Molecular Epidemiological Characterisation of ESBL- and Plasmid-Mediated AmpC-Producing Escherichia coli and Klebsiella pneumoniae at Kamuzu Central Hospital, Lilongwe, Malawi

The global rise in infections caused by multidrug resistant (MDR) Enterobacterales poses a public health problem. We have performed a molecular epidemiological characterisation of representative plasmid-mediated AmpC (pAmpC) and ESBL-positive clinical isolates of Escherichia coli (n = 38) and Klebsiella pneumoniae (n = 17) from a tertiary hospital in Malawi collected in 2017. BlaCTX-M-15 was the most prevalent ESBL-determinant in E. coli (n = 30/38) and K. pneumoniae (n = 17/17), whereas blaCMY-2 was detected in nearly all AmpC-phenotype E. coli (n = 15/17). Whole genome sequencing revealed dominant globally disseminated E. coli sequence types (STs); ST410 (n = 16), ST131 (n = 7), and ST617 (n = 6). The ST distribution in K. pneumoniae was more diverse but included ST101 (n = 2), ST14 (n = 2), and ST340 (n = 2), all considered high-risk MDR clones. The isolates expressed an MDR profile, including resistance against commonly used antibiotics, such as fluoroquinolones, aminoglycosides, and/or trimethoprim-sulfamethoxazole, and harboured corresponding resistance determinants. Clonal analyses of the major STs of E. coli revealed closely related genetic clusters within ST410, ST131, and ST617 supporting within-hospital transmission between patients and/or via a common reservoir. The overall findings add to the limited knowledge on the molecular epidemiology of MDR E. coli and K. pneumoniae in Malawi and may help health policy makers to identify areas to target when addressing this major threat of antibiotic resistance

Virulence factors and antibiotic resistance patterns of uropathogenic Escherichia coli

This is an article cover page

Virulence factors and antibiotic resistance patterns of uropathogenic Escherichia coli

This is a journal article.,Urinary tract infections (UTIs)are one of the most common infections in humans and the commonest cause is Uropathogenic Escherichia coli (UPEC). UPEC possess various virulence factors which enable them to survive and grow in urine and other extra-intestinal environments. Similarly, avian pathogenic E.coli (APEC) are known for their ability to cause extra-intestinal diseases in birds. Since APEC and UPEC may encounter similar challenges when establishing infection in these locations, they may share a similar content of virulence genes and capacity to cause disease. In this study, 40 UPEC isolates were obtained from patients with suspected UTIs. Multiplex polymerase chain reaction (PCR) was then used to screen the 40 UPEC isolates for 12 virulence genes usually associated with APEC isolates. The iutA (35%), frimH (32,5%), VAT (17.5%), sitA (17.5%), sitD (15%), hlyF (12,5%), pstB (10%) and frz (7.5%) genes were detected. None of the isolates had the kpsM, ompT, unvrY and sopB genes. Antibiotic resistance patterns were also determined for all 40 isolates. A high resistance to ampicillin (90%) and tetracycline (75%) accompanied by a high sensitivity to gentamycin (82.5%) and nitrofurantoin (62.5%) was observed. Eleven multi-drug resistance patterns were observed in 65% (26/40) of the isolates. The studied UPEC isolates were shown to possess APEC associated virulence genes at low percentage frequencies suggesting a slight overlap in virulence genotypes. Antibiotic resistance patterns suggest surveillance programs to monitor drug resistance should be put in place

An evaluation of the antimicrobial activities of aloe barbadensis:A. chabaudii and A. arborescens leaf extracts used in folklore veterinary medicine in Zimbabwe

