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.

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.

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 antibiotic 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 antibiotic 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 creation 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 resistance 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 according to their field of research (humans, animals or the environment). Initially there was no rationale for the recruitment 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 mechanism of resistance. Specific panels of antibiotics were tested according to the bacteria species (e.g. Enterobacteriaceae, nonfermentative Gram-negative bacteria, Gram-positive bacteria). 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 presented 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 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).

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.

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.

Table 1

Samples and publications studied according to countries in Institut Hospitalo-Universitaire Méditerranée Infection from 2011 to 2017

Country	Year	Strain type	Studied strains	No. of samples	No. of positive samples with an AR gene detected	Tested phenotype	Type of antibiotic resistance genes detected (n)	Study
Algeria	2008–2011	Clinical isolates	Klebsiella pneumoniae	211	194	ESBLCephalosporinasesPenicillinaseHLP		[19]
	2008–2012	Clinical isolates	K. pneumoniae	221	190	ESBLCephalosporinasesPenicillinaseHLP	blaTEM (146)blaSHV (154)blaCTX-M (130)	[20]
	2017	Animal (45) and human (37) isolates	Salmonella spp.	92	18	ESBL	blaCTX-M-1 (12)blaCTX-M-15 (5)blaTEM (8)	[21]
	2011	Clinical isolates	Escherichia coli	1	1	Coli R	mcr-1	[22]
	2015	Animal isolates	E. coli (30)K. pneumoniae (17)	47	47	Coli RESBL	blaCTX-M-15 (47)blaTEM-1 (25)	[23]
	2014	Clinical and environmental isolates	K. pneumoniaeEnterobacter cloacaeAcinetobacter baumanniiPseudomonas aeruginosa	89	32	ESBLCarbapenemases	blaOXA-48 (5)blaNDM-1 (7)blaOXA-43 (2)blaTEM (6)blaSHV + blaCTX-M (7)	[24]
	2013–2015	Environmental isolates	A. baumannii	1	1	CarbapenemasesESBLFluoroquinolones	blaNDM-1 (1)	[25]
	2010–2013	Clinical isolates	Enterococcus spp.	85	85	Vanco R	vanC	[26]
	2010–2013	Clinical isolates	A. baumannii	43	43	Carbapenemases	blaNDM-1 (7)blaOXA-23 (28)blaOXA-24 (1)blaOXA-58 (6)blaOXA-51 (43)blaOXA-23 + blaNDM-1 (2)blaOXA-58 + blaNDM-1 (1)	[27]
	2013–2015	Clinical isolates	Enterobacteriaceae (161)P. aeruginosa (18)A. baumannii (7)	186	36	CarbapenemasesESBL	blaOXA-48 (2)blaVIM-4 (2)blaNDM-1 (2)blaOXA-23 (5)	[28]
	2011–2013	Environmental isolates	A. baumannii	67	61	Carbapenemases	blaOXA-23 (29)blaNDM-1 (32)	[29]
