TEM-145 and TEM-146 &#223-lactamases produced by Escherichia coli isolates from state hospitals in KwaZulu-Natal, South Africa

Two Escherichia coli isolates which were isolated from the urine of patients in state hospitals in KwaZulu-Natal, South Africa were investigated to determine the sequence of the TEM -lactamases responsible for their resistance to -lactamase inhibitors. The isolates were subjected to MICdeterminations, iso-electric focusing analysis, plasmid analysis, polymerase chain reaction (PCR) for the detection of -lactamase genes and sequencing of the blaTEM. Analysis of the nucleotide sequencesrevealed the presence of two novel TEM -lactamases, TEM-145 and TEM-146 which had the R244H mutation. Mutations at position 244 have been previously reported in other inhibitor-resistant TEMs (IRTs)

Detection of mutations in the gyrA of clinical Salmonella spp.

The high prevalence of resistance to nalidixic acid and reduced susceptibility to ciprofloxacin of Salmonella spp. obtained from stool samples of neonates presenting with acute diarrhea in 2001 at the King Edward VIII hospital in Durban, South Africa, prompted this study to determine if there were any mutations in the QRDR of these isolates and to search for the qnrA gene. All isolates with nalidixic acid MICs > 48 μg/ml had the single mutation D87N, or D87G in the QRDR of the gyrA gene, and only 2 strains had an additional mutation; S83L and S83F respectively. The mutation S83T was present in only one isolate with the nalidixic acid MIC of 10 μg/ml whilst the 6 other strains with nalidixic acid MICs < 10 μg/ml had no changes in the QRDR of the gyrA gene. The qnrA gene was not found. These findings indicate that there are mutations in the gyrA of Salmonella isolates which could contribute to resistance to nalidixic acid with reduced susceptibility to ciprofloxacin and there is the co-expression of quinolone and extended-spectrum ß-lactam resistance among Salmonella spp

Molecular characterization of methicillin-resistant Staphylococcus aureus isolates from a hospital in Ghana

Background: Methicillin-resistant  Staphylococcus aureus (MRSA) are a major cause of hospital- and community-acquired infection. They can colonize humans and cause a wide range of infections including pneumonia, endocarditis and bacteraemia. We investigated the molecular mechanism of resistance and virulence of MRSA isolates from a teaching hospital in Ghana.Methodology: A total of 91 S. aureus isolates constituted the initial bacterial sample. Identification of S. aureus was confirmed by the VITEK 2 system. The cefoxitin screen test was used to detect MRSA and antibiotic susceptibility was determined using the VITEK 2 system. The resistance (mecA, blaZ, aac-aph, ermC, and tetK) and virulence (lukS/F-PV, hla, hld and eta) genes were amplified by polymerase chain reaction (PCR) and positive samples subjected to DNA sequencing. Pulsed field gel electrophoresis (PFGE) was used to ascertain the relatedness of the isolates.Results: Fifty-eight of 91 (63.7%) isolates were putatively methicillin resistant by the phenotypic cefoxitin screen test and oxacillin MICs. However, 43 (47%) of the isolates were genotypically confirmed as MRSA based on PCR detection of the mecA gene. Furthermore, 37.9% of isolates displayed resistance to tetracycline, 19% to trimethoprim-sulphamethoxazole, 15.5% to clindamycin, 12.1% to gentamicin, 13.8% to ciprofloxacin and erythromycin, 6.9% to moxifloxacin and 7.0% to rifampicin. None of the isolates was positive for inducible clindamycin resistance. The prevalence of resistance (mecA, blaZ, aac(6’)-aph(2’’), tetK, and ermC) and virulence (hla and lukS/F-PV) genes respectively were 74%, 33%, 22%, 19%, 3%, 5% and 3%, with isolates organized in two highly related clades.Conclusion: Results indicate a fairly high occurrence of MRSA, which can complicate the effective therapy of S. aureus infections, necessitating surveillance and stringent infection control programmes to forestall its spread.Keywords: MRSA, mecA, blaZ, hla, lukS/F-P

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The effect of mutations in the AmpC promoter region on &#946-lactam resistance from an Escherichia coli clinical isolate in a public sector hospital in KwaZulu-Natal, South Africa

The ampC promoter and attenuator regions of an Escherichia coli clinical isolate from a public hospital in KwaZulu-Natal was investigated to detect the presence of mutations in these regions. The isolate was subjected to MIC determinations, IEF analysis, PCR for the presence of &beta;-lactamases and sequencing of the ampC gene. Analysis of the ampC promoter and attenuator regions of the isolate showed that the isolate had mutations in the promoter region and this included insertions of nucleotides in the spacer region between the -10 and -35 Pribnow boxes. The insertion of an extra nucleotide in the spacer region between the -10 and -35 boxes affects the resistance of bacteria to &beta;-lactam antibiotics

Geographical evolution of the CTX-M &#223-lactamase – an update

The CTX-M- type extended spectrum -lactamases (ESBLs) that preferentially hydrolyze cefotaxime are emerging globally and comprise of more than 50 enzymes. The emergence of novel CTX-M - lactamases in several countries is noted as opposed to the transfer of established CTX-M genes from one country to another, suggestive of a de novo dissemination of CTX-M genes

Additional file 1: of Faecal colonization of E. coli and Klebsiella spp. producing extended-spectrum beta-lactamases and plasmid-mediated AmpC in Mozambican university students

Table S1. Resistance genes identified and sensitivity results of E. coli and Klebsiella spp. (DOCX 38 kb