Antimicrobial Resistance in the WHO African Region: A Systematic Literature Review 2016-2020.

Antimicrobial resistance (AMR) is a significant global public health threat. This review presents the most recent in-depth review of the situation of the main AMR types in relation to the most commonly prescribed antibiotics in the World Health Organization (WHO) African Region. Underlying genes of resistance have been analyzed where possible. A search to capture published research data on AMR from articles published between 2016 and 2020 was done using PubMed and Google Scholar, with rigorous inclusion/exclusion criteria. Out of 48003 articles, only 167 were included. Among the tested gram-negative bacteria species, Klebsiella spp. remain the most tested, and generally the most resistant. The highest overall phenotypic resistance for imipenem was reported in E. coli, whereas for meropenem, E. coli and Haemophilus spp. showed an equal resistance proportion at 2.5%. For gram-positive bacteria, Streptococcus pneumoniae displayed high resistance percentages to trimethoprim/sulfamethoxazole (64.3%), oxacillin (32.2%), penicillin (23.2%), and tetracycline (28.3%), whereas Staphylococcus aureus contributed to 22.8% and 10% resistance to penicillin and oxacillin, respectively. This review shows that AMR remains a major public health threat. The present findings will help public health decision-makers in developing efficient preventive strategies and adequate policies for antibiotic stewardship and surveillance in line with the global action plan for AMR.

Implementation of a prospective study for enhancing surveillance of invasive bacterial infections in North Africa.

OBJECTIVES: We implemented a project named MENINGSTOP in three countries of North Africa (Algeria, Morocco and Tunisia). The main objective was to use real-time PCR to detect, identify and type the three main agents (Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae) responsible for invasive bacterial infections (IBI). METHODS: The protocol of WHO and US CDC for real-time PCR was used to detect and type the three bacterial agents in clinical samples. We also designated two quality exercises using an external interlaboratory study and cross-testing of 10% of randomly selected samples. RESULTS: Among the 752 samples tested, 18% were positive for one of the three agents. N. meningitidis was the most frequent globally reaching 9% of all samples (7% to 17% range) followed by S. pneumoniae 8% of all samples (6% to 15%). Group B meningococci was the most frequent (74% of all positive samples for meningococci and ranging from 50% to 90%). Quality assurance showed >85% correlation scores. CONCLUSIONS: Real-time PCR can help improving epidemiological surveillance. Data confirm the prevalence of meningococci B. Our project adds a reliable tool to enhance surveillance and to help decision making in vaccination strategies against IBI.

Vancomycin-resistant Enterococcus faecium in Algeria: phenotypic and genotypic characterization of clinical isolates.

INTRODUCTION: vancomycin-resistant Enterococcus faecium (VREfm) is a major public health problem worldwide. The aim of our study was to determine the microbiological, epidemiological and molecular characteristics of VREfm isolated in north-central, eastern and western Algeria. METHODOLOGY: a collection of 48 VREfm isolated from September 2010 to April 2017 in several Algerian hospitals were studied. Minimum inhibitory concentrations (MICs) were determined by E-test method according to CLSI guidelines. the detection of van genotype of all strains was performed by PCR. Clonal relationship of five VREfm targeted by region were characterized using multilocus sequence typing (MLST). RESULTS: All isolates have multidrug-resistance (MDR) and were resistant to at least five classes of antibiotics; however, all were susceptible to tigecycline and daptomycin with MIC50 at 0.094 µg/mL and 2 µg/mL respectively. All strains belonged to vanA genotype and have high level of resistance to vancomycin and teicoplanin. MLST revealed two sequence types (STs): ST80 (from the four regions of Algeria) and ST789, both belonging to the former hospital-adapted clonal complex CC17. CONCLUSIONS: the alarming dissemination of MDR E. faecium vanA and the ST80 in several regions of Algeria suggest a clonal spread of VREfm strains, which urgently require implementation of adequate infection control measures.

Phenotypic and genotypic characterization of multidrug-resistant Acinetobacter baumannii isolated in Algerian hospitals.