	2013–2014	Clinical isolates	Streptococcus agalactiae	93	74	MLSB R	ermB (18)ermAmef(A)mef(E)	[30]
	2015	Animal isolates	E. coli	1	1	Carbapenemase	blaNDM-5 (1)	[31]
	2014–2016	Animal isolates	Enterobacteriaceae	380	3	CarbapenemasesESBLCephalosporinases	blaOXA-48 (3)	[32]
	2012–2014	Environmental isolates	K. pneumoniae	44	44	ESBLCephalosporinasesFluoroquinolonesAminoglycosides	blaCTX-M-15 (41)blaCTX-M-3 (3)	[33]
	2014–2015	Animal isolates	Samples	503	389	CarbapenemasesESBL	blaTEM (128)blaSHV (83)blaCTX-M (46)blaOXA-58 (132)	[34]
	2015	Animal isolates	Enterobacteriaceae	32	32	CarbapenemasesESBL	blaOXA-48 (32)blaCTX-M-15 (1)blaTEM (2)	[35]
	2013–2014	Animal (3) and human (1) isolates	E. coli	4	4	Coli R	mcr-1 (4)	[36]
	2016	Animal isolates	E. coli	8	8	Coli R	In progress	Unpublished results
	2017	Animal (4) and environmental (5) isolates	E. coli (8)E. cloacae (1)	9	9	Coli R	In progress	Unpublished results
	2016	Clinical isolates	K. pneumoniae	3	3	Coli R	In progress	Unpublished results
	2015–2016	Environmental isolates	Staphylococcus aureus	200	153	Methi R	In progress	Unpublished results
	2011–2013	Clinical isolates	A. baumannii	47	47	CarbapenemasesAminoglycosidesFluoroquinolones	blaOXA-23 (33)blaOXA-24 (10)blaNDM (11)armA (4)aph(3′)VI (24)aadA (6)ant(2′)I (10)aac(3)Ia (33)Mutation in gyrA, parC (45)	[37]
	2013–2014	Clinical isolates	A. baumannii	12	12	Coli RCarbapenemases	blaOXA-24 (4)blaOXA-23 (6)blaOXA-51 (12)blaNDM-1 (2)	[38]
	2016–2017	Animal isolates	Samples	200	4	ESBL	In progress	Unpublished results
	2013	Clinical isolates	Enterococcus hirae	1	1			[39]
	2016	Clinical isolates	K. pneumoniae (20)A. baumannii (12)P. aeruginosa (9)E. coli (27)	68	68	CarbapenemasesESBL	In progress	Unpublished results
	2011–2012	Clinical isolates	A. baumannii	30	24	Carbapenemases	blaOXA-23 (22)blaOXA-58 (1)blaOXA-23 + blaOXA-58 (1)	[40]
	2011	Clinical isolates	P. aeruginosa	17	17	Carbapenemases	blaVIM-2 (14)Mutation in oprD (3)	[41]
	2012–2013	Clinical isolates	E. coli	105	3	CarbapenemasesESBLAminoglycosidesFluoroquinolones	blaNDM-5 (3)blaTEM (3)blaCTX-M (3)aadA (3)	[42]
	2010–2011	Clinical isolates	E. coli (3)K. pneumoniae (24)E. cloacae (11)Serratia marcescens (4)	42	39	ESBL	blaCTX-M (10)blaTEM (14)blaSHV (15)	[43]
	2010–2011	Clinical isolates	K. pneumoniae	100	100	ESBLAminoglycosidesFluoroquinolones	blaCTX-M (76)blaTEM (74)blaSHV (73)armA (23)aadA (35)aac(6′)Ib (50)qnrB (22)	[44]
	2013	Animal isolates	Acinetobacter spp.	33	4	Carbapenemases	blaOXA-23 + blaOXA-58 + blaOXA-51 (1)blaOXA-58 + blaOXA-51 (1)blaOXA-58 (2)	[45]
	2014–2015	Clinical isolates	K. pneumoniae	7	7	ESBLCarbapenemases	blaOXA-48 + blaCTX-M-15 + blaSHV-1 + blaTEM-1D (7)	[46]
	2015	Environmental isolates	Enterobacteriaceae	12	9	CarbapenemasesESBL	blaCTX-M-15 (9)blaOXA-48 (1)blaTEM (1)	[47]
	2015	Animal isolates	Pseudomonas putida	1	1	CarbapenemasesESBL	blaVIM-2	[48]
