of resistance in these areas as

well as in African countries that historically have links to France. Thus, over the last 6 years, the institute has become a reference centre for the surveillance of antibiotic resistance and the training of students from countries in the Mediterranean basin and Africa. Such a collaborative network will expand in the future, permitting real-time surveillance of antibiotic resistance determinants that may emerge and spread in these areas [89].

## Acknowledgement

We are grateful to IHU-MI.

## Conflict of interest

None declared.

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