INTRODUCTION: The aim of this study was to investigate the drug-resistance and the molecular characterization of carbapenemases, ESBL, and aminoglycoside-modifying enzymes among Acinetobacter baumannii clinical isolates in Algerian hospitals. METHODOLOGY: A total of 92 A. baumannii isolates were collected between 2012 and 2016. Antimicrobial susceptibility testings were performed for ß-lactams, aminoglycosides, fluoroquinolones, trimethoprim-sulfamethoxazole, rifampicin and colistin. The phenotypic characterization of ß-lactamases was investigated. For 30 randomly targeted strains, the carriage of the carbapenemases, ESBL and aminoglycoside-modifying enzymes -encoding genes was determined by PCR. Sequencing was carried out for carbapenemases and ESBL genes. RESULTS: Most of the 92 isolates studied were recovered from hospitalized patients (93.5%) and were mainly from intensive care units (51.1%) and orthopedics (19.6%). The strains were collected primarily from low respiratory tract (33.7%), wounds (23.9%) and urine (16.3%). Multidrug-resistant A. baumannii strains were prevalent (96.7%). High rates of resistance were observed for almost all antibiotics tested (>70%) excluding rifampicin (7.6%) and colistin (5.4%). For the five colistin-resistant strains, MICs ranged between 4 and 128 µg/mL. Positive MBL (83.7%) and ESBL (23.9%) strains were identified. Regarding ß-lactams, the blaNDM and both blaSHV and blaCTX-M1 genes were detected in five and two strains respectively. Sequencing of the genes revealed the presence of blaNDM-1, blaCTX-M-15, and blaSHV-33. For aminoglycosides, aac(6')-Ib, ant(2'')-I and aph(3')-VI genes were detected in three, seven and six strains respectively. CONCLUSIONS: Here, we report the first co-occurrence of extended-spectrum ß-lactamases SHV-33 and CTX-M-15, the carbapenemase NDM-1 and the emergence of colistin-resistant A. baumannii in Algerian hospitals.

Detection of multidrug resistant Escherichia coli in the ovaries of healthy broiler breeders with emphasis on extended-spectrum ß-lactamases producers.

In the last few years, antimicrobial resistant (AMR) Escherichia coli have been detected in newborn chickens suggesting their vertical transmission from breeding birds to their offspring. However, little is known about the presence of AMR E. coli in the reproductive organs of broiler breeders. The aim of this study was to investigate the presence of E. coli in the ovaries of healthy broiler breeders and to study their antimicrobial resistance. Samples from broiler breeders (n = 80) collected from 80 different broiler breeder flocks were included in this study. Antibiotic susceptibility testing was performed using disk diffusion method according to Clinical and Laboratory Standards Institute guidelines. Minimal inhibitory concentrations (MICs) of five antimicrobial agents were determined by Etest. PCR and sequencing were used to detect the blaESBL genes. E. coli were detected in the ovaries of thirty seven out of 80 (46.25%) sampled flocks. High levels of resistance to various first-line antimicrobial agents were recorded in E. coli isolates. This study showed that 89.18% of E. coli isolates were multidrug resistant (MDR). Furthermore, MDR extended-spectrum ß-lactamases (ESBL)-producing E. coli were detected in the ovaries of four different broiler breeder flocks. Molecular characterization revealed that three isolates harboured blaCTX-M-1 gene and one isolate expressed blaSHV-12 gene. In addition, one blaCTX-M-1 -producing E. coli co-harboured the blaTEM-1 gene. These findings would contribute to a better epidemiological understanding of MDR E. coli for improve existing preventive strategies in order to reduce the dissemination of antimicrobial resistance in the broiler production system.

Isolation of Escherichia coli carrying the blaCTX-M-1 and qnrS1 genes from reproductive organs of broiler breeders and internal contents of hatching eggs.

This study aimed to characterize two third-generation cephalosporins- and quinolone-resistant Escherichia coli (TGCs- and Q-R-Ec) isolates recovered from the ovaries of a broiler breeder flock and the internal contents of hatching eggs produced by the broiler breeder flock. Clonal relatedness was determined by multilocus sequence typing (MLST). The isolates displayed the same multidrug resistance profile, with resistance to ampicillin, ticarcillin, piperacillin, cefazollin, cephalothin, cefotaxime, nalidixic acid, tetracycline and sulfonamides. Double disk synergy test demonstrated that the two isolates presented an ESBL phenotype. PCR and sequencing results showed that both the isolates harbored the blaCTX-M-1 and qnrS1 genes. MLST revealed a novel allele combination, designated as ST461, in these isolates. This study would contribute to the molecular epidemiological understanding of TGCs- and/or Q-R-Ec.

Immune responses to vaccine-preventable diseases among toddlers and preschool children after primary immunization and first booster in Northwestern Algiers, Algeria.

