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1.
J Glob Antimicrob Resist ; 24: 175-177, 2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-33460845

RESUMO

OBJECTIVES: The underlying resistance mechanisms, defence systems, mobilome, virulome, clonality and global phylogenetic relationship of a novel sequence type (ST) 658 Aeromonas hydrophilia (A34a) isolated from a pig abattoir in South Africa was determined using whole-genome sequence (WGS) technology. METHODS: Following isolation on chromogenic agar (CHROMID® CARBA SMART), microbial identification and antibiotic susceptibility testing were performed using a VITEK®2 platform. Genotyping involved WGS performed with an Illumina MiSeq platform. RESULTS: The antibiotic resistome agreed with the resistance phenotype of the isolate and included antibiotic resistance determinants for ß-lactams (blaCPHA3 and blaOXA-724). BLASTn analysis of resistome-encoding contigs affirmed chromosomally-mediated resistance. BURST algorithmic analysis identified the novel ST658 as a satellite variant. Virulome analysis predicted virulence genes of Aeromonas whose expression are critical for establishing infection in the host. Global phylogenomic analyses showed strain A34a is closely related to two international isolates from Sri Lanka (Ae25) and the USA (RU34A), although there is little to suggest that it was imported from abroad. CONCLUSION: This is the first report on the genomic analysis of a novel ST658 A. hydrophilia, offering useful insights into its pathogenicity and global phylogenetics.

2.
Microorganisms ; 8(12)2020 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-33339176

RESUMO

The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed. All the isolates had similar resistance phenotypes, which corroborated their chromosomally mediated resistome (blaCPHA3 and blaOXA-12) and belonged to a novel sequence type, ST657 (a satellite clone). Isolates in the same sub-clades clustered according to their clonal lineages and host. Mobilome analysis revealed the presence of chromosome-borne insertion sequence families. The estimated pathogenicity score (Pscore ≈ 0.60) indicated their potential pathogenicity in humans. Furthermore, these isolates carried several virulence factors (adherence factors, toxins, and immune evasion), in different permutations and combinations, indicating a differential ability to establish infection. Phylogenomic and metadata analyses revealed a predilection for water environments and aquatic animals, with more recent reports in humans and food animals across geographies, making A. veronii a potential One Health indicator bacterium.

3.
Int J Infect Dis ; 2020 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-33212262

RESUMO

Botulism, a rare life-threatening toxaemia, is probably underdiagnosed in all of its forms in Africa. Here we report the first laboratory-supported case of infant botulism on the African continent. A 10-week-old previously-well infant presented with progressive global weakness, feeding difficulty, and aspiration pneumonia. During a lengthy hospitalization, a rare bivalent Clostridium botulinum strain producing subtype B3 and F8 toxins, with a new multi-locus sequence type, was isolated from stool. The infant was successfully treated with a heptavalent botulinum antitoxin infusion and pyridostigmine. Despite the relative rarity of infant botulism, this case illustrates the importance of maintaining a high level of clinical suspicion when assessing hypotonic infants. The value of modern diagnostic modalities to identify and characterize this under-recognized condition is also demonstrated.

4.
Transfus Apher Sci ; : 102918, 2020 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-32900597

RESUMO

Coronavirus disease 2019 (COVID-19) is a disease spreading rapidly in Sudan, the rest of the African continent and the world with no known definitive treatment or vaccines. However, among many treatment interventions being tested globally, beneficial effects and clinical improvements have been reported when convalescent plasma is used for treating COVID-19 patients. We prepared a guiding protocol for treating early to moderate COVID-19 patients with plasma transfusion from convalescent COVID-19 patients. This protocol was deduced based on previously published reports and studies that evaluated and tested convalescent plasma as a prospective therapy for COVID-19 patients. The protocol covers instructions on patient and donor selection criteria, plasma harvesting, plasma product specifications, dosage and precautions for convalescent plasma collection and transfusion process. Altogether, we prepared a treatment protocol that is tailored to the context of Sudan to be adopted by Sudan's health authority. Moreover, it will also provide reference for researchers to design open label clinical trials for convalescent plasma transfusion.

