Implementation of the WHO Tricycle protocol for surveillance of extended-spectrum ß-lactamase producing Escherichia coli in humans, chickens, and the environment in Madagascar: a prospective genomic epidemiology study.

BACKGROUND: Antimicrobial resistance (AMR) is a major public health threat, affecting not only people but also animals and the environment. The One Health dimension of AMR is well known; however, data are lacking on the circulation of resistance-conferring genes, particularly in low-income countries. In 2017, WHO proposed a protocol called Tricycle, focusing on extended-spectrum ß-lactamase (ESBL)-Escherichia coli surveillance in the three sectors (humans, animals, and the environment). We implemented Tricycle in Madagascar to assess ESBL-E coli prevalence and describe intrasector and intersector circulation of ESBL-E coli and plasmids. METHODS: In this prospective study, we collected blood culture data from hospitalised patients with a suspected bloodstream infection processed from May 1, 2018, to April 30, 2019, and rectal swabs from healthy pregnant women from July 30, 2018, to April 27, 2019, both from three hospitals in Antananarivo, Madagascar; and caeca from farm chickens and surface waters from the Ikopa river, wastewater, and slaughterhouse effluents in the Antananarivo area, Madagascar, from April 9, 2018, to April 30, 2019. All samples were tested for ESBL-E coli. The genomes of all isolates were sequenced using a short-read method on NextSeq 500 and NovaSeq 6000 platforms (Illumina, San Diego, CA, USA) and those carrying plasmid replicons using an additional long-read method on a MinION platform (Oxford Nanopore Technologies, Oxford, UK). We characterised genomes of isolated strains (sequence type, resistance and virulence gene content, and plasmid replicons). We then compared isolates using the variant calling method (single-nucleotide polymorphism). FINDINGS: Data from 1056 blood cultures were collected and 289 pregnant women, 246 chickens, and 28 surface waters were sampled. Of the blood cultures, 18 contained E coli, of which seven (39%) were ESBL. ESBL-E coli was present in samples from 86 (30%) of 289 pregnant women, 140 (57%) of 246 chickens, and 28 (100%) of 28 surface water samples. The wet season (November to April) was associated with higher rates of carriage in humans (odds ratio 3·08 [1·81-5·27]) and chickens (2·79 [1·65-4·81]). Sequencing of 277 non-duplicated isolates (82 from pregnant women, 118 from chickens, and 77 from environmental samples) showed high genetic diversity (90 sequence types identified) with sector-specific genomic features. Single nucleotide polymorphism (SNP) analysis revealed that 169 (61%) of 277 isolates grouped into 44 clusters (two or more isolates) of closely related isolates (<40 SNPs), of which 24 clusters contained isolates from two sectors and five contained isolates from all three sectors. ESBL genes were all blaCTX-M variants (215 [78%] of 277 being blaCTX-M-15) and were located on a plasmid in 113 (41%) of 277 isolates. These ESBL-carrying plasmids were mainly IncF (63 [55%] of 114; one strain carried two plasmids) and IncY (42 [37%] of 114). The F31/36:A4:B1 (n=13) and F-:A-:B53 (n=8) pMLST subtypes, and the IncY plasmids, which were all highly conserved, were observed in isolates of differing genetic backgrounds from all sectors and were transferable in vitro by conjugation. INTERPRETATION: Despite sector-specific population structures, both ESBL-E coli strains and plasmids are circulating among humans, chickens, and the environment in Antananarivo, Madagascar. The Tricycle protocol can be implemented in a low-income country and represents a powerful tool for investigating dissemination of AMR from a One Health perspective. FUNDING: Fondation Mérieux and INSERM, Université Paris Cité.

Implementation of an antibiotic resistance surveillance tool in Madagascar, the TSARA project: a prospective, observational, multicentre, hospital-based study protocol.

INTRODUCTION: Antimicrobial resistance (AMR) has become a significant public health threat. Without any interventions, it has been modelled that AMR will account for an estimated 10 million deaths annually by 2050, this mainly affects low/middle-income countries. AMR has a systemic negative perspective affecting the overall healthcare system down to the patient's personal outcome. In response to this issue, the WHO urged countries to provide antimicrobial stewardship programmes (ASPs). ASPs in hospitals are a vital component of national action plans for AMR, and have been shown to significantly reduce AMR, in particular in low-income countries such as Madagascar.As part of an ASP, AMR surveillance provides essential information needed to guide medical practice. We developed an AMR surveillance tool-Technique de Surveillance Actualisée de la Résistance aux Antimicrobiens (TSARA)-with the support of the Mérieux Foundation. TSARA combines bacteriological and clinical information to provide a better understanding of the scope and the effects of AMR in Madagascar, where no such surveillance tool exists. METHODS AND ANALYSIS: A prospective, observational, hospital-based study was carried out for data collection using a standardised data collection tool, called TSARA deployed in 2023 in 10 hospitals in Madagascar participating in the national Malagasy laboratory network (Réseau des Laboratoires à Madagascar (RESAMAD)). Any hospitalised patient where the clinician decided to take a bacterial sample is included. As a prospective study, individual isolate-level data and antimicrobial susceptibility information on pathogens were collected routinely from the bacteriology laboratory and compiled with clinical information retrieved from face-to-face interviews with the patient and completed using medical records where necessary. Analysis of the local ecology, resistance rates and antibiotic prescription patterns were collected. ETHICS AND DISSEMINATION: This protocol obtained ethical approval from the Malagasy Ethical Committee n°07-MSANP/SG/AGMED/CNPV/CERBM on 24 January 2023. Findings generated were shared with national health stakeholders, microbiologists, members of the RESAMAD network and the Malagasy academic society of infectious diseases.

