Functional host-specific adaptation of the intestinal microbiome in hominids.

Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.

New technologies for controlling emerging infectious diseases in Guinea and the Democratic Republic of the Congo: their role in response to the Ebola epidemic.

Emerging infectious diseases appear recurrently and represent a threat to global health security. Africa is particularly exposed to the risks of infectious epidemics, due to both the number of circulating infectious agents, especially in wildlife, and the social and environmental factors that promote their epidemic spread. Ebola outbreaks in West Africa in 2014 and those in the DRC that began in 2018 were an opportunity to develop and deploy new diagnostic techniques in laboratories in Guinea and the Democratic Republic of the Congo (DRC). These tools made it possible to identify the infectious agent rapidly, to trace contamination chains in real time to enable effective interventions, and to develop a reliable serological tool for differential diagnoses. Today, equipped and functional facilities exist in both countries, led by Guinean and Congolese researchers trained to high levels of competence and benefiting from unique experience and field knowledge.

Unveiling the molecular basis of antimicrobial resistance in Staphylococcus aureus from the Democratic Republic of the Congo using whole genome sequencing.

Staphylococcus aureus from sub-Saharan Africa is frequently resistant to antimicrobial agents that are commonly used to treat invasive infections in resource-limited settings. The underlying mechanisms of resistance are largely unknown. We therefore performed whole genome sequencing (WGS) on S. aureus from the Democratic Republic of the Congo (DRC) to analyse the genetic determinants of antimicrobial resistance. One hundred S. aureus samples were collected from community-associated asymptomatic nasal carriers in the metropolitan area of Kinshasa, DRC, between 2013 and 2014. Phenotypic resistance against 15 antimicrobial agents was compared to the genotypic results that were extracted from WGS data using Mykrobe predictor and the SeqSphere(+) software that screened for 106 target genes associated with resistance. Isolates were phenotypically resistant against penicillin (97%, n=97), trimethoprim (72%, n=72) and tetracycline (54%, n=45). Thirty-three isolates (33%) were methicillin-resistant S. aureus (MRSA). Of these, nine isolates (27.3%) were oxacillin-susceptible MRSA (OS-MRSA) and belonged to ST8 (t1476). The Y195F mutation of FemA was associated with OS-MRSA (p 0.015). The majority of trimethoprim resistant isolates carried dfrG. Tetracycline resistance was associated with tet(K). The concordance between phenotypic susceptibility testing and both WGS analysis tools was similar and ranged between 96% and 100%. In conclusion, a high proportion of OS-MRSA in the DRC was linked to mutations of FemA. Genotypic and phenotypical antimicrobial susceptibility testing showed high concordance. This encourages the future use of WGS in routine antimicrobial susceptibility testing.

Complete coding regions of the prototypes enterovirus B93 and C95: phylogenetic analyses of the P1 and P3 regions of EV-B and EV-C strains.

Complete coding regions were sequenced for two new enterovirus genomes: EV-B93 previously identified by VP1 sequencing, derived from a child with acute flaccid paralysis in the Democratic Republic of Congo; and EV-C95 from a French soldier with acute gastroenteritis in Djibouti. The EV-B93 P1 had more than 30% nucleotide divergence from other EV-B types, with highest similarity to E-15 and EV-B80. The P1 nucleotide sequence of EV-C95 was most similar, 71%, to CV-A21. Complete coding regions for the new enteroviruses were compared with those of 135 EV-B and 176 EV-C strains representing all types available in GenBank. When strains from the same outbreak or strains isolated during the same year in the same geographical region were excluded, 27 of the 58 EV-B, and 16 of the 23 EV-C types were represented by more than one sequence. However, for EV-B the P3 sequences formed three clades mainly according to origin or time of isolation, irrespective of type, while for EV-C the P3 sequences segregated mainly according to disease manifestation, with most strains causing paralysis, including polioviruses, forming one clade, and strains causing respiratory illness forming another. There was no intermixing of types between these two clades, apart from two EV-C96 strains. The EV-B P3 sequences had lower inter-clade and higher intra-clade variability as compared to the EV-C sequences, which may explain why inter-clade recombinations are more frequent in EV-B. Further analysis of more isolates may shed light on the role of recombinations in the evolution of EV-B in geographical context.

