Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of infections. It is well recognized that nasal carriage of S. aureus represents a potent and increasingly prevalent risk factor for subsequent S. aureus infection. However, in Madagascar no data exist concerning this nasal carriage of S. aureus. Methodology: Nasal swabs from 304 different patients attending the Laboratory of Training and Research in Medical Biology of Madagascar were cultured for methicillin sensitive (MSSA) and MRSA. Results: One hundred and sixteen patients had S. aureus in their noses (38.16 ± 5.46%) of whom 45 (14.80 ± 3.99%) had MRSA. A risk factor for MSSA nasal carriage included a history of hospitalization when antibiotics were administered (odds ratio [OR] 2.25, 1.09 -4.64). Among MRSA nasal isolates, high rate of resistance to other antibiotics was observed, particularly for trimethoprim-sulfamethoxazole (68.89%), erythromycin (66.67%) and ofloxacin (53.33%). Conclusion: Our data showed a high rate of MRSA nasal carriage and a high rate of multidrug resistance. A strategic policy against the spread of multidrug resistant strains is desirable.

Antimicrobial resistance is a major public health concern worldwide affecting humans, animals and the environment. However, data is lacking especially in developing countries. Thus, the World Health Organization developed a One-Health surveillance project called Tricycle focusing on the prevalence of ESBL-producing Escherichia coli in humans, animals, and the environment. Here we present the first results of the human community component of Tricycle in Madagascar. From July 2018 to April 2019, rectal swabs from 492 pregnant women from Antananarivo, Mahajanga, Ambatondrazaka, and Toamasina were tested for ESBL-E. coli carriage. Demographic, sociological and environmental risk factors were investigated, and E. coli isolates were characterized (antibiotic susceptibility, resistance and virulence genes, plasmids, and genomic diversity). ESBL-E. coli prevalence carriage in pregnant women was 34% varying from 12% (Toamasina) to 65% (Ambatondrazaka). The main risk factor associated with ESBL-E. coli carriage was the rainy season (OR = 2.9, 95% CI 1.3–5.6, p = 0.009). Whole genome sequencing was performed on 168 isolates from 144 participants. blaCTX–M–15 was the most frequent ESBL gene (86%). One isolate was resistant to carbapenems and carried the blaNDM–5 gene. Most isolates belonged to commensalism associated phylogenetic groups A, B1, and C (90%) and marginally to extra-intestinal virulence associated phylogenetic groups B2, D and F (10%). Multi locus sequence typing showed 67 different sequence types gathered in 17 clonal complexes (STc), the most frequent being STc10/phylogroup A (35%), followed distantly by the emerging STc155/phylogroup B1 (7%), STc38/phylogroup D (4%) and STc131/phylogroup B2 (3%). While a wide diversity of clones has been observed, SNP analysis revealed several genetically close isolates (n = 34/168) which suggests human-to-human transmissions. IncY plasmids were found with an unusual prevalence (23%), all carrying a blaCTX–M–15. Most of them (85%) showed substantial homology (≥85%) suggesting a dissemination of IncY ESBL plasmids in Madagascar. This large-scale study reveals a high prevalence of ESBL-E. coli among pregnant women in four cities in Madagascar associated with warmth and rainfall. It shows the great diversity of E. coli disseminating throughout the country but also transmission of specific clones and spread of plasmids. This highlights the urgent need of public-health interventions to control antibiotic resistance in the country.

