Seroprevalence of SARS-CoV-2 IgG antibodies among workers in the University Hospital of Guadeloupe.

OBJECTIVE: The Covid-19 pandemic is the major global health crisis of our time. The purpose of this study is to estimate the seroprevalence of IgG against SARS-CoV-2 among workers in the University Hospi-tal of Guadeloupe and to assess this seroprevalence in asymptomatic personnel as well as the proportion of asymptomatic agents among seropositive agents. SETTING AND METHODS: We carried out a seroprevalence study in the staff of the University Hospital of Guadeloupe. The presence of IgG anti SARS-CoV-2 was determined by a micro-particulate immunolo-gical assay using the chemiluminescence technique (CMIA, Architect i2000SR, Abbott). Data on the previous presence of symptoms sugge-stive of COVID-19, were identified using a standardized questionnaire. Statistical analyses were performed using Epi Info® software. RESULTS: From 07/05/2020 to 28/10/2020, 892 serologies were performed, 45 of which were positive for SARS-CoV-2 : a prevalence of 5.0% [95% CI: 3.6% - 6.5%]. Seroprevalence was 1.5% [95% CI: 0.6% - 2.3%] among agents who reported being asymptomatic. Among seropositive individuals, 24.4% [95% CI:12% - 36%] was totally asymptomatic. CONCLUSION: Our results highlight the importance of continuing seroprevalence studies for SARS-CoV-2 in hospital staff, which can provide important information on the level of exposure in healthcare workers and asymptomatic transmission of SARS-CoV-2 in clinical set-tings.

Prevalence and characterization of extended-spectrum ß-lactamase-producing clinical Salmonella enterica isolates in Dakar, Senegal, from 1999 to 2009.

A total of 1623 clinical isolates of Salmonella belonging to 229 serotypes were received by the Senegalese Reference Center for Enterobacteria from January 1999 to December 2009. The most common serotypes were Enteritidis (19% of the isolates), Typhi (8%), Typhimurium (7%) and Kentucky (4%). A significant increase in the prevalence of resistance to amoxicillin (0.9% in 1999 to 11.1% in 2009) and nalidixic acid (0.9% in 1999 to 26.7% in 2009) was observed in non-typhoidal Salmonella serotypes. For critically important antibiotics, notably ciprofloxacin and extended-spectrum cephalosporins (ESCs), the rates of resistance were low: 0.3% and 0.5%, respectively. Seven ESC-resistant Salmonella strains and three additional ESC-resistant strains from Senegal (1990) and Mali (2007) were studied to identify the genetic basis of their antibiotic resistance. All ESC-resistant strains produced an extended-spectrum ß-lactamase (ESBL). These were CTX-M-15 (n = 6; 2000-2008), SHV-12 (n = 3; 2000-2001) and SHV-2 (n = 1; 1990). A large IncHI2 ST1 pK29-like plasmid was found in six strains (three producing SHV-12 and three CTX-M-15), whereas IncN and IncF plasmids were found in three strains and one strain, respectively. The association of plasmid-mediated quinolone resistance (PMQR) genes qnrB1 and aac(6')-Ib-cr was found in four ESBL-producing strains, leading to decreased susceptibility and even full resistance to ciprofloxacin (MIC range 0.75-2 mg/L) despite the absence of mutations in the quinolone resistance-determining region (QRDR) of gyrA, gyrB, parC and parE. This association of ESBL and multiple PMQR mechanisms within the same strains is therefore a serious concern as it hampers the use of both ESCs and fluoroquinolones for severe Salmonella infections.

Klebsiella pneumoniae resistant to third-generation cephalosporins in five African and two Vietnamese major towns: multiclonal population structure with two major international clonal groups, CG15 and CG258.