Ebola virus outbreaks in Africa: past and present.

Ebola haemorrhagic fever (EHF) is a zoonosis affecting both human and non-human primates (NHP). Outbreaks in Africa occur mainly in the Congo and Nile basins. The first outbreaks of EHF occurred nearly simultaneously in 1976 in the Democratic Republic of the Congo (DRC, former Zaire) and Sudan with very high case fatality rates of 88% and 53%, respectively. The two outbreaks were caused by two distinct species of Ebola virus named Zaire ebolavirus (ZEBOV) and Sudan ebolavirus (SEBOV). The source of transmission remains unknown. After a long period of silence (1980-1993), EHF outbreaks in Africa caused by the two species erupted with increased frequency and new species were discovered, namely Côte d'Ivoire ebolavirus (CIEBOV) in 1994 in the Ivory Coast and Bundibugyo ebolavirus (BEBOV) in 2007 in Uganda. The re-emergence of EHF outbreaks in Gabon and Republic of the Congo were concomitant with an increase in mortality amongst gorillas and chimpanzees infected with ZEBOV. The human outbreaks were related to multiple, unrelated index cases who had contact with dead gorillas or chimpanzees. However, in areas where NHP were rare or absent, as in Kikwit (DRC) in 1995, Mweka (DRC) in 2007, Gulu (Uganda) in 2000 and Yambio (Sudan) in 2004, the hunting and eating of fruit bats may have resulted in the primary transmission of Ebola virus to humans. Human-to-human transmission is associated with direct contact with body fluids or tissues from an infected subject or contaminated objects. Despite several, often heroic field studies, the epidemiology and ecology of Ebola virus, including identification of its natural reservoir hosts, remains a formidable challenge for public health and scientific communities.

Characterization of human rotavirus recovered from children with acute diarrhea in Kinshasa, Democratic Republic Of Congo.

Between July and October of 2003, 2004, and 2005, outbreaks of acute gastroenteritis occurred among children <5 years of age in Kinshasa, Democratic Republic of the Congo. Stool specimens (67 in 2003, 108 in 2004, and 116 in 2005) were collected and screened for rotaviruses using either latex agglutination (Diarlex LAA; Orion Diagnostics) or enzyme immunoassay (IDEIA; DakoCytomation). The molecular characteristics of the rotavirus strains were then determined. Group A rotavirus was detected in 195 (76%) of 258 stool specimens. Polyacrylamide gel electrophoresis was used to observe the 11 rotavirus double-stranded RNA segments in 83% of the 195 rotavirus-positive specimens. Six rotavirus group A electropherotypic patterns were noted, predominantly within the short classic pattern (111 [69%]) and the long pattern (37 [23%]). Mixed patterns were noted in the 14 remaining specimens (9%). Of the 29 samples subjected to subgrouping VP6 enzyme immunoassay, subgroup I predominated. Some of the specimens collected in 2003 (n = 26), 2004 (n = 38), and 2005 (n = 52) were analyzed by reverse-transcription polymerase chain reaction, which showed that t G8P[6] and G8P[8] strains predominated in 2003, and G1P[6] strains with short electropherotypic patterns predominated in 2004 and 2005. The emergence in Kinshasa of G8 serotypes, unusually associated with the P[6] genotype, as well as uncommon G1 rotavirus strains showing a short RNA pattern, is significant in relation to the introduction of a rotavirus vaccine and underscores the need for continued rotavirus serotype surveillance in the Democratic Republic of the Congo.

[Relapse after surgical treatment of mycobacterium ulcerans infection (buruli ulcer): study of risk factors in 84 patients in the Democratic Republic of the Congo]. / Rechutes après traitement chirurgical exclusif de l'infection à Mycobacterium ulcerans (ulcère de Buruli): étude des facteurs de risque chez 84 patients congolais.

