Q Fever as a Cause of Community-Acquired Pneumonia in French Guiana.

In French Guiana, community-acquired pneumonia (CAP) represents over 90% of Coxiella burnetii acute infections. Between 2004 and 2007, we reported that C. burnetii was responsible for 24.4% of the 131 CAP hospitalized in Cayenne. The main objective of the present study was to determine whether the prevalence of Q fever pneumonia remained at such high levels. The secondary objectives were to identify new clinical characteristics and risk factors for C. burnetii pneumonia. A retrospective case-control study was conducted on patients admitted in Cayenne Hospital, between 2009 and 2012. All patients with CAP were included. The diagnosis of acute Q fever relied on titers of phase II IgG ≥ 200 and/or IgM ≥ 50 or seroconversion between two serum samples. Patients with Q fever were compared with patients with non-C. burnetii CAP in bivariate and multivariate analyses. During the 5-year study, 275 patients with CAP were included. The etiology of CAP was identified in 54% of the patients. C. burnetii represented 38.5% (106/275; 95% CI: 31.2-45.9%). In multivariate analysis, living in Cayenne area, being aged 30-60 years, C-reactive protein (CRP) > 185 mg/L, and leukocyte count < 10 G/L were independently associated with Q fever. The prevalence of Q fever among CAP increased to 38.5%. This is the highest prevalence ever reported in the world. This high prevalence justifies the systematic use of doxycycline in addition to antipneumococcal antibiotic regimens.

First cases of Burkholderia cenocepacia IIIA neonatal sepsis in Central African Republic.

Bacteria of the Burkholderia cepacia complex cause frequent infections in immunocompromised and hospitalized patients, with a significant mortality rate. Phenotypic identification of those bacteria is difficult and therefore rarely reported from developing countries. This study presents the first ever reported case series of Burkholderia cenocepacia neonatal sepsis in Central African Republic. It demonstrates the superiority of molecular methods to accurately identify B. cenocepacia IIIA species compared to the phenotypic methods.

Burkholderia cepacia meningitis in the Central African Republic.

Burkholderia cepacia causes frequent infections in immunocompromised and hospitalized patients, with a significant mortality rate. This bacterial species has also been associated with epidemic outbreaks due to contamination of antiseptic solutions and parenteral and nebulized medications. In 2016, in the town of Bongonon in the north of the Central African Republic (CAR), a three-year-old boy with febrile meningeal syndrome (fever, neck stiffness and altered general condition) was admitted for a medical consultation provided by the nongovernmental organization MSF-Spain. On 20 March 2016, a sample of the boy's cerebrospinal fluid was sent to the Bacteriology Laboratory of the Pasteur Institute of Bangui for analysis. Conventional bacteriology showed that the isolate was a Gram-negative bacillus, which was identified as B. cepacia by using API 20 NE, with 99.9%confidence. In addition, the strain presented an acquired resistance to ticarcillin-clavulanate, ceftazidime and imipenem but remained susceptible to cotrimoxazole. As B. cepacia had never previously been isolated from cerebrospinal fluid in Africa, we chose to identify the strain by 16S rRNA gene sequencing. The molecular data showed that the isolate belonged to B. cepacia group. This is the first report of a case of meningitis caused by B. cepacia in CAR and developing countries.

Surveillance of Rifampicin Resistance With GeneXpert MTB/RIF in the National Reference Laboratory for Tuberculosis at the Institut Pasteur in Bangui, 2015-2017.