The molecular epidemiology of third-generation cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in developing countries is poorly documented. From February 2007 to March 2008, we collected 135 3GC-R K. pneumoniae isolates from seven major towns in Maghreb (Morocco), West Africa (Senegal, Côte d'Ivoire), Central Africa (Cameroon), East Africa (Madagascar) and Southeast Asia (Vietnam). Their genetic diversity, assessed by multilocus sequence typing, was high (60 sequence types), reflecting multiclonality. However, two major clonal groups, CG15 (n = 23, 17% of isolates) and CG258 (n = 18, 13%), were detected in almost all participating centres. The two major clonal groups have previously been described in other parts of the world, indicating their global spread. The high diversity of enterobacterial repetitive intergenic consensus sequence-PCR banding patterns at the local level indicates that most isolates were epidemiologically unrelated. The isolates were characterized by the presence of multiple resistance determinants, most notably the concomitant presence of the aac(6')-Ib-cr, qnr and blaCTX-M-15 genes in 61 isolates (45%) belonging to 31 sequence types. These isolates were detected across a large geographical area including Cameroon (n = 1), Vietnam (n = 4), Madagascar (n = 10), Côte d'Ivoire (n = 12), Morocco (n = 13) and Senegal (n = 21). These results have major implications for patient management and highlight a potential reservoir for resistance determinants.

Clinical relevance of cagA and vacA gene polymorphisms in Helicobacter pylori isolates from Senegalese patients.

The molecular epidemiology of Helicobacter pylori in Africa is poorly documented. From January 2007 to December 2008, we investigated 187 patients with gastric symptoms in one of the main tertiary hospitals in Dakar, Senegal. One hundred and seventeen patients were culture-positive for H. pylori. Polymorphisms in vacA and cagA status were investigated by PCR; the 3'-region of cagA was sequenced, and EPIYA motifs were identified. Bacterial heterogeneity within individuals was extensively assessed by using an approach based on vacA and cagA heterogeneity. Fourteen per cent of H. pylori-positive patients displayed evidence of mixed infection, which may affect disease outcome. Patients with multiple vacA alleles were excluded from subsequent analyses. Among the final study population of 105 patients, 29 had gastritis only, 61 had ulcerated lesions, and 15 had suspicion of neoplasia based on endoscopic findings. All cases of suspected neoplasia were histologically confirmed as gastric cancer (GC). The cagA gene was present in 73.3% of isolates. CagA proteins contained zero (3.7%), one (93.9%) or two (2.4%) EPIYA-C segments, and all were western CagA. Most of the isolates possessed presumed high-vacuolization isotypes (s1i1m1 (57.1%) or s1i1m2 (21.9%)). Despite the small number of cases, GC was associated with cagA (p 0.03), two EPIYA-C segments in the C-terminal region of CagA (p 0.03), and the s1 vacA allele (p 0.002). Multiple EPIYA-C segments were less frequent than reported in other countries, possibly contributing to the low incidence of GC in Senegal.

Epidemiology of methicillin-resistant Staphylococcus aureus lineages in five major African towns: emergence and spread of atypical clones.

The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in Africa is poorly documented. From January 2007 to March 2008, we collected 86 MRSA isolates from five African towns, one each in Cameroon, Madagascar, Morocco, Niger and Senegal. Although one or two major clones, defined by the sequence type and staphylococcal cassette chromosome mec type, predominated at each site, genetic diversity (ten clones) was relatively limited in view of the large geographical area studied. Most of the isolates (n = 76, 88%) belonged to three major clones, namely ST239/241-III, a well-known pandemic clone (n = 34, 40%), ST88-IV (n = 24, 28%) and ST5-IV (n = 18, 21%). The latter two clones have only been sporadically described in other parts of the world. The spread of community-associated MRSA carrying the Panton-Valentine leukocidin genes is a cause for concern, especially in Dakar and possibly throughout Africa.

Epidemiology of methicillin-susceptible Staphylococcus aureus lineages in five major African towns: high prevalence of Panton-Valentine leukocidin genes.