OBJECTIVE: To identify risk factors for relapse after exclusively surgical treatment of Mycobacterium ulcerans infection (Buruli ulcer). METHODS: Study was carried out in 102 patients treated exclusively by surgery for Buruli ulcer at various care facilities in the Congo from January 1, 2000 to January 1, 2005. RESULTS: Outcomes included relapse in 22 patients (21.5%), cure in 62 (60.7%), and unknown in 18 (17.6%). Statistical analysis identified the following variables as independent risk factors for relapse after exclusively surgical treatment: incomplete surgical excision (OR = 91.83; P = 0.0000; IC to 95%), age under 16 years (OR = 14.80; P = 0.0000; IC to 95%) and pre-ulcerative Buruli lesions (edema and plaque) (OR = 3.18; P = 0.0215; IC to 95%). CONCLUSION: Quality of excision, patient age, and clinical form of lesion are the main predictors of relapse after isolated surgical treatment of Buruli ulcer.

An outbreak of peritonitis caused by multidrug-resistant Salmonella Typhi in Kinshasa, Democratic Republic of Congo.

Between October 2004 and January 2005, 144 patients with peritonitis were admitted to the surgical wards of Kinshasa General Hospital and a few private city clinics. 63 patients (44%) underwent surgical intervention because of intestinal perforation consistent with typhoid fever; the case fatality rate was 53%. The majority of patients had received a course of first-line antibiotics such as chloramphenicol, ampicillin or co-trimoxazole before admission. On bacteriological investigation, Salmonella Typhi was isolated from the blood of 11 patients with peritonitis. The isolates were all resistant to ampicillin, chloramphenicol, tetracycline and co-trimoxazole, but sensitive to third-generation cephalosporins, quinolone (nalidixic acid, ciprofloxacine) and amoxicillin-clavulanic acid. Several factors contributed to the poor outcome of this disease including a) the use of inappropriate antibiotics, b) long delay in diagnosis, c) difficult access to health facilities. This is the first documented outbreak of typhoid fever caused by a multidrug-resistant S. Typhi in Kinshasa.

[Follow-up of the first case of Mycobacterium ulcerans infection documented by PCR, genotyping and culture in the Republic of Congo-Brazzaville]. / Suivi du premier cas d'infection à Mycobacterium ulcerans confirmé par culture, PCR et génotypage République du Congo-Brazzaville.

This article presents follow-up data from the first patient in whom Mycobacterium ulcerans infection (MUI) was documented by PCR, genotyping and culture in the Republic of Congo-Brazzaville. Findings show the importance of regular clinical and microbiological evaluation for the disseminated form of the disease. The patient was probably infected in Pointe Noire where MUI has been described but never documented. Culture of specimens collected before antibiotic treatment showed that the bacterium was sensitive to the antibiotics being administered (streptomycin and rifampin) and was identical to isolates from Atlantic-coast regions of West Africa where MUI is endemic. The patient was treated with streptomycin and rifampin for 12 weeks in association with surgery. During treatment clinical examination was performed every day and microbiological analysis every two weeks. The duration of follow-up from the end of specific antibiotic treatment was 26 months. Medical treatment failed to prevent bone involvement and fistulae that were treated by surgery. However medical treatment may have limited dissemination of the disease. Serial microbiological evaluation was useful to detect bone involvement in this patient, but persistent positive gene amplification is not a proof of active disease. This study confirms that MUI is still endemic in the region of Pointe Noire. This finding underlines the need to optimize epidemiologic surveillance, laboratory diagnostic capabilities, and therapeutic management in the Republic of Congo-Brazzaville.

[Primary resistance of Mycobacterium tuberculosis to anti-tuberculosis drugs in Kinshasa, (DRC)]. / Résistance primaire de Mycobacterium tuberculosis aux anti-tuberculeux à Kinshasa, République Démocratique du Congo.