Molecular characterization of Staphylococcus aureus isolates derived from severe pneumonia: a retrospective monocentre study.

BACKGROUND: Staphylococcus aureus is endowed with a repertoire of virulence factors potentially implicated in its pathogenicity and ability to cause invasive disease. The main objective of this study was to describe the bacterial genotype, including virulence genes and affiliation to clonal complexes (CCs), encountered in severe pneumonia. METHODS: DNA microarray was used to analyse 18 S. aureus isolates from patients hospitalized with severe pneumonia between 2017 and 2019. RESULTS: Among 18 S. aureus isolates, 14 were methicillin-susceptible S. aureus (MSSA), and 4 methicillin-resistant S. aureus (MRSA). There were 14 community-acquired, 3 healthcare-associated, and 1 hospital-acquired infections. Different radiological presentations were observed: necrotizing pneumonia (n = 8, 44%), alveolar consolidation (n = 7, 39%), alveolar-interstitial infiltrates (n = 3, 17%). Sixteen patients (89%) required ICU hospitalization, 13 (72%) an invasive mechanical ventilation, and 12 (67%) a vasopressor support. Mortality affected 6 patients (33%). Panton-Valentine leukocidin (PVL), staphylococcal enterotoxins, toxic shock syndrome toxine-1 (TSST-1) encoding genes were documented in nine (50%), 12 (67%), one (6%) of the isolates, respectively. Accessory regulator gene group I was the most reported (n = 9, 50%) and was found in five deaths. The majority of isolates were affiliated to CC152 (n = 6), followed by CC15 (n = 3), CC45 (n = 2), CC30 (n = 2), CC1 (n = 2), CC8 (n = 1), CC9 (n = 1), and CC25 (n = 1). All the CC152 isolates were PVL-positive. CONCLUSION: CC152-PVL positive S. aureus strains were the most prevalent in severe pneumonia. Other virulence gene profiles were found coupled to additional clonal lineages. A genotyping strategy contributes to describe the current circulating strains and bacterial genetic backgrounds.

Prevalence, Risk Factors, and Genetic Characterization of Extended-Spectrum Beta-Lactamase Escherichia coli Isolated From Healthy Pregnant Women in Madagascar.

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. bla CTX-M-15 was the most frequent ESBL gene (86%). One isolate was resistant to carbapenems and carried the bla NDM-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 bla CTX-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.

Novel Streptococcus suis Sequence Type 834 among Humans, Madagascar.

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.

[Resistant phenotypes of Escherichia coli strains responsible for urinary tract infection in the laboratory of the University Hospital Joseph Raseta Befelatanana, Antananarivo]. / Phénotypes de résistance des souches d'Escherichia coli responsables d'infection urinaire au laboratoire du Centre Hospitalo-Universitaire de Befelatanana Antananarivo.

INTRODUCTION: Urinary tract infection caused by Escherichia coli frequently occurs in the hospital environment. This study aims to describe resistant phenotypes of Escherichia coli strains to monitor their occurrence. METHODS: We conducted a descriptive retrospective study of 102 Escherchia coli strains responsible for urinary tract infection in the laboratory of the University Hospital Joseph Raseta Befelatanana, Antananarivo from January 2014 to October 2016. RESULTS: Beta-lactam antibiotic resistance screening identified high-level penicillinases 50% (n=51), Escherichia coli producing extended-spectrum beta-lactamases (ESBLs) 22.5% (n=23), high-level cephalosporinases 14.7% (n=15), penicillinases low level 5.9% (n=6), wild type strains 5.9% (n=6) and a strain ofEscherichia coli emerging strain high-level resistance. Aminoglycosides resistance was identified in 58 (56.9%) wild type phenotype, 29 (28.4%) strains sensitive to amikacin and 15 (14.7%) resistant to all aminoglycosides. Fluoroquinolones resistance was identified in 52 (51%) wild type strains, 9 (8.8%) strains sensitive to ciprofloxacin and 41 (40.2%) resistant to all fluoroquinolones. Women (25, 7%) (p= 0.25, NS), patients more than 60 years (38.7%) (p=0.02), patients hospitalized in the Department of Nephrology (53.8%) (p=0.04), with urinary disorder and kidney disease (29, 7%) (p= 0.2, NS) were the most affected by E-ESBL. CONCLUSION: Based on high multidrug resistance in Escherichia coli strains guidelines for the empirical treatment of urinary tract infections need to be revised.

Resurgence of Neisseria meningitidis serogroup W ST-11 (cc11) in Madagascar, 2015-2016.

The resurgence of invasive meningococcal disease caused by Neisseria meningitidis serogroup W with sequence type ST-11 (cc11) was observed in Madagascar in 2015-2016. Three cases were investigated in this study. Molecular characterization of the strains suggests the local transmission of a single genotype that may have been circulating for years.

Evaluation of methicillin-resistant Staphylococcus aureus nasal carriage in Malagasy patients.

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%). CONCLUSIONS: 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.