BACKGROUND: The Central African Republic (CAR) has one of the heaviest burdens of tuberculosis (TB) in the world, with an incidence of 423 cases per 100 000 population. Surveillance of resistance to rifampicin with GeneXpert MTB/RIF was instituted in the National TB Reference Laboratory in 2015. The aim of this study was to evaluate, after 3 years, resistance to rifampicin, the most effective firstline drug against TB. METHODS: The surveillance database on cases of rifampicin resistance was retrospectively analyzed. The populations targeted by the National TB Programme were failure, relapse, default, and contacts of multidrug-resistant TB (MDR-TB). Statistical analyses were performed with Stata software, version 14, using chi-square tests and odds ratios. RESULTS: Six hundred seventeen cases were registered; 63.7% were male, 36.3% were female, and the mean age was 35.5 years (range from 2 to 81). GeneXpert MTB/RIF tests were positive in 79.1% (488/617), and resistance to rifampicin was positive in 42.2% (206/488), with 49.1% (56/114) in 2015, 34.7% (57/164) in 2016, and 44.3% (93/210) in 2017. Failure cases had the highest rate of resistance (70.4%), with a significant difference (P < .0001; odds ratio, 9.5; 95% confidence interval, 4.4-20.5). Resistance was observed in 40% of contacts of MDR-TB, 28.2% of the relapses and 20% of the defaults without significant difference. CONCLUSIONS: Resistance to rifampicin is still high in the CAR and is most strongly associated with treatment failure. The Ministry of Health must to deploy GeneXpert MTB/RIF tests in the provinces to evaluate resistance to TB drugs in the country.

Epidemiology of Human Leptospirosis in French Guiana (2007-2014): A Retrospective Study.

Leptospirosis is a worldwide zoonotic bacterial infection with a rising incidence. French Guiana is mostly covered by Amazonian rain forest. Despite a potentially favorable environment, leptospirosis has been barely studied in French Guiana. The objective of this study was to describe the current trends of leptospirosis epidemiology in French Guiana. A cross-sectional study was performed in the two main hospitals of French Guiana. Cases of leptospirosis from 2007 to 2014 were retrospectively identified with a systematic screening of serological and polymerase chain reaction results to classify them as confirmed, probable, or excluded cases. Medical files were reviewed to collect epidemiological data. Among the 72 included patients, 55 (76.4%) cases were confirmed and 17 (23.6%) were probable. The median age was 39 years (range: 16-82 years) and the M/F sex ratio 6.2. Sixty-two (86.1%) patients required hospitalization, including 12 (16.7%) in the intensive care unit. Three (4.2%) patients died. The monthly distribution of cases was correlated with rainfall (P = 0.004) and moisture (P = 0.038). Professional exposure was frequently identified (especially gold mining and construction). Among 16 different serogroups identified by microagglutination test, Icterohaemorrhagiae was the most frequent (38.0%). This study revealed an epidemiology close to that observed in Brazilian regions, and professional and climatic risk factors. The high diversity of serogroups may reveal a complex environmental reservoir requiring further investigations. Only 20% of leptospirosis patients were suspected as such on hospital admission, thus emphasizing the need to inform local physicians.

Mycobacterium ulcerans infection (Buruli ulcer) in French Guiana, South America, 1969-2013: an epidemiological study.

BACKGROUND: Mycobacterium ulcerans infection is the third most common mycobacterial disease in the world after tuberculosis and leprosy. To date, transmission pathways from its environmental reservoir to humans are still unknown. In South America, French Guiana has the highest reported number of M ulcerans infections across the continent. This empirical study aimed to characterise the epidemiology of M ulcerans infection in French Guiana between 1969 and 2013. METHODS: Data were collected prospectively mainly by two dermatologists at Cayenne Hospital's dermatology department between Jan 1, 1969, and Dec 31, 2013, for age, date of diagnosis, sex, residence, location of the lesion, type of lesion, associated symptoms, and diagnostic method (smear, culture, PCR, or histology) for all confirmed and suspected cases of M ulcerans. We obtained population data from censuses. We calculated mean M ulcerans infection incidences, presented as the number of cases per 100 000 person-years. FINDINGS: 245 patients with M ulcerans infections were reported at Cayenne Hospital's dermatology department during the study period. M ulcerans infection incidence decreased over time, from 6·07 infections per 100 000 person-years (95% CI 4·46-7·67) in 1969-83 to 4·77 infections per 100 000 person-years (3·75-5·79) in 1984-98 and to 3·49 infections per 100 000 person-years (2·83-4·16) in 1999-2013. The proportion of children with infections also declined with time, from 42 (76%) of 55 patients in 1969-83 to 26 (31%) of 84 in 1984-98 and to 22 (21%) of 106 in 1999-2013. Most cases occurred in coastal areas surrounded by marshy savannah (incidence of 21·08 per 100 000 person-years in Sinnamary and 21·18 per 100 000 person-years in Mana). Lesions mainly affected limbs (lower limbs 161 [66%] patients; upper limbs 60 [24%] patients). We diagnosed no bone infections. INTERPRETATION: The decrease of M ulcerans infection incidence and the proportion of children with infections over a 45 year period in this ultra-peripheral French territory might have been mostly driven by improving living conditions, prophylactic recommendations, and access to health care. FUNDING: Agence Nationale de la Recherche.