5.
Microbiol Resour Announc ; 9(33)2020 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-32817153

RESUMO

We describe here the draft genome sequence of AY1MRC, a Mycobacterium tuberculosis strain belonging to lineage 1 (Indo-Oceanic) and the East African Indian spoligotype, isolated from a patient with tuberculosis in Jazan, Saudi Arabia.

6.
Microorganisms ; 8(8)2020 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-32759699

RESUMO

Bacillus sporothermodurans currently possesses one of the most highly heat-resistant spores (HRS), which can withstand ultra-high temperature (UHT) processing. Determination of multiple whole genome sequences of B. sporothermodurans provided an opportunity to perform the first comparative genome analysis between strains and with B. oleronius, B. cereus, and B. subtilis groups. In this study, five whole genome sequences of B. sporothermodurans strains, including those belonging to the HRS clone (SAD and BR12) normally isolated from UHT milk, were compared with the aforementioned Bacillus species for gene clusters responsible for heat resistance. In the phylogenomic analysis, B. sporothermodurans, with its closest phylogenetic neighbor, B. oleronius, clustered with B. thermoamylovorans and B. thermotolerans. Heat shock proteins GrpE, GroES, GroEL, and DnaK presented identical sequences for all B. sporothermodurans strains, indicating that differences in functional efficiency are not involved in the thermal resistance variations. However, comparing all species evaluated, B. sporothermodurans exhibited a different gene configuration in the chromosomal region of the heat shock protein GrpE. Furthermore, only B. sporothermodurans strains presented the stage II sporulation protein P gene located in this region. Multisequence alignment and phylogenetic analysis of the ClpB protein showed differences for HRS and non-HRS strains. The study identified ClpC, ClpE, and ClpX as the three ATPases putatively involved in protein disaggregation in B. sporothermodurans. Bacillussporothermodurans exhibits high homology with other Bacillus species in the DnaK, DnaJ, GroEL, and GroES cluster of genes involved in heat resistance. The data presented here pave the way to select and evaluate the phenotypic effects of genes putatively involved in heat resistance.

7.
BMC Infect Dis ; 20(1): 621, 2020 Aug 24.
Artigo em Inglês | MEDLINE | ID: mdl-32831057

RESUMO

BACKGROUND: We aimed to describe an outbreak of cutaneous abscesses caused by Panton-Valentine leukocidin (PVL)-producing methicillin-susceptible Staphylococcus aureus (MSSA) among gold mine workers. METHODS: In February 2018, we retrospectively reviewed a random sample of 50 medical records from 243 cases and conducted face-to-face interviews using a structured questionnaire. Pus aspirates were sent to the National Institute for Communicable Diseases from prospectively-identified cases (November 2017-March 2018). Nasopharyngeal swabs were collected during a colonisation survey in February 2018. Staphylococcus aureus isolates were screened with a conventional PCR for lukS/F-PV. Pulsed-field gel electrophoresis (PFGE) was performed to determine the genetic relatedness among the isolates. A sample of isolates were selected for whole genome sequencing (WGS). We conducted an assessment on biological risks associated with mining activities. RESULTS: From January 2017 to February 2018, 10% (350/3582) of mine workers sought care for cutaneous abscesses. Forty-seven medical files were available for review, 96% were male (n = 45) with a mean age of 43 years (SD = 7). About 52% (24/46) were involved in stoping and 28% (13/47) worked on a particular level. We cultured S. aureus from 79% (30/38) of cases with a submitted specimen and 14% (12/83) from colonisation swabs. All isolates were susceptible to cloxacillin. Seventy-one percent of S. aureus isolates (30/42) were PVL-PCR-positive. Six PFGE clusters were identified, 57% (21/37) were closely related. WGS analysis found nine different sequence types. PFGE and WGS analysis showed more than one cluster of S. aureus infections involving closely related isolates. Test reports for feed and product water of the mine showed that total plate counts were above the limits of 1000 cfu/ml, coliform counts > 10 cfu/100 ml and presence of faecal coliforms. Best practices were poorly implemented as some mine workers washed protective clothing with untreated water and hung them for drying at the underground surface. CONCLUSIONS: PVL-producing MSSA caused an outbreak of cutaneous abscesses among underground workers at a gold mining company. To our knowledge, no other outbreaks of PVL-producing S. aureus involving skin and soft tissue infections have been reported in mining facilities in South Africa. We recommend that worker awareness of infection prevention and control practices be strengthened.