OBJECTIVES: To determine immune responses to selected vaccine-preventable communicable diseases: pertussis, diphtheria and Haemophilus influenzae type b (Hib) in Algerian toddlers and preschool children after primary vaccination and first booster, recruited from three local healthcare facilities in Northwestern Algiers. METHODS: The information of demographic characteristics and vaccination status were collected for each subject by questionnaire. Specific antibody levels and Hib antibody avidity were determined using commercial ELISA kits. RESULTS: A total of eighty-one subjects aged between 19 and 55 months were studied. Almost all subjects were fully protected against diphtheria (76/81; 93.83%; 95% CI: 86.35-97.33) and invasive Hib disease (29/30; 96.67%; 95% CI: 83.33-99.41), while only 20/78 (25.64%; 95% CI: 17.26-36.31) had anti-PT (pertussis toxin) antibody levels above 25 IU/ml. A significant decrease of anti-PT antibody levels was observed until the age of 36 months (p = 0.02). GMTs (geometric mean titers) of anti-PT antibodies were low, but remain significantly higher in children ≤36 months of age (p = 0.02). Both GMT and rates of ≥0.15 µg/ml, ≥1 µg/ml, and ≥5 µg/ml titers were significantly higher in Hib-vaccinated subjects (p < 0.01). Relative Hib-avidity index (≥50%) and GMAI (geometric mean avidity index) were high in both Hib-vaccinated and -unvaccinated groups. CONCLUSIONS: As shown in the present study, young children were fully protected against diphtheria and Hib, but showed low immunity to pertussis. Further sero-epidemiological studies including a large number of subjects with a wider range of age are needed to explore the immunity level in older children, adolescents and adults.

Characterization of quinolone-resistant Enterobacteriaceae strains isolated from poultry in Western Algeria: First report of qnrS in an Enterobacter cloacae.

AIM: Multidrug-resistant (MDR) Enterobacteriaceae have frequently been reported, in both human and veterinary medicine, from different parts of the world as a consequence of antibiotic usage. However, there is a lack of published data regarding antimicrobial resistance in non-Escherichia coli (E. coli) Enterobacteriaceae from animals in Algeria. This study aimed to evaluate the frequency of resistance to antibiotics with a focus on quinolones and to investigate the presence of qnr genes inEnterobacteriaceaeof poultry origin. MATERIALS AND METHODS: A total of 310 samples of poultry origin were collected from 2010 to 2014 from broiler and layer farms and hatcheries located in different geographic areas of Western Algeria (including Mostaganem, Oran, Mascara, Relizane, Chlef, Tiaret, and Tissemsilt). Antimicrobial susceptibility testing was performed using disc diffusion assay. Polymerase chain reaction and sequencing accomplished the characterization of qnr genes (qnrA, qnrB, and qnrS). RESULTS: A total of 253 Enterobacteriaceaestrains were isolated in this study. These isolates exhibited high levels of resistance to quinolones and other families of antibiotics. All the strains isolated in this study were resistant to at least one antibiotic. Among them, 233 (92.09%) were considered MDR. Among the 18 randomly selected nalidixic acid (NA)-resistant Enterobacteriaceaeisolates, one E. coli and one Enterobacter cloacae were carrying qnrS1. By contrast, qnrA and qnrB were not detected in this study. CONCLUSION: This is the first report on the identification of the qnrS gene in E. cloacae isolated from animal source in Algeria. Further studies have to be conducted to determine the real prevalence of qnr genes.

Wide spread of OXA-48-producing Enterobacteriaceae in Algerian hospitals: A four years' study.

INTRODUCTION: The aim of this study was to investigate the presence of carbapenemase-producing Enterobacteriaceae (CPE) in Algerian hospitals and to characterize the molecular types of carbapenemases found. METHODOLOGY: During a four years study lasting between 2012 and 2015, 81 strains of Enterobacteriaceae with reduced susceptibility to carbapenems were collected from different hospitals. Carbapenemase genes were detected by PCR. Multi locus sequence typing was used to study genetic relationships between carbapenemase- producing Klebsiella pneumoniae isolates. RESULTS: Among 56 confirmed CPE, blaOXA-48 was detected in 98.21% of isolates. Two isolates co-expressed NDM, and a single one was only an NDM producer. The strains displayed various susceptibility patterns to antibiotics with variable levels of resistance to carbapenems. Multilocus sequence typing (MLST) revealed the presence of multiple sequence types in circulation. CONCLUSIONS: This report highlights the wide distribution of several clones of OXA-48-producing Enterobacteriaceae in Algeria. Urgent action should be taken to avoid epidemic situations.