HIV-1 Pol Gene Polymorphism and Antiretroviral Resistance Mutations in Treatment-Naive Adult Patients in French Guiana Between 2006 and 2012.

Little information is available on the molecular epidemiologic profile of HIV-1 in French Guiana, the French department with the highest HIV/AIDS incidence. To follow the evolution of HIV-1 diversity, we carried out a molecular analysis of HIV-1 isolates from 305 treatment-naive patients between 2006 and 2012. Protease and reverse-transcriptase sequences were obtained for subtype characterization, polymorphism analysis, and identification of drug resistance mutations. Of 305 HIV-1 strains, 95.1% were subtype B viruses. The overall prevalence of transmitted drug-resistance mutations (TDRMs) was 4.6% (14/305), ranging from 1.9% to 7.1% depending on the year. This study shows a low level of HIV-1 genetic diversity and a moderate prevalence of TDRMs with no evidence of an increasing trend over the study period. Nevertheless, the strong genetic polymorphism observed on both genes may be of concern for long-term treatment of people living with HIV-1 and thus deserves continuous monitoring.

Aetiology of community-acquired pneumonia in hospitalized adult patients in New Caledonia.

OBJECTIVE: To describe the aetiology of community-acquired pneumonia (CAP) in hospitalized adult patients in New Caledonia, a French archipelago in the South Pacific. METHODS: Confirmed CAP patients (n=137) were enrolled prospectively. Pathogens were detected by culture, molecular methods, serology on paired sera, immunofluorescence on nasopharyngeal swabs and antigen detection in urine. RESULTS: The aetiology of CAP was determined in 82 of 137 cases (59.8%), of which 31 exhibited two or more pathogens (37.8%). Hundred and seventeen pathogens were detected: Streptococcus pneumoniae was the most common one (41.0%), followed by influenza virus A (22.1%) and Haemophilus influenzae (10.2%). The frequency of atypical bacteria was low (6.0%). The most frequent and significant coinfection was S. pneumoniae with influenza A virus (P=0.004). Influenza virus was detected from nasopharyngeal swabs in four patients (15.4% of patients tested for influenza) and by PCR from pulmonary specimens in 15 patients (57.7%). CONCLUSIONS : Pneumoniae is the leading cause of CAP in New Caledonian adults. Viral-bacterial co-infections involving S. pneumoniae and influenza virus are very common during the winter. Such adult patients hospitalized with CAP are a clear sentinel group for surveillance of influenza. Vaccination against influenza and S. pneumoniae should be strengthened when risk factors are identified.

Comparison of PanBio dengue IgM ELISA assay with pentax dengue IgM particle agglutination assay to evaluate factors affecting false positive results.