Assuntos
Abscesso/microbiologia , Dermatopatias/epidemiologia , Infecções dos Tecidos Moles/epidemiologia , Infecções Estafilocócicas/epidemiologia , Staphylococcus aureus/patogenicidade , Adulto , Toxinas Bacterianas/metabolismo , Surtos de Doenças , Eletroforese em Gel de Campo Pulsado , Exotoxinas/metabolismo , Feminino , Ouro , Humanos , Leucocidinas/metabolismo , Masculino , Meticilina/farmacologia , Pessoa de Meia-Idade , Mineradores , Estudos Retrospectivos , Dermatopatias/microbiologia , Infecções dos Tecidos Moles/microbiologia , África do Sul/epidemiologia , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/genética , Staphylococcus aureus/metabolismo
8.
Microbiol Resour Announc ; 9(27)2020 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-32616644

RESUMO

As a contribution to the global efforts to track and trace the ongoing coronavirus pandemic, here we present the sequence, phylogenetic analysis, and modeling of nonsynonymous mutations for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome that was detected in a South African patient with coronavirus disease 2019 (COVID-19).

10.
Microbiol Resour Announc ; 9(11)2020 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-32165387

RESUMO

We report here the whole-genome sequence of Escherichia coli NUBRI-E, a representative of E. coli clone O25:H4 sequence type 131 with bla CTX-M-15, which was obtained from a Sudanese patient with a urinary tract infection.

11.
Pathogens ; 9(2)2020 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-32024012

RESUMO

Pathogenomic analysis was performed on a novel carbapenem-resistant Citrobacter freundii isolate (H2730R) from a rectal swab of an adult male patient admitted to a tertiary hospital, Durban, South Africa. H2730R was identified using selective media and API 20e kit. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK II. H2730R was whole-genome sequenced on the Illumina MiSeq platform. H2730R was resistant to all tested antibiotics except tigecycline and was defined as ST498 by the C. freundii multilocus sequence typing (MLST) database. The estimated pathogenic potential predicted a higher probability (Pscore ≈ 0.875), supporting H2730R as a human pathogen. H2730R harbored 25 putative acquired resistance genes, 4 plasmid replicons, 4 intact prophages, a class 1 integron (IntI1), 2 predominant insertion sequences (IS3 and IS5), numerous efflux genes, and virulome. BLASTn analysis of the blaNDM-1 encoding contig (00022) and its flanking sequences revealed the blaNDM-1 was located on a plasmid similar to the multireplicon p18-43_01 plasmid reported for the spread of carbapenem resistance in South Africa. Phylogenomic analysis showed clustering of H2730R with CF003/CF004 strains in the same clade, suggesting a possible association between C. freundii strains/clones. Acquiring the p18-43_01 plasmid containing blaNDM-1, the diversity, and complex resistome, virulome, and mobilome of this pathogen makes its incidence very worrying regarding mobilized resistance. This study presents the background genomic information for future surveillance and tracking of the spread of carbapenem-resistant Enterobacteriaceae in South Africa.

12.
Influenza Other Respir Viruses ; 14(3): 266-273, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32058677

RESUMO

BACKGROUND: In June 2017, an outbreak of the highly pathogenic avian influenza A(H5N8) was detected in commercial poultry farms in South Africa, which rapidly spread to all nine South African provinces. OBJECTIVES: We conducted active surveillance for the transmission of influenza A(H5N8) to humans working with infected birds during the South African outbreak. METHODS: Influenza A(H5N8)-positive veterinary specimens were used to evaluate the ability of real-time PCR-based assays to detect contemporary avian influenza A(H5N8) strains. Whole genome sequences were generated from these specimens by next-generation sequencing for phylogenetic characterization and screening for mammalian-adaptive mutations. RESULTS: Human respiratory samples from 74 individuals meeting our case definition, all tested negative for avian influenza A(H5) by real-time PCR, but 2 (3%) were positive for human influenza A(H3N2). 54% (40/74) reported wearing personal protective equipment including overalls, boots, gloves, masks, and goggles. 94% (59/63) of veterinary specimens positive for H5N8 were detected on an influenza A(H5) assay for human diagnostics. A commercial H5N8 assay detected H5 in only 6% (3/48) and N8 in 92% (44/48). Thirteen (13/25; 52%) A(H5N8) genomes generated from veterinary specimens clustered in a single monophyletic clade. These sequences contained the NS (P42S) and PB2 (L89V) mutations noted as markers of mammalian adaptation. CONCLUSIONS: Diagnostic assays were able to detect and characterize influenza A(H5N8) viruses, but poor performance is reported for a commercial assay. Absence of influenza A(H5N8) in humans with occupational exposure and no clear impression of molecular adaptation for mammalian infection suggest that this avian pathogen continues to be low-risk human pathogen.