The epidemiology of methicillin-susceptible Staphylococcus aureus (MSSA) in Africa is poorly documented. From January 2007 to March 2008, 555 S. aureus isolates were collected from five African towns in Cameroon, Madagascar, Morocco, Niger, and Senegal; among these, 456 unique isolates were susceptible to methicillin. Approximately 50% of the MSSA isolates from each different participating centre were randomly selected for further molecular analysis. Of the 228 isolates investigated, 132 (58%) belonged to five major multilocus sequence typing (MLST) clonal complexes (CCs) (CC1, CC15, CC30, CC121 and CC152) that were not related to any successful methicillin-resistant S. aureus (MRSA) clones previously identified in the same study population. The luk-PV genes encoding Panton-Valentine leukocidin (PVL), present in 130 isolates overall (57%), were highly prevalent in isolates from Cameroon, Niger, and Senegal (West and Central Africa). This finding is of major concern, with regard to both a source of severe infections and a potential reservoir for PVL genes. This overrepresentation of PVL in MSSA could lead to the emergence and spread of successful, highly virulent PVL-positive MRSA clones, a phenomenon that has already started in Africa.

Invasive serotype 1 Streptococcus pneumoniae outbreaks in the South Pacific from 2000 to 2007.

In New Caledonia, Wallis and Futuna, and French Polynesia, an active surveillance system was established to monitor pneumococcal serotype prevalence between 2000 and 2007. The most prevalent serotype was serotype 1, which belonged to the major clonal complex sequence type 306 (ST306) and was responsible for invasive pneumococcal disease outbreaks.

Antimicrobial Resistance in Outpatient Escherichia coli Urinary Isolates in Dakar; Senegal

Background: Data regarding the evolution of antimicrobial resistance are needed to suggest appropriate empirical treatment of urinary tract infections (UTI) in developing countries. To assess the antimicrobial susceptibility of Escherichia coli; the predominant pathogen in community-acquired UTI; a prospective multicenter study was carried out in Dakar; Senegal. Methodology: From February 2004 to October 2006; 1010 non-duplicate E. coli strains were collected from four centres. Antimicrobial susceptibility testing was performed using disk diffusion method according to the recommendations of the CA-SFM (2004). Results: Most of the isolates were resistant to amoxicillin (73.1); amoxicillin- clavulanic acid (67.5); cephalothin (55.8); and trimethoprim/sulfamethoxazole (68.1). Extended spectrum beta-lactamase was detected in 38 strains. The overall resistance rates to nalidixic acid; norfloxacin and ciprofloxacin were 23.9; 16.4and 15.5; respectively. Most of the strains were susceptible to gentamicin; nitrofurantoin and fosfomycin (respective susceptibility rates; 93.8; 89.9; and 99.3). During this period; a significant decrease in sensitivity was observed for cephalothin; fluoroquinolones and trimethoprim/sulfamethoxazole (p0.001). Conclusions: These data suggest that trimethoprim/sulfamethoxazole may no longer be used as empirical treatment for community- acquired UTI in Dakar. In order to preserve the activity of fluoroquinolones for future years; alternatives such as fosfomycin or nitrofurantoin should be considered

Class 2 integron-associated antibiotic resistance in Shigella sonnei isolates in Dakar, Senegal.

Forty-three Shigella sonnei isolates from adult patients with diarrhoea in Dakar were analysed for the presence of integrons. Isolates were resistant to sulphamethoxazole, trimethoprim, tetracycline, streptomycin and spectinomycin. A high prevalence of class 2 integrons (93%) was found. These integrons showed three distinct structures: a class 2 integron, part of the Tn7 family and its derivatives, carrying four cassettes in the order dfrA1-sat-aadA1-orfX; a truncated class 2 integron, without orfX; and a third type ca. 4 kb in size. These class 2 integrons probably play a role in the spread of multiresistance in S. sonnei isolates. To our knowledge, this is the first description of class 2 integrons in S. sonnei isolated in sub-Saharan Africa.

Distribution of Streptococcus pneumoniae serotypes responsible for penicillin resistance and the potential role of new conjugate vaccines in New Caledonia.