	2017	Clinical isolates	K. pneumoniae	1	1	CarbapenemasesESBL	blaOXA-48 (1)blaSHV-27 (1)	[49]
	2010–2011	Clinical isolates	A. baumannii	71	71	Carbapenemases	blaOXA-23 (31)blaOXA-24 (5)blaOXA-51 (71)	[50]
	2010–2011	Clinical isolates	A. baumannii	71	71	CarbapenemasesESBLAminoglycosidesFluoroquinolones	blaTEM (53)ampC (69)aph(3′)VI (36)aadA (45)ant(2′)I (10)aac(3)Ia (64)aac(6′)Ib (3)Mutation gyrA, parC (67)	[51]
	2013	Clinical isolates	K. pneumoniae	1	1	CarbapenemasesESBLAminoglycosidesFluoroquinolones	blaKPC-3blaTEMblaSHVaac(6′)IbaadA	[52]
	2015	Environmental isolates	E. coli (12)K. pneumoniae (3)Raoultella ornithinolytica (3)Citrobacter freundii (1)Citrobacter braakii (1)	20	20	ESBLCarbapenemases	blaOXA-48 (17)blaOXA-244 (3)blaTEM-1 (9)blaCTX-M-15 + blaTEM-1 (3)	[13]
	2016	Environmental isolates	K. pneumoniae	87	3	ESBLCarbapenemases	blaOXA-48 (3)blaTEM-1 (1)	[16]
	2014	Animal isolates	E. coli	20	20	CarbapenemasesESBLAminoglycosides	blaTEM-1 (20)blaCTX-M-1 (2)blaSHV-12 (14)CMY-2 (4)aadA (20)	[12]
	2015	Environmental isolates	Shewanella xiamenensis	4	4	Carbapenemases	blaOXA-48 (1)blaOXA-199 (1)blaOXA-181 (2)	[11]
	2016	Animal isolates	Enterobacteriaceae	86	1	Coli R	mcr-1blaCTX-M-15blaTEM-1qnrB19	[17]
	2014	Clinical isolates	S. aureus	250	171	Methi R	In progress	Unpublished results
	2005–2007	Clinical isolates	S. aureus	64	64	Methi R	mecA (64)	[53]
	2011	Clinical isolates	Proteus mirablisMorganella spp.Providencia spp.	106	72	ESBLCarbapenemases Aminoglycosides Fluoroquinolones	In progress	Unpublished results
	2014–2015	Clinical (60) and environmental (39) isolates	EnterobacteriaceaeAcinetobacter spp.	99	10	CarbapenemasesESBLCephalosporinasesAminoglycosides	blaNDM-1 (5)blaOXA-23 (3)blaOXA-48 (2)blaSHV-148 + blaTEM-163 (2)aph(3′)VI–ant(2″)I (2)aac(3)Ia aadA (3)AME-encoding genes (5)	[54]
	2009–2012	Clinical isolates	P. aeruginosa	89	39	CarbapenemasesAminoglycosides	blaVIM-2 (2)aadA (10)aac(3)Ia (3)	[55]
	2008–2012	Clinical isolates	Acinetobacter spp.	113	113	CarbapenemasesESBLAminoglycosidesFluoroquinolones	blaOXA-23 (40)blaOXA-24 (17)blaNDM (5)aph(3′)VI (70)aadA (57)ant(2′)I (60)aac(3)Ia (77)aac(6′)Ib (1)	[56]
	2012	Clinical isolates	A. baumannii	123	77	CarbapenemasesESBL	blaOXA-23 (40)blaOXA-24 (3)blaOXA-23 + blaOXA-24 (3)	[57]
Benin	2015	Clinical isolates	Staphylococcus saprophyticus (31)S. aureus (21)Staphylococcus sciuri (17)Staphylococcus conhii (5)Staphylococcus haemolyticus (2)Staphylococcus xylosus (1)Staphylococcus hominis (1)	78	21	Methi R	mecA (19)	[58]
	2015	Clinical isolates	Enterobacteriaceae	157	103	ESBLCarbapenemases	In progress	Unpublished results
	2016	Clinical isolates	P. aeruginosa	3	3	Carbapenemases	In progress	Unpublished results
Egypt	2012–2013	Clinical isolates	A. baumannii	150	150	CarbapenemasesAminoglycosides	blaNDM-1 (59)blaOXA-23 (115)armA (141)blaOXA-51 (150)blaNDM-1 + blaOXA-23 (53)armA + blaNDM-1 + blaOXA-23 (52)	[59]