13.
N Engl J Med ; 382(7): 632-643, 2020 02 13.
Artigo em Inglês | MEDLINE | ID: mdl-32053299

RESUMO

BACKGROUND: An outbreak of listeriosis was identified in South Africa in 2017. The source was unknown. METHODS: We conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type Listeria monocytogenes isolates. A case was defined as laboratory-confirmed L. monocytogenes infection during the period from June 11, 2017, to April 7, 2018. RESULTS: A total of 937 cases were identified, of which 465 (50%) were associated with pregnancy; 406 of the pregnancy-associated cases (87%) occurred in neonates. Of the 937 cases, 229 (24%) occurred in patients 15 to 49 years of age (excluding those who were pregnant). Among the patients in whom human immunodeficiency virus (HIV) status was known, 38% of those with pregnancy-associated cases (77 of 204) and 46% of the remaining patients (97 of 211) were infected with HIV. Among 728 patients with a known outcome, 193 (27%) died. Clinical isolates from 609 patients were sequenced, and 567 (93%) were identified as sequence type 6 (ST6). In a case-control analysis, patients with ST6 infections were more likely to have eaten polony (a ready-to-eat processed meat) than those with non-ST6 infections (odds ratio, 8.55; 95% confidence interval, 1.66 to 43.35). Polony and environmental samples also yielded ST6 isolates, which, together with the isolates from the patients, belonged to the same core-genome multilocus sequence typing cluster with no more than 4 allelic differences; these findings showed that polony produced at a single facility was the outbreak source. A recall of ready-to-eat processed meat products from this facility was associated with a rapid decline in the incidence of L. monocytogenes ST6 infections. CONCLUSIONS: This investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons. Whole-genome sequencing facilitated the detection of the outbreak and guided the trace-back investigations that led to the identification of the source.


Assuntos
Surtos de Doenças , Doenças Transmitidas por Alimentos/epidemiologia , Listeria monocytogenes/isolamento & purificação , Listeriose/epidemiologia , Produtos da Carne/microbiologia , Adolescente , Adulto , Idoso , Técnicas de Tipagem Bacteriana , Estudos de Casos e Controles , Feminino , Doenças Transmitidas por Alimentos/etiologia , Doenças Transmitidas por Alimentos/mortalidade , Infecções por HIV/complicações , HIV-1 , Humanos , Recém-Nascido , Listeria monocytogenes/genética , Listeriose/etiologia , Listeriose/mortalidade , Masculino , Produtos da Carne/efeitos adversos , Pessoa de Meia-Idade , Gravidez , Complicações Infecciosas na Gravidez/epidemiologia , Recall e Retirada de Produto , Distribuição por Sexo , África do Sul/epidemiologia , Sequenciamento Completo do Genoma , Adulto Jovem
14.
Microorganisms ; 8(1)2020 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-31963608

