Whole-genome sequences of multidrug-resistant Escherichia coli in South-Kivu Province, Democratic Republic of Congo: characterization of phylogenomic changes, virulence and resistance genes.

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are responsible for severe infections worldwide. Whereas their genotypic and pathogenic characteristics are not documented in Democratic Republic of Congo (DRC), recent studies conducted at the Bukavu General Hospital in the South Kivu province highlighted their high prevalence in extra-intestinal infections. Here we provide data on molecular characterization of ESBL producing-Escherichia coli isolates from patients with extra-intestinal infections at this provincial hospital. Whole-genome sequencing was carried out on 21 of these ESBL-producing Extra-intestinal Pathogenic Escherichia coli (ExPEC) for analysis of phylogenomic evolution, virulence factor and antimicrobial resistance (AMR) genes. Data were compared to phylogenetically close genomes using Multi-Locus Sequence Typing and Single Nucleotide Polymorphism-based phylogenetic approaches. The distribution of E. coli sequence types (ST) was as follows: ST 131 (n = 7), ST405 (n = 4), ST410 (n = 2), and other STs (ST10, ST58, ST95, ST393, ST443, S617, ST648, and ST2450). All ST131 belonged to the O25b-ST131 pandemic clone. Unexpectedly, they harbored more virulence genes than their GenBank counterparts. IncF plasmid replicons included novel FIB 69, FII 105 and FII 107 alleles. ESBL-genes included the plasmid-mediated CTX-M-15 in all isolates, and the SHV-12 allele. Other AMR genes included blaOXA-1, blaTEM-1, as well as genes encoding resistance against aminoglycosides, quinolones, chloramphenicol, rifampicin, tetracyclines, sulfonamides and trimethoprim. Current data confirm the clonal spread of ESBL-producing ST131 and ST405 clones in patients from South Kivu, and the acquisition of resistance and virulence genes. A closer survey of AMR and virulence should therefore be prompted in this high-risk area

A qPCR and multiplex pyrosequencing assay combined with automated data processing for rapid and unambiguous detection of ESBL-producers Enterobacteriaceae.

Rapid and specific detection of extended-spectrum β-lactamase-producing (ESBL) bacteria is crucial both for timely antibiotic therapy when treating infected patients as well as for appropriate infection control measures aimed at curbing the spread of ESBL-producing isolates. Whereas a variety of phenotypic methods are currently available for ESBL detection, they remain time consuming and sometimes difficult to interpret while being also affected by a lack of sensitivity and specificity. Considering the longer turnaround time (TAT) of susceptibility testing and culture results, DNA-based ESBL identification would be a valuable surrogate for phenotypic-based methods. Putative ESBL-positive Enterobacteriaceae isolates (n = 330) from clinical specimen were prospectively collected in Bulgaria, Romania and Democratic Republic of Congo and tested in this study. All isolates were assessed for ESBL-production by the E-test method and those giving undetermined ESBL status were re-tested using the combination disk test. A genotypic assay successively combining qPCR detection of blaCTX-M, blaTEM and blaSHV genes with a multiplex pyrosequencing of blaTEM and blaSHV genes was developed in order to detect the most common ESBL-associated TEM and SHV single nucleotides polymorphisms, irrespective of their plasmid and/or chromosomal location. This assay was applied on all Enterobacteriaceae isolates (n = 330). Phenotypic and genotypic results matched in 324/330 (98.2%). Accordingly, real-time PCR combined with multiplex pyrosequencing appears to be a reliable and easy-to-perform assay with high-throughput identification and fast TAT (~5 h)

Antimicrobial resistance of bacteria isolated from patients with bloodstream infections at a tertiary care hospital in the Democratic Republic of the Congo