Meningococcal disease in the Middle East and Africa: Findings and updates from the Global Meningococcal Initiative.

The Global Meningococcal Initiative (GMI) has recently considered current issues in Middle Eastern and African countries, and produced two recommendations: (i) that vaccination of attendees should be considered for some types of mass-gathering events, as some countries mandate for the Hajj, and (ii) vaccination of people with human immunodeficiency virus should be used routinely, because of increased meningococcal disease (MD) risk. Differences exist between Middle Eastern and African countries regarding case and syndrome definitions, surveillance, and epidemiologic data gaps. Sentinel surveillance provides an overview of trends and prevalence of different capsular groups supporting vaccine selection and planning, whereas cost-effectiveness decisions require comprehensive disease burden data, ideally counting every case. Surveillance data showed importance of serogroup B MD in North Africa and serogroup W expansion in Turkey and South Africa. Success of MenAfriVac® in the African "meningitis belt" was reviewed; the GMI believes similar benefits may follow development of a low-cost meningococcal pentavalent vaccine, currently in phase 1 clinical trial, by 2022. The importance of carriage and herd protection for controlling invasive MD and the importance of advocacy and awareness campaigns were also highlighted.

Pertussis in north-central and northwestern regions of Algeria.

INTRODUCTION: Pertussis outbreaks continue to occur in many countries despite high vaccination coverage. Under-diagnosed cases in adolescents and adults may result in increased transmission to infants, who are at risk of severe pertussis. Additional measures to protect both groups should be considered. METHODOLOGY: Nasopharyngeal samples and sera were collected from patients and household contacts with clinically suspected pertussis. Diagnoses were confirmed by culture, real-time polymerase chain reaction (PCR), and serology. Bordetella pertussis isolates were characterized by antimicrobial sensitivity and fimbrial serotyping. RESULTS: Of 392 participants, 134/248 patients (54%) and 66/144 contacts (45.8%) had confirmed pertussis infections. B. parapertussis was not detected. All B. pertussis isolates were sensitive to the antibiotics tested, and all expressed the Fim3, not the Fim2, fimbrial serotype. Most patients (81.2%) were <6 months (51.8% of whom were <3 months) of age; 77.6% were unvaccinated, and most positive contacts were mothers 20-40 years of age. CONCLUSIONS: Despite high vaccination coverage, pertussis is circulating in Algeria. Most infections occur in unvaccinated infants <6 months of age, with mothers as the main source of infection. An adolescent/adult booster should be considered. Adoption of sensitive and specific laboratory tests would improve pertussis diagnosis and surveillance.

Emergence of plasmid mediated carbapenemase OXA-48 in a Klebsiella pneumoniae strain in Algeria.

A carbapenem resistant Klebsiella pneumoniae strain was isolated in October 2011 in the pediatric unit of the Hôpital central de l'armée in Algeria, this strain have been confirmed for the production of OXA-48 carbapenemase. The blaOXA-48 gene was located on a self conjugative plasmid of 70kb. Multilocus sequence typing indicated the presence of the sequence type ST-307. This is the first isolation of OXA-48-producing K. pneumoniae in Algeria.

[Emergence of glycopeptide resistant Enterococcus faecium in Algeria: a case report]. / Émergence d'Enterococcus faecium résistant aux glycopeptides en Algérie : à propos d'un cas.

A glycopeptide-resistant Enterococcus faecium (EFRG) was isolated from a wound in a patient hospitalized in a university hospital in Algiers. This strain was resistant to several antibiotics. This patient was carrying this strain in the digestive tract which may partly explain its origin. Genotypic comparison of the two strains by pulsed field gel electrophoresis showed that it was the same strain. Glycopeptide resistance was due to the presence of the vanA gene. Vigilance is required facing the emergence of strains of EFRG in our hospitals.

Biomedical research in developing countries. I--The Algerian case (1993-1998).

Biomedical articles emerging from Algeria between 1993 an 1998 were analysed in order to evaluate the scientific output. By developing a search strategy based on complementary bibliographic databases, 221 articles were retrieved, which geographic location, research topic, language, journal name and impact factor were analysed. International collaborations resulted in a profound change of the publication profile in terms of language, journal impact factor, and above all a change in research interests. This study might encourage initiatives to improve literature access and contribute to define incentives for scientific research policy in Algeria as well as in other developing countries.