Invasive pneumococcal disease is a significant cause of morbidity and mortality worldwide. The aim of this study was to establish the serotypes responsible for pneumococcal disease and the serotypes responsible for penicillin resistance in Noumea, New Caledonia. Isolates of Streptococcus pneumoniae from all body sites referred to the Microbiology Department of the Pasteur Institute in New Caledonia between May 1999 and May 2001 had serotyping and susceptibility testing performed. Basic demographic data on patients were also collected. A total of 298 isolates were included in the study. The most common serotypes were types 1 (20%), 23F (10%), 12F (8%), 19F (8%), and 6B (5%). The serotype distribution differed significantly with age, site of collection, and ethnicity. Overall, 280 of 298 (94%) of the isolates had serogroups that are included in the 23-valent vaccine. However, only 14 of 20 (70%) of the isolates associated with invasive disease from children younger than 5 years of age and 26 of 113 (23%) of invasive isolates from patients more than 5 years of age were included in the new 7-valent conjugate vaccine. Overall, reduced susceptibility to penicillin was found in 43 of 298 (14.4%) of the isolates, with 13% falling into the intermediate resistance category and only 5 (2%) being high-level resistant. A higher prevalence of penicillin resistance occurred in younger age groups and in European patients and involved specifically certain serotypes. The 7-valent conjugate pneumococcal vaccine has potential benefit for the New Caledonian population under 5 years of age and should be considered for future vaccines schedules.

[Nasopharyngeal carriage of Streptococcus pneumoniae in healthy children, 2 to 24 months of age, in New-Caledonia]. / Etude du portage rhinopharyngé de Streptococcus pneumoniae chez les enfants sains âgés de 2 à 24 mois en Nouvelle-Calédonie.

OBJECTIVES: The aims of this study were to determine the prevalence of pneumococcal nasopharyngeal carriage in New-Caledonian children less than two years of age, to define risk factors for carriage, and to document the serotypes present in New Caledonia prior to the implementation of the conjugate pneumococcal vaccine. METHOD AND RESULTS: From August 2002 to April 2003, nasopharyngeal samples were collected on 1040 children less than two years of age during scheduled visits to dispensaries for routine immunization. Of the 1040 samples, 544 (52%) were positive for Streptococcus pneumoniae. The percentage of pneumococcal strains with reduced susceptibility to penicillin (PRSP) was 21%. Several risk factors for pneumococcal carriage were identified. These included the Province that the child lived in, the ethnic group, age, and having a sibling less than 6 years of age. Risk factors for carriage of PRSP carriage were similar but also included additional risk factors such as attendance at day care and a history of antibiotic treatment. The eight most frequent serotypes were 6B, 19F, 14, 23F, 6A, 19A, 11A, and 16F. These serotypes accounted for 60% of all strains detected. The most frequent serotypes of PRSP were 14, 9 V, 19F, 23F, and 6B. They were more often identified in european children and 80% were vaccine serotypes. However, overall 250/544 (46%) of all pneumococcal isolates were those included in the 7 serotype vaccine.

Multicenter study of street foods in 13 towns on four continents by the food and environmental hygiene study group of the international network of pasteur and associated institutes.

An international multicenter study of ready-to-eat foods, sandwiches, and ice creams or sorbets sold in the streets and their vendors was carried out to assess the microbiological quality of these foods and to identify characteristics of the vendors possibly associated with pathogens. Thirteen towns in Africa, America, Asia, and Oceania were involved in the study. A single protocol was used in all 13 centers: representative sampling was by random selection of vendors and a sample of foods bought from each of these vendors at a time and date selected at random. Microbiological analyses were carried out using standardized Association Française de Normalisation methods, and the use of a standardized questionnaire to collect data concerning the characteristics of the vendors. Fifteen surveys were carried out, with 3,003 food samples from 1,268 vendors. The proportion of unsatisfactory food samples was between 12.7 and 82.9% for ice creams and sorbets and between 11.3 and 92% for sandwiches. For ice creams and sorbets, the sale of a large number of units (>80 per day) increased the risk of unsatisfactory food by a factor of 2.8 (95% confidence interval [CI]: 1.5 to 5.1), lack of training in food hygiene by 6.6 (95% CI: 1.1 to 50). and by a factor of 2.8 (95% CI: 1.4 to 5.4) for mobile vendors. These risk factors were not identified for sandwiches, this difference may be due to the presence of a cooking step in their preparation. These results show that the poor microbiological quality of these street foods constitutes a potential hazard to public health, that the extent of this hazard varies between the cities studied, and that vendors' health education in food safety is a crucial factor in the prevention of foodborne infections.