The objectives of this study were to conduct a further evaluation of performance characteristics (sensitivity/specificity, predictive values, cross-reactivity) of PanBio Dengue IgM (IgM-EIA test), particularly during non-epidemic periods in New Caledonia, and (ii) to evaluate an alternative test, Pentax Dengue IgM-Particle Agglutination (PA-lgM) test. A total of 1,808 samples were first tested with the IgM-EIA test and reactive specimens were then re-tested with IgM-PA test. Sensitivity and specificity were measured on a prospective mode from 2005 and 2006. Other etiologies were also investigated to confirm the non-specific reactive results. One hundred fifty-three samples were initially reactive with IgM-EIA test. Of these, 147 were classified as non specific and only 16 were reactive with the particle agglutination test (89.1% reduction of this interference). The specificity and positive predictive value of the ELISA test was 91.8% and 5.8%, respectively. The extrapolated specificity and positive predictive value for the particle agglutination test was 99.1% and 33.3%, respectively. Hepatitis A was identified as a major source of false positive, followed by rheumatoid factor and leptospirosis. Sensitivity of both tests was100% on samples taken from the fifth day of the disease.

Isolation of Trichophyton concentricum from chronic cutaneous lesions in patients from the Solomon Islands.

Tinea imbricata, also known as 'Tokelau', is an uncommon superficial mycosis caused by the anthropophilic dermatophyte Trichophyton concentricum. Cutaneous lesions appear characteristically as scaly and concentric rings that may cover all parts of the body. Often acquired in childhood, tinea imbricata is a chronic disease and lichenification is extremely common due to pruritus. The dermatophytosis mainly occurs in the South Pacific, but also in some regions of Southeast Asia and Central or South America. Tinea imbricata usually affects people living in primitive and isolated conditions. Mycological analysis is required for the diagnosis. The epidemiological and mycological study reported here took place in the Solomon Islands from June-September 2006. Skin scrapings were collected from 29 Melanesian patients (aged 8 months to 58 years) with chronic cutaneous lesions and were analysed mycologically in the Laboratory of Parasitology and Mycology of Angers University Hospital (France). Ten patients showed very evocative lesions with a positive direct examination, but T. concentricum was only isolated from three patients. Identification of the strains was confirmed by sequencing of the internal transcribed spacer (ITS) regions. With the increase in international travel, one cannot disregard that this very rare species may be isolated by mycologists in temperate areas from patients coming from endemic foci.

Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient.

Between 2000 and 2004, dengue virus type 1 (DENV-1) genotypes I and II from Asia were introduced into the Pacific region and co-circulated in some localities. Envelope protein gene sequences of DENV-1 from 12 patients infected on the island of New Caledonia were obtained, five of which carried genotype I viruses and six, genotype II viruses. One patient harboured a mixed infection, containing viruses assigned to both genotypes I and II, as well as a number of inter-genotypic recombinants. This is the first report of a population of dengue viruses isolated from a patient containing both parental and recombinant viruses.

Multicentre survey of incidence and public health impact of leptospirosis in the Western Pacific.

The objectives of the study were to describe the mode of circulation (endemic or epidemic) of human leptospirosis in various Pacific island states and territories by identifying predominant Leptospira serogroups and the most probable routes of human exposure, and to recommend a feasible laboratory strategy for leptospirosis in the Pacific. From September 2003 to December 2005, 263 leptospirosis suspect patients were recruited by public practitioners on 11 Pacific islands, using the WHO case definition. Diagnosis was confirmed using a three-level serology algorithm and a regional laboratory network. Sixty-nine leptospirosis cases were identified from seven islands: Futuna, Raiatea and the Marquesas Islands where outbreaks were apparent, and Vanuatu, Fiji, Palau and Wallis where sporadic cases indicated at least the presence of the disease. Most patients were men aged 17-40 years. The infection appeared to occur during the course of normal daily activities more often than following specific professional exposure. The dominant presumptive serogroups were Icterohaemorrhagiae and Australis, highly suggestive of a rodent reservoir. This study confirms the widespread presence of leptospirosis in the Pacific region. It should help in the implementation of local leptospirosis control plans and highlights the role of on-site laboratory confirmation.

