ObjectiveWe aimed to provide an analysis of A. baumannii complex (ABC) isolated from blood cultures in South Africa.Materials and methodsABC surveillance was conducted from 1 April 2017 to 30 ...September 2019 at 19 hospital sites from blood cultures of any age and sex. Organism identification was performed using the MALDI-TOF MS and antimicrobial susceptibility testing (AST), MicroScan Walkaway System. We confirmed colistin resistance with Sensititre, FRCOL panel, and selected for whole-genome sequencing.ResultsDuring the study period, we identified 4822 cases of ABC, of which 2152 cases were from 19 enhanced surveillance sites were reported during the enhanced surveillance period (1 August 2018 to 30 September 2019). Males accounted for 54% (2611/4822). Of the cases with known age, 41% (1968/4822) were infants (< 1-year-old). Seventy-eight percent (1688/2152) of cases had a known hospital outcome, of which 36% (602/1688) died. HIV status was known for 69% (1168/1688) of cases, and 14% (238/1688) were positive. Eighty-two percent (1389/1688) received antimicrobial treatment in admission. Three percent (35/1389) of cases received single colistin. Four percent (75/2033) were resistant to colistin. At least 75% of the isolates (1530/2033) can be classified as extensively drug-resistant (XDR), with resistance to most antibiotics except for colistin. The majority, 83% (20/24), of the colistin-resistant isolates were of the sequence type (ST) 1. Resistance genes, both plasmid- and chromosomal- mediated were not observed. Although all isolates had, nine efflux pump genes related to antimicrobial resistance.ConclusionOur surveillance data contributed to a better understanding of the natural course of A. baumannii disease, the patient characteristics among infants, and the level of resistance. At least two-thirds of the isolates were extensively drug-resistant, and four percent of isolates were resistant to colistin.
Candida auris is an invasive healthcare-associated fungal pathogen. Cases of candidemia, defined as illness in patients with Candida cultured from blood, were detected through national ...laboratory-based surveillance in South Africa during 2016-2017. We identified viable isolates by using mass spectrometry and sequencing. Among 6,669 cases (5,876 with species identification) from 269 hospitals, 794 (14%) were caused by C. auris. The incidence risk for all candidemia at 133 hospitals was 83.8 (95% CI 81.2-86.4) cases/100,000 admissions. Prior systemic antifungal drug therapy was associated with a 40% increased adjusted odds of C. auris fungemia compared with bloodstream infection caused by other Candida species (adjusted odds ratio 1.4 95% CI 0.8-2.3). The crude in-hospital case-fatality ratio did not differ between Candida species and was 45% for C. auris candidemia, compared with 43% for non-C. auris candidemia. C. auris has caused a major epidemiologic shift in candidemia in South Africa.
Bordetella bronchiseptica is a rare cause of invasive human infection. The most common infection in humans is the respiratory tract infection and it is usually associated with immunosuppression, ...particularly acquired immunodeficiency syndrome (AIDS). We report a case of a pneumonia and peritonitis in a 42-year-old female with alcoholic liver disease. The patient died despite treatment with antibiotics. This case illustrates the potential virulence of B. bronchiseptica in susceptible patients and to our knowledge it is the first case of primary peritonitis due to this organism.
Salmonella is well recognized as an aetiological agent of gastrointestinal and diarrhoeal disease. Salmonella enterica serotype Enteritidis (Salmonella Enteritidis) is one of the commonest serotypes ...associated with foodborne illness. In South Africa, we compared Salmonella Enteritidis strains isolated from humans with gastroenteritis and strains isolated from captive wild animals, between June 2011 and July 2012.
Bacteria were phenotypically characterized using standard microbiological techniques. Genotypic relatedness of isolates was investigated by pulsed-field gel electrophoresis (PFGE) analysis.
a diversity of 27 PFGE patterns amongst 196 human non-invasive isolates was shown; two PFGE patterns predominated and accounted for 74% of all human isolates. Human isolates showed a 12% prevalence rate for nalidixic acid resistance. Animal isolates from 5 different sources were investigated. With the exception of an isolate from a ground hornbill, all animal isolates (jaguar, crocodile, lion and poultry) showed PFGE pattern matches to a human isolate. Animal isolates showed susceptibility to all antimicrobial agents tested, with the exception of nalidixic acid resistance in isolates from the lion and poultry source.