Molecular epidemiology of human herpesvirus 8 in africa: both B and A5 K1 genotypes, as well as the M and P genotypes of K14.1/K15 loci, are frequent and widespread.

We have studied 52 new HHV8 strains by sequencing the complete hypervariable K1 gene and genotyping the K14.1/K15 loci located at both sides, respectively, of the viral genome. The samples originated from 49 patients with Kaposi's sarcoma (KS; 32 patients), multicentric Castleman's disease (MCD; 12 patients), or primary effusion lymphoma (PEL; 5 patients). Among these patients, 32 were of African origin (West and Central African countries and Creoles from French Guiana) and the 17 others were mostly French homosexuals. Comprehensive phylogenetic studies allowed the identification of distinct groups within the three already known main subtypes. Interestingly, two new sequences that did not cluster within a known subtype or group could be considered as prototypes of early/ancient variants of the C subtype and A/C set, respectively. Among the 32 African strains, the majority were either of the B subtype (13 cases) or of the A5 group (11 cases), indicating that this latter genotype is frequent and widespread in Africa. In contrast, a subtype C strain infected most of the 17 other patients. PCR-based genotyping of the K14.1/K15 loci revealed an overall predominance of P subtype, except in the A5 and B K1 groups, in which the P and M alleles were equally represented. The implications of these data on the evolution and spread of HHV8 among human African populations are discussed.

Compartmentalization of the IgG immune response to HIV-1 in breast milk.

OBJECTIVE: To evaluate the IgG immune response to HIV-1 in colostrum. METHODS: Paired serum and colostrum were collected from 16 asymptomatic HIV-1-infected women. IgG to gp160 and to four peptides (gp41 immunodominant DI domain, gp41/Id; EDLKWA epitope of DIII domain, gp41/K; gp120 C-terminus, gp120/Ct; V3 loop, gp120/V3) were evaluated in all samples. Functional activity of purified IgG was assessed for the ability to block transcytosis of cell-associated HIV-1 through a tight monolayer of endometrial epithelial cell line HEC1. RESULTS: IgG antibody to gp160 and to the four env-encoded synthetic peptides were detected in all specimens. The mean specific activity of IgG to gp41/K was 4.2 fold higher in colostrum than in paired serum. In contrast, mean specific activities of IgG to gp160 and gp41/Id were twofold higher in serum than in paired colostrum. Mean specific activities of IgG to gp120/V3 and to gp120/Ct were similar in systemic and milk compartments. Functional activity of IgG was evaluated in six paired serum and colostrum: in two women, serum IgG was 3.0 and 7.6 fold more efficient in blocking transcytosis than colostrum IgG; in one patient, colostrum IgG exhibited a 28 fold higher inhibitory capacity than serum IgG; in the remaining patients, serum and colostrum IgG demonstrated similar inhibitory activities against transcytosis of HIV. CONCLUSION: These features are consistent with a compartmentalization of the humoral IgG immune response to HIV within the mammary gland. Some HIV-1 antigens are able to induce a strong humoral mucosal immune response which may be of relevance for the design of a mucosal vaccine against HIV-1.

High mortality rates among patients with tuberculosis in Bangui, Central African Republic.

PIP: Survival time until death was investigated in a prospective cohort of 224 tuberculosis patients from Bangui, Central African Republic, who were randomly selected from among 1492 such patients registered in 1993 and 1994. 6 patients (2.7%) presented with extrapulmonary tuberculosis, 186 (83%) were smear-positive, and 139 (62%) were infected with HIV-1. 23 (10.3%) had multidrug-resistant tuberculosis strains. The treatment regimen (isoniazid, rifampicin, ethambutol, and pyrazinamide for 2 months, followed by isoniazid and ethambutol for another 6 months) was successful in 46.4% of HIV-infected patients compared with 67.1% of HIV-negative patients. At the end of 8 months, 39.1% of HIV-infected patients but only 8.2% of HIV-negative patients had died. 24 months after the start of tuberculosis treatment, the cumulative death rate was 58% in HIV-seropositive patients compared with 20% in seronegative patients. Median life expectancy to death among HIV-infected tuberculosis patients was 15 months. Decreased survival was significantly associated with HIV-seropositivity, older age, failure to complete the full treatment regimen, and a low CD4 cell count. Multidrug-resistant tuberculosis was not linked to increased mortality.^ieng

High-level ability of secretory IgA to block HIV type 1 transcytosis: contrasting secretory IgA and IgG responses to glycoprotein 160.