Greece	2013–2017	Clinical isolates	P. mirablis (4)P. putida (1)C. freundii (1)Enterobacter aerogenes (2)Providencia stuartii (8)P. aeruginosa (79)A. baumannii (158)E. cloacae (10)E. coli (33)K. pneumoniae (314)	610	610	CarbapenemasesESBLColi RFluoroquinolones	In progress	Unpublished results
Israel	2011	Clinical isolates	Providencia rettgeri	1	1	Carbapenemase	blaNDM-1 (1)	[60]
	2008–2011	Clinical isolates	K. pneumoniae	15	15	CarbapenemasesColi RAminoglycosides	In progress	Unpublished results
	2010–2011	Clinical isolates	K. pneumoniae (1)E. coli (1)P. mirabilis (1)P. rettgeri (1)Morganella morganii (1)	5	5	Carbapenemases	blaNDM-1 (5)	[61]
	2014	Clinical isolates	M. morganii	1	1	Carbapenemases	blaNDM-1 (1)	[62]
Ivory Coast	2012–2015	Clinical isolates	Enterobacteriaceae	153	153	ESBLAminoglycosidesFluoroquinolones	In progress	Unpublished results
Lebanon	2013	Clinical isolates	P. aeruginosa	35	35	CarbapenemasesCephalosporinases	blaVIM-2 (16)blaIMP-15 (2)ampC (8)	[14]
	2013	Animal isolates	E. coli	1	1	ESBLCarbapenemases	blaOXA-48 (1)blaCTX-M-14 (1)blaTEM-1 (1)	[63]
	2013	Animal isolates	P. aeruginosa (4)A. baumannii (5)	9	9	Carbapenemases	blaOXA-23 (4)blaOXA-58 (1)blaVIM-2 (4)	[64]
	2015	Clinical isolates	R. ornithinolytica	1	1	CarbapenemasesCephalosporinaseBLSEMLSB RChloramphenicolFluoroquinolones	blaOXA-48ampCampHblaTEM-166macAmacBcmrcatgyrA mutated	[10]
	2015	Animal isolates	E. coli	1	1	ESBLColi R	blaTEM-135-like (1)mcr-1 (1)	[18]
	2015	Animal isolates	E. cloacae	1	1	CephalosporinaseColi R	In progress	Unpublished results
	2015	Animal isolates	E. coli (217)K. pneumoniae (8)Escherichia fergusonii (1)A. baumannii (1)P. mirabilis (3)E. cloacae (2)	235	235	ESBLCephalosporinases	In progress	Unpublished results
	2017	Animal isolates	E. coli (105)E. fergusonii (2)K. pneumoniae (4)	111	111	ESBLCephalosporinaseColi R	In progress	Unpublished results
	2017	Animal (346)Environmental (53)Human (11) isolates	E. coli (341)K. pneumoniae (31)Enterobacter asburiae (1)Stenotrophomonas maltophilia (4)Serratia rubidae (1)A. baumannii (4)Acinetobacter genomospecies (4)Pseudomonas spp. (8)Ochrobactrum spp. (1)E. cloacae (4)	399	399	ESBLCephalosporinaseColi R	In progress	Unpublished results
	2016–2017	Clinical isolates	Enterobacter faecium	4	4	Glycopeptides	In progress	Unpublished results
	2016	Clinical isolates	A. baumannii	31	31	ESBLCarbapenemases	In progress	Unpublished results
	2016	Clinical isolates	Campylobacter jejuni	1	1	ESBLCarbapenemases	In progress	Unpublished results
	2010–2016	Clinical isolates	E. coli	43	43	ESBL	In progress	Unpublished results
	2015	Clinical isolates	K. pneumoniae	3	3	ESBLColi R	blaCTX-M-15 + blaTEM-12 + blaSHV-5 (2)blaSHV-5 (1)Mutation mgrB (2)phoQ (1)pmrA (1)	[65]