Appears in the Journal of Animal and Veterinary Advances 9 (23): 2918-2923, Medwell Journals, 2010,The antimicrobial activities of Aloe barbadensis Miller(Aloe vera), A. chabaudii and A. Arborescens sap extracts on selected microorganisms were determined. Methanol as well as aqueous extracts of these plants were obtained and then tested for their antimicrobial activities using the disc diffusion assay. The extracts were assayed againstgram positive bacteria (Staphylococcus aureus, Bacillus substilis), gram negative bacteria (Escherichia coli, Salmonella typhimurium, S. gallinarum, Klebsiellasp., Proteussp.) and Candida albicans. The study showed that the sap extracts of the three Aloes had antimicrobial activity against all the tested microorganisms. The antimicrobial activity of the methanol extracts were significantly higher than those of the aqueous (warm and cold) extracts (one tailed t-test, p<0.05). There was no significant difference in the antimicrobial activities of the aqueous extracts (one tailed t-test, p<0.05). S. typhimurium and S. gallinarum were the least susceptible to the extracts tested E. coli, Proteussp., Klebsiellasp. and C. albicans were the most sensitive.,National University of Science and Technology (NUST) Research Board

Molecular characterization and antibiotic resistance patterns of avian fecal Escherichia coli from turkeys, geese, and ducks

Background and Aim: Avian fecal Escherichia coli (AFEC) are considered to be the natural reservoir of pathogenic strains in extraintestinal infections as such characterization of AFEC gives insight into the spread of the potential pathogenic lineage. The aim of the study was to investigate the reservoirs of avian pathogenic E. coli (APEC) from fecal samples of healthy ducks, geese, and turkeys by determining the antibiotic resistance patterns of AFEC isolates from turkeys, geese and ducks and characterization of the isolates using virulence genes, plasmid profiles, and phylogenetic grouping. Materials and Methods: The disc diffusion method was used to determine antibiotic resistance of 100 AFEC isolates from turkeys (9), geese (29), and ducks (62) to 8 antibiotics. Molecular characterization of the isolates was done by multiplex polymerase chain reaction to investigate the presence of 12 virulence genes, plasmid profiling, and phylogenetic grouping based on the 16S rRNA sequences. Results: Antibiogram profiles indicated maximum resistance to cloxacillin (100%) and bacitracin (100%) for all AFEC isolates and high sensitivity to ciprofloxacin; however, all isolates exhibited multi-drug resistance. The AFEC isolates from turkeys (6) and geese (12) did not contain virulence genes. The frz (3.7%), sitD (29.6%), and fimH (92.5%) were detected in the duck isolates. None of the isolates had the KpsM, iutA, vat, sitA, hlyF, pstB, ompT, uvrY, and sopB genes. Plasmid profiling gave four plasmid profiles with the plasmids ranging from 1.5 to 55 kb. Phylogenetic analysis of 16S rRNA sequences revealed similarities between AFEC isolates from the different poultry species, as the isolates did not cluster according to avian species. Conclusion: AFEC isolates are potential reservoirs of APEC as they contain some of the virulence genes associated with APEC. Multidrug resistance is high in AFEC isolated from healthy birds. This is a public health concern

Occurrence of multidrug-resistant Escherichia coli and antibiotic resistance genes in a wastewater treatment plant and its associated river water in Harare, Zimbabwe

Wastewater treatment plants (WWTPs) have been identified as point sources of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARG). Due to variations in antibiotic use and prescribing patterns in different countries, it is imperative to establish the presence of ARB and ARGs in water environments on a country-by-country basis. This study investigated the occurrence of 11 antibiotic-resistance genes (QNRB, DFR14, CTX-M, KPC, Sul1, QNRA, Sul2, ERMB,&nbsp; ERMA, SHV, NDM), and antibiotic-resistant Escherichia coli in a WWTP and its associated river water in Harare, Zimbabwe. 24 water samples were collected across 3 sites: upstream and downstream of the WWTP; final effluent of the WWTP. The samples were collected weekly for 8 weeks. Pure cultures of the E. coli isolates were obtained by membrane filtration (0.45 µm) and repeated streaking on Tryptone Bile X-glucuronide followed by biochemical tests (indole test; citrate test; motility, indole, and ornithine). Antibiotic resistance profiling was done for 12 antibiotics using the disc diffusion method. Total genomic DNA was extracted from the 21 water samples and the occurrence of 11 antibiotic-resistant genes investigated using conventional PCR. 86 E. coli isolates were obtained from the sampled sites: 28 from the upstream site, 26 from the WWTP effluent, and 32 from the downstream site. The results from chi-squared analysis showed a significant association (p &lt; 0.05) between the sampling site and the percentage of antibiotic-resistant E. coli for all 12 antibiotics investigated. The percentage of E. coli isolates resistant to the tested antibiotics varied from 29% (ertapenem) to 80.2% (ciprofloxacin). 81 (94.2%) E. coli isolates were resistant to antibiotics from ≥3 classes.&nbsp; Eight (8/11, 72.7%) ARGs were detected in the WWTP effluent and river water samples. Results indicate that the investigated WWTP and associated river water are reservoirs of ARGs and antibiotic-resistant E. coli, which is a public health concern