The IgG and secretory IgA (S-IgA) responses to the HIV-1 envelope (gp160 antigen) were analyzed in the colostrum (Col) and in the cervicovaginal fluid (CVF) of HIV-l-infected women. We show IgG antibodies (Abs) to the recombinant gp160 to be predominant as compared with the corresponding S-IgA isotype. The low level of the S-IgA response cannot be related to a general disturbance of the mucosal-associated Iymphoid tissue (MALT) because the level of a current Ab to a caries-associated antigen from Streptococcus sobrinus was in the normal range in these secretions. The major subclass of IgA to gp160 was of the alpha1 isotype both in Col and in CVF. However, the specific activities of S-IgA1 and S-IgA2 were different when expressed as the ratio of the anti-gp160 related to total Ig of each subclass. Indeed, the specific activity of the S-IgA2 was predominant over S-IgA1 in the Col, whereas the reciprocal results were found in CVF, showing a subcompartmentalization of these secretions. The ability of S-IgA and IgG to block one of the pathways involved in the HIV-1 penetration across mucosa, i.e., transcytosis through epithelial cells, was evaluated using a functional in vitro assay. Both S-IgA and IgG Abs impaired virus transcytosis, irrespective of the level of antigp160 specific activities. However, specific S-IgA was more efficient than IgG. These features suggest that mucosal specific S-IgA to HIV-1 could be relevant in decreasing infectivity of HIV-1 in corporal fluids.

Molecular epidemiology of 58 new African human T-cell leukemia virus type 1 (HTLV-1) strains: identification of a new and distinct HTLV-1 molecular subtype in Central Africa and in Pygmies.

To gain new insights on the origin, evolution, and modes of dissemination of human T-cell leukemia virus type I (HTLV-1), we performed a molecular analysis of 58 new African HTLV-1 strains (18 from West Africa, 36 from Central Africa, and 4 from South Africa) originating from 13 countries. Of particular interest were eight strains from Pygmies of remote areas of Cameroon and the Central African Republic (CAR), considered to be the oldest inhabitants of these regions. Eight long-term activated T-cell lines producing HTLV-1 gag and env antigens were established from peripheral blood mononuclear cell cultures of HTLV-1 seropositive individuals, including three from Pygmies. A fragment of the env gene encompassing most of the gp21 transmembrane region was sequenced for the 58 new strains, while the complete long terminal repeat (LTR) region was sequenced for 9 strains, including 4 from Pygmies. Comparative sequence analyses and phylogenetic studies performed on both the env and LTR regions by the neighbor-joining and DNA parsimony methods demonstrated that all 22 strains from West and South Africa belong to the widespread cosmopolitan subtype (also called HTLV-1 subtype A). Within or alongside the previously described Zairian cluster (HTLV-1 subtype B), we discovered a number of new HTLV-1 variants forming different subgroups corresponding mainly to the geographical origins of the infected persons, Cameroon, Gabon, and Zaire. Six of the eight Pygmy strains clustered together within this Central African subtype, suggesting a common origin. Furthermore, three new strains (two originating from Pygmies from Cameroon and the CAR, respectively, and one from a Gabonese individual) were particularly divergent and formed a distinct new phylogenetic cluster, characterized by specific mutations and occupying in most analyses a unique phylogenetic position between the large Central African genotype (HTLV-1 subtype B) and the Melanesian subtype (HTLV-1 subtype C). We have tentatively named this new HTLV-1 genotype HTLV-1 subtype D. While the HTLV-1 subtype D strains were not closely related to any known African strain of simian T-cell leukemia virus type 1 (STLV-1), other Pygmy strains and some of the new Cameroonian and Gabonese HTLV-1 strains were very similar (>98% nucleotide identity) to chimpanzee STLV-1 strains, reinforcing the hypothesis of interspecies transmission between humans and monkeys in Central Africa.