Dataset Information

Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo.

ABSTRACT: Multidrug-resistant (MDR) and extended spectrum β-lactamase (ESBL)-producing extra-intestinal K. pneumoniae are associated with increased morbidity and mortality. This study aimed to characterize the resistance and virulence profiles of extra-intestinal MDR ESBL-producing K. pneumoniae associated with infections at a tertiary hospital in South-Kivu province, DRC. Whole-genome sequencing (WGS) was carried out on 37 K. pneumoniae isolates displaying MDR and ESBL-producing phenotype. The assembled genomes were analysed for phylogeny, virulence factors and antimicrobial resistance genes (ARG) determinants. These isolates were compared to sub-Saharan counterparts. K. pneumoniae isolates displayed a high genetic variability with up to 16 sequence types (ST). AMR was widespread against β-lactamases (including third and fourth-generation cephalosporins, but not carbapenems), aminoglycosides, ciprofloxacin, tetracycline, erythromycin, nitrofurantoin, and cotrimoxazole. The bla_CTX-M-15 gene was the most common β-lactamase gene among K. pneumoniae isolates. No carbapenemase gene was found. ARG for aminoglycosides, quinolones, phenicols, tetracyclines, sulfonamides, nitrofurantoin were widely distributed among the isolates. Nine isolates had the colistin-resistant R256G substitution in the pmrB efflux pump gene without displaying reduced susceptibility to colistin. Despite carrying virulence genes, none had hypervirulence genes. Our results highlight the genetic diversity of MDR ESBL-producing K. pneumoniae isolates and underscore the importance of monitoring simultaneously the evolution of phenotypic and genotypic AMR in Bukavu and DRC, while calling for caution in administering colistin and carbapenem to patients.

SUBMITTER: Irenge LM

PROVIDER: S-EPMC9960421 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo.

Irenge Leonid M LM Ambroise Jérôme J Bearzatto Bertrand B Durant Jean-François JF Bonjean Maxime M Gala Jean-Luc JL

Microorganisms 20230218 2

Multidrug-resistant (MDR) and extended spectrum β-lactamase (ESBL)-producing extra-intestinal K. pneumoniae are associated with increased morbidity and mortality. This study aimed to characterize the resistance and virulence profiles of extra-intestinal MDR ESBL-producing K. pneumoniae associated with infections at a tertiary hospital in South-Kivu province, DRC. Whole-genome sequencing (WGS) was carried out on 37 K. pneumoniae isolates displaying MDR and ESBL-producing phen ...[more]

PMID: 36838490

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Project description:BackgroundSchistosomiasis, caused by Schistosoma mansoni, is of great significance to public health in sub-Saharan Africa. In the Democratic Republic of Congo (DRC), information on the burden of S. mansoni infection is scarce, which hinders the implementation of adequate control measures. We assessed the geographical distribution of S. mansoni infection across Ituri province in north-eastern DRC and determined the prevailing risk factors.Methods/principal findingsTwo province-wide, community-based studies were conducted. In 2016, a geographical distribution study was carried out in 46 randomly selected villages across Ituri. In 2017, an in-depth study was conducted in 12 purposively-selected villages, across the province. Households were randomly selected, and members were enrolled. In 2016, one stool sample was collected per participant, while in 2017, several samples were collected per participant. S. mansoni eggs were detected using the Kato-Katz technique. In 2017, a point-of-care circulating cathodic S. mansoni antigen (POC-CCA) urine test was the second used diagnostic approach. Household and individual questionnaires were used to collect data on demographic, socioeconomic, environmental, behavioural and knowledge risk factors. Of the 2,131 participants in 2016, 40.0% were positive of S. mansoni infection. Infection prevalence in the villages ranged from 0 to 90.2%. Of the 707 participants in 2017, 73.1% were tested positive for S. mansoni. Prevalence ranged from 52.8 to 95.0% across the health districts visited. Infection prevalence increased from north to south and from west to east. Exposure to the waters of Lake Albert and the villages' altitude above sea level were associated with the distribution. Infection prevalence and intensity peaked in the age groups between 10 and 29 years. Preschool children were highly infected (62.3%). Key risk factors were poor housing structure (odds ratio [OR] 2.1, 95% 95% confidence interval [CI] 1.02-4.35), close proximity to water bodies (OR 1.72, 95% CI 1.1-2.49), long-term residence in a community (OR 1.41, 95% CI 1.11-1.79), lack of latrine in the household (OR 2.00, 95% CI 1.11-3.60), and swimming (OR 2.53, 95% CI 1.20-5.32) and washing (OR 1.75, 95% CI 1.10-2.78) in local water bodies.Conclusions/significanceOur results show that S. mansoni is highly endemic and a major health concern in Ituri province, DRC. Infection prevalence and intensity, and the prevailing socioeconomic, environmental, and behavioural risk factors in Ituri reflect intense exposure and alarming transmission rates. A robust plan of action is urgently needed in the province.