	2016–2017	Clinical isolates	Enterobacteriaceae (8)P. aeruginosa (1)	9	9	ESBLCarbapenemasesColi R	In progress	Unpublished results
	2012	Clinical isolates	A. baumannii	4	4	Carbapenemases	blaNDM-1 (4)blaOXA-94 (4)	[15]
	2016	Clinical isolates	Neisseria meningitidis	58	1		In progress	Unpublished results
Libya	2013–2014	Clinical isolates	P. aeruginosa (24)A. baumannii (25)	49	43	Carbapenemases	blaOXA-24 (3)blaOXA-23 (19)blaVIM-2 (19)	[66]
	2015	Clinical isolates	A. baumannii	36	36	Carbapenemases	blaOXA-23 (29)blaNDM-1 (8)blaNDM (36)	[67]
Nigeria	2012	Clinical isolates	A. baumannii	3	3	Carbapenemases	blaOXA-23 (3)	[68]
	2012–2013	Clinical isolates	Klebsiella spp.	139	1	Coli R	mgrB (1)	[69]
	2012	Animal (2) and human (1) isolates	E. coli	3	1	Coli R	mcr-1 (1)	[70]
Qatar	2011–2012	Clinical isolates	A. baumannii	48	48	Carbapenemases	blaOXA-23 (48)	[68]
Saudi Arabia	2013–2014	Clinical isolates	E. coli (10)K. pneumoniae (1)	11	11	Coli RESBL	mcr-1 (11)blaTEM-1 (10)blaSHV-1 (1)blaCTX-M-15 (1)	[71]
	2014	Clinical isolates	A. baumannii	42	28	CarbapenemasesESBLAminoglycosides	oxa-72 (1)blaNDM-5 (1)blaNDM-1 (1)blaOXA-48 (1)blaOXA-58 (22)blaOXA-51 + blaOXA-72 (1)blaNDM-5 + blaCTX-M-15 + blaTEM-1 + aadA2 (1)blaNDM-5 + blaTEM-1 + aadA2 (1)	[72]
	2013–2014	Clinical isolates	E. coli (23)K. pneumoniae (5)	28	28	ESBL	blaCTX-M (27)blaTEM (19)blaSHV (4)	[73]
	2013–2014	Clinical isolates						[74]
	2013–2014	Clinical isolates	Samples	218	73	ESBL	blaCTX-M (73)	[75]
Senegal	2011	Clinical isolates	A. baumannii	5	3	Carbapenemases	blaOXA-23 (3)	[76]
	2014	Clinical isolates	M. morganii	112	112	ESBL	blaCTX (112)blaTEM (86)blaSHV (63)	[77]
	2015–2017	Clinical isolates	Enterobacteriaceae	161	120	CarbapenemasesESBLAminoglycosidesFluoroquinolonesColi R	In progress	Unpublished results
Spain	2015	Clinical isolates	Acinetobacter nosocomialis	1	1	Coli R		[78]
Tunisia	2013–2016	Clinical isolates	A. baumannii	25	25	Carbapenemases	blaOXA-51 + blaOXA-23 (25)blaOXA-58 (1)	[79]
	2015	Clinical isolates	E. coli (51)K. pneumoniae (36)	87	68	CarbapenemasesESBL	blaCTX (47)blaTEM-1 (31)blaSHV (18)blaOXA (10)	[80]
Yemen	2013	Clinical isolates	A. baumannii	3	3	CarbapenemasesAminoglycosidesFluoroquinolones	blaOXA-23 (3)armA (3)aac(6′)Ib (1)Mutated gyrA (3)	[81]
			Total studied samples	7280			Total no. of publications	97
			Total studied strains	6359

‘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.

The main antibiotic resistance determinants detected and characterized were extended-spectrum β-lactamases (ESBLs) and carbapenemases including blaCTX-M, blaSHV, blaTEM [12], blaOXA-48 [13], blaNDM [82] and blaVIM [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.

Fig. 2

Global distribution of samples in Mediterranean basin and African countries.

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].

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].