In a descriptive cross-sectional study carried out in Kinshasa between July 2003 and January 2004, we determined the prevalence of the primary resistance of M. tuberculosis to first-line anti-tuberculosis drugs. The antibiogram was performed with the proportion method on 301 isolats from patients who all had a first episode of pulmonary tuberculosis with positive microscopy (TPM+) and who had not received any anti-tuberculosis treatment before. The primary resistance rate reached 43.5%; it reached 31.6% in 1990. The multi-drug-resistance rate (MDR-TB) notified as resistant to both rifamicine and isoniazide rose to 5.3%. This rate of primary resistance is among the highest in Africa. The emergence of the resistant strains and specially the multi-drug-resistant strains (MDR-TB) in Kinshasa requires a regular assessment of these phenomena which threaten seriously the implementation of the national tuberculosis control programme.

Epidemic resurgence of Chikungunya virus in democratic Republic of the Congo: identification of a new central African strain.

The resurgence of Chikungunya virus is described during an urban epidemic in Kinshasa Democratic Republic of the Congo, after 39 years without any isolation of the virus. Chikungunya virus was isolated in sera from nine patients with clinical symptoms. A 1,200 bp long partial sequence of the E1/3'UTR genomic region was determined for each isolate. All sequences clustered in the central African lineage. They constitute Chikungunya virus reference sequences for the Democratic Republic of the Congo.

Surveillance virologique des paralysies flasques aiguës en Republique Démocratique du Congo (RDC) 1997-2001

Lesauteursrap p o rtent les résultatsde l'analyse de la surveillance viro l ogiquedespara lysies flasques aiguës (PFA )en République Démocratique du Congo (RDC),pays longtemps ravagé par des conflits armés. Au total,3658 échantillons deselles de cas de PFA en provenance des provinces sous contrôle gouvernemental,ont été analysés selon les méthodes recom-mandées par l'OMS. L' a m é l i o ration de la surveillance épidémiologique des PFA s'est traduite par l'accroissement sensible dunombre d'échantillons traités qui est passé de 32 en 1997 à 2471 en 2001. Les performances du laboratoire national de réfé-rence accrédité en 1999,ontétéappréciées par le taux annuel d'isolement desentérov i rusnon poliov i rus qui estpassé de10%en 1999 à 20% en 2001,et par le rendu des résultats qui est passé de 50% en 1999 pour dépasser en 2001 le seuil de 80% exigépar l'OMS. De 1997 à 2001,68 souches de poliovirus sauvages ont été isolées dont 52 souches de type 1,une souche de type 2et 15de type 3. Quat re-vingt un pour cent des casdepoliomyélitesurve nus entre 1997 et 2001ontétéobservés chezdes enfa n t sâgés de 0 à 5 ans. Seulement 12% ont été détectés chez des enfants âgés de 6 à 14 ans contre 3% chez de jeunes adolescents.Soixante-sept pour cent des 45 sujets atteints de poliomyélite et dont l'état vaccinal était connu,avaient reçu 0 à 3 doses devaccinanti-poliomyélitiqueoral. Parcontre15sujets(33%) bien qu'ayant reçuplusde4 dosesrequises deva c c i n ,avaient quandmême développélamaladie. Depuis1997,t roisprovinces dela RDC sontexemptesde poliov i russauvage :la ville deKinshasa,leBas-Congoet leNord - K ivu. En 2001,lacirc u l ation depoliov i russauvage aétéinterrompuesurtoutel'étenduedupaysgr â c eaux activités de vaccination de routine et surtout à l'organisation des journées nationales de vaccination

[Prevalence of HIV and HBs antigen in blood donors. Residual risk of contamination in blood recipients in East Kinshasa, Democratic Republic of the Congo]. / Prévalence du VIH et de l'antigène HBs chez les donneurs du sang. Risque résiduel de contamination chez les receveurs de sang à Kinshasa-est, Rèpublique Démocratique du Congo.