Our data showed similarities between Salmonella Enteritidis strains isolated from humans and captive wild animals, suggesting a probable common source for strains from humans and animals.
A thesis submitted to the Faculty of Health Science, University of the Witwatersrand,;
Johannesburg, South Africa, in fulfilment of the requirements for the degree, Doctorate of;
Philosophy in ...Medicine, 2009-2015
Cholera is an acute diarrhoeal disease that generally presents as abrupt watery diarrhoea and;
vomiting. For the years 2008 to 2009, South Africa experienced two major outbreaks of;
cholera. The first outbreak was reported from May to July 2008 (Chapter Three) and the;
second outbreak from November 2008 to April 2009 (Chapter Four). Within both events,;
Vibrio cholerae (V. cholerae) O1 identified at peripheral laboratories displayed resistance to;
three or more routinely tested antimicrobial agents. The molecular epidemiology and;
mechanism of antimicrobial resistance of V. cholerae O1 isolates was investigated. This was;
achieved by using various molecular techniques, which included pulsed-field gel;
electrophoresis (PFGE) analysis, polymerase chain reaction (PCR), nucleotide sequencing,;
identification of plasmid DNA and Southern blot hybridization analysis.;
Methods;
As part of routine characterization of V. cholerae isolates at the Centre for Enteric Diseases;
(CED), isolates underwent serological and biochemical confirmatory identification as well as;
antimicrobial susceptibility testing using the Etest method. PFGE analysis was performed on;
V. cholerae O1 isolates digested with NotI restriction enzyme. One-hundred V. cholerae O1;
isolates, ten isolates characterized in Chapter Three and 90 isolates characterized in Chapter;
Four were selected for further analysis to ensure that all PFGE banding patterns were;
represented. Three probable mechanisms of antimicrobial resistance were investigated.;
Firstly, PCR was used to detect for the presence of class 1 integrons (3’-CS and 5’-CS), class;
2 integrons (intI2), plasmid-mediated quinolone resistance (PMQR) genes (qnrA, qnrB, qnrS,;
qnrC and qepA), quinolone resistance determinant (qnrVC3), ESBL producing genes (blaTEM,;
blaSHV and blaCTX-M), genes coding for the quinolone resistance-determining region (QRDR);
of DNA gyrase (gyrA/gyrB) and topoisomerase IV (parC/parE), SXT element-integrase gene;
(SXTint) and associated SXT resistance genes (floR, sul2, dfrA1, dfr18, strA and strB) and;
the class A tetracycline resistance determinant (tetA).;
The presence of resistance plasmids was investigated by isolation of intact bacterial plasmid;
DNA. Southern blotting and DNA probing was used to investigate the location of resistance;
genes on the plasmids. Secondly, nucleotide sequencing was used to detect amino acid;
mutations in the QRDR of DNA gyrase and topoisomerase IV respectively. Thirdly, to;
determine the role of an active efflux pump in quinolone resistance, susceptibility testing to;
nalidixic acid was investigated in ten V. cholerae O1 isolates characterised in Chapter Three;
using agar dilution in the presence and absence of two efflux pump inhibitors, reserpine and;
phenylalanyl arginine- -naphthylamide. PCR analysis was used to detect for virulence;
determinants, which included the enzymatic A subunit of the cholera toxin (CT), ctxA and the;
gene encoding for the toxin co-regulated pilus (TCP), tcpA respectively. In addition, the;
complete coding region of the ctxAB gene was amplified and sequenced from four V.;
cholerae O1 isolates, two isolates characterized in Chapter Three and two isolates;
characterized in Chapter Four as several V. cholerae O1 atypical El Tor isolates have been;
described in Africa. Minimum inhibitory concentration (MIC) values for azithromycin were;
determined for all 100 V. cholerae O1 isolates using both the Etest and agar dilution methods;
(Chapter Five). PCR-analysis was used to determine the presence of seven macrolide;
