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

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)

Évaluation comparée de la pollution des rivières Kahuwa et Mpungwe par l'utilisation des macroinvertébrés benthiques

Les perturbations environnementales dues aux activités anthropogéniques se multiplient dans de nombreuses régions du globe et entraînent diverses pollutions des eaux. Ces pollutions sont importantes et causent un grand problème régional et local de santé publique. Dans la ville de Bukavu et ses environs, il y a suffisamment des systèmes aquatiques qui présentent des signes de pollution résultant des activités humaines. En vue d’estimer l’impact des activités anthropogéniques sur l’environnement des rivières, cette étude a été menée sur les rivières Kahuwa, située en milieu urbain, la ville de Bukavu et Mpungwe, située en milieu rural, à 20 km de la même ville. Des analyses physico-chimiques et biologiques réalisées in situ et au laboratoire du Centre de recherche en sciences naturelles de Lwiro, République Démocratique du Congo dans 7 sites des deux rivières (4 dans la rivière Kahuwa et 3 dans la rivière Mpungwe). Les résultats obtenus ont montré que la rivière Kahuwa est plus polluée que la rivière Mpungwe durant la période d’étude. Les paramètres physico-chimiques étudiés varient de l’amont en aval dans les deux rivières. Les concentrations en nutriments (phosphore et azote) sont en générales très élevées dans les sites où les activités anthropogéniques sont intenses (Kibonge, Cheche et SNCC pour la rivière Kahuwa et Usine Murhesa pour la rivière Mpungwe). Ces concentrations montrent bien que la pollution organique est intensifiée par les apports anthropogéniques. En général, la différence des concentrations des paramètres physico-chimiques dans les deux rivières est significative (p < 0,05). Les sources de ces nutriments sont généralement les effluents domestiques, les fosses septiques, les érosions provenant de l’agriculture, les rejets des industries et rejets des déchets divers qui ne sont pas réglementés. Les sites de la rivière Kahuwa ont moins d’espèces (14) que les sites de la rivière Mpungwe (31). La différence est significative entre les deux rivières (p < 0,001) en ce qui concerne la richesse spécifique. Cette faible richesse spécifique de la rivière Kahuwa serait due à la dégradation de la qualité des eaux comme déjà observée dans les facteurs physico-chimiques. En effet, il a été remarqué que l’utilisation des terres dans le bassin versant avait un impact significatif sur la distribution des macroinvertébrés. L’indice de Shannon et Weaver H’, l’indice biotique de pollution des macroinvertébrés l’indice de Hilsenhof, l’indice de Simpson et l’indice de Margalef montrent des variations entre les sites de prélèvement et les rivières. Des mesures de lutte antiérosive dans le bassin versant de la rivière Kahuwa et de mesures d’éco-sanitation (utilisation des toilettes VIP) sont recommandées pour diminuer la quantité des matières organiques apportées par la rivière Kahuwa dans le Lac Kivu.The environmental disturbances due to human activities increase in many countries and draw away various types of water pollutions. These pollutions are important and cause a serious regional and local problem in public health. In Bukavu and the surrounding areas, there are enough aquatic systems which shown signs of pollution resulting from human activities. In order to estimate the impact of human activities on the water quality within rivers, this study was carried out in the Kahuwa river, located in Bukavu, urban area, and Mpungwe river, located in rural area, so far at 20 Km of Bukavu. The physico-chemical and biological parameters from 7 sampling sites of both rivers (4 in the Kahuwa river and 3 in the Mpungwe river) was assessed in-situ and in the laboratory of the Lwiro Research Centre in Natural Sciences, Democratic Republic of Congo. According to the results obtained, Kahuwa river is more polluted than Mpungwe river during the period of this study. The physico-chemical parameters reach from upstream to downstream in both rivers Kahuwa and Mpungwe. The nutrients (phosphorus and nitrogen) increased in the sites which is intensively anthropogenic activities (Kibonge, Cheche and SNCC for the Kahuwa river and Murhesa factory for the Mpungwe river). The organic pollution is intensified by anthropogenic used. In general the physico-chemical water quality parameters show a significant difference (p <0,05). The major sources of the high levels of nutrients are in general the waste dumping, the mechanical erosion of rocks and soil particles due to agriculture blocks, the septic hole, the domestic sewers and industrial effluents in the water bodies, which are not regulated. The taxanomic diversity presents fewer species in Kahuwa river (14) than Mpungwe river (31). The difference is significant between both rivers (p <0,001) as regards species richness. The water quality was found to be the major factor contributing to the species richness of Kahuwa river and the impact of agriculture land use in the catchment on benthic macroinvertebrates distribution is significant. The several diversity (Shannon-Weaver, Hilsenhof, Simpson and Maragelf Indices) and pollution biotic macroinvertebrates indices show variations of the population diversity between the samples sites and rivers. In order to reduce the organic materials loading from Kahuwa micro catchment and Lake Kivu, there is need of erosion prevention and sanitation program (VIP toilet)

Évaluation comparée de la pollution des rivières Kahuwa et Mpungwe par l'utilisation des macroinvertébrés benthiques

The environmental disturbances due to human activities increase in many countries and draw away various types of water pollutions. These pollutions are important and cause a serious regional and local problem in public health. In Bukavu and the surrounding areas, there are enough aquatic systems which shown signs of pollution resulting from human activities. In order to estimate the impact of human activities on the water quality within rivers, this study was carried out in the Kahuwa river, located in Bukavu, urban area, and Mpungwe river, located in rural area, so far at 20 Km of Bukavu. The physico-chemical and biological parameters from 7 sampling sites of both rivers (4 in the Kahuwa river and 3 in the Mpungwe river) was assessed in-situ and in the laboratory of the Lwiro Research Centre in Natural Sciences, Democratic Republic of Congo. According to the results obtained, Kahuwa river is more polluted than Mpungwe river during the period of this study. The physico-chemical parameters reach from upstream to downstream in both rivers Kahuwa and Mpungwe. The nutrients (phosphorus and nitrogen) increased in the sites which is intensively anthropogenic activities (Kibonge, Cheche and SNCC for the Kahuwa river and Murhesa factory for the Mpungwe river). The organic pollution is intensified by anthropogenic used. In general the physico-chemical water quality parameters show a significant difference (p &#60;0,05). The major sources of the high levels of nutrients are in general the waste dumping, the mechanical erosion of rocks and soil particles due to agriculture blocks, the septic hole, the domestic sewers and industrial effluents in the water bodies, which are not regulated. The taxanomic diversity presents fewer species in Kahuwa river (14) than Mpungwe river (31). The difference is significant between both rivers (p &#60;0,001) as regards species richness. The water quality was found to be the major factor contributing to the species richness of Kahuwa river and the impact of agriculture land use in the catchment on benthic macroinvertebrates distribution is significant. The several diversity (Shannon-Weaver, Hilsenhof, Simpson and Maragelf Indices) and pollution biotic macroinvertebrates indices show variations of the population diversity between the samples sites and rivers. In order to reduce the organic materials loading from Kahuwa micro catchment and Lake Kivu, there is need of erosion prevention and sanitation program (VIP toilet)

Primers used for PCR amplification of the ACE cDNA (NM_000789.3) region encompassing the IVS25 splice-junction site.

<p>Primers used for PCR amplification of the ACE cDNA (NM_000789.3) region encompassing the IVS25 splice-junction site.</p