Between January and August 1999, a total of 7277 blood donors at various health centers in Kinshasa, Democratic Republic of the Congo were screened for human immunodeficiency virus 1 (HIV1) and hepatitis B surface antigen (HbsAg) using the ELISA technique. Findings showed an incidence of 6.4% for HIV1 antibodies, 9.2% for HbsAg, and 1% for HIV1 and HbsAg. Young females (under 39 years of age) from lower socio-economic classes were the most likely to be infected by HIV1. The risk of HIV transmission by transfusion of contaminated blood was 3%, which is close to the incidence of HIV in the general population. The findings of this study document the need to speed up implementation of blood donor screening in the city of Kinshasa and the rest of the country.

Viewpoint: filovirus haemorrhagic fever outbreaks: much ado about nothing?

The recent outbreak of Marburg haemorrhagic fever in the Democratic Republic of Congo has put the filovirus threat back on the international health agenda. This paper gives an overview of Marburg and Ebola outbreaks so far observed and puts them in a public health perspective. Damage on the local level has been devastating at times, but was marginal on the international level despite the considerable media attention these outbreaks received. The potential hazard of outbreaks, however, after export of filovirus from its natural environment into metropolitan areas, is argued to be considerable. Some avenues for future research and intervention are explored. Beyond the obvious need to find the reservoir and study the natural history, public health strategies for a more timely and efficient response are urgently needed.

High prevalence of GB virus C/hepatitis G virus in Kinshasa, Democratic Republic of Congo: a phylogenetic analysis.

A prevalence of 10.3% of GB virus C (GBV-C)/hepatitis G virus (HGV) carriers was found in 97 pregnant women from Kinshasa, Congo (formerly Zaire), while prevalences of 1%, 4.1%, and 0% were found for hepatitis C virus, human immunodeficiency virus, and human T-lymphotropic virus respectively. Phylogenetic analysis of the ten GBV-C/HGV positives based on the 5' non-coding region using three different methods identified consistently three GBV-C/HGV genotypes. Four main clades were found within the type 1 sequences. All the Congolese isolates are GBV-C/HGV type 1 in two different clades. The clustering of seven Congolese isolates was inconsistent in different methods. Further likelihood-mapping analysis showed a well-resolved phylogeny, confirming the clustering of the seven Congolese isolates with a Belgian strain representing a new clade in the GBV-C/HGV type 1 sequences.

Ebola hemorrhagic fever: lessons from Kikwit, Democratic Republic of the Congo.

The outbreak of Ebola hemorrhagic fever in Kikwit, Democratic Republic of the Congo, clearly signaled an end to the days when physicians and researchers could work in relative obscurity on problems of international importance, and it provided many lessons to the international public health and scientific communities. In particular, the outbreak signaled a need for stronger infectious disease surveillance and control worldwide, for improved international preparedness to provide support when similar outbreaks occur, and for accommodating the needs of the press in providing valid information. A need for more broad-based international health regulations and electronic information systems within the World Health Organization also became evident, as did the realization that there are new and more diverse partners able to rapidly respond to international outbreaks. Finally, a need for continued and coordinated Ebola research was identified, especially as concerns development of simple and valid diagnostic tests, better patient management procedures, and identification of the natural reservoir.

Ebola hemorrhagic fever in Kikwit, Democratic Republic of the Congo: clinical observations in 103 patients.

During the 1995 outbreak of Ebola hemorrhagic fever in the Democratic Republic of the Congo, a series of 103 cases (one-third of the total number of cases) had clinical symptoms and signs accurately recorded by medical workers, mainly in the setting of the urban hospital in Kikwit. Clinical diagnosis was confirmed retrospectively in cases for which serum samples were available (n = 63, 61% of the cases). The disease began unspecifically with fever, asthenia, diarrhea, headaches, myalgia, arthralgia, vomiting, and abdominal pain. Early inconsistent signs and symptoms included conjunctival injection, sore throat, and rash. Overall, bleeding signs were observed in <45% of the cases. Typically, terminally ill patients presented with obtundation, anuria, shock, tachypnea, and normothermia. Late manifestations, most frequently arthralgia and ocular diseases, occurred in convalescent patients. This series is the most extensive number of cases of Ebola hemorrhagic fever observed during an outbreak.