Virulence gene profiles of avian pathogenic <i>Escherichia coli</i> isolated from chickens with colibacillosis in Bulawayo, Zimbabwe

Colibacillosis, a disease caused by avian pathogenic Escherichia coli (APEC), is one of the main causes of economic losses in the poultry industry worldwide. This study was carried out in order to determine the APEC-associated virulence genes contained by E. coli isolates causing colibacillosis in chickens. A total of 45 E. coli isolates were obtained from the diagnostics and research branch of the Central Veterinary Laboratories, Bulawayo, Zimbabwe. These isolates were obtained from chickens with confirmed cases of colibacillosis after postmortem examination. The presence of the iutA, hlyF, ompT, frz, sitD, fimH, kpsM, sitA, sopB, uvrY, pstB and vat genes were investigated by multiplex polymerase chain reaction (PCR) assay. Of the 45 isolates, 93% were positive for the presence of at least one virulence gene. The three most prevalent virulence genes were iutA (80%), fimH (33.3%) and hlyF (24.4%). The kpsM, pstB and ompT genes had the lowest prevalence, having been detected in only 2.2% of the isolates. All 12 virulence genes studied were detected in the 45 APEC isolates. Virulence gene profiles were constructed for each APEC isolate from the multiplex data. The APEC isolates were profiled as 62.2% fitting profile A, 31.1% profile B and 6.7% profile C. None of the isolates had more than seven virulence genes. Virulence profiles of Zimbabwean APEC isolates are different from those previously reported. Zimbabwean APEC isolates appear to be less pathogenic and may rely on environmental factors and stress in hosts to establish infection

Evolution of antimicrobial resistance of Salmonella enteritidis (1972?2005)

This is a journal article.With the extensive use of antibiotics in livestock production, surveillance revealed an increase in salmonella resistance to the commonly used antimicrobials in veterinary and public health. This serious threat to health care is further exacerbated by the limited epidemiological information about the common zoonotic agent, Salmonella enteritidis, required to determine antibiotic therapy. The aim was to characterise the antimicrobial resistance patterns of S. enteritidis isolates across different timelines (1972?2005) with accompanying genetic changes being investigated. Thirty-seven stored S. enteritidis isolates were collected from the Central Veterinary Laboratory, Harare, with antimicrobial susceptibility determined against eight antibiotics. Plasmids were isolated to analyse any genetic variation. An overall significant increase in resistance (p < 0.05) to nalidixic acid (0% ? 10%), ampicillin (14.3% ?50%), tetracycline (14.3% ? 30%) and erythromycin (71.4% ? 100%) was observed across the timeline. However, the highest rates of susceptibility were maintained for gentamicin, sulphamethoxazole-trimethoprim, kanamycin and chloramphenicol. We report an increase in multidrug resistance (MDR) of 14.2% ? 50% with an increase in resistotypes and plasmid profiles across the timeline. Eleven plasmid profiles were obtained in the 37 isolates studied with a minority of isolates (21.6%, 8/37) harbouring a 54 kb plasmid, commonly serovarspecific. A concerning increase in antimicrobial resistance to commonly administered drugs was observed across the timeline. The surge in MDR is of great concern and implies the need for consistent antimicrobial stewardship. No correlation was observed between the plasmid and antibiotic profiles