RESUMO

Whole-genome sequence (WGS) analyses were employed to investigate the genomic epidemiology of extensively drug-resistant Klebsiella pneumoniae strains, focusing on the carbapenem resistance-encoding determinants, mobile genetic support, clonal and epidemiological relationships. A total of ten isolates were obtained from patients admitted to the intensive care unit (ICU) in a public hospital in South Africa. Five isolates were from rectal swabs of colonized patients and five from blood cultures of patients with invasive carbapenem-resistant infections. Following microbial identification and antibiotic susceptibility tests, the isolates were subjected to WGS on the Illumina MiSeq platform. All the isolates showed genotypic resistance to tested ß-lactams (NDM-1, OXA-1, CTX-M-15, TEM-1B, SHV-1) and other antibiotics. All but one isolate belonged to the ST152 with a novel sequence type, ST3136, differing by a single-locus variant. The isolates had the same plasmid multilocus sequence type (IncF[K12:A-:B36]) and capsular serotype (KL149), supporting the epidemiological linkage between the clones. Resistance to carbapenems in the 10 isolates was conferred by the blaNDM-1 mediated by the acquisition of multi-replicon [ColRNAI, IncFIB(pB171), Col440I, IncFII, IncFIB(K) and IncFII(Yp)] p18-43_01 plasmid. These findings suggest that the acquisition of blaNDM-1-bearing plasmid structure (p18-43_01), horizontal transfer and clonal dissemination facilitate the spread of carbapenemases in South Africa. This emphasizes the importance of targeted infection control measures to prevent dissemination.

15.
J Clin Microbiol ; 58(3)2020 02 24.
Artigo em Inglês | MEDLINE | ID: mdl-31896663

RESUMO

We reevaluated 20 cases of blastomycosis diagnosed in South Africa between 1967 and 2014, with Blastomyces dermatitidis considered to be the etiological agent, in light of newly described species and the use of more advanced technologies. In addition to histopathological and/or culture-based methods, all 20 isolates were phenotypically and genotypically characterized, including multilocus typing of five genes and whole-genome sequencing. Antifungal susceptibility testing was performed as outlined by Clinical and Laboratory Standards Institute documents M27-A3 and M38-A2. We merged laboratory and corresponding clinical case data, where available. Morphological characteristics and phylogenetic analyses of five-gene and whole-genome sequences revealed two groups, both of which were closely related to but distinct from B. dermatitidis, Blastomyces gilchristii, and Blastomyces parvus The first group (n = 12) corresponded to the recently described species Blastomyces percursus, and the other (n = 8) is described here as Blastomyces emzantsi sp. nov. Both species exhibited incomplete conversion to the yeast phase at 37°C and were heterothallic for mating types. All eight B. emzantsi isolates belonged to the α mating type. Whole-genome sequencing confirmed distinct species identities as well as the absence of a full orthologue of the BAD-1 gene. Extrapulmonary (skin or bone) disease, probably resulting from hematogenous spread from a primary lung infection, was more common than pulmonary disease alone. Voriconazole, posaconazole, itraconazole, amphotericin B, and micafungin had the most potent in vitro activity. Over the 5 decades, South African cases of blastomycosis were caused by species that are distinct from B. dermatitidis Increasing clinical awareness and access to simple rapid diagnostics may improve the diagnosis of blastomycosis in resource-limited countries.

16.
J Glob Antimicrob Resist ; 20: 16-17, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31655135

RESUMO

OBJECTIVES: Here we describe the draft genome sequence of a clinical Acinetobacter haemolyticus isolate (A109R1B4) from a rectal swab of a hospitalised patient in South Africa. METHODS: Genomic DNA from the isolate was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using Qiagen CLC Genomics Workbench. The assembled contigs were annotated and antimicrobial resistance genes and sequence type were identified. RESULTS: The genome comprised 281 contigs with a total assembly length of 3 371 389bp, a G+C content of 39.9% and an N50 value of 58 196bp, and reference coverage was 93.08 while the coverage was 88.08. A total of 3387 genes, 3292 coding sequences (CDS), 3175 coding genes and 95 RNA genes were detected. The antimicrobial resistance genes blaOXA-264 and aac(6')-Ig were detected. CONCLUSION: The genome sequence reported will serve as a reference point for molecular epidemiological studies of antibiotic-resistant A. haemolyticus in Africa.

17.
Microbiol Resour Announc ; 8(50)2019 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-31831607

RESUMO

Here, we present the complete genome sequence of Staphylococcus aureus NP66, isolated from a South African mine worker.