Background. Bloodstream infection (BSI) is a life-threatening condition that requires rapid antimicrobial treatment. Methods. We determined the prevalence of bacterial isolates associated with BSI at Bukavu General Hospital (BGH), South Kivu Province, Democratic Republic of the Congo, and their patterns of susceptibility to antimicrobial drugs, from February 2013 to January 2014. Results. We cultured 112 clinically relevant isolates from 320 blood cultures. Of these isolates, 104 (92.9%) were Gram-negative bacteria (GNB), with 103 bacilli (92.0%) and one coccus (0.9%). Among GNB, Escherichia coli (51.9%), Klebsiella spp. (20.2%), Enterobacter spp. (6.7%), Shigella spp. (5.8%) and Salmonella spp. (4.8%) were the most frequent agents causing BSIs. Other GNB isolates included Proteus spp., Citrobacter spp. and Pseudomonas aeruginosa (both 2.9%), and Acinetobacter spp. and Neisseria spp. (both 0.9%). High rates of resistance to co-trimoxazole (100%), erythromycin (100%) and ampicillin (66.7 - 100%) and moderate to high resistance to ciprofloxacin, ceftazidime, ceftriaxone, cefuroxime and cefepime were observed among GNB. Furthermore, there were high rates of multidrug resistance and of extended-spectrum β-lactamase (ESBL) production phenotype among Enterobacteriaceae. Gram-positive bacteria included three Staphylococcus aureus isolates (2.7%), four oxacillin-resistant coagulase-negative staphylococci (CoNS) isolates (3.6%) and one Streptococcus pneumoniae (0.9%). No oxacillin-resistant S. aureus was isolated. Among clinically relevant staphylococci, susceptibility to co-trimoxazole and ampicillin was low (0 - 25%). In addition, 58 contaminant CoNS were isolated from blood cultures, and the calculated ratio of contaminants to pathogens in blood cultures was 1:2. Conclusions. Multidrug-resistant and ESBL-producing GNB are the leading cause of BSI at BGH

Caractéristiques épidémiologiques et histopathologiques de 1280 cancers du col utérin à Kinshasa

OBJECTIF : Vu le manque de registre du cancer et de programme de dépistage à grande échelle du cancer du col utérin dans la plupart des pays africains, des modèles mathématiques sont à la base des données disponibles. Cette étude vise à cerner concrètement les particularités épidémiologiques et histopathologiques du cancer du col utérin. MÉTHODES : Parmi les cancers (n = 5801) diagnostiqués dans cinq laboratoires d’anatomie pathologique de Kinshasa durant 10 ans, les lames histologiques des cancers du col ont fait l’objet d’une relecture et d’une classification selon l’OMS 2014. RÉSULTATS : Les cancers du col utérin (n = 1280) ont représenté 22 % de l’ensemble des cancers et 40,4 % des cancers mammaires et gynécologiques. La tranche d’âge la plus touchée était celle de 49 à 58 ans. Le carcinome malpighien correspond à 73,2 %, l’adénocarcinome à 18,4 % et le carcinome adénosquameux à 8,4 % des cancers cervicaux. Les sous-types se distribuaient comme suit : le carcinome kératinisant 47,2 %, le non kératinisant 20,8 %, l’adénocarcinome usuel 9,6 % et le villoglandulaire 5,3 %. Dans le sous-type des carcinomes mucineux, seul le variant à cellules en bague à chaton (1,3 %) était représenté. Parmi les cancers du col utérin, 69 % étaient de grade histologique I, 20 % de grade II et 11 % de grade III. CONCLUSION : Cette étude des particularités épidémiologiques et histopathologiques du cancer du col utérin à Kinshasa fournit une base de données concrètes pour initier un registre du cancer et des campagnes de dépistage et de vaccination contre le HPV.[Epidemiologic and histopathologic characteristics of 1280 uterine cervical cancers in Kinshasa]. OBJECTIVE: Due to the lack of both cancer registry and large scale cervical screening in most african countries, only theoretical studies are available. The objective of our work was to provide epidemiological and histopathological characteristics of cervical cancer based on concrete observations. METHODS: This study was carried out on all cancers (n=5801) collected in the last 10 years from 5 pathology laboratories of Kinshasa; the histologic slides of the cervical cancers (n=1280) were reviewed by at least two pathologists and classified according to the 2014 OMS classification. RESULTS: The cervical cancers accounted for 22% of all cancers and 40,4% of breast and gynecological cancers. The cervical cancer was the most common among women aged 49-58. Squamous cell carcinomas were the most observed type (73,2%) followed by adenocarcinomas (18,4%) and adenosquamous carcinomas (8,4%). Keratinized (47,2%) and non keratinized squamous carcinoma (20,8%) were the most frequent subtypes among squamous carcinomas and the usual adenocarcinoma among adenocarcinomas (9,6%). In the mucinous adenocarcinoma subtype, only the signet ring cells (1,3%) variant was found. Among cervical cancers, 69% were grade I, 20% grade II and 11% grade III. CONCLUSION: Our study provides a concrete database of epidemiological and histopathological cervical cancer particularities in Kinshasa, useful to initiate a cancer register, as well as cervical screening and HPV vaccine campaigns