resistance determinants (mefA, ereA, ereB, ermB, mphA, mphB and mphD) in all 100 V.;
cholerae O1 isolates.;
Results;
For both cholera outbreaks, a total of 751 isolates were received and available for analysis.;
All 31 isolates recovered from the first outbreak (Chapter Three) were characterized as V.;
cholerae O1 serotype Ogawa. For the second outbreak (Chapter Four) 708 isolates were;
characterized as serotype Ogawa, while the remaining 12 isolates were characterized as;
serotype Inaba. All isolates analyzed from both outbreaks were susceptible to ciprofloxacin;
and imipenem, but resistant to six or more antimicrobial agents tested for surveillance;
purposes. All V. cholerae O1 isolates were shown to be resistant to nalidixic acid, cotrimoxazole,;
trimethoprim, sulfamethoxazoleand streptomycin. Extended-spectrum -;
lactamase (ESBL) activity was observed in V. cholerae O1 isolates (MIC 64 μg/ml) from;
both outbreaks. In the second outbreak reduced susceptibility to ampicillin, tetracycline,;
kanamycin, chloramphenicol, erythromycin and furazolidone were observed. Dendrogram;
analysis produced two main PFGE clusters. PFGE fingerprint patterns from V. cholerae O1;
isolates recovered from the first outbreak clustered away from V. cholerae O1 isolates;
recovered from the second outbreak (data not shown in this study). Class 1 integrons, class 2;
integrons and PMQR genes were not detected by PCR.All 100 V. cholerae O1 isolates were;
PCR-positive for the SXTint gene and five of the six associated SXT resistance genes;
encoding for chloramphenicol (floR), sulfamethoxazole (sul2), trimethoprim (dfrA1) and;
streptomycin (strA and strB). Seventeen V. cholerae O1 isolates (ten isolates characterized in;
Chapter Three and seven isolates characterized in Chapter Four) were PCR-positive for the;
tetA resistance determinant. Nucleotide sequencing of the QRDR, showed that all nalidixic;
acid-resistant isolates harboured the same mutations in GyrA (S83-I) and ParC (S85-L) but;
none were observed in GyrB and ParE.There was no involvement of an active efflux pump in;
quinolone resistance in ten isolates characterised in Chapter Three. Sixteen V. cholerae O1;
isolates (ten isolates characterized in Chapter Three and six isolates characterized in Chapter;
Four) harboured a single plasmid of approximately 140 kilobase pairs in size and showed to;
harbour the blaTEM gene, which produced the TEM-63 -lactamase.PCR analysis showed that;
all 100 V. cholerae O1 isolates were positive for the CT, and all were PCR-positive for the El;
Tor variant of the TCP. Nucleotide sequencing of the ctxAB gene of the four selected isolates;
showed that all four isolates expressed the encoded ctxB allele for the CT of the classical;
biotype and were defined as “altered El Tor”. A mobilome is characterized by related genome;
sequences that differ by combinations of genomic islands, prophages and integrative;
conjugative elements. All four isolates contained an identical mobilome profile pattern,;
profile B. Comparative analysis using both the Etest and agar dilution methods (Chapter;
Five) showed that all V. cholerae O1 isolates were susceptible to azithromycin provided that;
the tentative breakpoint of 16μg/ml is applied. All 100 isolates were PCR-negative for all;
seven macrolide resistance determinants, which are commonly associated in the family;
Enterobacteriaceae respectively.;
Conclusion;
This is the first incidence of TEM-63 -lactamase-producing, antimicrobial-resistant,;
toxigenic V. cholerae O1 altered El Tor isolates in South Africa. This study highlights the;
need to further analyze antimicrobial resistance and track emerging epidemic isolates of V;
cholerae O1. The MIC values and PCR results reported in this study for azithromycin;
provides a foundation for the surveillance of azithromycin susceptibility and to determine;
MIC breakpoints in V. cholerae O1 isolates circulating in South Africa.
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