Laboratory characterisation of Salmonella enterica serotype Typhi isolates from Zimbabwe, 2009–2017

Background Typhoid fever remains a major public health problem in Zimbabwe with recurrent outbreaks reported since 2009. To provide guidance on appropriate treatment choice in order to minimise the morbidity and mortality of typhoid fever and prevent large scale outbreaks, we investigated the antimicrobial susceptibility patterns, prevalence of Salmonella enterica serotype Typhi (S. Typhi) H58 haplotype and molecular subtypes of S. Typhi from outbreak strains isolated from 2009 to 2017 in Zimbabwe and compared these to isolates from neighbouring African countries. Methods Antimicrobial susceptibility testing was performed on all isolates using the disk diffusion, and E-Test, and results were interpreted using Clinical and Laboratory Standards Institute (CLSI) guidelines (2017). S. Typhi H58 haplotype screening was performed on 161 (58.3%) isolates. Pulsed-field gel electrophoresis (PFGE) was performed on 91 selected isolates across timelines using antibiotic susceptibility results and geographical distribution (2009 to 2016). Results Between 2009 and 2017, 16,398 suspected cases and 550 confirmed cases of typhoid fever were notified in Zimbabwe. A total of 276 (44.6%) of the culture-confirmed S. Typhi isolates were analysed and 243 isolates (88.0%) were resistant to two or more first line drugs (ciprofloxacin, ampicillin and chloramphenicol) for typhoid. The most common resistance was to ampicillin-chloramphenicol (172 isolates; 62.3%). Increasing ciprofloxacin resistance was observed from 2012 to 2017 (4.2 to 22.0%). Out of 161 screened isolates, 150 (93.2%) were haplotype H58. Twelve PFGE patterns were observed among the 91 isolates analysed, suggesting some diversity exists among strains circulating in Zimbabwe. PFGE analysis of 2013, 2014 and 2016 isolates revealed a common strain with an indistinguishable PFGE pattern (100% similarity) and indistinguishable from PFGE patterns previously identified in strains isolated from South Africa, Zambia and Tanzania. Conclusions Resistance to first line antimicrobials used for typhoid fever is emerging in Zimbabwe and the multidrug resistant S. Typhi H58 haplotype is widespread. A predominant PFGE clone circulating in Zimbabwe, South Africa, Zambia and Tanzania, argues for cross-border cooperation in the control of this disease

Strategies and opportunities for promoting bioinformatics in Zimbabwe.

CITATION: Shoko, R., et al. 2018. Strategies and opportunities for promoting bioinformatics in Zimbabwe. PLoS Computational Biology, 14(11):e1006480, doi:10.1371/journal.pcbi.1006480.The original publication is available at https://journals.plos.org/ploscompbiolIntroduction: The increasing applications of advanced technologies in life sciences are fueling the growth of data from genome sequencing, functional genomics experiments, and macromolecular structure determination. Bioinformatics (sometimes interchangeably used with the term “computational biology”) permits researchers to collect, manage, and sift through these massive data sets and derive scientific insight from them [1,2]. Bioinformatics holds a big promise in addressing many of the problems that are facing humanity today, including human health, agriculture, and the environment [3–8]. Consequently, the demand for skilled scientists with the ability to use information technology to solve life science problems has been rising steadily globally. Similar to other developing countries in Africa, bioinformatics is slowly gaining popularity among Zimbabwean scientists. In this paper, we review the progress made by Zimbabwean scientists in bioinformatics and propose strategies for boosting bioinformatics capacity in the country. To our knowledge, this work is the first attempt to give a comprehensive report of bioinformatics activities in the country. As such, it is inevitable that our review may not be exhaustive and may fall short of mentioning or acknowledging groups or scientists who have contributed or presented their work on other platforms.https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006480Publisher's versio