18.
Pathogens ; 8(4)2019 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-31569754

RESUMO

This study undertook genome mining and comparative genomics to gain genetic insights into the dominance of the methicillin-resistant Staphylococcus aureus (MRSA) endemic clone ST612-CC8-t1257-SCCmec_IVd(2B), obtained from the poultry food chain in South Africa. Functional annotation of the genome revealed a vast array of similar central metabolic, cellular and biochemical networks within the endemic clone crucial for its survival in the microbial community. In-silico analysis of the clone revealed the possession of uniform defense systems, restriction-modification system (type I and IV), accessory gene regulator (type I), arginine catabolic mobile element (type II), and type 1 clustered, regularly interspaced, short palindromic repeat (CRISPR)Cas array (N = 7 ± 1), which offer protection against exogenous attacks. The estimated pathogenic potential predicted a higher probability (average Pscore ≈ 0.927) of the clone being pathogenic to its host. The clone carried a battery of putative virulence determinants whose expression are critical for establishing infection. However, there was a slight difference in their possession of adherence factors (biofilm operon system) and toxins (hemolysins and enterotoxins). Further analysis revealed a conserved environmental tolerance and persistence mechanisms related to stress (oxidative and osmotic), heat shock, sporulation, bacteriocins, and detoxification, which enable it to withstand lethal threats and contribute to its success in diverse ecological niches. Phylogenomic analysis with close sister lineages revealed that the clone was closely related to the MRSA isolate SHV713 from Australia. The results of this bioinformatic analysis provide valuable insights into the biology of this endemic clone.

19.
Microbiol Resour Announc ; 8(40)2019 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-31582453

RESUMO

Pseudomonas aeruginosa is a common nosocomial pathogen often associated with a high mortality rate in vulnerable populations. Here, we describe the genomic sequence of a pan-resistant, high-risk clone of P. aeruginosa sequence type 111 (ST111) isolated from a hospital patient in Sudan.

20.
Microb Genom ; 5(10)2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31617841

RESUMO

Most pneumococci express a polysaccharide capsule, a key virulence factor and target for pneumococcal vaccines. However, pneumococci showing no serological evidence of capsule expression [nontypeable pneumococci (NTPn)] are more frequently isolated from carriage studies than in invasive disease. Limited data exist about the population structure of carriage NTPn from the African continent. We aimed to characterize carriage NTPn and compare them to previously described invasive NTPn. Carriage and invasive NTPn isolates were obtained from South African cross-sectional studies (2009 and 2012) and laboratory-based surveillance for invasive pneumococcal disease (2003-2013), respectively. Isolates were characterized by capsular locus sequence analysis, multilocus sequence typing, antimicrobial non-susceptibility patterns and phylogenetic analysis. NTPn represented 3.7 % (137/3721) of carriage isolates compared to 0.1 % (39/32 824) of invasive isolates (P<0.001), and 24 % (33/137) of individuals were co-colonized with encapsulated pneumococci. Non-susceptibility to cotrimoxazole [84 % (112/133) vs 44 % (17/39)], penicillin [77 % (102/133) vs 36 % (14/39)], erythromycin [53 % (70/133) vs 31 % (12/39)] and clindamycin [36 % (48/133) vs 18 % (7/39)] was higher (P=0.03) among carriage than invasive NTPn. Ninety-one per cent (124/137) of carriage NTPn had complete deletion of the capsular locus and 9 % (13/137) had capsule genes, compared to 44 % (17/39) and 56 % (22/39) of invasive NTPn, respectively. Carriage NTPn were slightly less diverse [Simpson's diversity index (D)=0.92] compared to invasive NTPn [D=0.97]. Sixty-seven per cent (92/137) of carriage NTPn belonged to a lineage exclusive to NTPn strains compared to 23 % (9/39) of invasive NTPn. We identified 293 and 275 genes that were significantly associated with carriage and invasive NTPn, respectively. NTPn isolates detected in carriage differed from those causing invasive disease, which may explain their success in colonisation or in causing invasive disease.


Assuntos
Portador Sadio/microbiologia , Farmacorresistência Bacteriana/genética , Infecções Pneumocócicas/microbiologia , Streptococcus pneumoniae , Fatores de Virulência/genética , Proteínas de Bactérias/genética , Portador Sadio/epidemiologia , Estudos Transversais , Genômica , Humanos , Filogenia , Infecções Pneumocócicas/epidemiologia , Sorotipagem , África do Sul/epidemiologia , Streptococcus pneumoniae/classificação , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/isolamento & purificação
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