A rapid and quantitative method for the detection of Leptospira species in human leptospirosis.

Prompt laboratory diagnosis of leptospirosis infection facilitates patient management and initiation of therapy. A cost effective real-time PCR assay using SYBR Green I was developed for detection of pathogenic leptospires in serum specimens. Specific PCR products were obtained only with DNA of pathogenic Leptospira genomospecies. LightCycler PCR ability to distinguish between species was possible using melting curves, providing an approach for identification with a specific Tm assigned to a single species or set of species. Assay sensitivity was approximately 50 leptospires/ml, corresponding to one to two genome copies in a PCR mixture. Fifty-one patients who had clinical symptoms consistent with leptospirosis were tested both with a previously described rrs amplification and our real-time assay. Our LFB1 real-time assay confirmed the diagnosis for 25 patients (49%, 25/51) and revealed an estimated density of 8.0x10(1)-3.9x10(4) leptospires/ml of blood. The total assay time for 12 clinical samples from sample to data analysis was less than 3 h. These data illustrate the potential of our LFB1 real-time assay for the rapid detection of leptospires in serum samples and their subsequent quantification in a single run.

Laboratory-based influenza surveillance in New Caledonia, 1999-2003.

We aimed to evaluate the annual incidence of influenza in New Caledonia and to identify the circulating viral types and subtypes in order to gather information for the local vaccination programme and regional influenza surveillance. A surveillance network was set up in 1999; it included sentinel practitioners in Noumea and the virology department of the Pasteur Institute. Influenza circulated in New Caledonia every year, regularly during the southern hemisphere winter and occasionally during March-May. Isolates were generally consistent with world surveillance, except in 1999, when a new A/H1N1 variant was identified. This study emphasises the need for regular influenza surveillance, even when performed on a limited scale. Importantly the optimal time for local vaccination was found to be in December or January each year.

Sustained transmission of dengue virus type 1 in the Pacific due to repeated introductions of different Asian strains.

Outbreaks of dengue due to dengue virus type 1 (DENV-1) occurred almost simultaneously in 2001 in Myanmar and at multiple sites almost 10,000 km away in the Pacific. Phylogenetic analyses of the E protein genes of DENV-1 strains recovered from Asia and the Pacific revealed three major viral genotypes (I, II, and III) with distinct clades within each. The majority of strains from the Pacific and Myanmar, and a number of other Asian strains fell into genotype I. Genotype II comprised a smaller set of Asian and Pacific strains, while genotype III contained viruses from diverse geographical localities. These analyses suggested that the continuing outbreak of dengue in the Pacific has been due to multiple, direct, introductions of dengue viruses from a variety of locations in Asia followed by local transmission. There was no evidence that the introduction of these viruses into the Pacific was associated with any adaptive changes in the E protein of the viruses.

10 year assessment of infant hepatitis B vaccination program, in the Loyalty Islands (New Caledonia).

OBJECTIVES OF THE STUDY: To evaluate the decrease of hepatitis B prevalence in New Caledonia 10 years after the implementation of a neonatal vaccination program and discuss the need of any booster in preadolescents. METHOD: A survey was conducted in the Loyalty Islands, involving 593 children aged 8-11 years. Serological profiles were determined using three parameters: antibodies to core and surface antigens and HBs Ag. RESULTS: The vaccine coverage rate is 93 and 89% of the children are protected against hepatitis B. However, 8% of them did have contact with the virus and 1.3% are carriers. Thirty-eight percent of the vaccinated children had their first injection later than the age of 3 months. CONCLUSION: This study attests that the neonatal immunisation is accepted and followed. The prevalence reduction is not as great as expected, probably due to excess delay in primary vaccination. Hepatitis B eradication could be achieved in New Caledonia by starting immunisation at birth, and by implementing a global catch-up program among preadolescents.