Project description:IntroductionIn the field of tuberculosis (TB), and particularly in regard to paediatric TB (PedTB), clinical skills of health professionals play an important role in determining quality of care. In an era where novel diagnostic technologies and efficient treatment regimens are being made available for the poorest, we must not divert our attention from the importance of clinical skills, as this deliverable remains the cornerstone of individualized patient care and ultimately the best assurance for optimal use of resources. The aim of our work was to study the epidemiology of PedTB and the determinants of PedTB under-detection in the South-Kivu Province of the Democratic Republic of Congo (DRC), a setting with nearly no technical resources allowing to support the clinical diagnosis of PedTB, i.e. chest X-rays, rapid molecular tests or culture laboratories.MethodsWe collected TB notification data from 2010 to 2015 and analysed the space-time variations in notification for the different forms of TB among the 113 health facilities (HF) the South-Kivu Province, a region with a low HIV incidence. The different forms of TB notified were: smear positive pulmonary TB (SS+PTB), smear negative pulmonary TB (SS-PTB) and extra-pulmonary TB (EPTB). We further analysed the distribution of these different forms of the disease per age group and explored the possibility to predict the detection of PedTB.ResultsSignificant differences were observed between HF in regard to the proportion of paediatric TB and the proportion of SS-TB among adults. We found a strong correlation between the proportion of PedTB and three major factors: the proportion of TB cases with no bacteriological confirmation (SS-TB) among adults, the number of TB cases notified by the HF and the fact that the HF was supported or not by Médecins Sans Frontières (MSF). The proportion of SS-TB among adults was found to be a valid indicator for predicting the level of detection of PedTB at the same HF.ConclusionOur observations strongly suggest that under-detection of PedTB is associated with insufficient clinical skills and technical resources at the HF level which similarly affects other forms of the disease, in particular SS-TB. We demonstrated that, in the specific context of South-Kivu, under-detection of PedTB can be predicted by a low SS-TB/SS+PTB ratio in the adult population. In the context of severely under-resourced settings, this ratio could be used to rapidly identify HF that should benefit in priority from deeper evaluation, and eventually targeted interventions.

Project description:African swine fever (ASF) is the most important disease constraining smallholder pig production in the Democratic Republic of Congo, causing high mortality in domestic pigs with severe impacts on the livelihoods of local populations. This study was conducted with the aim of determining the prevalence of ASF and circulating virus genotypes in asymptomatic pigs raised on smallholder farms in the South Kivu province to understand the transmission dynamics of ASF and ultimately improving disease control. A cross-sectional survey was carried out in 5 districts where 267 pig blood were screened for both antibody and viral genome using indirect Enzyme Linked Immunosorbent Assay (ELISA) and polymerase chain reaction (PCR) respectively. Additionally, amplicons from PCR positive samples were sequenced by Sanger method for genetic analysis of ASF virus (ASFV) based on the C-terminal region of the B646L gene that encodes the major capsid protein p72 and the gene E183L encoding the p54 protein. The overall seroprevalence obtained based on antibody to p30 protein was 37 % and was significantly higher (P < 0.05) in adult (>1 year) animals (44.7 %) than in younger (<1 year) ones (33.5 %). Moreover, the seropositivity varied significantly (P < 0.05) according to the pig husbandry system practiced within the districts investigated with Uvira (55 %) and Mwenga (42.2 %) having the highest ASFV antibodies, while the lowest (10.5 %) were in Kalehe. Free-range pigs exhibited a higher level of seropositivity to ASFV antibody (68.9 %) than pigs kept in the pigsty housing system (21.6 %). However, no statistically significant differences (P > 0.05) were observed when sex of the animal and breed were factored. PCR detection of ASFV amplified a specific band of expected size (257 bp) in 61 out of 267 blood samples, confirming the presence of the viral DNA in 22.8 % of asymptomatic domestic pigs. Statistical analysis revealed that ASFV infection in domestic pigs varied significantly (p < 0.001) according to geographical location and breed, with the highest infection rate found in Walungu district (33.7 %) while the lowest was registered in Kalehe (15.8 %). Local pigs (27.2 %) were more infected than crosses (9.2 %). Phylogenetic analyses based on partial sequences of the p72 and p54 genes revealed that all the ASFV detected belonged to genotype IX, which has previously been reported in other parts of DR Congo, and was clustered together with isolates from Kenya, Uganda and Republic of Congo. This study avails the first evidence of the presence of ASF virus in domestic pigs in the absence of outbreaks in South Kivu province, eastern DR Congo, indicating a need to raise awareness among pig farmers and veterinary authorities on the application of biosecurity measures and good husbandry practices to control the disease.

Dataset Information

Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo.

Publications

Genomic Characterization of Multidrug-Resistant Extended Spectrum β-Lactamase-Producing <i>Klebsiella pneumoniae</i> from Clinical Samples of a Tertiary Hospital in South Kivu Province, Eastern Democratic Republic of Congo.

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