IntroductionI’infection urinaire à Escherichia coli est fréquente en milieu hospitalier. Cette étude se propose de décrire les différents phénotypes de résistance des souches d’Escherichia coli afin de surveiller leur émergence.MéthodesIl s’agit d’une étude rétrospective de type descriptif de 102 souches d’Escherchia coli responsables d’infection urinaire sur une période allant du mois de Janvier 2014 au mois d’Octobre 2016 au Laboratoire du Centre Hospitalo-Universitaire Befelatanana Antananarivo.RésultatsLa résistance aux béta-lactamines a identifié des pénicillinases de haut niveau 50% (n=51), des Escherichia coli sécrétrices de Béta-Lactamase à Spectre Etendu E-BLSE 22,5% (n=23), des céphalosporinases de haut niveau 14,7% (n=15), des pénicillinases de bas niveau 5,9% (n=6), des souches sauvages 5,9% (n=6) et une souche d’Escherichia coli hautement résistante émergente. La résistance aux aminosides a concerné 58 (56,9%) phénotypes sauvages, 29 (28,4%) souches sensibles à l’amikacine et 15 (14,7%) résistants à tous les aminosides. La résistance aux fluoroquinolones a identifiée 52 (51%) souches sauvages, 9 (8,8%) souches sensibles à la ciprofloxacine et 41 (40,2%) résistantes à tous les fluoroquinolones. Les femmes (25, 7%) (p= 0,25, NS), les sujets de plus de 60 ans (38,7%) (p=0,02), les sujets hospitalisés dans le service de néphrologie (53,8%) (p=0,04), ayant présenté des troubles urinaires et rénaux (29, 7%) (p= 0,2, NS), ont été les plus affectés par les E-BLSE.ConclusionLa multi-résistance élevée des souches d’Escherichia coli interpelle sur une révision du traitement empirique des infections urinaires.

Background: Antimicrobial resistance is a major public health threat, affecting not only humans but also animals and the environment. Although the "One Health" dimension of resistance is well recognized, data are lacking on the circulation of resistance, particularly in low-income countries. The World Health Organization has proposed a protocol called Tricycle, focusing on extended-spectrum beta-lactamase (ESBL)-Escherichia coli surveillance in the three sectors. We implemented Tricycle in Madagascar to assess ESBL-E. coli prevalence and describe intra- and inter-sector circulation of ESBL-E. coli and plasmids. Methods: 289 pregnant women, 246 farm chickens and 28 surface waters were sampled in Antananarivo (the capital city) area and tested for ESBL-E. coli. Isolates were sequenced by short- (Illumina) and long- (Nanopore) read methods. Findings: ESBL-E. coli prevalence was 29.8%, 56.9% and 100% in pregnant women, chickens, and the environment, respectively. The wet season was associated with higher rates of carriage in humans (OR=3.1, 95%CI 1.8-5.3) and animals (OR=2.8 95%CI 1.7-4.8). Sequencing of 277 non-duplicated isolates (82, 118 and 77 from each sector, respectively) showed high genetic diversity (90 STs identified) with differences between sectors. Single nucleotide polymorphism (SNP) analysis revealed 169/277 (61%) isolates grouped into 44 clusters (≥2 isolates) of closely related isolates (<40 SNPs), of which 24 contained isolates from two sectors and five contained isolates from all three sectors. ESBL genes were all blaCTX-M (77.6% blaCTX-M-15), chromosomally integrated in 57.4% (159/277) of isolates, and plasmidic in 40.8% (113/277). The 114 ESBL-carrying plasmids were mainly IncF (55.2%, n=63) and IncY (36.8%, n=42). The F31/36:A4:B1 (n=13) and F-:A-:B53 (n=8) subtypes, and all IncY plasmids, highly conserved, were observed in isolates of differing genetic backgrounds from all sectors. Interpretation: Despite varying strain population structures in the three sectors, both ESBL-E. coli strains and plasmids are circulating among humans, chickens and the environment in the capital of Madagascar. Funding: Fondation Merieux, INSERM, Universite Paris Cite. Keywords: Extended spectrum beta-lactamase (ESBL), Escherichia coli, Tricycle, One Health, circulation

Two cases of meningitis caused by Streptococcus suis occurred in Madagascar, 1 in 2015 and 1 in 2016. We report the characterization of the novel sequence type, 834, which carried the mrp+/sly+/epf+ virulence marker and a mutation G→T at position 174, leading to a substitution mutS1 to mutS284.